patch 29Jun18

fix typo in python module

.github/CODEOWNERS

@@ -16,6 +16,7 @@ src/COMPRESS/*        @akohlmey
 src/GPU/*             @ndtrung81
 src/KOKKOS/*          @stanmoore1
 src/KIM/*             @ellio167
+src/LATTE/*           @cnegre
 src/USER-CGDNA/*      @ohenrich
 src/USER-CGSDK/*      @akohlmey
 src/USER-COLVARS/*    @giacomofiorin

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

@@ -6,11 +6,12 @@ cmake_minimum_required(VERSION 2.8.12)
 
 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})
@@ -23,21 +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)
 
-file(GLOB SRC_FILES ${LAMMPS_SOURCE_DIR}/*.cpp)
-list(SORT SRC_FILES)
-# check for files installed by make-based buildsystem 
-# only run this time consuming check if there are new files
-if(NOT SRC_FILES STREQUAL SRC_FILES_CACHED)
-  file(GLOB SRC_PKG_FILES ${LAMMPS_SOURCE_DIR}/*/*.cpp)
-  message(STATUS "Running check for installed package (this might take a while)")
-  foreach(_SRC SRC_PKG_FILES)
-    get_filename_component(FILENAME "${_SRC}" NAME)
-    if(EXISTS ${LAMMPS_SOURCE_DIR}/${FILENAME})
-      message(FATAL_ERROR "Found packages installed by the make-based buildsystem, please run 'make -C ${LAMMPS_SOURCE_DIR} no-all purge'")
-    endif()
-  endforeach()
-  set(SRC_FILES_CACHED "${SRC_FILES}" CACHE INTERNAL "List of file in LAMMPS_SOURCE_DIR" FORCE)
-endif()
+# 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
@@ -49,18 +52,59 @@ if (${CMAKE_CXX_COMPILER_ID} STREQUAL "Intel")
   set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -restrict")
 endif()
 
-option(ENABLE_COVERAGE "Enable code coverage" OFF)
-if(ENABLE_COVERAGE)
-  set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} --coverage")
+# GNU compiler features
+if (${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)
@@ -102,12 +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)
@@ -115,19 +153,16 @@ if(ENABLE_TESTING)
   enable_testing()
 endif(ENABLE_TESTING)
 
-option(ENABLE_ALL "Build all default packages" OFF)
 set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GRANULAR
-  KSPACE MANYBODY MC MEAM MISC MOLECULE PERI QEQ
-  REAX REPLICA RIGID SHOCK SNAP SRD)
-set(OTHER_PACKAGES KIM PYTHON MSCG MPIIO VORONOI POEMS LATTE
-  USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-MESO
-  USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF
-  USER-FEP USER-H5MD USER-LB USER-MANIFOLD USER-MEAMC USER-MGPT USER-MISC
+  KSPACE MANYBODY MC MEAM MISC MOLECULE PERI QEQ REAX REPLICA RIGID SHOCK SPIN SNAP
+  SRD KIM PYTHON MSCG MPIIO VORONOI POEMS LATTE USER-ATC USER-AWPMD USER-BOCS
+  USER-CGDNA USER-MESO USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE
+  USER-EFF USER-FEP USER-H5MD USER-LB USER-MANIFOLD USER-MEAMC USER-MGPT USER-MISC
   USER-MOFFF USER-MOLFILE USER-NETCDF USER-PHONON USER-QTB USER-REAXC USER-SMD
   USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM)
 set(ACCEL_PACKAGES USER-OMP KOKKOS OPT USER-INTEL GPU)
 foreach(PKG ${DEFAULT_PACKAGES})
-  option(PKG_${PKG} "Build ${PKG} Package" ${ENABLE_ALL})
+  option(PKG_${PKG} "Build ${PKG} Package" OFF)
 endforeach()
 foreach(PKG ${ACCEL_PACKAGES} ${OTHER_PACKAGES})
   option(PKG_${PKG} "Build ${PKG} Package" OFF)
@@ -213,7 +248,7 @@ if(PKG_PYTHON)
   add_definitions(-DLMP_PYTHON)
   include_directories(${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}'))"
@@ -296,8 +331,8 @@ if(PKG_LATTE)
     message(STATUS "LATTE not found - we will build our own")
     include(ExternalProject)
     ExternalProject_Add(latte_build
-      URL https://github.com/lanl/LATTE/archive/v1.1.1.tar.gz
-      URL_MD5 cb86f1d2473ce00aa61ff6a023154b03
+      URL https://github.com/lanl/LATTE/archive/v1.2.1.tar.gz
+      URL_MD5 bed76e7e76c545c36dd848a8f1fd35eb
       SOURCE_SUBDIR cmake
       CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR> -DCMAKE_POSITION_INDEPENDENT_CODE=${CMAKE_POSITION_INDEPENDENT_CODE}
       )
@@ -445,6 +480,9 @@ endforeach(HEADER)
 set(MATH_LIBRARIES "m" CACHE STRING "math library")
 mark_as_advanced( MATH_LIBRARIES )
 include(CheckLibraryExists)
+if (CMAKE_VERSION VERSION_LESS "3.4")
+  enable_language(C) # check_library_exists isn't supported without a c compiler before v3.4
+endif()
 foreach(FUNC sin cos)
   check_library_exists(${MATH_LIBRARIES} ${FUNC} "" FOUND_${FUNC}_${MATH_LIBRARIES})
   if(NOT FOUND_${FUNC}_${MATH_LIBRARIES})
@@ -462,23 +500,14 @@ RegisterStyles(${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()
-
-  foreach(PKG_FILE in ${${PKG}_HEADERS})
-      get_filename_component(FNAME ${PKG_FILE} NAME)
-      DetectAndRemovePackageHeader(${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})
 
   if(PKG_${PKG})
     # detects styles in package and adds them to global list
@@ -489,6 +518,17 @@ 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
 ############################################
@@ -623,6 +663,10 @@ if(PKG_USER-INTEL)
         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)
@@ -687,8 +731,7 @@ if(PKG_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 ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_pppm.cu)
@@ -797,35 +840,64 @@ GenerateStyleHeaders(${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 ${LIB_SOURCES})
 get_property(LANGUAGES GLOBAL PROPERTY ENABLED_LANGUAGES)
 list (FIND LANGUAGES "Fortran" _index)
 if (${_index} GREATER -1)
   list(APPEND LAMMPS_LINK_LIBS ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
 endif()
 list(REMOVE_DUPLICATES LAMMPS_LINK_LIBS)
-target_link_libraries(lammps ${LAMMPS_LINK_LIBS})
-if(LAMMPS_DEPS)
-  add_dependencies(lammps ${LAMMPS_DEPS})
-endif()
-set_target_properties(lammps PROPERTIES OUTPUT_NAME lammps${LAMMPS_MACHINE})
-if(BUILD_SHARED_LIBS)
-  set_target_properties(lammps PROPERTIES SOVERSION ${SOVERSION})
-  install(TARGETS lammps LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
-  install(FILES ${LAMMPS_SOURCE_DIR}/library.h DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps)
-  configure_file(pkgconfig/liblammps.pc.in ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_MACHINE}.pc @ONLY)
-  install(FILES ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_MACHINE}.pc DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
+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()
 
 ###############################################################################
@@ -860,7 +932,7 @@ endif()
 ###############################################################################
 # Print package summary
 ###############################################################################
-foreach(PKG ${DEFAULT_PACKAGES} ${OTHER_PACKAGES} ${ACCEL_PACKAGES})
+foreach(PKG ${DEFAULT_PACKAGES} ${ACCEL_PACKAGES})
   if(PKG_${PKG})
     message(STATUS "Building package: ${PKG}")
   endif()
@@ -869,7 +941,7 @@ endforeach()
 string(TOUPPER "${CMAKE_BUILD_TYPE}" BTYPE)
 get_directory_property(CPPFLAGS DIRECTORY ${CMAKE_SOURCE_DIR} COMPILE_DEFINITIONS)
 include(FeatureSummary)
-feature_summary(INCLUDE_QUIET_PACKAGES WHAT ALL)
+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}
@@ -907,13 +979,17 @@ 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(ENABLED_GPU)
+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")

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/README.md

@@ -22,6 +22,7 @@ tasks, act as a reference and provide examples of typical use cases.
    * [Building LAMMPS using cmake](#building-lammps-using-cmake-1)
       * [Prerequisites](#prerequisites)
       * [Build directory vs. Source Directory](#build-directory-vs-source-directory)
+   * [Defining and using presets](#defining-and-using-presets)
    * [Reference](#reference)
       * [Common CMAKE Configuration Options](#common-cmake-configuration-options)
       * [LAMMPS Configuration Options](#lammps-configuration-options)
@@ -150,6 +151,31 @@ build directory.
 ```
 make
 ```
+# Defining and using presets
+
+The CMake build exposes a lot of different options. In the old build system
+some of the package selections were possible by using special make target like
+`make yes-std` or `make no-lib`. Achieving the same result with cmake requires
+specifying all options manually. This can quickly become a very long command
+line that is hard to handle.  While these could be stored in a simple script
+file, there is another way of defining "presets" to compile LAMMPS in a certain
+way.
+
+A preset is a regular CMake script file that can use constructs such as
+variables, lists and for-loops to manipulate configuration options and create
+an [*initial cache*](https://cmake.org/cmake/help/v3.12/manual/cmake.1.html).
+Options must be set with the `CACHE` and `FORCE` flag to ensure they are
+considered even during a second cmake run.
+
+Such a file can then be passed to cmake via the `-C` flag. Several examples of
+presets can be found in the `cmake/presets` folder.
+
+```bash
+# build LAMMPS with all "standard" packages which don't use libraries and enable GPU package
+mkdir build
+cd build
+cmake -C ../cmake/presets/std_nolib.cmake ../cmake -DPKG_GPU=on
+```
 
 # Reference
 
@@ -374,16 +400,6 @@ make
 </tr>
 </thead>
 <tbody>
-<tr>
-  <td><code>ENABLE_ALL</code></td>
-  <td>Enable all default packages</td>
-  <td>
-  <dl>
-    <dt><code>off</code> (default)</dt>
-    <dt><code>on</code></dt>
-  </dl>
-  </td>
-</tr>
 <tr>
   <td><code>PKG_ASPHERE</code></td>
   <td>Computes, time-integration fixes, and pair styles for aspherical particle models including ellipsoids, 2d lines, and 3d triangles.</td>

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/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="22 Jun 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
-22 Jun 2018 version :c,h2
+29 Jun 2018 version :c,h2
 
 Version info: :h3
 

doc/src/Section_commands.txt

@@ -594,6 +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,
@@ -617,6 +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,
@@ -629,6 +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,
@@ -835,6 +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,
@@ -863,6 +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,
@@ -1028,6 +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,

doc/src/Section_howto.txt

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

doc/src/Section_packages.txt

@@ -114,6 +114,7 @@ Package, Description, Doc page, Example, Library
 "RIGID"_#RIGID, rigid bodies and constraints, "fix rigid"_fix_rigid.html, rigid, -
 "SHOCK"_#SHOCK, shock loading methods, "fix msst"_fix_msst.html, -, -
 "SNAP"_#SNAP, quantum-fitted potential, "pair_style snap"_pair_snap.html, snap, -
+"SPIN"_#SPIN, magnetic atomic spin dynamics, "Section 6.6.28"_Section_howto.html#howto_28, SPIN, -
 "SRD"_#SRD, stochastic rotation dynamics, "fix srd"_fix_srd.html, srd, -
 "VORONOI"_#VORONOI, Voronoi tesselation, "compute voronoi/atom"_compute_voronoi_atom.html, -, ext :tb(ea=c,ca1=l)
 
@@ -1415,6 +1416,38 @@ examples/snap :ul
 
 :line
 
+SPIN package :link(SPIN),h4
+
+[Contents:]
+
+Model atomic magnetic spins classically, coupled to atoms moving in
+the usual manner via MD.  Various pair, fix, and compute styles.
+
+[Author:] Julian Tranchida (Sandia).
+
+[Install or un-install:]
+
+make yes-spin
+make machine :pre
+
+make no-spin
+make machine :pre
+
+[Supporting info:]
+
+src/SPIN: filenames -> commands
+"Section 6.28"_Section_howto.html#howto_28
+"pair_style spin/dmi"_pair_spin_dmi.html
+"pair_style spin/exchange"_pair_spin_exchange.html
+"pair_style spin/magelec"_pair_spin_magelec.html
+"pair_style spin/neel"_pair_spin_neel.html
+"fix nve/spin"_fix_nve_spin.html
+"fix precession/spin"_fix_precession_spin.html
+"compute spin"_compute_spin.html
+examples/SPIN :ul
+
+:line
+
 SRD package :link(SRD),h4
 
 [Contents:]

doc/src/atom_style.txt

@@ -15,7 +15,7 @@ atom_style style args :pre
 style = {angle} or {atomic} or {body} or {bond} or {charge} or {dipole} or \
         {dpd} or {edpd} or {mdpd} or {tdpd} or {electron} or {ellipsoid} or \
         {full} or {line} or {meso} or {molecular} or {peri} or {smd} or \
-        {sphere} or {tri} or {template} or {hybrid} :ulb,l
+        {sphere} or {spin} or {tri} or {template} or {hybrid} :ulb,l
   args = none for any style except the following
     {body} args = bstyle bstyle-args
       bstyle = style of body particles
@@ -38,6 +38,7 @@ atom_style full
 atom_style body nparticle 2 10
 atom_style hybrid charge bond
 atom_style hybrid charge body nparticle 2 5
+atom_style spin
 atom_style template myMols 
 atom_style tdpd 2 :pre
 
@@ -89,6 +90,7 @@ quantities.
 {peri} | mass, volume | mesocopic Peridynamic models |
 {smd} | volume, kernel diameter, contact radius, mass | solid and fluid SPH particles |
 {sphere} | diameter, mass, angular velocity | granular models |
+{spin} | magnetic moment | system with magnetic particles |
 {template} | template index, template atom | small molecules with fixed topology |
 {tri} | corner points, angular momentum | rigid bodies |
 {wavepacket} | charge, spin, eradius, etag, cs_re, cs_im | AWPMD :tb(c=3,s=|)
@@ -175,6 +177,9 @@ used for calculating the field variables (e.g. stress and deformation)
 and a contact radius for calculating repulsive forces which prevent
 individual physical bodies from penetrating each other.
 
+For the {spin} style, a magnetic spin is associated to each atom.
+Those spins have a norm (their magnetic moment) and a direction.
+
 The {wavepacket} style is similar to {electron}, but the electrons may
 consist of several Gaussian wave packets, summed up with coefficients
 cs= (cs_re,cs_im).  Each of the wave packets is treated as a separate
@@ -312,6 +317,8 @@ The {meso} style is part of the USER-SPH package for smoothed particle
 hydrodynamics (SPH).  See "this PDF
 guide"_USER/sph/SPH_LAMMPS_userguide.pdf to using SPH in LAMMPS.
 
+The {spin} style is part of the SPIN package.
+
 The {wavepacket} style is part of the USER-AWPMD package for the
 "antisymmetrized wave packet MD method"_pair_awpmd.html.
 

doc/src/compute_entropy_atom.txt

@@ -0,0 +1,130 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+compute entropy/atom command :h3
+
+[Syntax:]
+
+compute ID group-ID entropy/atom sigma cutoff keyword value ... :pre
+
+ID, group-ID are documented in "compute"_compute.html command :l
+entropy/atom = style name of this compute command :l
+sigma = width of gaussians used in the g(r) smoothening :l
+cutoff = cutoff for the g(r) calculation :l
+one or more keyword/value pairs may be appended :l
+keyword = {avg} or {local}
+  {avg} values = {yes} or {no} cutoff2
+    {yes} = average the pair entropy over neighbors
+    {no} = do not average the pair entropy over neighbors
+    cutoff2 = cutoff for the averaging over neighbors
+  {local} values = {yes} or {no} = use the local density around each atom to normalize the g(r) :pre
+:ule
+
+[Examples:]
+
+compute 1 all entropy/atom 0.25 5.
+compute 1 all entropy/atom 0.25 5. avg yes 5.
+compute 1 all entropy/atom 0.125 7.3 avg yes 5.1 local yes :pre
+
+[Description:]
+
+Define a computation that calculates the pair entropy fingerprint for
+each atom in the group. The fingerprint is useful to distinguish between
+ordered and disordered environments, for instance liquid and solid-like 
+environments, or glassy and crystalline-like environments. Some 
+applications could be the identification of grain boundaries, a 
+melt-solid interface, or a solid cluster emerging from the melt. 
+The advantage of this parameter over others is that no a priori 
+information about the solid structure is required.
+
+This parameter for atom i is computed using the following formula from
+"(Piaggi)"_#Piaggi and "(Nettleton)"_#Nettleton ,
+
+:c,image(Eqs/pair_entropy.jpg)
+
+where r is a distance, g(r) is the radial distribution function of atom 
+i and rho is the density of the system. The g(r) computed for each 
+atom i can be noisy and therefore it is smoothened using:
+
+:c,image(Eqs/pair_entropy2.jpg)
+
+where the sum in j goes through the neighbors of atom i, and sigma is a
+parameter to control the smoothening.
+
+The input parameters are {sigma} the smoothening parameter, and the
+{cutoff} for the calculation of g(r). 
+
+If the keyword {avg} has the setting {yes}, then this compute also
+averages the parameter over the neighbors  of atom i according to:
+
+:c,image(Eqs/pair_entropy3.jpg)
+
+where the sum j goes over the neighbors of atom i and N is the number
+of neighbors. This procedure provides a sharper distinction between
+order and disorder environments. In this case the input parameter 
+{cutoff2} is the cutoff for the averaging over the neighbors and 
+must also be specified.
+
+If the {avg yes} option is used, the effective cutoff of the neighbor
+list should be {cutoff}+{cutoff2} and therefore it might be necessary 
+to increase the skin of the neighbor list with:
+
+neighbor skin bin :pre
+
+See "neighbor"_neighbor.html for details.
+
+If the {local yes} option is used, the g(r) is normalized by the 
+local density around each atom, that is to say the density around each 
+atom  is the number of neighbors within the neighbor list cutoff divided 
+by the corresponding volume. This option can be useful when dealing with 
+inhomogeneus systems such as those that have surfaces.
+
+Here are typical input parameters for fcc aluminum (lattice 
+constant 4.05 Angstroms),
+
+compute 1 all entropy/atom 0.25 5.7 avg yes 3.7 :pre
+
+and for bcc sodium (lattice constant 4.23 Angstroms),
+
+compute 1 all entropy/atom 0.25 7.3 avg yes 5.1 :pre
+
+
+[Output info:]
+
+By default, this compute calculates the pair entropy value for each
+atom as a per-atom vector, which can be accessed by any command that
+uses per-atom values from a compute as input.  See "Section
+6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
+options.
+
+The pair entropy values have units of the Boltzmann constant. They are 
+always negative, and lower values (lower entropy) correspond to more
+ordered environments.
+
+[Restrictions:]
+
+This compute is part of the USER-MISC package.  It is only enabled if
+LAMMPS was built with that package.  See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
+
+[Related commands:]
+
+"compute cna/atom"_compute_cna_atom.html
+"compute centro/atom"_compute_centro_atom.html
+
+[Default:]
+
+The default values for the optional keywords are avg = no and local = no.
+
+:line
+
+:link(Piaggi)
+[(Piaggi)] Piaggi and Parrinello, J Chem Phys, 147, 114112 (2017).
+
+:link(Nettleton)
+[(Nettleton)] Nettleton and Green, J Chem Phys, 29, 6 (1958).

doc/src/compute_property_atom.txt

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

doc/src/compute_spin.txt

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

doc/src/computes.txt

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

doc/src/dump_modify.txt

@@ -486,7 +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
@@ -600,13 +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.

doc/src/fix_langevin_spin.txt

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

doc/src/fix_nve_spin.txt

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

doc/src/fix_precession_spin.txt

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

doc/src/fix_rigid.txt

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

doc/src/fixes.txt

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

doc/src/lammps.book

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

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_spin_dmi.txt

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

doc/src/pair_spin_exchange.txt

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

doc/src/pair_spin_magelec.txt

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

doc/src/pair_spin_neel.txt

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

doc/src/pairs.txt

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

examples/SPIN/bfo/in.spin.bfo

@@ -0,0 +1,53 @@
+# layer sc iron atoms (in the [001] plane) in bismuth oxide 
+
+clear 
+units 		metal
+atom_style 	spin
+
+dimension 	3
+boundary 	p p f
+
+# necessary for the serial algorithm (sametag)
+atom_modify 	map array 
+
+lattice 	sc 3.96
+region 		box block 0.0 34.0 0.0 34.0 0.0 5.0
+create_box 	1 box
+create_atoms 	1 box
+
+# setting mass, mag. moments, and interactions for bfo
+
+mass		1 1.0
+
+set 		group all spin/random 11 2.50
+
+pair_style 	hybrid/overlay spin/exchange 6.0 spin/magelec 4.5
+pair_coeff 	* * spin/exchange exchange 6.0 -0.01575 0.0 1.965
+pair_coeff 	* * spin/magelec magelec 4.5 0.000109 1.0 1.0 1.0
+
+neighbor 	0.1 bin
+neigh_modify 	every 10 check yes delay 20
+
+fix 		1 all precession/spin anisotropy 0.0000033 0.0 0.0 1.0
+fix 		2 all langevin/spin 0.0 0.1 21
+fix 		3 all nve/spin lattice no
+
+timestep	0.0002
+
+compute 	out_mag	 all compute/spin
+compute 	out_pe	 all pe
+compute 	out_ke	 all ke
+compute 	out_temp all temp
+
+variable 	magz	 equal c_out_mag[3]
+variable 	magnorm	 equal c_out_mag[4]
+variable 	emag	 equal c_out_mag[5]
+variable 	tmag	 equal c_out_mag[6]
+
+thermo_style    custom step time v_magnorm v_emag temp etotal
+thermo          50
+
+compute outsp all property/atom spx spy spz sp fmx fmy fmz
+dump 100 all custom 1 dump_bfo.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
+
+run 		5000

examples/SPIN/bfo/log.11May18.spin.bfo.g++.1

@@ -0,0 +1,212 @@
+LAMMPS (11 May 2018)
+# layer sc iron atoms (in the [001] plane) in bismuth oxide
+
+clear
+units 		metal
+atom_style 	spin
+
+dimension 	3
+boundary 	p p f
+
+# necessary for the serial algorithm (sametag)
+atom_modify 	map array
+
+lattice 	sc 3.96
+Lattice spacing in x,y,z = 3.96 3.96 3.96
+region 		box block 0.0 34.0 0.0 34.0 0.0 5.0
+create_box 	1 box
+Created orthogonal box = (0 0 0) to (134.64 134.64 19.8)
+  1 by 1 by 1 MPI processor grid
+create_atoms 	1 box
+Created 5780 atoms
+  Time spent = 0.0013566 secs
+
+# setting mass, mag. moments, and interactions for bfo
+
+mass		1 1.0
+
+set 		group all spin/random 11 2.50
+  5780 settings made for spin/random
+
+pair_style 	hybrid/overlay spin/exchange 6.0 spin/magelec 4.5
+pair_coeff 	* * spin/exchange exchange 6.0 -0.01575 0.0 1.965
+pair_coeff 	* * spin/magelec magelec 4.5 0.000109 1.0 1.0 1.0
+
+neighbor 	0.1 bin
+neigh_modify 	every 10 check yes delay 20
+
+fix 		1 all precession/spin anisotropy 0.0000033 0.0 0.0 1.0
+fix 		2 all langevin/spin 0.0 0.1 21
+fix 		3 all nve/spin lattice no
+
+timestep	0.0002
+
+compute 	out_mag	 all compute/spin
+compute 	out_pe	 all pe
+compute 	out_ke	 all ke
+compute 	out_temp all temp
+
+variable 	magz	 equal c_out_mag[3]
+variable 	magnorm	 equal c_out_mag[4]
+variable 	emag	 equal c_out_mag[5]
+variable 	tmag	 equal c_out_mag[6]
+
+thermo_style    custom step time v_magnorm v_emag temp etotal
+thermo          50
+
+compute outsp all property/atom spx spy spz sp fmx fmy fmz
+dump 100 all custom 1 dump_bfo.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
+
+run 		5000
+Neighbor list info ...
+  update every 10 steps, delay 20 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 6.1
+  ghost atom cutoff = 6.1
+  binsize = 3.05, bins = 45 45 7
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair spin/exchange, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (2) pair spin/magelec, perpetual, copy from (1)
+      attributes: full, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 7.272 | 7.272 | 7.272 Mbytes
+Step Time v_magnorm v_emag Temp TotEng 
+       0            0  0.010071723  -0.13298298            0  -0.12034311 
+      50         0.01 0.0098643821   -1.3898985            0   -1.3772103 
+     100         0.02 0.0096526211   -2.6381677            0   -2.6254222 
+     150         0.03 0.0094342235   -3.8784006            0   -3.8656019 
+     200         0.04 0.0092074832    -5.111441            0   -5.0986001 
+     250         0.05 0.0089713115   -6.3380611            0   -6.3251904 
+     300         0.06 0.0087256081   -7.5587787            0   -7.5458894 
+     350         0.07 0.0084715548   -8.7738491            0   -8.7609521 
+     400         0.08  0.008211486   -9.9833855            0   -9.9704932 
+     450         0.09 0.0079483243    -11.18751            0   -11.174637 
+     500          0.1 0.0076849713   -12.386462            0    -12.37362 
+     550         0.11  0.007424064   -13.580633            0   -13.567832 
+     600         0.12 0.0071680699   -14.770519            0   -14.757759 
+     650         0.13 0.0069192726   -15.956579            0   -15.943853 
+     700         0.14 0.0066793495   -17.139049            0   -17.126343 
+     750         0.15 0.0064488038   -18.317803            0   -18.305099 
+     800         0.16 0.0062267571   -19.492336            0   -19.479616 
+     850         0.17 0.0060112235   -20.661925            0   -20.649176 
+     900         0.18 0.0057995251   -21.825931            0   -21.813141 
+     950         0.19 0.0055886511    -22.98413            0   -22.971297 
+    1000          0.2 0.0053757923   -24.136967            0   -24.124095 
+    1050         0.21 0.0051592263   -25.285621            0   -25.272717 
+    1100         0.22 0.0049391661   -26.431928            0   -26.419004 
+    1150         0.23 0.0047179149   -27.578212            0   -27.565281 
+    1200         0.24 0.0044991004   -28.727051            0   -28.714128 
+    1250         0.25 0.0042864034   -29.880967            0   -29.868062 
+    1300         0.26 0.0040824475   -31.042054            0   -31.029173 
+    1350         0.27 0.0038883007    -32.21165            0   -32.198795 
+    1400         0.28 0.0037036595   -33.390159            0   -33.377326 
+    1450         0.29 0.0035274815   -34.577121            0   -34.564302 
+    1500          0.3 0.0033587207   -35.771483            0   -35.758672 
+    1550         0.31 0.0031969501   -36.971996            0    -36.95919 
+    1600         0.32 0.0030429081   -38.177601            0   -38.164801 
+    1650         0.33 0.0028989804   -39.387757            0   -39.374962 
+    1700         0.34 0.0027692024   -40.602665            0   -40.589873 
+    1750         0.35 0.0026581403   -41.823341            0    -41.81054 
+    1800         0.36 0.0025686991    -43.05145            0   -43.038628 
+    1850         0.37  0.002500124   -44.288966            0   -44.276111 
+    1900         0.38 0.0024477804   -45.537752            0    -45.52486 
+    1950         0.39 0.0024050049   -46.799255            0   -46.786336 
+    2000          0.4 0.0023657031   -48.074388            0   -48.061466 
+    2050         0.41 0.0023260844   -49.363587            0   -49.350695 
+    2100         0.42 0.0022848329   -50.666866            0   -50.654039 
+    2150         0.43 0.0022419759   -51.983781            0   -51.971055 
+    2200         0.44 0.0021972506    -53.31336            0   -53.300764 
+    2250         0.45 0.0021488322   -54.654121            0   -54.641676 
+    2300         0.46 0.0020929483   -56.004207            0   -55.991918 
+    2350         0.47 0.0020244601   -57.361586            0   -57.349442 
+    2400         0.48  0.001938225    -58.72428            0   -58.712247 
+    2450         0.49 0.0018309419    -60.09064            0   -60.078671 
+    2500          0.5 0.0017030436   -61.459658            0   -61.447705 
+    2550         0.51 0.0015599449   -62.831213            0   -62.819237 
+    2600         0.52 0.0014117554   -64.206088            0   -64.194074 
+    2650         0.53 0.0012709942   -65.585701            0   -65.573657 
+    2700         0.54 0.0011490452   -66.971565            0   -66.959515 
+    2750         0.55  0.001053009   -68.364663            0   -68.352635 
+    2800         0.56 0.00098415327   -69.765002            0   -69.753017 
+    2850         0.57 0.00093809306   -71.171532            0   -71.159598 
+    2900         0.58 0.00090656933    -72.58234            0   -72.570459 
+    2950         0.59 0.00088069677   -73.994931            0   -73.983099 
+    3000          0.6 0.00085472643   -75.406507            0    -75.39472 
+    3050         0.61 0.00082842902   -76.814319            0   -76.802575 
+    3100         0.62 0.00080642618   -78.216074            0   -78.204373 
+    3150         0.63 0.00079463972   -79.610246            0   -79.598589 
+    3200         0.64 0.0007962304   -80.996103            0   -80.984494 
+    3250         0.65 0.00080980411    -82.37346            0   -82.361903 
+    3300         0.66 0.00083070982   -83.742356            0   -83.730855 
+    3350         0.67 0.00085389185   -85.102808            0   -85.091374 
+    3400         0.68 0.00087624091   -86.454619            0   -86.443259 
+    3450         0.69 0.00089741986   -87.797089            0   -87.785814 
+    3500          0.7 0.00091910796    -89.12875            0   -89.117567 
+    3550         0.71 0.00094318459   -90.447312            0   -90.436232 
+    3600         0.72 0.00096989367   -91.750008            0   -91.739046 
+    3650         0.73 0.00099713096   -93.034224            0   -93.023402 
+    3700         0.74 0.0010212995   -94.298186            0   -94.287529 
+    3750         0.75 0.0010391164     -95.5414            0   -95.530926 
+    3800         0.76 0.0010491462   -96.764626            0   -96.754338 
+    3850         0.77 0.0010521238   -97.969346            0    -97.95923 
+    3900         0.78 0.0010500324   -99.156875            0   -99.146899 
+    3950         0.79 0.0010447043   -100.32743            0   -100.31756 
+    4000          0.8 0.0010368986    -101.4796            0   -101.46978 
+    4050         0.81 0.0010263632   -102.61044            0   -102.60064 
+    4100         0.82 0.0010126933   -103.71619            0   -103.70639 
+    4150         0.83 0.00099631895   -104.79338            0   -104.78358 
+    4200         0.84 0.0009789075    -105.8398            0   -105.82998 
+    4250         0.85 0.00096287608   -106.85496            0   -106.84515 
+    4300         0.86 0.00095034023   -107.84011            0   -107.83029 
+    4350         0.87 0.00094219078    -108.7976            0   -108.78778 
+    4400         0.88 0.00093779428   -109.73016            0   -109.72031 
+    4450         0.89 0.0009354459   -110.63996            0   -110.63008 
+    4500          0.9 0.00093342614   -111.52805            0   -111.51812 
+    4550         0.91 0.0009311077   -112.39417            0   -112.38416 
+    4600         0.92 0.00092926689   -113.23706            0   -113.22697 
+    4650         0.93 0.00092921566   -114.05512            0   -114.04495 
+    4700         0.94 0.00093142598   -114.84701            0   -114.83675 
+    4750         0.95 0.00093479851   -115.61197            0   -115.60164 
+    4800         0.96 0.0009369799    -116.3499            0   -116.33951 
+    4850         0.97 0.00093516768   -117.06128            0   -117.05084 
+    4900         0.98 0.00092684411   -117.74695            0   -117.73645 
+    4950         0.99 0.00091046222   -118.40798            0   -118.39742 
+    5000            1 0.00088619957   -119.04554            0   -119.03492 
+Loop time of 128.304 on 1 procs for 5000 steps with 5780 atoms
+
+Performance: 0.673 ns/day, 35.640 hours/ns, 38.970 timesteps/s
+99.6% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 24.227     | 24.227     | 24.227     |   0.0 | 18.88
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.081048   | 0.081048   | 0.081048   |   0.0 |  0.06
+Output  | 39.796     | 39.796     | 39.796     |   0.0 | 31.02
+Modify  | 64.112     | 64.112     | 64.112     |   0.0 | 49.97
+Other   |            | 0.08788    |            |       |  0.07
+
+Nlocal:    5780 ave 5780 max 5780 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    1065 ave 1065 max 1065 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  92480 ave 92480 max 92480 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 92480
+Ave neighs/atom = 16
+Neighbor list builds = 0
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:02:08

examples/SPIN/bfo/log.11May18.spin.bfo.g++.4

@@ -0,0 +1,212 @@
+LAMMPS (11 May 2018)
+# layer sc iron atoms (in the [001] plane) in bismuth oxide
+
+clear
+units 		metal
+atom_style 	spin
+
+dimension 	3
+boundary 	p p f
+
+# necessary for the serial algorithm (sametag)
+atom_modify 	map array
+
+lattice 	sc 3.96
+Lattice spacing in x,y,z = 3.96 3.96 3.96
+region 		box block 0.0 34.0 0.0 34.0 0.0 5.0
+create_box 	1 box
+Created orthogonal box = (0 0 0) to (134.64 134.64 19.8)
+  2 by 2 by 1 MPI processor grid
+create_atoms 	1 box
+Created 5780 atoms
+  Time spent = 0.000355959 secs
+
+# setting mass, mag. moments, and interactions for bfo
+
+mass		1 1.0
+
+set 		group all spin/random 11 2.50
+  5780 settings made for spin/random
+
+pair_style 	hybrid/overlay spin/exchange 6.0 spin/magelec 4.5
+pair_coeff 	* * spin/exchange exchange 6.0 -0.01575 0.0 1.965
+pair_coeff 	* * spin/magelec magelec 4.5 0.000109 1.0 1.0 1.0
+
+neighbor 	0.1 bin
+neigh_modify 	every 10 check yes delay 20
+
+fix 		1 all precession/spin anisotropy 0.0000033 0.0 0.0 1.0
+fix 		2 all langevin/spin 0.0 0.1 21
+fix 		3 all nve/spin lattice no
+
+timestep	0.0002
+
+compute 	out_mag	 all compute/spin
+compute 	out_pe	 all pe
+compute 	out_ke	 all ke
+compute 	out_temp all temp
+
+variable 	magz	 equal c_out_mag[3]
+variable 	magnorm	 equal c_out_mag[4]
+variable 	emag	 equal c_out_mag[5]
+variable 	tmag	 equal c_out_mag[6]
+
+thermo_style    custom step time v_magnorm v_emag temp etotal
+thermo          50
+
+compute outsp all property/atom spx spy spz sp fmx fmy fmz
+dump 100 all custom 1 dump_bfo.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
+
+run 		5000
+Neighbor list info ...
+  update every 10 steps, delay 20 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 6.1
+  ghost atom cutoff = 6.1
+  binsize = 3.05, bins = 45 45 7
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair spin/exchange, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (2) pair spin/magelec, perpetual, copy from (1)
+      attributes: full, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 6.862 | 6.862 | 6.862 Mbytes
+Step Time v_magnorm v_emag Temp TotEng 
+       0            0  0.010071723  -0.13298298            0  -0.12034311 
+      50         0.01 0.0098643821   -1.3898985            0   -1.3772103 
+     100         0.02  0.009652621   -2.6381677            0   -2.6254222 
+     150         0.03 0.0094342234   -3.8784007            0   -3.8656019 
+     200         0.04  0.009207483   -5.1114411            0   -5.0986001 
+     250         0.05 0.0089713114   -6.3380611            0   -6.3251904 
+     300         0.06 0.0087256079   -7.5587787            0   -7.5458894 
+     350         0.07 0.0084715546   -8.7738491            0   -8.7609521 
+     400         0.08 0.0082114858   -9.9833855            0   -9.9704932 
+     450         0.09 0.0079483242    -11.18751            0   -11.174637 
+     500          0.1 0.0076849711   -12.386462            0    -12.37362 
+     550         0.11 0.0074240638   -13.580633            0   -13.567832 
+     600         0.12 0.0071680697   -14.770519            0   -14.757759 
+     650         0.13 0.0069192724   -15.956579            0   -15.943853 
+     700         0.14 0.0066793493   -17.139049            0   -17.126343 
+     750         0.15 0.0064488035   -18.317803            0   -18.305099 
+     800         0.16 0.0062267569   -19.492336            0   -19.479616 
+     850         0.17 0.0060112233   -20.661925            0   -20.649176 
+     900         0.18  0.005799525   -21.825931            0   -21.813141 
+     950         0.19 0.0055886511    -22.98413            0   -22.971297 
+    1000          0.2 0.0053757923   -24.136967            0   -24.124095 
+    1050         0.21 0.0051592265   -25.285621            0   -25.272717 
+    1100         0.22 0.0049391664   -26.431928            0   -26.419004 
+    1150         0.23 0.0047179153   -27.578212            0   -27.565281 
+    1200         0.24 0.0044991009   -28.727051            0   -28.714128 
+    1250         0.25 0.0042864039   -29.880967            0   -29.868062 
+    1300         0.26  0.004082448   -31.042054            0   -31.029174 
+    1350         0.27 0.0038883012    -32.21165            0   -32.198795 
+    1400         0.28 0.0037036599   -33.390159            0   -33.377326 
+    1450         0.29 0.0035274817   -34.577121            0   -34.564302 
+    1500          0.3 0.0033587208   -35.771483            0   -35.758672 
+    1550         0.31 0.0031969501   -36.971996            0    -36.95919 
+    1600         0.32 0.0030429079   -38.177601            0   -38.164801 
+    1650         0.33 0.0028989801   -39.387757            0   -39.374962 
+    1700         0.34 0.0027692022   -40.602666            0   -40.589873 
+    1750         0.35 0.0026581401   -41.823341            0    -41.81054 
+    1800         0.36  0.002568699    -43.05145            0   -43.038628 
+    1850         0.37 0.0025001242   -44.288966            0   -44.276111 
+    1900         0.38 0.0024477808   -45.537752            0    -45.52486 
+    1950         0.39 0.0024050056   -46.799255            0   -46.786336 
+    2000          0.4  0.002365704   -48.074388            0   -48.061466 
+    2050         0.41 0.0023260854   -49.363587            0   -49.350695 
+    2100         0.42  0.002284834   -50.666866            0   -50.654039 
+    2150         0.43 0.0022419771   -51.983781            0   -51.971055 
+    2200         0.44 0.0021972518    -53.31336            0   -53.300764 
+    2250         0.45 0.0021488333   -54.654121            0   -54.641676 
+    2300         0.46 0.0020929494   -56.004207            0   -55.991918 
+    2350         0.47 0.0020244612   -57.361586            0   -57.349441 
+    2400         0.48 0.0019382262    -58.72428            0   -58.712247 
+    2450         0.49  0.001830943   -60.090639            0   -60.078671 
+    2500          0.5 0.0017030446   -61.459658            0   -61.447704 
+    2550         0.51 0.0015599459   -62.831213            0   -62.819237 
+    2600         0.52 0.0014117562   -64.206088            0   -64.194074 
+    2650         0.53  0.001270995     -65.5857            0   -65.573657 
+    2700         0.54  0.001149046   -66.971565            0   -66.959515 
+    2750         0.55 0.0010530098   -68.364663            0   -68.352635 
+    2800         0.56 0.00098415418   -69.765002            0   -69.753017 
+    2850         0.57 0.00093809402   -71.171532            0   -71.159598 
+    2900         0.58 0.00090657031    -72.58234            0   -72.570459 
+    2950         0.59 0.00088069773   -73.994931            0   -73.983099 
+    3000          0.6 0.00085472731   -75.406507            0    -75.39472 
+    3050         0.61 0.00082842975   -76.814319            0   -76.802575 
+    3100         0.62 0.00080642669   -78.216074            0   -78.204373 
+    3150         0.63   0.00079464   -79.610246            0    -79.59859 
+    3200         0.64 0.00079623049   -80.996103            0   -80.984494 
+    3250         0.65 0.00080980416   -82.373461            0   -82.361903 
+    3300         0.66 0.00083070997   -83.742356            0   -83.730856 
+    3350         0.67 0.00085389223   -85.102809            0   -85.091374 
+    3400         0.68 0.00087624159   -86.454619            0    -86.44326 
+    3450         0.69 0.00089742086    -87.79709            0   -87.785815 
+    3500          0.7 0.00091910931    -89.12875            0   -89.117568 
+    3550         0.71 0.00094318635   -90.447312            0   -90.436233 
+    3600         0.72 0.00096989594   -91.750008            0   -91.739047 
+    3650         0.73 0.00099713386   -93.034224            0   -93.023403 
+    3700         0.74 0.0010213031   -94.298186            0   -94.287529 
+    3750         0.75 0.0010391209   -95.541401            0   -95.530926 
+    3800         0.76 0.0010491514   -96.764626            0   -96.754339 
+    3850         0.77 0.0010521296   -97.969347            0   -97.959231 
+    3900         0.78 0.0010500386   -99.156876            0   -99.146899 
+    3950         0.79 0.0010447106   -100.32743            0   -100.31756 
+    4000          0.8 0.0010369046    -101.4796            0   -101.46978 
+    4050         0.81 0.0010263688   -102.61044            0   -102.60064 
+    4100         0.82 0.0010126985   -103.71619            0   -103.70639 
+    4150         0.83 0.00099632366   -104.79338            0   -104.78358 
+    4200         0.84 0.00097891183    -105.8398            0   -105.82998 
+    4250         0.85 0.00096288003   -106.85496            0   -106.84515 
+    4300         0.86 0.00095034371   -107.84011            0   -107.83029 
+    4350         0.87 0.00094219371    -108.7976            0   -108.78778 
+    4400         0.88 0.00093779663   -109.73016            0   -109.72031 
+    4450         0.89 0.00093544766   -110.63996            0   -110.63008 
+    4500          0.9 0.00093342739   -111.52805            0   -111.51812 
+    4550         0.91 0.00093110855   -112.39417            0   -112.38416 
+    4600         0.92 0.00092926746   -113.23706            0   -113.22697 
+    4650         0.93 0.00092921608   -114.05512            0   -114.04495 
+    4700         0.94 0.0009314263   -114.84701            0   -114.83675 
+    4750         0.95 0.0009347987   -115.61197            0   -115.60164 
+    4800         0.96 0.00093697985    -116.3499            0   -116.33951 
+    4850         0.97 0.00093516726   -117.06128            0   -117.05084 
+    4900         0.98 0.00092684316   -117.74695            0   -117.73645 
+    4950         0.99 0.00091046061   -118.40798            0   -118.39742 
+    5000            1 0.00088619727   -119.04554            0   -119.03492 
+Loop time of 37.142 on 4 procs for 5000 steps with 5780 atoms
+
+Performance: 2.326 ns/day, 10.317 hours/ns, 134.619 timesteps/s
+98.7% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 6.2804     | 6.3487     | 6.4569     |   2.7 | 17.09
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.15385    | 0.27957    | 0.36215    |  14.6 |  0.75
+Output  | 10.573     | 10.784     | 10.994     |   4.8 | 29.03
+Modify  | 19.48      | 19.707     | 19.925     |   3.7 | 53.06
+Other   |            | 0.02255    |            |       |  0.06
+
+Nlocal:    1445 ave 1445 max 1445 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost:    555 ave 555 max 555 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs:    0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs:  23120 ave 23120 max 23120 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 92480
+Ave neighs/atom = 16
+Neighbor list builds = 0
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:37

examples/SPIN/cobalt_fcc/exchange_fit_fcc_co/exchange_fcc_cobalt.dat

@@ -0,0 +1,5 @@
+2.503 0.01476
+3.54  0.001497
+4.33  0.001578
+5.01  -0.001224
+5.597 0.000354

examples/SPIN/cobalt_fcc/exchange_fit_fcc_co/exchange_fit.py

@@ -0,0 +1,32 @@
+#Program fitting the exchange interaction
+#Model curve: Bethe-Slater function
+import numpy as np, pylab, tkinter
+import matplotlib.pyplot as plt
+from scipy.optimize import curve_fit
+from decimal import *
+
+print("Loop begin")
+
+#Definition of the Bethe-Slater function
+def func(x,a,b,c):
+    return 4*a*((x/c)**2)*(1-b*(x/c)**2)*np.exp(-(x/c)**2)
+
+#Exchange coeff table (data to fit)
+rdata, Jdata = np.loadtxt('exchange_fcc_cobalt.dat', usecols=(0,1), unpack=True)
+plt.plot(rdata, Jdata, 'b-', label='data')
+
+#Perform the fit
+popt, pcov = curve_fit(func, rdata, Jdata, bounds=(0, [500.,5.,5.]))
+plt.plot(rdata, func(rdata, *popt), 'r--', label='fit')
+
+#Print the fitted params
+print("Parameters: a={:.10} (in meV), b={:.10} (adim), c={:.10} (in Ang)".format(*popt))
+
+#Ploting the result
+plt.xlabel('r_ij')
+pylab.xlim([0,6.5])
+plt.ylabel('J_ij')
+plt.legend()
+plt.show()
+
+print("Loop end")

examples/SPIN/cobalt_fcc/in.spin.cobalt_fcc

@@ -0,0 +1,63 @@
+# fcc cobalt in a 3d periodic box
+
+clear 
+units		metal
+atom_style 	spin
+
+dimension 	3
+boundary 	p p p
+
+# necessary for the serial algorithm (sametag)
+atom_modify 	map array 
+
+lattice fcc 	3.54
+region box 	block 0.0 5.0 0.0 5.0 0.0 5.0
+create_box 	1 box
+create_atoms 	1 box
+
+# setting mass, mag. moments, and interactions for fcc cobalt
+
+mass		1 58.93
+
+#set 		group all spin/random 31 1.72
+set 		group all spin 1.72 0.0 0.0 1.0
+velocity 	all create 100 4928459 rot yes dist gaussian
+
+pair_style 	hybrid/overlay eam/alloy spin/exchange 4.0
+pair_coeff 	* * eam/alloy Co_PurjaPun_2012.eam.alloy Co
+pair_coeff 	* * spin/exchange exchange 4.0 0.0446928 0.003496 1.4885 
+
+neighbor 	0.1 bin
+neigh_modify 	every 10 check yes delay 20
+
+fix 		1 all precession/spin zeeman 1.0 0.0 0.0 1.0
+fix_modify 	1 energy yes
+
+fix 		2 all langevin/spin 0.0 0.0 21
+
+fix 		3 all nve/spin lattice yes
+timestep	0.0001
+
+# compute and output options
+
+compute 	out_mag    all compute/spin
+compute 	out_pe     all pe
+compute 	out_ke     all ke
+compute 	out_temp   all temp
+
+thermo_style	custom f_1
+
+variable 	magx      equal c_out_mag[1]
+variable 	magy      equal c_out_mag[2]
+variable 	magz      equal c_out_mag[3]
+variable 	magnorm   equal c_out_mag[4]
+variable 	emag      equal c_out_mag[5]
+variable 	tmag      equal c_out_mag[6]
+
+thermo_style    custom step time f_1 v_magx v_magy v_magnorm v_emag temp etotal
+thermo          50
+
+#compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
+#dump 		100 all custom 1 dump_cobalt_fcc.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
+
+run 		1000

examples/SPIN/cobalt_fcc/log.11May18.spin.cobalt_fcc.g++.1

@@ -0,0 +1,142 @@
+LAMMPS (11 May 2018)
+# fcc cobalt in a 3d periodic box
+
+clear
+units		metal
+atom_style 	spin
+
+dimension 	3
+boundary 	p p p
+
+# necessary for the serial algorithm (sametag)
+atom_modify 	map array
+
+lattice fcc 	3.54
+Lattice spacing in x,y,z = 3.54 3.54 3.54
+region box 	block 0.0 5.0 0.0 5.0 0.0 5.0
+create_box 	1 box
+Created orthogonal box = (0 0 0) to (17.7 17.7 17.7)
+  1 by 1 by 1 MPI processor grid
+create_atoms 	1 box
+Created 500 atoms
+  Time spent = 0.000651121 secs
+
+# setting mass, mag. moments, and interactions for fcc cobalt
+
+mass		1 58.93
+
+#set 		group all spin/random 31 1.72
+set 		group all spin 1.72 0.0 0.0 1.0
+  500 settings made for spin
+velocity 	all create 100 4928459 rot yes dist gaussian
+
+pair_style 	hybrid/overlay eam/alloy spin/exchange 4.0
+pair_coeff 	* * eam/alloy Co_PurjaPun_2012.eam.alloy Co
+pair_coeff 	* * spin/exchange exchange 4.0 0.0446928 0.003496 1.4885
+
+neighbor 	0.1 bin
+neigh_modify 	every 10 check yes delay 20
+
+fix 		1 all precession/spin zeeman 1.0 0.0 0.0 1.0
+fix_modify 	1 energy yes
+
+fix 		2 all langevin/spin 0.0 0.0 21
+
+fix 		3 all nve/spin lattice yes
+timestep	0.0001
+
+# compute and output options
+
+compute 	out_mag    all compute/spin
+compute 	out_pe     all pe
+compute 	out_ke     all ke
+compute 	out_temp   all temp
+
+thermo_style	custom f_1
+
+variable 	magx      equal c_out_mag[1]
+variable 	magy      equal c_out_mag[2]
+variable 	magz      equal c_out_mag[3]
+variable 	magnorm   equal c_out_mag[4]
+variable 	emag      equal c_out_mag[5]
+variable 	tmag      equal c_out_mag[6]
+
+thermo_style    custom step time f_1 v_magx v_magy v_magnorm v_emag temp etotal
+thermo          50
+
+#compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
+#dump 		100 all custom 1 dump_cobalt_fcc.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
+
+run 		1000
+Neighbor list info ...
+  update every 10 steps, delay 20 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 6.59954
+  ghost atom cutoff = 6.59954
+  binsize = 3.29977, bins = 6 6 6
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair eam/alloy, perpetual, half/full from (2)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+  (2) pair spin/exchange, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 5.218 | 5.218 | 5.218 Mbytes
+Step Time f_1 v_magx v_magy v_magnorm v_emag Temp TotEng 
+       0            0  0.049785486            0            0            1   -187.94116    100.00543   -2372.4636 
+      50        0.005  0.049785486            0            0            1   -187.94112    95.094679   -2372.4636 
+     100         0.01  0.049785486            0            0            1   -187.94071    81.578321   -2372.4636 
+     150        0.015  0.049785486            0            0            1   -187.93912    62.802727   -2372.4636 
+     200         0.02  0.049785486            0            0            1   -187.93551     43.35108   -2372.4636 
+     250        0.025  0.049785486            0            0            1   -187.92942    27.749821   -2372.4636 
+     300         0.03  0.049785486            0            0            1   -187.92118    19.149389   -2372.4636 
+     350        0.035  0.049785486            0            0            1   -187.91199    18.453387   -2372.4636 
+     400         0.04  0.049785486            0            0            1   -187.90364    24.249423   -2372.4636 
+     450        0.045  0.049785486            0            0            1   -187.89806    33.548008   -2372.4636 
+     500         0.05  0.049785486            0            0            1   -187.89668    42.973172   -2372.4636 
+     550        0.055  0.049785486            0            0            1       -187.9    49.902539   -2372.4636 
+     600         0.06  0.049785486            0            0            1   -187.90735    53.166772   -2372.4636 
+     650        0.065  0.049785486            0            0            1   -187.91706    53.153416   -2372.4636 
+     700         0.07  0.049785486            0            0            1   -187.92692    51.377187   -2372.4636 
+     750        0.075  0.049785486            0            0            1    -187.9348    49.725449   -2372.4636 
+     800         0.08  0.049785486            0            0            1   -187.93921    49.663576   -2372.4636 
+     850        0.085  0.049785486            0            0            1   -187.93974    51.681567   -2372.4636 
+     900         0.09  0.049785486            0            0            1     -187.937    55.166554   -2372.4636 
+     950        0.095  0.049785486            0            0            1   -187.93239    58.718232   -2372.4636 
+    1000          0.1  0.049785486            0            0            1   -187.92755     60.75567   -2372.4636 
+Loop time of 4.1303 on 1 procs for 1000 steps with 500 atoms
+
+Performance: 2.092 ns/day, 11.473 hours/ns, 242.113 timesteps/s
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 2.142      | 2.142      | 2.142      |   0.0 | 51.86
+Neigh   | 0.0094573  | 0.0094573  | 0.0094573  |   0.0 |  0.23
+Comm    | 0.023293   | 0.023293   | 0.023293   |   0.0 |  0.56
+Output  | 0.00031972 | 0.00031972 | 0.00031972 |   0.0 |  0.01
+Modify  | 1.9488     | 1.9488     | 1.9488     |   0.0 | 47.18
+Other   |            | 0.006488   |            |       |  0.16
+
+Nlocal:    500 ave 500 max 500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    1956 ave 1956 max 1956 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    24065 ave 24065 max 24065 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  48130 ave 48130 max 48130 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 48130
+Ave neighs/atom = 96.26
+Neighbor list builds = 6
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:04

examples/SPIN/cobalt_fcc/log.11May18.spin.cobalt_fcc.g++.4

@@ -0,0 +1,142 @@
+LAMMPS (11 May 2018)
+# fcc cobalt in a 3d periodic box
+
+clear
+units		metal
+atom_style 	spin
+
+dimension 	3
+boundary 	p p p
+
+# necessary for the serial algorithm (sametag)
+atom_modify 	map array
+
+lattice fcc 	3.54
+Lattice spacing in x,y,z = 3.54 3.54 3.54
+region box 	block 0.0 5.0 0.0 5.0 0.0 5.0
+create_box 	1 box
+Created orthogonal box = (0 0 0) to (17.7 17.7 17.7)
+  1 by 2 by 2 MPI processor grid
+create_atoms 	1 box
+Created 500 atoms
+  Time spent = 0.000240088 secs
+
+# setting mass, mag. moments, and interactions for fcc cobalt
+
+mass		1 58.93
+
+#set 		group all spin/random 31 1.72
+set 		group all spin 1.72 0.0 0.0 1.0
+  500 settings made for spin
+velocity 	all create 100 4928459 rot yes dist gaussian
+
+pair_style 	hybrid/overlay eam/alloy spin/exchange 4.0
+pair_coeff 	* * eam/alloy Co_PurjaPun_2012.eam.alloy Co
+pair_coeff 	* * spin/exchange exchange 4.0 0.0446928 0.003496 1.4885
+
+neighbor 	0.1 bin
+neigh_modify 	every 10 check yes delay 20
+
+fix 		1 all precession/spin zeeman 1.0 0.0 0.0 1.0
+fix_modify 	1 energy yes
+
+fix 		2 all langevin/spin 0.0 0.0 21
+
+fix 		3 all nve/spin lattice yes
+timestep	0.0001
+
+# compute and output options
+
+compute 	out_mag    all compute/spin
+compute 	out_pe     all pe
+compute 	out_ke     all ke
+compute 	out_temp   all temp
+
+thermo_style	custom f_1
+
+variable 	magx      equal c_out_mag[1]
+variable 	magy      equal c_out_mag[2]
+variable 	magz      equal c_out_mag[3]
+variable 	magnorm   equal c_out_mag[4]
+variable 	emag      equal c_out_mag[5]
+variable 	tmag      equal c_out_mag[6]
+
+thermo_style    custom step time f_1 v_magx v_magy v_magnorm v_emag temp etotal
+thermo          50
+
+#compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
+#dump 		100 all custom 1 dump_cobalt_fcc.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
+
+run 		1000
+Neighbor list info ...
+  update every 10 steps, delay 20 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 6.59954
+  ghost atom cutoff = 6.59954
+  binsize = 3.29977, bins = 6 6 6
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair eam/alloy, perpetual, half/full from (2)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+  (2) pair spin/exchange, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 5.163 | 5.163 | 5.163 Mbytes
+Step Time f_1 v_magx v_magy v_magnorm v_emag Temp TotEng 
+       0            0  0.049785486            0            0            1   -187.94116    100.00543   -2372.4636 
+      50        0.005  0.049785486            0            0            1   -187.94101    95.174807   -2372.4636 
+     100         0.01  0.049785486            0            0            1   -187.94029    81.854304   -2372.4636 
+     150        0.015  0.049785486            0            0            1   -187.93834    63.270938   -2372.4636 
+     200         0.02  0.049785486            0            0            1   -187.93446    43.867262   -2372.4636 
+     250        0.025  0.049785486            0            0            1   -187.92831    28.075261   -2372.4636 
+     300         0.03  0.049785486            0            0            1   -187.92031    19.046222   -2372.4636 
+     350        0.035  0.049785486            0            0            1   -187.91161     17.79071   -2372.4636 
+     400         0.04  0.049785486            0            0            1    -187.9039    23.079994   -2372.4636 
+     450        0.045  0.049785486            0            0            1   -187.89895    32.127316   -2372.4636 
+     500         0.05  0.049785486            0            0            1   -187.89801    41.709644   -2372.4636 
+     550        0.055  0.049785486            0            0            1   -187.90146    49.246292   -2372.4636 
+     600         0.06  0.049785486            0            0            1   -187.90859    53.465535   -2372.4636 
+     650        0.065  0.049785486            0            0            1   -187.91778    54.522857   -2372.4636 
+     700         0.07  0.049785486            0            0            1    -187.9269    53.635521   -2372.4636 
+     750        0.075  0.049785486            0            0            1   -187.93396    52.419678   -2372.4636 
+     800         0.08  0.049785486            0            0            1    -187.9376    52.176558   -2372.4636 
+     850        0.085  0.049785486            0            0            1   -187.93744    53.380592   -2372.4636 
+     900         0.09  0.049785486            0            0            1   -187.93412    55.551378   -2372.4636 
+     950        0.095  0.049785486            0            0            1   -187.92902    57.540047   -2372.4636 
+    1000          0.1  0.049785486            0            0            1   -187.92378    58.088674   -2372.4636 
+Loop time of 1.71411 on 4 procs for 1000 steps with 500 atoms
+
+Performance: 5.041 ns/day, 4.761 hours/ns, 583.392 timesteps/s
+97.7% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.54717    | 0.57392    | 0.58784    |   2.1 | 33.48
+Neigh   | 0.0023484  | 0.0025793  | 0.0026793  |   0.3 |  0.15
+Comm    | 0.058548   | 0.073335   | 0.10006    |   5.9 |  4.28
+Output  | 0.00042272 | 0.00079203 | 0.0018559  |   0.0 |  0.05
+Modify  | 1.0577     | 1.0611     | 1.0625     |   0.2 | 61.90
+Other   |            | 0.00239    |            |       |  0.14
+
+Nlocal:    125 ave 133 max 116 min
+Histogram: 1 0 0 0 0 2 0 0 0 1
+Nghost:    1099 ave 1108 max 1091 min
+Histogram: 1 0 0 0 2 0 0 0 0 1
+Neighs:    6032.5 ave 6417 max 5489 min
+Histogram: 1 0 0 0 0 0 1 1 0 1
+FullNghs:  12065 ave 13062 max 10970 min
+Histogram: 1 0 0 0 0 2 0 0 0 1
+
+Total # of neighbors = 48260
+Ave neighs/atom = 96.52
+Neighbor list builds = 6
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:01

examples/SPIN/cobalt_hcp/Co_PurjaPun_2012.eam.alloy

@@ -0,0 +1 @@
+../cobalt_fcc/Co_PurjaPun_2012.eam.alloy

examples/SPIN/cobalt_hcp/exchange_fit_hcp_co/exchange_fit.py

@@ -0,0 +1,32 @@
+#Program fitting the exchange interaction
+#Model curve: Bethe-Slater function
+import numpy as np, pylab, tkinter
+import matplotlib.pyplot as plt
+from scipy.optimize import curve_fit
+from decimal import *
+
+print("Loop begin")
+
+#Definition of the Bethe-Slater function
+def func(x,a,b,c):
+    return 4*a*((x/c)**2)*(1-b*(x/c)**2)*np.exp(-(x/c)**2)
+
+#Exchange coeff table (data to fit)
+rdata, Jdata = np.loadtxt('exchange_hcp_co.dat', usecols=(0,1), unpack=True)
+plt.plot(rdata, Jdata, 'b-', label='data')
+
+#Perform the fit
+popt, pcov = curve_fit(func, rdata, Jdata, bounds=(0, [500.,5.,5.]))
+plt.plot(rdata, func(rdata, *popt), 'r--', label='fit')
+
+#Print the fitted params
+print("Parameters: a={:.10} (in meV), b={:.10} (adim), c={:.10} (in Ang)".format(*popt))
+
+#Ploting the result
+plt.xlabel('r_ij')
+pylab.xlim([0,6.5])
+plt.ylabel('J_ij')
+plt.legend()
+plt.show()
+
+print("Loop end")

examples/SPIN/cobalt_hcp/exchange_fit_hcp_co/exchange_hcp_co.dat

@@ -0,0 +1,9 @@
+2.25569176882662 73.37931034482759
+2.3817863397548162 47.99999999999999
+2.4518388791593697 34.39080459770115
+2.507880910683012 31.816091954022987
+2.5359019264448337 28.137931034482747
+2.5779334500875657 25.011494252873554
+2.6339754816112086 19.126436781609186
+2.760070052539404 13.241379310344826
+3.5446584938704033 6.068965517241367

examples/SPIN/cobalt_hcp/in.spin.cobalt_hcp

@@ -0,0 +1,59 @@
+# hcp cobalt in a 3d periodic box
+
+clear 
+units	 	metal
+atom_style 	spin
+
+dimension 	3
+boundary 	p p p
+
+# necessary for the serial algorithm (sametag)
+atom_modify 	map array 
+
+lattice 	hcp 2.5071
+region 		box block 0.0 5.0 0.0 5.0 0.0 5.0
+create_box 	1 box
+create_atoms 	1 box
+
+# setting mass, mag. moments, and interactions for hcp cobalt
+
+mass		1 58.93
+
+#set 		group all spin/random 31 1.72
+set 		group all spin 1.72 0.0 0.0 1.0 
+velocity 	all create 100 4928459 rot yes dist gaussian
+
+#pair_style 	hybrid/overlay eam/alloy spin/exchange 4.0 spin/neel 4.0
+pair_style 	hybrid/overlay eam/alloy spin/exchange 4.0
+pair_coeff 	* * eam/alloy Co_PurjaPun_2012.eam.alloy Co
+pair_coeff 	* * spin/exchange exchange 4.0 0.3593 1.135028015e-05 1.064568567
+#pair_coeff 	* * spin/neel neel 4.0 0.0048 0.234 1.168 2.6905 0.705 0.652  
+
+
+neighbor 	0.1 bin
+neigh_modify 	every 10 check yes delay 20
+
+fix 		1 all precession/spin zeeman 1.0 0.0 0.0 1.0
+fix 		2 all langevin/spin 0.0 0.0 21
+fix 		3 all nve/spin lattice yes
+
+timestep	0.0001
+
+
+compute 	out_mag    all compute/spin
+compute 	out_pe     all pe
+compute 	out_ke     all ke
+compute 	out_temp   all temp
+
+variable 	magz      equal c_out_mag[3]
+variable 	magnorm   equal c_out_mag[4]
+variable 	emag      equal c_out_mag[5]
+variable 	tmag      equal c_out_mag[6]
+
+thermo_style    custom step time v_magnorm v_emag temp etotal
+thermo          10
+
+compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
+dump 		100 all custom 1 dump_cobalt_hcp.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
+
+run 		2000

examples/SPIN/cobalt_hcp/log.11May18.spin.cobalt_hcp.g++.1

@@ -0,0 +1,318 @@
+LAMMPS (11 May 2018)
+# hcp cobalt in a 3d periodic box
+
+clear
+units	 	metal
+atom_style 	spin
+
+dimension 	3
+boundary 	p p p
+
+# necessary for the serial algorithm (sametag)
+atom_modify 	map array
+
+lattice 	hcp 2.5071
+Lattice spacing in x,y,z = 2.5071 4.34242 4.09408
+region 		box block 0.0 5.0 0.0 5.0 0.0 5.0
+create_box 	1 box
+Created orthogonal box = (0 0 0) to (12.5355 21.7121 20.4704)
+  1 by 1 by 1 MPI processor grid
+create_atoms 	1 box
+Created 500 atoms
+  Time spent = 0.000801802 secs
+
+# setting mass, mag. moments, and interactions for hcp cobalt
+
+mass		1 58.93
+
+#set 		group all spin/random 31 1.72
+set 		group all spin 1.72 0.0 0.0 1.0
+  500 settings made for spin
+velocity 	all create 100 4928459 rot yes dist gaussian
+
+#pair_style 	hybrid/overlay eam/alloy spin/exchange 4.0 spin/neel 4.0
+pair_style 	hybrid/overlay eam/alloy spin/exchange 4.0
+pair_coeff 	* * eam/alloy Co_PurjaPun_2012.eam.alloy Co
+pair_coeff 	* * spin/exchange exchange 4.0 0.3593 1.135028015e-05 1.064568567
+#pair_coeff 	* * spin/neel neel 4.0 0.0048 0.234 1.168 2.6905 0.705 0.652
+
+
+neighbor 	0.1 bin
+neigh_modify 	every 10 check yes delay 20
+
+fix 		1 all precession/spin zeeman 1.0 0.0 0.0 1.0
+fix 		2 all langevin/spin 0.0 0.0 21
+fix 		3 all nve/spin lattice yes
+
+timestep	0.0001
+
+
+compute 	out_mag    all compute/spin
+compute 	out_pe     all pe
+compute 	out_ke     all ke
+compute 	out_temp   all temp
+
+variable 	magz      equal c_out_mag[3]
+variable 	magnorm   equal c_out_mag[4]
+variable 	emag      equal c_out_mag[5]
+variable 	tmag      equal c_out_mag[6]
+
+thermo_style    custom step time v_magnorm v_emag temp etotal
+thermo          10
+
+compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
+dump 		100 all custom 1 dump_cobalt_hcp.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
+
+run 		2000
+Neighbor list info ...
+  update every 10 steps, delay 20 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 6.59954
+  ghost atom cutoff = 6.59954
+  binsize = 3.29977, bins = 4 7 7
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair eam/alloy, perpetual, half/full from (2)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+  (2) pair spin/exchange, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 7.401 | 7.401 | 7.401 Mbytes
+Step Time v_magnorm v_emag Temp TotEng 
+       0            0            1   -187.29499    100.00543   -2375.8943 
+      10        0.001            1   -187.29714    99.845593   -2375.8943 
+      20        0.002            1   -187.30356    99.367234   -2375.8943 
+      30        0.003            1   -187.31419    98.573996   -2375.8943 
+      40        0.004            1   -187.32896    97.472027   -2375.8943 
+      50        0.005            1   -187.34772    96.069944   -2375.8943 
+      60        0.006            1   -187.37032    94.378764   -2375.8943 
+      70        0.007            1   -187.39656    92.411827   -2375.8943 
+      80        0.008            1    -187.4262    90.184697   -2375.8943 
+      90        0.009            1     -187.459    87.715037   -2375.8943 
+     100         0.01            1   -187.49466    85.022479   -2375.8943 
+     110        0.011            1   -187.53289    82.128462   -2375.8943 
+     120        0.012            1   -187.57334     79.05606   -2375.8943 
+     130        0.013            1   -187.61568     75.82979   -2375.8943 
+     140        0.014            1   -187.65953    72.475403   -2375.8943 
+     150        0.015            1   -187.70453    69.019658   -2375.8943 
+     160        0.016            1   -187.75028    65.490086   -2375.8943 
+     170        0.017            1   -187.79642    61.914735   -2375.8943 
+     180        0.018            1   -187.84254    58.321911   -2375.8943 
+     190        0.019            1   -187.88828    54.739907   -2375.8943 
+     200         0.02            1   -187.93324    51.196728   -2375.8943 
+     210        0.021            1   -187.97708    47.719812   -2375.8943 
+     220        0.022            1   -188.01947    44.335762   -2375.8943 
+     230        0.023            1   -188.06003     41.07007   -2375.8943 
+     240        0.024            1   -188.09853    37.946852   -2375.8944 
+     250        0.025            1   -188.13457    34.988599   -2375.8944 
+     260        0.026            1   -188.16795    32.215943   -2375.8944 
+     270        0.027            1   -188.19851    29.647465   -2375.8944 
+     280        0.028            1   -188.22593    27.299481   -2375.8944 
+     290        0.029            1   -188.25011    25.185896   -2375.8944 
+     300         0.03            1   -188.27095    23.318075   -2375.8945 
+     310        0.031            1    -188.2883     21.70475   -2375.8945 
+     320        0.032            1   -188.30213     20.35194   -2375.8945 
+     330        0.033            1   -188.31251    19.262946   -2375.8945 
+     340        0.034            1   -188.31928    18.438347   -2375.8945 
+     350        0.035            1   -188.32258    17.876036   -2375.8945 
+     360        0.036            1   -188.32249    17.571322   -2375.8945 
+     370        0.037            1   -188.31913    17.517032   -2375.8945 
+     380        0.038            1   -188.31264    17.703653   -2375.8945 
+     390        0.039            1   -188.30321    18.119513   -2375.8945 
+     400         0.04            1   -188.29102    18.750969   -2375.8945 
+     410        0.041            1    -188.2763    19.582631   -2375.8945 
+     420        0.042            1   -188.25929    20.597597   -2375.8945 
+     430        0.043            1   -188.24025    21.777699   -2375.8945 
+     440        0.044            1   -188.21945    23.103765   -2375.8945 
+     450        0.045            1   -188.19719    24.555878   -2375.8946 
+     460        0.046            1   -188.17368    26.113643   -2375.8946 
+     470        0.047            1    -188.1493    27.756439   -2375.8946 
+     480        0.048            1   -188.12429    29.463677   -2375.8946 
+     490        0.049            1   -188.09895     31.21504   -2375.8946 
+     500         0.05            1   -188.07354    32.990713   -2375.8946 
+     510        0.051            1   -188.04832    34.771601   -2375.8945 
+     520        0.052            1   -188.02358    36.539517   -2375.8945 
+     530        0.053            1   -187.99951     38.27736   -2375.8945 
+     540        0.054            1   -187.97636    39.969275   -2375.8945 
+     550        0.055            1   -187.95437    41.600775   -2375.8945 
+     560        0.056            1   -187.93364    43.158863   -2375.8944 
+     570        0.057            1    -187.9144    44.632119   -2375.8944 
+     580        0.058            1   -187.89669    46.010765   -2375.8944 
+     590        0.059            1   -187.88074    47.286714   -2375.8944 
+     600         0.06            1   -187.86658    48.453573   -2375.8944 
+     610        0.061            1   -187.85422    49.506668   -2375.8943 
+     620        0.062            1   -187.84377    50.443021   -2375.8943 
+     630        0.063            1    -187.8352    51.261297   -2375.8943 
+     640        0.064            1    -187.8285    51.961764   -2375.8943 
+     650        0.065            1    -187.8236     52.54622   -2375.8943 
+     660        0.066            1    -187.8205    53.017899   -2375.8943 
+     670        0.067            1   -187.81909    53.381374   -2375.8943 
+     680        0.068            1   -187.81926     53.64244   -2375.8943 
+     690        0.069            1   -187.82092    53.807997   -2375.8943 
+     700         0.07            1   -187.82391    53.885909   -2375.8943 
+     710        0.071            1   -187.82814    53.884865   -2375.8943 
+     720        0.072            1   -187.83339    53.814238   -2375.8943 
+     730        0.073            1   -187.83952     53.68392   -2375.8943 
+     740        0.074            1   -187.84635    53.504185   -2375.8943 
+     750        0.075            1   -187.85375    53.285525   -2375.8943 
+     760        0.076            1   -187.86153    53.038494   -2375.8943 
+     770        0.077            1   -187.86952    52.773567   -2375.8943 
+     780        0.078            1   -187.87758    52.500994   -2375.8943 
+     790        0.079            1   -187.88549    52.230655   -2375.8943 
+     800         0.08            1   -187.89313    51.971933   -2375.8943 
+     810        0.081            1   -187.90035    51.733593   -2375.8943 
+     820        0.082            1   -187.90702    51.523671   -2375.8943 
+     830        0.083            1   -187.91302    51.349376   -2375.8943 
+     840        0.084            1   -187.91824    51.217006   -2375.8943 
+     850        0.085            1    -187.9226    51.131875   -2375.8943 
+     860        0.086            1   -187.92602    51.098259   -2375.8943 
+     870        0.087            1   -187.92844    51.119356   -2375.8943 
+     880        0.088            1   -187.92979    51.197261   -2375.8943 
+     890        0.089            1   -187.93011    51.332955   -2375.8943 
+     900         0.09            1   -187.92937    51.526314   -2375.8943 
+     910        0.091            1   -187.92757     51.77613   -2375.8943 
+     920        0.092            1   -187.92475    52.080145   -2375.8943 
+     930        0.093            1   -187.92096    52.435106   -2375.8943 
+     940        0.094            1   -187.91624    52.836825   -2375.8943 
+     950        0.095            1   -187.91068    53.280251   -2375.8943 
+     960        0.096            1   -187.90435    53.759559   -2375.8943 
+     970        0.097            1   -187.89734    54.268246   -2375.8943 
+     980        0.098            1   -187.88981    54.799223   -2375.8943 
+     990        0.099            1   -187.88185    55.344928   -2375.8943 
+    1000          0.1            1   -187.87357    55.897438   -2375.8943 
+    1010        0.101            1   -187.86511    56.448585   -2375.8943 
+    1020        0.102            1    -187.8566    56.990069   -2375.8943 
+    1030        0.103            1   -187.84817    57.513575   -2375.8943 
+    1040        0.104            1   -187.83995    58.010887   -2375.8943 
+    1050        0.105            1   -187.83208    58.474004   -2375.8943 
+    1060        0.106            1    -187.8247     58.89524   -2375.8943 
+    1070        0.107            1   -187.81789    59.267328   -2375.8943 
+    1080        0.108            1   -187.81177    59.583518   -2375.8943 
+    1090        0.109            1   -187.80646    59.837665   -2375.8943 
+    1100         0.11            1   -187.80204    60.024306   -2375.8943 
+    1110        0.111            1   -187.79861    60.138734   -2375.8943 
+    1120        0.112            1   -187.79625    60.177056   -2375.8943 
+    1130        0.113            1   -187.79497    60.136244   -2375.8943 
+    1140        0.114            1   -187.79485    60.014176   -2375.8943 
+    1150        0.115            1    -187.7959    59.809665   -2375.8943 
+    1160        0.116            1   -187.79811     59.52248   -2375.8943 
+    1170        0.117            1   -187.80157    59.153353   -2375.8943 
+    1180        0.118            1   -187.80618    58.703971   -2375.8943 
+    1190        0.119            1   -187.81193    58.176956   -2375.8943 
+    1200         0.12            1   -187.81879    57.575849   -2375.8943 
+    1210        0.121            1   -187.82668    56.905072   -2375.8943 
+    1220        0.122            1   -187.83554    56.169878   -2375.8943 
+    1230        0.123            1   -187.84528    55.376297   -2375.8943 
+    1240        0.124            1   -187.85581     54.53107   -2375.8943 
+    1250        0.125            1   -187.86702    53.641573   -2375.8943 
+    1260        0.126            1    -187.8788    52.715739   -2375.8943 
+    1270        0.127            1   -187.89103    51.761969   -2375.8943 
+    1280        0.128            1   -187.90358    50.789036   -2375.8943 
+    1290        0.129            1   -187.91632    49.805988   -2375.8943 
+    1300         0.13            1   -187.92911    48.822045   -2375.8943 
+    1310        0.131            1   -187.94182    47.846491   -2375.8943 
+    1320        0.132            1   -187.95428    46.888574   -2375.8943 
+    1330        0.133            1   -187.96643    45.957394   -2375.8943 
+    1340        0.134            1    -187.9781    45.061794   -2375.8943 
+    1350        0.135            1    -187.9892    44.210263   -2375.8943 
+    1360        0.136            1   -187.99955    43.410832   -2375.8943 
+    1370        0.137            1   -188.00907    42.670979   -2375.8943 
+    1380        0.138            1   -188.01767    41.997547   -2375.8943 
+    1390        0.139            1   -188.02525    41.396655   -2375.8943 
+    1400         0.14            1   -188.03177    40.873631   -2375.8944 
+    1410        0.141            1   -188.03711    40.432952   -2375.8944 
+    1420        0.142            1   -188.04124    40.078172   -2375.8944 
+    1430        0.143            1   -188.04413    39.811902   -2375.8944 
+    1440        0.144            1   -188.04575    39.635775   -2375.8944 
+    1450        0.145            1   -188.04607    39.550435   -2375.8943 
+    1460        0.146            1   -188.04515    39.555512   -2375.8943 
+    1470        0.147            1   -188.04298    39.649651   -2375.8943 
+    1480        0.148            1   -188.03961    39.830523   -2375.8943 
+    1490        0.149            1   -188.03508    40.094865   -2375.8943 
+    1500         0.15            1   -188.02944    40.438519   -2375.8943 
+    1510        0.151            1   -188.02275    40.856491   -2375.8943 
+    1520        0.152            1   -188.01515    41.343019   -2375.8943 
+    1530        0.153            1   -188.00671    41.891643   -2375.8943 
+    1540        0.154            1   -187.99753    42.495295   -2375.8943 
+    1550        0.155            1   -187.98772     43.14639   -2375.8943 
+    1560        0.156            1    -187.9774    43.836918   -2375.8943 
+    1570        0.157            1    -187.9667    44.558553   -2375.8943 
+    1580        0.158            1   -187.95576    45.302751   -2375.8943 
+    1590        0.159            1   -187.94466    46.060862   -2375.8943 
+    1600         0.16            1   -187.93356    46.824226   -2375.8943 
+    1610        0.161            1   -187.92257    47.584289   -2375.8943 
+    1620        0.162            1   -187.91183    48.332703   -2375.8943 
+    1630        0.163            1   -187.90145    49.061422   -2375.8943 
+    1640        0.164            1   -187.89155    49.762798   -2375.8943 
+    1650        0.165            1   -187.88222    50.429671   -2375.8943 
+    1660        0.166            1   -187.87357    51.055445   -2375.8943 
+    1670        0.167            1   -187.86569    51.634167   -2375.8943 
+    1680        0.168            1   -187.85864    52.160588   -2375.8943 
+    1690        0.169            1   -187.85249    52.630219   -2375.8943 
+    1700         0.17            1    -187.8473    53.039377   -2375.8943 
+    1710        0.171            1   -187.84311    53.385221   -2375.8943 
+    1720        0.172            1   -187.83994    53.665778   -2375.8943 
+    1730        0.173            1   -187.83781    53.879954   -2375.8943 
+    1740        0.174            1   -187.83671    54.027539   -2375.8943 
+    1750        0.175            1   -187.83663    54.109201   -2375.8943 
+    1760        0.176            1   -187.83753    54.126472   -2375.8943 
+    1770        0.177            1   -187.83941    54.081708   -2375.8943 
+    1780        0.178            1    -187.8422     53.97806   -2375.8943 
+    1790        0.179            1   -187.84584    53.819424   -2375.8943 
+    1800         0.18            1   -187.85025    53.610389   -2375.8943 
+    1810        0.181            1   -187.85535    53.356163   -2375.8943 
+    1820        0.182            1   -187.86105     53.06251   -2375.8943 
+    1830        0.183            1   -187.86723    52.735671   -2375.8943 
+    1840        0.184            1   -187.87384    52.382262   -2375.8943 
+    1850        0.185            1   -187.88075    52.009201   -2375.8943 
+    1860        0.186            1   -187.88784    51.623613   -2375.8943 
+    1870        0.187            1   -187.89501    51.232726   -2375.8943 
+    1880        0.188            1   -187.90214    50.843782   -2375.8943 
+    1890        0.189            1   -187.90912    50.463929   -2375.8943 
+    1900         0.19            1   -187.91585    50.100133   -2375.8943 
+    1910        0.191            1   -187.92222    49.759075   -2375.8943 
+    1920        0.192            1   -187.92814    49.447064   -2375.8943 
+    1930        0.193            1   -187.93351    49.169949   -2375.8943 
+    1940        0.194            1   -187.93826    48.933036   -2375.8943 
+    1950        0.195            1   -187.94232    48.741013   -2375.8943 
+    1960        0.196            1   -187.94561    48.597888   -2375.8943 
+    1970        0.197            1   -187.94809    48.506926   -2375.8943 
+    1980        0.198            1   -187.94972    48.470605   -2375.8943 
+    1990        0.199            1   -187.95047    48.490576   -2375.8943 
+    2000          0.2            1   -187.95033    48.567643   -2375.8943 
+Loop time of 10.5391 on 1 procs for 2000 steps with 500 atoms
+
+Performance: 1.640 ns/day, 14.638 hours/ns, 189.770 timesteps/s
+99.6% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 4.9958     | 4.9958     | 4.9958     |   0.0 | 47.40
+Neigh   | 0.020741   | 0.020741   | 0.020741   |   0.0 |  0.20
+Comm    | 0.05899    | 0.05899    | 0.05899    |   0.0 |  0.56
+Output  | 1.1598     | 1.1598     | 1.1598     |   0.0 | 11.00
+Modify  | 4.2885     | 4.2885     | 4.2885     |   0.0 | 40.69
+Other   |            | 0.01522    |            |       |  0.14
+
+Nlocal:    500 ave 500 max 500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    2444 ave 2444 max 2444 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    27041 ave 27041 max 27041 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  54082 ave 54082 max 54082 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 54082
+Ave neighs/atom = 108.164
+Neighbor list builds = 12
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:10

examples/SPIN/cobalt_hcp/log.11May18.spin.cobalt_hcp.g++.4

@@ -0,0 +1,318 @@
+LAMMPS (11 May 2018)
+# hcp cobalt in a 3d periodic box
+
+clear
+units	 	metal
+atom_style 	spin
+
+dimension 	3
+boundary 	p p p
+
+# necessary for the serial algorithm (sametag)
+atom_modify 	map array
+
+lattice 	hcp 2.5071
+Lattice spacing in x,y,z = 2.5071 4.34242 4.09408
+region 		box block 0.0 5.0 0.0 5.0 0.0 5.0
+create_box 	1 box
+Created orthogonal box = (0 0 0) to (12.5355 21.7121 20.4704)
+  1 by 2 by 2 MPI processor grid
+create_atoms 	1 box
+Created 500 atoms
+  Time spent = 0.000241518 secs
+
+# setting mass, mag. moments, and interactions for hcp cobalt
+
+mass		1 58.93
+
+#set 		group all spin/random 31 1.72
+set 		group all spin 1.72 0.0 0.0 1.0
+  500 settings made for spin
+velocity 	all create 100 4928459 rot yes dist gaussian
+
+#pair_style 	hybrid/overlay eam/alloy spin/exchange 4.0 spin/neel 4.0
+pair_style 	hybrid/overlay eam/alloy spin/exchange 4.0
+pair_coeff 	* * eam/alloy Co_PurjaPun_2012.eam.alloy Co
+pair_coeff 	* * spin/exchange exchange 4.0 0.3593 1.135028015e-05 1.064568567
+#pair_coeff 	* * spin/neel neel 4.0 0.0048 0.234 1.168 2.6905 0.705 0.652
+
+
+neighbor 	0.1 bin
+neigh_modify 	every 10 check yes delay 20
+
+fix 		1 all precession/spin zeeman 1.0 0.0 0.0 1.0
+fix 		2 all langevin/spin 0.0 0.0 21
+fix 		3 all nve/spin lattice yes
+
+timestep	0.0001
+
+
+compute 	out_mag    all compute/spin
+compute 	out_pe     all pe
+compute 	out_ke     all ke
+compute 	out_temp   all temp
+
+variable 	magz      equal c_out_mag[3]
+variable 	magnorm   equal c_out_mag[4]
+variable 	emag      equal c_out_mag[5]
+variable 	tmag      equal c_out_mag[6]
+
+thermo_style    custom step time v_magnorm v_emag temp etotal
+thermo          10
+
+compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
+dump 		100 all custom 1 dump_cobalt_hcp.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
+
+run 		2000
+Neighbor list info ...
+  update every 10 steps, delay 20 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 6.59954
+  ghost atom cutoff = 6.59954
+  binsize = 3.29977, bins = 4 7 7
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair eam/alloy, perpetual, half/full from (2)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+  (2) pair spin/exchange, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 7.313 | 7.314 | 7.314 Mbytes
+Step Time v_magnorm v_emag Temp TotEng 
+       0            0            1   -187.29499    100.00543   -2375.8943 
+      10        0.001            1   -187.29721    99.841045   -2375.8943 
+      20        0.002            1   -187.30385    99.349208   -2375.8943 
+      30        0.003            1   -187.31485    98.533905   -2375.8943 
+      40        0.004            1   -187.33011    97.401749   -2375.8943 
+      50        0.005            1   -187.34949    95.961938   -2375.8943 
+      60        0.006            1   -187.37283     94.22618   -2375.8943 
+      70        0.007            1   -187.39992    92.208606   -2375.8943 
+      80        0.008            1   -187.43051     89.92566   -2375.8943 
+      90        0.009            1   -187.46434     87.39597   -2375.8943 
+     100         0.01            1    -187.5011    84.640195   -2375.8943 
+     110        0.011            1   -187.54047    81.680862   -2375.8943 
+     120        0.012            1    -187.5821    78.542172   -2375.8943 
+     130        0.013            1   -187.62564    75.249797   -2375.8943 
+     140        0.014            1   -187.67069    71.830656   -2375.8943 
+     150        0.015            1   -187.71686    68.312673   -2375.8943 
+     160        0.016            1   -187.76377    64.724523   -2375.8943 
+     170        0.017            1   -187.81099    61.095365   -2375.8943 
+     180        0.018            1   -187.85814    57.454566   -2375.8943 
+     190        0.019            1   -187.90481    53.831412   -2375.8943 
+     200         0.02            1   -187.95061    50.254822   -2375.8943 
+     210        0.021            1   -187.99517    46.753056   -2375.8943 
+     220        0.022            1   -188.03812    43.353428   -2375.8943 
+     230        0.023            1   -188.07913    40.082023   -2375.8943 
+     240        0.024            1   -188.11787    36.963429   -2375.8943 
+     250        0.025            1   -188.15409    34.020481   -2375.8943 
+     260        0.026            1    -188.1875     31.27403   -2375.8943 
+     270        0.027            1   -188.21782     28.74271   -2375.8943 
+     280        0.028            1    -188.2449     26.44276   -2375.8943 
+     290        0.029            1   -188.26857    24.387875   -2375.8943 
+     300         0.03            1   -188.28877    22.589076   -2375.8944 
+     310        0.031            1   -188.30529    21.054615   -2375.8944 
+     320        0.032            1   -188.31814    19.789913   -2375.8944 
+     330        0.033            1    -188.3273    18.797563   -2375.8944 
+     340        0.034            1   -188.33284    18.077336   -2375.8944 
+     350        0.035            1   -188.33478    17.626237   -2375.8945 
+     360        0.036            1   -188.33319    17.438611   -2375.8945 
+     370        0.037            1   -188.32824    17.506247   -2375.8945 
+     380        0.038            1   -188.32007    17.818564   -2375.8945 
+     390        0.039            1   -188.30888    18.362769   -2375.8945 
+     400         0.04            1    -188.2949    19.124086   -2375.8945 
+     410        0.041            1   -188.27837    20.085983   -2375.8945 
+     420        0.042            1   -188.25957    21.230423   -2375.8945 
+     430        0.043            1   -188.23868    22.538112   -2375.8945 
+     440        0.044            1   -188.21604    23.988778   -2375.8945 
+     450        0.045            1   -188.19195    25.561447   -2375.8945 
+     460        0.046            1   -188.16672    27.234703   -2375.8945 
+     470        0.047            1   -188.14064    28.986964   -2375.8946 
+     480        0.048            1   -188.11402    30.796738   -2375.8946 
+     490        0.049            1   -188.08713    32.642869   -2375.8945 
+     500         0.05            1   -188.06032    34.504776   -2375.8945 
+     510        0.051            1   -188.03383    36.362662   -2375.8945 
+     520        0.052            1   -188.00793    38.197721   -2375.8945 
+     530        0.053            1   -187.98284    39.992314   -2375.8945 
+     540        0.054            1   -187.95884    41.730127   -2375.8945 
+     550        0.055            1   -187.93612    43.396298   -2375.8945 
+     560        0.056            1   -187.91489     44.97754   -2375.8945 
+     570        0.057            1   -187.89524    46.462224   -2375.8945 
+     580        0.058            1   -187.87735    47.840443   -2375.8945 
+     590        0.059            1    -187.8613    49.104064   -2375.8945 
+     600         0.06            1   -187.84719    50.246744   -2375.8945 
+     610        0.061            1   -187.83509     51.26393   -2375.8944 
+     620        0.062            1   -187.82506    52.152839   -2375.8944 
+     630        0.063            1   -187.81706    52.912413   -2375.8944 
+     640        0.064            1   -187.81109    53.543272   -2375.8944 
+     650        0.065            1   -187.80708    54.047636   -2375.8944 
+     660        0.066            1   -187.80499    54.429234   -2375.8944 
+     670        0.067            1    -187.8047    54.693202   -2375.8944 
+     680        0.068            1   -187.80613    54.845965   -2375.8944 
+     690        0.069            1   -187.80914    54.895106   -2375.8944 
+     700         0.07            1   -187.81356    54.849238   -2375.8944 
+     710        0.071            1   -187.81923     54.71786   -2375.8943 
+     720        0.072            1   -187.82608    54.511181   -2375.8943 
+     730        0.073            1   -187.83388    54.239987   -2375.8943 
+     740        0.074            1   -187.84244     53.91548   -2375.8943 
+     750        0.075            1   -187.85158    53.549112   -2375.8943 
+     760        0.076            1   -187.86112    53.152433   -2375.8943 
+     770        0.077            1   -187.87086    52.736925   -2375.8943 
+     780        0.078            1   -187.88063    52.313858   -2375.8943 
+     790        0.079            1   -187.89026    51.894138   -2375.8943 
+     800         0.08            1   -187.89958    51.488169   -2375.8943 
+     810        0.081            1   -187.90842    51.105725   -2375.8943 
+     820        0.082            1   -187.91663    50.755829   -2375.8943 
+     830        0.083            1   -187.92411    50.446651   -2375.8943 
+     840        0.084            1   -187.93071    50.185404   -2375.8943 
+     850        0.085            1   -187.93637    49.978262   -2375.8943 
+     860        0.086            1   -187.94099    49.830307   -2375.8943 
+     870        0.087            1    -187.9445    49.745473   -2375.8943 
+     880        0.088            1   -187.94685    49.726517   -2375.8943 
+     890        0.089            1   -187.94802    49.774999   -2375.8943 
+     900         0.09            1   -187.94799    49.891282   -2375.8943 
+     910        0.091            1   -187.94678    50.074549   -2375.8943 
+     920        0.092            1   -187.94441    50.322833   -2375.8943 
+     930        0.093            1   -187.94093    50.633063   -2375.8943 
+     940        0.094            1   -187.93639    51.001126   -2375.8943 
+     950        0.095            1   -187.93089    51.421938   -2375.8943 
+     960        0.096            1    -187.9245    51.889531   -2375.8943 
+     970        0.097            1   -187.91733    52.397148   -2375.8943 
+     980        0.098            1    -187.9095    52.937345   -2375.8943 
+     990        0.099            1   -187.90113    53.502108   -2375.8943 
+    1000          0.1            1   -187.89236    54.082966   -2375.8943 
+    1010        0.101            1   -187.88332    54.671115   -2375.8943 
+    1020        0.102            1   -187.87415    55.257545   -2375.8943 
+    1030        0.103            1   -187.86501    55.833162   -2375.8943 
+    1040        0.104            1   -187.85602    56.388915   -2375.8943 
+    1050        0.105            1   -187.84734    56.915918   -2375.8943 
+    1060        0.106            1   -187.83909    57.405575   -2375.8943 
+    1070        0.107            1   -187.83143    57.849686   -2375.8943 
+    1080        0.108            1   -187.82446    58.240564   -2375.8943 
+    1090        0.109            1    -187.8183    58.571132   -2375.8943 
+    1100         0.11            1   -187.81306    58.835016   -2375.8943 
+    1110        0.111            1   -187.80883    59.026633   -2375.8943 
+    1120        0.112            1    -187.8057    59.141258   -2375.8943 
+    1130        0.113            1   -187.80372     59.17509   -2375.8943 
+    1140        0.114            1   -187.80295    59.125305   -2375.8943 
+    1150        0.115            1   -187.80341    58.990092   -2375.8943 
+    1160        0.116            1   -187.80515     58.76868   -2375.8943 
+    1170        0.117            1   -187.80814    58.461352   -2375.8943 
+    1180        0.118            1   -187.81244    58.069457   -2375.8943 
+    1190        0.119            1   -187.81794    57.595377   -2375.8944 
+    1200         0.12            1   -187.82458    57.042514   -2375.8944 
+    1210        0.121            1   -187.83233    56.415256   -2375.8944 
+    1220        0.122            1   -187.84112    55.718931   -2375.8944 
+    1230        0.123            1   -187.85086    54.959744   -2375.8944 
+    1240        0.124            1   -187.86145    54.144707   -2375.8944 
+    1250        0.125            1   -187.87277    53.281562   -2375.8944 
+    1260        0.126            1   -187.88471    52.378686   -2375.8944 
+    1270        0.127            1   -187.89713       51.445   -2375.8944 
+    1280        0.128            1    -187.9099    50.489858   -2375.8944 
+    1290        0.129            1   -187.92288    49.522943   -2375.8944 
+    1300         0.13            1   -187.93591    48.554147   -2375.8944 
+    1310        0.131            1   -187.94886    47.593456   -2375.8944 
+    1320        0.132            1   -187.96157    46.650829   -2375.8944 
+    1330        0.133            1   -187.97391    45.736073   -2375.8944 
+    1340        0.134            1   -187.98573    44.858733   -2375.8944 
+    1350        0.135            1   -187.99691    44.027964   -2375.8944 
+    1360        0.136            1   -188.00731    43.252426   -2375.8944 
+    1370        0.137            1   -188.01678    42.540178   -2375.8943 
+    1380        0.138            1   -188.02529    41.898568   -2375.8943 
+    1390        0.139            1    -188.0327    41.334152   -2375.8943 
+    1400         0.14            1   -188.03894    40.852606   -2375.8943 
+    1410        0.141            1   -188.04396     40.45866   -2375.8944 
+    1420        0.142            1   -188.04768    40.156041   -2375.8944 
+    1430        0.143            1   -188.05007    39.947416   -2375.8944 
+    1440        0.144            1   -188.05107    39.834367   -2375.8944 
+    1450        0.145            1    -188.0507    39.817378   -2375.8944 
+    1460        0.146            1   -188.04898    39.895828   -2375.8944 
+    1470        0.147            1   -188.04595    40.068005   -2375.8945 
+    1480        0.148            1   -188.04164    40.331129   -2375.8945 
+    1490        0.149            1   -188.03603    40.681394   -2375.8945 
+    1500         0.15            1   -188.02929    41.114003   -2375.8945 
+    1510        0.151            1   -188.02148    41.623259   -2375.8945 
+    1520        0.152            1    -188.0127     42.20263   -2375.8945 
+    1530        0.153            1   -188.00302    42.844846   -2375.8945 
+    1540        0.154            1   -187.99255    43.541977   -2375.8945 
+    1550        0.155            1   -187.98148    44.285554   -2375.8945 
+    1560        0.156            1   -187.96989    45.066666   -2375.8945 
+    1570        0.157            1   -187.95793    45.876084   -2375.8945 
+    1580        0.158            1   -187.94574    46.704378   -2375.8945 
+    1590        0.159            1   -187.93346    47.542032   -2375.8945 
+    1600         0.16            1   -187.92122    48.379564   -2375.8945 
+    1610        0.161            1   -187.90916    49.207642   -2375.8945 
+    1620        0.162            1   -187.89742      50.0172   -2375.8945 
+    1630        0.163            1   -187.88613    50.799541   -2375.8945 
+    1640        0.164            1   -187.87536    51.546446   -2375.8944 
+    1650        0.165            1   -187.86531    52.250265   -2375.8944 
+    1660        0.166            1   -187.85604    52.904001   -2375.8944 
+    1670        0.167            1   -187.84765    53.501394   -2375.8944 
+    1680        0.168            1   -187.84021    54.036987   -2375.8944 
+    1690        0.169            1   -187.83379    54.506178   -2375.8944 
+    1700         0.17            1   -187.82846    54.905273   -2375.8944 
+    1710        0.171            1   -187.82424    55.231514   -2375.8944 
+    1720        0.172            1   -187.82117    55.483104   -2375.8944 
+    1730        0.173            1   -187.81922    55.659221   -2375.8944 
+    1740        0.174            1   -187.81843    55.760007   -2375.8944 
+    1750        0.175            1   -187.81881    55.786556   -2375.8944 
+    1760        0.176            1   -187.82029    55.740888   -2375.8944 
+    1770        0.177            1   -187.82284    55.625916   -2375.8944 
+    1780        0.178            1   -187.82639    55.445397   -2375.8944 
+    1790        0.179            1   -187.83088    55.203871   -2375.8944 
+    1800         0.18            1   -187.83623    54.906597   -2375.8944 
+    1810        0.181            1   -187.84235    54.559471   -2375.8944 
+    1820        0.182            1   -187.84913    54.168949   -2375.8944 
+    1830        0.183            1   -187.85646    53.741952   -2375.8943 
+    1840        0.184            1   -187.86424     53.28578   -2375.8943 
+    1850        0.185            1   -187.87239    52.807988   -2375.8943 
+    1860        0.186            1   -187.88077      52.3163   -2375.8943 
+    1870        0.187            1   -187.88925     51.81851   -2375.8943 
+    1880        0.188            1   -187.89772    51.322368   -2375.8943 
+    1890        0.189            1   -187.90605    50.835483   -2375.8943 
+    1900         0.19            1   -187.91415    50.365218   -2375.8943 
+    1910        0.191            1   -187.92189      49.9186   -2375.8943 
+    1920        0.192            1   -187.92917    49.502222   -2375.8943 
+    1930        0.193            1   -187.93591    49.122167   -2375.8943 
+    1940        0.194            1   -187.94198    48.783928   -2375.8943 
+    1950        0.195            1   -187.94737    48.492348   -2375.8943 
+    1960        0.196            1   -187.95199     48.25154   -2375.8943 
+    1970        0.197            1   -187.95576    48.064862   -2375.8943 
+    1980        0.198            1   -187.95866    47.934875   -2375.8943 
+    1990        0.199            1   -187.96065    47.863314   -2375.8943 
+    2000          0.2            1   -187.96171    47.851079   -2375.8943 
+Loop time of 4.40076 on 4 procs for 2000 steps with 500 atoms
+
+Performance: 3.927 ns/day, 6.112 hours/ns, 454.467 timesteps/s
+96.2% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 1.2934     | 1.3683     | 1.432      |   4.2 | 31.09
+Neigh   | 0.005039   | 0.0053418  | 0.0054908  |   0.2 |  0.12
+Comm    | 0.12642    | 0.1922     | 0.26891    |  11.6 |  4.37
+Output  | 0.39256    | 0.40875    | 0.43431    |   2.5 |  9.29
+Modify  | 2.395      | 2.4202     | 2.4352     |   1.0 | 54.99
+Other   |            | 0.006007   |            |       |  0.14
+
+Nlocal:    125 ave 130 max 122 min
+Histogram: 1 1 0 1 0 0 0 0 0 1
+Nghost:    1324 ave 1330 max 1316 min
+Histogram: 1 0 0 1 0 0 0 0 0 2
+Neighs:    6747 ave 6959 max 6652 min
+Histogram: 2 1 0 0 0 0 0 0 0 1
+FullNghs:  13494 ave 14060 max 13186 min
+Histogram: 2 0 0 1 0 0 0 0 0 1
+
+Total # of neighbors = 53976
+Ave neighs/atom = 107.952
+Neighbor list builds = 12
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:04

examples/SPIN/iron/exchange_fit_bcc_iron/exchange_bcc_iron.dat

@@ -0,0 +1,5 @@
+2.4824 0.01948336
+2.8665 0.01109
+4.0538 -0.0002176
+4.753 -0.001714
+4.965 -0.001986

examples/SPIN/iron/exchange_fit_bcc_iron/exchange_fit.py

@@ -0,0 +1,32 @@
+#Program fitting the exchange interaction
+#Model curve: Bethe-Slater function
+import numpy as np, pylab, tkinter
+import matplotlib.pyplot as plt
+from scipy.optimize import curve_fit
+from decimal import *
+
+print("Loop begin")
+
+#Definition of the Bethe-Slater function
+def func(x,a,b,c):
+    return 4*a*((x/c)**2)*(1-b*(x/c)**2)*np.exp(-(x/c)**2)
+
+#Exchange coeff table (data to fit)
+rdata, Jdata = np.loadtxt('exchange_bcc_iron.dat', usecols=(0,1), unpack=True)
+plt.plot(rdata, Jdata, 'b-', label='data')
+
+#Perform the fit
+popt, pcov = curve_fit(func, rdata, Jdata, bounds=(0, [500.,5.,5.]))
+plt.plot(rdata, func(rdata, *popt), 'r--', label='fit')
+
+#Print the fitted params
+print("Parameters: a={:.10} (in meV), b={:.10} (adim), c={:.10} (in Ang)".format(*popt))
+
+#Ploting the result
+plt.xlabel('r_ij')
+pylab.xlim([0,6.5])
+plt.ylabel('J_ij')
+plt.legend()
+plt.show()
+
+print("Loop end")

examples/SPIN/iron/fe_dd.dat

@@ -0,0 +1,19 @@
+            6            8
+ Optimal parameter set
+            1    4.100199340884814       F
+            2    1.565647547483517       F
+            1   0.9332056681088162       T    3.000000000000000     
+            2   -1.162558782567700       T    2.866666666666670     
+            3  -0.3502026949249225       T    2.733333333333330     
+            4   0.4287820835430028       T    2.600000000000000     
+            5    4.907925057809273       T    2.400000000000000     
+            6   -5.307049068415304       T    2.300000000000000     
+            1  -0.1960674387419232       F    4.100000000000000     
+            2   0.3687525935422963       F    3.800000000000000     
+            3   -1.505333614924853       F    3.500000000000000     
+            4    4.948907078156191       T    3.200000000000000     
+            5   -4.894613262753399       T    2.900000000000000     
+            6    3.468897724782442       T    2.600000000000000     
+            7   -1.792218099820337       T    2.400000000000000     
+            8    80.22069592246987       T    2.300000000000000     
+

examples/SPIN/iron/in.spin.iron

@@ -0,0 +1,56 @@
+# bcc iron in a 3d periodic box
+
+clear 
+units 		metal
+atom_style 	spin
+
+dimension 	3
+boundary 	p p p
+
+# necessary for the serial algorithm (sametag)
+atom_modify 	map array 
+
+lattice 	bcc 2.8665
+region 		box block 0.0 5.0 0.0 5.0 0.0 5.0
+create_box 	1 box
+create_atoms 	1 box
+
+# setting mass, mag. moments, and interactions for bcc iron
+
+mass		1 55.845
+
+set 		group all spin/random 31 2.2
+velocity 	all create 100 4928459 rot yes dist gaussian
+
+pair_style 	hybrid/overlay eam/alloy spin/exchange 3.5
+pair_coeff 	* * eam/alloy Fe_Mishin2006.eam.alloy Fe
+pair_coeff 	* * spin/exchange exchange 3.4 0.02726 0.2171 1.841
+
+neighbor 	0.1 bin
+neigh_modify 	every 10 check yes delay 20
+
+fix 		1 all precession/spin zeeman 0.0 0.0 0.0 1.0
+fix 		2 all langevin/spin 0.0 0.0 21
+
+fix 		3 all nve/spin lattice yes
+timestep	0.0001
+
+# compute and output options
+
+compute 	out_mag    all compute/spin
+compute 	out_pe     all pe
+compute 	out_ke     all ke
+compute 	out_temp   all temp
+
+variable 	magz      equal c_out_mag[3]
+variable 	magnorm   equal c_out_mag[4]
+variable 	emag      equal c_out_mag[5]
+variable 	tmag      equal c_out_mag[6]
+
+thermo_style    custom step time v_magnorm v_tmag temp v_emag ke pe etotal
+thermo          50
+
+compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
+dump 		100 all custom 1 dump_iron.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
+
+run 		50000

examples/SPIN/nickel/exchange_fit_fcc_ni/exchange_fcc_ni.dat

@@ -0,0 +1,5 @@
+2.492 0.0028027
+3.524 0.0000816
+4.316 0.0003537
+4.984 0.0001632
+5.572 0.0000408

examples/SPIN/nickel/exchange_fit_fcc_ni/exchange_fcc_ni2.dat

@@ -0,0 +1,5 @@
+2.495 8.3
+3.524 -3.99
+4.31 0.998
+4.99 -0.955
+5.56 0.213

examples/SPIN/nickel/exchange_fit_fcc_ni/exchange_fit.py

@@ -0,0 +1,33 @@
+# program fitting the exchange interaction
+# model curve: Bethe-Slater function
+import numpy as np, pylab, tkinter
+import matplotlib.pyplot as plt
+from scipy.optimize import curve_fit
+from decimal import *
+
+print("Loop begin")
+
+# definition of the Bethe-Slater function
+def func(x,a,b,c):
+    return 4*a*((x/c)**2)*(1-b*(x/c)**2)*np.exp(-(x/c)**2)
+
+# exchange coeff table (data to fit)
+rdata, Jdata = np.loadtxt('exchange_fcc_ni.dat', usecols=(0,1), unpack=True)
+plt.plot(rdata, Jdata, 'b-', label='data')
+
+# perform the fit
+popt, pcov = curve_fit(func, rdata, Jdata, bounds=([0.0,-1.0,0.0], [100.,5.,5.]))
+plt.plot(rdata, func(rdata, *popt), 'r--', label='fit')
+
+# print the fitted parameters
+print("Parameters: a={:.10} (in meV), b={:.10} (adim), c={:.10} (in Ang)".format(*popt))
+
+# ploting the result
+plt.xlabel('r_ij')
+pylab.xlim([0.0,6.5])
+#pylab.ylim([-2.0,10.0])
+plt.ylabel('J_ij')
+plt.legend()
+plt.show()
+
+print("Loop end")

examples/SPIN/nickel/in.spin.nickel

@@ -0,0 +1,58 @@
+# fcc nickel in a 3d periodic box
+
+clear 
+units 		metal
+atom_style 	spin
+
+dimension 	3
+boundary 	p p p
+
+# necessary for the serial algorithm (sametag)
+atom_modify 	map array 
+
+lattice 	fcc 3.524
+region 		box block 0.0 5.0 0.0 5.0 0.0 5.0
+create_box 	1 box
+create_atoms 	1 box
+
+# setting mass, mag. moments, and interactions for cobalt
+
+mass		1 58.69
+
+set 		group all spin/random 31 0.63
+#set 		group all spin 0.63 0.0 0.0 1.0 
+velocity 	all create 100 4928459 rot yes dist gaussian
+
+pair_style 	hybrid/overlay eam/alloy spin/exchange 4.0
+pair_coeff 	* * eam/alloy Ni99.eam.alloy Ni
+pair_coeff 	* * spin/exchange exchange 4.0 0.50 0.2280246862 1.229983475
+
+neighbor 	0.1 bin
+neigh_modify 	every 10 check yes delay 20
+
+fix 		1 all precession/spin zeeman 0.0 0.0 0.0 1.0
+fix 		2 all langevin/spin 0.0 0.0 21
+
+fix 		3 all nve/spin lattice yes
+timestep	0.0001
+
+# compute and output options
+
+compute 	out_mag    all compute/spin
+compute 	out_pe     all pe
+compute 	out_ke     all ke
+compute 	out_temp   all temp
+
+variable 	magz      equal c_out_mag[3]
+variable 	magnorm   equal c_out_mag[4]
+variable 	emag      equal c_out_mag[5]
+variable 	tmag      equal c_out_mag[6]
+
+thermo_style    custom step time v_magnorm v_emag temp v_tmag etotal
+thermo          50
+
+compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
+dump 		50 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
+
+run 		2000
+

examples/SPIN/nickel/log.11May18.spin.nickel.g++.1

@@ -0,0 +1,157 @@
+LAMMPS (11 May 2018)
+# fcc nickel in a 3d periodic box
+
+clear
+units 		metal
+atom_style 	spin
+
+dimension 	3
+boundary 	p p p
+
+# necessary for the serial algorithm (sametag)
+atom_modify 	map array
+
+lattice 	fcc 3.524
+Lattice spacing in x,y,z = 3.524 3.524 3.524
+region 		box block 0.0 5.0 0.0 5.0 0.0 5.0
+create_box 	1 box
+Created orthogonal box = (0 0 0) to (17.62 17.62 17.62)
+  1 by 1 by 1 MPI processor grid
+create_atoms 	1 box
+Created 500 atoms
+  Time spent = 0.000804186 secs
+
+# setting mass, mag. moments, and interactions for cobalt
+
+mass		1 58.69
+
+set 		group all spin/random 31 0.63
+  500 settings made for spin/random
+#set 		group all spin 0.63 0.0 0.0 1.0
+velocity 	all create 100 4928459 rot yes dist gaussian
+
+pair_style 	hybrid/overlay eam/alloy spin/exchange 4.0
+pair_coeff 	* * eam/alloy Ni99.eam.alloy Ni
+pair_coeff 	* * spin/exchange exchange 4.0 0.50 0.2280246862 1.229983475
+
+neighbor 	0.1 bin
+neigh_modify 	every 10 check yes delay 20
+
+fix 		1 all precession/spin zeeman 0.0 0.0 0.0 1.0
+fix 		2 all langevin/spin 0.0 0.0 21
+
+fix 		3 all nve/spin lattice yes
+timestep	0.0001
+
+# compute and output options
+
+compute 	out_mag    all compute/spin
+compute 	out_pe     all pe
+compute 	out_ke     all ke
+compute 	out_temp   all temp
+
+variable 	magz      equal c_out_mag[3]
+variable 	magnorm   equal c_out_mag[4]
+variable 	emag      equal c_out_mag[5]
+variable 	tmag      equal c_out_mag[6]
+
+thermo_style    custom step time v_magnorm v_emag temp v_tmag etotal
+thermo          50
+
+compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
+dump 		50 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
+
+run 		2000
+Neighbor list info ...
+  update every 10 steps, delay 20 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 5.90375
+  ghost atom cutoff = 5.90375
+  binsize = 2.95187, bins = 6 6 6
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair eam/alloy, perpetual, half/full from (2)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+  (2) pair spin/exchange, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 7.384 | 7.384 | 7.384 Mbytes
+Step Time v_magnorm v_emag Temp v_tmag TotEng 
+       0            0  0.028733803   0.40997576    100.03408   -9550.1342   -2218.1018 
+      50        0.005  0.028733807  0.070491717    101.47879   -56307.038   -2218.1018 
+     100         0.01  0.028733815  -0.70937134     101.7311    5851.6355   -2218.1018 
+     150        0.015  0.028733823    -1.853981     99.63039    2395.8677   -2218.1018 
+     200         0.02  0.028733828   -3.2679239    94.850105    1482.3486   -2218.1018 
+     250        0.025  0.028733824    -4.863967    88.444584    1100.7396   -2218.1018 
+     300         0.03  0.028733807   -6.5763457    82.689581    899.56642   -2218.1018 
+     350        0.035  0.028733783   -8.3489158    80.108798    768.64457   -2218.1018 
+     400         0.04  0.028733763   -10.120216    82.374947    670.03091   -2218.1018 
+     450        0.045  0.028733755   -11.828932    89.814597    593.77931   -2218.1018 
+     500         0.05  0.028733762   -13.423712    101.39613    535.03371   -2218.1018 
+     550        0.055  0.028733783   -14.866724    115.07399    489.92024   -2218.1018 
+     600         0.06  0.028733801   -16.135279    128.57849    458.66654   -2218.1018 
+     650        0.065  0.028733804   -17.222838    140.22402    440.11437   -2218.1018 
+     700         0.07  0.028733795   -18.154813    149.61295    425.91356   -2218.1018 
+     750        0.075  0.028733781   -18.996903     157.5814    412.82654   -2218.1018 
+     800         0.08  0.028733768   -19.804249    164.92075    407.77954   -2218.1018 
+     850        0.085  0.028733752   -20.579151    171.67278    406.84726   -2218.1018 
+     900         0.09  0.028733728   -21.294277    177.67238    399.69633   -2218.1018 
+     950        0.095  0.028733715   -21.943945     183.2621    389.92281   -2218.1018 
+    1000          0.1   0.02873374   -22.551277    188.99284    383.19592   -2218.1018 
+    1050        0.105  0.028733783   -23.120147    194.51391    375.87245   -2218.1018 
+    1100         0.11  0.028733792   -23.602325    198.18631    365.37753   -2218.1018 
+    1150        0.115  0.028733774   -23.976048    199.04022    354.04863   -2218.1018 
+    1200         0.12   0.02873376    -24.31575    198.41999    346.40397   -2218.1018 
+    1250        0.125  0.028733759   -24.718347     198.3669     343.1701   -2218.1018 
+    1300         0.13  0.028733765   -25.189073    199.57949    336.90052   -2218.1018 
+    1350        0.135  0.028733774   -25.650252    201.45897    329.07023   -2218.1018 
+    1400         0.14  0.028733785   -26.042702     203.6926    327.97373   -2218.1018 
+    1450        0.145  0.028733791   -26.373965    206.80469    327.38747   -2218.1018 
+    1500         0.15  0.028733791   -26.691802    211.43923    322.75885   -2218.1018 
+    1550        0.155  0.028733794   -27.021573    217.10969    315.55781   -2218.1018 
+    1600         0.16  0.028733792   -27.344066    222.16052     310.6743   -2218.1018 
+    1650        0.165  0.028733788   -27.640017    225.28449    310.49671   -2218.1018 
+    1700         0.17  0.028733803   -27.907241    226.37676     310.9389   -2218.1018 
+    1750        0.175  0.028733828   -28.143477    226.31095    313.28034   -2218.1018 
+    1800         0.18  0.028733833   -28.363397    226.43633    317.31668   -2218.1018 
+    1850        0.185  0.028733811    -28.58153    227.36287    318.98645   -2218.1018 
+    1900         0.19  0.028733796   -28.785208    228.39889     316.9972   -2218.1018 
+    1950        0.195  0.028733826     -28.9724    228.84666     309.8027   -2218.1018 
+    2000          0.2   0.02873386   -29.175039      228.918    297.88519   -2218.1018 
+Loop time of 10.033 on 1 procs for 2000 steps with 500 atoms
+
+Performance: 1.722 ns/day, 13.935 hours/ns, 199.342 timesteps/s
+99.4% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 3.909      | 3.909      | 3.909      |   0.0 | 38.96
+Neigh   | 0.031031   | 0.031031   | 0.031031   |   0.0 |  0.31
+Comm    | 0.046559   | 0.046559   | 0.046559   |   0.0 |  0.46
+Output  | 2.4087     | 2.4087     | 2.4087     |   0.0 | 24.01
+Modify  | 3.625      | 3.625      | 3.625      |   0.0 | 36.13
+Other   |            | 0.01268    |            |       |  0.13
+
+Nlocal:    500 ave 500 max 500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    1956 ave 1956 max 1956 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    19508 ave 19508 max 19508 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  39016 ave 39016 max 39016 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 39016
+Ave neighs/atom = 78.032
+Neighbor list builds = 21
+Dangerous builds = 0
+
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:10

examples/SPIN/nickel/log.11May18.spin.nickel.g++.4

@@ -0,0 +1,157 @@
+LAMMPS (11 May 2018)
+# fcc nickel in a 3d periodic box
+
+clear
+units 		metal
+atom_style 	spin
+
+dimension 	3
+boundary 	p p p
+
+# necessary for the serial algorithm (sametag)
+atom_modify 	map array
+
+lattice 	fcc 3.524
+Lattice spacing in x,y,z = 3.524 3.524 3.524
+region 		box block 0.0 5.0 0.0 5.0 0.0 5.0
+create_box 	1 box
+Created orthogonal box = (0 0 0) to (17.62 17.62 17.62)
+  1 by 2 by 2 MPI processor grid
+create_atoms 	1 box
+Created 500 atoms
+  Time spent = 0.000523567 secs
+
+# setting mass, mag. moments, and interactions for cobalt
+
+mass		1 58.69
+
+set 		group all spin/random 31 0.63
+  500 settings made for spin/random
+#set 		group all spin 0.63 0.0 0.0 1.0
+velocity 	all create 100 4928459 rot yes dist gaussian
+
+pair_style 	hybrid/overlay eam/alloy spin/exchange 4.0
+pair_coeff 	* * eam/alloy Ni99.eam.alloy Ni
+pair_coeff 	* * spin/exchange exchange 4.0 0.50 0.2280246862 1.229983475
+
+neighbor 	0.1 bin
+neigh_modify 	every 10 check yes delay 20
+
+fix 		1 all precession/spin zeeman 0.0 0.0 0.0 1.0
+fix 		2 all langevin/spin 0.0 0.0 21
+
+fix 		3 all nve/spin lattice yes
+timestep	0.0001
+
+# compute and output options
+
+compute 	out_mag    all compute/spin
+compute 	out_pe     all pe
+compute 	out_ke     all ke
+compute 	out_temp   all temp
+
+variable 	magz      equal c_out_mag[3]
+variable 	magnorm   equal c_out_mag[4]
+variable 	emag      equal c_out_mag[5]
+variable 	tmag      equal c_out_mag[6]
+
+thermo_style    custom step time v_magnorm v_emag temp v_tmag etotal
+thermo          50
+
+compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
+dump 		50 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
+
+run 		2000
+Neighbor list info ...
+  update every 10 steps, delay 20 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 5.90375
+  ghost atom cutoff = 5.90375
+  binsize = 2.95187, bins = 6 6 6
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair eam/alloy, perpetual, half/full from (2)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+  (2) pair spin/exchange, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 7.298 | 7.298 | 7.298 Mbytes
+Step Time v_magnorm v_emag Temp v_tmag TotEng 
+       0            0  0.028733803   0.40997576    100.03408   -9550.1342   -2218.1018 
+      50        0.005  0.028733805   0.25324083    98.741633   -15727.749   -2218.1018 
+     100         0.01  0.028733812  -0.37320751    97.073875    11244.373   -2218.1018 
+     150        0.015  0.028733819   -1.3971549    94.073447    3250.0517   -2218.1018 
+     200         0.02  0.028733825   -2.7238372    89.419944     1838.752   -2218.1018 
+     250        0.025  0.028733829   -4.2684428     84.07494    1304.3675   -2218.1018 
+     300         0.03  0.028733824   -5.9636712     80.06368    1025.7815   -2218.1018 
+     350        0.035   0.02873381   -7.7386326    79.366702    844.49729   -2218.1018 
+     400         0.04  0.028733802   -9.5148059    83.052751    715.20758   -2218.1018 
+     450        0.045  0.028733806   -11.234935    91.282747    621.75552   -2218.1018 
+     500         0.05   0.02873381   -12.875184    103.49836    550.04479   -2218.1018 
+     550        0.055  0.028733808   -14.413473    118.16526    495.70417   -2218.1018 
+     600         0.06  0.028733803   -15.812466    132.83837    461.35805   -2218.1018 
+     650        0.065  0.028733808   -17.061311    145.41049    444.38951   -2218.1018 
+     700         0.07  0.028733818   -18.181903    154.83414    438.85866   -2218.1018 
+     750        0.075  0.028733823   -19.176259    160.58645    436.90462   -2218.1018 
+     800         0.08  0.028733825   -20.035157    163.02829    429.73193   -2218.1018 
+     850        0.085  0.028733825   -20.806548     164.4197    419.73763   -2218.1018 
+     900         0.09  0.028733829   -21.571419     167.8571    411.59699   -2218.1018 
+     950        0.095  0.028733825   -22.365879    175.00875    402.66175   -2218.1018 
+    1000          0.1  0.028733821   -23.133464    184.68305    391.05824   -2218.1018 
+    1050        0.105  0.028733833   -23.770507    193.83795    379.23354   -2218.1018 
+    1100         0.11   0.02873385   -24.249882     200.5039    372.08521   -2218.1018 
+    1150        0.115  0.028733864   -24.630489    204.46984    367.92135   -2218.1018 
+    1200         0.12  0.028733877   -24.956281    205.96624    363.72367   -2218.1018 
+    1250        0.125  0.028733884   -25.227332    205.18503    361.09236   -2218.1018 
+    1300         0.13  0.028733877    -25.43568    202.76969    359.10924   -2218.1018 
+    1350        0.135  0.028733868   -25.588748    199.85462    358.69556   -2218.1018 
+    1400         0.14  0.028733866   -25.723582    197.99165    360.27856   -2218.1018 
+    1450        0.145  0.028733851   -25.866283    198.30283    360.46623   -2218.1018 
+    1500         0.15  0.028733812   -26.014569    200.95517    354.66722   -2218.1018 
+    1550        0.155   0.02873379   -26.192673    205.95485    348.37935   -2218.1018 
+    1600         0.16  0.028733795   -26.444059    212.87557    345.53576   -2218.1018 
+    1650        0.165  0.028733838    -26.75551    219.86449     338.9224   -2218.1018 
+    1700         0.17  0.028733868   -27.068513    224.47868    327.81241   -2218.1018 
+    1750        0.175  0.028733862   -27.344118    225.62318    319.85486   -2218.1018 
+    1800         0.18  0.028733849    -27.57563    224.07463    320.07064   -2218.1018 
+    1850        0.185  0.028733852   -27.774274    221.70618    323.12599   -2218.1018 
+    1900         0.19  0.028733864   -27.967999    220.53947     322.9504   -2218.1018 
+    1950        0.195  0.028733863   -28.173041    221.61407    318.63401   -2218.1018 
+    2000          0.2  0.028733853   -28.362177    224.22281    310.55185   -2218.1018 
+Loop time of 3.95094 on 4 procs for 2000 steps with 500 atoms
+
+Performance: 4.374 ns/day, 5.487 hours/ns, 506.208 timesteps/s
+98.1% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 1.0289     | 1.0467     | 1.0811     |   2.0 | 26.49
+Neigh   | 0.0079527  | 0.0081946  | 0.0084369  |   0.2 |  0.21
+Comm    | 0.094456   | 0.13311    | 0.15138    |   6.2 |  3.37
+Output  | 0.69702    | 0.71998    | 0.74483    |   2.1 | 18.22
+Modify  | 2.0107     | 2.0383     | 2.0598     |   1.3 | 51.59
+Other   |            | 0.004668   |            |       |  0.12
+
+Nlocal:    125 ave 132 max 120 min
+Histogram: 2 0 0 0 0 1 0 0 0 1
+Nghost:    1099 ave 1104 max 1092 min
+Histogram: 1 0 0 0 1 0 0 0 0 2
+Neighs:    4876.5 ave 5100 max 4721 min
+Histogram: 2 0 0 0 0 1 0 0 0 1
+FullNghs:  9753 ave 10296 max 9362 min
+Histogram: 2 0 0 0 0 1 0 0 0 1
+
+Total # of neighbors = 39012
+Ave neighs/atom = 78.024
+Neighbor list builds = 21
+Dangerous builds = 0
+
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:04

examples/SPIN/read_restart/Co_PurjaPun_2012.eam.alloy

@@ -0,0 +1 @@
+../cobalt_fcc/Co_PurjaPun_2012.eam.alloy

examples/SPIN/read_restart/in.spin.read_data

@@ -0,0 +1,45 @@
+units 		metal
+dimension 	3
+boundary 	p p p 
+
+atom_style 	spin
+
+# necessary for the serial algorithm (sametag)
+atom_modify 	map array
+read_data 	Norm_randXY_8x8x32.data
+
+mass		1 58.93
+
+pair_style 	hybrid/overlay eam/alloy spin/exchange 4.0
+pair_coeff 	* * eam/alloy Co_PurjaPun_2012.eam.alloy Co
+pair_coeff 	* * spin/exchange exchange 4.0 0.0446928 0.003496 1.4885 
+
+neighbor 	1.0 bin
+neigh_modify 	every 1 check no delay 0
+
+fix 		1 all precession/spin zeeman 0.0 0.0 0.0 1.0
+fix 		2 all langevin/spin 0.0 0.0 21
+
+fix 		3 all nve/spin lattice yes
+timestep	0.0001
+
+# define outputs and computes
+
+compute 	out_mag    all compute/spin
+compute 	out_pe     all pe
+compute 	out_ke     all ke
+compute 	out_temp   all temp
+
+variable 	magz      equal c_out_mag[3]
+variable 	magnorm   equal c_out_mag[4]
+variable 	emag      equal c_out_mag[5]
+variable 	tmag      equal c_out_mag[6]
+
+thermo          10
+thermo_style    custom step time v_magnorm v_emag v_tmag temp etotal
+thermo_modify   format float %20.15g
+
+compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
+dump 		10 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
+
+run 		100

examples/SPIN/read_restart/in.spin.restart

@@ -0,0 +1,49 @@
+# start a spin-lattice simulation from a data file
+units 		metal
+atom_style 	spin
+
+dimension 	3
+boundary 	p p p 
+
+# necessary for the serial algorithm (sametag)
+atom_modify 	map array 
+
+read_restart	restart_hcp_cobalt.equil
+
+# setting mass, mag. moments, and interactions
+
+mass		1 58.93
+
+pair_style 	hybrid/overlay eam/alloy spin/exchange 4.0
+pair_coeff 	* * eam/alloy Co_PurjaPun_2012.eam.alloy Co
+pair_coeff 	* * spin/exchange exchange 4.0 0.3593 1.135028015e-05 1.064568567
+
+neighbor 	1.0 bin
+neigh_modify 	every 1 check no delay 0
+
+fix 		1 all precession/spin zeeman 0.0 0.0 0.0 1.0
+fix 		2 all langevin/spin 0.0 0.0 21
+
+fix 		3 all nve/spin lattice yes
+timestep	0.0001
+
+# define outputs
+
+compute 	out_mag    all compute/spin
+compute 	out_pe     all pe
+compute 	out_ke     all ke
+compute 	out_temp   all temp
+
+variable 	magz      equal c_out_mag[3]
+variable 	magnorm   equal c_out_mag[4]
+variable 	emag      equal c_out_mag[5]
+variable 	tmag      equal c_out_mag[6]
+
+thermo          10
+thermo_style    custom step time v_magnorm v_emag v_tmag temp etotal
+thermo_modify   format float %20.15g
+
+compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
+dump 		100 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
+
+run 		100