patch 22Jun18

made latte.in compatible with v1.1.1 and updated log files

.github/CODEOWNERS

@@ -9,13 +9,48 @@ lib/kokkos/*          @stanmoore1
 lib/molfile/*         @akohlmey
 lib/qmmm/*            @akohlmey
 lib/vtk/*             @rbberger
+lib/kim/*             @ellio167
 
-# packages
-src/KOKKOS            @stanmoore1
-src/USER-CGSDK        @akohlmey
-src/USER-COLVARS      @giacomofiorin
-src/USER-OMP          @akohlmey
-src/USER-QMMM         @akohlmey
+# whole packages
+src/COMPRESS/*        @akohlmey
+src/GPU/*             @ndtrung81
+src/KOKKOS/*          @stanmoore1
+src/KIM/*             @ellio167
+src/USER-CGDNA/*      @ohenrich
+src/USER-CGSDK/*      @akohlmey
+src/USER-COLVARS/*    @giacomofiorin
+src/USER-DPD/*        @timattox
+src/USER-INTEL/*      @wmbrownintel
+src/USER-MANIFOLD/*   @Pakketeretet2
+src/USER-MEAMC/*      @martok
+src/USER-MOFFF/*      @hheenen
+src/USER-MOLFILE/*    @akohlmey
+src/USER-NETCDF/*     @pastewka
+src/USER-PHONON/*     @lingtikong
+src/USER-OMP/*        @akohlmey
+src/USER-QMMM/*       @akohlmey
+src/USER-REAXC/*      @hasanmetin
+src/USER-TALLY/*      @akohlmey
+src/USER-UEF/*        @danicholson
+src/USER-VTK/*        @rbberger
+
+# individual files in packages
+src/GPU/pair_vashishta_gpu.*        @andeplane
+src/KOKKOS/pair_vashishta_kokkos.*  @andeplane
+src/MANYBODY/pair_vashishta_table.* @andeplane
+src/USER-MISC/fix_bond_react.*      @jrgissing
+src/USER-MISC/*_grem.*              @dstelter92
 
 # tools
 tools/msi2lmp/*       @akohlmey
+
+# cmake
+cmake/*               @junghans @rbberger
+
+# python
+python/*              @rbberger
+
+# docs
+doc/utils/*/*         @rbberger
+doc/Makefile          @rbberger
+doc/README            @rbberger

cmake/CMakeLists.txt

@@ -2,9 +2,9 @@
 # CMake build system
 # This file is part of LAMMPS
 # Created by Christoph Junghans and Richard Berger
-cmake_minimum_required(VERSION 3.1)
+cmake_minimum_required(VERSION 2.8.12)
 
-project(lammps)
+project(lammps CXX)
 set(SOVERSION 0)
 set(LAMMPS_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../src)
 set(LAMMPS_LIB_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../lib)
@@ -23,14 +23,22 @@ if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CXX_FLAGS)
   set(CMAKE_BUILD_TYPE Release CACHE STRING "Choose the type of build, options are: None Debug Release RelWithDebInfo MinSizeRel." FORCE)
 endif(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CXX_FLAGS)
 
-# remove any style headers in the src dir
-file(GLOB SRC_STYLE_FILES ${LAMMPS_SOURCE_DIR}/style_*.h)
-if(SRC_STYLE_FILES)
-  file(REMOVE ${SRC_STYLE_FILES})
+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()
 
-enable_language(CXX)
-
 ######################################################################
 # compiler tests
 # these need ot be done early (before further tests).
@@ -41,6 +49,11 @@ 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")
+endif()
+
 ########################################################################
 # User input options                                                   #
 ########################################################################
@@ -48,21 +61,27 @@ option(BUILD_SHARED_LIBS "Build shared libs" OFF)
 if(BUILD_SHARED_LIBS) # for all pkg libs, mpi_stubs and linalg
   set(CMAKE_POSITION_INDEPENDENT_CODE ON)
 endif()
+option(DEVELOPER_MODE "Enable developer mode" OFF)
+mark_as_advanced(DEVELOPER_MODE)
+option(CMAKE_VERBOSE_MAKEFILE "Generate verbose Makefiles" OFF)
 include(GNUInstallDirs)
 
 set(LAMMPS_LINK_LIBS)
 set(LAMMPS_DEPS)
 set(LAMMPS_API_DEFINES)
-option(ENABLE_MPI "Build MPI version" OFF)
-if(ENABLE_MPI)
+
+find_package(MPI QUIET)
+option(BUILD_MPI "Build MPI version" ${MPI_FOUND})
+if(BUILD_MPI)
   find_package(MPI REQUIRED)
-  include_directories(${MPI_C_INCLUDE_PATH})
+  include_directories(${MPI_CXX_INCLUDE_PATH})
   list(APPEND LAMMPS_LINK_LIBS ${MPI_CXX_LIBRARIES})
   option(LAMMPS_LONGLONG_TO_LONG "Workaround if your system or MPI version does not recognize 'long long' data types" OFF)
   if(LAMMPS_LONGLONG_TO_LONG)
     add_definitions(-DLAMMPS_LONGLONG_TO_LONG)
   endif()
 else()
+  enable_language(C)
   file(GLOB MPI_SOURCES ${LAMMPS_SOURCE_DIR}/STUBS/mpi.c)
   add_library(mpi_stubs STATIC ${MPI_SOURCES})
   include_directories(${LAMMPS_SOURCE_DIR}/STUBS)
@@ -101,21 +120,21 @@ set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GRANU
   KSPACE MANYBODY MC MEAM MISC MOLECULE PERI QEQ
   REAX REPLICA RIGID SHOCK SNAP SRD)
 set(OTHER_PACKAGES KIM PYTHON MSCG MPIIO VORONOI POEMS LATTE
-  USER-ATC USER-AWPMD USER-CGDNA USER-MESO
+  USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-MESO
   USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF
   USER-FEP USER-H5MD USER-LB USER-MANIFOLD USER-MEAMC USER-MGPT USER-MISC
   USER-MOFFF USER-MOLFILE USER-NETCDF USER-PHONON USER-QTB USER-REAXC USER-SMD
   USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM)
 set(ACCEL_PACKAGES USER-OMP KOKKOS OPT USER-INTEL GPU)
 foreach(PKG ${DEFAULT_PACKAGES})
-  option(ENABLE_${PKG} "Build ${PKG} Package" ${ENABLE_ALL})
+  option(PKG_${PKG} "Build ${PKG} Package" ${ENABLE_ALL})
 endforeach()
 foreach(PKG ${ACCEL_PACKAGES} ${OTHER_PACKAGES})
-  option(ENABLE_${PKG} "Build ${PKG} Package" OFF)
+  option(PKG_${PKG} "Build ${PKG} Package" OFF)
 endforeach()
 
 macro(pkg_depends PKG1 PKG2)
-  if(ENABLE_${PKG1} AND NOT ENABLE_${PKG2})
+  if(PKG_${PKG1} AND NOT (PKG_${PKG2} OR BUILD_${PKG2}))
     message(FATAL_ERROR "${PKG1} package needs LAMMPS to be build with ${PKG2}")
   endif()
 endmacro()
@@ -123,43 +142,51 @@ endmacro()
 pkg_depends(MPIIO MPI)
 pkg_depends(QEQ MANYBODY)
 pkg_depends(USER-ATC MANYBODY)
-pkg_depends(USER-H5MD MPI)
 pkg_depends(USER-LB MPI)
 pkg_depends(USER-MISC MANYBODY)
 pkg_depends(USER-PHONON KSPACE)
-
-if(ENABLE_BODY AND ENABLE_POEMS)
-  message(FATAL_ERROR "BODY and POEMS cannot be enabled at the same time")
-endif()
+pkg_depends(CORESHELL KSPACE)
 
 ######################################################
 # packages with special compiler needs or external libs
 ######################################################
-if(ENABLE_REAX OR ENABLE_MEAM OR ENABLE_USER-QUIP OR ENABLE_USER-QMMM OR ENABLE_LATTE)
+if(PKG_REAX OR PKG_MEAM OR PKG_USER-QUIP OR PKG_USER-QMMM OR PKG_LATTE)
   enable_language(Fortran)
-  include(CheckFortranCompilerFlag)
-  check_Fortran_compiler_flag("-fno-second-underscore" FC_HAS_NO_SECOND_UNDERSCORE)
 endif()
 
-if(ENABLE_KOKKOS OR ENABLE_MSCG)
-  # starting with CMake 3.1 this is all you have to do to enforce C++11
-  set(CMAKE_CXX_STANDARD 11) # C++11...
-  set(CMAKE_CXX_STANDARD_REQUIRED ON) #...is required...
-  set(CMAKE_CXX_EXTENSIONS OFF) #...without compiler extensions like gnu++11
+if(PKG_MEAM OR PKG_USER-H5MD OR PKG_USER-QMMM)
+  enable_language(C)
 endif()
 
-if(ENABLE_USER-OMP OR ENABLE_KOKKOS OR ENABLE_USER-INTEL)
+find_package(OpenMP QUIET)
+option(BUILD_OMP "Build with OpenMP support" ${OpenMP_FOUND})
+if(BUILD_OMP OR PKG_USER-OMP OR PKG_KOKKOS OR PKG_USER-INTEL)
   find_package(OpenMP REQUIRED)
   set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")
   set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
 endif()
 
-if(ENABLE_KSPACE)
-  set(FFT "KISSFFT" CACHE STRING "FFT library for KSPACE package")
-  set_property(CACHE FFT PROPERTY STRINGS KISSFFT FFTW3 MKL FFTW2)
+if(PKG_KSPACE)
+  option(FFT_SINGLE "Use single precision FFT instead of double" OFF)
+  set(FFTW "FFTW3")
+  if(FFT_SINGLE)
+    set(FFTW "FFTW3F")
+    add_definitions(-DFFT_SINGLE)
+  endif()
+  find_package(${FFTW} QUIET)
+  if(${FFTW}_FOUND)
+    set(FFT "${FFTW}" CACHE STRING "FFT library for KSPACE package")
+  else()
+    set(FFT "KISSFFT" CACHE STRING "FFT library for KSPACE package")
+  endif()
+  set_property(CACHE FFT PROPERTY STRINGS KISSFFT ${FFTW} MKL)
   if(NOT FFT STREQUAL "KISSFFT")
     find_package(${FFT} REQUIRED)
-    add_definitions(-DFFT_${FFT})
+    if(NOT FFT STREQUAL "FFTW3F")
+      add_definitions(-DFFT_FFTW)
+    else()
+      add_definitions(-DFFT_${FFT})
+    endif()
     include_directories(${${FFT}_INCLUDE_DIRS})
     list(APPEND LAMMPS_LINK_LIBS ${${FFT}_LIBRARIES})
   endif()
@@ -170,22 +197,17 @@ if(ENABLE_KSPACE)
   endif()
 endif()
 
-if(ENABLE_MSCG OR ENABLE_USER-ATC OR ENABLE_USER-AWPMD OR ENABLE_USER-QUIP OR ENABLE_LATTE)
+if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE)
   find_package(LAPACK)
   if(NOT LAPACK_FOUND)
     enable_language(Fortran)
-    file(GLOB LAPACK_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/linalg/*.f)
+    file(GLOB LAPACK_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/linalg/*.[fF])
     add_library(linalg STATIC ${LAPACK_SOURCES})
-    include(CheckFortranCompilerFlag)
-    check_Fortran_compiler_flag("-fno-second-underscore" FC_HAS_NO_SECOND_UNDERSCORE)
-    if(FC_HAS_NO_SECOND_UNDERSCORE)
-      target_compile_options(linalg PRIVATE -fno-second-underscore)
-    endif()
     set(LAPACK_LIBRARIES linalg)
   endif()
 endif()
 
-if(ENABLE_PYTHON)
+if(PKG_PYTHON)
   find_package(PythonInterp REQUIRED)
   find_package(PythonLibs REQUIRED)
   add_definitions(-DLMP_PYTHON)
@@ -201,16 +223,25 @@ if(ENABLE_PYTHON)
   endif()
 endif()
 
-find_package(JPEG)
-if(JPEG_FOUND)
+find_package(JPEG QUIET)
+option(WITH_JPEG "Enable JPEG support" ${JPEG_FOUND})
+if(WITH_JPEG)
+  find_package(JPEG REQUIRED)
   add_definitions(-DLAMMPS_JPEG)
   include_directories(${JPEG_INCLUDE_DIR})
   list(APPEND LAMMPS_LINK_LIBS ${JPEG_LIBRARIES})
 endif()
 
-find_package(PNG)
-find_package(ZLIB)
+find_package(PNG QUIET)
+find_package(ZLIB QUIET)
 if(PNG_FOUND AND ZLIB_FOUND)
+  option(WITH_PNG "Enable PNG support" ON)
+else()
+  option(WITH_PNG "Enable PNG support" OFF)
+endif()
+if(WITH_PNG)
+  find_package(PNG REQUIRED)
+  find_package(ZLIB REQUIRED)
   include_directories(${PNG_INCLUDE_DIRS} ${ZLIB_INCLUDE_DIRS})
   list(APPEND LAMMPS_LINK_LIBS ${PNG_LIBRARIES} ${ZLIB_LIBRARIES})
   add_definitions(-DLAMMPS_PNG)
@@ -218,113 +249,194 @@ endif()
 
 find_program(GZIP_EXECUTABLE gzip)
 find_package_handle_standard_args(GZIP REQUIRED_VARS GZIP_EXECUTABLE)
-if(GZIP_FOUND)
+option(WITH_GZIP "Enable GZIP support" ${GZIP_FOUND})
+if(WITH_GZIP)
+  if(NOT GZIP_FOUND)
+    message(FATAL_ERROR "gzip executable not found")
+  endif()
   add_definitions(-DLAMMPS_GZIP)
 endif()
 
 find_program(FFMPEG_EXECUTABLE ffmpeg)
 find_package_handle_standard_args(FFMPEG REQUIRED_VARS FFMPEG_EXECUTABLE)
-if(FFMPEG_FOUND)
+option(WITH_FFMPEG "Enable FFMPEG support" ${FFMPEG_FOUND})
+if(WITH_FFMPEG)
+  if(NOT FFMPEG_FOUND)
+    message(FATAL_ERROR "ffmpeg executable not found")
+  endif()
   add_definitions(-DLAMMPS_FFMPEG)
 endif()
 
-if(ENABLE_VORONOI)
-  find_package(VORO REQUIRED) #some distros
+if(PKG_VORONOI)
+  option(DOWNLOAD_VORO "Download voro++ (instead of using the system's one)" OFF)
+  if(DOWNLOAD_VORO)
+    include(ExternalProject)
+    ExternalProject_Add(voro_build
+      URL http://math.lbl.gov/voro++/download/dir/voro++-0.4.6.tar.gz
+      URL_MD5 2338b824c3b7b25590e18e8df5d68af9
+      CONFIGURE_COMMAND "" BUILD_IN_SOURCE 1 INSTALL_COMMAND "" 
+      )
+    ExternalProject_get_property(voro_build SOURCE_DIR)
+    set(VORO_LIBRARIES ${SOURCE_DIR}/src/libvoro++.a)
+    set(VORO_INCLUDE_DIRS ${SOURCE_DIR}/src)
+    list(APPEND LAMMPS_DEPS voro_build)
+  else()
+    find_package(VORO)
+    if(NOT VORO_FOUND)
+      message(FATAL_ERROR "VORO not found, help CMake to find it by setting VORO_LIBRARY and VORO_INCLUDE_DIR, or set DOWNLOAD_VORO=ON to download it")
+    endif()
+  endif()
   include_directories(${VORO_INCLUDE_DIRS})
   list(APPEND LAMMPS_LINK_LIBS ${VORO_LIBRARIES})
 endif()
 
-if(ENABLE_LATTE)
-  find_package(LATTE QUIET)
-  if(NOT LATTE_FOUND)
+if(PKG_LATTE)
+  option(DOWNLOAD_LATTE "Download latte (instead of using the system's one)" OFF)
+  if(DOWNLOAD_LATTE)
     message(STATUS "LATTE not found - we will build our own")
     include(ExternalProject)
     ExternalProject_Add(latte_build
-      URL https://github.com/lanl/LATTE/archive/v1.0.1.tar.gz
-      URL_MD5 5137e28cb1a64444bd571c98c98a6eee
+      URL https://github.com/lanl/LATTE/archive/v1.1.1.tar.gz
+      URL_MD5 cb86f1d2473ce00aa61ff6a023154b03
       SOURCE_SUBDIR cmake
       CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR> -DCMAKE_POSITION_INDEPENDENT_CODE=${CMAKE_POSITION_INDEPENDENT_CODE}
       )
     ExternalProject_get_property(latte_build INSTALL_DIR)
     set(LATTE_LIBRARIES ${INSTALL_DIR}/${CMAKE_INSTALL_LIBDIR}/liblatte.a)
     list(APPEND LAMMPS_DEPS latte_build)
+  else()
+    find_package(LATTE)
+    if(NOT LATTE_FOUND)
+      message(FATAL_ERROR "LATTE not found, help CMake to find it by setting LATTE_LIBRARY, or set DOWNLOAD_LATTE=ON to download it")
+    endif()
   endif()
-  list(APPEND LAMMPS_LINK_LIBS ${LATTE_LIBRARIES} ${LAPACK_LIBRARIES} ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
+  list(APPEND LAMMPS_LINK_LIBS ${LATTE_LIBRARIES} ${LAPACK_LIBRARIES})
 endif()
 
-if(ENABLE_USER-MOLFILE)
+if(PKG_USER-MOLFILE)
   add_library(molfile INTERFACE)
   target_include_directories(molfile INTERFACE ${LAMMPS_LIB_SOURCE_DIR}/molfile)
   target_link_libraries(molfile INTERFACE ${CMAKE_DL_LIBS})
   list(APPEND LAMMPS_LINK_LIBS molfile)
 endif()
 
-if(ENABLE_USER-NETCDF)
+if(PKG_USER-NETCDF)
   find_package(NetCDF REQUIRED)
   include_directories(NETCDF_INCLUDE_DIR)
   list(APPEND LAMMPS_LINK_LIBS ${NETCDF_LIBRARY})
   add_definitions(-DLMP_HAS_NETCDF -DNC_64BIT_DATA=0x0020)
 endif()
 
-if(ENABLE_USER-SMD)
-  find_package(Eigen3 REQUIRED)
+if(PKG_USER-SMD)
+  option(DOWNLOAD_Eigen3 "Download Eigen3 (instead of using the system's one)" OFF)
+  if(DOWNLOAD_Eigen3)
+    include(ExternalProject)
+    ExternalProject_Add(Eigen3_build
+      URL http://bitbucket.org/eigen/eigen/get/3.3.4.tar.gz 
+      URL_MD5 1a47e78efe365a97de0c022d127607c3
+      CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
+    )
+    ExternalProject_get_property(Eigen3_build SOURCE_DIR)
+    set(EIGEN3_INCLUDE_DIR ${SOURCE_DIR})
+    list(APPEND LAMMPS_DEPS Eigen3_build)
+  else()
+    find_package(Eigen3)
+    if(NOT Eigen3_FOUND)
+      message(FATAL_ERROR "Eigen3 not found, help CMake to find it by setting EIGEN3_INCLUDE_DIR, or set DOWNLOAD_Eigen3=ON to download it")
+    endif()
+  endif()
   include_directories(${EIGEN3_INCLUDE_DIR})
 endif()
 
-if(ENABLE_USER-QUIP)
+if(PKG_USER-QUIP)
   find_package(QUIP REQUIRED)
-  list(APPEND LAMMPS_LINK_LIBS ${QUIP_LIBRARIES} ${LAPACK_LIBRARIES} ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
+  list(APPEND LAMMPS_LINK_LIBS ${QUIP_LIBRARIES} ${LAPACK_LIBRARIES})
 endif()
 
-if(ENABLE_USER-QMMM)
+if(PKG_USER-QMMM)
+  message(WARNING "Building QMMM with CMake is still experimental")
   find_package(QE REQUIRED)
   include_directories(${QE_INCLUDE_DIRS})
-  list(APPEND LAMMPS_LINK_LIBS ${QE_LIBRARIES} ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
+  list(APPEND LAMMPS_LINK_LIBS ${QE_LIBRARIES})
 endif()
 
-if(ENABLE_USER-VTK)
+if(PKG_USER-VTK)
   find_package(VTK REQUIRED NO_MODULE)
   include(${VTK_USE_FILE})
   add_definitions(-DLAMMPS_VTK)
   list(APPEND LAMMPS_LINK_LIBS ${VTK_LIBRARIES})
 endif()
 
-if(ENABLE_KIM)
-  find_package(KIM REQUIRED)
+if(PKG_KIM)
+  option(DOWNLOAD_KIM "Download kim-api (instead of using the system's one)" OFF)
+  if(DOWNLOAD_KIM)
+    include(ExternalProject)
+    ExternalProject_Add(kim_build
+      URL https://github.com/openkim/kim-api/archive/v1.9.5.tar.gz
+      URL_MD5 9f66efc128da33039e30659f36fc6d00
+      BUILD_IN_SOURCE 1
+      CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR>
+      )
+    ExternalProject_get_property(kim_build INSTALL_DIR)
+    set(KIM_INCLUDE_DIRS ${INSTALL_DIR}/include/kim-api-v1)
+    set(KIM_LIBRARIES ${INSTALL_DIR}/lib/libkim-api-v1.so)
+    list(APPEND LAMMPS_DEPS kim_build)
+  else()
+    find_package(KIM)
+    if(NOT KIM_FOUND)
+      message(FATAL_ERROR "KIM not found, help CMake to find it by setting KIM_LIBRARY and KIM_INCLUDE_DIR, or set DOWNLOAD_KIM=ON to download it")
+    endif()
+  endif()
   list(APPEND LAMMPS_LINK_LIBS ${KIM_LIBRARIES})
   include_directories(${KIM_INCLUDE_DIRS})
 endif()
 
-if(ENABLE_MSCG)
+if(PKG_MSCG)
   find_package(GSL REQUIRED)
-  set(LAMMPS_LIB_MSCG_BIN_DIR ${LAMMPS_LIB_BINARY_DIR}/mscg)
-  set(MSCG_TARBALL ${LAMMPS_LIB_MSCG_BIN_DIR}/MS-CG-master.zip)
-  set(LAMMPS_LIB_MSCG_BIN_DIR ${LAMMPS_LIB_MSCG_BIN_DIR}/MSCG-release-master/src)
-  if(NOT EXISTS ${LAMMPS_LIB_MSCG_BIN_DIR})
-    if(NOT EXISTS ${MSCG_TARBALL})
-      message(STATUS "Downloading ${MSCG_TARBALL}")
-      file(DOWNLOAD
-        https://github.com/uchicago-voth/MSCG-release/archive/master.zip
-        ${MSCG_TARBALL} SHOW_PROGRESS) #EXPECTED_MD5 cannot be due due to master
+  option(DOWNLOAD_MSCG "Download latte (instead of using the system's one)" OFF)
+  if(DOWNLOAD_MSCG)
+    include(ExternalProject)
+    if(NOT LAPACK_FOUND)
+      set(EXTRA_MSCG_OPTS "-DLAPACK_LIBRARIES=${CMAKE_CURRENT_BINARY_DIR}/liblinalg.a")
+    endif()
+    ExternalProject_Add(mscg_build
+      URL https://github.com/uchicago-voth/MSCG-release/archive/1.7.3.1.tar.gz
+      URL_MD5 8c45e269ee13f60b303edd7823866a91
+      SOURCE_SUBDIR src/CMake
+      CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR> -DCMAKE_POSITION_INDEPENDENT_CODE=${CMAKE_POSITION_INDEPENDENT_CODE} ${EXTRA_MSCG_OPTS}
+      BUILD_COMMAND make mscg INSTALL_COMMAND ""
+      )
+    ExternalProject_get_property(mscg_build BINARY_DIR)
+    set(MSCG_LIBRARIES ${BINARY_DIR}/libmscg.a)
+    ExternalProject_get_property(mscg_build SOURCE_DIR)
+    set(MSCG_INCLUDE_DIRS ${SOURCE_DIR}/src)
+    list(APPEND LAMMPS_DEPS mscg_build)
+    if(NOT LAPACK_FOUND)
+      file(MAKE_DIRECTORY ${MSCG_INCLUDE_DIRS})
+      add_dependencies(mscg_build linalg)
+    endif()
+  else()
+    find_package(MSCG)
+    if(NOT MSCG_FOUND)
+      message(FATAL_ERROR "MSCG not found, help CMake to find it by setting MSCG_LIBRARY and MSCG_INCLUDE_DIRS, or set DOWNLOAD_MSCG=ON to download it")
     endif()
-    message(STATUS "Unpacking ${MSCG_TARBALL}")
-    execute_process(COMMAND ${CMAKE_COMMAND} -E tar xvf ${MSCG_TARBALL}
-      WORKING_DIRECTORY ${LAMMPS_LIB_BINARY_DIR}/mscg)
   endif()
-  file(GLOB MSCG_SOURCES ${LAMMPS_LIB_MSCG_BIN_DIR}/*.cpp)
-  add_library(mscg STATIC ${MSCG_SOURCES})
-  list(APPEND LAMMPS_LINK_LIBS mscg)
-  target_compile_options(mscg PRIVATE -DDIMENSION=3 -D_exclude_gromacs=1)
-  target_include_directories(mscg PUBLIC ${LAMMPS_LIB_MSCG_BIN_DIR})
-  target_link_libraries(mscg ${GSL_LIBRARIES} ${LAPACK_LIBRARIES})
+  list(APPEND LAMMPS_LINK_LIBS ${MSCG_LIBRARIES} ${GSL_LIBRARIES} ${LAPACK_LIBRARIES})
+  include_directories(${MSCG_INCLUDE_DIRS})
+endif()
+
+if(PKG_COMPRESS)
+  find_package(ZLIB REQUIRED)
+  include_directories(${ZLIB_INCLUDE_DIRS})
+  list(APPEND LAMMPS_LINK_LIBS ${ZLIB_LIBRARIES})
 endif()
 
 ########################################################################
 # Basic system tests (standard libraries, headers, functions, types)   #
 ########################################################################
-include(CheckIncludeFile)
+include(CheckIncludeFileCXX)
 foreach(HEADER math.h)
-  check_include_file(${HEADER} FOUND_${HEADER})
+  check_include_file_cxx(${HEADER} FOUND_${HEADER})
   if(NOT FOUND_${HEADER})
     message(FATAL_ERROR "Could not find needed header - ${HEADER}")
   endif(NOT FOUND_${HEADER})
@@ -368,7 +480,7 @@ foreach(PKG ${DEFAULT_PACKAGES} ${OTHER_PACKAGES})
       DetectAndRemovePackageHeader(${LAMMPS_SOURCE_DIR}/${FNAME})
   endforeach()
 
-  if(ENABLE_${PKG})
+  if(PKG_${PKG})
     # detects styles in package and adds them to global list
     RegisterStyles(${${PKG}_SOURCES_DIR})
 
@@ -382,7 +494,7 @@ endforeach()
 ############################################
 foreach(SIMPLE_LIB REAX MEAM POEMS USER-ATC USER-AWPMD USER-COLVARS USER-H5MD
   USER-QMMM)
-  if(ENABLE_${SIMPLE_LIB})
+  if(PKG_${SIMPLE_LIB})
     string(REGEX REPLACE "^USER-" "" PKG_LIB "${SIMPLE_LIB}")
     string(TOLOWER "${PKG_LIB}" PKG_LIB)
     file(GLOB_RECURSE ${PKG_LIB}_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/*.F
@@ -403,40 +515,26 @@ foreach(SIMPLE_LIB REAX MEAM POEMS USER-ATC USER-AWPMD USER-COLVARS USER-H5MD
   endif()
 endforeach()
 
-if(ENABLE_USER-AWPMD)
+if(PKG_USER-AWPMD)
   target_link_libraries(awpmd ${LAPACK_LIBRARIES})
 endif()
 
-if(ENABLE_USER-ATC)
+if(PKG_USER-ATC)
   target_link_libraries(atc ${LAPACK_LIBRARIES})
 endif()
 
-if(ENABLE_USER-H5MD)
+if(PKG_USER-H5MD)
   find_package(HDF5 REQUIRED)
   target_link_libraries(h5md ${HDF5_LIBRARIES})
   target_include_directories(h5md PRIVATE ${HDF5_INCLUDE_DIRS})
 endif()
 
-if(ENABLE_MEAM AND FC_HAS_NO_SECOND_UNDERSCORE)
-  foreach(FSRC ${meam_SOURCES})
-    string(REGEX REPLACE "^.*\\." "" FEXT "${FSRC}")
-    list(FIND CMAKE_Fortran_SOURCE_FILE_EXTENSIONS "${FEXT}" FINDEX)
-    if(FINDEX GREATER -1)
-      set_property(SOURCE ${FSRC} APPEND PROPERTY COMPILE_FLAGS "-fno-second-underscore")
-    endif()
-  endforeach()
-endif()
-
-if(ENABLE_REAX AND FC_HAS_NO_SECOND_UNDERSCORE)
-  target_compile_options(reax PRIVATE -fno-second-underscore)
-endif()
-
 
 ######################################################################
 # packages which selectively include variants based on enabled styles
 # e.g. accelerator packages
 ######################################################################
-if(ENABLE_USER-OMP)
+if(PKG_USER-OMP)
     set(USER-OMP_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/USER-OMP)
     set(USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/thr_data.cpp
                          ${USER-OMP_SOURCES_DIR}/thr_omp.cpp
@@ -453,7 +551,7 @@ if(ENABLE_USER-OMP)
     include_directories(${USER-OMP_SOURCES_DIR})
 endif()
 
-if(ENABLE_KOKKOS)
+if(PKG_KOKKOS)
   set(LAMMPS_LIB_KOKKOS_SRC_DIR ${LAMMPS_LIB_SOURCE_DIR}/kokkos)
   set(LAMMPS_LIB_KOKKOS_BIN_DIR ${LAMMPS_LIB_BINARY_DIR}/kokkos)
   add_definitions(-DLMP_KOKKOS)
@@ -489,7 +587,7 @@ if(ENABLE_KOKKOS)
   RegisterNBinStyle(${KOKKOS_PKG_SOURCES_DIR}/nbin_kokkos.h)
   RegisterNPairStyle(${KOKKOS_PKG_SOURCES_DIR}/npair_kokkos.h)
 
-  if(ENABLE_USER-DPD)
+  if(PKG_USER-DPD)
     get_property(KOKKOS_PKG_SOURCES GLOBAL PROPERTY KOKKOS_PKG_SOURCES)
     list(APPEND KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/npair_ssa_kokkos.cpp)
     RegisterNPairStyle(${KOKKOS_PKG_SOURCES_DIR}/npair_ssa_kokkos.h)
@@ -502,7 +600,7 @@ if(ENABLE_KOKKOS)
   include_directories(${KOKKOS_PKG_SOURCES_DIR})
 endif()
 
-if(ENABLE_OPT)
+if(PKG_OPT)
     set(OPT_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/OPT)
     set(OPT_SOURCES)
     set_property(GLOBAL PROPERTY "OPT_SOURCES" "${OPT_SOURCES}")
@@ -516,7 +614,30 @@ if(ENABLE_OPT)
     include_directories(${OPT_SOURCES_DIR})
 endif()
 
-if(ENABLE_USER-INTEL)
+if(PKG_USER-INTEL)
+    if(NOT DEVELOPER_MODE)
+      if(NOT CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
+        message(FATAL_ERROR "USER-INTEL is only useful together with intel compiler")
+      endif()
+      if(CMAKE_CXX_COMPILER_VERSION VERSION_LESS 16)
+        message(FATAL_ERROR "USER-INTEL is needed at least 2016 intel compiler, found ${CMAKE_CXX_COMPILER_VERSION}")
+      endif()
+    endif()
+    option(INJECT_INTEL_FLAG "Inject OMG fast flags for USER-INTEL" ON)
+    if(INJECT_INTEL_FLAG AND CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
+      if(CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.3 OR CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.4)
+        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -xCOMMON-AVX512")
+      else()
+        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -xHost")
+      endif()
+      include(CheckCXXCompilerFlag)
+      foreach(_FLAG -qopenmp -qno-offload -fno-alias -ansi-alias -restrict -DLMP_INTEL_USELRT -DLMP_USE_MKL_RNG -O2 "-fp-model fast=2" -no-prec-div -qoverride-limits -qopt-zmm-usage=high)
+        check_cxx_compiler_flag("${__FLAG}" COMPILER_SUPPORTS${_FLAG})
+        if(COMPILER_SUPPORTS${_FLAG})
+          set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${_FLAG}")
+        endif()
+      endforeach()
+    endif()
     set(USER-INTEL_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/USER-INTEL)
     set(USER-INTEL_SOURCES ${USER-INTEL_SOURCES_DIR}/intel_preprocess.h
                            ${USER-INTEL_SOURCES_DIR}/intel_buffers.h
@@ -540,7 +661,10 @@ if(ENABLE_USER-INTEL)
     include_directories(${USER-INTEL_SOURCES_DIR})
 endif()
 
-if(ENABLE_GPU)
+if(PKG_GPU)
+    if (CMAKE_VERSION VERSION_LESS "3.1") 
+      message(FATAL_ERROR "For the GPU package you need at least cmake-3.1")
+    endif()
     set(GPU_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/GPU)
     set(GPU_SOURCES ${GPU_SOURCES_DIR}/gpu_extra.h
                     ${GPU_SOURCES_DIR}/fix_gpu.h
@@ -637,7 +761,7 @@ if(ENABLE_GPU)
       add_library(gpu STATIC ${GPU_LIB_SOURCES})
       target_link_libraries(gpu ${OpenCL_LIBRARIES})
       target_include_directories(gpu PRIVATE ${CMAKE_CURRENT_BINARY_DIR}/gpu ${OpenCL_INCLUDE_DIRS})
-      target_compile_definitions(gpu PRIVATE -D_${GPU_PREC} -DMPI_GERYON -DUCL_NO_EXIT)
+      target_compile_definitions(gpu PRIVATE -D_${GPU_PREC} -D${OCL_TUNE}_OCL -DMPI_GERYON -DUCL_NO_EXIT)
       target_compile_definitions(gpu PRIVATE -DUSE_OPENCL)
 
       list(APPEND LAMMPS_LINK_LIBS gpu)
@@ -677,6 +801,12 @@ include_directories(${LAMMPS_STYLE_HEADERS_DIR})
 # 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 ${LAMMPS_DEPS})
@@ -698,35 +828,93 @@ if(ENABLE_TESTING)
   add_test(ShowHelp lmp${LAMMPS_MACHINE} -help)
 endif()
 
-##################################
+###############################################################################
+# Testing
+#
+# Requires latest gcovr (for GCC 8.1 support):#
+# pip install git+https://github.com/gcovr/gcovr.git
+###############################################################################
+if(ENABLE_COVERAGE)
+    find_program(GCOVR_BINARY gcovr)
+    find_package_handle_standard_args(GCOVR DEFAULT_MSG GCOVR_BINARY)
+
+    if(GCOVR_FOUND)
+        get_filename_component(ABSOLUTE_LAMMPS_SOURCE_DIR ${LAMMPS_SOURCE_DIR} ABSOLUTE)
+
+        add_custom_target(
+            gen_coverage_xml
+            COMMAND ${GCOVR_BINARY} -s -x -r ${ABSOLUTE_LAMMPS_SOURCE_DIR} --object-directory=${CMAKE_BINARY_DIR} -o coverage.xml
+            WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
+            COMMENT "Generating XML Coverage Report..."
+        )
+
+        add_custom_target(
+            gen_coverage_html
+            COMMAND ${GCOVR_BINARY} -s  --html --html-details -r ${ABSOLUTE_LAMMPS_SOURCE_DIR} --object-directory=${CMAKE_BINARY_DIR} -o coverage.html
+            WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
+            COMMENT "Generating HTML Coverage Report..."
+        )
+    endif()
+endif()
+
+###############################################################################
 # Print package summary
-##################################
+###############################################################################
 foreach(PKG ${DEFAULT_PACKAGES} ${OTHER_PACKAGES} ${ACCEL_PACKAGES})
-  if(ENABLE_${PKG})
+  if(PKG_${PKG})
     message(STATUS "Building package: ${PKG}")
   endif()
 endforeach()
 
 string(TOUPPER "${CMAKE_BUILD_TYPE}" BTYPE)
+get_directory_property(CPPFLAGS DIRECTORY ${CMAKE_SOURCE_DIR} COMPILE_DEFINITIONS)
+include(FeatureSummary)
+feature_summary(INCLUDE_QUIET_PACKAGES WHAT ALL)
 message(STATUS "<<< Build configuration >>>
    Build type       ${CMAKE_BUILD_TYPE}
    Install path     ${CMAKE_INSTALL_PREFIX}
    Compilers and Flags:
    C++ Compiler     ${CMAKE_CXX_COMPILER}
        Type         ${CMAKE_CXX_COMPILER_ID}
-   C++ Flags        ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_${BTYPE}}")
+       Version      ${CMAKE_CXX_COMPILER_VERSION}
+   C++ Flags        ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_${BTYPE}}
+   Defines          ${CPPFLAGS}")
 get_property(LANGUAGES GLOBAL PROPERTY ENABLED_LANGUAGES)
-if(LANGUAGES MATCHES ".*Fortran.*")
+list (FIND LANGUAGES "Fortran" _index)
+if (${_index} GREATER -1)
   message(STATUS "Fortran Compiler ${CMAKE_Fortran_COMPILER} 
            Type     ${CMAKE_Fortran_COMPILER_ID}
+           Version  ${CMAKE_Fortran_COMPILER_VERSION}
    Fortran Flags    ${CMAKE_Fortran_FLAGS} ${CMAKE_Fortran_FLAGS_${BTYPE}}")
 endif()
-message(STATUS "Linker flags:
+list (FIND LANGUAGES "C" _index)
+if (${_index} GREATER -1)
+  message(STATUS "C Compiler ${CMAKE_C_COMPILER} 
+     Type     ${CMAKE_C_COMPILER_ID}
+     Version  ${CMAKE_C_COMPILER_VERSION}
+     C Flags  ${CMAKE_C_FLAGS} ${CMAKE_C_FLAGS_${BTYPE}}")
+endif()
+if(CMAKE_EXE_LINKER_FLAGS)
+  message(STATUS "Linker flags:
    Executable      ${CMAKE_EXE_LINKER_FLAGS}")
+  endif()
 if(BUILD_SHARED_LIBS)
-  message(STATUS "Shared libries  ${CMAKE_SHARED_LINKER_FLAGS}")
+  message(STATUS "Shared libraries  ${CMAKE_SHARED_LINKER_FLAGS}")
 else()
-  message(STATUS "Static libries  ${CMAKE_STATIC_LINKER_FLAGS}")
+  message(STATUS "Static libraries  ${CMAKE_STATIC_LINKER_FLAGS}")
 endif()
 message(STATUS "Link libraries: ${LAMMPS_LINK_LIBS}")
-
+if(BUILD_MPI)
+  message(STATUS "Using mpi with headers in ${MPI_CXX_INCLUDE_PATH} and ${MPI_CXX_LIBRARIES}")
+endif()
+if(ENABLED_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()
+endif()
+if(PKG_KSPACE)
+  message(STATUS "Using ${FFT} as FFT")
+endif()

cmake/Modules/FindFFTW2.cmake

@@ -1,22 +0,0 @@
-# - Find fftw2
-# Find the native FFTW2 headers and libraries.
-#
-#  FFTW2_INCLUDE_DIRS - where to find fftw2.h, etc.
-#  FFTW2_LIBRARIES    - List of libraries when using fftw2.
-#  FFTW2_FOUND        - True if fftw2 found.
-#
-
-find_path(FFTW2_INCLUDE_DIR fftw.h)
-
-find_library(FFTW2_LIBRARY NAMES fftw)
-
-set(FFTW2_LIBRARIES ${FFTW2_LIBRARY})
-set(FFTW2_INCLUDE_DIRS ${FFTW2_INCLUDE_DIR})
-
-include(FindPackageHandleStandardArgs)
-# handle the QUIETLY and REQUIRED arguments and set FFTW2_FOUND to TRUE
-# if all listed variables are TRUE
-
-find_package_handle_standard_args(FFTW2 DEFAULT_MSG FFTW2_LIBRARY FFTW2_INCLUDE_DIR)
-
-mark_as_advanced(FFTW2_INCLUDE_DIR FFTW2_LIBRARY )

cmake/Modules/FindFFTW3F.cmake

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

cmake/Modules/FindMSCG.cmake

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

doc/Makefile

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

doc/src/Developer/developer.tex

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

doc/src/Eqs/dihedral_table_cut.tex

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

doc/src/Manual.txt

@@ -1,7 +1,7 @@
 <!-- HTML_ONLY -->
 <HEAD>
 <TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="30 Mar 2018 version">
+<META NAME="docnumber" CONTENT="22 Jun 2018 version">
 <META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
 <META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
 </HEAD>
@@ -19,7 +19,7 @@
 :line
 
 LAMMPS Documentation :c,h1
-30 Mar 2018 version :c,h2
+22 Jun 2018 version :c,h2
 
 Version info: :h3
 

doc/src/Section_commands.txt

@@ -129,6 +129,17 @@ region 1 block $((xlo+xhi)/2+sqrt(v_area)) 2 INF INF EDGE EDGE :pre
 
 so that you do not have to define (or discard) a temporary variable X.
 
+Additionally, the "immediate" variable expression may be followed by a
+colon, followed by a C-style format string, e.g. ":%f" or ":%.10g".
+The format string must be appropriate for a double-precision
+floating-point value.  The format string is used to output the result
+of the variable expression evaluation.  If a format string is not
+specified a high-precision "%.20g" is used as the default.
+
+This can be useful for formatting print output to a desired precion:
+
+print "Final energy per atom: $(pe/atoms:%10.3f) eV/atom" :pre
+
 Note that neither the curly-bracket or immediate form of variables can
 contain nested $ characters for other variables to substitute for.
 Thus you cannot do this:
@@ -684,6 +695,7 @@ package"_Section_start.html#start_3.
 "addtorque"_fix_addtorque.html,
 "atc"_fix_atc.html,
 "ave/correlate/long"_fix_ave_correlate_long.html,
+"bond/react"_fix_bond_react.html,
 "colvars"_fix_colvars.html,
 "dpd/energy (k)"_fix_dpd_energy.html,
 "drude"_fix_drude.html,
@@ -1211,7 +1223,8 @@ package"_Section_start.html#start_3.
 "nharmonic (o)"_dihedral_nharmonic.html,
 "quadratic (o)"_dihedral_quadratic.html,
 "spherical (o)"_dihedral_spherical.html,
-"table (o)"_dihedral_table.html :tb(c=4,ea=c)
+"table (o)"_dihedral_table.html,
+"table/cut"_dihedral_table_cut.html :tb(c=4,ea=c)
 
 :line
 

doc/src/Section_errors.txt

@@ -803,6 +803,13 @@ lo value must be less than the hi value for all 3 dimensions. :dd
 The box command cannot be used after a read_data, read_restart, or
 create_box command. :dd
 
+{BUG: restartinfo=1 but no restart support in pair style} :dt
+
+The pair style has a bug, where it does not support reading
+and writing information to a restart file, but does not set
+the member variable restartinfo to 0 as required in that case. :dd
+
+
 {CPU neighbor lists must be used for ellipsoid/sphere mix.} :dt
 
 When using Gay-Berne or RE-squared pair styles with both ellipsoidal and
@@ -1565,15 +1572,6 @@ This operation is not allowed. :dd
 
 This operation is not allowed. :dd
 
-{Cannot use -cuda on and -kokkos on together} :dt
-
-This is not allowed since both packages can use GPUs. :dd
-
-{Cannot use -cuda on without USER-CUDA installed} :dt
-
-The USER-CUDA package must be installed via "make yes-user-cuda"
-before LAMMPS is built. :dd
-
 {Cannot use -kokkos on without KOKKOS installed} :dt
 
 Self-explanatory. :dd
@@ -1597,11 +1595,6 @@ solver/pair style. :dd
 
 This is a current restriction of this command. :dd
 
-{Cannot use GPU package with USER-CUDA package enabled} :dt
-
-You cannot use both the GPU and USER-CUDA packages
-together.  Use one or the other. :dd
-
 {Cannot use Kokkos pair style with rRESPA inner/middle} :dt
 
 Self-explanatory. :dd
@@ -8252,12 +8245,6 @@ Self-explanatory. :dd
 The package command cannot be used afer a read_data, read_restart, or
 create_box command. :dd
 
-{Package cuda command without USER-CUDA package enabled} :dt
-
-The USER-CUDA package must be installed via "make yes-user-cuda"
-before LAMMPS is built, and the "-c on" must be used to enable the
-package. :dd
-
 {Package gpu command without GPU package installed} :dt
 
 The GPU package must be installed via "make yes-gpu" before LAMMPS is
@@ -10230,22 +10217,6 @@ it in different ways. :dd
 
 Self-explanatory. :dd
 
-{USER-CUDA mode requires CUDA variant of min style} :dt
-
-CUDA mode is enabled, so the min style must include a cuda suffix. :dd
-
-{USER-CUDA mode requires CUDA variant of run style} :dt
-
-CUDA mode is enabled, so the run style must include a cuda suffix. :dd
-
-{USER-CUDA package does not yet support comm_style tiled} :dt
-
-Self-explanatory. :dd
-
-{USER-CUDA package requires a cuda enabled atom_style} :dt
-
-Self-explanatory. :dd
-
 {Unable to initialize accelerator for use} :dt
 
 There was a problem initializing an accelerator for the gpu package :dd
@@ -10494,10 +10465,6 @@ Must use remap v option with fix deform with this pair style. :dd
 
 If fix deform is used, the remap v option is required. :dd
 
-{Using suffix cuda without USER-CUDA package enabled} :dt
-
-Self-explanatory. :dd
-
 {Using suffix gpu without GPU package installed} :dt
 
 Self-explanatory. :dd

doc/src/Section_intro.txt

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

doc/src/Section_packages.txt

@@ -122,6 +122,7 @@ Package, Description, Doc page, Example, Library
 Package, Description, Doc page, Example, Library
 "USER-ATC"_#USER-ATC, atom-to-continuum coupling, "fix atc"_fix_atc.html, USER/atc, int
 "USER-AWPMD"_#USER-AWPMD, wave-packet MD, "pair_style awpmd/cut"_pair_awpmd.html, USER/awpmd, int
+"USER-BOCS"_#USER-BOCS, BOCS bottom up coarse graining, "fix bocs"_fix_bocs.html, USER/bocs, -
 "USER-CGDNA"_#USER-CGDNA, coarse-grained DNA force fields, src/USER-CGDNA/README, USER/cgdna, -
 "USER-CGSDK"_#USER-CGSDK, SDK coarse-graining model, "pair_style lj/sdk"_pair_sdk.html, USER/cgsdk, -
 "USER-COLVARS"_#USER-COLVARS, collective variables library, "fix colvars"_fix_colvars.html, USER/colvars, int
@@ -1625,6 +1626,43 @@ examples/USER/awpmd :ul
 
 :line
 
+USER-BOCS package :link(USER-BOCS),h4
+
+[Contents:]
+
+This package provides "fix bocs"_fix_bocs.html, a modified version
+of "fix npt"_fix_nh.html which includes the pressure correction to
+the barostat as outlined in:
+
+N. J. H. Dunn and W. G. Noid, "Bottom-up coarse-grained models that 
+accurately describe the structure, pressure, and compressibility of
+molecular liquids," J. Chem. Phys. 143, 243148 (2015).
+
+[Authors:] Nicholas J. H. Dunn and Michael R. DeLyser (The Pennsylvania State University)
+
+[Install or un-install:]
+
+make yes-user-bocs
+make machine :pre
+
+make no-user-bocs
+make machine :pre
+
+[Supporting info:]
+
+The USER-BOCS user package for LAMMPS is part of the BOCS software package:
+"https://github.com/noid-group/BOCS"_https://github.com/noid-group/BOCS
+
+See the following reference for information about the entire package:
+
+Dunn, NJH; Lebold, KM; DeLyser, MR; Rudzinski, JF; Noid, WG.
+"BOCS: Bottom-Up Open-Source Coarse-Graining Software."
+J. Phys. Chem. B. 122, 13, 3363-3377 (2018).
+
+Example inputs are in the examples/USER/bocs folder.
+
+:line
+
 USER-CGDNA package :link(USER-CGDNA),h4
 
 [Contents:]

doc/src/bond_oxdna.txt

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

doc/src/compute_ackland_atom.txt

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

doc/src/compute_displace_atom.txt

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

doc/src/compute_heat_flux.txt

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

doc/src/compute_sna_atom.txt

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

doc/src/create_bonds.txt

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

doc/src/dihedral_table_cut.txt

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

doc/src/dihedrals.txt

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

doc/src/dump_modify.txt

@@ -15,7 +15,7 @@ dump_modify dump-ID keyword values ... :pre
 dump-ID = ID of dump to modify :ulb,l
 one or more keyword/value pairs may be appended :l
 these keywords apply to various dump styles :l
-keyword = {append} or {at} or {buffer} or {delay} or {element} or {every} or {fileper} or {first} or {flush} or {format} or {image} or {label} or {nfile} or {pad} or {precision} or {region} or {scale} or {sort} or {thresh} or {unwrap} :l
+keyword = {append} or {at} or {buffer} or {delay} or {element} or {every} or {fileper} or {first} or {flush} or {format} or {image} or {label} or {maxfiles} or {nfile} or {pad} or {precision} or {region} or {scale} or {sort} or {thresh} or {unwrap} :l
   {append} arg = {yes} or {no}
   {at} arg = N
     N = index of frame written upon first dump
@@ -37,6 +37,8 @@ keyword = {append} or {at} or {buffer} or {delay} or {element} or {every} or {fi
   {image} arg = {yes} or {no}
   {label} arg = string
     string = character string (e.g. BONDS) to use in header of dump local file
+  {maxfiles} arg = Fmax
+    Fmax = keep only the most recent {Fmax} snapshots (one snapshot per file)
   {nfile} arg = Nf
     Nf = write this many files, one from each of Nf processors
   {pad} arg = Nchar = # of characters to convert timestep to
@@ -364,6 +366,20 @@ e.g. BONDS or ANGLES.
 
 :line
 
+The {maxfiles} keyword can only be used when a '*' wildcard is
+included in the dump file name, i.e. when writing a new file(s) for
+each snapshot.  The specified {Fmax} is how many snapshots will be
+kept.  Once this number is reached, the file(s) containing the oldest
+snapshot is deleted before a new dump file is written.  If the
+specified {Fmax} <= 0, then all files are retained.
+
+This can be useful for debugging, especially if you don't know on what
+timestep something bad will happen, e.g. when LAMMPS will exit with an
+error.  You can dump every timestep, and limit the number of dump
+files produced, even if you run for 1000s of steps.
+
+:line
+
 The {nfile} or {fileper} keywords can be used in conjunction with the
 "%" wildcard character in the specified dump file name, for all dump
 styles except the {dcd}, {image}, {movie}, {xtc}, and {xyz} styles
@@ -901,6 +917,7 @@ flush = yes
 format = %d and %g for each integer or floating point value
 image = no
 label = ENTRIES
+maxifiles = -1
 nfile = 1
 pad = 0
 pbc = no

doc/src/fix_adapt.txt

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

doc/src/fix_bocs.txt

@@ -0,0 +1,112 @@
+<"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+fix bocs command :h3
+
+[Syntax:]
+
+fix  ID group-ID bocs keyword values ... :pre
+
+keyword = {temp} or {cgiso} or {analytic} or {linear_spline} or {cubic_spline}
+  {temp} values = Tstart Tstop Tdamp
+  {cgiso} values = Pstart Pstop Pdamp
+  {basis set}
+    {analytic} values = V_avg N_particles N_coeff Coeff_1 Coeff_2 ... Coeff_N
+    {linear_spline} values = input_filename
+    {cubic_spline} values = input_filename :pre
+:ule
+
+[Examples:]
+
+fix 1 all bocs temp 300.0 300.0 100.0 cgiso 0.986 0.986 1000.0 analytic 66476.015 968 2 245030.10 8962.20 :pre
+ 
+fix 1 all bocs temp 300.0 300.0 100.0 cgiso 0.986 0.986 1000.0 cubic_spline input_Fv.dat :pre
+
+thermo_modify press 1_press :pre
+
+
+[Description:]
+
+These commands incorporate a pressure correction as described by 
+Dunn and Noid in "(Dunn1)"_#bocs-Dunn1 to the standard MTTK
+barostat by Martyna et. al. in "(Martyna)"_#bocs-Martyna .
+The first half of the command mimics a standard fix npt command:
+
+fix 1 all bocs temp Tstart Tstop Tcoupl cgiso Pstart Pstop Pdamp :pre
+
+The two differences are replacing {npt} with {bocs}, and replacing 
+{iso}/{aniso}/{etc} with {cgiso}.
+The rest of the command details what form you would like to use for 
+the pressure correction equation. The choices are: {analytic}, {linear_spline}, 
+or {cubic_spline}. 
+
+With either spline method, the only argument that needs to follow it 
+is the name of a file that contains the desired pressure correction 
+as a function of volume. The file should be formatted so each line has:
+
+Volume_i, PressureCorrection_i :pre
+
+Note both the COMMA and the SPACE separating the volume's 
+value and its corresponding pressure correction. The volumes in the file 
+should be uniformly spaced. Both the volumes and the pressure corrections 
+should be provided in the proper units, e.g. if you are using {units real}, 
+the volumes should all be in cubic angstroms, and the pressure corrections 
+should all be in atomspheres. Furthermore, the table should start/end at a 
+volume considerably smaller/larger than you expect your system to sample 
+during the simulation. If the system ever reaches a volume outside of the 
+range provided, the simulation will stop.
+
+With the {analytic} option, the arguments are as follows:
+
+... analytic V_avg N_particles N_coeff Coeff_1 Coeff_2 ... Coeff_N :pre
+
+Note that {V_avg} and {Coeff_i} should all be in the proper units, e.g. if you 
+are using {units real}, {V_avg} should be in cubic angstroms, and the 
+coefficients should all be in atmospheres * cubic angstroms.
+
+[Restrictions:]
+
+As this is computing a (modified) pressure, group-ID should be {all}.
+
+The pressure correction has only been tested for use with an isotropic 
+pressure coupling in 3 dimensions.   
+
+By default, LAMMPS will still report the normal value for the pressure
+if the pressure is printed via a {thermo} command, or if the pressures
+are written to a file every so often. In order to have LAMMPS report the
+modified pressure, you must include the {thermo_modify} command given in 
+the examples. For the last argument in the command, you should put 
+XXXX_press, where XXXX is the ID given to the fix bocs command (in the
+example, the ID of the fix bocs command is 1 ).
+
+This fix is part of the USER-BOCS package.  It is only enabled if
+LAMMPS was built with that package.  See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
+
+[Related:]
+
+For more details about the pressure correction and the entire BOCS software 
+package, visit the "BOCS package on github"_bocsgithub and read the release 
+paper by Dunn et. al. "(Dunn2)"_#bocs-Dunn2 .
+
+
+:link(bocsgithub,https://github.com/noid-group/BOCS)
+
+:line
+
+:link(bocs-Dunn1)
+[(Dunn1)] Dunn and Noid, J Chem Phys, 143, 243148 (2015).
+
+:link(bocs-Martyna)
+[(Martyna)] Martyna, Tobias, and Klein, J Chem Phys, 101, 4177 (1994).
+
+:link(bocs-Dunn2)
+[(Dunn2)] Dunn, Lebold, DeLyser, Rudzinski, and Noid, J. Phys. Chem. B, 122, 3363 (2018).
+
+
+

doc/src/fix_bond_react.txt

@@ -0,0 +1,332 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+fix bond/react command :h3
+
+[Syntax:]
+
+fix ID group-ID bond/react common_keyword values ...
+  react react-ID react-group-ID Nevery Rmin Rmax template-ID(pre-reacted) template-ID(post-reacted) map_file individual_keyword values ...
+  react react-ID react-group-ID Nevery Rmin Rmax template-ID(pre-reacted) template-ID(post-reacted) map_file individual_keyword values ...
+  react react-ID react-group-ID Nevery Rmin Rmax template-ID(pre-reacted) template-ID(post-reacted) map_file individual_keyword values ...
+  ... :pre
+
+ID, group-ID are documented in "fix"_fix.html command. Group-ID is ignored. :ulb,l
+bond/react = style name of this fix command :l
+zero or more common keyword/value pairs may be appended directly after 'bond/react' :l
+these apply to all reaction specifications (below) :l
+common_keyword = {stabilization} :l
+  {stabilization} values = {no} or {yes} {group-ID} {xmax}
+    {no} = no reaction site stabilization
+    {yes} = perform reaction site stabilization
+      {group-ID} = user-assigned ID for all non-reacting atoms (group created internally)
+      {xmax} = xmax value that is used by an internally created "nve/limit"_fix_nve_limit.html integrator :pre
+react = mandatory argument indicating new reaction specification :l
+  react-ID = user-assigned name for the reaction :l
+  react-group-ID = only atoms in this group are available for the reaction :l
+  Nevery = attempt reaction every this many steps :l
+  Rmin = bonding pair atoms must be separated by more than Rmin to initiate reaction (distance units) :l
+  Rmax = bonding pair atoms must be separated by less than Rmax to initiate reaction (distance units) :l
+  template-ID(pre-reacted) = ID of a molecule template containing pre-reaction topology :l
+  template-ID(post-reacted) = ID of a molecule template containing post-reaction topology :l
+  map_file = name of file specifying corresponding atomIDs in the pre- and post-reacted templates :l
+  zero or more individual keyword/value pairs may be appended to each react argument :l
+  individual_keyword = {prob} or {stabilize_steps} :l
+    {prob} values = fraction seed
+      fraction = initiate reaction with this probability if otherwise eligible
+      seed = random number seed (positive integer)
+    {stabilize_steps} value = timesteps
+      timesteps = number of timesteps to apply internally created nve/limit.html :pre
+:ule
+
+[Examples:]
+
+molecule mol1 pre_reacted_topology.txt
+molecule mol2 post_reacted_topology.txt
+fix 5 all bond/react stabilization no react myrxn1 all 1 0 3.25 mol1 mol2 map_file.txt :pre
+
+molecule mol1 pre_reacted_rxn1.txt
+molecule mol2 post_reacted_rxn1.txt
+molecule mol3 pre_reacted_rxn2.txt
+molecule mol4 post_reacted_rxn2.txt
+fix 5 all bond/react stabilization yes nvt_grp .03 &
+  react myrxn1 all 1 0 3.25 mol1 mol2 map_file_rxn1.txt prob 0.50 12345 &
+  react myrxn2 all 1 0 2.75 mol3 mol4 map_file_rxn2.txt prob 0.25 12345
+fix 6 nvt_grp nvt temp 300 300 100 # set thermostat after bond/react :pre
+
+[Description:]
+
+Initiate complex covalent bonding (topology) changes. These topology
+changes will be referred to as 'reactions' throughout this
+documentation. Topology changes are defined in pre- and post-reaction
+molecule templates and can include creation and deletion of bonds,
+angles, dihedrals, impropers, bond-types, angle-types, dihedral-types,
+atom-types, or atomic charges.
+
+Fix bond/react does not use quantum mechanical (eg. fix qmmm) or
+pairwise bond-order potential (eg. Tersoff or AIREBO) methods to
+determine bonding changes a priori. Rather, it uses a distance-based
+probabilistic criteria to effect predetermined topology changes in
+simulations using standard force fields.
+
+This fix was created to facilitate the dynamic creation of polymeric,
+amorphous or highly-crosslinked systems. A suggested workflow for
+using this fix is: 1) identify a reaction to be simulated 2) build a
+molecule template of the reaction site before the reaction has
+occurred 3) build a molecule template of the reaction site after the
+reaction has occurred 4) create a map that relates the
+template-atom-IDs of each atom between pre- and post-reaction molecule
+templates 5) fill a simulation box with molecules and run a simulation
+with fix bond/react.
+
+Only one 'fix bond/react' command can be used at a time. Multiple
+reactions can be simultaneously applied by specifying multiple {react}
+arguments to a single 'fix bond/react' command. This syntax is
+necessary because the 'common keywords' are applied to all reactions.
+
+The {stabilization} keyword enables reaction site stabilization.
+Reaction site stabilization is performed by including reacting atoms
+in an internally created fix "nve/limit"_fix_nve_limit.html time
+integrator for a set number of timesteps given by the
+{stabilize_steps} keyword. While reacting atoms are being time
+integrated by the internal nve/limit, they are prevented from being
+involved in any new reactions. The {xmax} value keyword should
+typically be set to the maximum distance that non-reacting atoms move
+during the simulation.
+
+The group-ID set using the {stabilization} keyword should be a
+previously unused group-ID. It cannot be specified as 'all'. The fix
+bond/react command creates a "dynamic group"_group.html of this name
+that includes all non-reacting atoms. This dynamic group-ID should
+then be used by a subsequent system-wide time integrator such as nvt,
+npt, or nve, as shown in the second example above. It is currently
+necessary to place the time integration command after the fix
+bond/react command due to the internal dynamic grouping performed by
+fix bond/react.
+
+NOTE: The internally created group currently applies to all atoms in
+the system, i.e. you should generally not have a separate thermostat
+which acts on the 'all' group.
+
+The following comments pertain to each {react} argument:
+
+A check for possible new reaction sites is performed every {Nevery}
+timesteps.
+
+Two conditions must be met for a reaction to occur. First a bonding
+atom pair must be identified. Second, the topology surrounding the
+bonding atom pair must match the topology of the pre-reaction
+template. If both these conditions are met, the reaction site is
+modified to match the post-reaction template.
+
+A bonding atom pair will be identified if several conditions are met.
+First, a pair of atoms within the specified react-group-ID of type
+typei and typej must separated by a distance between {Rmin} and
+{Rmax}. It is possible that multiple bonding atom pairs are
+identified: if the bonding atoms in the pre-reacted template are not
+1-2, 1-3, or 1-4 neighbors, the closest bonding atom partner is set as
+its bonding partner; otherwise, the farthest potential partner is
+chosen. Then, if both an atomi and atomj have each other as their
+nearest bonding partners, these two atoms are identified as the
+bonding atom pair of the reaction site. Once this unique bonding atom
+pair is identified for each reaction, there could two or more
+reactions that involve a given atom on the same timestep. If this is
+the case, only one such reaction is permitted to occur. This reaction
+is chosen randomly from all potential reactions. This capability
+allows e.g. for different reaction pathways to proceed from identical
+reaction sites with user-specified probabilities.
+
+The pre-reacted molecule template is specified by a molecule command.
+This molecule template file contains a sample reaction site and its
+surrounding topology. As described below, the bonding atom pairs of
+the pre-reacted template are specified by atom ID in the map file. The
+pre-reacted molecule template should contain as few atoms as possible
+while still completely describing the topology of all atoms affected
+by the reaction. For example, if the force field contains dihedrals,
+the pre-reacted template should contain any atom within three bonds of
+reacting atoms.
+
+Some atoms in the pre-reacted template that are not reacting may have
+missing topology with respect to the simulation. For example, the
+pre-reacted template may contain an atom that would connect to the
+rest of a long polymer chain. These are referred to as edge atoms, and
+are also specified in the map file.
+
+Note that some care must be taken when a building a molecule template
+for a given simulation. All atom types in the pre-reacted template
+must be the same as those of a potential reaction site in the
+simulation. A detailed discussion of matching molecule template atom
+types with the simulation is provided on the "molecule"_molecule.html
+command page.
+
+The post-reacted molecule template contains a sample of the reaction
+site and its surrounding topology after the reaction has occurred. It
+must contain the same number of atoms as the pre-reacted template. A
+one-to-one correspondence between the atom IDs in the pre- and
+post-reacted templates is specified in the map file as described
+below. Note that during a reaction, an atom, bond, etc. type may
+change to one that was previously not present in the simulation. These
+new types must also be defined during the setup of a given simulation.
+A discussion of correctly handling this is also provided on the
+"molecule"_molecule.html command page.
+
+The map file is a text document with the following format:
+
+A map file has a header and a body. The header of map file the
+contains one mandatory keyword and one optional keyword. The mandatory
+keyword is 'equivalences' and the optional keyword is 'edgeIDs':
+
+N {equivalences} = # of atoms N in the reaction molecule templates
+N {edgeIDs} = # of edge atoms N in the pre-reacted molecule template :pre
+
+The body of the map file contains two mandatory sections and one
+optional section. The first mandatory section begins with the keyword
+'BondingIDs' and lists the atom IDs of the bonding atom pair in the
+pre-reacted molecule template. The second mandatory section begins
+with the keyword 'Equivalences' and lists a one-to-one correspondence
+between atom IDs of the pre- and post-reacted templates. The first
+column is an atom ID of the pre-reacted molecule template, and the
+second column is the corresponding atom ID of the post-reacted
+molecule template. The optional section begins with the keyword
+'EdgeIDs' and lists the atom IDs of edge atoms in the pre-reacted
+molecule template.
+
+A sample map file is given below:
+
+:line
+
+# this is a map file :pre
+
+2 edgeIDs
+7 equivalences :pre
+
+BondingIDs :pre
+
+3
+5 :pre
+
+EdgeIDs :pre
+
+1
+7 :pre
+
+Equivalences :pre
+
+1   1
+2   2
+3   3
+4   4
+5   5
+6   6
+7   7 :pre
+
+:line
+
+Once a reaction site has been successfully identified, data structures
+within LAMMPS that store bond topology are updated to reflect the
+post-reacted molecule template. All force fields with fixed bonds,
+angles, dihedrals or impropers are supported.
+
+A few capabilities to note: 1) You may specify as many {react}
+arguments as desired. For example, you could break down a complicated
+reaction mechanism into several reaction steps, each defined by its
+own {react} argument. 2) While typically a bond is formed or removed
+between the bonding atom pairs specified in the pre-reacted molecule
+template, this is not required. 3) By reversing the order of the pre-
+and post- reacted molecule templates in another {react} argument, you
+can allow for the possibility of one or more reverse reactions.
+
+The optional keywords deal with the probability of a given reaction
+occurring as well as the stable equilibration of each reaction site as
+it occurs.
+
+The {prob} keyword can affect whether an eligible reaction actually
+occurs. The fraction setting must be a value between 0.0 and 1.0. A
+uniform random number between 0.0 and 1.0 is generated and the
+eligible reaction only occurs if the random number is less than the
+fraction.
+
+The {stabilize_steps} keyword allows for the specification of how many
+timesteps a reaction site is stabilized before being returned to the
+overall system thermostat.
+
+In order to produce the most physical behavior, this 'reaction site
+equilibration time' should be tuned to be as small as possible while
+retaining stability for a given system or reaction step. After a
+limited number of case studies, this number has been set to a default
+of 60 timesteps. Ideally, it should be individually tuned for each fix
+reaction step. Note that in some situations, decreasing rather than
+increasing this parameter will result in an increase in stability.
+
+A few other considerations:
+
+It may be beneficial to ensure reacting atoms are at a certain
+temperature before being released to the overall thermostat. For this,
+you can use the internally-created dynamic group named
+"bond_react_MASTER_group." For example, adding the following command
+would thermostat the group of all atoms currently involved in a
+reaction:
+
+fix 1 bond_react_MASTER_group temp/rescale 1 300 300 10 1 :pre
+
+NOTE: This command must be added after the fix bond/react command, and
+will apply to all reactions.
+
+Computationally, each timestep this fix operates, it loops over
+neighbor lists (for bond-forming reactions) and computes distances
+between pairs of atoms in the list. It also communicates between
+neighboring processors to coordinate which bonds  are created and/or
+removed. All of these operations increase the cost of a timestep. Thus
+you should be cautious about invoking this fix too frequently.
+
+You can dump out snapshots of the current bond topology via the dump
+local command.
+
+:line
+
+[Restart, fix_modify, output, run start/stop, minimize info:]
+
+No information about this fix is written to "binary restart
+files"_restart.html, aside from internally-created per-atom
+properties. None of the "fix_modify"_fix_modify.html options are
+relevant to this fix.
+
+This fix computes one statistic for each {react} argument that it
+stores in a global vector, of length 'number of react arguments', that
+can be accessed by various "output
+commands"_Section_howto.html#howto_15. The vector values calculated by
+this fix are "intensive".
+
+These is 1 quantity for each react argument:
+
+(1) cumulative # of reactions occurred :ul
+
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command.  This fix is not invoked during "energy
+minimization"_minimize.html.
+
+[Restrictions:]
+
+This fix is part of the USER-MISC package.  It is only enabled if
+LAMMPS was built with that package.  See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
+
+[Related commands:]
+
+"fix bond/create"_fix_bond_create.html, "fix
+bond/break"_fix_bond_break.html, "fix bond/swap"_fix_bond_swap.html,
+"dump local"_dump.html, "special_bonds"_special_bonds.html
+
+[Default:]
+
+The option defaults are stabilization = no, stabilize_steps = 60
+
+:line
+
+:link(Gissinger)
+[(Gissinger)] Gissinger, Jensen and Wise, Polymer, 128, 211 (2017).

doc/src/fix_dt_reset.txt

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

doc/src/fix_langevin_drude.txt

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

doc/src/fix_modify.txt

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

doc/src/fix_poems.txt

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

doc/src/fix_reax_bonds.txt

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

doc/src/fix_restrain.txt

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

doc/src/fix_rigid.txt

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

doc/src/fixes.txt

@@ -20,9 +20,11 @@ Fixes :h1
    fix_ave_time
    fix_aveforce
    fix_balance
+   fix_bocs
    fix_bond_break
    fix_bond_create
    fix_bond_swap
+   fix_bond_react
    fix_box_relax
    fix_cmap
    fix_colvars

doc/src/lammps.book

@@ -135,8 +135,10 @@ fix_ave_histo.html
 fix_ave_time.html
 fix_aveforce.html
 fix_balance.html
+fix_bocs.html
 fix_bond_break.html
 fix_bond_create.html
+fix_bond_react.html
 fix_bond_swap.html
 fix_box_relax.html
 fix_cmap.html
@@ -580,6 +582,7 @@ dihedral_opls.html
 dihedral_quadratic.html
 dihedral_spherical.html
 dihedral_table.html
+dihedral_table_cut.html
 dihedral_zero.html
 
 lammps_commands_improper.html

doc/src/molecule.txt

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

doc/src/pair_born.txt

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

doc/src/pair_coul.txt

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

doc/src/pair_gw.txt

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

doc/src/pair_kolmogorov_crespi_z.txt

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

doc/src/pair_oxdna.txt

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

doc/src/pair_oxdna2.txt

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

doc/src/pair_reaxc.txt

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

doc/src/pair_sw.txt

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

doc/src/variable.txt

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

doc/src/write_data.txt

@@ -16,6 +16,7 @@ file = name of data file to write out :ulb,l
 zero or more keyword/value pairs may be appended :l
 keyword = {pair} or {nocoeff} :l
   {nocoeff} = do not write out force field info
+  {nofix} = do not write out extra sections read by fixes
   {pair} value = {ii} or {ij}
     {ii} = write one line of pair coefficient info per atom type
     {ij} = write one line of pair coefficient info per IJ atom type pair :pre
@@ -83,6 +84,12 @@ be written to the data file. This can be very helpful, if one wants
 to make significant changes to the force field or if the parameters
 are read in separately anyway, e.g. from an include file.
 
+The {nofix} keyword requests that no extra sections read by fixes
+should be written to the data file (see the {fix} option of the
+"read_data"_read_data.html command for details). For example, this
+option excludes sections for user-created per-atom properties 
+from "fix property/atom"_fix_property_atom.html.
+
 The {pair} keyword lets you specify in what format the pair
 coefficient information is written into the data file.  If the value
 is specified as {ii}, then one line per atom type is written, to
@@ -120,4 +127,3 @@ setup, atom masses initialized, etc).
 [Default:]
 
 The option defaults are pair = ii.
-

examples/COUPLE/lammps_quest/lmpqst.cpp

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

examples/COUPLE/lammps_spparks/lmpspk.cpp

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

examples/COUPLE/library/error.cpp

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

examples/COUPLE/library/files.cpp

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

examples/COUPLE/library/irregular.cpp

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

examples/COUPLE/library/lammps_data_write.cpp

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

examples/COUPLE/library/lammps_data_write.h

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

examples/COUPLE/library/many2many.cpp

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

examples/COUPLE/library/many2one.cpp

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

examples/COUPLE/library/memory.cpp

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

examples/COUPLE/library/one2many.cpp

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

examples/COUPLE/library/send2one.cpp

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

examples/COUPLE/multiple/multiple.cpp

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

examples/COUPLE/simple/simple.cpp

@@ -19,15 +19,16 @@
 //         in.lammps = LAMMPS input script
 // See README for compilation instructions
 
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
-#include "mpi.h"
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
+#include <mpi.h>
 
-#include "lammps.h"         // these are LAMMPS include files
-#include "input.h"
-#include "atom.h"
-#include "library.h"
+// these are LAMMPS include files
+#include <lammps/lammps.h>
+#include <lammps/input.h>
+#include <lammps/atom.h>
+#include <lammps/library.h>
 
 using namespace LAMMPS_NS;
 

examples/USER/bocs/README

@@ -0,0 +1,6 @@
+This folder contains the files to run a NPT simulation of 1 site CG methanol
+while employing a correction to the barostat.
+The pair force was computed via the Multi-Scale Coarse-Graining method.
+The resulting model was then iteratively pressure matched.
+The model accurately reproduces both structural (RDF) and thermodynamic 
+(Pressure-Volume EoS) properties of the underlying OPLS-AA model of methanol.

examples/USER/bocs/in.methanol

@@ -0,0 +1,69 @@
+units		real
+dimension	3
+boundary	p p p
+atom_style      atomic
+
+newton		on
+timestep	1.0
+
+read_data	methanol.data
+
+velocity	all create 300.0 16802 dist gaussian
+
+pair_style	table spline 15000
+
+pair_coeff	1 1 lammps_nb_MET-MET.table nb_METMET 12.0
+
+neigh_modify	delay 0 every 1 check yes one 10000
+neighbor	12.0 bin
+
+thermo		500
+thermo_style	custom step temp pe etotal press vol
+
+variable STEP equal step
+variable TEMP equal temp
+## volume from cubic angstroms to cubic nm
+variable VOL equal vol/1000.0
+## pressure from atm to bar
+variable PRESS equal press*1.01325
+variable PXX equal pxx*1.01325
+variable PYY equal pyy*1.01325
+variable PZZ equal pzz*1.01325
+variable PXY equal pxy*1.01325
+variable PXZ equal pxz*1.01325
+variable PYZ equal pyz*1.01325
+## energy from kcal/mol to kJ/mol
+variable KE equal ke*4.184
+variable PE equal pe*4.184
+variable UVDW equal evdwl*4.184
+
+
+#####     SPECIAL COMMANDS FOR FIX_BOCS     #####
+#       ID group-ID style_name thermostat T_init T_end T_couple barostat P_start P_end  P_couple pmatch_basis avg_vol     N_sites N_coeffs coeff1      coeff2
+fix 	1  all      bocs       temp       300.0  300.0 100.0    cgiso    0.986   0.986  1000.0   analytic     66476.015   968     2        245030.10   8962.20 
+
+# Report the modified pressure
+thermo_modify 	press 1_press
+
+
+
+## Uncomment to save some data from simulation to files
+#fix             print_temp all print 500 "${STEP} ${TEMP}" file temp.dat screen no
+#fix             print_vol all print 500 "${STEP} ${VOL}" file vol.dat screen no
+#fix             print_press all print 500 "${STEP} ${PRESS}" file press.dat screen no
+#fix             print_ke all print 500 "${STEP} ${KE}" file kinetic_E.dat screen no
+#fix             print_pe all print 500 "${STEP} ${PE}" file potential_E.dat screen no
+#fix             print_ve all print 500 "${STEP} ${UVDW}" file vdw_E.dat screen no
+#fix             print_press_tens all print 500 "${STEP} ${PXX} ${PYY} ${PZZ} ${PXY} ${PXZ} ${PYZ}" file press_tens.dat screen no
+#fix		print_PV_eos all print 500 "${VOL} ${PRESS}" file pv_eos.dat screen no
+
+## Prints a configuration to dump.txt every 500 steps
+#dump		1 all custom 500 dump.txt id type x y z fx fy fz
+
+# Write restart files to continue simulations
+#restart 10000 state1.restart state2.restart
+
+## Run for this many steps
+run_style       verlet
+run 10000
+

examples/USER/bocs/log.20Apr18.methanol.g++.1

@@ -0,0 +1,143 @@
+LAMMPS (20 Apr 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+  using 1 OpenMP thread(s) per MPI task
+units		real
+dimension	3
+boundary	p p p
+atom_style      atomic
+
+newton		on
+timestep	1.0
+
+read_data	methanol.data
+  orthogonal box = (0 0 0) to (40.4635 40.4635 40.4635)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  968 atoms
+
+velocity	all create 300.0 16802 dist gaussian
+
+pair_style	table spline 15000
+
+pair_coeff	1 1 lammps_nb_MET-MET.table nb_METMET 12.0
+WARNING: 78 of 2500 force values in table are inconsistent with -dE/dr.
+  Should only be flagged at inflection points (../pair_table.cpp:481)
+
+neigh_modify	delay 0 every 1 check yes one 10000
+neighbor	12.0 bin
+
+thermo		500
+thermo_style	custom step temp pe etotal press vol
+
+variable STEP equal step
+variable TEMP equal temp
+## volume from cubic angstroms to cubic nm
+variable VOL equal vol/1000.0
+## pressure from atm to bar
+variable PRESS equal press*1.01325
+variable PXX equal pxx*1.01325
+variable PYY equal pyy*1.01325
+variable PZZ equal pzz*1.01325
+variable PXY equal pxy*1.01325
+variable PXZ equal pxz*1.01325
+variable PYZ equal pyz*1.01325
+## energy from kcal/mol to kJ/mol
+variable KE equal ke*4.184
+variable PE equal pe*4.184
+variable UVDW equal evdwl*4.184
+
+
+#####     SPECIAL COMMANDS FOR FIX_BOCS     #####
+#       ID group-ID style_name thermostat T_init T_end T_couple barostat P_start P_end  P_couple pmatch_basis avg_vol     N_sites N_coeffs coeff1      coeff2
+fix 	1  all      bocs       temp       300.0  300.0 100.0    cgiso    0.986   0.986  1000.0   analytic     66476.015   968     2        245030.10   8962.20
+
+# Report the modified pressure
+thermo_modify 	press 1_press
+
+
+
+## Uncomment to save some data from simulation to files
+#fix             print_temp all print 500 "${STEP} ${TEMP}" file temp.dat screen no
+#fix             print_vol all print 500 "${STEP} ${VOL}" file vol.dat screen no
+#fix             print_press all print 500 "${STEP} ${PRESS}" file press.dat screen no
+#fix             print_ke all print 500 "${STEP} ${KE}" file kinetic_E.dat screen no
+#fix             print_pe all print 500 "${STEP} ${PE}" file potential_E.dat screen no
+#fix             print_ve all print 500 "${STEP} ${UVDW}" file vdw_E.dat screen no
+#fix             print_press_tens all print 500 "${STEP} ${PXX} ${PYY} ${PZZ} ${PXY} ${PXZ} ${PYZ}" file press_tens.dat screen no
+#fix		print_PV_eos all print 500 "${VOL} ${PRESS}" file pv_eos.dat screen no
+
+## Prints a configuration to dump.txt every 500 steps
+#dump		1 all custom 500 dump.txt id type x y z fx fy fz
+
+# Write restart files to continue simulations
+#restart 10000 state1.restart state2.restart
+
+## Run for this many steps
+run_style       verlet
+run 10000
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 10000, page size: 100000
+  master list distance cutoff = 24
+  ghost atom cutoff = 24
+  binsize = 12, bins = 4 4 4
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair table, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 4.691 | 4.691 | 4.691 Mbytes
+Step Temp PotEng TotEng Press Volume 
+       0          300    1061.5961    1926.3291      107.006    66250.679 
+     500    314.54728    1034.1091    1940.7738    194.42689    65660.282 
+    1000    301.41603    1030.7027    1899.5173   -91.966709    66262.543 
+    1500     298.8308    1014.8276    1876.1905   -80.178606    67053.605 
+    2000    294.78476    1046.8207     1896.521    50.592942    66316.735 
+    2500    301.18564    1033.9214    1902.0719     40.48255    66607.667 
+    3000    301.06632    1022.0381    1889.8447    47.582344    66341.947 
+    3500    297.98361    989.80983    1848.7307   -204.69879    67462.078 
+    4000    299.03493    1034.6571    1896.6083    89.188888    66457.385 
+    4500    306.03351     985.4121    1867.5363   -51.102407    67519.446 
+    5000     305.6903    1013.8613    1894.9963   -141.13704    67240.467 
+    5500    292.23444    1029.5558     1871.905    20.764579    66683.876 
+    6000    287.87735    1017.7325    1847.5226   -35.288049    66630.031 
+    6500    305.26461    960.08118    1839.9891   -352.42596    67612.317 
+    7000    300.34449    1055.0664    1920.7923     22.04027     66187.27 
+    7500    305.48612    1038.6651    1919.2115    17.807254    66324.168 
+    8000    316.03232    1034.6809    1945.6262    27.482857    66502.198 
+    8500    294.28636    1038.8213     1887.085   -72.840559    66851.661 
+    9000    316.69029    1065.7481    1978.5899    245.61677    65678.385 
+    9500    297.46127    1034.5547      1891.97     54.23428    66892.627 
+   10000    301.24799    1036.5432    1904.8735    7.7134029    66150.506 
+Loop time of 34.426 on 1 procs for 10000 steps with 968 atoms
+
+Performance: 25.097 ns/day, 0.956 hours/ns, 290.478 timesteps/s
+99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 33.324     | 33.324     | 33.324     |   0.0 | 96.80
+Neigh   | 0.12198    | 0.12198    | 0.12198    |   0.0 |  0.35
+Comm    | 0.42865    | 0.42865    | 0.42865    |   0.0 |  1.25
+Output  | 0.00059938 | 0.00059938 | 0.00059938 |   0.0 |  0.00
+Modify  | 0.42553    | 0.42553    | 0.42553    |   0.0 |  1.24
+Other   |            | 0.1252     |            |       |  0.36
+
+Nlocal:    968 ave 968 max 968 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    9112 ave 9112 max 9112 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    404392 ave 404392 max 404392 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 404392
+Ave neighs/atom = 417.76
+Neighbor list builds = 13
+Dangerous builds = 0
+
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:34

examples/USER/bocs/log.20Apr18.methanol.g++.4

@@ -0,0 +1,143 @@
+LAMMPS (20 Apr 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+  using 1 OpenMP thread(s) per MPI task
+units		real
+dimension	3
+boundary	p p p
+atom_style      atomic
+
+newton		on
+timestep	1.0
+
+read_data	methanol.data
+  orthogonal box = (0 0 0) to (40.4635 40.4635 40.4635)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  968 atoms
+
+velocity	all create 300.0 16802 dist gaussian
+
+pair_style	table spline 15000
+
+pair_coeff	1 1 lammps_nb_MET-MET.table nb_METMET 12.0
+WARNING: 78 of 2500 force values in table are inconsistent with -dE/dr.
+  Should only be flagged at inflection points (../pair_table.cpp:481)
+
+neigh_modify	delay 0 every 1 check yes one 10000
+neighbor	12.0 bin
+
+thermo		500
+thermo_style	custom step temp pe etotal press vol
+
+variable STEP equal step
+variable TEMP equal temp
+## volume from cubic angstroms to cubic nm
+variable VOL equal vol/1000.0
+## pressure from atm to bar
+variable PRESS equal press*1.01325
+variable PXX equal pxx*1.01325
+variable PYY equal pyy*1.01325
+variable PZZ equal pzz*1.01325
+variable PXY equal pxy*1.01325
+variable PXZ equal pxz*1.01325
+variable PYZ equal pyz*1.01325
+## energy from kcal/mol to kJ/mol
+variable KE equal ke*4.184
+variable PE equal pe*4.184
+variable UVDW equal evdwl*4.184
+
+
+#####     SPECIAL COMMANDS FOR FIX_BOCS     #####
+#       ID group-ID style_name thermostat T_init T_end T_couple barostat P_start P_end  P_couple pmatch_basis avg_vol     N_sites N_coeffs coeff1      coeff2
+fix 	1  all      bocs       temp       300.0  300.0 100.0    cgiso    0.986   0.986  1000.0   analytic     66476.015   968     2        245030.10   8962.20
+
+# Report the modified pressure
+thermo_modify 	press 1_press
+
+
+
+## Uncomment to save some data from simulation to files
+#fix             print_temp all print 500 "${STEP} ${TEMP}" file temp.dat screen no
+#fix             print_vol all print 500 "${STEP} ${VOL}" file vol.dat screen no
+#fix             print_press all print 500 "${STEP} ${PRESS}" file press.dat screen no
+#fix             print_ke all print 500 "${STEP} ${KE}" file kinetic_E.dat screen no
+#fix             print_pe all print 500 "${STEP} ${PE}" file potential_E.dat screen no
+#fix             print_ve all print 500 "${STEP} ${UVDW}" file vdw_E.dat screen no
+#fix             print_press_tens all print 500 "${STEP} ${PXX} ${PYY} ${PZZ} ${PXY} ${PXZ} ${PYZ}" file press_tens.dat screen no
+#fix		print_PV_eos all print 500 "${VOL} ${PRESS}" file pv_eos.dat screen no
+
+## Prints a configuration to dump.txt every 500 steps
+#dump		1 all custom 500 dump.txt id type x y z fx fy fz
+
+# Write restart files to continue simulations
+#restart 10000 state1.restart state2.restart
+
+## Run for this many steps
+run_style       verlet
+run 10000
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 10000, page size: 100000
+  master list distance cutoff = 24
+  ghost atom cutoff = 24
+  binsize = 12, bins = 4 4 4
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair table, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.37 | 3.37 | 3.371 Mbytes
+Step Temp PotEng TotEng Press Volume 
+       0          300    1061.5961    1926.3291      107.006    66250.679 
+     500    314.54728    1034.1091    1940.7738    194.42689    65660.282 
+    1000    301.41603    1030.7027    1899.5173   -91.966709    66262.543 
+    1500     298.8308    1014.8276    1876.1905   -80.178606    67053.605 
+    2000    294.78476    1046.8207     1896.521    50.592942    66316.735 
+    2500    301.18564    1033.9214    1902.0719    40.482557    66607.667 
+    3000    301.06631    1022.0381    1889.8447    47.582403    66341.947 
+    3500    297.98353    989.81011    1848.7308   -204.69823    67462.076 
+    4000    299.03465    1034.6603    1896.6108    89.196235    66457.338 
+    4500    306.04532    985.37017    1867.5285   -51.094929    67519.735 
+    5000    304.72903    1014.9543    1893.3184   -127.04402    67238.517 
+    5500    292.52622    1025.6599    1868.8502   -19.753932    66716.551 
+    6000    296.82719    1031.5184    1887.1059   -1.2609328    66368.611 
+    6500    298.63312    1018.4299    1879.2229    -24.75835    66524.898 
+    7000    303.25389    1005.9283    1880.0404   -96.273504    67349.674 
+    7500    292.45089    1068.2863    1911.2595    103.23295     65778.08 
+    8000    301.22765    1040.6294    1908.9011  -0.83635353    66831.038 
+    8500    300.19765    1047.5856    1912.8883   -31.582343    66316.305 
+    9000     295.1108    1023.8234    1874.4635   -88.165532    67192.344 
+    9500     302.1087    1003.6348    1874.4459   -18.707065    66369.361 
+   10000     296.3083     1004.126    1858.2178   -28.293045    66862.576 
+Loop time of 28.8053 on 4 procs for 10000 steps with 968 atoms
+
+Performance: 29.994 ns/day, 0.800 hours/ns, 347.159 timesteps/s
+95.2% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 19.929     | 21.765     | 23.391     |  27.8 | 75.56
+Neigh   | 0.067397   | 0.071231   | 0.077313   |   1.5 |  0.25
+Comm    | 3.9226     | 5.5183     | 7.3214     |  53.7 | 19.16
+Output  | 0.00069928 | 0.0016099  | 0.0043275  |   3.9 |  0.01
+Modify  | 1.0874     | 1.1376     | 1.1888     |   4.2 |  3.95
+Other   |            | 0.3112     |            |       |  1.08
+
+Nlocal:    242 ave 244 max 239 min
+Histogram: 1 0 0 0 0 0 1 0 1 1
+Nghost:    5718.5 ave 5736 max 5702 min
+Histogram: 1 0 0 0 1 1 0 0 0 1
+Neighs:    100703 ave 108064 max 93454 min
+Histogram: 1 0 0 1 0 0 1 0 0 1
+
+Total # of neighbors = 402813
+Ave neighs/atom = 416.129
+Neighbor list builds = 14
+Dangerous builds = 0
+
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:28

examples/USER/bocs/methanol.data

@@ -0,0 +1,991 @@
+LAMMPS Description
+
+     968  atoms
+     0  bonds
+     0  angles
+     0  dihedrals
+     0  impropers
+
+     1  atom types
+     0  bond types
+     0  angle types
+     0  dihedral types
+
+  0  40.4635 xlo xhi
+  0  40.4635 ylo yhi
+  0  40.4635 zlo zhi
+
+Masses
+
+    1 32.0424
+
+Atoms
+
+1 1 36.39 8.05 27.55
+2 1 18.38 15.72 26.03
+3 1 3.52 1.77 23.57
+4 1 31.09 11.38 12.17
+5 1 13.3 34.8 2.89
+6 1 1.72 38.55 10.36
+7 1 38.6 23.16 6.19
+8 1 0.74 33.21 0.17
+9 1 26.97 9.53 11.24
+10 1 31.68 12.19 17.04
+11 1 15.19 9.06 0.2
+12 1 34.39 20.63 35.71
+13 1 21.79 4.93 6.49
+14 1 28.08 33.01 24.51
+15 1 37.03 20.52 32.9
+16 1 32.69 20 30.11
+17 1 23.77 38.59 18.79
+18 1 16.01 2.31 20.15
+19 1 5.65 15.5 28.5
+20 1 8.35 17.35 20.48
+21 1 31.24 24.68 27.4
+22 1 29.41 16.64 19.79
+23 1 37.42 31.93 26.68
+24 1 18.76 39.06 30.68
+25 1 22.97 35 20.81
+26 1 39.47 18.28 29.6
+27 1 34.37 19.4 0.17
+28 1 5.94 9.53 10.95
+29 1 11.45 38.44 14.64
+30 1 39.57 11.04 1.57
+31 1 25.91 20.97 12.79
+32 1 36.3 22.1 1.68
+33 1 21.87 22.49 3.43
+34 1 5.77 18.66 3.97
+35 1 7 7.59 18.42
+36 1 39.76 27.63 17.98
+37 1 10.26 23.18 5.11
+38 1 23.23 21.37 17.38
+39 1 7.47 37.37 5.57
+40 1 0.73 21.6 14.78
+41 1 2.27 30.22 14.93
+42 1 7.39 28.22 14.88
+43 1 27.48 1.11 25.02
+44 1 8.37 13.19 14.64
+45 1 7.11 33.57 0.65
+46 1 34.19 35.11 3.17
+47 1 7.52 3.2 20.33
+48 1 1.02 17.69 37.85
+49 1 8.59 6.21 10.26
+50 1 2.89 16.81 30.02
+51 1 27.05 9.07 32.8
+52 1 12.32 14.79 21.11
+53 1 26.63 22.69 16.75
+54 1 31.6 2.79 20.45
+55 1 35.11 0.74 12.16
+56 1 29.71 31.23 37.63
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+642 1 15.72 22.91 30.66
+643 1 37.42 3.13 5.51
+644 1 1.51 38.14 20.78
+645 1 12.55 18.16 25.81
+646 1 18.98 15.88 29.21
+647 1 17.33 32.04 27.87
+648 1 31.21 37.38 22.84
+649 1 11.88 32.4 31
+650 1 25.1 2.19 12.69
+651 1 38.85 39.1 27.87
+652 1 5.9 16.14 33.34
+653 1 6.3 17.5 36.46
+654 1 2.28 25.02 12.53
+655 1 19.33 25.49 6.78
+656 1 8.57 37.22 8.4
+657 1 22 38.61 24.14
+658 1 35.63 3.23 2.15
+659 1 37.35 22.64 9.99
+660 1 25.46 28.22 33.18
+661 1 13.99 4.21 9.07
+662 1 9.04 40.64 37.59
+663 1 17.46 6.49 27.93
+664 1 1.42 6.14 30.2
+665 1 25.82 28.28 10.33
+666 1 30.71 30.2 -0.02
+667 1 8.05 29.32 0.62
+668 1 6.49 3.17 6.65
+669 1 7.77 39.88 26.03
+670 1 28.53 12.14 30.96
+671 1 6.25 12.64 39.55
+672 1 3.78 7.96 25.83
+673 1 28.69 29.58 6.61
+674 1 5.32 18.55 8.6
+675 1 5.3 11.44 14.19
+676 1 39 12.03 36.99
+677 1 11.08 32.51 19.12
+678 1 38.48 1.03 20.34
+679 1 38.47 11.31 10.12
+680 1 3.65 20.3 11.99
+681 1 27.18 11.39 3.4
+682 1 29.61 20.72 38.86
+683 1 31.88 4.82 24.75
+684 1 14.52 36.61 25.66
+685 1 21.68 19.96 24.58
+686 1 1.2 13.59 23.16
+687 1 37.71 5.97 35.28
+688 1 19.81 22.04 37.54
+689 1 40.67 27.07 10.14
+690 1 38.57 13.96 13.75
+691 1 18.15 17.19 21.63
+692 1 3.76 27.51 30.32
+693 1 11.39 25.09 7.96
+694 1 28.95 22.02 13.33
+695 1 31.72 35.46 35.33
+696 1 15.17 6.03 23.94
+697 1 9.63 9.42 22.18
+698 1 27.76 4.1 38.61
+699 1 27.37 37.46 11.07
+700 1 35.69 15.24 6.39
+701 1 21.92 33.09 36.84
+702 1 4.79 15.51 13.28
+703 1 9.31 26.44 22.8
+704 1 30.14 38.31 6.98
+705 1 4.33 6.66 13.77
+706 1 3.66 27.15 37.83
+707 1 0.44 24.06 29.62
+708 1 35.4 9.59 9.8
+709 1 33.77 39.44 21.41
+710 1 29.2 18.74 24.38
+711 1 34.14 30 7.36
+712 1 16.02 4.37 6.43
+713 1 35.75 39.41 40.58
+714 1 15.32 11.84 23.24
+715 1 32.52 24.39 20.97
+716 1 11.45 2.9 7.16
+717 1 7.07 34.28 36.04
+718 1 11.41 8.83 7.57
+719 1 29.29 27.79 16.55
+720 1 2.41 9.16 16.14
+721 1 13.14 38.07 12.01
+722 1 37.45 14.26 18.3
+723 1 34.64 18.37 16.65
+724 1 29.26 34.28 33.46
+725 1 13.67 19.83 3.04
+726 1 19.64 2.6 32.95
+727 1 23.61 23.55 11.34
+728 1 6.87 22.5 36.5
+729 1 36.78 28.34 22.96
+730 1 11.3 13.98 9.84
+731 1 20.82 19.73 9.16
+732 1 12.65 12.61 6.16
+733 1 9.25 7.81 25.28
+734 1 25.4 29.36 5.84
+735 1 17.86 9.06 4.45
+736 1 35.84 40.51 26.06
+737 1 26.97 21.28 31.59
+738 1 39.94 38.14 24.86
+739 1 3.16 17.07 2.49
+740 1 14.08 15.4 36.99
+741 1 26.1 13.88 29.68
+742 1 26.36 20 20.56
+743 1 12.02 6.35 27.65
+744 1 11.21 19.14 15.27
+745 1 35.86 22.93 26.81
+746 1 32.26 12.62 2.68
+747 1 29.36 4.91 6.86
+748 1 20.14 7.97 29.32
+749 1 25.53 11.2 36.18
+750 1 30.36 14.25 24.79
+751 1 29.84 38.37 39.29
+752 1 15.79 36.4 4.26
+753 1 32.59 14.17 10.29
+754 1 13.89 34.54 15.42
+755 1 12.13 33.62 7.27
+756 1 25.86 23.81 33.97
+757 1 18.4 31.27 34.96
+758 1 6.58 40.49 17.57
+759 1 5.64 39.86 23.05
+760 1 25.32 33 16.24
+761 1 0.98 10.99 12.21
+762 1 32.86 23.75 12.41
+763 1 32.91 1.3 26.94
+764 1 9.46 8.66 31.47
+765 1 17.49 15.53 1.82
+766 1 8.17 18.16 15.3
+767 1 4.84 30.63 26.32
+768 1 6.75 37.1 30.8
+769 1 7.16 5.72 15.74
+770 1 20.09 17.82 19.18
+771 1 1.02 27.99 32.54
+772 1 21.44 1.28 38.4
+773 1 21.06 14.62 37.08
+774 1 27.82 18.99 15.96
+775 1 33.51 21.46 22.82
+776 1 8.29 2.79 17.09
+777 1 18.14 11.41 28.62
+778 1 17.94 28.54 32.73
+779 1 36.1 9.54 40.1
+780 1 36.55 2.62 22.97
+781 1 27.29 10.41 39.35
+782 1 22.04 37.76 2.02
+783 1 23.01 30.08 16.58
+784 1 6.34 15.31 21.61
+785 1 7.3 22.39 7.74
+786 1 38 5.77 21.04
+787 1 32.93 12.85 26.58
+788 1 22.43 15.36 16.72
+789 1 18.54 2.38 8.35
+790 1 0.62 31.88 23.84
+791 1 39.56 30.3 21.7
+792 1 7.56 11.78 25.2
+793 1 16.05 3.98 26.72
+794 1 24.33 36.16 13.16
+795 1 26.38 31.24 35.77
+796 1 14.94 26.46 -0.44
+797 1 3.53 28 19.79
+798 1 11.94 32.27 25.88
+799 1 34.59 15.06 19.23
+800 1 3.51 10.62 24.22
+801 1 13.18 21.59 35.52
+802 1 19.95 13.15 16.23
+803 1 24.48 9.63 19.58
+804 1 37.7 34.42 19.19
+805 1 22.84 19.59 5.52
+806 1 34.62 36.75 12.26
+807 1 10.33 21.85 25.15
+808 1 21.51 29.7 7.23
+809 1 34.05 3 30.58
+810 1 12.43 29.67 5.59
+811 1 18.94 21.82 29.31
+812 1 39.21 17.7 4
+813 1 7.04 2.97 37.09
+814 1 30.87 10.8 22.09
+815 1 33.54 7.16 23.15
+816 1 32.82 32.27 11.47
+817 1 21.8 14.54 21.61
+818 1 38.83 6.69 13.68
+819 1 30.37 39.05 18.66
+820 1 31.21 15.08 13.79
+821 1 1.07 11.97 35.04
+822 1 26.02 35.8 35.47
+823 1 27.64 33.32 8.04
+824 1 39.57 36.88 4.39
+825 1 14.48 30.97 36.87
+826 1 36.86 27.04 8.96
+827 1 34.73 26.27 19.55
+828 1 29.24 29.12 10.86
+829 1 8.35 39.9 13.92
+830 1 5.43 5.1 31.85
+831 1 18.36 22.31 5.89
+832 1 2.46 27.35 16.36
+833 1 21.76 37.05 27.45
+834 1 29.32 17.11 2.28
+835 1 3.58 21.98 3.09
+836 1 10.61 9.17 10.69
+837 1 25.15 17.54 6.05
+838 1 3.4 22.81 7.03
+839 1 16.12 23.66 38.29
+840 1 8.67 4.79 31.8
+841 1 27.82 0.02 20.45
+842 1 4.46 2.44 29.46
+843 1 39.11 22.69 36.33
+844 1 4.26 2.45 34.43
+845 1 13.47 3.5 30.9
+846 1 26.92 22.55 26.54
+847 1 5.66 30.07 30.65
+848 1 31.58 35.68 25.46
+849 1 31.23 5.65 27.78
+850 1 8.76 19.49 28.61
+851 1 24.13 8.02 2.3
+852 1 8.27 6.8 4.93
+853 1 15.31 34.36 37.63
+854 1 3.96 35.82 26.97
+855 1 24.95 4.01 29.96
+856 1 26.54 25.95 19.15
+857 1 17.76 29.23 5.35
+858 1 16.95 21.79 0.78
+859 1 17.52 39.02 13.01
+860 1 20.5 22.86 10.41
+861 1 27.67 27.07 2.78
+862 1 37.1 31.02 2.03
+863 1 37.17 2.24 16.34
+864 1 24.51 34.69 10.28
+865 1 17.38 13.41 21.4
+866 1 38 9.37 17.94
+867 1 35.67 25.27 5.3
+868 1 22.66 4.47 0.97
+869 1 20.06 28.17 27.42
+870 1 27.33 2.38 9.79
+871 1 36.4 10.73 31.42
+872 1 0.53 9.45 6.96
+873 1 12.89 9.03 25.13
+874 1 37.5 23.54 21.33
+875 1 7.19 28.87 19.11
+876 1 21.45 32.81 22.71
+877 1 8.76 8.3 13.51
+878 1 10.24 31.46 3.73
+879 1 15.93 9.7 35.82
+880 1 14.92 19.46 39.91
+881 1 13.02 22.03 27.3
+882 1 34.57 1.59 34.73
+883 1 0.5 21.04 30.77
+884 1 24.84 32.67 4.97
+885 1 30.96 4.24 17.34
+886 1 23.63 8.84 32.7
+887 1 6.84 3.83 26.13
+888 1 31.57 9.23 27.06
+889 1 14.99 35.15 0.07
+890 1 36.29 40.01 8.22
+891 1 18 36.86 35.66
+892 1 11.5 29.22 0.37
+893 1 35.18 36.03 24.88
+894 1 14.49 9.41 27.73
+895 1 10.12 12.91 0.99
+896 1 11.91 29.4 27.3
+897 1 25.51 28.68 14.56
+898 1 29.32 12.95 35.59
+899 1 2.96 0.59 0.53
+900 1 5.47 5.35 9.88
+901 1 8.93 39.33 1.78
+902 1 39.68 38.49 12.33
+903 1 3.78 1.24 11.85
+904 1 29.54 33.76 11.99
+905 1 7.48 6.16 28.8
+906 1 10.83 33.63 36.96
+907 1 22.03 19.06 21.39
+908 1 31.68 31 3.71
+909 1 35.32 0.3 30.88
+910 1 9.93 35.42 14.85
+911 1 21.01 10.66 12.97
+912 1 22.54 21.62 33.81
+913 1 12.48 12.46 25.15
+914 1 0.64 27.93 39.01
+915 1 13.88 27.29 3.8
+916 1 13.03 20.93 19.25
+917 1 5.7 37.48 34.09
+918 1 2.27 35.08 14.29
+919 1 21.75 26.44 13.48
+920 1 10.66 11.35 17.49
+921 1 36.67 34.72 27.69
+922 1 8.23 22.8 33.36
+923 1 4.79 4.05 3.48
+924 1 35.61 35 35.21
+925 1 31.38 37.67 10.06
+926 1 26.44 35.58 27.52
+927 1 25.53 4.47 8.03
+928 1 38.81 33.08 31.55
+929 1 29.62 39.68 34.32
+930 1 0.76 3.88 10.61
+931 1 24.06 30.13 24.84
+932 1 18.77 8.38 37.02
+933 1 2.81 24.14 24.45
+934 1 11.33 1.25 19.69
+935 1 1.61 26.53 6.48
+936 1 9.52 29.81 35.98
+937 1 7.83 31.75 20.77
+938 1 9.67 23.93 20.57
+939 1 33.96 16.95 24.79
+940 1 37.55 37.31 37.17
+941 1 6.2 24.19 31.13
+942 1 17.79 4.35 30.56
+943 1 13.51 20.25 30.45
+944 1 14.76 12.48 13.13
+945 1 32.56 27.52 30.41
+946 1 35.81 40.1 4.85
+947 1 39.01 25.43 27.07
+948 1 22.8 5.53 32.22
+949 1 2.35 39.55 32.5
+950 1 3.31 31.51 34.19
+951 1 40.63 37.01 15.9
+952 1 18.43 35.86 30.77
+953 1 37.01 39.18 15.57
+954 1 6.74 6.26 21.64
+955 1 5.22 24.94 22.53
+956 1 25.2 11.08 13.98
+957 1 14.66 -0.14 5
+958 1 14.96 8.38 20.32
+959 1 1.89 23.03 10.1
+960 1 33.01 11.23 39.32
+961 1 32.68 6.79 32.04
+962 1 6.25 25.81 3.82
+963 1 18.37 31.97 14.57
+964 1 9.74 30.21 22.71
+965 1 3.09 1.52 19.38
+966 1 33.98 37.34 5.63
+967 1 32.19 28.35 15.8
+968 1 24.4 15.49 19.39

examples/USER/misc/bond_react/nylon,6-6_melt/in.large_nylon_melt

@@ -0,0 +1,52 @@
+# 35,000 atom nylon melt example
+
+units real
+
+boundary p p p
+
+atom_style full
+
+kspace_style pppm 1.0e-4
+
+pair_style lj/class2/coul/long 8.5
+
+angle_style class2
+
+bond_style class2
+
+dihedral_style class2
+
+improper_style class2
+
+read_data large_nylon_melt.data.gz
+
+velocity all create 800.0 4928459 dist gaussian
+
+molecule mol1 rxn1_stp1_unreacted.data_template
+molecule mol2 rxn1_stp1_reacted.data_template
+molecule mol3 rxn1_stp2_unreacted.data_template
+molecule mol4 rxn1_stp2_reacted.data_template
+
+thermo 50
+
+# dump 1 all xyz 100 test_vis.xyz
+
+fix myrxns all bond/react stabilization yes statted_grp .03 &
+  react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map &
+  react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
+
+# stable at 800K
+fix 1 statted_grp nvt temp 800 800 100
+
+# in order to customize behavior of reacting atoms,
+# you can use the internally created 'bond_react_MASTER_group', like so:
+# fix 2 bond_react_MASTER_group temp/rescale 1 800 800 10 1
+
+thermo_style custom step temp press density f_myrxns[1] f_myrxns[2] # cumulative reaction counts
+
+# restart 100 restart1 restart2
+
+run 200
+
+# write_restart restart_longrun
+# write_data restart_longrun.data

examples/USER/misc/bond_react/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.1

@@ -0,0 +1,175 @@
+LAMMPS (20 Apr 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+  using 1 OpenMP thread(s) per MPI task
+# 35,000 atom nylon melt example
+
+units real
+
+boundary p p p
+
+atom_style full
+
+kspace_style pppm 1.0e-4
+
+pair_style lj/class2/coul/long 8.5
+
+angle_style class2
+
+bond_style class2
+
+dihedral_style class2
+
+improper_style class2
+
+read_data large_nylon_melt.data.gz
+  orthogonal box = (-2.68344 -2.06791 -2.21988) to (73.4552 73.2448 73.4065)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  35200 atoms
+  reading velocities ...
+  35200 velocities
+  scanning bonds ...
+  9 = max bonds/atom
+  scanning angles ...
+  21 = max angles/atom
+  scanning dihedrals ...
+  31 = max dihedrals/atom
+  scanning impropers ...
+  29 = max impropers/atom
+  reading bonds ...
+  33600 bonds
+  reading angles ...
+  59200 angles
+  reading dihedrals ...
+  80000 dihedrals
+  reading impropers ...
+  35200 impropers
+  4 = max # of 1-2 neighbors
+  6 = max # of 1-3 neighbors
+  12 = max # of 1-4 neighbors
+  41 = max # of special neighbors
+
+velocity all create 800.0 4928459 dist gaussian
+
+molecule mol1 rxn1_stp1_unreacted.data_template
+Read molecule mol1:
+  18 atoms with max type 8
+  16 bonds with max type 12
+  25 angles with max type 24
+  23 dihedrals with max type 33
+  14 impropers with max type 9
+molecule mol2 rxn1_stp1_reacted.data_template
+Read molecule mol2:
+  18 atoms with max type 9
+  17 bonds with max type 11
+  31 angles with max type 23
+  39 dihedrals with max type 30
+  20 impropers with max type 1
+molecule mol3 rxn1_stp2_unreacted.data_template
+Read molecule mol3:
+  15 atoms with max type 9
+  14 bonds with max type 11
+  25 angles with max type 23
+  30 dihedrals with max type 30
+  16 impropers with max type 1
+molecule mol4 rxn1_stp2_reacted.data_template
+Read molecule mol4:
+  15 atoms with max type 11
+  13 bonds with max type 13
+  19 angles with max type 25
+  16 dihedrals with max type 29
+  10 impropers with max type 11
+
+thermo 50
+
+# dump 1 all xyz 100 test_vis.xyz
+
+fix myrxns all bond/react stabilization yes statted_grp .03   react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map   react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
+WARNING: An atom in 'react #1' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489)
+WARNING: An atom in 'react #2' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489)
+dynamic group bond_react_MASTER_group defined
+dynamic group statted_grp defined
+dynamic group bond_react_MASTER_group defined
+dynamic group statted_grp defined
+
+# stable at 800K
+fix 1 statted_grp nvt temp 800 800 100
+
+# in order to customize behavior of reacting atoms,
+# you can use the internally created 'bond_react_MASTER_group', like so:
+# fix 2 bond_react_MASTER_group temp/rescale 1 800 800 10 1
+
+thermo_style custom step temp press density f_myrxns[1] f_myrxns[2] # cumulative reaction counts
+
+# restart 100 restart1 restart2
+
+run 200
+PPPM initialization ...
+  using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+  G vector (1/distance) = 0.20765
+  grid = 18 18 18
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0333156
+  estimated relative force accuracy = 0.000100329
+  using double precision FFTs
+  3d grid and FFT values/proc = 12167 5832
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 10.5
+  ghost atom cutoff = 10.5
+  binsize = 5.25, bins = 15 15 15
+  2 neighbor lists, perpetual/occasional/extra = 1 1 0
+  (1) pair lj/class2/coul/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+  (2) fix bond/react, occasional, copy from (1)
+      attributes: half, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 209.1 | 209.1 | 209.1 Mbytes
+Step Temp Press Density f_myrxns[1] f_myrxns[2] 
+       0          800    3666.3948   0.80366765            0            0 
+      50    673.95238   -9670.9169   0.80366765           31            0 
+     100    697.22819   -4624.0512   0.80366765           57           22 
+     150    723.60507   -17175.571   0.80366765           76           48 
+     200    736.71277   -12961.963   0.80366765           84           64 
+Loop time of 102.825 on 1 procs for 200 steps with 35200 atoms
+
+Performance: 0.168 ns/day, 142.812 hours/ns, 1.945 timesteps/s
+99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 27.193     | 27.193     | 27.193     |   0.0 | 26.45
+Bond    | 11.324     | 11.324     | 11.324     |   0.0 | 11.01
+Kspace  | 4.1878     | 4.1878     | 4.1878     |   0.0 |  4.07
+Neigh   | 54.724     | 54.724     | 54.724     |   0.0 | 53.22
+Comm    | 0.40662    | 0.40662    | 0.40662    |   0.0 |  0.40
+Output  | 0.0011101  | 0.0011101  | 0.0011101  |   0.0 |  0.00
+Modify  | 4.9422     | 4.9422     | 4.9422     |   0.0 |  4.81
+Other   |            | 0.04545    |            |       |  0.04
+
+Nlocal:    35200 ave 35200 max 35200 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    38403 ave 38403 max 38403 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    6.9281e+06 ave 6.9281e+06 max 6.9281e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 6928101
+Ave neighs/atom = 196.821
+Ave special neighs/atom = 9.83727
+Neighbor list builds = 200
+Dangerous builds = 0
+
+# write_restart restart_longrun
+# write_data restart_longrun.data
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:01:43

examples/USER/misc/bond_react/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.4

@@ -0,0 +1,175 @@
+LAMMPS (20 Apr 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+  using 1 OpenMP thread(s) per MPI task
+# 35,000 atom nylon melt example
+
+units real
+
+boundary p p p
+
+atom_style full
+
+kspace_style pppm 1.0e-4
+
+pair_style lj/class2/coul/long 8.5
+
+angle_style class2
+
+bond_style class2
+
+dihedral_style class2
+
+improper_style class2
+
+read_data large_nylon_melt.data.gz
+  orthogonal box = (-2.68344 -2.06791 -2.21988) to (73.4552 73.2448 73.4065)
+  2 by 1 by 2 MPI processor grid
+  reading atoms ...
+  35200 atoms
+  reading velocities ...
+  35200 velocities
+  scanning bonds ...
+  9 = max bonds/atom
+  scanning angles ...
+  21 = max angles/atom
+  scanning dihedrals ...
+  31 = max dihedrals/atom
+  scanning impropers ...
+  29 = max impropers/atom
+  reading bonds ...
+  33600 bonds
+  reading angles ...
+  59200 angles
+  reading dihedrals ...
+  80000 dihedrals
+  reading impropers ...
+  35200 impropers
+  4 = max # of 1-2 neighbors
+  6 = max # of 1-3 neighbors
+  12 = max # of 1-4 neighbors
+  41 = max # of special neighbors
+
+velocity all create 800.0 4928459 dist gaussian
+
+molecule mol1 rxn1_stp1_unreacted.data_template
+Read molecule mol1:
+  18 atoms with max type 8
+  16 bonds with max type 12
+  25 angles with max type 24
+  23 dihedrals with max type 33
+  14 impropers with max type 9
+molecule mol2 rxn1_stp1_reacted.data_template
+Read molecule mol2:
+  18 atoms with max type 9
+  17 bonds with max type 11
+  31 angles with max type 23
+  39 dihedrals with max type 30
+  20 impropers with max type 1
+molecule mol3 rxn1_stp2_unreacted.data_template
+Read molecule mol3:
+  15 atoms with max type 9
+  14 bonds with max type 11
+  25 angles with max type 23
+  30 dihedrals with max type 30
+  16 impropers with max type 1
+molecule mol4 rxn1_stp2_reacted.data_template
+Read molecule mol4:
+  15 atoms with max type 11
+  13 bonds with max type 13
+  19 angles with max type 25
+  16 dihedrals with max type 29
+  10 impropers with max type 11
+
+thermo 50
+
+# dump 1 all xyz 100 test_vis.xyz
+
+fix myrxns all bond/react stabilization yes statted_grp .03   react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map   react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
+WARNING: An atom in 'react #1' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489)
+WARNING: An atom in 'react #2' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489)
+dynamic group bond_react_MASTER_group defined
+dynamic group statted_grp defined
+dynamic group bond_react_MASTER_group defined
+dynamic group statted_grp defined
+
+# stable at 800K
+fix 1 statted_grp nvt temp 800 800 100
+
+# in order to customize behavior of reacting atoms,
+# you can use the internally created 'bond_react_MASTER_group', like so:
+# fix 2 bond_react_MASTER_group temp/rescale 1 800 800 10 1
+
+thermo_style custom step temp press density f_myrxns[1] f_myrxns[2] # cumulative reaction counts
+
+# restart 100 restart1 restart2
+
+run 200
+PPPM initialization ...
+  using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+  G vector (1/distance) = 0.20765
+  grid = 18 18 18
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0333156
+  estimated relative force accuracy = 0.000100329
+  using double precision FFTs
+  3d grid and FFT values/proc = 4508 1620
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 10.5
+  ghost atom cutoff = 10.5
+  binsize = 5.25, bins = 15 15 15
+  2 neighbor lists, perpetual/occasional/extra = 1 1 0
+  (1) pair lj/class2/coul/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+  (2) fix bond/react, occasional, copy from (1)
+      attributes: half, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 81.11 | 81.13 | 81.15 Mbytes
+Step Temp Press Density f_myrxns[1] f_myrxns[2] 
+       0          800    3666.3948   0.80366765            0            0 
+      50    673.95238   -9670.9169   0.80366765           31            0 
+     100    697.22819   -4624.0512   0.80366765           57           22 
+     150    724.40407   -17166.729   0.80366765           76           49 
+     200    737.28582   -12968.224   0.80366765           84           65 
+Loop time of 51.171 on 4 procs for 200 steps with 35200 atoms
+
+Performance: 0.338 ns/day, 71.071 hours/ns, 3.908 timesteps/s
+98.4% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 12.926     | 13.247     | 13.493     |   6.7 | 25.89
+Bond    | 5.2132     | 5.2733     | 5.3367     |   1.9 | 10.31
+Kspace  | 2.3601     | 2.6534     | 3.0067     |  16.0 |  5.19
+Neigh   | 25.93      | 25.934     | 25.937     |   0.1 | 50.68
+Comm    | 0.73273    | 0.75464    | 0.78505    |   2.3 |  1.47
+Output  | 0.00045228 | 0.00067407 | 0.0013323  |   0.0 |  0.00
+Modify  | 3.2682     | 3.2686     | 3.2692     |   0.0 |  6.39
+Other   |            | 0.03995    |            |       |  0.08
+
+Nlocal:    8800 ave 8913 max 8652 min
+Histogram: 1 0 0 0 1 0 0 0 1 1
+Nghost:    18366 ave 18461 max 18190 min
+Histogram: 1 0 0 0 0 0 0 1 1 1
+Neighs:    1.73203e+06 ave 1.77261e+06 max 1.68165e+06 min
+Histogram: 1 0 1 0 0 0 0 0 0 2
+
+Total # of neighbors = 6928132
+Ave neighs/atom = 196.822
+Ave special neighs/atom = 9.83608
+Neighbor list builds = 200
+Dangerous builds = 0
+
+# write_restart restart_longrun
+# write_data restart_longrun.data
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:52

examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp1_map

@@ -0,0 +1,35 @@
+this is a nominal superimpose file
+
+2 edgeIDs
+18 equivalences
+
+BondingIDs
+
+10
+1
+
+EdgeIDs
+
+16
+8
+
+Equivalences
+
+1	1
+2	2
+3	3
+4	4
+5	5
+6	6
+7	7
+8	8
+9	9
+10	10
+11	11
+12	12
+13	13
+14	14
+15	15
+16	16
+17	17
+18	18

examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp1_reacted.data_template

@@ -0,0 +1,189 @@
+this is a molecule template for: initial nylon crosslink, post-reacting
+
+18 atoms           
+17 bonds           
+31 angles           
+39 dihedrals           
+20 impropers           
+
+Types
+
+1 9
+2 1
+3 1
+4 4
+5 4
+6 3
+7 3
+8 1
+9 1
+10 5
+11 8
+12 6
+13 3
+14 3
+15 7
+16 1
+17 3
+18 3
+
+Charges
+
+1 -0.300000
+2 0.000000
+3 0.000000
+4 0.000000
+5 0.000000
+6 0.000000
+7 0.000000
+8 0.000000
+9 0.000000
+10 0.300000
+11 0.000000
+12 0.000000
+13 0.000000
+14 0.000000
+15 0.000000
+16 0.000000
+17 0.000000
+18 0.000000
+
+Coords
+
+1 -5.522237 -0.752722 1.631158
+2 -5.170398 -0.545733 0.178130
+3 -6.469695 -0.553072 -0.648889
+4 -6.052076 -1.721152 1.744648
+5 -6.183059 0.071387 1.971497
+6 -4.489340 -1.389197 -0.173156
+7 -4.637591 0.453703 0.051252
+8 -5.618658 0.138919 4.386107
+9 -4.669492 -0.989819 3.943591
+10 -4.270194 -0.766405 2.474102
+11 -3.348470 -1.875393 2.024289
+12 -3.569794 0.564183 2.345995
+13 -5.201079 -1.993301 4.044219
+14 -3.736682 -0.984819 4.598305
+15 -4.255402 1.370923 2.679069
+16 -6.136394 -0.339866 -2.136775
+17 -6.996331 -1.555519 -0.517408
+18 -7.153308 0.284949 -0.289930
+
+Bonds
+
+1 9 1 2
+2 10 1 4
+3 10 1 5
+4 11 1 10
+5 1 2 3
+6 2 2 6
+7 2 2 7
+8 1 3 16
+9 2 3 17
+10 2 3 18
+11 1 8 9
+12 6 9 10
+13 2 9 13
+14 2 9 14
+15 7 10 11
+16 5 10 12
+17 8 12 15
+
+Angles
+
+1 14 2 1 4
+2 14 2 1 5
+3 15 2 1 10
+4 16 4 1 5
+5 17 4 1 10
+6 17 5 1 10
+7 18 1 2 3
+8 19 1 2 6
+9 19 1 2 7
+10 1 3 2 6
+11 1 3 2 7
+12 3 6 2 7
+13 2 2 3 16
+14 1 2 3 17
+15 1 2 3 18
+16 1 16 3 17
+17 1 16 3 18
+18 3 17 3 18
+19 12 8 9 10
+20 1 8 9 13
+21 1 8 9 14
+22 13 13 9 10
+23 13 14 9 10
+24 3 13 9 14
+25 10 9 10 11
+26 8 9 10 12
+27 20 1 10 9
+28 21 11 10 12
+29 22 1 10 11
+30 23 1 10 12
+31 11 10 12 15
+
+Dihedrals
+
+1 16 4 1 2 3
+2 17 4 1 2 6
+3 17 4 1 2 7
+4 16 5 1 2 3
+5 17 5 1 2 6
+6 17 5 1 2 7
+7 18 10 1 2 3
+8 19 10 1 2 6
+9 19 10 1 2 7
+10 20 2 1 10 9
+11 21 2 1 10 11
+12 22 2 1 10 12
+13 23 4 1 10 9
+14 24 4 1 10 11
+15 25 4 1 10 12
+16 23 5 1 10 9
+17 24 5 1 10 11
+18 25 5 1 10 12
+19 26 1 2 3 16
+20 27 1 2 3 17
+21 27 1 2 3 18
+22 4 16 3 2 6
+23 2 6 2 3 17
+24 2 6 2 3 18
+25 4 16 3 2 7
+26 2 7 2 3 17
+27 2 7 2 3 18
+28 14 8 9 10 11
+29 12 8 9 10 12
+30 28 8 9 10 1
+31 15 13 9 10 11
+32 13 13 9 10 12
+33 29 13 9 10 1
+34 15 14 9 10 11
+35 13 14 9 10 12
+36 29 14 9 10 1
+37 10 9 10 12 15
+38 11 11 10 12 15
+39 30 1 10 12 15
+
+Impropers
+
+1 1 2 1 4 5
+2 1 2 1 4 10
+3 1 2 1 5 10
+4 1 4 1 5 10
+5 1 1 2 3 6
+6 1 1 2 3 7
+7 1 1 2 6 7
+8 1 3 2 6 7
+9 1 2 3 16 17
+10 1 2 3 16 18
+11 1 2 3 17 18
+12 1 16 3 17 18
+13 1 8 9 13 10
+14 1 8 9 14 10
+15 1 8 9 13 14
+16 1 13 9 14 10
+17 1 9 10 11 12
+18 1 1 10 9 11
+19 1 1 10 9 12
+20 1 1 10 11 12

examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp1_unreacted.data_template

@@ -0,0 +1,160 @@
+this is a molecule template for: initial nylon crosslink, pre-reacting
+
+18 atoms           
+16 bonds           
+25 angles           
+23 dihedrals           
+14 impropers           
+
+Types
+
+1 2
+2 1
+3 1
+4 4
+5 4
+6 3
+7 3
+8 1
+9 1
+10 5
+11 8
+12 6
+13 3
+14 3
+15 7
+16 1
+17 3
+18 3
+
+Charges
+
+1 -0.300000
+2 0.000000
+3 0.000000
+4 0.000000
+5 0.000000
+6 0.000000
+7 0.000000
+8 0.000000
+9 0.000000
+10 0.300000
+11 0.000000
+12 0.000000
+13 0.000000
+14 0.000000
+15 0.000000
+16 0.000000
+17 0.000000
+18 0.000000
+
+Coords
+
+1 -4.922858 -0.946982 1.146055
+2 -5.047195 -0.935267 -0.358173
+3 -6.526281 -0.755366 -0.743523
+4 -5.282604 0.020447 1.552710
+5 -3.860697 -1.095850 1.428305
+6 -4.662382 -1.920900 -0.781524
+7 -4.433977 -0.072765 -0.784071
+8 -5.506279 0.202610 4.825816
+9 -4.449177 -0.844592 4.423366
+10 -4.103916 -0.749629 2.925195
+11 -3.376249 -1.886171 2.245643
+12 -4.493235 0.477214 2.137199
+13 -4.849053 -1.888877 4.663994
+14 -3.491823 -0.662913 5.018510
+15 -5.020777 1.189745 2.805427
+16 -3.964987 2.900602 -1.551341
+17 -4.460694 2.836102 0.668882
+18 -4.828494 3.219656 -0.122111
+
+Bonds
+
+1 12 1 2
+2 4 1 4
+3 4 1 5
+4 1 2 3
+5 2 2 6
+6 2 2 7
+7 1 3 16
+8 2 3 17
+9 2 3 18
+10 1 8 9
+11 6 9 10
+12 2 9 13
+13 2 9 14
+14 7 10 11
+15 5 10 12
+16 8 12 15
+
+Angles
+
+1 6 2 1 4
+2 6 2 1 5
+3 7 4 1 5
+4 24 1 2 3
+5 5 1 2 6
+6 5 1 2 7
+7 1 3 2 6
+8 1 3 2 7
+9 3 6 2 7
+10 2 2 3 16
+11 1 2 3 17
+12 1 2 3 18
+13 1 16 3 17
+14 1 16 3 18
+15 3 17 3 18
+16 12 8 9 10
+17 1 8 9 13
+18 1 8 9 14
+19 13 13 9 10
+20 13 14 9 10
+21 3 13 9 14
+22 10 9 10 11
+23 8 9 10 12
+24 21 11 10 12
+25 11 10 12 15
+
+Dihedrals
+
+1 31 4 1 2 3
+2 32 4 1 2 6
+3 32 4 1 2 7
+4 31 5 1 2 3
+5 32 5 1 2 6
+6 32 5 1 2 7
+7 33 1 2 3 16
+8 1 1 2 3 17
+9 1 1 2 3 18
+10 4 16 3 2 6
+11 2 6 2 3 17
+12 2 6 2 3 18
+13 4 16 3 2 7
+14 2 7 2 3 17
+15 2 7 2 3 18
+16 14 8 9 10 11
+17 12 8 9 10 12
+18 15 13 9 10 11
+19 13 13 9 10 12
+20 15 14 9 10 11
+21 13 14 9 10 12
+22 10 9 10 12 15
+23 11 11 10 12 15
+
+Impropers
+
+1 1 2 1 4 5
+2 9 9 10 11 12
+3 1 1 2 3 6
+4 1 1 2 3 7
+5 1 1 2 6 7
+6 1 3 2 6 7
+7 1 2 3 16 17
+8 1 2 3 16 18
+9 1 2 3 17 18
+10 1 16 3 17 18
+11 1 8 9 13 10
+12 1 8 9 14 10
+13 1 8 9 13 14
+14 1 13 9 14 10

examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp2_map

@@ -0,0 +1,32 @@
+this is a nominal superimpose file
+
+2 edgeIDs
+15 equivalences
+
+BondingIDs
+
+4
+12
+
+EdgeIDs
+
+8
+3
+
+Equivalences
+
+1	1
+2	2
+3	3
+4	4
+5	5
+6	6
+7	7
+8	8
+9	9
+10	10
+11	11
+12	12
+13	13
+14	14
+15	15

examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp2_reacted.data_template

@@ -0,0 +1,131 @@
+this is a molecule template for: water condensation, post-reacting
+
+15 atoms           
+13 bonds           
+19 angles           
+16 dihedrals           
+10 impropers           
+
+Types
+
+1 9
+2 1
+3 1
+4 10
+5 4
+6 3
+7 3
+8 1
+9 1
+10 5
+11 8
+12 11
+13 3
+14 3
+15 10
+
+Charges
+
+1 -0.300000
+2 0.000000
+3 0.000000
+4 0.410000
+5 0.000000
+6 0.000000
+7 0.000000
+8 0.000000
+9 0.000000
+10 0.300000
+11 0.000000
+12 -0.820000
+13 0.000000
+14 0.000000
+15 0.410000
+
+Coords
+
+1 -4.856280 -1.050468 1.432625
+2 -5.047195 -0.935267 -0.358173
+3 -6.526281 -0.755366 -0.743523
+4 -5.282604 0.020447 1.552710
+5 -3.860697 -1.095850 1.428305
+6 -4.662382 -1.920900 -0.781524
+7 -4.433977 -0.072765 -0.784071
+8 -5.506279 0.202610 4.825816
+9 -4.449177 -0.844592 4.423366
+10 -4.103916 -0.749629 2.925195
+11 -3.376249 -1.886171 2.245643
+12 -4.493235 0.477214 2.137199
+13 -4.849053 -1.888877 4.663994
+14 -3.491823 -0.662913 5.018510
+15 -5.020777 1.189745 2.805427
+
+Bonds
+
+1 9 1 2
+2 10 1 5
+3 11 1 10
+4 1 2 3
+5 2 2 6
+6 2 2 7
+7 13 4 12
+8 1 8 9
+9 6 9 10
+10 2 9 13
+11 2 9 14
+12 7 10 11
+13 13 15 12
+
+Angles
+
+1 14 2 1 5
+2 15 2 1 10
+3 17 5 1 10
+4 18 1 2 3
+5 19 1 2 6
+6 19 1 2 7
+7 1 3 2 6
+8 1 3 2 7
+9 3 6 2 7
+10 12 8 9 10
+11 1 8 9 13
+12 1 8 9 14
+13 13 13 9 10
+14 13 14 9 10
+15 3 13 9 14
+16 10 9 10 11
+17 20 1 10 9
+18 22 1 10 11
+19 25 15 12 4
+
+Dihedrals
+
+1 16 5 1 2 3
+2 17 5 1 2 6
+3 17 5 1 2 7
+4 18 10 1 2 3
+5 19 10 1 2 6
+6 19 10 1 2 7
+7 20 2 1 10 9
+8 21 2 1 10 11
+9 23 5 1 10 9
+10 24 5 1 10 11
+11 14 8 9 10 11
+12 28 8 9 10 1
+13 15 13 9 10 11
+14 29 13 9 10 1
+15 15 14 9 10 11
+16 29 14 9 10 1
+
+Impropers
+
+1 10 2 1 5 10
+2 11 1 10 9 11
+3 1 1 2 3 6
+4 1 1 2 3 7
+5 1 1 2 6 7
+6 1 3 2 6 7
+7 1 8 9 13 10
+8 1 8 9 14 10
+9 1 8 9 13 14
+10 1 13 9 14 10

examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp2_unreacted.data_template

@@ -0,0 +1,158 @@
+this is a molecule template for: water condensation, pre-reacting
+
+15 atoms           
+14 bonds           
+25 angles           
+30 dihedrals           
+16 impropers           
+
+Types
+
+1 9
+2 1
+3 1
+4 4
+5 4
+6 3
+7 3
+8 1
+9 1
+10 5
+11 8
+12 6
+13 3
+14 3
+15 7
+
+Charges
+
+1 -0.300000
+2 0.000000
+3 0.000000
+4 0.000000
+5 0.000000
+6 0.000000
+7 0.000000
+8 0.000000
+9 0.000000
+10 0.300000
+11 0.000000
+12 0.000000
+13 0.000000
+14 0.000000
+15 0.000000
+
+Coords
+
+1 -4.922858 -0.946982 1.146055
+2 -5.047195 -0.935267 -0.358173
+3 -6.526281 -0.755366 -0.743523
+4 -5.282604 0.020447 1.552710
+5 -3.860697 -1.095850 1.428305
+6 -4.662382 -1.920900 -0.781524
+7 -4.433977 -0.072765 -0.784071
+8 -5.506279 0.202610 4.825816
+9 -4.449177 -0.844592 4.423366
+10 -4.103916 -0.749629 2.925195
+11 -3.376249 -1.886171 2.245643
+12 -4.493235 0.477214 2.137199
+13 -4.849053 -1.888877 4.663994
+14 -3.491823 -0.662913 5.018510
+15 -5.020777 1.189745 2.805427
+
+Bonds
+
+1 9 1 2
+2 10 1 4
+3 10 1 5
+4 11 1 10
+5 1 2 3
+6 2 2 6
+7 2 2 7
+8 1 8 9
+9 6 9 10
+10 2 9 13
+11 2 9 14
+12 7 10 11
+13 5 10 12
+14 8 12 15
+
+Angles
+
+1 14 2 1 4
+2 14 2 1 5
+3 15 2 1 10
+4 16 4 1 5
+5 17 4 1 10
+6 17 5 1 10
+7 18 1 2 3
+8 19 1 2 6
+9 19 1 2 7
+10 1 3 2 6
+11 1 3 2 7
+12 3 6 2 7
+13 12 8 9 10
+14 1 8 9 13
+15 1 8 9 14
+16 13 13 9 10
+17 13 14 9 10
+18 3 13 9 14
+19 10 9 10 11
+20 8 9 10 12
+21 20 1 10 9
+22 21 11 10 12
+23 22 1 10 11
+24 23 1 10 12
+25 11 10 12 15
+
+Dihedrals
+
+1 16 4 1 2 3
+2 17 4 1 2 6
+3 17 4 1 2 7
+4 16 5 1 2 3
+5 17 5 1 2 6
+6 17 5 1 2 7
+7 18 10 1 2 3
+8 19 10 1 2 6
+9 19 10 1 2 7
+10 20 2 1 10 9
+11 21 2 1 10 11
+12 22 2 1 10 12
+13 23 4 1 10 9
+14 24 4 1 10 11
+15 25 4 1 10 12
+16 23 5 1 10 9
+17 24 5 1 10 11
+18 25 5 1 10 12
+19 14 8 9 10 11
+20 12 8 9 10 12
+21 28 8 9 10 1
+22 15 13 9 10 11
+23 13 13 9 10 12
+24 29 13 9 10 1
+25 15 14 9 10 11
+26 13 14 9 10 12
+27 29 14 9 10 1
+28 10 9 10 12 15
+29 11 11 10 12 15
+30 30 1 10 12 15
+
+Impropers
+
+1 1 2 1 4 5
+2 1 2 1 4 10
+3 1 2 1 5 10
+4 1 4 1 5 10
+5 1 1 2 3 6
+6 1 1 2 3 7
+7 1 1 2 6 7
+8 1 3 2 6 7
+9 1 8 9 13 10
+10 1 8 9 14 10
+11 1 8 9 13 14
+12 1 13 9 14 10
+13 1 9 10 11 12
+14 1 1 10 9 11
+15 1 1 10 9 12
+16 1 1 10 11 12

examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon

@@ -0,0 +1,50 @@
+# two monomer nylon example
+# reaction produces a condensed water molecule
+
+units real
+
+boundary p p p
+
+atom_style full
+
+kspace_style pppm 1.0e-4
+
+pair_style lj/class2/coul/long 8.5
+
+angle_style class2
+
+bond_style class2
+
+dihedral_style class2
+
+improper_style class2
+
+read_data tiny_nylon.data
+
+velocity all create 300.0 4928459 dist gaussian
+
+molecule mol1 rxn1_stp1_unreacted.data_template
+molecule mol2 rxn1_stp1_reacted.data_template
+molecule mol3 rxn1_stp2_unreacted.data_template
+molecule mol4 rxn1_stp2_reacted.data_template
+
+thermo 50
+
+# dump 1 all xyz 1 test_vis.xyz
+
+fix myrxns all bond/react stabilization yes statted_grp .03 &
+  react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map &
+  react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
+
+fix 1 statted_grp nvt temp 300 300 100
+
+fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1
+
+thermo_style custom step temp press density f_myrxns[1] f_myrxns[2]
+
+# restart 100 restart1 restart2
+
+run 10000
+
+# write_restart restart_longrun
+# write_data restart_longrun.data

examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.1

@@ -0,0 +1,370 @@
+LAMMPS (20 Apr 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+  using 1 OpenMP thread(s) per MPI task
+# two monomer nylon example
+# reaction produces a condensed water molecule
+
+units real
+
+boundary p p p
+
+atom_style full
+
+kspace_style pppm 1.0e-4
+
+pair_style lj/class2/coul/long 8.5
+
+angle_style class2
+
+bond_style class2
+
+dihedral_style class2
+
+improper_style class2
+
+read_data tiny_nylon.data
+  orthogonal box = (-25 -25 -25) to (25 25 25)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  44 atoms
+  reading velocities ...
+  44 velocities
+  scanning bonds ...
+  9 = max bonds/atom
+  scanning angles ...
+  21 = max angles/atom
+  scanning dihedrals ...
+  29 = max dihedrals/atom
+  scanning impropers ...
+  29 = max impropers/atom
+  reading bonds ...
+  42 bonds
+  reading angles ...
+  74 angles
+  reading dihedrals ...
+  100 dihedrals
+  reading impropers ...
+  44 impropers
+  4 = max # of 1-2 neighbors
+  6 = max # of 1-3 neighbors
+  12 = max # of 1-4 neighbors
+  41 = max # of special neighbors
+
+velocity all create 300.0 4928459 dist gaussian
+
+molecule mol1 rxn1_stp1_unreacted.data_template
+Read molecule mol1:
+  18 atoms with max type 8
+  16 bonds with max type 14
+  25 angles with max type 28
+  23 dihedrals with max type 36
+  14 impropers with max type 11
+molecule mol2 rxn1_stp1_reacted.data_template
+Read molecule mol2:
+  18 atoms with max type 9
+  17 bonds with max type 13
+  31 angles with max type 27
+  39 dihedrals with max type 33
+  20 impropers with max type 1
+molecule mol3 rxn1_stp2_unreacted.data_template
+Read molecule mol3:
+  15 atoms with max type 9
+  14 bonds with max type 13
+  25 angles with max type 27
+  30 dihedrals with max type 33
+  16 impropers with max type 1
+molecule mol4 rxn1_stp2_reacted.data_template
+Read molecule mol4:
+  15 atoms with max type 11
+  13 bonds with max type 15
+  19 angles with max type 29
+  16 dihedrals with max type 32
+  10 impropers with max type 13
+
+thermo 50
+
+# dump 1 all xyz 1 test_vis.xyz
+
+fix myrxns all bond/react stabilization yes statted_grp .03   react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map   react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
+WARNING: An atom in 'react #1' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489)
+WARNING: An atom in 'react #2' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489)
+dynamic group bond_react_MASTER_group defined
+dynamic group statted_grp defined
+dynamic group bond_react_MASTER_group defined
+dynamic group statted_grp defined
+
+fix 1 statted_grp nvt temp 300 300 100
+
+fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1
+
+thermo_style custom step temp press density f_myrxns[1] f_myrxns[2]
+
+# restart 100 restart1 restart2
+
+run 10000
+PPPM initialization ...
+  using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+  G vector (1/distance) = 0.0534597
+  grid = 2 2 2
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0402256
+  estimated relative force accuracy = 0.000121138
+  using double precision FFTs
+  3d grid and FFT values/proc = 343 8
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 10.5
+  ghost atom cutoff = 10.5
+  binsize = 5.25, bins = 10 10 10
+  2 neighbor lists, perpetual/occasional/extra = 1 1 0
+  (1) pair lj/class2/coul/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+  (2) fix bond/react, occasional, copy from (1)
+      attributes: half, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+WARNING: Inconsistent image flags (../domain.cpp:786)
+Per MPI rank memory allocation (min/avg/max) = 33.34 | 33.34 | 33.34 Mbytes
+Step Temp Press Density f_myrxns[1] f_myrxns[2] 
+       0          300    346.78165 0.0034851739            0            0 
+      50    296.70408    -51.30066 0.0034851739            1            0 
+     100    274.25324    46.715512 0.0034851739            1            1 
+     150    471.61579    31.321598 0.0034851739            1            1 
+     200    362.87766    42.061118 0.0034851739            1            1 
+     250    367.58058    65.303109 0.0034851739            1            1 
+     300    372.38236   -52.421725 0.0034851739            1            1 
+     350    297.69957    17.869945 0.0034851739            1            1 
+     400    258.30433     49.19156 0.0034851739            1            1 
+     450    253.34384   -5.8162637 0.0034851739            1            1 
+     500    269.96465   -43.337517 0.0034851739            1            1 
+     550    303.23718    10.180246 0.0034851739            1            1 
+     600    329.59579    -48.97461 0.0034851739            1            1 
+     650    350.42568    50.983183 0.0034851739            1            1 
+     700    342.03272     35.43465 0.0034851739            1            1 
+     750    269.23405   -41.873166 0.0034851739            1            1 
+     800    245.15025    13.953092 0.0034851739            1            1 
+     850    257.85421   -3.1492141 0.0034851739            1            1 
+     900    316.15644    7.7798301 0.0034851739            1            1 
+     950     299.9124    -15.77014 0.0034851739            1            1 
+    1000    302.89968   -17.049693 0.0034851739            1            1 
+    1050    308.91651     71.84632 0.0034851739            1            1 
+    1100    348.43932   -18.742012 0.0034851739            1            1 
+    1150    309.03036    50.536311 0.0034851739            1            1 
+    1200     318.9761   -16.905746 0.0034851739            1            1 
+    1250    320.42806 -0.057975092 0.0034851739            1            1 
+    1300     289.7824    18.200772 0.0034851739            1            1 
+    1350    284.79836   -9.1978427 0.0034851739            1            1 
+    1400    325.43292    42.082833 0.0034851739            1            1 
+    1450     261.5041   -37.823325 0.0034851739            1            1 
+    1500    298.88723   -5.1647385 0.0034851739            1            1 
+    1550    291.37403   -7.7764201 0.0034851739            1            1 
+    1600    293.83475      22.2458 0.0034851739            1            1 
+    1650    293.80611    24.202512 0.0034851739            1            1 
+    1700    291.70205   -23.397884 0.0034851739            1            1 
+    1750    292.32437   -10.671214 0.0034851739            1            1 
+    1800    302.01367   -11.671025 0.0034851739            1            1 
+    1850     322.1651    24.438331 0.0034851739            1            1 
+    1900    310.45076    45.343592 0.0034851739            1            1 
+    1950    325.91745   -19.847809 0.0034851739            1            1 
+    2000    276.89662    63.387098 0.0034851739            1            1 
+    2050    311.33783   -24.683247 0.0034851739            1            1 
+    2100     346.2336   -27.526891 0.0034851739            1            1 
+    2150    345.30604   -15.722411 0.0034851739            1            1 
+    2200     346.7718   -17.857633 0.0034851739            1            1 
+    2250    304.28676   -1.9965581 0.0034851739            1            1 
+    2300    322.56372   -31.786868 0.0034851739            1            1 
+    2350    282.64326    6.1982735 0.0034851739            1            1 
+    2400    286.65759   -63.207781 0.0034851739            1            1 
+    2450    257.05528    32.931491 0.0034851739            1            1 
+    2500    283.64386    26.912373 0.0034851739            1            1 
+    2550    299.54005    27.277039 0.0034851739            1            1 
+    2600    283.92503    14.660972 0.0034851739            1            1 
+    2650    321.93453   -18.977358 0.0034851739            1            1 
+    2700     376.7189    31.826935 0.0034851739            1            1 
+    2750    372.20075   -32.821697 0.0034851739            1            1 
+    2800    361.40604    83.035183 0.0034851739            1            1 
+    2850    332.27269   -23.927452 0.0034851739            1            1 
+    2900    331.14638  -0.12328446 0.0034851739            1            1 
+    2950    303.67489   -24.078857 0.0034851739            1            1 
+    3000    311.40462    21.563537 0.0034851739            1            1 
+    3050    284.72849   -23.849667 0.0034851739            1            1 
+    3100    303.48477    39.347763 0.0034851739            1            1 
+    3150     264.2739  -0.22299879 0.0034851739            1            1 
+    3200    300.03351    31.545323 0.0034851739            1            1 
+    3250    288.56663    5.7225228 0.0034851739            1            1 
+    3300    200.13238   -31.239655 0.0034851739            1            1 
+    3350    231.32512    16.631728 0.0034851739            1            1 
+    3400    260.57402    2.1717992 0.0034851739            1            1 
+    3450    301.47128   -42.210623 0.0034851739            1            1 
+    3500    321.77414    40.074365 0.0034851739            1            1 
+    3550    353.21858    28.387783 0.0034851739            1            1 
+    3600    331.45989   -57.800858 0.0034851739            1            1 
+    3650    303.88123     44.86596 0.0034851739            1            1 
+    3700    329.73833  -0.80615652 0.0034851739            1            1 
+    3750    297.55588  -0.49626039 0.0034851739            1            1 
+    3800    286.38794   -10.010003 0.0034851739            1            1 
+    3850    290.17417    -43.51187 0.0034851739            1            1 
+    3900    247.88933     51.23735 0.0034851739            1            1 
+    3950    332.31324   -18.194985 0.0034851739            1            1 
+    4000    325.56802    18.402825 0.0034851739            1            1 
+    4050    338.37593    36.430977 0.0034851739            1            1 
+    4100    370.95478    39.290285 0.0034851739            1            1 
+    4150    348.47859   -7.0779678 0.0034851739            1            1 
+    4200    241.30632   -33.371788 0.0034851739            1            1 
+    4250    242.17258    -9.986197 0.0034851739            1            1 
+    4300    300.85311   -7.9244294 0.0034851739            1            1 
+    4350    273.15684   -21.257283 0.0034851739            1            1 
+    4400    305.77463   -5.8720722 0.0034851739            1            1 
+    4450    314.97697      45.0373 0.0034851739            1            1 
+    4500    310.77723    16.958773 0.0034851739            1            1 
+    4550     302.1742    12.156862 0.0034851739            1            1 
+    4600    319.74799      6.84889 0.0034851739            1            1 
+    4650    270.86805   -13.767905 0.0034851739            1            1 
+    4700    249.81731   -31.197487 0.0034851739            1            1 
+    4750    285.86481   -9.8916364 0.0034851739            1            1 
+    4800    233.98321    7.1338571 0.0034851739            1            1 
+    4850    302.60551    49.262889 0.0034851739            1            1 
+    4900    316.55056    34.663247 0.0034851739            1            1 
+    4950    357.32741    11.583006 0.0034851739            1            1 
+    5000    400.21045   -8.1781061 0.0034851739            1            1 
+    5050    390.01845   -20.490275 0.0034851739            1            1 
+    5100    378.84247   -41.328757 0.0034851739            1            1 
+    5150    324.02038   -15.023862 0.0034851739            1            1 
+    5200    262.08429    10.937354 0.0034851739            1            1 
+    5250    255.75508    16.381455 0.0034851739            1            1 
+    5300    277.84989     40.68232 0.0034851739            1            1 
+    5350    302.92832    9.1989494 0.0034851739            1            1 
+    5400     283.7196   -1.6584671 0.0034851739            1            1 
+    5450    300.71266   -4.7030295 0.0034851739            1            1 
+    5500     343.5499  -0.30550044 0.0034851739            1            1 
+    5550    369.51271    21.691649 0.0034851739            1            1 
+    5600    372.69789    -38.67994 0.0034851739            1            1 
+    5650    327.41266    11.352137 0.0034851739            1            1 
+    5700    278.98614   -23.827304 0.0034851739            1            1 
+    5750    308.30054   -20.756187 0.0034851739            1            1 
+    5800    341.45594    28.058441 0.0034851739            1            1 
+    5850    322.97844   -10.731921 0.0034851739            1            1 
+    5900    304.53591    32.825279 0.0034851739            1            1 
+    5950     287.1752   -36.780091 0.0034851739            1            1 
+    6000    296.52681    18.781896 0.0034851739            1            1 
+    6050    314.25442    15.992829 0.0034851739            1            1 
+    6100    313.86576    3.4342714 0.0034851739            1            1 
+    6150    325.64196    32.392039 0.0034851739            1            1 
+    6200    367.42931   -27.160706 0.0034851739            1            1 
+    6250    369.30798    39.020934 0.0034851739            1            1 
+    6300    328.92285   -23.175157 0.0034851739            1            1 
+    6350    305.63077    4.9024453 0.0034851739            1            1 
+    6400    241.70341   -13.676629 0.0034851739            1            1 
+    6450    265.66717      2.40612 0.0034851739            1            1 
+    6500    249.36037    13.420255 0.0034851739            1            1 
+    6550    294.53814    10.853462 0.0034851739            1            1 
+    6600     308.2025    18.995308 0.0034851739            1            1 
+    6650    305.43797    -49.56785 0.0034851739            1            1 
+    6700    320.27344    11.336281 0.0034851739            1            1 
+    6750    321.78666   -23.463899 0.0034851739            1            1 
+    6800    303.40388    7.6224553 0.0034851739            1            1 
+    6850    297.18966     51.52256 0.0034851739            1            1 
+    6900    284.18909   -8.4947203 0.0034851739            1            1 
+    6950    331.03663    13.233655 0.0034851739            1            1 
+    7000    311.37928   -43.265479 0.0034851739            1            1 
+    7050    286.81661   -14.174683 0.0034851739            1            1 
+    7100    302.84119    12.048954 0.0034851739            1            1 
+    7150    297.19357   -43.111968 0.0034851739            1            1 
+    7200    332.47359    26.048249 0.0034851739            1            1 
+    7250    262.70677    41.176242 0.0034851739            1            1 
+    7300    250.61405   -23.413982 0.0034851739            1            1 
+    7350    296.91117     35.88133 0.0034851739            1            1 
+    7400    245.09229   -13.447194 0.0034851739            1            1 
+    7450    272.28131   -23.322585 0.0034851739            1            1 
+    7500    209.04985    13.871239 0.0034851739            1            1 
+    7550    255.00955    4.9325621 0.0034851739            1            1 
+    7600    312.30937   -37.368274 0.0034851739            1            1 
+    7650    305.65903    55.245496 0.0034851739            1            1 
+    7700    325.09504   -18.347711 0.0034851739            1            1 
+    7750    363.28282   -22.479686 0.0034851739            1            1 
+    7800    350.17429    26.849547 0.0034851739            1            1 
+    7850    271.70853   -17.764575 0.0034851739            1            1 
+    7900    272.66484   -11.701967 0.0034851739            1            1 
+    7950    298.60202   -12.765675 0.0034851739            1            1 
+    8000    274.58852    49.641532 0.0034851739            1            1 
+    8050    304.72347  -0.55414183 0.0034851739            1            1 
+    8100    328.30757   -39.861301 0.0034851739            1            1 
+    8150    406.67601    2.8999409 0.0034851739            1            1 
+    8200    332.20083   -51.217399 0.0034851739            1            1 
+    8250    354.50609    53.128769 0.0034851739            1            1 
+    8300     337.2758     20.68562 0.0034851739            1            1 
+    8350    361.89708   -54.185869 0.0034851739            1            1 
+    8400    305.63496    24.058529 0.0034851739            1            1 
+    8450    303.27461     4.304683 0.0034851739            1            1 
+    8500    253.53694   -10.909021 0.0034851739            1            1 
+    8550    277.03017    23.241479 0.0034851739            1            1 
+    8600    291.41844   -22.240665 0.0034851739            1            1 
+    8650    307.85368    31.919587 0.0034851739            1            1 
+    8700    309.19724   0.53529642 0.0034851739            1            1 
+    8750     354.6583    11.565515 0.0034851739            1            1 
+    8800    329.78598      19.5996 0.0034851739            1            1 
+    8850    240.79198    21.803515 0.0034851739            1            1 
+    8900    318.40749   -59.816923 0.0034851739            1            1 
+    8950    308.47211   -57.808635 0.0034851739            1            1 
+    9000    271.51207    50.943482 0.0034851739            1            1 
+    9050     249.4005    6.7529187 0.0034851739            1            1 
+    9100     221.8772    47.196092 0.0034851739            1            1 
+    9150     297.9351    4.0058184 0.0034851739            1            1 
+    9200    274.85051   -24.774393 0.0034851739            1            1 
+    9250    336.04757    5.3799028 0.0034851739            1            1 
+    9300    380.44956   -22.389381 0.0034851739            1            1 
+    9350     336.9824    23.050616 0.0034851739            1            1 
+    9400    304.46425    32.530218 0.0034851739            1            1 
+    9450    317.55591   -22.265425 0.0034851739            1            1 
+    9500    323.70901   -7.0159787 0.0034851739            1            1 
+    9550    316.07308    28.062131 0.0034851739            1            1 
+    9600    262.74608  -0.78519192 0.0034851739            1            1 
+    9650    271.55045   -21.430123 0.0034851739            1            1 
+    9700     239.6022    14.483637 0.0034851739            1            1 
+    9750     338.1437  -0.72765302 0.0034851739            1            1 
+    9800    334.50189    19.495144 0.0034851739            1            1 
+    9850    354.87554    19.272719 0.0034851739            1            1 
+    9900    334.02141   -22.393457 0.0034851739            1            1 
+    9950    293.63651    19.178873 0.0034851739            1            1 
+   10000    319.81736    21.904414 0.0034851739            1            1 
+Loop time of 1.84987 on 1 procs for 10000 steps with 44 atoms
+
+Performance: 467.059 ns/day, 0.051 hours/ns, 5405.774 timesteps/s
+99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.26152    | 0.26152    | 0.26152    |   0.0 | 14.14
+Bond    | 0.74069    | 0.74069    | 0.74069    |   0.0 | 40.04
+Kspace  | 0.30505    | 0.30505    | 0.30505    |   0.0 | 16.49
+Neigh   | 0.39991    | 0.39991    | 0.39991    |   0.0 | 21.62
+Comm    | 0.02261    | 0.02261    | 0.02261    |   0.0 |  1.22
+Output  | 0.0034585  | 0.0034585  | 0.0034585  |   0.0 |  0.19
+Modify  | 0.099979   | 0.099979   | 0.099979   |   0.0 |  5.40
+Other   |            | 0.01666    |            |       |  0.90
+
+Nlocal:    44 ave 44 max 44 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    44 ave 44 max 44 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    823 ave 823 max 823 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 823
+Ave neighs/atom = 18.7045
+Ave special neighs/atom = 9.77273
+Neighbor list builds = 10000
+Dangerous builds = 0
+
+# write_restart restart_longrun
+# write_data restart_longrun.data
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:01

examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.4

@@ -0,0 +1,370 @@
+LAMMPS (20 Apr 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+  using 1 OpenMP thread(s) per MPI task
+# two monomer nylon example
+# reaction produces a condensed water molecule
+
+units real
+
+boundary p p p
+
+atom_style full
+
+kspace_style pppm 1.0e-4
+
+pair_style lj/class2/coul/long 8.5
+
+angle_style class2
+
+bond_style class2
+
+dihedral_style class2
+
+improper_style class2
+
+read_data tiny_nylon.data
+  orthogonal box = (-25 -25 -25) to (25 25 25)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  44 atoms
+  reading velocities ...
+  44 velocities
+  scanning bonds ...
+  9 = max bonds/atom
+  scanning angles ...
+  21 = max angles/atom
+  scanning dihedrals ...
+  29 = max dihedrals/atom
+  scanning impropers ...
+  29 = max impropers/atom
+  reading bonds ...
+  42 bonds
+  reading angles ...
+  74 angles
+  reading dihedrals ...
+  100 dihedrals
+  reading impropers ...
+  44 impropers
+  4 = max # of 1-2 neighbors
+  6 = max # of 1-3 neighbors
+  12 = max # of 1-4 neighbors
+  41 = max # of special neighbors
+
+velocity all create 300.0 4928459 dist gaussian
+
+molecule mol1 rxn1_stp1_unreacted.data_template
+Read molecule mol1:
+  18 atoms with max type 8
+  16 bonds with max type 14
+  25 angles with max type 28
+  23 dihedrals with max type 36
+  14 impropers with max type 11
+molecule mol2 rxn1_stp1_reacted.data_template
+Read molecule mol2:
+  18 atoms with max type 9
+  17 bonds with max type 13
+  31 angles with max type 27
+  39 dihedrals with max type 33
+  20 impropers with max type 1
+molecule mol3 rxn1_stp2_unreacted.data_template
+Read molecule mol3:
+  15 atoms with max type 9
+  14 bonds with max type 13
+  25 angles with max type 27
+  30 dihedrals with max type 33
+  16 impropers with max type 1
+molecule mol4 rxn1_stp2_reacted.data_template
+Read molecule mol4:
+  15 atoms with max type 11
+  13 bonds with max type 15
+  19 angles with max type 29
+  16 dihedrals with max type 32
+  10 impropers with max type 13
+
+thermo 50
+
+# dump 1 all xyz 1 test_vis.xyz
+
+fix myrxns all bond/react stabilization yes statted_grp .03   react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map   react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
+WARNING: An atom in 'react #1' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489)
+WARNING: An atom in 'react #2' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489)
+dynamic group bond_react_MASTER_group defined
+dynamic group statted_grp defined
+dynamic group bond_react_MASTER_group defined
+dynamic group statted_grp defined
+
+fix 1 statted_grp nvt temp 300 300 100
+
+fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1
+
+thermo_style custom step temp press density f_myrxns[1] f_myrxns[2]
+
+# restart 100 restart1 restart2
+
+run 10000
+PPPM initialization ...
+  using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+  G vector (1/distance) = 0.0534597
+  grid = 2 2 2
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0402256
+  estimated relative force accuracy = 0.000121138
+  using double precision FFTs
+  3d grid and FFT values/proc = 252 2
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 10.5
+  ghost atom cutoff = 10.5
+  binsize = 5.25, bins = 10 10 10
+  2 neighbor lists, perpetual/occasional/extra = 1 1 0
+  (1) pair lj/class2/coul/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+  (2) fix bond/react, occasional, copy from (1)
+      attributes: half, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+WARNING: Inconsistent image flags (../domain.cpp:786)
+Per MPI rank memory allocation (min/avg/max) = 33.34 | 33.69 | 34.37 Mbytes
+Step Temp Press Density f_myrxns[1] f_myrxns[2] 
+       0          300    346.78165 0.0034851739            0            0 
+      50    296.70408    -51.30066 0.0034851739            1            0 
+     100    274.25324    46.715512 0.0034851739            1            1 
+     150    471.61579    31.321598 0.0034851739            1            1 
+     200    362.87766    42.061118 0.0034851739            1            1 
+     250    367.58058    65.303109 0.0034851739            1            1 
+     300    372.38236   -52.421725 0.0034851739            1            1 
+     350    297.69957    17.869945 0.0034851739            1            1 
+     400    258.30433     49.19156 0.0034851739            1            1 
+     450    253.34384   -5.8162637 0.0034851739            1            1 
+     500    269.96465   -43.337517 0.0034851739            1            1 
+     550    303.23718    10.180246 0.0034851739            1            1 
+     600    329.59579    -48.97461 0.0034851739            1            1 
+     650    350.42568    50.983183 0.0034851739            1            1 
+     700    342.03272     35.43465 0.0034851739            1            1 
+     750    269.23405   -41.873166 0.0034851739            1            1 
+     800    245.15025    13.953092 0.0034851739            1            1 
+     850    257.85421   -3.1492141 0.0034851739            1            1 
+     900    316.15644    7.7798301 0.0034851739            1            1 
+     950     299.9124    -15.77014 0.0034851739            1            1 
+    1000    302.89968   -17.049693 0.0034851739            1            1 
+    1050    308.91651     71.84632 0.0034851739            1            1 
+    1100    348.43932   -18.742012 0.0034851739            1            1 
+    1150    309.03036    50.536311 0.0034851739            1            1 
+    1200     318.9761   -16.905746 0.0034851739            1            1 
+    1250    320.42806 -0.057975092 0.0034851739            1            1 
+    1300     289.7824    18.200772 0.0034851739            1            1 
+    1350    284.79836   -9.1978427 0.0034851739            1            1 
+    1400    325.43292    42.082833 0.0034851739            1            1 
+    1450     261.5041   -37.823325 0.0034851739            1            1 
+    1500    298.88723   -5.1647385 0.0034851739            1            1 
+    1550    291.37403   -7.7764201 0.0034851739            1            1 
+    1600    293.83475      22.2458 0.0034851739            1            1 
+    1650    293.80611    24.202512 0.0034851739            1            1 
+    1700    291.70205   -23.397884 0.0034851739            1            1 
+    1750    292.32437   -10.671214 0.0034851739            1            1 
+    1800    302.01367   -11.671025 0.0034851739            1            1 
+    1850     322.1651    24.438331 0.0034851739            1            1 
+    1900    310.45076    45.343592 0.0034851739            1            1 
+    1950    325.91745   -19.847809 0.0034851739            1            1 
+    2000    276.89662    63.387098 0.0034851739            1            1 
+    2050    311.33783   -24.683247 0.0034851739            1            1 
+    2100     346.2336   -27.526891 0.0034851739            1            1 
+    2150    345.30604   -15.722411 0.0034851739            1            1 
+    2200     346.7718   -17.857633 0.0034851739            1            1 
+    2250    304.28676   -1.9965581 0.0034851739            1            1 
+    2300    322.56372   -31.786868 0.0034851739            1            1 
+    2350    282.64326    6.1982735 0.0034851739            1            1 
+    2400    286.65759   -63.207781 0.0034851739            1            1 
+    2450    257.05528    32.931491 0.0034851739            1            1 
+    2500    283.64386    26.912373 0.0034851739            1            1 
+    2550    299.54005    27.277039 0.0034851739            1            1 
+    2600    283.92503    14.660972 0.0034851739            1            1 
+    2650    321.93453   -18.977358 0.0034851739            1            1 
+    2700     376.7189    31.826935 0.0034851739            1            1 
+    2750    372.20075   -32.821697 0.0034851739            1            1 
+    2800    361.40604    83.035183 0.0034851739            1            1 
+    2850    332.27269   -23.927452 0.0034851739            1            1 
+    2900    331.14638  -0.12328446 0.0034851739            1            1 
+    2950    303.67489   -24.078857 0.0034851739            1            1 
+    3000    311.40462    21.563537 0.0034851739            1            1 
+    3050    284.72849   -23.849667 0.0034851739            1            1 
+    3100    303.48477    39.347763 0.0034851739            1            1 
+    3150     264.2739  -0.22299878 0.0034851739            1            1 
+    3200    300.03351    31.545323 0.0034851739            1            1 
+    3250    288.56663    5.7225229 0.0034851739            1            1 
+    3300    200.13238   -31.239655 0.0034851739            1            1 
+    3350    231.32512    16.631728 0.0034851739            1            1 
+    3400    260.57402    2.1717992 0.0034851739            1            1 
+    3450    301.47128   -42.210623 0.0034851739            1            1 
+    3500    321.77414    40.074365 0.0034851739            1            1 
+    3550    353.21858    28.387783 0.0034851739            1            1 
+    3600    331.45989   -57.800858 0.0034851739            1            1 
+    3650    303.88123     44.86596 0.0034851739            1            1 
+    3700    329.73833   -0.8061567 0.0034851739            1            1 
+    3750    297.55588  -0.49626022 0.0034851739            1            1 
+    3800    286.38794   -10.010003 0.0034851739            1            1 
+    3850    290.17417    -43.51187 0.0034851739            1            1 
+    3900    247.88933     51.23735 0.0034851739            1            1 
+    3950    332.31324   -18.194985 0.0034851739            1            1 
+    4000    325.56802    18.402825 0.0034851739            1            1 
+    4050    338.37594    36.430977 0.0034851739            1            1 
+    4100    370.95478    39.290285 0.0034851739            1            1 
+    4150    348.47859   -7.0779683 0.0034851739            1            1 
+    4200    241.30632   -33.371789 0.0034851739            1            1 
+    4250    242.17258   -9.9861962 0.0034851739            1            1 
+    4300    300.85311    -7.924429 0.0034851739            1            1 
+    4350    273.15684   -21.257282 0.0034851739            1            1 
+    4400    305.77464   -5.8720712 0.0034851739            1            1 
+    4450    314.97697    45.037299 0.0034851739            1            1 
+    4500    310.77723    16.958771 0.0034851739            1            1 
+    4550    302.17421    12.156862 0.0034851739            1            1 
+    4600    319.74799    6.8488914 0.0034851739            1            1 
+    4650    270.86805   -13.767907 0.0034851739            1            1 
+    4700    249.81731   -31.197484 0.0034851739            1            1 
+    4750    285.86481   -9.8916332 0.0034851739            1            1 
+    4800    233.98321    7.1338518 0.0034851739            1            1 
+    4850    302.60551    49.262886 0.0034851739            1            1 
+    4900    316.55055    34.663238 0.0034851739            1            1 
+    4950    357.32741    11.583013 0.0034851739            1            1 
+    5000    400.21044   -8.1780861 0.0034851739            1            1 
+    5050    390.01845   -20.490268 0.0034851739            1            1 
+    5100    378.84249   -41.328772 0.0034851739            1            1 
+    5150    324.02039   -15.023852 0.0034851739            1            1 
+    5200    262.08427    10.937367 0.0034851739            1            1 
+    5250    255.75506    16.381495 0.0034851739            1            1 
+    5300    277.84991    40.682283 0.0034851739            1            1 
+    5350    302.92834    9.1989644 0.0034851739            1            1 
+    5400    283.71964   -1.6583895 0.0034851739            1            1 
+    5450    300.71261    -4.703054 0.0034851739            1            1 
+    5500    343.54987  -0.30546396 0.0034851739            1            1 
+    5550    369.51272    21.691639 0.0034851739            1            1 
+    5600    372.69786   -38.679919 0.0034851739            1            1 
+    5650    327.41256    11.352201 0.0034851739            1            1 
+    5700     278.9861    -23.82728 0.0034851739            1            1 
+    5750    308.30037   -20.756238 0.0034851739            1            1 
+    5800     341.4559    28.058314 0.0034851739            1            1 
+    5850     322.9786   -10.731862 0.0034851739            1            1 
+    5900    304.53598    32.825105 0.0034851739            1            1 
+    5950    287.17515   -36.780057 0.0034851739            1            1 
+    6000    296.52688    18.782156 0.0034851739            1            1 
+    6050    314.25411     15.99272 0.0034851739            1            1 
+    6100    313.86572    3.4344108 0.0034851739            1            1 
+    6150    325.64197     32.39212 0.0034851739            1            1 
+    6200     367.4298   -27.161154 0.0034851739            1            1 
+    6250    369.30937    39.020881 0.0034851739            1            1 
+    6300    328.92245   -23.175612 0.0034851739            1            1 
+    6350     305.6293    4.9011587 0.0034851739            1            1 
+    6400    241.70456   -13.675247 0.0034851739            1            1 
+    6450    265.66574    2.4049735 0.0034851739            1            1 
+    6500     249.3592    13.420453 0.0034851739            1            1 
+    6550     294.5367    10.856753 0.0034851739            1            1 
+    6600    308.20246    18.992923 0.0034851739            1            1 
+    6650    305.43756    -49.57151 0.0034851739            1            1 
+    6700    320.27395    11.339101 0.0034851739            1            1 
+    6750     321.7875   -23.463361 0.0034851739            1            1 
+    6800    303.40316    7.6256997 0.0034851739            1            1 
+    6850    297.18652     51.52186 0.0034851739            1            1 
+    6900    284.19084    -8.496294 0.0034851739            1            1 
+    6950    331.04173    13.227745 0.0034851739            1            1 
+    7000    311.38027    -43.26105 0.0034851739            1            1 
+    7050    286.82046   -14.171194 0.0034851739            1            1 
+    7100    302.81691    12.058085 0.0034851739            1            1 
+    7150    297.18018   -43.110658 0.0034851739            1            1 
+    7200    332.46131    26.051496 0.0034851739            1            1 
+    7250    262.72288    41.161451 0.0034851739            1            1 
+    7300    250.62739   -23.440907 0.0034851739            1            1 
+    7350    296.92141    35.869216 0.0034851739            1            1 
+    7400    245.06807   -13.467896 0.0034851739            1            1 
+    7450     272.2659   -23.292836 0.0034851739            1            1 
+    7500    209.05776    13.888665 0.0034851739            1            1 
+    7550    255.03716    4.9662624 0.0034851739            1            1 
+    7600    312.26011   -37.350427 0.0034851739            1            1 
+    7650     305.5823    55.208039 0.0034851739            1            1 
+    7700    325.13382   -18.370791 0.0034851739            1            1 
+    7750    363.24898   -22.473126 0.0034851739            1            1 
+    7800    350.19254    26.792307 0.0034851739            1            1 
+    7850    271.76418   -17.843445 0.0034851739            1            1 
+    7900    272.70301   -11.709349 0.0034851739            1            1 
+    7950     298.5993   -12.736235 0.0034851739            1            1 
+    8000    274.52611    49.657345 0.0034851739            1            1 
+    8050    304.73711  -0.52485689 0.0034851739            1            1 
+    8100    328.29239   -39.901891 0.0034851739            1            1 
+    8150    406.52096    2.8669076 0.0034851739            1            1 
+    8200    332.17309   -51.168754 0.0034851739            1            1 
+    8250    354.68419    53.003157 0.0034851739            1            1 
+    8300    337.28934    20.766408 0.0034851739            1            1 
+    8350    361.81133   -54.159227 0.0034851739            1            1 
+    8400    305.59597    24.011667 0.0034851739            1            1 
+    8450    303.25823     4.423341 0.0034851739            1            1 
+    8500    253.50747   -11.026949 0.0034851739            1            1 
+    8550    277.13504    23.204625 0.0034851739            1            1 
+    8600    291.40211   -22.253861 0.0034851739            1            1 
+    8650    307.93765     32.14162 0.0034851739            1            1 
+    8700     309.1529   0.36279434 0.0034851739            1            1 
+    8750    355.10326    11.677219 0.0034851739            1            1 
+    8800    330.21328    19.235269 0.0034851739            1            1 
+    8850    241.29109    21.707386 0.0034851739            1            1 
+    8900    319.15363   -60.010115 0.0034851739            1            1 
+    8950    308.88552   -57.637014 0.0034851739            1            1 
+    9000    272.22373     51.15837 0.0034851739            1            1 
+    9050    248.84947    7.3390565 0.0034851739            1            1 
+    9100    221.91564    48.387079 0.0034851739            1            1 
+    9150    298.03506    2.9058639 0.0034851739            1            1 
+    9200    274.25114   -24.597819 0.0034851739            1            1 
+    9250    334.08373    5.1079577 0.0034851739            1            1 
+    9300    383.07285   -23.274763 0.0034851739            1            1 
+    9350    335.00581     20.94212 0.0034851739            1            1 
+    9400    309.23862    34.074744 0.0034851739            1            1 
+    9450    312.62262   -28.468057 0.0034851739            1            1 
+    9500    324.54274     2.851136 0.0034851739            1            1 
+    9550    313.32781    22.468182 0.0034851739            1            1 
+    9600    269.04372     4.064934 0.0034851739            1            1 
+    9650    270.98476   -21.520127 0.0034851739            1            1 
+    9700     236.8736    16.250728 0.0034851739            1            1 
+    9750    333.94686    1.6864148 0.0034851739            1            1 
+    9800    330.91875    12.150018 0.0034851739            1            1 
+    9850     343.8603    25.338853 0.0034851739            1            1 
+    9900    330.93364   -28.292992 0.0034851739            1            1 
+    9950    291.25518    25.795948 0.0034851739            1            1 
+   10000    319.25565    25.323846 0.0034851739            1            1 
+Loop time of 3.55353 on 4 procs for 10000 steps with 44 atoms
+
+Performance: 243.139 ns/day, 0.099 hours/ns, 2814.105 timesteps/s
+93.4% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.0030422  | 0.10454    | 0.35211    |  44.8 |  2.94
+Bond    | 0.0063896  | 0.29222    | 0.94356    |  71.3 |  8.22
+Kspace  | 0.88508    | 1.6486     | 1.979      |  35.1 | 46.39
+Neigh   | 0.61154    | 0.62212    | 0.63307    |   1.0 | 17.51
+Comm    | 0.18944    | 0.24549    | 0.29196    |   7.9 |  6.91
+Output  | 0.0050066  | 0.011804   | 0.032134   |  10.8 |  0.33
+Modify  | 0.52282    | 0.60522    | 0.69588    |   7.9 | 17.03
+Other   |            | 0.02359    |            |       |  0.66
+
+Nlocal:    11 ave 44 max 0 min
+Histogram: 3 0 0 0 0 0 0 0 0 1
+Nghost:    33 ave 44 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 3
+Neighs:    205.75 ave 823 max 0 min
+Histogram: 3 0 0 0 0 0 0 0 0 1
+
+Total # of neighbors = 823
+Ave neighs/atom = 18.7045
+Ave special neighs/atom = 9.77273
+Neighbor list builds = 10000
+Dangerous builds = 0
+
+# write_restart restart_longrun
+# write_data restart_longrun.data
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:03

examples/USER/misc/bond_react/tiny_nylon/rxn1_stp1_map

@@ -0,0 +1,35 @@
+this is a nominal superimpose file
+
+2 edgeIDs
+18 equivalences
+
+BondingIDs
+
+10
+1
+
+EdgeIDs
+
+16
+8
+
+Equivalences
+
+1	1
+2	2
+3	3
+4	4
+5	5
+6	6
+7	7
+8	8
+9	9
+10	10
+11	11
+12	12
+13	13
+14	14
+15	15
+16	16
+17	17
+18	18

examples/USER/misc/bond_react/tiny_nylon/rxn1_stp1_reacted.data_template

@@ -0,0 +1,189 @@
+this is a molecule template for: initial nylon crosslink, post-reacting
+
+18 atoms
+17 bonds
+31 angles
+39 dihedrals
+20 impropers
+
+Types
+
+1 9
+2 1
+3 1
+4 8
+5 8
+6 4
+7 4
+8 1
+9 1
+10 2
+11 6
+12 3
+13 4
+14 4
+15 5
+16 1
+17 4
+18 4
+
+Charges
+
+1 -0.300000
+2 0.000000
+3 0.000000
+4 0.000000
+5 0.000000
+6 0.000000
+7 0.000000
+8 0.000000
+9 0.000000
+10 0.300000
+11 0.000000
+12 0.000000
+13 0.000000
+14 0.000000
+15 0.000000
+16 0.000000
+17 0.000000
+18 0.000000
+
+Coords
+
+1 -5.522237 -0.752722 1.631158
+2 -5.170398 -0.545733 0.178130
+3 -6.469695 -0.553072 -0.648889
+4 -6.052076 -1.721152 1.744648
+5 -6.183059 0.071387 1.971497
+6 -4.489340 -1.389197 -0.173156
+7 -4.637591 0.453703 0.051252
+8 -5.618658 0.138919 4.386107
+9 -4.669492 -0.989819 3.943591
+10 -4.270194 -0.766405 2.474102
+11 -3.348470 -1.875393 2.024289
+12 -3.569794 0.564183 2.345995
+13 -5.201079 -1.993301 4.044219
+14 -3.736682 -0.984819 4.598305
+15 -4.255402 1.370923 2.679069
+16 -6.136394 -0.339866 -2.136775
+17 -6.996331 -1.555519 -0.517408
+18 -7.153308 0.284949 -0.289930
+
+Bonds
+
+1 11 1 2
+2 12 1 4
+3 12 1 5
+4 13 1 10
+5 2 2 3
+6 1 2 6
+7 1 2 7
+8 2 3 16
+9 1 3 17
+10 1 3 18
+11 2 8 9
+12 4 9 10
+13 1 9 13
+14 1 9 14
+15 5 10 11
+16 3 10 12
+17 6 12 15
+
+Angles
+
+1 17 2 1 4
+2 17 2 1 5
+3 18 2 1 10
+4 19 4 1 5
+5 20 4 1 10
+6 20 5 1 10
+7 21 1 2 3
+8 22 1 2 6
+9 22 1 2 7
+10 2 3 2 6
+11 2 3 2 7
+12 1 6 2 7
+13 3 2 3 16
+14 2 2 3 17
+15 2 2 3 18
+16 2 16 3 17
+17 2 16 3 18
+18 1 17 3 18
+19 8 8 9 10
+20 2 8 9 13
+21 2 8 9 14
+22 23 13 9 10
+23 23 14 9 10
+24 1 13 9 14
+25 6 9 10 11
+26 4 9 10 12
+27 24 1 10 9
+28 25 11 10 12
+29 26 1 10 11
+30 27 1 10 12
+31 7 10 12 15
+
+Dihedrals
+
+1 19 4 1 2 3
+2 20 4 1 2 6
+3 20 4 1 2 7
+4 19 5 1 2 3
+5 20 5 1 2 6
+6 20 5 1 2 7
+7 21 10 1 2 3
+8 22 10 1 2 6
+9 22 10 1 2 7
+10 23 2 1 10 9
+11 24 2 1 10 11
+12 25 2 1 10 12
+13 26 4 1 10 9
+14 27 4 1 10 11
+15 28 4 1 10 12
+16 26 5 1 10 9
+17 27 5 1 10 11
+18 28 5 1 10 12
+19 29 1 2 3 16
+20 30 1 2 3 17
+21 30 1 2 3 18
+22 4 16 3 2 6
+23 2 6 2 3 17
+24 2 6 2 3 18
+25 4 16 3 2 7
+26 2 7 2 3 17
+27 2 7 2 3 18
+28 10 8 9 10 11
+29 8 8 9 10 12
+30 31 8 9 10 1
+31 11 13 9 10 11
+32 9 13 9 10 12
+33 32 13 9 10 1
+34 11 14 9 10 11
+35 9 14 9 10 12
+36 32 14 9 10 1
+37 6 9 10 12 15
+38 7 11 10 12 15
+39 33 1 10 12 15
+
+Impropers
+
+1 1 2 1 4 5
+2 1 2 1 4 10
+3 1 2 1 5 10
+4 1 4 1 5 10
+5 1 1 2 3 6
+6 1 1 2 3 7
+7 1 1 2 6 7
+8 1 3 2 6 7
+9 1 2 3 16 17
+10 1 2 3 16 18
+11 1 2 3 17 18
+12 1 16 3 17 18
+13 1 8 9 13 10
+14 1 8 9 14 10
+15 1 8 9 13 14
+16 1 13 9 14 10
+17 1 9 10 11 12
+18 1 1 10 9 11
+19 1 1 10 9 12
+20 1 1 10 11 12

examples/USER/misc/bond_react/tiny_nylon/rxn1_stp1_unreacted.data_template

@@ -0,0 +1,160 @@
+this is a molecule template for: initial nylon crosslink, pre-reacting
+
+18 atoms
+16 bonds
+25 angles
+23 dihedrals
+14 impropers
+
+Types
+
+1 7
+2 1
+3 1
+4 8
+5 8
+6 4
+7 4
+8 1
+9 1
+10 2
+11 6
+12 3
+13 4
+14 4
+15 5
+16 1
+17 4
+18 4
+
+Charges
+
+1 -0.300000
+2 0.000000
+3 0.000000
+4 0.000000
+5 0.000000
+6 0.000000
+7 0.000000
+8 0.000000
+9 0.000000
+10 0.300000
+11 0.000000
+12 0.000000
+13 0.000000
+14 0.000000
+15 0.000000
+16 0.000000
+17 0.000000
+18 0.000000
+
+Coords
+
+1 -4.922858 -0.946982 1.146055
+2 -5.047195 -0.935267 -0.358173
+3 -6.526281 -0.755366 -0.743523
+4 -5.282604 0.020447 1.552710
+5 -3.860697 -1.095850 1.428305
+6 -4.662382 -1.920900 -0.781524
+7 -4.433977 -0.072765 -0.784071
+8 -5.506279 0.202610 4.825816
+9 -4.449177 -0.844592 4.423366
+10 -4.103916 -0.749629 2.925195
+11 -3.376249 -1.886171 2.245643
+12 -4.493235 0.477214 2.137199
+13 -4.849053 -1.888877 4.663994
+14 -3.491823 -0.662913 5.018510
+15 -5.020777 1.189745 2.805427
+16 -3.964987 2.900602 -1.551341
+17 -4.460694 2.836102 0.668882
+18 -4.828494 3.219656 -0.122111
+
+Bonds
+
+1 14 1 2
+2 10 1 4
+3 10 1 5
+4 2 2 3
+5 1 2 6
+6 1 2 7
+7 2 3 16
+8 1 3 17
+9 1 3 18
+10 2 8 9
+11 4 9 10
+12 1 9 13
+13 1 9 14
+14 5 10 11
+15 3 10 12
+16 6 12 15
+
+Angles
+
+1 15 2 1 4
+2 15 2 1 5
+3 16 4 1 5
+4 28 1 2 3
+5 14 1 2 6
+6 14 1 2 7
+7 2 3 2 6
+8 2 3 2 7
+9 1 6 2 7
+10 3 2 3 16
+11 2 2 3 17
+12 2 2 3 18
+13 2 16 3 17
+14 2 16 3 18
+15 1 17 3 18
+16 8 8 9 10
+17 2 8 9 13
+18 2 8 9 14
+19 23 13 9 10
+20 23 14 9 10
+21 1 13 9 14
+22 6 9 10 11
+23 4 9 10 12
+24 25 11 10 12
+25 7 10 12 15
+
+Dihedrals
+
+1 34 4 1 2 3
+2 35 4 1 2 6
+3 35 4 1 2 7
+4 34 5 1 2 3
+5 35 5 1 2 6
+6 35 5 1 2 7
+7 36 1 2 3 16
+8 12 1 2 3 17
+9 12 1 2 3 18
+10 4 16 3 2 6
+11 2 6 2 3 17
+12 2 6 2 3 18
+13 4 16 3 2 7
+14 2 7 2 3 17
+15 2 7 2 3 18
+16 10 8 9 10 11
+17 8 8 9 10 12
+18 11 13 9 10 11
+19 9 13 9 10 12
+20 11 14 9 10 11
+21 9 14 9 10 12
+22 6 9 10 12 15
+23 7 11 10 12 15
+
+Impropers
+
+1 6 2 1 4 5
+2 11 9 10 11 12
+3 1 1 2 3 6
+4 1 1 2 3 7
+5 1 1 2 6 7
+6 1 3 2 6 7
+7 1 2 3 16 17
+8 1 2 3 16 18
+9 1 2 3 17 18
+10 1 16 3 17 18
+11 1 8 9 13 10
+12 1 8 9 14 10
+13 1 8 9 13 14
+14 1 13 9 14 10

examples/USER/misc/bond_react/tiny_nylon/rxn1_stp2_map

@@ -0,0 +1,32 @@
+this is a nominal superimpose file
+
+2 edgeIDs
+15 equivalences
+
+BondingIDs
+
+4
+12
+
+EdgeIDs
+
+8
+3
+
+Equivalences
+
+1	1
+2	2
+3	3
+4	4
+5	5
+6	6
+7	7
+8	8
+9	9
+10	10
+11	11
+12	12
+13	13
+14	14
+15	15

examples/USER/misc/bond_react/tiny_nylon/rxn1_stp2_reacted.data_template

@@ -0,0 +1,131 @@
+this is a molecule template for: water condensation, post-reacting
+
+15 atoms
+13 bonds
+19 angles
+16 dihedrals
+10 impropers
+
+Types
+
+1 9
+2 1
+3 1
+4 10
+5 8
+6 4
+7 4
+8 1
+9 1
+10 2
+11 6
+12 11
+13 4
+14 4
+15 10
+
+Charges
+
+1 -0.300000
+2 0.000000
+3 0.000000
+4 0.410000
+5 0.000000
+6 0.000000
+7 0.000000
+8 0.000000
+9 0.000000
+10 0.300000
+11 0.000000
+12 -0.820000
+13 0.000000
+14 0.000000
+15 0.410000
+
+Coords
+
+1 -4.856280 -1.050468 1.432625
+2 -5.047195 -0.935267 -0.358173
+3 -6.526281 -0.755366 -0.743523
+4 -5.282604 0.020447 1.552710
+5 -3.860697 -1.095850 1.428305
+6 -4.662382 -1.920900 -0.781524
+7 -4.433977 -0.072765 -0.784071
+8 -5.506279 0.202610 4.825816
+9 -4.449177 -0.844592 4.423366
+10 -4.103916 -0.749629 2.925195
+11 -3.376249 -1.886171 2.245643
+12 -4.493235 0.477214 2.137199
+13 -4.849053 -1.888877 4.663994
+14 -3.491823 -0.662913 5.018510
+15 -5.020777 1.189745 2.805427
+
+Bonds
+
+1 11 1 2
+2 12 1 5
+3 13 1 10
+4 2 2 3
+5 1 2 6
+6 1 2 7
+7 15 4 12
+8 2 8 9
+9 4 9 10
+10 1 9 13
+11 1 9 14
+12 5 10 11
+13 15 15 12
+
+Angles
+
+1 17 2 1 5
+2 18 2 1 10
+3 20 5 1 10
+4 21 1 2 3
+5 22 1 2 6
+6 22 1 2 7
+7 2 3 2 6
+8 2 3 2 7
+9 1 6 2 7
+10 8 8 9 10
+11 2 8 9 13
+12 2 8 9 14
+13 23 13 9 10
+14 23 14 9 10
+15 1 13 9 14
+16 6 9 10 11
+17 24 1 10 9
+18 26 1 10 11
+19 29 15 12 4
+
+Dihedrals
+
+1 19 5 1 2 3
+2 20 5 1 2 6
+3 20 5 1 2 7
+4 21 10 1 2 3
+5 22 10 1 2 6
+6 22 10 1 2 7
+7 23 2 1 10 9
+8 24 2 1 10 11
+9 26 5 1 10 9
+10 27 5 1 10 11
+11 10 8 9 10 11
+12 31 8 9 10 1
+13 11 13 9 10 11
+14 32 13 9 10 1
+15 11 14 9 10 11
+16 32 14 9 10 1
+
+Impropers
+
+1 12 2 1 5 10
+2 13 1 10 9 11
+3 1 1 2 3 6
+4 1 1 2 3 7
+5 1 1 2 6 7
+6 1 3 2 6 7
+7 1 8 9 13 10
+8 1 8 9 14 10
+9 1 8 9 13 14
+10 1 13 9 14 10

examples/USER/misc/bond_react/tiny_nylon/rxn1_stp2_unreacted.data_template

@@ -0,0 +1,158 @@
+this is a molecule template for: water condensation, pre-reacting
+
+15 atoms
+14 bonds
+25 angles
+30 dihedrals
+16 impropers
+
+Types
+
+1 9
+2 1
+3 1
+4 8
+5 8
+6 4
+7 4
+8 1
+9 1
+10 2
+11 6
+12 3
+13 4
+14 4
+15 5
+
+Charges
+
+1 -0.300000
+2 0.000000
+3 0.000000
+4 0.000000
+5 0.000000
+6 0.000000
+7 0.000000
+8 0.000000
+9 0.000000
+10 0.300000
+11 0.000000
+12 0.000000
+13 0.000000
+14 0.000000
+15 0.000000
+
+Coords
+
+1 -4.922858 -0.946982 1.146055
+2 -5.047195 -0.935267 -0.358173
+3 -6.526281 -0.755366 -0.743523
+4 -5.282604 0.020447 1.552710
+5 -3.860697 -1.095850 1.428305
+6 -4.662382 -1.920900 -0.781524
+7 -4.433977 -0.072765 -0.784071
+8 -5.506279 0.202610 4.825816
+9 -4.449177 -0.844592 4.423366
+10 -4.103916 -0.749629 2.925195
+11 -3.376249 -1.886171 2.245643
+12 -4.493235 0.477214 2.137199
+13 -4.849053 -1.888877 4.663994
+14 -3.491823 -0.662913 5.018510
+15 -5.020777 1.189745 2.805427
+
+Bonds
+
+1 11 1 2
+2 12 1 4
+3 12 1 5
+4 13 1 10
+5 2 2 3
+6 1 2 6
+7 1 2 7
+8 2 8 9
+9 4 9 10
+10 1 9 13
+11 1 9 14
+12 5 10 11
+13 3 10 12
+14 6 12 15
+
+Angles
+
+1 17 2 1 4
+2 17 2 1 5
+3 18 2 1 10
+4 19 4 1 5
+5 20 4 1 10
+6 20 5 1 10
+7 21 1 2 3
+8 22 1 2 6
+9 22 1 2 7
+10 2 3 2 6
+11 2 3 2 7
+12 1 6 2 7
+13 8 8 9 10
+14 2 8 9 13
+15 2 8 9 14
+16 23 13 9 10
+17 23 14 9 10
+18 1 13 9 14
+19 6 9 10 11
+20 4 9 10 12
+21 24 1 10 9
+22 25 11 10 12
+23 26 1 10 11
+24 27 1 10 12
+25 7 10 12 15
+
+Dihedrals
+
+1 19 4 1 2 3
+2 20 4 1 2 6
+3 20 4 1 2 7
+4 19 5 1 2 3
+5 20 5 1 2 6
+6 20 5 1 2 7
+7 21 10 1 2 3
+8 22 10 1 2 6
+9 22 10 1 2 7
+10 23 2 1 10 9
+11 24 2 1 10 11
+12 25 2 1 10 12
+13 26 4 1 10 9
+14 27 4 1 10 11
+15 28 4 1 10 12
+16 26 5 1 10 9
+17 27 5 1 10 11
+18 28 5 1 10 12
+19 10 8 9 10 11
+20 8 8 9 10 12
+21 31 8 9 10 1
+22 11 13 9 10 11
+23 9 13 9 10 12
+24 32 13 9 10 1
+25 11 14 9 10 11
+26 9 14 9 10 12
+27 32 14 9 10 1
+28 6 9 10 12 15
+29 7 11 10 12 15
+30 33 1 10 12 15
+
+Impropers
+
+1 1 2 1 4 5
+2 1 2 1 4 10
+3 1 2 1 5 10
+4 1 4 1 5 10
+5 1 1 2 3 6
+6 1 1 2 3 7
+7 1 1 2 6 7
+8 1 3 2 6 7
+9 1 8 9 13 10
+10 1 8 9 14 10
+11 1 8 9 13 14
+12 1 13 9 14 10
+13 1 9 10 11 12
+14 1 1 10 9 11
+15 1 1 10 9 12
+16 1 1 10 11 12

examples/USER/misc/bond_react/tiny_nylon/tiny_nylon.data

@@ -0,0 +1,795 @@
+this is LAMMPS data file containing two nylon monomers
+
+44 atoms
+11 atom types
+42 bonds
+15 bond types
+74 angles
+29 angle types
+100 dihedrals
+36 dihedral types
+44 impropers
+13 improper types
+5 extra bond per atom
+15 extra angle per atom
+15 extra dihedral per atom
+25 extra improper per atom
+25 extra special per atom
+
+-25 25 xlo xhi
+-25 25 ylo yhi
+-25 25 zlo zhi
+
+Masses
+
+1 12.0112
+2 12.0112
+3 15.9994
+4 1.00797
+5 1.00797
+6 15.9994
+7 14.0067
+8 1.00797
+9 14.0067
+10 1.00797
+11 15.9994
+
+Pair Coeffs # lj/class2/coul/cut
+
+1 0.054 4.01
+2 0.12 3.81
+3 0.24 3.535
+4 0.02 2.7
+5 0.013 1.098
+6 0.267 3.3
+7 0.065 4.07
+8 0.013 1.098
+9 0.106 4.07
+10 0.013 1.098
+11 0.26 3.61
+
+Bond Coeffs # class2
+
+1 1.101 345 -691.89 844.6
+2 1.53 299.67 -501.77 679.81
+3 1.3649 368.731 -832.478 1274.02
+4 1.5202 253.707 -423.037 396.9
+5 1.202 851.14 -1918.49 2160.77
+6 0.965 532.506 -1282.9 2004.77
+7 1.53 299.67 -501.77 679.81
+8 1.101 345 -691.89 844.6
+9 1.457 365.805 -699.637 998.484
+10 1.006 466.74 -1073.6 1251.11
+11 1.452 327.166 -547.899 526.5
+12 1.01 462.75 -1053.63 1545.76
+13 1.416 359.159 -558.473 1146.38
+14 1.457 365.805 -699.637 998.484
+15 0.97 563.28 -1428.22 1902.12
+
+Angle Coeffs # class2
+
+1 107.66 39.641 -12.921 -2.4318
+2 110.77 41.453 -10.604 5.129
+3 112.67 39.516 -7.443 -9.5583
+4 123.145 55.5431 -17.2123 0.1348
+5 118.986 98.6813 -22.2485 10.3673
+6 123.145 55.5431 -17.2123 0.1348
+7 111.254 53.5303 -11.8454 -11.5405
+8 108.53 51.9747 -9.4851 -10.9985
+9 107.734 40.6099 -28.8121 0
+10 110.77 41.453 -10.604 5.129
+11 112.67 39.516 -7.443 -9.5583
+12 107.66 39.641 -12.921 -2.4318
+13 111.91 60.7147 -13.3366 -13.0785
+14 110.62 51.3137 -6.7198 -2.6003
+15 110.954 50.8652 -4.4522 -10.0298
+16 107.067 45.252 -7.5558 -9.512
+17 113.868 45.9271 -20.0824 0
+18 111.037 31.8958 -6.6942 -6.837
+19 116.94 37.5749 -8.6676 0
+20 117.961 37.4964 -8.1837 0
+21 114.302 42.6589 -10.5464 -9.3243
+22 108.937 57.401 2.9374 0
+23 107.734 40.6099 -28.8121 0
+24 116.926 39.4193 -10.9945 -8.7733
+25 118.986 98.6813 -22.2485 10.3673
+26 125.542 92.572 -34.48 -11.1871
+27 0 0 0 0
+28 111.91 60.7147 -13.3366 -13.0785
+29 103.7 49.84 -11.6 -8
+
+BondBond Coeffs
+
+1 5.3316 1.101 1.101
+2 3.3872 1.53 1.101
+3 0 1.53 1.53
+4 0 1.5202 1.3649
+5 0 1.3649 1.202
+6 46.0685 1.5202 1.202
+7 0 1.3649 0.965
+8 5.4199 1.53 1.5202
+9 0.7115 1.5202 1.101
+10 3.3872 1.53 1.101
+11 0 1.53 1.53
+12 5.3316 1.101 1.101
+13 4.6217 1.53 1.457
+14 12.426 1.457 1.101
+15 -6.4168 1.457 1.006
+16 -1.8749 1.006 1.006
+17 -3.471 1.452 1.01
+18 12.1186 1.452 1.416
+19 -0.5655 1.01 1.01
+20 -4.3126 1.01 1.416
+21 3.5446 1.452 1.53
+22 15.2994 1.452 1.101
+23 0.7115 1.101 1.5202
+24 0 1.416 1.5202
+25 0 1.202 1.3649
+26 138.495 1.416 1.202
+27 0 1.416 1.3649
+28 4.6217 1.457 1.53
+29 -9.5 0.97 0.97
+
+BondAngle Coeffs
+
+1 18.103 18.103 1.101 1.101
+2 20.754 11.421 1.53 1.101
+3 8.016 8.016 1.53 1.53
+4 0 0 1.5202 1.3649
+5 0 0 1.3649 1.202
+6 34.9982 37.1298 1.5202 1.202
+7 0 0 1.3649 0.965
+8 18.1678 15.8758 1.53 1.5202
+9 12.4632 9.1765 1.5202 1.101
+10 20.754 11.421 1.53 1.101
+11 8.016 8.016 1.53 1.53
+12 18.103 18.103 1.101 1.101
+13 6.0876 16.5702 1.53 1.457
+14 42.4332 13.4582 1.457 1.101
+15 31.8096 20.5799 1.457 1.006
+16 28.0322 28.0322 1.006 1.006
+17 11.8828 5.9339 1.452 1.01
+18 3.7812 14.8633 1.452 1.416
+19 19.8125 19.8125 1.01 1.01
+20 10.8422 29.5743 1.01 1.416
+21 4.6031 -5.479 1.452 1.53
+22 34.8907 10.6917 1.452 1.101
+23 9.1765 12.4632 1.101 1.5202
+24 0 0 1.416 1.5202
+25 0 0 1.202 1.3649
+26 62.7124 52.4045 1.416 1.202
+27 0 0 1.416 1.3649
+28 16.5702 6.0876 1.457 1.53
+29 22.35 22.35 0.97 0.97
+
+Dihedral Coeffs # class2
+
+1 -0.0228 0 0.028 0 -0.1863 0
+2 -0.1432 0 0.0617 0 -0.1083 0
+3 0.0972 0 0.0722 0 -0.2581 0
+4 0 0 0.0316 0 -0.1681 0
+5 0 0 0.0514 0 -0.143 0
+6 0 0 0 0 0 0
+7 -2.7332 0 2.9646 0 -0.0155 0
+8 0 0 0 0 0 0
+9 0 0 0 0 0 0
+10 0.0442 0 0.0292 0 0.0562 0
+11 -0.1804 0 0.0012 0 0.0371 0
+12 -0.2428 0 0.4065 0 -0.3079 0
+13 -0.1432 0 0.0617 0 -0.1083 0
+14 0.1764 0 0.1766 0 -0.5206 0
+15 0 0 0.0316 0 -0.1681 0
+16 0 0 0.0514 0 -0.143 0
+17 -1.1506 0 -0.6344 0 -0.1845 0
+18 -0.5187 0 -0.4837 0 -0.1692 0
+19 -0.0483 0 -0.0077 0 -0.0014 0
+20 -0.0148 0 -0.0791 0 -0.0148 0
+21 0.0143 0 -0.0132 0 0.0091 0
+22 0.0219 0 -0.026 0 0.0714 0
+23 -0.7532 0 2.7392 0 0.0907 0
+24 0.8297 0 3.7234 0 -0.0495 0
+25 0 0 0 0 0 0
+26 0 0 0 0 0 0
+27 -1.6938 0 2.7386 0 -0.336 0
+28 0 0 0 0 0 0
+29 0.0972 0 0.0722 0 -0.2581 0
+30 -0.0228 0 0.028 0 -0.1863 0
+31 0.1693 0 -0.009 0 -0.0687 0
+32 0.1693 0 -0.009 0 -0.0687 0
+33 0 0 0 0 0 0
+34 -1.1506 0 -0.6344 0 -0.1845 0
+35 -0.5187 0 -0.4837 0 -0.1692 0
+36 0.1764 0 0.1766 0 -0.5206 0
+
+AngleAngleTorsion Coeffs
+
+1 -5.3624 108.53 110.77
+2 -12.564 110.77 110.77
+3 -0.3801 112.67 108.53
+4 -16.164 112.67 110.77
+5 -22.045 112.67 112.67
+6 0 0 111.254
+7 0 118.985 111.254
+8 0 108.53 0
+9 0 107.734 0
+10 -8.019 108.53 123.145
+11 -15.3496 107.734 123.145
+12 -15.7572 111.91 110.77
+13 -12.564 110.77 110.77
+14 -27.3953 112.67 111.91
+15 -16.164 112.67 110.77
+16 -22.045 112.67 112.67
+17 -7.5499 111.91 110.954
+18 -10.4258 110.62 110.954
+19 -4.6337 113.868 114.302
+20 -6.659 113.868 108.937
+21 -7.4314 111.037 114.302
+22 -8.1335 111.037 108.937
+23 -6.5335 111.037 116.926
+24 -15.5547 111.037 125.542
+25 0 111.037 0
+26 -1.3234 117.961 116.926
+27 -7.3186 117.961 125.542
+28 0 117.961 0
+29 -1.0631 114.302 112.67
+30 -12.7974 114.302 110.77
+31 -5.4514 108.53 116.926
+32 -12.2417 107.734 116.926
+33 0 0 111.254
+34 -7.5499 110.954 111.91
+35 -10.4258 110.954 110.62
+36 -27.3953 111.91 112.67
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+EndBondTorsion Coeffs
+
+1 -0.0204 0.3628 -0.4426 -0.0097 -0.0315 -0.0755 1.5202 1.101
+2 0.213 0.312 0.0777 0.213 0.312 0.0777 1.101 1.101
+3 0.0062 -0.0002 0.0036 0.0055 0.006 -0.0009 1.53 1.5202
+4 0.2486 0.2422 -0.0925 0.0814 0.0591 0.2219 1.53 1.101
+5 -0.0732 0 0 -0.0732 0 0 1.53 1.53
+6 0 0 0 0 0 0 1.5202 0.965
+7 0 0 0 0 0 0 1.202 0.965
+8 0 0 0 0 0 0 1.53 1.3649
+9 0 0 0 0 0 0 1.101 1.3649
+10 0.2654 0.0503 0.1046 -0.281 0.0816 -0.1522 1.53 1.202
+11 1.2143 0.2831 0.3916 -0.2298 0.0354 0.3853 1.101 1.202
+12 0.1022 0.209 0.6433 0.196 0.7056 0.112 1.457 1.101
+13 0.213 0.312 0.0777 0.213 0.312 0.0777 1.101 1.101
+14 0.1032 0.5896 -0.4836 0.0579 -0.0043 -0.1906 1.53 1.457
+15 0.2486 0.2422 -0.0925 0.0814 0.0591 0.2219 1.53 1.101
+16 -0.0732 0 0 -0.0732 0 0 1.53 1.53
+17 -0.9466 0.9356 -0.5542 0.057 0.0625 0.4112 1.53 1.006
+18 -1.1685 0.9266 -0.0993 0.085 0.3061 0.2104 1.101 1.006
+19 -0.0992 -0.0727 -0.4139 0.132 0.0015 0.1324 1.01 1.53
+20 -0.4894 0.1644 0.3105 -0.8983 0.2826 0.0881 1.01 1.101
+21 -0.1245 -0.9369 0.7781 -0.2033 0.0035 0.056 1.416 1.53
+22 0.2292 1.1732 -0.058 -0.3667 0.8197 0.1335 1.416 1.101
+23 0.2299 -0.1141 -0.1424 0.0933 -0.4631 0.2883 1.452 1.5202
+24 0.1598 0.7253 -0.1007 0.1226 -2.1326 0.5581 1.452 1.202
+25 0 0 0 0 0 0 1.452 1.3649
+26 0.6413 0.1676 0.144 -0.6979 0.5619 0.4212 1.01 1.5202
+27 0.1214 0.1936 0.0816 -0.7604 -2.6431 1.2467 1.01 1.202
+28 0 0 0 0 0 0 1.01 1.3649
+29 -0.0797 -0.0406 0.0255 0.0742 0.0105 0.0518 1.452 1.53
+30 0.3022 0.2513 0.4641 -0.0601 -0.3763 -0.1876 1.452 1.101
+31 -0.2631 -0.0076 -0.1145 -0.2751 -0.3058 -0.1767 1.53 1.416
+32 -0.0268 0.7836 0.0035 0.3552 -0.2685 0.5834 1.101 1.416
+33 0 0 0 0 0 0 1.416 0.965
+34 0.057 0.0625 0.4112 -0.9466 0.9356 -0.5542 1.006 1.53
+35 0.085 0.3061 0.2104 -1.1685 0.9266 -0.0993 1.006 1.101
+36 0.0579 -0.0043 -0.1906 0.1032 0.5896 -0.4836 1.457 1.53
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+1 -3.5039 1.2458 -0.761 1.53
+2 -14.261 -0.5322 -0.4864 1.53
+3 -1.5945 0.2267 -0.6911 1.53
+4 -14.879 -3.6581 -0.3138 1.53
+5 -17.787 -7.1877 0 1.53
+6 0 0 0 1.3649
+7 0 0 0 1.3649
+8 0 0 0 1.5202
+9 0 0 0 1.5202
+10 0.3388 -0.1096 0.1219 1.5202
+11 0.2359 0.9139 0.9594 1.5202
+12 -10.4959 -0.7647 -0.0545 1.53
+13 -14.261 -0.5322 -0.4864 1.53
+14 -15.4174 -7.3055 -1.0749 1.53
+15 -14.879 -3.6581 -0.3138 1.53
+16 -17.787 -7.1877 0 1.53
+17 -2.2208 0.5479 -0.3527 1.457
+18 -3.4611 1.6996 -0.6007 1.457
+19 -3.5406 -3.3866 0.0352 1.452
+20 -1.1752 2.8058 0.8083 1.452
+21 -3.9501 -0.4002 -0.6798 1.452
+22 -0.6899 -2.2646 1.1579 1.452
+23 0 0 0 1.416
+24 -8.8301 14.3079 -1.7716 1.416
+25 0 0 0 1.416
+26 0 0 0 1.416
+27 -0.9084 6.1447 -0.4852 1.416
+28 0 0 0 1.416
+29 -4.2324 -3.3023 -1.3244 1.53
+30 -4.1028 -0.5941 -0.047 1.53
+31 0 0 0 1.5202
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+35 -3.4611 1.6996 -0.6007 1.457
+36 -15.4174 -7.3055 -1.0749 1.53
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+BondBond13 Coeffs
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+1 0 1.5202 1.101
+2 0 1.101 1.101
+3 0 1.53 1.5202
+4 0 1.53 1.101
+5 0 1.53 1.53
+6 0 1.5202 0.965
+7 0 1.202 0.965
+8 0 1.53 1.3649
+9 0 1.101 1.3649
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+11 0 1.101 1.202
+12 0 1.457 1.101
+13 0 1.101 1.101
+14 0 1.53 1.457
+15 0 1.53 1.101
+16 0 1.53 1.53
+17 0 1.53 1.006
+18 0 1.101 1.006
+19 0 1.01 1.53
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+21 0 1.416 1.53
+22 0 1.416 1.101
+23 0 1.452 1.5202
+24 0 1.452 1.202
+25 0 1.452 1.3649
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+28 0 1.01 1.3649
+29 0 1.452 1.53
+30 0 1.452 1.101
+31 0 1.53 1.416
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+33 0 1.416 0.965
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+AngleTorsion Coeffs
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+3 -0.2607 0.3203 -0.2283 0.0515 -0.0674 -0.0474 112.67 108.53
+4 -0.2454 0 -0.1136 0.3113 0.4516 -0.1988 112.67 110.77
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+6 0 0 0 0 0 0 0 111.254
+7 0 0 0 0 0 0 118.985 111.254
+8 0 0 0 0 0 0 108.53 0
+9 0 0 0 0 0 0 107.734 0
+10 0.0885 -1.3703 -0.5452 0.675 0.5965 0.6725 108.53 123.145
+11 9.1299 -0.4847 0.3582 -1.4946 0.7308 -0.2083 107.734 123.145
+12 -1.1075 0.282 0.8318 0.5111 1.6328 -1.0155 111.91 110.77
+13 -0.8085 0.5569 -0.2466 -0.8085 0.5569 -0.2466 110.77 110.77
+14 -1.9225 -1.345 0.221 2.0125 0.944 -2.7612 112.67 111.91
+15 -0.2454 0 -0.1136 0.3113 0.4516 -0.1988 112.67 110.77
+16 0.3886 -0.3139 0.1389 0.3886 -0.3139 0.1389 112.67 112.67
+17 -3.343 4.4558 -0.0346 0.2873 -0.8072 -0.096 111.91 110.954
+18 -3.9582 2.0063 0.3213 -0.4294 -0.4442 -0.6141 110.62 110.954
+19 -0.5807 0.2041 -0.1384 -2.8967 2.7084 -0.0375 113.868 114.302
+20 -0.3868 0.2041 0.0445 -3.7022 1.3876 0.2393 113.868 108.937
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+23 5.916 1.7856 0.4052 4.2133 2.9302 3.2903 111.037 116.926
+24 7.4427 2.1505 -0.2206 4.4466 4.0317 1.7129 111.037 125.542
+25 0 0 0 0 0 0 111.037 0
+26 1.9306 0.2105 0.0557 -2.2134 1.2909 0.9726 117.961 116.926
+27 2.3848 0.703 0.1399 -2.6238 0.3606 0.5474 117.961 125.542
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+29 0.2039 0.1602 -0.7946 -0.5501 -1.6982 0.2485 114.302 112.67
+30 -1.982 0.2325 -0.3928 -1.2469 1.6933 -1.2081 114.302 110.77
+31 2.1802 -0.0335 -1.3816 2.1221 0.5032 -0.0767 108.53 116.926
+32 7.095 0.0075 0.691 2.0013 0.5068 0.8406 107.734 116.926
+33 0 0 0 0 0 0 0 111.254
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+36 2.0125 0.944 -2.7612 -1.9225 -1.345 0.221 111.91 112.67
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+Improper Coeffs # class2
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+1 0 0
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+3 -1.3199 -1.3199 0.1184 112.67 110.77 110.77
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+5 -3.3867 -3.4976 -3.3867 107.734 107.66 107.734
+6 0 0 0 110.954 107.067 110.954
+7 0.2738 -0.4825 0.2738 110.77 107.66 110.77
+8 -1.3199 -1.3199 0.1184 112.67 110.77 110.77
+9 -2.5301 0.5381 2.4286 111.91 110.62 110.77
+10 2.4321 -3.5496 2.4321 110.62 107.66 110.62
+11 0 0 0 123.145 118.985 0
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+13 0 0 0 116.926 123.145 125.542
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+70 10 26 42 43
+71 10 26 42 44
+72 10 39 42 43
+73 10 39 42 44
+74 12 43 42 44
+
+Dihedrals
+
+1 2 5 1 7 14
+2 2 5 1 7 15
+3 2 4 1 7 14
+4 2 4 1 7 15
+5 3 8 1 7 2
+6 4 8 1 7 14
+7 4 8 1 7 15
+8 2 5 1 8 16
+9 2 5 1 8 17
+10 2 4 1 8 16
+11 2 4 1 8 17
+12 5 7 1 8 9
+13 4 7 1 8 16
+14 4 7 1 8 17
+15 6 7 2 3 6
+16 7 11 2 3 6
+17 1 2 7 1 5
+18 1 2 7 1 4
+19 8 1 7 2 3
+20 9 14 7 2 3
+21 9 15 7 2 3
+22 10 1 7 2 11
+23 11 14 7 2 11
+24 11 15 7 2 11
+25 4 9 8 1 5
+26 4 9 8 1 4
+27 3 1 8 9 10
+28 4 1 8 9 18
+29 4 1 8 9 19
+30 2 16 8 9 18
+31 2 16 8 9 19
+32 2 17 8 9 18
+33 2 17 8 9 19
+34 1 10 9 8 16
+35 1 10 9 8 17
+36 10 8 9 10 12
+37 8 8 9 10 13
+38 11 18 9 10 12
+39 9 18 9 10 13
+40 11 19 9 10 12
+41 9 19 9 10 13
+42 6 9 10 13 20
+43 7 12 10 13 20
+44 13 27 21 22 29
+45 13 27 21 22 30
+46 13 28 21 22 29
+47 13 28 21 22 30
+48 14 39 21 22 23
+49 15 39 21 22 29
+50 15 39 21 22 30
+51 15 22 21 39 40
+52 15 22 21 39 41
+53 16 22 21 39 42
+54 13 27 21 39 40
+55 13 27 21 39 41
+56 13 28 21 39 40
+57 13 28 21 39 41
+58 12 23 22 21 27
+59 12 23 22 21 28
+60 17 21 22 23 31
+61 17 21 22 23 32
+62 18 29 22 23 31
+63 18 29 22 23 32
+64 18 30 22 23 31
+65 18 30 22 23 32
+66 17 26 25 24 33
+67 18 35 25 24 33
+68 18 36 25 24 33
+69 17 26 25 24 34
+70 18 35 25 24 34
+71 18 36 25 24 34
+72 12 24 25 26 37
+73 12 24 25 26 38
+74 13 35 25 26 37
+75 13 35 25 26 38
+76 13 36 25 26 37
+77 13 36 25 26 38
+78 14 42 26 25 24
+79 15 42 26 25 35
+80 15 42 26 25 36
+81 16 25 26 42 39
+82 15 25 26 42 43
+83 15 25 26 42 44
+84 13 37 26 42 43
+85 13 37 26 42 44
+86 13 38 26 42 43
+87 13 38 26 42 44
+88 15 42 39 21 27
+89 15 42 39 21 28
+90 16 21 39 42 26
+91 15 21 39 42 43
+92 15 21 39 42 44
+93 13 40 39 42 43
+94 13 40 39 42 44
+95 13 41 39 42 43
+96 13 41 39 42 44
+97 15 39 42 26 37
+98 15 39 42 26 38
+99 15 26 42 39 40
+100 15 26 42 39 41
+
+Impropers
+
+1 2 7 1 4 5
+2 2 8 1 4 5
+3 3 7 1 8 5
+4 3 7 1 8 4
+5 1 7 2 3 11
+6 4 1 7 2 14
+7 4 1 7 2 15
+8 2 1 7 14 15
+9 5 2 7 14 15
+10 3 1 8 9 16
+11 3 1 8 9 17
+12 2 1 8 16 17
+13 2 9 8 16 17
+14 4 8 9 10 18
+15 4 8 9 10 19
+16 2 8 9 18 19
+17 5 10 9 18 19
+18 1 9 10 13 12
+19 7 22 21 27 28
+20 8 22 21 39 27
+21 8 22 21 39 28
+22 7 39 21 28 27
+23 9 21 22 23 29
+24 9 21 22 23 30
+25 7 21 22 29 30
+26 10 23 22 29 30
+27 6 22 23 31 32
+28 6 25 24 33 34
+29 9 26 25 24 35
+30 9 26 25 24 36
+31 10 24 25 35 36
+32 7 26 25 35 36
+33 7 25 26 37 38
+34 8 25 26 42 37
+35 8 25 26 42 38
+36 7 42 26 38 37
+37 7 21 39 40 41
+38 8 21 39 42 40
+39 8 21 39 42 41
+40 7 42 39 41 40
+41 8 26 42 39 43
+42 8 26 42 39 44
+43 7 26 42 43 44
+44 7 39 42 43 44

examples/gcmc/in.gcmc.co2

@@ -59,7 +59,9 @@ timestep        1.0
 # rigid constraints with thermostat 
 
 fix             myrigidnvt co2 rigid/nvt/small molecule temp ${temp} ${temp} 100 mol co2mol
-fix_modify	myrigidnvt dynamic/dof no
+
+# dynamically update  fix rigid/nvt/small temperature ndof
+fix_modify	myrigidnvt dynamic/dof yes
 
 # gcmc
 
@@ -82,7 +84,10 @@ variable	tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1)
 variable	iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1)
 variable	dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1)
 variable	racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1)
+
+# dynamically update default temperature ndof
 compute_modify  thermo_temp dynamic/dof yes
+
 thermo_style    custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc v_nC v_nO
 thermo          1000
 

examples/gcmc/in.gcmc.h2o

@@ -30,8 +30,6 @@ create_box      2 box                       &
                 extra/angle/per/atom 1      &
                 extra/special/per/atom 2
 
-# we can load multiple molecule templates, but don't have to use them all
-molecule        co2mol CO2.txt
 molecule        h2omol H2O.txt
 create_atoms   	0 box mol h2omol 464563 units box
                         
@@ -58,18 +56,24 @@ timestep        1.0
 
 minimize 0.0 0.0 100 1000
 reset_timestep 0
+
 # rigid constraints with thermostat 
 
-fix             mynvt all nvt temp ${temp} ${temp} 100
-fix             wshake  all shake 0.0001 50 0 b 1 a 1 mol h2omol
-# gcmc
+fix             mynvt h2o nvt temp ${temp} ${temp} 100
+fix             wshake h2o shake 0.0001 50 0 b 1 a 1 mol h2omol
 
+# important to make temperature dofs dynamic
 
+compute_modify  thermo_temp dynamic/dof yes
+compute_modify  mynvt_temp dynamic/dof yes
 
 run 1000
+reset_timestep 0
+
+# gcmc
 
 variable        tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans)
-fix             mygcmc all gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol &
+fix             mygcmc h2o gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol &
                 h2omol tfac_insert ${tfac} group h2o shake wshake
 
 # atom counts
@@ -87,7 +91,6 @@ variable	tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1)
 variable	iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1)
 variable	dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1)
 variable	racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1)
-compute_modify  thermo_temp dynamic/dof yes
 thermo_style    custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc v_nO v_nH
 thermo          1000
 

examples/gcmc/log.23Oct17.gcmc.co2.g++.4

@@ -1,192 +0,0 @@
-LAMMPS (23 Oct 2017)
-  using 1 OpenMP thread(s) per MPI task
-# GCMC for CO2 molecular fluid, rigid/small/nvt dynamics
-# Rigid CO2 TraPPE model
-# [Potoff and J.I. Siepmann, Vapor-liquid equilibria of
-# mixtures containing alkanes, carbon dioxide and
-# nitrogen AIChE J., 47,1676-1682 (2001)].
-
-# variables available on command line
-
-variable        mu index -8.1
-variable	disp index 0.5
-variable        temp index 338.0
-variable        lbox index 10.0
-variable        spacing index 5.0
-
-# global model settings
-
-units           real
-atom_style      full
-boundary        p p p
-pair_style      lj/cut/coul/long  14
-pair_modify     mix arithmetic tail yes
-kspace_style    ewald 0.0001
-bond_style      harmonic
-angle_style     harmonic
-
-# box, start molecules on simple cubic lattice
-
-lattice 	sc ${spacing}
-lattice 	sc 5.0
-Lattice spacing in x,y,z = 5 5 5
-region          box block 0 ${lbox} 0 ${lbox} 0 ${lbox} units box
-region          box block 0 10.0 0 ${lbox} 0 ${lbox} units box
-region          box block 0 10.0 0 10.0 0 ${lbox} units box
-region          box block 0 10.0 0 10.0 0 10.0 units box
-create_box      2 box                                       bond/types 1                                angle/types 1                               extra/bond/per/atom 2                       extra/angle/per/atom 1                      extra/special/per/atom 2
-Created orthogonal box = (0 0 0) to (10 10 10)
-  1 by 2 by 2 MPI processor grid
-molecule        co2mol CO2.txt
-Read molecule co2mol:
-  3 atoms with 2 types
-  2 bonds with 1 types
-  1 angles with 1 types
-  0 dihedrals with 0 types
-  0 impropers with 0 types
-create_atoms   	0 box mol co2mol 464563 units box
-Created 24 atoms
-  Time spent = 0.00261331 secs
-
-# rigid CO2 TraPPE model
-
-pair_coeff      1   1  0.053649   2.8
-pair_coeff      2   2  0.156973   3.05
-bond_coeff      1       0       1.16
-angle_coeff     1       0       180
-
-# masses
-
-mass 1 12.0107
-mass 2 15.9994
-
-# MD settings
-
-group           co2 type 1 2
-24 atoms in group co2
-neighbor        2.0 bin
-neigh_modify    every 1 delay 10 check yes
-velocity       	all create ${temp} 54654
-velocity       	all create 338.0 54654
-timestep        1.0
-
-# rigid constraints with thermostat
-
-fix             myrigidnvt all rigid/nvt/small molecule temp ${temp} ${temp} 100 mol co2mol
-fix             myrigidnvt all rigid/nvt/small molecule temp 338.0 ${temp} 100 mol co2mol
-fix             myrigidnvt all rigid/nvt/small molecule temp 338.0 338.0 100 mol co2mol
-8 rigid bodies with 24 atoms
-  1.16 = max distance from body owner to body atom
-fix_modify	myrigidnvt dynamic/dof no
-
-# gcmc
-
-variable        tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans)
-fix             mygcmc all gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol                 co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
-fix             mygcmc all gcmc 100 100 0 0 54341 338.0 ${mu} ${disp} mol                 co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
-fix             mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol                 co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
-fix             mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol                 co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
-fix             mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol                 co2mol tfac_insert 1.66666666666667 group co2 rigid myrigidnvt
-
-# atom counts
-
-variable 	carbon atom "type==1"
-variable        oxygen atom "type==2"
-group 		carbon dynamic all var carbon
-dynamic group carbon defined
-group 	        oxygen dynamic all var oxygen
-dynamic group oxygen defined
-variable        nC equal count(carbon)
-variable        nO equal count(oxygen)
-
-# output
-
-variable	tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1)
-variable	iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1)
-variable	dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1)
-variable	racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1)
-compute_modify  thermo_temp dynamic/dof yes
-thermo_style    custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc v_nC v_nO
-thermo          1000
-
-# run
-
-run             20000
-Ewald initialization ...
-WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
-  G vector (1/distance) = 0.164636
-  estimated absolute RMS force accuracy = 0.0332064
-  estimated relative force accuracy = 0.0001
-  KSpace vectors: actual max1d max3d = 16 2 62
-                  kxmax kymax kzmax  = 2 2 2
-WARNING: Fix gcmc using full_energy option (../fix_gcmc.cpp:445)
-0 atoms in group FixGCMC:gcmc_exclusion_group:mygcmc
-0 atoms in group FixGCMC:rotation_gas_atoms:mygcmc
-WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (../neighbor.cpp:472)
-Neighbor list info ...
-  update every 1 steps, delay 10 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 16
-  ghost atom cutoff = 16
-  binsize = 8, bins = 2 2 2
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair lj/cut/coul/long, perpetual
-      attributes: half, newton on
-      pair build: half/bin/newton
-      stencil: half/bin/3d/newton
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 15.41 | 15.41 | 15.41 Mbytes
-Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_racc v_nC v_nO 
-       0    386.52184    23582.465   -3.2433417    14.209828    0.5846359       24            0            0            0            0            8           16 
-WARNING: Using kspace solver on system with no charge (../kspace.cpp:289)
-    1000    335.66829   -3.7743052   -4.6268612    7.3374649   0.36539744       15   0.20601899   0.20787963            0            0            5           10 
-    2000    459.73529    238.91592  -0.42937831    5.4815343   0.21923846        9   0.30392058   0.30105616            0            0            3            6 
-    3000    255.47773   -479.67802   -36.850434    15.738299   0.95003334       39   0.22220744    0.2197582            0            0           13           26 
-    4000    182.70803   -1059.2262   -43.044833    12.163134    1.0231128       42   0.16781689   0.16716177            0            0           14           28 
-    5000    234.00907   -1821.0444    -46.04795    15.578317    1.0231128       42   0.13498091   0.13704201            0            0           14           28 
-    6000    163.42759   -774.67294   -49.686261    11.691518    1.0961923       45   0.11401677   0.11296973            0            0           15           30 
-    7000    171.64616   -355.23516   -49.323434     12.27947    1.0961923       45  0.098302308  0.098552065            0            0           15           30 
-    8000    251.29791   -905.47863   -37.841209    15.480807   0.95003334       39  0.086856972   0.08638658            0            0           13           26 
-    9000    143.69498   -849.95393   -49.073188    10.279858    1.0961923       45  0.078261061  0.077955243            0            0           15           30 
-   10000    239.35727   -1158.1879   -43.562047    15.934355    1.0231128       42  0.070789792  0.070807529            0            0           14           28 
-   11000    169.51213   -1574.7885   -51.125228    12.126803    1.0961923       45  0.065008734   0.06498871            0            0           15           30 
-   12000    181.39739    160.11631   -46.850937    12.977068    1.0961923       45  0.059648717  0.059514803            0            0           15           30 
-   13000    164.14601   -1107.7629   -50.726722    11.742914    1.0961923       45  0.055207333  0.055097701            0            0           15           30 
-   14000    287.26285    418.51463   -41.664766    19.123497    1.0231128       42  0.051346789  0.051222285            0            0           14           28 
-   15000    256.94593   -532.36615   -41.651618    17.105257    1.0231128       42  0.047870301  0.047861685            0            0           14           28 
-   16000    166.92132    151.15933   -39.957018     11.11219    1.0231128       42  0.045205599  0.045042211            0            0           14           28 
-   17000    163.22452   -1299.8119   -42.677558    10.866089    1.0231128       42  0.043122086  0.042993687            0            0           14           28 
-   18000    158.01154    475.77329   -48.803162    11.304057    1.0961923       45  0.041016683  0.040647229            0            0           15           30 
-   19000    138.49297   -1585.1508   -47.517099    9.9077098    1.0961923       45  0.038929287  0.038436764            0            0           15           30 
-   20000    173.84439   -1362.6301   -53.002743    12.436731    1.0961923       45  0.036973919  0.036523816            0            0           15           30 
-Loop time of 32.4481 on 4 procs for 20000 steps with 45 atoms
-
-Performance: 53.254 ns/day, 0.451 hours/ns, 616.369 timesteps/s
-98.4% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 1.1687     | 1.6702     | 2.1864     |  30.8 |  5.15
-Bond    | 0.018828   | 0.020035   | 0.020975   |   0.6 |  0.06
-Kspace  | 0.57506    | 1.0931     | 1.5898     |  37.7 |  3.37
-Neigh   | 0.068863   | 0.069524   | 0.070128   |   0.2 |  0.21
-Comm    | 2.0735     | 2.0865     | 2.0979     |   0.7 |  6.43
-Output  | 0.0025017  | 0.0025966  | 0.0027781  |   0.2 |  0.01
-Modify  | 27.335     | 27.344     | 27.363     |   0.2 | 84.27
-Other   |            | 0.1621     |            |       |  0.50
-
-Nlocal:    11.25 ave 14 max 8 min
-Histogram: 1 0 0 0 0 1 1 0 0 1
-Nghost:    2639.75 ave 2656 max 2617 min
-Histogram: 1 0 0 0 0 0 2 0 0 1
-Neighs:    4320 ave 5824 max 2201 min
-Histogram: 1 0 0 0 0 0 1 1 0 1
-
-Total # of neighbors = 17280
-Ave neighs/atom = 384
-Ave special neighs/atom = 2
-Neighbor list builds = 20394
-Dangerous builds = 0
-
-Total wall time: 0:00:32

examples/gcmc/log.23Oct17.gcmc.h2o.g++.4

@@ -1,293 +0,0 @@
-LAMMPS (23 Oct 2017)
-  using 1 OpenMP thread(s) per MPI task
-# fix gcmc example with fix shake
-
-# variables available on command line
-
-variable        mu index -8.1
-variable	disp index 0.5
-variable        temp index 338.0
-variable        lbox index 10.0
-variable        spacing index 5.0
-
-# global model settings
-
-units           real
-atom_style      full
-boundary        p p p
-pair_style      lj/cut/coul/long  14
-pair_modify     mix arithmetic tail yes
-kspace_style    ewald 0.0001
-bond_style      harmonic
-angle_style     harmonic
-
-# box, start molecules on simple cubic lattice
-
-lattice 	sc ${spacing}
-lattice 	sc 5.0
-Lattice spacing in x,y,z = 5 5 5
-region          box block 0 ${lbox} 0 ${lbox} 0 ${lbox} units box
-region          box block 0 10.0 0 ${lbox} 0 ${lbox} units box
-region          box block 0 10.0 0 10.0 0 ${lbox} units box
-region          box block 0 10.0 0 10.0 0 10.0 units box
-create_box      2 box                                       bond/types 1                                angle/types 1                               extra/bond/per/atom 2                       extra/angle/per/atom 1                      extra/special/per/atom 2
-Created orthogonal box = (0 0 0) to (10 10 10)
-  1 by 2 by 2 MPI processor grid
-
-# we can load multiple molecule templates, but don't have to use them all
-molecule        co2mol CO2.txt
-Read molecule co2mol:
-  3 atoms with 2 types
-  2 bonds with 1 types
-  1 angles with 1 types
-  0 dihedrals with 0 types
-  0 impropers with 0 types
-molecule        h2omol H2O.txt
-Read molecule h2omol:
-  3 atoms with 2 types
-  2 bonds with 1 types
-  1 angles with 1 types
-  0 dihedrals with 0 types
-  0 impropers with 0 types
-create_atoms   	0 box mol h2omol 464563 units box
-Created 24 atoms
-  Time spent = 0.00174451 secs
-
-# rigid SPC/E water model
-
-pair_coeff      1 1 0.15535 3.166
-pair_coeff      * 2 0.0000 0.0000
-
-bond_coeff      1     1000       1.0
-angle_coeff     1      100       109.47
-
-# masses
-
-mass 1 15.9994
-mass 2 1.0
-
-# MD settings
-
-group           h2o type 1 2
-24 atoms in group h2o
-neighbor        2.0 bin
-neigh_modify    every 1 delay 1 check yes
-velocity       	all create ${temp} 54654
-velocity       	all create 338.0 54654
-timestep        1.0
-
-minimize 0.0 0.0 100 1000
-WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:168)
-Ewald initialization ...
-WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
-  G vector (1/distance) = 0.170448
-  estimated absolute RMS force accuracy = 0.0332064
-  estimated relative force accuracy = 0.0001
-  KSpace vectors: actual max1d max3d = 16 2 62
-                  kxmax kymax kzmax  = 2 2 2
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 16
-  ghost atom cutoff = 16
-  binsize = 8, bins = 2 2 2
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair lj/cut/coul/long, perpetual
-      attributes: half, newton on
-      pair build: half/bin/newton
-      stencil: half/bin/3d/newton
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 11.85 | 11.85 | 11.85 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0          338   -4.9610706 9.2628112e-06    18.211756    730.90791 
-     100          338   -15.742442   0.14954269     7.579918   -637.49568 
-Loop time of 0.0566185 on 4 procs for 100 steps with 24 atoms
-
-98.8% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-Minimization stats:
-  Stopping criterion = max iterations
-  Energy initial, next-to-last, final = 
-        -4.96106135393     -15.5388622715      -15.592899346
-  Force two-norm initial, final = 15.474 18.1478
-  Force max component initial, final = 5.80042 7.56514
-  Final line search alpha, max atom move = 0.00151131 0.0114333
-  Iterations, force evaluations = 100 328
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.0085177  | 0.016083   | 0.026787   |   5.3 | 28.41
-Bond    | 0.00022459 | 0.00031394 | 0.00037575 |   0.0 |  0.55
-Kspace  | 0.0049062  | 0.014122   | 0.02044    |   5.0 | 24.94
-Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.018515   | 0.02086    | 0.023246   |   1.2 | 36.84
-Output  | 2.4796e-05 | 2.6047e-05 | 2.9802e-05 |   0.0 |  0.05
-Modify  | 0          | 0          | 0          |   0.0 |  0.00
-Other   |            | 0.005213   |            |       |  9.21
-
-Nlocal:    6 ave 8 max 3 min
-Histogram: 1 0 0 0 1 0 0 0 0 2
-Nghost:    1722 ave 1725 max 1720 min
-Histogram: 2 0 0 0 0 0 1 0 0 1
-Neighs:    1256.75 ave 2101 max 667 min
-Histogram: 1 0 1 0 1 0 0 0 0 1
-
-Total # of neighbors = 5027
-Ave neighs/atom = 209.458
-Ave special neighs/atom = 2
-Neighbor list builds = 0
-Dangerous builds = 0
-reset_timestep 0
-# rigid constraints with thermostat
-
-fix             mynvt all nvt temp ${temp} ${temp} 100
-fix             mynvt all nvt temp 338.0 ${temp} 100
-fix             mynvt all nvt temp 338.0 338.0 100
-fix             wshake  all shake 0.0001 50 0 b 1 a 1 mol h2omol
-  0 = # of size 2 clusters
-  0 = # of size 3 clusters
-  0 = # of size 4 clusters
-  8 = # of frozen angles
-# gcmc
-
-
-
-run 1000
-Ewald initialization ...
-WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
-  G vector (1/distance) = 0.170448
-  estimated absolute RMS force accuracy = 0.0332064
-  estimated relative force accuracy = 0.0001
-  KSpace vectors: actual max1d max3d = 16 2 62
-                  kxmax kymax kzmax  = 2 2 2
-Per MPI rank memory allocation (min/avg/max) = 11.6 | 11.6 | 11.6 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0    518.26667   -15.742442            0    7.4303753    -613.0781 
-    1000    369.81793   -54.202686            0   -37.667331    294.98823 
-Loop time of 0.154891 on 4 procs for 1000 steps with 24 atoms
-
-Performance: 557.810 ns/day, 0.043 hours/ns, 6456.135 timesteps/s
-98.3% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.0154     | 0.028993   | 0.040525   |   5.5 | 18.72
-Bond    | 0.00016999 | 0.0001902  | 0.00023293 |   0.0 |  0.12
-Kspace  | 0.019093   | 0.028112   | 0.038976   |   4.3 | 18.15
-Neigh   | 0.0020263  | 0.0022184  | 0.002408   |   0.4 |  1.43
-Comm    | 0.04947    | 0.053627   | 0.058009   |   1.4 | 34.62
-Output  | 2.5749e-05 | 2.7537e-05 | 3.2187e-05 |   0.0 |  0.02
-Modify  | 0.035275   | 0.036815   | 0.038425   |   0.7 | 23.77
-Other   |            | 0.004909   |            |       |  3.17
-
-Nlocal:    6 ave 8 max 3 min
-Histogram: 1 0 0 0 0 0 1 0 1 1
-Nghost:    1331.5 ave 1369 max 1290 min
-Histogram: 1 0 0 0 0 2 0 0 0 1
-Neighs:    1259.75 ave 1642 max 428 min
-Histogram: 1 0 0 0 0 0 0 1 0 2
-
-Total # of neighbors = 5039
-Ave neighs/atom = 209.958
-Ave special neighs/atom = 2
-Neighbor list builds = 27
-Dangerous builds = 0
-
-variable        tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans)
-fix             mygcmc all gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol                 h2omol tfac_insert ${tfac} group h2o shake wshake
-fix             mygcmc all gcmc 100 100 0 0 54341 338.0 ${mu} ${disp} mol                 h2omol tfac_insert ${tfac} group h2o shake wshake
-fix             mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol                 h2omol tfac_insert ${tfac} group h2o shake wshake
-fix             mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol                 h2omol tfac_insert ${tfac} group h2o shake wshake
-fix             mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol                 h2omol tfac_insert 1.66666666666667 group h2o shake wshake
-
-# atom counts
-
-variable 	oxygen atom "type==1"
-variable 	hydrogen atom "type==2"
-group 	        oxygen dynamic all var oxygen
-dynamic group oxygen defined
-group 		hydrogen dynamic all var hydrogen
-dynamic group hydrogen defined
-variable        nO equal count(oxygen)
-variable        nH equal count(hydrogen)
-
-# output
-
-variable	tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1)
-variable	iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1)
-variable	dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1)
-variable	racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1)
-compute_modify  thermo_temp dynamic/dof yes
-thermo_style    custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc v_nO v_nH
-thermo          1000
-
-# run
-
-run             20000
-Ewald initialization ...
-WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
-  G vector (1/distance) = 0.170448
-  estimated absolute RMS force accuracy = 0.0332064
-  estimated relative force accuracy = 0.0001
-  KSpace vectors: actual max1d max3d = 16 2 62
-                  kxmax kymax kzmax  = 2 2 2
-WARNING: Fix gcmc using full_energy option (../fix_gcmc.cpp:445)
-0 atoms in group FixGCMC:gcmc_exclusion_group:mygcmc
-0 atoms in group FixGCMC:rotation_gas_atoms:mygcmc
-WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (../neighbor.cpp:472)
-Per MPI rank memory allocation (min/avg/max) = 11.6 | 11.6 | 11.6 Mbytes
-Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_racc v_nO v_nH 
-    1000    369.81793    295.32434   -54.202686    16.535355   0.23910963       24            0            0            0            0            8           16 
-    2000    84.544466   -2810.9047   -344.81664    14.364627   0.86677242       87  0.052198354 0.0099581757            0            0           29           58 
-    3000    75.188527    -3688.256   -425.02228    14.567977   0.98632724       99  0.030546787 0.0049111089            0            0           33           66 
-    4000    75.019396   -5669.3063   -427.69454    14.535207   0.98632724       99  0.019972039 0.0033375609            0            0           33           66 
-    5000    90.415371   -2141.7596   -434.65925    17.518218   0.98632724       99  0.014909796  0.002514964            0            0           33           66 
-    6000    78.212628   -943.75125   -428.80584    15.153904   0.98632724       99   0.01181521 0.0020316119            0            0           33           66 
-    7000    71.754139   -2028.5122    -435.2139    13.902555   0.98632724       99 0.0099466198 0.0016755471            0            0           33           66 
-    8000    84.446231   -1969.1657   -428.27313    16.361681   0.98632724       99 0.0084791272 0.0014442102            0            0           33           66 
-    9000    70.952348   -2476.9812   -446.33824    14.170197    1.0162159      102 0.0077150892 0.0012556189            0            0           34           68 
-   10000    71.418543   -1875.7083    -443.7214    14.263302    1.0162159      102 0.0068355714 0.0011197957            0            0           34           68 
-   11000    86.094994   -4508.7581   -444.82687    17.194399    1.0162159      102 0.0061494515 0.0010082475            0            0           34           68 
-   12000    81.906091   -1547.8105   -442.36719    16.357815    1.0162159      102 0.0055834729 0.00091775114            0            0           34           68 
-   13000    57.221548   -4607.6222   -448.30939     11.42796    1.0162159      102 0.0051230355 0.00084046326            0            0           34           68 
-   14000    61.288344   -2518.1779   -445.70636    12.240157    1.0162159      102 0.0047276997 0.00077602396            0            0           34           68 
-   15000    85.787669   -2407.7111    -443.3834    17.133022    1.0162159      102 0.0043983485 0.00071920715            0            0           34           68 
-   16000    74.845939   -3288.3403    -445.8247    14.947802    1.0162159      102 0.0042321884 0.00080654918            0            0           34           68 
-   17000    73.835431   -1926.9566   -445.67476    14.745989    1.0162159      102 0.0039751059 0.00075470749            0            0           34           68 
-   18000    72.634985    -3997.552    -447.2351    14.506243    1.0162159      102 0.0037395847 0.00071063946            0            0           34           68 
-   19000    96.776472   -714.44132   -453.65552    19.904587    1.0461046      105 0.0036487876 0.00066993446            0            0           35           70 
-   20000    75.470786    183.16972   -464.04688    15.522521    1.0461046      105 0.0034630763 0.00063350614            0            0           35           70 
-   21000    65.658309   -773.41266   -466.27068    13.504331    1.0461046      105  0.003289113 0.00060198052            0            0           35           70 
-Loop time of 84.4085 on 4 procs for 20000 steps with 105 atoms
-
-Performance: 20.472 ns/day, 1.172 hours/ns, 236.943 timesteps/s
-98.8% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 6.3571     | 9.7574     | 13.984     |  90.7 | 11.56
-Bond    | 0.026374   | 0.031321   | 0.035482   |   2.1 |  0.04
-Kspace  | 0.57402    | 4.7894     | 8.1754     | 129.0 |  5.67
-Neigh   | 0.34952    | 0.34987    | 0.35021    |   0.1 |  0.41
-Comm    | 2.4028     | 2.4228     | 2.4372     |   0.9 |  2.87
-Output  | 0.0012269  | 0.0012826  | 0.0014355  |   0.2 |  0.00
-Modify  | 66.819     | 66.828     | 66.837     |   0.1 | 79.17
-Other   |            | 0.2281     |            |       |  0.27
-
-Nlocal:    26.25 ave 31 max 22 min
-Histogram: 1 0 1 0 0 0 1 0 0 1
-Nghost:    6049.25 ave 6133 max 5962 min
-Histogram: 1 0 0 0 1 0 1 0 0 1
-Neighs:    23613 ave 35083 max 14025 min
-Histogram: 1 0 0 1 1 0 0 0 0 1
-
-Total # of neighbors = 94452
-Ave neighs/atom = 899.543
-Ave special neighs/atom = 2
-Neighbor list builds = 20428
-Dangerous builds = 0
-
-Total wall time: 0:01:24

examples/gcmc/log.30Mar18.gcmc.co2.g++.1

@@ -1,4 +1,4 @@
-LAMMPS (23 Oct 2017)
+LAMMPS (30 Mar 2018)
   using 1 OpenMP thread(s) per MPI task
 # GCMC for CO2 molecular fluid, rigid/small/nvt dynamics
 # Rigid CO2 TraPPE model
@@ -39,14 +39,14 @@ Created orthogonal box = (0 0 0) to (10 10 10)
   1 by 1 by 1 MPI processor grid
 molecule        co2mol CO2.txt
 Read molecule co2mol:
-  3 atoms with 2 types
-  2 bonds with 1 types
-  1 angles with 1 types
-  0 dihedrals with 0 types
-  0 impropers with 0 types
+  3 atoms with max type 2
+  2 bonds with max type 1
+  1 angles with max type 1
+  0 dihedrals with max type 0
+  0 impropers with max type 0
 create_atoms   	0 box mol co2mol 464563 units box
 Created 24 atoms
-  Time spent = 0.00196958 secs
+  Time spent = 0.00241756 secs
 
 # rigid CO2 TraPPE model
 
@@ -72,29 +72,31 @@ timestep        1.0
 
 # rigid constraints with thermostat
 
-fix             myrigidnvt all rigid/nvt/small molecule temp ${temp} ${temp} 100 mol co2mol
-fix             myrigidnvt all rigid/nvt/small molecule temp 338.0 ${temp} 100 mol co2mol
-fix             myrigidnvt all rigid/nvt/small molecule temp 338.0 338.0 100 mol co2mol
+fix             myrigidnvt co2 rigid/nvt/small molecule temp ${temp} ${temp} 100 mol co2mol
+fix             myrigidnvt co2 rigid/nvt/small molecule temp 338.0 ${temp} 100 mol co2mol
+fix             myrigidnvt co2 rigid/nvt/small molecule temp 338.0 338.0 100 mol co2mol
 8 rigid bodies with 24 atoms
   1.16 = max distance from body owner to body atom
-fix_modify	myrigidnvt dynamic/dof no
+
+# dynamically update  fix rigid/nvt/small temperature ndof
+fix_modify	myrigidnvt dynamic/dof yes
 
 # gcmc
 
 variable        tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans)
-fix             mygcmc all gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol                 co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
-fix             mygcmc all gcmc 100 100 0 0 54341 338.0 ${mu} ${disp} mol                 co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
-fix             mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol                 co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
-fix             mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol                 co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
-fix             mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol                 co2mol tfac_insert 1.66666666666667 group co2 rigid myrigidnvt
+fix             mygcmc co2 gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol                 co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
+fix             mygcmc co2 gcmc 100 100 0 0 54341 338.0 ${mu} ${disp} mol                 co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
+fix             mygcmc co2 gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol                 co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
+fix             mygcmc co2 gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol                 co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
+fix             mygcmc co2 gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol                 co2mol tfac_insert 1.66666666666667 group co2 rigid myrigidnvt
 
 # atom counts
 
 variable 	carbon atom "type==1"
 variable        oxygen atom "type==2"
-group 		carbon dynamic all var carbon
+group 		carbon dynamic co2 var carbon
 dynamic group carbon defined
-group 	        oxygen dynamic all var oxygen
+group 	        oxygen dynamic co2 var oxygen
 dynamic group oxygen defined
 variable        nC equal count(carbon)
 variable        nO equal count(oxygen)
@@ -105,7 +107,10 @@ variable	tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1)
 variable	iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1)
 variable	dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1)
 variable	racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1)
+
+# dynamically update default temperature ndof
 compute_modify  thermo_temp dynamic/dof yes
+
 thermo_style    custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc v_nC v_nO
 thermo          1000
 
@@ -113,13 +118,13 @@ thermo          1000
 
 run             20000
 Ewald initialization ...
-WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+  using 12-bit tables for long-range coulomb (../kspace.cpp:321)
   G vector (1/distance) = 0.164636
   estimated absolute RMS force accuracy = 0.0332064
   estimated relative force accuracy = 0.0001
   KSpace vectors: actual max1d max3d = 16 2 62
                   kxmax kymax kzmax  = 2 2 2
-WARNING: Fix gcmc using full_energy option (../fix_gcmc.cpp:445)
+WARNING: Fix gcmc using full_energy option (../fix_gcmc.cpp:485)
 0 atoms in group FixGCMC:gcmc_exclusion_group:mygcmc
 0 atoms in group FixGCMC:rotation_gas_atoms:mygcmc
 WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (../neighbor.cpp:472)
@@ -138,55 +143,54 @@ Neighbor list info ...
 Per MPI rank memory allocation (min/avg/max) = 15.62 | 15.62 | 15.62 Mbytes
 Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_racc v_nC v_nO 
        0    364.27579    4238.8631   -9.6809388    13.391989    0.5846359       24            0            0            0            0            8           16 
-WARNING: Using kspace solver on system with no charge (../kspace.cpp:289)
-    1000    420.43475    1722.4052   -9.6956123    15.456579    0.5846359       24   0.20879341   0.20713005            0            0            8           16 
-    2000    302.29516   -547.83641   -22.017674     14.11699   0.73079488       30    0.1742478    0.1678018            0            0           10           20 
-    3000     316.6934   -1080.2672   -8.2218891    10.069364   0.51155641       21   0.13544917   0.13720634            0            0            7           14 
-    4000    246.81618   -679.83642   -14.577244     10.29997   0.65771539       27    0.1568939   0.15860229            0            0            9           18 
-    5000    260.22849   -896.29914   -16.097593    10.859684   0.65771539       27   0.13138744   0.13547049            0            0            9           18 
-    6000    291.70796     -1521.99   -22.303136    13.622574   0.73079488       30   0.12615476   0.12717694            0            0           10           20 
-    7000    236.02638   -599.92186   -27.580831    13.367447   0.87695385       36     0.119703   0.12145398            0            0           12           24 
-    8000    321.45341    688.10577    -10.09204    11.817696    0.5846359       24   0.10917411   0.11032646            0            0            8           16 
-    9000    502.85382   -302.31056  -0.22330142   0.99927447  0.073079488        3    0.1254105   0.12905828            0            0            1            2 
-   10000    249.98239    -510.0091   -32.815145    15.399767   0.95003334       39    0.1274504   0.12875623            0            0           13           26 
-   11000    247.59424   -1129.0274   -25.320205    12.792544   0.80387436       33   0.11739076   0.11916784            0            0           11           22 
-   12000            0    -20.39554  -0.14872889           -0            0        0    0.1254933   0.12920375            0            0            0            0 
-   13000    1272.2738   -474.79484  -0.29450485    8.8489483   0.14615898        6   0.13767133   0.14112496            0            0            2            4 
-   14000    516.54246   -36.296516   -5.0012009    11.291243   0.36539744       15   0.15632744   0.15955377            0            0            5           10 
-   15000    307.09233    1951.9301   -14.820362    12.815375   0.65771539       27   0.15393544   0.15716192            0            0            9           18 
-   16000    198.31989   -559.48443   -30.459487    11.231925   0.87695385       36    0.1482565   0.15025652            0            0           12           24 
-   17000    246.99311    657.85683   -18.579206     11.53442   0.73079488       30   0.14143958   0.14375423            0            0           10           20 
-   18000    467.13468    167.03738   -1.0945268     5.569759   0.21923846        9   0.13847359   0.14098533            0            0            3            6 
-   19000    359.54027   -1413.5407   -12.156233    13.217895    0.5846359       24   0.15169146   0.15294205            0            0            8           16 
-   20000    227.79597   -1204.5652    -23.24144    10.637925   0.73079488       30   0.14917199   0.15022946            0            0           10           20 
-Loop time of 20.6928 on 1 procs for 20000 steps with 30 atoms
+    1000    330.05964    -376.0111   -13.936335    13.773831   0.65771539       27   0.21142067   0.21453147            0            0            9           18 
+    2000    293.79769    -321.3209   -19.049256    13.720163   0.73079488       30   0.25170944   0.25426294            0            0           10           20 
+    3000     348.9085    259.04079  -0.23347965    2.4267366   0.14615898        6   0.22016906   0.23200597            0            0            2            4 
+    4000    360.54577   -329.12072   -16.584234    15.046059   0.65771539       27   0.19173099   0.19785362            0            0            9           18 
+    5000    275.58628   -58.283006   -12.520856    11.500585   0.65771539       27   0.16490585   0.17329884            0            0            9           18 
+    6000    338.59574    364.93514   -19.866569    17.494353   0.80387436       33   0.17971759   0.18331589            0            0           11           22 
+    7000    286.11586   -1252.5069   -19.588667    13.361427   0.73079488       30   0.15729895   0.16220459            0            0           10           20 
+    8000    454.86786   -642.89382   -20.818357    21.242037   0.73079488       30   0.15500235   0.15802382            0            0           10           20 
+    9000    326.36695   -364.71382   -31.376162     18.48392   0.87695385       36   0.14203985   0.14510714            0            0           12           24 
+   10000    348.46961   -387.75245   -21.068466     18.00451   0.80387436       33   0.14000907   0.14343389            0            0           11           22 
+   11000    409.74257   -15.843895   -20.648252    21.170323   0.80387436       33   0.14689306   0.15117074            0            0           11           22 
+   12000    523.93502    1003.0729   -6.0563102    14.055757   0.43847693       18   0.15337575    0.1580166            0            0            6           12 
+   13000    278.14441    -717.1097   -2.3488496    4.6982087   0.29231795       12   0.15952356   0.16422306            0            0            4            8 
+   14000    367.89375    1239.0841   -11.203323    13.524997    0.5846359       24   0.17002439   0.17460294            0            0            8           16 
+   15000    197.05319   -471.14343   -9.3890758    6.2653668   0.51155641       21   0.17702612   0.18155802            0            0            7           14 
+   16000    138.17147   -935.93437   -2.3846783    2.3338898   0.29231795       12   0.17884346   0.18268758            0            0            4            8 
+   17000    245.61833    -166.1694   -5.0970057    5.3690384   0.36539744       15   0.18909252   0.19317817            0            0            5           10 
+   18000     232.0142     -175.732   -14.320198    9.6822635   0.65771539       27   0.18977089   0.19280537            0            0            9           18 
+   19000    362.01189    864.87258   -6.4515321    9.7117982   0.43847693       18   0.19207244   0.19488984            0            0            6           12 
+   20000    441.19548    186.19779   -18.147268    20.603546   0.73079488       30   0.19713351     0.199073            0            0           10           20 
+Loop time of 16.4949 on 1 procs for 20000 steps with 30 atoms
 
-Performance: 83.507 ns/day, 0.287 hours/ns, 966.519 timesteps/s
-99.2% CPU use with 1 MPI tasks x 1 OpenMP threads
+Performance: 104.760 ns/day, 0.229 hours/ns, 1212.498 timesteps/s
+99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 2.5462     | 2.5462     | 2.5462     |   0.0 | 12.30
-Bond    | 0.029783   | 0.029783   | 0.029783   |   0.0 |  0.14
-Kspace  | 0.26167    | 0.26167    | 0.26167    |   0.0 |  1.26
-Neigh   | 0.10705    | 0.10705    | 0.10705    |   0.0 |  0.52
-Comm    | 0.23409    | 0.23409    | 0.23409    |   0.0 |  1.13
-Output  | 0.0013416  | 0.0013416  | 0.0013416  |   0.0 |  0.01
-Modify  | 17.458     | 17.458     | 17.458     |   0.0 | 84.37
-Other   |            | 0.05433    |            |       |  0.26
+Pair    | 1.8955     | 1.8955     | 1.8955     |   0.0 | 11.49
+Bond    | 0.026564   | 0.026564   | 0.026564   |   0.0 |  0.16
+Kspace  | 0.21215    | 0.21215    | 0.21215    |   0.0 |  1.29
+Neigh   | 0.088336   | 0.088336   | 0.088336   |   0.0 |  0.54
+Comm    | 0.19828    | 0.19828    | 0.19828    |   0.0 |  1.20
+Output  | 0.001025   | 0.001025   | 0.001025   |   0.0 |  0.01
+Modify  | 14.024     | 14.024     | 14.024     |   0.0 | 85.02
+Other   |            | 0.0491     |            |       |  0.30
 
 Nlocal:    30 ave 30 max 30 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    2310 ave 2310 max 2310 min
+Nghost:    2094 ave 2094 max 2094 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    7736 ave 7736 max 7736 min
+Neighs:    7664 ave 7664 max 7664 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
 
-Total # of neighbors = 7736
-Ave neighs/atom = 257.867
+Total # of neighbors = 7664
+Ave neighs/atom = 255.467
 Ave special neighs/atom = 2
-Neighbor list builds = 20349
+Neighbor list builds = 20076
 Dangerous builds = 0
 
-Total wall time: 0:00:20
+Total wall time: 0:00:16

examples/gcmc/log.30Mar18.gcmc.co2.g++.4

@@ -0,0 +1,131 @@
+LAMMPS (30 Mar 2018)
+  using 1 OpenMP thread(s) per MPI task
+# GCMC for CO2 molecular fluid, rigid/small/nvt dynamics
+# Rigid CO2 TraPPE model
+# [Potoff and J.I. Siepmann, Vapor-liquid equilibria of
+# mixtures containing alkanes, carbon dioxide and
+# nitrogen AIChE J., 47,1676-1682 (2001)].
+
+# variables available on command line
+
+variable        mu index -8.1
+variable	disp index 0.5
+variable        temp index 338.0
+variable        lbox index 10.0
+variable        spacing index 5.0
+
+# global model settings
+
+units           real
+atom_style      full
+boundary        p p p
+pair_style      lj/cut/coul/long  14
+pair_modify     mix arithmetic tail yes
+kspace_style    ewald 0.0001
+bond_style      harmonic
+angle_style     harmonic
+
+# box, start molecules on simple cubic lattice
+
+lattice 	sc ${spacing}
+lattice 	sc 5.0
+Lattice spacing in x,y,z = 5 5 5
+region          box block 0 ${lbox} 0 ${lbox} 0 ${lbox} units box
+region          box block 0 10.0 0 ${lbox} 0 ${lbox} units box
+region          box block 0 10.0 0 10.0 0 ${lbox} units box
+region          box block 0 10.0 0 10.0 0 10.0 units box
+create_box      2 box                                       bond/types 1                                angle/types 1                               extra/bond/per/atom 2                       extra/angle/per/atom 1                      extra/special/per/atom 2
+Created orthogonal box = (0 0 0) to (10 10 10)
+  1 by 2 by 2 MPI processor grid
+molecule        co2mol CO2.txt
+Read molecule co2mol:
+  3 atoms with max type 2
+  2 bonds with max type 1
+  1 angles with max type 1
+  0 dihedrals with max type 0
+  0 impropers with max type 0
+create_atoms   	0 box mol co2mol 464563 units box
+Created 24 atoms
+  Time spent = 0.00257635 secs
+
+# rigid CO2 TraPPE model
+
+pair_coeff      1   1  0.053649   2.8
+pair_coeff      2   2  0.156973   3.05
+bond_coeff      1       0       1.16
+angle_coeff     1       0       180
+
+# masses
+
+mass 1 12.0107
+mass 2 15.9994
+
+# MD settings
+
+group           co2 type 1 2
+24 atoms in group co2
+neighbor        2.0 bin
+neigh_modify    every 1 delay 10 check yes
+velocity       	all create ${temp} 54654
+velocity       	all create 338.0 54654
+timestep        1.0
+
+# rigid constraints with thermostat
+
+fix             myrigidnvt co2 rigid/nvt/small molecule temp ${temp} ${temp} 100 mol co2mol
+fix             myrigidnvt co2 rigid/nvt/small molecule temp 338.0 ${temp} 100 mol co2mol
+fix             myrigidnvt co2 rigid/nvt/small molecule temp 338.0 338.0 100 mol co2mol
+8 rigid bodies with 24 atoms
+  1.16 = max distance from body owner to body atom
+
+# dynamically update  fix rigid/nvt/small temperature ndof
+fix_modify	myrigidnvt dynamic/dof yes
+
+# gcmc
+
+variable        tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans)
+fix             mygcmc co2 gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol                 co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
+fix             mygcmc co2 gcmc 100 100 0 0 54341 338.0 ${mu} ${disp} mol                 co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
+fix             mygcmc co2 gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol                 co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
+fix             mygcmc co2 gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol                 co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
+fix             mygcmc co2 gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol                 co2mol tfac_insert 1.66666666666667 group co2 rigid myrigidnvt
+
+# atom counts
+
+variable 	carbon atom "type==1"
+variable        oxygen atom "type==2"
+group 		carbon dynamic co2 var carbon
+dynamic group carbon defined
+group 	        oxygen dynamic co2 var oxygen
+dynamic group oxygen defined
+variable        nC equal count(carbon)
+variable        nO equal count(oxygen)
+
+# output
+
+variable	tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1)
+variable	iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1)
+variable	dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1)
+variable	racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1)
+
+# dynamically update default temperature ndof
+compute_modify  thermo_temp dynamic/dof yes
+
+thermo_style    custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc v_nC v_nO
+thermo          1000
+
+# run
+
+run             20000
+Ewald initialization ...
+  using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+  G vector (1/distance) = 0.164636
+  estimated absolute RMS force accuracy = 0.0332064
+  estimated relative force accuracy = 0.0001
+  KSpace vectors: actual max1d max3d = 16 2 62
+                  kxmax kymax kzmax  = 2 2 2
+WARNING: Fix gcmc using full_energy option (../fix_gcmc.cpp:485)
+0 atoms in group FixGCMC:gcmc_exclusion_group:mygcmc
+0 atoms in group FixGCMC:rotation_gas_atoms:mygcmc
+ERROR: fix gcmc does currently not support full_energy option with molecules on more than 1 MPI process. (../fix_gcmc.cpp:721)
+Last command: run             20000

examples/gcmc/log.30Mar18.gcmc.h2o.g++.1

@@ -1,4 +1,4 @@
-LAMMPS (23 Oct 2017)
+LAMMPS (30 Mar 2018)
   using 1 OpenMP thread(s) per MPI task
 # fix gcmc example with fix shake
 
@@ -34,24 +34,16 @@ create_box      2 box                                       bond/types 1
 Created orthogonal box = (0 0 0) to (10 10 10)
   1 by 1 by 1 MPI processor grid
 
-# we can load multiple molecule templates, but don't have to use them all
-molecule        co2mol CO2.txt
-Read molecule co2mol:
-  3 atoms with 2 types
-  2 bonds with 1 types
-  1 angles with 1 types
-  0 dihedrals with 0 types
-  0 impropers with 0 types
 molecule        h2omol H2O.txt
 Read molecule h2omol:
-  3 atoms with 2 types
-  2 bonds with 1 types
-  1 angles with 1 types
-  0 dihedrals with 0 types
-  0 impropers with 0 types
+  3 atoms with max type 2
+  2 bonds with max type 1
+  1 angles with max type 1
+  0 dihedrals with max type 0
+  0 impropers with max type 0
 create_atoms   	0 box mol h2omol 464563 units box
 Created 24 atoms
-  Time spent = 0.00201297 secs
+  Time spent = 0.00204968 secs
 
 # rigid SPC/E water model
 
@@ -79,7 +71,7 @@ timestep        1.0
 minimize 0.0 0.0 100 1000
 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:168)
 Ewald initialization ...
-WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+  using 12-bit tables for long-range coulomb (../kspace.cpp:321)
   G vector (1/distance) = 0.170448
   estimated absolute RMS force accuracy = 0.0332064
   estimated relative force accuracy = 0.0001
@@ -101,9 +93,9 @@ Per MPI rank memory allocation (min/avg/max) = 11.88 | 11.88 | 11.88 Mbytes
 Step Temp E_pair E_mol TotEng Press 
        0          338   -4.1890564 9.2628112e-06     18.98377    739.06991 
      100          338   -30.182886   0.85607237   -6.1539961   -2535.3207 
-Loop time of 0.0507543 on 1 procs for 100 steps with 24 atoms
+Loop time of 0.0512006 on 1 procs for 100 steps with 24 atoms
 
-99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
+99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
 
 Minimization stats:
   Stopping criterion = max iterations
@@ -117,14 +109,14 @@ Minimization stats:
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.042597   | 0.042597   | 0.042597   |   0.0 | 83.93
-Bond    | 0.00047708 | 0.00047708 | 0.00047708 |   0.0 |  0.94
-Kspace  | 0.0031135  | 0.0031135  | 0.0031135  |   0.0 |  6.13
+Pair    | 0.04303    | 0.04303    | 0.04303    |   0.0 | 84.04
+Bond    | 0.00047088 | 0.00047088 | 0.00047088 |   0.0 |  0.92
+Kspace  | 0.0029728  | 0.0029728  | 0.0029728  |   0.0 |  5.81
 Neigh   | 0.00045919 | 0.00045919 | 0.00045919 |   0.0 |  0.90
-Comm    | 0.0032997  | 0.0032997  | 0.0032997  |   0.0 |  6.50
-Output  | 1.359e-05  | 1.359e-05  | 1.359e-05  |   0.0 |  0.03
+Comm    | 0.003406   | 0.003406   | 0.003406   |   0.0 |  6.65
+Output  | 2.265e-05  | 2.265e-05  | 2.265e-05  |   0.0 |  0.04
 Modify  | 0          | 0          | 0          |   0.0 |  0.00
-Other   |            | 0.0007946  |            |       |  1.57
+Other   |            | 0.0008392  |            |       |  1.64
 
 Nlocal:    24 ave 24 max 24 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -139,23 +131,26 @@ Ave special neighs/atom = 2
 Neighbor list builds = 2
 Dangerous builds = 0
 reset_timestep 0
+
 # rigid constraints with thermostat
 
-fix             mynvt all nvt temp ${temp} ${temp} 100
-fix             mynvt all nvt temp 338.0 ${temp} 100
-fix             mynvt all nvt temp 338.0 338.0 100
-fix             wshake  all shake 0.0001 50 0 b 1 a 1 mol h2omol
+fix             mynvt h2o nvt temp ${temp} ${temp} 100
+fix             mynvt h2o nvt temp 338.0 ${temp} 100
+fix             mynvt h2o nvt temp 338.0 338.0 100
+fix             wshake h2o shake 0.0001 50 0 b 1 a 1 mol h2omol
   0 = # of size 2 clusters
   0 = # of size 3 clusters
   0 = # of size 4 clusters
   8 = # of frozen angles
-# gcmc
 
+# important to make temperature dofs dynamic
 
+compute_modify  thermo_temp dynamic/dof yes
+compute_modify  mynvt_temp dynamic/dof yes
 
 run 1000
 Ewald initialization ...
-WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+  using 12-bit tables for long-range coulomb (../kspace.cpp:321)
   G vector (1/distance) = 0.170448
   estimated absolute RMS force accuracy = 0.0332064
   estimated relative force accuracy = 0.0001
@@ -164,23 +159,23 @@ WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
 Per MPI rank memory allocation (min/avg/max) = 11.63 | 11.63 | 11.63 Mbytes
 Step Temp E_pair E_mol TotEng Press 
        0    518.26667   -30.182886            0   -7.0100684     993.1985 
-    1000     326.9865   -62.258445            0   -47.638175   -5.3440813 
-Loop time of 0.141449 on 1 procs for 1000 steps with 24 atoms
+    1000     326.9865   -62.258443            0   -47.638173   -5.3439918 
+Loop time of 0.139436 on 1 procs for 1000 steps with 24 atoms
 
-Performance: 610.819 ns/day, 0.039 hours/ns, 7069.663 timesteps/s
-99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
+Performance: 619.641 ns/day, 0.039 hours/ns, 7171.773 timesteps/s
+99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.10788    | 0.10788    | 0.10788    |   0.0 | 76.27
-Bond    | 0.00018954 | 0.00018954 | 0.00018954 |   0.0 |  0.13
-Kspace  | 0.011867   | 0.011867   | 0.011867   |   0.0 |  8.39
-Neigh   | 0.0045254  | 0.0045254  | 0.0045254  |   0.0 |  3.20
-Comm    | 0.011277   | 0.011277   | 0.011277   |   0.0 |  7.97
-Output  | 1.5497e-05 | 1.5497e-05 | 1.5497e-05 |   0.0 |  0.01
-Modify  | 0.00383    | 0.00383    | 0.00383    |   0.0 |  2.71
-Other   |            | 0.001868   |            |       |  1.32
+Pair    | 0.10588    | 0.10588    | 0.10588    |   0.0 | 75.94
+Bond    | 0.00015759 | 0.00015759 | 0.00015759 |   0.0 |  0.11
+Kspace  | 0.011144   | 0.011144   | 0.011144   |   0.0 |  7.99
+Neigh   | 0.00459    | 0.00459    | 0.00459    |   0.0 |  3.29
+Comm    | 0.011396   | 0.011396   | 0.011396   |   0.0 |  8.17
+Output  | 1.7166e-05 | 1.7166e-05 | 1.7166e-05 |   0.0 |  0.01
+Modify  | 0.0043328  | 0.0043328  | 0.0043328  |   0.0 |  3.11
+Other   |            | 0.001914   |            |       |  1.37
 
 Nlocal:    24 ave 24 max 24 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -194,13 +189,16 @@ Ave neighs/atom = 213
 Ave special neighs/atom = 2
 Neighbor list builds = 25
 Dangerous builds = 0
+reset_timestep 0
+
+# gcmc
 
 variable        tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans)
-fix             mygcmc all gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol                 h2omol tfac_insert ${tfac} group h2o shake wshake
-fix             mygcmc all gcmc 100 100 0 0 54341 338.0 ${mu} ${disp} mol                 h2omol tfac_insert ${tfac} group h2o shake wshake
-fix             mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol                 h2omol tfac_insert ${tfac} group h2o shake wshake
-fix             mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol                 h2omol tfac_insert ${tfac} group h2o shake wshake
-fix             mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol                 h2omol tfac_insert 1.66666666666667 group h2o shake wshake
+fix             mygcmc h2o gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol                 h2omol tfac_insert ${tfac} group h2o shake wshake
+fix             mygcmc h2o gcmc 100 100 0 0 54341 338.0 ${mu} ${disp} mol                 h2omol tfac_insert ${tfac} group h2o shake wshake
+fix             mygcmc h2o gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol                 h2omol tfac_insert ${tfac} group h2o shake wshake
+fix             mygcmc h2o gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol                 h2omol tfac_insert ${tfac} group h2o shake wshake
+fix             mygcmc h2o gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol                 h2omol tfac_insert 1.66666666666667 group h2o shake wshake
 
 # atom counts
 
@@ -219,7 +217,6 @@ variable	tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1)
 variable	iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1)
 variable	dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1)
 variable	racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1)
-compute_modify  thermo_temp dynamic/dof yes
 thermo_style    custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc v_nO v_nH
 thermo          1000
 
@@ -227,67 +224,67 @@ thermo          1000
 
 run             20000
 Ewald initialization ...
-WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+  using 12-bit tables for long-range coulomb (../kspace.cpp:321)
   G vector (1/distance) = 0.170448
   estimated absolute RMS force accuracy = 0.0332064
   estimated relative force accuracy = 0.0001
   KSpace vectors: actual max1d max3d = 16 2 62
                   kxmax kymax kzmax  = 2 2 2
-WARNING: Fix gcmc using full_energy option (../fix_gcmc.cpp:445)
+WARNING: Fix gcmc using full_energy option (../fix_gcmc.cpp:485)
 0 atoms in group FixGCMC:gcmc_exclusion_group:mygcmc
 0 atoms in group FixGCMC:rotation_gas_atoms:mygcmc
 WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (../neighbor.cpp:472)
 Per MPI rank memory allocation (min/avg/max) = 11.63 | 11.63 | 11.63 Mbytes
 Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_racc v_nO v_nH 
-    1000     326.9865   -4.3509713   -62.258445     14.62027   0.23910963       24            0            0            0            0            8           16 
-    2000    116.99793   -5344.1527   -286.61595    17.088682   0.74721761       75  0.048183096  0.013941446            0            0           25           50 
-    3000    106.86746   -3920.4926   -361.60598    18.794545   0.89666113       90  0.035637919  0.012768883            0            0           30           60 
-    4000    75.002668    540.46846    -414.8511    14.531966   0.98632724       99  0.025963651 0.0093451705            0            0           33           66 
-    5000    79.924788   -2131.1173   -437.21216    15.962121    1.0162159      102  0.019879728 0.0070418993            0            0           34           68 
-    6000    95.552773   -3647.0233   -438.24276    19.083253    1.0162159      102  0.015753613 0.0056885133            0            0           34           68 
-    7000    79.501736   -2071.5369   -440.77351    15.877631    1.0162159      102   0.01326216 0.0046915318            0            0           34           68 
-    8000    62.567091   -3102.9616   -442.21884    12.495541    1.0162159      102  0.011305503 0.0040437885            0            0           34           68 
-    9000    68.324047   -3812.7866   -440.46835    13.645287    1.0162159      102 0.0099549538 0.0035157329            0            0           34           68 
-   10000    83.857631   -2158.2659    -444.8183    16.747566    1.0162159      102 0.0088200922 0.0031354281            0            0           34           68 
-   11000    68.350984   -2084.0789   -440.14081    13.650667    1.0162159      102 0.0081331455 0.0030247424            0            0           34           68 
-   12000    76.867315   -1585.6723   -443.36199      15.3515    1.0162159      102 0.0073845932 0.0027532534            0            0           34           68 
-   13000     59.74266   -2211.0211   -446.07791    11.931462    1.0162159      102 0.0067756276 0.0025213898            0            0           34           68 
-   14000    81.154979    -907.0176   -441.53368    16.207808    1.0162159      102 0.0062527642 0.0023280719            0            0           34           68 
-   15000    66.814346   -2804.5134   -455.80704      13.7421    1.0461046      105 0.0059590528 0.0021576214            0            0           35           70 
-   16000     71.42983   -3930.4004   -458.43218    14.691394    1.0461046      105 0.0055547473 0.0020163729            0            0           35           70 
-   17000    89.624855   -3569.8136   -455.18164    18.433672    1.0461046      105 0.0052173265 0.0018867687            0            0           35           70 
-   18000    63.519962   -1882.8157   -456.58939    13.064525    1.0461046      105 0.0049082049 0.0017765986            0            0           35           70 
-   19000    71.872698   -2243.5046   -454.93359    14.782481    1.0461046      105 0.0046439115 0.0016748361            0            0           35           70 
-   20000    73.660765   -2285.3173   -476.35473    15.589381    1.0759934      108 0.0045124933 0.0015837653            0            0           36           72 
-   21000    95.675868    987.92089   -475.46736    20.248603    1.0759934      108  0.004285814 0.0015049513            0            0           36           72 
-Loop time of 220.662 on 1 procs for 20000 steps with 108 atoms
+       0     326.9865   -4.3508819   -62.258443     14.62027   0.23910963       24            0            0            0            0            8           16 
+    1000      354.423   -3760.1354   -235.34169    51.766914   0.74721761       75  0.046175467  0.011949811            0            0           25           50 
+    2000    335.19661    -3018.659   -270.44089    52.955344   0.80699501       81  0.026473882 0.0068755525            0            0           27           54 
+    3000    333.47175    2657.2052   -336.48359    64.611037   0.98632724       99  0.022634978 0.0060076096            0            0           33           66 
+    4000    321.48504    2055.4786   -345.06113    62.288579   0.98632724       99  0.016897769 0.0045269353            0            0           33           66 
+    5000    333.45735    1918.5375    -368.5463    66.596193    1.0162159      102  0.013784412 0.0036569014            0            0           34           68 
+    6000    301.90666   -698.74074   -371.32122    60.295069    1.0162159      102   0.01160439 0.0030159847            0            0           34           68 
+    7000    336.42505    1537.9483   -378.51731    69.194524    1.0461046      105  0.010174953 0.0025995783            0            0           35           70 
+    8000    338.95331   -1032.1084    -390.7067    69.714524    1.0461046      105 0.0089594585  0.002260114            0            0           35           70 
+    9000    311.44605   -1494.7788    -383.9272    64.056945    1.0461046      105  0.007938083 0.0020156323            0            0           35           70 
+   10000    330.70877    2082.4597   -366.57249    68.018822    1.0461046      105 0.0071412985 0.0018148454            0            0           35           70 
+   11000    286.34718    2238.3752   -370.91119    60.601806    1.0759934      108 0.0066641451 0.0016519521            0            0           36           72 
+   12000    371.02522    3048.7157   -398.51333    78.522854    1.0759934      108 0.0061145907 0.0015128339            0            0           36           72 
+   13000    392.87611    4486.1134   -387.07077    83.147323    1.0759934      108 0.0056427384 0.0013968431            0            0           36           72 
+   14000    332.80747    3586.2698   -406.12151    70.434545    1.0759934      108 0.0052496417 0.0012945729            0            0           36           72 
+   15000    325.61844    4198.3864    -387.5733    68.913077    1.0759934      108 0.0048934679 0.0012098238            0            0           36           72 
+   16000    254.10285     1560.976   -409.98615    55.292559    1.1058821      111 0.0047204383 0.0011320612            0            0           37           74 
+   17000    367.46414    2750.8283   -412.22037    79.959878    1.1058821      111 0.0044407568 0.0010659592            0            0           37           74 
+   18000    407.74215    2308.5027   -408.73046    88.724338    1.1058821      111 0.0042016342 0.0010049017            0            0           37           74 
+   19000    341.53799    5777.9814   -407.00637     74.31837    1.1058821      111 0.0039877848 0.00095025921            0            0           37           74 
+   20000    395.75303    3159.4677   -403.82798    86.115516    1.1058821      111 0.0037874635 0.00090297077            0            0           37           74 
+Loop time of 231.351 on 1 procs for 20000 steps with 111 atoms
 
-Performance: 7.831 ns/day, 3.065 hours/ns, 90.637 timesteps/s
-99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
+Performance: 7.469 ns/day, 3.213 hours/ns, 86.449 timesteps/s
+99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 37.459     | 37.459     | 37.459     |   0.0 | 16.98
-Bond    | 0.087067   | 0.087067   | 0.087067   |   0.0 |  0.04
-Kspace  | 0.90234    | 0.90234    | 0.90234    |   0.0 |  0.41
-Neigh   | 1.2299     | 1.2299     | 1.2299     |   0.0 |  0.56
-Comm    | 0.95437    | 0.95437    | 0.95437    |   0.0 |  0.43
-Output  | 0.0010636  | 0.0010636  | 0.0010636  |   0.0 |  0.00
-Modify  | 179.85     | 179.85     | 179.85     |   0.0 | 81.51
-Other   |            | 0.1754     |            |       |  0.08
+Pair    | 39.09      | 39.09      | 39.09      |   0.0 | 16.90
+Bond    | 0.092728   | 0.092728   | 0.092728   |   0.0 |  0.04
+Kspace  | 0.87751    | 0.87751    | 0.87751    |   0.0 |  0.38
+Neigh   | 3.9658     | 3.9658     | 3.9658     |   0.0 |  1.71
+Comm    | 1.0608     | 1.0608     | 1.0608     |   0.0 |  0.46
+Output  | 0.00096035 | 0.00096035 | 0.00096035 |   0.0 |  0.00
+Modify  | 186.07     | 186.07     | 186.07     |   0.0 | 80.43
+Other   |            | 0.1892     |            |       |  0.08
 
-Nlocal:    108 ave 108 max 108 min
+Nlocal:    111 ave 111 max 111 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    7850 ave 7850 max 7850 min
+Nghost:    8070 ave 8070 max 8070 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    99828 ave 99828 max 99828 min
+Neighs:    105469 ave 105469 max 105469 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
 
-Total # of neighbors = 99828
-Ave neighs/atom = 924.333
+Total # of neighbors = 105469
+Ave neighs/atom = 950.171
 Ave special neighs/atom = 2
-Neighbor list builds = 20439
+Neighbor list builds = 20910
 Dangerous builds = 0
 
-Total wall time: 0:03:40
+Total wall time: 0:03:51

examples/gcmc/log.30Mar18.gcmc.h2o.g++.4

@@ -0,0 +1,237 @@
+LAMMPS (30 Mar 2018)
+  using 1 OpenMP thread(s) per MPI task
+# fix gcmc example with fix shake
+
+# variables available on command line
+
+variable        mu index -8.1
+variable	disp index 0.5
+variable        temp index 338.0
+variable        lbox index 10.0
+variable        spacing index 5.0
+
+# global model settings
+
+units           real
+atom_style      full
+boundary        p p p
+pair_style      lj/cut/coul/long  14
+pair_modify     mix arithmetic tail yes
+kspace_style    ewald 0.0001
+bond_style      harmonic
+angle_style     harmonic
+
+# box, start molecules on simple cubic lattice
+
+lattice 	sc ${spacing}
+lattice 	sc 5.0
+Lattice spacing in x,y,z = 5 5 5
+region          box block 0 ${lbox} 0 ${lbox} 0 ${lbox} units box
+region          box block 0 10.0 0 ${lbox} 0 ${lbox} units box
+region          box block 0 10.0 0 10.0 0 ${lbox} units box
+region          box block 0 10.0 0 10.0 0 10.0 units box
+create_box      2 box                                       bond/types 1                                angle/types 1                               extra/bond/per/atom 2                       extra/angle/per/atom 1                      extra/special/per/atom 2
+Created orthogonal box = (0 0 0) to (10 10 10)
+  1 by 2 by 2 MPI processor grid
+
+molecule        h2omol H2O.txt
+Read molecule h2omol:
+  3 atoms with max type 2
+  2 bonds with max type 1
+  1 angles with max type 1
+  0 dihedrals with max type 0
+  0 impropers with max type 0
+create_atoms   	0 box mol h2omol 464563 units box
+Created 24 atoms
+  Time spent = 0.00285625 secs
+
+# rigid SPC/E water model
+
+pair_coeff      1 1 0.15535 3.166
+pair_coeff      * 2 0.0000 0.0000
+
+bond_coeff      1     1000       1.0
+angle_coeff     1      100       109.47
+
+# masses
+
+mass 1 15.9994
+mass 2 1.0
+
+# MD settings
+
+group           h2o type 1 2
+24 atoms in group h2o
+neighbor        2.0 bin
+neigh_modify    every 1 delay 1 check yes
+velocity       	all create ${temp} 54654
+velocity       	all create 338.0 54654
+timestep        1.0
+
+minimize 0.0 0.0 100 1000
+WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:168)
+Ewald initialization ...
+  using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+  G vector (1/distance) = 0.170448
+  estimated absolute RMS force accuracy = 0.0332064
+  estimated relative force accuracy = 0.0001
+  KSpace vectors: actual max1d max3d = 16 2 62
+                  kxmax kymax kzmax  = 2 2 2
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 16
+  ghost atom cutoff = 16
+  binsize = 8, bins = 2 2 2
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut/coul/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 11.85 | 11.85 | 11.85 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0          338   -4.9610706 9.2628112e-06    18.211756    730.90791 
+     100          338   -15.742442   0.14954269     7.579918   -637.49568 
+Loop time of 0.0695416 on 4 procs for 100 steps with 24 atoms
+
+94.4% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+Minimization stats:
+  Stopping criterion = max iterations
+  Energy initial, next-to-last, final = 
+        -4.96106135393     -15.5388622715      -15.592899346
+  Force two-norm initial, final = 15.474 18.1478
+  Force max component initial, final = 5.80042 7.56514
+  Final line search alpha, max atom move = 0.00151131 0.0114333
+  Iterations, force evaluations = 100 328
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.0093951  | 0.017625   | 0.028943   |   5.3 | 25.34
+Bond    | 0.00035357 | 0.00042325 | 0.00055075 |   0.0 |  0.61
+Kspace  | 0.00664    | 0.019695   | 0.029924   |   6.1 | 28.32
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.022505   | 0.02509    | 0.027851   |   1.3 | 36.08
+Output  | 3.3855e-05 | 3.5942e-05 | 4.1485e-05 |   0.0 |  0.05
+Modify  | 0          | 0          | 0          |   0.0 |  0.00
+Other   |            | 0.006672   |            |       |  9.59
+
+Nlocal:    6 ave 8 max 3 min
+Histogram: 1 0 0 0 1 0 0 0 0 2
+Nghost:    1722 ave 1725 max 1720 min
+Histogram: 2 0 0 0 0 0 1 0 0 1
+Neighs:    1256.75 ave 2101 max 667 min
+Histogram: 1 0 1 0 1 0 0 0 0 1
+
+Total # of neighbors = 5027
+Ave neighs/atom = 209.458
+Ave special neighs/atom = 2
+Neighbor list builds = 0
+Dangerous builds = 0
+reset_timestep 0
+
+# rigid constraints with thermostat
+
+fix             mynvt h2o nvt temp ${temp} ${temp} 100
+fix             mynvt h2o nvt temp 338.0 ${temp} 100
+fix             mynvt h2o nvt temp 338.0 338.0 100
+fix             wshake h2o shake 0.0001 50 0 b 1 a 1 mol h2omol
+  0 = # of size 2 clusters
+  0 = # of size 3 clusters
+  0 = # of size 4 clusters
+  8 = # of frozen angles
+
+# important to make temperature dofs dynamic
+
+compute_modify  thermo_temp dynamic/dof yes
+compute_modify  mynvt_temp dynamic/dof yes
+
+run 1000
+Ewald initialization ...
+  using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+  G vector (1/distance) = 0.170448
+  estimated absolute RMS force accuracy = 0.0332064
+  estimated relative force accuracy = 0.0001
+  KSpace vectors: actual max1d max3d = 16 2 62
+                  kxmax kymax kzmax  = 2 2 2
+Per MPI rank memory allocation (min/avg/max) = 11.6 | 11.6 | 11.6 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0    518.26667   -15.742442            0    7.4303753    -613.0781 
+    1000    369.81793   -54.202682            0   -37.667327    294.98832 
+Loop time of 0.191619 on 4 procs for 1000 steps with 24 atoms
+
+Performance: 450.894 ns/day, 0.053 hours/ns, 5218.680 timesteps/s
+96.4% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.015873   | 0.028989   | 0.040172   |   5.3 | 15.13
+Bond    | 0.00024271 | 0.00027657 | 0.00034404 |   0.0 |  0.14
+Kspace  | 0.022896   | 0.034492   | 0.047924   |   5.1 | 18.00
+Neigh   | 0.0025764  | 0.0025961  | 0.0026152  |   0.0 |  1.35
+Comm    | 0.068467   | 0.070095   | 0.071535   |   0.4 | 36.58
+Output  | 4.8161e-05 | 5.0783e-05 | 5.7936e-05 |   0.0 |  0.03
+Modify  | 0.049141   | 0.049894   | 0.05072    |   0.3 | 26.04
+Other   |            | 0.005226   |            |       |  2.73
+
+Nlocal:    6 ave 8 max 3 min
+Histogram: 1 0 0 0 0 0 1 0 1 1
+Nghost:    1331.5 ave 1369 max 1290 min
+Histogram: 1 0 0 0 0 2 0 0 0 1
+Neighs:    1259.75 ave 1642 max 428 min
+Histogram: 1 0 0 0 0 0 0 1 0 2
+
+Total # of neighbors = 5039
+Ave neighs/atom = 209.958
+Ave special neighs/atom = 2
+Neighbor list builds = 27
+Dangerous builds = 0
+reset_timestep 0
+
+# gcmc
+
+variable        tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans)
+fix             mygcmc h2o gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol                 h2omol tfac_insert ${tfac} group h2o shake wshake
+fix             mygcmc h2o gcmc 100 100 0 0 54341 338.0 ${mu} ${disp} mol                 h2omol tfac_insert ${tfac} group h2o shake wshake
+fix             mygcmc h2o gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol                 h2omol tfac_insert ${tfac} group h2o shake wshake
+fix             mygcmc h2o gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol                 h2omol tfac_insert ${tfac} group h2o shake wshake
+fix             mygcmc h2o gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol                 h2omol tfac_insert 1.66666666666667 group h2o shake wshake
+
+# atom counts
+
+variable 	oxygen atom "type==1"
+variable 	hydrogen atom "type==2"
+group 	        oxygen dynamic all var oxygen
+dynamic group oxygen defined
+group 		hydrogen dynamic all var hydrogen
+dynamic group hydrogen defined
+variable        nO equal count(oxygen)
+variable        nH equal count(hydrogen)
+
+# output
+
+variable	tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1)
+variable	iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1)
+variable	dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1)
+variable	racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1)
+thermo_style    custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc v_nO v_nH
+thermo          1000
+
+# run
+
+run             20000
+Ewald initialization ...
+  using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+  G vector (1/distance) = 0.170448
+  estimated absolute RMS force accuracy = 0.0332064
+  estimated relative force accuracy = 0.0001
+  KSpace vectors: actual max1d max3d = 16 2 62
+                  kxmax kymax kzmax  = 2 2 2
+WARNING: Fix gcmc using full_energy option (../fix_gcmc.cpp:485)
+0 atoms in group FixGCMC:gcmc_exclusion_group:mygcmc
+0 atoms in group FixGCMC:rotation_gas_atoms:mygcmc
+ERROR: fix gcmc does currently not support full_energy option with molecules on more than 1 MPI process. (../fix_gcmc.cpp:721)
+Last command: run             20000

examples/gcmc/log.30Mar18.gcmc.lj.g++.1

@@ -1,4 +1,4 @@
-LAMMPS (23 Oct 2017)
+LAMMPS (30 Mar 2018)
   using 1 OpenMP thread(s) per MPI task
 # GCMC for LJ simple fluid, no dynamics
 # T = 2.0
@@ -36,17 +36,22 @@ Created orthogonal box = (0 0 0) to (5 5 5)
 pair_coeff	* * 1.0 1.0
 mass		* 1.0
 
+# we recommend setting up a dedicated group for gcmc
+
+group		gcmcgroup type 1
+0 atoms in group gcmcgroup
+
 # gcmc
 
-fix             mygcmc all gcmc 1 100 100 1 29494 ${temp} ${mu} ${disp}
-fix             mygcmc all gcmc 1 100 100 1 29494 2.0 ${mu} ${disp}
-fix             mygcmc all gcmc 1 100 100 1 29494 2.0 -1.25 ${disp}
-fix             mygcmc all gcmc 1 100 100 1 29494 2.0 -1.25 1.0
+fix             mygcmc gcmcgroup gcmc 1 100 100 1 29494 ${temp} ${mu} ${disp}
+fix             mygcmc gcmcgroup gcmc 1 100 100 1 29494 2.0 ${mu} ${disp}
+fix             mygcmc gcmcgroup gcmc 1 100 100 1 29494 2.0 -1.25 ${disp}
+fix             mygcmc gcmcgroup gcmc 1 100 100 1 29494 2.0 -1.25 1.0
 
 # atom count
 
 variable 	type1 atom "type==1"
-group 		type1 dynamic all var type1
+group 		type1 dynamic gcmcgroup var type1
 dynamic group type1 defined
 variable        n1 equal count(type1)
 
@@ -97,40 +102,40 @@ Neighbor list info ...
 Per MPI rank memory allocation (min/avg/max) = 0.433 | 0.433 | 0.433 Mbytes
 Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_rhoav v_pav v_muexav v_n1av 
        0            0            0            0           -0            0        0            0            0            0            0            0            0            0 
-    1000    2.4038954    2.1735585   -2.7041368    3.5476844        0.496       62  0.064790036   0.06313096    0.1081294      0.54304    1.4513524 -0.025479219        64.98 
-    2000    2.0461168    1.1913842   -2.9880181    3.0212194        0.512       64  0.067416408  0.066335853   0.11306166      0.52736    1.3274665  0.034690004        62.97 
-    3000    1.7930436    1.3788681   -3.2212667    2.6505861        0.552       69  0.067733191  0.066877836    0.1133516       0.5344    1.3834744 0.0070582537         63.5 
-    4000     1.981449    1.2541054   -2.8222868    2.9217977        0.472       59  0.068546991  0.067856412   0.11442807      0.52504    1.3815629  0.043309657        62.17 
-    5000    2.0946818    1.0701629   -3.5213291    3.0977688        0.568       71   0.06813743  0.067567891   0.11342906      0.53824    1.4049567 -0.0054539777        64.15 
-    6000    1.9793484   0.68224187    -3.410211    2.9247088        0.536       67  0.067797628  0.067420108   0.11295333       0.5384     1.401683 -0.0066894359        64.37 
-    7000    2.1885798    1.6745012    -3.185499    3.2345922        0.544       68  0.068630201  0.068261832   0.11403705       0.5244     1.449239  0.045987399        62.33 
-    8000    2.2175324    1.5897263    -3.078898    3.2759002        0.528       66  0.068180395  0.067899629   0.11332691      0.53928    1.5488388  -0.01075766        64.29 
-    9000    1.8610779    1.0396231    -2.923262    2.7465908        0.496       62  0.068346453  0.068028117    0.1134132      0.52912    1.4352871  0.027082544        62.87 
-   10000    2.1079271    1.1746643   -2.9112062    3.1091925         0.48       60  0.068352878  0.068054948   0.11335434       0.5316    1.4462327  0.018503094         63.2 
-Loop time of 20.4081 on 1 procs for 10000 steps with 60 atoms
+    1000    2.0603874    2.9024736   -3.2576986    3.0482443        0.584       73  0.069266074  0.066959582   0.11158434      0.53624    1.3978532 0.0014407586        64.19 
+    2000    2.1586837    1.5581387   -2.8420766    3.1857993        0.496       62  0.068487803  0.067570935    0.1126652      0.53128    1.3713694  0.020274019        63.41 
+    3000    2.4664064   0.65471138   -3.3428236    3.6435549        0.528       66  0.068182273  0.067547792   0.11226502      0.53472    1.3892234 0.0070204504        63.68 
+    4000    1.8880496    1.4802782   -2.7846019     2.785647        0.488       61  0.068250075  0.067843541   0.11299989      0.52744     1.299496  0.033918563         63.1 
+    5000    2.0578649    1.3204331   -3.5571862    3.0433213        0.568       71  0.067858571  0.067732262   0.11271981       0.5364    1.4237505 0.00065741209           64 
+    6000    2.3627973   0.97064566   -3.1107668    3.4879388        0.504       63  0.067846204   0.06757018   0.11272207       0.5332    1.3945131  0.014216594         63.7 
+    7000    1.6629817   0.98138972   -2.7780297    2.4514644        0.464       58  0.067451389  0.067269791   0.11263692      0.53688    1.4207486 -0.0012887793        63.82 
+    8000    2.2135488    2.0878792   -3.0471089    3.2707661        0.536       67  0.067926473  0.067738312    0.1135594      0.52736    1.4348314  0.034380623        62.43 
+    9000    1.8904287   0.52639383   -3.3548657    2.7920177         0.52       65   0.06818197  0.068003094   0.11356319      0.53072    1.4528143  0.021683615        63.23 
+   10000    2.2353281   0.73275312   -3.2197702    3.3006016        0.512       64  0.068465059  0.068208485   0.11414748      0.52712    1.4143492   0.03497858        62.44 
+Loop time of 21.2409 on 1 procs for 10000 steps with 64 atoms
 
-Performance: 211680.375 tau/day, 490.001 timesteps/s
-98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
+Performance: 203381.368 tau/day, 470.790 timesteps/s
+99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.46484    | 0.46484    | 0.46484    |   0.0 |  2.28
-Neigh   | 1.1447     | 1.1447     | 1.1447     |   0.0 |  5.61
-Comm    | 0.1696     | 0.1696     | 0.1696     |   0.0 |  0.83
-Output  | 0.000319   | 0.000319   | 0.000319   |   0.0 |  0.00
-Modify  | 18.607     | 18.607     | 18.607     |   0.0 | 91.17
-Other   |            | 0.02194    |            |       |  0.11
+Pair    | 0.45931    | 0.45931    | 0.45931    |   0.0 |  2.16
+Neigh   | 1.1637     | 1.1637     | 1.1637     |   0.0 |  5.48
+Comm    | 0.17294    | 0.17294    | 0.17294    |   0.0 |  0.81
+Output  | 0.00027394 | 0.00027394 | 0.00027394 |   0.0 |  0.00
+Modify  | 19.416     | 19.416     | 19.416     |   0.0 | 91.41
+Other   |            | 0.02919    |            |       |  0.14
 
-Nlocal:    60 ave 60 max 60 min
+Nlocal:    64 ave 64 max 64 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    663 ave 663 max 663 min
+Nghost:    714 ave 714 max 714 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    2133 ave 2133 max 2133 min
+Neighs:    2423 ave 2423 max 2423 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
 
-Total # of neighbors = 2133
-Ave neighs/atom = 35.55
+Total # of neighbors = 2423
+Ave neighs/atom = 37.8594
 Neighbor list builds = 10000
 Dangerous builds = 0
-Total wall time: 0:00:20
+Total wall time: 0:00:21

examples/gcmc/log.30Mar18.gcmc.lj.g++.4

@@ -1,4 +1,4 @@
-LAMMPS (23 Oct 2017)
+LAMMPS (30 Mar 2018)
   using 1 OpenMP thread(s) per MPI task
 # GCMC for LJ simple fluid, no dynamics
 # T = 2.0
@@ -36,17 +36,22 @@ Created orthogonal box = (0 0 0) to (5 5 5)
 pair_coeff	* * 1.0 1.0
 mass		* 1.0
 
+# we recommend setting up a dedicated group for gcmc
+
+group		gcmcgroup type 1
+0 atoms in group gcmcgroup
+
 # gcmc
 
-fix             mygcmc all gcmc 1 100 100 1 29494 ${temp} ${mu} ${disp}
-fix             mygcmc all gcmc 1 100 100 1 29494 2.0 ${mu} ${disp}
-fix             mygcmc all gcmc 1 100 100 1 29494 2.0 -1.25 ${disp}
-fix             mygcmc all gcmc 1 100 100 1 29494 2.0 -1.25 1.0
+fix             mygcmc gcmcgroup gcmc 1 100 100 1 29494 ${temp} ${mu} ${disp}
+fix             mygcmc gcmcgroup gcmc 1 100 100 1 29494 2.0 ${mu} ${disp}
+fix             mygcmc gcmcgroup gcmc 1 100 100 1 29494 2.0 -1.25 ${disp}
+fix             mygcmc gcmcgroup gcmc 1 100 100 1 29494 2.0 -1.25 1.0
 
 # atom count
 
 variable 	type1 atom "type==1"
-group 		type1 dynamic all var type1
+group 		type1 dynamic gcmcgroup var type1
 dynamic group type1 defined
 variable        n1 equal count(type1)
 
@@ -97,40 +102,40 @@ Neighbor list info ...
 Per MPI rank memory allocation (min/avg/max) = 0.4477 | 0.4477 | 0.4477 Mbytes
 Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_rhoav v_pav v_muexav v_n1av 
        0            0            0            0           -0            0        0            0            0            0            0            0            0            0 
-    1000     1.956397    1.7699101   -2.7889468    2.8864874        0.488       61  0.068894746  0.067229075    0.1141726      0.53288    1.3832798  0.013392866        63.44 
-    2000     2.040943   0.56060899   -2.8001647    3.0077055        0.456       57  0.069858594  0.068831934   0.11629114       0.5232    1.3587174  0.049995794        62.19 
-    3000    2.0004866    1.5736515   -3.3098044    2.9572411        0.552       69  0.069594029  0.068727791   0.11592543      0.53096    1.4129434  0.020022578        63.23 
-    4000    2.1127942     2.642809   -2.8865084    3.1211733        0.528       66  0.070268697  0.069533235   0.11693806      0.52424    1.3444615  0.046884078        62.57 
-    5000    2.3663648     1.354269   -3.1917346    3.4957662        0.528       66  0.070519633  0.069960064   0.11710321      0.52688    1.3595814  0.036270867        62.56 
-    6000    1.9224136   0.82756699      -3.1965     2.839257         0.52       65   0.06985018  0.069474645   0.11628632        0.536      1.47062   0.00141549        63.76 
-    7000    2.0266192    1.5593811   -2.9972341    2.9931606         0.52       65  0.070244693  0.069880791   0.11666541      0.52528    1.3246332  0.040754793         62.2 
-    8000    1.7790467    1.8680568   -2.8028819    2.6275151         0.52       65  0.070454494  0.070172368   0.11736806        0.524    1.4213649  0.047985191        62.03 
-    9000    1.7968847    1.3195587    -3.261001    2.6550983        0.536       67  0.069952011  0.069618327   0.11650087      0.53904    1.4624201  -0.01069837        64.36 
-   10000    2.1566109    1.1015729   -3.4999837    3.1880335        0.552       69  0.069603309  0.069284134   0.11625548      0.53128    1.3587249   0.02075238        63.24 
-Loop time of 23.8213 on 4 procs for 10000 steps with 69 atoms
+    1000    2.4378552    1.9014939     -3.23439    3.6030066        0.544       68  0.073050445  0.070796636   0.11934255      0.52552    1.3006333   0.04152087        62.56 
+    2000    1.9339159    1.0360287   -3.5001391    2.8594327         0.56       70  0.069588893  0.068587488   0.11319584        0.542    1.4012888 -0.020696665        64.56 
+    3000    1.8891807    2.2857708   -3.3755633    2.7954769        0.592       74  0.068329031  0.067640916   0.11187803      0.53536    1.3380926 0.0062359288        64.21 
+    4000    2.0436517    1.7600211   -3.4067452    3.0229014        0.576       72  0.067464211  0.067003868   0.11060324      0.54144    1.4484907 -0.016246603        64.75 
+    5000    2.1512268    1.0811095   -3.2418366    3.1786785        0.536       67  0.066830654  0.066717982    0.1094094      0.54368    1.4962073 -0.025791643        65.04 
+    6000     2.128931    1.5444487   -3.1904474    3.1450116        0.528       66  0.067479197  0.067193531    0.1104464      0.53112    1.4247377  0.019908014        63.01 
+    7000    1.8194311   0.72981963   -3.6601329    2.6912418        0.576       72  0.068131849  0.067910074   0.11182024      0.51968    1.4517098  0.063444774        61.72 
+    8000     1.947817   0.74570466   -3.0935809    2.8753489        0.504       63  0.068034071  0.067855883   0.11217045      0.53304    1.4924302  0.012298733        63.45 
+    9000    1.8942389    1.3367401   -2.8925016    2.7962574        0.504       63  0.068117479  0.067943081   0.11236152        0.536    1.4091106 0.0011494886        63.73 
+   10000    2.2092799   0.95517153   -2.9117781    3.2586879         0.48       60  0.068264792  0.068016591   0.11310789      0.52272    1.4774174  0.051284873        62.04 
+Loop time of 29.2417 on 4 procs for 10000 steps with 60 atoms
 
-Performance: 181350.388 tau/day, 419.793 timesteps/s
-97.6% CPU use with 4 MPI tasks x 1 OpenMP threads
+Performance: 147733.999 tau/day, 341.977 timesteps/s
+96.3% CPU use with 4 MPI tasks x 1 OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.10935    | 0.11844    | 0.12741    |   2.1 |  0.50
-Neigh   | 0.33       | 0.33945    | 0.35091    |   1.6 |  1.42
-Comm    | 0.49249    | 0.51745    | 0.53856    |   2.7 |  2.17
-Output  | 0.00053334 | 0.0007208  | 0.0007906  |   0.0 |  0.00
-Modify  | 22.82      | 22.822     | 22.825     |   0.0 | 95.81
-Other   |            | 0.02289    |            |       |  0.10
+Pair    | 0.11648    | 0.1221     | 0.13001    |   1.5 |  0.42
+Neigh   | 0.34452    | 0.35618    | 0.36328    |   1.2 |  1.22
+Comm    | 0.63561    | 0.65617    | 0.67542    |   1.8 |  2.24
+Output  | 0.00056601 | 0.00069755 | 0.00074744 |   0.0 |  0.00
+Modify  | 28.069     | 28.076     | 28.082     |   0.1 | 96.01
+Other   |            | 0.03094    |            |       |  0.11
 
-Nlocal:    17.25 ave 23 max 10 min
-Histogram: 1 0 0 0 0 0 2 0 0 1
-Nghost:    506.5 ave 519 max 490 min
-Histogram: 1 0 1 0 0 0 0 0 0 2
-Neighs:    705.75 ave 998 max 369 min
-Histogram: 1 0 0 0 0 1 1 0 0 1
+Nlocal:    15 ave 16 max 14 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Nghost:    437 ave 446 max 431 min
+Histogram: 2 0 0 0 0 0 1 0 0 1
+Neighs:    529 ave 595 max 437 min
+Histogram: 1 0 0 0 1 0 0 0 0 2
 
-Total # of neighbors = 2823
-Ave neighs/atom = 40.913
+Total # of neighbors = 2116
+Ave neighs/atom = 35.2667
 Neighbor list builds = 10000
 Dangerous builds = 0
-Total wall time: 0:00:23
+Total wall time: 0:00:29