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)
@@ -218,25 +249,50 @@ 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
@@ -248,55 +304,76 @@ if(ENABLE_LATTE)
     ExternalProject_get_property(latte_build INSTALL_DIR)
     set(LATTE_LIBRARIES ${INSTALL_DIR}/${CMAKE_INSTALL_LIBDIR}/liblatte.a)
     list(APPEND LAMMPS_DEPS latte_build)
+  else()
+    find_package(LATTE)
+    if(NOT LATTE_FOUND)
+      message(FATAL_ERROR "LATTE not found, help CMake to find it by setting LATTE_LIBRARY, or set DOWNLOAD_LATTE=ON to download it")
+    endif()
   endif()
-  list(APPEND LAMMPS_LINK_LIBS ${LATTE_LIBRARIES} ${LAPACK_LIBRARIES} ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
+  list(APPEND LAMMPS_LINK_LIBS ${LATTE_LIBRARIES} ${LAPACK_LIBRARIES})
 endif()
 
-if(ENABLE_USER-MOLFILE)
+if(PKG_USER-MOLFILE)
   add_library(molfile INTERFACE)
   target_include_directories(molfile INTERFACE ${LAMMPS_LIB_SOURCE_DIR}/molfile)
   target_link_libraries(molfile INTERFACE ${CMAKE_DL_LIBS})
   list(APPEND LAMMPS_LINK_LIBS molfile)
 endif()
 
-if(ENABLE_USER-NETCDF)
+if(PKG_USER-NETCDF)
   find_package(NetCDF REQUIRED)
   include_directories(NETCDF_INCLUDE_DIR)
   list(APPEND LAMMPS_LINK_LIBS ${NETCDF_LIBRARY})
   add_definitions(-DLMP_HAS_NETCDF -DNC_64BIT_DATA=0x0020)
 endif()
 
-if(ENABLE_USER-SMD)
-  find_package(Eigen3 REQUIRED)
+if(PKG_USER-SMD)
+  option(DOWNLOAD_Eigen3 "Download Eigen3 (instead of using the system's one)" OFF)
+  if(DOWNLOAD_Eigen3)
+    include(ExternalProject)
+    ExternalProject_Add(Eigen3_build
+      URL http://bitbucket.org/eigen/eigen/get/3.3.4.tar.gz 
+      URL_MD5 1a47e78efe365a97de0c022d127607c3
+      CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
+    )
+    ExternalProject_get_property(Eigen3_build SOURCE_DIR)
+    set(EIGEN3_INCLUDE_DIR ${SOURCE_DIR})
+    list(APPEND LAMMPS_DEPS Eigen3_build)
+  else()
+    find_package(Eigen3)
+    if(NOT Eigen3_FOUND)
+      message(FATAL_ERROR "Eigen3 not found, help CMake to find it by setting EIGEN3_INCLUDE_DIR, or set DOWNLOAD_Eigen3=ON to download it")
+    endif()
+  endif()
   include_directories(${EIGEN3_INCLUDE_DIR})
 endif()
 
-if(ENABLE_USER-QUIP)
+if(PKG_USER-QUIP)
   find_package(QUIP REQUIRED)
-  list(APPEND LAMMPS_LINK_LIBS ${QUIP_LIBRARIES} ${LAPACK_LIBRARIES} ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
+  list(APPEND LAMMPS_LINK_LIBS ${QUIP_LIBRARIES} ${LAPACK_LIBRARIES})
 endif()
 
-if(ENABLE_USER-QMMM)
+if(PKG_USER-QMMM)
+  message(WARNING "Building QMMM with CMake is still experimental")
   find_package(QE REQUIRED)
   include_directories(${QE_INCLUDE_DIRS})
-  list(APPEND LAMMPS_LINK_LIBS ${QE_LIBRARIES} ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
+  list(APPEND LAMMPS_LINK_LIBS ${QE_LIBRARIES})
 endif()
 
-if(ENABLE_USER-VTK)
+if(PKG_USER-VTK)
   find_package(VTK REQUIRED NO_MODULE)
   include(${VTK_USE_FILE})
   add_definitions(-DLAMMPS_VTK)
   list(APPEND LAMMPS_LINK_LIBS ${VTK_LIBRARIES})
 endif()
 
-if(ENABLE_KIM)
-  find_package(KIM QUIET)
-  if(NOT KIM_FOUND)
-    message(STATUS "KIM not found - we will build our own")
+if(PKG_KIM)
+  option(DOWNLOAD_KIM "Download kim-api (instead of using the system's one)" OFF)
+  if(DOWNLOAD_KIM)
     include(ExternalProject)
     ExternalProject_Add(kim_build
-      URL https://github.com/openkim/kim-api/archive/v1.9.4.tar.gz
-      URL_MD5 f4d35a1705eed46d64c7c0ab448ff3e0
+      URL https://github.com/openkim/kim-api/archive/v1.9.5.tar.gz
+      URL_MD5 9f66efc128da33039e30659f36fc6d00
       BUILD_IN_SOURCE 1
       CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR>
       )
@@ -304,41 +381,62 @@ if(ENABLE_KIM)
     set(KIM_INCLUDE_DIRS ${INSTALL_DIR}/include/kim-api-v1)
     set(KIM_LIBRARIES ${INSTALL_DIR}/lib/libkim-api-v1.so)
     list(APPEND LAMMPS_DEPS kim_build)
+  else()
+    find_package(KIM)
+    if(NOT KIM_FOUND)
+      message(FATAL_ERROR "KIM not found, help CMake to find it by setting KIM_LIBRARY and KIM_INCLUDE_DIR, or set DOWNLOAD_KIM=ON to download it")
+    endif()
   endif()
   list(APPEND LAMMPS_LINK_LIBS ${KIM_LIBRARIES})
   include_directories(${KIM_INCLUDE_DIRS})
 endif()
 
-if(ENABLE_MSCG)
+if(PKG_MSCG)
   find_package(GSL REQUIRED)
-  set(LAMMPS_LIB_MSCG_BIN_DIR ${LAMMPS_LIB_BINARY_DIR}/mscg)
-  set(MSCG_TARBALL ${LAMMPS_LIB_MSCG_BIN_DIR}/MS-CG-master.zip)
-  set(LAMMPS_LIB_MSCG_BIN_DIR ${LAMMPS_LIB_MSCG_BIN_DIR}/MSCG-release-master/src)
-  if(NOT EXISTS ${LAMMPS_LIB_MSCG_BIN_DIR})
-    if(NOT EXISTS ${MSCG_TARBALL})
-      message(STATUS "Downloading ${MSCG_TARBALL}")
-      file(DOWNLOAD
-        https://github.com/uchicago-voth/MSCG-release/archive/master.zip
-        ${MSCG_TARBALL} SHOW_PROGRESS) #EXPECTED_MD5 cannot be due due to master
+  option(DOWNLOAD_MSCG "Download latte (instead of using the system's one)" OFF)
+  if(DOWNLOAD_MSCG)
+    include(ExternalProject)
+    if(NOT LAPACK_FOUND)
+      set(EXTRA_MSCG_OPTS "-DLAPACK_LIBRARIES=${CMAKE_CURRENT_BINARY_DIR}/liblinalg.a")
+    endif()
+    ExternalProject_Add(mscg_build
+      URL https://github.com/uchicago-voth/MSCG-release/archive/1.7.3.1.tar.gz
+      URL_MD5 8c45e269ee13f60b303edd7823866a91
+      SOURCE_SUBDIR src/CMake
+      CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR> -DCMAKE_POSITION_INDEPENDENT_CODE=${CMAKE_POSITION_INDEPENDENT_CODE} ${EXTRA_MSCG_OPTS}
+      BUILD_COMMAND make mscg INSTALL_COMMAND ""
+      )
+    ExternalProject_get_property(mscg_build BINARY_DIR)
+    set(MSCG_LIBRARIES ${BINARY_DIR}/libmscg.a)
+    ExternalProject_get_property(mscg_build SOURCE_DIR)
+    set(MSCG_INCLUDE_DIRS ${SOURCE_DIR}/src)
+    list(APPEND LAMMPS_DEPS mscg_build)
+    if(NOT LAPACK_FOUND)
+      file(MAKE_DIRECTORY ${MSCG_INCLUDE_DIRS})
+      add_dependencies(mscg_build linalg)
+    endif()
+  else()
+    find_package(MSCG)
+    if(NOT MSCG_FOUND)
+      message(FATAL_ERROR "MSCG not found, help CMake to find it by setting MSCG_LIBRARY and MSCG_INCLUDE_DIRS, or set DOWNLOAD_MSCG=ON to download it")
     endif()
-    message(STATUS "Unpacking ${MSCG_TARBALL}")
-    execute_process(COMMAND ${CMAKE_COMMAND} -E tar xvf ${MSCG_TARBALL}
-      WORKING_DIRECTORY ${LAMMPS_LIB_BINARY_DIR}/mscg)
   endif()
-  file(GLOB MSCG_SOURCES ${LAMMPS_LIB_MSCG_BIN_DIR}/*.cpp)
-  add_library(mscg STATIC ${MSCG_SOURCES})
-  list(APPEND LAMMPS_LINK_LIBS mscg)
-  target_compile_options(mscg PRIVATE -DDIMENSION=3 -D_exclude_gromacs=1)
-  target_include_directories(mscg PUBLIC ${LAMMPS_LIB_MSCG_BIN_DIR})
-  target_link_libraries(mscg ${GSL_LIBRARIES} ${LAPACK_LIBRARIES})
+  list(APPEND LAMMPS_LINK_LIBS ${MSCG_LIBRARIES} ${GSL_LIBRARIES} ${LAPACK_LIBRARIES})
+  include_directories(${MSCG_INCLUDE_DIRS})
+endif()
+
+if(PKG_COMPRESS)
+  find_package(ZLIB REQUIRED)
+  include_directories(${ZLIB_INCLUDE_DIRS})
+  list(APPEND LAMMPS_LINK_LIBS ${ZLIB_LIBRARIES})
 endif()
 
 ########################################################################
 # Basic system tests (standard libraries, headers, functions, types)   #
 ########################################################################
-include(CheckIncludeFile)
+include(CheckIncludeFileCXX)
 foreach(HEADER math.h)
-  check_include_file(${HEADER} FOUND_${HEADER})
+  check_include_file_cxx(${HEADER} FOUND_${HEADER})
   if(NOT FOUND_${HEADER})
     message(FATAL_ERROR "Could not find needed header - ${HEADER}")
   endif(NOT FOUND_${HEADER})
@@ -382,7 +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})
 
@@ -396,7 +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
@@ -417,40 +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
                          ${USER-OMP_SOURCES_DIR}/thr_omp.cpp
@@ -467,7 +551,7 @@ if(ENABLE_USER-OMP)
     include_directories(${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 ${LAMMPS_LIB_BINARY_DIR}/kokkos)
   add_definitions(-DLMP_KOKKOS)
@@ -503,7 +587,7 @@ if(ENABLE_KOKKOS)
   RegisterNBinStyle(${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)
@@ -516,7 +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}")
@@ -530,7 +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
                            ${USER-INTEL_SOURCES_DIR}/intel_buffers.h
@@ -554,7 +661,10 @@ if(ENABLE_USER-INTEL)
     include_directories(${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
@@ -651,7 +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)
@@ -691,6 +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 ${LAMMPS_DEPS})
@@ -712,35 +828,93 @@ if(ENABLE_TESTING)
   add_test(ShowHelp lmp${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/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="20 Apr 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
-20 Apr 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

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_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

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
+57 1 38.22 19.02 18.12
+58 1 10.95 17.4 0.39
+59 1 1.65 19.87 6.67
+60 1 5.15 1.94 14.61
+61 1 8.2 31.43 15.72
+62 1 0.55 20.85 2.45
+63 1 15.27 31.74 0.33
+64 1 17.9 9.84 23.87
+65 1 1.46 8.39 19.24
+66 1 37.79 25.11 12.24
+67 1 14.11 27.19 30.7
+68 1 29.39 24.12 38.92
+69 1 39.15 20.32 39.86
+70 1 11.79 11.38 30.6
+71 1 29.87 30.18 32.5
+72 1 11.06 37.8 30.18
+73 1 20.11 4.59 35.57
+74 1 37.19 27.23 1.44
+75 1 18.83 26.13 35.26
+76 1 29.27 7.86 36.75
+77 1 34.83 29.59 37.82
+78 1 22.16 34.68 25.27
+79 1 5.95 14.65 25.55
+80 1 -0.04 3.48 29.91
+81 1 14.69 6.75 38.06
+82 1 16.8 23.69 3.14
+83 1 14.52 38.72 21.61
+84 1 37.36 15.13 27.98
+85 1 29.79 17.03 27.55
+86 1 21.01 0.39 0.9
+87 1 35.3 6.45 14.41
+88 1 13.74 34.69 10.01
+89 1 13.83 7.92 31.88
+90 1 26.88 37.81 22.36
+91 1 31.76 7.34 10.03
+92 1 11.98 37.49 19.61
+93 1 29.19 31.74 20.69
+94 1 39.15 10.97 21.06
+95 1 1.47 5 22.21
+96 1 -0.1 1.33 16.26
+97 1 34.74 34.78 30.66
+98 1 22.09 26.78 2.27
+99 1 36.58 34.8 16.19
+100 1 19.09 24.88 15.75
+101 1 2.21 31.42 38.32
+102 1 28.02 8.18 29.77
+103 1 15.99 16.78 17.61
+104 1 32.43 12.2 35.3
+105 1 26.54 38.8 30.88
+106 1 35.58 22.23 18.31
+107 1 28.3 30.81 2.96
+108 1 8.95 32.9 9.02
+109 1 28.51 30.02 29.39
+110 1 13 5.35 34.26
+111 1 37.9 36.79 1.37
+112 1 12.78 1.99 40.66
+113 1 21.19 34.55 17.45
+114 1 10.5 20 5.07
+115 1 16.19 21.64 18.49
+116 1 14.62 26.41 19.88
+117 1 27.97 2.89 28.03
+118 1 29.44 14.35 39.04
+119 1 2.29 24.16 33.8
+120 1 39.22 15.81 32.02
+121 1 7.31 19.66 18.18
+122 1 27.67 7.98 15.53
+123 1 31.23 4.04 33
+124 1 29.52 39.44 28.71
+125 1 30.86 20.28 15.84
+126 1 32.25 7.44 19.79
+127 1 34.68 15.68 1.18
+128 1 16.58 27.98 27.97
+129 1 32.27 24.24 15.82
+130 1 3.86 6.57 39.8
+131 1 9.1 2.88 13.12
+132 1 17.84 27.8 11.79
+133 1 4.77 10.88 6.75
+134 1 16.58 24.21 24.5
+135 1 10.17 19.31 38.32
+136 1 6.27 7.81 36.44
+137 1 34.76 37.89 29.76
+138 1 40.99 38.22 35.21
+139 1 25.04 21.79 36.88
+140 1 4.78 15.35 16.44
+141 1 19.24 5.77 40.18
+142 1 13.59 11.27 37.14
+143 1 1.61 23.83 39.61
+144 1 6.02 33.07 3.77
+145 1 0.85 7.4 35.42
+146 1 6.47 40.34 4.65
+147 1 16.45 36.52 15.44
+148 1 19.58 9.5 1.64
+149 1 1.36 1.72 35.53
+150 1 11.74 5.48 4.98
+151 1 25.45 40.36 15.44
+152 1 19.09 0.74 36.18
+153 1 31.78 37.98 1.84
+154 1 23.26 18.47 38.56
+155 1 7.29 22.87 25.86
+156 1 2.36 7.83 8.78
+157 1 39.61 25.94 21.12
+158 1 7.78 18.97 25.29
+159 1 36.56 19.61 26.7
+160 1 4.64 12.06 19.9
+161 1 21.05 33.08 0.87
+162 1 33.93 22.87 39.71
+163 1 33.62 29.48 20.83
+164 1 0.64 18.79 9.52
+165 1 27.53 16.7 22.51
+166 1 17.66 9.84 14.61
+167 1 31.23 22.44 24.98
+168 1 39.3 34.88 11.03
+169 1 24.01 10.56 0.09
+170 1 15.81 33.44 18.52
+171 1 19.92 30.61 19.25
+172 1 16.49 3.95 38.28
+173 1 18.6 38.87 24.98
+174 1 33.04 25.55 8.57
+175 1 16.9 35.09 22.94
+176 1 15.18 6.74 2.33
+177 1 40.54 12.58 31.65
+178 1 21.21 37.62 14.35
+179 1 33.52 38.19 14.89
+180 1 22.06 12.49 29.81
+181 1 19.49 29.03 2.52
+182 1 26.97 18.55 38.45
+183 1 24.1 11.86 17.22
+184 1 12.02 0.55 10.39
+185 1 3.8 35.94 19.94
+186 1 8.31 14.31 37.4
+187 1 29.03 8.28 22.92
+188 1 18.92 0.22 27.87
+189 1 26.79 24.9 24.62
+190 1 36.59 18.86 21.13
+191 1 33.06 13.58 30.17
+192 1 32.37 2.02 39.69
+193 1 22.65 25.97 32.59
+194 1 21.81 38.04 33.85
+195 1 36.82 37.68 19.22
+196 1 32.48 31.43 33.66
+197 1 8.75 36.66 20.34
+198 1 14.88 15.11 28.76
+199 1 22.83 28.55 29.5
+200 1 2.98 12.06 2.88
+201 1 3.01 37 6.91
+202 1 14.79 16.69 3.66
+203 1 12.62 38.28 0.97
+204 1 40.07 21.27 25.25
+205 1 34.58 6.14 39.48
+206 1 11.51 30.52 33.53
+207 1 32.22 9.28 30.52
+208 1 0.7 4.01 38.87
+209 1 32.66 39.86 36.84
+210 1 27.34 34.57 21.76
+211 1 13.7 23.12 8.34
+212 1 28 9.71 6.29
+213 1 31.69 26.39 38.19
+214 1 2.04 20.93 36.95
+215 1 30.31 26.61 12.31
+216 1 25.37 20.63 9.4
+217 1 16.29 5.62 14.04
+218 1 1.36 1.95 4.97
+219 1 38.75 26.8 5.62
+220 1 40.28 29.89 12.27
+221 1 0.52 31.22 7.58
+222 1 15.64 21.64 14.71
+223 1 10.11 28.8 9.67
+224 1 19.03 37.3 38.87
+225 1 12.07 6.46 19.25
+226 1 36.22 21.11 15.02
+227 1 12.49 15.69 7.21
+228 1 25.2 30.8 19.71
+229 1 8.24 35.22 23.02
+230 1 9.94 4.1 1.86
+231 1 4.31 19.07 26.23
+232 1 22.03 19.99 14.19
+233 1 30.84 5.24 2.75
+234 1 35.51 30.52 32.3
+235 1 3.88 20.41 39.48
+236 1 30.86 0.39 31.56
+237 1 25.91 27.12 39.04
+238 1 33.39 5.37 4.51
+239 1 20.58 28.33 37.53
+240 1 11.83 21.81 39.11
+241 1 39.94 5.2 5.73
+242 1 29.89 33.21 15.44
+243 1 23.42 15.38 30.98
+244 1 28.66 11.56 16.13
+245 1 16.74 20.43 21.72
+246 1 9.31 0.26 22.42
+247 1 4.38 37.78 14.12
+248 1 13.86 4.65 16.99
+249 1 6.72 27.43 8.14
+250 1 33.45 18.74 19.98
+251 1 17.34 14.55 35.57
+252 1 14.21 37.39 28.76
+253 1 26.29 29.06 22.26
+254 1 36.52 26.18 15.62
+255 1 17.6 8.81 10.14
+256 1 21.95 25.19 17.69
+257 1 17.4 7.46 18.59
+258 1 6.15 29.7 35.99
+259 1 9.73 37.39 24.96
+260 1 28.58 28.21 36.19
+261 1 8.24 13.72 32.2
+262 1 13.25 34.6 22.71
+263 1 38.58 7.98 10.3
+264 1 18.29 29.75 23.51
+265 1 3.74 13.22 31.05
+266 1 30.78 0.7 24.57
+267 1 24.5 12.94 10.81
+268 1 33.88 26.44 1.96
+269 1 29.92 22.6 9.59
+270 1 15.87 21.94 33.44
+271 1 23.63 8.41 10.95
+272 1 26.53 0.01 7.58
+273 1 33.88 8.73 2.52
+274 1 39.74 31.46 36.87
+275 1 13.28 39.54 37
+276 1 24.74 35.41 32.14
+277 1 17.3 34.32 6.85
+278 1 24.43 13.36 5.63
+279 1 31.23 17.12 7.11
+280 1 15.58 37.85 34.06
+281 1 25.93 38.17 3.13
+282 1 31.84 34.34 39.67
+283 1 14.41 17.74 14.43
+284 1 9.4 1.78 29.53
+285 1 8.29 29.61 6.81
+286 1 7.13 17.36 -0.19
+287 1 38.04 19.52 11.25
+288 1 34.87 32.77 38.75
+289 1 27.18 22.49 5.69
+290 1 29.69 27.11 20.29
+291 1 25.23 2.22 39.75
+292 1 35.8 17.1 36.09
+293 1 20.53 17.67 35.47
+294 1 23.41 31.36 2.24
+295 1 25.17 20.09 29.2
+296 1 0.32 9.28 39.74
+297 1 22.49 18.77 29.89
+298 1 38.64 0.85 39.43
+299 1 18.55 5.87 9.15
+300 1 35.21 28.69 25.76
+301 1 39.24 15.68 6.36
+302 1 5.91 13.29 3.92
+303 1 0.5 21.25 21.62
+304 1 34.39 9.43 18.59
+305 1 22.7 1.03 8.79
+306 1 40.15 16.25 24.87
+307 1 16.52 13.69 10.25
+308 1 6.88 36.77 39.57
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+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 
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+   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 
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+     200    362.87766    42.061118 0.0034851739            1            1 
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+    4900    316.55055    34.663238 0.0034851739            1            1 
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+    5000    400.21044   -8.1780861 0.0034851739            1            1 
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+    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 
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+    6100    313.86572    3.4344108 0.0034851739            1            1 
+    6150    325.64197     32.39212 0.0034851739            1            1 
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+    6250    369.30937    39.020881 0.0034851739            1            1 
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+    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 
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+    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 
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+    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
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+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
+
+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
+
+MiddleBondTorsion Coeffs
+
+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
+32 0 0 0 1.5202
+33 0 0 0 1.3649
+34 -2.2208 0.5479 -0.3527 1.457
+35 -3.4611 1.6996 -0.6007 1.457
+36 -15.4174 -7.3055 -1.0749 1.53
+
+BondBond13 Coeffs
+
+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
+10 0 1.53 1.202
+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
+20 0 1.01 1.101
+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
+26 0 1.01 1.5202
+27 0 1.01 1.202
+28 0 1.01 1.3649
+29 0 1.452 1.53
+30 0 1.452 1.101
+31 0 1.53 1.416
+32 0 1.101 1.416
+33 0 1.416 0.965
+34 0 1.006 1.53
+35 0 1.006 1.101
+36 0 1.457 1.53
+
+AngleTorsion Coeffs
+
+1 -0.7466 -0.9448 -0.6321 0.0162 1.4211 -1.4092 108.53 110.77
+2 -0.8085 0.5569 -0.2466 -0.8085 0.5569 -0.2466 110.77 110.77
+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
+5 0.3886 -0.3139 0.1389 0.3886 -0.3139 0.1389 112.67 112.67
+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
+21 -1.523 1.1296 0.7167 -0.7555 0.0564 1.2177 111.037 114.302
+22 0.0372 -0.3418 -0.0775 -1.5157 2.0781 0.5364 111.037 108.937
+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
+28 0 0 0 0 0 0 117.961 0
+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
+34 0.2873 -0.8072 -0.096 -3.343 4.4558 -0.0346 110.954 111.91
+35 -0.4294 -0.4442 -0.6141 -3.9582 2.0063 0.3213 110.954 110.62
+36 2.0125 0.944 -2.7612 -1.9225 -1.345 0.221 111.91 112.67
+
+Improper Coeffs # class2
+
+1 0 0
+2 0 0
+3 0 0
+4 0 0
+5 0 0
+6 0 0
+7 0 0
+8 0 0
+9 0 0
+10 0 0
+11 0 0
+12 0 0
+13 24.3329 0
+
+AngleAngle Coeffs
+
+1 0 0 0 0 118.985 123.145
+2 0.2738 -0.4825 0.2738 110.77 107.66 110.77
+3 -1.3199 -1.3199 0.1184 112.67 110.77 110.77
+4 2.0403 -1.8202 1.0827 108.53 107.734 110.77
+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
+12 0 0 0 113.868 117.961 111.037
+13 0 0 0 116.926 123.145 125.542
+
+Atoms # full
+
+1 1 1 0.0000000000000000e+00   12.288168        0.738732        4.374280 0 0 0
+2 1 2 2.9999999999999999e-01   13.959928       -0.883144        5.090597 0 0 0
+3 1 3 0.0000000000000000e+00   14.411288       -1.994419        5.682160 0 0 0
+4 1 4 0.0000000000000000e+00   12.881083        0.872503        3.506176 0 0 0
+5 1 4 0.0000000000000000e+00   11.232775        0.801641        3.998777 0 0 0
+6 1 5 0.0000000000000000e+00   13.704366       -2.470396        6.130105 0 0 0
+7 1 1 0.0000000000000000e+00   12.489752       -0.793693        4.710639 0 0 0
+8 1 1 0.0000000000000000e+00   12.455071        1.866388        5.385870 0 0 0
+9 1 1 0.0000000000000000e+00   11.248961        1.901849        6.347664 0 0 0
+10 1 2 2.9999999999999999e-01  10.005971        2.466710        5.772840 -1 1 0
+11 1 6 0.0000000000000000e+00  14.795360       -0.034436        4.807367 0 0 0
+12 1 6 0.0000000000000000e+00   9.115239        1.654547        5.617002 -1 0 0
+13 1 3 0.0000000000000000e+00   9.745096        3.807654        5.573585 -1 1 0
+14 1 4 0.0000000000000000e+00  12.248215       -1.371492        3.808598 0 0 0
+15 1 4 0.0000000000000000e+00  11.715755       -1.036825        5.500449 0 0 0
+16 1 4 0.0000000000000000e+00  12.559724        2.807687        4.858452 0 1 0
+17 1 4 0.0000000000000000e+00  13.299968        1.616570        6.123781 0 0 0
+18 1 4 0.0000000000000000e+00  11.650505        2.330454        7.282410 0 1 0
+19 1 4 0.0000000000000000e+00  10.888420        0.913219        6.637162 -1 0 0
+20 1 5 0.0000000000000000e+00  10.550073        4.294209        5.758192 -1 1 0
+21 2 1 0.0000000000000000e+00   5.851425        1.929552        6.038335 0 0 0
+22 2 1 0.0000000000000000e+00   6.741509        3.160751        6.233074 0 0 0
+23 2 7 -2.9999999999999999e-01  7.957761        3.121780        5.252257 1 0 0
+24 2 7 -2.9999999999999999e-01  2.599653       -2.258940        5.985863 0 -1 0
+25 2 1 0.0000000000000000e+00   3.834337       -1.907078        5.441528 0 -1 0
+26 2 1 0.0000000000000000e+00   4.810793       -1.083699        6.310184 0 -1 0
+27 2 4 0.0000000000000000e+00   6.505912        1.182799        5.449104 0 0 0
+28 2 4 0.0000000000000000e+00   5.156429        2.256468        5.348423 0 0 0
+29 2 4 0.0000000000000000e+00   7.232782        3.178785        7.181911 0 0 0
+30 2 4 0.0000000000000000e+00   6.251671        4.103621        6.222913 0 0 0
+31 2 8 0.0000000000000000e+00   8.249909        4.070668        4.881297 1 0 0
+32 2 8 0.0000000000000000e+00   7.813025        2.623184        4.400744 1 0 0
+33 2 8 0.0000000000000000e+00   2.626695       -2.857547        6.817247 0 -1 0
+34 2 8 0.0000000000000000e+00   1.955281       -2.684319        5.328460 0 -1 0
+35 2 4 0.0000000000000000e+00   3.637708       -1.322842        4.469265 0 -1 0
+36 2 4 0.0000000000000000e+00   4.415570       -2.739689        4.997336 0 -1 0
+37 2 4 0.0000000000000000e+00   5.710714       -1.010014        5.642798 0 -1 0
+38 2 4 0.0000000000000000e+00   5.103831       -1.696423        7.160345 0 -1 0
+39 2 1 0.0000000000000000e+00   5.270763        1.286629        7.308822 0 0 0
+40 2 4 0.0000000000000000e+00   4.834381        2.168531        7.931687 0 0 1
+41 2 4 0.0000000000000000e+00   6.118354        0.786724        7.794709 0 0 1
+42 2 1 0.0000000000000000e+00   4.273849        0.167695        6.957862 0 -1 0
+43 2 4 0.0000000000000000e+00   3.792544       -0.081782        7.904418 0 -1 1
+44 2 4 0.0000000000000000e+00   3.527495        0.674238        6.348869 0 0 0
+
+Velocities
+
+1 -2.4626989626218821e-03 -1.5920230003311222e-03 -3.0621927786115238e-03
+2 9.5082416704385837e-03 -6.9903166167507250e-03 1.3702671335945608e-02
+3 2.3431518493187576e-03 -2.9261683108242173e-03 1.4269399726982105e-03
+4 -1.8184451408256214e-02 3.1103803691687960e-02 -1.3358827768357973e-02
+5 2.6084132471017967e-02 -1.0819576493517332e-02 3.0403384454794881e-02
+6 -4.7312115958218744e-03 -1.9111462399478338e-02 -3.6793354156497558e-02
+7 -7.5068797595949869e-03 6.5661422055962489e-03 1.3226575122695422e-03
+8 3.3807881380161281e-03 3.0458732663557089e-03 2.2368826795446284e-03
+9 -3.1113905793879316e-03 8.2908867720754773e-03 -1.7561238039496530e-03
+10 2.4685206571693056e-03 1.3194776209841030e-03 -2.8041877032800441e-03
+11 -3.4945605770565296e-03 3.2323777135621814e-03 1.6223017668450866e-03
+12 -6.1153483612847778e-03 -5.1534857074262185e-03 1.7735747357354274e-03
+13 2.1384296781859011e-04 -4.5398902942729667e-03 6.1649769894413760e-03
+14 2.5004619864373401e-03 -1.5709184283264888e-03 2.0837548254667757e-02
+15 6.0547939205643532e-03 -1.2650704436910937e-02 -5.4430753266962190e-03
+16 -1.0374605775698001e-02 9.1408658463889240e-03 -1.1306875858287088e-02
+17 -1.2736499128987409e-02 -9.1726811852506501e-03 5.1136502685461254e-03
+18 7.6741778607048112e-03 1.8629856635459279e-02 -1.1300096447670932e-02
+19 -1.8616138775281121e-02 1.0848388547730185e-03 -5.7118433687798576e-03
+20 5.4137572241479059e-03 -1.4564578166395727e-02 -1.2618420441909540e-02
+21 5.8473521452312256e-03 -4.0595286000332086e-03 -6.2517801580146415e-03
+22 3.6402033824753104e-03 -1.4629540504663154e-03 -4.0030712318898046e-03
+23 9.0266305019107689e-03 -2.7511425384659687e-03 4.5576402565437142e-03
+24 -1.3102302415548614e-02 -4.7286703965305791e-03 -1.8966887841189517e-03
+25 7.8621682621103171e-03 -4.2046313540949568e-03 9.6887957374751301e-04
+26 -4.7380176438337968e-03 9.6090441940775827e-03 -8.7592431387039336e-03
+27 5.4311658811632517e-03 2.0032224663495989e-02 -9.4952076489808503e-03
+28 -2.9056381493904374e-03 3.3317109723156875e-03 1.6650350064426677e-02
+29 -6.4569944033489122e-03 2.8423983541959541e-03 -2.6066912906505167e-02
+30 -2.2173867823429387e-02 1.4628839880961319e-02 -2.3330833961402380e-02
+31 9.1925713381983114e-03 -2.5697556639281928e-03 -1.2822203161488303e-02
+32 -8.3206975051927905e-03 -2.2538429924858707e-03 7.7620244118580314e-03
+33 1.9920685674825727e-02 5.0317764848494097e-03 -2.1106672824976403e-02
+34 1.4118463330250982e-02 1.7455545466840316e-02 -1.2482101375598437e-02
+35 -6.1116505640437966e-03 1.3353021777303568e-02 -2.5492434283827668e-02
+36 9.1001521565859649e-03 5.5737774505222404e-03 1.4573768978939985e-02
+37 1.6523593470528035e-03 -2.2107518020000917e-02 2.0311423445130115e-02
+38 -1.0346275393471860e-02 1.6055856586351790e-02 5.5489127019262424e-03
+39 -3.2054811383248638e-03 1.6779208962376315e-03 2.9390509537535661e-03
+40 1.9649219364916443e-02 4.0815776523222859e-03 -9.8422441166041274e-03
+41 5.6961697588160361e-04 7.1361132234741477e-04 4.6335764220256257e-03
+42 2.2221300208006252e-03 3.6217319632558197e-03 -6.3299398503455151e-03
+43 2.5710172734841170e-03 8.0029179814482924e-03 1.9992986928468189e-02
+44 -6.0827581822674656e-03 -1.1834273655641976e-02 2.0526923045885208e-02
+
+Bonds
+
+1 1 1 5
+2 1 1 4
+3 2 1 7
+4 2 1 8
+5 3 2 3
+6 5 2 11
+7 6 3 6
+8 4 7 2
+9 1 7 14
+10 1 7 15
+11 2 8 9
+12 1 8 16
+13 1 8 17
+14 4 9 10
+15 1 9 18
+16 1 9 19
+17 5 10 12
+18 3 10 13
+19 6 13 20
+20 7 21 22
+21 8 21 27
+22 8 21 28
+23 7 21 39
+24 9 22 23
+25 8 22 29
+26 8 22 30
+27 10 23 31
+28 10 23 32
+29 10 24 33
+30 10 24 34
+31 9 25 24
+32 7 25 26
+33 8 25 35
+34 8 25 36
+35 8 26 37
+36 8 26 38
+37 7 26 42
+38 8 39 40
+39 8 39 41
+40 7 39 42
+41 8 42 43
+42 8 42 44
+
+Angles
+
+1 1 5 1 4
+2 2 7 1 5
+3 2 8 1 5
+4 2 7 1 4
+5 2 8 1 4
+6 3 7 1 8
+7 4 7 2 3
+8 5 3 2 11
+9 6 7 2 11
+10 7 2 3 6
+11 8 1 7 2
+12 2 1 7 14
+13 2 1 7 15
+14 9 2 7 14
+15 9 2 7 15
+16 1 14 7 15
+17 3 1 8 9
+18 2 1 8 16
+19 2 1 8 17
+20 2 9 8 16
+21 2 9 8 17
+22 1 16 8 17
+23 8 8 9 10
+24 2 8 9 18
+25 2 8 9 19
+26 9 10 9 18
+27 9 10 9 19
+28 1 18 9 19
+29 6 9 10 12
+30 4 9 10 13
+31 5 13 10 12
+32 7 10 13 20
+33 10 22 21 27
+34 10 22 21 28
+35 11 22 21 39
+36 12 27 21 28
+37 10 39 21 27
+38 10 39 21 28
+39 13 21 22 23
+40 10 21 22 29
+41 10 21 22 30
+42 14 23 22 29
+43 14 23 22 30
+44 12 29 22 30
+45 15 22 23 31
+46 15 22 23 32
+47 16 31 23 32
+48 15 25 24 33
+49 15 25 24 34
+50 16 33 24 34
+51 13 26 25 24
+52 14 24 25 35
+53 14 24 25 36
+54 10 26 25 35
+55 10 26 25 36
+56 12 35 25 36
+57 10 25 26 37
+58 10 25 26 38
+59 11 25 26 42
+60 12 37 26 38
+61 10 42 26 37
+62 10 42 26 38
+63 10 21 39 40
+64 10 21 39 41
+65 11 21 39 42
+66 12 40 39 41
+67 10 42 39 40
+68 10 42 39 41
+69 11 26 42 39
+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/latte/data.graphene.boxrel

@@ -0,0 +1,49 @@
+ LAMMPS Description
+ 
+          32 atoms
+ 
+           1 atom types
+ 
+   0.0000000000000000        10.000000000000000      xlo xhi
+   0.0000000000000000        8.0000000000000000      ylo yhi
+   0.0000000000000000        20.000000000000000      zlo zhi
+   4.8985871965894128E-016   1.2246467991473533E-015   1.2246467991473533E-015 xy xz yz
+ 
+ Masses
+ 
+              1   12.010000000000000     
+ 
+ Atoms
+ 
+    1    1    1   0.0   4.93100   4.25000   0.00500
+    2    1    1   0.0   8.62100   2.12100   0.14000
+    3    1    1   0.0   3.70700   2.12600   0.14700
+    4    1    1   0.0   7.38200   4.25400   0.07800
+    5    1    1   0.0   2.47900   4.25400   0.08000
+    6    1    1   0.0   6.15800   6.37400  -0.01000
+    7    1    1   0.0   1.23700   6.38300   0.06600
+    8    1    1   0.0   1.24000   2.12100   0.14600
+    9    1    1   0.0   6.15500   2.12600   0.12900
+   10    1    1   0.0   0.00700   4.25200   0.12200
+   11    1    1   0.0   8.62100   6.38500   0.04100
+   12    1    1   0.0   3.70000   6.37400  -0.01000
+   13    1    1   0.0   0.00600   1.41600   0.13000
+   14    1    1   0.0   4.93000   1.40800   0.14700
+   15    1    1   0.0   8.61800   3.54600   0.11500
+   16    1    1   0.0   3.70800   3.55300   0.08400
+   17    1    1   0.0   7.39400   5.68000   0.03500
+   18    1    1   0.0   2.46500   5.68000   0.03500
+   19    1    1   0.0   6.16000   7.80500   0.02700
+   20    1    1   0.0   1.23800   7.81100   0.06000
+   21    1    1   0.0   2.47300   1.41800   0.16100
+   22    1    1   0.0   7.38900   1.41700   0.14800
+   23    1    1   0.0   1.24200   3.54700   0.12600
+   24    1    1   0.0   6.15300   3.55300   0.07400
+   25    1    1   0.0   0.00700   5.67800   0.09700
+   26    1    1   0.0   4.93100   5.66800  -0.03100
+   27    1    1   0.0   8.62000   7.81300   0.03900
+   28    1    1   0.0   3.70100   7.80200   0.03700
+   29    1    1   0.0   0.00700  -0.01000   0.08900
+   30    1    1   0.0   4.93100  -0.01500   0.16100
+   31    1    1   0.0   2.47300  -0.01200   0.14400
+   32    1    1   0.0   7.38900  -0.01300   0.14800

examples/latte/in.graphene.boxrel

@@ -0,0 +1,44 @@
+# Simple water model with LATTE
+
+units		metal
+atom_style	full
+atom_modify     sort 0 0.0    # turn off sorting of the coordinates
+
+read_data       data.graphene.boxrel
+
+# replicate system if requested
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+
+variable        nrep equal v_x*v_y*v_z
+if              "${nrep} > 1" then "replicate $x $y $z"
+
+# initialize system
+
+velocity	all create 0.0 87287 loop geom
+
+pair_style      zero 1.0
+pair_coeff	* *  
+
+neighbor	1.0 bin
+neigh_modify    every 1 delay 0 check yes 
+
+timestep        0.00025
+
+fix 1 all box/relax iso 0.0 vmax 0.001
+
+fix             2 all latte NULL
+fix_modify      2 energy yes
+
+thermo_style    custom   etotal
+
+# minimization
+
+thermo          1
+fix 3 all print 1 "Total Energy ="
+min_style cg
+min_modify dmax 0.1
+min_modify line quadratic
+minimize        1.0e-4 1.0e-4 10000 10000

examples/latte/in.latte.water.min

@@ -37,5 +37,6 @@ thermo_style    custom step temp pe etotal press
 # minimization
 
 thermo          10
-min_style fire
-minimize        1.0e-9 1.0e-9 500 500
+
+min_style       fire
+minimize        1.0e-4 1.0e-4 500 500

examples/latte/latte.in

@@ -11,7 +11,6 @@ LATTE INPUT FILE
 CONTROL{
   xControl= 1
   BASISTYPE= NONORTHO
-  COORDSFILE= "./coords.dat"
   PARAMPATH= "./TBparam"
   KBT= 0.0
   ENTROPYKIND= 1
@@ -32,9 +31,3 @@ CONTROL{
   XBODISORDER= 5
   KON= 0
 }
-
-#Controls for QMD (if using lammps MAXITER must be set to -1)
-MDCONTROL{
-  MAXITER= -1
-}
-

examples/latte/log.19Sep17.latte.sucrose.g++.1

@@ -1,406 +0,0 @@
- The log file for latte_lib
- 
- CONTROL{                                          }                                                 
-  
- WARNING: variable JobName= is missing. I will use a default value instead ...
- WARNING: variable PARAMPATH= is missing. I will use a default value instead ...
- WARNING: variable DEBUGON= is missing. I will use a default value instead ...
- WARNING: variable FERMIM= is missing. I will use a default value instead ...
- WARNING: variable CGORLIB= is missing. I will use a default value instead ...
- WARNING: variable NORECS= is missing. I will use a default value instead ...
- WARNING: variable VDWON= is missing. I will use a default value instead ...
- WARNING: variable ORDERNMOL= is missing. I will use a default value instead ...
- WARNING: variable LCNON= is missing. I will use a default value instead ...
- WARNING: variable LCNITER= is missing. I will use a default value instead ...
- WARNING: variable MDON= is missing. I will use a default value instead ...
- WARNING: variable PBCON= is missing. I will use a default value instead ...
- WARNING: variable RESTART= is missing. I will use a default value instead ...
- WARNING: variable NGPU= is missing. I will use a default value instead ...
- WARNING: variable COMPFORCE= is missing. I will use a default value instead ...
- WARNING: variable DOSFIT= is missing. I will use a default value instead ...
- WARNING: variable INTS2FIT= is missing. I will use a default value instead ...
- WARNING: variable NFITSTEP= is missing. I will use a default value instead ...
- WARNING: variable QFIT= is missing. I will use a default value instead ...
- WARNING: variable PPFITON= is missing. I will use a default value instead ...
- WARNING: variable ALLFITON= is missing. I will use a default value instead ...
- WARNING: variable PPSTEP= is missing. I will use a default value instead ...
- WARNING: variable BISTEP= is missing. I will use a default value instead ...
- WARNING: variable PP2FIT= is missing. I will use a default value instead ...
- WARNING: variable BINT2FIT= is missing. I will use a default value instead ...
- WARNING: variable PPNMOL= is missing. I will use a default value instead ...
- WARNING: variable PPNGEOM= is missing. I will use a default value instead ...
- WARNING: variable PARREP= is missing. I will use a default value instead ...
- WARNING: variable VERBOSE= is missing. I will use a default value instead ...
- WARNING: variable MIXER= is missing. I will use a default value instead ...
- WARNING: variable RESTARTLIB= is missing. I will use a default value instead ...
- WARNING: variable CGTOL= is missing. I will use a default value instead ...
- WARNING: variable ELEC_ETOL= is missing. I will use a default value instead ...
- WARNING: variable COULACC= is missing. I will use a default value instead ...
- WARNING: variable COULCUT= is missing. I will use a default value instead ...
- WARNING: variable COULR1= is missing. I will use a default value instead ...
- WARNING: variable CHTOL= is missing. I will use a default value instead ...
- WARNING: variable BETA= is missing. I will use a default value instead ...
- WARNING: variable MCSIGMA= is missing. I will use a default value instead ...
- WARNING: variable PPBETA= is missing. I will use a default value instead ...
- WARNING: variable PPSIGMA= is missing. I will use a default value instead ...
- WARNING: variable ER= is missing. I will use a default value instead ...
- WARNING: variable INITIALIZED= is missing. I will use a default value instead ...
-  
-  
- ############### Parameters used for this run ################
-  CONTROL{                                          
-  xControl=           1
-  DEBUGON=           0
-  FERMIM=           6
-  CGORLIB=           1
-  NORECS=           1
-  ENTROPYKIND=           1
-  PPOTON=           1
-  VDWON=           0
-  SPINON=           0
-  ELECTRO=           1
-  ELECMETH=           0
-  MAXSCF=         450
-  MINSP2ITER=          22
-  FULLQCONV=           1
-  QITER=           3
-  ORDERNMOL=           0
-  SPARSEON=           1
-  THRESHOLDON=           1
-  FILLINSTOP=         100
-  BLKSZ=           4
-  MSPARSE=        1500
-  LCNON=           0
-  LCNITER=           4
-  RELAX=           0
-  MAXITER=      100000
-  MDON=           1
-  PBCON=           1
-  RESTART=           0
-  CHARGE=           0
-  XBO=           1
-  XBODISON=           1
-  XBODISORDER=           5
-  NGPU=           2
-  KON=           0
-  COMPFORCE=           1
-  DOSFIT=           0
-  INTS2FIT=           1
-  NFITSTEP=        5000
-  QFIT=           0
-  PPFITON=           0
-  ALLFITON=           0
-  PPSTEP=         500
-  BISTEP=         500
-  PP2FIT=           2
-  BINT2FIT=           6
-  PPNMOL=          10
-  PPNGEOM=         200
-  PARREP=           0
-  VERBOSE=           0
-  MIXER=           0
-  RESTARTLIB=           0
-  CGTOL=   9.9999999747524271E-007
-  KBT=   0.0000000000000000     
-  SPINTOL=   1.0000000000000000E-004
-  ELEC_ETOL=   1.0000000474974513E-003
-  ELEC_QTOL=   1.0000000000000000E-008
-  COULACC=   9.9999999747524271E-007
-  COULCUT=  -500.00000000000000     
-  COULR1=   500.00000000000000     
-  BREAKTOL=   9.9999999999999995E-007
-  QMIX=  0.25000000000000000     
-  SPINMIX=  0.25000000000000000     
-  MDMIX=  0.25000000000000000     
-  NUMTHRESH=   9.9999999999999995E-007
-  CHTOL=   9.9999997764825821E-003
-  SKIN=   1.0000000000000000     
-  RLXFTOL=   9.9999999999999995E-008
-  BETA=   1000.0000000000000     
-  MCSIGMA=  0.20000000298023224     
-  PPBETA=   1000.0000000000000     
-  PPSIGMA=   9.9999997764825821E-003
-  ER=   1.0000000000000000     
-  JobName=MyJob                                                                                               
-  BASISTYPE=NONORTHO                                                                                            
-  SP2CONV=REL                                                                                                 
-  RELAXTYPE=SD                                                                                                  
-  PARAMPATH=./TBparam                                                                                           
-  COORDSFILE=./coords.dat                                                                                        
-  INITIALIZED= F
-  }                                                 
-  
- ./TBparam/electrons.dat
- MDCONTROL{                                        }                                                 
-  
- WARNING: variable RNDIST= is missing. I will use a default value instead ...
- WARNING: variable SEEDINIT= is missing. I will use a default value instead ...
- WARNING: variable NPTTYPE= is missing. I will use a default value instead ...
- WARNING: variable UDNEIGH= is missing. I will use a default value instead ...
- WARNING: variable DUMPFREQ= is missing. I will use a default value instead ...
- WARNING: variable RSFREQ= is missing. I will use a default value instead ...
- WARNING: variable WRTFREQ= is missing. I will use a default value instead ...
- WARNING: variable TOINITTEMP5= is missing. I will use a default value instead ...
- WARNING: variable THERMPER= is missing. I will use a default value instead ...
- WARNING: variable THERMRUN= is missing. I will use a default value instead ...
- WARNING: variable NVTON= is missing. I will use a default value instead ...
- WARNING: variable NPTON= is missing. I will use a default value instead ...
- WARNING: variable AVEPER= is missing. I will use a default value instead ...
- WARNING: variable SEED= is missing. I will use a default value instead ...
- WARNING: variable SHOCKON= is missing. I will use a default value instead ...
- WARNING: variable SHOCKSTART= is missing. I will use a default value instead ...
- WARNING: variable SHOCKDIR= is missing. I will use a default value instead ...
- WARNING: variable MDADAPT= is missing. I will use a default value instead ...
- WARNING: variable GETHUG= is missing. I will use a default value instead ...
- WARNING: variable RSLEVEL= is missing. I will use a default value instead ...
- WARNING: variable DT= is missing. I will use a default value instead ...
- WARNING: variable TEMPERATURE= is missing. I will use a default value instead ...
- WARNING: variable FRICTION= is missing. I will use a default value instead ...
- WARNING: variable PTARGET= is missing. I will use a default value instead ...
- WARNING: variable UPARTICLE= is missing. I will use a default value instead ...
- WARNING: variable USHOCK= is missing. I will use a default value instead ...
- WARNING: variable C0= is missing. I will use a default value instead ...
- WARNING: variable E0= is missing. I will use a default value instead ...
- WARNING: variable V0= is missing. I will use a default value instead ...
- WARNING: variable P0= is missing. I will use a default value instead ...
- WARNING: variable DUMMY= is missing. I will use a default value instead ...
-  
-  
- ############### Parameters used for this run ################
-  MDCONTROL{                                        
-  MAXITER=          -1
-  UDNEIGH=           1
-  DUMPFREQ=         250
-  RSFREQ=         500
-  WRTFREQ=          25
-  TOINITTEMP5=           1
-  THERMPER=         500
-  THERMRUN=       50000
-  NVTON=           0
-  NPTON=           0
-  AVEPER=        1000
-  SEED=          54
-  SHOCKON=           0
-  SHOCKSTART=      100000
-  SHOCKDIR=           1
-  MDADAPT=           0
-  GETHUG=           0
-  RSLEVEL=           0
-  DT=  0.25000000000000000     
-  TEMPERATURE=   300.00000000000000     
-  FRICTION=   1000.0000000000000     
-  PTARGET=   0.0000000000000000     
-  UPARTICLE=   500.00000000000000     
-  USHOCK=  -4590.0000000000000     
-  C0=   1300.0000000000000     
-  E0=  -795.72497558593750     
-  V0=   896.98486328125000     
-  P0=   8.3149001002311707E-002
-  RNDIST=GAUSSIAN                                                                                            
-  SEEDINIT=UNIFORM                                                                                             
-  NPTTYPE=ISO                                                                                                 
-  DUMMY= F
-  }                                                 
-  
- LIBCALLS           0
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- LIBCALLS           1
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.15142147081917        13.850596160685321        0.0000000000000000        3.9653428217526296     
- LIBCALLS           2
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.15072431717670        13.849902902335046        0.0000000000000000        3.9653556077235628     
- LIBCALLS           3
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.14958682134301        13.848772166382796        0.0000000000000000        3.9653762812719782     
- LIBCALLS           4
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.14804481054080        13.847240065975685        0.0000000000000000        3.9654039257311324     
- LIBCALLS           5
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.14614669298459        13.845355347298943        0.0000000000000000        3.9654372593625880     
- LIBCALLS           6
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.14395200541782        13.843177681164811        0.0000000000000000        3.9654747563744728     
- LIBCALLS           7
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.14152950027858        13.840775605612510        0.0000000000000000        3.9655146828204026     
- LIBCALLS           8
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.13895477239572        13.838224210058369        0.0000000000000000        3.9655551214573213     
- LIBCALLS           9
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.13630808318862        13.835602658269416        0.0000000000000000        3.9655940696401335     
- LIBCALLS          10
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.13367156672246        13.832991646694552        0.0000000000000000        3.9656294961085377     
- LIBCALLS          11
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.13112695791978        13.830470890853416        0.0000000000000000        3.9656594331001127     
- LIBCALLS          12
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.12875304084571        13.828116721514562        0.0000000000000000        3.9656820468287637     
- LIBCALLS          13
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.12662314462005        13.825999860613845        0.0000000000000000        3.9656956633599689     
- LIBCALLS          14
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.12480303363179        13.824183432931337        0.0000000000000000        3.9656988576578489     
- LIBCALLS          15
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.12334906554690        13.822721254684298        0.0000000000000000        3.9656905013961525     
- LIBCALLS          16
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.12230649281338        13.821656427050725        0.0000000000000000        3.9656697961568699     
- LIBCALLS          17
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.12170820445976        13.821020251989051        0.0000000000000000        3.9656362957330207     
- LIBCALLS          18
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.12157378544725        13.820831478957400        0.0000000000000000        3.9655899465557289     
- LIBCALLS          19
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.12190902409918        13.821095885466233        0.0000000000000000        3.9655310732858191     
- LIBCALLS          20
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.12270578464654        13.821806190548854        0.0000000000000000        3.9654603894825375     
- LIBCALLS          21
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.12394226924755        13.822942298269552        0.0000000000000000        3.9653789701528157     
- LIBCALLS          22
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.12558369933174        13.824471866833779        0.0000000000000000        3.9652882392864672     
- LIBCALLS          23
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.12758334335854        13.826351196916939        0.0000000000000000        3.9651899208403507     
- LIBCALLS          24
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.12988392857540        13.828526429544008        0.0000000000000000        3.9650859962581815     
- LIBCALLS          25
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.13241933900565        13.830935038404082        0.0000000000000000        3.9649786471076300     
- LIBCALLS          26
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.13511663668885        13.833507593821677        0.0000000000000000        3.9648702062183578     
- LIBCALLS          27
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.13789821166085        13.836169765592846        0.0000000000000000        3.9647630647732250     
- LIBCALLS          28
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.14068416314257        13.838844520440762        0.0000000000000000        3.9646596094056243     
- LIBCALLS          29
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.14339478125902        13.841454456993119        0.0000000000000000        3.9645621614306648     
- LIBCALLS          30
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.14595299166797        13.843924209084781        0.0000000000000000        3.9644728862209537     
- LIBCALLS          31
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.14828672908391        13.846182838096166        0.0000000000000000        3.9643937231592781     
- LIBCALLS          32
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.15033121417270        13.848166127650318        0.0000000000000000        3.9643263326484774     
- LIBCALLS          33
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.15203097820654        13.849818691045462        0.0000000000000000        3.9642720350529470     
- LIBCALLS          34
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.15334158494318        13.851095804201121        0.0000000000000000        3.9642317563508436     
- LIBCALLS          35
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.15423101277941        13.851964884709183        0.0000000000000000        3.9642060118064197     
- LIBCALLS          36
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.15468060067406        13.852406550643760        0.0000000000000000        3.9641948735126151     
- LIBCALLS          37
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.15468556770435        13.852415210893483        0.0000000000000000        3.9641979705462513     
- LIBCALLS          38
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.15425506702360        13.851999160128511        0.0000000000000000        3.9642145018322728     
- LIBCALLS          39
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.15341177086162        13.851180175004831        0.0000000000000000        3.9642432622019754     
- LIBCALLS          40
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.15219100341108        13.849992631968849        0.0000000000000000        3.9642826797086155     
- LIBCALLS          41
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.15063948253476        13.848482189284203        0.0000000000000000        3.9643308764467280     
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- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.14881366363778        13.846704095034502        0.0000000000000000        3.9643857194231229     
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- LIBCALLS          46
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.14012416839108        13.838239201362184        0.0000000000000000        3.9646244709241216     
- LIBCALLS          47
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.13796944534135        13.836138629087953        0.0000000000000000        3.9646771958199687     
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- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.13596436459642        13.834182058508610        0.0000000000000000        3.9647228360374207     
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- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.13264918465853        13.830937266579358        0.0000000000000000        3.9647862263274365     
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- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.13144121811348        13.829746970164395        0.0000000000000000        3.9648015300858930     
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- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.13058418584075        13.828893856279002        0.0000000000000000        3.9648049379175174     
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- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.13000675986638        13.828280567696357        0.0000000000000000        3.9647757005033171     
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- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.13029725443062        13.828531873218640        0.0000000000000000        3.9647439679967813     
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- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.13096031859556        13.829143196581525        0.0000000000000000        3.9647021412055241     
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- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.13197071275096        13.830091344339912        0.0000000000000000        3.9646517009757813     
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- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.13329208290526        13.831342554670950        0.0000000000000000        3.9645944691057076     
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- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.13487817952188        13.832853532802908        0.0000000000000000        3.9645325717081379     
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- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.13667431785007        13.834572772174083        0.0000000000000000        3.9644683636269380     
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- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.13861917436014        13.836442137716100        0.0000000000000000        3.9644043716683206     
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- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.14064674344610        13.838398678492441        0.0000000000000000        3.9643432117931376     
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- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.14268847880851        13.840376626541268        0.0000000000000000        3.9642875107994442     
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- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.14467552446979        13.842309527587247        0.0000000000000000        3.9642398279114381     
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- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.14654097615647        13.844132438475109        0.0000000000000000        3.9642025589783412     
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- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.14822207995957        13.845784117078871        0.0000000000000000        3.9641778771678413     
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- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.14966231911774        13.847209123749478        0.0000000000000000        3.9641676470155103     
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- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.15081329445576        13.848359751049152        0.0000000000000000        3.9641733618391299     
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- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.15163634076458        13.849197700537186        0.0000000000000000        3.9641960937768981     
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- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.15210380659516        13.849695432596437        0.0000000000000000        3.9642364336978391     
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- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.15219997215792        13.849837127658775        0.0000000000000000        3.9642944914660605     
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- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.15192153900722        13.849619213627008        0.0000000000000000        3.9643698667021590     
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- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.15127769530471        13.849050434626310        0.0000000000000000        3.9644616585289247     
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- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.15028974592457        13.848151458176057        0.0000000000000000        3.9645684873567908     
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- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.14899032381624        13.846954040343237        0.0000000000000000        3.9646885325372980     
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- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.14742221364327        13.845499789571511        0.0000000000000000        3.9648195821504211     
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- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.14563684020112        13.843838588134755        0.0000000000000000        3.9649591055666282     
- LIBCALLS          78
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.14369246883172        13.842026744273829        0.0000000000000000        3.9651043223068876     
- LIBCALLS          79
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.14165219754119        13.840124957235691        0.0000000000000000        3.9652522794782556     
- LIBCALLS          80
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.13958181195608        13.838196181062383        0.0000000000000000        3.9653999492835532     
- LIBCALLS          81
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.13754757713065        13.836303471774007        0.0000000000000000        3.9655443071963385     
- LIBCALLS          82
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.13561405478509        13.834507896249461        0.0000000000000000        3.9656824354232736     
- LIBCALLS          83
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.13384198639028        13.832866571528193        0.0000000000000000        3.9658115908515681     
- LIBCALLS          84
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.13228634940748        13.831430891696755        0.0000000000000000        3.9659292903699495     
- LIBCALLS          85
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.13099461122306        13.830244986101496        0.0000000000000000        3.9660333724384569     
- LIBCALLS          86
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.13000526350720        13.829344440260281        0.0000000000000000        3.9661220782532145     
- LIBCALLS          87
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.12934661713206        13.828755299191645        0.0000000000000000        3.9661940662588862     
- LIBCALLS          88
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.12903595764971        13.828493364127572        0.0000000000000000        3.9662484623936765     
- LIBCALLS          89
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.12907904533250        13.828563786156602        0.0000000000000000        3.9662848954537067     
- LIBCALLS          90
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.12946994320248        13.828960955791626        0.0000000000000000        3.9663034756730777     
- LIBCALLS          91
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.13019123489619        13.829668684955367        0.0000000000000000        3.9663048073711558     
- LIBCALLS          92
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.13121457766835        13.830660675785223        0.0000000000000000        3.9662899643566578     
- LIBCALLS          93
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.13250159637499        13.831901269302985        0.0000000000000000        3.9662604605307470     
- LIBCALLS          94
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.13400508153813        13.833346464674193        0.0000000000000000        3.9662181906403653     
- LIBCALLS          95
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.13567049003717        13.834945196074795        0.0000000000000000        3.9661653991148187     
- LIBCALLS          96
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.13743766487022        13.836640848231452        0.0000000000000000        3.9661045863001441     
- LIBCALLS          97
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.13924277096038        13.838372983906890        0.0000000000000000        3.9660384593805307     
- LIBCALLS          98
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.14102036682124        13.840079246589914        0.0000000000000000        3.9659698320311318     
- LIBCALLS          99
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.14270555407057        13.841697390518378        0.0000000000000000        3.9659015537535014     
- LIBCALLS         100
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.14423615166146        13.843167378892108        0.0000000000000000        3.9658364191978137     

examples/latte/log.19Sep17.latte.water.g++.1

@@ -1,406 +0,0 @@
- The log file for latte_lib
- 
- CONTROL{                                          }                                                 
-  
- WARNING: variable JobName= is missing. I will use a default value instead ...
- WARNING: variable PARAMPATH= is missing. I will use a default value instead ...
- WARNING: variable DEBUGON= is missing. I will use a default value instead ...
- WARNING: variable FERMIM= is missing. I will use a default value instead ...
- WARNING: variable CGORLIB= is missing. I will use a default value instead ...
- WARNING: variable NORECS= is missing. I will use a default value instead ...
- WARNING: variable VDWON= is missing. I will use a default value instead ...
- WARNING: variable ORDERNMOL= is missing. I will use a default value instead ...
- WARNING: variable LCNON= is missing. I will use a default value instead ...
- WARNING: variable LCNITER= is missing. I will use a default value instead ...
- WARNING: variable MDON= is missing. I will use a default value instead ...
- WARNING: variable PBCON= is missing. I will use a default value instead ...
- WARNING: variable RESTART= is missing. I will use a default value instead ...
- WARNING: variable NGPU= is missing. I will use a default value instead ...
- WARNING: variable COMPFORCE= is missing. I will use a default value instead ...
- WARNING: variable DOSFIT= is missing. I will use a default value instead ...
- WARNING: variable INTS2FIT= is missing. I will use a default value instead ...
- WARNING: variable NFITSTEP= is missing. I will use a default value instead ...
- WARNING: variable QFIT= is missing. I will use a default value instead ...
- WARNING: variable PPFITON= is missing. I will use a default value instead ...
- WARNING: variable ALLFITON= is missing. I will use a default value instead ...
- WARNING: variable PPSTEP= is missing. I will use a default value instead ...
- WARNING: variable BISTEP= is missing. I will use a default value instead ...
- WARNING: variable PP2FIT= is missing. I will use a default value instead ...
- WARNING: variable BINT2FIT= is missing. I will use a default value instead ...
- WARNING: variable PPNMOL= is missing. I will use a default value instead ...
- WARNING: variable PPNGEOM= is missing. I will use a default value instead ...
- WARNING: variable PARREP= is missing. I will use a default value instead ...
- WARNING: variable VERBOSE= is missing. I will use a default value instead ...
- WARNING: variable MIXER= is missing. I will use a default value instead ...
- WARNING: variable RESTARTLIB= is missing. I will use a default value instead ...
- WARNING: variable CGTOL= is missing. I will use a default value instead ...
- WARNING: variable ELEC_ETOL= is missing. I will use a default value instead ...
- WARNING: variable COULACC= is missing. I will use a default value instead ...
- WARNING: variable COULCUT= is missing. I will use a default value instead ...
- WARNING: variable COULR1= is missing. I will use a default value instead ...
- WARNING: variable CHTOL= is missing. I will use a default value instead ...
- WARNING: variable BETA= is missing. I will use a default value instead ...
- WARNING: variable MCSIGMA= is missing. I will use a default value instead ...
- WARNING: variable PPBETA= is missing. I will use a default value instead ...
- WARNING: variable PPSIGMA= is missing. I will use a default value instead ...
- WARNING: variable ER= is missing. I will use a default value instead ...
- WARNING: variable INITIALIZED= is missing. I will use a default value instead ...
-  
-  
- ############### Parameters used for this run ################
-  CONTROL{                                          
-  xControl=           1
-  DEBUGON=           0
-  FERMIM=           6
-  CGORLIB=           1
-  NORECS=           1
-  ENTROPYKIND=           1
-  PPOTON=           1
-  VDWON=           0
-  SPINON=           0
-  ELECTRO=           1
-  ELECMETH=           0
-  MAXSCF=         450
-  MINSP2ITER=          22
-  FULLQCONV=           1
-  QITER=           3
-  ORDERNMOL=           0
-  SPARSEON=           1
-  THRESHOLDON=           1
-  FILLINSTOP=         100
-  BLKSZ=           4
-  MSPARSE=        1500
-  LCNON=           0
-  LCNITER=           4
-  RELAX=           0
-  MAXITER=      100000
-  MDON=           1
-  PBCON=           1
-  RESTART=           0
-  CHARGE=           0
-  XBO=           1
-  XBODISON=           1
-  XBODISORDER=           5
-  NGPU=           2
-  KON=           0
-  COMPFORCE=           1
-  DOSFIT=           0
-  INTS2FIT=           1
-  NFITSTEP=        5000
-  QFIT=           0
-  PPFITON=           0
-  ALLFITON=           0
-  PPSTEP=         500
-  BISTEP=         500
-  PP2FIT=           2
-  BINT2FIT=           6
-  PPNMOL=          10
-  PPNGEOM=         200
-  PARREP=           0
-  VERBOSE=           0
-  MIXER=           0
-  RESTARTLIB=           0
-  CGTOL=   9.9999999747524271E-007
-  KBT=   0.0000000000000000     
-  SPINTOL=   1.0000000000000000E-004
-  ELEC_ETOL=   1.0000000474974513E-003
-  ELEC_QTOL=   1.0000000000000000E-008
-  COULACC=   9.9999999747524271E-007
-  COULCUT=  -500.00000000000000     
-  COULR1=   500.00000000000000     
-  BREAKTOL=   9.9999999999999995E-007
-  QMIX=  0.25000000000000000     
-  SPINMIX=  0.25000000000000000     
-  MDMIX=  0.25000000000000000     
-  NUMTHRESH=   9.9999999999999995E-007
-  CHTOL=   9.9999997764825821E-003
-  SKIN=   1.0000000000000000     
-  RLXFTOL=   9.9999999999999995E-008
-  BETA=   1000.0000000000000     
-  MCSIGMA=  0.20000000298023224     
-  PPBETA=   1000.0000000000000     
-  PPSIGMA=   9.9999997764825821E-003
-  ER=   1.0000000000000000     
-  JobName=MyJob                                                                                               
-  BASISTYPE=NONORTHO                                                                                            
-  SP2CONV=REL                                                                                                 
-  RELAXTYPE=SD                                                                                                  
-  PARAMPATH=./TBparam                                                                                           
-  COORDSFILE=./coords.dat                                                                                        
-  INITIALIZED= F
-  }                                                 
-  
- ./TBparam/electrons.dat
- MDCONTROL{                                        }                                                 
-  
- WARNING: variable RNDIST= is missing. I will use a default value instead ...
- WARNING: variable SEEDINIT= is missing. I will use a default value instead ...
- WARNING: variable NPTTYPE= is missing. I will use a default value instead ...
- WARNING: variable UDNEIGH= is missing. I will use a default value instead ...
- WARNING: variable DUMPFREQ= is missing. I will use a default value instead ...
- WARNING: variable RSFREQ= is missing. I will use a default value instead ...
- WARNING: variable WRTFREQ= is missing. I will use a default value instead ...
- WARNING: variable TOINITTEMP5= is missing. I will use a default value instead ...
- WARNING: variable THERMPER= is missing. I will use a default value instead ...
- WARNING: variable THERMRUN= is missing. I will use a default value instead ...
- WARNING: variable NVTON= is missing. I will use a default value instead ...
- WARNING: variable NPTON= is missing. I will use a default value instead ...
- WARNING: variable AVEPER= is missing. I will use a default value instead ...
- WARNING: variable SEED= is missing. I will use a default value instead ...
- WARNING: variable SHOCKON= is missing. I will use a default value instead ...
- WARNING: variable SHOCKSTART= is missing. I will use a default value instead ...
- WARNING: variable SHOCKDIR= is missing. I will use a default value instead ...
- WARNING: variable MDADAPT= is missing. I will use a default value instead ...
- WARNING: variable GETHUG= is missing. I will use a default value instead ...
- WARNING: variable RSLEVEL= is missing. I will use a default value instead ...
- WARNING: variable DT= is missing. I will use a default value instead ...
- WARNING: variable TEMPERATURE= is missing. I will use a default value instead ...
- WARNING: variable FRICTION= is missing. I will use a default value instead ...
- WARNING: variable PTARGET= is missing. I will use a default value instead ...
- WARNING: variable UPARTICLE= is missing. I will use a default value instead ...
- WARNING: variable USHOCK= is missing. I will use a default value instead ...
- WARNING: variable C0= is missing. I will use a default value instead ...
- WARNING: variable E0= is missing. I will use a default value instead ...
- WARNING: variable V0= is missing. I will use a default value instead ...
- WARNING: variable P0= is missing. I will use a default value instead ...
- WARNING: variable DUMMY= is missing. I will use a default value instead ...
-  
-  
- ############### Parameters used for this run ################
-  MDCONTROL{                                        
-  MAXITER=          -1
-  UDNEIGH=           1
-  DUMPFREQ=         250
-  RSFREQ=         500
-  WRTFREQ=          25
-  TOINITTEMP5=           1
-  THERMPER=         500
-  THERMRUN=       50000
-  NVTON=           0
-  NPTON=           0
-  AVEPER=        1000
-  SEED=          54
-  SHOCKON=           0
-  SHOCKSTART=      100000
-  SHOCKDIR=           1
-  MDADAPT=           0
-  GETHUG=           0
-  RSLEVEL=           0
-  DT=  0.25000000000000000     
-  TEMPERATURE=   300.00000000000000     
-  FRICTION=   1000.0000000000000     
-  PTARGET=   0.0000000000000000     
-  UPARTICLE=   500.00000000000000     
-  USHOCK=  -4590.0000000000000     
-  C0=   1300.0000000000000     
-  E0=  -795.72497558593750     
-  V0=   896.98486328125000     
-  P0=   8.3149001002311707E-002
-  RNDIST=GAUSSIAN                                                                                            
-  SEEDINIT=UNIFORM                                                                                             
-  NPTTYPE=ISO                                                                                                 
-  DUMMY= F
-  }                                                 
-  
- LIBCALLS           0
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -110.94281402417451        9.3197859655447317        0.0000000000000000        3.3331152608769714     
- LIBCALLS           1
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -111.00875524736128        9.3653691493930946        0.0000000000000000        3.3307590218500454     
- LIBCALLS           2
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -111.20542679804305        9.5022104076319209        0.0000000000000000        3.3237269236958826     
- LIBCALLS           3
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -111.52938059528239        9.7304811436977623        0.0000000000000000        3.3121168872278743     
- LIBCALLS           4
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -111.97463249071366        10.050121693432235        0.0000000000000000        3.2961492065207088     
- LIBCALLS           5
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -112.53270518796754        10.460328095449432        0.0000000000000000        3.2761112890303719     
- LIBCALLS           6
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -113.19233973551384        10.958848347453728        0.0000000000000000        3.2524094948032394     
- LIBCALLS           7
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -113.93936061504219        11.541120618354967        0.0000000000000000        3.2255715906285793     
- LIBCALLS           8
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -114.75657630591589        12.199315594286325        0.0000000000000000        3.1962412869596100     
- LIBCALLS           9
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -115.62363727592754        12.921383532128770        0.0000000000000000        3.1652236023838971     
- LIBCALLS          10
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -116.51738028417616        13.690253224922545        0.0000000000000000        3.1333864449223818     
- LIBCALLS          11
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -117.41167836078414        14.483370804317431        0.0000000000000000        3.1018474945925432     
- LIBCALLS          12
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -118.27888830961329        15.272791625586624        0.0000000000000000        3.0716022180609772     
- LIBCALLS          13
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -119.09006809777934        16.026020995592610        0.0000000000000000        3.0437832241644842     
- LIBCALLS          14
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -119.81665859965702        16.707725410478066        0.0000000000000000        3.0194382402972129     
- LIBCALLS          15
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -120.43171665196000        17.282293509806884        0.0000000000000000        2.9995944159949395     
- LIBCALLS          16
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -120.91202932933264        17.717025741135480        0.0000000000000000        2.9850159611897484     
- LIBCALLS          17
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -121.23935305628714        17.985521384886379        0.0000000000000000        2.9763132734231292     
- LIBCALLS          18
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -121.40195013006486        18.070687763205626        0.0000000000000000        2.9738279411203812     
- LIBCALLS          19
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -121.39540873020161        17.966785565900089        0.0000000000000000        2.9776410698341418     
- LIBCALLS          20
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -121.22299732491055        17.680085363043698        0.0000000000000000        2.9875419962840417     
- LIBCALLS          21
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -120.89520311723561        17.228004261852682        0.0000000000000000        3.0030824758482719     
- LIBCALLS          22
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -120.42892991839108        16.636927104987372        0.0000000000000000        3.0235548851138652     
- LIBCALLS          23
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -119.84603562384113        15.939176953031323        0.0000000000000000        3.0480682132279808     
- LIBCALLS          24
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -119.17151378155378        15.169713318754383        0.0000000000000000        3.0757033760823562     
- LIBCALLS          25
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -118.43237009319661        14.363090728730079        0.0000000000000000        3.1053593079625457     
- LIBCALLS          26
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -117.65587959220025        13.551051330611342        0.0000000000000000        3.1359367589132958     
- LIBCALLS          27
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -116.86794783202731        12.760928656005802        0.0000000000000000        3.1665525874091585     
- LIBCALLS          28
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -116.09314111752745        12.014864684105008        0.0000000000000000        3.1962157162544820     
- LIBCALLS          29
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -115.35329645548983        11.329720850249741        0.0000000000000000        3.2241713466126849     
- LIBCALLS          30
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -114.66766945168203        10.717501941208962        0.0000000000000000        3.2497326120829619     
- LIBCALLS          31
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -114.05267853351812        10.186102377105355        0.0000000000000000        3.2723439005172468     
- LIBCALLS          32
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -113.52195471723405        9.7402032028335377        0.0000000000000000        3.2915777178346559     
- LIBCALLS          33
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -113.08654808143162        9.3821857555240076        0.0000000000000000        3.3070881064986164     
- LIBCALLS          34
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -112.75494140290169        9.1129669843369658        0.0000000000000000        3.3186769594405297     
- LIBCALLS          35
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -112.53346080566452        8.9326971516334606        0.0000000000000000        3.3261797960311763     
- LIBCALLS          36
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -112.42631053676025        8.8412887543407273        0.0000000000000000        3.3295101207595583     
- LIBCALLS          37
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -112.43567911088179        8.8387604511711384        0.0000000000000000        3.3286360397306387     
- LIBCALLS          38
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -112.56180874683180        8.9253908783870841        0.0000000000000000        3.3235794828927934     
- LIBCALLS          39
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -112.80290981416660        9.1016780459478674        0.0000000000000000        3.3144303393175201     
- LIBCALLS          40
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -113.15529209572232        9.3681021116147463        0.0000000000000000        3.3012719922659173     
- LIBCALLS          41
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -113.61284717182851        9.7246892073080176        0.0000000000000000        3.2843276907821406     
- LIBCALLS          42
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -114.16711238367500        10.170382433756300        0.0000000000000000        3.2638758866524444     
- LIBCALLS          43
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -114.80697882175535        10.702240750749448        0.0000000000000000        3.2402928278295451     
- LIBCALLS          44
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -115.51862249254057        11.314512276989859        0.0000000000000000        3.2140189987358694     
- LIBCALLS          45
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -116.28534475502829        11.997664972113199        0.0000000000000000        3.1855791836729437     
- LIBCALLS          46
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -117.08723294353808        12.737504349188432        0.0000000000000000        3.1557205936583181     
- LIBCALLS          47
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -117.90172272355942        13.514542609912253        0.0000000000000000        3.1252466759266087     
- LIBCALLS          48
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -118.70392627447073        14.303827027310493        0.0000000000000000        3.0950533786893732     
- LIBCALLS          49
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -119.46728361372288        15.075425279261220        0.0000000000000000        3.0661202668284480     
- LIBCALLS          50
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -120.16480071670361        15.795723720235596        0.0000000000000000        3.0394030522382605     
- LIBCALLS          51
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -120.77012122199473        16.429579578207949        0.0000000000000000        3.0158910566711334     
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- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -121.25943485841766        16.943195338409559        0.0000000000000000        2.9964108616830281     
- LIBCALLS          53
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -121.61275582007269        17.307379355481601        0.0000000000000000        2.9817016064731785     
- LIBCALLS          54
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -121.81557415209883        17.500688554193868        0.0000000000000000        2.9722905637821611     
- LIBCALLS          55
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -121.85979389563140        17.511877645177901        0.0000000000000000        2.9685356305551474     
- LIBCALLS          56
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -121.74454585055143        17.341170281709367        0.0000000000000000        2.9705149057151141     
- LIBCALLS          57
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -121.47625724150488        17.000096879575938        0.0000000000000000        2.9780008785307088     
- LIBCALLS          58
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -121.06771474420596        16.509959464438374        0.0000000000000000        2.9906138266349656     
- LIBCALLS          59
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -120.53702830874704        15.899266098308772        0.0000000000000000        3.0078351734174715     
- LIBCALLS          60
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -119.90667912574422        15.200652842845301        0.0000000000000000        3.0288733658622142     
- LIBCALLS          61
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -119.20142467775943        14.447825469624703        0.0000000000000000        3.0529481020908245     
- LIBCALLS          62
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -118.44747494197328        13.672949108115853        0.0000000000000000        3.0790791220573088     
- LIBCALLS          63
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -117.67063237406208        12.904741667499017        0.0000000000000000        3.1063745183559131     
- LIBCALLS          64
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -116.89550228683500        12.167344616151606        0.0000000000000000        3.1339818740985033     
- LIBCALLS          65
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -116.14487351718614        11.479908971904207        0.0000000000000000        3.1610748652786995     
- LIBCALLS          66
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -115.43917601644073        10.856755674815151        0.0000000000000000        3.1869042214936911     
- LIBCALLS          67
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -114.79630542914917        10.307930318909381        0.0000000000000000        3.2107896540741994     
- LIBCALLS          68
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -114.23118520942130        9.8399835349372715        0.0000000000000000        3.2322754400486997     
- LIBCALLS          69
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -113.75645667348935        9.4568320682906393        0.0000000000000000        3.2508686207040949     
- LIBCALLS          70
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -113.38220191758144        9.1605931457952803        0.0000000000000000        3.2662052636761625     
- LIBCALLS          71
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -113.11651461323785        8.9523172650382463        0.0000000000000000        3.2778578161416640     
- LIBCALLS          72
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -112.96490300473705        8.8325758589074610        0.0000000000000000        3.2856373346184280     
- LIBCALLS          73
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -112.93101384064629        8.8018792766284140        0.0000000000000000        3.2893376450243901     
- LIBCALLS          74
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -113.01657988020818        8.8609123616606951        0.0000000000000000        3.2887786713823335     
- LIBCALLS          75
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -113.22122702505257        9.0105808374276855        0.0000000000000000        3.2838806809960044     
- LIBCALLS          76
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -113.54255812607462        9.2518619694254909        0.0000000000000000        3.2746170980725564     
- LIBCALLS          77
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -113.97595003796289        9.5854566564348804        0.0000000000000000        3.2610495238703536     
- LIBCALLS          78
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -114.51445216471619        10.011242264155852        0.0000000000000000        3.2433103887056101     
- LIBCALLS          79
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -115.14835871057100        10.527538366743359        0.0000000000000000        3.2217018278255036     
- LIBCALLS          80
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -115.86512618816471        11.130220642932718        0.0000000000000000        3.1966546818138903     
- LIBCALLS          81
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -116.64916580084807        11.811746817430592        0.0000000000000000        3.1687509169099037     
- LIBCALLS          82
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -117.48162972769103        12.560201275368994        0.0000000000000000        3.1387793445426220     
- LIBCALLS          83
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -118.34080112521505        13.358507776606700        0.0000000000000000        3.1076005013428842     
- LIBCALLS          84
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -119.20206255799097        14.183999576696523        0.0000000000000000        3.0762625451098367     
- LIBCALLS          85
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -120.03875955947012        15.008549885925623        0.0000000000000000        3.0458557745855401     
- LIBCALLS          86
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -120.82281065648482        15.799445052997022        0.0000000000000000        3.0175902569508040     
- LIBCALLS          87
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -121.52638053902615        16.521105731022047        0.0000000000000000        2.9925661691795984     
- LIBCALLS          88
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -122.12297505178334        17.137613862262167        0.0000000000000000        2.9718740800190462     
- LIBCALLS          89
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -122.58954501498538        17.615819283155187        0.0000000000000000        2.9563457612376758     
- LIBCALLS          90
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -122.90768650775293        17.928615619513138        0.0000000000000000        2.9466637669908935     
- LIBCALLS          91
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -123.06510359278838        18.057846294334183        0.0000000000000000        2.9432773288779130     
- LIBCALLS          92
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -123.05653995529889        17.996310208253615        0.0000000000000000        2.9463730237128352     
- LIBCALLS          93
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -122.88443709725219        17.748486968230267        0.0000000000000000        2.9557418006906766     
- LIBCALLS          94
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -122.55804625906457        17.329857520510558        0.0000000000000000        2.9710497340098647     
- LIBCALLS          95
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -122.09316916859144        16.764989519228550        0.0000000000000000        2.9916333369114647     
- LIBCALLS          96
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -121.51050736457847        16.084787212290774        0.0000000000000000        3.0167038701280053     
- LIBCALLS          97
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -120.83475656442954        15.323405512114466        0.0000000000000000        3.0451593241515909     
- LIBCALLS          98
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -120.09218577985371        14.515310319889227        0.0000000000000000        3.0759929793994090     
- LIBCALLS          99
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -119.30969482099719        13.692843612811791        0.0000000000000000        3.1081426979179545     
- LIBCALLS         100
- Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -118.51358261827596        12.884492109393644        0.0000000000000000        3.1405428597121636     

examples/latte/log.19Sep17.latte.water.min.g++.1

@@ -1,152 +0,0 @@
-LAMMPS (1 Sep 2017)
-# simple water model with LATTE
-
-units		metal
-atom_style	full
-atom_modify     sort 0 0.0    # turn off sorting of the coordinates
-
-read_data       data.water
-  orthogonal box = (0 0 0) to (6.267 6.267 6.267)
-  1 by 1 by 1 MPI processor grid
-  reading atoms ...
-  24 atoms
-  0 = max # of 1-2 neighbors
-  0 = max # of 1-3 neighbors
-  0 = max # of 1-4 neighbors
-  1 = max # of special neighbors
-
-# replicate system if requested
-
-variable	x index 1
-variable	y index 1
-variable	z index 1
-
-variable        nrep equal v_x*v_y*v_z
-if              "${nrep} > 1" then "replicate $x $y $z"
-
-# initialize system
-
-velocity	all create 0.0 87287 loop geom
-
-pair_style      zero 1.0
-pair_coeff	* *
-
-neighbor	1.0 bin
-neigh_modify    every 1 delay 0 check yes
-
-timestep        0.00025
-
-fix		1 all nve
-
-fix             2 all latte NULL
-fix_modify      2 energy yes
-
-thermo_style    custom step temp pe etotal press
-
-# minimization
-
-thermo          10
-min_style fire
-minimize        1.0e-9 1.0e-9 500 500
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 2
-  ghost atom cutoff = 2
-  binsize = 1, bins = 7 7 7
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair zero, 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) = 5.629 | 5.629 | 5.629 Mbytes
-Step Temp PotEng TotEng Press 
-       0            0   -104.95614   -104.95614    48229.712 
-      10    349.44219   -105.50971   -104.47083    62149.591 
-      20    1253.6752   -107.00898   -103.28182    116444.44 
-      30    134.63588   -107.56184   -107.16157    59854.143 
-      40    2.4043703   -108.15301   -108.14586     32685.77 
-      50    162.13426   -108.40551   -107.92349    62104.273 
-      60    134.03149   -108.70118   -108.30271    49400.525 
-      70    64.159014   -108.78034    -108.5896    37243.303 
-      80    240.49926   -109.10766   -108.39266    42158.884 
-      90   0.60467192   -109.61818   -109.61639    14107.515 
-     100    1.4691163   -109.65556   -109.65119    21596.775 
-     110    30.500628   -109.69267     -109.602    16104.639 
-     120    120.62379   -109.83749   -109.47888     9474.971 
-     130    8.4742975   -109.99986   -109.97467    10104.102 
-     140    3.4732679   -110.01209   -110.00176    11990.442 
-     150    24.749482   -110.04313   -109.96955    10851.569 
-     160    4.1106505   -110.13288   -110.12066    8257.3969 
-     170 0.0065628716   -110.18061   -110.18059    7876.8748 
-     180    2.0542078    -110.1837   -110.17759    7996.0533 
-     190    20.134782   -110.21071   -110.15085    7556.1811 
-     200    2.3397267    -110.3244   -110.31745     3767.062 
-     210    4.3544709   -110.34438   -110.33143     4889.145 
-     220    1.1872367   -110.37457   -110.37104    4162.6543 
-     230    2.2798399   -110.38081   -110.37403    4321.0943 
-     240    11.835907   -110.39611   -110.36092    4187.5757 
-     250   0.13741849   -110.41453   -110.41412    3720.7527 
-     260    4.2283185   -110.42036   -110.40779    3743.3494 
-     270   0.47243724   -110.44349   -110.44208    3172.1866 
-     280   0.06090137   -110.45428    -110.4541    3065.9348 
-     290    5.3413962   -110.46285   -110.44697    3121.2924 
-     300    8.2032986   -110.48519    -110.4608    2705.5001 
-     310    2.0783529   -110.48807   -110.48189    2740.7989 
-     320    16.629185   -110.51002   -110.46058    2581.7434 
-     330   0.19723065   -110.53444   -110.53385    1942.0228 
-     340    6.2758334   -110.54361   -110.52495    1924.0965 
-     350    1.4539052   -110.59108   -110.58676   -449.41056 
-     360    0.0514233   -110.60143   -110.60128    1284.8259 
-     370    1.7240145   -110.60394   -110.59881    1468.0004 
-     380     13.28516   -110.62337   -110.58387    1573.4714 
-     390    1.2247432   -110.63525   -110.63161    1113.4557 
-     400    0.3946985   -110.63694   -110.63576    1083.0801 
-     410    2.9831433     -110.641   -110.63213     1112.419 
-     420  0.068550589   -110.66029   -110.66009    897.09211 
-     430   0.83976182   -110.66259   -110.66009    918.69832 
-     440    4.4760907   -110.66844   -110.65513    915.24435 
-     450    1.2841241   -110.67482     -110.671    953.30422 
-     460    2.5707455   -110.68509   -110.67745    775.21273 
-     470   0.99721544   -110.68646    -110.6835    812.74984 
-     480    6.8379261   -110.69468   -110.67435     787.9705 
-     490   0.18134438   -110.69628   -110.69574    675.52792 
-     500    2.0946523   -110.69918   -110.69295    696.82065 
-Loop time of 31.775 on 1 procs for 500 steps with 24 atoms
-
-884.8% CPU use with 1 MPI tasks x no OpenMP threads
-
-Minimization stats:
-  Stopping criterion = max iterations
-  Energy initial, next-to-last, final = 
-         -104.95614332     -110.698546127     -110.699182193
-  Force two-norm initial, final = 19.119 0.234621
-  Force max component initial, final = 11.7759 0.0903198
-  Final line search alpha, max atom move = 0 0
-  Iterations, force evaluations = 500 500
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.00016952 | 0.00016952 | 0.00016952 |   0.0 |  0.00
-Bond    | 2.8372e-05 | 2.8372e-05 | 2.8372e-05 |   0.0 |  0.00
-Neigh   | 3.0994e-05 | 3.0994e-05 | 3.0994e-05 |   0.0 |  0.00
-Comm    | 0.00060034 | 0.00060034 | 0.00060034 |   0.0 |  0.00
-Output  | 0.00057817 | 0.00057817 | 0.00057817 |   0.0 |  0.00
-Modify  | 31.771     | 31.771     | 31.771     |   0.0 | 99.99
-Other   |            | 0.002469   |            |       |  0.01
-
-Nlocal:    24 ave 24 max 24 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    71 ave 71 max 71 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    27 ave 27 max 27 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 27
-Ave neighs/atom = 1.125
-Ave special neighs/atom = 0
-Neighbor list builds = 2
-Dangerous builds = 0
-Total wall time: 0:00:31

examples/latte/log.21Jun18.latte.graphene.boxrelax.g++.1

@@ -0,0 +1,170 @@
+LAMMPS (11 May 2018)
+# Simple water model with LATTE
+
+units		metal
+atom_style	full
+atom_modify     sort 0 0.0    # turn off sorting of the coordinates
+
+read_data       data.graphene.boxrel
+  triclinic box = (0 0 0) to (10 8 20) with tilt (4.89859e-16 1.22465e-15 1.22465e-15)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  32 atoms
+  0 = max # of 1-2 neighbors
+  0 = max # of 1-3 neighbors
+  0 = max # of 1-4 neighbors
+  1 = max # of special neighbors
+
+# replicate system if requested
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+
+variable        nrep equal v_x*v_y*v_z
+if              "${nrep} > 1" then "replicate $x $y $z"
+
+# initialize system
+
+velocity	all create 0.0 87287 loop geom
+
+pair_style      zero 1.0
+pair_coeff	* *
+
+neighbor	1.0 bin
+neigh_modify    every 1 delay 0 check yes
+
+timestep        0.00025
+
+fix 1 all box/relax iso 0.0 vmax 0.001
+
+fix             2 all latte NULL
+fix_modify      2 energy yes
+
+thermo_style    custom   etotal
+
+# minimization
+
+thermo          1
+fix 3 all print 1 "Total Energy ="
+min_style cg
+min_modify dmax 0.1
+min_modify line quadratic
+minimize        1.0e-4 1.0e-4 10000 10000
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2
+  ghost atom cutoff = 2
+  binsize = 1, bins = 11 9 20
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair zero, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton/tri
+      stencil: half/bin/3d/newton/tri
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 6.779 | 6.779 | 6.779 Mbytes
+TotEng 
+  -247.46002 
+  -247.67224 
+  -247.87937 
+  -248.08148 
+  -248.27865 
+  -248.47096 
+  -248.65851 
+  -248.84137 
+  -249.01964 
+  -249.19342 
+  -249.36281 
+  -249.52791 
+  -249.68883 
+   -249.8457 
+  -249.99865 
+   -250.1478 
+  -250.29332 
+  -250.43535 
+  -250.57409 
+  -250.70972 
+  -250.84247 
+  -250.97258 
+  -251.10035 
+   -251.2261 
+  -251.35021 
+  -251.47314 
+  -251.59543 
+  -251.71776 
+  -251.84096 
+   -251.9661 
+  -252.09459 
+  -252.22833 
+  -252.37003 
+  -252.52371 
+  -252.69578 
+  -252.89752 
+  -253.15197 
+  -253.52044 
+  -254.31418 
+   -255.6175 
+   -256.8162 
+   -258.1227 
+  -259.38401 
+  -260.74831 
+  -262.03991 
+   -263.5463 
+  -264.70486 
+  -267.69144 
+  -267.88682 
+  -269.03519 
+  -270.60187 
+  -270.65382 
+  -270.74279 
+  -271.55883 
+  -271.81248 
+  -271.87529 
+  -273.01494 
+  -273.23948 
+  -273.28719 
+  -273.35272 
+  -273.41591 
+  -273.46274 
+  -273.54755 
+  -273.58318 
+  -273.73111 
+  -273.75754 
+Loop time of 39.4155 on 1 procs for 65 steps with 32 atoms
+
+1582.4% CPU use with 1 MPI tasks x no OpenMP threads
+
+Minimization stats:
+  Stopping criterion = energy tolerance
+  Energy initial, next-to-last, final = 
+        -247.460020579     -273.731112592     -273.757543461
+  Force two-norm initial, final = 201.608 9.43485
+  Force max component initial, final = 188.924 2.41297
+  Final line search alpha, max atom move = 0.000223273 0.00053875
+  Iterations, force evaluations = 65 65
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.00012159 | 0.00012159 | 0.00012159 |   0.0 |  0.00
+Bond    | 5.1975e-05 | 5.1975e-05 | 5.1975e-05 |   0.0 |  0.00
+Neigh   | 4.1962e-05 | 4.1962e-05 | 4.1962e-05 |   0.0 |  0.00
+Comm    | 0.00026107 | 0.00026107 | 0.00026107 |   0.0 |  0.00
+Output  | 0.0013342  | 0.0013342  | 0.0013342  |   0.0 |  0.00
+Modify  | 39.412     | 39.412     | 39.412     |   0.0 | 99.99
+Other   |            | 0.00127    |            |       |  0.00
+
+Nlocal:    32 ave 32 max 32 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    100 ave 100 max 100 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    48 ave 48 max 48 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 48
+Ave neighs/atom = 1.5
+Ave special neighs/atom = 0
+Neighbor list builds = 1
+Dangerous builds = 0
+Total wall time: 0:00:40

examples/latte/log.21Jun18.latte.sucrose.g++.1

@@ -0,0 +1,103 @@
+LAMMPS (11 May 2018)
+# simple sucrose model with LATTE
+
+units		metal
+atom_style	full
+atom_modify     sort 0 0.0    # turn off sorting of the coordinates
+
+read_data       data.sucrose
+  orthogonal box = (0 0 0) to (17.203 18.009 21.643)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  45 atoms
+  0 = max # of 1-2 neighbors
+  0 = max # of 1-3 neighbors
+  0 = max # of 1-4 neighbors
+  1 = max # of special neighbors
+
+# replicate system if requested
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+
+variable        nrep equal v_x*v_y*v_z
+if              "${nrep} > 1" then "replicate $x $y $z"
+
+# initialize system
+
+velocity	all create 0.0 87287 loop geom
+
+pair_style      zero 1.0
+pair_coeff	* *
+
+neighbor	1.0 bin
+neigh_modify    every 1 delay 0 check yes
+
+timestep        0.00025
+
+fix		1 all nve
+
+fix             2 all latte NULL
+fix_modify      2 energy yes
+
+thermo_style    custom step temp pe etotal press
+
+# dynamics
+
+thermo          10
+run		100
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2
+  ghost atom cutoff = 2
+  binsize = 1, bins = 18 19 22
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair zero, 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) = 0.5064 | 0.5064 | 0.5064 Mbytes
+Step Temp PotEng TotEng Press 
+       0            0   -251.26617   -251.26617    16.617234 
+      10  0.025263709   -251.26631   -251.26617    8.0576708 
+      20  0.034232467   -251.26636   -251.26617    1.6673442 
+      30  0.059079556    -251.2665   -251.26617    11.058458 
+      40  0.055499766   -251.26648   -251.26617    14.837775 
+      50  0.058499509    -251.2665   -251.26617    6.7183113 
+      60  0.071094535   -251.26657   -251.26617    6.6133687 
+      70  0.084309439   -251.26665   -251.26617    12.372721 
+      80    0.1089929   -251.26679   -251.26617    8.8355516 
+      90   0.11378257   -251.26681   -251.26617    5.1177922 
+     100   0.13003966   -251.26691   -251.26617    8.2431185 
+Loop time of 27.8386 on 1 procs for 100 steps with 45 atoms
+
+Performance: 0.078 ns/day, 309.318 hours/ns, 3.592 timesteps/s
+1799.6% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 8.3685e-05 | 8.3685e-05 | 8.3685e-05 |   0.0 |  0.00
+Bond    | 7.4148e-05 | 7.4148e-05 | 7.4148e-05 |   0.0 |  0.00
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.00016689 | 0.00016689 | 0.00016689 |   0.0 |  0.00
+Output  | 0.00032401 | 0.00032401 | 0.00032401 |   0.0 |  0.00
+Modify  | 27.837     | 27.837     | 27.837     |   0.0 |100.00
+Other   |            | 0.0005403  |            |       |  0.00
+
+Nlocal:    45 ave 45 max 45 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    59 ave 59 max 59 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 59
+Ave neighs/atom = 1.31111
+Ave special neighs/atom = 0
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:28

examples/latte/log.21Jun18.latte.water.g++.1

@@ -0,0 +1,103 @@
+LAMMPS (11 May 2018)
+# simple water model with LATTE
+
+units		metal
+atom_style	full
+atom_modify     sort 0 0.0    # turn off sorting of the coordinates
+
+read_data       data.water
+  orthogonal box = (0 0 0) to (6.267 6.267 6.267)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  24 atoms
+  0 = max # of 1-2 neighbors
+  0 = max # of 1-3 neighbors
+  0 = max # of 1-4 neighbors
+  1 = max # of special neighbors
+
+# replicate system if requested
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+
+variable        nrep equal v_x*v_y*v_z
+if              "${nrep} > 1" then "replicate $x $y $z"
+
+# initialize system
+
+velocity	all create 0.0 87287 loop geom
+
+pair_style      zero 1.0
+pair_coeff	* *
+
+neighbor	1.0 bin
+neigh_modify    every 1 delay 0 check yes
+
+timestep        0.00025
+
+fix		1 all nve
+
+fix             2 all latte NULL
+fix_modify      2 energy yes
+
+thermo_style    custom step temp pe etotal press
+
+# dynamics
+
+thermo          10
+run		100
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2
+  ghost atom cutoff = 2
+  binsize = 1, bins = 7 7 7
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair zero, 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) = 5.629 | 5.629 | 5.629 Mbytes
+Step Temp PotEng TotEng Press 
+       0            0   -104.95594   -104.95594    48236.006 
+      10     336.5303   -105.96026   -104.95976    97997.303 
+      20    529.06385   -106.53021   -104.95731    131520.49 
+      30    753.62616    -107.1995   -104.95898    49297.371 
+      40     716.6565   -107.08802   -104.95741    28307.272 
+      50    824.04417   -107.40822   -104.95835    102167.48 
+      60    933.56056   -107.73478   -104.95932    92508.792 
+      70    851.18518   -107.48766   -104.95711     13993.28 
+      80    999.80265   -107.93146   -104.95906    36700.417 
+      90    998.77707   -107.92569   -104.95634     107233.7 
+     100    1281.4446   -108.76961   -104.95989    49703.193 
+Loop time of 10.6388 on 1 procs for 100 steps with 24 atoms
+
+Performance: 0.203 ns/day, 118.209 hours/ns, 9.400 timesteps/s
+6459.7% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 7.6771e-05 | 7.6771e-05 | 7.6771e-05 |   0.0 |  0.00
+Bond    | 7.5817e-05 | 7.5817e-05 | 7.5817e-05 |   0.0 |  0.00
+Neigh   | 4.6015e-05 | 4.6015e-05 | 4.6015e-05 |   0.0 |  0.00
+Comm    | 0.00031829 | 0.00031829 | 0.00031829 |   0.0 |  0.00
+Output  | 0.00032401 | 0.00032401 | 0.00032401 |   0.0 |  0.00
+Modify  | 10.637     | 10.637     | 10.637     |   0.0 | 99.99
+Other   |            | 0.00052    |            |       |  0.00
+
+Nlocal:    24 ave 24 max 24 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    77 ave 77 max 77 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    31 ave 31 max 31 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 31
+Ave neighs/atom = 1.29167
+Ave special neighs/atom = 0
+Neighbor list builds = 2
+Dangerous builds = 0
+Total wall time: 0:00:10

examples/latte/log.21Jun18.latte.water.min.g++.1

@@ -0,0 +1,108 @@
+LAMMPS (11 May 2018)
+# simple water model with LATTE
+
+units		metal
+atom_style	full
+atom_modify     sort 0 0.0    # turn off sorting of the coordinates
+
+read_data       data.water
+  orthogonal box = (0 0 0) to (6.267 6.267 6.267)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  24 atoms
+  0 = max # of 1-2 neighbors
+  0 = max # of 1-3 neighbors
+  0 = max # of 1-4 neighbors
+  1 = max # of special neighbors
+
+# replicate system if requested
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+
+variable        nrep equal v_x*v_y*v_z
+if              "${nrep} > 1" then "replicate $x $y $z"
+
+# initialize system
+
+velocity	all create 0.0 87287 loop geom
+
+pair_style      zero 1.0
+pair_coeff	* *
+
+neighbor	1.0 bin
+neigh_modify    every 1 delay 0 check yes
+
+timestep        0.00025
+
+fix		1 all nve
+
+fix             2 all latte NULL
+fix_modify      2 energy yes
+
+thermo_style    custom step temp pe etotal press
+
+# minimization
+
+thermo          10
+
+min_style       fire
+minimize        1.0e-4 1.0e-4 500 500
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2
+  ghost atom cutoff = 2
+  binsize = 1, bins = 7 7 7
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair zero, 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) = 5.629 | 5.629 | 5.629 Mbytes
+Step Temp PotEng TotEng Press 
+       0            0   -104.95594   -104.95594    48236.006 
+      10     349.4534   -105.50948   -104.47056    62157.729 
+      20    1253.6636   -107.00863   -103.28151    116456.71 
+      30    134.64051   -107.56155   -107.16127    59864.196 
+      40    2.4044989    -108.1527   -108.14556    32695.648 
+      47    137.26885   -108.30413   -107.89603    60177.442 
+Loop time of 6.42677 on 1 procs for 47 steps with 24 atoms
+
+6481.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+Minimization stats:
+  Stopping criterion = energy tolerance
+  Energy initial, next-to-last, final = 
+        -104.955944301     -108.302982895     -108.304126127
+  Force two-norm initial, final = 19.119 3.44609
+  Force max component initial, final = 11.7758 1.3408
+  Final line search alpha, max atom move = 0 0
+  Iterations, force evaluations = 47 47
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 4.6253e-05 | 4.6253e-05 | 4.6253e-05 |   0.0 |  0.00
+Bond    | 3.1948e-05 | 3.1948e-05 | 3.1948e-05 |   0.0 |  0.00
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.00014353 | 0.00014353 | 0.00014353 |   0.0 |  0.00
+Output  | 0.00012302 | 0.00012302 | 0.00012302 |   0.0 |  0.00
+Modify  | 6.426      | 6.426      | 6.426      |   0.0 | 99.99
+Other   |            | 0.0004699  |            |       |  0.01
+
+Nlocal:    24 ave 24 max 24 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    71 ave 71 max 71 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    37 ave 37 max 37 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 37
+Ave neighs/atom = 1.54167
+Ave special neighs/atom = 0
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:06

examples/rigid/in.rigid.early

@@ -0,0 +1,83 @@
+# Simple rigid body system
+
+units		lj
+atom_style	atomic
+
+pair_style	lj/cut 2.5
+
+read_data	data.rigid
+
+velocity 	all create 100.0 4928459
+
+# unconnected bodies
+
+group		clump1 id <> 1 9
+group		clump2 id <> 10 18
+group		clump3 id <> 19 27
+group		clump4 id <> 28 36
+group		clump5 id <> 37 45
+group		clump6 id <> 46 54
+group		clump7 id <> 55 63
+group		clump8 id <> 64 72
+group		clump9 id <> 73 81
+
+fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 &
+	  	      clump6 clump7 clump8 clump9
+
+fix_modify 1 bodyforces early
+
+# 1 chain of connected bodies
+
+#group		clump1 id <> 1 9
+#group		clump2 id <> 9 18
+#group		clump3 id <> 18 27
+#group		clump4 id <> 27 36
+#group		clump5 id <> 36 45
+#group		clump6 id <> 45 54
+#group		clump7 id <> 54 63
+#group		clump8 id <> 63 72
+#group		clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 &
+#	  	      clump6 clump7 clump8 clump9
+
+# 2 chains of connected bodies
+
+#group		clump1 id <> 1 9
+#group		clump2 id <> 9 18
+#group		clump3 id <> 18 27
+#group		clump4 id <> 27 36
+#group		clump5 id <> 37 45
+#group		clump6 id <> 45 54
+#group		clump7 id <> 54 63
+#group		clump8 id <> 63 72
+#group		clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4
+#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
+
+neigh_modify	exclude group clump1 clump1
+neigh_modify	exclude group clump2 clump2
+neigh_modify	exclude group clump3 clump3
+neigh_modify	exclude group clump4 clump4
+neigh_modify	exclude group clump5 clump5
+neigh_modify	exclude group clump6 clump6
+neigh_modify	exclude group clump7 clump7
+neigh_modify	exclude group clump8 clump8
+neigh_modify	exclude group clump9 clump9
+
+thermo		100
+
+#dump		1 all atom 50 dump.rigid
+
+#dump		2 all image 100 image.*.jpg type type &
+#		axes yes 0.8 0.02 view 60 -30
+#dump_modify	2 pad 5
+
+#dump		3 all movie 100 movie.mpg type type &
+#		axes yes 0.8 0.02 view 60 -30
+#dump_modify	3 pad 5
+
+timestep 	0.0001
+thermo		50
+run		10000