Merge pull request #1623 from akohlmey/next-version

Step version string for stable release

cmake/CMakeLists.txt

@@ -133,6 +133,24 @@ foreach(PKG ${DEFAULT_PACKAGES} ${ACCEL_PACKAGES})
   option(PKG_${PKG} "Build ${PKG} Package" OFF)
 endforeach()
 
+######################################################
+# download and unpack support binaries for compilation
+# of windows binaries.
+######################################################
+if(${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
+  set(LAMMPS_THIRDPARTY_URL "http://download.lammps.org/thirdparty")
+  file(DOWNLOAD "${LAMMPS_THIRDPARTY_URL}/opencl-win-devel.tar.gz" "${CMAKE_CURRENT_BINARY_DIR}/opencl-win-devel.tar.gz"
+          EXPECTED_MD5 2c00364888d5671195598b44c2e0d44d)
+  execute_process(COMMAND ${CMAKE_COMMAND} -E tar xzf opencl-win-devel.tar.gz WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
+  if(${CMAKE_SYSTEM_PROCESSOR} STREQUAL "x86")
+    set(OpenCL_LIBRARY "${CMAKE_CURRENT_BINARY_DIR}/OpenCL/lib_win32/libOpenCL.dll")
+  elseif(${CMAKE_SYSTEM_PROCESSOR} STREQUAL "x86_64")
+    set(OpenCL_LIBRARY "${CMAKE_CURRENT_BINARY_DIR}/OpenCL/lib_win64/libOpenCL.dll")
+  endif()
+  set(OpenCL_INCLUDE_DIR "${CMAKE_CURRENT_BINARY_DIR}/OpenCL/include")
+endif()
+
+######################################################
 ######################################################
 # packages with special compiler needs or external libs
 ######################################################
@@ -148,6 +166,7 @@ if(PKG_USER-ADIOS)
 endif()
 
 # do MPI detection after language activation, if MPI for these language is required
+set(MPI_CXX_SKIP_MPICXX TRUE)
 find_package(MPI QUIET)
 option(BUILD_MPI "Build MPI version" ${MPI_FOUND})
 if(BUILD_MPI)
@@ -175,11 +194,13 @@ add_definitions(-DLAMMPS_${LAMMPS_SIZES})
 set(LAMMPS_API_DEFINES "${LAMMPS_API_DEFINES} -DLAMMPS_${LAMMPS_SIZES}")
 
 # posix_memalign is not available on Windows
-if(NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
+if(${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
+  set(LAMMPS_MEMALIGN "0" CACHE STRING "posix_memalign() is not available on Windows" FORCE)
+else()
   set(LAMMPS_MEMALIGN "64" CACHE STRING "enables the use of the posix_memalign() call instead of malloc() when large chunks or memory are allocated by LAMMPS. Set to 0 to disable")
-  if(NOT ${LAMMPS_MEMALIGN} STREQUAL "0")
-    add_definitions(-DLAMMPS_MEMALIGN=${LAMMPS_MEMALIGN})
-  endif()
+endif()
+if(NOT ${LAMMPS_MEMALIGN} STREQUAL "0")
+  add_definitions(-DLAMMPS_MEMALIGN=${LAMMPS_MEMALIGN})
 endif()
 
 option(LAMMPS_EXCEPTIONS "enable the use of C++ exceptions for error messages (useful for library interface)" OFF)
@@ -219,8 +240,7 @@ if(BUILD_OMP)
   set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
 endif()
 
-
-if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-PLUMED OR PKG_USER-QUIP OR PKG_LATTE)
+if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE)
   find_package(LAPACK)
   find_package(BLAS)
   if(NOT LAPACK_FOUND OR NOT BLAS_FOUND)
@@ -230,6 +250,7 @@ if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-PLUMED OR PKG_USER-QUI
     enable_language(Fortran)
     file(GLOB LAPACK_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/linalg/[^.]*.[fF])
     add_library(linalg STATIC ${LAPACK_SOURCES})
+    set(BLAS_LIBRARIES linalg)
     set(LAPACK_LIBRARIES linalg)
   else()
     list(APPEND LAPACK_LIBRARIES ${BLAS_LIBRARIES})
@@ -497,10 +518,43 @@ if(BUILD_LIB)
   if(LAMMPS_DEPS)
     add_dependencies(lammps ${LAMMPS_DEPS})
   endif()
+  set(LAMMPS_CXX_HEADERS
+    ${LAMMPS_SOURCE_DIR}/angle.h
+    ${LAMMPS_SOURCE_DIR}/atom.h
+    ${LAMMPS_SOURCE_DIR}/bond.h
+    ${LAMMPS_SOURCE_DIR}/citeme.h
+    ${LAMMPS_SOURCE_DIR}/comm.h
+    ${LAMMPS_SOURCE_DIR}/compute.h
+    ${LAMMPS_SOURCE_DIR}/dihedral.h
+    ${LAMMPS_SOURCE_DIR}/domain.h
+    ${LAMMPS_SOURCE_DIR}/error.h
+    ${LAMMPS_SOURCE_DIR}/fix.h
+    ${LAMMPS_SOURCE_DIR}/force.h
+    ${LAMMPS_SOURCE_DIR}/group.h
+    ${LAMMPS_SOURCE_DIR}/improper.h
+    ${LAMMPS_SOURCE_DIR}/input.h
+    ${LAMMPS_SOURCE_DIR}/kspace.h
+    ${LAMMPS_SOURCE_DIR}/lammps.h
+    ${LAMMPS_SOURCE_DIR}/lattice.h
+    ${LAMMPS_SOURCE_DIR}/lmppython.h
+    ${LAMMPS_SOURCE_DIR}/memory.h
+    ${LAMMPS_SOURCE_DIR}/modify.h
+    ${LAMMPS_SOURCE_DIR}/neighbor.h
+    ${LAMMPS_SOURCE_DIR}/neigh_list.h
+    ${LAMMPS_SOURCE_DIR}/output.h
+    ${LAMMPS_SOURCE_DIR}/pair.h
+    ${LAMMPS_SOURCE_DIR}/pointers.h
+    ${LAMMPS_SOURCE_DIR}/region.h
+    ${LAMMPS_SOURCE_DIR}/timer.h
+    ${LAMMPS_SOURCE_DIR}/universe.h
+    ${LAMMPS_SOURCE_DIR}/update.h
+    ${LAMMPS_SOURCE_DIR}/variable.h)
+
   set_target_properties(lammps PROPERTIES OUTPUT_NAME lammps${LAMMPS_LIB_SUFFIX})
   set_target_properties(lammps PROPERTIES SOVERSION ${SOVERSION})
   install(TARGETS lammps LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
   install(FILES ${LAMMPS_SOURCE_DIR}/library.h DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps)
+  install(FILES ${LAMMPS_CXX_HEADERS} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps)
   configure_file(pkgconfig/liblammps.pc.in ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_LIB_SUFFIX}.pc @ONLY)
   install(FILES ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_LIB_SUFFIX}.pc DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
   configure_file(FindLAMMPS.cmake.in ${CMAKE_CURRENT_BINARY_DIR}/FindLAMMPS${LAMMPS_LIB_SUFFIX}.cmake @ONLY)
@@ -551,11 +605,11 @@ include(Documentation)
 ###############################################################################
 # Install potential and force field files in data directory
 ###############################################################################
-set(LAMMPS_INSTALL_POTENTIALS_DIR ${CMAKE_INSTALL_FULL_DATADIR}/lammps/potentials)
-install(DIRECTORY ${LAMMPS_POTENTIALS_DIR} DESTINATION ${LAMMPS_INSTALL_POTENTIALS_DIR})
-
-set(LAMMPS_INSTALL_FRC_FILES_DIR ${CMAKE_INSTALL_FULL_DATADIR}/lammps/frc_files)
-install(DIRECTORY ${LAMMPS_TOOLS_DIR}/msi2lmp/frc_files/ DESTINATION ${LAMMPS_INSTALL_FRC_FILES_DIR})
+set(LAMMPS_INSTALL_DATADIR ${CMAKE_INSTALL_FULL_DATADIR}/lammps)
+install(DIRECTORY ${LAMMPS_POTENTIALS_DIR} DESTINATION ${LAMMPS_INSTALL_DATADIR})
+if(BUILD_TOOLS)
+  install(DIRECTORY ${LAMMPS_TOOLS_DIR}/msi2lmp/frc_files DESTINATION ${LAMMPS_INSTALL_DATADIR})
+endif()
 
 configure_file(etc/profile.d/lammps.sh.in ${CMAKE_BINARY_DIR}/etc/profile.d/lammps.sh @ONLY)
 configure_file(etc/profile.d/lammps.csh.in ${CMAKE_BINARY_DIR}/etc/profile.d/lammps.csh @ONLY)

cmake/Modules/Packages/KIM.cmake

@@ -9,6 +9,9 @@ if(PKG_KIM)
   if(KIM-API_FOUND)
     set(DOWNLOAD_KIM_DEFAULT OFF)
   else()
+    if (NOT DOWNLOAD_KIM)
+      message(WARNING "KIM-API package not found.  We will download and build our own")
+    endif()
     set(DOWNLOAD_KIM_DEFAULT ON)
   endif()
   option(DOWNLOAD_KIM "Download KIM-API from OpenKIM instead of using an already installed one" ${DOWNLOAD_KIM_DEFAULT})
@@ -17,12 +20,16 @@ if(PKG_KIM)
       message(FATAL_ERROR "Cannot build downloaded KIM-API library with Ninja build tool")
     endif()
     message(STATUS "KIM-API download requested - we will build our own")
-    enable_language(C)
-    enable_language(Fortran)
+    include(CheckLanguage)
     include(ExternalProject)
+    enable_language(C)
+    check_language(Fortran)
+    if(NOT CMAKE_Fortran_COMPILER)
+      message(FATAL_ERROR "Compiling the KIM-API library requires a Fortran compiler")
+    endif()
     ExternalProject_Add(kim_build
-      URL https://s3.openkim.org/kim-api/kim-api-2.0.2.txz
-      URL_MD5 537d9c0abd30f85b875ebb584f9143fa
+      URL https://s3.openkim.org/kim-api/kim-api-2.1.2.txz
+      URL_MD5 6ac52e14ef52967fc7858220b208cba5
       BINARY_DIR build
       CMAKE_ARGS -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
                  -DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}

cmake/Modules/Packages/USER-PLUMED.cmake

@@ -1,11 +1,23 @@
 if(PKG_USER-PLUMED)
-  find_package(GSL REQUIRED)
   set(PLUMED_MODE "static" CACHE STRING "Linkage mode for Plumed2 library")
   set(PLUMED_MODE_VALUES static shared runtime)
   set_property(CACHE PLUMED_MODE PROPERTY STRINGS ${PLUMED_MODE_VALUES})
   validate_option(PLUMED_MODE PLUMED_MODE_VALUES)
   string(TOUPPER ${PLUMED_MODE} PLUMED_MODE)
 
+  set(PLUMED_LINK_LIBS "")
+  if(PLUMED_MODE STREQUAL "STATIC")
+    find_package(LAPACK REQUIRED)
+    find_package(BLAS REQUIRED)
+    find_package(GSL REQUIRED)
+    list(APPEND LAPACK_LIBRARIES ${BLAS_LIBRARIES})
+    list(APPEND PLUMED_LINK_LIBS ${LAPACK_LIBRARIES} ${GSL_LIBRARIES})
+    find_package(ZLIB QUIET)
+    if(ZLIB_FOUND)
+      list(APPEND PLUMED_LINK_LIBS ${ZLIB_LIBRARIES})
+    endif()
+  endif()
+
   find_package(PkgConfig QUIET)
   set(DOWNLOAD_PLUMED_DEFAULT ON)
   if(PKG_CONFIG_FOUND)
@@ -37,8 +49,8 @@ if(PKG_USER-PLUMED)
     message(STATUS "PLUMED download requested - we will build our own")
     include(ExternalProject)
     ExternalProject_Add(plumed_build
-      URL https://github.com/plumed/plumed2/releases/download/v2.5.1/plumed-src-2.5.1.tgz
-      URL_MD5 c2a7b519e32197a120cdf47e0f194f81
+      URL https://github.com/plumed/plumed2/releases/download/v2.5.2/plumed-src-2.5.2.tgz
+      URL_MD5 bd2f18346c788eb54e1e52f4f6acf41a
       BUILD_IN_SOURCE 1
       CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR>
                                                ${CONFIGURE_REQUEST_PIC}
@@ -53,11 +65,11 @@ if(PKG_USER-PLUMED)
     list(APPEND LAMMPS_DEPS plumed_build)
     if(PLUMED_MODE STREQUAL "STATIC")
       add_definitions(-D__PLUMED_WRAPPER_CXX=1)
-      list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/libplumed.a ${GSL_LIBRARIES} ${LAPACK_LIBRARIES} ${CMAKE_DL_LIBS})
+      list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/libplumed.a ${PLUMED_LINK_LIBS} ${CMAKE_DL_LIBS})
     elseif(PLUMED_MODE STREQUAL "SHARED")
-      list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/libplumed.so ${PLUMED_INSTALL_DIR}/lib/libplumedKernel.so ${CMAKE_DL_LIBS})
+      list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/libplumed${CMAKE_SHARED_LIBRARY_SUFFIX} ${PLUMED_INSTALL_DIR}/lib/libplumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX} ${CMAKE_DL_LIBS})
     elseif(PLUMED_MODE STREQUAL "RUNTIME")
-      add_definitions(-D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_DEFAULT_KERNEL=${PLUMED_INSTALL_DIR}/lib/libplumedKernel.so)
+      add_definitions(-D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_DEFAULT_KERNEL=${PLUMED_INSTALL_DIR}/lib/libplumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX})
       list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/libplumedWrapper.a -rdynamic ${CMAKE_DL_LIBS})
     endif()
     set(PLUMED_INCLUDE_DIRS "${PLUMED_INSTALL_DIR}/include")
@@ -70,7 +82,7 @@ if(PKG_USER-PLUMED)
     elseif(PLUMED_MODE STREQUAL "SHARED")
       include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.shared)
     elseif(PLUMED_MODE STREQUAL "RUNTIME")
-      add_definitions(-D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_DEFAULT_KERNEL=${PLUMED_LIBDIR}/libplumedKernel.so)
+      add_definitions(-D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_DEFAULT_KERNEL=${PLUMED_LIBDIR}/libplumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX})
       include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.runtime)
     endif()
     list(APPEND LAMMPS_LINK_LIBS ${PLUMED_LOAD})

cmake/Modules/Packages/VORONOI.cmake

@@ -18,8 +18,12 @@ if(PKG_VORONOI)
     else()
       set(VORO_BUILD_CFLAGS "${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_${BTYPE}}")
     endif()
-    string(APPEND VORO_BUILD_CFLAGS ${CMAKE_CXX_FLAGS})
-    set(VORO_BUILD_OPTIONS CXX=${CMAKE_CXX_COMPILER} CFLAGS=${VORO_BUILD_CFLAGS})
+    if(APPLE)
+      get_filename_component(VORO_CXX ${CMAKE_CXX_COMPILER} NAME_WE)
+      set(VORO_BUILD_OPTIONS CXX=${VORO_CXX} CFLAGS=${VORO_BUILD_CFLAGS})
+    else()
+      set(VORO_BUILD_OPTIONS CXX=${CMAKE_CXX_COMPILER} CFLAGS=${VORO_BUILD_CFLAGS})
+    endif()
 
     ExternalProject_Add(voro_build
       URL https://download.lammps.org/thirdparty/voro++-0.4.6.tar.gz

cmake/README.md

@@ -33,12 +33,17 @@ tasks, act as a reference and provide examples of typical use cases.
       * [Package-Specific Configuration Options](#package-specific-configuration-options)
          * [KSPACE Package](#kspace-package)
          * [MKL](#mkl)
-         * [FFTW2](#fftw2)
          * [FFTW3](#fftw3)
+         * [BLAS](#blas)
          * [LAPACK](#lapack)
          * [PYTHON Package](#python-package)
          * [GPU Package](#gpu-package)
+         * [MESSAGE Package](#message-package)
+         * [MSCG Package](#mscg-package)
          * [VORONOI Package](#voronoi-package)
+         * [USER-LATTE Package](#user-latte-package)
+         * [USER-PLUMED Package](#user-plumed-package)
+         * [USER-SCAFACOS Package](#user-scafacos-package)
          * [USER-SMD Package](#user-smd-package)
       * [Optional Features](#optional-features)
          * [zlib support](#zlib-support)
@@ -50,8 +55,6 @@ tasks, act as a reference and provide examples of typical use cases.
          * [Building with GNU Compilers](#building-with-gnu-compilers)
          * [Building with Intel Compilers](#building-with-intel-compilers)
          * [Building with LLVM/Clang Compilers](#building-with-llvmclang-compilers)
-      * [Examples](#examples)
-
 
 ## Quick Start for the Impatient
 If you want to skip ahead and just run the compilation using `cmake`, please
@@ -205,8 +208,10 @@ cmake -C ../cmake/presets/all_on.cmake -C ../cmake/presets/nolib.cmake -D PKG_GP
   <td>Controls if debugging symbols are added to the generated binaries</td>
   <td>
   <dl>
-  <dt><code>Release</code> (default)</dt>
+  <dt><code>RelWithDebInfo (default)</code></dt>
+  <dt><code>Release</code></dt>
   <dt><code>Debug</code></dt>
+  <dt><code>MinSizeRel</code></dt>
   </dl>
   </td>
 </tr>
@@ -249,6 +254,16 @@ cmake -C ../cmake/presets/all_on.cmake -C ../cmake/presets/nolib.cmake -D PKG_GP
   </dl>
   </td>
 </tr>
+<tr>
+  <td><code>LAMMPS_LONGLONG_TO_LONG</code></td>
+  <td>Workaround if your system or MPI version does not recognize <code>long long</code> data types</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
 <tr>
   <td><code>LAMMPS_MEMALIGN</code></td>
   <td>controls the alignment of blocks of memory allocated by LAMMPS</td>
@@ -271,7 +286,16 @@ cmake -C ../cmake/presets/all_on.cmake -C ../cmake/presets/nolib.cmake -D PKG_GP
 </tr>
 <tr>
   <td><code>LAMMPS_MACHINE</code></td>
-  <td>allows appending a machine suffix to the generate LAMMPS binary</td>
+  <td>allows appending a machine suffix to the generated LAMMPS binary</td>
+  <td>
+  <dl>
+    <dt>*none*  (default)</dt>
+  </dl>
+  </td>
+</tr>
+<tr>
+  <td><code>LAMMPS_LIB_SUFFIX</code></td>
+  <td>allows appending a suffix to the generated LAMMPS library</td>
   <td>
   <dl>
     <dt>*none*  (default)</dt>
@@ -319,8 +343,8 @@ cmake -C ../cmake/presets/all_on.cmake -C ../cmake/presets/nolib.cmake -D PKG_GP
   </td>
 </tr>
 <tr>
-  <td><code>LAMMPS_LONGLONG_TO_LONG</code></td>
-  <td>Workaround if your system or MPI version does not recognize <code>long long</code> data types</td>
+  <td><code>BUILD_TOOLS</code></td>
+  <td>control whether to build LAMMPS tools</td>
   <td>
   <dl>
     <dt><code>off</code> (default)</dt>
@@ -561,23 +585,6 @@ cmake -C ../cmake/presets/all_on.cmake -C ../cmake/presets/nolib.cmake -D PKG_GP
   </dl>
   </td>
 </tr>
-<tr>
-  <td><code>PKG_MEAM</code></td>
-  <td>
-<p>A pair style for the modified embedded atom (MEAM) potential.</p>
-
-<p><strong>Please note that the MEAM package has been superseded by the USER-MEAMC package,
-which is a direct translation of the MEAM package to C++. USER-MEAMC contains
-additional optimizations making it run faster than MEAM on most machines, while
-providing the identical features and USER interface.</strong></p>
-  </td>
-  <td>
-  <dl>
-    <dt><code>off</code> (default)</dt>
-    <dt><code>on</code></dt>
-  </dl>
-  </td>
-</tr>
 <tr>
   <td><code>PKG_MISC</code></td>
   <td>
@@ -634,21 +641,6 @@ providing the identical features and USER interface.</strong></p>
   </dl>
   </td>
 </tr>
-<tr>
-  <td><code>PKG_REAX</code></td>
-  <td>
-  A pair style which wraps a Fortran library which implements the ReaxFF
-  potential, which is a universal reactive force field. See the USER-REAXC
-  package for an alternate implementation in C/C++. Also a fix reax/bonds
-  command for monitoring molecules as bonds are created and destroyed.
-  </td>
-  <td>
-  <dl>
-    <dt><code>off</code> (default)</dt>
-    <dt><code>on</code></dt>
-  </dl>
-  </td>
-</tr>
 <tr>
   <td><code>PKG_REPLICA</code></td>
   <td>
@@ -695,6 +687,16 @@ providing the identical features and USER interface.</strong></p>
   </dl>
   </td>
 </tr>
+<tr>
+  <td><code>PKG_SPIN</code></td>
+  <td>Model atomic magnetic spins classically, coupled to atoms moving in the usual manner via MD. Various pair, fix, and compute styles.</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
 <tr>
   <td><code>PKG_SNAP</code></td>
   <td>
@@ -757,6 +759,16 @@ providing the identical features and USER interface.</strong></p>
   </dl>
   </td>
 </tr>
+<tr>
+  <td><code>PKG_MESSAGE</code></td>
+  <td>Commands to use LAMMPS as either a client or server and couple it to another application.</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
 <tr>
   <td><code>PKG_MSCG</code></td>
   <td>
@@ -811,6 +823,18 @@ providing the identical features and USER interface.</strong></p>
   </dl>
   </td>
 </tr>
+<tr>
+  <td><code>PKG_VORONOI</code></td>
+  <td>
+  A compute command which calculates the Voronoi tesselation of a collection of atoms by wrapping the Voro++ library. This can be used to calculate the local volume or each atoms or its near neighbors.
+  </td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
 </tbody>
 </table>
 
@@ -825,6 +849,16 @@ providing the identical features and USER interface.</strong></p>
 </tr>
 </thead>
 <tbody>
+<tr>
+  <td><code>PKG_USER-ADIOS</code></td>
+  <td>ADIOS is a high-performance I/O library. This package implements the dump “atom/adios” and dump “custom/adios” commands to write data using the ADIOS library.</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
 <tr>
   <td><code>PKG_USER-ATC</code></td>
   <td>
@@ -853,6 +887,18 @@ providing the identical features and USER interface.</strong></p>
   </dl>
   </td>
 </tr>
+<tr>
+  <td><code>PKG_USER-BOCS</code></td>
+  <td>
+  This package provides fix bocs, a modified version of fix npt 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).
+  </td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
 <tr>
   <td><code>PKG_USER-CGDNA</code></td>
   <td>
@@ -1142,6 +1188,30 @@ providing the identical features and USER interface.</strong></p>
   </dl>
   </td>
 </tr>
+<tr>
+  <td><code>PKG_USER-PLUMED</code></td>
+  <td>
+  The fix plumed command allows you to use the PLUMED free energy plugin for molecular dynamics to analyze and bias your LAMMPS trajectory on the fly. The PLUMED library is called from within the LAMMPS input script by using the <code>fix plumed</code> command.
+  </td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
+<tr>
+  <td><code>PKG_USER-PTM</code></td>
+  <td>
+  A <code>compute ptm/atom</code> command that calculates local structure characterization using the Polyhedral Template Matching methodology.
+  </td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
 <tr>
   <td><code>PKG_USER-QTB</code></td>
   <td>
@@ -1197,6 +1267,33 @@ providing the identical features and USER interface.</strong></p>
   </dl>
   </td>
 </tr>
+<tr>
+  <td><code>PKG_USER-SCAFACOS</code></td>
+  <td>
+  A KSpace style which wraps the ScaFaCoS Coulomb solver library to compute long-range Coulombic interactions.
+  </td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
+<tr>
+  <td><code>PKG_USER-SDPD</code></td>
+  <td>
+  A pair style for smoothed dissipative particle dynamics (SDPD), which is an
+  extension of smoothed particle hydrodynamics (SPH) to mesoscale where thermal
+  fluctuations are important (see the USER-SPH package). Also two fixes for
+  moving and rigid body integration of SPH/SDPD particles (particles of
+  <code>atom_style meso</code>).</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
 <tr>
   <td><code>PKG_USER-SMD</code></td>
   <td>
@@ -1280,6 +1377,23 @@ providing the identical features and USER interface.</strong></p>
   </dl>
   </td>
 </tr>
+<tr>
+  <td><code>PKG_USER-YAFF</code></td>
+  <td>
+  Some potentials that are also implemented in the Yet Another Force Field (YAFF) code.
+  The expressions and their use are discussed in the following papers:
+  <ul>
+    <li><a href="http://dx.doi.org/10.1002/jcc.23877" target="_blank">Vanduyfhuys et al., J. Comput. Chem., 36 (13), 1015-1027 (2015)</a></li>
+    <li><a href="http://dx.doi.org/10.1002/jcc.25173" target="_blank">Vanduyfhuys et al., J. Comput. Chem., 39 (16), 999-1011 (2018)</a></li>
+  </ul>
+  </td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
 </tbody>
 </table>
 
@@ -1300,14 +1414,27 @@ providing the identical features and USER interface.</strong></p>
   <td><code>FFT</code></td>
   <td>
     <p>FFT library for KSPACE package</p>
-    <p>If either MKL or FFTW is selected <code>cmake</code> will try to locate these libraries automatically. To control which one should be used please see the options below for each FFT library.</p>
+    <p>If either MKL or FFTW is selected <code>cmake</code> will try to locate
+    these libraries automatically. To control which one should be used please see
+    the options below for each FFT library.  Otherwise it will default to KISS
+    FFT.</p>
   </td>
   <td>
   <dl>
-    <dt><code>KISS</code></dt>
     <dt><code>FFTW3</code></dt>
     <dt><code>FFTW2</code></dt>
     <dt><code>MKL</code></dt>
+    <dt><code>KISS</code> (default)</dt>
+  </dl>
+  </td>
+</tr>
+<tr>
+  <td><code>FFT_SINGLE</code></td>
+  <td>Use single-precision floating-point in FFT</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default = double precision)</dt>
+    <dt><code>on</code></dt>
   </dl>
   </td>
 </tr>
@@ -1325,60 +1452,6 @@ providing the identical features and USER interface.</strong></p>
 </tbody>
 </table>
 
-### MKL
-
-<table>
-<thead>
-<tr>
-  <th>Option</th>
-  <th>Description</th>
-  <th>Values</th>
-</tr>
-</thead>
-<tbody>
-<tr>
-  <td><code>MKL_INCLUDE_DIRS</code></td>
-  <td></td>
-  <td>
-  </td>
-</tr>
-<tr>
-  <td><code>MKL_LIBRARIES</code></td>
-  <td></td>
-  <td>
-  </td>
-</tr>
-</tbody>
-</table>
-
-TODO static vs dynamic linking
-
-### FFTW2
-
-<table>
-<thead>
-<tr>
-  <th>Option</th>
-  <th>Description</th>
-  <th>Values</th>
-</tr>
-</thead>
-<tbody>
-<tr>
-  <td><code>FFTW2_INCLUDE_DIRS</code></td>
-  <td></td>
-  <td>
-  </td>
-</tr>
-<tr>
-  <td><code>FFTW2_LIBRARIES</code></td>
-  <td></td>
-  <td>
-  </td>
-</tr>
-</tbody>
-</table>
-
 ### FFTW3
 
 <table>
@@ -1392,24 +1465,57 @@ TODO static vs dynamic linking
 <tbody>
 <tr>
   <td><code>FFTW3_INCLUDE_DIRS</code></td>
-  <td></td>
+  <td>path to FFTW3 include files</td>
   <td>
   </td>
 </tr>
 <tr>
   <td><code>FFTW3_LIBRARIES</code></td>
-  <td></td>
+  <td>list of paths to FFTW3 libraries</td>
   <td>
   </td>
 </tr>
 </tbody>
 </table>
 
+### MKL
+
+<table>
+<thead>
+<tr>
+  <th>Option</th>
+  <th>Description</th>
+  <th>Values</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+  <td><code>MKL_INCLUDE_DIRS</code></td>
+  <td>path to MKL include files</td>
+  <td>
+  </td>
+</tr>
+<tr>
+  <td><code>MKL_LIBRARIES</code></td>
+  <td>list of paths to MKL libraries</td>
+  <td>
+  </td>
+</tr>
+</tbody>
+</table>
+
+### BLAS
+
+See [FindBLAS documentation](https://cmake.org/cmake/help/latest/module/FindBLAS.html)
+
 ### LAPACK
-TODO
+
+See [FindLAPACK documentation](https://cmake.org/cmake/help/latest/module/FindLAPACK.html)
 
 ### PYTHON Package
 
+See [FindPYTHON documentation](https://cmake.org/cmake/help/latest/module/FindPython.html)
+
 ### USER-INTEL Package
 
 <table>
@@ -1499,10 +1605,11 @@ target API.
   <td>
   <dl>
     <dt><code>sm_20</code> (Fermi)</dt>
-    <dt><code>sm_30</code> (Kepler)</dt>
+    <dt><code>sm_30</code> (Kepler) (default)</dt>
     <dt><code>sm_50</code> (Maxwell)</dt>
     <dt><code>sm_60</code> (Pascal)</dt>
     <dt><code>sm_70</code> (Volta)</dt>
+    <dt><code>sm_75</code> (Turing)</dt>
   </dl>
   </td>
 </tr>
@@ -1534,13 +1641,14 @@ target API.
 </tbody>
 </table>
 
-### VORONOI Package
+### KIM Package
 
-TODO
+Requires installation of the KIM library with API v2
 
-### USER-SMD Package
-
-Requires a Eigen3 installation
+If `DOWNLOAD_KIM` is set, the KIM library will be downloaded and built inside
+the CMake build directory. If the KIM library is already on your system (in a
+location CMake cannot find it), set the `PKG_CONFIG_PATH` environment variable
+so that `libkim-api` can be found.
 
 <table>
 <thead>
@@ -1551,9 +1659,323 @@ Requires a Eigen3 installation
 </tr>
 </thead>
 <tbody>
+<tr>
+  <td><code>DOWNLOAD_KIM</code></td>
+  <td>Download KIM API v2 and compile it as part of the build.</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
+</tbody>
+</table>
+
+### MESSAGE Package
+
+This package can optionally include support for messaging via sockets, using the open-source [ZeroMQ library](http://zeromq.org/), which must be installed on your system.
+
+<table>
+<thead>
+<tr>
+  <th>Option</th>
+  <th>Description</th>
+  <th>Values</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+  <td><code>MESSAGE_ZMQ</code></td>
+  <td>Build with ZeroMQ support</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
+<tr>
+  <td><code>ZMQ_LIBRARY</code></td>
+  <td>
+    ZMQ library file (only needed if at custom location)
+  </td>
+  <td>
+  </td>
+</tr>
+<tr>
+  <td><code>ZMG_INCLUDE_DIR</code></td>
+  <td>
+    Provide include directory of existing ZMQ installation (only needed if at custom location)
+  </td>
+  <td>
+  </td>
+</tr>
+</tbody>
+</table>
+
+### MSCG Package
+
+Requires installation of the MSCG library
+
+<table>
+<thead>
+<tr>
+  <th>Option</th>
+  <th>Description</th>
+  <th>Values</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+  <td><code>DOWNLOAD_MSCG</code></td>
+  <td>Download MSCG and compile it as part of the build</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
+<tr>
+  <td><code>MSCG_LIBRARY</code></td>
+  <td>
+    MSCG library file (only needed if at custom location)
+  </td>
+  <td>
+  </td>
+</tr>
+<tr>
+  <td><code>MSCG_INCLUDE_DIR</code></td>
+  <td>
+    Provide include directory of existing MSCG installation (only needed if at custom location)
+  </td>
+  <td>
+  </td>
+</tr>
+</tbody>
+</table>
+
+### VORONOI Package
+
+Requires installation of the Voro++ library
+
+<table>
+<thead>
+<tr>
+  <th>Option</th>
+  <th>Description</th>
+  <th>Values</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+  <td><code>DOWNLOAD_VORO</code></td>
+  <td>Download Voro++ and compile it as part of the build</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
+<tr>
+  <td><code>VORO_LIBRARY</code></td>
+  <td>
+    Voro++ library file (only needed if at custom location)
+  </td>
+  <td>
+  </td>
+</tr>
+<tr>
+  <td><code>VORO_INCLUDE_DIR</code></td>
+  <td>
+    Provide include directory of existing Voro++ installation (only needed if at custom location)
+  </td>
+  <td>
+  </td>
+</tr>
+</tbody>
+</table>
+
+### USER-LATTE Package
+
+Requires installation of the LATTE library
+
+<table>
+<thead>
+<tr>
+  <th>Option</th>
+  <th>Description</th>
+  <th>Values</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+  <td><code>DOWNLOAD_LATTE</code></td>
+  <td>Download LATTE and compile it as part of the build</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
+<tr>
+  <td><code>LATTE_LIBRARY</code></td>
+  <td>
+    LATTE library file (only needed if at custom location)
+  </td>
+  <td>
+  </td>
+</tr>
+</tbody>
+</table>
+
+### USER-PLUMED Package
+
+Requires installation of the PLUMED library
+
+<table>
+<thead>
+<tr>
+  <th>Option</th>
+  <th>Description</th>
+  <th>Values</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+  <td><code>DOWNLOAD_PLUMED</code></td>
+  <td>Download PLUMED and compile it as part of the build</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
+<tr>
+  <td><code>PLUMED_MODE</code></td>
+  <td>
+    Determines the linkage mode for the PLUMED library.
+  </td>
+  <td>
+  <dl>
+    <dt><code>static</code> (default)</dt>
+    <dt><code>shared</code></dt>
+    <dt><code>runtime</code></dt>
+  </dl>
+  </td>
+</tr>
+</tbody>
+</table>
+
+### USER-LATTE Package
+
+Requires installation of the LATTE library
+
+<table>
+<thead>
+<tr>
+  <th>Option</th>
+  <th>Description</th>
+  <th>Values</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+  <td><code>DOWNLOAD_LATTE</code></td>
+  <td>Download LATTE and compile it as part of the build</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
+<tr>
+  <td><code>LATTE_LIBRARY</code></td>
+  <td>
+    LATTE library file (only needed if at custom location)
+  </td>
+  <td>
+  </td>
+</tr>
+</tbody>
+</table>
+
+### USER-SMD Package
+
+Requires installation of the Eigen3 library
+
+<table>
+<thead>
+<tr>
+  <th>Option</th>
+  <th>Description</th>
+  <th>Values</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+  <td><code>DOWNLOAD_EIGEN3</code></td>
+  <td>Download Eigen3 and compile it as part of the build</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
 <tr>
   <td><code>EIGEN3_INCLUDE_DIR</code></td>
-  <td></td>
+  <td>
+    Provide include directory of existing Eigen3 installation (only needed if at custom location)
+  </td>
+  <td>
+  </td>
+</tr>
+</tbody>
+</table>
+
+
+### USER-SCAFACOS Package
+
+To build with this package, you must download and build the [ScaFaCoS Coulomb solver library](http://www.scafacos.de/)
+
+<table>
+<thead>
+<tr>
+  <th>Option</th>
+  <th>Description</th>
+  <th>Values</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+  <td><code>DOWNLOAD_SCAFACOS</code></td>
+  <td>Download SCAFACOS and compile it as part of the build</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
+<tr>
+  <td><code>SCAFACOS_LIBRARY</code></td>
+  <td>
+    SCAFACOS library file (only needed if at custom location)
+  </td>
+  <td>
+  </td>
+</tr>
+<tr>
+  <td><code>SCAFACOS_INCLUDE_DIR</code></td>
+  <td>
+    SCAFACOS include directory (only needed if at custom location)
+  </td>
   <td>
   </td>
 </tr>
@@ -1791,5 +2213,82 @@ cmake -D CMAKE_C_COMPILER=icc -D CMAKE_CXX_COMPILER=icpc -D CMAKE_Fortran_COMPIL
 cmake -D CMAKE_C_COMPILER=clang -D CMAKE_CXX_COMPILER=clang++ -D CMAKE_Fortran_COMPILER=flang ../cmake
 ```
 
+## LAMMPS Developer Options
 
-## Examples
+
+<table>
+<thead>
+<tr>
+  <th>Option</th>
+  <th>Description</th>
+  <th>Values</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+  <td><code>ENABLE_TESTING</code></td>
+  <td>Control wheather to add tests via CTest</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
+<tr>
+  <td><code>LAMMPS_TESTING_SOURCE_DIR</code></td>
+  <td>Custom location of lammps-testing repository (optional). If not specified it will download it via Git</td>
+  <td>
+  </td>
+</tr>
+<tr>
+  <td><code>LAMMPS_TESTING_GIT_TAG</code></td>
+  <td>If lammps-testing repository is cloned, this is the tag/commit that will be checked out</td>
+  <td>
+  <dl>
+    <dt><code>master</code> (default)</dt>
+  </dl>
+  </td>
+</tr>
+<tr>
+  <td><code>ENABLE_COVERAGE</code></td>
+  <td>Enables code coverage support via gcov and adds a gcovr build target to generate a coverage report.</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
+<tr>
+  <td><code>ENABLE_SANITIZE_ADDRESS</code></td>
+  <td>Enables Address Sanitizer support when compiling using GCC or Clang for detecting memory leaks in binaries while running them. See https://clang.llvm.org/docs/AddressSanitizer.html</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
+<tr>
+  <td><code>ENABLE_SANITIZE_UNDEFINED</code></td>
+  <td>Enables Undefined Behavior Sanitizer support when compiling using GCC or Clang for detecting code that is running into undefined behavior of the language. See https://clang.llvm.org/docs/UndefinedBehaviorSanitizer.html</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
+<tr>
+  <td><code>ENABLE_SANITIZE_THREAD</code></td>
+  <td>Enables Thread Sanitizer support when compiling using GCC or Clang for detecting data races in binaries while running them. See https://clang.llvm.org/docs/ThreadSanitizer.html</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
+</tbody>
+</table>

cmake/etc/profile.d/lammps.csh.in

@@ -1,4 +1,4 @@
 # set environment for LAMMPS and msi2lmp executables
 # to find potential and force field files
-if ( "$?LAMMPS_POTENTIALS" == 0 ) setenv LAMMPS_POTENTIALS @LAMMPS_POTENTIALS_DIR@
-if ( "$?MSI2LMP_LIBRARY" == 0 ) setenv MSI2LMP_LIBRARY @LAMMPS_FRC_FILES_DIR@
+if ( "$?LAMMPS_POTENTIALS" == 0 ) setenv LAMMPS_POTENTIALS @LAMMPS_INSTALL_DATADIR@/potentials
+if ( "$?MSI2LMP_LIBRARY" == 0 ) setenv MSI2LMP_LIBRARY @LAMMPS_INSTALL_DATADIR@/frc_files

cmake/etc/profile.d/lammps.sh.in

@@ -1,5 +1,5 @@
 # set environment for LAMMPS and msi2lmp executables
 # to find potential and force field files
-LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS-@LAMMPS_POTENTIALS_DIR@}
-MSI2LMP_LIBRARY=${MSI2LMP_LIBRARY-@LAMMPS_FRC_FILES_DIR@}
+LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS-@LAMMPS_INSTALL_DATADIR@/potentials}
+MSI2LMP_LIBRARY=${MSI2LMP_LIBRARY-@LAMMPS_INSTALL_DATADIR@/frc_files}
 export LAMMPS_POTENTIALS MSI2LMP_LIBRARY

cmake/presets/mingw-cross.cmake

@@ -3,9 +3,9 @@ set(WIN_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
                  REPLICA RIGID SHOCK SNAP SPIN SRD VORONOI USER-ATC USER-AWPMD
                  USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS USER-DIFFRACTION
                  USER-DPD USER-DRUDE USER-EFF USER-FEP USER-INTEL USER-MANIFOLD
-                 USER-MEAMC USER-MESO USER-MISC USER-MOFFF USER-MOLFILE USER-OMP
-                 USER-PHONON USER-PTM USER-QTB USER-REAXC USER-SDPD USER-SMD
-                 USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-YAFF)
+                 USER-MEAMC USER-MESO USER-MISC USER-MGPT USER-MOFFF USER-MOLFILE
+                 USER-OMP USER-PHONON USER-PTM USER-QTB USER-REAXC USER-SDPD
+                 USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-YAFF)
 
 foreach(PKG ${WIN_PACKAGES})
   set(PKG_${PKG} ON CACHE BOOL "" FORCE)
@@ -14,4 +14,4 @@ endforeach()
 set(DOWNLOAD_VORO ON CACHE BOOL "" FORCE)
 set(DOWNLOAD_EIGEN3 ON CACHE BOOL "" FORCE)
 set(LAMMPS_MEMALIGN "0" CACHE STRING "" FORCE)
-set(INTEL_LRT_MODE "none" CACHE STRING "" FORCE)
+set(CMAKE_INSTALL_PREFIX "${CMAKE_CURRENT_BINARY_DIR}/lammps-installer")

doc/include-file-conventions.md

@@ -0,0 +1,133 @@
+# Outline of include file conventions in LAMMPS
+
+This purpose of this document is to provide a point of reference
+for LAMMPS developers and contributors as to what include files
+and definitions to put where into LAMMPS source.
+Last change 2019-07-05
+
+## Table of Contents
+
+  * [Motivation](#motivation)
+  * [Rules](#rules)
+  * [Tools](#tools)
+  * [Legacy Code](#legacy-code)
+
+## Motivation
+
+The conventions outlined in this document are supposed to help make
+maintenance of the LAMMPS software easier.  By trying to achieve
+consistency across files contributed by different developers, it will
+become easier for the code maintainers to modify and adjust files and,
+overall, the chance for errors or portability issues will be reduced.
+The rules employed are supposed to minimize naming conflicts and
+simplify dependencies between files and thus speed up compilation. They
+may, as well, make otherwise hidden dependencies visible.
+
+## Rules
+
+Below are the various rules that are applied.  Not all are enforced
+strictly and automatically.  If there are no significant side effects,
+exceptions may be possible for cases where a full compliance to the
+rules may require a large effort compared to the benefit.
+
+### Core Files Versus Package Files
+
+All rules listed below are most strictly observed for core LAMMPS files,
+which are the files that are not part of a package, and the files of the
+packages MOLECULE, MANYBODY, KSPACE, and RIGID.  On the other end of
+the spectrum are USER packages and legacy packages that predate these
+rules and thus may not be fully compliant.  Also, new contributions
+will be checked more closely, while existing code will be incrementally
+adapted to the rules as time and required effort permits.
+
+### System Versus Local Header Files
+
+All system- or library-provided include files are included with angular
+brackets (examples: `#include <cstring>` or `#include <mpi.h>`) while
+include files provided with LAMMPS are included with double quotes
+(examples: `#include "pointers.h"` or `#include "compute_temp.h"`).
+
+For headers declaring functions of the C-library, the corresponding
+C++ versions should be included (examples: `#include <cstdlib>` or
+`#include <cctypes>`).  However, these includes are limited to those defined
+in the C++98 standard.  Some files thus must use the older style until
+the minimum C++ standard requirement of LAMMPS is lifted to C++11 or
+even beyond (examples: `#include <stdint.h>` versus `#include <cstdint>`
+or `#include <inttypes.h>` versus `#include <cinttypes>`).
+
+### C++ Standard Compliance
+
+LAMMPS core files currently correspond to the C++98 standard. Files
+requiring C++11 or later are only permitted in (optional) packages
+and particularly packages that are not part of the list of commonly
+used packages such as MOLECULE, KSPACE, MANYBODY, or RIGID.
+
+Also, LAMMPS uses the C-style stdio library for I/O instead of iostreams.
+Since using both at the same time can cause problems, iostreams should
+be avoided where possible.
+
+### Lean Header Files
+
+Header files will typically contain the definition of a (single) class.
+These header files should have as few include statements as possible.
+This is particularly important for classes that implement a "style" and
+thus use a macro of the kind `SomeStyle(some/name,SomeName)`. These will
+all be included in the auto-generated `"some_style.h"` files which 
+results in a high potential for direct or indirect symbol name clashes.
+
+In the ideal case, the header would only include one file defining the
+parent class. That would typically be either `#include "pointers.h"` for
+the `Pointers` class, or a header of a class derived from it like
+`#include "pair.h"` for the `Pair` class and so on.  References to other
+classes inside the class should be make through pointers, for which forward
+declarations (inside the `LAMMPS_NS` or the new class' namespace) can
+be employed.  The full definition will then be included into the corresponding
+implementation file.  In the given example from above, the header file
+would be called `some_name.h` and the implementation `some_name.cpp` (all
+lower case with underscores, while the class itself would be in camel case
+and no underscores `SomeName`, and the style name with lower case names separated by
+a forward slash).
+
+### Implementation Files
+
+In the implementation files (typically, those would have the same base name
+as the corresponding header with a .cpp extension instead of .h) include
+statements should follow the "include what you use" principle.
+
+### Order of Include Statements
+
+Include files should be included in this order:
+* the header matching the implementation (`some_class.h` for file `some_class.cpp`)
+* mpi.h
+* system and library headers (anything that is using angular brackets; C-library headers first, then C++)
+* LAMMPS local headers (preferably in alphabetical order)
+
+### Special Cases and Exceptions
+
+#### pointers.h
+
+The `pointer.h` header file also includes `cstdio` and `lmptype.h`
+(and through it `stdint.h`, `intttypes.h`, cstdlib, and `climits`).
+This means any header including `pointers.h` can assume that `FILE`,
+`NULL`, `INT_MAX` are defined.
+
+## Tools
+
+The [Include What You Use tool](https://include-what-you-use.org/)
+can be used to provide supporting information about compliance with
+the rules listed here.  There are some limitations and the IWYU tool
+may give incorrect advice.  The tools is activated by setting the
+CMake variable `CMAKE_CXX_INCLUDE_WHAT_YOU_USE` variable to the
+path of the `include-what-you-use` command.  When activated, the
+tool will be run after each compilation and provide suggestions for
+which include files should be added or removed.
+
+## Legacy Code
+
+A lot of code predates the application of the rules in this document
+and the rules themselves are a moving target.  So there are going to be
+significant chunks of code that do not fully comply.  This applies
+for example to the USER-REAXC, or the USER-ATC package.  The LAMMPS
+developers are dedicated to make an effort to improve the compliance
+and welcome volunteers wanting to help with the process.
+

doc/lammps.1

@@ -1,4 +1,4 @@
-.TH LAMMPS "19 July 2019" "2019-07-19"
+.TH LAMMPS "7 August 2019" "2019-08-07"
 .SH NAME
 .B LAMMPS
 \- Molecular Dynamics Simulator.

doc/src/Build.txt

@@ -29,6 +29,7 @@ as described on the "Install"_Install.html doc page.
    Build_package
    Build_extras
    Build_windows
+   Build_development
 
 END_RST -->
 
@@ -41,7 +42,8 @@ END_RST -->
 "Optional build settings"_Build_settings.html
 "Include packages in build"_Build_package.html
 "Packages with extra build options"_Build_extras.html
-"Notes for building LAMMPS on Windows"_Build_windows.html  :all(b)
+"Notes for building LAMMPS on Windows"_Build_windows.html
+"Development build options (CMake only)"_Build_development.html  :all(b)
 
 If you have problems building LAMMPS, it is often due to software
 issues on your local machine.  If you can, find a local expert to

doc/src/Build_basics.txt

@@ -235,12 +235,16 @@ running LAMMPS from Python via its library interface.
 
 -D BUILD_EXE=value           # yes (default) or no
 -D BUILD_LIB=value           # yes or no (default)
--D BUILD_SHARED_LIBS=value   # yes or no (default) :pre
+-D BUILD_SHARED_LIBS=value   # yes or no (default)
+-D LAMMPS_LIB_SUFFIX=name    # name = mpi, serial, mybox, titan, laptop, etc
+                             # no default value :pre
+
 
 Setting BUILD_EXE=no will not produce an executable.  Setting
 BUILD_LIB=yes will produce a static library named liblammps.a.
 Setting both BUILD_LIB=yes and BUILD_SHARED_LIBS=yes will produce a
-shared library named liblammps.so.
+shared library named liblammps.so. If LAMMPS_LIB_SUFFIX is set the generated
+libraries will be named liblammps_name.a or liblammps_name.so instead.
 
 [Traditional make]:
 
@@ -310,6 +314,30 @@ current LAMMPS version (HTML and PDF files), from the website
 
 :line
 
+Build LAMMPS tools :h4,link(tools)
+
+Some tools described in "Auxiliary tools"_Tools.html can be built directly
+using CMake or Make.
+
+[CMake variable]:
+
+-D BUILD_TOOLS=value       # yes or no (default) :pre
+
+The generated binaries will also become part of the LAMMPS installation (see below)
+
+[Traditional make]:
+
+cd lammps/tools
+make all              # build all binaries of tools
+make binary2txt       # build only binary2txt tool
+make chain            # build only chain tool
+make micelle2d        # build only micelle2d tool
+make thermo_extract   # build only thermo_extract tool
+:pre
+
+:line
+
+
 Install LAMMPS after a build :h4,link(install)
 
 After building LAMMPS, you may wish to copy the LAMMPS executable of

doc/src/Build_cmake.txt

@@ -52,11 +52,17 @@ LAMMPS or need to re-compile LAMMPS repeatedly, installation of the
 ccache (= Compiler Cache) software may speed up repeated compilation
 even more.
 
-After compilation, you can optionally copy the LAMMPS executable and
-library into your system folders (by default under $HOME/.local) with:
+After compilation, you may optionally install the LAMMPS executable into
+your system with:
 
 make install    # optional, copy LAMMPS executable & library elsewhere :pre
 
+This will install the lammps executable and library (if requested), some
+tools (if configured) and additional files like library API headers,
+manpages, potential and force field files. The location of the installation
+tree is set by the CMake variable "CMAKE_INSTALL_PREFIX" which defaults
+to $\{HOME\}/.local
+
 :line
 
 There are 3 variants of CMake: a command-line version (cmake), a text mode
@@ -114,7 +120,7 @@ The argument can be preceeded or followed by various CMake
 command-line options.  Several useful ones are:
 
 -D CMAKE_INSTALL_PREFIX=path  # where to install LAMMPS executable/lib if desired
--D CMAKE_BUILD_TYPE=type      # type = Release or Debug
+-D CMAKE_BUILD_TYPE=type      # type = RelWithDebInfo (default), Release, MinSizeRel, or Debug
 -G output                     # style of output CMake generates
 -DVARIABLE=value              # setting for a LAMMPS feature to enable
 -D VARIABLE=value             # ditto, but cannot come after CMakeLists.txt dir

doc/src/Build_development.txt

@@ -0,0 +1,86 @@
+"Higher level section"_Build.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Development build options (CMake only) :h3
+
+The CMake build of LAMMPS has a few extra options which are useful during
+development,  testing or debugging.
+
+:line
+
+Verify compilation flags :h4,link(compilation)
+
+Sometimes it is necessary to verify the complete sequence of compilation flags
+generated by the CMake build. To enable a more verbose output during
+compilation you can use the following option.
+
+-D CMAKE_VERBOSE_MAKEFILE=value    # value = no (default) or yes :pre
+
+Another way of doing this without reconfiguration is calling make with variable VERBOSE set to 1:
+
+make VERBOSE=1 :pre
+
+:line
+
+Address, Undefined Behavior, and Thread Sanitizer Support :h4,link(sanitizer)
+
+Compilers such as GCC and Clang support generating binaries which use different
+sanitizers to detect problems in code during run-time. They can detect "memory leaks"_https://clang.llvm.org/docs/AddressSanitizer.html,
+code that runs into "undefined behavior"_https://clang.llvm.org/docs/UndefinedBehaviorSanitizer.html of the
+language and "data races"_https://clang.llvm.org/docs/ThreadSanitizer.html in threaded code.
+
+The following settings allow you enable these features if your compiler supports
+it. Please note that they come with a performance hit. However, they are
+usually faster than using tools like Valgrind.
+
+-D ENABLE_SANITIZE_ADDRESS=value    # enable Address Sanitizer, value = no (default) or yes
+-D ENABLE_SANITIZE_UNDEFINED=value  # enable Undefined Behaviour Sanitizer, value = no (default) or yes
+-D ENABLE_SANITIZE_THREAD=value     # enable Thread Sanitizer, value = no (default) or yes
+:pre
+
+:line
+
+Code Coverage and Testing :h4,link(testing)
+
+We do extensive regression testing of the LAMMPS code base on a continuous
+basis. Some of the logic to do this has been added to the CMake build so
+developers can run the tests directly on their workstation. 
+
+NOTE: this is incomplete and only represents a small subset of tests that we run
+
+-D ENABLE_TESTING=value               # enable simple run tests of LAMMPS, value = no (default) or yes
+-D LAMMPS_TESTING_SOURCE_DIR=path     # path to lammps-testing repository (option if in custom location)
+-D LAMMPS_TESTING_GIT_TAG=value       # version of lammps-testing repository that should be used, value = master (default) or custom git commit or tag
+:pre
+
+If you enable testing in the CMake build it will create an additional target called "test". You can run them with:
+
+make test
+:pre
+
+The test cases used come from the lammps-testing repository. They are
+derivatives of the examples folder with some modifications to make the run
+faster.
+
+You can also collect code coverage metrics while running the tests by enabling
+coverage support during building.
+
+-D ENABLE_COVERAGE=value  # enable coverage measurements, value = no (default) or yes :pre
+
+This will also add the following targets to generate coverage reports after running the LAMMPS executable:
+
+make test               # run tests first!
+make gen_coverage_html  # generate coverage report in HTML format
+make gen_coverage_xml   # generate coverage report in XML format
+:pre
+
+These reports require GCOVR to be installed. The easiest way to do this to install it via pip:
+
+pip install git+https://github.com/gcovr/gcovr.git :pre
+:pre

doc/src/Build_extras.txt

@@ -88,7 +88,7 @@ which GPU hardware to build for.
                           # generic (default) or intel (Intel CPU) or fermi, kepler, cypress (NVIDIA)
 -D GPU_ARCH=value         # primary GPU hardware choice for GPU_API=cuda
                           # value = sm_XX, see below
-                          # default is Cuda-compiler dependent, but typically sm_20
+                          # default is sm_30
 -D CUDPP_OPT=value        # optimization setting for GPU_API=cuda
                           # enables CUDA Performance Primitives Optimizations
                           # value = yes (default) or no
@@ -172,22 +172,17 @@ KIM package :h4,link(kim)
 
 To build with this package, the KIM library with API v2 must be downloaded
 and built on your system.  It must include the KIM models that you want to
-use with LAMMPS. If you want to use the "kim_query"_kim_query.html
+use with LAMMPS. If you want to use the "kim_query"_kim_commands.html
 command, you also need to have libcurl installed with the matching
 development headers and the curl-config tool.
 
-Note that in LAMMPS lingo, a KIM model driver is a pair style
-(e.g. EAM or Tersoff).  A KIM model is a pair style for a particular
-element or alloy and set of parameters, e.g. EAM for Cu with a
-specific EAM potential file.  Also note that downloading and installing
-the KIM API library with all its models, may take a long time (10s of
-minutes to hours) to build.  Of course you only need to do that once.
+See "Obtaining KIM Models"_http://openkim.org/doc/usage/obtaining-models to
+learn how to install a pre-build binary of the OpenKIM Repository of Models.
+See the list of all KIM models here: https://openkim.org/browse/models
 
-See the list of KIM model drivers here:
-https://openkim.org/browse/model-drivers/alphabetical
-
-See the list of all KIM models here:
-https://openkim.org/browse/models/by-model-drivers
+(Also note that when downloading and installing from source
+the KIM API library with all its models, may take a long time (tens of
+minutes to hours) to build.  Of course you only need to do that once.)
 
 [CMake build]:
 
@@ -359,6 +354,9 @@ be installed on your system.
 [CMake build]:
 
 -D MESSAGE_ZMQ=value    # build with ZeroMQ support, value = no (default) or yes
+-D ZMQ_LIBRARY=path     # ZMQ library file (only needed if a custom location)
+-D ZMQ_INCLUDE_DIR=path # ZMQ include directory (only needed if a custom location)
+:pre
 
 [Traditional make]:
 
@@ -371,6 +369,7 @@ simply invoke the lib/message/Install.py script with the specified args:
 make lib-message               # print help message
 make lib-message args="-m -z"  # build with MPI and socket (ZMQ) support
 make lib-message args="-s"     # build as serial lib with no ZMQ support
+:pre
 
 The build should produce two files: lib/message/cslib/src/libmessage.a
 and lib/message/Makefile.lammps.  The latter is copied from an

doc/src/Commands_all.txt

@@ -68,7 +68,9 @@ An alphabetic list of all general LAMMPS commands.
 "improper_style"_improper_style.html,
 "include"_include.html,
 "jump"_jump.html,
-"kim_query"_kim_query.html,
+"kim_init"_kim_commands.html,
+"kim_interactions"_kim_commands.html,
+"kim_query"_kim_commands.html,
 "kspace_modify"_kspace_modify.html,
 "kspace_style"_kspace_style.html,
 "label"_label.html,

doc/src/Commands_compute.txt

@@ -66,6 +66,7 @@ KOKKOS, o = USER-OMP, t = OPT.
 "group/group"_compute_group_group.html,
 "gyration"_compute_gyration.html,
 "gyration/chunk"_compute_gyration_chunk.html,
+"gyration/shape"_compute_gyration_shape.html,
 "heat/flux"_compute_heat_flux.html,
 "heat/flux/tally"_compute_tally.html,
 "hexorder/atom"_compute_hexorder_atom.html,
@@ -80,6 +81,7 @@ KOKKOS, o = USER-OMP, t = OPT.
 "meso/e/atom"_compute_meso_e_atom.html,
 "meso/rho/atom"_compute_meso_rho_atom.html,
 "meso/t/atom"_compute_meso_t_atom.html,
+"momentum"_compute_momentum.html,
 "msd"_compute_msd.html,
 "msd/chunk"_compute_msd_chunk.html,
 "msd/nongauss"_compute_msd_nongauss.html,

doc/src/Eqs/compute_shape_parameters.tex

@@ -0,0 +1,13 @@
+\documentclass[12pt]{article}
+
+\pagestyle{empty}
+\begin{document}
+
+\begin{eqnarray*}
+ c = l_z - 0.5(l_y+l_x) \\
+ b = l_y - l_x \\
+ k = \frac{3}{2} \frac{l_x^2+l_y^2+l_z^2}{(l_x+l_y+l_z)^2} - \frac{1}{2} 
+\end{eqnarray*}
+
+\end{document}
+

doc/src/Eqs/pair_kolmogorov_crespi_full.tex

@@ -27,7 +27,7 @@
   V_{ij} & = & e^{-\lambda (r_{ij} -z_0)} \left [ C + f(\rho_{ij}) + f(\rho_{ji}) - A \left ( \frac{r_{ij}}{z_0}\right )^{-6} \right ] \\
   \rho_{ij}^2 & = & r_{ij}^2 - ({\bf r}_{ij}\cdot {\bf n}_{i})^2 \\[15pt]
   \rho_{ji}^2 & = & r_{ij}^2 - ({\bf r}_{ij}\cdot  {\bf n}_{j})^2 \\[15pt]
-  f(\rho) & = &  e^{-(\rho/\delta)^2} \sum_{n=0}^2 C_{2n} { \rho/\delta }^{2n}
+  f(\rho) & = &  e^{-(\rho/\delta)^2} \sum_{n=0}^2 C_{2n} { (\rho/\delta) }^{2n}
 \end{eqnarray*}
 \endgroup
 \end{document}

doc/src/Errors_messages.txt

@@ -2438,6 +2438,14 @@ Self-explanatory. :dd
 
 Self-explanatory. :dd
 
+{Compute gyration ID does not exist for compute gyration/shape} :dt
+
+Self-explanatory. Provide a valid compute ID. :dd
+
+{Compute gyration/shape compute ID does not point to a gyration compute} :dt
+
+Self-explanatory. Provide and ID of a compute gyration command. :dd
+
 {Compute ID for compute reduce does not exist} :dt
 
 Self-explanatory. :dd
@@ -5777,6 +5785,16 @@ definitions. :dd
 
 The data file header lists improper but no improper types. :dd
 
+{Incompatible KIM Simulator Model} :dt
+
+The requested KIM Simulator Model was defined for a different MD code
+and thus is not compatible with LAMMPS. :dd
+
+{Incompatible units for KIM Simulator Model} :dt
+
+The selected unit style is not compatible with the requested KIM
+Simulator Model. :dd
+
 {Incomplete use of variables in create_atoms command} :dt
 
 The var and set options must be used together. :dd
@@ -7047,6 +7065,12 @@ The atom style defined does not have this attribute. :dd
 
 The atom style defined does not have these attributes. :dd
 
+{KIM Simulator Model has no Model definition} :dt
+
+There is no model definition (key: model-defn) in the KIM Simulator
+Model.  Please contact the OpenKIM database maintainers to verify
+and potentially correct this. :dd
+
 {KOKKOS package does not yet support comm_style tiled} :dt
 
 Self-explanatory. :dd
@@ -7551,6 +7575,18 @@ Self-explanatory. :dd
 
 Self-explanatory. :dd
 
+{Must use 'kim_style init' command before simulation box is defined} :dt
+
+Self-explanatory. :dd
+
+{Must use 'kim_style define' command after simulation box is defined} :dt
+
+Self-explanatory. :dd
+
+{Must use 'kim_style init' command before 'kim_style define'} :dt
+
+Self-explanatory. :dd
+
 {Must use 'kspace_modify pressure/scalar no' for rRESPA with kspace_style MSM} :dt
 
 The kspace scalar pressure option cannot (yet) be used with rRESPA. :dd
@@ -9494,6 +9530,11 @@ See the "read_data extra/special/per/atom" command
 for info on how to leave space in the special bonds
 list to allow for additional bonds to be formed. :dd
 
+{Species XXX is not supported by this KIM Simulator Model} :dt
+
+The kim_style define command was referencing a species that is not
+present in the requested KIM Simulator Model. :dd
+
 {Specified processors != physical processors} :dt
 
 The 3d grid of processors defined by the processors command does not

doc/src/Errors_warnings.txt

@@ -129,6 +129,16 @@ Self-explanatory. :dd
 
 Self-explanatory. :dd
 
+{Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost} :dt
+
+The communication cutoff defaults to the maximum of what is inferred from
+pair and bond styles (will be zero, if none are defined) and what is specified
+via "comm_modify cutoff"_comm_modify.html (defaults to 0.0).  If this results
+to 0.0, no ghost atoms will be generated and LAMMPS may lose atoms or use
+incorrect periodic images of atoms in interaction lists.  To avoid, either use
+"pair style zero"_pair_zero.html with a suitable cutoff or use "comm_modify
+cutoff"_comm_modify.html. :dd
+
 {Communication cutoff is too small for SNAP micro load balancing, increased to %lf} :dt
 
 Self-explanatory. :dd

doc/src/Examples.txt

@@ -73,7 +73,7 @@ granregion: use of fix wall/region/gran as boundary on granular particles
 hugoniostat: Hugoniostat shock dynamics
 hyper:    global and local hyperdynamics of diffusion on Pt surface
 indent:   spherical indenter into a 2d solid
-kim:      use of potentials in Knowledge Base for Interatomic Models (KIM)
+kim:      use of potentials from the "OpenKIM Repository"_openkim
 latte:    examples for using fix latte for DFTB via the LATTE library
 meam:     MEAM test for SiC and shear (same as shear examples)
 melt:     rapid melt of 3d LJ system
@@ -153,3 +153,5 @@ illustrate how to use the command(s) provided in that package.  Many
 of the sub-directories have their own README files which give further
 instructions.  See the "Packages_details"_Packages_details.html doc
 page for more info on specific USER packages.
+
+:link(openkim,https://openkim.org)

doc/src/Install_mac.txt

@@ -10,47 +10,34 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 Download an executable for Mac :h3
 
 LAMMPS can be downloaded, built, and configured for OS X on a Mac with
-"Homebrew"_homebrew.  Only four of the LAMMPS packages are unavailable
-at this time because of additional needs not yet met: KIM, GPU,
-USER-INTEL, USER-ATC.
+"Homebrew"_homebrew.  The following LAMMPS packages are unavailable at this
+time because of additional needs not yet met: GPU, KOKKOS, LATTE, MSCG,
+MESSAGE, MPIIO POEMS VORONOI.
 
 After installing Homebrew, you can install LAMMPS on your system with
 the following commands:
 
-% brew tap homebrew/science
-% brew install lammps              # serial version
-% brew install lammps --with-mpi   # mpi support :pre
+% brew install lammps :pre
 
-This will install the executable "lammps", a python module named
-"lammps", and additional resources with all the standard packages.  To
-get the location of the additional resources type this:
-
-% brew info lammps :pre
-
-This command also tells you additional installation options available.
-The user-packages are available as options, just install them like
-this example for the USER-OMP package:
-
-% brew install lammps --enable-user-omp :pre
-
-It is usually best to install LAMMPS with the most up to date source
-files, which can be done with the "--HEAD" option:
-
-% brew install lammps --HEAD :pre
-
-To re-install the LAMMPS HEAD, run this command occasionally (make sure
-to use the desired options).
-
-% brew install --force lammps --HEAD $\{options\} :pre
+This will install the executables "lammps_serial" and "lammps_mpi", as well as
+the LAMMPS "doc", "potentials", "tools", "bench", and "examples" directories.
 
 Once LAMMPS is installed, you can test the installation with the
 Lennard-Jones benchmark file:
 
 % brew test lammps -v :pre
 
+The LAMMPS binary is built with the "KIM package"_Build_extras#kim which
+results in Homebrew also installing the `kim-api` binaries when LAMMPS is
+installed.  In order to use potentials from "openkim.org"_openkim, you can
+install the `openkim-models` package
+
+% brew install openkim-models :pre
+
 If you have problems with the installation you can post issues to
 "this link"_homebrew.
 
 Thanks to Derek Thomas (derekt at cello.t.u-tokyo.ac.jp) for setting
 up the Homebrew capability.
-:link(homebrew,https://github.com/Homebrew/homebrew-science/issues)
+:link(homebrew,https://github.com/Homebrew/homebrew-core/issues)
+:link(openkim,https://openkim.org)

doc/src/Intro_features.txt

@@ -92,8 +92,8 @@ commands)
   implicit solvent potentials: hydrodynamic lubrication, Debye
   force-field compatibility with common CHARMM, AMBER, DREIDING, \
     OPLS, GROMACS, COMPASS options
-  access to "KIM archive"_http://openkim.org of potentials via \
-    "pair kim"_pair_kim.html
+  access to the "OpenKIM Repository"_http://openkim.org of potentials via \
+    "kim_init, kim_interactions, and kim_query"_kim_commands.html commands
   hybrid potentials: multiple pair, bond, angle, dihedral, improper \
     potentials can be used in one simulation
   overlaid potentials: superposition of multiple pair potentials :ul

doc/src/Manual.txt

@@ -1,7 +1,7 @@
 <!-- HTML_ONLY -->
 <HEAD>
 <TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="19 Jul 2019 version">
+<META NAME="docnumber" CONTENT="7 Aug 2019 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>
@@ -21,7 +21,7 @@
 :line
 
 LAMMPS Documentation :c,h1
-19 Jul 2019 version :c,h2
+7 Aug 2019 version :c,h2
 
 "What is a LAMMPS version?"_Manual_version.html
 

doc/src/Packages_details.txt

@@ -338,22 +338,37 @@ KIM package :link(PKG-KIM),h4
 
 [Contents:]
 
-A "pair_style kim"_pair_kim.html command which is a wrapper on the
-Knowledge Base for Interatomic Models (KIM) repository of interatomic
-potentials, enabling any of them to be used in LAMMPS simulations.
-Also a "kim_query"_kim_query.html command, which allows to query
-the OpenKIM database for stored properties.
+This package contains a set of commands that serve as a wrapper on the
+"Open Knowledgebase of Interatomic Models (OpenKIM)"_https://openkim.org
+repository of interatomic models (IMs)
+enabling compatible ones to be used in LAMMPS simulations.
+This includes "kim_init and kim_interactions"_kim_commands.html
+commands to select, initialize and instantiate the IM, and a
+"kim_query"_kim_commands.html command to perform web queries
+for material property predictions of OpenKIM IMs.
+Support for KIM IMs that conform to the
+"KIM Application Programming Interface (API)"_https://openkim.org/kim-api/
+is provided by the "pair_style kim"_pair_kim.html command.
 
-To use this package you must have the KIM library available on your
-system.
+NOTE: The command {pair_style kim} is called by {kim_interactions} and
+is not recommended to be directly used in input scripts.
+
+To use this package you must have the KIM API library available on your
+system. The KIM API is available for download on the
+"OpenKIM website"_https://openkim.org/kim-api/.
+When installing LAMMPS from binary, the kim-api package
+is a dependency that is automatically downloaded and installed.
 
 Information about the KIM project can be found at its website:
-https://openkim.org.  The KIM project is led by Ellad Tadmor and Ryan
-Elliott (U Minnesota).
+"https://openkim.org"_https://openkim.org.
+The KIM project is led by Ellad Tadmor and Ryan Elliott (U Minnesota)
+and is funded by the "National Science Foundation"_https://www.nsf.gov/.
 
 [Authors:] Ryan Elliott (U Minnesota) is the main developer for the KIM
-API which the "pair_style kim"_pair_kim.html command uses.  He
-developed the pair style.
+API and the {pair_style kim} command. Axel Kohlmeyer (Temple U) and
+Ellad Tadmor (U Minnesota) contributed to the "kim_commands"_kim_commands.html
+interface in close collaboration with Ryan Elliott.
+
 
 [Install:]
 
@@ -363,10 +378,11 @@ extras"_Build_extras.html doc page.
 
 [Supporting info:]
 
+"kim_commands"_kim_commands.html
+"pair_style kim"_pair_kim.html
 src/KIM: filenames -> commands
 src/KIM/README
 lib/kim/README
-"pair_style kim"_pair_kim.html
 examples/kim :ul
 
 :line
@@ -984,9 +1000,9 @@ USER-ADIOS package :link(PKG-USER-ADIOS),h4
 
 [Contents:]
 
-ADIOS is a high-performance I/O library. This package implements the 
+ADIOS is a high-performance I/O library. This package implements the
 dump "atom/adios" and dump "custom/adios" commands to write data using
-the ADIOS library. 
+the ADIOS library.
 
 [Authors:] Norbert Podhorszki (ORNL) from the ADIOS developer team.
 
@@ -1175,7 +1191,7 @@ USER-PLUMED package :link(PKG-USER-PLUMED),h4
 The fix plumed command allows you to use the PLUMED free energy plugin
 for molecular dynamics to analyze and bias your LAMMPS trajectory on
 the fly.  The PLUMED library is called from within the LAMMPS input
-script by using the "fix plumed _fix_plumed.html command.
+script by using the "fix plumed"_fix_plumed.html command.
 
 [Authors:] The "PLUMED library"_#PLUMED is written and maintained by
 Massimilliano Bonomi, Giovanni Bussi, Carlo Camiloni and Gareth

doc/src/Speed_kokkos.txt

@@ -46,16 +46,15 @@ software version 7.5 or later must be installed on your system. See
 the discussion for the "GPU package"_Speed_gpu.html for details of how
 to check and do this.
 
-NOTE: Kokkos with CUDA currently implicitly assumes that the MPI
-library is CUDA-aware and has support for GPU-direct. This is not
-always the case, especially when using pre-compiled MPI libraries
-provided by a Linux distribution. This is not a problem when using
-only a single GPU and a single MPI rank on a desktop. When running
-with multiple MPI ranks, you may see segmentation faults without
-GPU-direct support.  These can be avoided by adding the flags "-pk
-kokkos gpu/direct off"_Run_options.html to the LAMMPS command line or
-by using the command "package kokkos gpu/direct off"_package.html in
-the input file.
+NOTE: Kokkos with CUDA currently implicitly assumes that the MPI library 
+is CUDA-aware. This is not always the case, especially when using 
+pre-compiled MPI libraries provided by a Linux distribution. This is not 
+a problem when using only a single GPU with a single MPI rank. When 
+running with multiple MPI ranks, you may see segmentation faults without 
+CUDA-aware MPI support. These can be avoided by adding the flags "-pk 
+kokkos cuda/aware off"_Run_options.html to the LAMMPS command line or by 
+using the command "package kokkos cuda/aware off"_package.html in the 
+input file.
 
 [Building LAMMPS with the KOKKOS package:]
 
@@ -217,9 +216,8 @@ case, also packing/unpacking communication buffers on the host may give
 speedup (see the KOKKOS "package"_package.html command). Using CUDA MPS 
 is recommended in this scenario.
 
-Using a CUDA-aware MPI library with 
-support for GPU-direct is highly recommended. GPU-direct use can be 
-avoided by using "-pk kokkos gpu/direct no"_package.html. As above for 
+Using a CUDA-aware MPI library is highly recommended. CUDA-aware MPI use can be 
+avoided by using "-pk kokkos cuda/aware no"_package.html. As above for 
 multi-core CPUs (and no GPU), if N is the number of physical cores/node, 
 then the number of MPI tasks/node should not exceed N.
 

doc/src/angle_table.txt

@@ -143,6 +143,16 @@ instructions on how to use the accelerated styles effectively.
 
 :line
 
+[Restart info:]
+
+This angle style writes the settings for the "angle_style table"
+command to "binary restart files"_restart.html, so a angle_style
+command does not need to specified in an input script that reads a
+restart file.  However, the coefficient information is not stored in
+the restart file, since it is tabulated in the potential files.  Thus,
+angle_coeff commands do need to be specified in the restart input
+script.
+
 [Restrictions:]
 
 This angle style can only be used if LAMMPS was built with the

doc/src/bond_table.txt

@@ -140,6 +140,16 @@ instructions on how to use the accelerated styles effectively.
 
 :line
 
+[Restart info:]
+
+This bond style writes the settings for the "bond_style table"
+command to "binary restart files"_restart.html, so a bond_style
+command does not need to specified in an input script that reads a
+restart file.  However, the coefficient information is not stored in
+the restart file, since it is tabulated in the potential files.  Thus,
+bond_coeff commands do need to be specified in the restart input
+script.
+
 [Restrictions:]
 
 This bond style can only be used if LAMMPS was built with the MOLECULE

doc/src/comm_modify.txt

@@ -69,9 +69,15 @@ processors.  By default the ghost cutoff = neighbor cutoff = pairwise
 force cutoff + neighbor skin.  See the "neighbor"_neighbor.html command
 for more information about the skin distance.  If the specified Rcut is
 greater than the neighbor cutoff, then extra ghost atoms will be acquired.
-If the provided cutoff is smaller, the provided value will be ignored
-and the ghost cutoff is set to the neighbor cutoff. Specifying a
-cutoff value of 0.0 will reset any previous value to the default.
+If the provided cutoff is smaller, the provided value will be ignored,
+the ghost cutoff is set to the neighbor cutoff and a warning will be
+printed. Specifying a cutoff value of 0.0 will reset any previous value
+to the default. If bonded interactions exist and equilibrium bond length
+information is available, then also a heuristic based on that bond length
+is computed. It is used as communication cutoff, if there is no pair
+style present and no {comm_modify cutoff} command used. Otherwise a
+warning is printed, if this bond based estimate is larger than the
+communication cutoff used. A
 
 The {cutoff/multi} option is equivalent to {cutoff}, but applies to
 communication mode {multi} instead. Since in this case the communication

doc/src/commands_list.txt

@@ -53,7 +53,7 @@ Commands :h1
    include
    info
    jump
-   kim_query
+   kim_commands
    kspace_modify
    kspace_style
    label

doc/src/compute.txt

@@ -177,7 +177,7 @@ compute"_Commands_compute.html doc page are followed by one or more of
 "angle"_compute_angle.html - energy of each angle sub-style
 "angle/local"_compute_angle_local.html - theta and energy of each angle
 "angmom/chunk"_compute_angmom_chunk.html - angular momentum for each chunk
-"basal/atom"_compute_basal_atom.html - calculates the hexagonal close-packed “c” lattice vector of each atom
+"basal/atom"_compute_basal_atom.html - calculates the hexagonal close-packed "c" lattice vector of each atom
 "body/local"_compute_body_local.html - attributes of body sub-particles
 "bond"_compute_bond.html - energy of each bond sub-style
 "bond/local"_compute_bond_local.html - distance and energy of each bond
@@ -213,6 +213,7 @@ compute"_Commands_compute.html doc page are followed by one or more of
 "group/group"_compute_group_group.html - energy/force between two groups of atoms
 "gyration"_compute_gyration.html - radius of gyration of group of atoms
 "gyration/chunk"_compute_gyration_chunk.html - radius of gyration for each chunk
+"gyration/shape"_compute_gyration_shape.html - compute shape parameters from radius of gyration tensor
 "heat/flux"_compute_heat_flux.html - heat flux through a group of atoms
 "heat/flux/tally"_compute_tally.html -
 "hexorder/atom"_compute_hexorder_atom.html - bond orientational order parameter q6
@@ -227,6 +228,7 @@ compute"_Commands_compute.html doc page are followed by one or more of
 "meso/e/atom"_compute_meso_e_atom.html - per-atom internal energy of Smooth-Particle Hydrodynamics atoms
 "meso/rho/atom"_compute_meso_rho_atom.html - per-atom mesoscopic density of Smooth-Particle Hydrodynamics atoms
 "meso/t/atom"_compute_meso_t_atom.html - per-atom internal temperature of Smooth-Particle Hydrodynamics atoms
+"momentum"_compute_momentum.html - translational momentum
 "msd"_compute_msd.html - mean-squared displacement of group of atoms
 "msd/chunk"_compute_msd_chunk.html - mean-squared displacement for each chunk
 "msd/nongauss"_compute_msd_nongauss.html - MSD and non-Gaussian parameter of group of atoms

doc/src/compute_gyration.txt

@@ -67,6 +67,7 @@ distance^2 "units"_units.html respectively.
 
 [Related commands:]
 
-"compute gyration/chunk"_compute_gyration_chunk.html
+"compute gyration/chunk"_compute_gyration_chunk.html,
+"compute gyration/shape"_compute_gyration_shape.html
 
 [Default:] none

doc/src/compute_gyration_shape.txt

@@ -0,0 +1,86 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+compute gyration/shape command :h3
+
+[Syntax:]
+
+compute ID group-ID gyration compute-ID :pre
+
+ID, group-ID are documented in "compute"_compute.html command
+gyration/shape = style name of this compute command
+compute-ID = ID of "compute gyration"_compute_gyration.html command :ul
+
+[Examples:]
+
+compute 1 molecule gyration/shape pe :pre
+
+[Description:]
+
+Define a computation that calculates the eigenvalues of the gyration tensor of a
+group of atoms and three shape parameters. The computation includes all effects
+due to atoms passing thru periodic boundaries.
+
+The three computed shape parameters are the asphericity, b, the acylindricity, c,
+and the relative shape anisotropy, k:
+
+:c,image(Eqs/compute_shape_parameters.jpg)
+
+where lx <= ly <= lz are the three eigenvalues of the gyration tensor.
+The asphericity  is always non-negative and zero only when the three principal
+moments are equal. This zero condition is met when the distribution of particles
+is spherically symmetric (hence the name asphericity) but also whenever the particle
+distribution is symmetric with respect to the three coordinate axes, e.g.,
+when the particles are distributed uniformly on a cube, tetrahedron or other Platonic
+solid. The acylindricity is always non-negative and zero only when the two principal
+moments are equal. This zero condition is met when the distribution of particles is
+cylindrically symmetric (hence the name, acylindricity), but also whenever the particle
+distribution is symmetric with respect to the two coordinate axes, e.g., when the
+particles are distributed uniformly on a regular prism. the relative shape anisotropy
+is bounded between zero (if all points are spherically symmetric) and one
+(if all points lie on a line).
+
+NOTE: The coordinates of an atom contribute to the gyration tensor in
+"unwrapped" form, by using the image flags associated with each atom.
+See the "dump custom"_dump.html command for a discussion of "unwrapped"
+coordinates. See the Atoms section of the "read_data"_read_data.html
+command for a discussion of image flags and how they are set for each
+atom.  You can reset the image flags (e.g. to 0) before invoking this
+compute by using the "set image"_set.html command.
+
+[Output info:]
+
+This compute calculates a global vector of
+length 6, which can be accessed by indices 1-6. The first three values are the
+eigenvalues of the gyration tensor followed by the asphericity, the acylindricity
+and the relative shape anisotropy.  The computed values can be used by any command
+that uses global  vector values from a compute as input.  See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
+options.
+
+The vector values calculated by this compute are
+"intensive".  The first five vector values will be in
+distance^2 "units"_units.html while the sixth one is dimensionless.
+
+[Restrictions:]
+
+This compute is part of the USER-MISC package.  It is only enabled if
+LAMMPS was built with that package.  See the "Build
+package"_Build_package.html doc page for more info.
+
+[Related commands:]
+
+"compute gyration"_compute_gyration.html
+
+[Default:] none
+
+:line
+
+:link(Theodorou)
+[(Theodorou)] Theodorou, Suter, Macromolecules, 18, 1206 (1985).
+

doc/src/compute_hexorder_atom.txt

@@ -65,7 +65,7 @@ In an isotropic liquid, local neighborhoods may still exhibit
 weak hexagonal symmetry, but because the orientational correlation
 decays quickly with distance, the value of phi will be different for
 different atoms, and so when {q}6 is averaged over all the atoms
-in the system, \|<{q}6>\| << 1.
+in the system, |<{q}6>| << 1.
 
 The value of {qn} is set to zero for atoms not in the
 specified compute group, as well as for atoms that have less than

doc/src/compute_momentum.txt

@@ -0,0 +1,49 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+compute momentum command :h3
+
+[Syntax:]
+
+compute ID group-ID momentum :pre
+
+ID, group-ID are documented in "compute"_compute.html command
+momentum = style name of this compute command :ul
+
+[Examples:]
+
+compute 1 all momentum :pre
+
+[Description:]
+
+Define a computation that calculates the translational momentum
+of a group of particles.
+
+The momentum of each particles is computed as m v, where m and v are
+the mass and velocity of the particle.
+
+[Output info:]
+
+This compute calculates a global vector (the summed momentum) of
+length 3. This value can be used by any command that uses a global
+vector value from a compute as input. See the "Howto
+output"_Howto_output.html doc page for an overview of LAMMPS output
+options.
+
+The vector value calculated by this compute is "extensive". The vector
+value will be in mass*velocity "units"_units.html.
+
+[Restrictions:]
+
+This compute is part of the USER-MISC package.  It is only enabled if
+LAMMPS was built with that package.  See the "Build
+package"_Build_package.html doc page for more info.
+
+[Related commands:]
+
+[Default:] none

doc/src/compute_pressure.txt

@@ -16,12 +16,13 @@ ID, group-ID are documented in "compute"_compute.html command
 pressure = style name of this compute command
 temp-ID = ID of compute that calculates temperature, can be NULL if not needed
 zero or more keywords may be appended
-keyword = {ke} or {pair} or {bond} or {angle} or {dihedral} or {improper} or {kspace} or {fix} or {virial} :ul
+keyword = {ke} or {pair} or {bond} or {angle} or {dihedral} or {improper} or {kspace} or {fix} or {virial} or {pair/hybrid} :ul
 
 [Examples:]
 
 compute 1 all pressure thermo_temp
-compute 1 all pressure NULL pair bond :pre
+compute 1 all pressure NULL pair bond
+compute 1 all pressure NULL pair/hybrid lj/cut :pre
 
 [Description:]
 
@@ -67,6 +68,9 @@ extra keywords are listed, then only those components are summed to
 compute temperature or ke and/or the virial.  The {virial} keyword
 means include all terms except the kinetic energy {ke}.
 
+The {pair/hybrid} keyword means to only include contribution
+from a sub-style in a {hybrid} or {hybrid/overlay} pair style.
+
 Details of how LAMMPS computes the virial efficiently for the entire
 system, including for many-body potentials and accounting for the
 effects of periodic boundary conditions are discussed in

doc/src/computes.txt

@@ -44,6 +44,7 @@ Computes :h1
    compute_group_group
    compute_gyration
    compute_gyration_chunk
+   compute_gyration_shape
    compute_heat_flux
    compute_hexorder_atom
    compute_improper
@@ -57,6 +58,7 @@ Computes :h1
    compute_meso_e_atom
    compute_meso_rho_atom
    compute_meso_t_atom
+   compute_momentum
    compute_msd
    compute_msd_chunk
    compute_msd_nongauss

doc/src/create_atoms.txt

@@ -242,9 +242,8 @@ write_dump      all atom sinusoid.lammpstrj :pre
 
 :c,image(JPG/sinusoid_small.jpg,JPG/sinusoid.jpg)
 
-The {rotate} keyword can only be used with the {single} style and
-when adding a single molecule. It allows to specify the orientation
-at which the molecule is inserted.  The axis of rotation is
+The {rotate} keyword allows specification of the orientation
+at which molecules are inserted.  The axis of rotation is
 determined by the rotation vector (Rx,Ry,Rz) that goes through the
 insertion point.  The specified {theta} determines the angle of
 rotation around that axis.  Note that the direction of rotation for

doc/src/dihedral_table.txt

@@ -191,6 +191,16 @@ switch"_Run_options.html when you invoke LAMMPS, or you can use the
 See the "Speed packages"_Speed_packages.html doc page for more
 instructions on how to use the accelerated styles effectively.
 
+[Restart info:]
+
+This dihedral style writes the settings for the "dihedral_style table"
+command to "binary restart files"_restart.html, so a dihedral_style
+command does not need to specified in an input script that reads a
+restart file.  However, the coefficient information is not stored in
+the restart file, since it is tabulated in the potential files.  Thus,
+dihedral_coeff commands do need to be specified in the restart input
+script.
+
 [Restrictions:]
 
 This dihedral style can only be used if LAMMPS was built with the

doc/src/dihedral_table_cut.txt

@@ -189,6 +189,16 @@ 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.
 
+[Restart info:]
+
+This dihedral style writes the settings for the "dihedral_style table/cut"
+command to "binary restart files"_restart.html, so a dihedral_style
+command does not need to specified in an input script that reads a
+restart file.  However, the coefficient information is not stored in
+the restart file, since it is tabulated in the potential files.  Thus,
+dihedral_coeff commands do need to be specified in the restart input
+script.
+
 [Restrictions:]
 
 This dihedral style can only be used if LAMMPS was built with the

doc/src/fix.txt

@@ -165,40 +165,40 @@ page are followed by one or more of (g,i,k,o,t) to indicate which
 accelerated styles exist.
 
 "adapt"_fix_adapt.html - change a simulation parameter over time
-"adapt/fep"_fix_adapt_fep.html -
+"adapt/fep"_fix_adapt_fep.html - enhanced version of fix adapt
 "addforce"_fix_addforce.html - add a force to each atom
-"addtorque"_fix_addtorque.html -
+"addtorque"_fix_addtorque.html - add a torque to a group of atoms
 "append/atoms"_fix_append_atoms.html - append atoms to a running simulation
-"atc"_fix_atc.html -
+"atc"_fix_atc.html - initiates a coupled MD/FE simulation
 "atom/swap"_fix_atom_swap.html - Monte Carlo atom type swapping
 "ave/atom"_fix_ave_atom.html - compute per-atom time-averaged quantities
 "ave/chunk"_fix_ave_chunk.html - compute per-chunk time-averaged quantities
 "ave/correlate"_fix_ave_correlate.html - compute/output time correlations
 "ave/correlate/long"_fix_ave_correlate_long.html -
 "ave/histo"_fix_ave_histo.html - compute/output time-averaged histograms
-"ave/histo/weight"_fix_ave_histo.html -
+"ave/histo/weight"_fix_ave_histo.html - weighted version of fix ave/histo
 "ave/time"_fix_ave_time.html - compute/output global time-averaged quantities
 "aveforce"_fix_aveforce.html - add an averaged force to each atom
 "balance"_fix_balance.html - perform dynamic load-balancing
-"bocs"_fix_bocs.html -
+"bocs"_fix_bocs.html - NPT style time integration with pressure correction
 "bond/break"_fix_bond_break.html - break bonds on the fly
 "bond/create"_fix_bond_create.html - create bonds on the fly
-"bond/react"_fix_bond_react.html -
+"bond/react"_fix_bond_react.html - apply topology changes to model reactions
 "bond/swap"_fix_bond_swap.html - Monte Carlo bond swapping
 "box/relax"_fix_box_relax.html - relax box size during energy minimization
-"client/md"_fix_client_md.html -
-"cmap"_fix_cmap.html -
-"colvars"_fix_colvars.html -
-"controller"_fix_controller.html -
+"client/md"_fix_client_md.html - MD client for client/server simulations
+"cmap"_fix_cmap.html - enables CMAP cross-terms of the CHARMM force field
+"colvars"_fix_colvars.html - interface to the collective variables “Colvars” library
+"controller"_fix_controller.html - apply control loop feedback mechanism
 "deform"_fix_deform.html - change the simulation box size/shape
 "deposit"_fix_deposit.html - add new atoms above a surface
-"dpd/energy"_fix_dpd_energy.html -
+"dpd/energy"_fix_dpd_energy.html - constant energy dissipative particle dynamics
 "drag"_fix_drag.html - drag atoms towards a defined coordinate
-"drude"_fix_drude.html -
-"drude/transform/direct"_fix_drude_transform.html -
-"drude/transform/inverse"_fix_drude_transform.html -
+"drude"_fix_drude.html - part of Drude oscillator polarization model
+"drude/transform/direct"_fix_drude_transform.html -  part of Drude oscillator polarization model
+"drude/transform/inverse"_fix_drude_transform.html -  part of Drude oscillator polarization model
 "dt/reset"_fix_dt_reset.html - reset the timestep based on velocity, forces
-"edpd/source"_fix_dpd_source.html -
+"edpd/source"_fix_dpd_source.html - add heat source to eDPD simulations
 "efield"_fix_efield.html - impose electric field on system
 "ehex"_fix_ehex.html - enhanced heat exchange algorithm
 "electron/stopping"_fix_electron_stopping.html - electronic stopping power as a friction force
@@ -208,27 +208,26 @@ accelerated styles exist.
 "eos/table/rx"_fix_eos_table_rx.html -
 "evaporate"_fix_evaporate.html - remove atoms from simulation periodically
 "external"_fix_external.html - callback to an external driver program
-"ffl"_fix_ffl.html -
-"filter/corotate"_fix_filter_corotate.html -
-"flow/gauss"_fix_flow_gauss.html -
+"ffl"_fix_ffl.html - apply a Fast-Forward Langevin equation thermostat
+"filter/corotate"_fix_filter_corotate.html - implement corotation filter to allow larger timesteps with r-RESPA
+"flow/gauss"_fix_flow_gauss.html - Gaussian dynamics for constant mass flux
 "freeze"_fix_freeze.html - freeze atoms in a granular simulation
 "gcmc"_fix_gcmc.html - grand canonical insertions/deletions
-"gld"_fix_gcmc.html - generalized Langevin dynamics integrator
-"gld"_fix_gld.html -
-"gle"_fix_gle.html -
+"gld"_fix_gld.html - generalized Langevin dynamics integrator
+"gle"_fix_gle.html - generalized Langevin equation thermostat
 "gravity"_fix_gravity.html - add gravity to atoms in a granular simulation
-"grem"_fix_grem.html -
+"grem"_fix_grem.html - implements the generalized replica exchange method
 "halt"_fix_halt.html - terminate a dynamics run or minimization
 "heat"_fix_heat.html - add/subtract momentum-conserving heat
 "hyper/global"_fix_hyper_global.html - global hyperdynamics
 "hyper/local"_fix_hyper_local.html - local hyperdynamics
-"imd"_fix_imd.html -
+"imd"_fix_imd.html - implements the “Interactive MD” (IMD) protocol 
 "indent"_fix_indent.html - impose force due to an indenter
-"ipi"_fix_ipi.html -
+"ipi"_fix_ipi.html - enable LAMMPS to run as a client for i-PI path-integral simulations
 "langevin"_fix_langevin.html - Langevin temperature control
-"langevin/drude"_fix_langevin_drude.html -
-"langevin/eff"_fix_langevin_eff.html -
-"langevin/spin"_fix_langevin_spin.html -
+"langevin/drude"_fix_langevin_drude.html - Langevin temperature control of Drude oscillators
+"langevin/eff"_fix_langevin_eff.html - Langevin temperature control for the electron force field model
+"langevin/spin"_fix_langevin_spin.html - Langevin temperature control for a spin or spin-lattice system
 "latte"_fix_latte.html - wrapper on LATTE density-functional tight-binding code
 "lb/fluid"_fix_lb_fluid.html -
 "lb/momentum"_fix_lb_momentum.html -
@@ -236,64 +235,60 @@ accelerated styles exist.
 "lb/rigid/pc/sphere"_fix_lb_rigid_pc_sphere.html -
 "lb/viscous"_fix_lb_viscous.html -
 "lineforce"_fix_lineforce.html - constrain atoms to move in a line
-"manifoldforce"_fix_manifoldforce.html -
-"meso"_fix_meso.html -
-"meso"_fix_meso_move.html - move mesoscopic SPH/SDPD particles in a prescribed fashion
-"meso/move"_fix_meso_move.html -
+"manifoldforce"_fix_manifoldforce.html - restrain atoms to a manifold during minimization
+"meso"_fix_meso.html - time integration for SPH/DPDE particles
+"meso/move"_fix_meso_move.html - move mesoscopic SPH/SDPD particles in a prescribed fashion
 "meso/stationary"_fix_meso_stationary.html -
 "momentum"_fix_momentum.html - zero the linear and/or angular momentum of a group of atoms
 "move"_fix_move.html - move atoms in a prescribed fashion
-"mscg"_fix_mscg.html -
+"mscg"_fix_mscg.html - apply MSCG method for force-matching to generate coarse grain models
 "msst"_fix_msst.html - multi-scale shock technique (MSST) integration
-"mvv/dpd"_fix_mvv_dpd.html -
-"mvv/edpd"_fix_mvv_dpd.html -
-"mvv/tdpd"_fix_mvv_dpd.html -
+"mvv/dpd"_fix_mvv_dpd.html - DPD using the modified velocity-Verlet integration algorithm
+"mvv/edpd"_fix_mvv_dpd.html - constant energy DPD using the modified velocity-Verlet algrithm
+"mvv/tdpd"_fix_mvv_dpd.html - constant temperature DPD using the modified velocity-Verlet algorithm
 "neb"_fix_neb.html - nudged elastic band (NEB) spring forces
 "nph"_fix_nh.html - constant NPH time integration via Nose/Hoover
 "nph/asphere"_fix_nph_asphere.html - NPH for aspherical particles
-"nph/body"_fix_nph_body.html -
-"nph/body"_fix_nve_body.html - NPH for body particles
-"nph/eff"_fix_nh_eff.html -
+"nph/body"_fix_nph_body.html - NPH for body particles
+"nph/eff"_fix_nh_eff.html - NPH for  nuclei and electrons in the electron force field model
 "nph/sphere"_fix_nph_sphere.html - NPH for spherical particles
 "nphug"_fix_nphug.html - constant-stress Hugoniostat integration
 "npt"_fix_nh.html - constant NPT time integration via Nose/Hoover
 "npt/asphere"_fix_npt_asphere.html - NPT for aspherical particles
-"npt/body"_fix_npt_body.html -
-"npt/body"_fix_nve_body.html - NPT for body particles
-"npt/eff"_fix_nh_eff.html -
+"npt/body"_fix_npt_body.html - NPT for body particles
+"npt/eff"_fix_nh_eff.html - NPT for  nuclei and electrons in the electron force field model
 "npt/sphere"_fix_npt_sphere.html - NPT for spherical particles
-"npt/uef"_fix_nh_uef.html -
+"npt/uef"_fix_nh_uef.html - NPT style time integration with diagonal flow
 "nve"_fix_nve.html - constant NVE time integration
 "nve/asphere"_fix_nve_asphere.html - NVE for aspherical particles
-"nve/asphere/noforce"_fix_nve_asphere_noforce.html - NVE for aspherical particles without forces"
-"nve/awpmd"_fix_nve_awpmd.html -
+"nve/asphere/noforce"_fix_nve_asphere_noforce.html - NVE for aspherical particles without forces
+"nve/awpmd"_fix_nve_awpmd.html - NVE for the Antisymmetrized Wave Packet Molecular Dynamics model
 "nve/body"_fix_nve_body.html - NVE for body particles
-"nve/dot"_fix_nve_dot.html -
-"nve/dotc/langevin"_fix_nve_dotc_langevin.html -
-"nve/eff"_fix_nve_eff.html -
+"nve/dot"_fix_nve_dot.html - rigid body constant energy time integrator for coarse grain models
+"nve/dotc/langevin"_fix_nve_dotc_langevin.html - Langevin style rigid body time integrator for coarse grain models
+"nve/eff"_fix_nve_eff.html - NVE for  nuclei and electrons in the electron force field model
 "nve/limit"_fix_nve_limit.html - NVE with limited step length
 "nve/line"_fix_nve_line.html - NVE for line segments
 "nve/manifold/rattle"_fix_nve_manifold_rattle.html -
 "nve/noforce"_fix_nve_noforce.html - NVE without forces (v only)
 "nve/sphere"_fix_nve_sphere.html - NVE for spherical particles
-"nve/spin"_fix_nve_spin.html -
+"nve/spin"_fix_nve_spin.html - NVE for a spin or spin-lattice system
 "nve/tri"_fix_nve_tri.html - NVE for triangles
-"nvk"_fix_nvk.html -
-"nvt"_fix_nh.html - constant NVT time integration via Nose/Hoover
+"nvk"_fix_nvk.html - constant kinetic energy time integration
+"nvt"_fix_nh.html - NVT time integration via Nose/Hoover
 "nvt/asphere"_fix_nvt_asphere.html - NVT for aspherical particles
-"nvt/body"_fix_nve_body.html - NVT for body particles
-"nvt/body"_fix_nvt_body.html -
-"nvt/eff"_fix_nh_eff.html -
+"nvt/body"_fix_nvt_body.html - NVT for body particles
+"nvt/eff"_fix_nh_eff.html - NVE for  nuclei and electrons in the electron force field model
 "nvt/manifold/rattle"_fix_nvt_manifold_rattle.html -
 "nvt/sllod"_fix_nvt_sllod.html - NVT for NEMD with SLLOD equations
-"nvt/sllod/eff"_fix_nvt_sllod_eff.html -
+"nvt/sllod/eff"_fix_nvt_sllod_eff.html - NVT for NEMD with SLLOD equations for the electron force field model
 "nvt/sphere"_fix_nvt_sphere.html - NVT for spherical particles
-"nvt/uef"_fix_nh_uef.html -
+"nvt/uef"_fix_nh_uef.html - NVT style time integration with diagonal flow
 "oneway"_fix_oneway.html - constrain particles on move in one direction
 "orient/bcc"_fix_orient.html - add grain boundary migration force for BCC
 "orient/fcc"_fix_orient.html - add grain boundary migration force for FCC
-"phonon"_fix_phonon.html -
-"pimd"_fix_pimd.html -
+"phonon"_fix_phonon.html - calculate dynamical matrix from MD simulations
+"pimd"_fix_pimd.html - Feynman path integral molecular dynamics
 "planeforce"_fix_planeforce.html - constrain atoms to move in a plane
 "plumed"_fix_plumed.html - wrapper on PLUMED free energy library
 "poems"_fix_poems.html - constrain clusters of atoms to move as coupled rigid bodies
@@ -302,24 +297,24 @@ accelerated styles exist.
 "press/berendsen"_fix_press_berendsen.html - pressure control by Berendsen barostat
 "print"_fix_print.html - print text and variables during a simulation
 "property/atom"_fix_property_atom.html - add customized per-atom values
-"python/invoke"_fix_python_invoke.html -
-"python/move"_fix_python_move.html -
-"qbmsst"_fix_qbmsst.html -
+"python/invoke"_fix_python_invoke.html - call a Python function during a simulation
+"python/move"_fix_python_move.html -  call a Python function during a simulation run
+"qbmsst"_fix_qbmsst.html - quantum bath multi-scale shock technique time integrator
 "qeq/comb"_fix_qeq_comb.html - charge equilibration for COMB potential
 "qeq/dynamic"_fix_qeq.html - charge equilibration via dynamic method
 "qeq/fire"_fix_qeq.html - charge equilibration via FIRE minimizer
 "qeq/point"_fix_qeq.html - charge equilibration via point method
-"qeq/reax"_fix_qeq_reax.html -
+"qeq/reax"_fix_qeq_reax.html - charge equilibration for ReaxFF potential
 "qeq/shielded"_fix_qeq.html - charge equilibration via shielded method
 "qeq/slater"_fix_qeq.html - charge equilibration via Slater method
-"qmmm"_fix_qmmm.html -
-"qtb"_fix_qtb.html -
+"qmmm"_fix_qmmm.html - functionality to enable a quantum mechanics/molecular mechanics coupling
+"qtb"_fix_qtb.html - implement quantum thermal bath scheme
 "rattle"_fix_shake.html - RATTLE constraints on bonds and/or angles
 "reax/c/bonds"_fix_reaxc_bonds.html - write out ReaxFF bond information
 "reax/c/species"_fix_reaxc_species.html - write out ReaxFF molecule information
 "recenter"_fix_recenter.html - constrain the center-of-mass position of a group of atoms
 "restrain"_fix_restrain.html - constrain a bond, angle, dihedral
-"rhok"_fix_rhok.html -
+"rhok"_fix_rhok.html - add bias potential for long-range ordered systems
 "rigid"_fix_rigid.html - constrain one or more clusters of atoms to move as a rigid body with NVE integration
 "rigid/meso"_fix_rigid_meso.html - constrain clusters of mesoscopic SPH/SDPD particles to move as a rigid body
 "rigid/nph"_fix_rigid.html - constrain one or more clusters of atoms to move as a rigid body with NPH integration
@@ -332,11 +327,11 @@ accelerated styles exist.
 "rigid/nvt/small"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with NVT integration
 "rigid/small"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with NVE integration
 "rx"_fix_rx.html -
-"saed/vtk"_fix_saed_vtk.html -
+"saed/vtk"_fix_saed_vtk.html - 
 "setforce"_fix_setforce.html - set the force on each atom
 "shake"_fix_shake.html - SHAKE constraints on bonds and/or angles
-"shardlow"_fix_shardlow.html -
-"smd"_fix_smd.html -
+"shardlow"_fix_shardlow.html - integration of DPD equations of motion using the Shardlow splitting
+"smd"_fix_smd.html - applied a steered MD force to a group
 "smd/adjust_dt"_fix_smd_adjust_dt.html -
 "smd/integrate_tlsph"_fix_smd_integrate_tlsph.html -
 "smd/integrate_ulsph"_fix_smd_integrate_ulsph.html -
@@ -355,13 +350,13 @@ accelerated styles exist.
 "temp/csld"_fix_temp_csvr.html - canonical sampling thermostat with Langevin dynamics
 "temp/csvr"_fix_temp_csvr.html - canonical sampling thermostat with Hamiltonian dynamics
 "temp/rescale"_fix_temp_rescale.html - temperature control by velocity rescaling
-"temp/rescale/eff"_fix_temp_rescale_eff.html -
+"temp/rescale/eff"_fix_temp_rescale_eff.html - temperature control by velocity rescaling in the electron force field model
 "tfmc"_fix_tfmc.html - perform force-bias Monte Carlo with time-stamped method
 "thermal/conductivity"_fix_thermal_conductivity.html - Muller-Plathe kinetic energy exchange for thermal conductivity calculation
 "ti/spring"_fix_ti_spring.html -
 "tmd"_fix_tmd.html - guide a group of atoms to a new configuration
 "ttm"_fix_ttm.html - two-temperature model for electronic/atomic coupling
-"ttm/mod"_fix_ttm.html -
+"ttm/mod"_fix_ttm.html - enhanced two-temperature model with additional options
 "tune/kspace"_fix_tune_kspace.html - auto-tune KSpace parameters
 "vector"_fix_vector.html - accumulate a global vector every N timesteps
 "viscosity"_fix_viscosity.html - Muller-Plathe momentum exchange for viscosity calculation
@@ -369,7 +364,7 @@ accelerated styles exist.
 "wall/body/polygon"_fix_wall_body_polygon.html -
 "wall/body/polyhedron"_fix_wall_body_polyhedron.html -
 "wall/colloid"_fix_wall.html - Lennard-Jones wall interacting with finite-size particles
-"wall/ees"_fix_wall_ees.html -
+"wall/ees"_fix_wall_ees.html - wall for ellipsoidal particles
 "wall/gran"_fix_wall_gran.html - frictional wall(s) for granular simulations
 "wall/gran/region"_fix_wall_gran_region.html -
 "wall/harmonic"_fix_wall.html - harmonic spring wall
@@ -379,7 +374,7 @@ accelerated styles exist.
 "wall/piston"_fix_wall_piston.html - moving reflective piston wall
 "wall/reflect"_fix_wall_reflect.html - reflecting wall(s)
 "wall/region"_fix_wall_region.html - use region surface as wall
-"wall/region/ees"_fix_wall_ees.html -
+"wall/region/ees"_fix_wall_ees.html - use region surface as wall for ellipsoidal particles
 "wall/srd"_fix_wall_srd.html - slip/no-slip wall for SRD particles :ul
 
 [Restrictions:]

doc/src/fix_adapt.txt

@@ -149,8 +149,7 @@ meaning of these parameters:
 "spin/neel"_pair_spin_neel.html: coulombic_cutoff: type global:
 "table"_pair_table.html: table_cutoff: type pairs:
 "ufm"_pair_ufm.html: epsilon,sigma: type pairs:
-"soft"_pair_soft.html: a: type pairs:
-"kim"_pair_kim.html: PARAM_FREE_*&#58i,j,...: global :tb(c=3,s=:)
+"soft"_pair_soft.html: a: type pairs: :tb(c=3,s=:)
 
 NOTE: It is easy to add new pairwise potentials and their parameters
 to this list.  All it typically takes is adding an extract() method to

doc/src/fix_bocs.txt

@@ -47,13 +47,13 @@ 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:
+as a function of volume. The file must 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
+must 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 atmospheres. Furthermore, the table should start/end at a

doc/src/fix_bond_react.txt

@@ -24,7 +24,7 @@ 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 prefix for the dynamic group of non-reacting atoms
+      {group-ID} = user-assigned prefix for the dynamic group of atoms not currently involved in a reaction
       {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
@@ -52,6 +52,8 @@ react = mandatory argument indicating new reaction specification :l
 
 [Examples:]
 
+For unabridged example scripts and files, see examples/USER/misc/bond_react.
+
 molecule mol1 pre_reacted_topology.txt
 molecule mol2 post_reacted_topology.txt
 fix 5 all bond/react react myrxn1 all 1 0 3.25 mol1 mol2 map_file.txt :pre
@@ -106,6 +108,20 @@ 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.
 
+Fix bond/react creates and maintains two important dynamic groups of
+atoms when using the {stabilization} keyword. The first group contains
+all atoms currently involved in a reaction; this group is
+automatically thermostatted by an internally-created
+"nve/limit"_fix_nve_limit.html integrator. The second group contains
+all atoms currently not involved in a reaction. This group should be
+used by a thermostat in order to time integrate the system. The name
+of this group of non-reacting atoms is created by appending '_REACT'
+to the group-ID argument of the {stabilization} keyword, as shown in
+the second example above.
+
+NOTE: When using reaction stabilization, you should generally not have
+a separate thermostat which acts on the 'all' group.
+
 The group-ID set using the {stabilization} keyword can be an existing
 static group or a previously-unused group-ID. It cannot be specified
 as 'all'. If the group-ID is previously unused, the fix bond/react
@@ -116,20 +132,17 @@ internally-created dynamic group. In both cases, this new dynamic
 group is named by appending '_REACT' to the group-ID, e.g.
 nvt_grp_REACT. By specifying an existing group, you may thermostat
 constant-topology parts of your system separately. The dynamic group
-contains only non-reacting atoms at a given timestep, and therefore
-should be used by a subsequent system-wide time integrator such as
-nvt, npt, or nve, as shown in the second example above. The time
-integration command should be placed after the fix bond/react command
-due to the internal dynamic grouping performed by fix bond/react.
+contains only atoms not involved in a reaction at a given timestep,
+and therefore should be used by a subsequent system-wide time
+integrator such as nvt, npt, or nve, as shown in the second example
+above (full examples can be found at examples/USER/misc/bond_react).
+The time integration command should be placed after the fix bond/react
+command due to the internal dynamic grouping performed by fix
+bond/react.
 
 NOTE: If the group-ID is an existing static group, react-group-IDs
 should also be specified as this static group, or a subset.
 
-NOTE: If the group-ID is previously unused, the internally-created
-group applies to all atoms in the system, i.e. you should generally
-not have a separate thermostat which acts on the 'all' group, or any
-other group.
-
 The following comments pertain to each {react} argument (in other
 words, can be customized for each reaction, or reaction step):
 
@@ -352,12 +365,13 @@ an atom that is not deleted. In addition to deleting unwanted reaction
 by-products, this feature can be used to remove specific topologies,
 such as small rings, that may be otherwise indistinguishable.
 
-Also, 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:
+Optionally, you can enforce additional behaviors on reacting atoms.
+For example, it may be beneficial to force reacting atoms to remain at
+a certain temperature. For this, you can use the internally-created
+dynamic group named "bond_react_MASTER_group", which consists of all
+atoms currently involved in a reaction. For example, adding the
+following command would add an additional thermostat to the group of
+all currently-reacting atoms:
 
 fix 1 bond_react_MASTER_group temp/rescale 1 300 300 10 1 :pre
 

doc/src/fix_plumed.txt

@@ -114,5 +114,5 @@ The default options are plumedfile = NULL and outfile = NULL
 :link(PLUMED)
 [(PLUMED)] G.A. Tribello, M. Bonomi, D. Branduardi, C. Camilloni and G. Bussi, Comp. Phys. Comm 185, 604 (2014)
 
-:link(plumeddocs,http://www.plumed.org/documentation)
+:link(plumeddocs,http://www.plumed.org/doc.html)
 :link(plumedhome,http://www.plumed.org/)

doc/src/fix_rhok.txt

@@ -39,8 +39,8 @@ An example of using the interface pinning method is located in the
 
 [Restrictions:]
 
-This fix is part of the MISC package.  It is only enabled if LAMMPS
-was built with that package.  See the "Build
+This fix is part of the USER-MISC package.  It is only enabled if
+LAMMPS was built with that package.  See the "Build
 package"_Build_package.html doc page for more info.
 
 [Related commands:]

doc/src/kim_commands.txt

@@ -0,0 +1,522 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+kim_init command :h3
+kim_interactions command :h3
+kim_query command :h3
+
+[Syntax:]
+
+kim_init model user_units unitarg
+kim_interactions typeargs
+kim_query variable formatarg query_function queryargs :pre
+
+model = name of the KIM interatomic model (the KIM ID for models archived in OpenKIM)
+user_units = the LAMMPS "units"_units.html style assumed in the LAMMPS input script
+unitarg = {unit_conversion_mode} (optional)
+typeargs = atom type to species mapping (one entry per atom type) or {fixed_types} for models with a preset fixed mapping
+variable = name of a (string style) variable where the result of the query is stored
+formatarg = {split} (optional)
+query_function = name of the OpenKIM web API query function to be used
+queryargs = a series of {keyword=value} pairs that represent the web query; supported keywords depend on the query function :ul
+
+
+[Examples:]
+
+kim_init SW_StillingerWeber_1985_Si__MO_405512056662_005 metal
+kim_interactions Si
+kim_init Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 real
+kim_init Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 metal unit_conversion_mode
+kim_interactions C H O
+Sim_LAMMPS_IFF_PCFF_HeinzMishraLinEmami_2015Ver1v5_FccmetalsMineralsSolvents Polymers__SM_039297821658_000 real
+kim_interactions fixed_types
+kim_query a0 get_lattice_constant_cubic crystal=\["fcc"\] species=\["Al"\] units=\["angstrom"\] :pre
+
+[Description:]
+
+The set of {kim_commands} provide a high-level wrapper around the
+"Open Knowledgebase of Interatomic Models (OpenKIM)"_https://openkim.org
+repository of interatomic models (IMs) (potentials and force fields),
+so that they can be used by LAMMPS scripts.  These commands do not implement
+any computations directly, but rather generate LAMMPS input commands based
+on the information retrieved from the OpenKIM repository to initialize and
+activate OpenKIM IMs and query their predictions for use in the LAMMPS script.
+All LAMMPS input commands generated and executed by {kim_commands} are
+echoed to the LAMMPS log file.
+
+Benefits of Using OpenKIM IMs :h4
+
+Employing OpenKIM IMs provides LAMMPS users with multiple benefits:
+
+Reliability :h5
+
+All content archived in OpenKIM is reviewed by the "KIM Editor"_https://openkim.org/governance/ for quality.
+IMs in OpenKIM are archived with full provenance control. Each is associated with a maintainer responsible for the integrity of the content. All changes are tracked and recorded.
+IMs in OpenKIM are exhaustively tested using "KIM Tests"_https://openkim.org/doc/evaluation/kim-tests/ that compute a host of material properties, and "KIM Verification Checks"_https://openkim.org/doc/evaluation/kim-verification-checks/ that provide the user with information on various aspects of the IM behavior and coding correctness. This information is displayed on the IM's page accessible through the  "OpenKIM browse interface"_https://openkim.org/browse. :ul
+
+Reproducibility :h5
+
+Each IM in OpenKIM is issued a unique identifier ("KIM ID"_https://openkim.org/doc/schema/kim-ids/), which includes a version number (last three digits).  Any changes that can result in different numerical values lead to a version increment in the KIM ID. This makes it possible to reproduce simulations since the specific version of a specific IM used can be retrieved using its KIM ID.
+OpenKIM is a member organization of "DataCite"_https://datacite.org/ and issues digital object identifiers (DOIs) to all IMs archived in OpenKIM. This makes it possible to cite the IM code used in a simulation in a publications to give credit to the developers and further facilitate reproducibility. :ul
+
+Convenience :h5
+
+IMs in OpenKIM are distributed in binary form along with LAMMPS and can be used in a LAMMPS input script simply by providing their KIM ID in the {kim_init} command documented on this page.
+The {kim_query} web query tool provides the ability to use the predictions of IMs for supported material properties (computed via "KIM Tests"_https://openkim.org/doc/evaluation/kim-tests/) as part of a LAMMPS input script setup and analysis.
+Support is provided for unit conversion between the "unit style"_units.html used in the LAMMPS input script and the units required by the OpenKIM IM. This makes it possible to use a single input script with IMs using different units without change and minimizes the likelihood of errors due to incompatible units.  :ul
+
+:link(IM_types)
+Types of IMs in OpenKIM :h4
+
+There are two types of IMs archived in OpenKIM:
+
+The first type is called a {KIM Portable Model} (PM). A KIM PM is an independent computer implementation of an IM written in one of the languages supported by KIM (C, C++, Fortran) that conforms to the KIM Application Programming Interface ("KIM API"_https://openkim.org/kim-api/) Portable Model Interface (PMI) standard. A KIM PM will work seamlessly with any simulation code that supports the KIM API/PMI standard (including LAMMPS; see "complete list of supported codes"_https://openkim.org/projects-using-kim/).
+The second type is called a {KIM Simulator Model} (SM). A KIM SM is an IM that is implemented natively within a simulation code ({simulator}) that supports the KIM API Simulator Model Interface (SMI); in this case LAMMPS. A separate SM package is archived in OpenKIM for each parameterization of the IM, which includes all of the necessary parameter files, LAMMPS commands, and metadata (supported species, units, etc.) needed to run the IM in LAMMPS. :ol
+
+With these two IM types, OpenKIM can archive and test almost all IMs that
+can be used by LAMMPS. (It is easy to contribute new IMs to OpenKIM, see
+the "upload instructions"_https://openkim.org/doc/repository/adding-content/.)
+
+OpenKIM IMs are uniquely identified by a
+"KIM ID"_https://openkim.org/doc/schema/kim-ids/.
+The extended KIM ID consists of
+a human-readable prefix identifying the type of IM, authors, publication year,
+and supported species, separated by two underscores from the KIM ID itself,
+which begins with an IM code
+({MO} for a KIM Portable Model, and {SM} for a KIM Simulator Model)
+followed by a unique 12-digit code and a 3-digit version identifier.
+By convention SM prefixes begin with {Sim_} to readily identify them.
+
+SW_StillingerWeber_1985_Si__MO_405512056662_005
+Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 :pre
+
+Each OpenKIM IM has a dedicated "Model Page" on "OpenKIM"_https://openkim.org
+providing all the information on the IM including a title, description,
+authorship and citation information, test and verification check results,
+visualizations of results, a wiki with documentation and user comments, and
+access to raw files, and other information.
+The URL for the Model Page is constructed from the
+"extended KIM ID"_https://openkim.org/doc/schema/kim-ids/ of the IM:
+
+https://openkim.org/id/extended_KIM_ID
+:pre
+
+For example for the Stillinger-Weber potential
+listed above the Model Page is located at:
+
+"https://openkim.org/id/SW_StillingerWeber_1985_Si__MO_405512056662_005"_https://openkim.org/id/SW_StillingerWeber_1985_Si__MO_405512056662_005
+:pre
+
+See the "current list of KIM PMs and SMs archived in OpenKIM"_https://openkim.org/browse/models/by-species.
+This list is sorted by species and can be filtered to display only
+IMs for certain species combinations.
+
+See "Obtaining KIM Models"_http://openkim.org/doc/usage/obtaining-models to
+learn how to install a pre-build binary of the OpenKIM Repository of Models.
+
+NOTE: It is also possible to locally install IMs not archived in OpenKIM,
+in which case their names do not have to conform to the KIM ID format.
+
+Using OpenKIM IMs with LAMMPS :h4
+
+Two commands are employed when using OpenKIM IMs, one to select the
+IM and perform necessary initialization ({kim_init}), and the second
+to set up the IM for use by executing any necessary LAMMPS commands
+({kim_interactions}). Both are required.
+
+See the {examples/kim} directory for example input scripts that use KIM PMs
+and KIM SMs.
+
+OpenKIM IM Initialization ({kim_init}) :h5
+
+The {kim_init} mode command must be issued [before]
+the simulation box is created (normally at the top of the file).
+This command sets the OpenKIM IM that will be used and may issue
+additional commands changing LAMMPS default settings that are required
+for using the selected IM (such as "units"_units.html or
+"atom_style"_atom_style.html). If needed, those settings can be overridden,
+however, typically a script containing a {kim_init} command
+would not include {units} and {atom_style} commands.
+
+The required arguments of {kim_init} are the {model} name of the
+IM to be used in the simulation (for an IM archived in OpenKIM this is
+its "extended KIM ID"_https://openkim.org/doc/schema/kim-ids/, and
+the {user_units}, which are the LAMMPS "units style"_units.html used
+in the input script.  (Any dimensioned numerical values in the input
+script and values read in from files are expected to be in the
+{user_units} system.)
+
+The selected IM can be either a "KIM PM or a KIM SM"_#IM_types.
+For a KIM SM, the {kim_init} command verifies that the SM is designed
+to work with LAMMPS (and not another simulation code).
+In addition, the LAMMPS version used for defining
+the SM and the LAMMPS version being currently run are
+printed to help diagnose any incompatible changes to input script or
+command syntax between the two LAMMPS versions.
+
+Based on the selected model {kim_init} may modify the
+"atom_style"_atom_style.html.
+Some SMs have requirements for this setting. If this is the case, then
+{atom_style} will be set to the required style. Otherwise, the value is left
+unchanged (which in the absence of an {atom_style} command in the input script
+is the "default atom_style value"_atom_style.html).
+
+Regarding units, the {kim_init} command behaves in different ways depending
+on whether or not {unit conversion mode} is activated as indicated by the
+optional {unitarg} argument.
+If unit conversion mode is [not] active, then {user_units} must
+either match the required units of the IM or the IM must be able
+to adjust its units to match. (The latter is only possible with some KIM PMs;
+SMs can never adjust their units.) If a match is possible, the LAMMPS
+"units"_units.html command is called to set the units to
+{user_units}. If the match fails, the simulation is terminated with
+an error.
+
+Here is an example of a LAMMPS script to compute the cohesive energy
+of a face-centered cubic (fcc) lattice for the Ercolessi and Adams (1994)
+potential for Al:
+
+kim_init         EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal
+boundary         p p p
+lattice          fcc 4.032
+region           simbox block 0 1 0 1 0 1 units lattice
+create_box       1 simbox
+create_atoms     1 box
+mass             1 26.981539
+kim_interactions Al
+run              0
+variable         Ec equal (pe/count(all))/$\{_u_energy\}
+print            "Cohesive Energy = $\{EcJ\} eV"
+:pre
+
+The above script will end with an error in the {kim_init} line if the
+IM is changed to another potential for Al that does not work with {metal}
+units. To address this {kim_init} offers the {unit_conversion_mode}.
+If unit conversion mode {is} active, then {kim_init} calls the LAMMPS
+"units"_units.html command to set the units to the IM's required or
+preferred units. Conversion factors between the IM's units and the {user_units}
+are defined for all "physical quantities"_units.html (mass, distance, etc.).
+(Note that converting to or from the "lj" unit style is not supported.)
+These factors are stored as "internal style variables"_variable.html with
+the following standard names:
+
+_u_mass
+_u_distance
+_u_time
+_u_energy
+_u_velocity
+_u_force
+_u_torque
+_u_temperature
+_u_pressure
+_u_viscosity
+_u_charge
+_u_dipole
+_u_efield
+_u_density :pre
+
+If desired, the input script can be designed to work with these conversion
+factors so that the script will work without change with any OpenKIM IM.
+(This approach is used in the
+"OpenKIM Testing Framework"_https://openkim.org/doc/evaluation/kim-tests/.)
+For example, the script given above for the cohesive energy of fcc Al
+can be rewritten to work with any IM regardless of units. The following
+script constructs an fcc lattice with a lattice parameter defined in
+meters, computes the total energy, and prints the cohesive energy in
+Joules regardless of the units of the IM.
+
+kim_init         EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 si unit_conversion_mode
+boundary         p p p
+lattice          fcc 4.032e-10*$\{_u_distance\}
+region           simbox block 0 1 0 1 0 1 units lattice
+create_box       1 simbox
+create_atoms     1 box
+mass             1 4.480134e-26*$\{_u_mass\}
+kim_interactions Al
+run              0
+variable         Ec_in_J equal (pe/count(all))/$\{_u_energy\}
+print            "Cohesive Energy = $\{Ec_in_J\} J" :pre
+
+Note the multiplication by $\{_u_distance\} and $\{_u_mass\} to convert
+from SI units (specified in the {kim_init} command) to whatever units the
+IM uses (metal in this case), and the division by $\{_u_energy\}
+to convert from the IM's energy units to SI units (Joule). This script
+will work correctly for any IM for Al (KIM PM or SM) selected by the
+{kim_init} command.
+
+Care must be taken to apply unit conversion to dimensional variables read in
+from a file. For example if a configuration of atoms is read in from a
+dump file using the "read_dump"_read_dump.html command, the following can
+be done to convert the box and all atomic positions to the correct units:
+
+variable xyfinal equal xy*$\{_u_distance\}
+variable xzfinal equal xz*$\{_u_distance\}
+variable yzfinal equal yz*$\{_u_distance\}
+change_box all x scale $\{_u_distance\} &
+                       y scale $\{_u_distance\} &
+                       z scale $\{_u_distance\} &
+                       xy final $\{xyfinal\} &
+                       xz final $\{xzfinal\} &
+                       yz final $\{yzfinal\} &
+                       remap  :pre
+
+NOTE: Unit conversion will only work if the conversion factors are placed in
+all appropriate places in the input script. It is up to the user to do this
+correctly.
+
+OpenKIM IM Execution ({kim_interactions}) :h5
+
+The second and final step in using an OpenKIM IM is to execute the
+{kim_interactions} command. This command must be preceded by a {kim_init}
+command and a command that defines the number of atom types {N} (such as
+"create_box"_create_box.html).
+The {kim_interactions} command has one argument {typeargs}. This argument
+contains either a list of {N} chemical species, which defines a mapping between
+atom types in LAMMPS to the available species in the OpenKIM IM, or the
+keyword {fixed_types} for models that have a preset fixed mapping (i.e.
+the mapping between LAMMPS atom types and chemical species is defined by
+the model and cannot be changed). In the latter case, the user must consult
+the model documentation to see how many atom types there are and how they
+map to the chemical species.
+
+For example, consider an OpenKIM IM that supports Si and C species.
+If the LAMMPS simulation has four atom types, where the first three are Si,
+and the fourth is C, the following {kim_interactions} command would be used:
+
+kim_interactions Si Si Si C
+:pre
+
+Alternatively, for a model with a fixed mapping the command would be:
+
+kim_interactions fixed_types
+:pre
+
+The {kim_interactions} command performs all the necessary steps to set up
+the OpenKIM IM selected in the {kim_init} command. The specific actions depend
+on whether the IM is a KIM PM or a KIM SM.  For a KIM PM,
+a "pair_style kim"_pair_kim.html command is executed followed by
+the appropriate {pair_coeff} command. For example, for the
+Ercolessi and Adams (1994) KIM PM for Al set by the following commands:
+
+kim_init EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal
+...
+...  box specification lines skipped
+...
+kim_interactions Al :pre
+
+the {kim_interactions} command executes the following LAMMPS input commands:
+
+pair_style kim EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005
+pair_coeff * * Al  :pre
+
+For a KIM SM, the generated input commands may be more complex
+and require that LAMMPS is built with the required packages included
+for the type of potential being used. The set of commands to be executed
+is defined in the SM specification file, which is part of the SM package.
+For example, for the Strachan et al. (2003) ReaxFF SM
+set by the following commands:
+
+kim_init Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 real
+...
+...  box specification lines skipped
+...
+kim_interactions C H N O  :pre
+
+the {kim_interactions} command executes the following LAMMPS input commands:
+
+pair_style reax/c lmp_control safezone 2.0 mincap 100
+pair_coeff * * ffield.reax.rdx C H N O
+fix reaxqeq all qeq/reax 1 0.0 10.0 1.0e-6 param.qeq  :pre
+
+Note that the files {lmp_control}, {ffield.reax.rdx} and {param.qeq}
+are specific to the Strachan et al. (2003) ReaxFF parameterization
+and are archived as part of the SM package in OpenKIM.
+Note also that parameters like cutoff radii and charge tolerances,
+which have an effect on IM predictions, are also included in the
+SM definition ensuring reproducibility.
+
+NOTE: When using {kim_init} and {kim_interactions} to select
+and set up an OpenKIM IM, other LAMMPS commands
+for the same functions (such as pair_style, pair_coeff, bond_style,
+bond_coeff, fixes related to charge equilibration, etc.) should normally
+not appear in the input script.
+
+Using OpenKIM Web Queries in LAMMPS ({kim_query}) :h5
+
+The {kim_query} command performs a web query to retrieve the predictions
+of the IM set by {kim_init} for material properties archived in
+"OpenKIM"_https://openkim.org.  The {kim_query} command must be preceded
+by a {kim_init} command. The result of the query is stored in a
+"string style variable"_variable.html, the name of which is given as the first
+argument of the {kim_query command}.  (For the case of multiple
+return values, the optional {split} keyword can be used after the
+variable name to separate the results into multiple variables; see
+the "example"_#split_example below.)
+The second required argument {query_function} is the name of the
+query function to be called (e.g. {get_lattice_constant_cubic}).
+All following "arguments"_Commands_parse.html are parameters handed over to
+the web query in the format {keyword=value}, where {value} is always
+an array of one or more comma-separated items in brackets.
+The list of supported keywords and the type and format of their values
+depend on the query function used. The current list of query functions
+is available on the OpenKIM webpage at
+"https://openkim.org/doc/usage/kim-query"_https://openkim.org/doc/usage/kim-query.
+
+NOTE: All query functions require the {model} keyword, which identifies
+the IM whose predictions are being queried. This keyword is automatically
+generated by {kim_query} based on the IM set in {kim_init} and must not
+be specified as an argument to {kim_query}.
+
+NOTE: Each {query_function} is associated with a default method (implemented
+as a "KIM Test"_https://openkim.org/doc/evaluation/kim-tests/)
+used to compute this property. In cases where there are multiple
+methods in OpenKIM for computing a property, a {method} keyword can
+be provided to select the method of choice.  See the
+"query documentation"_https://openkim.org/doc/repository/kim-query
+to see which methods are available for a given {query function}.
+
+{kim_query} Usage Examples and Further Clarifications: :h6
+
+The data obtained by {kim_query} commands can be used as part of the setup
+or analysis phases of LAMMPS simulations. Some examples are given below.
+
+[Define an equilibrium fcc crystal]
+
+kim_init         EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal
+boundary         p p p
+kim_query        a0 get_lattice_constant_cubic crystal=\["fcc"\] species=\["Al"\] units=\["angstrom"\]
+lattice          fcc $\{a0\}
+... :pre
+
+The {kim_query} command retrieves from "OpenKIM"_https://openkim.org
+the equilibrium lattice constant predicted by the Ercolessi and Adams (1994)
+potential for the fcc structure and places it in
+variable {a0}. This variable is then used on the next line to set up the
+crystal. By using {kim_query}, the user is saved the trouble and possible
+error of tracking this value down, or of having to perform an energy
+minimization to find the equilibrium lattice constant.
+
+Note that in {unit_conversion_mode} the results obtained from a
+{kim_query} would need to be converted to the appropriate units system.
+For example, in the above script, the lattice command would need to be
+changed to: "lattice fcc $\{a0\}*$\{_u_distance\}".
+
+:link(split_example)
+[Define an equilibrium hcp crystal]
+
+kim_init         EAM_Dynamo_Mendelev_2007_Zr__MO_848899341753_000 metal
+boundary         p p p
+kim_query        latconst split get_lattice_constant_hexagonal crystal=\["hcp"\] species=\["Zr"\] units=\["angstrom"\]
+variable         a0 equal latconst_1
+variable         c0 equal latconst_2
+variable         c_to_a equal $\{c0\}/$\{a0\}
+lattice          custom $\{a0\} a1 0.5 -0.866025 0 a2 0.5 0.866025 0 a3 0 0 $\{c_to_a\} &
+                 basis 0.333333 0.666666 0.25 basis 0.666666 0.333333 0.75
+... :pre
+
+In this case the {kim_query} returns two arguments (since the hexagonal
+close packed (hcp) structure has two independent lattice constants).
+The default behavior of {kim_query} returns the result as a string
+with the values separated by commas. The optional keyword {split}
+separates the result values into individual variables of the form
+{prefix_I}, where {prefix} is set to the the {kim_query} {variable} argument
+and {I} ranges from 1 to the number of returned values. The number and order of
+the returned values is determined by the type of query performed.
+
+[Define a crystal at finite temperature accounting for thermal expansion]
+
+kim_init         EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal
+boundary         p p p
+kim_query        a0 get_lattice_constant_cubic crystal=\["fcc"\] species=\["Al"\] units=\["angstrom"\]
+kim_query        alpha get_linear_thermal_expansion_coefficient_cubic  crystal=\["fcc"\] species=\["Al"\] units=\["1/K"\] temperature=\[293.15\] temperature_units=\["K"\]
+variable         DeltaT equal 300
+lattice          fcc $\{a0\}*$\{alpha\}*$\{DeltaT\}
+... :pre
+
+As in the previous example, the equilibrium lattice constant is obtained
+for the Ercolessi and Adams (1994) potential. However, in this case the
+crystal is scaled to the appropriate lattice constant at room temperature
+(293.15 K) by using the linear thermal expansion constant predicted by the
+potential.
+
+NOTE: When passing numerical values as arguments (as in the case
+of the temperature in the above example) it is also possible to pass a
+tolerance indicating how close to the value is considered a match.
+If no tolerance is passed a default value is used. If multiple results
+are returned (indicating that the tolerance is too large), {kim_query}
+will return an error. See the
+"query documentation"_https://openkim.org/doc/repository/kim-query
+to see which numerical arguments and tolerances are available for a
+given {query function}.
+
+[Compute defect formation energy]
+
+kim_init         EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal
+...
+... Build fcc crystal containing some defect and compute the total energy
+... which is stored in the variable {Etot}
+...
+kim_query        Ec get_cohesive_energy_cubic crystal=\["fcc"\] species=\["Al"\] units=\["eV"\]
+variable         Eform equal $\{Etot\} - count(all)*$\{Ec\}
+... :pre
+
+The defect formation energy {Eform} is computed by subtracting from {Etot} the
+ideal fcc cohesive energy of the atoms in the system obtained from
+"OpenKIM"_https://openkim.org for the Ercolessi and Adams (1994) potential.
+
+NOTE: {kim_query} commands return results archived in
+"OpenKIM"_https://openkim.org. These results are obtained
+using programs for computing material properties
+(KIM Tests and KIM Test Drivers) that were contributed to OpenKIM.
+In order to give credit to Test developers, the number of times results
+from these programs are queried is tracked. No other information about
+the nature of the query or its source is recorded.
+
+
+Citation of OpenKIM IMs :h4
+
+When publishing results obtained using OpenKIM IMs researchers are requested
+to cite the OpenKIM project "(Tadmor)"_#kim-mainpaper, KIM API
+"(Elliott)"_#kim-api, and the specific IM codes used in the simulations,
+in addition to the relevant scientific references for the IM.
+The citation format for an IM is displayed on its page on
+"OpenKIM"_https://openkim.org along with the corresponding BibTex file,
+and is automatically added to the LAMMPS {log.cite} file.
+
+Citing the IM software (KIM infrastructure and specific PM or SM codes)
+used in the simulation gives credit to the researchers who developed them
+and enables open source efforts like OpenKIM to function.
+
+
+[Restrictions:]
+
+The set of {kim_commands} is part of the KIM package.  It is only enabled if
+LAMMPS is built with that package. A requirement for the KIM package,
+is the KIM API library that must be downloaded from the
+"OpenKIM website"_https://openkim.org/kim-api/ and installed before
+LAMMPS is compiled. When installing LAMMPS from binary, the kim-api package
+is a dependency that is automatically downloaded and installed. See the KIM
+section of the "Packages details"_Packages_details.html for details.
+
+Furthermore, when using {kim_commands} to run KIM SMs, any packages required
+by the native potential being used or other commands or fixes that it invokes
+must be installed.
+
+[Related commands:]
+
+"pair_style kim"_pair_kim.html
+
+:line
+
+:link(kim-mainpaper)
+[(Tadmor)] Tadmor, Elliott, Sethna, Miller and Becker, JOM, 63, 17 (2011).
+doi: "https://doi.org/10.1007/s11837-011-0102-6"_https://doi.org/10.1007/s11837-011-0102-6
+
+:link(kim-api)
+[(Elliott)] Elliott, Tadmor and Bernstein, "https://openkim.org/kim-api"_https://openkim.org/kim-api (2011)
+doi: "https://doi.org/10.25950/FF8F563A"_https://doi.org/10.25950/FF8F563A

doc/src/kim_query.txt

@@ -1,46 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Commands_all.html)
-
-:line
-
-kim_query command :h3
-
-[Syntax:]
-
-kim_query variable query_function web_query_flags :pre
-
-variable = name of a (string style) variable where the result of the query is stored
-query_function = name of the OpenKIM web API query function to be used
-web_query_flags = a series of keyword=value pairs that represent the web query; supported keywords depend on query function :ul
-
-[Examples:]
-
-kim_query latconst get_test_result test=TE_156715955670 model=MO_800509458712 &
-  prop=structure-cubic-crystal-npt species=\["Al"\] keys=\["a"\] units=\["angstrom"\] :pre
-
-[Description:]
-
-The kim_query command allows to retrieve properties from the OpenKIM
-through a web query. The result is stored in a string style
-"variable"_variable.html, the name of which must be given as the first
-argument of the kim_query command.  The second required argument is the
-name of the actual query function (e.g. {get_test_result}).  All following
-arguments are parameters handed over to the web query in the format
-{keyword=value}.  The list of supported keywords and the type of how
-the value has to be encoded depends on the query function used.  This
-mirrors the functionality available on the OpenKIM webpage at
-"https://query.openkim.org"_https://query.openkim.org/
-
-[Restrictions:]
-
-This command is part of the KIM package.  It is only enabled if
-LAMMPS was built with that package.  Furthermore, its correct
-functioning depends on compiling LAMMPS with libcurl support.
-See the "Build package"_Build_package.html doc page for more info.
-
-[Related commands:]
-
-"pair_style kim"_pair_kim.html, "variable"_variable.html

doc/src/lammps.book

@@ -42,6 +42,7 @@ Commands_compute.html
 Commands_pair.html
 Commands_bond.html
 Commands_kspace.html
+Commands_removed.html
 Packages.html
 Packages_standard.html
 Packages_user.html
@@ -167,7 +168,7 @@ if.html
 include.html
 info.html
 jump.html
-kim_query.html
+kim_commands.html
 label.html
 lattice.html
 log.html
@@ -455,6 +456,7 @@ compute_global_atom.html
 compute_group_group.html
 compute_gyration.html
 compute_gyration_chunk.html
+compute_gyration_shape.html
 compute_heat_flux.html
 compute_hexorder_atom.html
 compute_improper.html
@@ -468,6 +470,7 @@ compute_ke_rigid.html
 compute_meso_e_atom.html
 compute_meso_rho_atom.html
 compute_meso_t_atom.html
+compute_momentum.html
 compute_msd.html
 compute_msd_chunk.html
 compute_msd_nongauss.html

doc/src/package.txt

@@ -64,7 +64,7 @@ args = arguments specific to the style :l
       {no_affinity} values = none
   {kokkos} args = keyword value ...
     zero or more keyword/value pairs may be appended
-    keywords = {neigh} or {neigh/qeq} or {neigh/thread} or {newton} or {binsize} or {comm} or {comm/exchange} or {comm/forward} or {comm/reverse} or {gpu/direct}
+    keywords = {neigh} or {neigh/qeq} or {neigh/thread} or {newton} or {binsize} or {comm} or {comm/exchange} or {comm/forward} or {comm/reverse} or {cuda/aware}
       {neigh} value = {full} or {half}
         full = full neighbor list
         half = half neighbor list built in thread-safe manner
@@ -87,9 +87,9 @@ args = arguments specific to the style :l
         no = perform communication pack/unpack in non-KOKKOS mode
         host = perform pack/unpack on host (e.g. with OpenMP threading)
         device = perform pack/unpack on device (e.g. on GPU)
-      {gpu/direct} = {off} or {on}
-        off = do not use GPU-direct
-        on = use GPU-direct (default)
+      {cuda/aware} = {off} or {on}
+        off = do not use CUDA-aware MPI
+        on = use CUDA-aware MPI (default)
   {omp} args = Nthreads keyword value ...
     Nthread = # of OpenMP threads to associate with each MPI process
     zero or more keyword/value pairs may be appended
@@ -520,19 +520,21 @@ pack/unpack communicated data. When running small systems on a GPU,
 performing the exchange pack/unpack on the host CPU can give speedup 
 since it reduces the number of CUDA kernel launches.
 
-The {gpu/direct} keyword chooses whether GPU-direct will be used. When 
+The {cuda/aware} keyword chooses whether CUDA-aware MPI will be used. When 
 this keyword is set to {on}, buffers in GPU memory are passed directly 
 through MPI send/receive calls. This reduces overhead of first copying 
-the data to the host CPU. However GPU-direct is not supported on all 
+the data to the host CPU. However CUDA-aware MPI is not supported on all 
 systems, which can lead to segmentation faults and would require using a 
-value of {off}. If LAMMPS can safely detect that GPU-direct is not 
+value of {off}. If LAMMPS can safely detect that CUDA-aware MPI is not 
 available (currently only possible with OpenMPI v2.0.0 or later), then 
-the {gpu/direct} keyword is automatically set to {off} by default. When 
-the {gpu/direct} keyword is set to {off} while any of the {comm} 
+the {cuda/aware} keyword is automatically set to {off} by default. When 
+the {cuda/aware} keyword is set to {off} while any of the {comm} 
 keywords are set to {device}, the value for these {comm} keywords will 
 be automatically changed to {host}. This setting has no effect if not 
-running on GPUs. GPU-direct is available for OpenMPI 1.8 (or later 
-versions), Mvapich2 1.9 (or later), and CrayMPI.
+running on GPUs. CUDA-aware MPI is available for OpenMPI 1.8 (or later 
+versions), Mvapich2 1.9 (or later) when the "MV2_USE_CUDA" environment
+variable is set to "1", CrayMPI, and IBM Spectrum MPI when the "-gpu"
+flag is used.
 
 :line
 
@@ -641,8 +643,8 @@ switch"_Run_options.html.
 
 For the KOKKOS package, the option defaults for GPUs are neigh = full, 
 neigh/qeq = full, newton = off, binsize for GPUs = 2x LAMMPS default 
-value, comm = device, gpu/direct = on. When LAMMPS can safely detect 
-that GPU-direct is not available, the default value of gpu/direct 
+value, comm = device, cuda/aware = on. When LAMMPS can safely detect 
+that CUDA-aware MPI is not available, the default value of cuda/aware 
 becomes "off". For CPUs or Xeon Phis, the option defaults are neigh = 
 half, neigh/qeq = half, newton = on, binsize = 0.0, and comm = no. The 
 option neigh/thread = on when there are 16K atoms or less on an MPI 

doc/src/pair_adp.txt

@@ -42,16 +42,17 @@ the ADP potential files themselves.  Likewise, the ADP potential files
 list atomic masses; thus you do not need to use the "mass"_mass.html
 command to specify them.
 
-The NIST WWW site distributes and documents ADP potentials:
+[ADP potentials are available from:]
 
-http://www.ctcms.nist.gov/potentials :pre
+The NIST WWW site at http://www.ctcms.nist.gov/potentials.
+Note that ADP potentials obtained from NIST must be converted
+into the extended DYNAMO {setfl} format discussed below.
+:l
 
-Note that these must be converted into the extended DYNAMO {setfl}
-format discussed below.
-
-The NIST site is maintained by Chandler Becker (cbecker at nist.gov)
-who is good resource for info on interatomic potentials and file
-formats.
+The OpenKIM Project at https://openkim.org/browse/models/by-type provides
+ADP potentials that can be used directly in LAMMPS with the "kim_commands
+interface"_kim_commands.html.
+:l
 
 :line
 

doc/src/pair_coul_shield.txt

@@ -13,7 +13,7 @@ pair_style coul/shield command :h3
 pair_style coul/shield cutoff tap_flag :pre
 
 cutoff = global cutoff (distance units)
-tap_flag = 0/1 to turn off/on the taper function
+tap_flag = 0/1 to turn off/on the taper function :ul
 
 [Examples:]
 

doc/src/pair_ilp_graphene_hbn.txt

@@ -13,17 +13,17 @@ pair_style ilp/graphene/hbn command :h3
 pair_style \[hybrid/overlay ...\] ilp/graphene/hbn cutoff tap_flag :pre
 
 cutoff = global cutoff (distance units)
-tap_flag = 0/1 to turn off/on the taper function
+tap_flag = 0/1 to turn off/on the taper function :ul
 
 [Examples:]
 
-pair_style hybrid/overlay ilp/graphene/hbn 16.0 1
-pair_coeff * * ilp/graphene/hbn  BNCH.ILP B N C :pre
+pair_style  hybrid/overlay ilp/graphene/hbn 16.0 1
+pair_coeff  * * ilp/graphene/hbn  BNCH.ILP B N C :pre
 
 pair_style  hybrid/overlay rebo tersoff ilp/graphene/hbn 16.0 coul/shield 16.0
-pair_coeff  * * rebo                 CH.rebo     NULL NULL C
-pair_coeff  * * tersoff              BNC.tersoff B    N    NULL
-pair_coeff  * * ilp/graphene/hbn     BNCH.ILP    B    N    C
+pair_coeff  * * rebo              CH.rebo     NULL NULL C
+pair_coeff  * * tersoff           BNC.tersoff B    N    NULL
+pair_coeff  * * ilp/graphene/hbn  BNCH.ILP    B    N    C
 pair_coeff  1 1 coul/shield 0.70
 pair_coeff  1 2 coul/shield 0.695
 pair_coeff  2 2 coul/shield 0.69 :pre
@@ -85,6 +85,22 @@ be found in "(Ouyang)"_#Ouyang.
 This potential must be used in combination with hybrid/overlay.
 Other interactions can be set to zero using pair_style {none}.
 
+This pair style tallies a breakdown of the total interlayer potential
+energy into sub-categories, which can be accessed via the "compute
+pair"_compute_pair.html command as a vector of values of length 2.
+The 2 values correspond to the following sub-categories:
+
+{E_vdW} = vdW (attractive) energy
+{E_Rep} = Repulsive energy :ol
+
+To print these quantities to the log file (with descriptive column
+headings) the following commands could be included in an input script:
+
+compute 0 all pair ilp/graphene/hbn
+variable Evdw  equal c_0\[1\]
+variable Erep  equal c_0\[2\]
+thermo_style custom step temp epair v_Erep v_Evdw :pre
+
 :line
 
 [Mixing, shift, table, tail correction, restart, rRESPA info]:

doc/src/pair_kim.txt

@@ -12,76 +12,72 @@ pair_style kim command :h3
 
 pair_style kim model :pre
 
-model = name of KIM model (potential)
+model = name of a KIM model (the KIM ID for models archived in OpenKIM)
 
 [Examples:]
 
-pair_style kim ex_model_Ar_P_LJ
-pair_coeff * * Ar Ar :pre
+pair_style kim SW_StillingerWeber_1985_Si__MO_405512056662_005
+pair_coeff * * Si :pre
 
 [Description:]
 
-This pair style is a wrapper on the "Knowledge Base for Interatomic
+This pair style is a wrapper on the "Open Knowledgebase of Interatomic
 Models (OpenKIM)"_https://openkim.org repository of interatomic
-potentials, so that they can be used by LAMMPS scripts.
+potentials to enable their use in LAMMPS scripts.
 
-Note that in LAMMPS lingo, a KIM model driver is a pair style
-(e.g. EAM or Tersoff).  A KIM model is a pair style for a particular
-element or alloy and set of parameters, e.g. EAM for Cu with a
-specific EAM potential file.
+The preferred interface for using interatomic models archived in
+OpenKIM is the "kim_commands interface"_kim_commands.html. That
+interface supports both "KIM Portable Models" (PMs) that conform to the
+KIM API Portable Model Interface (PMI) and can be used by any
+simulation code that conforms to the KIM API/PMI, and
+"KIM Simulator Models" that are natively implemented within a single
+simulation code (like LAMMPS) and can only be used with it.
+The {pair_style kim} command is limited to KIM PMs. It is
+used by the "kim_commands interface"_kim_commands.html as needed.
 
-See the current list of "KIM model
-drivers"_https://openkim.org/browse/model-drivers/alphabetical.
+NOTE: Since {pair_style kim} is called by {kim_interactions} as needed,
+is not recommended to be directly used in input scripts.
 
-See the current list of all "KIM
-models"_https://openkim.org/browse/models/by-model-drivers
-
-To use this pair style, you must first download and install the KIM
-API library from the "OpenKIM website"_https://openkim.org.  The KIM
-section of the "Packages details"_Packages_details.html doc page has
-instructions on how to do this with a simple make command, when
-building LAMMPS.
-
-See the examples/kim dir for an input script that uses a KIM model
-(potential) for Lennard-Jones.
- 
 :line
 
-The argument {model} is the name of the KIM model for a specific
-potential as KIM defines it.  In principle, LAMMPS can invoke any KIM
-model.  You should get an error or warning message from either LAMMPS
-or KIM if there is an incompatibility.
+The argument {model} is the name of the KIM PM.
+For potentials archived in OpenKIM
+this is the extended KIM ID (see "kim_commands"_kim_commands.html
+for details). LAMMPS can invoke any KIM PM, however there can
+be incompatibilities (for example due to unit matching issues).
+In the event of an incompatibility, the code will terminate with
+an error message. Check both the LAMMPS and KIM log files for details.
 
-Only a single pair_coeff command is used with the {kim} style which
-specifies the mapping of LAMMPS atom types to KIM elements.  This is
-done by specifying N additional arguments after the * * in the
-pair_coeff command, where N is the number of LAMMPS atom types:
+Only a single {pair_coeff} command is used with the {kim} style, which
+specifies the mapping of LAMMPS atom types to the species supported by
+the KIM PM.  This is done by specifying {N} additional arguments
+after the * * in the {pair_coeff} command, where {N} is the number of
+LAMMPS atom types:
 
 N element names = mapping of KIM elements to atom types :ul
 
-As an example, imagine the KIM model supports Si and C atoms.  If your
-LAMMPS simulation has 4 atom types and you want the 1st 3 to be Si,
-and the 4th to be C, you would use the following pair_coeff command:
+For example, consider a KIM PM that supports Si and C species.
+If the LAMMPS simulation has four atom types, where the first three are Si,
+and the fourth is C, the following {pair_coeff} command would be used:
 
 pair_coeff * * Si Si Si C :pre
 
-The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
-The first three Si arguments map LAMMPS atom types 1,2,3 to Si as
-defined within KIM.  The final C argument maps LAMMPS atom type 4 to C
-as defined within KIM.
+The first two arguments must be * * so as to span all LAMMPS atom types.
+The first three Si arguments map LAMMPS atom types 1, 2, and 3 to Si as
+defined within KIM PM.  The final C argument maps LAMMPS atom type 4 to C.
 
 :line
 
 In addition to the usual LAMMPS error messages, the KIM library itself
 may generate errors, which should be printed to the screen.  In this
-case it is also useful to check the kim.log file for additional error
-information.  The file kim.log should be generated in the same
+case it is also useful to check the {kim.log} file for additional error
+information.  The file {kim.log} should be generated in the same
 directory where LAMMPS is running.
 
 To download, build, and install the KIM library on your system, see
-the lib/kim/README file.  Once you have done this and built LAMMPS
+the {lib/kim/README} file.  Once you have done this and built LAMMPS
 with the KIM package installed you can run the example input scripts
-in examples/kim.
+in {examples/kim}.
 
 :line
 
@@ -103,15 +99,14 @@ This pair style can only be used via the {pair} keyword of the
 
 [Restrictions:]
 
-This pair style is part of the KIM package.  It is only enabled if
-LAMMPS was built with that package.  See the "Build
-package"_Build_package.html doc page for more info.
+This pair style is part of the KIM package. See details on
+restrictions in "kim_commands"_kim_commands.html.
 
 This current version of pair_style kim is compatible with the
 kim-api package version 2.0.0 and higher.
 
 [Related commands:]
 
-"pair_coeff"_pair_coeff.html
+"pair_coeff"_pair_coeff.html, "kim_commands"_kim_commands.html
 
 [Default:] none

doc/src/pair_kolmogorov_crespi_full.txt

@@ -13,7 +13,7 @@ pair_style kolmogorov/crespi/full command :h3
 pair_style hybrid/overlay kolmogorov/crespi/full cutoff tap_flag :pre
 
 cutoff = global cutoff (distance units)
-tap_flag = 0/1 to turn off/on the taper function
+tap_flag = 0/1 to turn off/on the taper function :ul
 
 [Examples:]
 
@@ -74,6 +74,22 @@ comparison of these parameters can be found in "(Ouyang)"_#Ouyang1.
 This potential must be used in combination with hybrid/overlay.
 Other interactions can be set to zero using pair_style {none}.
 
+This pair style tallies a breakdown of the total interlayer potential
+energy into sub-categories, which can be accessed via the "compute
+pair"_compute_pair.html command as a vector of values of length 2.
+The 2 values correspond to the following sub-categories:
+
+{E_vdW} = vdW (attractive) energy
+{E_Rep} = Repulsive energy :ol
+
+To print these quantities to the log file (with descriptive column
+headings) the following commands could be included in an input script:
+
+compute 0 all pair kolmogorov/crespi/full
+variable Evdw  equal c_0\[1\]
+variable Erep  equal c_0\[2\]
+thermo_style custom step temp epair v_Erep v_Evdw :pre
+
 :line
 
 [Mixing, shift, table, tail correction, restart, rRESPA info]:

doc/src/replicate.txt

@@ -14,7 +14,8 @@ replicate nx ny nz {keyword} :pre
 
 nx,ny,nz = replication factors in each dimension :ulb
 optional {keyword} = {bbox} :l
-  {bbox} = only check atoms in replicas that overlap with a processor's sub-domain :ule
+  {bbox} = only check atoms in replicas that overlap with a processor's sub-domain :pre
+:ule
 
 [Examples:]
 
@@ -45,11 +46,13 @@ file that crosses a periodic boundary should be between two atoms with
 image flags that differ by 1.  This will allow the bond to be
 unwrapped appropriately.
 
-The optional keyword {bbox} uses a bounding box to only check atoms
-in replicas that overlap with a processor's sub-domain when assigning
-atoms to processors, and thus can result in substantial speedups for
-calculations using a large number of processors. It does require
-temporarily using more memory.
+The optional keyword {bbox} uses a bounding box to only check atoms in
+replicas that overlap with a processor's sub-domain when assigning
+atoms to processors.  It typically results in a substantial speedup
+when using the replicate command on a large number of processors.  It
+does require temporary use of more memory, specifically that each
+processor can store all atoms in the entire system before it is
+replicated.
 
 [Restrictions:]
 

doc/utils/sphinx-config/false_positives.txt

@@ -20,6 +20,7 @@ acolor
 acos
 Acta
 actinide
+acylindricity
 addforce
 Addington
 addtorque
@@ -113,6 +114,7 @@ askoose
 asphere
 ASPHERE
 aspherical
+asphericity
 Asq
 assignee
 Asta
@@ -481,6 +483,7 @@ cvff
 cwiggle
 cygwin
 Cygwin
+cylindrically
 Cyrot
 cyrstals
 Daivis
@@ -526,6 +529,7 @@ decrementing
 deeppink
 deepskyblue
 defgrad
+defn
 deformable
 del
 deleteIDs
@@ -574,6 +578,7 @@ Dihedrals
 dihydride
 Dij
 dimdim
+dimensioned
 dimensionality
 dimgray
 dipolar
@@ -603,6 +608,7 @@ Dobson
 Dodds
 dodgerblue
 dof
+doi
 Donadio
 dotc
 Doty
@@ -754,6 +760,7 @@ equilibrating
 equilibration
 Equilibria
 equilization
+Ercolessi
 eradius
 erate
 erc
@@ -880,6 +887,7 @@ Fogarty
 Foiles
 fopenmp
 forestgreen
+formatarg
 formulae
 Forschungszentrum
 Fortran
@@ -1514,6 +1522,7 @@ lz
 Maaravi
 Mackay
 Mackrodt
+Macromolecules
 macroparticle
 Madura
 Magda
@@ -1539,6 +1548,7 @@ Mandelli
 Manh
 manifoldforce
 Manolopoulos
+manpages
 manybody
 MANYBODY
 Maras
@@ -1619,6 +1629,7 @@ meso
 mesoparticle
 mesoscale
 mesoscopic
+metadata
 metadynamics
 Metadynamics
 Methfessel
@@ -2257,6 +2268,7 @@ quati
 quatj
 quatk
 quatw
+queryargs
 Queteschiner
 qw
 qx
@@ -2286,6 +2298,7 @@ rcutfac
 rdc
 rdf
 RDideal
+rdx
 README
 realtime
 reamin
@@ -2312,6 +2325,8 @@ Rensselaer
 reparameterizing
 repo
 representable
+Reproducibility
+reproducibility
 repuls
 rescale
 rescaled
@@ -2428,6 +2443,8 @@ Salles
 sandia
 Sandia
 sandybrown
+Sanitizer
+sanitizers
 sc
 scafacos
 SCAFACOS
@@ -2602,6 +2619,7 @@ Stoll
 stopstep
 Stouch
 Straatsma
+Strachan
 Stratford
 Strathclyde
 Straub
@@ -2629,6 +2647,7 @@ superset
 supersphere
 Supinski
 surfactants
+Suter
 Sutmann
 svn
 sw
@@ -2690,6 +2709,7 @@ th
 Thakkar
 thb
 thei
+Theodorou
 Theor
 thermalization
 thermalize
@@ -2812,6 +2832,7 @@ txt
 typeI
 typeJ
 typeN
+typeargs
 Tz
 Tzou
 ub
@@ -2840,6 +2861,7 @@ undump
 uniaxial
 uniaxially
 unimodal
+unitarg
 unitless
 Universite
 unix

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

@@ -38,6 +38,8 @@ fix myrxns all bond/react stabilization yes statted_grp .03 &
 
 fix 1 statted_grp_REACT nvt temp 300 300 100
 
+# optionally, you can customize behavior of reacting atoms,
+# by using the internally-created 'bond_react_MASTER_group', like so:
 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]

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

@@ -0,0 +1,48 @@
+# 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 no &
+  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 all nve/limit .03
+
+thermo_style custom step temp press density f_myrxns[1] f_myrxns[2]
+
+# restart 100 restart1 restart2
+
+run 1000
+
+# write_restart restart_longrun
+# write_data restart_longrun.data

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

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

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

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

examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.stabilized.g++.1

@@ -0,0 +1,148 @@
+LAMMPS (5 Jun 2019)
+Reading data file ...
+  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
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:   0          0          0         
+  special bond factors coul: 0          0          0         
+  4 = max # of 1-2 neighbors
+  6 = max # of 1-3 neighbors
+  12 = max # of 1-4 neighbors
+  41 = max # of special neighbors
+  special bonds CPU = 0.000181113 secs
+  read_data CPU = 0.0251833 secs
+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
+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
+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
+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
+WARNING: Bond/react: Atom affected by reaction rxn1 too close to template edge (../fix_bond_react.cpp:1785)
+WARNING: Bond/react: Atom affected by reaction rxn2 too close to template edge (../fix_bond_react.cpp:1785)
+dynamic group bond_react_MASTER_group defined
+dynamic group statted_grp_REACT defined
+PPPM initialization ...
+  using 12-bit tables for long-range coulomb (../kspace.cpp:319)
+  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
+Setting up Verlet run ...
+  Unit style    : real
+  Current step  : 0
+  Time step     : 1
+WARNING: Inconsistent image flags (../domain.cpp:784)
+Per MPI rank memory allocation (min/avg/max) = 34.41 | 34.41 | 34.41 Mbytes
+Step Temp Press Density f_myrxns[1] f_myrxns[2] 
+       0          300    346.78165 0.0034851739            0            0 
+      50    293.70542   -52.547388 0.0034851739            1            0 
+     100    276.36755     54.81826 0.0034851739            1            1 
+     150    448.65869    16.874435 0.0034851739            1            1 
+     200    379.84257    11.578545 0.0034851739            1            1 
+     250    298.21983    90.656585 0.0034851739            1            1 
+     300     333.3111   -30.139607 0.0034851739            1            1 
+     350    266.57108    6.4505134 0.0034851739            1            1 
+     400    264.05476    10.513204 0.0034851739            1            1 
+     450    250.70418   -18.635379 0.0034851739            1            1 
+     500    261.21632    10.231013 0.0034851739            1            1 
+     550    309.89024   -8.8299506 0.0034851739            1            1 
+     600    373.45851    30.368993 0.0034851739            1            1 
+     650    338.26242    9.0362267 0.0034851739            1            1 
+     700    295.67794   -5.6007538 0.0034851739            1            1 
+     750    310.86563   -59.228181 0.0034851739            1            1 
+     800    286.22678   -9.9022407 0.0034851739            1            1 
+     850    218.42135    27.845352 0.0034851739            1            1 
+     900    259.62551    24.216336 0.0034851739            1            1 
+     950    250.21307   -14.560985 0.0034851739            1            1 
+    1000    274.29245  -0.38768626 0.0034851739            1            1 
+Loop time of 0.341061 on 1 procs for 1000 steps with 44 atoms
+
+Performance: 253.327 ns/day, 0.095 hours/ns, 2932.025 timesteps/s
+87.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.031135   | 0.031135   | 0.031135   |   0.0 |  9.13
+Bond    | 0.12623    | 0.12623    | 0.12623    |   0.0 | 37.01
+Kspace  | 0.036491   | 0.036491   | 0.036491   |   0.0 | 10.70
+Neigh   | 0.046395   | 0.046395   | 0.046395   |   0.0 | 13.60
+Comm    | 0.0025396  | 0.0025396  | 0.0025396  |   0.0 |  0.74
+Output  | 0.07775    | 0.07775    | 0.07775    |   0.0 | 22.80
+Modify  | 0.019219   | 0.019219   | 0.019219   |   0.0 |  5.64
+Other   |            | 0.001306   |            |       |  0.38
+
+Nlocal:    44 ave 44 max 44 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    2 ave 2 max 2 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    740 ave 740 max 740 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 740
+Ave neighs/atom = 16.8182
+Ave special neighs/atom = 9.77273
+Neighbor list builds = 1000
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:00

examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.stabilized.g++.4

@@ -0,0 +1,148 @@
+LAMMPS (5 Jun 2019)
+Reading data file ...
+  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
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:   0          0          0         
+  special bond factors coul: 0          0          0         
+  4 = max # of 1-2 neighbors
+  6 = max # of 1-3 neighbors
+  12 = max # of 1-4 neighbors
+  41 = max # of special neighbors
+  special bonds CPU = 0.000178751 secs
+  read_data CPU = 0.0385782 secs
+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
+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
+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
+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
+WARNING: Bond/react: Atom affected by reaction rxn1 too close to template edge (../fix_bond_react.cpp:1785)
+WARNING: Bond/react: Atom affected by reaction rxn2 too close to template edge (../fix_bond_react.cpp:1785)
+dynamic group bond_react_MASTER_group defined
+dynamic group statted_grp_REACT defined
+PPPM initialization ...
+  using 12-bit tables for long-range coulomb (../kspace.cpp:319)
+  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
+Setting up Verlet run ...
+  Unit style    : real
+  Current step  : 0
+  Time step     : 1
+WARNING: Inconsistent image flags (../domain.cpp:784)
+Per MPI rank memory allocation (min/avg/max) = 34.42 | 34.77 | 35.45 Mbytes
+Step Temp Press Density f_myrxns[1] f_myrxns[2] 
+       0          300    346.78165 0.0034851739            0            0 
+      50    293.70542   -52.547388 0.0034851739            1            0 
+     100    276.36755     54.81826 0.0034851739            1            1 
+     150    448.65869    16.874435 0.0034851739            1            1 
+     200    379.84257    11.578545 0.0034851739            1            1 
+     250    298.21983    90.656585 0.0034851739            1            1 
+     300     333.3111   -30.139607 0.0034851739            1            1 
+     350    266.57108    6.4505134 0.0034851739            1            1 
+     400    264.05476    10.513204 0.0034851739            1            1 
+     450    250.70418   -18.635379 0.0034851739            1            1 
+     500    261.21632    10.231013 0.0034851739            1            1 
+     550    309.89024   -8.8299506 0.0034851739            1            1 
+     600    373.45851    30.368993 0.0034851739            1            1 
+     650    338.26242    9.0362267 0.0034851739            1            1 
+     700    295.67794   -5.6007538 0.0034851739            1            1 
+     750    310.86563   -59.228181 0.0034851739            1            1 
+     800    286.22678   -9.9022407 0.0034851739            1            1 
+     850    218.42135    27.845352 0.0034851739            1            1 
+     900    259.62551    24.216336 0.0034851739            1            1 
+     950    250.21307   -14.560985 0.0034851739            1            1 
+    1000    274.29245  -0.38768626 0.0034851739            1            1 
+Loop time of 0.271242 on 4 procs for 1000 steps with 44 atoms
+
+Performance: 318.535 ns/day, 0.075 hours/ns, 3686.747 timesteps/s
+98.6% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.00023773 | 0.0077322  | 0.016042   |   8.4 |  2.85
+Bond    | 0.00073385 | 0.032108   | 0.08446    |  19.4 | 11.84
+Kspace  | 0.041659   | 0.098095   | 0.13373    |  12.3 | 36.16
+Neigh   | 0.028894   | 0.029247   | 0.029558   |   0.1 | 10.78
+Comm    | 0.012367   | 0.013642   | 0.01503    |   0.9 |  5.03
+Output  | 0.032475   | 0.040504   | 0.061019   |   5.9 | 14.93
+Modify  | 0.032934   | 0.049086   | 0.0577     |   4.3 | 18.10
+Other   |            | 0.0008281  |            |       |  0.31
+
+Nlocal:    11 ave 21 max 0 min
+Histogram: 1 1 0 0 0 0 0 0 0 2
+Nghost:    32.5 ave 43 max 23 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Neighs:    185 ave 376 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+
+Total # of neighbors = 740
+Ave neighs/atom = 16.8182
+Ave special neighs/atom = 9.77273
+Neighbor list builds = 1000
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:00

examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.1

@@ -0,0 +1,147 @@
+LAMMPS (5 Jun 2019)
+Reading data file ...
+  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
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:   0          0          0         
+  special bond factors coul: 0          0          0         
+  4 = max # of 1-2 neighbors
+  6 = max # of 1-3 neighbors
+  12 = max # of 1-4 neighbors
+  41 = max # of special neighbors
+  special bonds CPU = 0.000217102 secs
+  read_data CPU = 0.00630778 secs
+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
+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
+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
+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
+WARNING: Bond/react: Atom affected by reaction rxn1 too close to template edge (../fix_bond_react.cpp:1785)
+WARNING: Bond/react: Atom affected by reaction rxn2 too close to template edge (../fix_bond_react.cpp:1785)
+dynamic group bond_react_MASTER_group defined
+PPPM initialization ...
+  using 12-bit tables for long-range coulomb (../kspace.cpp:319)
+  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
+Setting up Verlet run ...
+  Unit style    : real
+  Current step  : 0
+  Time step     : 1
+WARNING: Inconsistent image flags (../domain.cpp:784)
+Per MPI rank memory allocation (min/avg/max) = 34.35 | 34.35 | 34.35 Mbytes
+Step Temp Press Density f_myrxns[1] f_myrxns[2] 
+       0          300    346.78165 0.0034851739            0            0 
+      50    416.49412   -20.293038 0.0034851739            1            0 
+     100    746.49323    91.912227 0.0034851739            1            1 
+     150    515.15907   -1.4024709 0.0034851739            1            1 
+     200    441.14572   -19.333087 0.0034851739            1            1 
+     250    376.40996    30.717679 0.0034851739            1            1 
+     300    326.15127   -3.0433799 0.0034851739            1            1 
+     350    326.21116     6.235391 0.0034851739            1            1 
+     400    366.48556    3.9807338 0.0034851739            1            1 
+     450    313.79097    7.6674629 0.0034851739            1            1 
+     500    278.89836    14.102052 0.0034851739            1            1 
+     550    267.50214    18.241417 0.0034851739            1            1 
+     600    276.28064    7.4649611 0.0034851739            1            1 
+     650    255.26713   -8.5258573 0.0034851739            1            1 
+     700    258.59752   -5.3341215 0.0034851739            1            1 
+     750    263.71264    33.369869 0.0034851739            1            1 
+     800    246.22976   -15.349137 0.0034851739            1            1 
+     850    255.93887    16.331669 0.0034851739            1            1 
+     900    239.72525  -0.20075789 0.0034851739            1            1 
+     950    213.73064     12.17619 0.0034851739            1            1 
+    1000    218.25094   -9.0955642 0.0034851739            1            1 
+Loop time of 0.348252 on 1 procs for 1000 steps with 44 atoms
+
+Performance: 248.096 ns/day, 0.097 hours/ns, 2871.483 timesteps/s
+91.8% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.031941   | 0.031941   | 0.031941   |   0.0 |  9.17
+Bond    | 0.13031    | 0.13031    | 0.13031    |   0.0 | 37.42
+Kspace  | 0.037554   | 0.037554   | 0.037554   |   0.0 | 10.78
+Neigh   | 0.047397   | 0.047397   | 0.047397   |   0.0 | 13.61
+Comm    | 0.0025814  | 0.0025814  | 0.0025814  |   0.0 |  0.74
+Output  | 0.083526   | 0.083526   | 0.083526   |   0.0 | 23.98
+Modify  | 0.013602   | 0.013602   | 0.013602   |   0.0 |  3.91
+Other   |            | 0.001336   |            |       |  0.38
+
+Nlocal:    44 ave 44 max 44 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    3 ave 3 max 3 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    818 ave 818 max 818 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 818
+Ave neighs/atom = 18.5909
+Ave special neighs/atom = 9.77273
+Neighbor list builds = 1000
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:00

examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.4

@@ -0,0 +1,147 @@
+LAMMPS (5 Jun 2019)
+Reading data file ...
+  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
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:   0          0          0         
+  special bond factors coul: 0          0          0         
+  4 = max # of 1-2 neighbors
+  6 = max # of 1-3 neighbors
+  12 = max # of 1-4 neighbors
+  41 = max # of special neighbors
+  special bonds CPU = 0.000163256 secs
+  read_data CPU = 0.0244579 secs
+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
+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
+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
+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
+WARNING: Bond/react: Atom affected by reaction rxn1 too close to template edge (../fix_bond_react.cpp:1785)
+WARNING: Bond/react: Atom affected by reaction rxn2 too close to template edge (../fix_bond_react.cpp:1785)
+dynamic group bond_react_MASTER_group defined
+PPPM initialization ...
+  using 12-bit tables for long-range coulomb (../kspace.cpp:319)
+  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
+Setting up Verlet run ...
+  Unit style    : real
+  Current step  : 0
+  Time step     : 1
+WARNING: Inconsistent image flags (../domain.cpp:784)
+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    416.49412   -20.293038 0.0034851739            1            0 
+     100    746.49323    91.912227 0.0034851739            1            1 
+     150    515.15907   -1.4024709 0.0034851739            1            1 
+     200    441.14572   -19.333087 0.0034851739            1            1 
+     250    376.40996    30.717679 0.0034851739            1            1 
+     300    326.15127   -3.0433799 0.0034851739            1            1 
+     350    326.21116     6.235391 0.0034851739            1            1 
+     400    366.48556    3.9807338 0.0034851739            1            1 
+     450    313.79097    7.6674629 0.0034851739            1            1 
+     500    278.89836    14.102052 0.0034851739            1            1 
+     550    267.50214    18.241417 0.0034851739            1            1 
+     600    276.28064    7.4649611 0.0034851739            1            1 
+     650    255.26713   -8.5258573 0.0034851739            1            1 
+     700    258.59752   -5.3341215 0.0034851739            1            1 
+     750    263.71264    33.369869 0.0034851739            1            1 
+     800    246.22976   -15.349137 0.0034851739            1            1 
+     850    255.93887    16.331669 0.0034851739            1            1 
+     900    239.72525  -0.20075789 0.0034851739            1            1 
+     950    213.73064     12.17619 0.0034851739            1            1 
+    1000    218.25094   -9.0955642 0.0034851739            1            1 
+Loop time of 0.254903 on 4 procs for 1000 steps with 44 atoms
+
+Performance: 338.952 ns/day, 0.071 hours/ns, 3923.053 timesteps/s
+99.8% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.00014252 | 0.0090715  | 0.021332   |   9.6 |  3.56
+Bond    | 0.00047028 | 0.037261   | 0.10789    |  22.7 | 14.62
+Kspace  | 0.051006   | 0.12756    | 0.1693     |  13.6 | 50.04
+Neigh   | 0.035644   | 0.036088   | 0.036523   |   0.2 | 14.16
+Comm    | 0.013984   | 0.016074   | 0.018676   |   1.6 |  6.31
+Output  | 0.0002816  | 0.00033726 | 0.00044251 |   0.0 |  0.13
+Modify  | 0.023697   | 0.027803   | 0.033552   |   2.5 | 10.91
+Other   |            | 0.0007123  |            |       |  0.28
+
+Nlocal:    11 ave 29 max 0 min
+Histogram: 1 1 0 0 1 0 0 0 0 1
+Nghost:    25 ave 31 max 12 min
+Histogram: 1 0 0 0 0 0 0 0 2 1
+Neighs:    204.5 ave 443 max 0 min
+Histogram: 2 0 0 0 0 0 0 0 1 1
+
+Total # of neighbors = 818
+Ave neighs/atom = 18.5909
+Ave special neighs/atom = 9.77273
+Neighbor list builds = 1000
+Dangerous builds = 0
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:00

examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/BNCH-old.ILP

@@ -1 +0,0 @@
-../../../../../potentials/BNCH-old.ILP

examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/CH.airebo

@@ -1 +0,0 @@
-../../../../../potentials/CH.airebo

examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/in.bilayer-graphene

@@ -1,61 +0,0 @@
-# Initialization
-units           metal
-boundary        p p p
-atom_style      full
-processors      * * 1     # domain decomposition over x and y
-
-# System and atom definition
-# we use 2 atom types so that inter- and intra-layer
-# interactions can be specified separately
-# read lammps data file
-read_data       Bi_gr_AB_stack_2L_noH_300K.data
-mass            1 12.0107   # carbon mass (g/mole) | membrane
-mass            2 12.0107   # carbon mass (g/mole) | adsorbate
-# Separate atom groups
-group membrane  type 1
-group adsorbate type 2
-
-######################## Potential defition ########################
-pair_style  hybrid/overlay  rebo  ilp/graphene/hbn 16.0
-####################################################################
-pair_coeff  * * rebo               CH.airebo      NULL C  # chemical
-pair_coeff  * * ilp/graphene/hbn   BNCH-old.ILP   C    C  # long range
-####################################################################
-# Neighbor update settings
-neighbor        2.0 bin
-neigh_modify    every 1
-neigh_modify    delay 0
-neigh_modify    check yes
-
-# calculate the COM
-variable        adsxcom equal xcm(adsorbate,x)
-variable        adsycom equal xcm(adsorbate,y)
-variable        adszcom equal xcm(adsorbate,z)
-variable        adsvxcom equal vcm(adsorbate,x)
-variable        adsvycom equal vcm(adsorbate,y)
-variable        adsvzcom equal vcm(adsorbate,z)
-
-#### Simulation settings ####
-timestep  0.001
-#velocity  adsorbate create 300.0 12345
-fix       subf membrane setforce 0.0 0.0 0.0
-fix       thermostat all nve
-
-compute   0 all pair rebo
-compute   1 all pair ilp/graphene/hbn
-variable  REBO     equal c_0
-variable  ILP      equal c_1
-
-############################
-
-# Output
-thermo          100
-thermo_style    custom step etotal pe ke v_REBO v_ILP temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
-thermo_modify   line one format float %.10f
-thermo_modify   flush yes norm no lost warn
-
-#dump            1 all custom 1000 traj.lammpstrj id mol type xu yu zu
-#dump_modify     1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
-
-###### Run molecular dynamics ######
-run 1000

examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/log.16Mar18.bilayer-graphene.g++.1

@@ -1,137 +0,0 @@
-LAMMPS (8 Mar 2018)
-  using 1 OpenMP thread(s) per MPI task
-# Initialization
-units           metal
-boundary        p p p
-atom_style      full
-processors      * * 1     # domain decomposition over x and y
-
-# System and atom definition
-# we use 2 atom types so that inter- and intra-layer
-# interactions can be specified separately
-# read lammps data file
-read_data       Bi_gr_AB_stack_2L_noH_300K.data
-  orthogonal box = (0 0 0) to (42.6 41.8117 100)
-  1 by 1 by 1 MPI processor grid
-  reading atoms ...
-  1360 atoms
-  reading velocities ...
-  1360 velocities
-  0 = max # of 1-2 neighbors
-  0 = max # of 1-3 neighbors
-  0 = max # of 1-4 neighbors
-  1 = max # of special neighbors
-mass            1 12.0107   # carbon mass (g/mole) | membrane
-mass            2 12.0107   # carbon mass (g/mole) | adsorbate
-# Separate atom groups
-group membrane  type 1
-680 atoms in group membrane
-group adsorbate type 2
-680 atoms in group adsorbate
-
-######################## Potential defition ########################
-pair_style  hybrid/overlay  rebo  ilp/graphene/hbn 16.0
-####################################################################
-pair_coeff  * * rebo               CH.airebo      NULL C  # chemical
-Reading potential file CH.airebo with DATE: 2011-10-25
-pair_coeff  * * ilp/graphene/hbn   BNCH-old.ILP   C    C  # long range
-####################################################################
-# Neighbor update settings
-neighbor        2.0 bin
-neigh_modify    every 1
-neigh_modify    delay 0
-neigh_modify    check yes
-
-# calculate the COM
-variable        adsxcom equal xcm(adsorbate,x)
-variable        adsycom equal xcm(adsorbate,y)
-variable        adszcom equal xcm(adsorbate,z)
-variable        adsvxcom equal vcm(adsorbate,x)
-variable        adsvycom equal vcm(adsorbate,y)
-variable        adsvzcom equal vcm(adsorbate,z)
-
-#### Simulation settings ####
-timestep  0.001
-#velocity  adsorbate create 300.0 12345
-fix       subf membrane setforce 0.0 0.0 0.0
-fix       thermostat all nve
-
-compute   0 all pair rebo
-compute   1 all pair ilp/graphene/hbn
-variable  REBO     equal c_0
-variable  ILP      equal c_1
-
-############################
-
-# Output
-thermo          100
-thermo_style    custom step etotal pe ke v_REBO v_ILP temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
-thermo_modify   line one format float %.10f
-thermo_modify   flush yes norm no lost warn
-
-#dump            1 all custom 1000 traj.lammpstrj id mol type xu yu zu
-#dump_modify     1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
-
-###### Run molecular dynamics ######
-run 1000
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 18
-  ghost atom cutoff = 18
-  binsize = 9, bins = 5 5 12
-  2 neighbor lists, perpetual/occasional/extra = 2 0 0
-  (1) pair rebo, perpetual, skip from (2)
-      attributes: full, newton on, ghost
-      pair build: skip/ghost
-      stencil: none
-      bin: none
-  (2) pair ilp/graphene/hbn, perpetual
-      attributes: full, newton on, ghost
-      pair build: full/bin/ghost
-      stencil: full/ghost/bin/3d
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 16.96 | 16.96 | 16.96 Mbytes
-Step TotEng PotEng KinEng v_REBO v_ILP Temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom 
-       0 -5029.3801131277 -5044.0700799791 14.6899668514 -5011.2636297759 -32.8064502032 83.6251135127 22.0155657205 20.2812150219 3.4623630945 0.0282287195 0.0535565745 0.2193320108 
-     100 -5029.3895815657 -5045.3201249690 15.9305434033 -5012.4897058028 -32.8304191662 90.6873047362 22.0181751545 20.2867946176 3.4502536831 0.0239131349 0.0576557373 -0.4387830564 
-     200 -5029.3874064119 -5045.8119502228 16.4245438109 -5012.7276250747 -33.0843251481 93.4994853617 22.0202931358 20.2926890775 3.3883512918 0.0180268639 0.0596894423 -0.6964675465 
-     300 -5029.3851410393 -5044.9928147367 15.6076736974 -5012.1131531405 -32.8796615962 88.8493144891 22.0216852689 20.2985091183 3.3368274018 0.0093519893 0.0546775051 -0.2110676539 
-     400 -5029.3900102082 -5045.6706717598 16.2806615516 -5012.7330095297 -32.9376622301 92.6804113372 22.0220931529 20.3035219616 3.3560233852 -0.0015365116 0.0454268927 0.5478139709 
-     500 -5029.3985510533 -5046.0433160610 16.6447650078 -5013.0924334585 -32.9508826025 94.7531316612 22.0214795944 20.3074656871 3.4232399722 -0.0107212024 0.0332249366 0.6595923534 
-     600 -5029.3929936746 -5045.4367231195 16.0437294449 -5012.7046931021 -32.7320300174 91.3316353653 22.0200027176 20.3101652565 3.4651727438 -0.0178110391 0.0210056002 0.1144372537 
-     700 -5029.3934435811 -5045.6074608403 16.2140172592 -5012.7886962164 -32.8187646239 92.3010274644 22.0178838793 20.3116257077 3.4432436715 -0.0242636237 0.0078323424 -0.5162836955 
-     800 -5029.3892931255 -5046.2270462380 16.8377531124 -5013.2383770824 -32.9886691555 95.8517489911 22.0151485191 20.3116305041 3.3780520461 -0.0302821178 -0.0083184719 -0.6710801515 
-     900 -5029.3930414672 -5046.0272003818 16.6341589146 -5013.2317798384 -32.7954205434 94.6927546874 22.0119224940 20.3099187654 3.3350551183 -0.0341747588 -0.0256858066 -0.0799872839 
-    1000 -5029.3908907831 -5045.6437703691 16.2528795861 -5012.6800867885 -32.9636835807 92.5222578135 22.0084902521 20.3065746721 3.3658243730 -0.0336536245 -0.0406018547 0.6191660974 
-Loop time of 137.46 on 1 procs for 1000 steps with 1360 atoms
-
-Performance: 0.629 ns/day, 38.183 hours/ns, 7.275 timesteps/s
-95.1% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 137.33     | 137.33     | 137.33     |   0.0 | 99.90
-Bond    | 0.00071788 | 0.00071788 | 0.00071788 |   0.0 |  0.00
-Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.067907   | 0.067907   | 0.067907   |   0.0 |  0.05
-Output  | 0.0016029  | 0.0016029  | 0.0016029  |   0.0 |  0.00
-Modify  | 0.036542   | 0.036542   | 0.036542   |   0.0 |  0.03
-Other   |            | 0.02574    |            |       |  0.02
-
-Nlocal:    1360 ave 1360 max 1360 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    7964 ave 7964 max 7964 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    0 ave 0 max 0 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-FullNghs:  265206 ave 265206 max 265206 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 265206
-Ave neighs/atom = 195.004
-Ave special neighs/atom = 0
-Neighbor list builds = 0
-Dangerous builds = 0
-Total wall time: 0:02:17

examples/USER/misc/ilp_graphene_hbn/bilayer-graphene/log.16Mar18.bilayer-graphene.g++.4

@@ -1,137 +0,0 @@
-LAMMPS (8 Mar 2018)
-  using 1 OpenMP thread(s) per MPI task
-# Initialization
-units           metal
-boundary        p p p
-atom_style      full
-processors      * * 1     # domain decomposition over x and y
-
-# System and atom definition
-# we use 2 atom types so that inter- and intra-layer
-# interactions can be specified separately
-# read lammps data file
-read_data       Bi_gr_AB_stack_2L_noH_300K.data
-  orthogonal box = (0 0 0) to (42.6 41.8117 100)
-  2 by 2 by 1 MPI processor grid
-  reading atoms ...
-  1360 atoms
-  reading velocities ...
-  1360 velocities
-  0 = max # of 1-2 neighbors
-  0 = max # of 1-3 neighbors
-  0 = max # of 1-4 neighbors
-  1 = max # of special neighbors
-mass            1 12.0107   # carbon mass (g/mole) | membrane
-mass            2 12.0107   # carbon mass (g/mole) | adsorbate
-# Separate atom groups
-group membrane  type 1
-680 atoms in group membrane
-group adsorbate type 2
-680 atoms in group adsorbate
-
-######################## Potential defition ########################
-pair_style  hybrid/overlay  rebo  ilp/graphene/hbn 16.0
-####################################################################
-pair_coeff  * * rebo               CH.airebo      NULL C  # chemical
-Reading potential file CH.airebo with DATE: 2011-10-25
-pair_coeff  * * ilp/graphene/hbn   BNCH-old.ILP   C    C  # long range
-####################################################################
-# Neighbor update settings
-neighbor        2.0 bin
-neigh_modify    every 1
-neigh_modify    delay 0
-neigh_modify    check yes
-
-# calculate the COM
-variable        adsxcom equal xcm(adsorbate,x)
-variable        adsycom equal xcm(adsorbate,y)
-variable        adszcom equal xcm(adsorbate,z)
-variable        adsvxcom equal vcm(adsorbate,x)
-variable        adsvycom equal vcm(adsorbate,y)
-variable        adsvzcom equal vcm(adsorbate,z)
-
-#### Simulation settings ####
-timestep  0.001
-#velocity  adsorbate create 300.0 12345
-fix       subf membrane setforce 0.0 0.0 0.0
-fix       thermostat all nve
-
-compute   0 all pair rebo
-compute   1 all pair ilp/graphene/hbn
-variable  REBO     equal c_0
-variable  ILP      equal c_1
-
-############################
-
-# Output
-thermo          100
-thermo_style    custom step etotal pe ke v_REBO v_ILP temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
-thermo_modify   line one format float %.10f
-thermo_modify   flush yes norm no lost warn
-
-#dump            1 all custom 1000 traj.lammpstrj id mol type xu yu zu
-#dump_modify     1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
-
-###### Run molecular dynamics ######
-run 1000
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 18
-  ghost atom cutoff = 18
-  binsize = 9, bins = 5 5 12
-  2 neighbor lists, perpetual/occasional/extra = 2 0 0
-  (1) pair rebo, perpetual, skip from (2)
-      attributes: full, newton on, ghost
-      pair build: skip/ghost
-      stencil: none
-      bin: none
-  (2) pair ilp/graphene/hbn, perpetual
-      attributes: full, newton on, ghost
-      pair build: full/bin/ghost
-      stencil: full/ghost/bin/3d
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 11.13 | 11.13 | 11.13 Mbytes
-Step TotEng PotEng KinEng v_REBO v_ILP Temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom 
-       0 -5029.3801131277 -5044.0700799791 14.6899668514 -5011.2636297759 -32.8064502032 83.6251135127 22.0155657205 20.2812150219 3.4623630945 0.0282287195 0.0535565745 0.2193320108 
-     100 -5029.3895815657 -5045.3201249690 15.9305434033 -5012.4897058028 -32.8304191662 90.6873047362 22.0181751545 20.2867946176 3.4502536831 0.0239131349 0.0576557373 -0.4387830564 
-     200 -5029.3874064119 -5045.8119502228 16.4245438109 -5012.7276250747 -33.0843251481 93.4994853617 22.0202931358 20.2926890775 3.3883512918 0.0180268639 0.0596894423 -0.6964675465 
-     300 -5029.3851410393 -5044.9928147367 15.6076736974 -5012.1131531405 -32.8796615962 88.8493144891 22.0216852689 20.2985091183 3.3368274018 0.0093519893 0.0546775051 -0.2110676539 
-     400 -5029.3900102082 -5045.6706717598 16.2806615516 -5012.7330095297 -32.9376622301 92.6804113371 22.0220931529 20.3035219616 3.3560233852 -0.0015365116 0.0454268927 0.5478139709 
-     500 -5029.3985510533 -5046.0433160611 16.6447650078 -5013.0924334585 -32.9508826025 94.7531316612 22.0214795944 20.3074656871 3.4232399722 -0.0107212024 0.0332249366 0.6595923534 
-     600 -5029.3929936746 -5045.4367231195 16.0437294449 -5012.7046931021 -32.7320300174 91.3316353653 22.0200027176 20.3101652565 3.4651727438 -0.0178110391 0.0210056002 0.1144372537 
-     700 -5029.3934435811 -5045.6074608403 16.2140172592 -5012.7886962164 -32.8187646239 92.3010274643 22.0178838793 20.3116257077 3.4432436715 -0.0242636237 0.0078323424 -0.5162836955 
-     800 -5029.3892931255 -5046.2270462380 16.8377531124 -5013.2383770824 -32.9886691555 95.8517489911 22.0151485191 20.3116305041 3.3780520461 -0.0302821178 -0.0083184719 -0.6710801515 
-     900 -5029.3930414671 -5046.0272003818 16.6341589146 -5013.2317798384 -32.7954205434 94.6927546874 22.0119224940 20.3099187654 3.3350551183 -0.0341747588 -0.0256858066 -0.0799872839 
-    1000 -5029.3908907831 -5045.6437703692 16.2528795861 -5012.6800867885 -32.9636835807 92.5222578135 22.0084902521 20.3065746721 3.3658243730 -0.0336536245 -0.0406018547 0.6191660974 
-Loop time of 36.0917 on 4 procs for 1000 steps with 1360 atoms
-
-Performance: 2.394 ns/day, 10.025 hours/ns, 27.707 timesteps/s
-97.6% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 33.204     | 34.289     | 35.893     |  17.3 | 95.01
-Bond    | 0.00038719 | 0.00065947 | 0.00097609 |   0.0 |  0.00
-Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.1539     | 1.7595     | 2.8464     |  76.7 |  4.88
-Output  | 0.0013447  | 0.0014529  | 0.0016887  |   0.4 |  0.00
-Modify  | 0.010811   | 0.012037   | 0.013764   |   1.0 |  0.03
-Other   |            | 0.0287     |            |       |  0.08
-
-Nlocal:    340 ave 344 max 334 min
-Histogram: 1 0 0 0 0 0 1 0 1 1
-Nghost:    4628 ave 4634 max 4624 min
-Histogram: 1 0 1 0 1 0 0 0 0 1
-Neighs:    0 ave 0 max 0 min
-Histogram: 4 0 0 0 0 0 0 0 0 0
-FullNghs:  66301.5 ave 67860 max 63963 min
-Histogram: 1 0 0 0 0 0 1 0 1 1
-
-Total # of neighbors = 265206
-Ave neighs/atom = 195.004
-Ave special neighs/atom = 0
-Neighbor list builds = 0
-Dangerous builds = 0
-Total wall time: 0:00:36

examples/USER/misc/ilp_graphene_hbn/gr-hBN/BNC.tersoff

@@ -1 +0,0 @@
-../../../../../potentials/BNC.tersoff

examples/USER/misc/ilp_graphene_hbn/gr-hBN/BNCH-old.ILP

@@ -1 +0,0 @@
-../../../../../potentials/BNCH-old.ILP

examples/USER/misc/ilp_graphene_hbn/gr-hBN/CH.airebo

@@ -1 +0,0 @@
-../../../../../potentials/CH.airebo

examples/USER/misc/ilp_graphene_hbn/gr-hBN/in.grhBN

@@ -1,71 +0,0 @@
-# Initialization
-units           metal
-boundary        p p p
-atom_style      full
-processors      * * 1     # domain decomposition over x and y
-
-# System and atom definition
-# we use 2 atom types so that inter- and intra-layer
-# interactions can be specified separately
-read_data       gr_hBN_Cstack_2L_noH.data
-mass            1 10.8110   # boron    mass (g/mole) | membrane
-mass            2 14.0067   # nitrogen mass (g/mole) | membrane
-mass            3 12.0107   # carbon   mass (g/mole) | adsorbate
-# Separate atom groups
-group membrane  type 1 2
-group adsorbate type 3
-
-######################## Potential defition ########################
-pair_style  hybrid/overlay rebo tersoff ilp/graphene/hbn 16.0 coul/shield 16.0
-####################################################################
-pair_coeff  * * rebo               CH.airebo     NULL NULL C    # chemical
-pair_coeff  * * tersoff            BNC.tersoff   B    N    NULL # chemical
-pair_coeff  * * ilp/graphene/hbn   BNCH-old.ILP  B    N    C    # long range
-pair_coeff  1 1 coul/shield 0.70
-pair_coeff  1 2 coul/shield 0.69498201415576216335
-pair_coeff  2 2 coul/shield 0.69
-####################################################################
-# Neighbor update settings
-neighbor        2.0 bin
-neigh_modify    every 1
-neigh_modify    delay 0
-neigh_modify    check yes
-
-# calculate the COM
-variable        adsxcom equal xcm(adsorbate,x)
-variable        adsycom equal xcm(adsorbate,y)
-variable        adszcom equal xcm(adsorbate,z)
-variable        adsvxcom equal vcm(adsorbate,x)
-variable        adsvycom equal vcm(adsorbate,y)
-variable        adsvzcom equal vcm(adsorbate,z)
-
-#### Simulation settings ####
-timestep  0.001
-velocity  all create 300.0 12345
-fix       thermostat all nve
-
-compute   0 all pair rebo
-compute   1 all pair tersoff
-compute   2 all pair ilp/graphene/hbn
-compute   3 all pair coul/shield
-variable  REBO     equal  c_0
-variable  Tersoff  equal  c_1
-variable  EILP     equal  c_2
-variable  Ecoul    equal  c_3
-
-# Calculate the pair potential between the substrate and slider
-compute         sldsub adsorbate group/group membrane
-variable        Evdw equal c_sldsub
-
-############################
-
-# Output
-thermo          100
-thermo_style    custom step etotal pe ke v_Evdw v_Tersoff v_REBO v_EILP v_Ecoul temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
-thermo_modify   line one format float %.10f
-
-#dump            1 all custom 1000 traj.lammpstrj id mol type xu yu zu
-#dump_modify     1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
-
-###### Run molecular dynamics ######
-run 1000

examples/USER/misc/ilp_graphene_hbn/gr-hBN/log.16Mar18.grhBN.g++.1

@@ -1,171 +0,0 @@
-LAMMPS (8 Mar 2018)
-  using 1 OpenMP thread(s) per MPI task
-# Initialization
-units           metal
-boundary        p p p
-atom_style      full
-processors      * * 1     # domain decomposition over x and y
-
-# System and atom definition
-# we use 2 atom types so that inter- and intra-layer
-# interactions can be specified separately
-read_data       gr_hBN_Cstack_2L_noH.data
-  orthogonal box = (0 0 0) to (44.583 42.9 100)
-  1 by 1 by 1 MPI processor grid
-  reading atoms ...
-  1440 atoms
-  0 = max # of 1-2 neighbors
-  0 = max # of 1-3 neighbors
-  0 = max # of 1-4 neighbors
-  1 = max # of special neighbors
-mass            1 10.8110   # boron    mass (g/mole) | membrane
-mass            2 14.0067   # nitrogen mass (g/mole) | membrane
-mass            3 12.0107   # carbon   mass (g/mole) | adsorbate
-# Separate atom groups
-group membrane  type 1 2
-720 atoms in group membrane
-group adsorbate type 3
-720 atoms in group adsorbate
-
-######################## Potential defition ########################
-pair_style  hybrid/overlay rebo tersoff ilp/graphene/hbn 16.0 coul/shield 16.0
-####################################################################
-pair_coeff  * * rebo               CH.airebo     NULL NULL C    # chemical
-Reading potential file CH.airebo with DATE: 2011-10-25
-pair_coeff  * * tersoff            BNC.tersoff   B    N    NULL # chemical
-Reading potential file BNC.tersoff with DATE: 2013-03-21
-pair_coeff  * * ilp/graphene/hbn   BNCH-old.ILP  B    N    C    # long range
-pair_coeff  1 1 coul/shield 0.70
-pair_coeff  1 2 coul/shield 0.69498201415576216335
-pair_coeff  2 2 coul/shield 0.69
-####################################################################
-# Neighbor update settings
-neighbor        2.0 bin
-neigh_modify    every 1
-neigh_modify    delay 0
-neigh_modify    check yes
-
-# calculate the COM
-variable        adsxcom equal xcm(adsorbate,x)
-variable        adsycom equal xcm(adsorbate,y)
-variable        adszcom equal xcm(adsorbate,z)
-variable        adsvxcom equal vcm(adsorbate,x)
-variable        adsvycom equal vcm(adsorbate,y)
-variable        adsvzcom equal vcm(adsorbate,z)
-
-#### Simulation settings ####
-timestep  0.001
-velocity  all create 300.0 12345
-fix       thermostat all nve
-
-compute   0 all pair rebo
-compute   1 all pair tersoff
-compute   2 all pair ilp/graphene/hbn
-compute   3 all pair coul/shield
-variable  REBO     equal  c_0
-variable  Tersoff  equal  c_1
-variable  EILP     equal  c_2
-variable  Ecoul    equal  c_3
-
-# Calculate the pair potential between the substrate and slider
-compute         sldsub adsorbate group/group membrane
-variable        Evdw equal c_sldsub
-
-############################
-
-# Output
-thermo          100
-thermo_style    custom step etotal pe ke v_Evdw v_Tersoff v_REBO v_EILP v_Ecoul temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
-thermo_modify   line one format float %.10f
-
-#dump            1 all custom 1000 traj.lammpstrj id mol type xu yu zu
-#dump_modify     1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
-
-###### Run molecular dynamics ######
-run 1000
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 18
-  ghost atom cutoff = 18
-  binsize = 9, bins = 5 5 12
-  7 neighbor lists, perpetual/occasional/extra = 6 1 0
-  (1) pair rebo, perpetual, skip from (3)
-      attributes: full, newton on, ghost
-      pair build: skip/ghost
-      stencil: none
-      bin: none
-  (2) pair tersoff, perpetual, skip from (6)
-      attributes: full, newton on
-      pair build: skip
-      stencil: none
-      bin: none
-  (3) pair ilp/graphene/hbn, perpetual
-      attributes: full, newton on, ghost
-      pair build: full/bin/ghost
-      stencil: full/ghost/bin/3d
-      bin: standard
-  (4) pair coul/shield, perpetual, half/full from (2)
-      attributes: half, newton on
-      pair build: halffull/newton/skip
-      stencil: none
-      bin: none
-  (5) compute group/group, occasional, copy from (7)
-      attributes: half, newton on
-      pair build: copy
-      stencil: none
-      bin: none
-  (6) neighbor class addition, perpetual, copy from (3)
-      attributes: full, newton on
-      pair build: copy
-      stencil: none
-      bin: none
-  (7) neighbor class addition, perpetual, half/full from (6)
-      attributes: half, newton on
-      pair build: halffull/newton
-      stencil: none
-      bin: none
-Per MPI rank memory allocation (min/avg/max) = 25.93 | 25.93 | 25.93 Mbytes
-Step TotEng PotEng KinEng v_Evdw v_Tersoff v_REBO v_EILP v_Ecoul Temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom 
-       0 -10708.4531746010 -10764.2547791975 55.8016045965 -66.8250335416 -5401.7347845703 -5322.2780762734 -40.2419183538 0.0000000000 300.0000000000 21.6722857297 22.1650000000 3.3300000000 0.1682661410 -0.0842226772 0.1056563755 
-     100 -10708.2491256387 -10738.4532793285 30.2041536898 -68.8603937785 -5389.4304136167 -5309.6361134033 -39.3867523085 0.0000000000 162.3832535368 21.6879886706 22.1574778199 3.3223279482 0.1346509596 -0.0580689194 -0.1274433614 
-     200 -10708.1985754490 -10736.7142682477 28.5156927987 -70.0276479251 -5388.8677096501 -5308.3263464524 -39.5202121452 0.0000000000 153.3057678444 21.6968427596 22.1541506320 3.3143666142 0.0334706445 -0.0081639882 -0.0055006321 
-     300 -10708.1878214116 -10736.9033486636 28.7155272520 -68.2422175765 -5388.5952548022 -5308.9505338445 -39.3575600169 0.0000000000 154.3801157314 21.6939171741 22.1551483321 3.3251666346 -0.0896064591 0.0248921781 0.1717740196 
-     400 -10708.2036103906 -10738.2295882994 30.0259779088 -67.4993928655 -5389.4510311345 -5309.1985887571 -39.5799684078 0.0000000000 161.4253467759 21.6806789605 22.1589742804 3.3300374170 -0.1615300496 0.0532638209 -0.1185426799 
-     500 -10708.1853082161 -10736.0245173060 27.8392090900 -69.9737746636 -5387.9379921501 -5308.5551693329 -39.5313558230 0.0000000000 149.6688632411 21.6641276776 22.1655659011 3.3143210751 -0.1579504334 0.0766822604 -0.1154029266 
-     600 -10708.1781001285 -10736.4254568396 28.2473567110 -69.9368770273 -5388.3515507737 -5308.6700567475 -39.4038493184 0.0000000000 151.8631421907 21.6516789999 22.1733266592 3.3149997184 -0.0805825343 0.0684349609 0.1419617624 
-     700 -10708.1867253590 -10736.6143955088 28.4276701498 -67.1597096579 -5387.8570063253 -5309.0676141640 -39.6897750195 0.0000000000 152.8325414049 21.6489884054 22.1774523945 3.3315351816 0.0259900263 0.0094570835 0.0707953688 
-     800 -10708.1733385055 -10736.0277775931 27.8544390876 -68.6354557276 -5388.1933954711 -5308.5094712719 -39.3249108500 0.0000000000 149.7507425941 21.6565725156 22.1751617515 3.3227650180 0.1222442823 -0.0531420670 -0.1677749693 
-     900 -10708.1827888042 -10737.2646739167 29.0818851126 -70.2218493216 -5387.9824857335 -5309.6527953488 -39.6293928345 0.0000000000 156.3497250098 21.6716950833 22.1680989334 3.3131455846 0.1650154385 -0.0820901425 0.0072049300 
-    1000 -10708.1804322657 -10736.1966428009 28.0162105352 -68.3753745517 -5388.2611029662 -5308.4521913187 -39.4833485160 0.0000000000 150.6204565501 21.6865468141 22.1602434319 3.3246621699 0.1213363701 -0.0688593023 0.1701174943 
-Loop time of 149.449 on 1 procs for 1000 steps with 1440 atoms
-
-Performance: 0.578 ns/day, 41.514 hours/ns, 6.691 timesteps/s
-96.7% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 149.06     | 149.06     | 149.06     |   0.0 | 99.74
-Bond    | 0.00082946 | 0.00082946 | 0.00082946 |   0.0 |  0.00
-Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.068351   | 0.068351   | 0.068351   |   0.0 |  0.05
-Output  | 0.25935    | 0.25935    | 0.25935    |   0.0 |  0.17
-Modify  | 0.030915   | 0.030915   | 0.030915   |   0.0 |  0.02
-Other   |            | 0.02702    |            |       |  0.02
-
-Nlocal:    1440 ave 1440 max 1440 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    8180 ave 8180 max 8180 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    140400 ave 140400 max 140400 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-FullNghs:  280800 ave 280800 max 280800 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 280800
-Ave neighs/atom = 195
-Ave special neighs/atom = 0
-Neighbor list builds = 0
-Dangerous builds = 0
-Total wall time: 0:02:29

examples/USER/misc/ilp_graphene_hbn/gr-hBN/log.16Mar18.grhBN.g++.4

@@ -1,171 +0,0 @@
-LAMMPS (8 Mar 2018)
-  using 1 OpenMP thread(s) per MPI task
-# Initialization
-units           metal
-boundary        p p p
-atom_style      full
-processors      * * 1     # domain decomposition over x and y
-
-# System and atom definition
-# we use 2 atom types so that inter- and intra-layer
-# interactions can be specified separately
-read_data       gr_hBN_Cstack_2L_noH.data
-  orthogonal box = (0 0 0) to (44.583 42.9 100)
-  2 by 2 by 1 MPI processor grid
-  reading atoms ...
-  1440 atoms
-  0 = max # of 1-2 neighbors
-  0 = max # of 1-3 neighbors
-  0 = max # of 1-4 neighbors
-  1 = max # of special neighbors
-mass            1 10.8110   # boron    mass (g/mole) | membrane
-mass            2 14.0067   # nitrogen mass (g/mole) | membrane
-mass            3 12.0107   # carbon   mass (g/mole) | adsorbate
-# Separate atom groups
-group membrane  type 1 2
-720 atoms in group membrane
-group adsorbate type 3
-720 atoms in group adsorbate
-
-######################## Potential defition ########################
-pair_style  hybrid/overlay rebo tersoff ilp/graphene/hbn 16.0 coul/shield 16.0
-####################################################################
-pair_coeff  * * rebo               CH.airebo     NULL NULL C    # chemical
-Reading potential file CH.airebo with DATE: 2011-10-25
-pair_coeff  * * tersoff            BNC.tersoff   B    N    NULL # chemical
-Reading potential file BNC.tersoff with DATE: 2013-03-21
-pair_coeff  * * ilp/graphene/hbn   BNCH-old.ILP  B    N    C    # long range
-pair_coeff  1 1 coul/shield 0.70
-pair_coeff  1 2 coul/shield 0.69498201415576216335
-pair_coeff  2 2 coul/shield 0.69
-####################################################################
-# Neighbor update settings
-neighbor        2.0 bin
-neigh_modify    every 1
-neigh_modify    delay 0
-neigh_modify    check yes
-
-# calculate the COM
-variable        adsxcom equal xcm(adsorbate,x)
-variable        adsycom equal xcm(adsorbate,y)
-variable        adszcom equal xcm(adsorbate,z)
-variable        adsvxcom equal vcm(adsorbate,x)
-variable        adsvycom equal vcm(adsorbate,y)
-variable        adsvzcom equal vcm(adsorbate,z)
-
-#### Simulation settings ####
-timestep  0.001
-velocity  all create 300.0 12345
-fix       thermostat all nve
-
-compute   0 all pair rebo
-compute   1 all pair tersoff
-compute   2 all pair ilp/graphene/hbn
-compute   3 all pair coul/shield
-variable  REBO     equal  c_0
-variable  Tersoff  equal  c_1
-variable  EILP     equal  c_2
-variable  Ecoul    equal  c_3
-
-# Calculate the pair potential between the substrate and slider
-compute         sldsub adsorbate group/group membrane
-variable        Evdw equal c_sldsub
-
-############################
-
-# Output
-thermo          100
-thermo_style    custom step etotal pe ke v_Evdw v_Tersoff v_REBO v_EILP v_Ecoul temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
-thermo_modify   line one format float %.10f
-
-#dump            1 all custom 1000 traj.lammpstrj id mol type xu yu zu
-#dump_modify     1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
-
-###### Run molecular dynamics ######
-run 1000
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 18
-  ghost atom cutoff = 18
-  binsize = 9, bins = 5 5 12
-  7 neighbor lists, perpetual/occasional/extra = 6 1 0
-  (1) pair rebo, perpetual, skip from (3)
-      attributes: full, newton on, ghost
-      pair build: skip/ghost
-      stencil: none
-      bin: none
-  (2) pair tersoff, perpetual, skip from (6)
-      attributes: full, newton on
-      pair build: skip
-      stencil: none
-      bin: none
-  (3) pair ilp/graphene/hbn, perpetual
-      attributes: full, newton on, ghost
-      pair build: full/bin/ghost
-      stencil: full/ghost/bin/3d
-      bin: standard
-  (4) pair coul/shield, perpetual, half/full from (2)
-      attributes: half, newton on
-      pair build: halffull/newton/skip
-      stencil: none
-      bin: none
-  (5) compute group/group, occasional, copy from (7)
-      attributes: half, newton on
-      pair build: copy
-      stencil: none
-      bin: none
-  (6) neighbor class addition, perpetual, copy from (3)
-      attributes: full, newton on
-      pair build: copy
-      stencil: none
-      bin: none
-  (7) neighbor class addition, perpetual, half/full from (6)
-      attributes: half, newton on
-      pair build: halffull/newton
-      stencil: none
-      bin: none
-Per MPI rank memory allocation (min/avg/max) = 14.25 | 14.25 | 14.25 Mbytes
-Step TotEng PotEng KinEng v_Evdw v_Tersoff v_REBO v_EILP v_Ecoul Temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom 
-       0 -10708.4531746011 -10764.2547791976 55.8016045965 -66.8250335415 -5401.7347845703 -5322.2780762735 -40.2419183538 0.0000000000 300.0000000000 21.6722857297 22.1650000000 3.3300000000 0.1682661410 -0.0842226772 0.1056563755 
-     100 -10708.2491256387 -10738.4532793285 30.2041536898 -68.8603937785 -5389.4304136167 -5309.6361134033 -39.3867523085 0.0000000000 162.3832535368 21.6879886706 22.1574778199 3.3223279482 0.1346509596 -0.0580689194 -0.1274433614 
-     200 -10708.1985754490 -10736.7142682477 28.5156927987 -70.0276479251 -5388.8677096501 -5308.3263464524 -39.5202121452 0.0000000000 153.3057678444 21.6968427596 22.1541506320 3.3143666142 0.0334706445 -0.0081639882 -0.0055006321 
-     300 -10708.1878214116 -10736.9033486636 28.7155272520 -68.2422175765 -5388.5952548022 -5308.9505338445 -39.3575600169 0.0000000000 154.3801157314 21.6939171741 22.1551483321 3.3251666346 -0.0896064591 0.0248921781 0.1717740196 
-     400 -10708.2036103906 -10738.2295882994 30.0259779088 -67.4993928655 -5389.4510311345 -5309.1985887571 -39.5799684078 0.0000000000 161.4253467759 21.6806789605 22.1589742804 3.3300374170 -0.1615300496 0.0532638209 -0.1185426799 
-     500 -10708.1853082161 -10736.0245173060 27.8392090900 -69.9737746636 -5387.9379921501 -5308.5551693329 -39.5313558230 0.0000000000 149.6688632411 21.6641276776 22.1655659011 3.3143210751 -0.1579504334 0.0766822604 -0.1154029266 
-     600 -10708.1781001285 -10736.4254568396 28.2473567110 -69.9368770273 -5388.3515507736 -5308.6700567475 -39.4038493184 0.0000000000 151.8631421907 21.6516789999 22.1733266592 3.3149997184 -0.0805825343 0.0684349609 0.1419617624 
-     700 -10708.1867253590 -10736.6143955089 28.4276701498 -67.1597096579 -5387.8570063253 -5309.0676141640 -39.6897750195 0.0000000000 152.8325414049 21.6489884054 22.1774523945 3.3315351816 0.0259900263 0.0094570835 0.0707953688 
-     800 -10708.1733385055 -10736.0277775930 27.8544390876 -68.6354557276 -5388.1933954711 -5308.5094712719 -39.3249108500 0.0000000000 149.7507425941 21.6565725156 22.1751617515 3.3227650180 0.1222442823 -0.0531420670 -0.1677749693 
-     900 -10708.1827888042 -10737.2646739167 29.0818851126 -70.2218493216 -5387.9824857335 -5309.6527953488 -39.6293928345 0.0000000000 156.3497250098 21.6716950833 22.1680989334 3.3131455846 0.1650154385 -0.0820901425 0.0072049300 
-    1000 -10708.1804322657 -10736.1966428009 28.0162105352 -68.3753745517 -5388.2611029662 -5308.4521913187 -39.4833485160 0.0000000000 150.6204565501 21.6865468141 22.1602434319 3.3246621699 0.1213363701 -0.0688593023 0.1701174943 
-Loop time of 39.6206 on 4 procs for 1000 steps with 1440 atoms
-
-Performance: 2.181 ns/day, 11.006 hours/ns, 25.239 timesteps/s
-98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 34.948     | 37.122     | 39.309     |  31.6 | 93.69
-Bond    | 0.00046444 | 0.0005914  | 0.00089121 |   0.0 |  0.00
-Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.20131    | 2.3895     | 4.565      | 124.7 |  6.03
-Output  | 0.069107   | 0.069157   | 0.069264   |   0.0 |  0.17
-Modify  | 0.010056   | 0.010403   | 0.010688   |   0.3 |  0.03
-Other   |            | 0.02875    |            |       |  0.07
-
-Nlocal:    360 ave 380 max 340 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-Nghost:    4716 ave 4736 max 4696 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-Neighs:    35100 ave 37050 max 33150 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-FullNghs:  70200 ave 74100 max 66300 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-
-Total # of neighbors = 280800
-Ave neighs/atom = 195
-Ave special neighs/atom = 0
-Neighbor list builds = 0
-Dangerous builds = 0
-Total wall time: 0:00:39

examples/USER/misc/ilp_graphene_hbn/in.bilayer-graphene

@@ -0,0 +1,51 @@
+# Initialization
+units           metal
+boundary        p p p
+atom_style      full
+processors      * * 1     # domain decomposition over x and y
+
+# System and atom definition
+# we use different molecule ids for each layer of hBN
+# so that inter- and intra-layer
+# interactions can be specified separately
+
+read_data       Bi_gr_AB_stack_2L_noH.data
+mass            1 12.0107   # carbon mass (g/mole) | membrane
+mass            2 12.0107   # carbon mass (g/mole) | adsorbate
+# Separate atom groups
+group		layer1 molecule 1
+group		layer2 molecule 2
+
+######################## Potential defition ########################
+pair_style  hybrid/overlay  rebo  ilp/graphene/hbn 16.0
+####################################################################
+pair_coeff  * * rebo               CH.rebo   C  C  # chemical
+pair_coeff  * * ilp/graphene/hbn   BNCH.ILP  C  C  # long range
+####################################################################
+# Neighbor update settings
+neighbor        2.0 bin
+neigh_modify    every 1
+neigh_modify    delay 0
+neigh_modify    check yes
+
+#### Simulation settings ####
+timestep	0.001
+velocity	all create 300.0 12345
+
+compute   	0 all pair rebo
+compute  	1 all pair ilp/graphene/hbn
+variable  	REBO  equal c_0     # REBO energy
+variable  	ILP   equal c_1     # total interlayer energy
+variable  	Evdw  equal c_1[1]  # attractive energy
+variable 	Erep  equal c_1[2]  # repulsive  energy
+
+############################
+
+# Output
+thermo          100
+thermo_style    custom step etotal pe ke v_REBO v_ILP v_Erep v_Evdw temp
+thermo_modify   lost warn
+
+###### Run molecular dynamics ######
+fix       	thermostat all nve
+run 	  	1000

examples/USER/misc/ilp_graphene_hbn/in.bilayer-hBN

@@ -0,0 +1,56 @@
+# Initialization
+units           metal
+boundary        p p p
+atom_style      full
+processors      * * 1     # domain decomposition over x and y
+
+# System and atom definition
+# we use different molecule ids for each layer of hBN
+# so that inter- and intra-layer
+# interactions can be specified separately
+read_data       hBN_AA_prime_stack_2L_noH.data
+mass            1 10.8110   # boron mass (g/mole) | membrane
+mass            2 14.0067   # nitrogen mass (g/mole) | adsorbate
+mass            3 10.8110   # boron mass (g/mole) | membrane
+mass            4 14.0067   # nitrogen mass (g/mole) | adsorbate
+# Separate atom groups
+group 		layer1 molecule 1
+group 		layer2 molecule 2
+
+######################## Potential defition ########################
+pair_style  hybrid/overlay  tersoff  ilp/graphene/hbn 16.0 coul/shield 16.0 1
+####################################################################
+pair_coeff  * * tersoff          BNC.tersoff B N B N  # chemical
+pair_coeff  * * ilp/graphene/hbn BNCH.ILP    B N B N  # long range
+pair_coeff  1 3 coul/shield 0.70
+pair_coeff  1 4 coul/shield 0.69498201415576216335
+pair_coeff  2 3 coul/shield 0.69498201415576216335
+pair_coeff  2 4 coul/shield 0.69
+####################################################################
+# Neighbor update settings
+neighbor        2.0 bin
+neigh_modify    every 1
+neigh_modify    delay 0
+neigh_modify    check yes
+
+#### Simulation settings ####
+timestep  	0.001
+velocity  	all create 300.0 12345 dist gaussian mom yes rot yes
+fix       	thermostat all nve
+
+compute   	0 all pair tersoff
+compute   	1 all pair coul/shield ecoul
+compute   	2 all pair ilp/graphene/hbn
+variable  	Tersoff  equal c_0     # Tersoff energy
+variable  	Ecoul    equal c_1     # Coulomb energy
+variable  	EILP     equal c_2     # total interlayer energy
+variable  	Evdw     equal c_2[1]  # attractive energy
+variable 	Erep     equal c_2[2]  # repulsive  energy
+
+############# Output ###############
+thermo          100
+thermo_style    custom step etotal pe ke v_Evdw v_Tersoff v_EILP v_Erep v_Evdw v_Ecoul temp
+thermo_modify   lost warn
+
+###### Run molecular dynamics ######
+run 		1000

examples/USER/misc/ilp_graphene_hbn/in.grhBN

@@ -0,0 +1,56 @@
+# Initialization
+units           metal
+boundary        p p p
+atom_style      full
+processors      * * 1     # domain decomposition over x and y
+
+# System and atom definition
+# we use different molecule ids for each layer
+# so that inter- and intra-layer
+# interactions can be specified separately
+read_data       gr_hBN_Cstack_2L_noH.data
+mass            1 10.8110   # boron    mass (g/mole) | membrane
+mass            2 14.0067   # nitrogen mass (g/mole) | membrane
+mass            3 12.0107   # carbon   mass (g/mole) | adsorbate
+# Separate atom groups
+group 		hBN molecule 1
+group 		gr  molecule 2
+
+######################## Potential defition ########################
+pair_style  hybrid/overlay rebo tersoff ilp/graphene/hbn 16.0 coul/shield 16.0
+####################################################################
+pair_coeff  * * rebo               CH.rebo     NULL NULL C    # chemical
+pair_coeff  * * tersoff            BNC.tersoff B    N    NULL # chemical
+pair_coeff  * * ilp/graphene/hbn   BNCH.ILP    B    N    C    # long range
+pair_coeff  1 1 coul/shield 0.70
+pair_coeff  1 2 coul/shield 0.69498201415576216335
+pair_coeff  2 2 coul/shield 0.69
+####################################################################
+# Neighbor update settings
+neighbor        2.0 bin
+neigh_modify    every 1
+neigh_modify    delay 0
+neigh_modify    check yes
+
+#### Simulation settings ####
+timestep  	0.001
+velocity  	all create 300.0 12345 dist gaussian mom yes rot yes
+fix       	thermostat all nve
+
+compute   	0 all pair rebo
+compute   	1 all pair tersoff
+compute   	2 all pair ilp/graphene/hbn
+compute   	3 all pair coul/shield
+variable  	REBO     equal  c_0
+variable  	Tersoff  equal  c_1
+variable  	EILP     equal  c_2     # total interlayer energy
+variable  	Evdw     equal  c_2[1]  # attractive energy
+variable 	Erep     equal  c_2[2]  # repulsive  energy
+variable  	Ecoul    equal  c_3
+
+############# Output ##############
+thermo          100
+thermo_style    custom step etotal pe ke v_Evdw v_Tersoff v_REBO v_EILP v_Erep v_Evdw v_Ecoul temp
+
+###### Run molecular dynamics ######
+run 		1000

examples/USER/misc/ilp_graphene_hbn/in.ilp_graphene_hbn

@@ -32,14 +32,6 @@ neigh_modify    every 1
 neigh_modify    delay 0
 neigh_modify    check yes
 
-# calculate the COM
-variable        adsxcom equal xcm(adsorbate,x)
-variable        adsycom equal xcm(adsorbate,y)
-variable        adszcom equal xcm(adsorbate,z)
-variable        adsvxcom equal vcm(adsorbate,x)
-variable        adsvycom equal vcm(adsorbate,y)
-variable        adsvzcom equal vcm(adsorbate,z)
-
 #### Simulation settings ####
 timestep  0.001
 #velocity  adsorbate create 300.0 12345
@@ -51,19 +43,16 @@ compute   1 all pair coul/shield ecoul
 compute   2 all pair ilp/graphene/hbn
 variable  Tersoff  equal c_0
 variable  Ecoul    equal c_1
-variable  EILP     equal c_2
-
-# Calculate the pair potential between the substrate and slider
-compute         sldsub adsorbate group/group membrane
-variable        Evdw equal c_sldsub
+variable  ILP      equal c_2
+variable  Evdw     equal c_2[1]
+variable  Erep     equal c_2[2]
 
 ############################
 
 # Output
 thermo          100
-thermo_style    custom step etotal pe ke v_Evdw v_Tersoff v_EILP v_Ecoul temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom f_subf[1] f_subf[2] f_subf[3]
-thermo_modify   line one format float %.10f
-thermo_modify   flush yes norm no lost warn #ignore
+thermo_style    custom step etotal pe ke v_Tersoff v_ILP v_Ecoul v_Erep v_Evdw temp
+thermo_modify   lost warn #ignore
 
 #dump            1 all custom 1000 traj.lammpstrj id mol type xu yu zu
 #dump_modify     1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes

examples/USER/misc/ilp_graphene_hbn/log.16Mar18.ilp_gr_hBN.g++.1

@@ -1,168 +0,0 @@
-LAMMPS (8 Mar 2018)
-  using 1 OpenMP thread(s) per MPI task
-# Initialization
-units           metal
-boundary        p p p
-atom_style      full
-processors      * * 1     # domain decomposition over x and y
-
-# System and atom definition
-# we use 2 atom types so that inter- and intra-layer
-# interactions can be specified separately
-read_data       hBN_AB_stack_2L_noH_equi_300K.data
-  orthogonal box = (0 0 0) to (43.38 42.5773 100)
-  1 by 1 by 1 MPI processor grid
-  reading atoms ...
-  1360 atoms
-  reading velocities ...
-  1360 velocities
-  0 = max # of 1-2 neighbors
-  0 = max # of 1-3 neighbors
-  0 = max # of 1-4 neighbors
-  1 = max # of special neighbors
-mass            1 10.8110   # boron mass (g/mole) | membrane
-mass            2 14.0067   # nitrogen mass (g/mole) | adsorbate
-mass            3 10.8110   # boron mass (g/mole) | membrane
-mass            4 14.0067   # nitrogen mass (g/mole) | adsorbate
-# Separate atom groups
-group membrane  type 1 2
-680 atoms in group membrane
-group adsorbate type 3 4
-680 atoms in group adsorbate
-
-######################## Potential defition ########################
-pair_style  hybrid/overlay  tersoff  ilp/graphene/hbn 16.0 coul/shield 16.0 1
-####################################################################
-pair_coeff  * * tersoff          BNC.tersoff   NULL NULL B N  # chemical
-Reading potential file BNC.tersoff with DATE: 2013-03-21
-pair_coeff  * * ilp/graphene/hbn BNCH-old.ILP  B N B N  # long range
-pair_coeff  1 3 coul/shield 0.70
-pair_coeff  1 4 coul/shield 0.69498201415576216335
-pair_coeff  2 3 coul/shield 0.69498201415576216335
-pair_coeff  2 4 coul/shield 0.69
-####################################################################
-# Neighbor update settings
-neighbor        2.0 bin
-neigh_modify    every 1
-neigh_modify    delay 0
-neigh_modify    check yes
-
-# calculate the COM
-variable        adsxcom equal xcm(adsorbate,x)
-variable        adsycom equal xcm(adsorbate,y)
-variable        adszcom equal xcm(adsorbate,z)
-variable        adsvxcom equal vcm(adsorbate,x)
-variable        adsvycom equal vcm(adsorbate,y)
-variable        adsvzcom equal vcm(adsorbate,z)
-
-#### Simulation settings ####
-timestep  0.001
-#velocity  adsorbate create 300.0 12345
-fix       subf membrane setforce 0.0 0.0 0.0
-fix       thermostat all nve
-
-compute   0 all pair tersoff
-compute   1 all pair coul/shield ecoul
-compute   2 all pair ilp/graphene/hbn
-variable  Tersoff  equal c_0
-variable  Ecoul    equal c_1
-variable  EILP     equal c_2
-
-# Calculate the pair potential between the substrate and slider
-compute         sldsub adsorbate group/group membrane
-variable        Evdw equal c_sldsub
-
-############################
-
-# Output
-thermo          100
-thermo_style    custom step etotal pe ke v_Evdw v_Tersoff v_EILP v_Ecoul temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom f_subf[1] f_subf[2] f_subf[3]
-thermo_modify   line one format float %.10f
-thermo_modify   flush yes norm no lost warn #ignore
-
-#dump            1 all custom 1000 traj.lammpstrj id mol type xu yu zu
-#dump_modify     1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
-
-###### Run molecular dynamics ######
-run 1000
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 18
-  ghost atom cutoff = 18
-  binsize = 9, bins = 5 5 12
-  6 neighbor lists, perpetual/occasional/extra = 5 1 0
-  (1) pair tersoff, perpetual, skip from (5)
-      attributes: full, newton on
-      pair build: skip
-      stencil: none
-      bin: none
-  (2) pair ilp/graphene/hbn, perpetual
-      attributes: full, newton on, ghost
-      pair build: full/bin/ghost
-      stencil: full/ghost/bin/3d
-      bin: standard
-  (3) pair coul/shield, perpetual, skip from (6)
-      attributes: half, newton on
-      pair build: skip
-      stencil: none
-      bin: none
-  (4) compute group/group, occasional, copy from (6)
-      attributes: half, newton on
-      pair build: copy
-      stencil: none
-      bin: none
-  (5) neighbor class addition, perpetual, copy from (2)
-      attributes: full, newton on
-      pair build: copy
-      stencil: none
-      bin: none
-  (6) neighbor class addition, perpetual, half/full from (5)
-      attributes: half, newton on
-      pair build: halffull/newton
-      stencil: none
-      bin: none
-Per MPI rank memory allocation (min/avg/max) = 57.85 | 57.85 | 57.85 Mbytes
-Step TotEng PotEng KinEng v_Evdw v_Tersoff v_EILP v_Ecoul Temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom f_subf[1] f_subf[2] f_subf[3] 
-       0 -5114.6628078598 -5127.8586355055 13.1958276458 -75.3652234209 -5091.4120857465 -36.0831137829 -0.3634359761 75.1194741238 20.9113202537 20.6582215878 3.2895976612 -0.0495147937 -0.0552233516 -0.0166592619 -0.1742790202 -0.0884665936 -0.8010816801 
-     100 -5114.6620580583 -5127.6958349342 13.0337768758 -75.2249487778 -5091.2407919311 -36.0927601416 -0.3622828614 74.1969727889 20.9076129631 20.6534162972 3.2908118318 -0.0234802196 -0.0397832410 0.0332404745 -0.2430042439 -0.1598109185 -0.5351246275 
-     200 -5114.6630637865 -5127.5945140906 12.9314503041 -74.6445167393 -5091.1507571912 -36.0866688941 -0.3570880053 73.6144615235 20.9067696105 20.6505240051 3.2976575241 0.0078967872 -0.0170385302 0.0850447973 -0.2934041648 -0.2405295165 0.2309200807 
-     300 -5114.6693830121 -5128.3286231421 13.6592401300 -74.2223518942 -5091.8645555419 -36.1107860098 -0.3532815904 77.7575278367 20.9090146500 20.6502445717 3.3024525026 0.0352437329 0.0112279015 -0.0021399216 -0.2166516175 -0.2410661267 0.9007458614 
-     400 -5114.6614035404 -5127.6423784754 12.9809749350 -74.6548295432 -5091.2348011465 -36.0496340516 -0.3579432773 73.8963888364 20.9136276183 20.6526810045 3.2977225951 0.0556629502 0.0358324354 -0.0738287296 -0.1431221016 -0.1626739623 0.0673046122 
-     500 -5114.6599876234 -5127.4097813122 12.7497936887 -75.2268687829 -5090.9284608504 -36.1195707042 -0.3617497575 72.5803506074 20.9197050770 20.6571510311 3.2909058903 0.0631939085 0.0530269602 -0.0516940297 -0.0112976844 -0.1217009147 -0.4713422319 
-     600 -5114.6672773464 -5128.0912983829 13.4240210364 -75.3848112535 -5091.6338883189 -36.0938401510 -0.3635699131 76.4185034811 20.9258252862 20.6628322031 3.2892805234 0.0573396226 0.0579085440 0.0291853982 0.1059950758 0.0102266125 -0.7683214794 
-     700 -5114.6609647250 -5127.7466720637 13.0857073388 -74.7981789470 -5091.2811095008 -36.1066385732 -0.3589239897 74.4925957063 20.9307092134 20.6683554324 3.2957959411 0.0396744013 0.0503347378 0.0818267711 0.1737903706 0.1258761156 0.1307185989 
-     800 -5114.6622627667 -5128.0130406264 13.3507778597 -74.2952448854 -5091.5693975625 -36.0897180314 -0.3539250325 76.0015543464 20.9334441079 20.6725125240 3.3019570181 0.0142277646 0.0313116646 0.0291673132 0.2457478793 0.1912082770 0.7239823553 
-     900 -5114.6675469561 -5128.1496933801 13.4821464240 -74.3644898573 -5091.6703861750 -36.1246785145 -0.3546286905 76.7493920516 20.9334403558 20.6744181494 3.3005582394 -0.0141399355 0.0063543986 -0.0561206619 0.2370151923 0.2115707560 0.7822017606 
-    1000 -5114.6683146144 -5128.3364609113 13.6681462969 -75.1091579020 -5091.9370210069 -36.0375964349 -0.3618434694 77.8082276935 20.9306643096 20.6737238853 3.2922181699 -0.0411219854 -0.0200694204 -0.0788193565 0.2225175431 0.2377413412 -0.5875288557 
-Loop time of 202.063 on 1 procs for 1000 steps with 1360 atoms
-
-Performance: 0.428 ns/day, 56.129 hours/ns, 4.949 timesteps/s
-91.0% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 201.4      | 201.4      | 201.4      |   0.0 | 99.67
-Bond    | 0.00092697 | 0.00092697 | 0.00092697 |   0.0 |  0.00
-Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.086005   | 0.086005   | 0.086005   |   0.0 |  0.04
-Output  | 0.50438    | 0.50438    | 0.50438    |   0.0 |  0.25
-Modify  | 0.038846   | 0.038846   | 0.038846   |   0.0 |  0.02
-Other   |            | 0.03093    |            |       |  0.02
-
-Nlocal:    1360 ave 1360 max 1360 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    7840 ave 7840 max 7840 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    249628 ave 249628 max 249628 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-FullNghs:  253390 ave 253390 max 253390 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 253390
-Ave neighs/atom = 186.316
-Ave special neighs/atom = 0
-Neighbor list builds = 0
-Dangerous builds = 0
-Total wall time: 0:03:22

examples/USER/misc/ilp_graphene_hbn/log.16Mar18.ilp_gr_hBN.g++.4

@@ -1,168 +0,0 @@
-LAMMPS (8 Mar 2018)
-  using 1 OpenMP thread(s) per MPI task
-# Initialization
-units           metal
-boundary        p p p
-atom_style      full
-processors      * * 1     # domain decomposition over x and y
-
-# System and atom definition
-# we use 2 atom types so that inter- and intra-layer
-# interactions can be specified separately
-read_data       hBN_AB_stack_2L_noH_equi_300K.data
-  orthogonal box = (0 0 0) to (43.38 42.5773 100)
-  2 by 2 by 1 MPI processor grid
-  reading atoms ...
-  1360 atoms
-  reading velocities ...
-  1360 velocities
-  0 = max # of 1-2 neighbors
-  0 = max # of 1-3 neighbors
-  0 = max # of 1-4 neighbors
-  1 = max # of special neighbors
-mass            1 10.8110   # boron mass (g/mole) | membrane
-mass            2 14.0067   # nitrogen mass (g/mole) | adsorbate
-mass            3 10.8110   # boron mass (g/mole) | membrane
-mass            4 14.0067   # nitrogen mass (g/mole) | adsorbate
-# Separate atom groups
-group membrane  type 1 2
-680 atoms in group membrane
-group adsorbate type 3 4
-680 atoms in group adsorbate
-
-######################## Potential defition ########################
-pair_style  hybrid/overlay  tersoff  ilp/graphene/hbn 16.0 coul/shield 16.0 1
-####################################################################
-pair_coeff  * * tersoff          BNC.tersoff   NULL NULL B N  # chemical
-Reading potential file BNC.tersoff with DATE: 2013-03-21
-pair_coeff  * * ilp/graphene/hbn BNCH-old.ILP  B N B N  # long range
-pair_coeff  1 3 coul/shield 0.70
-pair_coeff  1 4 coul/shield 0.69498201415576216335
-pair_coeff  2 3 coul/shield 0.69498201415576216335
-pair_coeff  2 4 coul/shield 0.69
-####################################################################
-# Neighbor update settings
-neighbor        2.0 bin
-neigh_modify    every 1
-neigh_modify    delay 0
-neigh_modify    check yes
-
-# calculate the COM
-variable        adsxcom equal xcm(adsorbate,x)
-variable        adsycom equal xcm(adsorbate,y)
-variable        adszcom equal xcm(adsorbate,z)
-variable        adsvxcom equal vcm(adsorbate,x)
-variable        adsvycom equal vcm(adsorbate,y)
-variable        adsvzcom equal vcm(adsorbate,z)
-
-#### Simulation settings ####
-timestep  0.001
-#velocity  adsorbate create 300.0 12345
-fix       subf membrane setforce 0.0 0.0 0.0
-fix       thermostat all nve
-
-compute   0 all pair tersoff
-compute   1 all pair coul/shield ecoul
-compute   2 all pair ilp/graphene/hbn
-variable  Tersoff  equal c_0
-variable  Ecoul    equal c_1
-variable  EILP     equal c_2
-
-# Calculate the pair potential between the substrate and slider
-compute         sldsub adsorbate group/group membrane
-variable        Evdw equal c_sldsub
-
-############################
-
-# Output
-thermo          100
-thermo_style    custom step etotal pe ke v_Evdw v_Tersoff v_EILP v_Ecoul temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom f_subf[1] f_subf[2] f_subf[3]
-thermo_modify   line one format float %.10f
-thermo_modify   flush yes norm no lost warn #ignore
-
-#dump            1 all custom 1000 traj.lammpstrj id mol type xu yu zu
-#dump_modify     1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
-
-###### Run molecular dynamics ######
-run 1000
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 18
-  ghost atom cutoff = 18
-  binsize = 9, bins = 5 5 12
-  6 neighbor lists, perpetual/occasional/extra = 5 1 0
-  (1) pair tersoff, perpetual, skip from (5)
-      attributes: full, newton on
-      pair build: skip
-      stencil: none
-      bin: none
-  (2) pair ilp/graphene/hbn, perpetual
-      attributes: full, newton on, ghost
-      pair build: full/bin/ghost
-      stencil: full/ghost/bin/3d
-      bin: standard
-  (3) pair coul/shield, perpetual, skip from (6)
-      attributes: half, newton on
-      pair build: skip
-      stencil: none
-      bin: none
-  (4) compute group/group, occasional, copy from (6)
-      attributes: half, newton on
-      pair build: copy
-      stencil: none
-      bin: none
-  (5) neighbor class addition, perpetual, copy from (2)
-      attributes: full, newton on
-      pair build: copy
-      stencil: none
-      bin: none
-  (6) neighbor class addition, perpetual, half/full from (5)
-      attributes: half, newton on
-      pair build: halffull/newton
-      stencil: none
-      bin: none
-Per MPI rank memory allocation (min/avg/max) = 30.63 | 30.63 | 30.64 Mbytes
-Step TotEng PotEng KinEng v_Evdw v_Tersoff v_EILP v_Ecoul Temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom f_subf[1] f_subf[2] f_subf[3] 
-       0 -5114.6628078598 -5127.8586355055 13.1958276458 -75.3652234209 -5091.4120857465 -36.0831137829 -0.3634359761 75.1194741238 20.9113202537 20.6582215878 3.2895976612 -0.0495147937 -0.0552233516 -0.0166592619 -0.1742790202 -0.0884665936 -0.8010816801 
-     100 -5114.6620580583 -5127.6958349342 13.0337768758 -75.2249487778 -5091.2407919311 -36.0927601416 -0.3622828614 74.1969727889 20.9076129631 20.6534162972 3.2908118318 -0.0234802196 -0.0397832410 0.0332404745 -0.2430042439 -0.1598109185 -0.5351246275 
-     200 -5114.6630637865 -5127.5945140906 12.9314503041 -74.6445167393 -5091.1507571912 -36.0866688941 -0.3570880053 73.6144615235 20.9067696105 20.6505240051 3.2976575241 0.0078967872 -0.0170385302 0.0850447973 -0.2934041648 -0.2405295165 0.2309200807 
-     300 -5114.6693830121 -5128.3286231421 13.6592401300 -74.2223518942 -5091.8645555419 -36.1107860098 -0.3532815904 77.7575278367 20.9090146500 20.6502445717 3.3024525026 0.0352437329 0.0112279015 -0.0021399216 -0.2166516175 -0.2410661267 0.9007458614 
-     400 -5114.6614035404 -5127.6423784754 12.9809749350 -74.6548295432 -5091.2348011465 -36.0496340516 -0.3579432773 73.8963888364 20.9136276183 20.6526810045 3.2977225951 0.0556629502 0.0358324354 -0.0738287296 -0.1431221016 -0.1626739623 0.0673046122 
-     500 -5114.6599876234 -5127.4097813122 12.7497936887 -75.2268687829 -5090.9284608504 -36.1195707042 -0.3617497575 72.5803506074 20.9197050770 20.6571510311 3.2909058903 0.0631939085 0.0530269602 -0.0516940297 -0.0112976844 -0.1217009147 -0.4713422319 
-     600 -5114.6672773464 -5128.0912983829 13.4240210364 -75.3848112535 -5091.6338883189 -36.0938401510 -0.3635699131 76.4185034811 20.9258252862 20.6628322031 3.2892805234 0.0573396226 0.0579085440 0.0291853982 0.1059950758 0.0102266125 -0.7683214794 
-     700 -5114.6609647250 -5127.7466720637 13.0857073388 -74.7981789470 -5091.2811095008 -36.1066385732 -0.3589239897 74.4925957063 20.9307092134 20.6683554324 3.2957959411 0.0396744013 0.0503347378 0.0818267711 0.1737903706 0.1258761156 0.1307185989 
-     800 -5114.6622627667 -5128.0130406264 13.3507778597 -74.2952448854 -5091.5693975625 -36.0897180314 -0.3539250325 76.0015543464 20.9334441079 20.6725125240 3.3019570181 0.0142277646 0.0313116646 0.0291673132 0.2457478793 0.1912082770 0.7239823553 
-     900 -5114.6675469561 -5128.1496933801 13.4821464240 -74.3644898573 -5091.6703861750 -36.1246785145 -0.3546286905 76.7493920516 20.9334403558 20.6744181494 3.3005582394 -0.0141399355 0.0063543986 -0.0561206619 0.2370151923 0.2115707560 0.7822017606 
-    1000 -5114.6683146144 -5128.3364609113 13.6681462969 -75.1091579020 -5091.9370210069 -36.0375964349 -0.3618434694 77.8082276935 20.9306643096 20.6737238853 3.2922181699 -0.0411219854 -0.0200694204 -0.0788193565 0.2225175431 0.2377413412 -0.5875288557 
-Loop time of 53.3155 on 4 procs for 1000 steps with 1360 atoms
-
-Performance: 1.621 ns/day, 14.810 hours/ns, 18.756 timesteps/s
-97.6% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 49.475     | 50.978     | 52.988     |  18.0 | 95.62
-Bond    | 0.00045061 | 0.00066602 | 0.00086665 |   0.0 |  0.00
-Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.16491    | 2.1759     | 3.679      |  87.0 |  4.08
-Output  | 0.11871    | 0.11882    | 0.11911    |   0.0 |  0.22
-Modify  | 0.012956   | 0.013504   | 0.01387    |   0.3 |  0.03
-Other   |            | 0.02828    |            |       |  0.05
-
-Nlocal:    340 ave 346 max 336 min
-Histogram: 1 0 1 0 1 0 0 0 0 1
-Nghost:    4537.5 ave 4540 max 4534 min
-Histogram: 1 0 0 0 0 0 2 0 0 1
-Neighs:    62407 ave 62413 max 62402 min
-Histogram: 1 0 0 1 1 0 0 0 0 1
-FullNghs:  63347.5 ave 65585 max 61866 min
-Histogram: 1 1 0 1 0 0 0 0 0 1
-
-Total # of neighbors = 253926
-Ave neighs/atom = 186.71
-Ave special neighs/atom = 0
-Neighbor list builds = 0
-Dangerous builds = 0
-Total wall time: 0:00:53

examples/USER/misc/ilp_graphene_hbn/log.31Jul19.bilayer-graphene.g++.1

@@ -0,0 +1,127 @@
+LAMMPS (31 Jul 2019)
+  using 1 OpenMP thread(s) per MPI task
+# Initialization
+units           metal
+boundary        p p p
+atom_style      full
+processors      * * 1     # domain decomposition over x and y
+
+# System and atom definition
+# we use different molecule ids for each layer of hBN
+# so that inter- and intra-layer
+# interactions can be specified separately
+
+read_data       Bi_gr_AB_stack_2L_noH.data
+  orthogonal box = (0 0 0) to (42.6 41.8117 100)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  1360 atoms
+  0 = max # of 1-2 neighbors
+  0 = max # of 1-3 neighbors
+  0 = max # of 1-4 neighbors
+  1 = max # of special neighbors
+  special bonds CPU = 0.000290871 secs
+  read_data CPU = 0.00159073 secs
+mass            1 12.0107   # carbon mass (g/mole) | membrane
+mass            2 12.0107   # carbon mass (g/mole) | adsorbate
+# Separate atom groups
+group		layer1 molecule 1
+680 atoms in group layer1
+group		layer2 molecule 2
+680 atoms in group layer2
+
+######################## Potential defition ########################
+pair_style  hybrid/overlay  rebo  ilp/graphene/hbn 16.0
+####################################################################
+pair_coeff  * * rebo               CH.rebo   C  C  # chemical
+Reading potential file CH.rebo with DATE: 2018-7-3
+pair_coeff  * * ilp/graphene/hbn   BNCH.ILP  C  C  # long range
+####################################################################
+# Neighbor update settings
+neighbor        2.0 bin
+neigh_modify    every 1
+neigh_modify    delay 0
+neigh_modify    check yes
+
+#### Simulation settings ####
+timestep	0.001
+velocity	all create 300.0 12345
+
+compute   	0 all pair rebo
+compute  	1 all pair ilp/graphene/hbn
+variable  	REBO  equal c_0     # REBO energy
+variable  	ILP   equal c_1     # total interlayer energy
+variable  	Evdw  equal c_1[1]  # attractive energy
+variable 	Erep  equal c_1[2]  # repulsive  energy
+
+############################
+
+# Output
+thermo          100
+thermo_style    custom step etotal pe ke v_REBO v_ILP v_Erep v_Evdw temp
+thermo_modify   lost warn
+
+###### Run molecular dynamics ######
+fix       	thermostat all nve
+run 	  	1000
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 18
+  ghost atom cutoff = 18
+  binsize = 9, bins = 5 5 12
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair rebo, perpetual
+      attributes: full, newton on, ghost
+      pair build: full/bin/ghost
+      stencil: full/ghost/bin/3d
+      bin: standard
+  (2) pair ilp/graphene/hbn, perpetual, copy from (1)
+      attributes: full, newton on, ghost
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 17.21 | 17.21 | 17.21 Mbytes
+Step TotEng PotEng KinEng v_REBO v_ILP v_Erep v_Evdw Temp 
+       0   -10037.285   -10089.985    52.699361   -10057.189   -32.795185    43.640104   -76.435288          300 
+     100   -10037.034   -10064.765     27.73131   -10032.181    -32.58421    34.730868   -67.315078    157.86516 
+     200   -10036.963   -10061.144     24.18111   -10028.856   -32.288132    28.179936   -60.468068    137.65505 
+     300   -10037.003     -10063.5    26.496726   -10030.823   -32.677105    34.923849   -67.600954    150.83708 
+     400   -10037.032   -10064.389    27.356526   -10031.853   -32.535415    44.242347   -76.777762    155.73164 
+     500   -10037.023   -10064.114    27.090279   -10031.431   -32.682418    37.229232    -69.91165    154.21598 
+     600   -10037.003   -10063.657    26.653718   -10031.327   -32.329664    28.509073   -60.838737    151.73078 
+     700   -10037.004    -10063.35    26.345697   -10030.801   -32.549231    32.564686   -65.113917    149.97732 
+     800   -10037.025   -10064.219    27.194765   -10031.766   -32.453653    43.381557    -75.83521    154.81078 
+     900   -10037.028   -10064.668    27.639127   -10032.167   -32.500121     39.99345   -72.493571    157.34039 
+    1000   -10037.003   -10063.662    26.658825   -10031.337   -32.325053    29.573578   -61.898631    151.75986 
+Loop time of 149.887 on 1 procs for 1000 steps with 1360 atoms
+
+Performance: 0.576 ns/day, 41.635 hours/ns, 6.672 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    | 149.75     | 149.75     | 149.75     |   0.0 | 99.91
+Bond    | 0.00024772 | 0.00024772 | 0.00024772 |   0.0 |  0.00
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.086328   | 0.086328   | 0.086328   |   0.0 |  0.06
+Output  | 0.00036383 | 0.00036383 | 0.00036383 |   0.0 |  0.00
+Modify  | 0.028636   | 0.028636   | 0.028636   |   0.0 |  0.02
+Other   |            | 0.01708    |            |       |  0.01
+
+Nlocal:    1360 ave 1360 max 1360 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    7964 ave 7964 max 7964 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  1.037e+06 ave 1.037e+06 max 1.037e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1037000
+Ave neighs/atom = 762.5
+Ave special neighs/atom = 0
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:02:30

examples/USER/misc/ilp_graphene_hbn/log.31Jul19.bilayer-graphene.g++.4

@@ -0,0 +1,127 @@
+LAMMPS (31 Jul 2019)
+  using 1 OpenMP thread(s) per MPI task
+# Initialization
+units           metal
+boundary        p p p
+atom_style      full
+processors      * * 1     # domain decomposition over x and y
+
+# System and atom definition
+# we use different molecule ids for each layer of hBN
+# so that inter- and intra-layer
+# interactions can be specified separately
+
+read_data       Bi_gr_AB_stack_2L_noH.data
+  orthogonal box = (0 0 0) to (42.6 41.8117 100)
+  2 by 2 by 1 MPI processor grid
+  reading atoms ...
+  1360 atoms
+  0 = max # of 1-2 neighbors
+  0 = max # of 1-3 neighbors
+  0 = max # of 1-4 neighbors
+  1 = max # of special neighbors
+  special bonds CPU = 0.000157118 secs
+  read_data CPU = 0.00145698 secs
+mass            1 12.0107   # carbon mass (g/mole) | membrane
+mass            2 12.0107   # carbon mass (g/mole) | adsorbate
+# Separate atom groups
+group		layer1 molecule 1
+680 atoms in group layer1
+group		layer2 molecule 2
+680 atoms in group layer2
+
+######################## Potential defition ########################
+pair_style  hybrid/overlay  rebo  ilp/graphene/hbn 16.0
+####################################################################
+pair_coeff  * * rebo               CH.rebo   C  C  # chemical
+Reading potential file CH.rebo with DATE: 2018-7-3
+pair_coeff  * * ilp/graphene/hbn   BNCH.ILP  C  C  # long range
+####################################################################
+# Neighbor update settings
+neighbor        2.0 bin
+neigh_modify    every 1
+neigh_modify    delay 0
+neigh_modify    check yes
+
+#### Simulation settings ####
+timestep	0.001
+velocity	all create 300.0 12345
+
+compute   	0 all pair rebo
+compute  	1 all pair ilp/graphene/hbn
+variable  	REBO  equal c_0     # REBO energy
+variable  	ILP   equal c_1     # total interlayer energy
+variable  	Evdw  equal c_1[1]  # attractive energy
+variable 	Erep  equal c_1[2]  # repulsive  energy
+
+############################
+
+# Output
+thermo          100
+thermo_style    custom step etotal pe ke v_REBO v_ILP v_Erep v_Evdw temp
+thermo_modify   lost warn
+
+###### Run molecular dynamics ######
+fix       	thermostat all nve
+run 	  	1000
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 18
+  ghost atom cutoff = 18
+  binsize = 9, bins = 5 5 12
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair rebo, perpetual
+      attributes: full, newton on, ghost
+      pair build: full/bin/ghost
+      stencil: full/ghost/bin/3d
+      bin: standard
+  (2) pair ilp/graphene/hbn, perpetual, copy from (1)
+      attributes: full, newton on, ghost
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 9.879 | 9.879 | 9.879 Mbytes
+Step TotEng PotEng KinEng v_REBO v_ILP v_Erep v_Evdw Temp 
+       0   -10037.285   -10089.985    52.699361   -10057.189   -32.795185    43.640104   -76.435288          300 
+     100   -10037.034   -10064.765     27.73131   -10032.181    -32.58421    34.730868   -67.315078    157.86516 
+     200   -10036.963   -10061.144     24.18111   -10028.856   -32.288132    28.179936   -60.468068    137.65505 
+     300   -10037.003     -10063.5    26.496726   -10030.823   -32.677105    34.923849   -67.600954    150.83708 
+     400   -10037.032   -10064.389    27.356526   -10031.853   -32.535415    44.242347   -76.777762    155.73164 
+     500   -10037.023   -10064.114    27.090279   -10031.431   -32.682418    37.229232    -69.91165    154.21598 
+     600   -10037.003   -10063.657    26.653718   -10031.327   -32.329664    28.509073   -60.838737    151.73078 
+     700   -10037.004    -10063.35    26.345697   -10030.801   -32.549231    32.564686   -65.113917    149.97732 
+     800   -10037.025   -10064.219    27.194765   -10031.766   -32.453653    43.381557    -75.83521    154.81078 
+     900   -10037.028   -10064.668    27.639127   -10032.167   -32.500121     39.99345   -72.493571    157.34039 
+    1000   -10037.003   -10063.662    26.658825   -10031.337   -32.325053    29.573578   -61.898631    151.75986 
+Loop time of 44.6551 on 4 procs for 1000 steps with 1360 atoms
+
+Performance: 1.935 ns/day, 12.404 hours/ns, 22.394 timesteps/s
+93.9% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 40.304     | 41.221     | 41.998     |   9.5 | 92.31
+Bond    | 0.00027633 | 0.00029379 | 0.00031424 |   0.0 |  0.00
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 2.5678     | 3.3334     | 4.2403     |  32.9 |  7.46
+Output  | 0.0051446  | 0.0054518  | 0.0059683  |   0.4 |  0.01
+Modify  | 0.0088317  | 0.009002   | 0.0090654  |   0.1 |  0.02
+Other   |            | 0.08586    |            |       |  0.19
+
+Nlocal:    340 ave 340 max 340 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost:    4628 ave 4628 max 4628 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs:    0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs:  259250 ave 259250 max 259250 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1037000
+Ave neighs/atom = 762.5
+Ave special neighs/atom = 0
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:44

examples/USER/misc/ilp_graphene_hbn/log.31Jul19.bilayer-hBN.g++.1

@@ -0,0 +1,142 @@
+LAMMPS (31 Jul 2019)
+  using 1 OpenMP thread(s) per MPI task
+# Initialization
+units           metal
+boundary        p p p
+atom_style      full
+processors      * * 1     # domain decomposition over x and y
+
+# System and atom definition
+# we use different molecule ids for each layer of hBN
+# so that inter- and intra-layer
+# interactions can be specified separately
+read_data       hBN_AA_prime_stack_2L_noH.data
+  orthogonal box = (0 0 0) to (43.38 42.5773 100)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  1360 atoms
+  0 = max # of 1-2 neighbors
+  0 = max # of 1-3 neighbors
+  0 = max # of 1-4 neighbors
+  1 = max # of special neighbors
+  special bonds CPU = 0.000375509 secs
+  read_data CPU = 0.00181293 secs
+mass            1 10.8110   # boron mass (g/mole) | membrane
+mass            2 14.0067   # nitrogen mass (g/mole) | adsorbate
+mass            3 10.8110   # boron mass (g/mole) | membrane
+mass            4 14.0067   # nitrogen mass (g/mole) | adsorbate
+# Separate atom groups
+group 		layer1 molecule 1
+680 atoms in group layer1
+group 		layer2 molecule 2
+680 atoms in group layer2
+
+######################## Potential defition ########################
+pair_style  hybrid/overlay  tersoff  ilp/graphene/hbn 16.0 coul/shield 16.0 1
+####################################################################
+pair_coeff  * * tersoff          BNC.tersoff B N B N  # chemical
+Reading potential file BNC.tersoff with DATE: 2013-03-21
+pair_coeff  * * ilp/graphene/hbn BNCH.ILP    B N B N  # long range
+pair_coeff  1 3 coul/shield 0.70
+pair_coeff  1 4 coul/shield 0.69498201415576216335
+pair_coeff  2 3 coul/shield 0.69498201415576216335
+pair_coeff  2 4 coul/shield 0.69
+####################################################################
+# Neighbor update settings
+neighbor        2.0 bin
+neigh_modify    every 1
+neigh_modify    delay 0
+neigh_modify    check yes
+
+#### Simulation settings ####
+timestep  	0.001
+velocity  	all create 300.0 12345 dist gaussian mom yes rot yes
+fix       	thermostat all nve
+
+compute   	0 all pair tersoff
+compute   	1 all pair coul/shield ecoul
+compute   	2 all pair ilp/graphene/hbn
+variable  	Tersoff  equal c_0     # Tersoff energy
+variable  	Ecoul    equal c_1     # Coulomb energy
+variable  	EILP     equal c_2     # total interlayer energy
+variable  	Evdw     equal c_2[1]  # attractive energy
+variable 	Erep     equal c_2[2]  # repulsive  energy
+
+############# Output ###############
+thermo          100
+thermo_style    custom step etotal pe ke v_Evdw v_Tersoff v_EILP v_Erep v_Evdw v_Ecoul temp
+thermo_modify   lost warn
+
+###### Run molecular dynamics ######
+run 		1000
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 18
+  ghost atom cutoff = 18
+  binsize = 9, bins = 5 5 12
+  4 neighbor lists, perpetual/occasional/extra = 4 0 0
+  (1) pair tersoff, perpetual
+      attributes: full, newton on
+      pair build: full/bin
+      stencil: full/bin/3d
+      bin: standard
+  (2) pair ilp/graphene/hbn, perpetual
+      attributes: full, newton on, ghost
+      pair build: full/bin/ghost
+      stencil: full/ghost/bin/3d
+      bin: standard
+  (3) pair coul/shield, perpetual, skip from (4)
+      attributes: half, newton on
+      pair build: skip
+      stencil: none
+      bin: none
+  (4) neighbor class addition, perpetual, half/full from (1)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 35.9 | 35.9 | 35.9 Mbytes
+Step TotEng PotEng KinEng v_Evdw v_Tersoff v_EILP v_Erep v_Evdw v_Ecoul Temp 
+       0   -10193.138   -10245.837    52.699361   -77.557069    -10208.73   -36.776483    40.780586   -77.557069  -0.33075117          300 
+     100   -10192.814   -10215.193     22.37957   -80.997619   -10177.878   -36.967736    44.029884   -80.997619  -0.34809915    127.39947 
+     200   -10192.922   -10221.807    28.884855   -86.370319   -10184.251   -37.168986    49.201334   -86.370319  -0.38644764    164.43191 
+     300   -10192.878   -10219.029    26.151464   -83.063924   -10182.349    -36.30412    46.759804   -83.063924  -0.37660157    148.87162 
+     400   -10192.892   -10218.834    25.942229   -78.394242   -10181.398   -37.110968    41.283274   -78.394242  -0.32494569    147.68051 
+     500   -10192.909   -10221.331    28.422213   -81.768531    -10184.03   -36.946226    44.822304   -81.768531  -0.35489965    161.79824 
+     600   -10192.886   -10219.371     26.48495   -86.278335   -10182.669    -36.29515    49.983185   -86.278335  -0.40636253    150.77004 
+     700   -10192.902    -10220.95    28.048108    -82.28873   -10183.208    -37.39374     44.89499    -82.28873  -0.34777958    159.66859 
+     800    -10192.88    -10218.51    25.630186   -78.011019   -10181.427   -36.754209    41.256811   -78.011019  -0.32904942    145.90415 
+     900   -10192.894    -10220.56    27.665437   -82.474379   -10183.801   -36.381157    46.093222   -82.474379  -0.37703328    157.49017 
+    1000   -10192.897    -10219.01     26.11313   -87.125683   -10181.252   -37.361898    49.763785   -87.125683  -0.39607952    148.65339 
+Loop time of 211.527 on 1 procs for 1000 steps with 1360 atoms
+
+Performance: 0.408 ns/day, 58.757 hours/ns, 4.728 timesteps/s
+99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 211.4      | 211.4      | 211.4      |   0.0 | 99.94
+Bond    | 0.00018859 | 0.00018859 | 0.00018859 |   0.0 |  0.00
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.082034   | 0.082034   | 0.082034   |   0.0 |  0.04
+Output  | 0.00037289 | 0.00037289 | 0.00037289 |   0.0 |  0.00
+Modify  | 0.027928   | 0.027928   | 0.027928   |   0.0 |  0.01
+Other   |            | 0.0159     |            |       |  0.01
+
+Nlocal:    1360 ave 1360 max 1360 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    7836 ave 7836 max 7836 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    249560 ave 249560 max 249560 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  1.00504e+06 ave 1.00504e+06 max 1.00504e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1005040
+Ave neighs/atom = 739
+Ave special neighs/atom = 0
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:03:31

examples/USER/misc/ilp_graphene_hbn/log.31Jul19.bilayer-hBN.g++.4

@@ -0,0 +1,142 @@
+LAMMPS (31 Jul 2019)
+  using 1 OpenMP thread(s) per MPI task
+# Initialization
+units           metal
+boundary        p p p
+atom_style      full
+processors      * * 1     # domain decomposition over x and y
+
+# System and atom definition
+# we use different molecule ids for each layer of hBN
+# so that inter- and intra-layer
+# interactions can be specified separately
+read_data       hBN_AA_prime_stack_2L_noH.data
+  orthogonal box = (0 0 0) to (43.38 42.5773 100)
+  2 by 2 by 1 MPI processor grid
+  reading atoms ...
+  1360 atoms
+  0 = max # of 1-2 neighbors
+  0 = max # of 1-3 neighbors
+  0 = max # of 1-4 neighbors
+  1 = max # of special neighbors
+  special bonds CPU = 0.000224352 secs
+  read_data CPU = 0.00160909 secs
+mass            1 10.8110   # boron mass (g/mole) | membrane
+mass            2 14.0067   # nitrogen mass (g/mole) | adsorbate
+mass            3 10.8110   # boron mass (g/mole) | membrane
+mass            4 14.0067   # nitrogen mass (g/mole) | adsorbate
+# Separate atom groups
+group 		layer1 molecule 1
+680 atoms in group layer1
+group 		layer2 molecule 2
+680 atoms in group layer2
+
+######################## Potential defition ########################
+pair_style  hybrid/overlay  tersoff  ilp/graphene/hbn 16.0 coul/shield 16.0 1
+####################################################################
+pair_coeff  * * tersoff          BNC.tersoff B N B N  # chemical
+Reading potential file BNC.tersoff with DATE: 2013-03-21
+pair_coeff  * * ilp/graphene/hbn BNCH.ILP    B N B N  # long range
+pair_coeff  1 3 coul/shield 0.70
+pair_coeff  1 4 coul/shield 0.69498201415576216335
+pair_coeff  2 3 coul/shield 0.69498201415576216335
+pair_coeff  2 4 coul/shield 0.69
+####################################################################
+# Neighbor update settings
+neighbor        2.0 bin
+neigh_modify    every 1
+neigh_modify    delay 0
+neigh_modify    check yes
+
+#### Simulation settings ####
+timestep  	0.001
+velocity  	all create 300.0 12345 dist gaussian mom yes rot yes
+fix       	thermostat all nve
+
+compute   	0 all pair tersoff
+compute   	1 all pair coul/shield ecoul
+compute   	2 all pair ilp/graphene/hbn
+variable  	Tersoff  equal c_0     # Tersoff energy
+variable  	Ecoul    equal c_1     # Coulomb energy
+variable  	EILP     equal c_2     # total interlayer energy
+variable  	Evdw     equal c_2[1]  # attractive energy
+variable 	Erep     equal c_2[2]  # repulsive  energy
+
+############# Output ###############
+thermo          100
+thermo_style    custom step etotal pe ke v_Evdw v_Tersoff v_EILP v_Erep v_Evdw v_Ecoul temp
+thermo_modify   lost warn
+
+###### Run molecular dynamics ######
+run 		1000
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 18
+  ghost atom cutoff = 18
+  binsize = 9, bins = 5 5 12
+  4 neighbor lists, perpetual/occasional/extra = 4 0 0
+  (1) pair tersoff, perpetual
+      attributes: full, newton on
+      pair build: full/bin
+      stencil: full/bin/3d
+      bin: standard
+  (2) pair ilp/graphene/hbn, perpetual
+      attributes: full, newton on, ghost
+      pair build: full/bin/ghost
+      stencil: full/ghost/bin/3d
+      bin: standard
+  (3) pair coul/shield, perpetual, skip from (4)
+      attributes: half, newton on
+      pair build: skip
+      stencil: none
+      bin: none
+  (4) neighbor class addition, perpetual, half/full from (1)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 18.99 | 18.99 | 18.99 Mbytes
+Step TotEng PotEng KinEng v_Evdw v_Tersoff v_EILP v_Erep v_Evdw v_Ecoul Temp 
+       0   -10193.138   -10245.837    52.699361   -77.557069    -10208.73   -36.776483    40.780586   -77.557069  -0.33075117          300 
+     100   -10192.814   -10215.193     22.37957   -80.997619   -10177.878   -36.967736    44.029884   -80.997619  -0.34809915    127.39947 
+     200   -10192.922   -10221.807    28.884855   -86.370319   -10184.251   -37.168986    49.201334   -86.370319  -0.38644764    164.43191 
+     300   -10192.878   -10219.029    26.151464   -83.063924   -10182.349    -36.30412    46.759804   -83.063924  -0.37660157    148.87162 
+     400   -10192.892   -10218.834    25.942229   -78.394242   -10181.398   -37.110968    41.283274   -78.394242  -0.32494569    147.68051 
+     500   -10192.909   -10221.331    28.422213   -81.768531    -10184.03   -36.946226    44.822304   -81.768531  -0.35489965    161.79824 
+     600   -10192.886   -10219.371     26.48495   -86.278335   -10182.669    -36.29515    49.983185   -86.278335  -0.40636253    150.77004 
+     700   -10192.902    -10220.95    28.048108    -82.28873   -10183.208    -37.39374     44.89499    -82.28873  -0.34777958    159.66859 
+     800    -10192.88    -10218.51    25.630186   -78.011019   -10181.427   -36.754209    41.256811   -78.011019  -0.32904942    145.90415 
+     900   -10192.894    -10220.56    27.665437   -82.474379   -10183.801   -36.381157    46.093222   -82.474379  -0.37703328    157.49017 
+    1000   -10192.897    -10219.01     26.11313   -87.125683   -10181.252   -37.361898    49.763785   -87.125683  -0.39607952    148.65339 
+Loop time of 68.3631 on 4 procs for 1000 steps with 1360 atoms
+
+Performance: 1.264 ns/day, 18.990 hours/ns, 14.628 timesteps/s
+98.5% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 64.58      | 66.38      | 67.402     |  13.2 | 97.10
+Bond    | 0.0001719  | 0.00021869 | 0.00024033 |   0.0 |  0.00
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.93767    | 1.9601     | 3.76       |  77.0 |  2.87
+Output  | 0.00033593 | 0.00061601 | 0.0014501  |   0.0 |  0.00
+Modify  | 0.0085733  | 0.0089303  | 0.0093236  |   0.4 |  0.01
+Other   |            | 0.01285    |            |       |  0.02
+
+Nlocal:    340 ave 340 max 340 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost:    4536 ave 4536 max 4536 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs:    62390 ave 62390 max 62390 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs:  251260 ave 251260 max 251260 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1005040
+Ave neighs/atom = 739
+Ave special neighs/atom = 0
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:01:08

examples/USER/misc/ilp_graphene_hbn/log.31Jul19.grhBN.g++.1

@@ -0,0 +1,153 @@
+LAMMPS (31 Jul 2019)
+  using 1 OpenMP thread(s) per MPI task
+# Initialization
+units           metal
+boundary        p p p
+atom_style      full
+processors      * * 1     # domain decomposition over x and y
+
+# System and atom definition
+# we use different molecule ids for each layer
+# so that inter- and intra-layer
+# interactions can be specified separately
+read_data       gr_hBN_Cstack_2L_noH.data
+  orthogonal box = (0 0 0) to (44.583 42.9 100)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  1440 atoms
+  0 = max # of 1-2 neighbors
+  0 = max # of 1-3 neighbors
+  0 = max # of 1-4 neighbors
+  1 = max # of special neighbors
+  special bonds CPU = 0.000282049 secs
+  read_data CPU = 0.00159025 secs
+mass            1 10.8110   # boron    mass (g/mole) | membrane
+mass            2 14.0067   # nitrogen mass (g/mole) | membrane
+mass            3 12.0107   # carbon   mass (g/mole) | adsorbate
+# Separate atom groups
+group 		hBN molecule 1
+720 atoms in group hBN
+group 		gr  molecule 2
+720 atoms in group gr
+
+######################## Potential defition ########################
+pair_style  hybrid/overlay rebo tersoff ilp/graphene/hbn 16.0 coul/shield 16.0
+####################################################################
+pair_coeff  * * rebo               CH.rebo     NULL NULL C    # chemical
+Reading potential file CH.rebo with DATE: 2018-7-3
+pair_coeff  * * tersoff            BNC.tersoff B    N    NULL # chemical
+Reading potential file BNC.tersoff with DATE: 2013-03-21
+pair_coeff  * * ilp/graphene/hbn   BNCH.ILP    B    N    C    # long range
+pair_coeff  1 1 coul/shield 0.70
+pair_coeff  1 2 coul/shield 0.69498201415576216335
+pair_coeff  2 2 coul/shield 0.69
+####################################################################
+# Neighbor update settings
+neighbor        2.0 bin
+neigh_modify    every 1
+neigh_modify    delay 0
+neigh_modify    check yes
+
+#### Simulation settings ####
+timestep  	0.001
+velocity  	all create 300.0 12345 dist gaussian mom yes rot yes
+fix       	thermostat all nve
+
+compute   	0 all pair rebo
+compute   	1 all pair tersoff
+compute   	2 all pair ilp/graphene/hbn
+compute   	3 all pair coul/shield
+variable  	REBO     equal  c_0
+variable  	Tersoff  equal  c_1
+variable  	EILP     equal  c_2     # total interlayer energy
+variable  	Evdw     equal  c_2[1]  # attractive energy
+variable 	Erep     equal  c_2[2]  # repulsive  energy
+variable  	Ecoul    equal  c_3
+
+############# Output ##############
+thermo          100
+thermo_style    custom step etotal pe ke v_Evdw v_Tersoff v_REBO v_EILP v_Erep v_Evdw v_Ecoul temp
+
+###### Run molecular dynamics ######
+run 		1000
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 18
+  ghost atom cutoff = 18
+  binsize = 9, bins = 5 5 12
+  6 neighbor lists, perpetual/occasional/extra = 6 0 0
+  (1) pair rebo, perpetual, skip from (3)
+      attributes: full, newton on, ghost
+      pair build: skip/ghost
+      stencil: none
+      bin: none
+  (2) pair tersoff, perpetual, skip from (5)
+      attributes: full, newton on
+      pair build: skip
+      stencil: none
+      bin: none
+  (3) pair ilp/graphene/hbn, perpetual
+      attributes: full, newton on, ghost
+      pair build: full/bin/ghost
+      stencil: full/ghost/bin/3d
+      bin: standard
+  (4) pair coul/shield, perpetual, half/full from (2)
+      attributes: half, newton on
+      pair build: halffull/newton/skip
+      stencil: none
+      bin: none
+  (5) neighbor class addition, perpetual, copy from (3)
+      attributes: full, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+  (6) neighbor class addition, perpetual, half/full from (5)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 22.52 | 22.52 | 22.52 Mbytes
+Step TotEng PotEng KinEng v_Evdw v_Tersoff v_REBO v_EILP v_Erep v_Evdw v_Ecoul Temp 
+       0   -10707.284   -10763.085    55.801605   -75.247726   -5401.7348   -5322.2781   -39.072409    36.175318   -75.247726            0          300 
+     100   -10707.074   -10737.127     30.05353   -73.217322   -5389.9568   -5309.2004   -37.970102     35.24722   -73.217322            0    161.57347 
+     200   -10707.016   -10734.932     27.91576   -71.603097   -5389.1294   -5307.7455   -38.056875    33.546222   -71.603097            0    150.08042 
+     300   -10707.013   -10734.987    27.973705   -75.082134   -5388.9196   -5308.1165   -37.950947    37.131186   -75.082134            0    150.39194 
+     400   -10707.012   -10735.498    28.486171   -76.339871   -5389.1657    -5308.153   -38.179442    38.160429   -76.339871            0    153.14706 
+     500   -10707.007   -10734.681    27.674101   -73.312354   -5388.7261   -5307.7384   -38.216944     35.09541   -73.312354            0    148.78121 
+     600   -10707.018   -10735.833    28.815132   -71.927763   -5389.0798    -5308.596   -38.157333     33.77043   -71.927763            0    154.91561 
+     700    -10707.02   -10735.656    28.635377   -74.679371   -5389.2971   -5308.1866   -38.172002    36.507368   -74.679371            0    153.94921 
+     800   -10707.004   -10734.352    27.347425   -76.371288   -5388.5923   -5307.7206   -38.038736    38.332552   -76.371288            0    147.02494 
+     900   -10707.014   -10735.832    28.817405   -73.699332   -5388.9674   -5308.7964   -38.068078    35.631254   -73.699332            0    154.92783 
+    1000   -10706.995   -10733.562     26.56615   -71.439868   -5388.0186   -5307.4414   -38.101452    33.338415   -71.439868            0    142.82466 
+Loop time of 152.66 on 1 procs for 1000 steps with 1440 atoms
+
+Performance: 0.566 ns/day, 42.406 hours/ns, 6.550 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    | 152.52     | 152.52     | 152.52     |   0.0 | 99.91
+Bond    | 0.00023174 | 0.00023174 | 0.00023174 |   0.0 |  0.00
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.087147   | 0.087147   | 0.087147   |   0.0 |  0.06
+Output  | 0.0004189  | 0.0004189  | 0.0004189  |   0.0 |  0.00
+Modify  | 0.029972   | 0.029972   | 0.029972   |   0.0 |  0.02
+Other   |            | 0.02057    |            |       |  0.01
+
+Nlocal:    1440 ave 1440 max 1440 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    8180 ave 8180 max 8180 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    140400 ave 140400 max 140400 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  280800 ave 280800 max 280800 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 280800
+Ave neighs/atom = 195
+Ave special neighs/atom = 0
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:02:32

examples/USER/misc/ilp_graphene_hbn/log.31Jul19.grhBN.g++.4

@@ -0,0 +1,153 @@
+LAMMPS (31 Jul 2019)
+  using 1 OpenMP thread(s) per MPI task
+# Initialization
+units           metal
+boundary        p p p
+atom_style      full
+processors      * * 1     # domain decomposition over x and y
+
+# System and atom definition
+# we use different molecule ids for each layer
+# so that inter- and intra-layer
+# interactions can be specified separately
+read_data       gr_hBN_Cstack_2L_noH.data
+  orthogonal box = (0 0 0) to (44.583 42.9 100)
+  2 by 2 by 1 MPI processor grid
+  reading atoms ...
+  1440 atoms
+  0 = max # of 1-2 neighbors
+  0 = max # of 1-3 neighbors
+  0 = max # of 1-4 neighbors
+  1 = max # of special neighbors
+  special bonds CPU = 0.00012207 secs
+  read_data CPU = 0.00357461 secs
+mass            1 10.8110   # boron    mass (g/mole) | membrane
+mass            2 14.0067   # nitrogen mass (g/mole) | membrane
+mass            3 12.0107   # carbon   mass (g/mole) | adsorbate
+# Separate atom groups
+group 		hBN molecule 1
+720 atoms in group hBN
+group 		gr  molecule 2
+720 atoms in group gr
+
+######################## Potential defition ########################
+pair_style  hybrid/overlay rebo tersoff ilp/graphene/hbn 16.0 coul/shield 16.0
+####################################################################
+pair_coeff  * * rebo               CH.rebo     NULL NULL C    # chemical
+Reading potential file CH.rebo with DATE: 2018-7-3
+pair_coeff  * * tersoff            BNC.tersoff B    N    NULL # chemical
+Reading potential file BNC.tersoff with DATE: 2013-03-21
+pair_coeff  * * ilp/graphene/hbn   BNCH.ILP    B    N    C    # long range
+pair_coeff  1 1 coul/shield 0.70
+pair_coeff  1 2 coul/shield 0.69498201415576216335
+pair_coeff  2 2 coul/shield 0.69
+####################################################################
+# Neighbor update settings
+neighbor        2.0 bin
+neigh_modify    every 1
+neigh_modify    delay 0
+neigh_modify    check yes
+
+#### Simulation settings ####
+timestep  	0.001
+velocity  	all create 300.0 12345 dist gaussian mom yes rot yes
+fix       	thermostat all nve
+
+compute   	0 all pair rebo
+compute   	1 all pair tersoff
+compute   	2 all pair ilp/graphene/hbn
+compute   	3 all pair coul/shield
+variable  	REBO     equal  c_0
+variable  	Tersoff  equal  c_1
+variable  	EILP     equal  c_2     # total interlayer energy
+variable  	Evdw     equal  c_2[1]  # attractive energy
+variable 	Erep     equal  c_2[2]  # repulsive  energy
+variable  	Ecoul    equal  c_3
+
+############# Output ##############
+thermo          100
+thermo_style    custom step etotal pe ke v_Evdw v_Tersoff v_REBO v_EILP v_Erep v_Evdw v_Ecoul temp
+
+###### Run molecular dynamics ######
+run 		1000
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 18
+  ghost atom cutoff = 18
+  binsize = 9, bins = 5 5 12
+  6 neighbor lists, perpetual/occasional/extra = 6 0 0
+  (1) pair rebo, perpetual, skip from (3)
+      attributes: full, newton on, ghost
+      pair build: skip/ghost
+      stencil: none
+      bin: none
+  (2) pair tersoff, perpetual, skip from (5)
+      attributes: full, newton on
+      pair build: skip
+      stencil: none
+      bin: none
+  (3) pair ilp/graphene/hbn, perpetual
+      attributes: full, newton on, ghost
+      pair build: full/bin/ghost
+      stencil: full/ghost/bin/3d
+      bin: standard
+  (4) pair coul/shield, perpetual, half/full from (2)
+      attributes: half, newton on
+      pair build: halffull/newton/skip
+      stencil: none
+      bin: none
+  (5) neighbor class addition, perpetual, copy from (3)
+      attributes: full, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+  (6) neighbor class addition, perpetual, half/full from (5)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 12.45 | 12.45 | 12.45 Mbytes
+Step TotEng PotEng KinEng v_Evdw v_Tersoff v_REBO v_EILP v_Erep v_Evdw v_Ecoul Temp 
+       0   -10707.284   -10763.085    55.801605   -75.247726   -5401.7348   -5322.2781   -39.072409    36.175318   -75.247726            0          300 
+     100   -10707.074   -10737.127     30.05353   -73.217322   -5389.9568   -5309.2004   -37.970102     35.24722   -73.217322            0    161.57347 
+     200   -10707.016   -10734.932     27.91576   -71.603097   -5389.1294   -5307.7455   -38.056875    33.546222   -71.603097            0    150.08042 
+     300   -10707.013   -10734.987    27.973705   -75.082134   -5388.9196   -5308.1165   -37.950947    37.131186   -75.082134            0    150.39194 
+     400   -10707.012   -10735.498    28.486171   -76.339871   -5389.1657    -5308.153   -38.179442    38.160429   -76.339871            0    153.14706 
+     500   -10707.007   -10734.681    27.674101   -73.312354   -5388.7261   -5307.7384   -38.216944     35.09541   -73.312354            0    148.78121 
+     600   -10707.018   -10735.833    28.815132   -71.927763   -5389.0798    -5308.596   -38.157333     33.77043   -71.927763            0    154.91561 
+     700    -10707.02   -10735.656    28.635377   -74.679371   -5389.2971   -5308.1866   -38.172002    36.507368   -74.679371            0    153.94921 
+     800   -10707.004   -10734.352    27.347425   -76.371288   -5388.5923   -5307.7206   -38.038736    38.332552   -76.371288            0    147.02494 
+     900   -10707.014   -10735.832    28.817405   -73.699332   -5388.9674   -5308.7964   -38.068078    35.631254   -73.699332            0    154.92783 
+    1000   -10706.995   -10733.562     26.56615   -71.439868   -5388.0186   -5307.4414   -38.101452    33.338415   -71.439868            0    142.82466 
+Loop time of 54.095 on 4 procs for 1000 steps with 1440 atoms
+
+Performance: 1.597 ns/day, 15.026 hours/ns, 18.486 timesteps/s
+84.8% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 42.138     | 45.531     | 49.106     |  42.0 | 84.17
+Bond    | 0.0003159  | 0.00037384 | 0.000489   |   0.0 |  0.00
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 4.71       | 8.2803     | 11.682     |  98.3 | 15.31
+Output  | 0.0021999  | 0.0055975  | 0.013382   |   6.0 |  0.01
+Modify  | 0.0092845  | 0.010981   | 0.012538   |   1.3 |  0.02
+Other   |            | 0.2673     |            |       |  0.49
+
+Nlocal:    360 ave 380 max 340 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Nghost:    4716 ave 4736 max 4696 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Neighs:    35100 ave 37050 max 33150 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+FullNghs:  70200 ave 74100 max 66300 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+
+Total # of neighbors = 280800
+Ave neighs/atom = 195
+Ave special neighs/atom = 0
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:54

examples/USER/misc/ilp_graphene_hbn/log.31Jul19.ilp_graphene_hbn.g++.1

@@ -0,0 +1,154 @@
+LAMMPS (31 Jul 2019)
+  using 1 OpenMP thread(s) per MPI task
+# Initialization
+units           metal
+boundary        p p p
+atom_style      full
+processors      * * 1     # domain decomposition over x and y
+
+# System and atom definition
+# we use 2 atom types so that inter- and intra-layer
+# interactions can be specified separately
+read_data       hBN_AB_stack_2L_noH_equi_300K.data
+  orthogonal box = (0 0 0) to (43.38 42.5773 100)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  1360 atoms
+  reading velocities ...
+  1360 velocities
+  0 = max # of 1-2 neighbors
+  0 = max # of 1-3 neighbors
+  0 = max # of 1-4 neighbors
+  1 = max # of special neighbors
+  special bonds CPU = 0.000251532 secs
+  read_data CPU = 0.00451231 secs
+mass            1 10.8110   # boron mass (g/mole) | membrane
+mass            2 14.0067   # nitrogen mass (g/mole) | adsorbate
+mass            3 10.8110   # boron mass (g/mole) | membrane
+mass            4 14.0067   # nitrogen mass (g/mole) | adsorbate
+# Separate atom groups
+group membrane  type 1 2
+680 atoms in group membrane
+group adsorbate type 3 4
+680 atoms in group adsorbate
+
+######################## Potential defition ########################
+pair_style  hybrid/overlay  tersoff  ilp/graphene/hbn 16.0 coul/shield 16.0 1
+####################################################################
+pair_coeff  * * tersoff          BNC.tersoff   NULL NULL B N  # chemical
+Reading potential file BNC.tersoff with DATE: 2013-03-21
+pair_coeff  * * ilp/graphene/hbn BNCH-old.ILP  B N B N  # long range
+pair_coeff  1 3 coul/shield 0.70
+pair_coeff  1 4 coul/shield 0.69498201415576216335
+pair_coeff  2 3 coul/shield 0.69498201415576216335
+pair_coeff  2 4 coul/shield 0.69
+####################################################################
+# Neighbor update settings
+neighbor        2.0 bin
+neigh_modify    every 1
+neigh_modify    delay 0
+neigh_modify    check yes
+
+#### Simulation settings ####
+timestep  0.001
+#velocity  adsorbate create 300.0 12345
+fix       subf membrane setforce 0.0 0.0 0.0
+fix       thermostat all nve
+
+compute   0 all pair tersoff
+compute   1 all pair coul/shield ecoul
+compute   2 all pair ilp/graphene/hbn
+variable  Tersoff  equal c_0
+variable  Ecoul    equal c_1
+variable  ILP      equal c_2
+variable  Evdw     equal c_2[1]
+variable  Erep     equal c_2[2]
+
+############################
+
+# Output
+thermo          100
+thermo_style    custom step etotal pe ke v_Tersoff v_ILP v_Ecoul v_Erep v_Evdw temp
+thermo_modify   lost warn #ignore
+
+#dump            1 all custom 1000 traj.lammpstrj id mol type xu yu zu
+#dump_modify     1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
+
+###### Run molecular dynamics ######
+run 1000
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 18
+  ghost atom cutoff = 18
+  binsize = 9, bins = 5 5 12
+  5 neighbor lists, perpetual/occasional/extra = 5 0 0
+  (1) pair tersoff, perpetual, skip from (4)
+      attributes: full, newton on
+      pair build: skip
+      stencil: none
+      bin: none
+  (2) pair ilp/graphene/hbn, perpetual
+      attributes: full, newton on, ghost
+      pair build: full/bin/ghost
+      stencil: full/ghost/bin/3d
+      bin: standard
+  (3) pair coul/shield, perpetual, skip from (5)
+      attributes: half, newton on
+      pair build: skip
+      stencil: none
+      bin: none
+  (4) neighbor class addition, perpetual, copy from (2)
+      attributes: full, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+  (5) neighbor class addition, perpetual, half/full from (4)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 54.59 | 54.59 | 54.59 Mbytes
+Step TotEng PotEng KinEng v_Tersoff v_ILP v_Ecoul v_Erep v_Evdw Temp 
+       0   -5114.6628   -5127.8586    13.195828   -5091.4121   -36.083114  -0.36343598    38.918674   -75.001787    75.119474 
+     100   -5114.6621   -5127.6958    13.033777   -5091.2408    -36.09276  -0.36228286    38.769906   -74.862666    74.196973 
+     200   -5114.6631   -5127.5945     12.93145   -5091.1508   -36.086669  -0.35708801     38.20076   -74.287429    73.614462 
+     300   -5114.6694   -5128.3286     13.65924   -5091.8646   -36.110786  -0.35328159    37.758284    -73.86907    77.757528 
+     400   -5114.6614   -5127.6424    12.980975   -5091.2348   -36.049634  -0.35794328    38.247252   -74.296886    73.896389 
+     500     -5114.66   -5127.4098    12.749794   -5090.9285   -36.119571  -0.36174976    38.745548   -74.865119    72.580351 
+     600   -5114.6673   -5128.0913    13.424021   -5091.6339    -36.09384  -0.36356991    38.927401   -75.021241    76.418503 
+     700    -5114.661   -5127.7467    13.085707   -5091.2811   -36.106639  -0.35892399    38.332616   -74.439255    74.492596 
+     800   -5114.6623    -5128.013    13.350778   -5091.5694   -36.089718  -0.35392503    37.851602    -73.94132    76.001554 
+     900   -5114.6675   -5128.1497    13.482146   -5091.6704   -36.124679  -0.35462869    37.885183   -74.009861    76.749392 
+    1000   -5114.6683   -5128.3365    13.668146    -5091.937   -36.037596  -0.36184347    38.709718   -74.747314    77.808228 
+Loop time of 207.028 on 1 procs for 1000 steps with 1360 atoms
+
+Performance: 0.417 ns/day, 57.508 hours/ns, 4.830 timesteps/s
+99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 206.9      | 206.9      | 206.9      |   0.0 | 99.94
+Bond    | 0.00019169 | 0.00019169 | 0.00019169 |   0.0 |  0.00
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.081397   | 0.081397   | 0.081397   |   0.0 |  0.04
+Output  | 0.00036597 | 0.00036597 | 0.00036597 |   0.0 |  0.00
+Modify  | 0.033408   | 0.033408   | 0.033408   |   0.0 |  0.02
+Other   |            | 0.01615    |            |       |  0.01
+
+Nlocal:    1360 ave 1360 max 1360 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    7840 ave 7840 max 7840 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    249628 ave 249628 max 249628 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  253390 ave 253390 max 253390 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 253390
+Ave neighs/atom = 186.316
+Ave special neighs/atom = 0
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:03:27

examples/USER/misc/ilp_graphene_hbn/log.31Jul19.ilp_graphene_hbn.g++.4

@@ -0,0 +1,154 @@
+LAMMPS (31 Jul 2019)
+  using 1 OpenMP thread(s) per MPI task
+# Initialization
+units           metal
+boundary        p p p
+atom_style      full
+processors      * * 1     # domain decomposition over x and y
+
+# System and atom definition
+# we use 2 atom types so that inter- and intra-layer
+# interactions can be specified separately
+read_data       hBN_AB_stack_2L_noH_equi_300K.data
+  orthogonal box = (0 0 0) to (43.38 42.5773 100)
+  2 by 2 by 1 MPI processor grid
+  reading atoms ...
+  1360 atoms
+  reading velocities ...
+  1360 velocities
+  0 = max # of 1-2 neighbors
+  0 = max # of 1-3 neighbors
+  0 = max # of 1-4 neighbors
+  1 = max # of special neighbors
+  special bonds CPU = 0.000332117 secs
+  read_data CPU = 0.00270581 secs
+mass            1 10.8110   # boron mass (g/mole) | membrane
+mass            2 14.0067   # nitrogen mass (g/mole) | adsorbate
+mass            3 10.8110   # boron mass (g/mole) | membrane
+mass            4 14.0067   # nitrogen mass (g/mole) | adsorbate
+# Separate atom groups
+group membrane  type 1 2
+680 atoms in group membrane
+group adsorbate type 3 4
+680 atoms in group adsorbate
+
+######################## Potential defition ########################
+pair_style  hybrid/overlay  tersoff  ilp/graphene/hbn 16.0 coul/shield 16.0 1
+####################################################################
+pair_coeff  * * tersoff          BNC.tersoff   NULL NULL B N  # chemical
+Reading potential file BNC.tersoff with DATE: 2013-03-21
+pair_coeff  * * ilp/graphene/hbn BNCH-old.ILP  B N B N  # long range
+pair_coeff  1 3 coul/shield 0.70
+pair_coeff  1 4 coul/shield 0.69498201415576216335
+pair_coeff  2 3 coul/shield 0.69498201415576216335
+pair_coeff  2 4 coul/shield 0.69
+####################################################################
+# Neighbor update settings
+neighbor        2.0 bin
+neigh_modify    every 1
+neigh_modify    delay 0
+neigh_modify    check yes
+
+#### Simulation settings ####
+timestep  0.001
+#velocity  adsorbate create 300.0 12345
+fix       subf membrane setforce 0.0 0.0 0.0
+fix       thermostat all nve
+
+compute   0 all pair tersoff
+compute   1 all pair coul/shield ecoul
+compute   2 all pair ilp/graphene/hbn
+variable  Tersoff  equal c_0
+variable  Ecoul    equal c_1
+variable  ILP      equal c_2
+variable  Evdw     equal c_2[1]
+variable  Erep     equal c_2[2]
+
+############################
+
+# Output
+thermo          100
+thermo_style    custom step etotal pe ke v_Tersoff v_ILP v_Ecoul v_Erep v_Evdw temp
+thermo_modify   lost warn #ignore
+
+#dump            1 all custom 1000 traj.lammpstrj id mol type xu yu zu
+#dump_modify     1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
+
+###### Run molecular dynamics ######
+run 1000
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 18
+  ghost atom cutoff = 18
+  binsize = 9, bins = 5 5 12
+  5 neighbor lists, perpetual/occasional/extra = 5 0 0
+  (1) pair tersoff, perpetual, skip from (4)
+      attributes: full, newton on
+      pair build: skip
+      stencil: none
+      bin: none
+  (2) pair ilp/graphene/hbn, perpetual
+      attributes: full, newton on, ghost
+      pair build: full/bin/ghost
+      stencil: full/ghost/bin/3d
+      bin: standard
+  (3) pair coul/shield, perpetual, skip from (5)
+      attributes: half, newton on
+      pair build: skip
+      stencil: none
+      bin: none
+  (4) neighbor class addition, perpetual, copy from (2)
+      attributes: full, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+  (5) neighbor class addition, perpetual, half/full from (4)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 28.9 | 28.9 | 28.9 Mbytes
+Step TotEng PotEng KinEng v_Tersoff v_ILP v_Ecoul v_Erep v_Evdw Temp 
+       0   -5114.6628   -5127.8586    13.195828   -5091.4121   -36.083114  -0.36343598    38.918674   -75.001787    75.119474 
+     100   -5114.6621   -5127.6958    13.033777   -5091.2408    -36.09276  -0.36228286    38.769906   -74.862666    74.196973 
+     200   -5114.6631   -5127.5945     12.93145   -5091.1508   -36.086669  -0.35708801     38.20076   -74.287429    73.614462 
+     300   -5114.6694   -5128.3286     13.65924   -5091.8646   -36.110786  -0.35328159    37.758284    -73.86907    77.757528 
+     400   -5114.6614   -5127.6424    12.980975   -5091.2348   -36.049634  -0.35794328    38.247252   -74.296886    73.896389 
+     500     -5114.66   -5127.4098    12.749794   -5090.9285   -36.119571  -0.36174976    38.745548   -74.865119    72.580351 
+     600   -5114.6673   -5128.0913    13.424021   -5091.6339    -36.09384  -0.36356991    38.927401   -75.021241    76.418503 
+     700    -5114.661   -5127.7467    13.085707   -5091.2811   -36.106639  -0.35892399    38.332616   -74.439255    74.492596 
+     800   -5114.6623    -5128.013    13.350778   -5091.5694   -36.089718  -0.35392503    37.851602    -73.94132    76.001554 
+     900   -5114.6675   -5128.1497    13.482146   -5091.6704   -36.124679  -0.35462869    37.885183   -74.009861    76.749392 
+    1000   -5114.6683   -5128.3365    13.668146    -5091.937   -36.037596  -0.36184347    38.709718   -74.747314    77.808228 
+Loop time of 65.9005 on 4 procs for 1000 steps with 1360 atoms
+
+Performance: 1.311 ns/day, 18.306 hours/ns, 15.174 timesteps/s
+98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 63.244     | 64.208     | 65.281     |  10.1 | 97.43
+Bond    | 0.00013971 | 0.00017679 | 0.00022101 |   0.0 |  0.00
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.58237    | 1.6612     | 2.6292     |  63.1 |  2.52
+Output  | 0.0003171  | 0.00062358 | 0.0015192  |   0.0 |  0.00
+Modify  | 0.010251   | 0.010509   | 0.01075    |   0.2 |  0.02
+Other   |            | 0.02025    |            |       |  0.03
+
+Nlocal:    340 ave 346 max 336 min
+Histogram: 1 0 1 0 1 0 0 0 0 1
+Nghost:    4537.5 ave 4540 max 4534 min
+Histogram: 1 0 0 0 0 0 2 0 0 1
+Neighs:    62407 ave 62413 max 62402 min
+Histogram: 1 0 0 1 1 0 0 0 0 1
+FullNghs:  63347.5 ave 65585 max 61866 min
+Histogram: 1 1 0 1 0 0 0 0 0 1
+
+Total # of neighbors = 253926
+Ave neighs/atom = 186.71
+Ave special neighs/atom = 0
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:01:06