Merge with current master

.github/PULL_REQUEST_TEMPLATE.md

@@ -4,7 +4,7 @@ _Briefly describe the new feature(s), enhancement(s), or bugfix(es) included in
 
 **Related Issues**
 
-__If this addresses an open GitHub Issue, mention the issue number here. Use the phrases `fixes #221` or `closes #135`, when you want those issues to be automatically closed when the pull request is merged_
+_If this addresses an open GitHub issue for this project, please mention the issue number here, and describe the relation. Use the phrases `fixes #221` or `closes #135`, when you want an issue to be automatically closed when the pull request is merged_
 
 **Author(s)**
 
@@ -16,7 +16,7 @@ By submitting this pull request, I agree, that my contribution will be included
 
 **Backward Compatibility**
 
-_Please state whether any changes in the pull request break backward compatibility for inputs, and - if yes - explain what has been changed and why_
+_Please state whether any changes in the pull request will break backward compatibility for inputs, and - if yes - explain what has been changed and why_
 
 **Implementation Notes**
 
@@ -24,7 +24,7 @@ _Provide any relevant details about how the changes are implemented, how correct
 
 **Post Submission Checklist**
 
-_Please check the fields below as they are completed **after** the pull request has been submitted_
+_Please check the fields below as they are completed **after** the pull request has been submitted. Delete lines that don't apply_
 
 - [ ] The feature or features in this pull request is complete
 - [ ] Licensing information is complete

cmake/CMakeLists.txt

@@ -11,6 +11,8 @@ get_filename_component(LAMMPS_LIB_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../lib
 get_filename_component(LAMMPS_LIB_BINARY_DIR ${CMAKE_BINARY_DIR}/lib ABSOLUTE)
 get_filename_component(LAMMPS_DOC_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../doc ABSOLUTE)
 
+find_package(Git)
+
 # by default, install into $HOME/.local (not /usr/local), so that no root access (and sudo!!) is needed
 if (CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
   set(CMAKE_INSTALL_PREFIX "$ENV{HOME}/.local" CACHE PATH "default install path" FORCE )
@@ -85,7 +87,7 @@ string(TOUPPER "${CMAKE_BUILD_TYPE}" BTYPE)
 # this is fast, so check for it all the time
 message(STATUS "Running check for auto-generated files from make-based build system")
 file(GLOB SRC_AUTOGEN_FILES ${LAMMPS_SOURCE_DIR}/style_*.h)
-list(APPEND SRC_AUTOGEN_FILES ${LAMMPS_SOURCE_DIR}/lmpinstalledpkgs.h)
+list(APPEND SRC_AUTOGEN_FILES ${LAMMPS_SOURCE_DIR}/lmpinstalledpkgs.h ${LAMMPS_SOURCE_DIR}/lmpgitversion.h)
 foreach(_SRC ${SRC_AUTOGEN_FILES})
   get_filename_component(FILENAME "${_SRC}" NAME)
   if(EXISTS ${LAMMPS_SOURCE_DIR}/${FILENAME})
@@ -320,7 +322,7 @@ pkg_depends(USER-SCAFACOS MPI)
 
 find_package(OpenMP QUIET)
 option(BUILD_OMP "Build with OpenMP support" ${OpenMP_FOUND})
-if(BUILD_OMP OR PKG_KOKKOS OR PKG_USER-INTEL)
+if(BUILD_OMP)
   find_package(OpenMP REQUIRED)
   set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")
   set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
@@ -379,19 +381,10 @@ if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE)
 endif()
 
 if(PKG_PYTHON)
-  find_package(PythonInterp REQUIRED)
   find_package(PythonLibs REQUIRED)
   add_definitions(-DLMP_PYTHON)
   include_directories(${PYTHON_INCLUDE_DIR})
   list(APPEND LAMMPS_LINK_LIBS ${PYTHON_LIBRARY})
-  if(BUILD_LIB AND BUILD_SHARED_LIBS)
-    if(NOT PYTHON_INSTDIR)
-      execute_process(COMMAND ${PYTHON_EXECUTABLE}
-        -c "import distutils.sysconfig as cg; print(cg.get_python_lib(1,0,prefix='${CMAKE_INSTALL_PREFIX}'))"
-        OUTPUT_VARIABLE PYTHON_INSTDIR OUTPUT_STRIP_TRAILING_WHITESPACE)
-    endif()
-    install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/../python/lammps.py DESTINATION ${PYTHON_INSTDIR})
-  endif()
 endif()
 
 find_package(JPEG QUIET)
@@ -567,6 +560,20 @@ if(PKG_USER-PLUMED)
 
   option(DOWNLOAD_PLUMED "Download Plumed package instead of using an already installed one" OFF)
   if(DOWNLOAD_PLUMED)
+    if(BUILD_MPI)
+      set(PLUMED_CONFIG_MPI "--enable-mpi")
+      set(PLUMED_CONFIG_CC  ${CMAKE_MPI_C_COMPILER})
+      set(PLUMED_CONFIG_CXX  ${CMAKE_MPI_CXX_COMPILER})
+    else()
+      set(PLUMED_CONFIG_MPI "--disable-mpi")
+      set(PLUMED_CONFIG_CC  ${CMAKE_C_COMPILER})
+      set(PLUMED_CONFIG_CXX  ${CMAKE_CXX_COMPILER})
+    endif()
+    if(BUILD_OMP)
+      set(PLUMED_CONFIG_OMP "--enable-openmp")
+    else()
+      set(PLUMED_CONFIG_OMP "--disable-openmp")
+    endif()
     message(STATUS "PLUMED download requested - we will build our own")
     include(ExternalProject)
     ExternalProject_Add(plumed_build
@@ -576,8 +583,10 @@ if(PKG_USER-PLUMED)
       CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR>
                                                ${CONFIGURE_REQUEST_PIC}
                                                --enable-modules=all
-                                               CXX=${CMAKE_MPI_CXX_COMPILER}
+                                               ${PLUMED_CONFIG_MPI}
-                                               CC=${CMAKE_MPI_C_COMPILER}
+                                               ${PLUMED_CONFIG_OMP}
+                                               CXX=${PLUMED_CONFIG_CXX}
+                                               CC=${PLUMED_CONFIG_CC}
     )
     ExternalProject_get_property(plumed_build INSTALL_DIR)
     set(PLUMED_INSTALL_DIR ${INSTALL_DIR})
@@ -611,9 +620,13 @@ if(PKG_USER-PLUMED)
 endif()
 
 if(PKG_USER-MOLFILE)
+  set(MOLFILE_INCLUDE_DIRS "${LAMMPS_LIB_SOURCE_DIR}/molfile" CACHE STRING "Path to VMD molfile plugin headers")
   add_library(molfile INTERFACE)
-  target_include_directories(molfile INTERFACE ${LAMMPS_LIB_SOURCE_DIR}/molfile)
+  target_include_directories(molfile INTERFACE ${MOLFILE_INCLUDE_DIRS})
+  # no need to link with -ldl on windows
+  if(NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
     target_link_libraries(molfile INTERFACE ${CMAKE_DL_LIBS})
+  endif()
   list(APPEND LAMMPS_LINK_LIBS molfile)
 endif()
 
@@ -624,7 +637,6 @@ if(PKG_USER-NETCDF)
   add_definitions(-DLMP_HAS_NETCDF -DNC_64BIT_DATA=0x0020)
 endif()
 
-
 if(PKG_USER-SMD)
   option(DOWNLOAD_EIGEN3 "Download Eigen3 instead of using an already installed one)" OFF)
   if(DOWNLOAD_EIGEN3)
@@ -668,15 +680,21 @@ if(PKG_USER-VTK)
 endif()
 
 if(PKG_KIM)
-  option(DOWNLOAD_KIM "Download KIM-API v2 from OpenKIM instead of using an already installed one" OFF)
+  find_package(CURL)
+  if(CURL_FOUND)
+    include_directories(${CURL_INCLUDE_DIRS})
+    list(APPEND LAMMPS_LINK_LIBS ${CURL_LIBRARIES})
+    add_definitions(-DLMP_KIM_CURL)
+  endif()
+  option(DOWNLOAD_KIM "Download KIM-API from OpenKIM instead of using an already installed one" OFF)
   if(DOWNLOAD_KIM)
-    message(STATUS "KIM-API v2 download requested - we will build our own")
+    message(STATUS "KIM-API download requested - we will build our own")
     enable_language(C)
     enable_language(Fortran)
     include(ExternalProject)
     ExternalProject_Add(kim_build
-      URL https://s3.openkim.org/kim-api/kim-api-v2-2.0.1.txz
+      URL https://s3.openkim.org/kim-api/kim-api-2.0.2.txz
-      URL_MD5 289c57f0c3bc2a549662283cac1c4ef1
+      URL_MD5 537d9c0abd30f85b875ebb584f9143fa
       BINARY_DIR build
       CMAKE_ARGS -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
                  -DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}
@@ -685,17 +703,17 @@ if(PKG_KIM)
                  -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
       )
     ExternalProject_get_property(kim_build INSTALL_DIR)
-    set(KIM-API-V2_INCLUDE_DIRS ${INSTALL_DIR}/include/kim-api-v2)
+    set(KIM-API_INCLUDE_DIRS ${INSTALL_DIR}/include/kim-api)
-    set(KIM-API-V2_LDFLAGS ${INSTALL_DIR}/${CMAKE_INSTALL_LIBDIR}/libkim-api-v2${CMAKE_SHARED_LIBRARY_SUFFIX})
+    set(KIM-API_LDFLAGS ${INSTALL_DIR}/${CMAKE_INSTALL_LIBDIR}/libkim-api${CMAKE_SHARED_LIBRARY_SUFFIX})
     list(APPEND LAMMPS_DEPS kim_build)
   else()
-    find_package(KIM-API-V2)
+    find_package(KIM-API)
-    if(NOT KIM-API-V2_FOUND)
+    if(NOT KIM-API_FOUND)
-      message(FATAL_ERROR "KIM-API v2 not found, help CMake to find it by setting PKG_CONFIG_PATH, or set DOWNLOAD_KIM=ON to download it")
+      message(FATAL_ERROR "KIM-API not found, help CMake to find it by setting PKG_CONFIG_PATH, or set DOWNLOAD_KIM=ON to download it")
     endif()
   endif()
-  list(APPEND LAMMPS_LINK_LIBS "${KIM-API-V2_LDFLAGS}")
+  list(APPEND LAMMPS_LINK_LIBS "${KIM-API_LDFLAGS}")
-  include_directories(${KIM-API-V2_INCLUDE_DIRS})
+  include_directories(${KIM-API_INCLUDE_DIRS})
 endif()
 
 if(PKG_MESSAGE)
@@ -710,6 +728,7 @@ if(PKG_MESSAGE)
     set_target_properties(cslib PROPERTIES OUTPUT_NAME "csmpi")
   else()
     target_compile_definitions(cslib PRIVATE -DMPI_NO)
+    target_include_directories(cslib PRIVATE ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/src/STUBS_MPI)
     set_target_properties(cslib PROPERTIES OUTPUT_NAME "csnompi")
   endif()
 
@@ -945,7 +964,7 @@ if(PKG_USER-OMP)
 
     # detects styles which have USER-OMP version
     RegisterStylesExt(${USER-OMP_SOURCES_DIR} omp OMP_SOURCES)
-    RegisterFixStyle("${USER-OMP_SOURCES_DIR}/fix_omp.h")
+    RegisterFixStyle(${USER-OMP_SOURCES_DIR}/fix_omp.h)
 
     get_property(USER-OMP_SOURCES GLOBAL PROPERTY OMP_SOURCES)
 
@@ -1058,24 +1077,10 @@ if(PKG_OPT)
 endif()
 
 if(PKG_USER-INTEL)
-    find_package(TBB REQUIRED)
+  if(LAMMPS_SIZES STREQUAL BIGBIG)
-    find_package(MKL REQUIRED)
+    message(FATAL_ERROR "The USER-INTEL Package is not compatible with -DLAMMPS_BIGBIG")
-
-    if(NOT CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
-      message(FATAL_ERROR "USER-INTEL is only useful together with intel compiler")
-    endif()
-
-    if(CMAKE_CXX_COMPILER_VERSION VERSION_LESS 16)
-        message(FATAL_ERROR "USER-INTEL needs at least a 2016 intel compiler, found ${CMAKE_CXX_COMPILER_VERSION}")
-    endif()
-
-    if(NOT BUILD_OMP)
-        message(FATAL_ERROR "USER-INTEL requires OpenMP")
-    endif()
-
-    if(NOT ${LAMMPS_MEMALIGN} STREQUAL "64")
-        message(FATAL_ERROR "USER-INTEL is only useful with LAMMPS_MEMALIGN=64")
   endif()
+  add_definitions(-DLMP_USER_INTEL)
 
   set(INTEL_ARCH "cpu" CACHE STRING "Architectures used by USER-INTEL (cpu or knl)")
   set(INTEL_ARCH_VALUES cpu knl)
@@ -1083,12 +1088,68 @@ if(PKG_USER-INTEL)
   validate_option(INTEL_ARCH INTEL_ARCH_VALUES)
   string(TOUPPER ${INTEL_ARCH} INTEL_ARCH)
 
+  find_package(Threads QUIET)
+  if(Threads_FOUND)
+    set(INTEL_LRT_MODE "threads" CACHE STRING "Long-range threads mode (none, threads, or c++11)")
+  else()
+    set(INTEL_LRT_MODE "none" CACHE STRING "Long-range threads mode (none, threads, or c++11)")
+  endif()
+  set(INTEL_LRT_VALUES none threads c++11)
+  set_property(CACHE INTEL_LRT_MODE PROPERTY STRINGS ${INTEL_LRT_VALUES})
+  validate_option(INTEL_LRT_MODE INTEL_LRT_VALUES)
+  string(TOUPPER ${INTEL_LRT_MODE} INTEL_LRT_MODE)
+  if(INTEL_LRT_MODE STREQUAL "THREADS")
+    if(Threads_FOUND)
+      add_definitions(-DLMP_INTEL_USELRT)
+      list(APPEND LAMMPS_LINK_LIBS ${CMAKE_THREAD_LIBS_INIT})
+    else()
+      message(FATAL_ERROR "Must have working threads library for Long-range thread support")
+    endif()
+  endif()
+  if(INTEL_LRT_MODE STREQUAL "C++11")
+    add_definitions(-DLMP_INTEL_USERLRT -DLMP_INTEL_LRT11)
+  endif()
+
+  if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
+    if(CMAKE_CXX_COMPILER_VERSION VERSION_LESS 16)
+      message(FATAL_ERROR "USER-INTEL needs at least a 2016 Intel compiler, found ${CMAKE_CXX_COMPILER_VERSION}")
+    endif()
+  else()
+    message(WARNING "USER-INTEL gives best performance with Intel compilers")
+  endif()
+
+  find_package(TBB QUIET)
+  if(TBB_FOUND)
+    list(APPEND LAMMPS_LINK_LIBS ${TBB_MALLOC_LIBRARIES})
+  else()
+    add_definitions(-DLMP_INTEL_NO_TBB)
+    if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
+      message(WARNING "USER-INTEL with Intel compilers should use TBB malloc libraries")
+    endif()
+  endif()
+
+  find_package(MKL QUIET)
+  if(MKL_FOUND)
+    add_definitions(-DLMP_USE_MKL_RNG)
+    list(APPEND LAMMPS_LINK_LIBS ${MKL_LIBRARIES})
+  else()
+    message(STATUS "Pair style dpd/intel will be faster with MKL libraries")
+  endif()
+
+  if((NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows") AND (NOT ${LAMMPS_MEMALIGN} STREQUAL "64") AND (NOT ${LAMMPS_MEMALIGN} STREQUAL "128") AND (NOT ${LAMMPS_MEMALIGN} STREQUAL "256"))
+    message(FATAL_ERROR "USER-INTEL only supports memory alignment of 64, 128 or 256 on this platform")
+  endif()
+
   if(INTEL_ARCH STREQUAL "KNL")
+    if(NOT CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
+      message(FATAL_ERROR "Must use Intel compiler with USER-INTEL for KNL architecture")
+    endif()
     set(CMAKE_EXE_LINKER_FLAGS  "${CMAKE_EXE_LINKER_FLAGS} -xHost -qopenmp -qoffload")
     set(MIC_OPTIONS "-qoffload-option,mic,compiler,\"-fp-model fast=2 -mGLOB_default_function_attrs=\\\"gather_scatter_loop_unroll=4\\\"\"")
     add_compile_options(-xMIC-AVX512 -qoffload -fno-alias -ansi-alias -restrict -qoverride-limits ${MIC_OPTIONS})
     add_definitions(-DLMP_INTEL_OFFLOAD)
   else()
+    if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
       if(CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.3 OR CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.4)
         set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -xCOMMON-AVX512")
       else()
@@ -1101,28 +1162,28 @@ if(PKG_USER-INTEL)
           add_compile_options(${_FLAG})
         endif()
       endforeach()
+    else()
+      add_compile_options(-O3 -ffast-math)
+    endif()
   endif()
 
-    add_definitions(-DLMP_INTEL_USELRT -DLMP_USE_MKL_RNG)
+  # collect sources
-
-    list(APPEND LAMMPS_LINK_LIBS ${TBB_MALLOC_LIBRARIES} ${MKL_LIBRARIES})
-
   set(USER-INTEL_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/USER-INTEL)
-    set(USER-INTEL_SOURCES ${USER-INTEL_SOURCES_DIR}/intel_preprocess.h
+  set(USER-INTEL_SOURCES ${USER-INTEL_SOURCES_DIR}/fix_intel.cpp
-                           ${USER-INTEL_SOURCES_DIR}/intel_buffers.h
+                         ${USER-INTEL_SOURCES_DIR}/fix_nh_intel.cpp
                          ${USER-INTEL_SOURCES_DIR}/intel_buffers.cpp
-                           ${USER-INTEL_SOURCES_DIR}/math_extra_intel.h
-                           ${USER-INTEL_SOURCES_DIR}/nbin_intel.h
                          ${USER-INTEL_SOURCES_DIR}/nbin_intel.cpp
-                           ${USER-INTEL_SOURCES_DIR}/npair_intel.h
                          ${USER-INTEL_SOURCES_DIR}/npair_intel.cpp
-                           ${USER-INTEL_SOURCES_DIR}/intel_simd.h
+                         ${USER-INTEL_SOURCES_DIR}/verlet_lrt_intel.cpp)
-                           ${USER-INTEL_SOURCES_DIR}/intel_intrinsics.h)
 
   set_property(GLOBAL PROPERTY "USER-INTEL_SOURCES" "${USER-INTEL_SOURCES}")
 
-    # detects styles which have USER-INTEL version
+  # detect styles which have a USER-INTEL version
-    RegisterStylesExt(${USER-INTEL_SOURCES_DIR} opt USER-INTEL_SOURCES)
+  RegisterStylesExt(${USER-INTEL_SOURCES_DIR} intel USER-INTEL_SOURCES)
+  RegisterNBinStyle(${USER-INTEL_SOURCES_DIR}/nbin_intel.h)
+  RegisterNPairStyle(${USER-INTEL_SOURCES_DIR}/npair_intel.h)
+  RegisterFixStyle(${USER-INTEL_SOURCES_DIR}/fix_intel.h)
+  RegisterIntegrateStyle(${USER-INTEL_SOURCES_DIR}/verlet_lrt_intel.h)
 
   get_property(USER-INTEL_SOURCES GLOBAL PROPERTY USER-INTEL_SOURCES)
 
@@ -1169,6 +1230,10 @@ if(PKG_GPU)
         message(FATAL_ERROR "Could not find bin2c, use -DBIN2C=/path/to/bin2c to help cmake finding it.")
       endif()
       option(CUDPP_OPT "Enable CUDPP_OPT" ON)
+      option(CUDA_MPS_SUPPORT "Enable tweaks to support CUDA Multi-process service (MPS)" OFF)
+      if(CUDA_MPS_SUPPORT)
+        set(GPU_CUDA_MPS_FLAGS "-DCUDA_PROXY")
+      endif()
 
       set(GPU_ARCH "sm_30" CACHE STRING "LAMMPS GPU CUDA SM primary architecture (e.g. sm_60)")
 
@@ -1232,7 +1297,7 @@ if(PKG_GPU)
       add_library(gpu STATIC ${GPU_LIB_SOURCES} ${GPU_LIB_CUDPP_SOURCES} ${GPU_OBJS})
       target_link_libraries(gpu ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY})
       target_include_directories(gpu PRIVATE ${LAMMPS_LIB_BINARY_DIR}/gpu ${CUDA_INCLUDE_DIRS})
-      target_compile_definitions(gpu PRIVATE -D_${GPU_PREC_SETTING} -DMPI_GERYON -DUCL_NO_EXIT)
+      target_compile_definitions(gpu PRIVATE -D_${GPU_PREC_SETTING} -DMPI_GERYON -DUCL_NO_EXIT ${GPU_CUDA_MPS_FLAGS})
       if(CUDPP_OPT)
         target_include_directories(gpu PRIVATE ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini)
         target_compile_definitions(gpu PRIVATE -DUSE_CUDPP)
@@ -1326,6 +1391,18 @@ message(STATUS "Generating lmpinstalledpkgs.h...")
 file(WRITE "${LAMMPS_STYLE_HEADERS_DIR}/lmpinstalledpkgs.h.tmp" "${temp}" )
 execute_process(COMMAND ${CMAKE_COMMAND} -E copy_if_different "${LAMMPS_STYLE_HEADERS_DIR}/lmpinstalledpkgs.h.tmp" "${LAMMPS_STYLE_HEADERS_DIR}/lmpinstalledpkgs.h")
 
+######################################
+# Generate lmpgitversion.h
+######################################
+add_custom_target(gitversion COMMAND ${CMAKE_COMMAND}
+  -DCMAKE_CURRENT_SOURCE_DIR="${CMAKE_CURRENT_SOURCE_DIR}"
+  -DGIT_EXECUTABLE="${GIT_EXECUTABLE}"
+  -DGIT_FOUND="${GIT_FOUND}"
+  -DLAMMPS_STYLE_HEADERS_DIR="${LAMMPS_STYLE_HEADERS_DIR}"
+  -P ${CMAKE_CURRENT_SOURCE_DIR}/Modules/generate_lmpgitversion.cmake)
+set_property(DIRECTORY APPEND PROPERTY ADDITIONAL_MAKE_CLEAN_FILES ${LAMMPS_STYLE_HEADERS_DIR}/gitversion.h)
+list(APPEND LAMMPS_DEPS gitversion)
+
 ###########################################
 # Actually add executable and lib to build
 ############################################
@@ -1447,6 +1524,49 @@ install(
   DESTINATION ${CMAKE_INSTALL_SYSCONFDIR}/profile.d
 )
 
+###############################################################################
+# Install LAMMPS lib and python module into site-packages folder with
+# "install-python" target.  Behaves exactly like "make install-python" for
+# conventional build.  Only available, if a shared library is built.
+# This is primarily for people that only want to use the Python wrapper.
+###############################################################################
+if(BUILD_LIB AND BUILD_SHARED_LIBS)
+  find_package(PythonInterp)
+  if (PYTHONINTERP_FOUND)
+    add_custom_target(
+      install-python
+      ${PYTHON_EXECUTABLE} install.py -v ${LAMMPS_SOURCE_DIR}/version.h
+      -m ${CMAKE_CURRENT_SOURCE_DIR}/../python/lammps.py
+      -l ${CMAKE_BINARY_DIR}/liblammps${CMAKE_SHARED_LIBRARY_SUFFIX}
+      WORKING_DIRECTORY  ${CMAKE_CURRENT_SOURCE_DIR}/../python
+      COMMENT "Installing LAMMPS Python module")
+  else()
+    add_custom_target(
+      install-python
+      ${CMAKE_COMMAND} -E echo "Must have Python installed to install the LAMMPS Python module")
+  endif()
+else()
+  add_custom_target(
+    install-python
+    ${CMAKE_COMMAND} -E echo "Must build LAMMPS as a shared library to use the Python module")
+endif()
+
+###############################################################################
+# Add LAMMPS python module to "install" target. This is taylored for building
+# LAMMPS for package managers and with different prefix settings.
+# This requires either a shared library or that the PYTHON package is included.
+###############################################################################
+if((BUILD_LIB AND BUILD_SHARED_LIBS) OR (PKG_PYTHON))
+  find_package(PythonInterp)
+  if (PYTHONINTERP_FOUND)
+    execute_process(COMMAND ${PYTHON_EXECUTABLE}
+      -c "import distutils.sysconfig as cg; print(cg.get_python_lib(1,0,prefix='${CMAKE_INSTALL_PREFIX}'))"
+      OUTPUT_VARIABLE PYTHON_DEFAULT_INSTDIR OUTPUT_STRIP_TRAILING_WHITESPACE)
+    set(PYTHON_INSTDIR ${PYTHON_DEFAULT_INSTDIR} CACHE PATH "Installation folder for LAMMPS Python module")
+    install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/../python/lammps.py DESTINATION ${PYTHON_INSTDIR})
+  endif()
+endif()
+
 ###############################################################################
 # Testing
 #

cmake/Modules/FindKIM-API.cmake

@@ -19,7 +19,7 @@
 #
 
 #
-# Copyright (c) 2013--2018, Regents of the University of Minnesota.
+# Copyright (c) 2013--2019, Regents of the University of Minnesota.
 # All rights reserved.
 #
 # Contributors:
@@ -28,23 +28,23 @@
 #    Ryan S. Elliott
 #
 
-# - Find KIM-API-V2
+# - Find KIM-API
 #
 # sets standard pkg_check_modules variables plus:
 #
-# KIM-API-V2-CMAKE_C_COMPILER
+# KIM-API-CMAKE_C_COMPILER
-# KIM-API-V2-CMAKE_CXX_COMPILER
+# KIM-API-CMAKE_CXX_COMPILER
-# KIM-API-V2-CMAKE_Fortran_COMPILER
+# KIM-API-CMAKE_Fortran_COMPILER
 #
 find_package(PkgConfig REQUIRED)
 include(FindPackageHandleStandardArgs)
 
-pkg_check_modules(KIM-API-V2 REQUIRED libkim-api-v2>=2.0)
+pkg_check_modules(KIM-API REQUIRED libkim-api>=2.0)
 
-pkg_get_variable(KIM-API-V2-CMAKE_C_COMPILER libkim-api-v2 CMAKE_C_COMPILER)
+pkg_get_variable(KIM-API-V2-CMAKE_C_COMPILER libkim-api CMAKE_C_COMPILER)
-pkg_get_variable(KIM-API-V2-CMAKE_CXX_COMPILER libkim-api-v2 CMAKE_CXX_COMPILER)
+pkg_get_variable(KIM-API-V2-CMAKE_CXX_COMPILER libkim-api CMAKE_CXX_COMPILER)
-pkg_get_variable(KIM-API-V2_CMAKE_Fortran_COMPILER libkim-api-v2 CMAKE_Fortran_COMPILER)
+pkg_get_variable(KIM-API-V2_CMAKE_Fortran_COMPILER libkim-api CMAKE_Fortran_COMPILER)
 
-# handle the QUIETLY and REQUIRED arguments and set KIM-API-V2_FOUND to TRUE
+# handle the QUIETLY and REQUIRED arguments and set KIM-API_FOUND to TRUE
 # if all listed variables are TRUE
-find_package_handle_standard_args(KIM-API-V2 REQUIRED_VARS KIM-API-V2_LIBRARIES)
+find_package_handle_standard_args(KIM-API REQUIRED_VARS KIM-API_LIBRARIES)

cmake/Modules/StyleHeaderUtils.cmake

@@ -91,6 +91,10 @@ function(RegisterFixStyle path)
     AddStyleHeader(${path} FIX)
 endfunction(RegisterFixStyle)
 
+function(RegisterIntegrateStyle path)
+    AddStyleHeader(${path} INTEGRATE)
+endfunction(RegisterIntegrateStyle)
+
 function(RegisterStyles search_path)
     FindStyleHeaders(${search_path} ANGLE_CLASS     angle_     ANGLE     ) # angle     ) # force
     FindStyleHeaders(${search_path} ATOM_CLASS      atom_vec_  ATOM_VEC  ) # atom      ) # atom      atom_vec_hybrid

cmake/Modules/generate_lmpgitversion.cmake

@@ -0,0 +1,30 @@
+set(temp "#ifndef LMP_GIT_VERSION_H\n#define LMP_GIT_VERSION_H\n")
+set(temp_git_commit "(unknown)")
+set(temp_git_branch "(unknown)")
+set(temp_git_describe "(unknown)")
+set(temp_git_info "false")
+if(GIT_FOUND AND EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/../.git)
+  set(temp_git_info "true")
+  execute_process(COMMAND ${GIT_EXECUTABLE} -C ${CMAKE_CURRENT_SOURCE_DIR}/.. rev-parse HEAD
+    OUTPUT_VARIABLE temp_git_commit
+    ERROR_QUIET
+    OUTPUT_STRIP_TRAILING_WHITESPACE)
+  execute_process(COMMAND ${GIT_EXECUTABLE} -C ${CMAKE_CURRENT_SOURCE_DIR}/.. rev-parse --abbrev-ref HEAD
+    OUTPUT_VARIABLE temp_git_branch
+    ERROR_QUIET
+    OUTPUT_STRIP_TRAILING_WHITESPACE)
+  execute_process(COMMAND ${GIT_EXECUTABLE} -C ${CMAKE_CURRENT_SOURCE_DIR}/.. describe --dirty=-modified
+    OUTPUT_VARIABLE temp_git_describe
+    ERROR_QUIET
+    OUTPUT_STRIP_TRAILING_WHITESPACE)
+endif()
+
+set(temp "${temp}const bool LAMMPS_NS::LAMMPS::has_git_info = ${temp_git_info};\n")
+set(temp "${temp}const char LAMMPS_NS::LAMMPS::git_commit[] = \"${temp_git_commit}\";\n")
+set(temp "${temp}const char LAMMPS_NS::LAMMPS::git_branch[] = \"${temp_git_branch}\";\n")
+set(temp "${temp}const char LAMMPS_NS::LAMMPS::git_descriptor[] = \"${temp_git_describe}\";\n")
+set(temp "${temp}#endif\n\n")
+
+message(STATUS "Generating lmpgitversion.h...")
+file(WRITE "${LAMMPS_STYLE_HEADERS_DIR}/lmpgitversion.h.tmp" "${temp}" )
+execute_process(COMMAND ${CMAKE_COMMAND} -E copy_if_different "${LAMMPS_STYLE_HEADERS_DIR}/lmpgitversion.h.tmp" "${LAMMPS_STYLE_HEADERS_DIR}/lmpgitversion.h")

cmake/README.md

@@ -155,11 +155,13 @@ make
 
 The CMake build exposes a lot of different options. In the old build system
 some of the package selections were possible by using special make target like
-`make yes-std` or `make no-lib`. Achieving the same result with cmake requires
+`make yes-std` or `make no-lib`. Achieving a similar result with cmake requires
 specifying all options manually. This can quickly become a very long command
 line that is hard to handle.  While these could be stored in a simple script
 file, there is another way of defining "presets" to compile LAMMPS in a certain
-way.
+way. Since the cmake build process - contrary to the conventional build system -
+includes the compilation of the bundled libraries into the standard build process,
+the grouping of those presets is somewhat different.
 
 A preset is a regular CMake script file that can use constructs such as
 variables, lists and for-loops to manipulate configuration options and create
@@ -171,10 +173,10 @@ Such a file can then be passed to cmake via the `-C` flag. Several examples of
 presets can be found in the `cmake/presets` folder.
 
 ```bash
-# build LAMMPS with all "standard" packages which don't use libraries and enable GPU package
+# build LAMMPS with all packages enabled which don't use external libraries and enable GPU package
 mkdir build
 cd build
-cmake -C ../cmake/presets/std_nolib.cmake -D PKG_GPU=on ../cmake
+cmake -C ../cmake/presets/all_on.cmake -C ../cmake/presets/nolib.cmake -D PKG_GPU=on ../cmake
 ```
 
 # Reference
@@ -1429,6 +1431,17 @@ TODO
   </dl>
   </td>
 </tr>
+<tr>
+  <td><code>INTEL_LRT_MODE</code></td>
+  <td>How to support Long-range thread mode in Verlet integration</td>
+  <td>
+  <dl>
+    <dt><code>threads</code> (default, if pthreads available)</dt>
+    <dt><code>none</code> (default, if pthreads not available)</dt>
+    <dt><code>c++11</code></dt>
+  </dl>
+  </td>
+</tr>
 </tbody>
 </table>
 
@@ -1503,6 +1516,16 @@ target API.
   </dl>
   </td>
 </tr>
+<tr>
+  <td><code>CUDA_MPS_SUPPORT</code> (CUDA only)</td>
+  <td>Enable tweaks for running with Nvidia CUDA Multi-process services daemon</td>
+  <td>
+  <dl>
+    <dt><code>on</code></dt>
+    <dt><code>off</code> (default)</dt>
+  </dl>
+  </td>
+</tr>
 <tr>
   <td><code>BIN2C</code> (CUDA only)</td>
   <td>Path to bin2c executable, will automatically pick up the first one in your $PATH.</td>

cmake/presets/all_off.cmake

@@ -1,21 +1,17 @@
-set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
+# preset that turns on all existing packages off. can be used to reset
-                      GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MEAM MISC
+# an existing package selection without losing any other settings
-                      MOLECULE MPIIO MSCG OPT PERI POEMS
-                      PYTHON QEQ REAX REPLICA RIGID SHOCK SNAP SRD VORONOI)
 
-set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS
+set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
-                  USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD
+        GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MISC MESSAGE MOLECULE
-                  USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO
+        MPIIO MSCG OPT PERI POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN
-                  USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE
+        SRD VORONOI
-                  USER-NETCDF USER-OMP USER-PHONON USER-QMMM USER-QTB
+        USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK
-                  USER-QUIP USER-REAXC USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY
+        USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP
-                  USER-UEF USER-VTK)
+        USER-H5MD USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO
-
+        USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP
-set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI
+        USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP
-                      USER-ATC USER-AWPMD USER-COLVARS USER-H5MD USER-LB USER-MOLFILE
+        USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH
-                      USER-NETCDF USER-PLUMED USER-QMMM USER-QUIP USER-SMD USER-VTK)
+        USER-TALLY USER-UEF USER-VTK USER-YAFF)
-
-set(ALL_PACKAGES ${STANDARD_PACKAGES} ${USER_PACKAGES})
 
 foreach(PKG ${ALL_PACKAGES})
   set(PKG_${PKG} OFF CACHE BOOL "" FORCE)

cmake/presets/all_on.cmake

@@ -1,21 +1,19 @@
-set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
+# preset that turns on all existing packages. using the combination
-                      GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MEAM MISC
+# this preset followed by the nolib.cmake preset should configure a
-                      MOLECULE MPIIO MSCG OPT PERI POEMS
+# LAMMPS binary, with as many packages included, that can be compiled
-                      PYTHON QEQ REAX REPLICA RIGID SHOCK SNAP SRD VORONOI)
+# with just a working C++ compiler and an MPI library.
 
-set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS
+set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
-                  USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD
+        GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MISC MESSAGE MOLECULE
-                  USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO
+        MPIIO MSCG OPT PERI POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN
-                  USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE
+        SRD VORONOI
-                  USER-NETCDF USER-OMP USER-PHONON USER-QMMM USER-QTB
+        USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK
-                  USER-QUIP USER-REAXC USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY
+        USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP
-                  USER-UEF USER-VTK)
+        USER-H5MD USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO
-
+        USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP
-set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI
+        USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP
-                      USER-ATC USER-AWPMD USER-COLVARS USER-H5MD USER-LB USER-MOLFILE
+        USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH
-                      USER-NETCDF USER-PLUMED USER-QMMM USER-QUIP USER-SMD USER-VTK)
+        USER-TALLY USER-UEF USER-VTK USER-YAFF)
-
-set(ALL_PACKAGES ${STANDARD_PACKAGES} ${USER_PACKAGES})
 
 foreach(PKG ${ALL_PACKAGES})
   set(PKG_${PKG} ON CACHE BOOL "" FORCE)

cmake/presets/manual_selection.cmake

@@ -1,71 +0,0 @@
-set(PKG_ASPHERE OFF CACHE BOOL "" FORCE)
-set(PKG_BODY OFF CACHE BOOL "" FORCE)
-set(PKG_CLASS2 OFF CACHE BOOL "" FORCE)
-set(PKG_COLLOID OFF CACHE BOOL "" FORCE)
-set(PKG_COMPRESS OFF CACHE BOOL "" FORCE)
-set(PKG_CORESHELL OFF CACHE BOOL "" FORCE)
-set(PKG_DIPOLE OFF CACHE BOOL "" FORCE)
-set(PKG_GPU OFF CACHE BOOL "" FORCE)
-set(PKG_GRANULAR OFF CACHE BOOL "" FORCE)
-set(PKG_KIM OFF CACHE BOOL "" FORCE)
-set(PKG_KOKKOS OFF CACHE BOOL "" FORCE)
-set(PKG_KSPACE OFF CACHE BOOL "" FORCE)
-set(PKG_LATTE OFF CACHE BOOL "" FORCE)
-set(PKG_LIB OFF CACHE BOOL "" FORCE)
-set(PKG_MANYBODY OFF CACHE BOOL "" FORCE)
-set(PKG_MC OFF CACHE BOOL "" FORCE)
-set(PKG_MEAM OFF CACHE BOOL "" FORCE)
-set(PKG_MISC OFF CACHE BOOL "" FORCE)
-set(PKG_MOLECULE OFF CACHE BOOL "" FORCE)
-set(PKG_MPIIO OFF CACHE BOOL "" FORCE)
-set(PKG_MSCG OFF CACHE BOOL "" FORCE)
-set(PKG_OPT OFF CACHE BOOL "" FORCE)
-set(PKG_PERI OFF CACHE BOOL "" FORCE)
-set(PKG_POEMS OFF CACHE BOOL "" FORCE)
-set(PKG_PYTHOFF OFF CACHE BOOL "" FORCE)
-set(PKG_QEQ OFF CACHE BOOL "" FORCE)
-set(PKG_REAX OFF CACHE BOOL "" FORCE)
-set(PKG_REPLICA OFF CACHE BOOL "" FORCE)
-set(PKG_RIGID OFF CACHE BOOL "" FORCE)
-set(PKG_SHOCK OFF CACHE BOOL "" FORCE)
-set(PKG_SNAP OFF CACHE BOOL "" FORCE)
-set(PKG_SRD OFF CACHE BOOL "" FORCE)
-set(PKG_VOROFFOI OFF CACHE BOOL "" FORCE)
-
-set(PKG_USER OFF CACHE BOOL "" FORCE)
-set(PKG_USER-ATC OFF CACHE BOOL "" FORCE)
-set(PKG_USER-AWPMD OFF CACHE BOOL "" FORCE)
-set(PKG_USER-BOCS OFF CACHE BOOL "" FORCE)
-set(PKG_USER-CGDNA OFF CACHE BOOL "" FORCE)
-set(PKG_USER-CGSDK OFF CACHE BOOL "" FORCE)
-set(PKG_USER-COLVARS OFF CACHE BOOL "" FORCE)
-set(PKG_USER-DIFFRACTIOFF OFF CACHE BOOL "" FORCE)
-set(PKG_USER-DPD OFF CACHE BOOL "" FORCE)
-set(PKG_USER-DRUDE OFF CACHE BOOL "" FORCE)
-set(PKG_USER-EFF OFF CACHE BOOL "" FORCE)
-set(PKG_USER-FEP OFF CACHE BOOL "" FORCE)
-set(PKG_USER-H5MD OFF CACHE BOOL "" FORCE)
-set(PKG_USER-INTEL OFF CACHE BOOL "" FORCE)
-set(PKG_USER-LB OFF CACHE BOOL "" FORCE)
-set(PKG_USER-MANIFOLD OFF CACHE BOOL "" FORCE)
-set(PKG_USER-MEAMC OFF CACHE BOOL "" FORCE)
-set(PKG_USER-MESO OFF CACHE BOOL "" FORCE)
-set(PKG_USER-MGPT OFF CACHE BOOL "" FORCE)
-set(PKG_USER-MISC OFF CACHE BOOL "" FORCE)
-set(PKG_USER-MOFFF OFF CACHE BOOL "" FORCE)
-set(PKG_USER-MOLFILE OFF CACHE BOOL "" FORCE)
-set(PKG_USER-NETCDF OFF CACHE BOOL "" FORCE)
-set(PKG_USER-OMP OFF CACHE BOOL "" FORCE)
-set(PKG_USER-PHONON OFF CACHE BOOL "" FORCE)
-set(PKG_USER-PLUMED OFF CACHE BOOL "" FORCE)
-set(PKG_USER-QMMM OFF CACHE BOOL "" FORCE)
-set(PKG_USER-QTB OFF CACHE BOOL "" FORCE)
-set(PKG_USER-QUIP OFF CACHE BOOL "" FORCE)
-set(PKG_USER-REAXC OFF CACHE BOOL "" FORCE)
-set(PKG_USER-SDPD OFF CACHE BOOL "" FORCE)
-set(PKG_USER-SMD OFF CACHE BOOL "" FORCE)
-set(PKG_USER-SMTBQ OFF CACHE BOOL "" FORCE)
-set(PKG_USER-SPH OFF CACHE BOOL "" FORCE)
-set(PKG_USER-TALLY OFF CACHE BOOL "" FORCE)
-set(PKG_USER-UEF OFF CACHE BOOL "" FORCE)
-set(PKG_USER-VTK OFF CACHE BOOL "" FORCE)

cmake/presets/mingw-cross.cmake

@@ -0,0 +1,17 @@
+set(WIN_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
+                 GRANULAR KSPACE MANYBODY MC MISC MOLECULE OPT PERI POEMS QEQ
+                 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)
+
+foreach(PKG ${WIN_PACKAGES})
+  set(PKG_${PKG} ON CACHE BOOL "" FORCE)
+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)

cmake/presets/minimal.cmake

@@ -0,0 +1,8 @@
+# preset that turns on just a few, frequently used packages
+# this will be compiled quickly and handle a lot of common inputs.
+
+set(ALL_PACKAGES KSPACE MANYBODY MOLECULE RIGID)
+
+foreach(PKG ${ALL_PACKAGES})
+  set(PKG_${PKG} ON CACHE BOOL "" FORCE)
+endforeach()

cmake/presets/most.cmake

@@ -0,0 +1,15 @@
+# preset that turns on a wide range of packages, some of which require
+# external libraries. Compared to all_on.cmake some more unusual packages
+# are removed. The resulting binary should be able to run most inputs.
+
+set(ALL_PACKAGES ASPHERE CLASS2 COLLOID CORESHELL DIPOLE
+        GRANULAR KSPACE MANYBODY MC MISC MOLECULE OPT PERI
+        PYTHON QEQ REPLICA RIGID SHOCK SRD VORONOI
+        USER-CGDNA USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD
+        USER-DRUDE USER-FEP USER-MEAMC USER-MESO
+        USER-MISC USER-MOFFF USER-OMP USER-PLUMED USER-PHONON USER-REAXC
+        USER-SPH USER-SMD USER-UEF USER-YAFF)
+
+foreach(PKG ${ALL_PACKAGES})
+  set(PKG_${PKG} ON CACHE BOOL "" FORCE)
+endforeach()

cmake/presets/nolib.cmake

@@ -1,21 +1,10 @@
-set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
+# preset that turns off all packages that require some form of external
-                      GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MEAM MISC
+# library or special compiler (fortran or cuda) or equivalent.
-                      MOLECULE MPIIO MSCG OPT PERI POEMS
-                      PYTHON QEQ REAX REPLICA RIGID SHOCK SNAP SRD VORONOI)
 
-set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS
+set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MPIIO MSCG PYTHON
-                  USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD
+        VORONOI USER-ADIOS USER-ATC USER-AWPMD USER-H5MD USER-LB
-                  USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO
+        USER-MOLFILE USER-NETCDF USER-PLUMED USER-QMMM USER-QUIP
-                  USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE
+        USER-SCAFACOS USER-SMD USER-VTK)
-                  USER-NETCDF USER-OMP USER-PHONON USER-QMMM USER-QTB
-                  USER-QUIP USER-REAXC USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY
-                  USER-UEF USER-VTK)
-
-set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI
-                      USER-ATC USER-AWPMD USER-COLVARS USER-H5MD USER-LB USER-MOLFILE
-                      USER-NETCDF USER-PLUMED USER-QMMM USER-QUIP USER-SMD USER-VTK)
-
-set(ALL_PACKAGES ${STANDARD_PACKAGES} ${USER_PACKAGES})
 
 foreach(PKG ${PACKAGES_WITH_LIB})
   set(PKG_${PKG} OFF CACHE BOOL "" FORCE)

cmake/presets/std.cmake

@@ -1,22 +0,0 @@
-set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
-                      GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MEAM MISC
-                      MOLECULE MPIIO MSCG OPT PERI POEMS
-                      PYTHON QEQ REAX REPLICA RIGID SHOCK SNAP SRD VORONOI)
-
-set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS
-                  USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD
-                  USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO
-                  USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE
-                  USER-NETCDF USER-OMP USER-PHONON USER-QMMM USER-QTB
-                  USER-QUIP USER-REAXC USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY
-                  USER-UEF USER-VTK)
-
-set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI
-                      USER-ATC USER-AWPMD USER-COLVARS USER-H5MD USER-LB USER-MOLFILE
-                      USER-NETCDF USER-QMMM USER-QUIP USER-SMD USER-VTK)
-
-set(ALL_PACKAGES ${STANDARD_PACKAGES} ${USER_PACKAGES})
-
-foreach(PKG ${STANDARD_PACKAGES})
-  set(PKG_${PKG} ON CACHE BOOL "" FORCE)
-endforeach()

cmake/presets/std_nolib.cmake

@@ -1,26 +0,0 @@
-set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
-                      GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MEAM MISC
-                      MOLECULE MPIIO MSCG OPT PERI POEMS
-                      PYTHON QEQ REAX REPLICA RIGID SHOCK SNAP SRD VORONOI)
-
-set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS
-                  USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD
-                  USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO
-                  USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE
-                  USER-NETCDF USER-OMP USER-PHONON USER-QMMM USER-QTB
-                  USER-QUIP USER-REAXC USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY
-                  USER-UEF USER-VTK)
-
-set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI
-                      USER-ATC USER-AWPMD USER-COLVARS USER-H5MD USER-LB USER-MOLFILE
-                      USER-NETCDF USER-QMMM USER-QUIP USER-SMD USER-VTK)
-
-set(ALL_PACKAGES ${STANDARD_PACKAGES} ${USER_PACKAGES})
-
-foreach(PKG ${STANDARD_PACKAGES})
-  set(PKG_${PKG} ON CACHE BOOL "" FORCE)
-endforeach()
-
-foreach(PKG ${PACKAGES_WITH_LIB})
-  set(PKG_${PKG} OFF CACHE BOOL "" FORCE)
-endforeach()

cmake/presets/user.cmake

@@ -1,22 +0,0 @@
-set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
-                      GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MEAM MISC
-                      MOLECULE MPIIO MSCG OPT PERI POEMS
-                      PYTHON QEQ REAX REPLICA RIGID SHOCK SNAP SRD VORONOI)
-
-set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS
-                  USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD
-                  USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO
-                  USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE
-                  USER-NETCDF USER-OMP USER-PHONON USER-QMMM USER-QTB
-                  USER-QUIP USER-REAXC USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY
-                  USER-UEF USER-VTK)
-
-set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI
-                      USER-ATC USER-AWPMD USER-COLVARS USER-H5MD USER-LB USER-MOLFILE
-                      USER-NETCDF USER-PLUMED USER-QMMM USER-QUIP USER-SMD USER-VTK)
-
-set(ALL_PACKAGES ${STANDARD_PACKAGES} ${USER_PACKAGES})
-
-foreach(PKG ${USER_PACKAGES})
-  set(PKG_${PKG} ON CACHE BOOL "" FORCE)
-endforeach()

doc/Makefile

@@ -116,6 +116,13 @@ mobi: epub
 	@echo "Conversion finished. The MOBI manual file is created."
 
 pdf: $(OBJECTS) $(ANCHORCHECK)
+	@(\
+		cd src/Developer; \
+		pdflatex developer; \
+		pdflatex developer; \
+		mv developer.pdf ../../Developer.pdf; \
+		cd ../../; \
+	)
 	@(\
                 . $(VENV)/bin/activate ;\
                 cp -r src/* $(RSTDIR)/ ;\
@@ -136,13 +143,6 @@ pdf: $(OBJECTS) $(ANCHORCHECK)
 	  make && \
 	  mv LAMMPS.pdf ../Manual.pdf && \
 	  cd ../;
-	@(\
-		cd src/Developer; \
-		pdflatex developer; \
-		pdflatex developer; \
-		mv developer.pdf ../../Developer.pdf; \
-		cd ../../; \
-	)
 	@rm -rf latex/_sources
 	@rm -rf latex/PDF
 	@rm -rf latex/USER
@@ -211,7 +211,7 @@ $(VENV):
 	@( \
 		$(VIRTUALENV) -p $(PYTHON) $(VENV); \
 		. $(VENV)/bin/activate; \
-		pip install Sphinx; \
+		pip install Sphinx==1.7.6; \
 		deactivate;\
 	)
 

doc/src/Build_cmake.txt

@@ -28,7 +28,7 @@ Makefile(s). Example:
 
 cd lammps                        # change to the LAMMPS distribution directory
 mkdir build; cd build            # create a new directory (folder) for build
-cmake ../cmake \[options ...\]   # configuration with (command-line) cmake
+cmake \[options ...\] ../cmake     # configuration with (command-line) cmake
 make                             # compilation :pre
 
 The cmake command will detect available features, enable selected
@@ -41,7 +41,8 @@ If your machine has multiple CPU cores (most do these days), using a
 command like "make -jN" (with N being the number of available local
 CPU cores) can be much faster.  If you plan to do development on
 LAMMPS or need to re-compile LAMMPS repeatedly, installation of the
-ccache (= Compiler Cache) software may speed up compilation even more.
+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:
@@ -108,7 +109,8 @@ command-line options.  Several useful ones are:
 -D CMAKE_BUILD_TYPE=type      # type = Release 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 :pre
+-D VARIABLE=value             # ditto, but cannot come after CMakeLists.txt dir
+-C path/to/preset/file        # load some CMake settings before configuring :pre
 
 All the LAMMPS-specific -D variables that a LAMMPS build supports are
 described on the pages linked to from the "Build"_Build.html doc page.

doc/src/Build_extras.txt

@@ -92,7 +92,9 @@ which GPU hardware to build for.
                           # default is Cuda-compiler dependent, but typically sm_20
 -D CUDPP_OPT=value        # optimization setting for GPU_API=cuda
                           # enables CUDA Performance Primitives Optimizations
-                      # yes (default) or no :pre
+                          # value = yes (default) or no
+-D CUDA_MPS_SUPPORT=value # enables some tweaks required to run with active nvidia-cuda-mps daemon
+                          # value = yes or no (default) :pre
 
 GPU_ARCH settings for different GPU hardware is as follows:
 
@@ -169,26 +171,24 @@ used to build the GPU library.
 
 KIM package :h4,link(kim)
 
-To build with this package, the KIM library must be downloaded and
+To build with this package, the KIM library with API v2 must be downloaded
-built on your system.  It must include the KIM models that you want to
+and built on your system.  It must include the KIM models that you want to
-use with LAMMPS.
+use with LAMMPS. If you want to use the "kim_query"_kim_query.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 installing the KIM API
+specific EAM potential file.  Also note that downloading and installing
-library with all its models, may take around 30 min to build.  Of
+the KIM API library with all its models, may take a long time (10s of
-course you only need to do that once.
+minutes to hours) to build.  Of course you only need to do that once.
 
 See the list of KIM model drivers here:
-https://openkim.org/kim-items/model-drivers/alphabetical
+https://openkim.org/browse/model-drivers/alphabetical
 
 See the list of all KIM models here:
-https://openkim.org/kim-items/models/by-model-drivers
+https://openkim.org/browse/models/by-model-drivers
-
-See the list of example KIM models included by default here:
-https://openkim.org/kim-api on the "What is in the KIM API source
-package?" page.
 
 [CMake build]:
 
@@ -197,7 +197,7 @@ package?" page.
 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-v2 can be found.
+environment variable so that libkim-api can be found.
 
 [Traditional make]:
 
@@ -859,23 +859,34 @@ file.
 USER-INTEL package :h4,link(user-intel)
 
 To build with this package, you must choose which hardware you want to
-build for, either Intel CPUs or Intel KNLs.  You should also typically
+build for, either x86 CPUs or Intel KNLs in offload mode.  You should
-"install the USER-OMP package"_#user-omp, as it can be used in tandem
+also typically "install the USER-OMP package"_#user-omp, as it can be
-with the USER-INTEL package to good effect, as explained on the "Speed
+used in tandem with the USER-INTEL package to good effect, as explained
-intel"_Speed_intel.html doc page.
+on the "Speed intel"_Speed_intel.html doc page.
 
 [CMake build]:
 
 -D INTEL_ARCH=value     # value = cpu (default) or knl
--D BUILD_OMP=yes        # also required to build with the USER-INTEl package :pre
+-D INTEL_LRT_MODE=value # value = threads, none, or c++11 :pre
 
-Requires an Intel compiler as well as the Intel TBB and MKL libraries.
+In Long-range thread mode (LRT) a modified verlet style is used, that
+operates the Kspace calculation in a separate thread concurrently to
+other calculations. This has to be enabled in the "package intel"_package.html
+command at runtime. With the setting "threads" it used the pthreads
+library, while c++11 will use the built-in thread support of C++11
+compilers. The option "none" skips compilation of this feature. The
+default is to use "threads" if pthreads is available and otherwise "none".
+
+Best performance is achieved with Intel hardware, Intel compilers, as well as
+the Intel TBB and MKL libraries. However, the code also compiles, links, and
+runs with other compilers and without TBB and MKL.
 
 [Traditional make]:
 
 Choose which hardware to compile for in Makefile.machine via the
 following settings.  See src/MAKE/OPTIONS/Makefile.intel_cpu* and
-Makefile.knl files for examples.
+Makefile.knl files for examples. and src/USER-INTEL/README for
+additional information.
 
 For CPUs:
 
@@ -897,7 +908,17 @@ USER-MOLFILE package :h4,link(user-molfile)
 
 [CMake build]:
 
-No additional settings are needed besides "-D PKG_USER-MOLFILE=yes".
+-D MOLFILE_INCLUDE_DIRS=path   # (optional) path where VMD molfile plugin headers are installed
+-D PKG_USER-MOLFILE=yes     :pre
+
+
+Using "-D PKG_USER-MOLFILE=yes" enables the package, and setting
+"-D MOLFILE_INCLUDE DIRS" allows to provide a custom location for
+the molfile plugin header files. These should match the ABI of the
+plugin files used, and thus one typically sets them to include
+folder of the local VMD installation in use. LAMMPS ships with a
+couple of default header files that correspond to a popular VMD
+version, usually the latest release.
 
 [Traditional make]:
 
@@ -906,7 +927,11 @@ loading library libdl.a that is typically present on all systems.  It
 is required for LAMMPS to link with this package.  If the setting is
 not valid for your system, you will need to edit the Makefile.lammps
 file.  See lib/molfile/README and lib/molfile/Makefile.lammps for
-details.
+details. It is also possible to configure a different folder with
+the VMD molfile plugin header files. LAMMPS ships with a couple of
+default headers, but these are not compatible with all VMD versions,
+so it is often best to change this setting to the location of the
+same include files of the local VMD installation in use.
 
 :line
 

doc/src/Build_package.txt

@@ -149,26 +149,39 @@ system. Using these files you can enable/disable portions of the
 available packages in LAMMPS. If you need a custom preset you can take
 one of them as a starting point and customize it to your needs.
 
-cmake -C ../cmake/presets/all_on.cmake \[OPTIONS\] ../cmake | enable all packages
+cmake -C ../cmake/presets/all_on.cmake  \[OPTIONS\] ../cmake |
-cmake -C ../cmake/presets/all_off.cmake \[OPTIONS\] ../cmake | disable all packages
+      enable all packages |
-cmake -C ../cmake/presets/std.cmake \[OPTIONS\] ../cmake | enable standard packages
+cmake -C ../cmake/presets/all_off.cmake \[OPTIONS\] ../cmake |
-cmake -C ../cmake/presets/user.cmake \[OPTIONS\] ../cmake | enable user packages
+      disable all packages |
-cmake -C ../cmake/presets/std_nolib.cmake \[OPTIONS\] ../cmake | enable standard packages that do not require extra libraries
+cmake -C ../cmake/presets/minimal.cmake \[OPTIONS\] ../cmake |
-cmake -C ../cmake/presets/nolib.cmake \[OPTIONS\] ../cmake | disable all packages that do not require extra libraries
+      enable just a few core packages |
-cmake -C ../cmake/presets/manual_selection.cmake \[OPTIONS\] ../cmake | example of how to create a manual selection of packages :tb(s=|,a=l)
+cmake -C ../cmake/presets/most.cmake    \[OPTIONS\] ../cmake |
+      enable most common packages |
+cmake -C ../cmake/presets/nolib.cmake   \[OPTIONS\] ../cmake |
+      disable packages that do require extra libraries or tools |
+cmake -C ../cmake/presets/mingw.cmake \[OPTIONS\] ../cmake |
+      enable all packages compatible with MinGW compilers :tb(c=2,s=|,a=l)
 
 NOTE: Running cmake this way manipulates the variable cache in your
-current build directory. You can combine presets and options with
+current build directory. You can combine multiple presets and options
-multiple cmake runs.
+in a single cmake run, or change settings incrementally by running
+cmake with new flags.
 
 [Example:]
 
-# build LAMMPS with all "standard" packages which don't
+# build LAMMPS with most commonly used packages, but then remove
-# use libraries and enable GPU package
+# those requiring additional library or tools, but still enable
+# GPU package and configure it for using CUDA. You can run.
 mkdir build
 cd build
-cmake -C ../cmake/presets/std_nolib.cmake -D PKG_GPU=on ../cmake :pre
+cmake -C ../cmake/presets/most.cmake -C ../cmake/presets/nolib.cmake -D PKG_GPU=on -D GPU_API=cuda ../cmake :pre
 
+# to add another package, say BODY to the previous configuration you can run:
+cmake -D PKG_BODY=on . :pre
+
+# to reset the package selection from above to the default of no packages
+# but leaving all other settings untouched. You can run:
+cmake -C ../cmake/presets/no_all.cmake . :pre
 :line
 
 [Make shortcuts for installing many packages]:

doc/src/Build_settings.txt

@@ -179,8 +179,11 @@ e.g. from 511 to -512, which can cause diagnostics like the
 mean-squared displacement, as calculated by the "compute
 msd"_compute_msd.html command, to be faulty.
 
-Note that the USER-ATC package is not currently compatible with the
+Note that the USER-ATC package and the USER-INTEL package are currently
-"bigbig" setting.
+not compatible with the "bigbig" setting. Also, there are limitations
+when using the library interface. Some functions with known issues
+have been replaced by dummy calls printing a corresponding error rather
+than crashing randomly or corrupting data.
 
 Also note that the GPU package requires its lib/gpu library to be
 compiled with the same size setting, or the link will fail.  A CMake

doc/src/Build_windows.txt

@@ -51,11 +51,10 @@ provides a unix/linux interface to low-level Windows functions, so LAMMPS
 can be compiled on Windows. The necessary (minor) modifications to LAMMPS
 are included, but may not always up-to-date for recently added functionality
 and the corresponding new code. A machine makefile for using cygwin for
-the old build system is provided. The CMake build system is untested
+the old build system is provided. Using CMake for this mode of compilation
-for this; you will have to request that makefiles are generated and
+is untested and not likely to work.
-manually set the compiler.
 
-When compiling for Windows [not] set the -DLAMMPS_MEMALIGN define
+When compiling for Windows do [not] set the -DLAMMPS_MEMALIGN define
 in the LMP_INC makefile variable and add -lwsock32 -lpsapi to the linker
 flags in LIB makefile variable. Try adding -static-libgcc or -static or
 both to the linker flags when your resulting LAMMPS Windows executable
@@ -79,7 +78,13 @@ probably the currently best tested and supported way to build LAMMPS
 executables for Windows.  There are makefiles provided for the
 traditional build system, but CMake has also been successfully tested
 using the mingw32-cmake and mingw64-cmake wrappers that are bundled
-with the cross-compiler environment on Fedora machines.
+with the cross-compiler environment on Fedora machines. A CMake preset
+selecting all packages compatible with this cross-compilation build
+is provided. You likely need to disable the GPU package unless you
+download and install the contents of the pre-compiled "OpenCL ICD loader
+library"_https://download.lammps.org/thirdparty/opencl-win-devel.tar.gz
+into your MinGW64 cross-compiler environment. The cross-compilation
+currently will only produce non-MPI serial binaries.
 
 Please keep in mind, though, that this only applies to compiling LAMMPS.
 Whether the resulting binaries do work correctly is no tested by the

doc/src/Commands_all.txt

@@ -68,6 +68,7 @@ An alphabetic list of all general LAMMPS commands.
 "improper_style"_improper_style.html,
 "include"_include.html,
 "jump"_jump.html,
+"kim_query"_kim_query.html,
 "kspace_modify"_kspace_modify.html,
 "kspace_style"_kspace_style.html,
 "label"_label.html,
@@ -78,6 +79,7 @@ An alphabetic list of all general LAMMPS commands.
 "minimize"_minimize.html,
 "min_modify"_min_modify.html,
 "min_style"_min_style.html,
+"min_style spin"_min_spin.html,
 "molecule"_molecule.html,
 "ndx2group"_group2ndx.html,
 "neb"_neb.html,

doc/src/Commands_fix.txt

@@ -224,7 +224,7 @@ OPT.
 "wall/body/polyhedron"_fix_wall_body_polyhedron.html,
 "wall/colloid"_fix_wall.html,
 "wall/ees"_fix_wall_ees.html,
-"wall/gran (o)"_fix_wall_gran.html,
+"wall/gran"_fix_wall_gran.html,
 "wall/gran/region"_fix_wall_gran_region.html,
 "wall/harmonic"_fix_wall.html,
 "wall/lj1043"_fix_wall.html,

doc/src/Commands_pair.txt

@@ -98,6 +98,7 @@ OPT.
 "gran/hertz/history (o)"_pair_gran.html,
 "gran/hooke (o)"_pair_gran.html,
 "gran/hooke/history (ko)"_pair_gran.html,
+"granular"_pair_granular.html,
 "gw"_pair_gw.html,
 "gw/zbl"_pair_gw.html,
 "hbond/dreiding/lj (o)"_pair_hbond_dreiding.html,

doc/src/Eqs/min_spin_damping.tex

@@ -0,0 +1,13 @@
+\documentclass[preview]{standalone}
+\usepackage{varwidth}
+\usepackage[utf8x]{inputenc}
+\usepackage{amsmath, amssymb, graphics, setspace}
+
+\begin{document}
+\begin{varwidth}{50in}
+  \begin{equation}
+    \frac{d \vec{s}_{i}}{dt} = \lambda\, \vec{s}_{i} \times\left( \vec{\omega}_{i} \times\vec{s}_{i} \right)
+    \nonumber
+  \end{equation}
+\end{varwidth}
+\end{document}

doc/src/Eqs/min_spin_timestep.tex

@@ -0,0 +1,14 @@
+\documentclass[preview]{standalone}
+\usepackage{varwidth}
+\usepackage[utf8x]{inputenc}
+\usepackage{amsmath, amssymb, graphics, setspace}
+
+\begin{document}
+\begin{varwidth}{50in}
+  \begin{equation}
+    {\Delta t}_{\rm max} = \frac{2\pi}{\kappa
+    \left|\vec{\omega}_{\rm max} \right|} 
+    \nonumber
+  \end{equation}
+\end{varwidth}
+\end{document}

doc/src/Howto_library.txt

@@ -166,9 +166,6 @@ void lammps_gather_atoms_subset(void *, char *, int, int, int, int *, void *)
 void lammps_scatter_atoms(void *, char *, int, int, void *)
 void lammps_scatter_atoms_subset(void *, char *, int, int, int, int *, void *) :pre
 
-void lammps_create_atoms(void *, int, tagint *, int *, double *, double *,
-                         imageint *, int) :pre
-
 The gather functions collect peratom info of the requested type (atom
 coords, atom types, forces, etc) from all processors, and returns the
 same vector of values to each calling processor.  The scatter
@@ -176,6 +173,11 @@ functions do the inverse.  They distribute a vector of peratom values,
 passed by all calling processors, to individual atoms, which may be
 owned by different processors.
 
+IMPORTANT NOTE: These functions are not compatible with the
+-DLAMMPS_BIGBIG setting when compiling LAMMPS.  Dummy functions
+that result in an error message and abort will be substituted
+instead of resulting in random crashes and memory corruption.
+
 The lammps_gather_atoms() function does this for all N atoms in the
 system, ordered by atom ID, from 1 to N.  The
 lammps_gather_atoms_concat() function does it for all N atoms, but
@@ -196,6 +198,9 @@ those values to each atom in the system.  The
 lammps_scatter_atoms_subset() function takes a subset of IDs as an
 argument and only scatters those values to the owning atoms.
 
+void lammps_create_atoms(void *, int, tagint *, int *, double *, double *,
+                         imageint *, int) :pre
+
 The lammps_create_atoms() function takes a list of N atoms as input
 with atom types and coords (required), an optionally atom IDs and
 velocities and image flags.  It uses the coords of each atom to assign

doc/src/Howto_pylammps.txt

@@ -57,6 +57,17 @@ library is then loaded by the Python interface. In this example we enable the
 MOLECULE package and compile LAMMPS with C++ exceptions, PNG, JPEG and FFMPEG
 output support enabled.
 
+Step 1a: For the CMake based build system, the steps are:
+
+mkdir $LAMMPS_DIR/build-shared
+cd  $LAMMPS_DIR/build-shared :pre
+
+# MPI, PNG, Jpeg, FFMPEG are auto-detected
+cmake ../cmake -DPKG_MOLECULE=yes -DLAMMPS_EXCEPTIONS=yes -DBUILD_LIB=yes -DBUILD_SHARED_LIBS=yes
+make :pre
+
+Step 1b: For the legacy, make based build system, the steps are:
+
 cd $LAMMPS_DIR/src :pre
 
 # add packages if necessary
@@ -68,10 +79,9 @@ make mpi mode=shlib LMP_INC="-DLAMMPS_PNG -DLAMMPS_JPEG -DLAMMPS_FFMPEG -DLAMMPS
 Step 2: Installing the LAMMPS Python package :h6
 
 PyLammps is part of the lammps Python package. To install it simply install
-that package into your current Python installation.
+that package into your current Python installation with:
 
-cd $LAMMPS_DIR/python
+make install-python :pre
-python install.py :pre
 
 NOTE: Recompiling the shared library requires re-installing the Python package
 
@@ -94,14 +104,21 @@ apt-get install python-virtualenv :pre
 
 Creating a virtualenv with lammps installed :h6
 
-# create virtualenv name 'testing' :pre
+# create virtualenv named 'testing'
+virtualenv $HOME/python/testing :pre
 
 # activate 'testing' environment
-source testing/bin/activate :pre
+source $HOME/python/testing/bin/activate :pre
+
+Now configure and compile the LAMMPS shared library as outlined above.
+When using CMake and the shared library has already been build, you
+need to re-run CMake to update the location of the python executable
+to the location in the virtual environment with:
+
+cmake . -DPYTHON_EXECUTABLE=$(which python) :pre
 
 # install LAMMPS package in virtualenv
-(testing) cd $LAMMPS_DIR/python
+(testing) make install-python :pre
-(testing) python install.py :pre
 
 # install other useful packages
 (testing) pip install matplotlib jupyter mpi4py :pre

doc/src/Manual.txt

@@ -1,7 +1,7 @@
 <!-- HTML_ONLY -->
 <HEAD>
 <TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="28 Feb 2019 version">
+<META NAME="docnumber" CONTENT="29 Mar 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
-28 Feb 2019 version :c,h2
+29 Mar 2019 version :c,h2
 
 "What is a LAMMPS version?"_Manual_version.html
 

doc/src/Packages_details.txt

@@ -341,6 +341,8 @@ KIM package :link(PKG-KIM),h4
 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.
 
 To use this package you must have the KIM library available on your
 system.

doc/src/Python_install.txt

@@ -12,16 +12,23 @@ Installing LAMMPS in Python :h3
 For Python to invoke LAMMPS, there are 2 files it needs to know about:
 
 python/lammps.py
-src/liblammps.so :ul
+liblammps.so or liblammps.dylib :ul
 
-Lammps.py is the Python wrapper on the LAMMPS library interface.
+The python source code in lammps.py is the Python wrapper on the
-Liblammps.so is the shared LAMMPS library that Python loads, as
+LAMMPS library interface. The liblammps.so or liblammps.dylib file
-described above.
+is the shared LAMMPS library that Python loads dynamically.
 
-You can insure Python can find these files in one of two ways:
+You can achieve that Python can find these files in one of two ways:
 
-set two environment variables
+set two environment variables pointing to the location in the source tree
-run the python/install.py script :ul
+run "make install-python" or run the python/install.py script explicitly :ul
+
+When calling "make install-python" LAMMPS will try to install the
+python module and the shared library into the python site-packages folders;
+either the system-wide ones, or the local users ones (in case of insufficient
+permissions for the global install). Python will then find the module
+and shared library file automatically. The exact location of these folders
+depends on your python version and your operating system.
 
 If you set the paths to these files as environment variables, you only
 have to do it once.  For the csh or tcsh shells, add something like
@@ -30,42 +37,28 @@ this to your ~/.cshrc file, one line for each of the two files:
 setenv PYTHONPATH $\{PYTHONPATH\}:/home/sjplimp/lammps/python
 setenv LD_LIBRARY_PATH $\{LD_LIBRARY_PATH\}:/home/sjplimp/lammps/src :pre
 
-If you use the python/install.py script, you need to invoke it every
+On MacOSX you may also need to set DYLD_LIBRARY_PATH accordingly.
-time you rebuild LAMMPS (as a shared library) or make changes to the
+For Bourne/Korn shells accordingly into the corresponding files using
-python/lammps.py file.
+the "export" shell builtin.
 
-You can invoke install.py from the python directory as
+If you use "make install-python" or the python/install.py script, you need
+to invoke it every time you rebuild LAMMPS (as a shared library) or
+make changes to the python/lammps.py file, so that the site-packages
+files are updated with the new version.
 
-% python install.py \[libdir\] \[pydir\] :pre
+If the default settings of "make install-python" are not what you want,
+you can invoke install.py from the python directory manually as
 
-The optional libdir is where to copy the LAMMPS shared library to; the
+% python install.py -m \<python module\> -l <shared library> -v <version.h file> \[-d \<pydir\>\] :pre
-default is /usr/local/lib.  The optional pydir is where to copy the
-lammps.py file to; the default is the site-packages directory of the
-version of Python that is running the install script.
 
-Note that libdir must be a location that is in your default
+The -m flag points to the lammps.py python module file to be installed,
-LD_LIBRARY_PATH, like /usr/local/lib or /usr/lib.  And pydir must be a
+the -l flag points to the LAMMPS shared library file to be installed,
-location that Python looks in by default for imported modules, like
+the -v flag points to the version.h file in the LAMMPS source
-its site-packages dir.  If you want to copy these files to
+and the optional -d flag to a custom (legacy) installation folder :ul
-non-standard locations, such as within your own user space, you will
-need to set your PYTHONPATH and LD_LIBRARY_PATH environment variables
-accordingly, as above.
 
-If the install.py script does not allow you to copy files into system
+If you use a legacy installation folder, you will need to set your
-directories, prefix the python command with "sudo".  If you do this,
+PYTHONPATH and LD_LIBRARY_PATH (and/or DYLD_LIBRARY_PATH) environment
-make sure that the Python that root runs is the same as the Python you
+variables accordingly, as described above.
-run.  E.g. you may need to do something like
-
-% sudo /usr/local/bin/python install.py \[libdir\] \[pydir\] :pre
-
-You can also invoke install.py from the make command in the src
-directory as
-
-% make install-python :pre
-
-In this mode you cannot append optional arguments.  Again, you may
-need to prefix this with "sudo".  In this mode you cannot control
-which Python is invoked by root.
 
 Note that if you want Python to be able to load different versions of
 the LAMMPS shared library (see "this section"_Python_shlib.html), you will

doc/src/Python_overview.txt

@@ -13,11 +13,11 @@ Overview of Python and LAMMPS :h3
 LAMMPS can work together with Python in three ways.  First, Python can
 wrap LAMMPS through the its "library interface"_Howto_library.html, so
 that a Python script can create one or more instances of LAMMPS and
-launch one or more simulations.  In Python lingo, this is "extending"
+launch one or more simulations.  In Python lingo, this is called
-Python with LAMMPS.
+"extending" Python with a LAMMPS module.
 
 Second, a lower-level Python interface can be used indirectly through
-provided PyLammps and IPyLammps wrapper classes, written in Python.
+the provided PyLammps and IPyLammps wrapper classes, written in Python.
 These wrappers try to simplify the usage of LAMMPS in Python by
 providing an object-based interface to common LAMMPS functionality.
 They also reduces the amount of code necessary to parameterize LAMMPS
@@ -25,11 +25,12 @@ scripts through Python and make variables and computes directly
 accessible.
 
 Third, LAMMPS can use the Python interpreter, so that a LAMMPS
-input script can invoke Python code directly, and pass information
+input script or styles can invoke Python code directly, and pass
-back-and-forth between the input script and Python functions you
+information back-and-forth between the input script and Python
-write.  This Python code can also callback to LAMMPS to query or change
+functions you write.  This Python code can also callback to LAMMPS
-its attributes.  In Python lingo, this is "embedding" Python in
+to query or change its attributes through the LAMMPS Python module
-LAMMPS.  When used in this mode, Python can perform operations that
+mentioned above.  In Python lingo, this is "embedding" Python in
-the simple LAMMPS input script syntax cannot.
+LAMMPS.  When used in this mode, Python can perform script operations
+that the simple LAMMPS input script syntax can not.
 
 

doc/src/Speed_intel.txt

@@ -24,7 +24,7 @@ LAMMPS to run on the CPU cores and co-processor cores simultaneously.
 
 Angle Styles: charmm, harmonic :ulb,l
 Bond Styles: fene, fourier, harmonic :l
-Dihedral Styles: charmm, harmonic, opls :l
+Dihedral Styles: charmm, fourier, harmonic, opls :l
 Fixes: nve, npt, nvt, nvt/sllod, nve/asphere :l
 Improper Styles: cvff, harmonic :l
 Pair Styles: airebo, airebo/morse, buck/coul/cut, buck/coul/long,
@@ -34,6 +34,10 @@ rebo, sw, tersoff :l
 K-Space Styles: pppm, pppm/disp :l
 :ule
 
+IMPORTANT NOTE: None of the styles in the USER-INTEL package currently
+support computing per-atom stress.  If any compute or fix in your
+input requires it, LAMMPS will abort with an error message.
+
 [Speed-ups to expect:]
 
 The speedups will depend on your simulation, the hardware, which

doc/src/commands_list.txt

@@ -53,6 +53,7 @@ Commands :h1
    include
    info
    jump
+   kim_query
    kspace_modify
    kspace_style
    label
@@ -61,6 +62,7 @@ Commands :h1
    mass
    message
    min_modify
+   min_spin
    min_style
    minimize
    molecule

doc/src/compute.txt

@@ -54,9 +54,10 @@ local quantities have the word "local" in their style,
 e.g. {bond/local}.  Styles with neither "atom" or "local" in their
 style produce global quantities.
 
-Note that a single compute produces either global or per-atom or local
+Note that a single compute can produce either global or per-atom or
-quantities, but never more than one of these (with only a few
+local quantities, but not both global and per-atom.  It can produce
-exceptions, as documented by individual compute commands).
+local quantities in tandem with global or per-atom quantities.  The
+compute doc page will explain.
 
 Global, per-atom, and local quantities each come in three kinds: a
 single scalar value, a vector of values, or a 2d array of values.  The

doc/src/fix.txt

@@ -83,8 +83,10 @@ not in the specified fix group.  Local quantities are calculated by
 each processor based on the atoms it owns, but there may be zero or
 more per atoms.
 
-Note that a single fix may produces either global or per-atom or local
+Note that a single fix can produce either global or per-atom or local
-quantities (or none at all), but never more than one of these.
+quantities (or none at all), but not both global and per-atom.  It can
+produce local quantities in tandem with global or per-atom quantities.
+The fix doc page will explain.
 
 Global, per-atom, and local quantities each come in three kinds: a
 single scalar value, a vector of values, or a 2d array of values.  The

doc/src/fix_ave_histo.txt

@@ -35,6 +35,7 @@ keyword = {mode} or {file} or {ave} or {start} or {beyond} or {overwrite} or {ti
   {mode} arg = {scalar} or {vector}
     scalar = all input values are scalars
     vector = all input values are vectors
+  {kind} arg = {global} or {peratom} or {local}
   {file} arg = filename
     filename = name of file to output histogram(s) to
   {ave} args = {one} or {running} or {window}
@@ -92,7 +93,8 @@ either all global, all per-atom, or all local quantities.  Inputs of
 different kinds (e.g. global and per-atom) cannot be mixed.  Atom
 attributes are per-atom vector values.  See the doc page for
 individual "compute" and "fix" commands to see what kinds of
-quantities they generate.
+quantities they generate.  See the optional {kind} keyword below for
+how to force the fix ave/histo command to disambiguate if necessary.
 
 Note that the output of this command is a single histogram for all
 input values combined together, not one histogram per input value.
@@ -231,6 +233,14 @@ keyword is set to {vector}, then all input values must be global or
 per-atom or local vectors, or columns of global or per-atom or local
 arrays.
 
+The {kind} keyword only needs to be set if a compute or fix produces
+more than one kind of output (global, per-atom, local).  If this is
+not the case, then LAMMPS will determine what kind of input is
+provided and whether all the input arguments are consistent.  If a
+compute or fix produces more than one kind of output, the {kind}
+keyword should be used to specify which output will be used.  The
+remaining input arguments must still be consistent.
+
 The {beyond} keyword determines how input values that fall outside the
 {lo} to {hi} bounds are treated.  Values such that {lo} <= value <=
 {hi} are assigned to one bin.  Values on a bin boundary are assigned
@@ -240,7 +250,7 @@ If {beyond} is set to {end} then values < {lo} are counted in the
 first bin and values > {hi} are counted in the last bin.  If {beyond}
 is set to {extend} then two extra bins are created, so that there are
 Nbins+2 total bins.  Values < {lo} are counted in the first bin and
-values > {hi} are counted in the last bin (Nbins+1).  Values between
+values > {hi} are counted in the last bin (Nbins+2).  Values between
 {lo} and {hi} (inclusive) are counted in bins 2 through Nbins+1.  The
 "coordinate" stored and printed for these two extra bins is {lo} and
 {hi}.
@@ -354,5 +364,6 @@ ave/chunk"_fix_ave_chunk.html, "fix ave/time"_fix_ave_time.html,
 
 [Default:] none
 
-The option defaults are mode = scalar, ave = one, start = 0, no file
+The option defaults are mode = scalar, kind = figured out from input
-output, beyond = ignore, and title 1,2,3 = strings as described above.
+arguments, ave = one, start = 0, no file output, beyond = ignore, and
+title 1,2,3 = strings as described above.

doc/src/fix_bond_react.txt

@@ -385,6 +385,10 @@ No parameter of this fix can be used with the {start/stop} keywords of
 the "run"_run.html command.  This fix is not invoked during "energy
 minimization"_minimize.html.
 
+When fix bond/react is 'unfixed,' all internally-created groups are
+deleted. Therefore, fix bond/react can only be unfixed after unfixing
+all other fixes that use any group created by fix bond/react.
+
 [Restrictions:]
 
 This fix is part of the USER-MISC package.  It is only enabled if

doc/src/fix_hyper_global.txt

@@ -102,7 +102,7 @@ Bi = exp(beta * Vij(max)) :pre
 where beta = 1/kTequil, and {Tequil} is the temperature of the system
 and an argument to this fix.  Note that Bi >= 1 at every step.
 
-NOTE: To run GHD, the input script must also use the "fix
+NOTE: To run a GHD simulation, the input script must also use the "fix
 langevin"_fix_langevin.html command to thermostat the atoms at the
 same {Tequil} as specified by this fix, so that the system is running
 constant-temperature (NVT) dynamics.  LAMMPS does not check that this
@@ -166,9 +166,9 @@ correctly.  There will just be fewer events because the hyper time
 
 NOTE: If you have no physical intuition as to the smallest barrier
 height in your system, a reasonable strategy to determine the largest
-{Vmax} you can use for an LHD model, is to run a sequence of
+{Vmax} you can use for a GHD model, is to run a sequence of
 simulations with smaller and smaller {Vmax} values, until the event
-rate does not change.
+rate does not change (as a function of hyper time).
 
 The {Tequil} argument is the temperature at which the system is
 simulated; see the comment above about the "fix
@@ -177,7 +177,8 @@ beta term in the exponential factor that determines how much boost is
 achieved as a function of the bias potential.
 
 In general, the lower the value of {Tequil} and the higher the value
-of {Vmax}, the more boost will be achievable by the GHD algorithm.
+of {Vmax}, the more time boost will be achievable by the GHD
+algorithm.
 
 :line
 
@@ -190,41 +191,43 @@ The "fix_modify"_fix_modify.html {energy} option is supported by this
 fix to add the energy of the bias potential to the the system's
 potential energy as part of "thermodynamic output"_thermo_style.html.
 
-This fix computes a global scalar and global vector of length 11, which
+This fix computes a global scalar and global vector of length 12, which
 can be accessed by various "output commands"_Howto_output.html.  The
 scalar is the magnitude of the bias potential (energy units) applied on
 the current timestep.  The vector stores the following quantities:
 
 1 = boost factor on this step (unitless)
-2 = max strain Eij of any bond on this step (unitless)
+2 = max strain Eij of any bond on this step (absolute value, unitless)
 3 = ID of first atom in the max-strain bond
 4 = ID of second atom in the max-strain bond
 5 = average # of bonds/atom on this step :ul
 
-6 = fraction of timesteps with bias = 0.0 during this run
+6 = fraction of timesteps where the biased bond has bias = 0.0 during this run
-7 = max drift distance of any atom during this run (distance units)
+7 = fraction of timesteps where the biased bond has negative strain during this run
-8 = max bond length during this run (distance units) :ul
+8 = max drift distance of any atom during this run (distance units)
+9 = max bond length during this run (distance units) :ul
 
-9 = cumulative hyper time since fix was defined (time units)
+10 = cumulative hyper time since fix was defined (time units)
-10 = cumulative count of event timesteps since fix was defined
+11 = cumulative count of event timesteps since fix was defined
-11 = cumulative count of atoms in events since fix was defined :ul
+12 = cumulative count of atoms in events since fix was defined :ul
 
-The first 5 quantities are for the current timestep.  Quantities 6-8
+The first 5 quantities are for the current timestep.  Quantities 6-9
-are for the current hyper run.  Quantities 9-11 are cumulative across
+are for the current hyper run.  They are reset each time a new hyper
-multiple runs (since the fix was defined in the input script).
+run is performed.  Quantities 19-12 are cumulative across multiple
+runs (since the point in the input script the fix was defined).
 
-For value 7, drift is the distance an atom moves between timesteps
+For value 8, drift is the distance an atom moves between two quenched
-when the bond list is reset, i.e. between events.  Atoms involved in
+states when the second quench determines an event has occurred.  Atoms
-an event will typically move the greatest distance since others are
+involved in an event will typically move the greatest distance since
-typically oscillating around their lattice site.
+others typically remain near their original quenched position.
 
-For value 10, events are checked for by the "hyper"_hyper.html command
+For value 11, events are checked for by the "hyper"_hyper.html command
 once every {Nevent} timesteps.  This value is the count of those
 timesteps on which one (or more) events was detected.  It is NOT the
 number of distinct events, since more than one event may occur in the
 same {Nevent} time window.
 
-For value 11, each time the "hyper"_hyper.html command checks for an
+For value 12, each time the "hyper"_hyper.html command checks for an
 event, it invokes a compute to flag zero or more atoms as
 participating in one or more events.  E.g. atoms that have displaced
 more than some distance from the previous quench state.  Value 11 is

doc/src/fix_hyper_local.txt

@@ -22,10 +22,9 @@ Dcut = minimum distance between boosted bonds (distance units) :l
 alpha = boostostat relaxation time (time units) :l
 Btarget = desired time boost factor (unitless) :l
 zero or more keyword/value pairs may be appended :l
-keyword = {lost} or {check/bias} or {check/coeff}
+keyword = {check/ghost} or {check/bias} :l
-  {lostbond} value = error/warn/ignore
+  {check/ghost} values = none
-  {check/bias} values = Nevery error/warn/ignore
+  {check/bias} values = Nevery error/warn/ignore :pre
-  {check/coeff} values = Nevery error/warn/ignore :pre
 :ule
 
 [Examples:]
@@ -65,8 +64,8 @@ To understand this description, you should first read the description
 of the GHD algorithm on the "fix hyper/global"_fix_hyper_global.html
 doc page.  This description of LHD builds on the GHD description.
 
-The definition of bonds, Eij, and Emax are the same for GHD and LHD.
+The definition of bonds and Eij are the same for GHD and LHD.  The
-The formulas for Vij(max) and Fij(max) are also the same except for a
+formulas for Vij(max) and Fij(max) are also the same except for a
 pre-factor Cij, explained below.
 
 The bias energy Vij applied to a bond IJ with maximum strain is
@@ -117,11 +116,11 @@ where Vkl(max) is the bias energy of the maxstrain bond KL within bond
 IJ's neighborhood, beta = 1/kTequil, and {Tequil} is the temperature
 of the system and an argument to this fix.
 
-NOTE: To run LHD, the input script must also use the "fix
+NOTE: To run an LHD simulation, the input script must also use the
-langevin"_fix_langevin.html command to thermostat the atoms at the
+"fix langevin"_fix_langevin.html command to thermostat the atoms at
-same {Tequil} as specified by this fix, so that the system is running
+the same {Tequil} as specified by this fix, so that the system is
-constant-temperature (NVT) dynamics.  LAMMPS does not check that this
+running constant-temperature (NVT) dynamics.  LAMMPS does not check
-is done.
+that this is done.
 
 Note that if IJ = KL, then bond IJ is a biased bond on that timestep,
 otherwise it is not.  But regardless, the boost factor Bij can be
@@ -216,20 +215,20 @@ each pair.  E.g. something like 2x the cutoff of the interatomic
 potential.  In practice a {Dcut} value of ~10 Angstroms seems to work
 well for many solid-state systems.
 
-NOTE: You must also insure that ghost atom communication is performed
+NOTE: You should insure that ghost atom communication is performed for
-for a distance of at least {Dcut} + {cutevent} where {cutevent} = the
+a distance of at least {Dcut} + {cutevent} = the distance one or more
-distance one or more atoms move (between quenched states) to be
+atoms move (between quenched states) to be considered an "event".  It
-considered an "event".  It is an argument to the "compute
+is an argument to the "compute event/displace" command used to detect
-event/displace" command used to detect events.  By default the ghost
+events.  By default the ghost communication distance is set by the
-communication distance is set by the pair_style cutoff, which will
+pair_style cutoff, which will typically be < {Dcut}.  The "comm_modify
-typically be < {Dcut}.  The "comm_modify cutoff"_comm_modify.html
+cutoff"_comm_modify.html command should be used to override the ghost
-command can be used to set the ghost cutoff explicitly, e.g.
+cutoff explicitly, e.g.
 
 comm_modify cutoff 12.0 :pre
 
-This fix does not know the {cutevent} parameter, but uses half the
+Note that this fix does not know the {cutevent} parameter, but uses
-bond length as an estimate to warn if the ghost cutoff is not long
+half the {cutbond} parameter as an estimate to warn if the ghost
-enough.
+cutoff is not long enough.
 
 As described above the {alpha} argument is a pre-factor in the
 boostostat update equation for each bond's Cij prefactor.  {Alpha} is
@@ -269,7 +268,30 @@ NOTE: If you have no physical intuition as to the smallest barrier
 height in your system, a reasonable strategy to determine the largest
 {Btarget} you can use for an LHD model, is to run a sequence of
 simulations with smaller and smaller {Btarget} values, until the event
-rate does not change.
+rate does not change (as a function of hyper time).
+
+:line
+
+Here is additional information on the optional keywords for this fix.
+
+The {check/ghost} keyword turns on extra computation each timestep to
+compute statistics about ghost atoms used to determine which bonds to
+bias.  The output of these stats are the vector values 14 and 15,
+described below.  If this keyword is not enabled, the output
+of the stats will be zero.
+
+The {check/bias} keyword turns on extra computation and communication
+to check if any biased bonds are closer than {Dcut} to each other,
+which should not be the case if LHD is operating correctly.  Thus it
+is a debugging check.  The {Nevery} setting determines how often the
+check is made.  The {error}, {warn}, or {ignore} setting determines
+what is done if the count of too-close bonds is not zero.  Either the
+code will exit, or issue a warning, or silently tally the count.  The
+count can be output as vector value 17, as described below.  If this
+keyword is not enabled, the output of that statistic will be 0.
+
+Note that both of these computations are costly, hence they are only
+enabled by these keywords.
 
 :line
 
@@ -282,95 +304,120 @@ The "fix_modify"_fix_modify.html {energy} option is supported by this
 fix to add the energy of the bias potential to the the system's
 potential energy as part of "thermodynamic output"_thermo_style.html.
 
-This fix computes a global scalar and global vector of length 23,
+This fix computes a global scalar and global vector of length 21,
-which can be accessed by various "output
+which can be accessed by various "output commands"_Howto_output.html.
-commands"_Howto_output.html.  The scalar is the magnitude of
+The scalar is the magnitude of the bias potential (energy units)
-the bias potential (energy units) applied on the current timestep,
+applied on the current timestep, summed over all biased bonds.  The
-summed over all biased bonds.  The vector stores the following
+vector stores the following quantities:
-quantities:
 
 1 = # of biased bonds on this step
-2 = max strain Eij of any bond on this step (unitless)
+2 = max strain Eij of any bond on this step (absolute value, unitless)
-3 = average bias potential for all biased bonds on this step (energy units)
+3 = average bias coeff for all bonds on this step (unitless)
 4 = average # of bonds/atom on this step
 5 = average neighbor bonds/bond on this step within {Dcut} :ul
 
-6 = fraction of steps and bonds with no bias during this run
+6 = max bond length during this run (distance units)
-7 = max drift distance of any atom during this run (distance units)
+7 = average # of biased bonds/step during this run
-8 = max bond length during this run (distance units)
+8 = fraction of biased bonds with no bias during this run
-9 = average # of biased bonds/step during this run
+9 = fraction of biased bonds with negative strain during this run
-10 = average bias potential for all biased bonds during this run (energy units)
+10 = average bias coeff for all bonds during this run (unitless)
-11 = max bias potential for any biased bond during this run (energy units)
+11 = min bias coeff for any bond during this run (unitless)
-12 = min bias potential for any biased bond during this run (energy units)
+12 = max bias coeff for any bond during this run (unitless)
-13 = max distance from my sub-box of any ghost atom with maxstrain < qfactor during this run (distance units)
-14 = max distance outside my box of any ghost atom with any maxstrain during this run (distance units)
-15 = count of ghost neighbor atoms not found on reneighbor steps during this run
-16 = count of lost bond partners during this run
-17 = average bias coeff for lost bond partners during this run
-18 = count of bias overlaps found during this run
-19 = count of non-matching bias coefficients found during this run :ul
 
-20 = cumulative hyper time since fix created (time units)
+13 = max drift distance of any bond atom during this run (distance units)
-21 = cumulative count of event timesteps since fix created
+14 = max distance from proc subbox of any ghost atom with maxstrain < qfactor during this run (distance units)
-22 = cumulative count of atoms in events since fix created
+15 = max distance outside my box of any ghost atom with any maxstrain during this run (distance units)
-23 = cumulative # of new bonds since fix created :ul
+16 = count of ghost atoms that could not be found on reneighbor steps during this run
+17 = count of bias overlaps (< Dcut) found during this run
+
+18 = cumulative hyper time since fix created (time units)
+19 = cumulative count of event timesteps since fix created
+20 = cumulative count of atoms in events since fix created
+21 = cumulative # of new bonds formed since fix created :ul
 
 The first quantities (1-5) are for the current timestep.  Quantities
-6-19 are for the current hyper run.  They are reset each time a new
+6-17 are for the current hyper run.  They are reset each time a new
-hyper run is performed.  Quantities 20-23 are cumulative across
+hyper run is performed.  Quantities 18-21 are cumulative across
-multiple runs (since the fix was defined in the input script).
+multiple runs (since the point in the input script the fix was
+defined).
 
-For value 6, the numerator is a count of all biased bonds on every
+For value 8, the numerator is a count of all biased bonds on each
 timestep whose bias energy = 0.0 due to Eij >= {qfactor}.  The
 denominator is the count of all biased bonds on all timesteps.
 
-For value 7, drift is the distance an atom moves between timesteps
+For value 9, the numerator is a count of all biased bonds on each
-when the bond list is reset, i.e. between events.  Atoms involved in
+timestep with negative strain.  The denominator is the count of all
-an event will typically move the greatest distance since others are
+biased bonds on all timesteps.
-typically oscillating around their lattice site.
 
-For values 13 and 14, the maxstrain of a ghost atom is the maxstrain
+Values 13-17 are mostly useful for debugging and diagnostic purposes.
-of any bond it is part of, and it is checked for ghost atoms within
-the bond neighbor cutoff.
 
-Values 15-19 are mostly useful for debugging and diagnostic purposes.
+For value 13, drift is the distance an atom moves between two quenched
+states when the second quench determines an event has occurred.  Atoms
+involved in an event will typically move the greatest distance since
+others typically remain near their original quenched position.
 
-For values 15-17, it is possible that a ghost atom owned by another
+For values 14-16, neighbor atoms in the full neighbor list with cutoff
-processor will move far enough (e.g. as part of an event-in-progress)
+{Dcut} may be ghost atoms outside a processor's sub-box.  Before the
-that it will no longer be within the communication cutoff distance for
+next event occurs they may move further than {Dcut} away from the
-acquiring ghost atoms.  Likewise it may be a ghost atom bond partner
+sub-box boundary.  Value 14 is the furthest (from the sub-box) any
-that cannot be found because it has moved too far.  These values count
+ghost atom in the neighbor list with maxstrain < {qfactor} was
-those occurrences.  Because they typically involve atoms that are part
+accessed during the run.  Value 15 is the same except that the ghost
-of events, they do not usually indicate bad dynamics.  Value 16 is the
+atom's maxstrain may be >= {qfactor}, which may mean it is about to
-average bias coefficient for bonds where a partner atom was lost.
+participate in an event.  Value 16 is a count of how many ghost atoms
+could not be found on reneighbor steps, presumably because they moved
+too far away due to their participation in an event (which will likely
+be detected at the next quench).
 
-For value 18, no two bonds should be biased if they are within a
+Typical values for 14 and 15 should be slightly larger than {Dcut},
+which accounts for ghost atoms initially at a {Dcut} distance moving
+thermally before the next event takes place.
+
+Note that for values 14 and 15 to be computed, the optional keyword
+{check/ghost} must be specified.  Otherwise these values will be zero.
+This is because computing them incurs overhead, so the values are only
+computed if requested.
+
+Value 16 should be zero or small.  As explained above a small count
+likely means some ghost atoms were participating in their own events
+and moved a longer distance.  If the value is large, it likely means
+the communication cutoff for ghosts is too close to {Dcut} leading to
+many not-found ghost atoms before the next event.  This may lead to a
+reduced number of bonds being selected for biasing, since the code
+assumes those atoms are part of highly strained bonds.  As explained
+above, the "comm_modify cutoff"_comm_modify.html command can be used
+to set a longer cutoff.
+
+For value 17, no two bonds should be biased if they are within a
 {Dcut} distance of each other.  This value should be zero, indicating
-that no pair of bonds "overlap", meaning they are closer than {Dcut}
+that no pair of biased bonds are closer than {Dcut} from each other.
-from each other.
 
-For value 19, the same bias coefficient is stored by both atoms in an
+Note that for values 17 to be computed, the optional keyword
-IJ bond.  This value should be zero, indicating that for all bonds,
+{check/bias} must be specified and it determines how often this check
-each atom in the bond stores the a bias coefficient with the same
+is performed.  This is because performing the check incurs overhead,
-value.
+so if only computed as often as requested.
 
-Value 20 is simply the specified {boost} factor times the number of
+The result at the end of the run is the cumulative total from every
-timestep times the timestep size.
+timestep the check was made.  Note that the value is a count of atoms
+in bonds which found other atoms in bonds too close, so it is almost
+always an over-count of the number of too-close bonds.
 
-For value 21, events are checked for by the "hyper"_hyper.html command
+Value 18 is simply the specified {boost} factor times the number of
+timesteps times the timestep size.
+
+For value 19, events are checked for by the "hyper"_hyper.html command
 once every {Nevent} timesteps.  This value is the count of those
 timesteps on which one (or more) events was detected.  It is NOT the
 number of distinct events, since more than one event may occur in the
 same {Nevent} time window.
 
-For value 22, each time the "hyper"_hyper.html command checks for an
+For value 20, each time the "hyper"_hyper.html command checks for an
 event, it invokes a compute to flag zero or more atoms as
 participating in one or more events.  E.g. atoms that have displaced
-more than some distance from the previous quench state.  Value 22 is
+more than some distance from the previous quench state.  Value 20 is
 the cumulative count of the number of atoms participating in any of
 the events that were found.
 
-Value 23 tallies the number of new bonds created by the bond reset
+Value 21 tallies the number of new bonds created by the bond reset
 operation.  Bonds between a specific I,J pair of atoms may persist for
 the entire hyperdynamics simulation if neither I or J are involved in
 an event.
@@ -378,6 +425,16 @@ an event.
 The scalar and vector values calculated by this fix are all
 "intensive".
 
+This fix also computes a local vector of length the number of bonds
+currently in the system.  The value for each bond is its Cij prefactor
+(bias coefficient).  These values can be can be accessed by various
+"output commands"_Howto_output.html.  A particularly useful one is the
+"fix ave/histo"_fix_ave_histo.html command which can be used to
+histogram the Cij values to see if they are distributed reasonably
+close to 1.0, which indicates a good choice of {Vmax}.
+
+The local values calculated by this fix are unitless.
+
 No parameter of this fix can be used with the {start/stop} keywords of
 the "run"_run.html command.  This fix is not invoked during "energy
 minimization"_minimize.html.
@@ -392,7 +449,9 @@ doc page for more info.
 
 "hyper"_hyper.html, "fix hyper/global"_fix_hyper_global.html
 
-[Default:] None
+[Default:]
+
+The check/ghost and check/bias keywords are not enabled by default.
 
 :line
 

doc/src/fix_wall_gran.txt

@@ -7,22 +7,24 @@
 :line
 
 fix wall/gran command :h3
-fix wall/gran/omp command :h3
 
 [Syntax:]
 
-fix ID group-ID wall/gran fstyle Kn Kt gamma_n gamma_t xmu dampflag wallstyle args keyword values ... :pre
+fix ID group-ID wall/gran fstyle fstyle_params wallstyle args keyword values ... :pre
 
 ID, group-ID are documented in "fix"_fix.html command :ulb,l
 wall/gran = style name of this fix command :l
 fstyle = style of force interactions between particles and wall :l
-  possible choices: hooke, hooke/history, hertz/history :pre
+  possible choices: hooke, hooke/history, hertz/history, granular :pre
-Kn = elastic constant for normal particle repulsion (force/distance units or pressure units - see discussion below) :l
+fstyle_params = parameters associated with force interaction style :l
-Kt = elastic constant for tangential contact (force/distance units or pressure units - see discussion below) :l
+  For {hooke}, {hooke/history}, and {hertz/history}, {fstyle_params} are: 
-gamma_n = damping coefficient for collisions in normal direction (1/time units or 1/time-distance units - see discussion below) :l
+	Kn = elastic constant for normal particle repulsion (force/distance units or pressure units - see discussion below) 
-gamma_t = damping coefficient for collisions in tangential direction (1/time units or 1/time-distance units - see discussion below) :l
+	Kt = elastic constant for tangential contact (force/distance units or pressure units - see discussion below) 
-xmu = static yield criterion (unitless value between 0.0 and 1.0e4) :l
+	gamma_n = damping coefficient for collisions in normal direction (1/time units or 1/time-distance units - see discussion below) 
-dampflag = 0 or 1 if tangential damping force is excluded or included :l
+	gamma_t = damping coefficient for collisions in tangential direction (1/time units or 1/time-distance units - see discussion below)  
+	xmu = static yield criterion (unitless value between 0.0 and 1.0e4) 
+	dampflag = 0 or 1 if tangential damping force is excluded or included :pre
+  For {granular}, {fstyle_params} are set using the same syntax as for the {pair_coeff} command of "pair_style granular"_pair_granular.html :pre
 wallstyle = {xplane} or {yplane} or {zplane} or {zcylinder} :l
 args = list of arguments for a particular style :l
   {xplane} or {yplane} or {zplane} args = lo hi
@@ -44,7 +46,10 @@ keyword = {wiggle} or {shear} :l
 
 fix 1 all wall/gran hooke  200000.0 NULL 50.0 NULL 0.5 0 xplane -10.0 10.0
 fix 1 all wall/gran hooke/history 200000.0 NULL 50.0 NULL 0.5 0 zplane 0.0 NULL
-fix 2 all wall/gran hooke 100000.0 20000.0 50.0 30.0 0.5 1 zcylinder 15.0 wiggle z 3.0 2.0 :pre
+fix 2 all wall/gran hooke 100000.0 20000.0 50.0 30.0 0.5 1 zcylinder 15.0 wiggle z 3.0 2.0 
+fix 3 all wall/gran granular hooke 1000.0 50.0 tangential linear_nohistory 1.0 0.4 zplane 0.0 NULL
+fix 4 all wall/gran granular jkr 1000.0 50.0 0.3 5.0 tangential mindlin 800.0 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall zcylinder 15.0 wiggle z 3.0 2.0
+fix 5 all wall/gran granular dmt 1000.0 50.0 0.3 10.0 tangential mindlin 800.0 0.5 0.1 roll sds 500.0 200.0 0.1 twisting marshall zplane 0.0 NULL :pre
 
 [Description:]
 
@@ -54,31 +59,40 @@ close enough to touch it.
 
 The nature of the wall/particle interactions are determined by the
 {fstyle} setting.  It can be any of the styles defined by the
-"pair_style granular"_pair_gran.html commands.  Currently this is
+"pair_style gran/*"_pair_gran.html or the more general "pair_style
-{hooke}, {hooke/history}, or {hertz/history}.  The equation for the
+granular"_pair_granular.html" commands.  Currently the options are
-force between the wall and particles touching it is the same as the
+{hooke}, {hooke/history}, or {hertz/history} for the former, and
-corresponding equation on the "pair_style granular"_pair_gran.html doc
+{granular} with all the possible options of the associated
-page, in the limit of one of the two particles going to infinite
+{pair_coeff} command for the latter.  The equation for the force
-radius and mass (flat wall).  Specifically, delta = radius - r =
+between the wall and particles touching it is the same as the
-overlap of particle with wall, m_eff = mass of particle, and the
+corresponding equation on the "pair_style gran/*"_pair_gran.html and
-effective radius of contact = RiRj/Ri+Rj is just the radius of the
+"pair_style_granular"_pair_granular.html doc pages, in the limit of
-particle.
+one of the two particles going to infinite radius and mass (flat
+wall).  Specifically, delta = radius - r = overlap of particle with
+wall, m_eff = mass of particle, and the effective radius of contact =
+RiRj/Ri+Rj is set to the radius of the particle.
 
 The parameters {Kn}, {Kt}, {gamma_n}, {gamma_t}, {xmu} and {dampflag}
 have the same meaning and units as those specified with the
-"pair_style granular"_pair_gran.html commands.  This means a NULL can
+"pair_style gran/*"_pair_gran.html commands.  This means a NULL can be
-be used for either {Kt} or {gamma_t} as described on that page.  If a
+used for either {Kt} or {gamma_t} as described on that page.  If a
 NULL is used for {Kt}, then a default value is used where {Kt} = 2/7
 {Kn}.  If a NULL is used for {gamma_t}, then a default value is used
 where {gamma_t} = 1/2 {gamma_n}.
 
+All the model choices for cohesion, tangential friction, rolling
+friction and twisting friction supported by the "pair_style
+granular"_pair_granular.html through its {pair_coeff} command are also
+supported for walls. These are discussed in greater detail on the doc
+page for "pair_style granular"_pair_granular.html.
+
 Note that you can choose a different force styles and/or different
-values for the 6 wall/particle coefficients than for particle/particle
+values for the wall/particle coefficients than for particle/particle
 interactions.  E.g. if you wish to model the wall as a different
 material.
 
 NOTE: As discussed on the doc page for "pair_style
-granular"_pair_gran.html, versions of LAMMPS before 9Jan09 used a
+gran/*"_pair_gran.html, versions of LAMMPS before 9Jan09 used a
 different equation for Hertzian interactions.  This means Hertizian
 wall/particle interactions have also changed.  They now include a
 sqrt(radius) term which was not present before.  Also the previous
@@ -108,14 +122,14 @@ Optionally, the wall can be moving, if the {wiggle} or {shear}
 keywords are appended.  Both keywords cannot be used together.
 
 For the {wiggle} keyword, the wall oscillates sinusoidally, similar to
-the oscillations of particles which can be specified by the
+the oscillations of particles which can be specified by the "fix
-"fix move"_fix_move.html command.  This is useful in packing
+move"_fix_move.html command.  This is useful in packing simulations of
-simulations of granular particles.  The arguments to the {wiggle}
+granular particles.  The arguments to the {wiggle} keyword specify a
-keyword specify a dimension for the motion, as well as it's
+dimension for the motion, as well as it's {amplitude} and {period}.
-{amplitude} and {period}.  Note that if the dimension is in the plane
+Note that if the dimension is in the plane of the wall, this is
-of the wall, this is effectively a shearing motion.  If the dimension
+effectively a shearing motion.  If the dimension is perpendicular to
-is perpendicular to the wall, it is more of a shaking motion.  A
+the wall, it is more of a shaking motion.  A {zcylinder} wall can only
-{zcylinder} wall can only be wiggled in the z dimension.
+be wiggled in the z dimension.
 
 Each timestep, the position of a wiggled wall in the appropriate {dim}
 is set according to this equation:
@@ -137,28 +151,6 @@ the clockwise direction for {vshear} > 0 or counter-clockwise for
 {vshear} < 0.  In this case, {vshear} is the tangential velocity of
 the wall at whatever {radius} has been defined.
 
-:line
-
-Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
-functionally the same as the corresponding style without the suffix.
-They have been optimized to run faster, depending on your available
-hardware, as discussed on the "Speed packages"_Speed_packages.html doc
-page.  The accelerated styles take the same arguments and should
-produce the same results, except for round-off and precision issues.
-
-These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
-USER-OMP and OPT packages, respectively.  They are only enabled if
-LAMMPS was built with those packages.  See the "Build
-package"_Build_package.html doc page for more info.
-
-You can specify the accelerated styles explicitly in your input script
-by including their suffix, or you can use the "-suffix command-line
-switch"_Run_options.html when you invoke LAMMPS, or you can use the
-"suffix"_suffix.html command in your input script.
-
-See the "Speed packages"_Speed_packages.html doc page for more
-instructions on how to use the accelerated styles effectively.
-
 [Restart, fix_modify, output, run start/stop, minimize info:]
 
 This fix writes the shear friction state of atoms interacting with the
@@ -188,6 +180,7 @@ Any dimension (xyz) that has a granular wall must be non-periodic.
 
 "fix move"_fix_move.html,
 "fix wall/gran/region"_fix_wall_gran_region.html,
-"pair_style granular"_pair_gran.html
+"pair_style gran/*"_pair_gran.html
+"pair_style granular"_pair_granular.html
 
 [Default:] none

doc/src/fix_wall_gran_region.txt

@@ -10,24 +10,30 @@ fix wall/gran/region command :h3
 
 [Syntax:]
 
-fix ID group-ID wall/gran/region fstyle Kn Kt gamma_n gamma_t xmu dampflag wallstyle regionID :pre
+fix ID group-ID wall/gran/region fstyle fstyle_params wallstyle regionID :pre
 
 ID, group-ID are documented in "fix"_fix.html command :ulb,l
 wall/region = style name of this fix command :l
 fstyle = style of force interactions between particles and wall :l
-  possible choices: hooke, hooke/history, hertz/history :pre
+  possible choices: hooke, hooke/history, hertz/history, granular :pre
-Kn = elastic constant for normal particle repulsion (force/distance units or pressure units - see discussion below) :l
+fstyle_params = parameters associated with force interaction style :l
-Kt = elastic constant for tangential contact (force/distance units or pressure units - see discussion below) :l
+  For {hooke}, {hooke/history}, and {hertz/history}, {fstyle_params} are: 
-gamma_n = damping coefficient for collisions in normal direction (1/time units or 1/time-distance units - see discussion below) :l
+	Kn = elastic constant for normal particle repulsion (force/distance units or pressure units - see discussion below) 
-gamma_t = damping coefficient for collisions in tangential direction (1/time units or 1/time-distance units - see discussion below) :l
+	Kt = elastic constant for tangential contact (force/distance units or pressure units - see discussion below) 
-xmu = static yield criterion (unitless value between 0.0 and 1.0e4) :l
+	gamma_n = damping coefficient for collisions in normal direction (1/time units or 1/time-distance units - see discussion below) 
-dampflag = 0 or 1 if tangential damping force is excluded or included :l
+	gamma_t = damping coefficient for collisions in tangential direction (1/time units or 1/time-distance units - see discussion below)  
+	xmu = static yield criterion (unitless value between 0.0 and 1.0e4) 
+	dampflag = 0 or 1 if tangential damping force is excluded or included :pre
+  For {granular}, {fstyle_params} are set using the same syntax as for the {pair_coeff} command of "pair_style granular"_pair_granular.html :pre
 wallstyle = region (see "fix wall/gran"_fix_wall_gran.html for options for other kinds of walls) :l
 region-ID = region whose boundary will act as wall :l,ule
 
 [Examples:]
 
-fix wall all wall/gran/region hooke/history 1000.0 200.0 200.0 100.0 0.5 1 region myCone :pre
+fix wall all wall/gran/region hooke/history 1000.0 200.0 200.0 100.0 0.5 1 region myCone 
+fix 3 all wall/gran/region granular hooke 1000.0 50.0 tangential linear_nohistory 1.0 0.4 region myBox
+fix 4 all wall/gran/region granular jkr 1000.0 50.0 tangential linear_history 800.0 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall region myCone
+fix 5 all wall/gran/region granular dmt 1000.0 50.0 0.3 10.0 tangential linear_history 800.0 0.5 0.1 roll sds 500.0 200.0 0.1 twisting marshall region myCone :pre
 
 [Description:]
 
@@ -42,8 +48,8 @@ Here are snapshots of example models using this command.
 Corresponding input scripts can be found in examples/granregion.
 Click on the images to see a bigger picture.  Movies of these
 simulations are "here on the Movies
-page"_http://lammps.sandia.gov/movies.html#granregion of the
+page"_http://lammps.sandia.gov/movies.html#granregion of the LAMMPS
-LAMMPS web site.
+web site.
 
 :image(JPG/gran_funnel_small.jpg,JPG/gran_funnel.png)
 :image(JPG/gran_mixer_small.jpg,JPG/gran_mixer.png)
@@ -123,12 +129,16 @@ to make the two faces differ by epsilon in their position.
 
 The nature of the wall/particle interactions are determined by the
 {fstyle} setting.  It can be any of the styles defined by the
-"pair_style granular"_pair_gran.html commands.  Currently this is
+"pair_style gran/*"_pair_gran.html or the more general "pair_style
-{hooke}, {hooke/history}, or {hertz/history}.  The equation for the
+granular"_pair_granular.html" commands.  Currently the options are
-force between the wall and particles touching it is the same as the
+{hooke}, {hooke/history}, or {hertz/history} for the former, and
-corresponding equation on the "pair_style granular"_pair_gran.html doc
+{granular} with all the possible options of the associated
-page, but the effective radius is calculated using the radius of the
+{pair_coeff} command for the latter.  The equation for the force
-particle and the radius of curvature of the wall at the contact point.
+between the wall and particles touching it is the same as the
+corresponding equation on the "pair_style gran/*"_pair_gran.html and
+"pair_style_granular"_pair_granular.html doc pages, but the effective
+radius is calculated using the radius of the particle and the radius
+of curvature of the wall at the contact point.
 
 Specifically, delta = radius - r = overlap of particle with wall,
 m_eff = mass of particle, and RiRj/Ri+Rj is the effective radius, with
@@ -141,12 +151,18 @@ particle.
 
 The parameters {Kn}, {Kt}, {gamma_n}, {gamma_t}, {xmu} and {dampflag}
 have the same meaning and units as those specified with the
-"pair_style granular"_pair_gran.html commands.  This means a NULL can
+"pair_style gran/*"_pair_gran.html commands.  This means a NULL can be
-be used for either {Kt} or {gamma_t} as described on that page.  If a
+used for either {Kt} or {gamma_t} as described on that page.  If a
 NULL is used for {Kt}, then a default value is used where {Kt} = 2/7
 {Kn}.  If a NULL is used for {gamma_t}, then a default value is used
 where {gamma_t} = 1/2 {gamma_n}.
 
+All the model choices for cohesion, tangential friction, rolling
+friction and twisting friction supported by the "pair_style
+granular"_pair_granular.html through its {pair_coeff} command are also
+supported for walls. These are discussed in greater detail on the doc
+page for "pair_style granular"_pair_granular.html.
+
 Note that you can choose a different force styles and/or different
 values for the 6 wall/particle coefficients than for particle/particle
 interactions.  E.g. if you wish to model the wall as a different
@@ -154,9 +170,9 @@ material.
 
 [Restart, fix_modify, output, run start/stop, minimize info:]
 
-Similar to "fix wall/gran"_fix_wall_gran.html command, this fix
+Similar to "fix wall/gran"_fix_wall_gran.html command, this fix writes
-writes the shear friction state of atoms interacting with the wall to
+the shear friction state of atoms interacting with the wall to "binary
-"binary restart files"_restart.html, so that a simulation can continue
+restart files"_restart.html, so that a simulation can continue
 correctly if granular potentials with shear "history" effects are
 being used.  This fix also includes info about a moving region in the
 restart file.  See the "read_restart"_read_restart.html command for
@@ -170,14 +186,14 @@ So you must re-define your region and if it is a moving region, define
 its motion attributes in a way that is consistent with the simulation
 that wrote the restart file.  In particular, if you want to change the
 region motion attributes (e.g. its velocity), then you should ensure
-the position/orientation of the region at the initial restart
+the position/orientation of the region at the initial restart timestep
-timestep is the same as it was on the timestep the restart file was
+is the same as it was on the timestep the restart file was written.
-written.  If this is not possible, you may need to ignore info in the
+If this is not possible, you may need to ignore info in the restart
-restart file by defining a new fix wall/gran/region command in your
+file by defining a new fix wall/gran/region command in your restart
-restart script, e.g. with a different fix ID.  Or if you want to keep
+script, e.g. with a different fix ID.  Or if you want to keep the
-the shear history info but discard the region motion information, you
+shear history info but discard the region motion information, you can
-can use the same fix ID for fix wall/gran/region, but assign it a
+use the same fix ID for fix wall/gran/region, but assign it a region
-region with a different region ID.
+with a different region ID.
 
 None of the "fix_modify"_fix_modify.html options are relevant to this
 fix.  No global or per-atom quantities are stored by this fix for

doc/src/kim_query.txt

@@ -0,0 +1,46 @@
+"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

@@ -167,6 +167,7 @@ if.html
 include.html
 info.html
 jump.html
+kim_query.html
 label.html
 lattice.html
 log.html
@@ -174,6 +175,7 @@ mass.html
 message.html
 min_modify.html
 min_style.html
+min_spin.html
 minimize.html
 molecule.html
 neb.html
@@ -578,6 +580,7 @@ pair_extep.html
 pair_gauss.html
 pair_gayberne.html
 pair_gran.html
+pair_granular.html
 pair_gromacs.html
 pair_gw.html
 pair_ilp_graphene_hbn.html

doc/src/min_modify.txt

@@ -13,11 +13,15 @@ min_modify command :h3
 min_modify keyword values ... :pre
 
 one or more keyword/value pairs may be listed :ulb,l
-keyword = {dmax} or {line}
+keyword = {dmax} or {line} or {alpha_damp} or {discrete_factor}
   {dmax} value = max
     max = maximum distance for line search to move (distance units)
   {line} value = {backtrack} or {quadratic} or {forcezero}
-    backtrack,quadratic,forcezero = style of linesearch to use :pre
+    backtrack,quadratic,forcezero = style of linesearch to use 
+  {alpha_damp} value = damping
+    damping = fictitious Gilbert damping for spin minimization (adim)
+  {discrete_factor} value = factor
+    factor = discretization factor for adaptive spin timestep (adim) :pre
 :ule
 
 [Examples:]
@@ -65,6 +69,17 @@ difference of two large values (energy before and energy after) and
 that difference may be smaller than machine epsilon even if atoms
 could move in the gradient direction to reduce forces further.
 
+Keywords {alpha_damp} and {discrete_factor} only make sense when
+a "min_spin"_min_spin.html command is declared. 
+Keyword {alpha_damp} defines an analog of a magnetic Gilbert
+damping. It defines a relaxation rate toward an equilibrium for
+a given magnetic system. 
+Keyword {discrete_factor} defines a discretization factor for the
+adaptive timestep used in the {spin} minimization. 
+See "min_spin"_min_spin.html for more information about those
+quantities. 
+Default values are {alpha_damp} = 1.0 and {discrete_factor} = 10.0.
+
 [Restrictions:] none
 
 [Related commands:]

doc/src/min_spin.txt

@@ -0,0 +1,65 @@
+"LAMMPS WWW Page"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+:line
+
+min_style spin command :h3
+
+[Syntax:]
+
+min_style spin :pre
+
+[Examples:]
+
+min_style 	spin :pre 
+
+[Description:]
+
+Apply a minimization algorithm to use when a "minimize"_minimize.html
+command is performed.
+
+Style {spin} defines a damped spin dynamics with an adaptive
+timestep, according to:
+
+:c,image(Eqs/min_spin_damping.jpg)
+
+with lambda a damping coefficient (similar to a Gilbert
+damping).
+Lambda can be defined by setting the {alpha_damp} keyword with the 
+"min_modify"_min_modify.html command. 
+
+The minimization procedure solves this equation using an
+adaptive timestep. The value of this timestep is defined 
+by the largest precession frequency that has to be solved in the 
+system:
+
+:c,image(Eqs/min_spin_timestep.jpg)
+
+with {|omega|_{max}} the norm of the largest precession frequency
+in the system (across all processes, and across all replicas if a
+spin/neb calculation is performed). 
+
+Kappa defines a discretization factor {discrete_factor} for the 
+definition of this timestep. 
+{discrete_factor} can be defined with the "min_modify"_min_modify.html
+command.
+
+NOTE: The {spin} style replaces the force tolerance by a torque
+tolerance. See "minimize"_minimize.html for more explanation. 
+
+[Restrictions:] 
+
+This minimization procedure is only applied to spin degrees of
+freedom for a frozen lattice configuration.
+
+[Related commands:]
+
+"min_style"_min_style.html, "minimize"_minimize.html, 
+"min_modify"_min_modify.html
+
+[Default:]
+
+The option defaults are {alpha_damp} = 1.0 and {discrete_factor} =
+10.0.

doc/src/min_style.txt

@@ -11,11 +11,12 @@ min_style command :h3
 
 min_style style :pre
 
-style = {cg} or {hftn} or {sd} or {quickmin} or {fire} :ul
+style = {cg} or {hftn} or {sd} or {quickmin} or {fire} or {spin} :ul
 
 [Examples:]
 
 min_style cg
+min_style spin
 min_style fire :pre
 
 [Description:]
@@ -61,6 +62,10 @@ the velocity non-parallel to the current force vector.  The velocity
 of each atom is initialized to 0.0 by this style, at the beginning of
 a minimization.
 
+Style {spin} is a damped spin dynamics with an adaptive 
+timestep.
+See the "min/spin"_min_spin.html doc page for more information.
+
 Either the {quickmin} and {fire} styles are useful in the context of
 nudged elastic band (NEB) calculations via the "neb"_neb.html command.
 

doc/src/minimize.txt

@@ -103,6 +103,13 @@ the line search fails because the step distance backtracks to 0.0
 the number of outer iterations or timesteps exceeds {maxiter}
 the number of total force evaluations exceeds {maxeval} :ul
 
+NOTE: the "minimization style"_min_style.html {spin} replaces
+the force tolerance {ftol} by a torque tolerance.
+The minimization procedure stops if the 2-norm (length) of the 
+global torque vector (defined as the cross product between the 
+spins and their precession vectors omega) is less than {ftol}, 
+or if any of the other criteria are met.
+
 NOTE: You can also use the "fix halt"_fix_halt.html command to specify
 a general criterion for exiting a minimization, that is a calculation
 performed on the state of the current system, as defined by an

doc/src/pair_granular.txt

@@ -0,0 +1,765 @@
+<script type="text/javascript"
+  src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
+</script>
+<script type="text/x-mathjax-config">
+  MathJax.Hub.Config({ TeX: { equationNumbers: {autoNumber: "AMS"} } });
+</script>
+
+"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
+
+pair_style granular command :h3
+
+[Syntax:]
+
+pair_style granular cutoff :pre
+
+cutoff = global cutoff (optional).  See discussion below. :ul
+
+[Examples:]
+
+pair_style granular
+pair_coeff * * hooke 1000.0 50.0 tangential linear_nohistory 1.0 0.4 :pre
+
+pair_style granular
+pair_coeff * * hertz 1000.0 50.0 tangential mindlin NULL 1.0 0.4 :pre
+
+pair_style granular
+pair_coeff * * hertz/material 1e8 0.3 tangential mindlin_rescale NULL 1.0 0.4 damping tsuji :pre
+
+pair_style granular
+pair_coeff 1 1 jkr 1000.0 50.0 tangential mindlin 800.0 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall
+pair_coeff 2 2 hertz 200.0 20.0 tangential linear_history 300.0 1.0 0.1 rolling sds 200.0 100.0 0.1 twisting marshall :pre
+
+pair_style granular
+pair_coeff 1 1 hertz 1000.0 50.0 tangential mindlin 800.0 0.5 0.5 rolling sds 500.0 200.0 0.5 twisting marshall
+pair_coeff 2 2 dmt 1000.0 50.0 0.3 10.0 tangential mindlin 800.0 0.5 0.1 roll sds 500.0 200.0 0.1 twisting marshall
+pair_coeff 1 2 dmt 1000.0 50.0 0.3 10.0 tangential mindlin 800.0 0.5 0.1 roll sds 500.0 200.0 0.1 twisting marshall :pre
+
+[Description:]
+
+The {granular} styles support a variety of options for the normal,
+tangential, rolling and twisting forces resulting from contact between
+two granular particles. This expands on the options offered by the
+"pair gran/*"_pair_gran.html pair styles. The total computed forces
+and torques are the sum of various models selected for the normal,
+tangential, rolling and twisting modes of motion.
+
+All model choices and parameters are entered in the
+"pair_coeff"_pair_coeff.html command, as described below.  Unlike
+e.g. "pair gran/hooke"_pair_gran.html, coefficient values are not
+global, but can be set to different values for different combinations
+of particle types, as determined by the "pair_coeff"_pair_coeff.html
+command.  If the contact model choice is the same for two particle
+types, the mixing for the cross-coefficients can be carried out
+automatically. This is shown in the second example, where model
+choices are the same for type 1 - type 1 as for type 2 - type2
+interactions, but coefficients are different. In this case, the
+coefficients for type 2 - type interactions can be determined from
+mixing rules discussed below.  For additional flexibility,
+coefficients as well as model forms can vary between particle types,
+as shown in the third example: type 1- type 1 interactions are based
+on a Hertzian normal contact model and 2-2 interactions are based on a
+DMT cohesive model (see below).  In that example, 1-1 and 2-2
+interactions have different model forms, in which case mixing of
+coefficients cannot be determined, so 1-2 interactions must be
+explicitly defined via the {pair_coeff 1 2} command, otherwise an
+error would result.
+
+:line
+
+The first required keyword for the {pair_coeff} command is the normal
+contact model. Currently supported options for normal contact models
+and their required arguments are:
+
+{hooke} : \(k_n\), \(\eta_\{n0\}\) (or \(e\))
+{hertz} : \(k_n\), \(\eta_\{n0\}\) (or \(e\))
+{hertz/material} : E, \(\eta_\{n0\}\) (or \(e\)), \(\nu\)
+{dmt} : E, \(\eta_\{n0\}\) (or \(e\)), \(\nu\), \(\gamma\)
+{jkr} : E, \(\eta_\{n0\}\) (or \(e\)), \(\nu\), \(\gamma\) :ol
+
+Here, \(k_n\) is spring stiffness (with units that depend on model
+choice, see below); \(\eta_\{n0\}\) is a damping prefactor (or, in its
+place a coefficient of restitution \(e\), depending on the choice of
+damping mode, see below); E is Young's modulus in units of
+{force}/{length}^2, i.e. {pressure}; \(\nu\) is Poisson's ratio and
+\(\gamma\) is a surface energy density, in units of
+{energy}/{length}^2.
+
+For the {hooke} model, the normal, elastic component of force acting
+on particle {i} due to contact with particle {j} is given by:
+
+\begin\{equation\}
+\mathbf\{F\}_\{ne, Hooke\} = k_N \delta_\{ij\} \mathbf\{n\}
+\end\{equation\}
+
+Where \(\delta = R_i + R_j - \|\mathbf\{r\}_\{ij\}\|\) is the particle
+overlap, \(R_i, R_j\) are the particle radii, \(\mathbf\{r\}_\{ij\} =
+\mathbf\{r\}_i - \mathbf\{r\}_j\) is the vector separating the two
+particle centers (note the i-j ordering so that \(F_\{ne\}\) is
+positive for repulsion), and \(\mathbf\{n\} =
+\frac\{\mathbf\{r\}_\{ij\}\}\{\|\mathbf\{r\}_\{ij\}\|\}\).  Therefore,
+for {hooke}, the units of the spring constant \(k_n\) are
+{force}/{distance}, or equivalently {mass}/{time^2}.
+
+For the {hertz} model, the normal component of force is given by:
+
+\begin\{equation\}
+\mathbf\{F\}_\{ne, Hertz\} = k_N R_\{eff\}^\{1/2\}\delta_\{ij\}^\{3/2\} \mathbf\{n\}
+\end\{equation\}
+
+Here, \(R_\{eff\} = \frac\{R_i R_j\}\{R_i + R_j\}\) is the effective
+radius, denoted for simplicity as {R} from here on.  For {hertz}, the
+units of the spring constant \(k_n\) are {force}/{length}^2, or
+equivalently {pressure}.
+
+For the {hertz/material} model, the force is given by:
+
+\begin\{equation\}
+\mathbf\{F\}_\{ne, Hertz/material\} = \frac\{4\}\{3\} E_\{eff\} R_\{eff\}^\{1/2\}\delta_\{ij\}^\{3/2\} \mathbf\{n\}
+\end\{equation\}
+
+Here, \(E_\{eff\} = E = \left(\frac\{1-\nu_i^2\}\{E_i\} +
+\frac\{1-\nu_j^2\}\{E_j\}\right)^\{-1\}\) is the effective Young's
+modulus, with \(\nu_i, \nu_j \) the Poisson ratios of the particles of
+types {i} and {j}. Note that if the elastic modulus and the shear
+modulus of the two particles are the same, the {hertz/material} model
+is equivalent to the {hertz} model with \(k_N = 4/3 E_\{eff\}\)
+
+The {dmt} model corresponds to the
+"(Derjaguin-Muller-Toporov)"_#DMT1975 cohesive model, where the force
+is simply Hertz with an additional attractive cohesion term:
+
+\begin\{equation\}
+\mathbf\{F\}_\{ne, dmt\} = \left(\frac\{4\}\{3\} E R^\{1/2\}\delta_\{ij\}^\{3/2\} - 4\pi\gamma R\right)\mathbf\{n\}
+\end\{equation\}
+
+The {jkr} model is the "(Johnson-Kendall-Roberts)"_#JKR1971 model,
+where the force is computed as:
+
+\begin\{equation\}
+\label\{eq:force_jkr\}
+\mathbf\{F\}_\{ne, jkr\} = \left(\frac\{4Ea^3\}\{3R\} - 2\pi a^2\sqrt\{\frac\{4\gamma E\}\{\pi a\}\}\right)\mathbf\{n\}
+\end\{equation\}
+
+Here, {a} is the radius of the contact zone, related to the overlap
+\(\delta\) according to:
+
+\begin\{equation\}
+\delta = a^2/R - 2\sqrt\{\pi \gamma a/E\}
+\end\{equation\}
+
+LAMMPS internally inverts the equation above to solve for {a} in terms
+of \(\delta\), then solves for the force in the previous
+equation. Additionally, note that the JKR model allows for a tensile
+force beyond contact (i.e. for \(\delta < 0\)), up to a maximum of
+\(3\pi\gamma R\) (also known as the 'pull-off' force).  Note that this
+is a hysteretic effect, where particles that are not contacting
+initially will not experience force until they come into contact
+\(\delta \geq 0\); as they move apart and (\(\delta < 0\)), they
+experience a tensile force up to \(3\pi\gamma R\), at which point they
+lose contact.
+
+:line
+
+In addition, the normal force is augmented by a damping term of the
+following general form:
+
+\begin\{equation\}
+\mathbf\{F\}_\{n,damp\} = -\eta_n \mathbf\{v\}_\{n,rel\}
+\end\{equation\}
+
+Here, \(\mathbf\{v\}_\{n,rel\} = (\mathbf\{v\}_j - \mathbf\{v\}_i)
+\cdot \mathbf\{n\}\) is the component of relative velocity along
+\(\mathbf\{n\}\).
+
+The optional {damping} keyword to the {pair_coeff} command followed by
+a keyword determines the model form of the damping factor \(\eta_n\),
+and the interpretation of the \(\eta_\{n0\}\) or \(e\) coefficients
+specified as part of the normal contact model settings. The {damping}
+keyword and corresponding model form selection may be appended
+anywhere in the {pair coeff} command.  Note that the choice of damping
+model affects both the normal and tangential damping (and depending on
+other settings, potentially also the twisting damping).  The options
+for the damping model currently supported are:
+
+{velocity}
+{viscoelastic}
+{tsuji} :ol
+
+If the {damping} keyword is not specified, the {viscoelastic} model is
+used by default.
+
+For {damping velocity}, the normal damping is simply equal to the
+user-specified damping coefficient in the {normal} model:
+
+\begin\{equation\}
+\eta_n = \eta_\{n0\}\
+\end\{equation\}
+
+Here, \(\gamma_n\) is the damping coefficient specified for the normal
+contact model, in units of {mass}/{time},
+
+The {damping viscoelastic} model is based on the viscoelastic
+treatment of "(Brilliantov et al)"_#Brill1996, where the normal
+damping is given by:
+
+\begin\{equation\}
+\eta_n = \eta_\{n0\}\ a m_\{eff\}
+\end\{equation\}
+
+Here, \(m_\{eff\} = m_i m_j/(m_i + m_j)\) is the effective mass, {a}
+is the contact radius, given by \(a =\sqrt\{R\delta\}\) for all models
+except {jkr}, for which it is given implicitly according to \(delta =
+a^2/R - 2\sqrt\{\pi \gamma a/E\}\).  In this case, \eta_\{n0\}\ is in
+units of 1/({time}*{distance}).
+
+The {tsuji} model is based on the work of "(Tsuji et
+al)"_#Tsuji1992. Here, the damping coefficient specified as part of
+the normal model is interpreted as a restitution coefficient
+\(e\). The damping constant \(\eta_n\) is given by:
+
+\begin\{equation\}
+\eta_n = \alpha (m_\{eff\}k_n)^\{1/2\}
+\end\{equation\}
+
+For normal contact models based on material parameters, \(k_n =
+4/3Ea\).  The parameter \(\alpha\) is related to the restitution
+coefficient {e} according to:
+
+\begin\{equation\}
+\alpha = 1.2728-4.2783e+11.087e^2-22.348e^3+27.467e^4-18.022e^5+4.8218e^6
+\end\{equation\}
+
+The dimensionless coefficient of restitution \(e\) specified as part
+of the normal contact model parameters should be between 0 and 1, but
+no error check is performed on this.
+
+The total normal force is computed as the sum of the elastic and
+damping components:
+
+\begin\{equation\}
+\mathbf\{F\}_n = \mathbf\{F\}_\{ne\} + \mathbf\{F\}_\{n,damp\}
+\end\{equation\}
+
+ :line
+
+The {pair_coeff} command also requires specification of the tangential
+contact model. The required keyword {tangential} is expected, followed
+by the model choice and associated parameters. Currently supported
+tangential model choices and their expected parameters are as follows:
+
+{linear_nohistory} : \(x_\{\gamma,t\}\), \(\mu_s\)
+{linear_history} : \(k_t\), \(x_\{\gamma,t\}\), \(\mu_s\)
+{mindlin} : \(k_t\) or NULL, \(x_\{\gamma,t\}\), \(\mu_s\)
+{mindlin_rescale} : \(k_t\) or NULL, \(x_\{\gamma,t\}\), \(\mu_s\) :ol
+
+Here, \(x_\{\gamma,t\}\) is a dimensionless multiplier for the normal
+damping \(\eta_n\) that determines the magnitude of the tangential
+damping, \(\mu_t\) is the tangential (or sliding) friction
+coefficient, and \(k_t\) is the tangential stiffness coefficient.
+
+For {tangential linear_nohistory}, a simple velocity-dependent Coulomb
+friction criterion is used, which mimics the behavior of the {pair
+gran/hooke} style. The tangential force (\mathbf\{F\}_t\) is given by:
+
+\begin\{equation\}
+\mathbf\{F\}_t =  -min(\mu_t F_\{n0\}, \|\mathbf\{F\}_\mathrm\{t,damp\}\|) \mathbf\{t\}
+\end\{equation\}
+
+The tangential damping force \(\mathbf\{F\}_\mathrm\{t,damp\}\) is given by:
+
+\begin\{equation\}
+\mathbf\{F\}_\mathrm\{t,damp\} = -\eta_t \mathbf\{v\}_\{t,rel\}
+\end\{equation\}
+
+The tangential damping prefactor \(\eta_t\) is calculated by scaling
+the normal damping \(\eta_n\) (see above):
+
+\begin\{equation\}
+\eta_t = -x_\{\gamma,t\} \eta_n
+\end\{equation\}
+
+The normal damping prefactor \(\eta_n\) is determined by the choice of
+the {damping} keyword, as discussed above.  Thus, the {damping}
+keyword also affects the tangential damping.  The parameter
+\(x_\{\gamma,t\}\) is a scaling coefficient. Several works in the
+literature use \(x_\{\gamma,t\} = 1\) ("Marshall"_#Marshall2009,
+"Tsuji et al"_#Tsuji1992, "Silbert et al"_#Silbert2001).  The relative
+tangential velocity at the point of contact is given by
+\(\mathbf\{v\}_\{t, rel\} = \mathbf\{v\}_\{t\} - (R_i\Omega_i +
+R_j\Omega_j) \times \mathbf\{n\}\), where \(\mathbf\{v\}_\{t\} =
+\mathbf\{v\}_r - \mathbf\{v\}_r\cdot\mathbf\{n\}\), \(\mathbf\{v\}_r =
+\mathbf\{v\}_j - \mathbf\{v\}_i\). The direction of the applied force
+is \(\mathbf\{t\} =
+\mathbf\{v_\{t,rel\}\}/\|\mathbf\{v_\{t,rel\}\}\|\).
+
+The normal force value \(F_\{n0\}\) used to compute the critical force
+depends on the form of the contact model. For non-cohesive models
+({hertz}, {hertz/material}, {hooke}), it is given by the magnitude of
+the normal force:
+
+\begin\{equation\}
+F_\{n0\} = \|\mathbf\{F\}_n\|
+\end\{equation\}
+
+For cohesive models such as {jkr} and {dmt}, the critical force is
+adjusted so that the critical tangential force approaches \(\mu_t
+F_\{pulloff\}\), see "Marshall"_#Marshall2009, equation 43, and
+"Thornton"_#Thornton1991.  For both models, \(F_\{n0\}\) takes the
+form:
+
+\begin\{equation\}
+F_\{n0\} = \|\mathbf\{F\}_ne + 2 F_\{pulloff\}\|
+\end\{equation\}
+
+Where \(F_\{pulloff\} = 3\pi \gamma R \) for {jkr}, and
+\(F_\{pulloff\} = 4\pi \gamma R \) for {dmt}.
+
+The remaining tangential options all use accumulated tangential
+displacement (i.e. contact history). This is discussed below in the
+context of the {linear_history} option, but the same treatment of the
+accumulated displacement applies to the other options as well.
+
+For {tangential linear_history}, the tangential force is given by:
+
+\begin\{equation\}
+\mathbf\{F\}_t =  -min(\mu_t F_\{n0\}, \|-k_t\mathbf\{\xi\} + \mathbf\{F\}_\mathrm\{t,damp\}\|) \mathbf\{t\}
+\end\{equation\}
+
+Here, \(\mathbf\{\xi\}\) is the tangential displacement accumulated
+during the entire duration of the contact:
+
+\begin\{equation\}
+\mathbf\{\xi\} = \int_\{t0\}^t \mathbf\{v\}_\{t,rel\}(\tau) \mathrm\{d\}\tau
+\end\{equation\}
+
+This accumulated tangential displacement must be adjusted to account
+for changes in the frame of reference of the contacting pair of
+particles during contact. This occurs due to the overall motion of the
+contacting particles in a rigid-body-like fashion during the duration
+of the contact. There are two modes of motion that are relevant: the
+'tumbling' rotation of the contacting pair, which changes the
+orientation of the plane in which tangential displacement occurs; and
+'spinning' rotation of the contacting pair about the vector connecting
+their centers of mass (\(\mathbf\{n\}\)).  Corrections due to the
+former mode of motion are made by rotating the accumulated
+displacement into the plane that is tangential to the contact vector
+at each step, or equivalently removing any component of the tangential
+displacement that lies along \(\mathbf\{n\}\), and rescaling to
+preserve the magnitude.  This follows the discussion in
+"Luding"_#Luding2008, see equation 17 and relevant discussion in that
+work:
+
+\begin\{equation\}
+\mathbf\{\xi\} = \left(\mathbf\{\xi'\} - (\mathbf\{n\} \cdot \mathbf\{\xi'\})\mathbf\{n\}\right) \frac\{\|\mathbf\{\xi'\}\|\}\{\|\mathbf\{\xi'\}\| - \mathbf\{n\}\cdot\mathbf\{\xi'\}\}
+\label\{eq:rotate_displacements\}
+\end\{equation\}
+
+Here, \(\mathbf\{\xi'\}\) is the accumulated displacement prior to the
+current time step and \(\mathbf\{\xi\}\) is the corrected
+displacement. Corrections to the displacement due to the second mode
+of motion described above (rotations about \(\mathbf\{n\}\)) are not
+currently implemented, but are expected to be minor for most
+simulations.
+
+Furthermore, when the tangential force exceeds the critical force, the
+tangential displacement is re-scaled to match the value for the
+critical force (see "Luding"_#Luding2008, equation 20 and related
+discussion):
+
+\begin\{equation\}
+\mathbf\{\xi\} = -\frac\{1\}\{k_t\}\left(\mu_t F_\{n0\}\mathbf\{t\} + \mathbf\{F\}_\{t,damp\}\right)
+\end\{equation\}
+
+The tangential force is added to the total normal force (elastic plus
+damping) to produce the total force on the particle. The tangential
+force also acts at the contact point (defined as the center of the
+overlap region) to induce a torque on each particle according to:
+
+\begin\{equation\}
+\mathbf\{\tau\}_i = -(R_i - 0.5 \delta) \mathbf\{n\} \times \mathbf\{F\}_t
+\end\{equation\}
+
+\begin\{equation\}
+\mathbf\{\tau\}_j = -(R_j - 0.5 \delta) \mathbf\{n\} \times \mathbf\{F\}_t
+\end\{equation\}
+
+For {tangential mindlin}, the "Mindlin"_#Mindlin1949 no-slip solution is used, which differs from the {linear_history}
+option by an additional factor of {a}, the radius of the contact region. The tangential force is given by:
+
+\begin\{equation\}
+\mathbf\{F\}_t =  -min(\mu_t F_\{n0\}, \|-k_t a \mathbf\{\xi\} + \mathbf\{F\}_\mathrm\{t,damp\}\|) \mathbf\{t\}
+\end\{equation\}
+
+Here, {a} is the radius of the contact region, given by \(a = \delta
+R\) for all normal contact models, except for {jkr}, where it is given
+implicitly by \(\delta = a^2/R - 2\sqrt\{\pi \gamma a/E\}\), see
+discussion above. To match the Mindlin solution, one should set \(k_t
+= 8G\), where \(G\) is the shear modulus, related to Young's modulus
+\(E\) by \(G = E/(2(1+\nu))\), where \(\nu\) is Poisson's ratio. This
+can also be achieved by specifying {NULL} for \(k_t\), in which case a
+normal contact model that specifies material parameters \(E\) and
+\(\nu\) is required (e.g. {hertz/material}, {dmt} or {jkr}). In this
+case, mixing of the shear modulus for different particle types {i} and
+{j} is done according to:
+
+\begin\{equation\}
+1/G = 2(2-\nu_i)(1+\nu_i)/E_i + 2(2-\nu_j)(1+\nu_j)/E_j
+\end\{equation\}
+
+The {mindlin_rescale} option uses the same form as {mindlin}, but the
+magnitude of the tangential displacement is re-scaled as the contact
+unloads, i.e. if \(a < a_\{t_\{n-1\}\}\):
+
+\begin\{equation\}
+\mathbf\{\xi\} = \mathbf\{\xi_\{t_\{n-1\}\}\} \frac\{a\}\{a_\{t_\{n-1\}\}\}
+\end\{equation\}
+
+Here, \(t_\{n-1\}\) indicates the value at the previous time
+step. This rescaling accounts for the fact that a decrease in the
+contact area upon unloading leads to the contact being unable to
+support the previous tangential loading, and spurious energy is
+created without the rescaling above ("Walton"_#WaltonPC ). See also
+discussion in "Thornton et al, 2013"_#Thornton2013 , particularly
+equation 18(b) of that work and associated discussion.
+
+:line
+
+The optional {rolling} keyword enables rolling friction, which resists
+pure rolling motion of particles. The options currently supported are:
+
+{none}
+{sds} : \(k_\{roll\}\), \(\gamma_\{roll\}\), \(\mu_\{roll\}\)  :ol
+
+If the {rolling} keyword is not specified, the model defaults to {none}.
+
+For {rolling sds}, rolling friction is computed via a
+spring-dashpot-slider, using a 'pseudo-force' formulation, as detailed
+by "Luding"_#Luding2008. Unlike the formulation in
+"Marshall"_#Marshall2009, this allows for the required adjustment of
+rolling displacement due to changes in the frame of reference of the
+contacting pair.  The rolling pseudo-force is computed analogously to
+the tangential force:
+
+\begin\{equation\}
+\mathbf\{F\}_\{roll,0\} =  k_\{roll\} \mathbf\{\xi\}_\{roll\}  - \gamma_\{roll\} \mathbf\{v\}_\{roll\}
+\end\{equation\}
+
+Here, \(\mathbf\{v\}_\{roll\} = -R(\mathbf\{\Omega\}_i -
+\mathbf\{\Omega\}_j) \times \mathbf\{n\}\) is the relative rolling
+velocity, as given in "Wang et al"_#Wang2015 and
+"Luding"_#Luding2008. This differs from the expressions given by "Kuhn
+and Bagi"_#Kuhn2004 and used in "Marshall"_#Marshall2009; see "Wang et
+al"_#Wang2015 for details. The rolling displacement is given by:
+
+\begin\{equation\}
+\mathbf\{\xi\}_\{roll\} = \int_\{t_0\}^t \mathbf\{v\}_\{roll\} (\tau) \mathrm\{d\} \tau
+\end\{equation\}
+
+A Coulomb friction criterion truncates the rolling pseudo-force if it
+exceeds a critical value:
+
+\begin\{equation\}
+\mathbf\{F\}_\{roll\} =  min(\mu_\{roll\} F_\{n,0\}, \|\mathbf\{F\}_\{roll,0\}\|)\mathbf\{k\}
+\end\{equation\}
+
+Here, \(\mathbf\{k\} =
+\mathbf\{v\}_\{roll\}/\|\mathbf\{v\}_\{roll\}\|\) is the direction of
+the pseudo-force.  As with tangential displacement, the rolling
+displacement is rescaled when the critical force is exceeded, so that
+the spring length corresponds the critical force. Additionally, the
+displacement is adjusted to account for rotations of the frame of
+reference of the two contacting particles in a manner analogous to the
+tangential displacement.
+
+The rolling pseudo-force does not contribute to the total force on
+either particle (hence 'pseudo'), but acts only to induce an equal and
+opposite torque on each particle, according to:
+
+\begin\{equation\}
+\tau_\{roll,i\} =  R_\{eff\} \mathbf\{n\} \times \mathbf\{F\}_\{roll\}
+\end\{equation\}
+
+\begin\{equation\}
+\tau_\{roll,j\} =  -\tau_\{roll,i\}
+\end\{equation\}
+
+:line
+
+The optional {twisting} keyword enables twisting friction, which
+resists rotation of two contacting particles about the vector
+\(\mathbf\{n\}\) that connects their centers. The options currently
+supported are:
+
+{none}
+{sds} : \(k_\{twist\}\), \(\gamma_\{twist\}\), \(\mu_\{twist\}\)
+{marshall} :ol
+
+If the {twisting} keyword is not specified, the model defaults to {none}.
+
+For both {twisting sds} and {twisting marshall}, a history-dependent
+spring-dashpot-slider is used to compute the twisting torque. Because
+twisting displacement is a scalar, there is no need to adjust for
+changes in the frame of reference due to rotations of the particle
+pair. The formulation in "Marshall"_#Marshall2009 therefore provides
+the most straightforward treatment:
+
+\begin\{equation\}
+\tau_\{twist,0\} = -k_\{twist\}\xi_\{twist\} - \gamma_\{twist\}\Omega_\{twist\}
+\end\{equation\}
+
+Here \(\xi_\{twist\} = \int_\{t_0\}^t \Omega_\{twist\} (\tau)
+\mathrm\{d\}\tau\) is the twisting angular displacement, and
+\(\Omega_\{twist\} = (\mathbf\{\Omega\}_i - \mathbf\{\Omega\}_j) \cdot
+\mathbf\{n\}\) is the relative twisting angular velocity. The torque
+is then truncated according to:
+
+\begin\{equation\}
+\tau_\{twist\} = min(\mu_\{twist\} F_\{n,0\}, \tau_\{twist,0\})
+\end\{equation\}
+
+Similar to the sliding and rolling displacement, the angular
+displacement is rescaled so that it corresponds to the critical value
+if the twisting torque exceeds this critical value:
+
+\begin\{equation\}
+\xi_\{twist\} = \frac\{1\}\{k_\{twist\}\} (\mu_\{twist\} F_\{n,0\}sgn(\Omega_\{twist\}) - \gamma_\{twist\}\Omega_\{twist\})
+\end\{equation\}
+
+For {twisting sds}, the coefficients \(k_\{twist\}, \gamma_\{twist\}\)
+and \(\mu_\{twist\}\) are simply the user input parameters that follow
+the {twisting sds} keywords in the {pair_coeff} command.
+
+For {twisting_marshall}, the coefficients are expressed in terms of
+sliding friction coefficients, as discussed in
+"Marshall"_#Marshall2009 (see equations 32 and 33 of that work):
+
+\begin\{equation\}
+k_\{twist\} = 0.5k_ta^2
+\end\{equation\}
+
+\begin\{equation\}
+\eta_\{twist\} = 0.5\eta_ta^2
+\end\{equation\}
+
+\begin\{equation\}
+\mu_\{twist\} = \frac\{2\}\{3\}a\mu_t
+\end\{equation\}
+
+Finally, the twisting torque on each particle is given by:
+
+\begin\{equation\}
+\mathbf\{\tau\}_\{twist,i\} = \tau_\{twist\}\mathbf\{n\}
+\end\{equation\}
+
+\begin\{equation\}
+\mathbf\{\tau\}_\{twist,j\} = -\mathbf\{\tau\}_\{twist,i\}
+\end\{equation\}
+
+:line
+
+LAMMPS automatically sets pairwise cutoff values for {pair_style
+granular} based on particle radii (and in the case of {jkr} pull-off
+distances). In the vast majority of situations, this is adequate.
+However, a cutoff value can optionally be appended to the {pair_style
+granular} command to specify a global cutoff (i.e. a cutoff for all
+atom types). Additionally, the optional {cutoff} keyword can be passed
+to the {pair_coeff} command, followed by a cutoff value.  This will
+set a pairwise cutoff for the atom types in the {pair_coeff} command.
+These options may be useful in some rare cases where the automatic
+cutoff determination is not sufficient, e.g.  if particle diameters
+are being modified via the {fix adapt} command. In that case, the
+global cutoff specified as part of the {pair_style granular} command
+is applied to all atom types, unless it is overridden for a given atom
+type combination by the {cutoff} value specified in the {pair coeff}
+command.  If {cutoff} is only specified in the {pair coeff} command
+and no global cutoff is appended to the {pair_style granular} command,
+then LAMMPS will use that cutoff for the specified atom type
+combination, and automatically set pairwise cutoffs for the remaining
+atom types.
+
+:line
+
+Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the "Build
+package"_Build_package.html doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the "-suffix command-line
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
+
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
+
+:line
+
+[Mixing, shift, table, tail correction, restart, rRESPA info]:
+
+The "pair_modify"_pair_modify.html mix, shift, table, and tail options
+are not relevant for granular pair styles.
+
+Mixing of coefficients is carried out using geometric averaging for
+most quantities, e.g. if friction coefficient for type 1-type 1
+interactions is set to \(\mu_1\), and friction coefficient for type
+2-type 2 interactions is set to \(\mu_2\), the friction coefficient
+for type1-type2 interactions is computed as \(\sqrt\{\mu_1\mu_2\}\)
+(unless explicitly specified to a different value by a {pair_coeff 1 2
+...} command. The exception to this is elastic modulus, only
+applicable to {hertz/material}, {dmt} and {jkr} normal contact
+models. In that case, the effective elastic modulus is computed as:
+
+\begin\{equation\}
+E_\{eff,ij\} = \left(\frac\{1-\nu_i^2\}\{E_i\} + \frac\{1-\nu_j^2\}\{E_j\}\right)^\{-1\}
+\end\{equation\}
+
+If the {i-j} coefficients \(E_\{ij\}\) and \(\nu_\{ij\}\) are
+explicitly specified, the effective modulus is computed as:
+
+\begin\{equation\}
+E_\{eff,ij\} = \left(\frac\{1-\nu_\{ij\}^2\}\{E_\{ij\}\} + \frac\{1-\nu_\{ij\}^2\}\{E_\{ij\}\}\right)^\{-1\}
+\end\{equation\}
+
+or
+
+\begin\{equation\}
+E_\{eff,ij\} = \frac\{E_\{ij\}\}\{2(1-\nu_\{ij\})\}
+\end\{equation\}
+
+These pair styles write their information to "binary restart
+files"_restart.html, so a pair_style command does not need to be
+specified in an input script that reads a restart file.
+
+These pair styles can only be used via the {pair} keyword of the
+"run_style respa"_run_style.html command.  They do not support the
+{inner}, {middle}, {outer} keywords.
+
+The single() function of these pair styles returns 0.0 for the energy
+of a pairwise interaction, since energy is not conserved in these
+dissipative potentials.  It also returns only the normal component of
+the pairwise interaction force.  However, the single() function also
+calculates 10 extra pairwise quantities.  The first 3 are the
+components of the tangential force between particles I and J, acting
+on particle I.  The 4th is the magnitude of this tangential force.
+The next 3 (5-7) are the components of the rolling torque acting on
+particle I. The next entry (8) is the magnitude of the rolling torque.
+The next entry (9) is the magnitude of the twisting torque acting
+about the vector connecting the two particle centers.
+The last 3 (10-12) are the components of the vector connecting
+the centers of the two particles (x_I - x_J).
+
+These extra quantities can be accessed by the "compute
+pair/local"_compute_pair_local.html command, as {p1}, {p2}, ...,
+{p12}.
+
+:line
+
+[Restrictions:]
+
+All the granular pair styles are part of the GRANULAR package.  It is
+only enabled if LAMMPS was built with that package.  See the "Build
+package"_Build_package.html doc page for more info.
+
+These pair styles require that atoms store torque and angular velocity
+(omega) as defined by the "atom_style"_atom_style.html.  They also
+require a per-particle radius is stored.  The {sphere} atom style does
+all of this.
+
+This pair style requires you to use the "comm_modify vel
+yes"_comm_modify.html command so that velocities are stored by ghost
+atoms.
+
+These pair styles will not restart exactly when using the
+"read_restart"_read_restart.html command, though they should provide
+statistically similar results.  This is because the forces they
+compute depend on atom velocities.  See the
+"read_restart"_read_restart.html command for more details.
+
+[Related commands:]
+
+"pair_coeff"_pair_coeff.html
+"pair gran/*"_pair_gran.html
+
+[Default:]
+
+For the {pair_coeff} settings: {damping viscoelastic}, {rolling none},
+{twisting none}.
+
+[References:]
+
+:link(Brill1996)
+[(Brilliantov et al, 1996)] Brilliantov, N. V., Spahn, F., Hertzsch,
+J. M., & Poschel, T. (1996).  Model for collisions in granular
+gases. Physical review E, 53(5), 5382.
+
+:link(Tsuji1992) 
+[(Tsuji et al, 1992)] Tsuji, Y., Tanaka, T., & Ishida,
+T. (1992). Lagrangian numerical simulation of plug flow of
+cohesionless particles in a horizontal pipe. Powder technology, 71(3),
+239-250.
+
+:link(JKR1971)
+[(Johnson et al, 1971)] Johnson, K. L., Kendall, K., & Roberts,
+A. D. (1971).  Surface energy and the contact of elastic
+solids. Proc. R. Soc. Lond. A, 324(1558), 301-313.
+
+:link(DMT1975)
+[Derjaguin et al, 1975)] Derjaguin, B. V., Muller, V. M., & Toporov,
+Y. P. (1975). Effect of contact deformations on the adhesion of
+particles. Journal of Colloid and interface science, 53(2), 314-326.
+
+:link(Luding2008)
+[(Luding, 2008)] Luding, S. (2008). Cohesive, frictional powders:
+contact models for tension. Granular matter, 10(4), 235.
+
+:link(Marshall2009)
+[(Marshall, 2009)] Marshall, J. S. (2009). Discrete-element modeling
+of particulate aerosol flows.  Journal of Computational Physics,
+228(5), 1541-1561.
+
+:link(Silbert2001)
+[(Silbert, 2001)] Silbert, L. E., Ertas, D., Grest, G. S., Halsey,
+T. C., Levine, D., & Plimpton, S. J. (2001).  Granular flow down an
+inclined plane: Bagnold scaling and rheology. Physical Review E,
+64(5), 051302.
+
+:link(Kuhn2004)
+[(Kuhn and Bagi, 2005)] Kuhn, M. R., & Bagi, K. (2004). Contact
+rolling and deformation in granular media.  International journal of
+solids and structures, 41(21), 5793-5820.
+
+:link(Wang2015)
+[(Wang et al, 2015)] Wang, Y., Alonso-Marroquin, F., & Guo,
+W. W. (2015).  Rolling and sliding in 3-D discrete element
+models. Particuology, 23, 49-55.
+
+:link(Thornton1991)
+[(Thornton, 1991)] Thornton, C. (1991). Interparticle sliding in the
+presence of adhesion.  J. Phys. D: Appl. Phys. 24 1942
+
+:link(Mindlin1949)
+[(Mindlin, 1949)] Mindlin, R. D. (1949). Compliance of elastic bodies
+in contact.  J. Appl. Mech., ASME 16, 259-268.
+
+:link(Thornton2013)
+[(Thornton et al, 2013)] Thornton, C., Cummins, S. J., & Cleary,
+P. W. (2013).  An investigation of the comparative behaviour of
+alternative contact force models during inelastic collisions. Powder
+Technology, 233, 30-46.
+
+:link(WaltonPC)
+[(Otis R. Walton)] Walton, O.R., Personal Communication	

doc/src/pair_kim.txt

@@ -31,14 +31,10 @@ element or alloy and set of parameters, e.g. EAM for Cu with a
 specific EAM potential file.
 
 See the current list of "KIM model
-drivers"_https://openkim.org/kim-items/model-drivers/alphabetical.
+drivers"_https://openkim.org/browse/model-drivers/alphabetical.
 
 See the current list of all "KIM
-models"_https://openkim.org/kim-items/models/by-model-drivers
+models"_https://openkim.org/browse/models/by-model-drivers
-
-See the list of "example KIM models"_https://openkim.org/kim-api which
-are included in the KIM library by default, in the "What is in the KIM
-API source package?" section.
 
 To use this pair style, you must first download and install the KIM
 API library from the "OpenKIM website"_https://openkim.org.  The KIM
@@ -46,11 +42,8 @@ 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)
+See the examples/kim dir for an input script that uses a KIM model
-for Lennard-Jones.  Note, for this example input script, the example models
+(potential) for Lennard-Jones.
-shipped with with kim-api package must be installed.  See the "Build
-package"_Build_package.html section and the ./lib/kim/README for details
-on how to build LAMMSPS with the kim-api and how to install the example models.
  
 :line
 

doc/src/pairs.txt

@@ -42,6 +42,7 @@ Pair Styles :h1
    pair_gauss
    pair_gayberne
    pair_gran
+   pair_granular
    pair_gromacs
    pair_gw
    pair_hbond_dreiding

doc/src/velocity.txt

@@ -134,7 +134,7 @@ The {mom} and {rot} keywords are used by {create}.  If mom = yes, the
 linear momentum of the newly created ensemble of velocities is zeroed;
 if rot = yes, the angular momentum is zeroed.
 
-*line
+:line
 
 If specified, the {temp} keyword is used by {create} and {scale} to
 specify a "compute"_compute.html that calculates temperature in a

doc/utils/sphinx-config/false_positives.txt

@@ -156,6 +156,8 @@ ba
 Babadi
 backcolor
 Baczewski
+Bagi
+Bagnold
 Bal
 balancer
 Balankura
@@ -250,6 +252,7 @@ Boresch
 Botero
 Botu
 Bouguet
+Bourne
 boxcolor
 bp
 bpls
@@ -346,6 +349,7 @@ Cij
 cis
 civ
 clearstore
+Cleary
 Clebsch
 clemson
 Clermont
@@ -372,6 +376,7 @@ Coeff
 CoefficientN
 coeffs
 Coeffs
+cohesionless
 Coker
 Colberg
 coleman
@@ -449,6 +454,7 @@ cuda
 Cuda
 CUDA
 CuH
+Cummins
 Curk
 customIDs
 cutbond
@@ -492,6 +498,7 @@ darkturquoise
 darkviolet
 Das
 Dasgupta
+dashpot
 dat
 datafile
 datums
@@ -529,6 +536,7 @@ Dequidt
 der
 derekt
 Derjagin
+Derjaguin
 Derlet
 Deserno
 Destree
@@ -627,6 +635,7 @@ dVx
 dW
 dx
 dy
+dylib
 dyn
 dyne
 dynes
@@ -1079,6 +1088,7 @@ Hyoungki
 hyperdynamics
 hyperradius
 hyperspherical
+hysteretic
 Ibanez
 ibar
 ibm
@@ -1138,6 +1148,7 @@ interconvert
 interial
 interlayer
 intermolecular
+Interparticle
 interstitials
 Intr
 intra
@@ -1156,6 +1167,7 @@ IPython
 Isele
 isenthalpic
 ish
+Ishida
 iso
 isodemic
 isoenergetic
@@ -1265,6 +1277,7 @@ kcl
 Kd
 KDevelop
 ke
+kepler
 KE
 Keblinski
 keflag
@@ -1298,6 +1311,7 @@ Kondor
 konglt
 Koning
 Kooser
+Korn
 Koskinen
 Koster
 Kosztin
@@ -1382,6 +1396,7 @@ libAtoms
 libawpmd
 libch
 libcolvars
+libcurl
 libdir
 libdl
 libfftw
@@ -1449,6 +1464,7 @@ logfile
 logfreq
 logicals
 Lomdahl
+Lond
 lookups
 Lookups
 LoopVar
@@ -1464,6 +1480,7 @@ lsfftw
 ltbbmalloc
 lubricateU
 lucy
+Luding
 Lussetti
 Lustig
 lwsock
@@ -1502,6 +1519,7 @@ manybody
 MANYBODY
 Maras
 Marrink
+Marroquin
 Marsaglia
 Marseille
 Martyna
@@ -1513,6 +1531,7 @@ masstotal
 Masuhiro
 Matchett
 Materias
+mathbf
 matlab
 matplotlib
 Mattox
@@ -1601,6 +1620,7 @@ Mie
 Mikami
 Militzer
 Minary
+Mindlin
 mincap
 mingw
 minima
@@ -1671,6 +1691,7 @@ mpiexec
 mpiio
 mpirun
 mplayer
+mps
 Mryglod
 mscg
 MSCG
@@ -1954,6 +1975,7 @@ oneway
 onn
 ons
 OO
+opencl
 openKIM
 OpenMP
 openmp
@@ -2286,6 +2308,7 @@ rg
 Rg
 Rhaphson
 rheological
+rheology
 rhodo
 Rhodo
 rhodopsin
@@ -2602,6 +2625,7 @@ Tait
 taitwater
 Tajkhorshid
 Tamaskovics
+Tanaka
 tanh
 Tartakovsky
 taskset
@@ -2689,6 +2713,7 @@ tokyo
 tol
 toolchain
 topologies
+Toporov
 Torder
 torsions
 Tosi
@@ -2733,6 +2758,7 @@ Tsrd
 Tstart
 tstat
 Tstop
+Tsuji
 Tsuzuki
 tt
 Tt

examples/SPIN/spinmin/in.spinmin.bfo

@@ -0,0 +1,55 @@
+# bfo in a 3d periodic box
+
+units 		metal
+dimension 	3
+boundary 	p p f
+atom_style 	spin
+
+# necessary for the serial algorithm (sametag)
+atom_modify 	map array 
+
+lattice 	sc 3.96
+region 		box block 0.0 34.0 0.0 34.0 0.0 1.0
+create_box 	1 box
+create_atoms 	1 box
+
+# setting mass, mag. moments, and interactions for bcc iron
+
+mass		1 1.0
+set 		group all spin/random 11 2.50
+
+pair_style 	hybrid/overlay spin/exchange 6.0 spin/magelec 4.5 spin/dmi 4.5
+pair_coeff 	* * spin/exchange exchange 6.0 -0.01575 0.0 1.965
+#pair_coeff 	* * spin/magelec magelec 4.5 0.000109 1.0 1.0 1.0
+pair_coeff 	* * spin/magelec magelec 4.5 0.00109 1.0 1.0 1.0
+pair_coeff 	* * spin/dmi dmi 4.5 0.00005 1.0 1.0 1.0
+
+neighbor 	0.1 bin
+neigh_modify 	every 10 check yes delay 20
+
+#fix 		1 all precession/spin zeeman 0.001 0.0 0.0 1.0 anisotropy 0.01 1.0 0.0 0.0 
+fix 		1 all precession/spin anisotropy 0.0000033 0.0 0.0 1.0
+fix_modify	1 energy yes
+
+timestep	0.0001
+
+compute 	out_mag    all spin
+compute 	out_pe     all pe
+compute 	out_ke     all ke
+compute 	out_temp   all temp
+
+variable 	magz      equal c_out_mag[3]
+variable 	magnorm   equal c_out_mag[4]
+variable 	emag      equal c_out_mag[5]
+variable 	tmag      equal c_out_mag[6]
+
+thermo          50
+thermo_style    custom step time v_magnorm v_emag v_tmag temp etotal
+thermo_modify   format float %20.15g
+
+compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
+dump 		1 all custom 50 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
+
+min_style	spin
+min_modify 	alpha_damp 1.0 discrete_factor 10.0
+minimize        1.0e-10 0.0 1000 100

examples/SPIN/spinmin/in.spinmin.iron

@@ -0,0 +1,55 @@
+# bcc iron in a 3d periodic box
+
+units 		metal
+dimension 	3
+boundary 	p p f
+atom_style 	spin
+
+# necessary for the serial algorithm (sametag)
+atom_modify 	map array 
+
+lattice 	bcc 2.8665
+region 		box block 0.0 4.0 0.0 4.0 0.0 4.0
+create_box 	1 box
+create_atoms 	1 box
+
+# setting mass, mag. moments, and interactions for bcc iron
+
+mass		1 55.845
+set 		group all spin/random 31 2.2
+#set 		group all spin 2.2 1.0 1.0 -1.0
+
+pair_style 	spin/exchange 3.5
+pair_coeff 	* * exchange 3.4 0.02726 0.2171 1.841
+
+neighbor 	0.1 bin
+neigh_modify 	every 10 check yes delay 20
+
+#fix 		1 all precession/spin zeeman 0.001 0.0 0.0 1.0 anisotropy 0.01 1.0 0.0 0.0 
+fix 		1 all precession/spin anisotropy 0.0001 0.0 0.0 1.0
+fix_modify	1 energy yes
+
+timestep	0.0001
+
+compute 	out_mag    all spin
+compute 	out_pe     all pe
+compute 	out_ke     all ke
+compute 	out_temp   all temp
+
+variable 	magx      equal c_out_mag[1]
+variable 	magy      equal c_out_mag[2]
+variable 	magz      equal c_out_mag[3]
+variable 	magnorm   equal c_out_mag[4]
+variable 	emag      equal c_out_mag[5]
+variable 	tmag      equal c_out_mag[6]
+
+thermo          100
+thermo_style    custom step time v_magx v_magz v_magnorm v_tmag etotal
+thermo_modify   format float %20.15g
+
+compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
+dump 		1 all custom 100 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
+
+min_style	spin
+min_modify 	alpha_damp 1.0 discrete_factor 10.0
+minimize        1.0e-10 1.0e-10 100000 1000

examples/hyper/in.hyper.global

@@ -12,6 +12,8 @@ variable        cutevent index 1.1
 variable        steps index 100000
 variable        nevent index 1000
 variable        zoom index 1.8
+variable        seed index 826626413
+variable        tol index 1.0e-15
 
 units           metal
 atom_style	atomic
@@ -45,7 +47,7 @@ neighbor	0.5 bin
 neigh_modify    every 1 delay 5 check yes
 
 fix		1 mobile nve
-fix		2 mobile langevin ${Tequil} ${Tequil} 1.0 858872873 zero yes
+fix		2 mobile langevin ${Tequil} ${Tequil} 1.0 ${seed} zero yes
 
 timestep	0.005
 
@@ -92,4 +94,4 @@ dump_modify	1 pad 6 amap 1 3 sa 1 3 blue red green
 
 # run
 
-hyper           ${steps} ${nevent} HG event min 1.0e-6 1.0e-6 100 100 dump 1
+hyper           ${steps} ${nevent} HG event min ${tol} ${tol} 1000 1000 dump 1

examples/hyper/in.hyper.local

@@ -107,6 +107,12 @@ dump		1 all image 10000000 local.*.jpg v_acolor type size 1024 1024 &
 		zoom ${zoom} adiam 2.5 view 0.0 0.0 up 0 1 0 axes yes 0.9 0.01
 dump_modify	1 pad 6 amap 1 3 sa 1 3 blue red green
 
+# test of histogramming and dump output of bias coeffs
+
+#fix            histo all ave/histo 10 100 1000 0.9 1.1 100 f_HL &
+#               mode vector kind local file tmp.histo
+#dump           2 all local 1000 tmp.local f_HL
+
 # run
 
 hyper           ${steps} ${nevent} HL event min ${tol} ${tol} 1000 1000 dump 1

examples/hyper/log.10Oct18.hyper.local.g++.16

@@ -1,993 +0,0 @@
-LAMMPS (10 Oct 2018)
-# 3d EAM surface for local HD
-
-# nearest neighbor distance = a * sqrt(2)/2 = 2.77 Angs for Pt with a = 3.92
-# hop event on (100) surface is same distance
-# exchange event is 2 atoms moving same distance
-
-variable        Tequil index 400.0
-variable        Vmax index 0.4
-variable        qfactor index 0.3
-variable        cutbond index 3.2
-variable        Dcut index 10.0
-variable        cutevent index 1.1
-variable        alpha index 200.0
-variable        boost index 4000.0
-variable        ghostcut index 12.0
-variable        steps index 1500
-variable        nevent index 100
-variable        nx index 8
-variable        ny index 8
-variable        zoom index 1.8
-variable        seed index 826626413
-variable        tol index 1.0e-15
-variable        add index 37K
-
-units           metal
-atom_style	atomic
-atom_modify     map array
-boundary        p p p
-comm_modify     cutoff ${ghostcut}
-comm_modify     cutoff 12.0
-
-lattice		fcc 3.92
-Lattice spacing in x,y,z = 3.92 3.92 3.92
-region		box block 0 6 0 6 0 4
-create_box	2 box
-Created orthogonal box = (0 0 0) to (23.52 23.52 15.68)
-  2 by 4 by 2 MPI processor grid
-create_atoms	1 box
-Created 576 atoms
-  Time spent = 0.00108504 secs
-
-mass            * 1.0
-
-change_box      all z final -0.1 5.0 boundary p p f
-  orthogonal box = (0 0 -0.392) to (23.52 23.52 19.6)
-
-# replicate in xy
-
-replicate       ${nx} ${ny} 1
-replicate       8 ${ny} 1
-replicate       8 8 1
-  orthogonal box = (0 0 -0.392) to (188.16 188.16 19.6)
-  4 by 4 by 1 MPI processor grid
-  36864 atoms
-  Time spent = 0.0028758 secs
-
-# add adatoms
-
-include         adatoms.list.${add}
-include         adatoms.list.37K
-create_atoms 1 single 27.5 9.5 4
-Created 1 atoms
-  Time spent = 0.000183105 secs
-create_atoms 1 single 16 9 4
-Created 1 atoms
-  Time spent = 0.000178099 secs
-create_atoms 1 single 10 12 4
-Created 1 atoms
-  Time spent = 0.000179768 secs
-create_atoms 1 single 31 44 4
-Created 1 atoms
-  Time spent = 0.000184059 secs
-create_atoms 1 single 13 17 4
-Created 1 atoms
-  Time spent = 0.000173807 secs
-create_atoms 1 single 8.5 28.5 4
-Created 1 atoms
-  Time spent = 0.000167847 secs
-create_atoms 1 single 23 26 4
-Created 1 atoms
-  Time spent = 0.000179052 secs
-create_atoms 1 single 38 27 4
-Created 1 atoms
-  Time spent = 0.000169992 secs
-create_atoms 1 single 37.5 4.5 4
-Created 1 atoms
-  Time spent = 0.000166178 secs
-create_atoms 1 single 41.5 47.5 4
-Created 1 atoms
-  Time spent = 0.000172138 secs
-create_atoms 1 single 20.5 37.5 4
-Created 1 atoms
-  Time spent = 0.000165939 secs
-create_atoms 1 single 5 8 4
-Created 1 atoms
-  Time spent = 0.00018096 secs
-create_atoms 1 single 2.5 16.5 4
-Created 1 atoms
-  Time spent = 0.000165939 secs
-create_atoms 1 single 38.5 45.5 4
-Created 1 atoms
-  Time spent = 0.000164986 secs
-create_atoms 1 single 9 0 4
-Created 1 atoms
-  Time spent = 0.000168085 secs
-create_atoms 1 single 39 32 4
-Created 1 atoms
-  Time spent = 0.000170946 secs
-create_atoms 1 single 45.5 11.5 4
-Created 1 atoms
-  Time spent = 0.00018096 secs
-create_atoms 1 single 40 0 4
-Created 1 atoms
-  Time spent = 0.000168085 secs
-create_atoms 1 single 44.5 2.5 4
-Created 1 atoms
-  Time spent = 0.000165939 secs
-create_atoms 1 single 4.5 44.5 4
-Created 1 atoms
-  Time spent = 0.000168085 secs
-create_atoms 1 single 24.5 13.5 4
-Created 1 atoms
-  Time spent = 0.000165939 secs
-create_atoms 1 single 47.5 23.5 4
-Created 1 atoms
-  Time spent = 0.00018096 secs
-create_atoms 1 single 1 20 4
-Created 1 atoms
-  Time spent = 0.000166893 secs
-create_atoms 1 single 38.5 31.5 4
-Created 1 atoms
-  Time spent = 0.000168085 secs
-create_atoms 1 single 12.5 12.5 4
-Created 1 atoms
-  Time spent = 0.000169992 secs
-create_atoms 1 single 2 27 4
-Created 1 atoms
-  Time spent = 0.000188828 secs
-create_atoms 1 single 21 5 4
-Created 1 atoms
-  Time spent = 0.000174999 secs
-create_atoms 1 single 47 12 4
-Created 1 atoms
-  Time spent = 0.000164986 secs
-create_atoms 1 single 32.5 46.5 4
-Created 1 atoms
-  Time spent = 0.000165939 secs
-create_atoms 1 single 9.5 40.5 4
-Created 1 atoms
-  Time spent = 0.000166893 secs
-create_atoms 1 single 8.5 2.5 4
-Created 1 atoms
-  Time spent = 0.000164986 secs
-create_atoms 1 single 41.5 22.5 4
-Created 1 atoms
-  Time spent = 0.000174046 secs
-create_atoms 1 single 29 11 4
-Created 1 atoms
-  Time spent = 0.000166893 secs
-create_atoms 1 single 3.5 3.5 4
-Created 1 atoms
-  Time spent = 0.000165224 secs
-create_atoms 1 single 5 21 4
-Created 1 atoms
-  Time spent = 0.000164986 secs
-create_atoms 1 single 46.5 31.5 4
-Created 1 atoms
-  Time spent = 0.000166178 secs
-create_atoms 1 single 35 46 4
-Created 1 atoms
-  Time spent = 0.000183105 secs
-create_atoms 1 single 40.5 41.5 4
-Created 1 atoms
-  Time spent = 0.000164986 secs
-create_atoms 1 single 10 22 4
-Created 1 atoms
-  Time spent = 0.000164986 secs
-create_atoms 1 single 43.5 14.5 4
-Created 1 atoms
-  Time spent = 0.000169992 secs
-create_atoms 1 single 42 42 4
-Created 1 atoms
-  Time spent = 0.000165939 secs
-create_atoms 1 single 4 26 4
-Created 1 atoms
-  Time spent = 0.000174999 secs
-create_atoms 1 single 19 34 4
-Created 1 atoms
-  Time spent = 0.000163078 secs
-create_atoms 1 single 33 9 4
-Created 1 atoms
-  Time spent = 0.000164986 secs
-create_atoms 1 single 0.5 45.5 4
-Created 1 atoms
-  Time spent = 0.000163078 secs
-create_atoms 1 single 30.5 32.5 4
-Created 1 atoms
-  Time spent = 0.000164986 secs
-create_atoms 1 single 25.5 5.5 4
-Created 1 atoms
-  Time spent = 0.000178099 secs
-create_atoms 1 single 47.5 39.5 4
-Created 1 atoms
-  Time spent = 0.000165939 secs
-create_atoms 1 single 15 13 4
-Created 1 atoms
-  Time spent = 0.000164986 secs
-create_atoms 1 single 21 21 4
-Created 1 atoms
-  Time spent = 0.000164986 secs
-create_atoms 1 single 14 28 4
-Created 1 atoms
-  Time spent = 0.000164986 secs
-create_atoms 1 single 9 34 4
-Created 1 atoms
-  Time spent = 0.000174999 secs
-create_atoms 1 single 7 38 4
-Created 1 atoms
-  Time spent = 0.000175953 secs
-create_atoms 1 single 11 35 4
-Created 1 atoms
-  Time spent = 0.000154972 secs
-create_atoms 1 single 20.5 45.5 4
-Created 1 atoms
-  Time spent = 0.000156879 secs
-create_atoms 1 single 30.5 31.5 4
-Created 1 atoms
-  Time spent = 0.000159979 secs
-create_atoms 1 single 32.5 2.5 4
-Created 1 atoms
-  Time spent = 0.000166178 secs
-create_atoms 1 single 21.5 3.5 4
-Created 1 atoms
-  Time spent = 0.000157833 secs
-create_atoms 1 single 23 12 4
-Created 1 atoms
-  Time spent = 0.000155926 secs
-create_atoms 1 single 4.5 33.5 4
-Created 1 atoms
-  Time spent = 0.000156879 secs
-create_atoms 1 single 46 43 4
-Created 1 atoms
-  Time spent = 0.000155926 secs
-create_atoms 1 single 42.5 45.5 4
-Created 1 atoms
-  Time spent = 0.000156879 secs
-create_atoms 1 single 4.5 10.5 4
-Created 1 atoms
-  Time spent = 0.000158072 secs
-create_atoms 1 single 33.5 15.5 4
-Created 1 atoms
-  Time spent = 0.000157833 secs
-create_atoms 1 single 24 5 4
-Created 1 atoms
-  Time spent = 0.000154018 secs
-create_atoms 1 single 13 16 4
-Created 1 atoms
-  Time spent = 0.000158072 secs
-create_atoms 1 single 16.5 23.5 4
-Created 1 atoms
-  Time spent = 0.000156164 secs
-create_atoms 1 single 45.5 28.5 4
-Created 1 atoms
-  Time spent = 0.000247002 secs
-create_atoms 1 single 44.5 5.5 4
-Created 1 atoms
-  Time spent = 0.000156164 secs
-create_atoms 1 single 27.5 46.5 4
-Created 1 atoms
-  Time spent = 0.000155926 secs
-create_atoms 1 single 44.5 12.5 4
-Created 1 atoms
-  Time spent = 0.000157833 secs
-create_atoms 1 single 12 41 4
-Created 1 atoms
-  Time spent = 0.000156879 secs
-create_atoms 1 single 6 4 4
-Created 1 atoms
-  Time spent = 0.0001688 secs
-create_atoms 1 single 31.5 10.5 4
-Created 1 atoms
-  Time spent = 0.00015521 secs
-create_atoms 1 single 1 44 4
-Created 1 atoms
-  Time spent = 0.000154972 secs
-create_atoms 1 single 31 4 4
-Created 1 atoms
-  Time spent = 0.000156879 secs
-create_atoms 1 single 21 33 4
-Created 1 atoms
-  Time spent = 0.000156879 secs
-create_atoms 1 single 3 33 4
-Created 1 atoms
-  Time spent = 0.000164032 secs
-create_atoms 1 single 15 10 4
-Created 1 atoms
-  Time spent = 0.0001719 secs
-create_atoms 1 single 28.5 22.5 4
-Created 1 atoms
-  Time spent = 0.000153065 secs
-create_atoms 1 single 43 1 4
-Created 1 atoms
-  Time spent = 0.000155926 secs
-create_atoms 1 single 3.5 0.5 4
-Created 1 atoms
-  Time spent = 0.000154972 secs
-create_atoms 1 single 41 37 4
-Created 1 atoms
-  Time spent = 0.000153065 secs
-create_atoms 1 single 18.5 43.5 4
-Created 1 atoms
-  Time spent = 0.000213146 secs
-create_atoms 1 single 17 27 4
-Created 1 atoms
-  Time spent = 0.000159979 secs
-create_atoms 1 single 3 5 4
-Created 1 atoms
-  Time spent = 0.000153065 secs
-create_atoms 1 single 18.5 23.5 4
-Created 1 atoms
-  Time spent = 0.000154972 secs
-create_atoms 1 single 31.5 14.5 4
-Created 1 atoms
-  Time spent = 0.000154972 secs
-create_atoms 1 single 41 31 4
-Created 1 atoms
-  Time spent = 0.000155926 secs
-create_atoms 1 single 22 3 4
-Created 1 atoms
-  Time spent = 0.00015521 secs
-create_atoms 1 single 14.5 40.5 4
-Created 1 atoms
-  Time spent = 0.000154018 secs
-create_atoms 1 single 9 38 4
-Created 1 atoms
-  Time spent = 0.000154018 secs
-create_atoms 1 single 36 42 4
-Created 1 atoms
-  Time spent = 0.000155926 secs
-create_atoms 1 single 33 22 4
-Created 1 atoms
-  Time spent = 0.000163078 secs
-create_atoms 1 single 15.5 47.5 4
-Created 1 atoms
-  Time spent = 0.000154972 secs
-create_atoms 1 single 3 0 4
-Created 1 atoms
-  Time spent = 0.000154972 secs
-create_atoms 1 single 25.5 27.5 4
-Created 1 atoms
-  Time spent = 0.000176907 secs
-create_atoms 1 single 2.5 28.5 4
-Created 1 atoms
-  Time spent = 0.000154972 secs
-create_atoms 1 single 29.5 28.5 4
-Created 1 atoms
-  Time spent = 0.000162125 secs
-create_atoms 1 single 44.5 18.5 4
-Created 1 atoms
-  Time spent = 0.000152826 secs
-create_atoms 1 single 26 40 4
-Created 1 atoms
-  Time spent = 0.000155926 secs
-create_atoms 1 single 41 27 4
-Created 1 atoms
-  Time spent = 0.000158072 secs
-create_atoms 1 single 39.5 5.5 4
-Created 1 atoms
-  Time spent = 0.000155926 secs
-create_atoms 1 single 3 38 4
-Created 1 atoms
-  Time spent = 0.000152826 secs
-create_atoms 1 single 35 29 4
-Created 1 atoms
-  Time spent = 0.000164986 secs
-create_atoms 1 single 11 19 4
-Created 1 atoms
-  Time spent = 0.000164986 secs
-create_atoms 1 single 18 1 4
-Created 1 atoms
-  Time spent = 0.000146866 secs
-create_atoms 1 single 39.5 40.5 4
-Created 1 atoms
-  Time spent = 0.000146866 secs
-create_atoms 1 single 46 17 4
-Created 1 atoms
-  Time spent = 0.000146151 secs
-create_atoms 1 single 1.5 23.5 4
-Created 1 atoms
-  Time spent = 0.000154018 secs
-create_atoms 1 single 28.5 23.5 4
-Created 1 atoms
-  Time spent = 0.000145912 secs
-create_atoms 1 single 10 28 4
-Created 1 atoms
-  Time spent = 0.000159979 secs
-create_atoms 1 single 19 47 4
-Created 1 atoms
-  Time spent = 0.000148058 secs
-create_atoms 1 single 10.5 16.5 4
-Created 1 atoms
-  Time spent = 0.000147104 secs
-create_atoms 1 single 38 45 4
-Created 1 atoms
-  Time spent = 0.000144958 secs
-create_atoms 1 single 42.5 41.5 4
-Created 1 atoms
-  Time spent = 0.000161886 secs
-create_atoms 1 single 47.5 42.5 4
-Created 1 atoms
-  Time spent = 0.000147104 secs
-create_atoms 1 single 38 7 4
-Created 1 atoms
-  Time spent = 0.000146151 secs
-create_atoms 1 single 10 44 4
-Created 1 atoms
-  Time spent = 0.000145912 secs
-create_atoms 1 single 29.5 27.5 4
-Created 1 atoms
-  Time spent = 0.000146151 secs
-create_atoms 1 single 45 30 4
-Created 1 atoms
-  Time spent = 0.000145912 secs
-create_atoms 1 single 3 9 4
-Created 1 atoms
-  Time spent = 0.000154018 secs
-create_atoms 1 single 8.5 35.5 4
-Created 1 atoms
-  Time spent = 0.000146151 secs
-create_atoms 1 single 24 44 4
-Created 1 atoms
-  Time spent = 0.000145912 secs
-create_atoms 1 single 47 4 4
-Created 1 atoms
-  Time spent = 0.000144958 secs
-create_atoms 1 single 7.5 8.5 4
-Created 1 atoms
-  Time spent = 0.000144958 secs
-create_atoms 1 single 32.5 41.5 4
-Created 1 atoms
-  Time spent = 0.000157833 secs
-create_atoms 1 single 0.5 34.5 4
-Created 1 atoms
-  Time spent = 0.000145912 secs
-create_atoms 1 single 11 8 4
-Created 1 atoms
-  Time spent = 0.000147104 secs
-create_atoms 1 single 2 40 4
-Created 1 atoms
-  Time spent = 0.000144958 secs
-create_atoms 1 single 25 24 4
-Created 1 atoms
-  Time spent = 0.000146151 secs
-create_atoms 1 single 47.5 6.5 4
-Created 1 atoms
-  Time spent = 0.000147104 secs
-create_atoms 1 single 39.5 28.5 4
-Created 1 atoms
-  Time spent = 0.000154972 secs
-create_atoms 1 single 17 21 4
-Created 1 atoms
-  Time spent = 0.000164032 secs
-create_atoms 1 single 32 43 4
-Created 1 atoms
-  Time spent = 0.000146151 secs
-create_atoms 1 single 16.5 29.5 4
-Created 1 atoms
-  Time spent = 0.000146151 secs
-create_atoms 1 single 34 34 4
-Created 1 atoms
-  Time spent = 0.000145912 secs
-create_atoms 1 single 11.5 3.5 4
-Created 1 atoms
-  Time spent = 0.000154018 secs
-create_atoms 1 single 39 22 4
-Created 1 atoms
-  Time spent = 0.000144958 secs
-create_atoms 1 single 24.5 36.5 4
-Created 1 atoms
-  Time spent = 0.000144958 secs
-create_atoms 1 single 33 31 4
-Created 1 atoms
-  Time spent = 0.000144958 secs
-create_atoms 1 single 35.5 35.5 4
-Created 1 atoms
-  Time spent = 0.000146151 secs
-create_atoms 1 single 14.5 34.5 4
-Created 1 atoms
-  Time spent = 0.000146866 secs
-create_atoms 1 single 34 28 4
-Created 1 atoms
-  Time spent = 0.000153065 secs
-create_atoms 1 single 37 41 4
-Created 1 atoms
-  Time spent = 0.000145912 secs
-create_atoms 1 single 33 46 4
-Created 1 atoms
-  Time spent = 0.000144958 secs
-create_atoms 1 single 27.5 28.5 4
-Created 1 atoms
-  Time spent = 0.000145197 secs
-create_atoms 1 single 40.5 22.5 4
-Created 1 atoms
-  Time spent = 0.000150919 secs
-create_atoms 1 single 27.5 1.5 4
-Created 1 atoms
-  Time spent = 0.000146151 secs
-create_atoms 1 single 12 2 4
-Created 1 atoms
-  Time spent = 0.000151873 secs
-create_atoms 1 single 36 43 4
-Created 1 atoms
-  Time spent = 0.000144005 secs
-create_atoms 1 single 28.5 9.5 4
-Created 1 atoms
-  Time spent = 0.000146151 secs
-create_atoms 1 single 20.5 25.5 4
-Created 1 atoms
-  Time spent = 0.000144958 secs
-create_atoms 1 single 3 3 4
-Created 1 atoms
-  Time spent = 0.000144005 secs
-create_atoms 1 single 38 33 4
-Created 1 atoms
-  Time spent = 0.000146151 secs
-create_atoms 1 single 3 20 4
-Created 1 atoms
-  Time spent = 0.000154972 secs
-create_atoms 1 single 35 11 4
-Created 1 atoms
-  Time spent = 0.000145912 secs
-create_atoms 1 single 5 25 4
-Created 1 atoms
-  Time spent = 0.000144005 secs
-create_atoms 1 single 36.5 6.5 4
-Created 1 atoms
-  Time spent = 0.000144005 secs
-create_atoms 1 single 19.5 24.5 4
-Created 1 atoms
-  Time spent = 0.000236988 secs
-create_atoms 1 single 27 41 4
-Created 1 atoms
-  Time spent = 0.000169992 secs
-create_atoms 1 single 39.5 11.5 4
-Created 1 atoms
-  Time spent = 0.000138998 secs
-create_atoms 1 single 21.5 2.5 4
-Created 1 atoms
-  Time spent = 0.000136852 secs
-create_atoms 1 single 46.5 15.5 4
-Created 1 atoms
-  Time spent = 0.000138998 secs
-create_atoms 1 single 13 24 4
-Created 1 atoms
-  Time spent = 0.000137091 secs
-create_atoms 1 single 11 37 4
-Created 1 atoms
-  Time spent = 0.000144005 secs
-create_atoms 1 single 11.5 31.5 4
-Created 1 atoms
-  Time spent = 0.000144958 secs
-create_atoms 1 single 47 0 4
-Created 1 atoms
-  Time spent = 0.000138044 secs
-create_atoms 1 single 25.5 17.5 4
-Created 1 atoms
-  Time spent = 0.00014019 secs
-create_atoms 1 single 32 11 4
-Created 1 atoms
-  Time spent = 0.000138044 secs
-create_atoms 1 single 8 17 4
-Created 1 atoms
-  Time spent = 0.000138044 secs
-create_atoms 1 single 27.5 12.5 4
-Created 1 atoms
-  Time spent = 0.000137806 secs
-create_atoms 1 single 25 7 4
-Created 1 atoms
-  Time spent = 0.000146151 secs
-create_atoms 1 single 25.5 37.5 4
-Created 1 atoms
-  Time spent = 0.000139952 secs
-create_atoms 1 single 12 15 4
-Created 1 atoms
-  Time spent = 0.000138044 secs
-create_atoms 1 single 1 7 4
-Created 1 atoms
-  Time spent = 0.000138998 secs
-create_atoms 1 single 18.5 47.5 4
-Created 1 atoms
-  Time spent = 0.000138044 secs
-create_atoms 1 single 5 38 4
-Created 1 atoms
-  Time spent = 0.000136852 secs
-create_atoms 1 single 42 19 4
-Created 1 atoms
-  Time spent = 0.000149012 secs
-create_atoms 1 single 30.5 7.5 4
-Created 1 atoms
-  Time spent = 0.000138044 secs
-create_atoms 1 single 42.5 7.5 4
-Created 1 atoms
-  Time spent = 0.000138998 secs
-create_atoms 1 single 26.5 18.5 4
-Created 1 atoms
-  Time spent = 0.000153065 secs
-create_atoms 1 single 18.5 1.5 4
-Created 1 atoms
-  Time spent = 0.000137091 secs
-create_atoms 1 single 41.5 10.5 4
-Created 1 atoms
-  Time spent = 0.000140905 secs
-
-# define frozen substrate and mobile atoms
-
-region          base block INF INF INF INF 0 1.8
-set             region base type 2
-  18432 settings made for type
-group           base type 2
-18432 atoms in group base
-group           mobile type 1
-18616 atoms in group mobile
-
-# pair style
-
-pair_style	eam/alloy
-pair_coeff	* * ptvoterlammps.eam Pt Pt
-
-neighbor	0.5 bin
-neigh_modify    every 1 delay 5 check yes
-
-fix		1 mobile nve
-fix		2 mobile langevin ${Tequil} ${Tequil} 1.0 ${seed} zero yes
-fix		2 mobile langevin 400.0 ${Tequil} 1.0 ${seed} zero yes
-fix		2 mobile langevin 400.0 400.0 1.0 ${seed} zero yes
-fix		2 mobile langevin 400.0 400.0 1.0 826626413 zero yes
-
-timestep	0.005
-
-compute         tmobile mobile temp
-
-thermo		100
-thermo_modify   temp tmobile
-WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:488)
-
-# thermal equilibration
-
-run             1000
-Neighbor list info ...
-  update every 1 steps, delay 5 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 6.07583
-  ghost atom cutoff = 12
-  binsize = 3.03792, bins = 62 62 7
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair eam/alloy, perpetual
-      attributes: half, newton on
-      pair build: half/bin/atomonly/newton
-      stencil: half/bin/3d/newton
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 3.359 | 3.359 | 3.36 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0            0   -206220.22            0   -206220.22   -52155.664 
-     100    188.18127   -206044.43            0   -205591.63    -25068.83 
-     200    274.34464   -205860.78            0   -205200.66   -40191.797 
-     300    325.66286   -205750.01            0    -204966.4   -31510.222 
-     400    352.48242   -205675.42            0   -204827.28   -35058.064 
-     500    370.88571   -205619.66            0   -204727.25   -32735.022 
-     600    388.62129   -205592.87            0   -204657.78   -33904.556 
-     700    389.54874   -205579.73            0    -204642.4   -32769.852 
-     800    395.56074   -205576.82            0   -204625.03   -33755.948 
-     900    398.03458   -205564.48            0   -204606.74   -32777.103 
-    1000    401.24089   -205562.85            0    -204597.4   -33785.341 
-Loop time of 4.3687 on 16 procs for 1000 steps with 37048 atoms
-
-Performance: 98.885 ns/day, 0.243 hours/ns, 228.901 timesteps/s
-98.4% CPU use with 16 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 3.2988     | 3.3828     | 3.4667     |   2.3 | 77.43
-Neigh   | 0.20856    | 0.23127    | 0.24382    |   1.9 |  5.29
-Comm    | 0.33313    | 0.45075    | 0.55485    |   9.2 | 10.32
-Output  | 0.00042987 | 0.00044042 | 0.00049591 |   0.0 |  0.01
-Modify  | 0.18811    | 0.28363    | 0.36798    |   9.7 |  6.49
-Other   |            | 0.01983    |            |       |  0.45
-
-Nlocal:    2315.5 ave 2332 max 2297 min
-Histogram: 2 0 0 3 4 0 2 1 2 2
-Nghost:    3186.31 ave 3205 max 3170 min
-Histogram: 2 1 3 0 2 3 2 1 0 2
-Neighs:    55590.9 ave 56174 max 55103 min
-Histogram: 2 2 1 1 4 1 3 0 0 2
-
-Total # of neighbors = 889454
-Ave neighs/atom = 24.0082
-Neighbor list builds = 105
-Dangerous builds = 0
-reset_timestep  0
-
-# pin base so will not move during quenches
-
-fix             freeze base setforce 0.0 0.0 0.0
-
-# event detection
-
-compute         event all event/displace ${cutevent}
-compute         event all event/displace 1.1
-
-# hyper/local
-
-fix             HL mobile hyper/local ${cutbond} ${qfactor} ${Vmax} ${Tequil}                 ${Dcut} ${alpha} ${boost}
-fix             HL mobile hyper/local 3.2 ${qfactor} ${Vmax} ${Tequil}                 ${Dcut} ${alpha} ${boost}
-fix             HL mobile hyper/local 3.2 0.3 ${Vmax} ${Tequil}                 ${Dcut} ${alpha} ${boost}
-fix             HL mobile hyper/local 3.2 0.3 0.4 ${Tequil}                 ${Dcut} ${alpha} ${boost}
-fix             HL mobile hyper/local 3.2 0.3 0.4 400.0                 ${Dcut} ${alpha} ${boost}
-fix             HL mobile hyper/local 3.2 0.3 0.4 400.0                 10.0 ${alpha} ${boost}
-fix             HL mobile hyper/local 3.2 0.3 0.4 400.0                 10.0 200.0 ${boost}
-fix             HL mobile hyper/local 3.2 0.3 0.4 400.0                 10.0 200.0 4000.0
-
-# thermo output
-
-thermo_style    custom step temp pe f_HL f_HL[*]
-WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:705)
-
-thermo_modify   lost ignore
-thermo_modify   temp tmobile
-WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:488)
-
-thermo          ${nevent}
-thermo          100
-
-# dump
-
-region          substrate block INF INF INF INF 1.8 3.8
-region          adatoms block INF INF INF INF 3.8 INF
-variable        acolor atom rmask(base)+2*rmask(substrate)+3*rmask(adatoms)
-
-dump		1 all image 10000000 local.*.jpg v_acolor type size 1024 1024 		zoom ${zoom} adiam 2.5 view 0.0 0.0 up 0 1 0 axes yes 0.9 0.01
-dump		1 all image 10000000 local.*.jpg v_acolor type size 1024 1024 		zoom 1.8 adiam 2.5 view 0.0 0.0 up 0 1 0 axes yes 0.9 0.01
-dump_modify	1 pad 6 amap 1 3 sa 1 3 blue red green
-
-# run
-
-hyper           ${steps} ${nevent} HL event min ${tol} ${tol} 1000 1000 dump 1
-hyper           1500 ${nevent} HL event min ${tol} ${tol} 1000 1000 dump 1
-hyper           1500 100 HL event min ${tol} ${tol} 1000 1000 dump 1
-hyper           1500 100 HL event min 1.0e-15 ${tol} 1000 1000 dump 1
-hyper           1500 100 HL event min 1.0e-15 1.0e-15 1000 1000 dump 1
-WARNING: Resetting reneighboring criteria during hyper (../hyper.cpp:133)
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 6.07583
-  ghost atom cutoff = 12
-  binsize = 3.03792, bins = 62 62 7
-  2 neighbor lists, perpetual/occasional/extra = 1 1 0
-  (1) pair eam/alloy, perpetual
-      attributes: half, newton on
-      pair build: half/bin/atomonly/newton
-      stencil: half/bin/3d/newton
-      bin: standard
-  (2) fix hyper/local, occasional
-      attributes: full, newton on, cut 10
-      pair build: full/bin/atomonly
-      stencil: full/bin/3d
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 7.566 | 7.567 | 7.567 Mbytes
-Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] 
-       0    401.24089   -205562.85            0            0            0            1            0            0            0            0            0            0            0            0        4e+19            0            0            0            0            0            0            0            0            0            0            0 
-      77    401.24089   -206534.96            0            0            0            1            0            0            0            0            0            0            0            0        4e+19            0            0            0            0            0            0            0         1540            0            0            0 
-Loop time of 0.540347 on 16 procs for 77 steps with 37048 atoms
-
-Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] 
-       0    401.24089   -205562.85    23.271302           74   0.18753621            1    6.0138739    703.62325            0   0.55802338    3.5350432            0            0            0        4e+19    10.115141    10.115141            0            0            0            0            0            0            0            0            0 
-     100    399.15639   -205546.21    22.904368           90   0.32935524   0.39929142    6.0138739    703.62325  0.026229865   0.91517139    3.9968927        91.88    0.3995539    0.4009724   0.39695676    10.262823    10.262823            0            0            0            0            0         2000            0            0            0 
-Loop time of 0.579085 on 16 procs for 100 steps with 37048 atoms
-
-Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] 
-     100    399.15639   -205546.21    22.904368           90   0.32935524   0.39929142    6.0138739    703.62325  0.026229865   0.91517139    3.9968927        91.88    0.3995539    0.4009724   0.39695676    10.262823    10.262823            0            0            0            0            0         2000            0            0            0 
-     184    399.15639   -206534.96    22.904368           90   0.32935524   0.39929142    6.0138739    703.62325  0.026229865   0.91517139    3.9968927    49.934783   0.21714886    0.4009724   0.39695676    10.262823    10.262823            0            0            0            0            0         3680            0            0            0 
-Loop time of 0.556056 on 16 procs for 84 steps with 37048 atoms
-
-Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] 
-     100    399.15639   -205546.21    22.903938           90   0.32935524   0.39929142    6.0138739    703.62325  0.026229865   0.91517139    3.9968927        91.88    0.3995539    0.4009724   0.39695676    10.262823    10.262823            0            0            0            0            0         2000            0            0            0 
-     200    403.01717   -205543.17    20.844359           90    0.3291605   0.39888693    6.0138739    703.62325  0.039527213   0.94418421    4.0368484        90.95   0.39930574    0.4019706   0.39554353    10.262823    10.262823            0            0            0            0            0         4000            0            0            0 
-Loop time of 0.581214 on 16 procs for 100 steps with 37048 atoms
-
-Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] 
-     200    403.01717   -205543.17    20.844359           90    0.3291605   0.39888693    6.0138739    703.62325  0.039527213   0.94418421    4.0368484        90.95   0.39930574    0.4019706   0.39554353    10.262823    10.262823            0            0            0            0            0         4000            0            0            0 
-     275    403.01717   -206534.96    20.844359           90    0.3291605   0.39888693    6.0138739    703.62325  0.039527213   0.94418421    4.0368484    66.145455   0.29040418    0.4019706   0.39554353    10.262823    10.262823            0            0            0            0            0         5500            0            0            0 
-Loop time of 0.481812 on 16 procs for 75 steps with 37048 atoms
-
-Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] 
-     200    403.01717   -205543.17    21.115577           91    0.3291605   0.39888693    6.0138739    703.62325  0.039527213   0.94418421    4.0368484        90.95   0.39930574    0.4019706   0.39554353    10.262823    10.262823            0            0            0            0            0         4000            0            0            0 
-     300    399.01963   -205541.46    19.137336           85   0.32442182   0.39862755    6.0138739    703.62325  0.046873868   0.94776891    4.0368484        92.02   0.39912484   0.40296919   0.39497622    10.288936    10.288936            0            0            0            0            0         6000            0            0            0 
-Loop time of 0.5757 on 16 procs for 100 steps with 37048 atoms
-
-Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] 
-     300    399.01963   -205541.46    19.137336           85   0.32442182   0.39862755    6.0138739    703.62325  0.046873868   0.94776891    4.0368484        92.02   0.39912484   0.40296919   0.39497622    10.288936    10.288936            0            0            0            0            0         6000            0            0            0 
-     377    399.01963   -206534.96    19.137336           85   0.32442182   0.39862755    6.0138739    703.62325  0.046873868   0.94776891    4.0368484    73.225464   0.31760598   0.40296919   0.39497622    10.288936    10.288936            0            0            0            0            0         7540            0            0            0 
-Loop time of 0.514907 on 16 procs for 77 steps with 37048 atoms
-
-Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] 
-     300    399.01963   -205541.46    19.137003           85   0.32442182   0.39862755    6.0138739    703.62325  0.046873868   0.94776891    4.0368484        92.02   0.39912484   0.40296919   0.39497622    10.288936    10.288936            0            0            0            0            0         6000            0            0            0 
-     400    398.15351   -205544.87    20.470844           93   0.34589451   0.39828754    6.0138739    703.62325  0.049952465   0.94776891    4.0779385      92.0375   0.39894967   0.40395328    0.3932824    10.307052    10.307052            0            0            0            0            0         8000            0            0            0 
-Loop time of 0.577371 on 16 procs for 100 steps with 37048 atoms
-
-Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] 
-     400    398.15351   -205544.87    20.470844           93   0.34589451   0.39828754    6.0138739    703.62325  0.049952465   0.94776891    4.0779385      92.0375   0.39894967   0.40395328    0.3932824    10.307052    10.307052            0            0            0            0            0         8000            0            0            0 
-     471    398.15351   -206534.96    20.470844           93   0.34589451   0.39828754    6.0138739    703.62325  0.049952465   0.94776891    4.0779385    78.163482   0.33881076   0.40395328    0.3932824    10.307052    10.307052            0            0            0            0            0         9420            0            0            0 
-Loop time of 0.465473 on 16 procs for 71 steps with 37048 atoms
-
-Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] 
-     400    398.15351   -205544.87    20.470689           93   0.34589451   0.39828754    6.0138739    703.62325  0.049952465   0.94776891    4.0779385      92.0375   0.39894967   0.40395328    0.3932824    10.307052    10.307052            0            0            0            0            0         8000            0            0            0 
-     500    400.29399   -205544.98    17.051242           83   0.42140172   0.39805251    6.0138739    703.62325  0.056986933    1.0907861    4.0779385       91.986   0.39879563   0.40493836   0.39165573    10.307052    10.307052            0            0            0            0            0        10000            0            0            0 
-Loop time of 0.579188 on 16 procs for 100 steps with 37048 atoms
-
-Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] 
-     500    400.29399   -205544.98    17.051242           83   0.42140172   0.39805251    6.0138739    703.62325  0.056986933    1.0907861    4.0779385       91.986   0.39879563   0.40493836   0.39165573    10.307052    10.307052            0            0            0            0            0        10000            0            0            0 
-     577    400.29399   -206534.96    17.051242           83   0.42140172   0.39805251    6.0138739    703.62325  0.056986933    1.0910651    4.0779385    79.710572    0.3455768   0.40493836   0.39165573    10.307052    10.307052            0            0            0            0            0        11540            0            0            0 
-Loop time of 0.502193 on 16 procs for 77 steps with 37048 atoms
-
-Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] 
-     500    400.29399   -205544.98    17.051107           83   0.42140172   0.39805251    6.0138739    703.62325  0.056986933    1.0910651    4.0779385       91.986   0.39879563   0.40493836   0.39165573    10.307052    10.307052            0            0            0            0            0        10000            0            0            0 
-     600    400.96099   -205544.56    20.904479           91   0.41219484   0.39780769    6.0138739    703.62325  0.061331691    1.1358732    4.0779385    92.013333   0.39864794   0.40593806   0.39067432    10.307052    10.307052            0            0            0            0            0        12000            0            0            0 
-Loop time of 0.694955 on 16 procs for 100 steps with 37048 atoms
-
-Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] 
-     600    400.96099   -205544.56    20.904479           91   0.41219484   0.39780769    6.0138739    703.62325  0.061331691    1.1358732    4.0779385    92.013333   0.39864794   0.40593806   0.39067432    10.307052    10.307052            0            0            0            0            0        12000            0            0            0 
-     680    400.96099   -206534.96    20.904479           91   0.41219484   0.39780769    6.0138739    703.62325  0.061331691    1.1358732    4.0779385    81.188235   0.35174818   0.40593806   0.39067432    10.307052    10.307052            0            0            0            0            0        13600            0            0            0 
-Loop time of 0.529041 on 16 procs for 80 steps with 37048 atoms
-
-Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] 
-     600    400.96099   -205544.56    20.904088           91   0.41219484   0.39780769    6.0138739    703.62325  0.061331691    1.1358732    4.0779385    92.013333   0.39864794   0.40593806   0.39067432    10.307052    10.307052            0            0            0            0            0        12000            0            0            0 
-     700    397.78618   -205534.96    20.361513           95   0.54466603   0.39757442    6.0138739    703.62325  0.061146951    1.1853748    4.1995704        92.12   0.39850836   0.40693553   0.38981834    10.307052    10.307052            0            0            0            0            0        14000            0            0            0 
-Loop time of 0.590093 on 16 procs for 100 steps with 37048 atoms
-
-Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] 
-     700    397.78618   -205534.96    20.361513           95   0.54466603   0.39757442    6.0138739    703.62325  0.061146951    1.2139704    4.1995704        92.12   0.39850836   0.40693553   0.38981834    10.307052    10.307052            0            0            0            0            0        14000            0            0            0 
-     790    397.78618   -206534.96    20.361513           95   0.54466603   0.39757442    6.0138739    703.62325  0.061146951    2.2107138    4.1995704    81.625316   0.35310868   0.40693553   0.38981834    10.307052    10.307052            0            0            0            0            0        15800            0            0            0 
-Loop time of 0.594281 on 16 procs for 90 steps with 37048 atoms
-
-Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] 
-     700    397.78618   -205534.96    20.236364           94   0.51088027   0.39757442    6.0138739    703.62325  0.061146951    2.2107138     4.205089        92.12   0.39850836   0.40693553   0.38981834    10.307052    10.307052            0            0            0            0            0        14000            1            2            6 
-     800    399.66919   -205547.44    21.285461           94   0.56079766   0.39739855    6.0138739    703.62325   0.06556778    2.2107138    4.3041291     92.36625    0.3983806   0.40793368      0.38875    10.307052    10.385797            0            0            0            0            0        16000            1            2            6 
-Loop time of 0.583824 on 16 procs for 100 steps with 37048 atoms
-
-Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] 
-     800    399.66919   -205547.44    21.285461           94   0.56079766   0.39739855    6.0138739    703.62325   0.06556778    2.2107138    4.3041291     92.36625    0.3983806   0.40793368      0.38875    10.307052    10.385797            0            0            0            0            0        16000            1            2            6 
-     872    399.66919   -206535.54    21.285461           94   0.56079766   0.39739855    6.0138739    703.62325   0.06556778    2.3177682    4.3041291    84.739679   0.36548679   0.40793368      0.38875    10.307052    10.385797            0            0            0            0            0        17440            1            2            6 
-Loop time of 0.46886 on 16 procs for 72 steps with 37048 atoms
-
-Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] 
-     800    399.66919   -205547.44      21.2852           94   0.44964213   0.39739855    6.0138739    703.62325   0.06556778    2.3177682    4.3041291     92.36625    0.3983806   0.40793368      0.38875    10.307052    10.385797            0            0            0            0            0        16000            2            4           13 
-     900     401.5853   -205544.22    19.308189           94   0.47610389   0.39719191    6.0138739    703.62325  0.066991886    2.3177682    4.3041291    92.017778   0.39825974   0.40893337    0.3878576    10.307052    10.385797            0            0            0            0            0        18000            2            4           13 
-Loop time of 0.585137 on 16 procs for 100 steps with 37048 atoms
-
-Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] 
-     900     401.5853   -205544.22    19.308189           94   0.47610389   0.39719191    6.0138739    703.62325  0.066991886    2.3177682    4.3041291    92.017778   0.39825974   0.40893337    0.3878576    10.307052    10.385797            0            0            0            0            0        18000            2            4           13 
-     975     401.5853   -206535.54    19.308189           94   0.47610389   0.39719191    6.0138739    703.62325  0.066991886    2.3177682    4.3041291    84.939487   0.36762438   0.40893337    0.3878576    10.307052    10.385797            0            0            0            0            0        19500            2            4           13 
-Loop time of 0.502012 on 16 procs for 75 steps with 37048 atoms
-
-Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] 
-     900     401.5853   -205544.22    19.307938           94   0.47610389   0.39719191    6.0138739    703.62325  0.066991886    2.3177682    4.3041291    92.017778   0.39825974   0.40893337    0.3878576    10.307052    10.385797            0            0            0            0            0        18000            2            4           13 
-    1000    395.06218   -205526.35    17.514295           91   0.42044925   0.39716259    6.0138739    703.62325  0.067937867    2.3177682    4.3041291       92.511   0.39814962   0.40993184    0.3867545    10.307052    10.385797            0            0            0            0            0        20000            2            4           13 
-Loop time of 0.588597 on 16 procs for 100 steps with 37048 atoms
-
-Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] 
-    1000    395.06218   -205526.35    17.514295           91   0.42044925   0.39716259    6.0138739    703.62325  0.067937867    2.3177682    4.3041291       92.511   0.39814962   0.40993184    0.3867545    10.307052    10.385797            0            0            0            0            0        20000            2            4           13 
-    1083    395.06218   -206535.54    17.514295           91   0.42044925   0.39716259    6.0138739    703.62325  0.067937867    2.3177682    4.3041291    85.421053   0.36763584   0.40993184    0.3867545    10.307052    10.385797            0            0            0            0            0        21660            2            4           13 
-Loop time of 0.543222 on 16 procs for 83 steps with 37048 atoms
-
-Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] 
-    1000    395.06218   -205526.35    17.514191           91   0.42044925   0.39716259    6.0138739    703.62325  0.067937867    2.3177682    4.3041291       92.511   0.39814962   0.40993184    0.3867545    10.307052    10.385797            0            0            0            0            0        20000            2            4           13 
-    1100    400.04484   -205545.92     19.52012           89   0.58919981   0.39704631    6.0138739    703.62325  0.069136967    2.3177682    4.4265979    92.517273   0.39805636   0.41093134   0.38574293    10.307052    10.385797            0            0            0            0            0        22000            2            4           13 
-Loop time of 0.590075 on 16 procs for 100 steps with 37048 atoms
-
-Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] 
-    1100    400.04484   -205545.92     19.52012           89   0.58919981   0.39704631    6.0138739    703.62325  0.069136967    2.3177682    4.4265979    92.517273   0.39805636   0.41093134   0.38574293    10.307052    10.385797            0            0            0            0            0        22000            2            4           13 
-    1177    400.04484   -206535.53     19.52012           89   0.58919981   0.39704631    6.0138739    703.62325  0.069136967    2.3177682    4.4265979    86.464741   0.37201529   0.41093134   0.38574293    10.307052    10.385797            0            0            0            0            0        23540            2            4           13 
-Loop time of 0.500839 on 16 procs for 77 steps with 37048 atoms
-
-Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] 
-    1100    400.04484   -205545.92    19.518413           89     0.429675   0.39705701    6.0137119     703.6043  0.069136967    2.3177682    4.4265979    92.517273   0.39805636   0.41093134   0.38574293    10.307052    10.385797            0            0            0            0            0        22000            3            6           19 
-    1200     400.7462    -205543.2    21.169548           91   0.32511134   0.39679665    6.0137119     703.6043   0.06750442    2.3177682    4.4265979    92.376667   0.39796198   0.41191655    0.3846039    10.307052    10.385797            0            0            0            0            0        24000            3            6           19 
-Loop time of 0.583971 on 16 procs for 100 steps with 37048 atoms
-
-Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] 
-    1200     400.7462    -205543.2    21.169548           91   0.32511134   0.39679665    6.0137119     703.6043   0.06750442    2.3177682    4.4265979    92.376667   0.39796198   0.41191655    0.3846039    10.307052    10.385797            0            0            0            0            0        24000            3            6           19 
-    1277     400.7462   -206535.53    21.169548           91   0.32511134   0.39679665    6.0137119     703.6043   0.06750442    2.3177682    4.4265979    86.806578   0.37396584   0.41191655    0.3846039    10.307052    10.385797            0            0            0            0            0        25540            3            6           19 
-Loop time of 0.509118 on 16 procs for 77 steps with 37048 atoms
-
-Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] 
-    1200     400.7462    -205543.2    21.169281           91   0.32511134   0.39679665    6.0137119     703.6043   0.06750442    2.3177682    4.4265979    92.376667   0.39796198   0.41191655    0.3846039    10.307052    10.385797            0            0            0            0            0        24000            3            6           19 
-    1300    398.53702   -205539.33     21.35815           94   0.38773898   0.39659935    6.0137119     703.6043  0.067808168    2.3177682    4.4265979    92.500769   0.39786514   0.41289519    0.3846039    10.307052    10.385797            0            0            0            0            0        26000            3            6           19 
-Loop time of 0.587306 on 16 procs for 100 steps with 37048 atoms
-
-Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] 
-    1300    398.53702   -205539.33     21.35815           94   0.38773898   0.39659935    6.0137119     703.6043  0.067808168    2.3177682    4.4265979    92.500769   0.39786514   0.41289519    0.3846039    10.307052    10.385797            0            0            0            0            0        26000            3            6           19 
-    1375    398.53702   -206535.53     21.35815           94   0.38773898   0.39659935    6.0137119     703.6043  0.067808168    2.3177682    4.4265979    87.455273   0.37616341   0.41289519    0.3846039    10.307052    10.385797            0            0            0            0            0        27500            3            6           19 
-Loop time of 0.483781 on 16 procs for 75 steps with 37048 atoms
-
-Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] 
-    1300    398.53702   -205539.33     21.35787           94   0.38773898   0.39659935    6.0137119     703.6043  0.067808168    2.3177682    4.4265979    92.500769   0.39786514   0.41289519    0.3846039    10.307052    10.385797            0            0            0            0            0        26000            3            6           19 
-    1400    402.80537    -205549.3    19.481887           95   0.32554201   0.39648737    6.0137119     703.6043  0.069550538    2.3177682    4.4265979    92.666429   0.39776836   0.41389491   0.38420043    10.307052    10.385797            0            0            0            0            0        28000            3            6           19 
-Loop time of 0.586411 on 16 procs for 100 steps with 37048 atoms
-
-Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] 
-    1400    402.80537    -205549.3    19.481887           95   0.32554201   0.39648737    6.0137119     703.6043  0.069550538    2.3177682    4.4265979    92.666429   0.39776836   0.41389491   0.38420043    10.307052    10.385797            0            0            0            0            0        28000            3            6           19 
-    1471    402.80537   -206535.53    19.481887           95   0.32554201   0.39648737    6.0137119     703.6043  0.069550538    2.3177682    4.4265979    88.193746   0.37856948   0.41389491   0.38420043    10.307052    10.385797            0            0            0            0            0        29420            3            6           19 
-Loop time of 0.473799 on 16 procs for 71 steps with 37048 atoms
-
-Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] 
-    1400    402.80537    -205549.3    19.481632           95   0.32554201   0.39648737    6.0137119     703.6043  0.069550538    2.3177682    4.4265979    92.666429   0.39776836   0.41389491   0.38420043    10.307052    10.385797            0            0            0            0            0        28000            3            6           19 
-    1500     402.0803    -205537.7    20.903964           99    0.3340498   0.39635609    6.0137119     703.6043  0.070409086    2.3177682    4.4265979    92.857333   0.39767858   0.41489448   0.38372784    10.333041    10.385797            0            0            0            0            0        30000            3            6           19 
-Loop time of 0.587342 on 16 procs for 100 steps with 37048 atoms
-
-Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] f_HL[22] f_HL[23] 
-    1500     402.0803    -205537.7    20.903964           99    0.3340498   0.39635609    6.0137119     703.6043  0.070409086    2.3177682    4.4265979    92.857333   0.39767858   0.41489448   0.38372784    10.333041    10.385797            0            0            0            0            0        30000            3            6           19 
-    1574     402.0803   -206535.53    20.903964           99    0.3340498   0.39635609    6.0137119     703.6043  0.070409086    2.3177682    4.4265979    88.491741   0.37898213   0.41489448   0.38372784    10.333041    10.385797            0            0            0            0            0        31480            3            6           19 
-Loop time of 0.493982 on 16 procs for 74 steps with 37048 atoms
-
-Final hyper stats ...
-
-Cummulative quantities for fix hyper:
-  hyper time = 30000
-  event timesteps = 3
-  # of atoms in events = 6
-Quantities for this hyper run:
-  event timesteps = 3
-  # of atoms in events = 6
-  max length of any bond = 4.4266
-  max drift distance of any atom = 2.31777
-  fraction of steps & bonds with zero bias = 0.0704091
-Current quantities:
-  ave bonds/atom = 6.01371
-Cummulative quantities specific tofix hyper/local:
-  # of new bonds formed = 19
-  max bonds/atom = 13
-Quantities for this hyper run specific to fix hyper/local:
-  ave boosted bonds/step = 92.8573
-  ave boost coeff of all bonds = 0.397679
-  max boost coeff of any bond = 0.414894
-  min boost coeff of any bond = 0.383728
-  max dist from my box of any non-maxstrain bond ghost atom = 10.333
-  max dist from my box of any bond ghost atom = 10.3858
-  count of ghost bond neighbors not found on reneighbor steps = 0
-  lost bond partners = 0
-  ave bias coeff for lost bond partners = 0
-  bias overlaps = 0
-  non-matching bias coeffs = 0
-  CPU time for bond builds = 0.044807
-Current quantities specific to fix hyper/local:
-  neighbor bonds/bond = 703.604
-  ave boost coeff for all bonds = 0.396356
-
-Loop time of 17.9972 on 16 procs for 1500 steps with 37048 atoms
-
-Performance: 36.006 ns/day, 0.667 hours/ns, 83.346 timesteps/s
-120.7% CPU use with 16 MPI tasks x no OpenMP threads
-
-Hyper stats:
-  Dynamics time (%) = 8.87027 (49.2869)
-  Quench   time (%) = 8.15972 (45.3388)
-  Other    time (%) = 1.2212 (6.78552)
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 11.6       | 11.848     | 12.043     |   3.9 | 65.83
-Neigh   | 0.50025    | 0.52638    | 0.55163    |   2.1 |  2.92
-Comm    | 0.34528    | 0.49905    | 0.66742    |  13.3 |  2.77
-Output  | 0.0021305  | 0.0021461  | 0.0022686  |   0.1 |  0.01
-Modify  | 3.7498     | 3.9009     | 3.9786     |   2.8 | 21.67
-Other   |            | 1.221      |            |       |  6.79
-
-Nlocal:    2315.5 ave 2361 max 2267 min
-Histogram: 1 1 0 4 2 1 3 3 0 1
-Nghost:    3187.88 ave 3236 max 3141 min
-Histogram: 1 0 3 2 2 1 4 1 1 1
-Neighs:    53950.6 ave 54989 max 53049 min
-Histogram: 2 0 3 2 1 2 4 1 0 1
-FullNghs:  542951 ave 554654 max 533224 min
-Histogram: 1 2 3 1 2 2 2 2 0 1
-
-Total # of neighbors = 8687214
-Ave neighs/atom = 234.485
-Neighbor list builds = 165
-Dangerous builds = 0
-Total wall time: 0:00:22

examples/kim/in.query

@@ -0,0 +1,11 @@
+
+# example for performing a query to the OpenKIM test database to retrieve
+# a parameter to be used in the input. here it requests the aluminium
+# lattice constant for a specific test used for a specific model and then
+# assigns it to the variable 'latconst'
+
+units metal
+info variables out log
+kim_query latconst get_test_result test=TE_156715955670 species=["Al"] model=MO_800509458712 prop=structure-cubic-crystal-npt keys=["a"] units=["angstrom"]
+info variables out log
+lattice fcc ${latconst}

examples/kim/log.22Mar2019.query.g++.1

@@ -0,0 +1,34 @@
+LAMMPS (28 Feb 2019)
+
+# example for performing a query to the OpenKIM test database to retrieve
+# a parameter to be used in the input. here it requests the aluminium
+# lattice constant for a specific test used for a specific model and then
+# assigns it to the variable 'latconst'
+
+units metal
+info variables out log
+
+Info-Info-Info-Info-Info-Info-Info-Info-Info-Info-Info
+Printed on Fri Mar 22 20:00:56 2019
+
+
+Variable information:
+
+Info-Info-Info-Info-Info-Info-Info-Info-Info-Info-Info
+
+kim_query latconst get_test_result test=TE_156715955670 species=["Al"] model=MO_800509458712 prop=structure-cubic-crystal-npt keys=["a"] units=["angstrom"]
+info variables out log
+
+Info-Info-Info-Info-Info-Info-Info-Info-Info-Info-Info
+Printed on Fri Mar 22 20:00:57 2019
+
+
+Variable information:
+Variable[  0]: latconst  ,  style = string    ,  def = 4.03208274841
+
+Info-Info-Info-Info-Info-Info-Info-Info-Info-Info-Info
+
+lattice fcc ${latconst}
+lattice fcc 4.03208274841
+Lattice spacing in x,y,z = 4.03208 4.03208 4.03208
+Total wall time: 0:00:00

examples/micelle/data.micelle

@@ -49,7 +49,7 @@
      22      0      1  25.100   0.000   0.000
      23      0      1  26.295   0.000   0.000
      24    110      2  27.490   0.000   0.000
-     25    128      2  28.685   0.000   0.000
+     25    128      2  28.685  35.85686 0.000
      26      0      1  29.881   0.000   0.000
      27      0      1  31.076   0.000   0.000
      28      0      1  32.271   0.000   0.000
@@ -175,7 +175,7 @@
     148      0      1  32.271   4.781   0.000
     149      0      1  33.466   4.781   0.000
     150      0      1  34.662   4.781   0.000
-    151     53      2   0.000   5.976   0.000
+    151     53      2 35.85686  5.976   0.000
     152      0      1   1.195   5.976   0.000
     153      0      1   2.390   5.976   0.000
     154      0      1   3.586   5.976   0.000
@@ -655,7 +655,7 @@
     628      0      1  32.271  23.905   0.000
     629      0      1  33.466  23.905   0.000
     630      0      1  34.662  23.905   0.000
-    631    148      2   0.000  25.100   0.000
+    631    148      2 35.85686 25.100   0.000
     632      0      1   1.195  25.100   0.000
     633      0      1   2.390  25.100   0.000
     634      0      1   3.586  25.100   0.000
@@ -976,7 +976,7 @@
     949     25      3   0.677  33.143   0.000
     950     25      4   1.353  32.819   0.000
     951     26      3  35.071  18.557   0.000
-    952     26      4  35.480  19.186   0.000
+    952     26      4 35.48000 19.186   0.000
     953     27      3  29.131  15.504   0.000
     954     27      4  28.382  15.470   0.000
     955     28      3  23.456  33.395   0.000
@@ -1096,7 +1096,7 @@
    1069     85      3  33.021  33.461   0.000
    1070     85      4  33.771  33.455   0.000
    1071     86      3   0.552  18.315   0.000
-   1072     86      4  35.766  18.701   0.000
+   1072     86      4 -0.09086 18.701   0.000
    1073     87      3  28.026  32.796   0.000
    1074     87      4  28.562  33.321   0.000
    1075     88      3  24.351  29.925   0.000
@@ -1112,7 +1112,7 @@
    1085     93      3  26.170  16.278   0.000
    1086     93      4  26.046  17.017   0.000
    1087     94      3  10.380   0.547   0.000
-   1088     94      4  10.003  35.755   0.000
+   1088     94      4  10.003 -0.10186  0.000
    1089     95      3   0.419  29.308   0.000
    1090     95      4   0.837  29.930   0.000
    1091     96      3  13.712  28.191   0.000

examples/micelle/in.micelle

@@ -58,7 +58,7 @@ pair_coeff	1 4 1.0 1.0 1.12246
 pair_coeff	2 3 1.0 0.88 1.12246
 pair_coeff	2 4 1.0 0.75 1.12246
 
-thermo		1000
+thermo		50
 
 #dump		1 all atom 2000 dump.micelle
 
@@ -69,4 +69,4 @@ thermo		1000
 #dump_modify	3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
 
 reset_timestep	0
-run		60000
+run		1000

examples/micelle/in.micelle-rigid

@@ -0,0 +1,87 @@
+# 2d micelle simulation
+
+dimension	2
+
+neighbor	0.3 bin
+neigh_modify	delay 5
+
+atom_style	bond
+
+# Soft potential push-off
+
+read_data	data.micelle
+special_bonds	fene
+
+pair_style	soft 1.12246
+pair_coeff	* * 0.0 1.12246
+
+bond_style 	harmonic
+bond_coeff	1 50.0 0.75
+
+velocity	all create 0.45 2349852
+
+variable	prefactor equal ramp(1.0,20.0)
+
+fix		1 all nve
+fix		2 all temp/rescale 100 0.45 0.45 0.02 1.0
+fix		3 all adapt 1 pair soft a * * v_prefactor
+fix		4 all enforce2d
+
+thermo		50
+run		500
+
+unfix		3
+
+# Main run
+
+pair_style	lj/cut 2.5
+
+# solvent/head - full-size and long-range
+
+pair_coeff	1 1 1.0 1.0 2.5
+pair_coeff	2 2 1.0 1.0 2.5
+pair_coeff	1 2 1.0 1.0 2.5
+
+# tail/tail - size-averaged and long-range
+
+pair_coeff	3 3 1.0 0.75 2.5
+pair_coeff	4 4 1.0 0.50 2.5
+pair_coeff	3 4 1.0 0.67 2.5
+
+# solvent/tail - full-size and repulsive
+
+pair_coeff	1 3 1.0 1.0 1.12246
+pair_coeff	1 4 1.0 1.0 1.12246
+
+# head/tail - size-averaged and repulsive
+
+pair_coeff	2 3 1.0 0.88 1.12246
+pair_coeff	2 4 1.0 0.75 1.12246
+
+thermo		50
+
+#dump		1 all atom 2000 dump.micelle
+
+#dump		2 all image 2000 image.*.jpg type type zoom 1.6
+#dump_modify	2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
+
+#dump		3 all movie 2000 movie.mpg type type zoom 1.6
+#dump_modify	3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
+
+reset_timestep	0
+group solvent   molecule 0
+group solute    subtract all solvent
+unfix 1
+unfix 2
+unfix 4
+fix		1 solvent nve
+fix		2 solvent temp/rescale 100 0.45 0.45 0.02 1.0
+fix		5 solute rigid molecule langevin 0.45 0.45 0.5 112211
+fix		4 all enforce2d
+run		500
+unfix 2
+unfix 4
+unfix 5
+fix		5 solute rigid/small molecule
+fix		4 all enforce2d
+run		500

examples/micelle/in.micelle.rigid

@@ -0,0 +1,86 @@
+# 2d micelle simulation
+
+dimension	2
+
+neighbor	0.3 bin
+neigh_modify	delay 5
+
+atom_style	bond
+
+# Soft potential push-off
+
+read_data	data.micelle
+special_bonds	fene
+
+pair_style	soft 1.12246
+pair_coeff	* * 0.0 1.12246
+
+bond_style 	harmonic
+bond_coeff	1 50.0 0.75
+
+velocity	all create 0.45 2349852
+
+variable	prefactor equal ramp(1.0,20.0)
+
+fix		1 all nve
+fix		2 all temp/rescale 100 0.45 0.45 0.02 1.0
+fix		3 all adapt 1 pair soft a * * v_prefactor
+fix		4 all enforce2d
+
+thermo		50
+run		1000
+
+unfix		3
+
+# Main run
+
+pair_style	lj/cut 2.5
+
+# solvent/head - full-size and long-range
+
+pair_coeff	1 1 1.0 1.0 2.5
+pair_coeff	2 2 1.0 1.0 2.5
+pair_coeff	1 2 1.0 1.0 2.5
+
+# tail/tail - size-averaged and long-range
+
+pair_coeff	3 3 1.0 0.75 2.5
+pair_coeff	4 4 1.0 0.50 2.5
+pair_coeff	3 4 1.0 0.67 2.5
+
+# solvent/tail - full-size and repulsive
+
+pair_coeff	1 3 1.0 1.0 1.12246
+pair_coeff	1 4 1.0 1.0 1.12246
+
+# head/tail - size-averaged and repulsive
+
+pair_coeff	2 3 1.0 0.88 1.12246
+pair_coeff	2 4 1.0 0.75 1.12246
+
+thermo		1000
+
+#dump		1 all atom 2000 dump.micelle
+
+#dump		2 all image 2000 image.*.jpg type type zoom 1.6
+#dump_modify	2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
+
+#dump		3 all movie 2000 movie.mpg type type zoom 1.6
+#dump_modify	3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
+
+reset_timestep	0
+group solvent   molecule 0
+group solute    subtract all solvent
+unfix 1
+unfix 2
+unfix 4
+fix		1 solvent nve
+fix		2 solvent temp/rescale 100 0.45 0.45 0.02 1.0
+fix		5 solute rigid molecule langevin 0.45 0.45 0.5 112211
+fix		4 all enforce2d
+run		20000
+unfix 5
+unfix 4
+fix		5 solute rigid/small molecule langevin 0.45 0.45 0.5 112211
+fix		4 all enforce2d
+run		20000

examples/micelle/log.27Nov18.micelle.g++.1

@@ -1,255 +0,0 @@
-LAMMPS (27 Nov 2018)
-  using 1 OpenMP thread(s) per MPI task
-# 2d micelle simulation
-
-dimension	2
-
-neighbor	0.3 bin
-neigh_modify	delay 5
-
-atom_style	bond
-
-# Soft potential push-off
-
-read_data	data.micelle
-  orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1)
-  1 by 1 by 1 MPI processor grid
-  reading atoms ...
-  1200 atoms
-  scanning bonds ...
-  1 = max bonds/atom
-  reading bonds ...
-  300 bonds
-  2 = max # of 1-2 neighbors
-  1 = max # of 1-3 neighbors
-  1 = max # of 1-4 neighbors
-  2 = max # of special neighbors
-special_bonds	fene
-  2 = max # of 1-2 neighbors
-  2 = max # of special neighbors
-
-pair_style	soft 1.12246
-pair_coeff	* * 0.0 1.12246
-
-bond_style 	harmonic
-bond_coeff	1 50.0 0.75
-
-velocity	all create 0.45 2349852
-
-variable	prefactor equal ramp(1.0,20.0)
-
-fix		1 all nve
-fix		2 all temp/rescale 100 0.45 0.45 0.02 1.0
-fix		3 all adapt 1 pair soft a * * v_prefactor
-fix		4 all enforce2d
-
-thermo		50
-run		1000
-Neighbor list info ...
-  update every 1 steps, delay 5 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 1.42246
-  ghost atom cutoff = 1.42246
-  binsize = 0.71123, bins = 51 51 1
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair soft, perpetual
-      attributes: half, newton on
-      pair build: half/bin/newton
-      stencil: half/bin/2d/newton
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 3.799 | 3.799 | 3.799 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0         0.45   0.40003481 2.2200223e-06   0.84966203   0.78952518 
-      50   0.47411013   0.67721272  0.057404514    1.2083323    1.3375852 
-     100         0.45   0.73046745  0.054836584     1.234929    2.3196516 
-     150   0.67521742   0.72402001  0.043490075    1.4421648    2.8744416 
-     200         0.45   0.78481891  0.076931503    1.3113754    3.0412388 
-     250   0.66479018   0.69790602  0.081075564    1.4432178    3.6917024 
-     300         0.45   0.76820218  0.066727591    1.2845548    3.7861054 
-     350   0.67619136     0.625715  0.072722727    1.3740656    4.2861621 
-     400         0.45   0.68527759  0.090724527    1.2256271    4.4725214 
-     450   0.56702844   0.64402767  0.080555563    1.2911391    4.7402211 
-     500         0.45   0.64883009  0.078376672    1.1768318    4.7919294 
-     550     0.564664   0.58260368  0.080779475    1.2275766    4.9855705 
-     600         0.45   0.58193041  0.088386617     1.119942     5.131481 
-     650   0.52110993    0.5415273  0.097683746    1.1598867    5.2500294 
-     700         0.45   0.50856787  0.088471208    1.0466641    5.2550165 
-     750   0.51510855   0.47441291  0.089429375    1.0785216     5.375763 
-     800         0.45   0.49926696  0.085958476    1.0348504    5.4665914 
-     850   0.50688494   0.46614429  0.088962292    1.0615691     5.556932 
-     900         0.45   0.47785593   0.10150857    1.0289895    5.7765975 
-     950   0.49590559   0.46050477  0.096404887     1.052402    5.8649245 
-    1000         0.45   0.47691182   0.08808163    1.0146185    6.0177568 
-Loop time of 0.167265 on 1 procs for 1000 steps with 1200 atoms
-
-Performance: 2582728.958 tau/day, 5978.539 timesteps/s
-99.1% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.096171   | 0.096171   | 0.096171   |   0.0 | 57.50
-Bond    | 0.006212   | 0.006212   | 0.006212   |   0.0 |  3.71
-Neigh   | 0.024826   | 0.024826   | 0.024826   |   0.0 | 14.84
-Comm    | 0.0047672  | 0.0047672  | 0.0047672  |   0.0 |  2.85
-Output  | 0.00029063 | 0.00029063 | 0.00029063 |   0.0 |  0.17
-Modify  | 0.028771   | 0.028771   | 0.028771   |   0.0 | 17.20
-Other   |            | 0.006227   |            |       |  3.72
-
-Nlocal:    1200 ave 1200 max 1200 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    195 ave 195 max 195 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    3136 ave 3136 max 3136 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 3136
-Ave neighs/atom = 2.61333
-Ave special neighs/atom = 0.5
-Neighbor list builds = 92
-Dangerous builds = 0
-
-unfix		3
-
-# Main run
-
-pair_style	lj/cut 2.5
-
-# solvent/head - full-size and long-range
-
-pair_coeff	1 1 1.0 1.0 2.5
-pair_coeff	2 2 1.0 1.0 2.5
-pair_coeff	1 2 1.0 1.0 2.5
-
-# tail/tail - size-averaged and long-range
-
-pair_coeff	3 3 1.0 0.75 2.5
-pair_coeff	4 4 1.0 0.50 2.5
-pair_coeff	3 4 1.0 0.67 2.5
-
-# solvent/tail - full-size and repulsive
-
-pair_coeff	1 3 1.0 1.0 1.12246
-pair_coeff	1 4 1.0 1.0 1.12246
-
-# head/tail - size-averaged and repulsive
-
-pair_coeff	2 3 1.0 0.88 1.12246
-pair_coeff	2 4 1.0 0.75 1.12246
-
-thermo		1000
-
-#dump		1 all atom 2000 dump.micelle
-
-#dump		2 all image 2000 image.*.jpg type type zoom 1.6
-#dump_modify	2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
-
-#dump		3 all movie 2000 movie.mpg type type zoom 1.6
-#dump_modify	3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
-
-reset_timestep	0
-run		60000
-Neighbor list info ...
-  update every 1 steps, delay 5 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 2.8
-  ghost atom cutoff = 2.8
-  binsize = 1.4, bins = 26 26 1
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair lj/cut, perpetual
-      attributes: half, newton on
-      pair build: half/bin/newton
-      stencil: half/bin/2d/newton
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 4.024 | 4.024 | 4.024 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0         0.45   -1.7056163   0.08808163   -1.1679097    3.9431686 
-    1000         0.45   -1.9727655  0.058608715   -1.4645318    1.9982298 
-    2000   0.46465361   -1.9897467  0.067008449   -1.4584719    1.5873463 
-    3000   0.46175071   -2.0129279  0.057865385   -1.4936966      1.41269 
-    4000   0.44386154   -2.0280304  0.067167835   -1.5173709    1.4022093 
-    5000   0.46127582   -2.0556041  0.068318674    -1.526394    1.1416711 
-    6000   0.45354052   -2.0463246   0.05461954   -1.5385425    1.1650258 
-    7000   0.44082313    -2.040263  0.060218047   -1.5395891    1.3258681 
-    8000   0.44353466   -2.0423792  0.061769402   -1.5374447    1.2696989 
-    9000   0.46192977   -2.0761348  0.064999109   -1.5495908    0.9205826 
-   10000   0.45278646   -2.0589872  0.059623919   -1.5469542     1.075581 
-   11000   0.45583355   -2.0661957  0.058197558   -1.5525445     1.127643 
-   12000   0.45881198   -2.0921508  0.066937896   -1.5667833   0.98383574 
-   13000   0.45339481    -2.079088   0.06292782   -1.5631432    1.0188637 
-   14000   0.43601312   -2.0624084  0.057999616    -1.568759    1.1452177 
-   15000   0.45941503   -2.0746606  0.062523373    -1.553105   0.86928343 
-   16000         0.45   -2.0743162   0.05517924    -1.569512   0.86849848 
-   17000   0.45603004   -2.0657683  0.058711872   -1.5514064   0.95544551 
-   18000   0.45320383   -2.1009711  0.060716634   -1.5874283    0.8343521 
-   19000   0.44072983   -2.0846408  0.062893297    -1.581385   0.90776246 
-   20000   0.44452441   -2.0921415  0.060341571    -1.587646   0.98180005 
-   21000   0.45964557   -2.0837047  0.054459432   -1.5699827    1.0213779 
-   22000   0.46351849   -2.1053613  0.058392027   -1.5838371   0.81579487 
-   23000   0.45576065   -2.1001888  0.057646538   -1.5871614   0.76090085 
-   24000   0.44671746   -2.0848717  0.058192801   -1.5803337   0.77003809 
-   25000   0.44371239   -2.0870872  0.054804981   -1.5889396   0.92295746 
-   26000   0.45381188    -2.097021  0.057195346    -1.586392    0.7743058 
-   27000   0.46158533   -2.1071056  0.061289644   -1.5846153   0.78981802 
-   28000   0.46534671   -2.1056151  0.054934755   -1.5857214   0.80778664 
-   29000    0.4505804   -2.0949318  0.065503451   -1.5792234   0.78274755 
-   30000   0.45730883   -2.1029161  0.063461968   -1.5825264   0.82507857 
-   31000    0.4620071   -2.1124989  0.059980378   -1.5908964   0.78583986 
-   32000   0.46934619   -2.1107818  0.056442616   -1.5853842   0.70535653 
-   33000   0.45800203   -2.1062502  0.054317859    -1.594312     0.726293 
-   34000   0.44634295    -2.110401  0.057764968    -1.606665   0.85401059 
-   35000    0.4431929   -2.1274759  0.062048133   -1.6226042   0.64243758 
-   36000   0.46049645   -2.1300979  0.068463634   -1.6015216   0.57252544 
-   37000   0.45366344   -2.0977407  0.053788554   -1.5906668   0.78046879 
-   38000   0.44155077   -2.1166674  0.056888683   -1.6185959   0.53429042 
-   39000   0.45631012    -2.096949   0.04860872   -1.5924104   0.86494908 
-   40000   0.44684402   -2.1229137  0.067190397   -1.6092516   0.65110818 
-   41000    0.4479377   -2.1105264  0.059375259   -1.6035867   0.79092862 
-   42000   0.46143191   -2.1174539  0.057418393   -1.5989882   0.69762908 
-   43000    0.4356786    -2.085826  0.056534028   -1.5939764   0.89541946 
-   44000   0.45806826    -2.126423  0.060905733   -1.6078307   0.66389027 
-   45000   0.44343688   -2.1116384  0.065870114    -1.602701   0.83947585 
-   46000   0.43844672   -2.1096265  0.064158652   -1.6073865   0.77278902 
-   47000   0.45794928   -2.1142786  0.058919562   -1.5977914   0.62611933 
-   48000   0.45412335   -2.1106058  0.059153304   -1.5977076   0.66190677 
-   49000   0.45927883   -2.1197656  0.068354598   -1.5925149   0.56008845 
-   50000   0.44117285   -2.1020783  0.064763249   -1.5965099   0.85935147 
-   51000   0.45325398   -2.1125154  0.062295387   -1.5973438   0.80951782 
-   52000   0.43896579   -2.1039004  0.057475908   -1.6078245   0.84753768 
-   53000   0.45180671   -2.1092446  0.063528598   -1.5942857   0.67065038 
-   54000    0.4554341   -2.1185135  0.059603337   -1.6038556   0.76399618 
-   55000   0.43861159   -2.0986406  0.057733879   -1.6026606   0.77334084 
-   56000   0.45522991   -2.1207166  0.063287543   -1.6025785   0.78669598 
-   57000   0.46125513   -2.1150202   0.06026261   -1.5938868   0.78148646 
-   58000   0.45236938   -2.1088894  0.062678374   -1.5942186   0.75643518 
-   59000   0.43927269   -2.1274165  0.055355076   -1.6331548   0.63495311 
-   60000   0.45331102   -2.1336193  0.051244399   -1.6294416   0.56706921 
-Loop time of 13.9361 on 1 procs for 60000 steps with 1200 atoms
-
-Performance: 1859917.639 tau/day, 4305.365 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    | 9.2211     | 9.2211     | 9.2211     |   0.0 | 66.17
-Bond    | 0.33763    | 0.33763    | 0.33763    |   0.0 |  2.42
-Neigh   | 2.3772     | 2.3772     | 2.3772     |   0.0 | 17.06
-Comm    | 0.37693    | 0.37693    | 0.37693    |   0.0 |  2.70
-Output  | 0.0011795  | 0.0011795  | 0.0011795  |   0.0 |  0.01
-Modify  | 1.2727     | 1.2727     | 1.2727     |   0.0 |  9.13
-Other   |            | 0.3493     |            |       |  2.51
-
-Nlocal:    1200 ave 1200 max 1200 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    405 ave 405 max 405 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    9565 ave 9565 max 9565 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 9565
-Ave neighs/atom = 7.97083
-Ave special neighs/atom = 0.5
-Neighbor list builds = 4876
-Dangerous builds = 0
-Total wall time: 0:00:14

examples/micelle/log.27Nov18.micelle.g++.4

@@ -1,255 +0,0 @@
-LAMMPS (27 Nov 2018)
-  using 1 OpenMP thread(s) per MPI task
-# 2d micelle simulation
-
-dimension	2
-
-neighbor	0.3 bin
-neigh_modify	delay 5
-
-atom_style	bond
-
-# Soft potential push-off
-
-read_data	data.micelle
-  orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1)
-  2 by 2 by 1 MPI processor grid
-  reading atoms ...
-  1200 atoms
-  scanning bonds ...
-  1 = max bonds/atom
-  reading bonds ...
-  300 bonds
-  2 = max # of 1-2 neighbors
-  1 = max # of 1-3 neighbors
-  1 = max # of 1-4 neighbors
-  2 = max # of special neighbors
-special_bonds	fene
-  2 = max # of 1-2 neighbors
-  2 = max # of special neighbors
-
-pair_style	soft 1.12246
-pair_coeff	* * 0.0 1.12246
-
-bond_style 	harmonic
-bond_coeff	1 50.0 0.75
-
-velocity	all create 0.45 2349852
-
-variable	prefactor equal ramp(1.0,20.0)
-
-fix		1 all nve
-fix		2 all temp/rescale 100 0.45 0.45 0.02 1.0
-fix		3 all adapt 1 pair soft a * * v_prefactor
-fix		4 all enforce2d
-
-thermo		50
-run		1000
-Neighbor list info ...
-  update every 1 steps, delay 5 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 1.42246
-  ghost atom cutoff = 1.42246
-  binsize = 0.71123, bins = 51 51 1
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair soft, perpetual
-      attributes: half, newton on
-      pair build: half/bin/newton
-      stencil: half/bin/2d/newton
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 3.758 | 3.85 | 4.126 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0         0.45   0.40003481 2.2200223e-06   0.84966203   0.78952518 
-      50   0.47411013   0.67721272  0.057404514    1.2083323    1.3375852 
-     100         0.45   0.73046745  0.054836584     1.234929    2.3196516 
-     150   0.67521742   0.72402001  0.043490075    1.4421648    2.8744416 
-     200         0.45   0.78481891  0.076931503    1.3113754    3.0412388 
-     250   0.66479018   0.69790602  0.081075564    1.4432178    3.6917024 
-     300         0.45   0.76820218  0.066727591    1.2845548    3.7861054 
-     350   0.67619136     0.625715  0.072722727    1.3740656    4.2861621 
-     400         0.45   0.68527759  0.090724527    1.2256271    4.4725214 
-     450   0.56702844   0.64402767  0.080555563    1.2911391    4.7402211 
-     500         0.45   0.64883009  0.078376672    1.1768318    4.7919294 
-     550     0.564664   0.58260368  0.080779475    1.2275766    4.9855705 
-     600         0.45   0.58193041  0.088386617     1.119942     5.131481 
-     650   0.52110993    0.5415273  0.097683746    1.1598867    5.2500294 
-     700         0.45   0.50856787  0.088471208    1.0466641    5.2550165 
-     750   0.51510855   0.47441291  0.089429375    1.0785216     5.375763 
-     800         0.45   0.49926696  0.085958476    1.0348504    5.4665914 
-     850   0.50688494   0.46614429  0.088962292    1.0615691     5.556932 
-     900         0.45   0.47785593   0.10150857    1.0289895    5.7765975 
-     950   0.49590559   0.46050477  0.096404887     1.052402    5.8649245 
-    1000         0.45   0.47691182   0.08808163    1.0146185    6.0177568 
-Loop time of 0.0641922 on 4 procs for 1000 steps with 1200 atoms
-
-Performance: 6729792.131 tau/day, 15578.223 timesteps/s
-90.9% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.020663   | 0.021445   | 0.022477   |   0.5 | 33.41
-Bond    | 0.0014422  | 0.0015128  | 0.001569   |   0.1 |  2.36
-Neigh   | 0.0067129  | 0.0067645  | 0.0068202  |   0.1 | 10.54
-Comm    | 0.018454   | 0.019275   | 0.020386   |   0.5 | 30.03
-Output  | 0.00038171 | 0.00040019 | 0.00044632 |   0.0 |  0.62
-Modify  | 0.010561   | 0.010904   | 0.011309   |   0.3 | 16.99
-Other   |            | 0.003891   |            |       |  6.06
-
-Nlocal:    300 ave 305 max 292 min
-Histogram: 1 0 0 0 0 0 1 0 1 1
-Nghost:    100.25 ave 108 max 93 min
-Histogram: 1 0 1 0 0 0 1 0 0 1
-Neighs:    784 ave 815 max 739 min
-Histogram: 1 0 0 0 0 0 1 1 0 1
-
-Total # of neighbors = 3136
-Ave neighs/atom = 2.61333
-Ave special neighs/atom = 0.5
-Neighbor list builds = 92
-Dangerous builds = 0
-
-unfix		3
-
-# Main run
-
-pair_style	lj/cut 2.5
-
-# solvent/head - full-size and long-range
-
-pair_coeff	1 1 1.0 1.0 2.5
-pair_coeff	2 2 1.0 1.0 2.5
-pair_coeff	1 2 1.0 1.0 2.5
-
-# tail/tail - size-averaged and long-range
-
-pair_coeff	3 3 1.0 0.75 2.5
-pair_coeff	4 4 1.0 0.50 2.5
-pair_coeff	3 4 1.0 0.67 2.5
-
-# solvent/tail - full-size and repulsive
-
-pair_coeff	1 3 1.0 1.0 1.12246
-pair_coeff	1 4 1.0 1.0 1.12246
-
-# head/tail - size-averaged and repulsive
-
-pair_coeff	2 3 1.0 0.88 1.12246
-pair_coeff	2 4 1.0 0.75 1.12246
-
-thermo		1000
-
-#dump		1 all atom 2000 dump.micelle
-
-#dump		2 all image 2000 image.*.jpg type type zoom 1.6
-#dump_modify	2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
-
-#dump		3 all movie 2000 movie.mpg type type zoom 1.6
-#dump_modify	3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
-
-reset_timestep	0
-run		60000
-Neighbor list info ...
-  update every 1 steps, delay 5 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 2.8
-  ghost atom cutoff = 2.8
-  binsize = 1.4, bins = 26 26 1
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair lj/cut, perpetual
-      attributes: half, newton on
-      pair build: half/bin/newton
-      stencil: half/bin/2d/newton
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 4.001 | 4.032 | 4.124 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0         0.45   -1.7056163   0.08808163   -1.1679097    3.9431686 
-    1000         0.45   -1.9727661   0.05860859   -1.4645325    1.9982402 
-    2000   0.45146247   -1.9766043  0.059408886   -1.4661092    1.7398826 
-    3000   0.43338517   -2.0028125  0.059884381   -1.5099041    1.4716488 
-    4000   0.46674519   -2.0200954  0.066548679   -1.4871905    1.2506693 
-    5000         0.45   -2.0207125  0.055926205   -1.5151613    1.3047457 
-    6000   0.45447759   -2.0585234  0.068004883   -1.5364197    1.1859762 
-    7000   0.43183018   -2.0170545  0.060800296   -1.5247839    1.3074223 
-    8000   0.46657547    -2.053224  0.063224367    -1.523813    1.1785643 
-    9000         0.45   -2.0691221  0.054959029    -1.564538    1.1833657 
-   10000    0.4428252   -2.0473987  0.054306905   -1.5506356     1.181794 
-   11000   0.45407036   -2.0746151  0.065849667   -1.5550734    1.1008545 
-   12000   0.46061944   -2.0580809  0.063129643   -1.5347156    1.0206491 
-   13000   0.45159068   -2.0640832  0.060059758   -1.5528091    1.0813494 
-   14000   0.44141594   -2.0467255  0.062785088   -1.5428923    1.1465772 
-   15000     0.454361   -2.0908595  0.057471037   -1.5794061   0.84297781 
-   16000   0.44061091   -2.0521452  0.064644196   -1.5472573    1.1478647 
-   17000   0.45118383    -2.081348  0.058660999   -1.5718791    1.0101404 
-   18000   0.44664866   -2.0845745  0.060435731   -1.5778623   0.96142277 
-   19000   0.45515339   -2.0914006  0.062174016   -1.5744525   0.87623323 
-   20000   0.45624408   -2.0837697  0.059263054   -1.5686428   0.92810644 
-   21000   0.46791657   -2.1062007  0.067355929   -1.5713181   0.88318793 
-   22000   0.43907391   -2.1005271  0.065885144   -1.5959339   0.77211644 
-   23000   0.43967354   -2.0723459  0.057613471   -1.5754253    1.0371548 
-   24000   0.45716384   -2.0987126  0.055157377   -1.5867723   0.89670061 
-   25000   0.45828285   -2.1041616  0.057736138   -1.5885245   0.79952286 
-   26000         0.45   -2.0743463  0.072455519   -1.5522658   0.88260204 
-   27000   0.46581599   -2.0804974  0.058113258   -1.5569564   0.93053891 
-   28000   0.46904194   -2.0920124  0.059748792   -1.5636125   0.79359618 
-   29000   0.46093196    -2.118556  0.063942334   -1.5940659   0.67707604 
-   30000   0.45733724   -2.1197827  0.066939064   -1.5958875   0.66886075 
-   31000   0.44580762   -2.0977175  0.056969121   -1.5953123   0.81042562 
-   32000   0.44403029   -2.1032264  0.063465127    -1.596101   0.71796412 
-   33000   0.45834072   -2.0934132  0.066035391    -1.569419   0.77873998 
-   34000   0.44981563   -2.0910902   0.07138738   -1.5702621   0.75679805 
-   35000   0.45383392   -2.0926654  0.067553478   -1.5716562    0.9064517 
-   36000   0.44447198   -2.1107114  0.062718917   -1.6038909    0.8538349 
-   37000   0.45838527   -2.1166464  0.062442606   -1.5962005    0.7300635 
-   38000   0.45014075   -2.1096258  0.059293718   -1.6005665   0.73988246 
-   39000   0.44377026    -2.080309  0.063545781   -1.5733628   0.99775641 
-   40000   0.44577324   -2.1134607  0.065271179   -1.6027878   0.64113168 
-   41000         0.45   -2.0937983  0.060881377   -1.5832919   0.78849829 
-   42000   0.46866695   -2.1142283  0.056417605   -1.5895343   0.73788436 
-   43000   0.43211727   -2.0819893  0.061463358   -1.5887688   0.95853724 
-   44000   0.44138397   -2.0921314  0.059643895   -1.5914713   0.89486208 
-   45000         0.45    -2.117209  0.054804331   -1.6127797   0.78564885 
-   46000   0.44285245   -2.1090975  0.057629006   -1.6089851   0.64549424 
-   47000   0.45537009   -2.1164296  0.068582324   -1.5928567   0.73629413 
-   48000   0.45046732   -2.1006362  0.057249591   -1.5932947   0.74317593 
-   49000   0.45425966   -2.1191703  0.064247719   -1.6010414   0.70962368 
-   50000   0.45506149   -2.1184671  0.064911797   -1.5988731   0.69958156 
-   51000   0.46047417   -2.1019719  0.058468259   -1.5834132   0.87219271 
-   52000   0.43808317    -2.092294  0.057280941    -1.597295   0.84156893 
-   53000   0.45012337   -2.1175234  0.064002667   -1.6037725   0.64562439 
-   54000   0.43854679   -2.1236444  0.061316257   -1.6241468   0.72478117 
-   55000   0.46382438   -2.1016563  0.060724666   -1.5774938   0.83311209 
-   56000   0.44951533   -2.0946157  0.055075217   -1.5903998   0.90066109 
-   57000   0.45937401   -2.0983442  0.061558996    -1.577794   0.58606161 
-   58000     0.446669   -2.1146838  0.062385166   -1.6060019   0.73443388 
-   59000   0.43847747   -2.1197461  0.060460257   -1.6211738    0.7230937 
-   60000   0.45294215   -2.1258513  0.061895006   -1.6113915   0.70722168 
-Loop time of 4.56226 on 4 procs for 60000 steps with 1200 atoms
-
-Performance: 5681397.232 tau/day, 13151.382 timesteps/s
-97.1% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 2.2114     | 2.2527     | 2.3592     |   4.1 | 49.38
-Bond    | 0.083713   | 0.09234    | 0.10244    |   2.3 |  2.02
-Neigh   | 0.72491    | 0.7277     | 0.72957    |   0.2 | 15.95
-Comm    | 0.79464    | 0.90036    | 0.94957    |   6.5 | 19.74
-Output  | 0.0014119  | 0.0024976  | 0.0057502  |   3.8 |  0.05
-Modify  | 0.33757    | 0.35202    | 0.36946    |   2.1 |  7.72
-Other   |            | 0.2346     |            |       |  5.14
-
-Nlocal:    300 ave 306 max 289 min
-Histogram: 1 0 0 0 0 0 0 1 1 1
-Nghost:    227.25 ave 250 max 216 min
-Histogram: 2 0 1 0 0 0 0 0 0 1
-Neighs:    2373.25 ave 2489 max 2283 min
-Histogram: 1 1 0 0 0 1 0 0 0 1
-
-Total # of neighbors = 9493
-Ave neighs/atom = 7.91083
-Ave special neighs/atom = 0.5
-Neighbor list builds = 4888
-Dangerous builds = 0
-Total wall time: 0:00:04

examples/micelle/log.29Mar2019.micelle-rigid.g++.1

@@ -0,0 +1,260 @@
+LAMMPS (29 Mar 2019)
+  using 1 OpenMP thread(s) per MPI task
+# 2d micelle simulation
+
+dimension	2
+
+neighbor	0.3 bin
+neigh_modify	delay 5
+
+atom_style	bond
+
+# Soft potential push-off
+
+read_data	data.micelle
+  orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  1200 atoms
+  scanning bonds ...
+  1 = max bonds/atom
+  reading bonds ...
+  300 bonds
+  2 = max # of 1-2 neighbors
+  1 = max # of 1-3 neighbors
+  1 = max # of 1-4 neighbors
+  2 = max # of special neighbors
+  special bonds CPU = 0.000473022 secs
+  read_data CPU = 0.0024147 secs
+special_bonds	fene
+  2 = max # of 1-2 neighbors
+  2 = max # of special neighbors
+  special bonds CPU = 0.00022316 secs
+
+pair_style	soft 1.12246
+pair_coeff	* * 0.0 1.12246
+
+bond_style 	harmonic
+bond_coeff	1 50.0 0.75
+
+velocity	all create 0.45 2349852
+
+variable	prefactor equal ramp(1.0,20.0)
+
+fix		1 all nve
+fix		2 all temp/rescale 100 0.45 0.45 0.02 1.0
+fix		3 all adapt 1 pair soft a * * v_prefactor
+fix		4 all enforce2d
+
+thermo		50
+run		500
+Neighbor list info ...
+  update every 1 steps, delay 5 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 1.42246
+  ghost atom cutoff = 1.42246
+  binsize = 0.71123, bins = 51 51 1
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair soft, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/2d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.799 | 3.799 | 3.799 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0         0.45   0.40003481 2.2200223e-06   0.84966203   0.78952518 
+      50   0.54981866   0.93548899  0.068440043    1.5532895    1.9232786 
+     100         0.45   0.99659327  0.079228519    1.5254468    3.2135679 
+     150   0.86965411   0.90456016   0.07493355    1.8484231    4.3821925 
+     200         0.45      1.01454   0.10663502       1.5708    4.7598476 
+     250   0.79636561   0.82567712   0.12105337    1.7424325    5.4983899 
+     300         0.45   0.86475538   0.11819875    1.4325791    5.8554758 
+     350   0.72135464   0.70693069   0.10912636    1.5368106    6.0388247 
+     400         0.45   0.75067331   0.14165013    1.3419484    6.3840708 
+     450   0.64839221   0.62402486   0.14173679    1.4136135    6.4791009 
+     500         0.45   0.66669513   0.13695201    1.2532721     6.807146 
+Loop time of 0.103162 on 1 procs for 500 steps with 1200 atoms
+
+Performance: 2093802.885 tau/day, 4846.766 timesteps/s
+99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.068308   | 0.068308   | 0.068308   |   0.0 | 66.21
+Bond    | 0.004235   | 0.004235   | 0.004235   |   0.0 |  4.11
+Neigh   | 0.014069   | 0.014069   | 0.014069   |   0.0 | 13.64
+Comm    | 0.0019219  | 0.0019219  | 0.0019219  |   0.0 |  1.86
+Output  | 0.00017262 | 0.00017262 | 0.00017262 |   0.0 |  0.17
+Modify  | 0.011728   | 0.011728   | 0.011728   |   0.0 | 11.37
+Other   |            | 0.002726   |            |       |  2.64
+
+Nlocal:    1200 ave 1200 max 1200 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    197 ave 197 max 197 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    3094 ave 3094 max 3094 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 3094
+Ave neighs/atom = 2.57833
+Ave special neighs/atom = 0.5
+Neighbor list builds = 52
+Dangerous builds = 0
+
+unfix		3
+
+# Main run
+
+pair_style	lj/cut 2.5
+
+# solvent/head - full-size and long-range
+
+pair_coeff	1 1 1.0 1.0 2.5
+pair_coeff	2 2 1.0 1.0 2.5
+pair_coeff	1 2 1.0 1.0 2.5
+
+# tail/tail - size-averaged and long-range
+
+pair_coeff	3 3 1.0 0.75 2.5
+pair_coeff	4 4 1.0 0.50 2.5
+pair_coeff	3 4 1.0 0.67 2.5
+
+# solvent/tail - full-size and repulsive
+
+pair_coeff	1 3 1.0 1.0 1.12246
+pair_coeff	1 4 1.0 1.0 1.12246
+
+# head/tail - size-averaged and repulsive
+
+pair_coeff	2 3 1.0 0.88 1.12246
+pair_coeff	2 4 1.0 0.75 1.12246
+
+thermo		50
+
+#dump		1 all atom 2000 dump.micelle
+
+#dump		2 all image 2000 image.*.jpg type type zoom 1.6
+#dump_modify	2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
+
+#dump		3 all movie 2000 movie.mpg type type zoom 1.6
+#dump_modify	3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
+
+reset_timestep	0
+group solvent   molecule 0
+750 atoms in group solvent
+group solute    subtract all solvent
+450 atoms in group solute
+unfix 1
+unfix 2
+unfix 4
+fix		1 solvent nve
+fix		2 solvent temp/rescale 100 0.45 0.45 0.02 1.0
+fix		5 solute rigid molecule langevin 0.45 0.45 0.5 112211
+150 rigid bodies with 450 atoms
+fix		4 all enforce2d
+run		500
+Neighbor list info ...
+  update every 1 steps, delay 5 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2.8
+  ghost atom cutoff = 2.8
+  binsize = 1.4, bins = 26 26 1
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/2d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 5.274 | 5.274 | 5.274 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0   0.45318168   -1.3753652   0.13695201   -0.8705807     1.975423 
+      50   0.77871641   -1.6955252   0.13695201  -0.92651507   0.64222539 
+     100    0.5336062   -1.7124572   0.13695201   -1.1423948  -0.11959696 
+     150   0.58789067   -1.7926109   0.13695201   -1.1784877    1.2592743 
+     200   0.47864796   -1.8040298   0.13695201   -1.2785752    3.6739793 
+     250   0.51124651   -1.8614797   0.13695201    -1.309566    2.5817722 
+     300   0.45695639   -1.8708384   0.13695201   -1.3629901    3.0833794 
+     350     0.477504   -1.8924359   0.13695201   -1.3679098   -5.1605926 
+     400   0.45328205     -1.87754   0.13695201    -1.372674   -4.0355858 
+     450   0.47465031   -1.9071924   0.13695201   -1.3849826    3.1949617 
+     500   0.45533691   -1.9072316   0.13695201   -1.4006978   0.48079061 
+Loop time of 0.178806 on 1 procs for 500 steps with 1200 atoms
+
+Performance: 1208012.705 tau/day, 2796.326 timesteps/s
+99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.086131   | 0.086131   | 0.086131   |   0.0 | 48.17
+Bond    | 0.0042472  | 0.0042472  | 0.0042472  |   0.0 |  2.38
+Neigh   | 0.021317   | 0.021317   | 0.021317   |   0.0 | 11.92
+Comm    | 0.0025985  | 0.0025985  | 0.0025985  |   0.0 |  1.45
+Output  | 0.000175   | 0.000175   | 0.000175   |   0.0 |  0.10
+Modify  | 0.061408   | 0.061408   | 0.061408   |   0.0 | 34.34
+Other   |            | 0.00293    |            |       |  1.64
+
+Nlocal:    1200 ave 1200 max 1200 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    416 ave 416 max 416 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    8769 ave 8769 max 8769 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 8769
+Ave neighs/atom = 7.3075
+Ave special neighs/atom = 0.5
+Neighbor list builds = 47
+Dangerous builds = 2
+unfix 2
+unfix 4
+unfix 5
+fix		5 solute rigid/small molecule
+  create bodies CPU = 0.00015378 secs
+150 rigid bodies with 450 atoms
+  1.30435 = max distance from body owner to body atom
+fix		4 all enforce2d
+run		500
+Per MPI rank memory allocation (min/avg/max) = 8.64 | 8.64 | 8.64 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+     500   0.45533691   -1.9072316   0.13695201   -1.4006978    2.4545793 
+     550   0.45627282    -1.912409   0.13695201   -1.4051155    2.1845065 
+     600   0.44734553   -1.8890695   0.13695201    -1.389022    2.3458965 
+     650   0.46444648   -1.9042462   0.13695201   -1.3903185    2.1609319 
+     700   0.47113236   -1.8977576   0.13695201   -1.3784032    2.2420351 
+     750   0.48554548   -1.9253545   0.13695201   -1.3943015     2.143907 
+     800   0.46350091   -1.8865749   0.13695201   -1.3734146     2.294431 
+     850    0.4766104   -1.9094039   0.13695201   -1.3856031    2.2077157 
+     900   0.48988467   -1.9051538   0.13695201   -1.3705787    2.0107056 
+     950   0.48351943   -1.9162485   0.13695201   -1.3868399    2.1891332 
+    1000   0.49033701   -1.9115165   0.13695201   -1.3765742    2.1508141 
+Loop time of 0.166502 on 1 procs for 500 steps with 1200 atoms
+
+Performance: 1297278.008 tau/day, 3002.958 timesteps/s
+99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.085767   | 0.085767   | 0.085767   |   0.0 | 51.51
+Bond    | 0.0042562  | 0.0042562  | 0.0042562  |   0.0 |  2.56
+Neigh   | 0.018039   | 0.018039   | 0.018039   |   0.0 | 10.83
+Comm    | 0.0024002  | 0.0024002  | 0.0024002  |   0.0 |  1.44
+Output  | 0.00018239 | 0.00018239 | 0.00018239 |   0.0 |  0.11
+Modify  | 0.052717   | 0.052717   | 0.052717   |   0.0 | 31.66
+Other   |            | 0.003141   |            |       |  1.89
+
+Nlocal:    1200 ave 1200 max 1200 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    415 ave 415 max 415 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    8743 ave 8743 max 8743 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 8743
+Ave neighs/atom = 7.28583
+Ave special neighs/atom = 0.5
+Neighbor list builds = 40
+Dangerous builds = 0
+Total wall time: 0:00:00

examples/micelle/log.29Mar2019.micelle-rigid.g++.4

@@ -0,0 +1,260 @@
+LAMMPS (29 Mar 2019)
+  using 1 OpenMP thread(s) per MPI task
+# 2d micelle simulation
+
+dimension	2
+
+neighbor	0.3 bin
+neigh_modify	delay 5
+
+atom_style	bond
+
+# Soft potential push-off
+
+read_data	data.micelle
+  orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1)
+  2 by 2 by 1 MPI processor grid
+  reading atoms ...
+  1200 atoms
+  scanning bonds ...
+  1 = max bonds/atom
+  reading bonds ...
+  300 bonds
+  2 = max # of 1-2 neighbors
+  1 = max # of 1-3 neighbors
+  1 = max # of 1-4 neighbors
+  2 = max # of special neighbors
+  special bonds CPU = 0.000422001 secs
+  read_data CPU = 0.00473404 secs
+special_bonds	fene
+  2 = max # of 1-2 neighbors
+  2 = max # of special neighbors
+  special bonds CPU = 0.000183344 secs
+
+pair_style	soft 1.12246
+pair_coeff	* * 0.0 1.12246
+
+bond_style 	harmonic
+bond_coeff	1 50.0 0.75
+
+velocity	all create 0.45 2349852
+
+variable	prefactor equal ramp(1.0,20.0)
+
+fix		1 all nve
+fix		2 all temp/rescale 100 0.45 0.45 0.02 1.0
+fix		3 all adapt 1 pair soft a * * v_prefactor
+fix		4 all enforce2d
+
+thermo		50
+run		500
+Neighbor list info ...
+  update every 1 steps, delay 5 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 1.42246
+  ghost atom cutoff = 1.42246
+  binsize = 0.71123, bins = 51 51 1
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair soft, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/2d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.758 | 3.85 | 4.126 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0         0.45   0.40003481 2.2200223e-06   0.84966203   0.78952518 
+      50   0.54981866   0.93548899  0.068440043    1.5532895    1.9232786 
+     100         0.45   0.99659327  0.079228519    1.5254468    3.2135679 
+     150   0.86965411   0.90456016   0.07493355    1.8484231    4.3821925 
+     200         0.45      1.01454   0.10663502       1.5708    4.7598476 
+     250   0.79636561   0.82567712   0.12105337    1.7424325    5.4983899 
+     300         0.45   0.86475538   0.11819875    1.4325791    5.8554758 
+     350   0.72135464   0.70693069   0.10912636    1.5368106    6.0388247 
+     400         0.45   0.75067331   0.14165013    1.3419484    6.3840708 
+     450   0.64839221   0.62402486   0.14173679    1.4136135    6.4791009 
+     500         0.45   0.66669513   0.13695201    1.2532721     6.807146 
+Loop time of 0.0426326 on 4 procs for 500 steps with 1200 atoms
+
+Performance: 5066547.720 tau/day, 11728.120 timesteps/s
+98.7% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.016784   | 0.019254   | 0.022154   |   1.5 | 45.16
+Bond    | 0.0010612  | 0.0012558  | 0.0014153  |   0.4 |  2.95
+Neigh   | 0.0046048  | 0.0046697  | 0.0047245  |   0.1 | 10.95
+Comm    | 0.0064592  | 0.0097114  | 0.012527   |   2.4 | 22.78
+Output  | 0.00022507 | 0.00026393 | 0.00033951 |   0.0 |  0.62
+Modify  | 0.0041659  | 0.0048084  | 0.0053945  |   0.8 | 11.28
+Other   |            | 0.002669   |            |       |  6.26
+
+Nlocal:    300 ave 304 max 292 min
+Histogram: 1 0 0 0 0 0 0 0 2 1
+Nghost:    103.5 ave 108 max 98 min
+Histogram: 1 0 0 1 0 0 0 0 0 2
+Neighs:    773.5 ave 792 max 735 min
+Histogram: 1 0 0 0 0 0 0 0 2 1
+
+Total # of neighbors = 3094
+Ave neighs/atom = 2.57833
+Ave special neighs/atom = 0.5
+Neighbor list builds = 52
+Dangerous builds = 0
+
+unfix		3
+
+# Main run
+
+pair_style	lj/cut 2.5
+
+# solvent/head - full-size and long-range
+
+pair_coeff	1 1 1.0 1.0 2.5
+pair_coeff	2 2 1.0 1.0 2.5
+pair_coeff	1 2 1.0 1.0 2.5
+
+# tail/tail - size-averaged and long-range
+
+pair_coeff	3 3 1.0 0.75 2.5
+pair_coeff	4 4 1.0 0.50 2.5
+pair_coeff	3 4 1.0 0.67 2.5
+
+# solvent/tail - full-size and repulsive
+
+pair_coeff	1 3 1.0 1.0 1.12246
+pair_coeff	1 4 1.0 1.0 1.12246
+
+# head/tail - size-averaged and repulsive
+
+pair_coeff	2 3 1.0 0.88 1.12246
+pair_coeff	2 4 1.0 0.75 1.12246
+
+thermo		50
+
+#dump		1 all atom 2000 dump.micelle
+
+#dump		2 all image 2000 image.*.jpg type type zoom 1.6
+#dump_modify	2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
+
+#dump		3 all movie 2000 movie.mpg type type zoom 1.6
+#dump_modify	3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
+
+reset_timestep	0
+group solvent   molecule 0
+750 atoms in group solvent
+group solute    subtract all solvent
+450 atoms in group solute
+unfix 1
+unfix 2
+unfix 4
+fix		1 solvent nve
+fix		2 solvent temp/rescale 100 0.45 0.45 0.02 1.0
+fix		5 solute rigid molecule langevin 0.45 0.45 0.5 112211
+150 rigid bodies with 450 atoms
+fix		4 all enforce2d
+run		500
+Neighbor list info ...
+  update every 1 steps, delay 5 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2.8
+  ghost atom cutoff = 2.8
+  binsize = 1.4, bins = 26 26 1
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/2d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 5.251 | 5.282 | 5.374 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0   0.45318168   -1.3753652   0.13695201   -0.8705807     1.975423 
+      50   0.77871641   -1.6955252   0.13695201  -0.92651507   0.64222539 
+     100    0.5336062   -1.7124572   0.13695201   -1.1423948  -0.11959696 
+     150   0.58789067   -1.7926109   0.13695201   -1.1784877    1.2592743 
+     200   0.47864796   -1.8040298   0.13695201   -1.2785752    3.6739793 
+     250   0.51124651   -1.8614797   0.13695201    -1.309566    2.5817722 
+     300   0.45695639   -1.8708384   0.13695201   -1.3629901    3.0833794 
+     350     0.477504   -1.8924359   0.13695201   -1.3679098   -5.1605926 
+     400   0.45328205     -1.87754   0.13695201    -1.372674   -4.0355858 
+     450   0.47465031   -1.9071924   0.13695201   -1.3849826    3.1949617 
+     500   0.45533691   -1.9072316   0.13695201   -1.4006978   0.48079061 
+Loop time of 0.0887392 on 4 procs for 500 steps with 1200 atoms
+
+Performance: 2434100.210 tau/day, 5634.491 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    | 0.022611   | 0.022839   | 0.023082   |   0.1 | 25.74
+Bond    | 0.0010793  | 0.0011569  | 0.0012515  |   0.2 |  1.30
+Neigh   | 0.0064609  | 0.0064996  | 0.0065265  |   0.0 |  7.32
+Comm    | 0.0071712  | 0.0073687  | 0.0077734  |   0.3 |  8.30
+Output  | 0.00023389 | 0.00025356 | 0.00030327 |   0.0 |  0.29
+Modify  | 0.047258   | 0.047683   | 0.048503   |   0.2 | 53.73
+Other   |            | 0.002938   |            |       |  3.31
+
+Nlocal:    300 ave 309 max 291 min
+Histogram: 1 0 0 1 0 0 1 0 0 1
+Nghost:    218.75 ave 223 max 216 min
+Histogram: 1 0 2 0 0 0 0 0 0 1
+Neighs:    2192.25 ave 2251 max 2113 min
+Histogram: 1 0 0 1 0 0 0 0 0 2
+
+Total # of neighbors = 8769
+Ave neighs/atom = 7.3075
+Ave special neighs/atom = 0.5
+Neighbor list builds = 47
+Dangerous builds = 2
+unfix 2
+unfix 4
+unfix 5
+fix		5 solute rigid/small molecule
+  create bodies CPU = 7.70092e-05 secs
+150 rigid bodies with 450 atoms
+  1.30435 = max distance from body owner to body atom
+fix		4 all enforce2d
+run		500
+Per MPI rank memory allocation (min/avg/max) = 8.565 | 8.597 | 8.69 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+     500   0.45533691   -1.9072316   0.13695201   -1.4006978    2.4545793 
+     550   0.45627282    -1.912409   0.13695201   -1.4051155    2.1845065 
+     600   0.44734553   -1.8890695   0.13695201    -1.389022    2.3458965 
+     650   0.46444648   -1.9042462   0.13695201   -1.3903185    2.1609319 
+     700   0.47113236   -1.8977576   0.13695201   -1.3784032    2.2420351 
+     750   0.48554548   -1.9253545   0.13695201   -1.3943015     2.143907 
+     800   0.46350091   -1.8865749   0.13695201   -1.3734146     2.294431 
+     850    0.4766104   -1.9094039   0.13695201   -1.3856031    2.2077157 
+     900   0.48988467   -1.9051538   0.13695201   -1.3705787    2.0107056 
+     950   0.48351942   -1.9162485   0.13695201   -1.3868399    2.1891332 
+    1000     0.490337   -1.9115164   0.13695201   -1.3765742    2.1508141 
+Loop time of 0.0588261 on 4 procs for 500 steps with 1200 atoms
+
+Performance: 3671840.233 tau/day, 8499.630 timesteps/s
+98.3% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.022407   | 0.022631   | 0.0229     |   0.1 | 38.47
+Bond    | 0.0010669  | 0.0011355  | 0.0012124  |   0.2 |  1.93
+Neigh   | 0.0052333  | 0.00528    | 0.0053182  |   0.0 |  8.98
+Comm    | 0.0063677  | 0.0066406  | 0.0068488  |   0.2 | 11.29
+Output  | 0.00023055 | 0.00024778 | 0.00028086 |   0.0 |  0.42
+Modify  | 0.020577   | 0.020651   | 0.020834   |   0.1 | 35.11
+Other   |            | 0.00224    |            |       |  3.81
+
+Nlocal:    300 ave 303 max 295 min
+Histogram: 1 0 0 0 0 0 1 0 1 1
+Nghost:    219 ave 224 max 215 min
+Histogram: 1 0 0 1 1 0 0 0 0 1
+Neighs:    2185.75 ave 2244 max 2143 min
+Histogram: 1 1 0 0 0 1 0 0 0 1
+
+Total # of neighbors = 8743
+Ave neighs/atom = 7.28583
+Ave special neighs/atom = 0.5
+Neighbor list builds = 40
+Dangerous builds = 0
+Total wall time: 0:00:00

examples/micelle/log.29Mar2019.micelle.g++.1

@@ -0,0 +1,218 @@
+LAMMPS (29 Mar 2019)
+  using 1 OpenMP thread(s) per MPI task
+# 2d micelle simulation
+
+dimension	2
+
+neighbor	0.3 bin
+neigh_modify	delay 5
+
+atom_style	bond
+
+# Soft potential push-off
+
+read_data	data.micelle
+  orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  1200 atoms
+  scanning bonds ...
+  1 = max bonds/atom
+  reading bonds ...
+  300 bonds
+  2 = max # of 1-2 neighbors
+  1 = max # of 1-3 neighbors
+  1 = max # of 1-4 neighbors
+  2 = max # of special neighbors
+  special bonds CPU = 0.00037837 secs
+  read_data CPU = 0.00206876 secs
+special_bonds	fene
+  2 = max # of 1-2 neighbors
+  2 = max # of special neighbors
+  special bonds CPU = 0.000177383 secs
+
+pair_style	soft 1.12246
+pair_coeff	* * 0.0 1.12246
+
+bond_style 	harmonic
+bond_coeff	1 50.0 0.75
+
+velocity	all create 0.45 2349852
+
+variable	prefactor equal ramp(1.0,20.0)
+
+fix		1 all nve
+fix		2 all temp/rescale 100 0.45 0.45 0.02 1.0
+fix		3 all adapt 1 pair soft a * * v_prefactor
+fix		4 all enforce2d
+
+thermo		50
+run		1000
+Neighbor list info ...
+  update every 1 steps, delay 5 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 1.42246
+  ghost atom cutoff = 1.42246
+  binsize = 0.71123, bins = 51 51 1
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair soft, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/2d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.799 | 3.799 | 3.799 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0         0.45   0.40003481 2.2200223e-06   0.84966203   0.78952518 
+      50   0.47411013   0.67721272  0.057404514    1.2083323    1.3375852 
+     100         0.45   0.73046745  0.054836584     1.234929    2.3196516 
+     150   0.67521742   0.72402001  0.043490075    1.4421648    2.8744416 
+     200         0.45   0.78481891  0.076931503    1.3113754    3.0412388 
+     250   0.66479018   0.69790602  0.081075564    1.4432178    3.6917024 
+     300         0.45   0.76820218  0.066727591    1.2845548    3.7861054 
+     350   0.67619136     0.625715  0.072722727    1.3740656    4.2861621 
+     400         0.45   0.68527759  0.090724527    1.2256271    4.4725214 
+     450   0.56702844   0.64402767  0.080555563    1.2911391    4.7402211 
+     500         0.45   0.64883009  0.078376672    1.1768318    4.7919294 
+     550     0.564664   0.58260368  0.080779475    1.2275766    4.9855705 
+     600         0.45   0.58193041  0.088386617     1.119942     5.131481 
+     650   0.52110993    0.5415273  0.097683746    1.1598867    5.2500294 
+     700         0.45   0.50856787  0.088471208    1.0466641    5.2550165 
+     750   0.51510855   0.47441291  0.089429375    1.0785216     5.375763 
+     800         0.45   0.49926696  0.085958476    1.0348504    5.4665914 
+     850   0.50688494   0.46614429  0.088962292    1.0615691     5.556932 
+     900         0.45   0.47785593   0.10150857    1.0289895    5.7765975 
+     950   0.49590559   0.46050477  0.096404887     1.052402    5.8649245 
+    1000         0.45   0.47691182   0.08808163    1.0146185    6.0177568 
+Loop time of 0.208895 on 1 procs for 1000 steps with 1200 atoms
+
+Performance: 2068027.282 tau/day, 4787.100 timesteps/s
+99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.14142    | 0.14142    | 0.14142    |   0.0 | 67.70
+Bond    | 0.008441   | 0.008441   | 0.008441   |   0.0 |  4.04
+Neigh   | 0.025716   | 0.025716   | 0.025716   |   0.0 | 12.31
+Comm    | 0.0036864  | 0.0036864  | 0.0036864  |   0.0 |  1.76
+Output  | 0.0003562  | 0.0003562  | 0.0003562  |   0.0 |  0.17
+Modify  | 0.023699   | 0.023699   | 0.023699   |   0.0 | 11.35
+Other   |            | 0.00558    |            |       |  2.67
+
+Nlocal:    1200 ave 1200 max 1200 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    195 ave 195 max 195 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    3136 ave 3136 max 3136 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 3136
+Ave neighs/atom = 2.61333
+Ave special neighs/atom = 0.5
+Neighbor list builds = 92
+Dangerous builds = 0
+
+unfix		3
+
+# Main run
+
+pair_style	lj/cut 2.5
+
+# solvent/head - full-size and long-range
+
+pair_coeff	1 1 1.0 1.0 2.5
+pair_coeff	2 2 1.0 1.0 2.5
+pair_coeff	1 2 1.0 1.0 2.5
+
+# tail/tail - size-averaged and long-range
+
+pair_coeff	3 3 1.0 0.75 2.5
+pair_coeff	4 4 1.0 0.50 2.5
+pair_coeff	3 4 1.0 0.67 2.5
+
+# solvent/tail - full-size and repulsive
+
+pair_coeff	1 3 1.0 1.0 1.12246
+pair_coeff	1 4 1.0 1.0 1.12246
+
+# head/tail - size-averaged and repulsive
+
+pair_coeff	2 3 1.0 0.88 1.12246
+pair_coeff	2 4 1.0 0.75 1.12246
+
+thermo		50
+
+#dump		1 all atom 2000 dump.micelle
+
+#dump		2 all image 2000 image.*.jpg type type zoom 1.6
+#dump_modify	2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
+
+#dump		3 all movie 2000 movie.mpg type type zoom 1.6
+#dump_modify	3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
+
+reset_timestep	0
+run		1000
+Neighbor list info ...
+  update every 1 steps, delay 5 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2.8
+  ghost atom cutoff = 2.8
+  binsize = 1.4, bins = 26 26 1
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/2d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 4.024 | 4.024 | 4.024 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0         0.45   -1.7056163   0.08808163   -1.1679097    3.9431686 
+      50   0.59734982   -1.8103783  0.076066922   -1.1374593    3.2770557 
+     100         0.45   -1.8347112  0.093132329   -1.2919539     3.024661 
+     150   0.51924311   -1.8943977  0.076004124   -1.2995832    2.5570373 
+     200         0.45   -1.8918672  0.082422107   -1.3598201    2.5629655 
+     250   0.50281134    -1.920406  0.074011331   -1.3440023    2.3518682 
+     300         0.45   -1.9351047  0.075337265   -1.4101424    2.3249947 
+     350   0.47650026   -1.9313687  0.072115117   -1.3831504    2.1987532 
+     400         0.45   -1.9554318  0.081603939   -1.4242028    2.0787066 
+     450   0.47220236   -1.9468502  0.065625624   -1.4094157    2.0984288 
+     500    0.4684673   -1.9444333  0.076696283   -1.3996601    2.0528682 
+     550   0.47683128    -1.958676  0.070589719   -1.4116523    2.0856022 
+     600   0.46851243   -1.9338267   0.07060548   -1.3950992      2.26405 
+     650   0.46874142   -1.9462493  0.069134685   -1.4087638    2.1070263 
+     700   0.46437384   -1.9309953  0.071977522   -1.3950309    2.2256923 
+     750   0.47326225   -1.9484255  0.075435845   -1.4001218    2.0880254 
+     800         0.45   -1.9646005  0.064159585   -1.4508159    2.0612696 
+     850   0.46748307    -1.970559  0.060384874   -1.4430806    1.9472879 
+     900   0.46909484    -1.953723  0.062470295   -1.4225488    2.0222909 
+     950   0.45631531   -1.9387753  0.067536568   -1.4153037    2.0638421 
+    1000         0.45   -1.9727646  0.058607721   -1.4645318    1.9982315 
+Loop time of 0.252254 on 1 procs for 1000 steps with 1200 atoms
+
+Performance: 1712557.882 tau/day, 3964.254 timesteps/s
+99.0% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.17177    | 0.17177    | 0.17177    |   0.0 | 68.09
+Bond    | 0.0084555  | 0.0084555  | 0.0084555  |   0.0 |  3.35
+Neigh   | 0.03991    | 0.03991    | 0.03991    |   0.0 | 15.82
+Comm    | 0.0049119  | 0.0049119  | 0.0049119  |   0.0 |  1.95
+Output  | 0.00039077 | 0.00039077 | 0.00039077 |   0.0 |  0.15
+Modify  | 0.021131   | 0.021131   | 0.021131   |   0.0 |  8.38
+Other   |            | 0.005685   |            |       |  2.25
+
+Nlocal:    1200 ave 1200 max 1200 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    415 ave 415 max 415 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    8586 ave 8586 max 8586 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 8586
+Ave neighs/atom = 7.155
+Ave special neighs/atom = 0.5
+Neighbor list builds = 86
+Dangerous builds = 0
+Total wall time: 0:00:00

examples/micelle/log.29Mar2019.micelle.g++.4

@@ -0,0 +1,218 @@
+LAMMPS (29 Mar 2019)
+  using 1 OpenMP thread(s) per MPI task
+# 2d micelle simulation
+
+dimension	2
+
+neighbor	0.3 bin
+neigh_modify	delay 5
+
+atom_style	bond
+
+# Soft potential push-off
+
+read_data	data.micelle
+  orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1)
+  2 by 2 by 1 MPI processor grid
+  reading atoms ...
+  1200 atoms
+  scanning bonds ...
+  1 = max bonds/atom
+  reading bonds ...
+  300 bonds
+  2 = max # of 1-2 neighbors
+  1 = max # of 1-3 neighbors
+  1 = max # of 1-4 neighbors
+  2 = max # of special neighbors
+  special bonds CPU = 0.000413656 secs
+  read_data CPU = 0.00487924 secs
+special_bonds	fene
+  2 = max # of 1-2 neighbors
+  2 = max # of special neighbors
+  special bonds CPU = 0.000178576 secs
+
+pair_style	soft 1.12246
+pair_coeff	* * 0.0 1.12246
+
+bond_style 	harmonic
+bond_coeff	1 50.0 0.75
+
+velocity	all create 0.45 2349852
+
+variable	prefactor equal ramp(1.0,20.0)
+
+fix		1 all nve
+fix		2 all temp/rescale 100 0.45 0.45 0.02 1.0
+fix		3 all adapt 1 pair soft a * * v_prefactor
+fix		4 all enforce2d
+
+thermo		50
+run		1000
+Neighbor list info ...
+  update every 1 steps, delay 5 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 1.42246
+  ghost atom cutoff = 1.42246
+  binsize = 0.71123, bins = 51 51 1
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair soft, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/2d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.758 | 3.85 | 4.126 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0         0.45   0.40003481 2.2200223e-06   0.84966203   0.78952518 
+      50   0.47411013   0.67721272  0.057404514    1.2083323    1.3375852 
+     100         0.45   0.73046745  0.054836584     1.234929    2.3196516 
+     150   0.67521742   0.72402001  0.043490075    1.4421648    2.8744416 
+     200         0.45   0.78481891  0.076931503    1.3113754    3.0412388 
+     250   0.66479018   0.69790602  0.081075564    1.4432178    3.6917024 
+     300         0.45   0.76820218  0.066727591    1.2845548    3.7861054 
+     350   0.67619136     0.625715  0.072722727    1.3740656    4.2861621 
+     400         0.45   0.68527759  0.090724527    1.2256271    4.4725214 
+     450   0.56702844   0.64402767  0.080555563    1.2911391    4.7402211 
+     500         0.45   0.64883009  0.078376672    1.1768318    4.7919294 
+     550     0.564664   0.58260368  0.080779475    1.2275766    4.9855705 
+     600         0.45   0.58193041  0.088386617     1.119942     5.131481 
+     650   0.52110993    0.5415273  0.097683746    1.1598867    5.2500294 
+     700         0.45   0.50856787  0.088471208    1.0466641    5.2550165 
+     750   0.51510855   0.47441291  0.089429375    1.0785216     5.375763 
+     800         0.45   0.49926696  0.085958476    1.0348504    5.4665914 
+     850   0.50688494   0.46614429  0.088962292    1.0615691     5.556932 
+     900         0.45   0.47785593   0.10150857    1.0289895    5.7765975 
+     950   0.49590559   0.46050477  0.096404887     1.052402    5.8649245 
+    1000         0.45   0.47691182   0.08808163    1.0146185    6.0177568 
+Loop time of 0.0906248 on 4 procs for 1000 steps with 1200 atoms
+
+Performance: 4766906.584 tau/day, 11034.506 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    | 0.036572   | 0.039266   | 0.041216   |   1.0 | 43.33
+Bond    | 0.0023205  | 0.0024512  | 0.0025697  |   0.2 |  2.70
+Neigh   | 0.0088909  | 0.0089301  | 0.0089679  |   0.0 |  9.85
+Comm    | 0.022308   | 0.024047   | 0.027175   |   1.3 | 26.53
+Output  | 0.00057411 | 0.00061274 | 0.00071025 |   0.0 |  0.68
+Modify  | 0.0083182  | 0.0092374  | 0.0098341  |   0.6 | 10.19
+Other   |            | 0.006081   |            |       |  6.71
+
+Nlocal:    300 ave 305 max 292 min
+Histogram: 1 0 0 0 0 0 1 0 1 1
+Nghost:    100.25 ave 108 max 93 min
+Histogram: 1 0 1 0 0 0 1 0 0 1
+Neighs:    784 ave 815 max 739 min
+Histogram: 1 0 0 0 0 0 1 1 0 1
+
+Total # of neighbors = 3136
+Ave neighs/atom = 2.61333
+Ave special neighs/atom = 0.5
+Neighbor list builds = 92
+Dangerous builds = 0
+
+unfix		3
+
+# Main run
+
+pair_style	lj/cut 2.5
+
+# solvent/head - full-size and long-range
+
+pair_coeff	1 1 1.0 1.0 2.5
+pair_coeff	2 2 1.0 1.0 2.5
+pair_coeff	1 2 1.0 1.0 2.5
+
+# tail/tail - size-averaged and long-range
+
+pair_coeff	3 3 1.0 0.75 2.5
+pair_coeff	4 4 1.0 0.50 2.5
+pair_coeff	3 4 1.0 0.67 2.5
+
+# solvent/tail - full-size and repulsive
+
+pair_coeff	1 3 1.0 1.0 1.12246
+pair_coeff	1 4 1.0 1.0 1.12246
+
+# head/tail - size-averaged and repulsive
+
+pair_coeff	2 3 1.0 0.88 1.12246
+pair_coeff	2 4 1.0 0.75 1.12246
+
+thermo		50
+
+#dump		1 all atom 2000 dump.micelle
+
+#dump		2 all image 2000 image.*.jpg type type zoom 1.6
+#dump_modify	2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
+
+#dump		3 all movie 2000 movie.mpg type type zoom 1.6
+#dump_modify	3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
+
+reset_timestep	0
+run		1000
+Neighbor list info ...
+  update every 1 steps, delay 5 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2.8
+  ghost atom cutoff = 2.8
+  binsize = 1.4, bins = 26 26 1
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/2d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 4.001 | 4.032 | 4.124 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0         0.45   -1.7056163   0.08808163   -1.1679097    3.9431686 
+      50   0.59734982   -1.8103783  0.076066922   -1.1374593    3.2770557 
+     100         0.45   -1.8347112  0.093132329   -1.2919539     3.024661 
+     150   0.51924311   -1.8943977  0.076004124   -1.2995832    2.5570373 
+     200         0.45   -1.8918672  0.082422107   -1.3598201    2.5629655 
+     250   0.50281134    -1.920406  0.074011331   -1.3440023    2.3518682 
+     300         0.45   -1.9351047  0.075337265   -1.4101424    2.3249947 
+     350   0.47650026   -1.9313687  0.072115117   -1.3831504    2.1987532 
+     400         0.45   -1.9554318  0.081603939   -1.4242028    2.0787066 
+     450   0.47220236   -1.9468502  0.065625625   -1.4094157    2.0984288 
+     500    0.4684673   -1.9444333  0.076696285   -1.3996601    2.0528682 
+     550   0.47683128    -1.958676  0.070589721   -1.4116523    2.0856023 
+     600   0.46851245   -1.9338267  0.070605469   -1.3950992      2.26405 
+     650   0.46874143   -1.9462493  0.069134686   -1.4087638    2.1070262 
+     700    0.4643739   -1.9309953  0.071977511   -1.3950309     2.225692 
+     750   0.47326259   -1.9484258  0.075435808   -1.4001218    2.0880235 
+     800         0.45   -1.9646003   0.06415956   -1.4508158    2.0612703 
+     850   0.46748278   -1.9705588   0.06038513   -1.4430804    1.9472884 
+     900   0.46909438   -1.9537221  0.062470305   -1.4225483    2.0223008 
+     950   0.45631508   -1.9387742  0.067536066   -1.4153033     2.063854 
+    1000         0.45   -1.9727651  0.058608085    -1.464532    1.9982447 
+Loop time of 0.0878521 on 4 procs for 1000 steps with 1200 atoms
+
+Performance: 4917357.613 tau/day, 11382.772 timesteps/s
+99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.043517   | 0.044455   | 0.046903   |   0.7 | 50.60
+Bond    | 0.0020199  | 0.0022303  | 0.0024347  |   0.4 |  2.54
+Neigh   | 0.012207   | 0.012335   | 0.012512   |   0.1 | 14.04
+Comm    | 0.014938   | 0.018265   | 0.020068   |   1.5 | 20.79
+Output  | 0.00061369 | 0.00064814 | 0.00073504 |   0.0 |  0.74
+Modify  | 0.0052264  | 0.0053691  | 0.0055039  |   0.2 |  6.11
+Other   |            | 0.00455    |            |       |  5.18
+
+Nlocal:    300 ave 305 max 296 min
+Histogram: 1 1 0 0 0 0 1 0 0 1
+Nghost:    219.5 ave 228 max 214 min
+Histogram: 1 0 1 1 0 0 0 0 0 1
+Neighs:    2146.5 ave 2201 max 2114 min
+Histogram: 1 1 0 1 0 0 0 0 0 1
+
+Total # of neighbors = 8586
+Ave neighs/atom = 7.155
+Ave special neighs/atom = 0.5
+Neighbor list builds = 86
+Dangerous builds = 0
+Total wall time: 0:00:00

lib/gpu/lal_device.cpp

@@ -237,7 +237,7 @@ int DeviceT::set_ocl_params(char *ocl_vendor) {
                         " -DBLOCK_CELL_ID="+params[11]+
                         " -DMAX_BIO_SHARED_TYPES="+params[12];
   }
-  _ocl_compile_string="-cl-fast-relaxed-math -cl-mad-enable "+std::string(OCL_INT_TYPE)+" "+
+  _ocl_compile_string="-cl-std=CL1.2 -cl-fast-relaxed-math -cl-mad-enable "+std::string(OCL_INT_TYPE)+" "+
                       std::string(OCL_PRECISION_COMPILE)+" "+_ocl_vendor_string;
   #endif
   return 0;

lib/kim/Install.py

@@ -18,7 +18,7 @@ parser = ArgumentParser(prog='Install.py',
 # settings
 
 thisdir = fullpath('.')
-version = "kim-api-v2-2.0.1"
+version = "kim-api-2.0.2"
 
 # help message
 
@@ -40,10 +40,10 @@ make lib-kim args="-b -a everything"   # install KIM API lib with all models
 make lib-kim args="-n -a EAM_Dynamo_Ackland_2003_W__MO_141627196590_005"    # only add one model or model driver
 
 See the list of KIM model drivers here:
-https://openkim.org/kim-items/model-drivers/alphabetical
+https://openkim.org/browse/model-drivers/alphabetical
 
 See the list of all KIM models here:
-https://openkim.org/kim-items/models/by-model-drivers
+https://openkim.org/browse/models/by-model-drivers
 """
 
 pgroup = parser.add_mutually_exclusive_group()
@@ -154,7 +154,7 @@ if buildflag:
   # add all OpenKIM models, if desired
   if everythingflag:
     print("Adding all OpenKIM models, this will take a while ...")
-    cmd = '%s/bin/kim-api-v2-collections-management install system OpenKIM' % (kimdir)
+    cmd = '%s/bin/kim-api-collections-management install system OpenKIM' % (kimdir)
     txt = subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True)
     if verboseflag:
       print(txt.decode("UTF-8"))
@@ -171,7 +171,7 @@ if addflag:
     sys.exit("\nkim-api is not installed")
 
   # download single model
-  cmd = '%s/bin/kim-api-v2-collections-management install system %s' % (kimdir.decode("UTF-8"), addmodelname)
+  cmd = '%s/bin/kim-api-collections-management install system %s' % (kimdir.decode("UTF-8"), addmodelname)
   txt = subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True)
   if verboseflag:
     print(txt.decode("UTF-8"))

lib/kim/Makefile.lammps

@@ -17,13 +17,18 @@
 ifeq ($(strip $(shell pkg-config --version)),)
   $(error 'pkg-config' not found, but is required to configure the KIM API)
 endif
-
 kim_PREFIX  := $(shell cat ../../lib/kim/kim-prefix.txt 2> /dev/null)
 kim_PREFIX  := $(if $(kim_PREFIX),$(kim_PREFIX)/lib/pkgconfig,)
 kim_PREFIX  := $(if $(shell printf -- "$${PKG_CONFIG_PATH}"),$(kim_PREFIX):$(shell printf -- "$${PKG_CONFIG_PATH}"),$(kim_PREFIX))
 
-kim_SYSINC  := $(shell export PKG_CONFIG_PATH="$(kim_PREFIX)"; pkg-config --cflags libkim-api-v2 2> /dev/null)
+# there is no usable libcurl installation
-kim_SYSLIB  := $(shell export PKG_CONFIG_PATH="$(kim_PREFIX)"; pkg-config --libs   libkim-api-v2 2> /dev/null)
+ifeq ($(shell curl-config --version 2> /dev/null),)
+kim_SYSINC  := $(shell export PKG_CONFIG_PATH="$(kim_PREFIX)"; pkg-config --cflags libkim-api 2> /dev/null)
+kim_SYSLIB  := $(shell export PKG_CONFIG_PATH="$(kim_PREFIX)"; pkg-config --libs   libkim-api 2> /dev/null)
+else
+kim_SYSINC  := $(shell export PKG_CONFIG_PATH="$(kim_PREFIX)"; pkg-config --cflags libkim-api 2> /dev/null) $(shell curl-config --cflags) -DLMP_KIM_CURL
+kim_SYSLIB  := $(shell export PKG_CONFIG_PATH="$(kim_PREFIX)"; pkg-config --libs   libkim-api 2> /dev/null) $(shell curl-config --libs)
+endif
 
 ifeq ($(strip $(kim_SYSINC)),)
   $(error 'pkg-config' could not find an installed KIM API library.)