Merge pull request #1423 from akohlmey/next-patch-release

Step version string for next patch release

cmake/CMakeLists.txt

@@ -320,10 +320,15 @@ pkg_depends(USER-LB MPI)
 pkg_depends(USER-PHONON KSPACE)
 pkg_depends(USER-SCAFACOS MPI)
 
+include(CheckIncludeFileCXX)
 find_package(OpenMP QUIET)
 option(BUILD_OMP "Build with OpenMP support" ${OpenMP_FOUND})
-if(BUILD_OMP OR PKG_KOKKOS OR PKG_USER-INTEL)
+if(BUILD_OMP)
   find_package(OpenMP REQUIRED)
+  check_include_file_cxx(omp.h HAVE_OMP_H_INCLUDE)
+  if(NOT HAVE_OMP_H_INCLUDE)
+    message(FATAL_ERROR "Cannot find required 'omp.h' header file")
+  endif()
   set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")
   set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
 endif()
@@ -367,7 +372,7 @@ if(PKG_KSPACE)
   endif()
 endif()
 
-if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE)
+if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-PLUMED OR PKG_USER-QUIP OR PKG_LATTE)
   find_package(LAPACK)
   find_package(BLAS)
   if(NOT LAPACK_FOUND OR NOT BLAS_FOUND)
@@ -443,7 +448,13 @@ endif()
 
 
 if(PKG_VORONOI)
-  option(DOWNLOAD_VORO "Download and compile the Voro++ library instead of using an already installed one" OFF)
+  find_package(VORO)
+  if(VORO_FOUND)
+    set(DOWNLOAD_VORO_DEFAULT OFF)
+  else()
+    set(DOWNLOAD_VORO_DEFAULT ON)
+  endif()
+  option(DOWNLOAD_VORO "Download and compile the Voro++ library instead of using an already installed one" ${DOWNLOAD_VORO_DEFAULT})
   if(DOWNLOAD_VORO)
     message(STATUS "Voro++ download requested - we will build our own")
     include(ExternalProject)
@@ -476,7 +487,13 @@ if(PKG_VORONOI)
 endif()
 
 if(PKG_LATTE)
-  option(DOWNLOAD_LATTE "Download the LATTE library instead of using an already installed one" OFF)
+  find_package(LATTE)
+  if(LATTE_FOUND)
+    set(DOWNLOAD_LATTE_DEFAULT OFF)
+  else()
+    set(DOWNLOAD_LATTE_DEFAULT ON)
+  endif()
+  option(DOWNLOAD_LATTE "Download the LATTE library instead of using an already installed one" ${DOWNLOAD_LATTE_DEFAULT})
   if(DOWNLOAD_LATTE)
     if (CMAKE_VERSION VERSION_LESS "3.7") # due to SOURCE_SUBDIR
       message(FATAL_ERROR "For downlading LATTE you need at least cmake-3.7")
@@ -487,7 +504,7 @@ if(PKG_LATTE)
       URL https://github.com/lanl/LATTE/archive/v1.2.1.tar.gz
       URL_MD5 85ac414fdada2d04619c8f936344df14
       SOURCE_SUBDIR cmake
-      CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR> ${CMAKE_REQUEST_PIC}
+      CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR> ${CMAKE_REQUEST_PIC} -DBLAS_LIBRARIES=${BLAS_LIBRARIES} -DLAPACK_LIBRARIES=${LAPACK_LIBRARIES}
     )
     ExternalProject_get_property(latte_build INSTALL_DIR)
     set(LATTE_LIBRARIES ${INSTALL_DIR}/${CMAKE_INSTALL_LIBDIR}/liblatte.a)
@@ -503,7 +520,15 @@ endif()
 
 if(PKG_USER-SCAFACOS)
   find_package(GSL REQUIRED)
-  option(DOWNLOAD_SCAFACOS "Download ScaFaCoS library instead of using an already installed one" OFF)
+  find_package(PkgConfig QUIET)
+  set(DOWNLOAD_SCAFACOS_DEFAULT ON)
+  if(PKG_CONFIG_FOUND)
+    pkg_check_modules(SCAFACOS QUIET scafacos)
+    if(SCAFACOS_FOUND)
+      set(DOWNLOAD_SCAFACOS_DEFAULT OFF)
+    endif()
+  endif()
+  option(DOWNLOAD_SCAFACOS "Download ScaFaCoS library instead of using an already installed one" ${DOWNLOAD_SCAFACOS_DEFAULT})
   if(DOWNLOAD_SCAFACOS)
     message(STATUS "ScaFaCoS download requested - we will build our own")
     include(ExternalProject)
@@ -543,8 +568,8 @@ if(PKG_USER-SCAFACOS)
     list(APPEND LAMMPS_LINK_LIBS ${MPI_Fortran_LIBRARIES})
     list(APPEND LAMMPS_LINK_LIBS ${MPI_C_LIBRARIES})
   else()
-    FIND_PACKAGE(PkgConfig REQUIRED)
-    PKG_CHECK_MODULES(SCAFACOS scafacos REQUIRED)
+    find_package(PkgConfig REQUIRED)
+    pkg_check_modules(SCAFACOS REQUIRED scafacos)
     list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_LDFLAGS})
   endif()
   include_directories(${SCAFACOS_INCLUDE_DIRS})
@@ -558,29 +583,53 @@ if(PKG_USER-PLUMED)
   validate_option(PLUMED_MODE PLUMED_MODE_VALUES)
   string(TOUPPER ${PLUMED_MODE} PLUMED_MODE)
 
-  option(DOWNLOAD_PLUMED "Download Plumed package instead of using an already installed one" OFF)
+  find_package(PkgConfig QUIET)
+  set(DOWNLOAD_PLUMED_DEFAULT ON)
+  if(PKG_CONFIG_FOUND)
+    pkg_check_modules(PLUMED QUIET plumed)
+    if(PLUMED_FOUND)
+      set(DOWNLOAD_PLUMED_DEFAULT OFF)
+    endif()
+  endif()
+
+  option(DOWNLOAD_PLUMED "Download Plumed package instead of using an already installed one" ${DOWNLOAD_PLUMED_DEFAULT})
   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
-      URL https://github.com/plumed/plumed2/releases/download/v2.4.4/plumed-src-2.4.4.tgz
-      URL_MD5 71ed465bdc7c2059e282dbda8d564e71
+      URL https://github.com/plumed/plumed2/releases/download/v2.5.1/plumed-src-2.5.1.tgz
+      URL_MD5 c2a7b519e32197a120cdf47e0f194f81
       BUILD_IN_SOURCE 1
       CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR>
                                                ${CONFIGURE_REQUEST_PIC}
-                                                --enable-modules=all
-                                               CXX=${CMAKE_MPI_CXX_COMPILER}
-                                               CC=${CMAKE_MPI_C_COMPILER}
+                                               --enable-modules=all
+                                               ${PLUMED_CONFIG_MPI}
+                                               ${PLUMED_CONFIG_OMP}
+                                               CXX=${PLUMED_CONFIG_CXX}
+                                               CC=${PLUMED_CONFIG_CC}
     )
     ExternalProject_get_property(plumed_build INSTALL_DIR)
     set(PLUMED_INSTALL_DIR ${INSTALL_DIR})
     list(APPEND LAMMPS_DEPS plumed_build)
     if(PLUMED_MODE STREQUAL "STATIC")
       add_definitions(-D__PLUMED_WRAPPER_CXX=1)
-      list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/plumed/obj/kernel.o
-        "${PLUMED_INSTALL_DIR}/lib/plumed/obj/PlumedStatic.o" ${GSL_LIBRARIES} ${CMAKE_DL_LIBS})
+      list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/libplumed.a ${GSL_LIBRARIES} ${LAPACK_LIBRARIES} ${CMAKE_DL_LIBS})
     elseif(PLUMED_MODE STREQUAL "SHARED")
-      list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/libplumed.so ${CMAKE_DL_LIBS})
+      list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/libplumed.so ${PLUMED_INSTALL_DIR}/lib/libplumedKernel.so ${CMAKE_DL_LIBS})
     elseif(PLUMED_MODE STREQUAL "RUNTIME")
       add_definitions(-D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_DEFAULT_KERNEL=${PLUMED_INSTALL_DIR}/lib/libplumedKernel.so)
       list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/libplumedWrapper.a -rdynamic ${CMAKE_DL_LIBS})
@@ -588,7 +637,7 @@ if(PKG_USER-PLUMED)
     set(PLUMED_INCLUDE_DIRS "${PLUMED_INSTALL_DIR}/include")
   else()
     find_package(PkgConfig REQUIRED)
-    pkg_check_modules(PLUMED plumed REQUIRED)
+    pkg_check_modules(PLUMED REQUIRED plumed)
     if(PLUMED_MODE STREQUAL "STATIC")
       add_definitions(-D__PLUMED_WRAPPER_CXX=1)
       include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.static)
@@ -607,7 +656,10 @@ if(PKG_USER-MOLFILE)
   set(MOLFILE_INCLUDE_DIRS "${LAMMPS_LIB_SOURCE_DIR}/molfile" CACHE STRING "Path to VMD molfile plugin headers")
   add_library(molfile INTERFACE)
   target_include_directories(molfile INTERFACE ${MOLFILE_INCLUDE_DIRS})
-  target_link_libraries(molfile INTERFACE ${CMAKE_DL_LIBS})
+  # 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()
 
@@ -619,7 +671,13 @@ if(PKG_USER-NETCDF)
 endif()
 
 if(PKG_USER-SMD)
-  option(DOWNLOAD_EIGEN3 "Download Eigen3 instead of using an already installed one)" OFF)
+  find_package(Eigen3 NO_MODULE)
+  if(EIGEN3_FOUND)
+    set(DOWNLOAD_EIGEN3_DEFAULT OFF)
+  else()
+    set(DOWNLOAD_EIGEN3_DEFAULT ON)
+  endif()
+  option(DOWNLOAD_EIGEN3 "Download Eigen3 instead of using an already installed one)" ${DOWNLOAD_EIGEN3_DEFAULT})
   if(DOWNLOAD_EIGEN3)
     message(STATUS "Eigen3 download requested - we will build our own")
     include(ExternalProject)
@@ -667,7 +725,13 @@ if(PKG_KIM)
     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)
+  find_package(KIM-API QUIET)
+  if(KIM-API_FOUND)
+    set(DOWNLOAD_KIM_DEFAULT OFF)
+  else()
+    set(DOWNLOAD_KIM_DEFAULT ON)
+  endif()
+  option(DOWNLOAD_KIM "Download KIM-API from OpenKIM instead of using an already installed one" ${DOWNLOAD_KIM_DEFAULT})
   if(DOWNLOAD_KIM)
     message(STATUS "KIM-API download requested - we will build our own")
     enable_language(C)
@@ -688,10 +752,7 @@ if(PKG_KIM)
     set(KIM-API_LDFLAGS ${INSTALL_DIR}/${CMAKE_INSTALL_LIBDIR}/libkim-api${CMAKE_SHARED_LIBRARY_SUFFIX})
     list(APPEND LAMMPS_DEPS kim_build)
   else()
-    find_package(KIM-API)
-    if(NOT KIM-API_FOUND)
-      message(FATAL_ERROR "KIM-API not found, help CMake to find it by setting PKG_CONFIG_PATH, or set DOWNLOAD_KIM=ON to download it")
-    endif()
+    find_package(KIM-API REQUIRED)
   endif()
   list(APPEND LAMMPS_LINK_LIBS "${KIM-API_LDFLAGS}")
   include_directories(${KIM-API_INCLUDE_DIRS})
@@ -709,6 +770,7 @@ 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()
 
@@ -728,7 +790,13 @@ endif()
 
 if(PKG_MSCG)
   find_package(GSL REQUIRED)
-  option(DOWNLOAD_MSCG "Download MSCG library instead of using an already installed one)" OFF)
+  find_package(MSCG QUIET)
+  if(MSGC_FOUND)
+    set(DOWNLOAD_MSCG_DEFAULT OFF)
+  else()
+    set(DOWNLOAD_MSCG_DEFAULT ON)
+  endif()
+  option(DOWNLOAD_MSCG "Download MSCG library instead of using an already installed one)" ${DOWNLOAD_MSCG_DEFAULT})
   if(DOWNLOAD_MSCG)
     if (CMAKE_VERSION VERSION_LESS "3.7") # due to SOURCE_SUBDIR
       message(FATAL_ERROR "For downlading MSCG you need at least cmake-3.7")
@@ -777,7 +845,6 @@ endif()
 ########################################################################
 # Basic system tests (standard libraries, headers, functions, types)   #
 ########################################################################
-include(CheckIncludeFileCXX)
 foreach(HEADER cmath)
   check_include_file_cxx(${HEADER} FOUND_${HEADER})
   if(NOT FOUND_${HEADER})
@@ -944,7 +1011,7 @@ 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)
 
@@ -1057,37 +1124,79 @@ if(PKG_OPT)
 endif()
 
 if(PKG_USER-INTEL)
-    find_package(TBB REQUIRED)
-    find_package(MKL REQUIRED)
+  if(LAMMPS_SIZES STREQUAL BIGBIG)
+    message(FATAL_ERROR "The USER-INTEL Package is not compatible with -DLAMMPS_BIGBIG")
+  endif()
+  add_definitions(-DLMP_USER_INTEL)
 
-    if(NOT CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
-      message(FATAL_ERROR "USER-INTEL is only useful together with intel compiler")
-    endif()
+  set(INTEL_ARCH "cpu" CACHE STRING "Architectures used by USER-INTEL (cpu or knl)")
+  set(INTEL_ARCH_VALUES cpu knl)
+  set_property(CACHE INTEL_ARCH PROPERTY STRINGS ${INTEL_ARCH_VALUES})
+  validate_option(INTEL_ARCH INTEL_ARCH_VALUES)
+  string(TOUPPER ${INTEL_ARCH} INTEL_ARCH)
 
-    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()
-
-    set(INTEL_ARCH "cpu" CACHE STRING "Architectures used by USER-INTEL (cpu or knl)")
-    set(INTEL_ARCH_VALUES cpu knl)
-    set_property(CACHE INTEL_ARCH PROPERTY STRINGS ${INTEL_ARCH_VALUES})
-    validate_option(INTEL_ARCH INTEL_ARCH_VALUES)
-    string(TOUPPER ${INTEL_ARCH} INTEL_ARCH)
-
-    if(INTEL_ARCH STREQUAL "KNL")
-      set(CMAKE_EXE_LINKER_FLAGS  "${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)
+  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()
@@ -1100,33 +1209,33 @@ 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
+  set(USER-INTEL_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/USER-INTEL)
+  set(USER-INTEL_SOURCES ${USER-INTEL_SOURCES_DIR}/fix_intel.cpp
+                         ${USER-INTEL_SOURCES_DIR}/fix_nh_intel.cpp
+                         ${USER-INTEL_SOURCES_DIR}/intel_buffers.cpp
+                         ${USER-INTEL_SOURCES_DIR}/nbin_intel.cpp
+                         ${USER-INTEL_SOURCES_DIR}/npair_intel.cpp
+                         ${USER-INTEL_SOURCES_DIR}/verlet_lrt_intel.cpp)
 
-    list(APPEND LAMMPS_LINK_LIBS ${TBB_MALLOC_LIBRARIES} ${MKL_LIBRARIES})
+  set_property(GLOBAL PROPERTY "USER-INTEL_SOURCES" "${USER-INTEL_SOURCES}")
 
-    set(USER-INTEL_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/USER-INTEL)
-    set(USER-INTEL_SOURCES ${USER-INTEL_SOURCES_DIR}/intel_preprocess.h
-                           ${USER-INTEL_SOURCES_DIR}/intel_buffers.h
-                           ${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
-                           ${USER-INTEL_SOURCES_DIR}/intel_intrinsics.h)
+  # detect styles which have a USER-INTEL version
+  RegisterStylesExt(${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)
 
-    set_property(GLOBAL PROPERTY "USER-INTEL_SOURCES" "${USER-INTEL_SOURCES}")
+  get_property(USER-INTEL_SOURCES GLOBAL PROPERTY USER-INTEL_SOURCES)
 
-    # detects styles which have USER-INTEL version
-    RegisterStylesExt(${USER-INTEL_SOURCES_DIR} opt USER-INTEL_SOURCES)
-
-    get_property(USER-INTEL_SOURCES GLOBAL PROPERTY USER-INTEL_SOURCES)
-
-    list(APPEND LIB_SOURCES ${USER-INTEL_SOURCES})
-    include_directories(${USER-INTEL_SOURCES_DIR})
+  list(APPEND LIB_SOURCES ${USER-INTEL_SOURCES})
+  include_directories(${USER-INTEL_SOURCES_DIR})
 endif()
 
 if(PKG_GPU)
@@ -1261,7 +1370,15 @@ if(PKG_GPU)
       set(OCL_COMMON_HEADERS ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_preprocessor.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_aux_fun1.h)
 
       file(GLOB GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu)
-      list(REMOVE_ITEM GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne.cu ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne_lj.cu)
+      list(REMOVE_ITEM GPU_LIB_CU
+        ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne.cu
+        ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne_lj.cu
+        ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_re_squared.cu
+        ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_re_squared_lj.cu
+        ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff.cu
+        ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_zbl.cu
+        ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_mod.cu
+      )
 
       foreach(GPU_KERNEL ${GPU_LIB_CU})
           get_filename_component(basename ${GPU_KERNEL} NAME_WE)
@@ -1272,7 +1389,21 @@ if(PKG_GPU)
 
       GenerateOpenCLHeader(gayberne ${CMAKE_CURRENT_BINARY_DIR}/gpu/gayberne_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_ellipsoid_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne.cu)
       GenerateOpenCLHeader(gayberne_lj ${CMAKE_CURRENT_BINARY_DIR}/gpu/gayberne_lj_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_ellipsoid_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne_lj.cu)
-      list(APPEND GPU_LIB_SOURCES ${CMAKE_CURRENT_BINARY_DIR}/gpu/gayberne_cl.h ${CMAKE_CURRENT_BINARY_DIR}/gpu/gayberne_lj_cl.h)
+      GenerateOpenCLHeader(re_squared ${CMAKE_CURRENT_BINARY_DIR}/gpu/re_squared_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_ellipsoid_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_re_squared.cu)
+      GenerateOpenCLHeader(re_squared_lj ${CMAKE_CURRENT_BINARY_DIR}/gpu/re_squared_lj_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_ellipsoid_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_re_squared_lj.cu)
+      GenerateOpenCLHeader(tersoff ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff.cu)
+      GenerateOpenCLHeader(tersoff_zbl ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_zbl_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_zbl_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_zbl.cu)
+      GenerateOpenCLHeader(tersoff_mod ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_mod_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_mod_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_mod.cu)
+
+      list(APPEND GPU_LIB_SOURCES
+        ${CMAKE_CURRENT_BINARY_DIR}/gpu/gayberne_cl.h
+        ${CMAKE_CURRENT_BINARY_DIR}/gpu/gayberne_lj_cl.h
+        ${CMAKE_CURRENT_BINARY_DIR}/gpu/re_squared_cl.h
+        ${CMAKE_CURRENT_BINARY_DIR}/gpu/re_squared_lj_cl.h
+        ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_cl.h
+        ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_zbl_cl.h
+        ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_mod_cl.h
+      )
 
       add_library(gpu STATIC ${GPU_LIB_SOURCES})
       target_link_libraries(gpu ${OpenCL_LIBRARIES})
@@ -1385,9 +1516,19 @@ if(BUILD_EXE)
   if(ENABLE_TESTING)
     add_test(ShowHelp ${LAMMPS_BINARY} -help)
   endif()
+
+  enable_language(C)
+  get_filename_component(MSI2LMP_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../tools/msi2lmp/src ABSOLUTE)
+  file(GLOB MSI2LMP_SOURCES ${MSI2LMP_SOURCE_DIR}/[^.]*.c)
+  add_executable(msi2lmp ${MSI2LMP_SOURCES})
+  target_link_libraries(msi2lmp m)
+  install(TARGETS msi2lmp DESTINATION ${CMAKE_INSTALL_BINDIR})
+  install(FILES ${LAMMPS_DOC_DIR}/msi2lmp.1 DESTINATION ${CMAKE_INSTALL_MANDIR}/man1)
+
 endif()
 
 
+
 ###############################################################################
 # Build documentation
 ###############################################################################
@@ -1449,11 +1590,14 @@ if(BUILD_DOC)
 endif()
 
 ###############################################################################
-# Install potential files in data directory
+# Install potential and force field files in data directory
 ###############################################################################
 set(LAMMPS_POTENTIALS_DIR ${CMAKE_INSTALL_FULL_DATADIR}/lammps/potentials)
 install(DIRECTORY ${LAMMPS_SOURCE_DIR}/../potentials/ DESTINATION ${LAMMPS_POTENTIALS_DIR})
 
+set(LAMMPS_FRC_FILES_DIR ${CMAKE_INSTALL_FULL_DATADIR}/lammps/frc_files)
+install(DIRECTORY ${LAMMPS_SOURCE_DIR}/../tools/msi2lmp/frc_files/ DESTINATION ${LAMMPS_FRC_FILES_DIR})
+
 configure_file(etc/profile.d/lammps.sh.in ${CMAKE_BINARY_DIR}/etc/profile.d/lammps.sh @ONLY)
 configure_file(etc/profile.d/lammps.csh.in ${CMAKE_BINARY_DIR}/etc/profile.d/lammps.csh @ONLY)
 install(

cmake/Modules/FindKIM-API.cmake

@@ -36,14 +36,23 @@
 # KIM-API-CMAKE_CXX_COMPILER
 # KIM-API-CMAKE_Fortran_COMPILER
 #
-find_package(PkgConfig REQUIRED)
+
+if(KIM-API_FIND_QUIETLY)
+  set(REQ_OR_QUI "QUIET")
+else()
+  set(REQ_OR_QUI "REQUIRED")
+endif()
+
+find_package(PkgConfig ${REQ_OR_QUI})
 include(FindPackageHandleStandardArgs)
 
-pkg_check_modules(KIM-API REQUIRED libkim-api>=2.0)
+pkg_check_modules(KIM-API ${REQ_OR_QUI} libkim-api>=2.0)
 
-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 CMAKE_CXX_COMPILER)
-pkg_get_variable(KIM-API-V2_CMAKE_Fortran_COMPILER libkim-api CMAKE_Fortran_COMPILER)
+if(KIM-API_FOUND)
+  pkg_get_variable(KIM-API-CMAKE_C_COMPILER libkim-api CMAKE_C_COMPILER)
+  pkg_get_variable(KIM-API-CMAKE_CXX_COMPILER libkim-api CMAKE_CXX_COMPILER)
+  pkg_get_variable(KIM-API_CMAKE_Fortran_COMPILER libkim-api CMAKE_Fortran_COMPILER)
+endif()
 
 # handle the QUIETLY and REQUIRED arguments and set KIM-API_FOUND to TRUE
 # if all listed variables are TRUE

cmake/Modules/OpenCLUtils.cmake

@@ -6,7 +6,7 @@ function(GenerateOpenCLHeader varname outfile files)
     foreach(IDX RANGE 2 ${ARG_END})
         list(GET ARGV ${IDX} filename)
         file(READ ${filename} content)
-        string(REGEX REPLACE "\\s*//[^\n]*\n" "" content "${content}")
+        string(REGEX REPLACE "\\s*//[^\n]*\n" "\n" content "${content}")
         string(REGEX REPLACE "\\\\" "\\\\\\\\" content "${content}")
         string(REGEX REPLACE "\"" "\\\\\"" content "${content}")
         string(REGEX REPLACE "([^\n]+)\n" "\"\\1\\\\n\"\n" content "${content}")

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/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
@@ -209,7 +211,7 @@ cmake -C ../cmake/presets/std_nolib.cmake -D PKG_GPU=on ../cmake
   </td>
 </tr>
 <tr>
-  <td><code><CMAKE_VERBOSE_MAKEFILE/code></td>
+  <td><code>CMAKE_VERBOSE_MAKEFILE</code></td>
   <td>Enable verbose output from Makefile builds (useful for debugging), the same can be achived by adding `VERBOSE=1` to the `make` call.</td>
   <td>
   <dl>
@@ -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>
 

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

@@ -1,2 +1,4 @@
-# set environment for LAMMPS executables to find potential files
+# set environment for LAMMPS and msi2lmp executables
+# to find potential and force field files
 if ( "$?LAMMPS_POTENTIALS" == 0 ) setenv LAMMPS_POTENTIALS @LAMMPS_POTENTIALS_DIR@
+if ( "$?MSI2LMP_LIBRARY" == 0 ) setenv MSI2LMP_LIBRARY @LAMMPS_FRC_FILES_DIR@

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

@@ -1,2 +1,5 @@
-# set environment for LAMMPS executables to find potential files
-export LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS-@LAMMPS_POTENTIALS_DIR@}
+# set environment for LAMMPS and msi2lmp executables
+# to find potential and force field files
+LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS-@LAMMPS_POTENTIALS_DIR@}
+MSI2LMP_LIBRARY=${MSI2LMP_LIBRARY-@LAMMPS_FRC_FILES_DIR@}
+export LAMMPS_POTENTIALS MSI2LMP_LIBRARY

cmake/presets/all_off.cmake

@@ -1,21 +1,17 @@
-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)
+# preset that turns on all existing packages off. can be used to reset
+# an existing package selection without losing any other settings
 
-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})
+set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
+        GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MISC MESSAGE MOLECULE
+        MPIIO MSCG OPT PERI POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN
+        SRD VORONOI
+        USER-ADIOS 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-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP
+        USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH
+        USER-TALLY USER-UEF USER-VTK USER-YAFF)
 
 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
-                      GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MEAM MISC
-                      MOLECULE MPIIO MSCG OPT PERI POEMS
-                      PYTHON QEQ REAX REPLICA RIGID SHOCK SNAP SRD VORONOI)
+# preset that turns on all existing packages. using the combination
+# this preset followed by the nolib.cmake preset should configure a
+# LAMMPS binary, with as many packages included, that can be compiled
+# 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
-                  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})
+set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
+        GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MISC MESSAGE MOLECULE
+        MPIIO MSCG OPT PERI POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN
+        SRD VORONOI
+        USER-ADIOS 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-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP
+        USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH
+        USER-TALLY USER-UEF USER-VTK USER-YAFF)
 
 foreach(PKG ${ALL_PACKAGES})
   set(PKG_${PKG} ON CACHE BOOL "" FORCE)

cmake/presets/clang.cmake

@@ -0,0 +1,17 @@
+# preset that will enable clang/clang++ with support for MPI and OpenMP (on Linux boxes)
+
+set(CMAKE_CXX_COMPILER "clang++" CACHE STRING "" FORCE)
+set(CMAKE_C_COMPILER "clang" CACHE STRING "" FORCE)
+set(CMAKE_CXX_FLAGS "-Wall -Wextra -g -O2 -DNDEBG" CACHE STRING "" FORCE)
+set(MPI_CXX "clang++" CACHE STRING "" FORCE)
+set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
+unset(HAVE_OMP_H_INCLUDE CACHE)
+
+set(OpenMP_C "clang" CACHE STRING "" FORCE)
+set(OpenMP_C_FLAGS "-fopenmp" CACHE STRING "" FORCE)
+set(OpenMP_C_LIB_NAMES "omp" CACHE STRING "" FORCE)
+set(OpenMP_CXX "clang++" CACHE STRING "" FORCE)
+set(OpenMP_CXX_FLAGS "-fopenmp" CACHE STRING "" FORCE)
+set(OpenMP_CXX_LIB_NAMES "omp" CACHE STRING "" FORCE)
+set(OpenMP_omp_LIBRARY "/usr/lib64/libomp.so" CACHE PATH "" 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
-                      GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MEAM MISC
-                      MOLECULE MPIIO MSCG OPT PERI POEMS
-                      PYTHON QEQ REAX REPLICA RIGID SHOCK SNAP SRD VORONOI)
+# preset that turns off all packages that require some form of external
+# library or special compiler (fortran or cuda) or equivalent.
 
-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})
+set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MPIIO MSCG PYTHON
+        VORONOI USER-ADIOS USER-ATC USER-AWPMD USER-H5MD USER-LB
+        USER-MOLFILE USER-NETCDF USER-PLUMED USER-QMMM USER-QUIP
+        USER-SCAFACOS USER-SMD USER-VTK)
 
 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/lammps.1

@@ -1,40 +1,259 @@
-.TH LAMMPS "2018-08-22"
+.TH LAMMPS "30 April 2019" "2019-04-30"
 .SH NAME
 .B LAMMPS
 \- Molecular Dynamics Simulator.
 
 .SH SYNOPSIS
-.B lmp 
--in in.file
+.B lmp
+\-in <input file> [OPTIONS] ...
 
 or
 
-mpirun \-np 2 
-.B lmp 
--in in.file
+mpirun \-np 2
+.B lmp
+<input file> [OPTIONS] ...
+
+or
+
+.B lmp
+\-r2data file.restart file.data
 
 .SH DESCRIPTION
-.B LAMMPS 
-LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale 
-Atomic/Molecular Massively Parallel Simulator. LAMMPS has potentials for soft 
-materials (biomolecules, polymers) and solid-state materials (metals, 
-semiconductors) and coarse-grained or mesoscopic systems. It can be used to 
-model atoms or, more generically, as a parallel particle simulator at the 
+.B LAMMPS
+is a classical molecular dynamics code, and an acronym for \fBL\fRarge-scale
+\fBA\fRtomic/\fBM\fRolecular \fBM\fRassively \fBP\fRarallel \fBS\fRimulator.
+.B LAMMPS
+has potentials for soft
+materials (bio-molecules, polymers) and solid-state materials (metals,
+semiconductors) and coarse-grained or mesoscopic systems. It can be used to
+model atoms or, more generically, as a parallel particle simulator at the
 atomic, meso, or continuum scale.
 
-See http://lammps.sandia.gov/ for documentation.
+See https://lammps.sandia.gov/ for more information and documentation.
+
+.SH EXECUTABLE NAME
+The
+.B LAMMPS
+executable can have different names depending on how it was configured,
+compiled and installed. It will be either
+.B lmp
+or
+.B lmp_<machine name>.
+The <machine name> suffix corresponds to the (machine specific) makefile
+used to compile
+.B LAMMPS
+when using the conventional build process. When building
+.B LAMMPS
+using
+.B CMake
+this <machine name> parameter can be chosen arbitrarily at configuration
+time, but more common is to just use
+.B lmp
+without a suffix. In this manpage we will use
+.B lmp
+to represent any of those names.
 
 .SH OPTIONS
-See https://lammps.sandia.gov/doc/Run_options.html for details on
-command-line options.
 
-.SH COPYRIGHT 
-© 2003--2018 Sandia Corporation
+.TP
+\fB\-h\fR or \fB\-help\fR
+Print a brief help summary and a list of settings and options compiled
+into this executable. It also explicitly lists all LAMMPS styles
+(atom_style, fix, compute, pair_style, bond_style, etc) available in
+the specific executable. This can tell you if the command you want to
+use was included via the appropriate package at compile time.
+LAMMPS will print the info and immediately exit if this switch is used.
+.TP
+\fB\-e\fR or \fB\-echo\fR
+Set the style of command echoing. The style can be
+.B none
+or
+.B screen
+or
+.B log
+or
+.B both.
+Depending on the style, each command read from the input script will
+be echoed to the screen and/or logfile. This can be useful to figure
+out which line of your script is causing an input error.
+The default value is
+.B log.
+.TP
+\fB\-i <input file>\fR or \fB\-in <input file>\fR
+Specify a file to use as an input script. If it is not specified,
+LAMMPS reads its script from standard input. This is a required
+switch when running LAMMPS in multi-partition mode.
+.TP
+\fB\-k on/off [keyword value]\fR or \fB\-kokkos on/off [keyword value]\fR
+Enable or disable general KOKKOS support, as provided by the KOKKOS
+package.  Even if LAMMPS is built with this package, this switch must
+be set to \fBon\fR to enable running with KOKKOS-enabled styles. More
+details on this switch and its optional keyword value pairs are discussed
+at: https://lammps.sandia.gov/doc/Run_options.html
+.TP
+\fB\-l <log file>\fR or \fB\-log <log file>\fR
+Specify a log file for LAMMPS to write status information to.
+The default value is "log.lammps". If the file name "none" is used,
+\fBLAMMPS\fR will not write a log file. In multi-partition mode only
+some high-level all-partition information is written to the "<log file>"
+file, the remainder is written in a per-partition file "<log file>.N"
+with "N" being the respective partition number, unless overridden
+by the \-plog flag (see below).
+.TP
+\fB\-m <number>\fR or \fB\-mpicolor <number>\fR
+If used, this must be the first command-line argument after the
+.B LAMMPS
+executable name. It is only used when
+.B LAMMPS
+is launched by an mpirun command which also launches one or more
+other executable(s) at the same time.
+.B LAMMPS
+and the other executable(s) perform an MPI_Comm_split(), each with
+their own different colors, to split the MPI_COMM_WORLD communicator
+for each executable to the subset of processors they are supposed to
+be actually running on. Currently, this is only used in
+.B LAMMPS
+to perform client/server messaging with another application.
+.B LAMMPS
+can act as either a client or server (or both).
+.TP
+\fB\-nc\fR or \fB\-nocite\fR
+Disable writing the "log.cite" file which is normally written to
+list references for specific cite-able features used during a
+.B LAMMPS
+run.
+.TP
+\fB\-pk <style> [options]\fR or \fB\-package <style> [options]\fR
+Invoke the \fBpackage\R command with <style> and optional arguments.
+The syntax is the same as if the command appeared in an input script.
+For example "-pk gpu 2" is the same as "package gpu 2" in the input
+script. The possible styles and options are discussed in the
+.B LAMMPS
+manual for the "package" command. This switch can be used multiple
+times, e.g. to set options for the USER-INTEL and USER-OMP packages
+when used together. Along with the "-sf" or "-suffix" switch, this
+is a convenient mechanism for invoking accelerator packages and their
+options without having to edit an input script.
+.TP
+\fB\-p\fR or \fB\-partition\fR
+Invoke
+.B LAMMPS
+in multi-partition mode. Without this,
+.B LAMMPS
+uses all P processors allocated via MPI to run a single simulation.
+If this switch is used, the P processors are split into separate
+partitions and each partition runs its own simulation. The arguments
+to the switch specify the number of processors in each partition.
+Arguments of the form "MxN" mean M partitions, each with N processors.
+Arguments of the form "N" mean a single partition with N processors.
+The sum of processors in all partitions must be equal P. Thus the
+command “-partition 8x2 4 5” has 10 partitions and runs on a total
+of 25 processors.  Running with multiple partitions is required for
+multi-replica simulations, where each replica runs on on one or more
+few processors.
+.TP
+\fB\-pl <basename>\fR or \fB\-plog <basename>\fR
+Specify the base name for the per-partition log files in multi-partition
+runs, where partition N writes log information to <basename>.N.
+If basename is set to "none", then no per-partition log files are created.
+This overrides the name specified in the \-log command-line option.
+.TP
+\fB\-ps <basename>\fR or \fB\-pscreen <basename>\fR
+Specify the base name for the per-partition screen files in multi-partition
+runs, where partition N writes screen output to <basename>.N.
+If basename is set to "none", then no per-partition screen files are created.
+The default value is "screen" or whatever is set by the \-screen flag.
+.TP
+\fB\-r2data <restart file> [remap] <data file>\fR or
+\fB\-restart2data <restart file> [remap] <data file>\fR
+Convert <restart file> previously written by
+.B LAMMPS
+into a data file and immediately exit. This option has replaced the
+external restart2data executable. Following <restart file>
+argument, the optional word "remap" may be used. This has the
+same effect like adding it to a "read_restart" command.
+The syntax following the <data file> name is identical to the
+arguments of the "write_data" command. See the
+.B LAMMPS
+manual for details on either of the two commands.
+.TP
+\fB\-r2dump <restart file> [remap] <dump file>\fR or
+\fB\-restart2dump <restart file> [remap] <dump file>\fR
+Convert <restart file> previously written by
+.B LAMMPS
+into a dump file and immediately exit. Following <restart file>
+argument, the optional word "remap" may be used. This has the
+same effect like adding it to a "read_restart" command.
+The syntax following the <dump file> name is identical to the
+arguments of the "dump" command. See the
+.B LAMMPS
+manual for details on either of the two commands.
+.TP
+\fB\-sc <file name>\fR or \fB\-screen <file name>\fR
+Specify a file for
+.B LAMMPS
+to write its screen information to. By default, this will be
+the standard output. If <file name> is "none", (most) screen
+output will be suppressed.  In multi-partition mode only
+some high-level all-partition information is written to the
+screen or "<file name>" file, the remainder is written in a
+per-partition file "screen.N" or "<file name>.N" 
+with "N" being the respective partition number, and unless
+overridden by the \-pscreen flag (see above).
+.TP
+\fB\-sf <suffix>\fR or \fB\-suffix <suffix>\fR
+Use variants of various styles in the input, if they exist. This is
+achieved by transparently trying to convert a style named <my/style>
+into <my/style/suffix> if that latter style exists, but otherwise
+fall back to the former. The most useful suffixes are  "gpu",
+"intel", "kk", "omp", "opt", or "hybrid". These refer to styles from
+optional packages that LAMMPS can be built with. The hybrid suffix is
+special, as it enables, having two suffixes tried (e.g. first "intel"
+and then "omp") and thus requires two arguments. Along with the
+"-package" command-line switch, this is a convenient mechanism for
+invoking styles from accelerator packages and setting their options
+without having to edit an input script.
+
+See https://lammps.sandia.gov/doc/Run_options.html for additional
+details and discussions on command-line options.
+
+.SH LAMMPS BASICS
+LAMMPS executes by reading commands from a input script (text file),
+one line at a time.  When the input script ends, LAMMPS exits.  Each
+command causes LAMMPS to take some action.  It may set or change an
+internal, read and parse a file, or run a simulation.  Most commands
+have default settings, which means you only need to use the command
+if you wish to change the default.
+
+The ordering of commands in an input script is usually not very important
+unless a command like "run" is encountered, which starts some calculation
+using the current internal state. Also, if a "pair_style" or "bond_style"
+other similar style command is issued that has a different name from what
+was previously active, it will replace the previous style and wipe out
+all corresponding "pair_coeff" or "bond_coeff" or equivalent settings.
+Some commands are only valid when they follow other commands.  For
+example you cannot set the temperature of a group of atoms until atoms
+have been defined and a group command is used to define which atoms
+belong to the group of a given name. Sometimes command B will use values
+that can be set by command A. This means command A must precede command
+B in the input to have the desired effect. Some commands must be issued
+.B before
+the simulation box is defined and others can only be issued
+.B after.
+Many input script errors are detected by
+.B LAMMPS
+and an ERROR or WARNING message is printed.  The documentation for
+each command lists restrictions on how the command can be used, and
+the chapter on errors in the
+.B LAMMPS
+manual gives some additional information about error messages, if possible.
+
+.SH COPYRIGHT
+© 2003--2019 Sandia Corporation
 
 This package is free software; you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation; either version 2 of the License, or
-(at your option) any later version.
+it under the terms of the GNU General Public License version 2 as
+published by the Free Software Foundation.
 
 This package is distributed in the hope that it will be useful,
 but WITHOUT ANY WARRANTY; without even the implied warranty of

doc/msi2lmp.1

@@ -0,0 +1,111 @@
+.TH MSI2LMP "v3.9.9" "2018-11-05"
+.SH NAME
+.B MSI2LMP
+\- Converter for Materials Studio files to LAMMPS
+
+.SH SYNOPSIS
+.B msi2lmp
+<ROOTNAME> [-class <I|1|II|2|O|0>] [-frc <path to frc file>] [-print #] [-ignore] [-nocenter] [-oldstyle] [-shift <x> <y> <z>]
+
+.SH DESCRIPTION
+.PP
+.B MSI2LMP
+is a tool bundled with LAMMPS to aide in the conversion of simulation
+inputs from Biovia's Materials Studio software for use with LAMMPS.
+It is a standalone program that generates a LAMMPS data file based on
+the information in an MS .car file (atom coordinates), an .mdf file
+(molecular topology and atom types) and an .frc (forcefield parameters)
+file.  The .car and .mdf files are specific to a molecular system while
+the .frc file is specific to a forcefield (variant).  The only coherency
+needed between .frc and .car/.mdf files are the atom types.
+.PP
+
+.SH OPTIONS
+.TP
+\fB\<ROOTNAME>\fR
+This has to be the first argument and is a
+.B mandatory
+argument. It defines the root of the file names; i.e. for a
+.B <ROOTNAME>
+of benzene, you have to provide the files 'benzene.car' and 'benzene.mdf'
+in the current working directory.
+.B msi2lmp
+will then read and process those files according to its remaining settings.
+All other settins are optional and have defaults as listed.
+.TP
+\fB\-c <I,1,II,2,O,0>\fR, \fB\-class <I,1,II,2,O,0>\fR
+The \-c or \-class option selects the force field class, i.e which pair
+styles and bond styles and so on are required in the LAMMPS input file.
+Class I or class 1 uses similar combination of functional forms as Amber
+and Charmm force field and support the force fields 
+.B cvff
+and
+.B clayff.
+Class II or class 2 corresponds to the more complex force fields
+.B COMPASS
+and
+.B pcff.
+Class O or class 0 finally is an experimental and incomplete extension
+and supports generating output for
+.B OPLS-AA
+.TP
+\fB\-f <ffname>\fR, \fB\-frc <ffname>\fR
+The \-c or \-frc option allows the selection of the force field parameter
+file
+.B<ffname>.frc.
+Valid names for <ffname> with this distribution are: cvff, clayff, cvff_aug,
+pcff, compass_published, cff91, and oplsaa. If the argument is a pathname,
+i.e. it starts with a '.' or a '/', then this absolute path is used to read
+the force field, otherwise
+.B msi2lmp
+will look in the folder pointed to by the environment variable
+$MSI2LMP_LIBRARY. If the variable is not set, then it will look in the current
+directory. The extension '.frc' is appended, if missing.
+Default is to look for the cvff.frc force field file.
+.TP
+\fB\-p <loglevel>\fR, \fB\-print <loglevel>\fR,
+Selects the amount of information messages about the progress of the
+conversion printed to the screen.
+.B <loglevel>
+can be a number from 0 (silent except for errors) to 3 (very detailed).
+.TP
+\fB\-i\fR, \fB\-ignore\fR,
+Ignore errors about missing parameters and use 0.0 for the respective
+force constants making these no-ops. Is correct to be used for a few
+molecules and settings, but often an indication, that either the atom
+type assignment have errors, or the force field file is missing entries.
+.TP
+\fB\-n\fR, \fB\-nocenter\fR,
+Do not center the box around the (geometrical) center of the atoms,
+but around the origin. Default is to recenter.
+.TP
+\fB\-o\fR, \fB\-oldstyle\fR,
+Write out a data file without style hint comments to be compatible
+with old LAMMPS versions. Default is to write out those comments.
+.TP
+\fB-s <x> <y> <z>\fR, \fB-shift <x> <y> <z>\fR,
+Shift the entire system (box and coordinates) by a vector
+(default: 0.0 0.0 0.0).
+.TP
+
+.SH EXAMPLES
+
+msi2lmp benzene -c 2 -p 1 -f ../frc_files/pcff.frc
+
+msi2lmp benzene-class1 -c I
+
+msi2lmp decane -c 0 -f oplsaa
+
+
+.SH COPYRIGHT
+© 2003--2019 Sandia Corporation
+
+This package is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License version 2 as
+published by the Free Software Foundation.
+
+This package is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+

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

@@ -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
-"install the USER-OMP package"_#user-omp, as it can be used in tandem
-with the USER-INTEL package to good effect, as explained on the "Speed
-intel"_Speed_intel.html doc page.
+build for, either x86 CPUs or Intel KNLs in offload mode.  You should
+also typically "install the USER-OMP package"_#user-omp, as it can be
+used in tandem with the USER-INTEL package to good effect, as explained
+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:
 

doc/src/Build_package.txt

@@ -149,26 +149,41 @@ 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_off.cmake \[OPTIONS\] ../cmake | disable all packages
-cmake -C ../cmake/presets/std.cmake \[OPTIONS\] ../cmake | enable standard packages
-cmake -C ../cmake/presets/user.cmake \[OPTIONS\] ../cmake | enable user packages
-cmake -C ../cmake/presets/std_nolib.cmake \[OPTIONS\] ../cmake | enable standard packages that do not require extra libraries
-cmake -C ../cmake/presets/nolib.cmake \[OPTIONS\] ../cmake | disable all packages that do not require extra libraries
-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/all_on.cmake  \[OPTIONS\] ../cmake |
+      enable all packages |
+cmake -C ../cmake/presets/all_off.cmake \[OPTIONS\] ../cmake |
+      disable all packages |
+cmake -C ../cmake/presets/minimal.cmake \[OPTIONS\] ../cmake |
+      enable just a few core packages |
+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/clang.cmake   \[OPTIONS\] ../cmake |
+      change settings to use the Clang compilers by default |
+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
-multiple cmake runs.
+current build directory. You can combine multiple presets and options
+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
-# use libraries and enable GPU package
+# build LAMMPS with most commonly used packages, but then remove
+# 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

@@ -57,10 +57,10 @@ FFT_INC = -DFFT_SINGLE        # do not specify for double precision
 FFT_INC = -DFFT_PACK_ARRAY    # or -DFFT_PACK_POINTER or -DFFT_PACK_MEMCPY :pre
                               # default is FFT_PACK_ARRAY if not specified
 
-FFT_INC =    	-I/usr/local/include
+FFT_INC =       -I/usr/local/include
 FFT_PATH =      -L/usr/local/lib
-FFT_LIB =	-lfftw3             # FFTW3 double precision
-FFT_LIB =	-lfftw3 -lfftw3f    # FFTW3 single precision
+FFT_LIB =       -lfftw3             # FFTW3 double precision
+FFT_LIB =       -lfftw3 -lfftw3f    # FFTW3 single precision
 FFT_LIB =       -lmkl_intel_lp64 -lmkl_sequential -lmkl_core  # MKL with Intel compiler
 FFT_LIB =       -lmkl_gf_lp64 -lmkl_sequential -lmkl_core     # MKL with GNU compier :pre
 
@@ -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
-"bigbig" setting.
+Note that the USER-ATC package and the USER-INTEL package are currently
+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
-for this; you will have to request that makefiles are generated and
-manually set the compiler.
+the old build system is provided. Using CMake for this mode of compilation
+is untested and not likely to work.
 
-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

@@ -83,6 +83,7 @@ An alphabetic list of all general LAMMPS commands.
 "molecule"_molecule.html,
 "ndx2group"_group2ndx.html,
 "neb"_neb.html,
+"neb_spin"_neb_spin.html,
 "neigh_modify"_neigh_modify.html,
 "neighbor"_neighbor.html,
 "newton"_newton.html,

doc/src/Commands_category.txt

@@ -116,6 +116,7 @@ Actions:
 
 "minimize"_minimize.html,
 "neb"_neb.html,
+"neb_spin"_neb_spin.html,
 "prd"_prd.html,
 "rerun"_rerun.html,
 "run"_run.html,

doc/src/Commands_fix.txt

@@ -61,6 +61,7 @@ OPT.
 "edpd/source"_fix_dpd_source.html,
 "efield"_fix_efield.html,
 "ehex"_fix_ehex.html,
+"electron/stopping"_fix_electron_stopping.html,
 "enforce2d (k)"_fix_enforce2d.html,
 "eos/cv"_fix_eos_cv.html,
 "eos/table"_fix_eos_table.html,
@@ -106,6 +107,7 @@ OPT.
 "mvv/edpd"_fix_mvv_dpd.html,
 "mvv/tdpd"_fix_mvv_dpd.html,
 "neb"_fix_neb.html,
+"neb_spin"_fix_neb_spin.html,
 "nph (ko)"_fix_nh.html,
 "nph/asphere (o)"_fix_nph_asphere.html,
 "nph/body"_fix_nph_body.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/neb_spin_angle.tex

@@ -0,0 +1,15 @@
+\documentclass[preview]{standalone}
+\usepackage{varwidth}
+\usepackage[utf8x]{inputenc}
+\usepackage{amsmath, amssymb, graphics, setspace}
+
+\begin{document}
+\begin{varwidth}{50in}
+  \begin{equation}
+    \omega_i^{\nu} = 
+    (\nu - 1) \Delta \omega_i
+    {\rm ~~and~~} \Delta \omega_i = \frac{\omega_i}{Q-1}
+  , \nonumber
+  \end{equation}
+\end{varwidth}
+\end{document}

doc/src/Eqs/neb_spin_k.tex

@@ -0,0 +1,16 @@
+\documentclass[preview]{standalone}
+\usepackage{varwidth}
+\usepackage[utf8x]{inputenc}
+\usepackage{amsmath, amssymb, graphics, setspace}
+
+\begin{document}
+\begin{varwidth}{50in}
+  \begin{equation}
+    \vec{k}_i =  
+    \frac{\vec{m}_i^I \times \vec{m}_i^F}{\left|\vec{m}_i^I 
+    \times \vec{m}_i^F\right|} 
+    %&{\rm ~if~}& \vec{m}_i^I \times \vec{m}_i^F  
+  , \nonumber
+  \end{equation}
+\end{varwidth}
+\end{document}

doc/src/Eqs/neb_spin_rodrigues_formula.tex

@@ -0,0 +1,16 @@
+\documentclass[preview]{standalone}
+\usepackage{varwidth}
+\usepackage[utf8x]{inputenc}
+\usepackage{amsmath, amssymb, graphics, setspace}
+
+\begin{document}
+\begin{varwidth}{50in}
+  \begin{equation}
+    \vec{m}_i^{\nu} = \vec{m}_i^{I} \cos(\omega_i^{\nu})
+    + (\vec{k}_i \times \vec{m}_i^{I}) \sin(\omega_i^{\nu})
+    + (1.0-\cos(\omega_i^{\nu})) \vec{k}_i (\vec{k}_i\cdot
+    \vec{m}_i^{I})
+  , \nonumber
+  \end{equation}
+\end{varwidth}
+\end{document}

doc/src/Howto.txt

@@ -148,7 +148,7 @@ END_RST -->
 
 <!-- HTML_ONLY -->
 
-"CHARMM, AMBER, and DREIDING force fields"_Howto_bioFF.html
+"CHARMM, AMBER, COMPASS, and DREIDING force fields"_Howto_bioFF.html
 "TIP3P water model"_Howto_tip3p.html
 "TIP4P water model"_Howto_tip4p.html
 "SPC water model"_Howto_spc.html :all(b)

doc/src/Howto_bioFF.txt

@@ -7,29 +7,31 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :line
 
-CHARMM, AMBER, and DREIDING force fields :h3
+CHARMM, AMBER, COMPASS, and DREIDING force fields :h3
 
 A force field has 2 parts: the formulas that define it and the
 coefficients used for a particular system.  Here we only discuss
 formulas implemented in LAMMPS that correspond to formulas commonly
-used in the CHARMM, AMBER, and DREIDING force fields.  Setting
-coefficients is done in the input data file via the
-"read_data"_read_data.html command or in the input script with
+used in the CHARMM, AMBER, COMPASS, and DREIDING force fields.  Setting
+coefficients is done either from special sections in an input data file
+via the "read_data"_read_data.html command or in the input script with
 commands like "pair_coeff"_pair_coeff.html or
-"bond_coeff"_bond_coeff.html.  See the "Tools"_Tools.html doc page for
-additional tools that can use CHARMM or AMBER to assign force field
-coefficients and convert their output into LAMMPS input.
+"bond_coeff"_bond_coeff.html and so on.  See the "Tools"_Tools.html doc
+page for additional tools that can use CHARMM, AMBER, or Materials
+Studio generated files to assign force field coefficients and convert
+their output into LAMMPS input.
 
 See "(MacKerell)"_#howto-MacKerell for a description of the CHARMM force
-field.  See "(Cornell)"_#howto-Cornell for a description of the AMBER force
-field.
+field.  See "(Cornell)"_#howto-Cornell for a description of the AMBER
+force field.  See "(Sun)"_#howto-Sun for a description of the COMPASS
+force field.
 
 :link(charmm,http://www.scripps.edu/brooks)
 :link(amber,http://amber.scripps.edu)
 
-These style choices compute force field formulas that are consistent
-with common options in CHARMM or AMBER.  See each command's
-documentation for the formula it computes.
+The interaction styles listed below compute force field formulas that
+are consistent with common options in CHARMM or AMBER.  See each
+command's documentation for the formula it computes.
 
 "bond_style"_bond_harmonic.html harmonic
 "angle_style"_angle_charmm.html charmm
@@ -44,28 +46,54 @@ documentation for the formula it computes.
 "special_bonds"_special_bonds.html charmm
 "special_bonds"_special_bonds.html amber :ul
 
-NOTE: For CHARMM, newer {charmmfsw} or {charmmfsh} styles were
-released in March 2017.  We recommend they be used instead of the
-older {charmm} styles.  See discussion of the differences on the "pair
-charmm"_pair_charmm.html and "dihedral charmm"_dihedral_charmm.html
-doc pages.
+NOTE: For CHARMM, newer {charmmfsw} or {charmmfsh} styles were released
+in March 2017.  We recommend they be used instead of the older {charmm}
+styles.  See discussion of the differences on the "pair
+charmm"_pair_charmm.html and "dihedral charmm"_dihedral_charmm.html doc
+pages.
+
+COMPASS is a general force field for atomistic simulation of common
+organic molecules, inorganic small molecules, and polymers which was
+developed using ab initio and empirical parameterization techniques.
+See the "Tools"_Tools.html doc page for the msi2lmp tool for creating
+LAMMPS template input and data files from BIOVIA’s Materials Studio
+files.  Please note that the msi2lmp tool is very old and largely
+unmaintained, so it does not support all features of Materials Studio
+provided force field files, especially additions during the last decade.
+You should watch the output carefully and compare results, where
+possible.  See "(Sun)"_#howto-Sun for a description of the COMPASS force
+field.
+
+These interaction styles listed below compute force field formulas that
+are consistent with the COMPASS force field.  See each command's
+documentation for the formula it computes.
+
+"bond_style"_bond_class2.html class2
+"angle_style"_angle_class2.html class2
+"dihedral_style"_dihedral_class2.html class2
+"improper_style"_improper_class2.html class2 :ul
+
+"pair_style"_pair_class2.html lj/class2
+"pair_style"_pair_class2.html lj/class2/coul/cut
+"pair_style"_pair_class2.html lj/class2/coul/long :ul
+
+"special_bonds"_special_bonds.html lj/coul 0 0 1 :ul
 
 DREIDING is a generic force field developed by the "Goddard
 group"_http://www.wag.caltech.edu at Caltech and is useful for
-predicting structures and dynamics of organic, biological and
-main-group inorganic molecules. The philosophy in DREIDING is to use
-general force constants and geometry parameters based on simple
-hybridization considerations, rather than individual force constants
-and geometric parameters that depend on the particular combinations of
-atoms involved in the bond, angle, or torsion terms. DREIDING has an
-"explicit hydrogen bond term"_pair_hbond_dreiding.html to describe
-interactions involving a hydrogen atom on very electronegative atoms
-(N, O, F).
+predicting structures and dynamics of organic, biological and main-group
+inorganic molecules. The philosophy in DREIDING is to use general force
+constants and geometry parameters based on simple hybridization
+considerations, rather than individual force constants and geometric
+parameters that depend on the particular combinations of atoms involved
+in the bond, angle, or torsion terms. DREIDING has an "explicit hydrogen
+bond term"_pair_hbond_dreiding.html to describe interactions involving a
+hydrogen atom on very electronegative atoms (N, O, F).
 
 See "(Mayo)"_#howto-Mayo for a description of the DREIDING force field
 
-These style choices compute force field formulas that are consistent
-with the DREIDING force field.  See each command's
+The interaction styles listed below compute force field formulas that
+are consistent with the DREIDING force field.  See each command's
 documentation for the formula it computes.
 
 "bond_style"_bond_harmonic.html harmonic
@@ -100,6 +128,9 @@ Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).
 [(Cornell)] Cornell, Cieplak, Bayly, Gould, Merz, Ferguson,
 Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995).
 
+:link(howto-Sun)
+[(Sun)] Sun, J. Phys. Chem. B, 102, 7338–7364 (1998).
+
 :link(howto-Mayo)
 [(Mayo)] Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
 (1990).

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_replica.txt

@@ -17,6 +17,7 @@ periodically.
 These are the relevant commands:
 
 "neb"_neb.html for nudged elastic band calculations
+"neb_spin"_neb_spin.html for magnetic nudged elastic band calculations
 "prd"_prd.html for parallel replica dynamics
 "tad"_tad.html for temperature accelerated dynamics
 "temper"_temper.html for parallel tempering

doc/src/Howto_spins.txt

@@ -10,7 +10,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 Magnetic spins :h3
 
 The magnetic spin simulations are enabled by the SPIN package, whose
-implementation is detailed in "Tranchida"_#Tranchida7.
+implementation is detailed in "Tranchida"_#Tranchida.
 
 The model represents the simulation of atomic magnetic spins coupled
 to lattice vibrations. The dynamics of those magnetic spins can be used
@@ -36,13 +36,28 @@ A Langevin thermostat can be applied to those magnetic spins using
 "fix langevin/spin"_fix_langevin_spin.html. Typically, this thermostat
 can be coupled to another Langevin thermostat applied to the atoms
 using "fix langevin"_fix_langevin.html in order to simulate
-thermostatted spin-lattice system.
+thermostatted spin-lattice systems.
 
 The magnetic Gilbert damping can also be applied using "fix
 langevin/spin"_fix_langevin_spin.html. It allows to either dissipate
 the thermal energy of the Langevin thermostat, or to perform a
 relaxation of the magnetic configuration toward an equilibrium state.
 
+The command "fix setforce/spin"_fix_setforce.html allows to set the 
+components of the magnetic precession vectors (while erasing and 
+replacing the previously computed magnetic precession vectors on 
+the atom). 
+This command can be used to freeze the magnetic moment of certain 
+atoms in the simulation by zeroing their precession vector. 
+
+The command "fix nve/spin"_fix_nve_spin.html can be used to
+perform a symplectic integration of the combined dynamics of spins 
+and atomic motions.
+
+The minimization style "min/spin"_min_spin.html can be applied
+to the spins to perform a minimization of the spin configuration. 
+
+
 All the computed magnetic properties can be output by two main
 commands. The first one is "compute spin"_compute_spin.html, that
 enables to evaluate magnetic averaged quantities, such as the total
@@ -54,6 +69,6 @@ magnetic spin, or the magnetic force acting on this spin.
 
 :line
 
-:link(Tranchida7)
+:link(Tranchida)
 [(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson,
-arXiv preprint arXiv:1801.10233, (2018).
+Journal of Computational Physics, 372, 406-425, (2018).

doc/src/Howto_tip3p.txt

@@ -10,7 +10,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 TIP3P water model :h3
 
 The TIP3P water model as implemented in CHARMM
-"(MacKerell)"_#howto-MacKerell specifies a 3-site rigid water molecule with
+"(MacKerell)"_#howto-tip3p specifies a 3-site rigid water molecule with
 charges and Lennard-Jones parameters assigned to each of the 3 atoms.
 In LAMMPS the "fix shake"_fix_shake.html command can be used to hold
 the two O-H bonds and the H-O-H angle rigid.  A bond style of
@@ -60,6 +60,10 @@ models"_http://en.wikipedia.org/wiki/Water_model.
 
 :line
 
+:link(howto-tip3p)
+[(MacKerell)] MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
+Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).
+
 :link(Jorgensen1)
 [(Jorgensen)] Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem
 Phys, 79, 926 (1983).

doc/src/Manual.txt

@@ -1,7 +1,7 @@
 <!-- HTML_ONLY -->
 <HEAD>
 <TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="29 Mar 2019 version">
+<META NAME="docnumber" CONTENT="30 Apr 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
-29 Mar 2019 version :c,h2
+30 Apr 2019 version :c,h2
 
 "What is a LAMMPS version?"_Manual_version.html
 

doc/src/Packages_details.txt

@@ -918,6 +918,7 @@ src/SPIN: filenames -> commands
 "fix nve/spin"_fix_nve_spin.html
 "fix precession/spin"_fix_precession_spin.html
 "compute spin"_compute_spin.html
+"neb/spin"_neb_spin.html
 examples/SPIN :ul
 
 :line

doc/src/Run_options.txt

@@ -79,7 +79,7 @@ stdin.
 Explicitly enable or disable KOKKOS support, as provided by the KOKKOS
 package.  Even if LAMMPS is built with this package, as described
 in "Speed kokkos"_Speed_kokkos.html, this switch must be set to enable
-running with the KOKKOS-enabled styles the package provides.  If the
+running with KOKKOS-enabled styles the package provides.  If the
 switch is not set (the default), LAMMPS will operate as if the KOKKOS
 package were not installed; i.e. you can run standard LAMMPS or with
 the GPU or USER-OMP packages, for testing or benchmarking purposes.
@@ -448,7 +448,7 @@ partition screen files file.N.
 [-suffix style args] :link(suffix)
 
 Use variants of various styles if they exist.  The specified style can
-be {cuda}, {gpu}, {intel}, {kk}, {omp}, {opt}, or {hybrid}.  These
+be {gpu}, {intel}, {kk}, {omp}, {opt}, or {hybrid}.  These
 refer to optional packages that LAMMPS can be built with, as described
 in "Accelerate performance"_Speed.html.  The "gpu" style corresponds to the
 GPU package, the "intel" style to the USER-INTEL package, the "kk"

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,

doc/src/commands_list.txt

@@ -67,6 +67,7 @@ Commands :h1
    minimize
    molecule
    neb
+   neb_spin
    neigh_modify
    neighbor
    newton

doc/src/fix.txt

@@ -201,6 +201,7 @@ accelerated styles exist.
 "edpd/source"_fix_dpd_source.html -
 "efield"_fix_efield.html - impose electric field on system
 "ehex"_fix_ehex.html - enhanced heat exchange algorithm
+"electron/stopping"_fix_electron_stopping.html - electronic stopping power as a friction force
 "enforce2d"_fix_enforce2d.html - zero out z-dimension velocity and force
 "eos/cv"_fix_eos_cv.html -
 "eos/table"_fix_eos_table.html -

doc/src/fix_electron_stopping.txt

@@ -0,0 +1,165 @@
+"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
+
+fix electron/stopping command :h3
+
+[Syntax:]
+
+fix ID group-ID electron/stopping Ecut file keyword value ... :pre
+
+ID, group-ID are documented in "fix"_fix.html command :ulb,l
+electron/stopping = style name of this fix command :l
+Ecut = minimum kinetic energy for electronic stopping (energy units) :l
+file = name of the file containing the electronic stopping power table :l
+zero or more keyword/value pairs may be appended to args :l
+keyword = {region} or {minneigh} :l
+  {region} value = region-ID
+    region-ID = region, whose atoms will be affected by this fix
+  {minneigh} value = minneigh
+    minneigh = minimum number of neighbors an atom to have stopping applied :pre
+:ule
+
+[Examples:]
+
+fix el all electron/stopping 10.0 elstop-table.txt
+fix el all electron/stopping 10.0 elstop-table.txt minneigh 3
+fix el mygroup electron/stopping 1.0 elstop-table.txt region bulk :pre
+
+[Description:]
+
+This fix implements inelastic energy loss for fast projectiles in solids. It
+applies a friction force to fast moving atoms to slow them down due to
+"electronic stopping"_#elstopping (energy lost via electronic collisions per
+unit of distance). This fix should be used for simulation of irradiation
+damage or ion implantation, where the ions can lose noticeable amounts of
+energy from electron excitations. If the electronic stopping power is not
+considered, the simulated range of the ions can be severely overestimated
+("Nordlund98"_#Nordlund98, "Nordlund95"_#Nordlund95).
+
+The electronic stopping is implemented by applying a friction force
+to each atom as:
+
+\begin\{equation\}
+\vec\{F\}_i = \vec\{F\}^0_i - \frac\{\vec\{v\}_i\}\{\|\vec\{v\}_i\|\} \cdot S_e
+\end\{equation\}
+
+where \(\vec\{F\}_i\) is the resulting total force on the atom.
+\(\vec\{F\}^0_i\) is the original force applied to the atom, \(\vec\{v\}_i\) is
+its velocity and \(S_e\) is the stopping power of the ion.
+
+NOTE: In addition to electronic stopping, atomic cascades and irradiation
+simulations require the use of an adaptive timestep (see
+"fix dt/reset"_fix_dt_reset.html) and the repulsive ZBL potential (see
+"ZBL"_pair_zbl.html potential) or similar. Without these settings the
+interaction between the ion and the target atoms will be faulty. It is also
+common to use in such simulations a thermostat ("fix_nvt"_fix_nh.html) in
+the borders of the simulation cell.
+
+NOTE: This fix removes energy from fast projectiles without depositing it as a
+heat to the simulation cell. Such implementation might lead to the unphysical
+results when the amount of energy deposited to the electronic system is large,
+e.g. simulations of Swift Heavy Ions (energy per nucleon of 100 keV/amu or
+higher) or multiple projectiles. You could compensate energy loss by coupling
+bulk atoms with some thermostat or control heat transfer between electronic and
+atomic subsystems with the two-temperature model ("fix_ttm"_fix_ttm.html).
+
+At low velocities the electronic stopping is negligible. The electronic
+friction is not applied to atoms whose kinetic energy is smaller than {Ecut},
+or smaller than the lowest energy value given in the table in {file}.
+Electronic stopping should be applied only when a projectile reaches bulk
+material. This fix scans neighbor list and excludes atoms with fewer than
+{minneigh} neighbors (by default one). If the pair potential cutoff is large,
+minneigh should be increased, though not above the number of nearest neighbors
+in bulk material. An alternative is to disable the check for neighbors by
+setting {minneigh} to zero and using the {region} keyword. This is necessary
+when running simulations of cluster bombardment.
+
+If the {region} keyword is used, the atom must also be in the specified
+geometric "region"_region.html in order to have electronic stopping applied to
+it. This is useful if the position of the bulk material is fixed. By default
+the electronic stopping is applied everywhere in the simulation cell.
+
+:line
+
+The energy ranges and stopping powers are read from the file {file}.
+Lines starting with {#} and empty lines are ignored. Otherwise each
+line must contain exactly [N+1] numbers, where [N] is the number of atom
+types in the simulation.
+
+The first column is the energy for which the stopping powers on that
+line apply. The energies must be sorted from the smallest to the largest.
+The other columns are the stopping powers \(S_e\) for each atom type,
+in ascending order, in force "units"_units.html. The stopping powers for
+intermediate energy values are calculated with linear interpolation between
+2 nearest points.
+
+For example:
+
+# This is a comment
+#       atom-1    atom-2
+# eV    eV/Ang    eV/Ang  # units metal
+ 10        0        0
+250       60       80
+750      100      150 :pre
+
+
+If an atom which would have electronic stopping applied to it has a
+kinetic energy higher than the largest energy given in {file}, LAMMPS
+will exit with an error message.
+
+The stopping power depends on the energy of the ion and the target
+material. The electronic stopping table can be obtained from
+scientific publications, experimental databases or by using
+"SRIM"_#SRIM software. Other programs such as "CasP"_#CasP or
+"PASS"_#PASS can calculate the energy deposited as a function
+of the impact parameter of the ion; these results can be used
+to derive the stopping power.
+
+[Restart, fix_modify, output, run start/stop, minimize info:]
+
+No information about this fix is written to "binary restart
+files"_restart.html.
+
+The "fix_modify"_fix_modify.html options are not supported.
+
+This fix computes a global scalar, which can be accessed by various
+"output commands"_Howto_output.html. The scalar is the total energy
+loss from electronic stopping applied by this fix since the start of
+the latest run. It is considered "intensive".
+
+The {start/stop} keywords of the "run"_run.html command have no effect
+on this fix.
+
+[Restrictions:]
+
+This pair style is part of the USER-MISC package. It is only enabled if
+LAMMPS was built with that package. See the "Build package"_Build_package.html
+doc page for more info.
+
+[Default:]
+
+The default is no limitation by region, and minneigh = 1.
+
+:line
+:link(elstopping)
+[(electronic stopping)] Wikipedia - Electronic Stopping Power: https://en.wikipedia.org/wiki/Stopping_power_%28particle_radiation%29
+
+:link(Nordlund98)
+[(Nordlund98)] Nordlund, Kai, et al.  Physical Review B 57.13 (1998): 7556.
+
+:link(Nordlund95)
+[(Nordlund95)] Nordlund, Kai. Computational materials science 3.4 (1995): 448-456.
+
+:link(SRIM)
+[(SRIM)] SRIM webpage: http://www.srim.org/
+
+:link(CasP)
+[(CasP)] CasP webpage: https://www.helmholtz-berlin.de/people/gregor-schiwietz/casp_en.html
+
+:link(PASS)
+[(PASS)] PASS webpage: https://www.sdu.dk/en/DPASS

doc/src/fix_langevin_spin.txt

@@ -99,4 +99,4 @@ integration fix (e.g. {fix nve/spin}).
 
 :link(Tranchida2)
 [(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson,
-Journal of Computational Physics, (2018).
+Journal of Computational Physics, 372, 406-425, (2018).

doc/src/fix_neb.txt

@@ -97,7 +97,7 @@ Note that in this case the specified {Kspring} is in force/distance
 units.
 
 With a value of {ideal}, the spring force is computed as suggested in
-"(WeinenE)"_#WeinenE :
+"(WeinanE)"_#WeinanE :
 
 Fnudge_parallel = -{Kspring} * (RD-RDideal) / (2 * meanDist) :pre
 
@@ -224,8 +224,8 @@ specified (no inter-replica force on the end replicas).
 [(Henkelman2)] Henkelman, Uberuaga, Jonsson, J Chem Phys, 113,
 9901-9904 (2000).
 
-:link(WeinenE)
-[(WeinenE)] E, Ren, Vanden-Eijnden, Phys Rev B, 66, 052301 (2002).
+:link(WeinanE)
+[(WeinanE)] E, Ren, Vanden-Eijnden, Phys Rev B, 66, 052301 (2002).
 
 :link(Jonsson)
 [(Jonsson)] Jonsson, Mills and Jacobsen, in Classical and Quantum

doc/src/fix_neb_spin.txt

@@ -0,0 +1,76 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+fix neb/spin command :h3
+
+[Syntax:]
+
+fix ID group-ID neb/spin Kspring :pre
+
+ID, group-ID are documented in "fix"_fix.html command :ulb,l
+neb/spin = style name of this fix command :l
+Kspring = spring constant for parallel nudging force
+(force/distance units or force units, see parallel keyword) :pre,ule
+
+[Examples:]
+
+fix 1 active neb/spin 1.0
+
+[Description:]
+
+Add nudging forces to spins in the group for a multi-replica
+simulation run via the "neb/spin"_neb_spin.html command to perform a 
+geodesic nudged elastic band (GNEB) calculation for finding the 
+transition state.
+Hi-level explanations of GNEB are given with the 
+"neb/spin"_neb_spin.html command and on the 
+"Howto replica"_Howto_replica.html doc page.  
+The fix neb/spin command must be used with the "neb/spin" command and 
+defines how inter-replica nudging forces are computed.  A GNEB 
+calculation is divided in two stages. In the first stage n replicas 
+are relaxed toward a MEP until convergence.  In the second stage, the 
+climbing image scheme is enabled, so that the replica having the highest 
+energy relaxes toward the saddle point (i.e. the point of highest energy 
+along the MEP), and a second relaxation is performed.
+
+The nudging forces are calculated as explained in
+"(BessarabB)"_#BessarabB).
+See this reference for more explanation about their expression.
+
+[Restart, fix_modify, output, run start/stop, minimize info:]
+
+No information about this fix is written to "binary restart
+files"_restart.html.  None of the "fix_modify"_fix_modify.html options
+are relevant to this fix.  No global or per-atom quantities are stored
+by this fix for access by various "output commands"_Howto_output.html.
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command.
+
+The forces due to this fix are imposed during an energy minimization,
+as invoked by the "minimize"_minimize.html command via the
+"neb/spin"_neb_spin.html command.
+
+[Restrictions:]
+
+This command can only be used if LAMMPS was built with the SPIN
+package.  See the "Build package"_Build_package.html doc
+page for more info.
+
+[Related commands:]
+
+"neb_spin"_neb_spin.html
+
+[Default:]
+
+none
+
+:line
+
+:link(BessarabB)
+[(BessarabB)] Bessarab, Uzdin, Jonsson, Comp Phys Comm, 196,
+335-347 (2015).

doc/src/fix_nve_spin.txt

@@ -73,4 +73,4 @@ instead of "array" is also valid.
 
 :link(Tranchida1)
 [(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson,
-Journal of Computational Physics, (2018).
+Journal of Computational Physics, 372, 406-425, (2018).

doc/src/fix_precession_spin.txt

@@ -31,7 +31,7 @@ fix 1 all precession/spin zeeman 0.1 0.0 0.0 1.0 anisotropy 0.001 0.0 0.0 1.0 :p
 
 [Description:]
 
-Impose a force torque to each magnetic spin in the group.
+This fix applies a precession torque to each magnetic spin in the group.
 
 Style {zeeman} is used for the simulation of the interaction
 between the magnetic spins in the defined group and an external

doc/src/fix_setforce.txt

@@ -8,6 +8,7 @@
 
 fix setforce command :h3
 fix setforce/kk command :h3
+fix setforce/spin command :h3
 
 [Syntax:]
 
@@ -27,6 +28,7 @@ keyword = {region}  :l
 
 fix freeze indenter setforce 0.0 0.0 0.0
 fix 2 edge setforce NULL 0.0 0.0
+fix 1 edge setforce/spin 0.0 0.0 0.0
 fix 2 edge setforce NULL 0.0 v_oscillate :pre
 
 [Description:]
@@ -65,6 +67,19 @@ to it.
 
 :line
 
+Style {spin} suffix sets the components of the magnetic precession 
+vectors instead of the mechanical forces. This also erases all 
+previously computed magnetic precession vectors on the atom, though 
+additional magnetic fixes could add new forces.
+
+This command can be used to freeze the magnetic moment of certain 
+atoms in the simulation by zeroing their precession vector. 
+
+All options defined above remain valid, they just apply to the magnetic 
+precession vectors instead of the forces.
+
+: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
@@ -117,7 +132,10 @@ forces to any value besides zero when performing a minimization.  Use
 the "fix addforce"_fix_addforce.html command if you want to apply a
 non-zero force to atoms during a minimization.
 
-[Restrictions:] none
+[Restrictions:] 
+
+The fix {setforce/spin} only makes sense when LAMMPS was built with the
+SPIN package.
 
 [Related commands:]
 

doc/src/fix_wall_gran.txt

@@ -17,13 +17,13 @@ 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, granular :pre
 fstyle_params = parameters associated with force interaction style :l
-  For {hooke}, {hooke/history}, and {hertz/history}, {fstyle_params} are: 
-	Kn = elastic constant for normal particle repulsion (force/distance units or pressure units - see discussion below) 
-	Kt = elastic constant for tangential contact (force/distance units or pressure units - see discussion below) 
-	gamma_n = damping coefficient for collisions in normal direction (1/time units or 1/time-distance units - see discussion below) 
-	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 {hooke}, {hooke/history}, and {hertz/history}, {fstyle_params} are:
+        Kn = elastic constant for normal particle repulsion (force/distance units or pressure units - see discussion below)
+        Kt = elastic constant for tangential contact (force/distance units or pressure units - see discussion below)
+        gamma_n = damping coefficient for collisions in normal direction (1/time units or 1/time-distance units - see discussion below)
+        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
@@ -46,10 +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 
-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
+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/region granular hooke 1000.0 50.0 tangential linear_nohistory 1.0 0.4 damping velocity region myBox
+fix 4 all wall/gran/region granular jkr 1e5 1500.0 0.3 10.0 tangential mindlin NULL 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall region myCone
+fix 5 all wall/gran/region granular dmt 1e5 0.2 0.3 10.0 tangential mindlin NULL 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall damping tsuji region myCone :pre
 
 [Description:]
 

doc/src/fix_wall_gran_region.txt

@@ -17,23 +17,23 @@ 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, granular :pre
 fstyle_params = parameters associated with force interaction style :l
-  For {hooke}, {hooke/history}, and {hertz/history}, {fstyle_params} are: 
-	Kn = elastic constant for normal particle repulsion (force/distance units or pressure units - see discussion below) 
-	Kt = elastic constant for tangential contact (force/distance units or pressure units - see discussion below) 
-	gamma_n = damping coefficient for collisions in normal direction (1/time units or 1/time-distance units - see discussion below) 
-	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 {hooke}, {hooke/history}, and {hertz/history}, {fstyle_params} are:
+        Kn = elastic constant for normal particle repulsion (force/distance units or pressure units - see discussion below)
+        Kt = elastic constant for tangential contact (force/distance units or pressure units - see discussion below)
+        gamma_n = damping coefficient for collisions in normal direction (1/time units or 1/time-distance units - see discussion below)
+        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 
-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
+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 damping velocity region myBox
+fix 4 all wall/gran/region granular jkr 1e5 1500.0 0.3 10.0 tangential mindlin NULL 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall region myCone
+fix 5 all wall/gran/region granular dmt 1e5 0.2 0.3 10.0 tangential mindlin NULL 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall damping tsuji region myCone :pre
 
 [Description:]
 

doc/src/fixes.txt

@@ -40,6 +40,7 @@ Fixes :h1
    fix_dt_reset
    fix_efield
    fix_ehex
+   fix_electron_stopping
    fix_enforce2d
    fix_eos_cv
    fix_eos_table
@@ -83,6 +84,7 @@ Fixes :h1
    fix_msst
    fix_mvv_dpd
    fix_neb
+   fix_neb_spin
    fix_nh
    fix_nh_eff
    fix_nh_uef

doc/src/kim_query.txt

@@ -26,12 +26,13 @@ kim_query latconst get_test_result test=TE_156715955670 model=MO_800509458712 &
 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
+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}. This list of supported keywords and the type of how
-the value has to be encoded depends on the query function used.
-For more details on this, please refer to the OpenKIM homepage.
+{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:]
 

doc/src/lammps.book

@@ -179,6 +179,7 @@ min_spin.html
 minimize.html
 molecule.html
 neb.html
+neb_spin.html
 neigh_modify.html
 neighbor.html
 newton.html
@@ -265,6 +266,7 @@ fix_drude_transform.html
 fix_dt_reset.html
 fix_efield.html
 fix_ehex.html
+fix_electron_stopping.html
 fix_enforce2d.html
 fix_eos_cv.html
 fix_eos_table.html
@@ -308,6 +310,7 @@ fix_mscg.html
 fix_msst.html
 fix_mvv_dpd.html
 fix_neb.html
+fix_neb_spin.html
 fix_nh.html
 fix_nh_eff.html
 fix_nph_asphere.html

doc/src/neb_spin.txt

@@ -0,0 +1,375 @@
+"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
+
+neb command :h3
+
+[Syntax:]
+
+neb/spin etol ttol N1 N2 Nevery file-style arg keyword :pre
+
+etol = stopping tolerance for energy (energy units) :ulb,l
+ttol = stopping tolerance for torque ( units) :l
+N1 = max # of iterations (timesteps) to run initial NEB :l
+N2 = max # of iterations (timesteps) to run barrier-climbing NEB :l
+Nevery = print replica energies and reaction coordinates every this many timesteps :l
+file-style = {final} or {each} or {none} :l
+  {final} arg = filename
+    filename = file with initial coords for final replica
+      coords for intermediate replicas are linearly interpolated
+      between first and last replica
+  {each} arg = filename
+    filename = unique filename for each replica (except first)
+      with its initial coords
+  {none} arg = no argument all replicas assumed to already have
+      their initial coords :pre
+keyword = {verbose}
+:ule
+
+[Examples:]
+
+neb/spin 0.1 0.0 1000 500 50 final coords.final
+neb/spin 0.0 0.001 1000 500 50 each coords.initial.$i
+neb/spin 0.0 0.001 1000 500 50 none verbose :pre
+
+[Description:]
+
+Perform a geodesic nudged elastic band (GNEB) calculation using multiple
+replicas of a system.  Two or more replicas must be used; the first
+and last are the end points of the transition path.
+
+GNEB is a method for finding both the spin configurations and height
+of the energy barrier associated with a transition state, e.g.
+spins to perform a collective rotation from one energy basin to
+another. 
+The implementation in LAMMPS follows the discussion in the
+following paper: "(BessarabA)"_#BessarabA.
+
+Each replica runs on a partition of one or more processors.  Processor
+partitions are defined at run-time using the "-partition command-line
+switch"_Run_options.html.  Note that if you have MPI installed, you
+can run a multi-replica simulation with more replicas (partitions)
+than you have physical processors, e.g you can run a 10-replica
+simulation on just one or two processors.  You will simply not get the
+performance speed-up you would see with one or more physical
+processors per replica.  See the "Howto replica"_Howto_replica.html
+doc page for further discussion.
+
+NOTE: As explained below, a GNEB calculation performs a damped dynamics
+minimization across all the replicas.  The "spin"_min_spin.html
+style minimizer has to be defined in your input script. 
+
+When a GNEB calculation is performed, it is assumed that each replica
+is running the same system, though LAMMPS does not check for this.
+I.e. the simulation domain, the number of magnetic atoms, the 
+interaction potentials, and the starting configuration when the neb 
+command is issued should be the same for every replica.
+
+In a GNEB calculation each replica is connected to other replicas by
+inter-replica nudging forces.  These forces are imposed by the "fix
+neb/spin"_fix_neb_spin.html command, which must be used in conjunction 
+with the neb command.  
+The group used to define the fix neb/spin command defines the
+GNEB magnetic atoms which are the only ones that inter-replica springs 
+are applied to.  
+If the group does not include all magnetic atoms, then non-GNEB
+magnetic atoms have no inter-replica springs and the torques they feel 
+and their precession motion is computed in the usual way due only 
+to other magnetic atoms within their replica.  
+Conceptually, the non-GNEB atoms provide a background force field for 
+the GNEB atoms.  
+Their magnetic spins can be allowed to evolve during the GNEB 
+minimization procedure.
+
+The initial spin configuration for each of the replicas can be
+specified in different manners via the {file-style} setting, as
+discussed below.  Only atomic spins whose initial coordinates should 
+differ from the current configuration need to be specified.
+
+Conceptually, the initial and final configurations for the first
+replica should be states on either side of an energy barrier.
+
+As explained below, the initial configurations of intermediate
+replicas can be spin coordinates interpolated in a linear fashion
+between the first and last replicas.  This is often adequate for
+simple transitions.  For more complex transitions, it may lead to slow
+convergence or even bad results if the minimum energy path (MEP, see
+below) of states over the barrier cannot be correctly converged to
+from such an initial path.  In this case, you will want to generate
+initial states for the intermediate replicas that are geometrically
+closer to the MEP and read them in.
+
+:line
+
+For a {file-style} setting of {final}, a filename is specified which
+contains atomic and spin coordinates for zero or more atoms, in the 
+format described below.  
+For each atom that appears in the file, the new coordinates are 
+assigned to that atom in the final replica.  Each intermediate replica 
+also assigns a new spin to that atom in an interpolated manner.  
+This is done by using the current direction of the spin at the starting 
+point and the read-in direction as the final point.  
+The "angular distance" between them is calculated, and the new direction 
+is assigned to be a fraction of the angular distance.
+
+NOTE: The "angular distance" between the starting and final point is 
+evaluated in the geodesic sense, as described in 
+"(BessarabA)"_#BessarabA. 
+
+NOTE: The angular interpolation between the starting and final point 
+is achieved using Rodrigues formula:
+
+:c,image(Eqs/neb_spin_rodrigues_formula.jpg)
+
+where m_i^I is the initial spin configuration for the spin i,
+omega_i^nu is a rotation angle defined as:
+
+:c,image(Eqs/neb_spin_angle.jpg)
+
+with nu the image number, Q the total number of images, and 
+omega_i the total rotation between the initial and final spins.
+k_i defines a rotation axis such as:
+
+:c,image(Eqs/neb_spin_k.jpg)
+
+if the initial and final spins are not aligned.
+If the initial and final spins are aligned, then their cross
+product is null, and the expression above does not apply.
+If they point toward the same direction, the intermediate images 
+conserve the same orientation.
+If the initial and final spins are aligned, but point toward
+opposite directions, an arbitrary rotation vector belonging to
+the plane perpendicular to initial and final spins is chosen. 
+In this case, a warning message is displayed.
+
+For a {file-style} setting of {each}, a filename is specified which is
+assumed to be unique to each replica. 
+See the "neb"_neb.html documentation page for more information about this 
+option.
+
+For a {file-style} setting of {none}, no filename is specified.  Each
+replica is assumed to already be in its initial configuration at the
+time the neb command is issued.  This allows each replica to define
+its own configuration by reading a replica-specific data or restart or
+dump file, via the "read_data"_read_data.html,
+"read_restart"_read_restart.html, or "read_dump"_read_dump.html
+commands.  The replica-specific names of these files can be specified
+as in the discussion above for the {each} file-style.  Also see the
+section below for how a NEB calculation can produce restart files, so
+that a long calculation can be restarted if needed.
+
+NOTE: None of the {file-style} settings change the initial
+configuration of any atom in the first replica.  The first replica
+must thus be in the correct initial configuration at the time the neb
+command is issued.
+
+:line
+
+A NEB calculation proceeds in two stages, each of which is a
+minimization procedure, performed via damped dynamics.  To enable
+this, you must first define a damped spin dynamics
+"min_style"_min_style.html, using the {spin} style (see
+"min_spin"_min_spin.html for more information).  
+The other styles cannot be used, since they relax the lattice
+degrees of freedom instead of the spins.
+
+The minimizer tolerances for energy and force are set by {etol} and
+{ttol}, the same as for the "minimize"_minimize.html command.
+
+A non-zero {etol} means that the GNEB calculation will terminate if the
+energy criterion is met by every replica.  The energies being compared
+to {etol} do not include any contribution from the inter-replica
+nudging forces, since these are non-conservative.  A non-zero {ttol}
+means that the GNEB calculation will terminate if the torque criterion
+is met by every replica.  The torques being compared to {ttol} include
+the inter-replica nudging forces.
+
+The maximum number of iterations in each stage is set by {N1} and
+{N2}.  These are effectively timestep counts since each iteration of
+damped dynamics is like a single timestep in a dynamics
+"run"_run.html.  During both stages, the potential energy of each
+replica and its normalized distance along the reaction path (reaction
+coordinate RD) will be printed to the screen and log file every
+{Nevery} timesteps.  The RD is 0 and 1 for the first and last replica.
+For intermediate replicas, it is the cumulative angular distance 
+(normalized by the total cumulative angular distance) between adjacent 
+replicas, where "distance" is defined as the length of the 3N-vector of 
+the geodesic distances in spin coordinates, with N the number of
+GNEB spins involved (see equation (13) in "(BessarabA)"_#BessarabA).
+These outputs allow you to monitor NEB's progress in
+finding a good energy barrier.  {N1} and {N2} must both be multiples
+of {Nevery}.
+
+In the first stage of GNEB, the set of replicas should converge toward
+a minimum energy path (MEP) of conformational states that transition
+over a barrier.  The MEP for a transition is defined as a sequence of
+3N-dimensional spin states, each of which has a potential energy 
+gradient parallel to the MEP itself.  
+The configuration of highest energy along a MEP corresponds to a saddle 
+point.  The replica states will also be roughly equally spaced along 
+the MEP due to the inter-replica nudging force added by the 
+"fix neb"_fix_neb.html command.
+
+In the second stage of GNEB, the replica with the highest energy is
+selected and the inter-replica forces on it are converted to a force
+that drives its spin coordinates to the top or saddle point of the
+barrier, via the barrier-climbing calculation described in
+"(BessarabA)"_#BessarabA.  As before, the other replicas rearrange
+themselves along the MEP so as to be roughly equally spaced.
+
+When both stages are complete, if the GNEB calculation was successful,
+the configurations of the replicas should be along (close to) the MEP
+and the replica with the highest energy should be a spin
+configuration at (close to) the saddle point of the transition. The
+potential energies for the set of replicas represents the energy
+profile of the transition along the MEP.
+
+:line
+
+An atom map must be defined which it is not by default for "atom_style
+atomic"_atom_style.html problems.  The "atom_modify
+map"_atom_modify.html command can be used to do this.
+
+An initial value can be defined for the timestep. Although, the {spin} 
+minimization algorithm is an adaptive timestep methodology, so that 
+this timestep is likely to evolve during the calculation.  
+
+The minimizers in LAMMPS operate on all spins in your system, even
+non-GNEB atoms, as defined above.  
+
+:line
+
+Each file read by the neb/spin command containing spin coordinates used
+to initialize one or more replicas must be formatted as follows.
+
+The file can be ASCII text or a gzipped text file (detected by a .gz
+suffix).  The file can contain initial blank lines or comment lines
+starting with "#" which are ignored.  The first non-blank, non-comment
+line should list N = the number of lines to follow.  The N successive
+lines contain the following information:
+
+ID1 g1 x1 y1 z1 sx1 sy1 sz1
+ID2 g2 x2 y2 z2 sx2 sy2 sz2
+...
+IDN gN yN zN sxN syN szN :pre
+
+The fields are the atom ID, the norm of the associated magnetic spin, 
+followed by the {x,y,z} coordinates and the {sx,sy,sz} spin coordinates.
+The lines can be listed in any order.  Additional trailing information on
+the line is OK, such as a comment.
+
+Note that for a typical GNEB calculation you do not need to specify
+initial spin coordinates for very many atoms to produce differing starting
+and final replicas whose intermediate replicas will converge to the
+energy barrier.  Typically only new spin coordinates for atoms
+geometrically near the barrier need be specified.
+
+Also note there is no requirement that the atoms in the file
+correspond to the GNEB atoms in the group defined by the "fix
+neb"_fix_neb.html command.  Not every GNEB atom need be in the file,
+and non-GNEB atoms can be listed in the file.
+
+:line
+
+Four kinds of output can be generated during a GNEB calculation: energy
+barrier statistics, thermodynamic output by each replica, dump files,
+and restart files.
+
+When running with multiple partitions (each of which is a replica in
+this case), the print-out to the screen and master log.lammps file
+contains a line of output, printed once every {Nevery} timesteps.  It
+contains the timestep, the maximum torque per replica, the maximum
+torque per atom (in any replica), potential gradients in the initial,
+final, and climbing replicas, the forward and backward energy
+barriers, the total reaction coordinate (RDT), and the normalized
+reaction coordinate and potential energy of each replica.
+
+The "maximum torque per replica" is the two-norm of the
+3N-length vector given by the cross product of a spin by its
+precession vector omega, in each replica, maximized across replicas, 
+which is what the {ttol} setting is checking against.  In this case, N is
+all the atoms in each replica.  The "maximum torque per atom" is the
+maximum torque component of any atom in any replica.  The potential
+gradients are the two-norm of the 3N-length magnetic precession vector 
+solely due to the interaction potential i.e. without adding in 
+inter-replica forces, and projected along the path tangent (as detailed 
+in Appendix D of "(BessarabA)"_#BessarabA).
+
+The "reaction coordinate" (RD) for each replica is the two-norm of the
+3N-length vector of geodesic distances between its spins and the preceding
+replica's spins (see equation (13) of "(BessarabA)"_#BessarabA), added to 
+the RD of the preceding replica. The RD of the first replica RD1 = 0.0; 
+the RD of the final replica RDN = RDT, the total reaction coordinate.  
+The normalized RDs are divided by RDT, so that they form a monotonically 
+increasing sequence from zero to one. When computing RD, N only includes 
+the spins being operated on by the fix neb/spin command.
+
+The forward (reverse) energy barrier is the potential energy of the
+highest replica minus the energy of the first (last) replica.
+
+Supplementary information for all replicas can be printed out to the
+screen and master log.lammps file by adding the verbose keyword. This
+information include the following. 
+The "GradVidottan" are the projections of the potential gradient for 
+the replica i on its tangent vector (as detailed in Appendix D of 
+"(BessarabA)"_#BessarabA).
+The "DNi" are the non normalized geodesic distances (see equation (13) 
+of "(BessarabA)"_#BessarabA), between a replica i and the next replica 
+i+1. For the last replica, this distance is not defined and a "NAN"
+value is the corresponding output. 
+
+When a NEB calculation does not converge properly, the supplementary
+information can help understanding what is going wrong. 
+
+When running on multiple partitions, LAMMPS produces additional log
+files for each partition, e.g. log.lammps.0, log.lammps.1, etc.  For a
+GNEB calculation, these contain the thermodynamic output for each
+replica.
+
+If "dump"_dump.html commands in the input script define a filename
+that includes a {universe} or {uloop} style "variable"_variable.html,
+then one dump file (per dump command) will be created for each
+replica.  At the end of the GNEB calculation, the final snapshot in
+each file will contain the sequence of snapshots that transition the
+system over the energy barrier.  Earlier snapshots will show the
+convergence of the replicas to the MEP.
+
+Likewise, "restart"_restart.html filenames can be specified with a
+{universe} or {uloop} style "variable"_variable.html, to generate
+restart files for each replica.  These may be useful if the GNEB
+calculation fails to converge properly to the MEP, and you wish to
+restart the calculation from an intermediate point with altered
+parameters.
+
+A c file script in provided in the tool/spin/interpolate_gneb
+directory, that interpolates the MEP given the information provided 
+by the verbose output option (as detailed in Appendix D of
+"(BessarabA)"_#BessarabA). 
+
+:line
+
+[Restrictions:]
+
+This command can only be used if LAMMPS was built with the SPIN
+package.  See the "Build package"_Build_package.html doc
+page for more info.
+
+:line
+
+[Related commands:]
+
+"min/spin"_min_spin.html, "fix neb/spin"_fix_neb_spin.html
+
+[Default:]
+
+none
+
+:line
+
+:link(BessarabA)
+[(BessarabA)] Bessarab, Uzdin, Jonsson, Comp Phys Comm, 196,
+335-347 (2015).

doc/src/pair_granular.txt

@@ -19,27 +19,29 @@ pair_style granular command :h3
 
 pair_style granular cutoff :pre
 
-cutoff = global cutoff (optional).  See discussion below. :l
+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_coeff * * hooke 1000.0 50.0 tangential linear_nohistory 1.0 0.4 damping mass_velocity :pre
 
 pair_style granular
-pair_coeff * * hertz 1000.0 50.0 tangential mindlin NULL 1.0 0.4 :pre
+pair_coeff * * hooke 1000.0 50.0 tangential linear_history 500.0 1.0 0.4 damping mass_velocity :pre
 
 pair_style granular
-pair_coeff * * hertz/material 1e8 0.3 tangential mindlin_rescale NULL 1.0 0.4 damping tsuji :pre
+pair_coeff * * hertz 1000.0 50.0 tangential mindlin 1000.0 1.0 0.4 :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_coeff * * hertz/material 1e8 0.3 0.3 tangential mindlin_rescale NULL 1.0 0.4 damping tsuji :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
+pair_coeff 1 * jkr 1000.0 500.0 0.3 10 tangential mindlin 800.0 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall
+pair_coeff 2 2 hertz 200.0 100.0 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 dmt 1000.0 50.0 0.3 0.0 tangential mindlin NULL 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 NULL 0.5 0.1 rolling sds 500.0 200.0 0.1 twisting marshall :pre
 
 [Description:]
 
@@ -57,18 +59,18 @@ 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
+automatically. This is shown in the last 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
+mixed coefficients for type 1 - type 2 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
+as shown in the fourth example: type 1 - type 1 interactions are based
+on a Johnson-Kendall-Roberts 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
+explicitly defined via the {pair_coeff 1 *} command, otherwise an
 error would result.
 
 :line
@@ -189,6 +191,7 @@ other settings, potentially also the twisting damping).  The options
 for the damping model currently supported are:
 
 {velocity}
+{mass_velocity}
 {viscoelastic}
 {tsuji} :ol
 
@@ -199,11 +202,23 @@ 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\}\
+\eta_n = \eta_\{n0\}
 \end\{equation\}
 
-Here, \(\gamma_n\) is the damping coefficient specified for the normal
-contact model, in units of {mass}/{time},
+Here, \(\eta_\{n0\}\) is the damping coefficient specified for the normal
+contact model, in units of {mass}/{time}.
+
+For {damping mass_velocity}, the normal damping is given by:
+
+\begin\{equation\}
+\eta_n = \eta_\{n0\} m_\{eff\}
+\end\{equation\}
+
+Here, \(\eta_\{n0\}\) is the damping coefficient specified for the normal
+contact model, in units of {mass}/{time} and
+\(m_\{eff\} = m_i m_j/(m_i + m_j)\) is the effective mass.
+Use {damping mass_velocity} to reproduce the damping behavior of
+{pair gran/hooke/*}.
 
 The {damping viscoelastic} model is based on the viscoelastic
 treatment of "(Brilliantov et al)"_#Brill1996, where the normal
@@ -213,11 +228,10 @@ damping is given by:
 \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}).
+Here, {a} is the contact radius, given by \(a =\sqrt\{R\delta\}\)
+for all models except {jkr}, for which it is given implicitly according
+to \(\delta = a^2/R - 2\sqrt\{\pi \gamma a/E\}\).  For {damping viscoelastic},
+\(\eta_\{n0\}\) 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
@@ -564,6 +578,20 @@ Finally, the twisting torque on each particle is given by:
 
 :line
 
+The {granular} pair style can reproduce the behavior of the
+{pair gran/*} styles with the appropriate settings (some very
+minor differences can be expected due to corrections in
+displacement history frame-of-reference, and the application
+of the torque at the center of the contact rather than
+at each particle). The first example above
+is equivalent to {pair gran/hooke 1000.0 NULL 50.0 50.0 0.4 1}.
+The second example is equivalent to
+{pair gran/hooke/history 1000.0 500.0 50.0 50.0 0.4 1}.
+The third example is equivalent to
+{pair gran/hertz/history 1000.0 500.0 50.0 50.0 0.4 1}.
+
+: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.
@@ -619,7 +647,7 @@ 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
+...} 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:
 
@@ -706,7 +734,7 @@ For the {pair_coeff} settings: {damping viscoelastic}, {rolling none},
 J. M., & Poschel, T. (1996).  Model for collisions in granular
 gases. Physical review E, 53(5), 5382.
 
-:link(Tsuji1992) 
+: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),

doc/src/pair_ilp_graphene_hbn.txt

@@ -47,11 +47,16 @@ equation can be found in "(Leven1)"_#Leven1 and "(Maaravi)"_#Maaravi2.
 It is important to include all the pairs to build the neighbor list for
 calculating the normals.
 
-NOTE: This potential is intended for interactions between two different
-layers of graphene or hexagonal boron nitride. Therefore, to avoid
-interaction within the same layers, each layer should have a separate
-molecule id and is recommended to use "full" atom style in the data
-file.
+NOTE: This potential (ILP) is intended for interlayer interactions between two
+different layers of graphene, hexagonal boron nitride (h-BN) and their hetero-junction.
+To perform a realistic simulation, this potential must be used in combination with
+intra-layer potential, such as "AIREBO"_pair_airebo.html or "Tersoff"_pair_tersoff.html potential.
+To keep the intra-layer properties unaffected, the interlayer interaction
+within the same layers should be avoided. Hence, each atom has to have a layer
+identifier such that atoms residing on the same layer interact via the
+appropriate intra-layer potential and atoms residing on different layers
+interact via the ILP. Here, the molecule id is chosen as the layer identifier,
+thus a data file with the "full" atom style is required to use this potential.
 
 The parameter file (e.g. BNCH.ILP), is intended for use with {metal}
 "units"_units.html, with energies in meV. Two additional parameters,
@@ -62,6 +67,10 @@ list for calculating the normals for each atom pair.
 NOTE: The parameters presented in the parameter file (e.g. BNCH.ILP),
 are fitted with taper function by setting the cutoff equal to 16.0
 Angstrom.  Using different cutoff or taper function should be careful.
+The parameters for atoms pairs between Boron and Nitrogen are fitted with
+a screened Coulomb interaction "coul/shield"_pair_coul_shield.html. Therefore,
+to simulated the properties of h-BN correctly, this potential must be used in
+combination with the pair style "coul/shield"_pair_coul_shield.html.
 
 NOTE: Two new sets of parameters of ILP for two-dimensional hexagonal
 Materials are presented in "(Ouyang)"_#Ouyang.  These parameters provide

doc/src/pair_kolmogorov_crespi_full.txt

@@ -42,10 +42,16 @@ the last term in the equation for {Vij} above. This is essential only
 when the tapper function is turned off. The formula of taper function
 can be found in pair style "ilp/graphene/hbn"_pair_ilp_graphene_hbn.html.
 
-NOTE: This potential is intended for interactions between two different
-graphene layers. Therefore, to avoid interaction within the same layers,
-each layer should have a separate molecule id and is recommended to use
-"full" atom style in the data file.
+NOTE: This potential (ILP) is intended for interlayer interactions between two
+different layers of graphene. To perform a realistic simulation, this potential 
+must be used in combination with intra-layer potential, such as 
+"AIREBO"_pair_airebo.html or "Tersoff"_pair_tersoff.html potential.
+To keep the intra-layer properties unaffected, the interlayer interaction
+within the same layers should be avoided. Hence, each atom has to have a layer
+identifier such that atoms residing on the same layer interact via the
+appropriate intra-layer potential and atoms residing on different layers
+interact via the ILP. Here, the molecule id is chosen as the layer identifier,
+thus a data file with the "full" atom style is required to use this potential.
 
 The parameter file (e.g. CH.KC), is intended for use with {metal}
 "units"_units.html, with energies in meV. Two additional parameters, {S},

doc/src/pair_meamc.txt

@@ -357,6 +357,13 @@ The {meam/c} style is provided in the USER-MEAMC package. It is
 only enabled if LAMMPS was built with that package.
 See the "Build package"_Build_package.html doc page for more info.
 
+The maximum number of elements, that can be read from the MEAM
+library file, is determined at compile time. The default is 5.
+If you need support for more elements, you have to change the
+define for the constant 'maxelt' at the beginning of the file
+src/USER-MEAMC/meam.h and update/recompile LAMMPS. There is no
+limit on the number of atoms types.
+
 [Related commands:]
 
 "pair_coeff"_pair_coeff.html, "pair_style eam"_pair_eam.html,

doc/src/pair_spin_dmi.txt

@@ -88,4 +88,4 @@ package"_Build_package.html doc page for more info.
 Physical Review B, 88(18), 184422. (2013).
 :link(Tranchida5)
 [(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson,
-Journal of Computational Physics, (2018).
+Journal of Computational Physics, 372, 406-425, (2018).

doc/src/pair_spin_exchange.txt

@@ -95,4 +95,4 @@ package"_Build_package.html doc page for more info.
 
 :link(Tranchida3)
 [(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson,
-Journal of Computational Physics, (2018).
+Journal of Computational Physics, 372, 406-425, (2018).

doc/src/pair_spin_magelec.txt

@@ -70,4 +70,4 @@ package"_Build_package.html doc page for more info.
 
 :link(Tranchida4)
 [(Tranchida)] Tranchida, Plimpton, Thibaudeau, and Thompson,
-Journal of Computational Physics, (2018).
+Journal of Computational Physics, 372, 406-425, (2018).

doc/src/pair_spin_neel.txt

@@ -80,4 +80,4 @@ package"_Build_package.html doc page for more info.
 
 :link(Tranchida6)
 [(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson,
-Journal of Computational Physics, (2018).
+Journal of Computational Physics, 372, 406-425, (2018).

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

@@ -200,6 +200,7 @@ Berkowitz
 berlin
 Berne
 Bertotti
+Bessarab
 Beutler
 bgq
 Bh
@@ -289,6 +290,7 @@ Cao
 Capolungo
 Caro
 cartesian
+CasP
 Caswell
 Cates
 Cavium
@@ -348,6 +350,7 @@ Cii
 Cij
 cis
 civ
+Clang
 clearstore
 Cleary
 Clebsch
@@ -590,6 +593,7 @@ Dmax
 dmg
 dmi
 dnf
+DNi
 Dobson
 Dodds
 dodgerblue
@@ -656,6 +660,7 @@ ec
 Ec
 ecoul
 ecp
+Ecut
 edgeIDs
 edihed
 edim
@@ -960,6 +965,8 @@ gmail
 gmake
 gmask
 Gmask
+gneb
+GNEB
 googlemail
 Gordan
 GPa
@@ -1134,6 +1141,7 @@ infty
 inhomogeneities
 inhomogeneous
 init
+initio
 initializations
 InP
 inregion
@@ -1255,6 +1263,7 @@ Jy
 Jz
 jzimmer
 Kadiri
+Kai
 Kalia
 Kamberaj
 Kapfer
@@ -1285,6 +1294,7 @@ Keir
 Kelchner
 Kelkar
 Kemper
+keV
 Keyes
 Khersonskii
 Khrapak
@@ -1538,6 +1548,7 @@ Mattox
 Mattson
 maxangle
 maxbond
+maxelt
 maxeval
 maxfiles
 Maxfoo
@@ -1627,6 +1638,7 @@ minima
 minimizations
 minimizer
 minimizers
+minneigh
 minorder
 minSteps
 mintcream
@@ -2360,6 +2372,7 @@ rNEMD
 ro
 Rochus
 Rockett
+Rodrigues
 Rohart
 Ronchetti
 Rosati
@@ -2764,6 +2777,7 @@ tt
 Tt
 TThis
 ttm
+ttol
 tu
 Tuckerman
 tue
@@ -2809,6 +2823,7 @@ unimodal
 unitless
 Universite
 unix
+unmaintained
 unoptimized
 unpadded
 unphysical
@@ -2835,6 +2850,7 @@ utsa
 Uttormark
 uvm
 uwo
+Uzdin
 vacf
 valent
 Valeriu
@@ -2934,7 +2950,7 @@ wB
 Wbody
 webpage
 Weckner
-WeinenE
+WeinanE
 Wennberg
 Westview
 wget
@@ -2944,6 +2960,7 @@ Wi
 Wicaksono
 wih
 Wijk
+Wikipedia
 wildcard
 Wildcard
 Wirnsberger

examples/SPIN/gneb/README

@@ -0,0 +1,13 @@
+Perform geodesic NEB calculations for spin configurations.
+The two examples are:
+- the magnetic switching of an iron nanoisland
+- the collapse of a magnetic skyrmion
+
+Run those examples as:
+
+mpirun -np 3 lmp_mpi -in in.gneb.iron -partition 3x1
+
+You should be able to use any number of replicas >= 3.
+
+In the interpolate/ directory, a c routine is provided to
+interpolate the MEP. 

examples/SPIN/gneb/iron/final.iron_spin

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examples/SPIN/gneb/iron/in.gneb.iron

@@ -0,0 +1,50 @@
+
+units 		metal
+dimension 	3
+boundary 	p p f
+atom_style 	spin
+
+# necessary for the serial algorithm (sametag)
+atom_modify 	map array 
+
+# setting mass, mag. moments, and interactions for bcc iron
+# (mass not necessary for fixed lattice calculation)
+
+read_data       initial.iron_spin
+mass		1 55.845
+
+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 0.1 0.0 0.0 1.0 anisotropy 0.0001 1.0 0.0 0.0 
+fix_modify	1 energy yes
+fix		3 all neb/spin 1.0  
+
+timestep	0.0001
+thermo		100
+
+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]
+
+thermo          100
+thermo_style    custom step time v_magx v_magz v_magnorm etotal
+thermo_modify   format float %20.15g
+
+compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
+variable	u universe 1 2 3 4
+dump 		1 all custom 200 dump.$u type x y z c_outsp[1] c_outsp[2] c_outsp[3]
+
+min_style	spin
+min_modify 	alpha_damp 1.0 discrete_factor 10.0
+neb/spin	1.0e-12 1.0e-12 200000 100000 1000 final final.iron_spin verbose

examples/SPIN/gneb/iron/initial.iron_spin

@@ -0,0 +1,82 @@
+LAMMPS data file via write_data, version 4 Jan 2019, timestep = 0
+
+32 atoms
+1 atom types
+
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+0.0000000000000000e+00 1.1465999999999999e+01 ylo yhi
+0.0000000000000000e+00 2.8664999999999998e+00 zlo zhi
+
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+
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+
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examples/SPIN/gneb/skyrmion/final.skyrmion

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+375 2.5 54.0 42.0 0.0 0.0 0.0 1.0
+376 2.5 54.0 45.0 0.0 0.0 0.0 1.0
+377 2.5 54.0 48.0 0.0 0.0 0.0 1.0
+378 2.5 54.0 51.0 0.0 0.0 0.0 1.0
+379 2.5 54.0 54.0 0.0 0.0 0.0 1.0
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+383 2.5 57.0 6.0 0.0 0.0 0.0 1.0
+384 2.5 57.0 9.0 0.0 0.0 0.0 1.0
+385 2.5 57.0 12.0 0.0 0.0 0.0 1.0
+386 2.5 57.0 15.0 0.0 0.0 0.0 1.0
+387 2.5 57.0 18.0 0.0 0.0 0.0 1.0
+388 2.5 57.0 21.0 0.0 0.0 0.0 1.0
+389 2.5 57.0 24.0 0.0 0.0 0.0 1.0
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+391 2.5 57.0 30.0 0.0 0.0 0.0 1.0
+392 2.5 57.0 33.0 0.0 0.0 0.0 1.0
+393 2.5 57.0 36.0 0.0 0.0 0.0 1.0
+394 2.5 57.0 39.0 0.0 0.0 0.0 1.0
+395 2.5 57.0 42.0 0.0 0.0 0.0 1.0
+396 2.5 57.0 45.0 0.0 0.0 0.0 1.0
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+398 2.5 57.0 51.0 0.0 0.0 0.0 1.0
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examples/SPIN/gneb/skyrmion/in.gneb.skyrmion

@@ -0,0 +1,47 @@
+
+units 		metal
+dimension 	3
+boundary 	p p f
+atom_style 	spin
+
+# necessary for the serial algorithm (sametag)
+atom_modify 	map array 
+
+# setting mass, mag. moments, and interactions for bcc iron
+# (mass not necessary for fixed lattice calculation)
+
+read_data       initial.skyrmion
+mass		1 55.845
+
+pair_style 	hybrid/overlay spin/exchange 3.1 spin/dmi 3.1
+pair_coeff 	* * spin/exchange exchange 3.1 0.01593 0.06626915552 1.211
+pair_coeff 	* * spin/dmi dmi 3.1 0.12e-03 0.0 0.0 1.0
+
+neighbor 	0.1 bin
+neigh_modify 	every 10 check yes delay 20
+
+fix 		1 all precession/spin zeeman 0.0 0.0 0.0 1.0 anisotropy 5e-05 0.0 0.0 1.0 
+fix_modify	1 energy yes
+fix 		2 all langevin/spin 0.0 0.0 21
+fix		3 all neb/spin 1.0  
+
+timestep	0.0001
+
+compute 	out_mag    all spin
+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]
+
+thermo          100
+thermo_style    custom step time v_magx v_magz v_magnorm etotal
+thermo_modify   format float %20.15g
+
+compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
+variable	u universe 1 2 3 4
+dump 		1 all custom 1 dump.$u type x y z c_outsp[1] c_outsp[2] c_outsp[3]
+
+min_style	spin
+min_modify 	alpha_damp 1.0 discrete_factor 10.0
+neb/spin	1.0e-9 1.0e-9 10000 10000 10 final final.skyrmion

examples/SPIN/gneb/skyrmion/initial.skyrmion

@@ -0,0 +1,818 @@
+LAMMPS data file via write_data, version 28 Feb 2019, timestep = 6
+
+400 atoms
+1 atom types
+
+0.0000000000000000e+00 6.0000000000000000e+01 xlo xhi
+0.0000000000000000e+00 6.0000000000000000e+01 ylo yhi
+0.0000000000000000e+00 3.0000000000000000e+00 zlo zhi
+
+Masses
+
+1 55.845
+
+Atoms # spin
+
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examples/SPIN/read_restart/in.spin.read_data

@@ -40,6 +40,6 @@ thermo_style    custom step time v_magnorm v_emag v_tmag temp etotal
 thermo_modify   format float %20.15g
 
 compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
-dump 		10 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
+dump 		1 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
 
 run 		100

examples/SPIN/setforce_spin/in.spinmin.setforce

@@ -0,0 +1,59 @@
+
+units 		metal
+dimension 	3
+boundary 	f f f
+atom_style 	spin
+
+# necessary for the serial algorithm (sametag)
+atom_modify 	map array 
+
+lattice 	sc 3.0
+region 		box block 0.0 10.0 0.0 10.0 0.0 1.0
+create_box 	2 box
+region		reg1 block 0.0 10.0 	0.0 5.0 	0.0 1.0
+region		reg2 block 0.0 10.0 	6.0 10.0 	0.0 1.0
+create_atoms 	1 region reg1 
+create_atoms 	2 region reg2
+
+# setting mass, mag. moments, and interactions for bcc iron
+
+mass		1 55.845
+mass		2 55.845
+set 		region reg1 spin 2.2 0.0 0.0 1.0
+set 		region reg2 spin/random 31 2.2
+
+group 		fixed_spin region reg1
+
+pair_style 	hybrid/overlay spin/exchange 3.1 spin/dmi 3.1
+pair_coeff 	* * spin/exchange exchange 3.1 -0.01593 0.06626915552 1.211
+pair_coeff	* * spin/dmi dmi 3.1 0.12e-03 0.0 0.0 1.0
+
+neighbor 	0.1 bin
+neigh_modify 	every 10 check yes delay 20
+
+fix 		1 all precession/spin zeeman 0.0 0.0 0.0 1.0 anisotropy 5e-05 0.0 0.0 1.0 
+fix_modify	1 energy yes
+fix 		2 fixed_spin setforce/spin 0.0 0.0 0.0
+fix 		3 all langevin/spin 0.0 0.1 21
+fix		4 all nve/spin lattice no 
+
+timestep	0.0001
+
+compute 	out_mag    all spin
+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          1000
+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 1000 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[5] c_outsp[6] c_outsp[7]
+
+min_style	spin
+min_modify 	alpha_damp 1.0 discrete_factor 20.0
+minimize        1.0e-16 1.0e-16 50000 1000

examples/USER/misc/electron_stopping/Si.Si.elstop

@@ -0,0 +1,14 @@
+# Electronic stopping for Si in Si
+# Uses metal units
+# Kinetic energy in eV, stopping power in eV/A
+# For other atom types, add columns.
+
+# energy    Si in Si
+  3918.2      6.541
+ 15672.9     13.091
+ 35263.9     19.660
+ 62691.5     26.257
+ 97955.4     32.889
+141055.9     39.566
+191992.0     46.292
+250766.1     53.074

examples/USER/misc/electron_stopping/Si.sw

@@ -0,0 +1 @@
+../../../../potentials/Si.sw

examples/USER/misc/electron_stopping/in.elstop

@@ -0,0 +1,38 @@
+# Test case / example for fix electron/stopping
+# Perfect Si lattice with one primary knock-on atom.
+#
+# Also uses fix dt/reset, as one should when energies are high
+# enough to require electronic stopping.
+
+units metal
+boundary p p p
+timestep 0.0001
+
+lattice fcc 5.431
+
+region rbox block -10 10 -10 10 -10 10
+create_box 1 rbox
+
+mass 1 28.0855
+
+create_atoms 1 box
+
+velocity all create 300 42534 mom yes rot yes
+
+group gPKA id 1
+velocity gPKA set 1120 1620 389
+
+pair_style sw
+pair_coeff * * Si.sw Si
+
+fix fdt all dt/reset 1 NULL 0.001 0.1 emax 20.0
+fix fel all electron/stopping 1.0 Si.Si.elstop
+fix fnve all nve
+
+thermo 10
+thermo_style custom step time dt f_fel
+
+#compute ek all ke/atom
+#dump mydump all custom 200 elstop.dump id x y z vx vy vz fx fy fz c_ek
+
+run 5000

examples/USER/misc/electron_stopping/in.elstop.only

@@ -0,0 +1,39 @@
+# Test case / example for fix electron/stopping
+# One fast atom, no other interactions.
+# Stopping only applied in a smaller box in the middle.
+#
+# Also uses fix dt/reset, as one should when energies are high
+# enough to require electronic stopping.
+
+units metal
+boundary p p p
+timestep 0.0001
+
+lattice fcc 1
+
+region rbox block -100 100 -100 100 -100 100
+region rsmallbox block -90 90 -90 90 -90 90
+
+create_box 1 rbox
+
+mass 1 28.0855
+
+create_atoms 1 single 0 0 0
+velocity all set 1120 1620 389
+
+pair_style zero 1
+pair_coeff * * 1
+
+fix fdt all dt/reset 1 NULL 0.001 0.1 emax 20.0
+fix fel all electron/stopping 1.0 Si.Si.elstop minneigh 0 region rsmallbox
+fix fnve all nve
+
+compute ek all ke/atom
+compute ektot all reduce sum c_ek
+
+thermo 100
+thermo_style custom step time dt f_fel c_ektot
+
+#dump mydump all custom 200 elstop.only.dump id x y z vx vy vz fx fy fz c_ek
+
+run 10000

examples/USER/misc/electron_stopping/log.20Mar19.elstop.g++.1

@@ -0,0 +1,597 @@
+LAMMPS (28 Feb 2019)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
+  using 1 OpenMP thread(s) per MPI task
+# Test case / example for fix electron/stopping
+# Perfect Si lattice with one primary knock-on atom.
+#
+# Also uses fix dt/reset, as one should when energies are high
+# enough to require electronic stopping.
+
+units metal
+boundary p p p
+timestep 0.0001
+
+lattice fcc 5.431
+Lattice spacing in x,y,z = 5.431 5.431 5.431
+
+region rbox block -10 10 -10 10 -10 10
+create_box 1 rbox
+Created orthogonal box = (-54.31 -54.31 -54.31) to (54.31 54.31 54.31)
+  1 by 1 by 1 MPI processor grid
+
+mass 1 28.0855
+
+create_atoms 1 box
+Created 32000 atoms
+  create_atoms CPU = 0.00282311 secs
+
+velocity all create 300 42534 mom yes rot yes
+
+group gPKA id 1
+1 atoms in group gPKA
+velocity gPKA set 1120 1620 389
+
+pair_style sw
+pair_coeff * * Si.sw Si
+Reading potential file Si.sw with DATE: 2007-06-11
+
+fix fdt all dt/reset 1 NULL 0.001 0.1 emax 20.0
+fix fel all electron/stopping 1.0 Si.Si.elstop
+fix fnve all nve
+
+thermo 10
+thermo_style custom step time dt f_fel
+
+#compute ek all ke/atom
+#dump mydump all custom 200 elstop.dump id x y z vx vy vz fx fy fz c_ek
+
+run 5000
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 5.77118
+  ghost atom cutoff = 5.77118
+  binsize = 2.88559, bins = 38 38 38
+  2 neighbor lists, perpetual/occasional/extra = 1 1 0
+  (1) pair sw, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (2) fix electron/stopping, occasional, copy from (1)
+      attributes: full, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 10.89 | 10.89 | 10.89 Mbytes
+Step Time Dt f_fel 
+       0            0  4.98128e-05            0 
+      10 0.00030141297 7.4132113e-06    143.83504 
+      20 0.00035951427 6.0316944e-06    171.53673 
+      30 0.00057458971 3.5117251e-05    274.07596 
+      40 0.00086591312 5.8243334e-06    412.87446 
+      50 0.00090045701 2.1026443e-06    429.31458 
+      60 0.00091828462 1.5368285e-06    437.79421 
+      70 0.00093305888 1.4643253e-06    444.81982 
+      80 0.00094860749 1.7487528e-06    452.21378 
+      90 0.00097032161 3.0786693e-06    462.54244 
+     100 0.0010787914 4.9354535e-05    514.16832 
+     110 0.0012080771 2.321306e-06    575.68374 
+     120 0.0012239682 1.0510328e-06    583.23471 
+     130 0.0012325497 6.8272619e-07    587.30872 
+     140 0.0012385196 5.1205819e-07    590.14077 
+     150  0.001243165 4.1524338e-07    592.34294 
+     160 0.0012470201 3.5380824e-07     594.1694 
+     170 0.0012503578 3.1203776e-07    595.74992 
+     180 0.0012533367 2.8236408e-07    597.15986 
+     190 0.0012560575 2.6071908e-07    598.44711 
+     200 0.0012585888 2.4474123e-07    599.64431 
+     210 0.0012609803 2.3298466e-07    600.77504 
+     220 0.0012632696 2.2453464e-07    601.85726 
+     230 0.0012654871 2.1880713e-07    602.90531 
+     240 0.0012676582 2.1543942e-07    603.93128 
+     250 0.0012698054 2.1422997e-07    604.94591 
+     260 0.0012719499 2.1510772e-07    605.95925 
+     270 0.0012741128 2.1812163e-07    606.98126 
+     280 0.0012763159 2.2344765e-07    608.02243 
+     290 0.0012785839 2.3141489e-07    609.09436 
+     300 0.0012809453 2.425587e-07    610.21066 
+     310 0.0012834353 2.577174e-07    611.38806 
+     320 0.0012860996 2.7820843e-07    612.64822 
+     330 0.0012890001 3.0616141e-07    614.02061 
+     340 0.0012922261 3.4518994e-07    615.54764 
+     350 0.0012959145 4.0187423e-07    617.29438 
+     360 0.0013002933 4.894618e-07    619.36917 
+     370 0.0013057872 6.3886828e-07    621.97388 
+     380 0.0013133355 9.4153332e-07    625.55502 
+     390 0.0013257779 1.8246429e-06    631.46263 
+     400 0.0013651328 1.4820738e-05    650.16503 
+     410 0.0016916358 4.5528312e-05     805.3327 
+     420 0.0020836696 2.6189823e-05    991.45963 
+     430  0.002192113 5.1312984e-06    1042.8979 
+     440 0.0022530638 1.1643276e-05    1071.7967 
+     450 0.0025312898 1.5833134e-05    1203.6961 
+     460 0.0028677695 3.9078523e-05    1363.0792 
+     470 0.0032653301 3.9299497e-05    1551.2027 
+     480 0.0036647478 4.1100578e-05    1739.9906 
+     490 0.0040772194 3.6017871e-05    1934.7262 
+     500  0.004246426 1.1620229e-05    2014.5366 
+     510 0.0045410379 2.1151987e-05    2153.4172 
+     520 0.0048951987 4.2067206e-05    2320.2216 
+     530 0.0051251181 5.9152255e-06    2428.4156 
+     540 0.0051740847 5.0188036e-06    2451.4388 
+     550 0.0053207575 4.1618335e-05    2520.4067 
+     560 0.0054412772 2.3641932e-06    2577.0541 
+     570  0.005457552 1.0847369e-06    2584.6937 
+     580 0.0054664476 7.1198746e-07    2588.8658 
+     590 0.0054726999 5.3933302e-07     2591.796 
+     600 0.0054776139 4.4178461e-07    2594.0976 
+     610 0.0054817341 3.8039473e-07    2596.0263 
+     620 0.0054853401 3.3924667e-07    2597.7135 
+     630 0.0054885957 3.1069211e-07    2599.2361 
+     640 0.0054916066 2.9064829e-07    2600.6439 
+     650 0.0054944462 2.7678405e-07    2601.9712 
+     660 0.0054971697 2.6772348e-07     2603.244 
+     670 0.0054998211 2.6266505e-07    2604.4829 
+     680 0.0055024383 2.6119265e-07    2605.7058 
+     690 0.0055050563 2.6318733e-07     2606.929 
+     700 0.0055077103 2.6880326e-07    2608.1691 
+     710 0.0055104383 2.7849814e-07    2609.4439 
+     720 0.0055132846 2.9313007e-07    2610.7742 
+     730 0.0055163044 3.141612e-07     2612.186 
+     740 0.0055195719 3.4406726e-07     2613.714 
+     750 0.0055231932 3.8719688e-07    2615.4081 
+     760 0.0055273329 4.5174267e-07    2617.3455 
+     770 0.0055322712 5.5490406e-07    2619.6579 
+     780 0.0055385515 7.3934538e-07    2622.6004 
+     790 0.0055474645 1.1452909e-06    2626.7792 
+     800 0.0055635927 2.6160295e-06    2634.3465 
+     810 0.0057044835 3.9642931e-05    2700.5132 
+     820 0.0060307501 2.9394558e-05    2853.6539 
+     830 0.0063374404 8.5188148e-06    2997.4768 
+     840 0.0063740052 1.4828325e-06    3014.6052 
+     850 0.0063848364 7.5985425e-07    3019.6727 
+     860 0.0063911095 5.0258852e-07    3022.6045 
+     870 0.0063954921 3.7335256e-07    3024.6508 
+     880 0.0063988506 2.9643864e-07    3026.2175 
+     890 0.0064015712 2.4575869e-07    3027.4855 
+     900 0.0064038584 2.1001191e-07    3028.5506 
+     910 0.0064058333 1.8353805e-07    3029.4694 
+     920  0.006407573 1.6320008e-07    3030.2782 
+     930 0.0064091297 1.4712417e-07    3031.0014 
+     940 0.0064105403 1.3412445e-07    3031.6562 
+     950 0.0064118317 1.2341509e-07    3032.2552 
+     960 0.0064130243 1.1445544e-07     3032.808 
+     970 0.0064141337 1.0686175e-07    3033.3219 
+     980 0.0064151722 1.0035437e-07    3033.8027 
+     990 0.0064161498 9.4724852e-08    3034.2549 
+    1000 0.0064170744 8.9814769e-08    3034.6824 
+    1010 0.0064179527 8.5501639e-08    3035.0882 
+    1020 0.0064187902 8.1689338e-08     3035.475 
+    1030 0.0064195915 7.8301418e-08    3035.8449 
+    1040 0.0064203606 7.5276356e-08    3036.1997 
+    1050 0.0064211009 7.2564109e-08     3036.541 
+    1060 0.0064218154 7.0123584e-08    3036.8703 
+    1070 0.0064225065 6.7920744e-08    3037.1886 
+    1080 0.0064231766 6.5927178e-08    3037.4971 
+    1090 0.0064238276 6.4119002e-08    3037.7967 
+    1100 0.0064244613 6.2476011e-08    3038.0882 
+    1110 0.0064250792 6.0981016e-08    3038.3724 
+    1120 0.0064256828 5.9619315e-08    3038.6498 
+    1130 0.0064262733 5.8378279e-08    3038.9212 
+    1140 0.0064268519 5.7247013e-08    3039.1869 
+    1150 0.0064274196 5.6216088e-08    3039.4476 
+    1160 0.0064279775 5.5277318e-08    3039.7037 
+    1170 0.0064285264 5.4423582e-08    3039.9556 
+    1180  0.006429067 5.3648672e-08    3040.2036 
+    1190 0.0064296003 5.294717e-08    3040.4482 
+    1200 0.0064301269 5.2314351e-08    3040.6897 
+    1210 0.0064306474 5.1746091e-08    3040.9283 
+    1220 0.0064311625 5.1238802e-08    3041.1644 
+    1230 0.0064316729 5.0789368e-08    3041.3983 
+    1240 0.0064321789 5.0395101e-08    3041.6301 
+    1250 0.0064326813 5.0053692e-08    3041.8603 
+    1260 0.0064331805 4.9763183e-08    3042.0889 
+    1270  0.006433677 4.9521937e-08    3042.3163 
+    1280 0.0064341713 4.9328614e-08    3042.5427 
+    1290 0.0064346639 4.9182151e-08    3042.7682 
+    1300 0.0064351552 4.9081752e-08    3042.9931 
+    1310 0.0064356458 4.9026872e-08    3043.2177 
+    1320  0.006436136 4.9017214e-08    3043.4421 
+    1330 0.0064366262 4.9052721e-08    3043.6666 
+    1340 0.0064371171 4.9133581e-08    3043.8912 
+    1350  0.006437609 4.9260223e-08    3044.1164 
+    1360 0.0064381023 4.9433327e-08    3044.3422 
+    1370 0.0064385976 4.9653831e-08     3044.569 
+    1380 0.0064390953 4.9922944e-08    3044.7968 
+    1390 0.0064395959 5.0242164e-08    3045.0261 
+    1400    0.0064401 5.0613297e-08    3045.2568 
+    1410  0.006440608 5.1038483e-08    3045.4895 
+    1420 0.0064411205 5.1520228e-08    3045.7242 
+    1430 0.0064416381 5.2061443e-08    3045.9613 
+    1440 0.0064421614 5.2665486e-08     3046.201 
+    1450  0.006442691 5.3336219e-08    3046.4437 
+    1460 0.0064432276 5.4078074e-08    3046.6896 
+    1470  0.006443772 5.4896126e-08    3046.9392 
+    1480 0.0064443249 5.5796191e-08    3047.1927 
+    1490 0.0064448873 5.6784937e-08    3047.4506 
+    1500 0.0064454599 5.7870017e-08    3047.7132 
+    1510 0.0064460439 5.9060235e-08    3047.9812 
+    1520 0.0064466403 6.0365742e-08    3048.2549 
+    1530 0.0064472503 6.1798287e-08    3048.5349 
+    1540 0.0064478752 6.337151e-08     3048.822 
+    1550 0.0064485166 6.5101323e-08    3049.1166 
+    1560  0.006449176 6.7006371e-08    3049.4197 
+    1570 0.0064498554 6.9108623e-08     3049.732 
+    1580 0.0064505567 7.1434118e-08    3050.0546 
+    1590 0.0064512824 7.4013931e-08    3050.3885 
+    1600 0.0064520352 7.6885409e-08    3050.7351 
+    1610 0.0064528182 8.0093813e-08    3051.0957 
+    1620  0.006453635 8.3694486e-08     3051.472 
+    1630 0.0064544898 8.7755778e-08    3051.8661 
+    1640 0.0064553876 9.2363047e-08    3052.2802 
+    1650 0.0064563343 9.7624226e-08    3052.7171 
+    1660 0.0064573371 1.0367771e-07    3053.1801 
+    1670 0.0064584046 1.1070379e-07    3053.6733 
+    1680 0.0064595476 1.1894157e-07    3054.2017 
+    1690 0.0064607796 1.2871484e-07    3054.7716 
+    1700 0.0064621178 1.4047265e-07     3055.391 
+    1710 0.0064635847 1.5485559e-07    3056.0705 
+    1720 0.0064652106 1.7280864e-07    3056.8241 
+    1730 0.0064670371 1.9578361e-07    3057.6713 
+    1740 0.0064691241 2.261258e-07    3058.6401 
+    1750 0.0064715615 2.6787347e-07    3059.7724 
+    1760 0.0064744931 3.2858822e-07    3061.1353 
+    1770 0.0064781697 4.2416554e-07    3062.8461 
+    1780 0.0064830857 5.9426003e-07    3065.1356 
+    1790 0.0064904338 9.7042692e-07    3068.5608 
+    1800  0.006504521 2.3570057e-06    3075.1339 
+    1810 0.0066489551 2.5350137e-05     3142.596 
+    1820 0.0067263358 2.0982567e-06    3178.7218 
+    1830 0.0067413263 1.0389873e-06    3185.7117 
+    1840 0.0067499639 7.021379e-07     3189.736 
+    1850 0.0067561793 5.4125252e-07    3192.6298 
+    1860   0.00676114 4.4920623e-07     3194.938 
+    1870 0.0067653505 3.911598e-07    3196.8961 
+    1880 0.0067690759 3.5254253e-07    3198.6279 
+    1890 0.0067724748 3.2626983e-07    3200.2074 
+    1900 0.0067756518 3.0855768e-07    3201.6834 
+    1910 0.0067786819 2.9728199e-07    3203.0908 
+    1920 0.0067816236 2.9125633e-07     3204.457 
+    1930 0.0067845263 2.8989566e-07    3205.8049 
+    1940 0.0067874357 2.9306921e-07     3207.156 
+    1950 0.0067903982 3.0106889e-07    3208.5318 
+    1960  0.006793465 3.1467844e-07    3209.9563 
+    1970 0.0067966982 3.3537556e-07    3211.4583 
+    1980 0.0068001793 3.6577201e-07    3213.0759 
+    1990 0.0068040239 4.1056728e-07     3214.863 
+    2000 0.0068084116 4.7878365e-07    3216.9034 
+    2010 0.0068136505 5.897605e-07    3219.3409 
+    2020 0.0068203489 7.9292336e-07    3222.4591 
+    2030 0.0068300039 1.259738e-06    3226.9568 
+    2040 0.0068484332 3.1869606e-06    3235.5484 
+    2050   0.00704302 3.1308435e-05    3326.3332 
+    2060 0.0073582601 1.9393034e-05    3473.3099 
+    2070 0.0076291992 6.1118973e-06    3599.5265 
+    2080 0.0076591273 1.397136e-06    3613.4525 
+    2090 0.0076695786 7.5324795e-07      3618.31 
+    2100 0.0076758692 5.1095756e-07    3621.2308 
+    2110 0.0076803593 3.8613872e-07    3623.3137 
+    2120 0.0076838539 3.1077232e-07    3624.9334 
+    2130 0.0076867208 2.6065521e-07    3626.2611 
+    2140 0.0076891581 2.2509342e-07    3627.3889 
+    2150  0.007691284 1.9865679e-07     3628.372 
+    2160 0.0076931748 1.7830513e-07    3629.2457 
+    2170 0.0076948825 1.6220815e-07    3630.0343 
+    2180 0.0076964439 1.4920028e-07    3630.7548 
+    2190 0.0076978861 1.3850522e-07      3631.42 
+    2200 0.0076992297 1.2958672e-07    3632.0393 
+    2210 0.0077004907 1.2206289e-07    3632.6203 
+    2220 0.0077016817 1.1565477e-07    3633.1687 
+    2230 0.0077028128 1.1015407e-07    3633.6892 
+    2240 0.0077038924 1.0540234e-07    3634.1859 
+    2250 0.0077049274 1.0127711e-07    3634.6618 
+    2260 0.0077059236 9.7682361e-08    3635.1197 
+    2270 0.0077068859 9.454193e-08    3635.5619 
+    2280 0.0077078187 9.1794781e-08    3635.9903 
+    2290 0.0077087255 8.9391579e-08    3636.4067 
+    2300 0.0077096098 8.7292175e-08    3636.8125 
+    2310 0.0077104742 8.5463727e-08    3637.2092 
+    2320 0.0077113216 8.3879281e-08     3637.598 
+    2330  0.007712154 8.2516693e-08    3637.9798 
+    2340 0.0077129738 8.1357804e-08    3638.3557 
+    2350 0.0077137829 8.0387796e-08    3638.7267 
+    2360 0.0077145831 7.9594705e-08    3639.0935 
+    2370 0.0077153761 7.8969036e-08     3639.457 
+    2380 0.0077161635 7.8503481e-08    3639.8178 
+    2390  0.007716947 7.8192701e-08    3640.1769 
+    2400 0.0077177281 7.8033171e-08    3640.5348 
+    2410 0.0077185083 7.8023089e-08    3640.8923 
+    2420  0.007719289 7.8162318e-08      3641.25 
+    2430 0.0077200718 7.8452384e-08    3641.6087 
+    2440 0.0077208582 7.8896522e-08    3641.9691 
+    2450 0.0077216498 7.9499759e-08    3642.3318 
+    2460 0.0077224481 8.026906e-08    3642.6977 
+    2470 0.0077232549 8.1213529e-08    3643.0675 
+    2480 0.0077240719 8.2344683e-08     3643.442 
+    2490 0.0077249012 8.3676812e-08    3643.8222 
+    2500 0.0077257448 8.5227445e-08     3644.209 
+    2510 0.0077266049 8.7017961e-08    3644.6035 
+    2520 0.0077274841 8.9074372e-08    3645.0068 
+    2530 0.0077283852 9.1428349e-08    3645.4203 
+    2540 0.0077293113 9.4118559e-08    3645.8454 
+    2550 0.0077302659 9.7192441e-08    3646.2837 
+    2560 0.0077312533 1.0070857e-07    3646.7372 
+    2570 0.0077322781 1.0473987e-07     3647.208 
+    2580 0.0077333458 1.0937801e-07    3647.6987 
+    2590  0.007734463 1.1473957e-07    3648.2124 
+    2600 0.0077356377 1.2097481e-07    3648.7528 
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+    2620 0.0077381998 1.3691837e-07    3649.9322 
+    2630 0.0077396139 1.4724543e-07    3650.5836 
+    2640 0.0077411406 1.5975888e-07    3651.2873 
+    2650 0.0077428048 1.7517253e-07    3652.0548 
+    2660 0.0077446398 1.9454711e-07    3652.9016 
+    2670 0.0077466922 2.1952673e-07    3653.8493 
+    2680 0.0077490288 2.5279733e-07     3654.929 
+    2690 0.0077517515 2.9905194e-07     3656.188 
+    2700 0.0077550252 3.6725589e-07    3657.7029 
+    2710 0.0077591434 4.7681009e-07    3659.6101 
+    2720 0.0077647038 6.7839241e-07    3662.1874 
+    2730  0.007773234 1.1552111e-06    3666.1446 
+    2740 0.0077911374 3.3406902e-06     3674.458 
+    2750    0.0079702 8.4184292e-06    3757.6696 
+    2760  0.008006114 1.4496754e-06    3774.3449 
+    2770 0.0080166835 7.3926386e-07    3779.2462 
+    2780 0.0080227734 4.8640717e-07    3782.0672 
+    2790 0.0080270055 3.5945058e-07    3784.0255 
+    2800 0.0080302318 2.8394384e-07     3785.517 
+    2810  0.008032832 2.3422206e-07    3786.7179 
+    2820 0.0080350072 1.9916814e-07    3787.7215 
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+    2840 0.0080385144 1.5327931e-07    3789.3377 
+    2850 0.0080399734 1.3751893e-07    3790.0091 
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+    2890 0.0080446097 9.7988142e-08    3792.1386 
+    2900 0.0080455599 9.1577084e-08    3792.5741 
+    2910   0.00804645 8.6019912e-08    3792.9818 
+    2920 0.0080472879 8.1161402e-08    3793.3653 
+    2930 0.0080480798 7.6881575e-08    3793.7275 
+    2940 0.0080488311 7.3086284e-08    3794.0709 
+    2950 0.0080495465 6.9700651e-08    3794.3977 
+    2960 0.0080502295 6.666441e-08    3794.7094 
+    2970 0.0080508836 6.3928523e-08    3795.0078 
+    2980 0.0080515116 6.1452701e-08    3795.2941 
+    2990 0.0080521158 5.9203545e-08    3795.5694 
+    3000 0.0080526985 5.7153146e-08    3795.8346 
+    3010 0.0080532614 5.5278009e-08    3796.0908 
+    3020 0.0080538063 5.3558217e-08    3796.3386 
+    3030 0.0080543347 5.1976785e-08    3796.5788 
+    3040 0.0080548478 5.051914e-08    3796.8119 
+    3050 0.0080553469 4.9172716e-08    3797.0385 
+    3060 0.0080558329 4.7926619e-08    3797.2591 
+    3070 0.0080563069 4.6771366e-08    3797.4741 
+    3080 0.0080567697 4.5698662e-08    3797.6839 
+    3090 0.0080572222 4.4701228e-08    3797.8889 
+    3100 0.0080576649 4.3772647e-08    3798.0895 
+    3110 0.0080580987 4.2907247e-08    3798.2858 
+    3120 0.0080585241 4.2099999e-08    3798.4784 
+    3130 0.0080589417 4.1346425e-08    3798.6672 
+    3140 0.0080593519 4.0642535e-08    3798.8527 
+    3150 0.0080597554 3.9984758e-08    3799.0351 
+    3160 0.0080601524 3.9369895e-08    3799.2145 
+    3170 0.0080605435 3.8795073e-08    3799.3911 
+    3180  0.008060929 3.8257705e-08    3799.5651 
+    3190 0.0080613093 3.7755461e-08    3799.7368 
+    3200 0.0080616847 3.7286239e-08    3799.9062 
+    3210 0.0080620556 3.6848135e-08    3800.0734 
+    3220 0.0080624222 3.6439432e-08    3800.2387 
+    3230 0.0080627848 3.6058573e-08    3800.4022 
+    3240 0.0080631438 3.5704146e-08     3800.564 
+    3250 0.0080634994 3.5374876e-08    3800.7241 
+    3260 0.0080638517 3.5069606e-08    3800.8828 
+    3270 0.0080642011 3.4787289e-08    3801.0402 
+    3280 0.0080645478 3.4526978e-08    3801.1962 
+    3290  0.008064892 3.4287819e-08    3801.3511 
+    3300 0.0080652339 3.4069042e-08     3801.505 
+    3310 0.0080655736 3.3869955e-08    3801.6578 
+    3320 0.0080659115 3.368994e-08    3801.8098 
+    3330 0.0080662477 3.3528444e-08     3801.961 
+    3340 0.0080665823 3.3384981e-08    3802.1115 
+    3350 0.0080669156 3.3259123e-08    3802.2613 
+    3360 0.0080672476 3.3150499e-08    3802.4106 
+    3370 0.0080675787 3.305879e-08    3802.5594 
+    3380  0.008067909 3.2983732e-08    3802.7078 
+    3390 0.0080682385 3.2925108e-08    3802.8559 
+    3400 0.0080685676 3.288275e-08    3803.0038 
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+    3420 0.0080692248 3.2846395e-08    3803.2991 
+    3430 0.0080695532 3.2852293e-08    3803.4466 
+    3440 0.0080698819 3.2874247e-08    3803.5943 
+    3450 0.0080702108 3.2912319e-08     3803.742 
+    3460 0.0080705401 3.2966617e-08      3803.89 
+    3470 0.0080708701 3.3037293e-08    3804.0382 
+    3480 0.0080712008 3.312455e-08    3804.1868 
+    3490 0.0080715325 3.3228638e-08    3804.3358 
+    3500 0.0080718653 3.3349858e-08    3804.4853 
+    3510 0.0080721995 3.3488567e-08    3804.6355 
+    3520  0.008072535 3.3645172e-08    3804.7862 
+    3530 0.0080728723 3.3820145e-08    3804.9378 
+    3540 0.0080732113 3.4014016e-08    3805.0901 
+    3550 0.0080735524 3.4227383e-08    3805.2434 
+    3560 0.0080738957 3.4460914e-08    3805.3977 
+    3570 0.0080742414 3.4715354e-08    3805.5532 
+    3580 0.0080745898 3.4991532e-08    3805.7098 
+    3590 0.0080749411 3.5290364e-08    3805.8677 
+    3600 0.0080752954 3.5612865e-08    3806.0271 
+    3610 0.0080756531 3.5960156e-08     3806.188 
+    3620 0.0080760143 3.6333475e-08    3806.3505 
+    3630 0.0080763794 3.6734187e-08    3806.5148 
+    3640 0.0080767487 3.7163802e-08     3806.681 
+    3650 0.0080771224 3.7623985e-08    3806.8492 
+    3660 0.0080775008 3.8116577e-08    3807.0196 
+    3670 0.0080778843 3.8643614e-08    3807.1924 
+    3680 0.0080782733 3.9207349e-08    3807.3676 
+    3690  0.008078668 3.9810283e-08    3807.5455 
+    3700  0.008079069 4.0455191e-08    3807.7262 
+    3710 0.0080794766 4.114516e-08      3807.91 
+    3720 0.0080798913 4.1883634e-08    3808.0971 
+    3730 0.0080803137 4.2674459e-08    3808.2877 
+    3740 0.0080807442 4.3521941e-08     3808.482 
+    3750 0.0080811834 4.4430917e-08    3808.6803 
+    3760 0.0080816321 4.5406834e-08     3808.883 
+    3770 0.0080820908 4.6455843e-08    3809.0902 
+    3780 0.0080825604 4.7584918e-08    3809.3025 
+    3790 0.0080830416 4.8801987e-08    3809.5201 
+    3800 0.0080835355 5.0116105e-08    3809.7436 
+    3810 0.0080840429 5.1537653e-08    3809.9733 
+    3820 0.0080845652 5.3078583e-08    3810.2097 
+    3830 0.0080851034 5.4752728e-08    3810.4535 
+    3840  0.008085659 5.6576175e-08    3810.7054 
+    3850 0.0080862335 5.8567743e-08    3810.9659 
+    3860 0.0080868289 6.0749572e-08     3811.236 
+    3870  0.008087447 6.3147889e-08    3811.5166 
+    3880 0.0080880901 6.5793981e-08    3811.8087 
+    3890  0.008088761 6.8725458e-08    3812.1136 
+    3900 0.0080894626 7.1987928e-08    3812.4327 
+    3910 0.0080901986 7.5637206e-08    3812.7675 
+    3920  0.008090973 7.9742316e-08    3813.1201 
+    3930 0.0080917909 8.4389592e-08    3813.4926 
+    3940  0.008092658 8.9688414e-08    3813.8879 
+    3950 0.0080935816 9.5779352e-08    3814.3091 
+    3960 0.0080945703 1.0284601e-07    3814.7604 
+    3970 0.0080956349 1.1113264e-07    3815.2467 
+    3980 0.0080967891 1.2097115e-07    3815.7742 
+    3990 0.0080980502 1.3282379e-07    3816.3511 
+    4000 0.0080994413 1.4735308e-07    3816.9878 
+    4010 0.0081009931 1.6554202e-07    3817.6987 
+    4020 0.0081027486 1.8891116e-07    3818.5035 
+    4030 0.0081047696 2.1993774e-07    3819.4308 
+    4040 0.0081071501 2.6293325e-07     3820.524 
+    4050 0.0081100418 3.2608623e-07    3821.8531 
+    4060 0.0081137136 4.2695471e-07    3823.5422 
+    4070 0.0081187073 6.1068659e-07    3825.8415 
+    4080 0.0081263808 1.0353843e-06    3829.3781 
+    4090 0.0081421033 2.8175459e-06    3836.6316 
+    4100 0.0083319479 3.0660994e-05     3924.296 
+    4110 0.0086521081 2.4031675e-05    4072.0381 
+    4120 0.0089367803 5.8263834e-06    4203.2922 
+    4130 0.0089679114 1.6262217e-06    4217.6293 
+    4140 0.0089805825 9.6546502e-07    4223.4594 
+    4150 0.0089889356 7.1159925e-07    4227.3001 
+    4160 0.0089954101 5.8311893e-07    4230.2754 
+    4170 0.0090008803 5.1000973e-07    4232.7881 
+    4180 0.0090057682 4.6713078e-07    4235.0326 
+    4190 0.0090103206 4.4370361e-07    4237.1225 
+    4200 0.0090147071 4.3491502e-07    4239.1361 
+    4210 0.0090190645 4.3912951e-07    4241.1362 
+    4220 0.0090235243 4.570826e-07    4243.1834 
+    4230 0.0090282367 4.9222468e-07    4245.3469 
+    4240 0.0090334045 5.5254852e-07      4247.72 
+    4250 0.0090393478 6.5600428e-07    4250.4502 
+    4260 0.0090466656 8.4827393e-07    4253.8133 
+    4270 0.0090567641 1.2818738e-06     4258.457 
+    4280 0.0090746835 2.9033891e-06    4266.7027 
+    4290 0.0092346752 2.9451638e-05    4340.3839 
+    4300 0.0093466586 4.9023913e-06    4391.9319 
+    4310 0.0093992941 7.8400922e-06     4416.149 
+    4320 0.0097053159 4.3362296e-05    4556.9393 
+    4330  0.010037349 4.9648086e-05    4709.5604 
+    4340  0.010297354 8.8232096e-06    4828.9697 
+    4350  0.010503113 4.4016316e-05    4923.4016 
+    4360  0.010926633 4.2142313e-05     5117.622 
+    4370  0.011318805 4.0285407e-05    5297.2575 
+    4380  0.011746199 4.3755472e-05    5492.8047 
+    4390  0.012044606 2.1150168e-05    5629.1924 
+    4400   0.01231664 7.0784321e-06    5753.4243 
+    4410   0.01236554 3.954763e-06    5775.7358 
+    4420     0.012415 8.8450437e-06    5798.2999 
+    4430  0.012723996 3.6113036e-05    5939.2622 
+    4440  0.013109261 4.5827638e-05    6114.8493 
+    4450  0.013251276 2.6649019e-06    6179.5172 
+    4460  0.013269544 1.2200106e-06    6187.8251 
+    4470  0.013279619 8.155501e-07    6192.4028 
+    4480  0.013286853 6.3300974e-07    6195.6879 
+    4490   0.01329269 5.3347649e-07    6198.3373 
+    4500  0.013297735 4.7451627e-07    6200.6261 
+    4510  0.013302306 4.392029e-07    6202.6992 
+    4520  0.013306599 4.1982963e-07    6204.6461 
+    4530  0.013310757 4.1285331e-07    6206.5311 
+    4540  0.013314895 4.1710029e-07    6208.4074 
+    4550  0.013319128 4.3324769e-07    6210.3267 
+    4560  0.013323586 4.6410935e-07     6212.348 
+    4570  0.013328439 5.1597347e-07    6214.5493 
+    4580   0.01333395 6.0235495e-07    6217.0498 
+    4590  0.013340584 7.5537668e-07    6220.0613 
+    4600  0.013349342 1.0699582e-06    6224.0388 
+    4610  0.013363183  1.98365e-06    6230.3293 
+    4620  0.013404081 1.4367775e-05    6248.9319 
+    4630  0.013593325 3.787203e-06    6335.0239 
+    4640   0.01361833 1.6441528e-06    6346.3866 
+    4650  0.013632159 1.1592769e-06    6352.6667 
+    4660  0.013642828 9.8623051e-07    6357.5101 
+    4670  0.013652418 9.4451692e-07    6361.8626 
+    4680  0.013662041 1.0034733e-06    6366.2295 
+    4690  0.013672824 1.2061779e-06    6371.1243 
+    4700  0.013686941 1.780995e-06    6377.5343 
+    4710  0.013713088 4.7634009e-06    6389.4131 
+    4720  0.013968014 3.9765415e-05    6505.2802 
+    4730  0.014228787 6.2632217e-06    6623.7185 
+    4740  0.014278333 4.7934169e-06    6646.2018 
+    4750  0.014382212 5.1069055e-05    6693.3424 
+    4760  0.014525205 2.0381123e-06    6758.2178 
+    4770  0.014538504 8.2250651e-07    6764.2412 
+    4780  0.014544984 4.9114353e-07    6767.1723 
+    4790  0.014549144 3.4212232e-07    6769.0518 
+    4800  0.014552156 2.589287e-07    6770.4109 
+    4810  0.014554491 2.0641662e-07    6771.4633 
+    4820  0.014556384 1.7052382e-07     6772.315 
+    4830  0.014557966 1.4457875e-07    6773.0262 
+    4840  0.014559319 1.250293e-07    6773.6339 
+    4850  0.014560498  1.09819e-07    6774.1626 
+    4860  0.014561539 9.7678962e-08     6774.629 
+    4870   0.01456247 8.7785899e-08    6775.0453 
+    4880   0.01456331 7.9583482e-08    6775.4205 
+    4890  0.014564074 7.2682934e-08    6775.7613 
+    4900  0.014564773 6.6804784e-08    6776.0732 
+    4910  0.014565418 6.1743238e-08    6776.3601 
+    4920  0.014566015 5.7343571e-08    6776.6256 
+    4930  0.014566571 5.3487327e-08    6776.8723 
+    4940   0.01456709 5.0082359e-08    6777.1026 
+    4950  0.014567577 4.7055963e-08    6777.3183 
+    4960  0.014568035 4.4350048e-08     6777.521 
+    4970  0.014568467 4.1917669e-08     6777.712 
+    4980  0.014568876 3.9720495e-08    6777.8926 
+    4990  0.014569265 3.7726941e-08    6778.0636 
+    5000  0.014569634 3.5910753e-08    6778.2261 
+Loop time of 24.155 on 1 procs for 5000 steps with 32000 atoms
+
+Performance: 0.001 ns/day, 37368.951 hours/ns, 206.996 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    | 15.795     | 15.795     | 15.795     |   0.0 | 65.39
+Neigh   | 1.5182     | 1.5182     | 1.5182     |   0.0 |  6.29
+Comm    | 0.58555    | 0.58555    | 0.58555    |   0.0 |  2.42
+Output  | 0.0064323  | 0.0064323  | 0.0064323  |   0.0 |  0.03
+Modify  | 5.619      | 5.619      | 5.619      |   0.0 | 23.26
+Other   |            | 0.6313     |            |       |  2.61
+
+Nlocal:    32000 ave 32000 max 32000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    13556 ave 13556 max 13556 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  576016 ave 576016 max 576016 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 576016
+Ave neighs/atom = 18.0005
+Neighbor list builds = 68
+Dangerous builds = 42
+Total wall time: 0:00:24

examples/USER/misc/electron_stopping/log.20Mar19.elstop.g++.4

@@ -0,0 +1,597 @@
+LAMMPS (28 Feb 2019)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
+  using 1 OpenMP thread(s) per MPI task
+# Test case / example for fix electron/stopping
+# Perfect Si lattice with one primary knock-on atom.
+#
+# Also uses fix dt/reset, as one should when energies are high
+# enough to require electronic stopping.
+
+units metal
+boundary p p p
+timestep 0.0001
+
+lattice fcc 5.431
+Lattice spacing in x,y,z = 5.431 5.431 5.431
+
+region rbox block -10 10 -10 10 -10 10
+create_box 1 rbox
+Created orthogonal box = (-54.31 -54.31 -54.31) to (54.31 54.31 54.31)
+  1 by 2 by 2 MPI processor grid
+
+mass 1 28.0855
+
+create_atoms 1 box
+Created 32000 atoms
+  create_atoms CPU = 0.000856161 secs
+
+velocity all create 300 42534 mom yes rot yes
+
+group gPKA id 1
+1 atoms in group gPKA
+velocity gPKA set 1120 1620 389
+
+pair_style sw
+pair_coeff * * Si.sw Si
+Reading potential file Si.sw with DATE: 2007-06-11
+
+fix fdt all dt/reset 1 NULL 0.001 0.1 emax 20.0
+fix fel all electron/stopping 1.0 Si.Si.elstop
+fix fnve all nve
+
+thermo 10
+thermo_style custom step time dt f_fel
+
+#compute ek all ke/atom
+#dump mydump all custom 200 elstop.dump id x y z vx vy vz fx fy fz c_ek
+
+run 5000
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 5.77118
+  ghost atom cutoff = 5.77118
+  binsize = 2.88559, bins = 38 38 38
+  2 neighbor lists, perpetual/occasional/extra = 1 1 0
+  (1) pair sw, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (2) fix electron/stopping, occasional, copy from (1)
+      attributes: full, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 3.825 | 3.825 | 3.825 Mbytes
+Step Time Dt f_fel 
+       0            0  4.98128e-05            0 
+      10 0.00030141235 7.4131221e-06    143.83474 
+      20 0.00035951242 6.0314282e-06    171.53584 
+      30 0.00057457861 3.511731e-05    274.07067 
+      40 0.00086591115 5.8248574e-06    412.87352 
+      50 0.00090045749 2.102773e-06    429.31482 
+      60 0.00091828633 1.5369556e-06    437.79502 
+      70 0.00093306208 1.4645168e-06    444.82135 
+      80 0.00094861336 1.7491631e-06    452.21657 
+      90 0.00097033523 3.0804023e-06    462.54893 
+     100 0.0010792154 4.9075683e-05    514.37014 
+     110 0.0012080866 2.3201427e-06    575.68827 
+     120 0.0012239719 1.0507964e-06    583.23648 
+     130 0.0012325518 6.8263389e-07    587.30975 
+     140 0.0012385211 5.1201217e-07    590.14147 
+     150 0.0012431661 4.1521773e-07    592.34347 
+     160  0.001247021 3.5379338e-07    594.16984 
+     170 0.0012503586 3.1202939e-07    595.75031 
+     180 0.0012533374 2.8236002e-07    597.16021 
+     190 0.0012560582 2.6071816e-07    598.44745 
+     200 0.0012585895 2.4474279e-07    599.64465 
+     210  0.001260981 2.3298831e-07     600.7754 
+     220 0.0012632704 2.2454021e-07    601.85763 
+     230  0.001265488 2.1881458e-07    602.90571 
+     240 0.0012676591 2.154488e-07    603.93173 
+     250 0.0012698064 2.1424147e-07    604.94641 
+     260 0.0012719511 2.1512161e-07     605.9598 
+     270 0.0012741141 2.1813836e-07    606.98189 
+     280 0.0012763174 2.2346783e-07    608.02314 
+     290 0.0012785856 2.3143942e-07    609.09518 
+     300 0.0012809473 2.4258888e-07     610.2116 
+     310 0.0012834376 2.5775518e-07    611.38916 
+     320 0.0012861023 2.7825685e-07    612.64953 
+     330 0.0012890034 3.062254e-07    614.02218 
+     340 0.0012922301 3.4527805e-07    615.54956 
+     350 0.0012959196 4.0200263e-07    617.29679 
+     360    0.0013003 4.8966484e-07    619.37233 
+     370 0.0013057965 6.3923294e-07     621.9783 
+     380   0.00131335 9.423535e-07    625.56194 
+     390 0.0013258073 1.8277087e-06    631.47661 
+     400 0.0013653313 1.4985239e-05    650.25939 
+     410 0.0016927117 4.5643592e-05    805.84388 
+     420  0.002085671 2.5698185e-05    992.40957 
+     430 0.0021935861 5.3102217e-06     1043.597 
+     440 0.0022614637 1.5788858e-05    1075.7807 
+     450 0.0025463923 1.6989456e-05    1210.8535 
+     460 0.0029095455 3.9205279e-05    1382.8591 
+     470  0.003309122 3.8882183e-05    1571.9128 
+     480 0.0037129772 4.0573389e-05    1762.7749 
+     490  0.004120209 2.7525742e-05    1955.0148 
+     500 0.0042711049 1.9373612e-05    2026.1805 
+     510 0.0045860203 2.4773305e-05    2174.6208 
+     520  0.004995259 3.8017877e-05    2367.3335 
+     530 0.0051457762 5.4205615e-06    2438.1475 
+     540  0.005203221 8.8625579e-06    2465.1577 
+     550 0.0054221421 5.7304442e-06    2568.0888 
+     560 0.0054524345 1.5599386e-06    2582.3169 
+     570 0.0054645073 9.1093243e-07    2587.9819 
+     580 0.0054723338 6.6033575e-07    2591.6518 
+     590 0.0054782965 5.3155858e-07     2594.446 
+     600  0.005483241 4.5581839e-07    2596.7619 
+     610 0.0054875675 4.0821885e-07    2598.7875 
+     620 0.0054915013 3.7775507e-07    2600.6287 
+     630 0.0054951861 3.5898561e-07    2602.3529 
+     640 0.0054987249 3.4911444e-07    2604.0086 
+     650 0.0055021998 3.4682698e-07    2605.6342 
+     660 0.0055056844 3.5182676e-07    2607.2643 
+     670 0.0055092538 3.6473743e-07    2608.9342 
+     680 0.0055129936 3.8730595e-07    2610.6841 
+     690 0.0055170145 4.2303997e-07     2612.566 
+     700 0.0055214749 4.7876507e-07    2614.6542 
+     710 0.0055266296 5.6863699e-07    2617.0684 
+     720 0.0055329452 7.2626141e-07    2620.0278 
+     730 0.0055414528 1.0527596e-06    2624.0166 
+     740 0.0055553208 2.0371511e-06     2630.523 
+     750 0.0056023478 2.2133456e-05    2652.6057 
+     760 0.0059007346 3.8610962e-05    2792.7168 
+     770 0.0062508505 3.9428337e-05    2956.9697 
+     780 0.0063682296 2.1223153e-06    3011.9927 
+     790 0.0063824196 9.0656948e-07    3018.6346 
+     800 0.0063896741 5.6137676e-07    3022.0266 
+     810 0.0063944906 4.0276465e-07    3024.2763 
+     820 0.0063980771 3.1284015e-07    3025.9499 
+     830 0.0064009279 2.5537602e-07    3027.2789 
+     840  0.006403292 2.1569057e-07    3028.3801 
+     850 0.0064053117 1.8674792e-07      3029.32 
+     860 0.0064070756 1.6477015e-07    3030.1402 
+     870 0.0064086425 1.4755386e-07    3030.8682 
+     880 0.0064100535 1.3373048e-07    3031.5232 
+     890 0.0064113381 1.2240666e-07    3032.1191 
+     900 0.0064125183 1.1297538e-07    3032.6662 
+     910 0.0064136112 1.0501022e-07    3033.1724 
+     920 0.0064146298 9.8203162e-08    3033.6439 
+     930 0.0064155847 9.2326368e-08    3034.0856 
+     940 0.0064164843 8.7207794e-08    3034.5015 
+     950 0.0064173357 8.2715188e-08    3034.8948 
+     960 0.0064181446 7.8745279e-08    3035.2682 
+     970 0.0064189159 7.5216291e-08    3035.6241 
+     980 0.0064196535 7.2062662e-08    3035.9642 
+     990 0.0064203612 6.9231241e-08    3036.2903 
+    1000 0.0064210418 6.6678502e-08    3036.6038 
+    1010  0.006421698 6.4368478e-08    3036.9059 
+    1020 0.0064223321 6.2271202e-08    3037.1976 
+    1030 0.0064229461 6.0361517e-08    3037.4799 
+    1040 0.0064235417 5.8618162e-08    3037.7537 
+    1050 0.0064241206 5.702305e-08    3038.0197 
+    1060 0.0064246841 5.556071e-08    3038.2784 
+    1070 0.0064252336 5.4217838e-08    3038.5306 
+    1080 0.0064257701 5.2982939e-08    3038.7768 
+    1090 0.0064262948 5.1846034e-08    3039.0174 
+    1100 0.0064268085 5.079843e-08    3039.2529 
+    1110  0.006427312 4.9832523e-08    3039.4837 
+    1120 0.0064278063 4.8941643e-08    3039.7101 
+    1130 0.0064282919 4.811992e-08    3039.9325 
+    1140 0.0064287697 4.7362175e-08    3040.1512 
+    1150 0.0064292401 4.6663831e-08    3040.3665 
+    1160 0.0064297038 4.6020833e-08    3040.5786 
+    1170 0.0064301613 4.5429586e-08    3040.7878 
+    1180 0.0064306131 4.4886899e-08    3040.9944 
+    1190 0.0064310597 4.4389937e-08    3041.1986 
+    1200 0.0064315016 4.3936183e-08    3041.4005 
+    1210  0.006431939 4.3523406e-08    3041.6003 
+    1220 0.0064323725 4.3149628e-08    3041.7984 
+    1230 0.0064328025 4.2813101e-08    3041.9947 
+    1240 0.0064332292 4.2512286e-08    3042.1896 
+    1250 0.0064336531 4.2245836e-08    3042.3831 
+    1260 0.0064340745 4.201258e-08    3042.5755 
+    1270 0.0064344937 4.1811507e-08    3042.7668 
+    1280  0.006434911 4.1641759e-08    3042.9572 
+    1290 0.0064353268 4.1502622e-08    3043.1469 
+    1300 0.0064357413 4.1393513e-08     3043.336 
+    1310 0.0064361549 4.1313982e-08    3043.5247 
+    1320 0.0064365678 4.1263699e-08     3043.713 
+    1330 0.0064369803 4.1242458e-08    3043.9012 
+    1340 0.0064373927 4.125017e-08    3044.0893 
+    1350 0.0064378054 4.1286866e-08    3044.2775 
+    1360 0.0064382185 4.1352691e-08     3044.466 
+    1370 0.0064386324 4.1447915e-08    3044.6548 
+    1380 0.0064390475 4.1572925e-08    3044.8441 
+    1390 0.0064394639 4.1728238e-08     3045.034 
+    1400 0.0064398819 4.1914501e-08    3045.2247 
+    1410  0.006440302 4.2132499e-08    3045.4163 
+    1420 0.0064407245 4.2383163e-08    3045.6091 
+    1430 0.0064411496 4.2667584e-08     3045.803 
+    1440 0.0064415776 4.2987016e-08    3045.9983 
+    1450 0.0064420091  4.33429e-08    3046.1952 
+    1460 0.0064424443 4.3736874e-08    3046.3938 
+    1470 0.0064428835 4.4170794e-08    3046.5944 
+    1480 0.0064433274 4.4646761e-08     3046.797 
+    1490 0.0064437761 4.5167139e-08    3047.0019 
+    1500 0.0064442303 4.5734596e-08    3047.2093 
+    1510 0.0064446904 4.6352132e-08    3047.4195 
+    1520 0.0064451569 4.7023127e-08    3047.6327 
+    1530 0.0064456303 4.7751389e-08     3047.849 
+    1540 0.0064461114 4.8541214e-08    3048.0689 
+    1550 0.0064466006 4.9397455e-08    3048.2926 
+    1560 0.0064470987 5.0325606e-08    3048.5204 
+    1570 0.0064476064 5.1331902e-08    3048.7527 
+    1580 0.0064481245 5.2423434e-08    3048.9899 
+    1590  0.006448654 5.3608296e-08    3049.2323 
+    1600 0.0064491958 5.4895757e-08    3049.4804 
+    1610  0.006449751 5.6296469e-08    3049.7347 
+    1620 0.0064503207 5.7822727e-08    3049.9959 
+    1630 0.0064509063 5.9488788e-08    3050.2644 
+    1640 0.0064515092 6.1311263e-08    3050.5409 
+    1650 0.0064521312 6.3309616e-08    3050.8263 
+    1660  0.006452774 6.5506785e-08    3051.1214 
+    1670 0.0064534398 6.7929981e-08    3051.4272 
+    1680 0.0064541309 7.0611714e-08    3051.7448 
+    1690 0.0064548502 7.3591127e-08    3052.0755 
+    1700 0.0064556007 7.6915753e-08    3052.4207 
+    1710 0.0064563863 8.064386e-08    3052.7823 
+    1720 0.0064572113 8.4847627e-08    3053.1621 
+    1730 0.0064580807 8.9617502e-08    3053.5627 
+    1740 0.0064590008 9.5068304e-08    3053.9869 
+    1750  0.006459979 1.0134793e-07    3054.4381 
+    1760 0.0064610244 1.0865003e-07    3054.9206 
+    1770 0.0064621483 1.1723301e-07    3055.4397 
+    1780 0.0064633651 1.2744917e-07    3056.0021 
+    1790 0.0064646931 1.3979108e-07    3056.6163 
+    1800 0.0064661566 1.5496815e-07    3057.2937 
+    1810 0.0064677883 1.7403894e-07    3058.0494 
+    1820  0.006469634 1.9865267e-07    3058.9049 
+    1830 0.0064717601 2.3152064e-07    3059.8912 
+    1840 0.0064742682 2.7741818e-07    3061.0556 
+    1850 0.0064773249 3.4556351e-07    3062.4759 
+    1860 0.0064812294 4.5619653e-07    3064.2917 
+    1870 0.0064866019 6.6337441e-07    3066.7924 
+    1880 0.0064950748 1.1706786e-06    3070.7399 
+    1890 0.0065140322 3.7878566e-06    3079.5809 
+    1900 0.0066957122 6.7105464e-06    3164.3691 
+    1910 0.0067279909 1.493224e-06    3179.4195 
+    1920 0.0067392058 8.1410321e-07    3184.6428 
+    1930 0.0067460435 5.5996376e-07    3187.8246 
+    1940 0.0067509948 4.2936252e-07    3190.1267 
+    1950 0.0067549055 3.5072462e-07    3191.9436 
+    1960 0.0067581623 2.9865016e-07    3193.4556 
+    1970 0.0067609737 2.6192794e-07    3194.7601 
+    1980 0.0067634648 2.3486813e-07    3195.9153 
+    1990 0.0067657165 2.1428715e-07    3196.9589 
+    2000 0.0067677841 1.9827071e-07    3197.9167 
+    2010 0.0067697074 1.8560268e-07    3198.8073 
+    2020  0.006771516 1.7547663e-07    3199.6445 
+    2030 0.0067732327 1.6733961e-07    3200.4388 
+    2040 0.0067748755 1.6080268e-07    3201.1987 
+    2050 0.0067764591 1.5558723e-07     3201.931 
+    2060 0.0067779957 1.5149159e-07    3202.6414 
+    2070 0.0067794958 1.4836976e-07    3203.3348 
+    2080 0.0067809687 1.4611749e-07    3204.0155 
+    2090 0.0067824227 1.4466322e-07    3204.6874 
+    2100 0.0067838655 1.4396229e-07    3205.3542 
+    2110 0.0067853047 1.4399348e-07    3206.0191 
+    2120 0.0067867474 1.4475745e-07    3206.6858 
+    2130 0.0067882012 1.4627671e-07    3207.3576 
+    2140 0.0067896737 1.4859736e-07    3208.0381 
+    2150 0.0067911733 1.5179256e-07    3208.7311 
+    2160 0.0067927092 1.5596849e-07    3209.4411 
+    2170 0.0067942917 1.6127347e-07    3210.1728 
+    2180 0.0067959331 1.6791214e-07    3210.9319 
+    2190 0.0067976479 1.7616698e-07    3211.7251 
+    2200 0.0067994539 1.8643208e-07    3212.5608 
+    2210 0.0068013736 1.9926751e-07    3213.4494 
+    2220 0.0068034361 2.154897e-07    3214.4044 
+    2230 0.0068056803 2.3632937e-07    3215.4441 
+    2240 0.0068081604 2.6372257e-07    3216.5937 
+    2250 0.0068109549 3.0088625e-07    3217.8897 
+    2260 0.0068141846 3.5356212e-07    3219.3884 
+    2270 0.0068180485 4.330391e-07    3221.1825 
+    2280 0.0068229109 5.6479966e-07    3223.4417 
+    2290 0.0068295488 8.2016289e-07    3226.5284 
+    2300 0.0068401389 1.4950446e-06    3231.4568 
+    2310 0.0068668194 6.4794351e-06    3243.8847 
+    2320 0.0071339944 2.3817631e-05    3368.3827 
+    2330 0.0074221156 3.4144405e-05    3502.5364 
+    2340  0.007650075 3.3142879e-06    3608.5998 
+    2350 0.0076703526 1.1927138e-06    3618.0215 
+    2360 0.0076797526 7.185434e-07    3622.3847 
+    2370 0.0076859146 5.1648342e-07    3625.2424 
+    2380 0.0076905359 4.0623045e-07    3627.3839 
+    2390 0.0076942651 3.3753265e-07    3629.1108 
+    2400 0.0076974175 2.910504e-07    3630.5697 
+    2410 0.0077001699 2.5780894e-07    3631.8426 
+    2420  0.007702631 2.3309498e-07    3632.9803 
+    2430  0.007704873 2.1420535e-07    3634.0161 
+    2440 0.0077069459 1.9948463e-07    3634.9733 
+    2450 0.0077088862 1.8786685e-07     3635.869 
+    2460 0.0077107216 1.7863849e-07     3636.716 
+    2470 0.0077124736 1.713078e-07    3637.5242 
+    2480 0.0077141595 1.6552875e-07    3638.3017 
+    2490 0.0077157937 1.6105508e-07    3639.0552 
+    2500 0.0077173883 1.5771154e-07    3639.7903 
+    2510 0.0077189541 1.553756e-07    3640.5121 
+    2520 0.0077205008 1.539658e-07    3641.2249 
+    2530 0.0077220373 1.534345e-07     3641.933 
+    2540 0.0077235724 1.5376384e-07    3642.6405 
+    2550 0.0077251148 1.5496427e-07    3643.3513 
+    2560 0.0077266731 1.5707538e-07    3644.0695 
+    2570  0.007728257 1.6016917e-07    3644.7995 
+    2580 0.0077298765 1.6435633e-07    3645.5461 
+    2590 0.0077315435 1.6979645e-07    3646.3147 
+    2600 0.0077332712 1.7671412e-07    3647.1115 
+    2610 0.0077350759 1.8542415e-07     3647.944 
+    2620 0.0077369773 1.9637153e-07    3648.8214 
+    2630 0.0077390006 2.1019669e-07    3649.7553 
+    2640 0.0077411783 2.2784614e-07    3650.7609 
+    2650 0.0077435548 2.5076917e-07    3651.8588 
+    2660 0.0077461922 2.8128932e-07    3653.0779 
+    2670 0.0077491826 3.233607e-07    3654.4608 
+    2680 0.0077526703 3.8426634e-07    3656.0746 
+    2690 0.0077569014 4.7896536e-07    3658.0337 
+    2700 0.0077623476 6.435095e-07    3660.5572 
+    2710 0.0077700972 9.9066415e-07    3664.1508 
+    2720 0.0077837321 2.1192489e-06    3670.4787 
+    2730 0.0078537309 5.0478452e-05    3702.9978 
+    2740 0.0080019842 2.234588e-06    3771.8639 
+    2750 0.0080167983 9.3912008e-07    3778.7349 
+    2760 0.0080243022 5.7998894e-07    3782.2116 
+    2770 0.0080292782 4.1619434e-07    3784.5147 
+    2780 0.0080329859 3.2365852e-07    3786.2291 
+    2790 0.0080359374 2.6464667e-07    3787.5927 
+    2800 0.0080383893 2.2394834e-07    3788.7244 
+    2810 0.0080404882 1.9429813e-07    3789.6924 
+    2820 0.0080423251 1.7180333e-07    3790.5389 
+    2830 0.0080439606 1.5419708e-07     3791.292 
+    2840 0.0080454366 1.4007294e-07    3791.9711 
+    2850 0.0080467835 1.2851365e-07    3792.5904 
+    2860 0.0080480239 1.1889632e-07    3793.1603 
+    2870 0.0080491753 1.1078364e-07     3793.689 
+    2880 0.0080502511 1.0385986e-07    3794.1826 
+    2890 0.0080512621 9.7891518e-08    3794.6462 
+    2900 0.0080522171 9.2702379e-08    3795.0838 
+    2910 0.0080531232 8.815703e-08    3795.4988 
+    2920 0.0080539863 8.4149767e-08    3795.8939 
+    2930 0.0080548115 8.0596927e-08    3796.2714 
+    2940 0.0080556029 7.7431468e-08    3796.6332 
+    2950 0.0080563642 7.4599072e-08    3796.9811 
+    2960 0.0080570985 7.2055292e-08    3797.3166 
+    2970 0.0080578086 6.9763432e-08    3797.6407 
+    2980 0.0080584967 6.7692955e-08    3797.9548 
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+    3080  0.008064541 5.5051058e-08    3800.7074 
+    3090 0.0080650882 5.4339406e-08    3800.9562 
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+    3200 0.0080707979 5.0563598e-08     3803.549 
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+    3340 0.0080780526 5.4903844e-08     3806.842 
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+    3430 0.0080833961 6.5449061e-08     3809.272 
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+    3580 0.0080968821 1.3697303e-07    3815.4361 
+    3590 0.0080983096 1.5031413e-07    3816.0912 
+    3600  0.008099884 1.6682798e-07    3816.8142 
+    3610 0.0081016421 1.877419e-07    3817.6222 
+    3620 0.0081036359 2.1499717e-07    3818.5391 
+    3630 0.0081059419 2.5184713e-07    3819.6004 
+    3640 0.0081086795 3.041685e-07    3820.8614 
+    3650 0.0081120491 3.8370792e-07    3822.4147 
+    3660 0.0081164246 5.1761443e-07    3824.4335 
+    3670 0.0081226282 7.8476649e-07    3827.2984 
+    3680 0.0081330874 1.5377267e-06     3832.133 
+    3690 0.0081640997 9.4754571e-06    3846.4828 
+    3700 0.0084647088 3.6520628e-05    3985.6105 
+    3710 0.0087788105 5.0607918e-05    4130.8576 
+    3720 0.0089496823 2.7369422e-06    4209.8144 
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+    3760 0.0089881163 4.3436406e-07    4227.5353 
+    3770 0.0089921427 3.689283e-07    4229.3876 
+    3780 0.0089956201 3.2480899e-07    4230.9866 
+    3790 0.0089987196 2.9368682e-07    4232.4111 
+    3800 0.0090015492 2.7114137e-07     4233.711 
+    3810 0.0090041821 2.5463023e-07    4234.9202 
+    3820 0.0090066711 2.4261002e-07    4236.0629 
+    3830 0.0090090563 2.3411372e-07    4237.1578 
+    3840 0.0090113701 2.2853263e-07    4238.2196 
+    3850 0.0090136398 2.2549889e-07    4239.2611 
+    3860 0.0090158898 2.2482231e-07    4240.2936 
+    3870 0.0090181435 2.264602e-07    4241.3277 
+    3880 0.0090204243 2.3051066e-07    4242.3742 
+    3890 0.0090227572 2.3722751e-07    4243.4449 
+    3900 0.0090251709 2.4706119e-07    4244.5528 
+    3910 0.0090276995 2.6073849e-07    4245.7136 
+    3920 0.0090303862 2.7940938e-07    4246.9474 
+    3930 0.0090332884 3.0492215e-07    4248.2805 
+    3940 0.0090364872 3.4036714e-07    4249.7505 
+    3950 0.0090401038 3.9124064e-07    4251.4133 
+    3960 0.0090443343 4.6822852e-07    4253.3593 
+    3970 0.0090495296 5.9498137e-07    4255.7504 
+    3980 0.0090564177 8.3552398e-07    4258.9229 
+    3990 0.0090669429 1.4384739e-06     4263.774 
+    4000 0.0090904831 4.9111984e-06    4274.6331 
+    4010 0.0092929124 8.3135371e-06    4368.0633 
+    4020 0.0093414419 3.1334206e-06    4390.4447 
+    4030 0.0093714047 3.1966251e-06    4404.2581 
+    4040 0.0094176451 9.8265197e-06    4425.5788 
+    4050 0.0097772862 4.2787238e-05    4591.3956 
+    4060  0.010043914 5.0703357e-05    4714.2148 
+    4070  0.010275503 5.9586189e-06    4820.8179 
+    4080  0.010329372 6.4730027e-06    4845.5948 
+    4090  0.010580719 3.2675549e-05    4961.1991 
+    4100   0.01097933 4.1824022e-05    5144.3777 
+    4110  0.011375225 4.4528389e-05    5326.1041 
+    4120  0.011791986 4.4629128e-05    5517.1914 
+    4130  0.012199057 3.8467532e-05    5703.6209 
+    4140  0.012388718 1.6598211e-05    5790.3997 
+    4150  0.012719145 2.6617697e-05    5941.4863 
+    4160  0.013138874 3.9714695e-05    6133.2127 
+    4170  0.013296898 5.7028372e-06    6205.3279 
+    4180  0.013359491 1.0623338e-05    6233.8756 
+    4190  0.013580279 4.9259166e-06    6334.5676 
+    4200  0.013608204 1.5476759e-06    6347.2885 
+    4210  0.013620408 9.4152281e-07    6352.8431 
+    4220  0.013628594 7.0110358e-07    6356.5664 
+    4230   0.01363499 5.7777895e-07     6359.474 
+    4240  0.013640419 5.071712e-07     6361.941 
+    4250  0.013645286 4.6571283e-07    6364.1515 
+    4260  0.013649829 4.4320314e-07    6366.2145 
+    4270  0.013654213 4.3508698e-07    6368.2055 
+    4280  0.013658575 4.3986766e-07     6370.186 
+    4290  0.013663045 4.5837677e-07    6372.2157 
+    4300  0.013667773 4.9416073e-07     6374.363 
+    4310  0.013672963 5.5535604e-07    6376.7211 
+    4320   0.01367894 6.6021298e-07    6379.4372 
+    4330  0.013686311 8.5526524e-07    6382.7882 
+    4340  0.013696507 1.296644e-06    6387.4262 
+    4350  0.013714701 2.9652221e-06    6395.7088 
+    4360  0.013881439 3.5899661e-05    6471.6738 
+    4370  0.014196617 3.1253608e-05    6615.1811 
+    4380  0.014504048 7.0683429e-06    6755.0394 
+    4390  0.014536871 1.4515319e-06    6769.9538 
+    4400  0.014547629 7.6742092e-07    6774.8365 
+    4410   0.01455401 5.1561918e-07    6777.7294 
+    4420  0.014558528 3.8717171e-07    6779.7758 
+    4430  0.014562024 3.1004583e-07    6781.3579 
+    4440  0.014564879 2.5893679e-07    6782.6486 
+    4450  0.014567296 2.2275131e-07    6783.7406 
+    4460  0.014569397 1.9588676e-07    6784.6888 
+    4470  0.014571258 1.7521879e-07    6785.5285 
+    4480  0.014572934 1.5887218e-07    6786.2838 
+    4490  0.014574461 1.4565562e-07    6786.9717 
+    4500  0.014575867 1.3477717e-07    6787.6046 
+    4510  0.014577173 1.2569059e-07    6788.1919 
+    4520  0.014578394 1.1800737e-07     6788.741 
+    4530  0.014579544 1.1144387e-07    6789.2576 
+    4540  0.014580632 1.0578845e-07    6789.7464 
+    4550  0.014581667 1.0088007e-07    6790.2111 
+    4560  0.014582656 9.6594222e-08    6790.6548 
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+    4580  0.014584518 8.9519251e-08    6791.4895 
+    4590    0.0145854 8.6590045e-08    6791.8845 
+    4600  0.014586254 8.3994895e-08     6792.267 
+    4610  0.014587083 8.1692339e-08    6792.6383 
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+    4630  0.014588679 7.7834097e-08    6793.3523 
+    4640   0.01458945 7.6226411e-08    6793.6971 
+    4650  0.014590205 7.4805352e-08     6794.035 
+    4660  0.014590948 7.3554327e-08    6794.3668 
+    4670  0.014591678 7.2459408e-08    6794.6932 
+    4680  0.014592398 7.1508917e-08     6795.015 
+    4690   0.01459311 7.0693097e-08    6795.3328 
+    4700  0.014593813 7.0003852e-08    6795.6471 
+    4710  0.014594511 6.9434537e-08    6795.9585 
+    4720  0.014595203 6.8979799e-08    6796.2676 
+    4730  0.014595891 6.8635445e-08    6796.5748 
+    4740  0.014596576 6.839835e-08    6796.8807 
+    4750   0.01459726 6.8266383e-08    6797.1857 
+    4760  0.014597942 6.823836e-08    6797.4903 
+    4770  0.014598625 6.8314021e-08     6797.795 
+    4780  0.014599309 6.849402e-08    6798.1003 
+    4790  0.014599995 6.8779943e-08    6798.4065 
+    4800  0.014600684 6.9174339e-08    6798.7143 
+    4810  0.014601378 6.9680779e-08    6799.0241 
+    4820  0.014602078 7.0303936e-08    6799.3364 
+    4830  0.014602784 7.1049693e-08    6799.6517 
+    4840  0.014603498 7.1925284e-08    6799.9707 
+    4850  0.014604222 7.2939475e-08     6800.294 
+    4860  0.014604956 7.4102791e-08    6800.6221 
+    4870  0.014605703 7.5427802e-08    6800.9557 
+    4880  0.014606464 7.6929481e-08    6801.2958 
+    4890  0.014607241 7.8625665e-08     6801.643 
+    4900  0.014608036 8.0537626e-08    6801.9983 
+    4910   0.01460885 8.2690811e-08    6802.3627 
+    4920  0.014609688 8.5115787e-08    6802.7374 
+    4930  0.014610551 8.7849474e-08    6803.1237 
+    4940  0.014611443 9.0936752e-08    6803.5231 
+    4950  0.014612368 9.4432608e-08    6803.9372 
+    4960   0.01461333 9.8405013e-08    6804.3681 
+    4970  0.014614334 1.0293885e-07    6804.8181 
+    4980  0.014615386 1.0814135e-07    6805.2899 
+    4990  0.014616494 1.1414984e-07    6805.7869 
+    5000  0.014617666 1.2114278e-07     6806.313 
+Loop time of 9.26846 on 4 procs for 5000 steps with 32000 atoms
+
+Performance: 0.006 ns/day, 4250.474 hours/ns, 539.464 timesteps/s
+96.0% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 4.6281     | 4.7789     | 5.1937     |  11.0 | 51.56
+Neigh   | 0.40488    | 0.41576    | 0.43895    |   2.1 |  4.49
+Comm    | 0.8478     | 1.2799     | 1.4349     |  22.1 | 13.81
+Output  | 0.0048099  | 0.016429   | 0.050251   |  15.2 |  0.18
+Modify  | 2.1042     | 2.1347     | 2.1706     |   1.6 | 23.03
+Other   |            | 0.6427     |            |       |  6.93
+
+Nlocal:    8000 ave 8033 max 7977 min
+Histogram: 1 0 1 1 0 0 0 0 0 1
+Nghost:    6061.25 ave 6085 max 6028 min
+Histogram: 1 0 0 0 0 1 0 1 0 1
+Neighs:    0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs:  144002 ave 144601 max 143596 min
+Histogram: 1 0 1 1 0 0 0 0 0 1
+
+Total # of neighbors = 576008
+Ave neighs/atom = 18.0003
+Neighbor list builds = 67
+Dangerous builds = 38
+Total wall time: 0:00:09

examples/USER/misc/electron_stopping/log.20Mar19.elstop.only.g++.1

@@ -0,0 +1,196 @@
+LAMMPS (28 Feb 2019)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
+  using 1 OpenMP thread(s) per MPI task
+# Test case / example for fix electron/stopping
+# One fast atom, no other interactions.
+# Stopping only applied in a smaller box in the middle.
+#
+# Also uses fix dt/reset, as one should when energies are high
+# enough to require electronic stopping.
+
+units metal
+boundary p p p
+timestep 0.0001
+
+lattice fcc 1
+Lattice spacing in x,y,z = 1 1 1
+
+region rbox block -100 100 -100 100 -100 100
+region rsmallbox block -90 90 -90 90 -90 90
+
+create_box 1 rbox
+Created orthogonal box = (-100 -100 -100) to (100 100 100)
+  1 by 1 by 1 MPI processor grid
+
+mass 1 28.0855
+
+create_atoms 1 single 0 0 0
+Created 1 atoms
+  create_atoms CPU = 4.05312e-06 secs
+velocity all set 1120 1620 389
+
+pair_style zero 1
+pair_coeff * * 1
+
+fix fdt all dt/reset 1 NULL 0.001 0.1 emax 20.0
+fix fel all electron/stopping 1.0 Si.Si.elstop minneigh 0 region rsmallbox
+fix fnve all nve
+
+compute ek all ke/atom
+compute ektot all reduce sum c_ek
+
+thermo 100
+thermo_style custom step time dt f_fel c_ektot
+
+#dump mydump all custom 200 elstop.only.dump id x y z vx vy vz fx fy fz c_ek
+
+run 10000
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 3
+  ghost atom cutoff = 3
+  binsize = 1.5, bins = 134 134 134
+  2 neighbor lists, perpetual/occasional/extra = 1 1 0
+  (1) pair zero, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+  (2) fix electron/stopping, occasional
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 13.31 | 13.31 | 13.31 Mbytes
+Step Time Dt f_fel c_ektot 
+       0            0  4.98128e-05            0    5865.5525 
+     100 0.0049972222 5.0137252e-05    76.048699     5789.883 
+     200  0.010027278 5.0467945e-05    151.67477    5714.2548 
+     300  0.015090636 5.0803375e-05     226.8806    5639.0469 
+     400  0.020187777 5.1143663e-05     301.6685    5564.2569 
+     500  0.025319192 5.1488933e-05    376.04082    5489.8825 
+     600  0.030485386 5.1839314e-05    449.99984    5415.9215 
+     700  0.035686876 5.2194938e-05    523.54788    5342.3714 
+     800  0.040924195 5.2555944e-05    596.68721      5269.23 
+     900  0.046197886 5.2922477e-05    669.42011    5196.4951 
+    1000   0.05150851 5.3294685e-05    741.74883    5124.1643 
+    1100  0.056856642 5.3672723e-05    813.67563    5052.2355 
+    1200  0.062229338 5.3731851e-05    824.43012    5041.1224 
+    1300  0.067602524 5.3731851e-05    824.43012    5041.1224 
+    1400  0.072978188 5.387166e-05    850.91948    5014.9907 
+    1500   0.07838447 5.425887e-05    922.23961    4943.6685 
+    1600   0.08382978 5.4652329e-05    993.16341    4872.7428 
+    1700  0.089299984 5.4705935e-05    1002.3545     4863.198 
+    1800  0.094770578 5.4705935e-05    1002.3545     4863.198 
+    1900   0.10024117 5.4705935e-05    1002.3545     4863.198 
+    2000   0.10571333 5.4819488e-05    1022.8338    4843.0716 
+    2100   0.11121515 5.5222127e-05    1093.1986    4772.7048 
+    2200   0.11675757 5.5631458e-05    1163.1724    4702.7291 
+    2300   0.12234126 5.6047675e-05    1232.7573    4633.1422 
+    2400   0.12796692 5.6470985e-05    1301.9555     4563.942 
+    2500   0.13363527 5.6901598e-05    1370.7692    4495.1264 
+    2600   0.13934706 5.7339739e-05    1439.2006    4426.6932 
+    2700   0.14510304 5.7785637e-05    1507.2516    4358.6403 
+    2800     0.150904 5.8239536e-05    1574.9245    4290.9655 
+    2900   0.15675076 5.8701688e-05    1642.2213    4223.6668 
+    3000   0.16264416 5.9172358e-05    1709.1441    4156.7422 
+    3100   0.16858505 5.9651822e-05     1775.695    4090.1894 
+    3200   0.17457434 6.0140369e-05    1841.8761    4024.0064 
+    3300   0.18061294 6.0638302e-05    1907.6894    3958.1913 
+    3400   0.18669814 6.0949329e-05    1947.6558    3917.8967 
+    3500   0.19279307 6.0949329e-05    1947.6558    3917.8967 
+    3600     0.198888 6.0949329e-05    1947.6558    3917.8967 
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+    3900    0.2171728 6.0949329e-05    1947.6558    3917.8967 
+    4000   0.22326773 6.0949329e-05    1947.6558    3917.8967 
+    4100   0.22936267 6.0949329e-05    1947.6558    3917.8967 
+    4200    0.2354576 6.0949329e-05    1947.6558    3917.8967 
+    4300   0.24155253 6.0949329e-05    1947.6558    3917.8967 
+    4400   0.24764747 6.0949329e-05    1947.6558    3917.8967 
+    4500    0.2537424 6.0949329e-05    1947.6558    3917.8967 
+    4600   0.25983733 6.0949329e-05    1947.6558    3917.8967 
+    4700   0.26593227 6.0949329e-05    1947.6558    3917.8967 
+    4800    0.2720272 6.0949329e-05    1947.6558    3917.8967 
+    4900   0.27812213 6.0949329e-05    1947.6558    3917.8967 
+    5000   0.28421706 6.0949329e-05    1947.6558    3917.8967 
+    5100     0.290312 6.0949329e-05    1947.6558    3917.8967 
+    5200   0.29640693 6.0949329e-05    1947.6558    3917.8967 
+    5300   0.30250186 6.0949329e-05    1947.6558    3917.8967 
+    5400    0.3085968 6.0949329e-05    1947.6558    3917.8967 
+    5500   0.31469173 6.0949329e-05    1947.6558    3917.8967 
+    5600   0.32078666 6.0949329e-05    1947.6558    3917.8967 
+    5700   0.32688159 6.0949329e-05    1947.6558    3917.8967 
+    5800   0.33297653 6.0949329e-05    1947.6558    3917.8967 
+    5900   0.33907146 6.0949329e-05    1947.6558    3917.8967 
+    6000   0.34516639 6.0949329e-05    1947.6558    3917.8967 
+    6100   0.35126133 6.0949329e-05    1947.6558    3917.8967 
+    6200   0.35735626 6.0949329e-05    1947.6558    3917.8967 
+    6300   0.36345119 6.0949329e-05    1947.6558    3917.8967 
+    6400   0.36954612 6.0949329e-05    1947.6558    3917.8967 
+    6500   0.37564106 6.0949329e-05    1947.6558    3917.8967 
+    6600   0.38173599 6.0949329e-05    1947.6558    3917.8967 
+    6700   0.38783092 6.0949329e-05    1947.6558    3917.8967 
+    6800   0.39392586 6.0949329e-05    1947.6558    3917.8967 
+    6900   0.40002079 6.0949329e-05    1947.6558    3917.8967 
+    7000   0.40611572 6.0949329e-05    1947.6558    3917.8967 
+    7100   0.41221066 6.0949329e-05    1947.6558    3917.8967 
+    7200   0.41830559 6.0949329e-05    1947.6558    3917.8967 
+    7300   0.42440052 6.0949329e-05    1947.6558    3917.8967 
+    7400   0.43049545 6.0949329e-05    1947.6558    3917.8967 
+    7500   0.43659039 6.0949329e-05    1947.6558    3917.8967 
+    7600   0.44268532 6.0949329e-05    1947.6558    3917.8967 
+    7700   0.44878025 6.0949329e-05    1947.6558    3917.8967 
+    7800   0.45487519 6.0949329e-05    1947.6558    3917.8967 
+    7900   0.46097012 6.0949329e-05    1947.6558    3917.8967 
+    8000   0.46706505 6.0949329e-05    1947.6558    3917.8967 
+    8100   0.47315998 6.0949329e-05    1947.6558    3917.8967 
+    8200   0.47925492 6.0949329e-05    1947.6558    3917.8967 
+    8300   0.48534985 6.0949329e-05    1947.6558    3917.8967 
+    8400   0.49144478 6.0949329e-05    1947.6558    3917.8967 
+    8500   0.49753972 6.0949329e-05    1947.6558    3917.8967 
+    8600   0.50363465 6.0949329e-05    1947.6558    3917.8967 
+    8700   0.50972958 6.0949329e-05    1947.6558    3917.8967 
+    8800   0.51582452 6.0949329e-05    1947.6558    3917.8967 
+    8900   0.52191945 6.0949329e-05    1947.6558    3917.8967 
+    9000   0.52801438 6.0949329e-05    1947.6558    3917.8967 
+    9100   0.53410931 6.0949329e-05    1947.6558    3917.8967 
+    9200   0.54020425 6.0949329e-05    1947.6558    3917.8967 
+    9300   0.54629918 6.0949329e-05    1947.6558    3917.8967 
+    9400   0.55239411 6.0949329e-05    1947.6558    3917.8967 
+    9500   0.55848905 6.0949329e-05    1947.6558    3917.8967 
+    9600   0.56458398 6.0949329e-05    1947.6558    3917.8967 
+    9700   0.57067891 6.0949329e-05    1947.6558    3917.8967 
+    9800   0.57677384 6.0949329e-05    1947.6558    3917.8967 
+    9900   0.58286878 6.0949329e-05    1947.6558    3917.8967 
+   10000   0.58896371 6.0949329e-05    1947.6558    3917.8967 
+Loop time of 1.25184 on 1 procs for 10000 steps with 1 atoms
+
+Performance: 42.066 ns/day, 0.571 hours/ns, 7988.216 timesteps/s
+99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.0005827  | 0.0005827  | 0.0005827  |   0.0 |  0.05
+Neigh   | 1.2134     | 1.2134     | 1.2134     |   0.0 | 96.93
+Comm    | 0.02822    | 0.02822    | 0.02822    |   0.0 |  2.25
+Output  | 0.0017159  | 0.0017159  | 0.0017159  |   0.0 |  0.14
+Modify  | 0.0052147  | 0.0052147  | 0.0052147  |   0.0 |  0.42
+Other   |            | 0.002664   |            |       |  0.21
+
+Nlocal:    1 ave 1 max 1 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 960
+Dangerous builds = 568
+Total wall time: 0:00:01

examples/USER/misc/electron_stopping/log.20Mar19.elstop.only.g++.4

@@ -0,0 +1,196 @@
+LAMMPS (28 Feb 2019)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
+  using 1 OpenMP thread(s) per MPI task
+# Test case / example for fix electron/stopping
+# One fast atom, no other interactions.
+# Stopping only applied in a smaller box in the middle.
+#
+# Also uses fix dt/reset, as one should when energies are high
+# enough to require electronic stopping.
+
+units metal
+boundary p p p
+timestep 0.0001
+
+lattice fcc 1
+Lattice spacing in x,y,z = 1 1 1
+
+region rbox block -100 100 -100 100 -100 100
+region rsmallbox block -90 90 -90 90 -90 90
+
+create_box 1 rbox
+Created orthogonal box = (-100 -100 -100) to (100 100 100)
+  1 by 2 by 2 MPI processor grid
+
+mass 1 28.0855
+
+create_atoms 1 single 0 0 0
+Created 1 atoms
+  create_atoms CPU = 1.19209e-05 secs
+velocity all set 1120 1620 389
+
+pair_style zero 1
+pair_coeff * * 1
+
+fix fdt all dt/reset 1 NULL 0.001 0.1 emax 20.0
+fix fel all electron/stopping 1.0 Si.Si.elstop minneigh 0 region rsmallbox
+fix fnve all nve
+
+compute ek all ke/atom
+compute ektot all reduce sum c_ek
+
+thermo 100
+thermo_style custom step time dt f_fel c_ektot
+
+#dump mydump all custom 200 elstop.only.dump id x y z vx vy vz fx fy fz c_ek
+
+run 10000
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 3
+  ghost atom cutoff = 3
+  binsize = 1.5, bins = 134 134 134
+  2 neighbor lists, perpetual/occasional/extra = 1 1 0
+  (1) pair zero, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+  (2) fix electron/stopping, occasional
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.637 | 4.2 | 5.887 Mbytes
+Step Time Dt f_fel c_ektot 
+       0            0  4.98128e-05            0    5865.5525 
+     100 0.0049972222 5.0137252e-05    76.048699     5789.883 
+     200  0.010027278 5.0467945e-05    151.67477    5714.2548 
+     300  0.015090636 5.0803375e-05     226.8806    5639.0469 
+     400  0.020187777 5.1143663e-05     301.6685    5564.2569 
+     500  0.025319192 5.1488933e-05    376.04082    5489.8825 
+     600  0.030485386 5.1839314e-05    449.99984    5415.9215 
+     700  0.035686876 5.2194938e-05    523.54788    5342.3714 
+     800  0.040924195 5.2555944e-05    596.68721      5269.23 
+     900  0.046197886 5.2922477e-05    669.42011    5196.4951 
+    1000   0.05150851 5.3294685e-05    741.74883    5124.1643 
+    1100  0.056856642 5.3672723e-05    813.67563    5052.2355 
+    1200  0.062229338 5.3731851e-05    824.43012    5041.1224 
+    1300  0.067602524 5.3731851e-05    824.43012    5041.1224 
+    1400  0.072978188 5.387166e-05    850.91948    5014.9907 
+    1500   0.07838447 5.425887e-05    922.23961    4943.6685 
+    1600   0.08382978 5.4652329e-05    993.16341    4872.7428 
+    1700  0.089299984 5.4705935e-05    1002.3545     4863.198 
+    1800  0.094770578 5.4705935e-05    1002.3545     4863.198 
+    1900   0.10024117 5.4705935e-05    1002.3545     4863.198 
+    2000   0.10571333 5.4819488e-05    1022.8338    4843.0716 
+    2100   0.11121515 5.5222127e-05    1093.1986    4772.7048 
+    2200   0.11675757 5.5631458e-05    1163.1724    4702.7291 
+    2300   0.12234126 5.6047675e-05    1232.7573    4633.1422 
+    2400   0.12796692 5.6470985e-05    1301.9555     4563.942 
+    2500   0.13363527 5.6901598e-05    1370.7692    4495.1264 
+    2600   0.13934706 5.7339739e-05    1439.2006    4426.6932 
+    2700   0.14510304 5.7785637e-05    1507.2516    4358.6403 
+    2800     0.150904 5.8239536e-05    1574.9245    4290.9655 
+    2900   0.15675076 5.8701688e-05    1642.2213    4223.6668 
+    3000   0.16264416 5.9172358e-05    1709.1441    4156.7422 
+    3100   0.16858505 5.9651822e-05     1775.695    4090.1894 
+    3200   0.17457434 6.0140369e-05    1841.8761    4024.0064 
+    3300   0.18061294 6.0638302e-05    1907.6894    3958.1913 
+    3400   0.18669814 6.0949329e-05    1947.6558    3917.8967 
+    3500   0.19279307 6.0949329e-05    1947.6558    3917.8967 
+    3600     0.198888 6.0949329e-05    1947.6558    3917.8967 
+    3700   0.20498294 6.0949329e-05    1947.6558    3917.8967 
+    3800   0.21107787 6.0949329e-05    1947.6558    3917.8967 
+    3900    0.2171728 6.0949329e-05    1947.6558    3917.8967 
+    4000   0.22326773 6.0949329e-05    1947.6558    3917.8967 
+    4100   0.22936267 6.0949329e-05    1947.6558    3917.8967 
+    4200    0.2354576 6.0949329e-05    1947.6558    3917.8967 
+    4300   0.24155253 6.0949329e-05    1947.6558    3917.8967 
+    4400   0.24764747 6.0949329e-05    1947.6558    3917.8967 
+    4500    0.2537424 6.0949329e-05    1947.6558    3917.8967 
+    4600   0.25983733 6.0949329e-05    1947.6558    3917.8967 
+    4700   0.26593227 6.0949329e-05    1947.6558    3917.8967 
+    4800    0.2720272 6.0949329e-05    1947.6558    3917.8967 
+    4900   0.27812213 6.0949329e-05    1947.6558    3917.8967 
+    5000   0.28421706 6.0949329e-05    1947.6558    3917.8967 
+    5100     0.290312 6.0949329e-05    1947.6558    3917.8967 
+    5200   0.29640693 6.0949329e-05    1947.6558    3917.8967 
+    5300   0.30250186 6.0949329e-05    1947.6558    3917.8967 
+    5400    0.3085968 6.0949329e-05    1947.6558    3917.8967 
+    5500   0.31469173 6.0949329e-05    1947.6558    3917.8967 
+    5600   0.32078666 6.0949329e-05    1947.6558    3917.8967 
+    5700   0.32688159 6.0949329e-05    1947.6558    3917.8967 
+    5800   0.33297653 6.0949329e-05    1947.6558    3917.8967 
+    5900   0.33907146 6.0949329e-05    1947.6558    3917.8967 
+    6000   0.34516639 6.0949329e-05    1947.6558    3917.8967 
+    6100   0.35126133 6.0949329e-05    1947.6558    3917.8967 
+    6200   0.35735626 6.0949329e-05    1947.6558    3917.8967 
+    6300   0.36345119 6.0949329e-05    1947.6558    3917.8967 
+    6400   0.36954612 6.0949329e-05    1947.6558    3917.8967 
+    6500   0.37564106 6.0949329e-05    1947.6558    3917.8967 
+    6600   0.38173599 6.0949329e-05    1947.6558    3917.8967 
+    6700   0.38783092 6.0949329e-05    1947.6558    3917.8967 
+    6800   0.39392586 6.0949329e-05    1947.6558    3917.8967 
+    6900   0.40002079 6.0949329e-05    1947.6558    3917.8967 
+    7000   0.40611572 6.0949329e-05    1947.6558    3917.8967 
+    7100   0.41221066 6.0949329e-05    1947.6558    3917.8967 
+    7200   0.41830559 6.0949329e-05    1947.6558    3917.8967 
+    7300   0.42440052 6.0949329e-05    1947.6558    3917.8967 
+    7400   0.43049545 6.0949329e-05    1947.6558    3917.8967 
+    7500   0.43659039 6.0949329e-05    1947.6558    3917.8967 
+    7600   0.44268532 6.0949329e-05    1947.6558    3917.8967 
+    7700   0.44878025 6.0949329e-05    1947.6558    3917.8967 
+    7800   0.45487519 6.0949329e-05    1947.6558    3917.8967 
+    7900   0.46097012 6.0949329e-05    1947.6558    3917.8967 
+    8000   0.46706505 6.0949329e-05    1947.6558    3917.8967 
+    8100   0.47315998 6.0949329e-05    1947.6558    3917.8967 
+    8200   0.47925492 6.0949329e-05    1947.6558    3917.8967 
+    8300   0.48534985 6.0949329e-05    1947.6558    3917.8967 
+    8400   0.49144478 6.0949329e-05    1947.6558    3917.8967 
+    8500   0.49753972 6.0949329e-05    1947.6558    3917.8967 
+    8600   0.50363465 6.0949329e-05    1947.6558    3917.8967 
+    8700   0.50972958 6.0949329e-05    1947.6558    3917.8967 
+    8800   0.51582452 6.0949329e-05    1947.6558    3917.8967 
+    8900   0.52191945 6.0949329e-05    1947.6558    3917.8967 
+    9000   0.52801438 6.0949329e-05    1947.6558    3917.8967 
+    9100   0.53410931 6.0949329e-05    1947.6558    3917.8967 
+    9200   0.54020425 6.0949329e-05    1947.6558    3917.8967 
+    9300   0.54629918 6.0949329e-05    1947.6558    3917.8967 
+    9400   0.55239411 6.0949329e-05    1947.6558    3917.8967 
+    9500   0.55848905 6.0949329e-05    1947.6558    3917.8967 
+    9600   0.56458398 6.0949329e-05    1947.6558    3917.8967 
+    9700   0.57067891 6.0949329e-05    1947.6558    3917.8967 
+    9800   0.57677384 6.0949329e-05    1947.6558    3917.8967 
+    9900   0.58286878 6.0949329e-05    1947.6558    3917.8967 
+   10000   0.58896371 6.0949329e-05    1947.6558    3917.8967 
+Loop time of 1.38891 on 4 procs for 10000 steps with 1 atoms
+
+Performance: 37.915 ns/day, 0.633 hours/ns, 7199.876 timesteps/s
+94.0% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.0004971  | 0.00060463 | 0.00069618 |   0.0 |  0.04
+Neigh   | 1.1005     | 1.1507     | 1.2839     |   7.2 | 82.85
+Comm    | 0.025918   | 0.026382   | 0.027041   |   0.3 |  1.90
+Output  | 0.0016336  | 0.005001   | 0.01507    |   8.2 |  0.36
+Modify  | 0.059378   | 0.20196    | 0.25453    |  18.3 | 14.54
+Other   |            | 0.00422    |            |       |  0.30
+
+Nlocal:    0.25 ave 1 max 0 min
+Histogram: 3 0 0 0 0 0 0 0 0 1
+Nghost:    0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs:    0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs:  0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 960
+Dangerous builds = 568
+Total wall time: 0:00:01

examples/granular/in.pour.drum

@@ -0,0 +1,98 @@
+# pour two types of particles (cohesive and non-cohesive) into cylinder
+# 'turn' cylinder by changing direction of gravity, then rotate it.
+# This simulates a rotating drum powder characterization experiment.
+
+variable	name string rotating_drum_two_types
+
+atom_style	sphere
+units		lj
+
+###############################################
+# Geometry-related parameters
+###############################################
+
+variable	boxx equal 30
+variable	boxy equal 30
+variable	boxz equal 50
+
+variable	drum_rad equal ${boxx}*0.5
+variable	drum_height equal 20
+
+variable	xc equal 0.5*${boxx}
+variable	yc equal 0.5*${boxx}
+variable	zc equal 0.5*${boxz}
+
+###############################################
+# Particle-related parameters
+###############################################
+variable	rlo equal 0.25
+variable	rhi equal 0.5
+variable	dlo equal 2.0*${rlo}
+variable	dhi equal 2.0*${rhi}
+
+variable	cyl_rad_inner equal ${drum_rad}-1.1*${rhi}
+
+variable	dens equal 1.0
+
+variable skin equal 0.4*${rhi}
+
+#############
+processors * * 1
+region		boxreg block 0 ${boxx} 0 ${boxy} 0 ${boxz}
+create_box	2 boxreg
+change_box	all boundary p p f
+comm_modify	vel yes
+
+variable	theta equal 0
+
+region		curved_wall cylinder z ${xc} ${yc} ${drum_rad} 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region		bottom_wall plane ${xc} ${yc} 0 0 0 1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
+
+region		insreg cylinder z ${xc} ${yc} ${cyl_rad_inner} ${drum_height} ${boxz}
+
+fix		0 all balance 100 1.0 shift xy 5 1.1
+fix		1 all nve/sphere
+fix		grav all gravity 10 vector 0 0 -1
+fix		ins1 all pour 2000 1 1234 region insreg diam range ${dlo} ${dhi} dens ${dens} ${dens}
+fix		ins2 all pour 2000 2 1234 region insreg diam range ${dlo} ${dhi} dens ${dens} ${dens}
+
+comm_modify	vel yes
+
+neighbor	${skin} bin
+neigh_modify	delay 0 every 1 check yes
+
+pair_style	granular 
+pair_coeff	1 * hertz/material 1e5 0.2 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji
+pair_coeff	2 2 jkr 1e5 0.1 0.3 50 tangential mindlin NULL 1.0 0.5 rolling sds 1e3 1e3 0.1 twisting marshall damping tsuji
+
+fix		3 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region curved_wall 
+fix		4 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region bottom_wall
+
+thermo_style	custom step atoms ke v_theta
+thermo_modify	lost warn
+thermo		100
+
+timestep	0.001
+
+#dump		1 all custom 100 ${name}.dump id type radius mass x y z 
+
+#For removal later
+compute		1 all property/atom radius
+variable	zmax atom z+c_1>0.5*${drum_height}
+group		delgroup dynamic all var zmax every 10000
+
+run		2000
+
+#Remove any particles that are above z > 0.5*drum_height
+delete_atoms	group delgroup
+
+#Add top lid
+region		top_wall plane ${xc} ${yc} ${drum_height} 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
+fix		5 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region top_wall
+
+# 'Turn' drum by switching the direction of gravity
+unfix		grav
+fix		grav all gravity 10 vector 0 -1 0
+
+variable	theta equal 2*PI*elapsed/20000.0
+run		3000

examples/granular/in.pour.flatwall

@@ -0,0 +1,67 @@
+# pour two types of particles (cohesive and non-cohesive) on flat wall
+
+variable   	name string pour_two_types
+
+atom_style	sphere
+units		lj
+
+###############################################
+# Geometry-related parameters
+###############################################
+
+variable	boxx equal 20
+variable	boxy equal 20
+variable	boxz equal 30
+
+variable	xc1 equal 0.3*${boxx}
+variable	xc2 equal 0.7*${boxx}
+variable	yc equal 0.5*${boxy}
+
+###############################################
+# Particle-related parameters
+###############################################
+variable	rlo equal 0.25
+variable	rhi equal 0.5
+variable	dlo equal 2.0*${rlo}
+variable	dhi equal 2.0*${rhi}
+
+variable	dens equal 1.0
+
+variable skin equal 0.3*${rhi}
+
+#############
+processors	* * 1
+region 		boxreg block 0 ${boxx} 0 ${boxy} 0 ${boxz}
+create_box	2 boxreg
+change_box	all boundary p p f
+
+comm_modify 	vel yes
+
+region		insreg1 cylinder z ${xc1} ${yc} 5 15 ${boxz}
+region		insreg2 cylinder z ${xc2} ${yc} 5 15 ${boxz}
+
+fix		1 all nve/sphere
+fix		grav all gravity 10.0 vector 0 0 -1
+fix		ins1 all pour 1500 1 3123 region insreg1 diam range ${dlo} ${dhi} dens ${dens} ${dens}
+fix		ins2 all pour 1500 2 3123 region insreg2 diam range ${dlo} ${dhi} dens ${dens} ${dens}
+
+comm_modify	vel yes
+
+neighbor	${skin} bin
+neigh_modify	delay 0 every 1 check yes
+
+pair_style	granular 
+pair_coeff 	1 * jkr 1000.0 50.0 0.3 10 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 
+
+fix		3 all wall/gran granular hertz/material 1e5 1e3 0.3 tangential mindlin NULL 1.0 0.5 zplane 0 NULL 
+
+thermo_style	custom step cpu atoms ke
+thermo_modify	lost warn
+thermo		100
+
+timestep	0.001
+
+#dump		1 all custom 100 ${name}.dump id type radius mass x y z 
+
+run		5000

examples/granular/log.29Mar19.pour.drum.g++.1

@@ -0,0 +1,271 @@
+LAMMPS (29 Mar 2019)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:88)
+  using 1 OpenMP thread(s) per MPI task
+# pour two types of particles (cohesive and non-cohesive) into cylinder
+# 'turn' cylinder by changing direction of gravity, then rotate it.
+# This simulates a rotating drum powder characterization experiment.
+
+variable	name string rotating_drum_two_types
+
+atom_style	sphere
+units		lj
+
+###############################################
+# Geometry-related parameters
+###############################################
+
+variable	boxx equal 30
+variable	boxy equal 30
+variable	boxz equal 50
+
+variable	drum_rad equal ${boxx}*0.5
+variable	drum_rad equal 30*0.5
+variable	drum_height equal 20
+
+variable	xc equal 0.5*${boxx}
+variable	xc equal 0.5*30
+variable	yc equal 0.5*${boxx}
+variable	yc equal 0.5*30
+variable	zc equal 0.5*${boxz}
+variable	zc equal 0.5*50
+
+###############################################
+# Particle-related parameters
+###############################################
+variable	rlo equal 0.25
+variable	rhi equal 0.5
+variable	dlo equal 2.0*${rlo}
+variable	dlo equal 2.0*0.25
+variable	dhi equal 2.0*${rhi}
+variable	dhi equal 2.0*0.5
+
+variable	cyl_rad_inner equal ${drum_rad}-1.1*${rhi}
+variable	cyl_rad_inner equal 15-1.1*${rhi}
+variable	cyl_rad_inner equal 15-1.1*0.5
+
+variable	dens equal 1.0
+
+variable skin equal 0.4*${rhi}
+variable skin equal 0.4*0.5
+
+#############
+processors * * 1
+region		boxreg block 0 ${boxx} 0 ${boxy} 0 ${boxz}
+region		boxreg block 0 30 0 ${boxy} 0 ${boxz}
+region		boxreg block 0 30 0 30 0 ${boxz}
+region		boxreg block 0 30 0 30 0 50
+create_box	2 boxreg
+Created orthogonal box = (0 0 0) to (30 30 50)
+  1 by 1 by 1 MPI processor grid
+change_box	all boundary p p f
+comm_modify	vel yes
+
+variable	theta equal 0
+
+region		curved_wall cylinder z ${xc} ${yc} ${drum_rad} 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region		curved_wall cylinder z 15 ${yc} ${drum_rad} 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region		curved_wall cylinder z 15 15 ${drum_rad} 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region		curved_wall cylinder z 15 15 15 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region		curved_wall cylinder z 15 15 15 0 20 side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region		curved_wall cylinder z 15 15 15 0 20 side in rotate v_theta 15 ${yc} 0 0 0 1
+region		curved_wall cylinder z 15 15 15 0 20 side in rotate v_theta 15 15 0 0 0 1
+region		bottom_wall plane ${xc} ${yc} 0 0 0 1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region		bottom_wall plane 15 ${yc} 0 0 0 1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region		bottom_wall plane 15 15 0 0 0 1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region		bottom_wall plane 15 15 0 0 0 1 side in rotate v_theta 15 ${yc} 0 0 0 1
+region		bottom_wall plane 15 15 0 0 0 1 side in rotate v_theta 15 15 0 0 0 1
+
+region		insreg cylinder z ${xc} ${yc} ${cyl_rad_inner} ${drum_height} ${boxz}
+region		insreg cylinder z 15 ${yc} ${cyl_rad_inner} ${drum_height} ${boxz}
+region		insreg cylinder z 15 15 ${cyl_rad_inner} ${drum_height} ${boxz}
+region		insreg cylinder z 15 15 14.45 ${drum_height} ${boxz}
+region		insreg cylinder z 15 15 14.45 20 ${boxz}
+region		insreg cylinder z 15 15 14.45 20 50
+
+fix		0 all balance 100 1.0 shift xy 5 1.1
+fix		1 all nve/sphere
+fix		grav all gravity 10 vector 0 0 -1
+fix		ins1 all pour 2000 1 1234 region insreg diam range ${dlo} ${dhi} dens ${dens} ${dens}
+fix		ins1 all pour 2000 1 1234 region insreg diam range 0.5 ${dhi} dens ${dens} ${dens}
+fix		ins1 all pour 2000 1 1234 region insreg diam range 0.5 1 dens ${dens} ${dens}
+fix		ins1 all pour 2000 1 1234 region insreg diam range 0.5 1 dens 1 ${dens}
+fix		ins1 all pour 2000 1 1234 region insreg diam range 0.5 1 dens 1 1
+Particle insertion: 9396 every 490 steps, 2000 by step 1
+fix		ins2 all pour 2000 2 1234 region insreg diam range ${dlo} ${dhi} dens ${dens} ${dens}
+fix		ins2 all pour 2000 2 1234 region insreg diam range 0.5 ${dhi} dens ${dens} ${dens}
+fix		ins2 all pour 2000 2 1234 region insreg diam range 0.5 1 dens ${dens} ${dens}
+fix		ins2 all pour 2000 2 1234 region insreg diam range 0.5 1 dens 1 ${dens}
+fix		ins2 all pour 2000 2 1234 region insreg diam range 0.5 1 dens 1 1
+Particle insertion: 9396 every 490 steps, 2000 by step 1
+
+comm_modify	vel yes
+
+neighbor	${skin} bin
+neighbor	0.2 bin
+neigh_modify	delay 0 every 1 check yes
+
+pair_style	granular
+pair_coeff	1 * hertz/material 1e5 0.2 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji
+pair_coeff	2 2 jkr 1e5 0.1 0.3 50 tangential mindlin NULL 1.0 0.5 rolling sds 1e3 1e3 0.1 twisting marshall damping tsuji
+
+fix		3 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region curved_wall
+fix		4 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region bottom_wall
+
+thermo_style	custom step atoms ke v_theta
+thermo_modify	lost warn
+thermo		100
+
+timestep	0.001
+
+dump		1 all custom 100 ${name}.dump id type radius mass x y z
+dump		1 all custom 100 rotating_drum_two_types.dump id type radius mass x y z
+
+#For removal later
+compute		1 all property/atom radius
+variable	zmax atom z+c_1>0.5*${drum_height}
+variable	zmax atom z+c_1>0.5*20
+group		delgroup dynamic all var zmax every 10000
+dynamic group delgroup defined
+
+run		2000
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 1.2
+  ghost atom cutoff = 1.2
+  binsize = 0.6, bins = 50 50 84
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair granular, perpetual
+      attributes: half, newton on, size, history
+      pair build: half/size/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 13.02 | 13.02 | 13.02 Mbytes
+Step Atoms KinEng v_theta 
+       0        0           -0            0 
+     100     4000           -0            0 
+     200     4000           -0            0 
+     300     4000           -0            0 
+     400     4000           -0            0 
+     500     4000           -0            0 
+     600     4000           -0            0 
+     700     4000           -0            0 
+     800     4000           -0            0 
+     900     4000           -0            0 
+    1000     4000           -0            0 
+    1100     4000           -0            0 
+    1200     4000           -0            0 
+    1300     4000           -0            0 
+    1400     4000           -0            0 
+    1500     4000           -0            0 
+    1600     4000           -0            0 
+    1700     4000           -0            0 
+    1800     4000           -0            0 
+    1900     4000           -0            0 
+    2000     4000           -0            0 
+Loop time of 3.54461 on 1 procs for 2000 steps with 4000 atoms
+
+Performance: 48750.057 tau/day, 564.237 timesteps/s
+99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.61949    | 0.61949    | 0.61949    |   0.0 | 17.48
+Neigh   | 1.2492     | 1.2492     | 1.2492     |   0.0 | 35.24
+Comm    | 0.046404   | 0.046404   | 0.046404   |   0.0 |  1.31
+Output  | 0.15901    | 0.15901    | 0.15901    |   0.0 |  4.49
+Modify  | 1.4165     | 1.4165     | 1.4165     |   0.0 | 39.96
+Other   |            | 0.05391    |            |       |  1.52
+
+Nlocal:    4000 ave 4000 max 4000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    166 ave 166 max 166 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    8195 ave 8195 max 8195 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 8195
+Ave neighs/atom = 2.04875
+Neighbor list builds = 1004
+Dangerous builds = 3
+
+#Remove any particles that are above z > 0.5*drum_height
+delete_atoms	group delgroup
+Deleted 0 atoms, new total = 4000
+
+#Add top lid
+region		top_wall plane ${xc} ${yc} ${drum_height} 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region		top_wall plane 15 ${yc} ${drum_height} 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region		top_wall plane 15 15 ${drum_height} 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region		top_wall plane 15 15 20 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region		top_wall plane 15 15 20 0 0 -1 side in rotate v_theta 15 ${yc} 0 0 0 1
+region		top_wall plane 15 15 20 0 0 -1 side in rotate v_theta 15 15 0 0 0 1
+fix		5 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region top_wall
+
+# 'Turn' drum by switching the direction of gravity
+unfix		grav
+fix		grav all gravity 10 vector 0 -1 0
+
+variable	theta equal 2*PI*elapsed/20000.0
+run		3000
+Per MPI rank memory allocation (min/avg/max) = 24.81 | 24.81 | 24.81 Mbytes
+Step Atoms KinEng v_theta 
+    2000     4000    64.333531            0 
+    2100     4000    106.69182  0.031415927 
+    2200     4000     121.8461  0.062831853 
+    2300     4000    88.767952   0.09424778 
+    2400     4000    82.850721   0.12566371 
+    2500     4000    91.683284   0.15707963 
+    2600     4000     31.56344   0.18849556 
+    2700     4000    4.5697672   0.21991149 
+    2800     4000    3.9879051   0.25132741 
+    2900     4000    4.4394235   0.28274334 
+    3000     4000    5.1212931   0.31415927 
+    3100     4000    5.8608892   0.34557519 
+    3200     4000     6.600714   0.37699112 
+    3300     4000    7.3497851   0.40840704 
+    3400     4000    8.0490988   0.43982297 
+    3500     4000    8.6712396    0.4712389 
+    3600     4000    9.1328667   0.50265482 
+    3700     4000    9.4683561   0.53407075 
+    3800     4000    9.5878145   0.56548668 
+    3900     4000     9.387745    0.5969026 
+    4000     4000    8.9117631   0.62831853 
+    4100     4000    8.2344368   0.65973446 
+    4200     4000    7.5335088   0.69115038 
+    4300     4000    6.8426179   0.72256631 
+    4400     4000    6.0567247   0.75398224 
+    4500     4000    5.4166132   0.78539816 
+    4600     4000    4.6012409   0.81681409 
+    4700     4000    3.8314982   0.84823002 
+    4800     4000    3.1916415   0.87964594 
+    4900     4000    2.7833964   0.91106187 
+    5000     4000    2.5051362    0.9424778 
+Loop time of 11.9545 on 1 procs for 3000 steps with 4000 atoms
+
+Performance: 21682.142 tau/day, 250.951 timesteps/s
+99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 4.8291     | 4.8291     | 4.8291     |   0.0 | 40.40
+Neigh   | 2.7489     | 2.7489     | 2.7489     |   0.0 | 22.99
+Comm    | 0.071249   | 0.071249   | 0.071249   |   0.0 |  0.60
+Output  | 0.20547    | 0.20547    | 0.20547    |   0.0 |  1.72
+Modify  | 4.0179     | 4.0179     | 4.0179     |   0.0 | 33.61
+Other   |            | 0.0819     |            |       |  0.69
+
+Nlocal:    4000 ave 4000 max 4000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    322 ave 322 max 322 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    14849 ave 14849 max 14849 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 14849
+Ave neighs/atom = 3.71225
+Neighbor list builds = 1290
+Dangerous builds = 672
+Total wall time: 0:00:15

examples/granular/log.29Mar19.pour.drum.g++.4

@@ -0,0 +1,271 @@
+LAMMPS (29 Mar 2019)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:88)
+  using 1 OpenMP thread(s) per MPI task
+# pour two types of particles (cohesive and non-cohesive) into cylinder
+# 'turn' cylinder by changing direction of gravity, then rotate it.
+# This simulates a rotating drum powder characterization experiment.
+
+variable	name string rotating_drum_two_types
+
+atom_style	sphere
+units		lj
+
+###############################################
+# Geometry-related parameters
+###############################################
+
+variable	boxx equal 30
+variable	boxy equal 30
+variable	boxz equal 50
+
+variable	drum_rad equal ${boxx}*0.5
+variable	drum_rad equal 30*0.5
+variable	drum_height equal 20
+
+variable	xc equal 0.5*${boxx}
+variable	xc equal 0.5*30
+variable	yc equal 0.5*${boxx}
+variable	yc equal 0.5*30
+variable	zc equal 0.5*${boxz}
+variable	zc equal 0.5*50
+
+###############################################
+# Particle-related parameters
+###############################################
+variable	rlo equal 0.25
+variable	rhi equal 0.5
+variable	dlo equal 2.0*${rlo}
+variable	dlo equal 2.0*0.25
+variable	dhi equal 2.0*${rhi}
+variable	dhi equal 2.0*0.5
+
+variable	cyl_rad_inner equal ${drum_rad}-1.1*${rhi}
+variable	cyl_rad_inner equal 15-1.1*${rhi}
+variable	cyl_rad_inner equal 15-1.1*0.5
+
+variable	dens equal 1.0
+
+variable skin equal 0.4*${rhi}
+variable skin equal 0.4*0.5
+
+#############
+processors * * 1
+region		boxreg block 0 ${boxx} 0 ${boxy} 0 ${boxz}
+region		boxreg block 0 30 0 ${boxy} 0 ${boxz}
+region		boxreg block 0 30 0 30 0 ${boxz}
+region		boxreg block 0 30 0 30 0 50
+create_box	2 boxreg
+Created orthogonal box = (0 0 0) to (30 30 50)
+  2 by 2 by 1 MPI processor grid
+change_box	all boundary p p f
+comm_modify	vel yes
+
+variable	theta equal 0
+
+region		curved_wall cylinder z ${xc} ${yc} ${drum_rad} 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region		curved_wall cylinder z 15 ${yc} ${drum_rad} 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region		curved_wall cylinder z 15 15 ${drum_rad} 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region		curved_wall cylinder z 15 15 15 0 ${drum_height} side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region		curved_wall cylinder z 15 15 15 0 20 side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region		curved_wall cylinder z 15 15 15 0 20 side in rotate v_theta 15 ${yc} 0 0 0 1
+region		curved_wall cylinder z 15 15 15 0 20 side in rotate v_theta 15 15 0 0 0 1
+region		bottom_wall plane ${xc} ${yc} 0 0 0 1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region		bottom_wall plane 15 ${yc} 0 0 0 1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region		bottom_wall plane 15 15 0 0 0 1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region		bottom_wall plane 15 15 0 0 0 1 side in rotate v_theta 15 ${yc} 0 0 0 1
+region		bottom_wall plane 15 15 0 0 0 1 side in rotate v_theta 15 15 0 0 0 1
+
+region		insreg cylinder z ${xc} ${yc} ${cyl_rad_inner} ${drum_height} ${boxz}
+region		insreg cylinder z 15 ${yc} ${cyl_rad_inner} ${drum_height} ${boxz}
+region		insreg cylinder z 15 15 ${cyl_rad_inner} ${drum_height} ${boxz}
+region		insreg cylinder z 15 15 14.45 ${drum_height} ${boxz}
+region		insreg cylinder z 15 15 14.45 20 ${boxz}
+region		insreg cylinder z 15 15 14.45 20 50
+
+fix		0 all balance 100 1.0 shift xy 5 1.1
+fix		1 all nve/sphere
+fix		grav all gravity 10 vector 0 0 -1
+fix		ins1 all pour 2000 1 1234 region insreg diam range ${dlo} ${dhi} dens ${dens} ${dens}
+fix		ins1 all pour 2000 1 1234 region insreg diam range 0.5 ${dhi} dens ${dens} ${dens}
+fix		ins1 all pour 2000 1 1234 region insreg diam range 0.5 1 dens ${dens} ${dens}
+fix		ins1 all pour 2000 1 1234 region insreg diam range 0.5 1 dens 1 ${dens}
+fix		ins1 all pour 2000 1 1234 region insreg diam range 0.5 1 dens 1 1
+Particle insertion: 9396 every 490 steps, 2000 by step 1
+fix		ins2 all pour 2000 2 1234 region insreg diam range ${dlo} ${dhi} dens ${dens} ${dens}
+fix		ins2 all pour 2000 2 1234 region insreg diam range 0.5 ${dhi} dens ${dens} ${dens}
+fix		ins2 all pour 2000 2 1234 region insreg diam range 0.5 1 dens ${dens} ${dens}
+fix		ins2 all pour 2000 2 1234 region insreg diam range 0.5 1 dens 1 ${dens}
+fix		ins2 all pour 2000 2 1234 region insreg diam range 0.5 1 dens 1 1
+Particle insertion: 9396 every 490 steps, 2000 by step 1
+
+comm_modify	vel yes
+
+neighbor	${skin} bin
+neighbor	0.2 bin
+neigh_modify	delay 0 every 1 check yes
+
+pair_style	granular
+pair_coeff	1 * hertz/material 1e5 0.2 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji
+pair_coeff	2 2 jkr 1e5 0.1 0.3 50 tangential mindlin NULL 1.0 0.5 rolling sds 1e3 1e3 0.1 twisting marshall damping tsuji
+
+fix		3 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region curved_wall
+fix		4 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region bottom_wall
+
+thermo_style	custom step atoms ke v_theta
+thermo_modify	lost warn
+thermo		100
+
+timestep	0.001
+
+dump		1 all custom 100 ${name}.dump id type radius mass x y z
+dump		1 all custom 100 rotating_drum_two_types.dump id type radius mass x y z
+
+#For removal later
+compute		1 all property/atom radius
+variable	zmax atom z+c_1>0.5*${drum_height}
+variable	zmax atom z+c_1>0.5*20
+group		delgroup dynamic all var zmax every 10000
+dynamic group delgroup defined
+
+run		2000
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 1.2
+  ghost atom cutoff = 1.2
+  binsize = 0.6, bins = 50 50 84
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair granular, perpetual
+      attributes: half, newton on, size, history
+      pair build: half/size/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 12.25 | 12.25 | 12.25 Mbytes
+Step Atoms KinEng v_theta 
+       0        0           -0            0 
+     100     4000           -0            0 
+     200     4000           -0            0 
+     300     4000           -0            0 
+     400     4000           -0            0 
+     500     4000           -0            0 
+     600     4000           -0            0 
+     700     4000           -0            0 
+     800     4000           -0            0 
+     900     4000           -0            0 
+    1000     4000           -0            0 
+    1100     4000           -0            0 
+    1200     4000           -0            0 
+    1300     4000           -0            0 
+    1400     4000           -0            0 
+    1500     4000           -0            0 
+    1600     4000           -0            0 
+    1700     4000           -0            0 
+    1800     4000           -0            0 
+    1900     4000           -0            0 
+    2000     4000           -0            0 
+Loop time of 2.0709 on 4 procs for 2000 steps with 4000 atoms
+
+Performance: 83442.024 tau/day, 965.764 timesteps/s
+97.7% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.24679    | 0.26336    | 0.28853    |   3.0 | 12.72
+Neigh   | 0.52279    | 0.5332     | 0.53858    |   0.9 | 25.75
+Comm    | 0.17418    | 0.20253    | 0.23266    |   4.7 |  9.78
+Output  | 0.092897   | 0.093531   | 0.09515    |   0.3 |  4.52
+Modify  | 0.88151    | 0.89571    | 0.90582    |   0.9 | 43.25
+Other   |            | 0.08257    |            |       |  3.99
+
+Nlocal:    1000 ave 1001 max 999 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Nghost:    267.75 ave 276 max 262 min
+Histogram: 1 0 1 0 1 0 0 0 0 1
+Neighs:    2031.5 ave 2091 max 1958 min
+Histogram: 1 0 0 0 1 0 0 1 0 1
+
+Total # of neighbors = 8126
+Ave neighs/atom = 2.0315
+Neighbor list builds = 1004
+Dangerous builds = 3
+
+#Remove any particles that are above z > 0.5*drum_height
+delete_atoms	group delgroup
+Deleted 0 atoms, new total = 4000
+
+#Add top lid
+region		top_wall plane ${xc} ${yc} ${drum_height} 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region		top_wall plane 15 ${yc} ${drum_height} 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region		top_wall plane 15 15 ${drum_height} 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region		top_wall plane 15 15 20 0 0 -1 side in rotate v_theta ${xc} ${yc} 0 0 0 1
+region		top_wall plane 15 15 20 0 0 -1 side in rotate v_theta 15 ${yc} 0 0 0 1
+region		top_wall plane 15 15 20 0 0 -1 side in rotate v_theta 15 15 0 0 0 1
+fix		5 all wall/gran/region granular hertz/material 1e5 0.1 0.3 tangential mindlin NULL 1.0 0.5 damping tsuji region top_wall
+
+# 'Turn' drum by switching the direction of gravity
+unfix		grav
+fix		grav all gravity 10 vector 0 -1 0
+
+variable	theta equal 2*PI*elapsed/20000.0
+run		3000
+Per MPI rank memory allocation (min/avg/max) = 21.6 | 22.6 | 23.82 Mbytes
+Step Atoms KinEng v_theta 
+    2000     4000    64.255821            0 
+    2100     4000    106.47082  0.031415927 
+    2200     4000    121.52634  0.062831853 
+    2300     4000    87.748818   0.09424778 
+    2400     4000    82.712784   0.12566371 
+    2500     4000    90.618713   0.15707963 
+    2600     4000    30.096031   0.18849556 
+    2700     4000    4.0838611   0.21991149 
+    2800     4000    3.7485959   0.25132741 
+    2900     4000    4.2159774   0.28274334 
+    3000     4000    4.8730048   0.31415927 
+    3100     4000    5.6109465   0.34557519 
+    3200     4000    6.4290528   0.37699112 
+    3300     4000    7.2699677   0.40840704 
+    3400     4000    8.0895944   0.43982297 
+    3500     4000    8.7222781    0.4712389 
+    3600     4000     9.133205   0.50265482 
+    3700     4000    9.3404584   0.53407075 
+    3800     4000    9.3359844   0.56548668 
+    3900     4000    9.0916854    0.5969026 
+    4000     4000    8.5596424   0.62831853 
+    4100     4000    7.9734883   0.65973446 
+    4200     4000    7.2154383   0.69115038 
+    4300     4000    6.7039232   0.72256631 
+    4400     4000    6.1542738   0.75398224 
+    4500     4000    5.4049454   0.78539816 
+    4600     4000    4.4603192   0.81681409 
+    4700     4000    3.6197985   0.84823002 
+    4800     4000    2.9895571   0.87964594 
+    4900     4000    2.5314553   0.91106187 
+    5000     4000    2.2645533    0.9424778 
+Loop time of 6.64209 on 4 procs for 3000 steps with 4000 atoms
+
+Performance: 39023.861 tau/day, 451.665 timesteps/s
+96.6% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 1.8376     | 2.126      | 2.3131     |  12.6 | 32.01
+Neigh   | 0.97762    | 1.0518     | 1.1337     |   5.4 | 15.84
+Comm    | 0.53699    | 0.84265    | 1.2325     |  27.6 | 12.69
+Output  | 0.13922    | 0.14159    | 0.14388    |   0.4 |  2.13
+Modify  | 1.8815     | 2.1026     | 2.3368     |  11.2 | 31.66
+Other   |            | 0.3774     |            |       |  5.68
+
+Nlocal:    1000 ave 1256 max 744 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Nghost:    579.5 ave 789 max 498 min
+Histogram: 2 1 0 0 0 0 0 0 0 1
+Neighs:    3696.25 ave 4853 max 2590 min
+Histogram: 2 0 0 0 0 0 0 0 1 1
+
+Total # of neighbors = 14785
+Ave neighs/atom = 3.69625
+Neighbor list builds = 1230
+Dangerous builds = 676
+Total wall time: 0:00:08

examples/granular/log.29Mar19.pour.flatwall.g++.1

@@ -0,0 +1,134 @@
+LAMMPS (29 Mar 2019)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:88)
+  using 1 OpenMP thread(s) per MPI task
+# pour two types of particles (cohesive and non-cohesive) on flat wall
+
+variable   	name string pour_two_types
+
+atom_style	sphere
+units		lj
+
+###############################################
+# Geometry-related parameters
+###############################################
+
+variable	boxx equal 20
+variable	boxy equal 20
+variable	boxz equal 30
+
+variable	xc1 equal 0.3*${boxx}
+variable	xc1 equal 0.3*20
+variable	xc2 equal 0.7*${boxx}
+variable	xc2 equal 0.7*20
+variable	yc equal 0.5*${boxy}
+variable	yc equal 0.5*20
+
+###############################################
+# Particle-related parameters
+###############################################
+variable	rlo equal 0.25
+variable	rhi equal 0.5
+variable	dlo equal 2.0*${rlo}
+variable	dlo equal 2.0*0.25
+variable	dhi equal 2.0*${rhi}
+variable	dhi equal 2.0*0.5
+
+variable	dens equal 1.0
+
+variable skin equal 0.3*${rhi}
+variable skin equal 0.3*0.5
+
+#############
+processors	* * 1
+region 		boxreg block 0 ${boxx} 0 ${boxy} 0 ${boxz}
+region 		boxreg block 0 20 0 ${boxy} 0 ${boxz}
+region 		boxreg block 0 20 0 20 0 ${boxz}
+region 		boxreg block 0 20 0 20 0 30
+create_box	2 boxreg
+Created orthogonal box = (0 0 0) to (20 20 30)
+  1 by 1 by 1 MPI processor grid
+change_box	all boundary p p f
+
+comm_modify 	vel yes
+
+region		insreg1 cylinder z ${xc1} ${yc} 5 15 ${boxz}
+region		insreg1 cylinder z 6 ${yc} 5 15 ${boxz}
+region		insreg1 cylinder z 6 10 5 15 ${boxz}
+region		insreg1 cylinder z 6 10 5 15 30
+region		insreg2 cylinder z ${xc2} ${yc} 5 15 ${boxz}
+region		insreg2 cylinder z 14 ${yc} 5 15 ${boxz}
+region		insreg2 cylinder z 14 10 5 15 ${boxz}
+region		insreg2 cylinder z 14 10 5 15 30
+
+fix		1 all nve/sphere
+fix		grav all gravity 10.0 vector 0 0 -1
+fix		ins1 all pour 1500 1 3123 region insreg1 diam range ${dlo} ${dhi} dens ${dens} ${dens}
+fix		ins1 all pour 1500 1 3123 region insreg1 diam range 0.5 ${dhi} dens ${dens} ${dens}
+fix		ins1 all pour 1500 1 3123 region insreg1 diam range 0.5 1 dens ${dens} ${dens}
+fix		ins1 all pour 1500 1 3123 region insreg1 diam range 0.5 1 dens 1 ${dens}
+fix		ins1 all pour 1500 1 3123 region insreg1 diam range 0.5 1 dens 1 1
+Particle insertion: 562 every 346 steps, 1500 by step 693
+fix		ins2 all pour 1500 2 3123 region insreg2 diam range ${dlo} ${dhi} dens ${dens} ${dens}
+fix		ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 ${dhi} dens ${dens} ${dens}
+fix		ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 1 dens ${dens} ${dens}
+fix		ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 1 dens 1 ${dens}
+fix		ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 1 dens 1 1
+Particle insertion: 562 every 346 steps, 1500 by step 693
+
+comm_modify	vel yes
+
+neighbor	${skin} bin
+neighbor	0.15 bin
+neigh_modify	delay 0 every 1 check yes
+
+pair_style	granular
+pair_coeff 	1 * jkr 1000.0 50.0 0.3 10 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
+
+fix		3 all wall/gran granular hertz/material 1e5 1e3 0.3 tangential mindlin NULL 1.0 0.5 zplane 0 NULL
+
+thermo_style	custom step cpu atoms ke
+thermo_modify	lost warn
+thermo		100
+
+timestep	0.001
+
+#dump		1 all custom 100 ${name}.dump id type radius mass x y z
+
+run		5000
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 1.15
+  ghost atom cutoff = 1.15
+  binsize = 0.575, bins = 35 35 53
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair granular, perpetual
+      attributes: half, newton on, size, history
+      pair build: half/size/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 12.22 | 12.22 | 12.22 Mbytes
+Step CPU Atoms KinEng 
+       0            0        0           -0 
+     100    3.8153191      855           -0 
+     200     4.195287      855           -0 
+     300    4.5890362      855           -0 
+     400    10.636087     1500           -0 
+     500    11.306909     1500           -0 
+     600    11.968198     1500           -0 
+     700    22.631892     2288           -0 
+     800    23.711387     2288           -0 
+     900    24.754344     2288           -0 
+    1000    25.811778     2288           -0 
+    1100    35.368869     2845           -0 
+    1200    37.149843     2845           -0 
+    1300    39.026458     2845           -0 
+    1400    41.757583     3000           -0 
+    1500    45.155503     3000           -0 
+    1600    48.570241     3000           -0 
+    1700    52.839322     3000           -0 
+    1800    59.772697     3000           -0 
+    1900    69.493305     3000           -0 
+    2000    114.61886     3000           -0 
+    2100    152.89232     3000           -0 

examples/granular/log.29Mar19.pour.flatwall.g++.4

@@ -0,0 +1,191 @@
+LAMMPS (29 Mar 2019)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:88)
+  using 1 OpenMP thread(s) per MPI task
+# pour two types of particles (cohesive and non-cohesive) on flat wall
+
+variable   	name string pour_two_types
+
+atom_style	sphere
+units		lj
+
+###############################################
+# Geometry-related parameters
+###############################################
+
+variable	boxx equal 20
+variable	boxy equal 20
+variable	boxz equal 30
+
+variable	xc1 equal 0.3*${boxx}
+variable	xc1 equal 0.3*20
+variable	xc2 equal 0.7*${boxx}
+variable	xc2 equal 0.7*20
+variable	yc equal 0.5*${boxy}
+variable	yc equal 0.5*20
+
+###############################################
+# Particle-related parameters
+###############################################
+variable	rlo equal 0.25
+variable	rhi equal 0.5
+variable	dlo equal 2.0*${rlo}
+variable	dlo equal 2.0*0.25
+variable	dhi equal 2.0*${rhi}
+variable	dhi equal 2.0*0.5
+
+variable	dens equal 1.0
+
+variable skin equal 0.3*${rhi}
+variable skin equal 0.3*0.5
+
+#############
+processors	* * 1
+region 		boxreg block 0 ${boxx} 0 ${boxy} 0 ${boxz}
+region 		boxreg block 0 20 0 ${boxy} 0 ${boxz}
+region 		boxreg block 0 20 0 20 0 ${boxz}
+region 		boxreg block 0 20 0 20 0 30
+create_box	2 boxreg
+Created orthogonal box = (0 0 0) to (20 20 30)
+  2 by 2 by 1 MPI processor grid
+change_box	all boundary p p f
+
+comm_modify 	vel yes
+
+region		insreg1 cylinder z ${xc1} ${yc} 5 15 ${boxz}
+region		insreg1 cylinder z 6 ${yc} 5 15 ${boxz}
+region		insreg1 cylinder z 6 10 5 15 ${boxz}
+region		insreg1 cylinder z 6 10 5 15 30
+region		insreg2 cylinder z ${xc2} ${yc} 5 15 ${boxz}
+region		insreg2 cylinder z 14 ${yc} 5 15 ${boxz}
+region		insreg2 cylinder z 14 10 5 15 ${boxz}
+region		insreg2 cylinder z 14 10 5 15 30
+
+fix		1 all nve/sphere
+fix		grav all gravity 10.0 vector 0 0 -1
+fix		ins1 all pour 1500 1 3123 region insreg1 diam range ${dlo} ${dhi} dens ${dens} ${dens}
+fix		ins1 all pour 1500 1 3123 region insreg1 diam range 0.5 ${dhi} dens ${dens} ${dens}
+fix		ins1 all pour 1500 1 3123 region insreg1 diam range 0.5 1 dens ${dens} ${dens}
+fix		ins1 all pour 1500 1 3123 region insreg1 diam range 0.5 1 dens 1 ${dens}
+fix		ins1 all pour 1500 1 3123 region insreg1 diam range 0.5 1 dens 1 1
+Particle insertion: 562 every 346 steps, 1500 by step 693
+fix		ins2 all pour 1500 2 3123 region insreg2 diam range ${dlo} ${dhi} dens ${dens} ${dens}
+fix		ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 ${dhi} dens ${dens} ${dens}
+fix		ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 1 dens ${dens} ${dens}
+fix		ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 1 dens 1 ${dens}
+fix		ins2 all pour 1500 2 3123 region insreg2 diam range 0.5 1 dens 1 1
+Particle insertion: 562 every 346 steps, 1500 by step 693
+
+comm_modify	vel yes
+
+neighbor	${skin} bin
+neighbor	0.15 bin
+neigh_modify	delay 0 every 1 check yes
+
+pair_style	granular
+pair_coeff 	1 * jkr 1000.0 50.0 0.3 10 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
+
+fix		3 all wall/gran granular hertz/material 1e5 1e3 0.3 tangential mindlin NULL 1.0 0.5 zplane 0 NULL
+
+thermo_style	custom step cpu atoms ke
+thermo_modify	lost warn
+thermo		100
+
+timestep	0.001
+
+dump		1 all custom 100 ${name}.dump id type radius mass x y z
+dump		1 all custom 100 pour_two_types.dump id type radius mass x y z
+
+run		5000
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 1.15
+  ghost atom cutoff = 1.15
+  binsize = 0.575, bins = 35 35 53
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair granular, perpetual
+      attributes: half, newton on, size, history
+      pair build: half/size/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 11.98 | 11.98 | 11.98 Mbytes
+Step CPU Atoms KinEng 
+       0            0        0           -0 
+     100   0.11584234      855           -0 
+     200   0.12743592      855           -0 
+     300   0.13925815      855           -0 
+     400   0.35203671     1500           -0 
+     500   0.37055922     1500           -0 
+     600   0.38671875     1500           -0 
+     700   0.71736908     2288           -0 
+     800   0.74506783     2288           -0 
+     900   0.77112222     2288           -0 
+    1000   0.79632139     2288           -0 
+    1100    1.0384252     2845           -0 
+    1200      1.08093     2845           -0 
+    1300    1.1224561     2845           -0 
+    1400    1.1811485     3000           -0 
+    1500    1.2414908     3000           -0 
+    1600    1.3105879     3000           -0 
+    1700     1.390928     3000           -0 
+    1800    1.4869275     3000           -0 
+    1900    1.5958266     3000           -0 
+    2000    1.7172487     3000           -0 
+    2100     1.851155     3000           -0 
+    2200    1.9957182     3000           -0 
+    2300    2.1593764     3000           -0 
+    2400    2.3433132     3000           -0 
+    2500     2.532742     3000           -0 
+    2600    2.7376895     3000           -0 
+    2700    2.9463468     3000           -0 
+    2800    3.1645725     3000           -0 
+    2900    3.3879526     3000           -0 
+    3000    3.6152103     3000           -0 
+    3100    3.8467371     3000           -0 
+    3200    4.0787683     3000           -0 
+    3300    4.3097105     3000           -0 
+    3400    4.5423617     3000           -0 
+    3500    4.7773693     3000           -0 
+    3600    5.0127218     3000           -0 
+    3700    5.2519271     3000           -0 
+    3800    5.4951298     3000           -0 
+    3900    5.7210469     3000           -0 
+    4000    5.9432652     3000           -0 
+    4100    6.1687591     3000           -0 
+    4200    6.3942792     3000           -0 
+    4300    6.6331475     3000           -0 
+    4400    6.8632154     3000           -0 
+    4500    7.0979366     3000           -0 
+    4600    7.3305347     3000           -0 
+    4700    7.5670528     3000           -0 
+    4800    7.8086057     3000           -0 
+    4900    8.0407174     3000           -0 
+    5000    8.2765219     3000           -0 
+Loop time of 8.27669 on 4 procs for 5000 steps with 3000 atoms
+
+Performance: 52194.788 tau/day, 604.106 timesteps/s
+97.7% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 1.6106     | 3.4073     | 5.4191     |  95.7 | 41.17
+Neigh   | 0.51456    | 0.64572    | 0.81542    |  16.6 |  7.80
+Comm    | 0.2808     | 2.5222     | 4.4998     | 121.9 | 30.47
+Output  | 0.15695    | 0.15919    | 0.16502    |   0.8 |  1.92
+Modify  | 1.3517     | 1.4192     | 1.4904     |   4.9 | 17.15
+Other   |            | 0.123      |            |       |  1.49
+
+Nlocal:    750 ave 1036 max 482 min
+Histogram: 2 0 0 0 0 0 0 0 1 1
+Nghost:    429.75 ave 475 max 386 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Neighs:    4051.75 ave 6274 max 2057 min
+Histogram: 2 0 0 0 0 0 0 0 1 1
+
+Total # of neighbors = 16207
+Ave neighs/atom = 5.40233
+Neighbor list builds = 1165
+Dangerous builds = 0
+Total wall time: 0:00:08

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/log.28Feb2019.micelle.g++.1

@@ -1,259 +0,0 @@
-LAMMPS (28 Feb 2019)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
-  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 = 0.000394821 secs
-  read_data CPU = 0.00212336 secs
-special_bonds	fene
-  2 = max # of 1-2 neighbors
-  2 = max # of special neighbors
-  special bonds CPU = 0.00018549 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 0.113919 on 1 procs for 1000 steps with 1200 atoms
-
-Performance: 3792167.464 tau/day, 8778.165 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    | 0.076825   | 0.076825   | 0.076825   |   0.0 | 67.44
-Bond    | 0.0041864  | 0.0041864  | 0.0041864  |   0.0 |  3.67
-Neigh   | 0.017061   | 0.017061   | 0.017061   |   0.0 | 14.98
-Comm    | 0.0019042  | 0.0019042  | 0.0019042  |   0.0 |  1.67
-Output  | 0.00017285 | 0.00017285 | 0.00017285 |   0.0 |  0.15
-Modify  | 0.011218   | 0.011218   | 0.011218   |   0.0 |  9.85
-Other   |            | 0.002551   |            |       |  2.24
-
-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   -1.9727644   0.05860769   -1.4645317    1.9982326 
-    2000   0.46143408   -1.9889684  0.058103225   -1.4698156    1.7806269 
-    3000   0.44459291   -1.9997961  0.068724164   -1.4868496    1.4369618 
-    4000   0.46939549   -2.0330437  0.073499424   -1.4905399    1.3780016 
-    5000   0.44411088   -2.0339936   0.05862049   -1.5316323    1.2544164 
-    6000   0.44034597   -2.0265475  0.066481992   -1.5200864    1.2362891 
-    7000   0.45097378   -2.0331083  0.058467565   -1.5240428    1.2762333 
-    8000   0.45797632   -2.0330255  0.060048036   -1.5153828    1.3862396 
-    9000   0.45297811   -2.0383417  0.067056519   -1.5186845    1.2762554 
-   10000         0.45   -2.0628269  0.065650067   -1.5475518    1.0566213 
-   11000   0.44466757   -2.0593977   0.06190999   -1.5531907    1.1452469 
-   12000   0.46743534   -2.0684295  0.061056278   -1.5403274    1.0824225 
-   13000   0.45601091   -2.0689708  0.054868536   -1.5584713   0.96703283 
-   14000   0.44111882   -2.0553174  0.058249816   -1.5563164    1.0986427 
-   15000   0.43894405   -2.0866829  0.064117804   -1.5839869   0.90031836 
-   16000   0.43856814   -2.0879319  0.056024166    -1.593705   0.96387323 
-   17000   0.45977841    -2.103188  0.058097306   -1.5856955   0.83352919 
-   18000   0.43423341   -2.0813151  0.066623991   -1.5808196   0.98157638 
-   19000   0.44245939   -2.0851261  0.057637655   -1.5853978   0.84228341 
-   20000   0.43144678   -2.0895403   0.06536727   -1.5930858   0.88177768 
-   21000   0.45014968    -2.106686  0.059137572   -1.5977739   0.89408935 
-   22000    0.4575126   -2.1024115  0.063013023   -1.5822672   0.84886734 
-   23000         0.45     -2.10897   0.06724784   -1.5920971   0.66205013 
-   24000   0.43055602   -2.0894725  0.061566464   -1.5977089   0.81764789 
-   25000    0.4366384   -2.0926743  0.059609321   -1.5967905   0.85549875 
-   26000    0.4521714   -2.0963996  0.062031863   -1.5825731   0.80137118 
-   27000   0.45734834   -2.1060987  0.061712636   -1.5874188   0.82899415 
-   28000   0.44803467   -2.0859226  0.061871856   -1.5763894   0.97007526 
-   29000         0.45   -2.1106243  0.063825481   -1.5971738   0.63798376 
-   30000   0.44932806   -2.1006036  0.053053934    -1.598596   0.63907113 
-   31000   0.44713779   -2.1096164  0.066470416   -1.5963808   0.66832708 
-   32000    0.4373357   -2.0941237  0.058871613   -1.5982808   0.78176106 
-   33000   0.44030485    -2.105644  0.058804306   -1.6069017   0.66286458 
-   34000   0.43781175   -2.1233209  0.064611206   -1.6212628   0.56342584 
-   35000   0.45670132   -2.1059408  0.053049584   -1.5965705   0.73992396 
-   36000   0.45555427   -2.1149877  0.057627709   -1.6021854   0.85854939 
-   37000   0.44134236   -2.1106202  0.064444306   -1.6052013   0.74674603 
-   38000   0.44812623   -2.1003681  0.057266258   -1.5953491   0.78239359 
-   39000   0.44167062     -2.11141     0.055354   -1.6147534    0.7066385 
-   40000   0.46103176   -2.1166687  0.062155412   -1.5938657   0.73620955 
-   41000   0.44537102   -2.0993898   0.05631213   -1.5980778   0.87348756 
-   42000   0.44752506   -2.1115212  0.057506521   -1.6068625   0.72999561 
-   43000    0.4483886   -2.1184719  0.066943915   -1.6035131   0.78112063 
-   44000   0.45944897   -2.0916657  0.055242781   -1.5773568   0.98660473 
-   45000   0.46238513   -2.1163075    0.0530031   -1.6013046   0.74416054 
-   46000   0.45979064   -2.1165545  0.060657581   -1.5964895   0.63516974 
-   47000   0.45936546   -2.1140678  0.049931919   -1.6051532   0.76425182 
-   48000   0.45424613   -2.1122681  0.061885599   -1.5965149   0.71981142 
-   49000   0.44449524   -2.1147361   0.06626748   -1.6043438   0.78720467 
-   50000    0.4641185   -2.1114668  0.055104874   -1.5926302   0.70195865 
-   51000   0.44220655   -2.1075773    0.0589109   -1.6068283   0.73806859 
-   52000   0.43097906   -2.1189493  0.061502241   -1.6268271   0.69622593 
-   53000         0.45    -2.137688  0.053631829   -1.6344311   0.48269158 
-   54000   0.43777118   -2.1089246  0.047098534   -1.6244197   0.70423814 
-   55000   0.46061985   -2.1129502  0.062520353   -1.5901938   0.72492307 
-   56000    0.4524841   -2.1195648   0.06580089   -1.6016569   0.52709892 
-   57000   0.44914574   -2.1041993  0.061040876    -1.594387    0.7979988 
-   58000   0.46446286   -2.1181238  0.055741995    -1.598306   0.51009146 
-   59000    0.4632674   -2.1169321  0.050672678   -1.6033781   0.83110911 
-   60000   0.46340478    -2.122846  0.058485209   -1.6013422   0.69966471 
-Loop time of 8.01683 on 1 procs for 60000 steps with 1200 atoms
-
-Performance: 3233199.903 tau/day, 7484.259 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    | 5.4027     | 5.4027     | 5.4027     |   0.0 | 67.39
-Bond    | 0.23585    | 0.23585    | 0.23585    |   0.0 |  2.94
-Neigh   | 1.5188     | 1.5188     | 1.5188     |   0.0 | 18.95
-Comm    | 0.14452    | 0.14452    | 0.14452    |   0.0 |  1.80
-Output  | 0.00060487 | 0.00060487 | 0.00060487 |   0.0 |  0.01
-Modify  | 0.56352    | 0.56352    | 0.56352    |   0.0 |  7.03
-Other   |            | 0.1508     |            |       |  1.88
-
-Nlocal:    1200 ave 1200 max 1200 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    395 ave 395 max 395 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    9652 ave 9652 max 9652 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 9652
-Ave neighs/atom = 8.04333
-Ave special neighs/atom = 0.5
-Neighbor list builds = 4886
-Dangerous builds = 0
-Total wall time: 0:00:08

examples/micelle/log.28Feb2019.micelle.g++.4

@@ -1,259 +0,0 @@
-LAMMPS (28 Feb 2019)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
-  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 = 0.000130415 secs
-  read_data CPU = 0.00132132 secs
-special_bonds	fene
-  2 = max # of 1-2 neighbors
-  2 = max # of special neighbors
-  special bonds CPU = 4.76837e-05 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 0.0377742 on 4 procs for 1000 steps with 1200 atoms
-
-Performance: 11436375.633 tau/day, 26473.092 timesteps/s
-96.6% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.016871   | 0.017299   | 0.018185   |   0.4 | 45.80
-Bond    | 0.0010128  | 0.0010633  | 0.001116   |   0.1 |  2.81
-Neigh   | 0.004832   | 0.0048565  | 0.0048807  |   0.0 | 12.86
-Comm    | 0.0066509  | 0.0077528  | 0.0084352  |   0.8 | 20.52
-Output  | 0.00022054 | 0.00028259 | 0.00046587 |   0.0 |  0.75
-Modify  | 0.0035386  | 0.0036086  | 0.0036943  |   0.1 |  9.55
-Other   |            | 0.002912   |            |       |  7.71
-
-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		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   -1.9727652  0.058608073   -1.4645321    1.9982444 
-    2000   0.44428815   -1.9902282  0.064240544   -1.4820698    1.7051263 
-    3000   0.46641766   -1.9856844  0.065017468   -1.4546379    1.6939772 
-    4000   0.45734058   -2.0242583  0.070494626   -1.4968042    1.3474276 
-    5000   0.44904747   -2.0086954  0.058801142    -1.501221    1.4632351 
-    6000   0.44961405   -2.0334509   0.05721299   -1.5269985    1.3093586 
-    7000   0.45474928   -2.0453645  0.064725006   -1.5262692    1.1581035 
-    8000   0.44274767   -2.0375379  0.062216035   -1.5329431     1.312914 
-    9000   0.46176571   -2.0473031  0.065581966   -1.5203402    1.2013868 
-   10000   0.45046977   -2.0540466  0.065402724   -1.5385495   0.95819581 
-   11000   0.45016671   -2.0610028  0.056993955   -1.5542172    1.0433435 
-   12000   0.43823039    -2.073155  0.065171939   -1.5701178    1.1400059 
-   13000   0.44482161   -2.0678338  0.063901045   -1.5594819   0.97993813 
-   14000         0.45   -2.0892562  0.061753632   -1.5778776   0.89841778 
-   15000   0.44328626   -2.0859346  0.059956258   -1.5830615   0.90664821 
-   16000   0.45666508   -2.0859262  0.059582346   -1.5700593    0.9702235 
-   17000   0.44832038   -2.0762124  0.059153394   -1.5691122   0.93020504 
-   18000    0.4555831   -2.0844959  0.057986324   -1.5713062   0.87398232 
-   19000   0.45257867   -2.0671736  0.062190389   -1.5527816   0.89208496 
-   20000   0.44010419   -2.1020944  0.062053708   -1.6003033   0.84140973 
-   21000   0.45239369   -2.0820308  0.060981799   -1.5690323   0.98502522 
-   22000   0.44607468   -2.0820602  0.051731316   -1.5846259   0.86120529 
-   23000   0.45088473   -2.0865286   0.05727778   -1.5787418    1.1479844 
-   24000   0.45526919   -2.1086678  0.057378327   -1.5963997   0.86944138 
-   25000   0.46536624   -2.1055425   0.05665328   -1.5839108   0.72895438 
-   26000   0.46716668   -2.1035267  0.057498747   -1.5792505   0.85105386 
-   27000   0.44374699   -2.0932213  0.060937242   -1.5889069   0.93200759 
-   28000   0.45944001   -2.0968869  0.053052954   -1.5847768   0.78909249 
-   29000    0.4543632     -2.10493  0.061511018   -1.5894345   0.85862527 
-   30000   0.44987776   -2.0942536  0.062431086   -1.5823197    0.7349894 
-   31000   0.43829016   -2.0951259  0.060245682   -1.5969553   0.86702973 
-   32000   0.45416601   -2.0991679  0.055978905   -1.5894015   0.75777153 
-   33000    0.4605079   -2.1118364  0.058205688   -1.5935066   0.86041104 
-   34000   0.43638213   -2.0925345  0.067533519   -1.5889825   0.85100425 
-   35000   0.46912252   -2.1082718  0.051646432   -1.5878938   0.73613751 
-   36000         0.45   -2.0966442  0.052507159   -1.5945121   0.88722487 
-   37000   0.44970507   -2.1029685  0.065454263    -1.588184   0.76033821 
-   38000   0.44910233    -2.097751   0.05767009   -1.5913528   0.95830923 
-   39000    0.4322161   -2.1060426  0.062453704    -1.611733   0.74681695 
-   40000   0.46143858   -2.1328575  0.057333011   -1.6144704   0.58326322 
-   41000   0.43180549   -2.1070656  0.064150563   -1.6114694   0.82842684 
-   42000   0.46738909   -2.1067947  0.058017036   -1.5817781   0.73292362 
-   43000   0.43699124   -2.1171964  0.062817262   -1.6177521   0.73354741 
-   44000   0.45262916   -2.1281307  0.055228619   -1.6206502   0.64167946 
-   45000   0.43905419    -2.088789  0.055597999   -1.5945027    0.8002542 
-   46000   0.44485569   -2.1035061  0.067828181   -1.5911929   0.71861494 
-   47000   0.44496824   -2.0968296    0.0632326   -1.5889996   0.75202899 
-   48000   0.46567244   -2.1235948  0.061032118   -1.5972783   0.64094556 
-   49000   0.43202506   -2.0986097  0.053464022   -1.6134806   0.83857984 
-   50000   0.45454698   -2.1263344  0.058119708   -1.6140465   0.67030037 
-   51000   0.43702766   -2.1292347  0.074047424   -1.6185238   0.52896462 
-   52000   0.46367081   -2.1177288   0.06726625   -1.5871781   0.74343227 
-   53000         0.45   -2.1341074  0.062769314   -1.6217131   0.51130365 
-   54000   0.44862492   -2.1272108  0.057723381   -1.6212364   0.54735429 
-   55000   0.44926027   -2.1350444  0.066186625   -1.6199719   0.66821299 
-   56000    0.4544227   -2.1325537  0.065298628   -1.6132111   0.63597556 
-   57000   0.45697003   -2.1323238  0.053312855   -1.6224218   0.55572633 
-   58000   0.45698902   -2.1043208  0.055835989   -1.5918766   0.63502658 
-   59000    0.4425306   -2.1120353  0.056617261   -1.6132563   0.65681272 
-   60000   0.44319296   -2.1171981  0.058330294   -1.6160442   0.63602511 
-Loop time of 2.63918 on 4 procs for 60000 steps with 1200 atoms
-
-Performance: 9821248.084 tau/day, 22734.371 timesteps/s
-97.3% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 1.1742     | 1.278      | 1.3471     |   5.9 | 48.43
-Bond    | 0.046621   | 0.06565    | 0.081322   |   5.1 |  2.49
-Neigh   | 0.46642    | 0.46917    | 0.47105    |   0.3 | 17.78
-Comm    | 0.47295    | 0.55928    | 0.67758    |  10.5 | 21.19
-Output  | 0.00073624 | 0.00173    | 0.0047016  |   4.1 |  0.07
-Modify  | 0.14511    | 0.15226    | 0.15887    |   1.5 |  5.77
-Other   |            | 0.1131     |            |       |  4.28
-
-Nlocal:    300 ave 309 max 281 min
-Histogram: 1 0 0 0 0 0 0 1 0 2
-Nghost:    232.75 ave 234 max 231 min
-Histogram: 1 0 0 1 0 0 0 0 0 2
-Neighs:    2450.25 ave 2576 max 2179 min
-Histogram: 1 0 0 0 0 0 0 0 1 2
-
-Total # of neighbors = 9801
-Ave neighs/atom = 8.1675
-Ave special neighs/atom = 0.5
-Neighbor list builds = 4887
-Dangerous builds = 0
-Total wall time: 0:00:02

examples/micelle/log.28Feb2019.micelle.rigid.g++.1

@@ -1,290 +0,0 @@
-LAMMPS (28 Feb 2019)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
-  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 = 0.000271559 secs
-  read_data CPU = 0.00115585 secs
-special_bonds	fene
-  2 = max # of 1-2 neighbors
-  2 = max # of special neighbors
-  special bonds CPU = 8.39233e-05 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 0.107201 on 1 procs for 1000 steps with 1200 atoms
-
-Performance: 4029800.456 tau/day, 9328.242 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    | 0.072035   | 0.072035   | 0.072035   |   0.0 | 67.20
-Bond    | 0.0039918  | 0.0039918  | 0.0039918  |   0.0 |  3.72
-Neigh   | 0.016078   | 0.016078   | 0.016078   |   0.0 | 15.00
-Comm    | 0.0018375  | 0.0018375  | 0.0018375  |   0.0 |  1.71
-Output  | 0.00016379 | 0.00016379 | 0.00016379 |   0.0 |  0.15
-Modify  | 0.010665   | 0.010665   | 0.010665   |   0.0 |  9.95
-Other   |            | 0.002429   |            |       |  2.27
-
-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
-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		20000
-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   0.44603578   -1.7056163   0.08808163   -1.2555023    3.4039736 
-    1000   0.46008168   -1.9040837   0.08808163   -1.4425691   0.93225457 
-    2000   0.44520658   -1.9317253   0.08808163   -1.4822843    3.8192896 
-    3000   0.43988556    -1.945898   0.08808163   -1.5007759    3.0371634 
-    4000    0.4646519   -1.9753553   0.08808163   -1.5101312   -1.8041178 
-    5000    0.4362993   -1.9763715   0.08808163   -1.5341603    1.5037284 
-    6000   0.47007384   -1.9833154   0.08808163   -1.5136905    2.1227653 
-    7000   0.44854623   -1.9914288   0.08808163   -1.5392772    3.9458099 
-    8000   0.43841372   -1.9779603   0.08808163   -1.5340328   -4.5429769 
-    9000    0.4518303   -1.9834387   0.08808163   -1.5286215    4.4230447 
-   10000   0.43562904    -2.001471   0.08808163   -1.5598038    1.8919582 
-   11000   0.44014575   -1.9820611   0.08808163   -1.5367278   -2.1189418 
-   12000   0.44466956   -2.0134014   0.08808163   -1.5643963   -2.5218497 
-   13000   0.45274369    -2.021443   0.08808163   -1.5658844    2.4795173 
-   14000   0.44742645    -2.011108   0.08808163   -1.5598653  -0.74697767 
-   15000    0.4674843    -2.024737   0.08808163   -1.5572139   -1.9539999 
-   16000   0.45610154   -2.0401029   0.08808163   -1.5818189  -0.53082066 
-   17000   0.44679292   -2.0365577   0.08808163   -1.5858291   -6.5040295 
-   18000   0.44279107   -2.0500326   0.08808163   -1.6025522 -0.051597102 
-   19000   0.45603993   -2.0306289   0.08808163   -1.5723948    1.0986608 
-   20000   0.44519606   -2.0412229   0.08808163   -1.5917904   -1.0406746 
-Loop time of 3.68102 on 1 procs for 20000 steps with 1200 atoms
-
-Performance: 2347175.802 tau/day, 5433.277 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    | 1.7349     | 1.7349     | 1.7349     |   0.0 | 47.13
-Bond    | 0.079483   | 0.079483   | 0.079483   |   0.0 |  2.16
-Neigh   | 0.49063    | 0.49063    | 0.49063    |   0.0 | 13.33
-Comm    | 0.049093   | 0.049093   | 0.049093   |   0.0 |  1.33
-Output  | 0.00022578 | 0.00022578 | 0.00022578 |   0.0 |  0.01
-Modify  | 1.273      | 1.273      | 1.273      |   0.0 | 34.58
-Other   |            | 0.05369    |            |       |  1.46
-
-Nlocal:    1200 ave 1200 max 1200 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    395 ave 395 max 395 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    8915 ave 8915 max 8915 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 8915
-Ave neighs/atom = 7.42917
-Ave special neighs/atom = 0.5
-Neighbor list builds = 1580
-Dangerous builds = 0
-unfix 5
-unfix 4
-fix		5 solute rigid/small molecule langevin 0.45 0.45 0.5 112211
-  create bodies CPU = 0.00012517 secs
-150 rigid bodies with 450 atoms
-  1.04536 = max distance from body owner to body atom
-fix		4 all enforce2d
-run		20000
-Per MPI rank memory allocation (min/avg/max) = 8.633 | 8.633 | 8.633 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-   20000   0.44519606   -2.0412229   0.08808163   -1.5917904    1.3058893 
-   21000    0.4353376   -2.0483342   0.08808163   -1.6069035   0.53023317 
-   22000   0.44034324   -2.0416876   0.08808163   -1.5961941    4.0327077 
-   23000    0.4685403     -2.05295   0.08808163   -1.5845698    3.6792349 
-   24000   0.44872075   -2.0320623   0.08808163    -1.579769   -2.0476923 
-   25000   0.46829594   -2.0671408   0.08808163   -1.5989589     2.180811 
-   26000   0.45257544   -2.0418792   0.08808163   -1.5864572    3.3924018 
-   27000   0.44269664   -2.0409905   0.08808163   -1.5935868  -0.17012673 
-   28000   0.46961216   -2.0552479   0.08808163   -1.5859978   -7.2870888 
-   29000   0.46683129   -2.0438334   0.08808163   -1.5768404    3.0583141 
-   30000   0.44262228    -2.036737   0.08808163   -1.5893937  0.087520915 
-   31000   0.43517227   -2.0479672   0.08808163   -1.6066708   -0.3426009 
-   32000   0.44543779   -2.0538031   0.08808163   -1.6041744   -0.2093148 
-   33000   0.44629079   -2.0409901   0.08808163   -1.5906691     3.310113 
-   34000   0.43058831   -2.0713827   0.08808163   -1.6338069   0.14128843 
-   35000   0.44546512   -2.0427068   0.08808163    -1.593056   -3.1386697 
-   36000   0.42971129   -2.0527435   0.08808163   -1.6158795   -2.7334963 
-   37000   0.44707969   -2.0461803   0.08808163    -1.595219   -3.8777678 
-   38000   0.43150818   -2.0435276   0.08808163   -1.6052052    0.2905487 
-   39000   0.44463343   -2.0522113   0.08808163   -1.6032355     3.543123 
-   40000   0.44582593    -2.052213   0.08808163   -1.6022693    1.1486536 
-Loop time of 3.69012 on 1 procs for 20000 steps with 1200 atoms
-
-Performance: 2341388.948 tau/day, 5419.882 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    | 1.756      | 1.756      | 1.756      |   0.0 | 47.59
-Bond    | 0.079221   | 0.079221   | 0.079221   |   0.0 |  2.15
-Neigh   | 0.49085    | 0.49085    | 0.49085    |   0.0 | 13.30
-Comm    | 0.048317   | 0.048317   | 0.048317   |   0.0 |  1.31
-Output  | 0.0002315  | 0.0002315  | 0.0002315  |   0.0 |  0.01
-Modify  | 1.2616     | 1.2616     | 1.2616     |   0.0 | 34.19
-Other   |            | 0.05386    |            |       |  1.46
-
-Nlocal:    1200 ave 1200 max 1200 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    393 ave 393 max 393 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    9091 ave 9091 max 9091 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 9091
-Ave neighs/atom = 7.57583
-Ave special neighs/atom = 0.5
-Neighbor list builds = 1582
-Dangerous builds = 0
-Total wall time: 0:00:07

examples/micelle/log.28Feb2019.micelle.rigid.g++.4

@@ -1,290 +0,0 @@
-LAMMPS (28 Feb 2019)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
-  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 = 0.000175714 secs
-  read_data CPU = 0.00145626 secs
-special_bonds	fene
-  2 = max # of 1-2 neighbors
-  2 = max # of special neighbors
-  special bonds CPU = 7.22408e-05 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 0.0389124 on 4 procs for 1000 steps with 1200 atoms
-
-Performance: 11101855.138 tau/day, 25698.739 timesteps/s
-95.7% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.016776   | 0.017405   | 0.018435   |   0.5 | 44.73
-Bond    | 0.0010033  | 0.0011995  | 0.0015519  |   0.6 |  3.08
-Neigh   | 0.0044944  | 0.0045093  | 0.0045218  |   0.0 | 11.59
-Comm    | 0.0080328  | 0.0093863  | 0.010242   |   0.9 | 24.12
-Output  | 0.00021577 | 0.00027579 | 0.00045323 |   0.0 |  0.71
-Modify  | 0.0034575  | 0.0036355  | 0.0040002  |   0.4 |  9.34
-Other   |            | 0.002501   |            |       |  6.43
-
-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
-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		20000
-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   0.44603578   -1.7056163   0.08808163   -1.2555023    3.4039736 
-    1000   0.46008163   -1.9040835   0.08808163   -1.4425689   0.93225869 
-    2000   0.44943348   -1.9355135   0.08808163   -1.4826417    3.8399671 
-    3000    0.4448437   -1.9480307   0.08808163   -1.4988842    2.5506553 
-    4000   0.46013872   -1.9783821   0.08808163   -1.5168212   -1.8963215 
-    5000   0.45520233   -1.9659462   0.08808163   -1.5083921    1.9238897 
-    6000   0.44942049   -1.9663403   0.08808163    -1.513479    3.0633512 
-    7000   0.45975758    -1.988462   0.08808163   -1.5272105    4.8267309 
-    8000   0.45125238   -1.9913522   0.08808163   -1.5370041   -4.6644852 
-    9000   0.45863606   -1.9792375   0.08808163   -1.5188962    4.3655071 
-   10000   0.46264541   -1.9864611   0.08808163   -1.5228656    2.2176464 
-   11000   0.45048361   -1.9907235   0.08808163   -1.5369994 -0.055360699 
-   12000   0.44536719    -2.012875   0.08808163   -1.5633037   -0.2583823 
-   13000   0.44212663   -2.0060111   0.08808163     -1.55907    3.3616171 
-   14000   0.44984353   -2.0335408   0.08808163   -1.5803361  -0.21585645 
-   15000   0.44896672   -2.0385265   0.08808163   -1.5860335   -4.6186206 
-   16000   0.46694997    -2.032795   0.08808163   -1.5657056   0.53443281 
-   17000   0.43208201   -2.0272255   0.08808163   -1.5884373   -6.5239975 
-   18000   0.43281873   -2.0331268   0.08808163   -1.5937406 -0.048319943 
-   19000   0.44704527   -2.0286742   0.08808163   -1.5777408    1.6356417 
-   20000   0.44279735   -2.0443561   0.08808163   -1.5968706   -3.8337952 
-Loop time of 1.71924 on 4 procs for 20000 steps with 1200 atoms
-
-Performance: 5025468.853 tau/day, 11633.030 timesteps/s
-98.2% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.39864    | 0.40873    | 0.42192    |   1.6 | 23.77
-Bond    | 0.02118    | 0.021816   | 0.022785   |   0.4 |  1.27
-Neigh   | 0.13931    | 0.14031    | 0.14117    |   0.2 |  8.16
-Comm    | 0.13974    | 0.15328    | 0.16884    |   3.3 |  8.92
-Output  | 0.00026131 | 0.00044435 | 0.00099206 |   0.0 |  0.03
-Modify  | 0.93275    | 0.94138    | 0.95072    |   0.7 | 54.76
-Other   |            | 0.05327    |            |       |  3.10
-
-Nlocal:    300 ave 303 max 298 min
-Histogram: 1 0 1 0 1 0 0 0 0 1
-Nghost:    218.5 ave 226 max 215 min
-Histogram: 2 1 0 0 0 0 0 0 0 1
-Neighs:    2258.75 ave 2283 max 2216 min
-Histogram: 1 0 0 0 0 0 1 0 1 1
-
-Total # of neighbors = 9035
-Ave neighs/atom = 7.52917
-Ave special neighs/atom = 0.5
-Neighbor list builds = 1580
-Dangerous builds = 0
-unfix 5
-unfix 4
-fix		5 solute rigid/small molecule langevin 0.45 0.45 0.5 112211
-  create bodies CPU = 5.43594e-05 secs
-150 rigid bodies with 450 atoms
-  0.916597 = max distance from body owner to body atom
-fix		4 all enforce2d
-run		20000
-Per MPI rank memory allocation (min/avg/max) = 8.568 | 8.6 | 8.691 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-   20000   0.44279735   -2.0443561   0.08808163   -1.5968706    -1.033643 
-   21000    0.4529129    -2.049461   0.08808163   -1.5937651   0.93160285 
-   22000   0.45039188   -2.0530092   0.08808163   -1.5993595  -0.10608965 
-   23000   0.45261583   -2.0336042   0.08808163   -1.5781494   -2.5769871 
-   24000    0.4608331   -2.0404645   0.08808163     -1.57834    3.1931675 
-   25000   0.43479001   -2.0617104   0.08808163   -1.6207242    2.8190122 
-   26000   0.47009651   -2.0754873   0.08808163    -1.605844   -0.9158501 
-   27000   0.45002704   -2.0782104   0.08808163   -1.6248568   0.98629661 
-   28000   0.45126136   -2.0592619   0.08808163   -1.6049065   0.03305448 
-   29000   0.44355328   -2.0572858   0.08808163   -1.6091868   -6.0797989 
-   30000   0.45053899   -2.0530953   0.08808163   -1.5993261   0.38382951 
-   31000   0.46931923   -2.0718827   0.08808163   -1.6028703    2.2346891 
-   32000   0.45348857   -2.0744024   0.08808163   -1.6182393    4.5028966 
-   33000   0.44767742   -2.0597127   0.08808163   -1.6082662   -2.8021641 
-   34000   0.45287544   -2.0857303   0.08808163   -1.6300648    -5.384091 
-   35000   0.44743898   -2.0927246   0.08808163   -1.6414717    1.4800508 
-   36000   0.45627028   -2.0720546   0.08808163   -1.6136336   -2.9961696 
-   37000    0.4641334   -2.0701098   0.08808163   -1.6053065    8.4186854 
-   38000   0.45922901   -2.0962331   0.08808163   -1.6354106   0.38361763 
-   39000    0.4692834   -2.0573815   0.08808163   -1.5883982   -2.2177345 
-   40000   0.46206931    -2.057851   0.08808163   -1.5947231   -1.0405727 
-Loop time of 1.25476 on 4 procs for 20000 steps with 1200 atoms
-
-Performance: 6885775.862 tau/day, 15939.296 timesteps/s
-98.1% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.40627    | 0.43037    | 0.45515    |   2.6 | 34.30
-Bond    | 0.020504   | 0.021573   | 0.022739   |   0.5 |  1.72
-Neigh   | 0.14337    | 0.14438    | 0.1453     |   0.2 | 11.51
-Comm    | 0.13776    | 0.16647    | 0.19351    |   5.0 | 13.27
-Output  | 0.00025082 | 0.00052994 | 0.0013635  |   0.0 |  0.04
-Modify  | 0.45467    | 0.45822    | 0.46259    |   0.5 | 36.52
-Other   |            | 0.03321    |            |       |  2.65
-
-Nlocal:    300 ave 304 max 293 min
-Histogram: 1 0 0 0 0 1 0 0 0 2
-Nghost:    215.25 ave 217 max 213 min
-Histogram: 1 0 0 0 0 1 0 1 0 1
-Neighs:    2340 ave 2378 max 2290 min
-Histogram: 1 0 0 1 0 0 0 0 0 2
-
-Total # of neighbors = 9360
-Ave neighs/atom = 7.8
-Ave special neighs/atom = 0.5
-Neighbor list builds = 1579
-Dangerous builds = 0
-Total wall time: 0:00:03

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