patch 23Oct17

Updated neighbor list history processing for USER-OMP

cmake/CMakeLists.txt

@@ -6,8 +6,8 @@ cmake_minimum_required(VERSION 3.1)
 
 project(lammps)
 set(SOVERSION 0)
-set(LAMMPS_SOURCE_DIR ${CMAKE_SOURCE_DIR}/../src)
-set(LAMMPS_LIB_SOURCE_DIR ${CMAKE_SOURCE_DIR}/../lib)
+set(LAMMPS_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../src)
+set(LAMMPS_LIB_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../lib)
 set(LAMMPS_LIB_BINARY_DIR ${CMAKE_BINARY_DIR}/lib)
 
 #To not conflict with old Makefile build system, we build everything here
@@ -16,20 +16,18 @@ file(GLOB LMP_SOURCES ${LAMMPS_SOURCE_DIR}/main.cpp)
 list(REMOVE_ITEM LIB_SOURCES ${LMP_SOURCES})
 
 # Cmake modules/macros are in a subdirectory to keep this file cleaner
-set(CMAKE_MODULE_PATH ${CMAKE_SOURCE_DIR}/Modules)
+set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/Modules)
 
 if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CXX_FLAGS)
   #release comes with -O3 by default
   set(CMAKE_BUILD_TYPE Release CACHE STRING "Choose the type of build, options are: None Debug Release RelWithDebInfo MinSizeRel." FORCE)
 endif(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CXX_FLAGS)
 
-foreach(STYLE_FILE style_angle.h style_atom.h style_body.h style_bond.h style_command.h style_compute.h style_dihedral.h style_dump.h
-             style_fix.h style_improper.h style_integrate.h style_kspace.h style_minimize.h style_nbin.h style_npair.h style_nstencil.h
-             style_ntopo.h style_pair.h style_reader.h style_region.h)
-  if(EXISTS ${LAMMPS_SOURCE_DIR}/${STYLE_FILE})
-    message(FATAL_ERROR "There is a ${STYLE_FILE} in ${LAMMPS_SOURCE_DIR}, please clean up the source directory first")
-  endif()
-endforeach()
+# remove any style headers in the src dir
+file(GLOB SRC_STYLE_FILES ${LAMMPS_SOURCE_DIR}/style_*.h)
+if(SRC_STYLE_FILES)
+  file(REMOVE ${SRC_STYLE_FILES})
+endif()
 
 enable_language(CXX)
 
@@ -39,14 +37,22 @@ enable_language(CXX)
 #####################################################################
 include(CheckCCompilerFlag)
 
+if (${CMAKE_CXX_COMPILER_ID} STREQUAL "Intel")
+  set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -restrict")
+endif()
+
 ########################################################################
 # User input options                                                   #
 ########################################################################
 option(BUILD_SHARED_LIBS "Build shared libs" OFF)
-option(INSTALL_LIB "Install lammps library and header" ON)
+if(BUILD_SHARED_LIBS) # for all pkg libs, mpi_stubs and linalg
+  set(CMAKE_POSITION_INDEPENDENT_CODE ON)
+endif()
 include(GNUInstallDirs)
 
 set(LAMMPS_LINK_LIBS)
+set(LAMMPS_DEPS)
+set(LAMMPS_API_DEFINES)
 option(ENABLE_MPI "Build MPI version" OFF)
 if(ENABLE_MPI)
   find_package(MPI REQUIRED)
@@ -58,13 +64,15 @@ if(ENABLE_MPI)
   endif()
 else()
   file(GLOB MPI_SOURCES ${LAMMPS_SOURCE_DIR}/STUBS/mpi.c)
-  list(APPEND LIB_SOURCES ${MPI_SOURCES})
+  add_library(mpi_stubs STATIC ${MPI_SOURCES})
   include_directories(${LAMMPS_SOURCE_DIR}/STUBS)
+  list(APPEND LAMMPS_LINK_LIBS mpi_stubs)
 endif()
 
 set(LAMMPS_SIZE_LIMIT "LAMMPS_SMALLBIG" CACHE STRING "Lammps size limit")
 set_property(CACHE LAMMPS_SIZE_LIMIT PROPERTY STRINGS LAMMPS_SMALLBIG LAMMPS_BIGBIG LAMMPS_SMALLSMALL)
 add_definitions(-D${LAMMPS_SIZE_LIMIT})
+set(LAMMPS_API_DEFINES "${LAMMPS_API_DEFINES} -D${LAMMPS_SIZE_LIMIT}")
 
 set(LAMMPS_MEMALIGN "64" CACHE STRING "enables the use of the posix_memalign() call instead of malloc() when large chunks or memory are allocated by LAMMPS")
 add_definitions(-DLAMMPS_MEMALIGN=${LAMMPS_MEMALIGN})
@@ -72,6 +80,13 @@ add_definitions(-DLAMMPS_MEMALIGN=${LAMMPS_MEMALIGN})
 option(LAMMPS_EXCEPTIONS "enable the use of C++ exceptions for error messages (useful for library interface)" OFF)
 if(LAMMPS_EXCEPTIONS)
   add_definitions(-DLAMMPS_EXCEPTIONS)
+  set(LAMMPS_API_DEFINES "${LAMMPS_API_DEFINES} -DLAMMPS_EXCEPTIONS")
+endif()
+
+set(LAMMPS_MACHINE "" CACHE STRING "Suffix to append to lmp binary and liblammps (WON'T enable any features automatically")
+mark_as_advanced(LAMMPS_MACHINE)
+if(LAMMPS_MACHINE)
+  set(LAMMPS_MACHINE "_${LAMMPS_MACHINE}")
 endif()
 
 option(CMAKE_VERBOSE_MAKEFILE "Verbose makefile" OFF)
@@ -85,12 +100,12 @@ option(ENABLE_ALL "Build all default packages" OFF)
 set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GRANULAR
   KSPACE MANYBODY MC MEAM MISC MOLECULE PERI QEQ
   REAX REPLICA RIGID SHOCK SNAP SRD)
-set(OTHER_PACKAGES KIM PYTHON MSCG MPIIO VORONOI POEMS
-   USER-ATC USER-AWPMD USER-CGDNA
+set(OTHER_PACKAGES KIM PYTHON MSCG MPIIO VORONOI POEMS LATTE
+  USER-ATC USER-AWPMD USER-CGDNA USER-MESO
   USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF
   USER-FEP USER-H5MD USER-LB USER-MANIFOLD USER-MEAMC USER-MGPT USER-MISC
-  USER-MOLFILE USER-NETCDF USER-PHONON USER-QTB USER-REAXC USER-SMD 
-  USER-SMTBQ USER-SPH USER-TALLY USER-VTK USER-QUIP USER-QMMM)
+  USER-MOLFILE USER-NETCDF USER-PHONON USER-QTB USER-REAXC USER-SMD
+  USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM)
 set(ACCEL_PACKAGES USER-OMP KOKKOS OPT USER-INTEL GPU)
 foreach(PKG ${DEFAULT_PACKAGES})
   option(ENABLE_${PKG} "Build ${PKG} Package" ${ENABLE_ALL})
@@ -120,8 +135,10 @@ endif()
 ######################################################
 # packages with special compiler needs or external libs
 ######################################################
-if(ENABLE_REAX OR ENABLE_MEAM OR ENABLE_USER-QUIP OR ENABLE_USER-QMMM)
+if(ENABLE_REAX OR ENABLE_MEAM OR ENABLE_USER-QUIP OR ENABLE_USER-QMMM OR ENABLE_LATTE)
   enable_language(Fortran)
+  include(CheckFortranCompilerFlag)
+  check_Fortran_compiler_flag("-fno-second-underscore" FC_HAS_NO_SECOND_UNDERSCORE)
 endif()
 
 if(ENABLE_KOKKOS OR ENABLE_MSCG)
@@ -156,18 +173,22 @@ endif()
 if(ENABLE_MISC)
   option(LAMMPS_XDR "include XDR compatibility files for doing particle dumps in XTC format" OFF)
   if(LAMMPS_XDR)
-    add_definitions(-DLAMMPS_XDR)
+    add_definitions(-DLAMMPS_XDR) # for liblammps
   endif()
 endif()
 
-if(ENABLE_MSCG OR ENABLE_USER-ATC OR ENABLE_USER-AWPMD OR ENABLE_USER-QUIP)
+if(ENABLE_MSCG OR ENABLE_USER-ATC OR ENABLE_USER-AWPMD OR ENABLE_USER-QUIP OR ENABLE_LATTE)
   find_package(LAPACK)
-  if(LAPACK_FOUND)
-    list(APPEND LAMMPS_LINK_LIBS ${LAPACK_LIBRARIES})
-  else()
+  if(NOT LAPACK_FOUND)
     enable_language(Fortran)
     file(GLOB LAPACK_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/linalg/*.f)
-    list(APPEND LIB_SOURCES ${LAPACK_SOURCES})
+    add_library(linalg STATIC ${LAPACK_SOURCES})
+    include(CheckFortranCompilerFlag)
+    check_Fortran_compiler_flag("-fno-second-underscore" FC_HAS_NO_SECOND_UNDERSCORE)
+    if(FC_HAS_NO_SECOND_UNDERSCORE)
+      target_compile_options(linalg PRIVATE -fno-second-underscore)
+    endif()
+    set(LAPACK_LIBRARIES linalg)
   endif()
 endif()
 
@@ -182,7 +203,7 @@ if(ENABLE_PYTHON)
 	  -c "import distutils.sysconfig as cg; print(cg.get_python_lib(1,0,prefix='${CMAKE_INSTALL_PREFIX}'))"
       OUTPUT_VARIABLE PYTHON_INSTDIR OUTPUT_STRIP_TRAILING_WHITESPACE)
   endif()
-  install(FILES ${CMAKE_SOURCE_DIR}/../python/lammps.py DESTINATION ${PYTHON_INSTDIR})
+  install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/../python/lammps.py DESTINATION ${PYTHON_INSTDIR})
   if(NOT BUILD_SHARED_LIBS)
     message(FATAL_ERROR "Python package need lammps to be build shared, use -DBUILD_SHARED_LIBS=ON")
   endif()
@@ -221,8 +242,29 @@ if(ENABLE_VORONOI)
   list(APPEND LAMMPS_LINK_LIBS ${VORO_LIBRARIES})
 endif()
 
+if(ENABLE_LATTE)
+  find_package(LATTE QUIET)
+  if(NOT LATTE_FOUND)
+    message(STATUS "LATTE not found - we will build our own")
+    include(ExternalProject)
+    ExternalProject_Add(latte_build
+      URL https://github.com/lanl/LATTE/archive/v1.0.1.tar.gz
+      URL_MD5 5137e28cb1a64444bd571c98c98a6eee
+      SOURCE_SUBDIR cmake
+      CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR> -DCMAKE_POSITION_INDEPENDENT_CODE=${CMAKE_POSITION_INDEPENDENT_CODE}
+      )
+    ExternalProject_get_property(latte_build INSTALL_DIR)
+    set(LATTE_LIBRARIES ${INSTALL_DIR}/${CMAKE_INSTALL_LIBDIR}/liblatte.a)
+    list(APPEND LAMMPS_DEPS latte_build)
+  endif()
+  list(APPEND LAMMPS_LINK_LIBS ${LATTE_LIBRARIES} ${LAPACK_LIBRARIES} ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
+endif()
+
 if(ENABLE_USER-MOLFILE)
-  list(APPEND LAMMPS_LINK_LIBS ${CMAKE_DL_LIBS})
+  add_library(molfile INTERFACE)
+  target_include_directories(molfile INTERFACE ${LAMMPS_LIB_SOURCE_DIR}/molfile)
+  target_link_libraries(molfile INTERFACE ${CMAKE_DL_LIBS})
+  list(APPEND LAMMPS_LINK_LIBS molfile)
 endif()
 
 if(ENABLE_USER-NETCDF)
@@ -239,7 +281,7 @@ endif()
 
 if(ENABLE_USER-QUIP)
   find_package(QUIP REQUIRED)
-  list(APPEND LAMMPS_LINK_LIBS ${QUIP_LIBRARIES} ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
+  list(APPEND LAMMPS_LINK_LIBS ${QUIP_LIBRARIES} ${LAPACK_LIBRARIES} ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
 endif()
 
 if(ENABLE_USER-QMMM)
@@ -248,17 +290,6 @@ if(ENABLE_USER-QMMM)
   list(APPEND LAMMPS_LINK_LIBS ${QE_LIBRARIES} ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
 endif()
 
-if(ENABLE_USER-AWPMD)
-  include_directories(${LAMMPS_LIB_SOURCE_DIR}/awpmd/systems/interact
-    ${LAMMPS_LIB_SOURCE_DIR}/awpmd/ivutils/include)
-endif()
-
-if(ENABLE_USER-H5MD)
-  find_package(HDF5 REQUIRED)
-  list(APPEND LAMMPS_LINK_LIBS ${HDF5_LIBRARIES})
-  include_directories(${HDF5_INCLUDE_DIRS} ${LAMMPS_LIB_SOURCE_DIR}/h5md/include)
-endif()
-
 if(ENABLE_USER-VTK)
   find_package(VTK REQUIRED NO_MODULE)
   include(${VTK_USE_FILE})
@@ -289,13 +320,11 @@ if(ENABLE_MSCG)
       WORKING_DIRECTORY ${LAMMPS_LIB_BINARY_DIR}/mscg)
   endif()
   file(GLOB MSCG_SOURCES ${LAMMPS_LIB_MSCG_BIN_DIR}/*.cpp)
-  list(APPEND LIB_SOURCES ${MSCG_SOURCES})
-  foreach(MSCG_SOURCE ${MSCG_SOURCES})
-    set_property(SOURCE ${MSCG_SOURCE} APPEND PROPERTY COMPILE_DEFINITIONS
-      DIMENSION=3 _exclude_gromacs=1)
-  endforeach()
-  include_directories(${LAMMPS_LIB_MSCG_BIN_DIR} ${GSL_INCLUDE_DIRS})
-  list(APPEND LAMMPS_LINK_LIBS ${GSL_LIBRARIES})
+  add_library(mscg STATIC ${MSCG_SOURCES})
+  list(APPEND LAMMPS_LINK_LIBS mscg)
+  target_compile_options(mscg PRIVATE -DDIMENSION=3 -D_exclude_gromacs=1)
+  target_include_directories(mscg PUBLIC ${LAMMPS_LIB_MSCG_BIN_DIR})
+  target_link_libraries(mscg ${GSL_LIBRARIES} ${LAPACK_LIBRARIES})
 endif()
 
 ########################################################################
@@ -321,7 +350,7 @@ endforeach(FUNC)
 list(APPEND LAMMPS_LINK_LIBS ${MATH_LIBRARIES})
 
 ######################################
-# Generate Basic Style files 
+# Generate Basic Style files
 ######################################
 include(StyleHeaderUtils)
 RegisterStyles(${LAMMPS_SOURCE_DIR})
@@ -330,13 +359,27 @@ RegisterStyles(${LAMMPS_SOURCE_DIR})
 # add sources of enabled packages
 ############################################
 foreach(PKG ${DEFAULT_PACKAGES} ${OTHER_PACKAGES})
-  if(ENABLE_${PKG})
-    set(${PKG}_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/${PKG})
+  set(${PKG}_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/${PKG})
 
+  # ignore PKG files which were manually installed in src folder
+  # headers are ignored during RegisterStyles
+  file(GLOB ${PKG}_SOURCES ${${PKG}_SOURCES_DIR}/*.cpp)
+  file(GLOB ${PKG}_HEADERS ${${PKG}_SOURCES_DIR}/*.h)
+
+  foreach(PKG_FILE in ${${PKG}_SOURCES})
+      get_filename_component(FNAME ${PKG_FILE} NAME)
+      list(REMOVE_ITEM LIB_SOURCES ${LAMMPS_SOURCE_DIR}/${FNAME})
+  endforeach()
+
+  foreach(PKG_FILE in ${${PKG}_HEADERS})
+      get_filename_component(FNAME ${PKG_FILE} NAME)
+      DetectAndRemovePackageHeader(${LAMMPS_SOURCE_DIR}/${FNAME})
+  endforeach()
+
+  if(ENABLE_${PKG})
     # detects styles in package and adds them to global list
     RegisterStyles(${${PKG}_SOURCES_DIR})
 
-    file(GLOB ${PKG}_SOURCES ${${PKG}_SOURCES_DIR}/*.cpp)
     list(APPEND LIB_SOURCES ${${PKG}_SOURCES})
     include_directories(${${PKG}_SOURCES_DIR})
   endif()
@@ -346,17 +389,53 @@ endforeach()
 # add lib sources of (simple) enabled packages
 ############################################
 foreach(SIMPLE_LIB REAX MEAM POEMS USER-ATC USER-AWPMD USER-COLVARS USER-H5MD
-  USER-MOLFILE USER-QMMM)
+  USER-QMMM)
   if(ENABLE_${SIMPLE_LIB})
-    string(REGEX REPLACE "^USER-" "" SIMPLE_LIB "${SIMPLE_LIB}")
-    string(TOLOWER "${SIMPLE_LIB}" INC_DIR)
-    file(GLOB_RECURSE ${SIMPLE_LIB}_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/${INC_DIR}/*.F
-      ${LAMMPS_LIB_SOURCE_DIR}/${INC_DIR}/*.c ${LAMMPS_LIB_SOURCE_DIR}/${INC_DIR}/*.cpp)
-    list(APPEND LIB_SOURCES ${${SIMPLE_LIB}_SOURCES})
-    include_directories(${LAMMPS_LIB_SOURCE_DIR}/${INC_DIR})
+    string(REGEX REPLACE "^USER-" "" PKG_LIB "${SIMPLE_LIB}")
+    string(TOLOWER "${PKG_LIB}" PKG_LIB)
+    file(GLOB_RECURSE ${PKG_LIB}_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/*.F
+      ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/*.c ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/*.cpp)
+    add_library(${PKG_LIB} STATIC ${${PKG_LIB}_SOURCES})
+    list(APPEND LAMMPS_LINK_LIBS ${PKG_LIB})
+    if(PKG_LIB STREQUAL awpmd)
+      target_include_directories(awpmd PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/awpmd/systems/interact ${LAMMPS_LIB_SOURCE_DIR}/awpmd/ivutils/include)
+    elseif(PKG_LIB STREQUAL h5md)
+      target_include_directories(h5md PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/h5md/include)
+    else()
+      target_include_directories(${PKG_LIB} PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB})
+    endif()
   endif()
 endforeach()
 
+if(ENABLE_USER-AWPMD)
+  target_link_libraries(awpmd ${LAPACK_LIBRARIES})
+endif()
+
+if(ENABLE_USER-ATC)
+  target_link_libraries(atc ${LAPACK_LIBRARIES})
+endif()
+
+if(ENABLE_USER-H5MD)
+  find_package(HDF5 REQUIRED)
+  target_link_libraries(h5md ${HDF5_LIBRARIES})
+  target_include_directories(h5md PRIVATE ${HDF5_INCLUDE_DIRS})
+endif()
+
+if(ENABLE_MEAM AND FC_HAS_NO_SECOND_UNDERSCORE)
+  foreach(FSRC ${meam_SOURCES})
+    string(REGEX REPLACE "^.*\\." "" FEXT "${FSRC}")
+    list(FIND CMAKE_Fortran_SOURCE_FILE_EXTENSIONS "${FEXT}" FINDEX)
+    if(FINDEX GREATER -1)
+      set_property(SOURCE ${FSRC} APPEND PROPERTY COMPILE_FLAGS "-fno-second-underscore")
+    endif()
+  endforeach()
+endif()
+
+if(ENABLE_REAX AND FC_HAS_NO_SECOND_UNDERSCORE)
+  target_compile_options(reax PRIVATE -fno-second-underscore)
+endif()
+
+
 ######################################################################
 # packages which selectively include variants based on enabled styles
 # e.g. accelerator packages
@@ -453,62 +532,130 @@ if(ENABLE_USER-INTEL)
 endif()
 
 if(ENABLE_GPU)
-    find_package(CUDA REQUIRED)
-    find_program(BIN2C bin2c)
-    if(NOT BIN2C)
-      message(FATAL_ERROR "Couldn't find bin2c, use -DBIN2C helping cmake to find it.")
-    endif()
-    include_directories(${CUDA_INCLUDE_DIRS})
-    list(APPEND LAMMPS_LINK_LIBS ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY})
-    set(GPU_PREC "SINGLE_DOUBLE" CACHE STRING "Lammps gpu precision size")
-    set_property(CACHE GPU_PREC PROPERTY STRINGS SINGLE_DOUBLE SINGLE_SINGLE DOUBLE_DOUBLE)
-    add_definitions(-D_${GPU_PREC})
-    add_definitions(-DNV_KERNEL -DUCL_CUDADR)
-    option(CUDPP_OPT "Enable CUDPP_OPT" ON)
-
     set(GPU_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/GPU)
-    set(GPU_SOURCES ${GPU_SOURCES_DIR}/gpu_extra.h)
+    set(GPU_SOURCES ${GPU_SOURCES_DIR}/gpu_extra.h
+                    ${GPU_SOURCES_DIR}/fix_gpu.h
+                    ${GPU_SOURCES_DIR}/fix_gpu.cpp)
+
+    set(GPU_API "OpenCL" CACHE STRING "API used by GPU package")
+    set_property(CACHE GPU_API PROPERTY STRINGS OpenCL CUDA)
+
+    set(GPU_PREC "SINGLE_DOUBLE" CACHE STRING "LAMMPS GPU precision size")
+    set_property(CACHE GPU_PREC PROPERTY STRINGS SINGLE_DOUBLE SINGLE_SINGLE DOUBLE_DOUBLE)
+
+    file(GLOB GPU_LIB_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/gpu/*.cpp)
+    file(MAKE_DIRECTORY ${LAMMPS_LIB_BINARY_DIR}/gpu)
+
+    if(GPU_API STREQUAL "CUDA")
+      find_package(CUDA REQUIRED)
+      find_program(BIN2C bin2c)
+      if(NOT BIN2C)
+        message(FATAL_ERROR "Couldn't find bin2c, use -DBIN2C helping cmake to find it.")
+      endif()
+      option(CUDPP_OPT "Enable CUDPP_OPT" ON)
+
+      set(GPU_ARCH "sm_30" CACHE STRING "LAMMPS GPU CUDA SM architecture")
+      set_property(CACHE GPU_ARCH PROPERTY STRINGS sm_10 sm_20 sm_30 sm_60)
+
+      file(GLOB GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/*.cu ${CMAKE_CURRENT_SOURCE_DIR}/gpu/*.cu)
+      list(REMOVE_ITEM GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_pppm.cu)
+
+      cuda_include_directories(${LAMMPS_LIB_SOURCE_DIR}/gpu ${LAMMPS_LIB_BINARY_DIR}/gpu)
+
+      if(CUDPP_OPT)
+        cuda_include_directories(${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini)
+        file(GLOB GPU_LIB_CUDPP_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/*.cpp)
+        file(GLOB GPU_LIB_CUDPP_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/*.cu)
+      endif()
+
+      cuda_compile_cubin(GPU_GEN_OBJS ${GPU_LIB_CU} OPTIONS
+                   -DUNIX -O3 -Xptxas -v --use_fast_math -DNV_KERNEL -DUCL_CUDADR -arch=${GPU_ARCH} -D_${GPU_PREC})
+
+      cuda_compile(GPU_OBJS ${GPU_LIB_CUDPP_CU} OPTIONS $<$<BOOL:${BUILD_SHARED_LIBS}>:-Xcompiler=-fPIC>
+                   -DUNIX -O3 -Xptxas -v --use_fast_math -DUCL_CUDADR -arch=${GPU_ARCH} -D_${GPU_PREC})
+
+      foreach(CU_OBJ ${GPU_GEN_OBJS})
+        get_filename_component(CU_NAME ${CU_OBJ} NAME_WE)
+        string(REGEX REPLACE "^.*_lal_" "" CU_NAME "${CU_NAME}")
+        add_custom_command(OUTPUT ${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}_cubin.h
+          COMMAND ${BIN2C} -c -n ${CU_NAME} ${CU_OBJ} > ${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}_cubin.h
+          DEPENDS ${CU_OBJ}
+          COMMENT "Generating ${CU_NAME}_cubin.h")
+        list(APPEND GPU_LIB_SOURCES ${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}_cubin.h)
+      endforeach()
+      set_directory_properties(PROPERTIES ADDITIONAL_MAKE_CLEAN_FILES "${LAMMPS_LIB_BINARY_DIR}/gpu/*_cubin.h")
+
+
+      add_library(gpu STATIC ${GPU_LIB_SOURCES} ${GPU_LIB_CUDPP_SOURCES} ${GPU_OBJS})
+      target_link_libraries(gpu ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY})
+      target_include_directories(gpu PRIVATE ${LAMMPS_LIB_BINARY_DIR}/gpu ${CUDA_INCLUDE_DIRS})
+      target_compile_definitions(gpu PRIVATE -D_${GPU_PREC} -DMPI_GERYON -DUCL_NO_EXIT)
+      if(CUDPP_OPT)
+        target_include_directories(gpu PRIVATE ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini)
+        target_compile_definitions(gpu PRIVATE -DUSE_CUDPP)
+      endif()
+
+      list(APPEND LAMMPS_LINK_LIBS gpu)
+
+      add_executable(nvc_get_devices ${LAMMPS_LIB_SOURCE_DIR}/gpu/geryon/ucl_get_devices.cpp)
+      target_compile_definitions(nvc_get_devices PRIVATE -DUCL_CUDADR)
+      target_link_libraries(nvc_get_devices PRIVATE ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY})
+      target_include_directories(nvc_get_devices PRIVATE ${CUDA_INCLUDE_DIRS})
+
+
+    elseif(GPU_API STREQUAL "OpenCL")
+      find_package(OpenCL REQUIRED)
+      set(OCL_TUNE "GENERIC" CACHE STRING "OpenCL Device Tuning")
+      set_property(CACHE OCL_TUNE PROPERTY STRINGS INTEL FERMI KEPLER CYPRESS GENERIC)
+
+      include(OpenCLUtils)
+      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)
+
+      foreach(GPU_KERNEL ${GPU_LIB_CU})
+          get_filename_component(basename ${GPU_KERNEL} NAME_WE)
+          string(SUBSTRING ${basename} 4 -1 KERNEL_NAME)
+          GenerateOpenCLHeader(${KERNEL_NAME} ${CMAKE_CURRENT_BINARY_DIR}/gpu/${KERNEL_NAME}_cl.h ${OCL_COMMON_HEADERS} ${GPU_KERNEL})
+          list(APPEND GPU_LIB_SOURCES ${CMAKE_CURRENT_BINARY_DIR}/gpu/${KERNEL_NAME}_cl.h)
+      endforeach()
+
+      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)
+
+      add_library(gpu STATIC ${GPU_LIB_SOURCES})
+      target_link_libraries(gpu ${OpenCL_LIBRARIES})
+      target_include_directories(gpu PRIVATE ${CMAKE_CURRENT_BINARY_DIR}/gpu ${OpenCL_INCLUDE_DIRS})
+      target_compile_definitions(gpu PRIVATE -D_${GPU_PREC} -DMPI_GERYON -DUCL_NO_EXIT)
+      target_compile_definitions(gpu PRIVATE -DUSE_OPENCL)
+
+      list(APPEND LAMMPS_LINK_LIBS gpu)
+
+      add_executable(ocl_get_devices ${LAMMPS_LIB_SOURCE_DIR}/gpu/geryon/ucl_get_devices.cpp)
+      target_compile_definitions(ocl_get_devices PRIVATE -DUCL_OPENCL)
+      target_link_libraries(ocl_get_devices PRIVATE ${OpenCL_LIBRARIES})
+      target_include_directories(ocl_get_devices PRIVATE ${OpenCL_INCLUDE_DIRS})
+    endif()
+
+    # GPU package
+    FindStyleHeaders(${GPU_SOURCES_DIR} FIX_CLASS fix_ FIX)
 
     set_property(GLOBAL PROPERTY "GPU_SOURCES" "${GPU_SOURCES}")
 
     # detects styles which have GPU version
-    RegisterStylesExt(${GPU_SOURCES_DIR} opt GPU_SOURCES)
+    RegisterStylesExt(${GPU_SOURCES_DIR} gpu GPU_SOURCES)
 
     get_property(GPU_SOURCES GLOBAL PROPERTY GPU_SOURCES)
-    
-    file(GLOB GPU_LIB_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/gpu/*.cpp)
-    file(GLOB GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/*.cu ${CMAKE_SOURCE_DIR}/gpu/*.cu)
-    file(GLOB_RECURSE GPU_NOT_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_pppm.cu)
-    list(REMOVE_ITEM GPU_LIB_CU ${GPU_NOT_LIB_CU})
-    include_directories(${GPU_SOURCES_DIR} ${LAMMPS_LIB_SOURCE_DIR}/gpu ${LAMMPS_LIB_BINARY_DIR}/gpu)
-    if(CUDPP_OPT)
-      include_directories(${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini)
-      add_definitions(-DCUDPP_OPT)
-      file(GLOB GPU_LIB_CUDPP_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/*.cpp)
-      file(GLOB GPU_LIB_CUDPP_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/*.cu)
-    endif()
-    cuda_compile(GPU_OBJS ${GPU_LIB_CU} ${GPU_LIB_CUDPP_CU} OPTIONS $<$<BOOL:${BUILD_SHARED_LIBS}>:-Xcompiler=-fPIC>)    
-    file(MAKE_DIRECTORY ${LAMMPS_LIB_BINARY_DIR}/gpu)
-    foreach(CU_OBJ ${GPU_OBJS})
-      get_filename_component(CU_NAME ${CU_OBJ} NAME_WE)
-      string(REGEX REPLACE "^.*_lal_" "" CU_NAME "${CU_NAME}")
-      add_custom_command(OUTPUT ${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}_cubin.h
-        COMMAND ${BIN2C} -c -n ${CU_NAME} ${CU_OBJ} > ${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}_cubin.h
-        DEPENDS ${CU_OBJ} 
-        COMMENT "Generating ${CU_NAME}_cubin.h")
-      list(APPEND LIB_SOURCES ${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}_cubin.h)
-      if(${CU_NAME} STREQUAL "pppm_d") #pppm_d doesn't get linked into the lib
-        set(CU_FORBIDDEN_OBJ "${CU_OBJ}") 
-      endif()
-    endforeach()
-    list(REMOVE_ITEM GPU_OBJS "${CU_FORBIDDEN_OBJ}")
-    list(APPEND LIB_SOURCES ${GPU_SOURCES} ${GPU_LIB_SOURCES} ${GPU_LIB_CUDPP_SOURCES} ${GPU_OBJS})
-    set_directory_properties(PROPERTIES ADDITIONAL_MAKE_CLEAN_FILES "${LAMMPS_LIB_BINARY_DIR}/gpu/*_cubin.h")
+
+    list(APPEND LIB_SOURCES ${GPU_SOURCES})
+    include_directories(${GPU_SOURCES_DIR})
 endif()
 
 ######################################################
 # Generate style headers based on global list of
-# styles registered during package selection           
+# styles registered during package selection
 ######################################################
 set(LAMMPS_STYLE_HEADERS_DIR ${CMAKE_CURRENT_BINARY_DIR}/styles)
 
@@ -522,19 +669,24 @@ include_directories(${LAMMPS_STYLE_HEADERS_DIR})
 ############################################
 add_library(lammps ${LIB_SOURCES})
 target_link_libraries(lammps ${LAMMPS_LINK_LIBS})
-set_target_properties(lammps PROPERTIES SOVERSION ${SOVERSION})
-if(INSTALL_LIB)
+if(LAMMPS_DEPS)
+  add_dependencies(lammps ${LAMMPS_DEPS})
+endif()
+set_target_properties(lammps PROPERTIES OUTPUT_NAME lammps${LAMMPS_MACHINE})
+if(BUILD_SHARED_LIBS)
+  set_target_properties(lammps PROPERTIES SOVERSION ${SOVERSION})
   install(TARGETS lammps LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
-  install(FILES ${LAMMPS_SOURCE_DIR}/lammps.h DESTINATION ${CMAKE_INSTALL_INCLUDEDIR})
-elseif(BUILD_SHARED_LIBS)
-  message(FATAL_ERROR "Shared library has to be installed, use -DINSTALL_LIB=ON to install lammps with a library")
+  install(FILES ${LAMMPS_SOURCE_DIR}/library.h DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps)
+  configure_file(pkgconfig/liblammps.pc.in ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_MACHINE}.pc @ONLY)
+  install(FILES ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_MACHINE}.pc DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
 endif()
 
 add_executable(lmp ${LMP_SOURCES})
 target_link_libraries(lmp lammps)
+set_target_properties(lmp PROPERTIES OUTPUT_NAME lmp${LAMMPS_MACHINE})
 install(TARGETS lmp DESTINATION ${CMAKE_INSTALL_BINDIR})
 if(ENABLE_TESTING)
-  add_test(ShowHelp ${CMAKE_CURRENT_BINARY_DIR}/lmp -help)
+  add_test(ShowHelp lmp${LAMMPS_MACHINE} -help)
 endif()
 
 ##################################
@@ -545,3 +697,27 @@ foreach(PKG ${DEFAULT_PACKAGES} ${OTHER_PACKAGES} ${ACCEL_PACKAGES})
     message(STATUS "Building package: ${PKG}")
   endif()
 endforeach()
+
+string(TOUPPER "${CMAKE_BUILD_TYPE}" BTYPE)
+message(STATUS "<<< Build configuration >>>
+   Build type       ${CMAKE_BUILD_TYPE}
+   Install path     ${CMAKE_INSTALL_PREFIX}
+   Compilers and Flags:
+   C++ Compiler     ${CMAKE_CXX_COMPILER}
+       Type         ${CMAKE_CXX_COMPILER_ID}
+   C++ Flags        ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_${BTYPE}}")
+get_property(LANGUAGES GLOBAL PROPERTY ENABLED_LANGUAGES)
+if(LANGUAGES MATCHES ".*Fortran.*")
+  message(STATUS "Fortran Compiler ${CMAKE_Fortran_COMPILER} 
+           Type     ${CMAKE_Fortran_COMPILER_ID}
+   Fortran Flags    ${CMAKE_Fortran_FLAGS} ${CMAKE_Fortran_FLAGS_${BTYPE}}")
+endif()
+message(STATUS "Linker flags:
+   Executable      ${CMAKE_EXE_LINKER_FLAGS}")
+if(BUILD_SHARED_LIBS)
+  message(STATUS "Shared libries  ${CMAKE_SHARED_LINKER_FLAGS}")
+else()
+  message(STATUS "Static libries  ${CMAKE_STATIC_LINKER_FLAGS}")
+endif()
+message(STATUS "Link libraries: ${LAMMPS_LINK_LIBS}")
+

cmake/Modules/FindLATTE.cmake

@@ -0,0 +1,18 @@
+# - Find latte
+# Find the native LATTE libraries.
+#
+#  LATTE_LIBRARIES    - List of libraries when using latte.
+#  LATTE_FOUND        - True if latte found.
+#
+
+find_library(LATTE_LIBRARY NAMES latte)
+
+set(LATTE_LIBRARIES ${LATTE_LIBRARY})
+
+include(FindPackageHandleStandardArgs)
+# handle the QUIETLY and REQUIRED arguments and set LATTE_FOUND to TRUE
+# if all listed variables are TRUE
+
+find_package_handle_standard_args(LATTE DEFAULT_MSG LATTE_LIBRARY)
+
+mark_as_advanced(LATTE_LIBRARY)

cmake/Modules/OpenCLUtils.cmake

@@ -0,0 +1,18 @@
+function(GenerateOpenCLHeader varname outfile files)
+    message("Creating ${outfile}...")
+    file(WRITE ${outfile} "const char * ${varname} = \n")
+    math(EXPR ARG_END   "${ARGC}-1")
+
+    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 "\\\\" "\\\\\\\\" content "${content}")
+        string(REGEX REPLACE "\"" "\\\\\"" content "${content}")
+        string(REGEX REPLACE "([^\n]+)\n" "\"\\1\\\\n\"\n" content "${content}")
+        string(REGEX REPLACE "\n+" "\n" content "${content}")
+        file(APPEND ${outfile} "${content}")
+    endforeach()
+
+    file(APPEND ${outfile} ";\n")
+endfunction(GenerateOpenCLHeader)

cmake/Modules/StyleHeaderUtils.cmake

@@ -85,6 +85,35 @@ function(RegisterStyles search_path)
     FindStyleHeaders(${search_path} REGION_CLASS    region_    REGION    ) # region    ) # domain
 endfunction(RegisterStyles)
 
+function(RemovePackageHeader headers pkg_header)
+    get_property(hlist GLOBAL PROPERTY ${headers})
+    list(REMOVE_ITEM hlist ${pkg_header})
+    set_property(GLOBAL PROPERTY ${headers} "${hlist}")
+endfunction(RemovePackageHeader)
+
+function(DetectAndRemovePackageHeader fname)
+    RemovePackageHeader(ANGLE     ${fname})
+    RemovePackageHeader(ATOM_VEC  ${fname})
+    RemovePackageHeader(BODY      ${fname})
+    RemovePackageHeader(BOND      ${fname})
+    RemovePackageHeader(COMMAND   ${fname})
+    RemovePackageHeader(COMPUTE   ${fname})
+    RemovePackageHeader(DIHEDRAL  ${fname})
+    RemovePackageHeader(DUMP      ${fname})
+    RemovePackageHeader(FIX       ${fname})
+    RemovePackageHeader(IMPROPER  ${fname})
+    RemovePackageHeader(INTEGRATE ${fname})
+    RemovePackageHeader(KSPACE    ${fname})
+    RemovePackageHeader(MINIMIZE  ${fname})
+    RemovePackageHeader(NBIN      ${fname})
+    RemovePackageHeader(NPAIR     ${fname})
+    RemovePackageHeader(NSTENCIL  ${fname})
+    RemovePackageHeader(NTOPO     ${fname})
+    RemovePackageHeader(PAIR      ${fname})
+    RemovePackageHeader(READER    ${fname})
+    RemovePackageHeader(REGION    ${fname})
+endfunction(DetectAndRemovePackageHeader)
+
 function(RegisterStylesExt search_path extension sources)
     FindStyleHeadersExt(${search_path} ANGLE_CLASS     ${extension}  ANGLE     ${sources})
     FindStyleHeadersExt(${search_path} ATOM_CLASS      ${extension}  ATOM_VEC  ${sources})

cmake/pkgconfig/liblammps.pc.in

@@ -0,0 +1,18 @@
+# pkg-config file for lammps
+# https://people.freedesktop.org/~dbn/pkg-config-guide.html
+# Usage: cc `pkg-config --cflags --libs liblammps` -o myapp myapp.c
+# after you added @CMAKE_INSTALL_FULL_LIBDIR@/pkg-config to PKG_CONFIG_PATH,
+# e.g. export PKG_CONFIG_PATH=@CMAKE_INSTALL_FULL_LIBDIR@/pkgconfig
+
+prefix=@CMAKE_INSTALL_FULL_PREFIX@
+libdir=@CMAKE_INSTALL_FULL_LIBDIR@
+includedir=@CMAKE_INSTALL_FULL_INCLUDEDIR@
+
+Name: liblammps@LAMMPS_MACHINE@
+Description: Large-scale Atomic/Molecular Massively Parallel Simulator Library
+URL: http://lammps.sandia.gov
+Version:
+Requires:
+Libs: -L${libdir} -llammps@LAMMPS_MACHINE@
+Libs.private: -lm
+Cflags: -I${includedir} @LAMMPS_API_DEFINES@

doc/src/Eqs/bond_gromos.tex

@@ -0,0 +1,10 @@
+\documentclass[12pt]{article}
+\pagestyle{empty}
+
+\begin{document}
+
+$$
+   E = K (r^2 - r_0^2)^2
+$$
+
+\end{document}

doc/src/Eqs/fix_rhok.tex

@@ -0,0 +1,11 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+\begin{eqnarray*}
+ U &=&  \frac{1}{2} K (|\rho_{\vec{k}}| - a)^2 \\
+ \rho_{\vec{k}} &=& \sum_j^N \exp(-i\vec{k} \cdot \vec{r}_j )/\sqrt{N} \\
+ \vec{k} &=& (2\pi n_x /L_x , 2\pi n_y  /L_y , 2\pi n_z/L_z ) 
+\end{eqnarray*}
+
+\end{document}

doc/src/Manual.txt

@@ -1,7 +1,7 @@
 <!-- HTML_ONLY -->
 <HEAD>
 <TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="1 Sep 2017 version">
+<META NAME="docnumber" CONTENT="23 Oct 2017 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 @@
 <H1></H1>
 
 LAMMPS Documentation :c,h3
-1 Sep 2017 version :c,h4
+23 Oct 2017 version :c,h4
 
 Version info: :h4
 

doc/src/Section_commands.txt

@@ -532,7 +532,8 @@ package"_Section_start.html#start_3.
 "dump vtk"_dump_vtk.html,
 "group2ndx"_group2ndx.html,
 "ndx2group"_group2ndx.html,
-"temper/grem"_temper_grem.html :tb(c=3,ea=c)
+"temper/grem"_temper_grem.html,
+"temper/npt"_temper_npt.html :tb(c=3,ea=c)
 
 :line
 
@@ -579,6 +580,7 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
 "halt"_fix_halt.html,
 "heat"_fix_heat.html,
 "indent"_fix_indent.html,
+"latte"_fix_latte.html,
 "langevin (k)"_fix_langevin.html,
 "lineforce"_fix_lineforce.html,
 "momentum (k)"_fix_momentum.html,
@@ -718,6 +720,8 @@ package"_Section_start.html#start_3.
 "nve/eff"_fix_nve_eff.html,
 "nvt/eff"_fix_nh_eff.html,
 "nvt/sllod/eff"_fix_nvt_sllod_eff.html,
+"npt/uef"_fix_nh_uef.html,
+"nvt/uef"_fix_nh_uef.html,
 "phonon"_fix_phonon.html,
 "pimd"_fix_pimd.html,
 "qbmsst"_fix_qbmsst.html,
@@ -726,6 +730,7 @@ package"_Section_start.html#start_3.
 "qtb"_fix_qtb.html,
 "reax/c/bonds"_fix_reax_bonds.html,
 "reax/c/species"_fix_reaxc_species.html,
+"rhok"_fix_rhok.html,
 "rx"_fix_rx.html,
 "saed/vtk"_fix_saed_vtk.html,
 "shardlow"_fix_shardlow.html,
@@ -755,6 +760,7 @@ package"_Section_accelerate.html.  This is indicated by additional
 letters in parenthesis: g = GPU, i = USER-INTEL, k =
 KOKKOS, o = USER-OMP, t = OPT.
 
+"aggregate/atom"_compute_cluster_atom.html,
 "angle"_compute_angle.html,
 "angle/local"_compute_angle_local.html,
 "angmom/chunk"_compute_angmom_chunk.html,
@@ -853,6 +859,7 @@ package"_Section_start.html#start_3.
 "meso/t/atom"_compute_meso_t_atom.html,
 "pe/tally"_compute_tally.html,
 "pe/mol/tally"_compute_tally.html,
+"pressure/uef"_compute_pressure_uef.html,
 "saed"_compute_saed.html,
 "smd/contact/radius"_compute_smd_contact_radius.html,
 "smd/damage"_compute_smd_damage.html,
@@ -881,6 +888,7 @@ package"_Section_start.html#start_3.
 "temp/deform/eff"_compute_temp_deform_eff.html,
 "temp/region/eff"_compute_temp_region_eff.html,
 "temp/rotate"_compute_temp_rotate.html,
+"temp/uef"_compute_temp_uef.html,
 "xrd"_compute_xrd.html :tb(c=6,ea=c)
 
 :line
@@ -912,11 +920,12 @@ KOKKOS, o = USER-OMP, t = OPT.
 "born/coul/long/cs"_pair_born.html,
 "born/coul/msm (o)"_pair_born.html,
 "born/coul/wolf (go)"_pair_born.html,
+"born/coul/wolf/cs"_pair_born.html,
 "brownian (o)"_pair_brownian.html,
 "brownian/poly (o)"_pair_brownian.html,
-"buck (gkio)"_pair_buck.html,
-"buck/coul/cut (gkio)"_pair_buck.html,
-"buck/coul/long (gkio)"_pair_buck.html,
+"buck (giko)"_pair_buck.html,
+"buck/coul/cut (giko)"_pair_buck.html,
+"buck/coul/long (giko)"_pair_buck.html,
 "buck/coul/long/cs"_pair_buck.html,
 "buck/coul/msm (o)"_pair_buck.html,
 "buck/long/coul/long (o)"_pair_buck_long.html,
@@ -931,12 +940,13 @@ KOKKOS, o = USER-OMP, t = OPT.
 "coul/msm"_pair_coul.html,
 "coul/streitz"_pair_coul.html,
 "coul/wolf (ko)"_pair_coul.html,
-"dpd (go)"_pair_dpd.html,
+"coul/wolf/cs"_pair_coul.html,
+"dpd (gio)"_pair_dpd.html,
 "dpd/tstat (go)"_pair_dpd.html,
 "dsmc"_pair_dsmc.html,
-"eam (gkiot)"_pair_eam.html,
-"eam/alloy (gkiot)"_pair_eam.html,
-"eam/fs (gkiot)"_pair_eam.html,
+"eam (gikot)"_pair_eam.html,
+"eam/alloy (gikot)"_pair_eam.html,
+"eam/fs (gikot)"_pair_eam.html,
 "eim (o)"_pair_eim.html,
 "gauss (go)"_pair_gauss.html,
 "gayberne (gio)"_pair_gayberne.html,
@@ -950,9 +960,9 @@ KOKKOS, o = USER-OMP, t = OPT.
 "kim"_pair_kim.html,
 "lcbop"_pair_lcbop.html,
 "line/lj"_pair_line_lj.html,
-"lj/charmm/coul/charmm (kio)"_pair_charmm.html,
+"lj/charmm/coul/charmm (iko)"_pair_charmm.html,
 "lj/charmm/coul/charmm/implicit (ko)"_pair_charmm.html,
-"lj/charmm/coul/long (gkio)"_pair_charmm.html,
+"lj/charmm/coul/long (giko)"_pair_charmm.html,
 "lj/charmm/coul/msm"_pair_charmm.html,
 "lj/charmmfsw/coul/charmmfsh"_pair_charmm.html,
 "lj/charmmfsw/coul/long"_pair_charmm.html,
@@ -1002,9 +1012,9 @@ KOKKOS, o = USER-OMP, t = OPT.
 "resquared (go)"_pair_resquared.html,
 "snap"_pair_snap.html,
 "soft (go)"_pair_soft.html,
-"sw (gkio)"_pair_sw.html,
+"sw (giko)"_pair_sw.html,
 "table (gko)"_pair_table.html,
-"tersoff (gkio)"_pair_tersoff.html,
+"tersoff (giko)"_pair_tersoff.html,
 "tersoff/mod (gko)"_pair_tersoff_mod.html,
 "tersoff/mod/c (o)"_pair_tersoff_mod.html,
 "tersoff/zbl (gko)"_pair_tersoff_zbl.html,
@@ -1108,6 +1118,7 @@ KOKKOS, o = USER-OMP, t = OPT.
 "class2 (ko)"_bond_class2.html,
 "fene (iko)"_bond_fene.html,
 "fene/expand (o)"_bond_fene_expand.html,
+"gromos (o)"_bond_gromos.html,
 "harmonic (ko)"_bond_harmonic.html,
 "morse (o)"_bond_morse.html,
 "nonlinear (o)"_bond_nonlinear.html,
@@ -1174,7 +1185,7 @@ USER-OMP, t = OPT.
 "none"_dihedral_none.html,
 "zero"_dihedral_zero.html,
 "hybrid"_dihedral_hybrid.html,
-"charmm (ko)"_dihedral_charmm.html,
+"charmm (iko)"_dihedral_charmm.html,
 "charmmfsw"_dihedral_charmm.html,
 "class2 (ko)"_dihedral_class2.html,
 "harmonic (io)"_dihedral_harmonic.html,
@@ -1187,7 +1198,7 @@ used if "LAMMPS is built with the appropriate
 package"_Section_start.html#start_3.
 
 "cosine/shift/exp (o)"_dihedral_cosine_shift_exp.html,
-"fourier (o)"_dihedral_fourier.html,
+"fourier (io)"_dihedral_fourier.html,
 "nharmonic (o)"_dihedral_nharmonic.html,
 "quadratic (o)"_dihedral_quadratic.html,
 "spherical (o)"_dihedral_spherical.html,
@@ -1210,7 +1221,7 @@ USER-OMP, t = OPT.
 "hybrid"_improper_hybrid.html,
 "class2 (ko)"_improper_class2.html,
 "cvff (io)"_improper_cvff.html,
-"harmonic (ko)"_improper_harmonic.html,
+"harmonic (iko)"_improper_harmonic.html,
 "umbrella (o)"_improper_umbrella.html :tb(c=4,ea=c)
 
 These are additional improper styles in USER packages, which can be

doc/src/Section_howto.txt

@@ -2859,8 +2859,8 @@ The nature of the atoms (core, Drude particle or non-polarizable) is
 specified via the "fix drude"_fix_drude.html command.  The special
 list of neighbors is automatically refactored to account for the
 equivalence of core and Drude particles as regards special 1-2 to 1-4
-screening. It may be necessary to use the {extra} keyword of the
-"special_bonds"_special_bonds.html command. If using "fix
+screening. It may be necessary to use the {extra/special/per/atom}
+keyword of the "read_data"_read_data.html command. If using "fix
 shake"_fix_shake.html, make sure no Drude particle is in this fix
 group.
 

doc/src/Section_packages.txt

@@ -96,6 +96,7 @@ Package, Description, Doc page, Example, Library
 "KIM"_#KIM, OpenKIM wrapper, "pair_style kim"_pair_kim.html, kim, ext
 "KOKKOS"_#KOKKOS, Kokkos-enabled styles, "Section 5.3.3"_accelerate_kokkos.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, -
 "KSPACE"_#KSPACE, long-range Coulombic solvers, "kspace_style"_kspace_style.html, peptide, -
+"LATTE"_#LATTE, quantum DFTB forces via LATTE, "fix latte"_fix_latte.html, latte, ext
 "MANYBODY"_#MANYBODY, many-body potentials, "pair_style tersoff"_pair_tersoff.html, shear, -
 "MC"_#MC, Monte Carlo options, "fix gcmc"_fix_gcmc.html, -, -
 "MEAM"_#MEAM, modified EAM potential, "pair_style meam"_pair_meam.html, meam, int
@@ -149,6 +150,7 @@ Package, Description, Doc page, Example, Library
 "USER-SMTBQ"_#USER-SMTBQ, second moment tight binding QEq potential,"pair_style smtbq"_pair_smtbq.html, USER/smtbq, -
 "USER-SPH"_#USER-SPH, smoothed particle hydrodynamics,"SPH User Guide"_PDF/SPH_LAMMPS_userguide.pdf, USER/sph, -
 "USER-TALLY"_#USER-TALLY, pairwise tally computes,"compute XXX/tally"_compute_tally.html, USER/tally, -
+"USER-UEF"_#USER-UEF, extensional flow,"fix nvt/uef"_fix_nh_uef.html, USER/uef, -
 "USER-VTK"_#USER-VTK, dump output via VTK, "compute vtk"_dump_vtk.html, -, ext :tb(ea=c,ca1=l)
 
 :line
@@ -695,6 +697,66 @@ bench/in.rhodo :ul
 
 :line
 
+LATTE package :link(LATTE),h4
+
+[Contents:]
+
+A fix command which wraps the LATTE DFTB code, so that molecular
+dynamics can be run with LAMMPS using density-functional tight-binding
+quantum forces calculated by LATTE.
+
+More information on LATTE can be found at this web site:
+"https://github.com/lanl/LATTE"_latte_home.  A brief technical
+description is given with the "fix latte"_fix_latte.html command.
+
+:link(latte_home,https://github.com/lanl/LATTE)
+
+[Authors:] Christian Negre (LANL) and Steve Plimpton (Sandia).  LATTE
+itself is developed at Los Alamos National Laboratory by Marc
+Cawkwell, Anders Niklasson, and Christian Negre.
+
+[Install or un-install:]
+
+Before building LAMMPS with this package, you must first download and
+build the LATTE library.  You can do this manually if you prefer;
+follow the instructions in lib/latte/README.  You can also do it in
+one step from the lammps/src dir, using a command like these, which
+simply invokes the lib/latte/Install.py script with the specified
+args:
+
+make lib-latte                          # print help message
+make lib-latte args="-b"                # download and build in lib/latte/LATTE-master
+make lib-latte args="-p $HOME/latte"    # use existing LATTE installation in $HOME/latte
+make lib-latte args="-b -m gfortran"    # download and build in lib/latte and 
+                                        #   copy Makefile.lammps.gfortran to Makefile.lammps
+:pre
+
+Note that 3 symbolic (soft) links, "includelink" and "liblink" and
+"filelink", are created in lib/latte to point into the LATTE home dir.
+When LAMMPS builds in src it will use these links.  You should 
+also check that the Makefile.lammps file you create is apporpriate
+for the compiler you use on your system to build LATTE.
+
+You can then install/un-install the package and build LAMMPS in the
+usual manner:
+
+make yes-latte
+make machine :pre
+
+make no-latte
+make machine :pre
+
+[Supporting info:]
+
+src/LATTE: filenames -> commands
+src/LATTE/README
+lib/latte/README
+"fix latte"_fix_latte.html
+examples/latte
+"LAMMPS-LATTE tutorial"_https://github.com/lanl/LATTE/wiki/Using-LATTE-through-LAMMPS :ul
+
+:line
+
 MANYBODY package :link(MANYBODY),h4
 
 [Contents:]
@@ -2191,7 +2253,7 @@ src/USER-MESO/README
 "pair_style edpd"_pair_meso.html
 "pair_style mdpd"_pair_meso.html
 "pair_style tdpd"_pair_meso.html
-"fix mvv/dpd"_fix_mvv.html
+"fix mvv/dpd"_fix_mvv_dpd.html
 examples/USER/meso
 http://lammps.sandia.gov/movies.html#mesodpd :ul
 
@@ -2710,13 +2772,44 @@ examples/USER/tally :ul
 
 :line
 
+USER-UEF package :link(USER-UEF),h4
+
+[Contents:]
+
+A fix style for the integration of the equations of motion under
+extensional flow with proper boundary conditions, as well as several
+supporting compute styles and an output option.
+
+[Author:] David Nicholson (MIT).
+
+[Install or un-install:]
+
+make yes-user-uef
+make machine :pre
+
+make no-user-uef
+make machine :pre
+
+[Supporting info:]
+
+src/USER-UEF: filenames -> commands
+src/USER-UEF/README
+"fix nvt/uef"_fix_nh_uef.html
+"fix npt/uef"_fix_nh_uef.html
+"compute pressure/uef"_compute_pressure_uef.html
+"compute temp/uef"_compute_temp_uef.html
+"dump cfg/uef"_dump_cfg_uef.html
+examples/uef :ul
+
+:line
+
 USER-VTK package :link(USER-VTK),h4
 
 [Contents:]
 
-A "dump vtk"_dump_vtk.html command which outputs
-snapshot info in the "VTK format"_vtk, enabling visualization by
-"Paraview"_paraview or other visuzlization packages.
+A "dump vtk"_dump_vtk.html command which outputs snapshot info in the
+"VTK format"_vtk, enabling visualization by "Paraview"_paraview or
+other visuzlization packages.
 
 :link(vtk,http://www.vtk.org)
 :link(paraview,http://www.paraview.org)

doc/src/Section_start.txt

@@ -920,7 +920,7 @@ CPUs and KNLs; the KOKKOS package builds for CPUs (OpenMP), GPUs
 Makefile.intel_cpu
 Makefile.intel_phi
 Makefile.kokkos_omp
-Makefile.kokkos_cuda
+Makefile.kokkos_cuda_mpi
 Makefile.kokkos_phi
 Makefile.omp
 Makefile.opt :ul

doc/src/accelerate_intel.txt

@@ -25,14 +25,14 @@ LAMMPS to run on the CPU cores and coprocessor cores simultaneously.
 [Currently Available USER-INTEL Styles:]
 
 Angle Styles: charmm, harmonic :ulb,l
-Bond Styles: fene, harmonic :l
+Bond Styles: fene, fourier, harmonic :l
 Dihedral Styles: charmm, harmonic, opls :l
-Fixes: nve, npt, nvt, nvt/sllod :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, 
-buck, eam, eam/alloy, eam/fs, gayberne, lj/charmm/coul/charmm, 
-lj/charmm/coul/long, lj/cut, lj/cut/coul/long, lj/long/coul/long, rebo,
-sw, tersoff :l
+buck, dpd, eam, eam/alloy, eam/fs, gayberne, lj/charmm/coul/charmm, 
+lj/charmm/coul/long, lj/cut, lj/cut/coul/long, lj/long/coul/long, 
+rebo, sw, tersoff :l
 K-Space Styles: pppm, pppm/disp :l
 :ule
 
@@ -54,11 +54,12 @@ warmup run (for use with offload benchmarks).
 :c,image(JPG/user_intel.png)
 
 Results are speedups obtained on Intel Xeon E5-2697v4 processors
-(code-named Broadwell) and Intel Xeon Phi 7250 processors
-(code-named Knights Landing) with "June 2017" LAMMPS built with
-Intel Parallel Studio 2017 update 2. Results are with 1 MPI task
-per physical core. See {src/USER-INTEL/TEST/README} for the raw
-simulation rates and instructions to reproduce.
+(code-named Broadwell), Intel Xeon Phi 7250 processors (code-named
+Knights Landing), and Intel Xeon Gold 6148 processors (code-named
+Skylake) with "June 2017" LAMMPS built with Intel Parallel Studio
+2017 update 2. Results are with 1 MPI task per physical core. See
+{src/USER-INTEL/TEST/README} for the raw simulation rates and
+instructions to reproduce.
 
 :line
 
@@ -82,6 +83,11 @@ this order :l
 The {newton} setting applies to all atoms, not just atoms shared
 between MPI tasks :l
 Vectorization can change the order for adding pairwise forces :l
+When using the -DLMP_USE_MKL_RNG define (all included intel optimized
+makefiles do) at build time, the random number generator for
+dissipative particle dynamics (pair style dpd/intel) uses the Mersenne
+Twister generator included in the Intel MKL library (that should be
+more robust than the default Masaglia random number generator) :l
 :ule
 
 The precision mode (described below) used with the USER-INTEL
@@ -108,7 +114,7 @@ $t should be 2 for Intel Xeon CPUs and 2 or 4 for Intel Xeon Phi :l
 For some of the simple 2-body potentials without long-range
 electrostatics, performance and scalability can be better with
 the "newton off" setting added to the input script :l
-For simulations on higher node counts, add "processors * * * grid 
+For simulations on higher node counts, add "processors * * * grid
 numa" to the beginning of the input script for better scalability :l
 If using {kspace_style pppm} in the input script, add
 "kspace_modify diff ad" for better performance :l
@@ -119,8 +125,8 @@ For Intel Xeon Phi CPUs:
 Runs should be performed using MCDRAM. :ulb,l
 :ule
 
-For simulations using {kspace_style pppm} on Intel CPUs
-supporting AVX-512:
+For simulations using {kspace_style pppm} on Intel CPUs supporting
+AVX-512:
 
 Add "kspace_modify diff ad" to the input script :ulb,l
 The command-line option should be changed to
@@ -237,14 +243,17 @@ However, if you do not have coprocessors on your system, building
 without offload support will produce a smaller binary.
 
 The general requirements for Makefiles with the USER-INTEL package
-are as follows. "-DLAMMPS_MEMALIGN=64" is required for CCFLAGS. When
-using Intel compilers, "-restrict" is required and "-qopenmp" is
-highly recommended for CCFLAGS and LINKFLAGS. LIB should include
-"-ltbbmalloc". For builds supporting offload, "-DLMP_INTEL_OFFLOAD"
-is required for CCFLAGS and "-qoffload" is required for LINKFLAGS.
-Other recommended CCFLAG options for best performance are
-"-O2 -fno-alias -ansi-alias -qoverride-limits fp-model fast=2
--no-prec-div".
+are as follows. When using Intel compilers, "-restrict" is required 
+and "-qopenmp" is highly recommended for CCFLAGS and LINKFLAGS. 
+CCFLAGS should include "-DLMP_INTEL_USELRT" (unless POSIX Threads
+are not supported in the build environment) and "-DLMP_USE_MKL_RNG"
+(unless Intel Math Kernel Library (MKL) is not available in the build
+environment). For Intel compilers, LIB should include "-ltbbmalloc" 
+or if the library is not available, "-DLMP_INTEL_NO_TBB" can be added
+to CCFLAGS. For builds supporting offload, "-DLMP_INTEL_OFFLOAD" is
+required for CCFLAGS and "-qoffload" is required for LINKFLAGS. Other
+recommended CCFLAG options for best performance are "-O2 -fno-alias
+-ansi-alias -qoverride-limits fp-model fast=2 -no-prec-div".
 
 NOTE: The vectorization and math capabilities can differ depending on
 the CPU. For Intel compilers, the "-x" flag specifies the type of
@@ -361,10 +370,14 @@ intel"_package.html command that can improve performance when using
 "PPPM"_kspace_style.html for long-range electrostatics on processors
 with SMT. It generates an extra pthread for each MPI task. The thread
 is dedicated to performing some of the PPPM calculations and MPI
-communications. On Intel Xeon Phi x200 series CPUs, this will likely
-always improve performance, even on a single node. On Intel Xeon
-processors, using this mode might result in better performance when
-using multiple nodes, depending on the machine. To use this mode,
+communications. This feature requires setting the preprocessor flag
+-DLMP_INTEL_USELRT in the makefile when compiling LAMMPS. It is unset
+in the default makefiles ({Makefile.mpi} and {Makefile.serial}) but
+it is set in all makefiles tuned for the USER-INTEL package.  On Intel
+Xeon Phi x200 series CPUs, the LRT feature will likely improve
+performance, even on a single node. On Intel Xeon processors, using
+this mode might result in better performance when using multiple nodes,
+depending on the specific machine configuration. To enable LRT mode,
 specify that the number of OpenMP threads is one less than would
 normally be used for the run and add the "lrt yes" option to the "-pk"
 command-line suffix or "package intel" command. For example, if a run

doc/src/accelerate_kokkos.txt

@@ -135,10 +135,10 @@ GPUs, or Phi.
 You can do any of these in one line, using the suitable make command
 line flags as described in "Section 4"_Section_packages.html of the
 manual. If run from the src directory, these
-commands will create src/lmp_kokkos_omp, lmp_kokkos_cuda, and
+commands will create src/lmp_kokkos_omp, lmp_kokkos_cuda_mpi, and
 lmp_kokkos_phi.  Note that the OMP and PHI options use
 src/MAKE/Makefile.mpi as the starting Makefile.machine.  The CUDA
-option uses src/MAKE/OPTIONS/Makefile.kokkos_cuda.
+option uses src/MAKE/OPTIONS/Makefile.kokkos_cuda_mpi.
 
 The latter two steps can be done using the "-k on", "-pk kokkos" and
 "-sf kk" "command-line switches"_Section_start.html#start_6
@@ -159,7 +159,7 @@ CPU-only (only MPI, no threading):
 
 cd lammps/src
 make yes-kokkos
-make kokkos_mpi :pre
+make kokkos_mpi_only :pre
 
 Intel Xeon Phi (Intel Compiler, Intel MPI):
 
@@ -167,11 +167,11 @@ cd lammps/src
 make yes-kokkos
 make kokkos_phi :pre
 
-CPUs and GPUs (with MPICH):
+CPUs and GPUs (with MPICH or OpenMPI):
 
 cd lammps/src
 make yes-kokkos
-make kokkos_cuda_mpich :pre
+make kokkos_cuda_mpi :pre
 
 These examples set the KOKKOS-specific OMP, MIC, CUDA variables on the
 make command line which requires a GNU-compatible make command.  Try

doc/src/atom_modify.txt

@@ -16,7 +16,7 @@ atom_modify keyword values ... :pre
 one or more keyword/value pairs may be appended :ulb,l
 keyword = {id} or {map} or {first} or {sort} :l
    {id} value = {yes} or {no}
-   {map} value = {array} or {hash}
+   {map} value = {yes} or {array} or {hash}
    {first} value = group-ID = group whose atoms will appear first in internal atom lists
    {sort} values = Nfreq binsize
      Nfreq = sort atoms spatially every this many time steps
@@ -25,8 +25,8 @@ keyword = {id} or {map} or {first} or {sort} :l
 
 [Examples:]
 
-atom_modify map hash
-atom_modify map array sort 10000 2.0
+atom_modify map yes
+atom_modify map hash sort 10000 2.0
 atom_modify first colloid :pre
 
 [Description:]
@@ -62,29 +62,33 @@ switch.  This is described in "Section 2.2"_Section_start.html#start_2
 of the manual.  If atom IDs are not used, they must be specified as 0
 for all atoms, e.g. in a data or restart file.
 
-The {map} keyword determines how atom ID lookup is done for molecular
-atom styles.  Lookups are performed by bond (angle, etc) routines in
-LAMMPS to find the local atom index associated with a global atom ID.
+The {map} keyword determines how atoms with specific IDs are found
+when required.  An example are the bond (angle, etc) methods which
+need to find the local index of an atom with a specific global ID
+which is a bond (angle, etc) partner.  LAMMPS performs this operation
+efficiently by creating a "map", which is either an {array} or {hash}
+table, as descibed below.
 
-When the {array} value is used, each processor stores a lookup table
-of length N, where N is the largest atom ID in the system.  This is a
+When the {map} keyword is not specified in your input script, LAMMPS
+only creates a map for "atom_styles"_atom_style.html for molecular
+systems which have permanent bonds (angles, etc).  No map is created
+for atomic systems, since it is normally not needed.  However some
+LAMMPS commands require a map, even for atomic systems, and will
+generate an error if one does not exist.  The {map} keyword thus
+allows you to force the creation of a map.  The {yes} value will
+create either an {array} or {hash} style map, as explained in the next
+paragraph.  The {array} and {hash} values create an atom-style or
+hash-style map respectively.
+
+For an {array}-style map, each processor stores a lookup table of
+length N, where N is the largest atom ID in the system.  This is a
 fast, simple method for many simulations, but requires too much memory
-for large simulations.  The {hash} value uses a hash table to perform
-the lookups.  This can be slightly slower than the {array} method, but
-its memory cost is proportional to the number of atoms owned by a
-processor, i.e. N/P when N is the total number of atoms in the system
-and P is the number of processors.
-
-When this setting is not specified in your input script, LAMMPS
-creates a map, if one is needed, as an array or hash.  See the
-discussion of default values below for how LAMMPS chooses which kind
-of map to build.  Note that atomic systems do not normally need to
-create a map.  However, even in this case some LAMMPS commands will
-create a map to find atoms (and then destroy it), or require a
-permanent map.  An example of the former is the "velocity loop
-all"_velocity.html command, which uses a map when looping over all
-atoms and insuring the same velocity values are assigned to an atom
-ID, no matter which processor owns it.
+for large simulations.  For a {hash}-style map, a hash table is
+created on each processor, which finds an atom ID in constant time
+(independent of the global number of atom IDs).  It can be slightly
+slower than the {array} map, but its memory cost is proportional to
+the number of atoms owned by a processor, i.e. N/P when N is the total
+number of atoms in the system and P is the number of processors.
 
 The {first} keyword allows a "group"_group.html to be specified whose
 atoms will be maintained as the first atoms in each processor's list

doc/src/bond_gromos.txt

@@ -0,0 +1,73 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+bond_style gromos command :h3
+bond_style gromos/omp command :h3
+
+[Syntax:]
+
+bond_style gromos :pre
+
+[Examples:]
+
+bond_style gromos
+bond_coeff 5 80.0 1.2 :pre
+
+[Description:]
+
+The {gromos} bond style uses the potential
+
+:c,image(Eqs/bond_gromos.jpg)
+
+where r0 is the equilibrium bond distance.  Note that the usual 1/4
+factor is included in K.
+
+The following coefficients must be defined for each bond type via the
+"bond_coeff"_bond_coeff.html command as in the example above, or in
+the data file or restart files read by the "read_data"_read_data.html
+or "read_restart"_read_restart.html commands:
+
+K (energy/distance^4)
+r0 (distance) :ul
+
+:line
+
+Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in "Section 5"_Section_accelerate.html
+of the manual.  The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the "-suffix command-line
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
+use the "suffix"_suffix.html command in your input script.
+
+See "Section 5"_Section_accelerate.html of the manual for
+more instructions on how to use the accelerated styles effectively.
+
+:line
+
+[Restrictions:]
+
+This bond style can only be used if LAMMPS was built with the
+MOLECULE package.  See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info on packages.
+
+[Related commands:]
+
+"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html
+
+[Default:] none

doc/src/bonds.txt

@@ -8,6 +8,7 @@ Bond Styles :h1
    bond_class2
    bond_fene
    bond_fene_expand
+   bond_gromos
    bond_harmonic
    bond_harmonic_shift
    bond_harmonic_shift_cut

doc/src/commands.txt

@@ -32,6 +32,7 @@ Commands :h1
    dimension
    displace_atoms
    dump
+   dump_cfg_uef
    dump_h5md
    dump_image
    dump_modify
@@ -92,6 +93,7 @@ Commands :h1
    tad
    temper
    temper_grem
+   temper_npt
    thermo
    thermo_modify
    thermo_style

doc/src/compute.txt

@@ -169,6 +169,7 @@ by users which are included in the LAMMPS distribution.  The list of
 these with links to the individual styles are given in the compute
 section of "this page"_Section_commands.html#cmd_5.
 
+"aggregate/atom"_compute_cluster_atom.html - aggregate ID for each atom
 "angle/local"_compute_bond_local.html - theta and energy of each angle
 "angmom/chunk"_compute_angmom_chunk.html - angular momentum for each chunk
 "body/local"_compute_body_local.html - attributes of body sub-particles
@@ -191,6 +192,7 @@ section of "this page"_Section_commands.html#cmd_5.
 "erotate/sphere"_compute_erotate_sphere.html - rotational energy of spherical particles
 "erotate/sphere/atom"_compute_erotate_sphere.html - rotational energy for each spherical particle
 "event/displace"_compute_event_displace.html - detect event on atom displacement
+"fragment/atom"_compute_cluster_atom.html - fragment ID for each atom
 "group/group"_compute_group_group.html - energy/force between two groups of atoms
 "gyration"_compute_gyration.html - radius of gyration of group of atoms
 "gyration/chunk"_compute_gyration_chunk.html - radius of gyration for each chunk

doc/src/compute_pressure_uef.txt

@@ -0,0 +1,61 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+compute pressure/uef command :h3
+
+[Syntax:]
+
+compute ID group-ID pressure/uef temp-ID keyword ... :pre
+
+ID, group-ID are documented in "compute"_compute.html command
+pressure/uef = style name of this compute command
+temp-ID = ID of compute that calculates temperature, can be NULL if not needed
+zero or more keywords may be appended
+keyword = {ke} or {pair} or {bond} or {angle} or {dihedral} or {improper} or {kspace} or {fix} or {virial} :ul
+
+[Examples:]
+
+compute 1 all pressure/uef my_temp_uef
+compute 2 all pressure/uef my_temp_uef virial :pre
+
+[Description:]
+
+This command is used to compute the pressure tensor in  
+the reference frame of the applied flow field when
+"fix nvt/uef"_fix_nh_uef.html" or 
+"fix npt/uef"_fix_nh_uef.html" is used. 
+It is not necessary to use this command to compute the scalar
+value of the pressure. A "compute pressure"_compute_pressure.html
+may be used for that purpose.
+
+The keywords and output information are documented in 
+"compute_pressure"_compute_pressure.html.
+
+[Restrictions:]
+
+This fix is part of the USER-UEF package. It is only enabled if
+LAMMPS was built with that package. See the
+"Making LAMMPS"_Section_start.html#start_3 section for more info.
+
+This command can only be used when "fix nvt/uef"_fix_nh_uef.html
+or "fix npt/uef"_fix_nh_uef.html is active.
+
+The kinetic contribution to the pressure tensor
+will be accurate only when 
+the compute specificed by {temp-ID} is a 
+"compute temp/uef"_compute_temp_uef.html.
+
+[Related commands:]
+
+"compute pressure"_compute_pressure.html,
+"fix nvt/uef"_fix_nh_uef.html,
+"compute temp/uef"_compute_temp_uef.html
+
+[Default:] none
+
+

doc/src/compute_temp_uef.txt

@@ -0,0 +1,52 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+compute temp/uef command :h3
+
+[Syntax:]
+
+compute ID group-ID temp/uef :pre
+
+ID, group-ID are documented in "compute"_compute.html command
+temp/uef = style name of this compute command :ul
+
+[Examples:]
+
+compute 1 all temp/uef 
+compute 2 sel temp/uef :pre
+
+[Description:]
+
+This command is used to compute the kinetic energy tensor in 
+the reference frame of the applied flow field when
+"fix nvt/uef"_fix_nh_uef.html" or
+"fix npt/uef"_fix_nh_uef.html" is used.
+It is not necessary to use this command to compute the scalar
+value of the temperature. A "compute temp"_compute_temp.html 
+may be used for that purpose.
+
+Output information for this command can be found in the
+documentation for "compute temp"_compute_temp.html.
+
+[Restrictions:]
+
+This fix is part of the USER-UEF package. It is only enabled if 
+LAMMPS was built with that package. See the 
+"Making LAMMPS"_Section_start.html#start_3 section for more info.
+
+This command can only be used when "fix nvt/uef"_fix_nh_uef.html 
+or "fix npt/uef"_fix_nh_uef.html is active.
+
+[Related commands:]
+
+"compute temp"_compute_temp.html,
+"fix nvt/uef"_fix_nh_uef.html,
+"compute pressure/uef"_compute_pressure_uef.html
+
+
+[Default:] none

doc/src/computes.txt

@@ -65,6 +65,7 @@ Computes :h1
    compute_pe_atom
    compute_plasticity_atom
    compute_pressure
+   compute_pressure_uef
    compute_property_atom
    compute_property_chunk
    compute_property_local
@@ -114,6 +115,7 @@ Computes :h1
    compute_temp_region_eff
    compute_temp_rotate
    compute_temp_sphere
+   compute_temp_uef
    compute_ti
    compute_torque_chunk
    compute_vacf

doc/src/dihedral_fourier.txt

@@ -7,6 +7,7 @@
 :line
 
 dihedral_style fourier command :h3
+dihedral_style fourier/intel command :h3
 dihedral_style fourier/omp command :h3
 
 [Syntax:]

doc/src/dump_cfg_uef.txt

@@ -0,0 +1,53 @@
+ "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+dump cfg/uef command :h3
+
+[Syntax:]
+
+dump ID group-ID cfg/uef N file mass type xs ys zs args :pre
+
+ID = user-assigned name for the dump :ulb,l
+group-ID = ID of the group of atoms to be dumped :l
+N = dump every this many timesteps :l
+file = name of file to write dump info to :l
+args = same as args for "dump custom"_dump.html :pre
+
+:ule
+
+[Examples:]
+
+dump 1 all cfg/uef 10 dump.*.cfg mass type xs ys zs
+dump 2 all cfg/uef 100 dump.*.cfg mass type xs ys zs id c_stress :pre
+
+[Description:]
+
+This command is used to dump atomic coordinates in the
+reference frame of the applied flow field when 
+"fix nvt/uef"_fix_nh_uef.html or
+"fix npt/uef"_fix_nh_uef.html or is used. Only the atomic 
+coordinates and frame-invariant scalar quantities 
+will be in the flow frame. If velocities are selected
+as output, for example, they will not be in the same
+reference frame as the atomic positions.
+
+[Restrictions:]
+
+This fix is part of the USER-UEF package. It is only enabled if
+LAMMPS was built with that package. See the
+"Making LAMMPS"_Section_start.html#start_3 section for more info.
+
+This command can only be used when "fix nvt/uef"_fix_nh_uef.html
+or "fix npt/uef"_fix_nh_uef.html is active.
+
+[Related commands:]
+
+"dump"_dump.html,
+"fix nvt/uef"_fix_nh_uef.html
+
+[Default:] none

doc/src/dump_modify.txt

@@ -15,8 +15,9 @@ dump_modify dump-ID keyword values ... :pre
 dump-ID = ID of dump to modify :ulb,l
 one or more keyword/value pairs may be appended :l
 these keywords apply to various dump styles :l
-keyword = {append} or {buffer} or {element} or {every} or {fileper} or {first} or {flush} or {format} or {image} or {label} or {nfile} or {pad} or {precision} or {region} or {scale} or {sort} or {thresh} or {unwrap} :l
-  {append} arg = {yes} or {no} or {at} N
+keyword = {append} or {at} or {buffer} or {element} or {every} or {fileper} or {first} or {flush} or {format} or {image} or {label} or {nfile} or {pad} or {precision} or {region} or {scale} or {sort} or {thresh} or {unwrap} :l
+  {append} arg = {yes} or {no}
+  {at} arg = N
     N = index of frame written upon first dump
   {buffer} arg = {yes} or {no}
   {element} args = E1 E2 ... EN, where N = # of atom types
@@ -141,13 +142,18 @@ and {dcd}.  It also applies only to text output files, not to binary
 or gzipped or image/movie files.  If specified as {yes}, then dump
 snapshots are appended to the end of an existing dump file.  If
 specified as {no}, then a new dump file will be created which will
-overwrite an existing file with the same name.  If the {at} option is present
-({netcdf} only), then the frame to append to can be specified.  Negative values
-are counted from the end of the file.  This keyword can only take effect if the
-dump_modify command is used after the "dump"_dump.html command, but before the
-first command that causes dump snapshots to be output, e.g. a "run"_run.html or
-"minimize"_minimize.html command.  Once the dump file has been opened, this
-keyword has no further effect.
+overwrite an existing file with the same name.
+
+:line
+
+The {at} keyword only applies to the {netcdf} dump style.  It can only
+be used if the {append yes} keyword is also used.  The {N} argument is
+the index of which frame to append to.  A negative value can be
+specified for {N}, which means a frame counted from the end of the
+file.  The {at} keyword can only be used if the dump_modify command is
+before the first command that causes dump snapshots to be output,
+e.g. a "run"_run.html or "minimize"_minimize.html command.  Once the
+dump file has been opened, this keyword has no further effect.
 
 :line
 

doc/src/dump_netcdf.txt

@@ -25,7 +25,8 @@ args = list of atom attributes, same as for "dump_style custom"_dump.html :l,ule
 
 dump 1 all netcdf 100 traj.nc type x y z vx vy vz
 dump_modify 1 append yes at -1 thermo yes
-dump 1 all netcdf/mpiio 1000 traj.nc id type x y z :pre
+dump 1 all netcdf/mpiio 1000 traj.nc id type x y z
+dump 1 all netcdf 1000 traj.*.nc id type x y z :pre
 
 [Description:]
 
@@ -73,4 +74,3 @@ section for more info.
 [Related commands:]
 
 "dump"_dump.html, "dump_modify"_dump_modify.html, "undump"_undump.html
-

doc/src/fix.txt

@@ -193,6 +193,7 @@ of "this page"_Section_commands.html#cmd_5.
 "halt"_fix_halt.html - terminate a dynamics run or minimization
 "heat"_fix_heat.html - add/subtract momentum-conserving heat
 "indent"_fix_indent.html - impose force due to an indenter
+"latte"_fix_latte.html - wrapper on LATTE density-functional tight-binding code
 "langevin"_fix_langevin.html - Langevin temperature control
 "lineforce"_fix_lineforce.html - constrain atoms to move in a line
 "momentum"_fix_momentum.html - zero the linear and/or angular momentum of a group of atoms

doc/src/fix_addforce.txt

@@ -139,6 +139,11 @@ forces added by this fix in a consistent manner.  I.e. there is a
 decrease in potential energy when atoms move in the direction of the
 added force.
 
+The "fix_modify"_fix_modify.html {virial} option is supported by this
+fix to add the contribution due to the added forces on atoms to the
+system's virial as part of "thermodynamic output"_thermo_style.html.
+The default is {virial no}
+
 The "fix_modify"_fix_modify.html {respa} option is supported by this
 fix. This allows to set at which level of the "r-RESPA"_run_style.html
 integrator the fix is adding its forces. Default is the outermost

doc/src/fix_cmap.txt

@@ -97,6 +97,11 @@ The "fix_modify"_fix_modify.html {energy} option is supported by this
 fix to add the potential "energy" of the CMAP interactions system's
 potential energy as part of "thermodynamic output"_thermo_style.html.
 
+The "fix_modify"_fix_modify.html {virial} option is supported by this
+fix to add the contribution due to the interaction between atoms to
+the system's virial as part of "thermodynamic output"_thermo_style.html.
+The default is {virial yes}
+
 This fix computes a global scalar which can be accessed by various
 "output commands"_Section_howto.html#howto_15.  The scalar is the
 potential energy discussed above.  The scalar value calculated by this

doc/src/fix_deform.txt

@@ -86,11 +86,16 @@ Change the volume and/or shape of the simulation box during a dynamics
 run.  Orthogonal simulation boxes have 3 adjustable parameters
 (x,y,z).  Triclinic (non-orthogonal) simulation boxes have 6
 adjustable parameters (x,y,z,xy,xz,yz).  Any or all of them can be
-adjusted independently and simultaneously by this command.  This fix
-can be used to perform non-equilibrium MD (NEMD) simulations of a
-continuously strained system.  See the "fix
+adjusted independently and simultaneously by this command.  
+
+This fix can be used to perform non-equilibrium MD (NEMD) simulations
+of a continuously strained system.  See the "fix
 nvt/sllod"_fix_nvt_sllod.html and "compute
-temp/deform"_compute_temp_deform.html commands for more details.
+temp/deform"_compute_temp_deform.html commands for more details.  Note
+that simulation of a continuously extended system (extensional flow)
+can be modeled using the "USER-UEF
+package"_Section_packages.html#USER-UEF and its "fix
+commands"_fix_nh_uef.html.
 
 For the {x}, {y}, {z} parameters, the associated dimension cannot be
 shrink-wrapped.  For the {xy}, {yz}, {xz} parameters, the associated

doc/src/fix_dpd_energy.txt

@@ -7,6 +7,7 @@
 :line
 
 fix dpd/energy command :h3
+fix dpd/energy/kk command :h3
 
 [Syntax:]
 
@@ -46,6 +47,29 @@ examples/USER/dpd directory.
 
 :line
 
+Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in "Section 5"_Section_accelerate.html
+of the manual.  The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the "-suffix command-line
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
+use the "suffix"_suffix.html command in your input script.
+
+See "Section 5"_Section_accelerate.html of the manual for
+more instructions on how to use the accelerated styles effectively.
+
+:line
+
 [Restrictions:]
 
 This command is part of the USER-DPD package.  It is only enabled if

doc/src/fix_efield.txt

@@ -124,6 +124,11 @@ can include the forces added by this fix in a consistent manner.
 I.e. there is a decrease in potential energy when atoms move in the
 direction of the added force due to the electric field.
 
+The "fix_modify"_fix_modify.html {virial} option is supported by this
+fix to add the contribution due to the added forces on atoms to the
+system's virial as part of "thermodynamic output"_thermo_style.html.
+The default is {virial no}
+
 The "fix_modify"_fix_modify.html {respa} option is supported by this
 fix. This allows to set at which level of the "r-RESPA"_run_style.html
 integrator the fix adding its forces. Default is the outermost level.

doc/src/fix_eos_table_rx.txt

@@ -7,6 +7,7 @@
 :line
 
 fix eos/table/rx command :h3
+fix eos/table/rx/kk command :h3
 
 [Syntax:]
 
@@ -152,6 +153,29 @@ no      0.93 0.00 0.000 -1.76 :pre
 
 :line
 
+Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in "Section 5"_Section_accelerate.html
+of the manual.  The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the "-suffix command-line
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
+use the "suffix"_suffix.html command in your input script.
+
+See "Section 5"_Section_accelerate.html of the manual for
+more instructions on how to use the accelerated styles effectively.
+
+:line
+
 [Restrictions:]
 
 This command is part of the USER-DPD package.  It is only enabled if

doc/src/fix_external.txt

@@ -131,6 +131,11 @@ forces added by this fix in a consistent manner.  I.e. there is a
 decrease in potential energy when atoms move in the direction of the
 added force.
 
+The "fix_modify"_fix_modify.html {virial} option is supported by this
+fix to add the contribution due to the interactions computed by the
+external program to the system's virial as part of "thermodynamic
+output"_thermo_style.html. The default is {virial yes}
+
 This fix computes a global scalar which can be accessed by various
 "output commands"_Section_howto.html#howto_15.  The scalar is the
 potential energy discussed above.  The scalar stored by this fix

doc/src/fix_latte.txt

@@ -0,0 +1,210 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+fix latte command :h3
+
+[Syntax:]
+
+fix ID group-ID latte peID :pre
+
+ID, group-ID are documented in "fix"_fix.html command
+latte = style name of this fix command
+peID = NULL or ID of compute used to calculate per-atom energy :ul
+
+[Examples:]
+
+fix dftb all latte NULL :pre
+
+[Description:]
+
+This fix style is a wrapper on the self-consistent charge transfer
+density functional based tight binding (DFTB) code LATTE. If you
+download and build LATTE, it can be called as a library by LAMMPS via
+this fix to run dynamics or perform energy minimization using DFTB
+forces and energies computed by LATTE.
+
+LATTE is principally developed and supported by Marc Cawkwell and
+co-workers at Los Alamos National Laboratory (LANL).  See the full
+list of contributors in the src/LATTE/README file.
+
+To use this fix, the LATTE program needs to be compiled as a library
+and linked with LAMMPS.  LATTE can be downloaded (or cloned) from
+"https://github.com/lanl/LATTE"_https://github.com/lanl/LATTE.
+Instructions on how to download and build LATTE on your system can be
+found in the lib/latte/README.  Note that you can also use the "make
+lib-latte" command from the LAMMPS src directory to automate this
+process.
+
+Once LAMMPS is built with the LATTE package, you can run the example
+input scripts for molecular dynamics or energy minimization that are
+found in examples/latte.
+
+A step-by-step tutorial can be follwed at: "LAMMPS-LATTE
+tutorial"_https://github.com/lanl/LATTE/wiki/Using-LATTE-through-LAMMPS
+
+The {peID} argument is not yet supported by fix latte, so it must be
+specified as NULL.  Eventually it will be used to enable LAMMPS to
+calculate a Coulomb potential as an alternative to LATTE performing
+the calculation.
+
+:line
+
+LATTE is a code for performing self-consistent charge transfer
+tight-binding (SC-TB) calculations of total energies and the forces
+acting on atoms in molecules and solids. This tight-binding method is
+becoming more and more popular and widely used in chemistry,
+biochemistry, material science, etc.  
+
+The SC-TB formalism is derived from an expansion of the Kohn-Sham
+density functional to second order in charge fluctuations about a
+reference charge of overlapping atom-centered densities and bond
+integrals are parameterized using a Slater-Koster tight-binding
+approach. This procedure, which usually is referred to as the DFTB
+method has been described in detail by ("Elstner"_#Elstner) and
+("Finnis"_#Finnis2) and coworkers. 
+
+The work of the LATTE developers follows that of Elstner closely with
+respect to the physical model.  However, the development of LATTE is
+geared principally toward large-scale, long duration, microcanonical
+quantum-based Born-Oppenheimer molecular dynamics (QMD) simulations.
+One of the main bottlenecks of an electronic structure calculation is
+the solution of the generalized eigenvalue problem which scales with
+the cube of the system size O(N^3).
+
+The Theoretical and Computer sciences divisions at Los Alamos National
+Laboratory have accumulated large experience addressing this issue by
+calculating the density matrix directly instead of using
+diagonalization. We typically use a recursive sparse Fermi-operator
+expansion using second-order spectral projection functions
+(SP2-algorithm), which was introduced by Niklasson in 2002
+("Niklasson2002"_#Niklasson2002), ("Rubensson"_#Rubensson),
+("Mniszewski"_#Mniszewski).  When the matrices involved in the
+recursive expansion are sufficiently sparse, the calculation of the
+density matrix scales linearly as a function of the system size O(N).
+
+Another important feature is the extended Lagrangian framework for
+Born-Oppenheimer molecular dynamics (XL-BOMD)
+("Niklasson2008"_#Niklasson2008) ("Niklasson2014"_#Niklasson2014),
+("Niklasson2017"_#Niklasson2017) that allows for a drastic reduction
+or even a complete removal of the iterative self-consistent field
+optimization.  Often only a single density matrix calculation per
+molecular dynamics time step is required, yet total energy stability
+is well maintained.  The SP2 and XL-BOMD techniques enables stable
+linear scaling MD simulations with a very small computational
+overhead.  This opens a number of opportunities in many different
+areas of chemistry and materials science, as we now can simulate
+larger system sizes and longer time scales
+("Cawkwell2012"_#Cawkwell2012), ("Negre2016"_#Negre2016).
+
+:line
+
+[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 {energy} option is supported by this
+fix to add the potential energy computed by LATTE to the system's
+potential energy as part of "thermodynamic output"_thermo_style.html.
+
+The "fix_modify"_fix_modify.html {virial} option is supported by this
+fix to add the LATTE DFTB contribution to the system's virial as part
+of "thermodynamic output"_thermo_style.html.  The default is {virial
+yes}
+
+This fix computes a global scalar which can be accessed by various
+"output commands"_Section_howto.html#howto_15.  The scalar is the
+potential energy discussed above.  The scalar value calculated by this
+fix is "extensive".
+
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command.
+
+The DFTB forces computed by LATTE via this fix are imposed during an
+energy minimization, invoked by the "minimize"_minimize.html command.
+
+NOTE: If you want the potential energy associated with the DFTB
+forces to be included in the total potential energy of the system (the
+quantity being minimized), you MUST enable the
+"fix_modify"_fix_modify.html {energy} option for this fix.
+
+[Restrictions:]
+
+This fix is part of the LATTE package.  It is only enabled if LAMMPS
+was built with that package.  See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
+
+You must use metal units, as set by the "units"_units command to use
+this fix.
+
+LATTE does not currently compute per-atom energy or per-atom virial
+contributions.  So they will not show up as part of the calculations
+performed by the "compute pe/atom"_compute_pe_atom.html or "compute
+stress/atom"_compute_stress_atom.html commands.
+
+Currently, LAMMPS must be run in serial or as a single MPI task, to
+use this fix.  This is typically not a bottleneck, since LATTE will be
+doing 99% or more of the work to compute quantum-accurate forces.
+
+NOTE: NEB calculations can be done using this fix using multiple
+replicas and running LAMMPS in parallel.  However, each replica must
+be run on a single MPI task.  For details, see the "neb"_neb.html
+command and -partition command-line explained in "Section
+2.6"_Section_start.html#start_6 of the manual.
+
+[Related commands:] none
+
+[Default:] none
+
+:line
+
+:link(Elstner)
+[(Elstner)] M. Elstner, D. Poresag, G. Jungnickel, J. Elsner,
+M. Haugk, T. Frauenheim, S. Suhai, and G. Seifert, Phys. Rev. B, 58,
+7260 (1998).
+
+:link(Elstner1)
+[(Elstner)] M. Elstner, D. Poresag, G. Jungnickel, J. Elsner,
+M. Haugk, T. Frauenheim, S. Suhai, and G. Seifert, Phys. Rev. B, 58,
+7260 (1998).
+
+:link(Finnis2)
+[(Finnis)] M. W. Finnis, A. T. Paxton, M. Methfessel, and M. van
+Schilfgarde, Phys. Rev. Lett., 81, 5149 (1998).
+
+:link(Mniszewski)
+[(Mniszewski)] S. M. Mniszewski, M. J. Cawkwell, M. E. Wall,
+J. Mohd-Yusof, N. Bock, T. C.  Germann, and A. M. N. Niklasson,
+J. Chem. Theory Comput., 11, 4644 (2015).
+
+:link(Niklasson2002)
+[(Niklasson2002)] A. M. N. Niklasson, Phys. Rev. B, 66, 155115 (2002).
+
+:link(Rubensson)
+[(Rubensson)] E. H. Rubensson, A. M. N. Niklasson, SIAM
+J. Sci. Comput. 36 (2), 147-170, (2014).
+
+:link(Niklasson2008)
+[(Niklasson2008)] A. M. N. Niklasson, Phys. Rev. Lett., 100, 123004
+(2008).
+
+:link(Niklasson2014)
+[(Niklasson2014)] A. M. N. Niklasson and M. Cawkwell, J. Chem. Phys.,
+141, 164123, (2014).
+
+:link(Niklasson2017)
+[(Niklasson2017)] A. M. N. Niklasson, J. Chem. Phys., 147, 054103 (2017).
+
+:link(Cawkwell2012)
+[(Cawkwell2012)] A. M. N. Niklasson, M. J. Cawkwell, Phys. Rev. B, 86
+(17), 174308 (2012).
+
+:link(Negre2016)
+[(Negre2016)] C. F. A. Negre, S. M. Mniszewski, M. J. Cawkwell,
+N. Bock, M. E. Wall, and A. M. N. Niklasson, J. Chem. Theory Comp.,
+12, 3063 (2016).

doc/src/fix_modify.txt

@@ -14,10 +14,11 @@ fix_modify fix-ID keyword value ... :pre
 
 fix-ID = ID of the fix to modify :ulb,l
 one or more keyword/value pairs may be appended :l
-keyword = {temp} or {press} or {energy} or {respa} or {dynamic/dof} :l
+keyword = {temp} or {press} or {energy} or {virial} or {respa} or {dynamic/dof} :l
   {temp} value = compute ID that calculates a temperature
   {press} value = compute ID that calculates a pressure
   {energy} value = {yes} or {no}
+  {virial} value = {yes} or {no}
   {respa} value = {1} to {max respa level} or {0} (for outermost level)
   {dynamic/dof} value = {yes} or {no}
     yes/no = do or do not recompute the number of degrees of freedom (DOF) contributing to the temperature :pre
@@ -52,11 +53,10 @@ define their own compute by default, as described in their
 documentation.  Thus this option allows the user to override the
 default method for computing P.
 
-For fixes that calculate a contribution to the potential energy of the
-system, the {energy} keyword will include that contribution in
-thermodynamic output of potential energy.  This is because the {energy
-yes} setting must be specified to include the fix's global or per-atom
-energy in the calculation performed by the "compute
+The {energy} keyword can be used with fixes that support it.
+{energy yes} adds a contribution to the potential energy of the
+system. The fix's global and per-atom
+energy is included in the calculation performed by the "compute
 pe"_compute_pe.html or "compute pe/atom"_compute_pe_atom.html
 commands.  See the "thermo_style"_thermo_style.html command for info
 on how potential energy is output.  For fixes that tally a global
@@ -69,6 +69,25 @@ are using it when performing an "energy minimization"_minimize.html
 and if you want the energy and forces it produces to be part of the
 optimization criteria.
 
+The {virial} keyword can be used with fixes that support it.
+{virial yes} adds a contribution to the virial of the
+system. The fix's global and per-atom
+virial is included in the calculation performed by the "compute
+pressure"_compute_pressure.html or
+"compute stress/atom"_compute_stress_atom.html
+commands.  See the "thermo_style"_thermo_style.html command for info
+on how pressure is output. 
+
+NOTE: You must specify the {virial yes} setting for a fix if you
+are doing "box relaxation"_fix_box_relax.html and
+if you want virial contribution of the fix to be part of the
+relaxation criteria, although this seems unlikely.
+
+NOTE: This option is only supported by fixes that explicitly say
+so. For some of these (e.g. the
+"fix shake"_fix_shake.html command) the default setting is
+{virial yes}, for others it is {virial no}.
+
 For fixes that set or modify forces, it may be possible to select at
 which "r-RESPA"_run_style.html level the fix operates via the {respa}
 keyword. The RESPA level at which the fix is active can be selected.
@@ -111,4 +130,4 @@ pressure"_compute_pressure.html, "thermo_style"_thermo_style.html
 [Default:]
 
 The option defaults are temp = ID defined by fix, press = ID defined
-by fix, energy = no, respa = 0.
+by fix, energy = no, virial = different for each fix style, respa = 0.

doc/src/fix_neb.txt

@@ -93,7 +93,7 @@ intermediate replica with the previous and the next image:
 
 Fnudge_parallel = {Kspring} * (|Ri+1 - Ri| - |Ri - Ri-1|) :pre
 
-Note that in this case the specified {Kspring) is in force/distance
+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
@@ -105,7 +105,7 @@ where RD is the "reaction coordinate" see "neb"_neb.html section, and
 RDideal is the ideal RD for which all the images are equally spaced.
 I.e. RDideal = (I-1)*meanDist when the climbing replica is off, where
 I is the replica number).  The meanDist is the average distance
-between replicas.  Note that in this case the specified {Kspring) is
+between replicas.  Note that in this case the specified {Kspring} is
 in force units.
 
 Note that the {ideal} form of nudging can often be more effective at

doc/src/fix_nh.txt

@@ -393,32 +393,36 @@ thermostatting and barostatting.
 :line
 
 These fixes compute a temperature and pressure each timestep.  To do
-this, the fix creates its own computes of style "temp" and "pressure",
-as if one of these two sets of commands had been issued:
+this, the thermostat and barostat fixes create their own computes of
+style "temp" and "pressure", as if one of these sets of commands had
+been issued:
 
+For fix nvt:
 compute fix-ID_temp group-ID temp
-compute fix-ID_press group-ID pressure fix-ID_temp :pre
 
+For fix npt and fix nph:
 compute fix-ID_temp all temp
 compute fix-ID_press all pressure fix-ID_temp :pre
 
-See the "compute temp"_compute_temp.html and "compute
-pressure"_compute_pressure.html commands for details.  Note that the
-IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID
-+ underscore + "press".  For fix nvt, the group for the new computes
-is the same as the fix group.  For fix nph and fix npt, the group for
-the new computes is "all" since pressure is computed for the entire
-system.
+For fix nvt, the group for the new temperature compute is the same as
+the fix group.  For fix npt and fix nph, the group for both the new
+temperature and pressure compute is "all" since pressure is computed
+for the entire system.  In the case of fix nph, the temperature
+compute is not used for thermostatting, but just for a kinetic-energy
+contribution to the pressure.  See the "compute
+temp"_compute_temp.html and "compute pressure"_compute_pressure.html
+commands for details.  Note that the IDs of the new computes are the
+fix-ID + underscore + "temp" or fix_ID + underscore + "press".
 
 Note that these are NOT the computes used by thermodynamic output (see
 the "thermo_style"_thermo_style.html command) with ID = {thermo_temp}
-and {thermo_press}.  This means you can change the attributes of this
+and {thermo_press}.  This means you can change the attributes of these
 fix's temperature or pressure via the
-"compute_modify"_compute_modify.html command or print this temperature
-or pressure during thermodynamic output via the "thermo_style
-custom"_thermo_style.html command using the appropriate compute-ID.
-It also means that changing attributes of {thermo_temp} or
-{thermo_press} will have no effect on this fix.
+"compute_modify"_compute_modify.html command.  Or you can print this
+temperature or pressure during thermodynamic output via the
+"thermo_style custom"_thermo_style.html command using the appropriate
+compute-ID.  It also means that changing attributes of {thermo_temp}
+or {thermo_press} will have no effect on this fix.
 
 Like other fixes that perform thermostatting, fix nvt and fix npt can
 be used with "compute commands"_compute.html that calculate a

doc/src/fix_nh_uef.txt

@@ -0,0 +1,228 @@
+<"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+fix nvt/uef command :h3
+fix npt/uef command :h3
+
+[Syntax:]
+
+fix ID group-ID style_name erate edot_x edot_y temp Tstart Tstop Tdamp keyword value ... :pre
+
+ID, group-ID are documented in "fix"_fix.html command :ulb,l
+style_name = {nvt/uef} or {npt/uef} :l
+{Tstart}, {Tstop}, and {Tdamp} are documented in the "fix npt"_fix_nh.html command :l
+{edot_x} and {edot_y} are the strain rates in the x and y directions (1/(time units)) :l
+one or more keyword/value pairs may be appended :l
+keyword = {ext} or {strain} or {iso} or {x} or {y} or {z} or {tchain} or {pchain} or {tloop} or {ploop} or {mtk}
+  {ext} value = {x} or {y} or {z} or {xy} or {yz} or {xz} = external dimensions
+    sets the external dimensions used to calculate the scalar pressure
+  {strain} values = e_x e_y = initial strain
+    usually not needed, but may be needed to resume a run with a data file.
+  {iso}, {x}, {y}, {z}, {tchain}, {pchain}, {tloop}, {ploop}, {mtk} keywords
+    documented by the "fix npt"_fix_nh.html command :pre
+:ule
+
+[Examples:]
+
+fix uniax_nvt all nvt/uef temp 400 400 100 erate 0.00001 -0.000005
+fix biax_nvt all nvt/uef temp 400 400 100 erate 0.000005 0.000005
+fix uniax_npt all npt/uef temp 400 400 300 iso 1 1 3000 erate 0.00001 -0.000005 ext yz
+fix biax_npt all npt/uef temp 400 400 100 erate -0.00001 0.000005 x 1 1 3000 :pre
+
+[Description:]
+
+This fix can be used to simulate non-equilibrium molecular dynamics
+(NEMD) under diagonal flow fields, including uniaxial and biaxial
+flow.  Simulations under continuous extensional flow may be carried
+out for an indefinite amount of time.  It is an implementation of the
+boundary conditions from "(Dobson)"_#Dobson, and also uses numerical
+lattice reduction as was proposed by "(Hunt)"_#Hunt. The lattice
+reduction algorithm is from "(Semaev)"_Semaev. The fix is intended for
+simulations of homogeneous flows, and integrates the SLLOD equations
+of motion, originally proposed by Hoover and Ladd (see "(Evans and
+Morriss)"_#Sllod).  Additional detail about this implementation can be
+found in "(Nicholson and Rutledge)"_#Nicholson.
+
+Note that NEMD simulations of a continuously strained system can be
+performed using the "fix deform"_fix_deform.html, "fix
+nvt/sllod"_fix_nvt_sllod.html, and "compute
+temp/deform"_compute_temp_deform.html commands.
+
+The applied flow field is set by the {eps} keyword. The values
+{edot_x} and {edot_y} correspond to the strain rates in the xx and yy
+directions.  It is implicitly assumed that the flow field is
+traceless, and therefore the strain rate in the zz direction is eqal
+to -({edot_x} + {edot_y}).
+
+NOTE: Due to an instability in the SLLOD equations under extension,
+"fix momentum"_fix_momentum.html should be used to regularly reset the
+linear momentum.
+
+The boundary conditions require a simulation box that does not have a
+consistent alignment relative to the applied flow field. Since LAMMPS
+utilizes an upper-triangular simulation box, it is not possible to
+express the evolving simulation box in the same coordinate system as
+the flow field.  This fix keeps track of two coordinate systems: the
+flow frame, and the upper triangular LAMMPS frame. The coordinate
+systems are related to each other through the QR decomposition, as is
+illustrated in the image below.
+
+:c,image(JPG/uef_frames.jpg)
+
+During most molecular dynamics operations, the system is represented
+in the LAMMPS frame. Only when the positions and velocities are
+updated is the system rotated to the flow frame, and it is rotated
+back to the LAMMPS frame immediately afterwards. For this reason, all
+vector-valued quantities (except for the tensors from
+"compute_pressure/uef"_compute_pressure_uef.html and
+"compute_temp/uef"_compute_temp_uef.html) will be computed in the
+LAMMPS frame. Rotationally invariant scalar quantities like the
+temperature and hydrostatic pressure are frame-invariant and will be
+computed correctly. Additionally, the system is in the LAMMPS frame
+during all of the output steps, and therefore trajectory files made
+using the dump command will be in the LAMMPS frame unless the
+"dump_cfg/uef"_dump_cfg_uef.html command is used.
+
+:line
+
+Temperature control is achieved with the default Nose-Hoover style
+thermostat documented in "fix npt"_fix_nh.html. When this fix is
+active, only the peculiar velocity of each atom is stored, defined as
+the velocity relative to the streaming velocity. This is in contrast
+to "fix nvt/sllod"_fix_nvt_sllod.html, which uses a lab-frame
+velocity, and removes the contribution from the streaming velocity in
+order to compute the temperature.
+
+Pressure control is achieved using the default Nose-Hoover barostat
+documented in "fix npt"_fix_nh.html. There are two ways to control the
+pressure using this fix. The first method involves using the {ext}
+keyword along with the {iso} pressure style. With this method, the
+pressure is controlled by scaling the simulation box isotropically to
+achieve the average pressure only in the directions specified by
+{ext}.  For example, if the {ext} value is set to {xy}, the average
+pressure (Pxx+Pyy)/2 will be controlled.
+
+This example command will control the total hydrostatic pressure under
+uniaxial tension:
+
+fix f1 all npt/uef temp 0.7 0.7 0.5 iso 1 1 5 erate -0.5 -0.5 ext xyz :pre
+
+This example command will control the average stress in compression
+directions, which would typically correspond to free surfaces under
+drawing with uniaxial tension:
+
+fix f2 all npt/uef temp 0.7 0.7 0.5 iso 1 1 5 erate -0.5 -0.5 ext xy :pre
+
+The second method for pressure control involves setting the normal
+stresses using the {x}, {y} , and/or {z} keywords. When using this
+method, the same pressure must be specified via {Pstart} and {Pstop}
+for all dimensions controlled. Any choice of pressure conditions that
+would cause LAMMPS to compute a deviatoric stress are not permissible
+and will result in an error. Additionally, all dimensions with
+controlled stress must have the same applied strain rate. The {ext}
+keyword must be set to the default value ({xyz}) when using this
+method.
+
+For example, the following commands will work:
+
+fix f3 all npt/uef temp 0.7 0.7 0.5 x 1 1 5 y 1 1 5 erate -0.5 -0.5
+fix f4 all npt/uef temp 0.7 0.7 0.5 z 1 1 5 erate 0.5 0.5 :pre
+
+The following commands will not work:
+
+fix f5 all npt/uef temp 0.7 0.7 0.5 x 1 1 5 z 1 1 5 erate -0.5 -0.5
+fix f6 all npt/uef temp 0.7 0.7 0.5 x 1 1 5 z 2 2 5 erate 0.5 0.5 :pre
+
+:line
+
+These fix computes a temperature and pressure each timestep.  To do
+this, it creates its own computes of style "temp/uef" and
+"pressure/uef", as if one of these two sets of commands had been
+issued:
+
+compute fix-ID_temp group-ID temp/uef
+compute fix-ID_press group-ID pressure/uef fix-ID_temp :pre
+
+compute fix-ID_temp all temp/uef
+compute fix-ID_press all pressure/uef fix-ID_temp :pre
+
+See the "compute temp/uef"_compute_temp_uef.html and "compute
+pressure/uef"_compute_pressure_uef.html commands for details.  Note
+that the IDs of the new computes are the fix-ID + underscore + "temp"
+or fix_ID + underscore + "press".
+
+[Restart, fix_modify, output, run start/stop, minimize info:]
+
+The fix writes the state of all the thermostat and barostat variables,
+as well as the cumulative strain applied, to "binary restart
+files"_restart.html.  See the "read_restart"_read_restart.html command
+for info on how to re-specify a fix in an input script that reads a
+restart file, so that the operation of the fix continues in an
+uninterrupted fashion.
+
+NOTE: It is not necessary to set the {strain} keyword when resuming a
+run from a restart file. Only for resuming from data files, which do
+not contain the cumulative applied strain, will this keyword be
+necessary.
+
+This fix can be used with the "fix_modify"_fix_modify.html {temp} and
+{press} options. The temperature and pressure computes used must be of
+type {temp/uef} and {pressure/uef}.
+
+This fix computes the same global scalar and vecor quantities as "fix
+npt"_fix_nh.html.
+
+The fix is not invoked during "energy minimization"_minimize.html.
+
+[Restrictions:]
+
+This fix is part of the USER-UEF package. It is only enabled if LAMMPS
+was built with that package. See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
+
+Due to requirements of the boundary conditions, when the {strain}
+keyword is set to zero (or unset), the initial simulation box must be
+cubic and have style triclinic. If the box is initially of type ortho,
+use "change_box"_change_box.html before invoking the fix.
+
+NOTE: When resuming from restart files, you may need to use "box tilt
+large"_box.html since lammps has internal criteria from lattice
+reduction that are not the same as the criteria in the numerical
+lattice reduction algorithm.
+
+[Related commands:]
+
+"fix nvt"_fix_nh.html, "fix nvt/sllod"_fix_nvt_sllod.html, "compute
+temp/uef"_compute_temp_uef.html, "compute
+pressure/uef"_compute_pressure_uef.html, "dump
+cfg/uef"_dump_cfg_uef.html
+
+[Default:]
+
+The default keyword values specific to this fix are exy = xyz, strain
+= 0 0.  The remaining defaults are the same as for {fix
+npt}_fix_nh.html except tchain = 1.  The reason for this change is
+given in "fix nvt/sllod"_fix_nvt_sllod.html.
+
+:line
+
+:link(Dobson)
+[(Dobson)] Dobson, J Chem Phys, 141, 184103 (2014).
+
+:link(Hunt)
+[(Hunt)] Hunt, Mol Simul, 42, 347 (2016).
+
+:link(Semaev)
+[(Semaev)] Semaev, Cryptography and Lattices, 181 (2001).
+
+:link(Sllod)
+[(Evans and Morriss)] Evans and Morriss, Phys Rev A, 30, 1528 (1984).
+
+:link(Nicholson)
+[(Nicholson and Rutledge)] Nicholson and Rutledge, J Chem Phys, 145,
+244903 (2016).

doc/src/fix_nve_dot.txt

@@ -44,7 +44,7 @@ A technical report with more information on this integrator can be found
 [Restrictions:]
 
 These pair styles can only be used if LAMMPS was built with the
-USER-CGDNA package and the MOLECULE and ASPHERE package.  See the "Making
+"USER-CGDNA"_#USER-CGDNA package and the MOLECULE and ASPHERE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.
 
 [Related commands:]

doc/src/fix_nve_dotc_langevin.txt

@@ -24,7 +24,8 @@ keyword = {angmom} :l
 
 [Examples:]
 
-fix 1 all nve/dotc/langevin 1.0 1.0 0.03 457145 angmom 10 :pre
+fix 1 all nve/dotc/langevin 1.0 1.0 0.03 457145 angmom 10 
+fix 1 all nve/dotc/langevin 0.1 0.1 78.9375 457145 angmom 10 :pre
 
 [Description:]
 
@@ -78,7 +79,9 @@ a Gaussian random number) for speed.
 :line
 
 {Tstart} and {Tstop} have to be constant values, i.e. they cannot
-be variables.
+be variables. If used together with the oxDNA force field for 
+coarse-grained simulation of DNA please note that T = 0.1 in oxDNA units
+corresponds to T = 300 K.  
 
 The {damp} parameter is specified in time units and determines how
 rapidly the temperature is relaxed.  For example, a value of 0.03
@@ -89,6 +92,10 @@ viscosity of the solvent, i.e. a small relaxation time implies a
 hi-viscosity solvent and vice versa.  See the discussion about gamma
 and viscosity in the documentation for the "fix
 viscous"_fix_viscous.html command for more details.
+Note that the value 78.9375 in the second example above corresponds 
+to a diffusion constant, which is about an order of magnitude larger 
+than realistic ones. This has been used to sample configurations faster
+in Brownian dynamics simulations. 
 
 The random # {seed} must be a positive integer. A Marsaglia random
 number generator is used.  Each processor uses the input seed to
@@ -115,12 +122,12 @@ A technical report with more information on this integrator can be found
 [Restrictions:]
 
 These pair styles can only be used if LAMMPS was built with the
-USER-CGDNA package and the MOLECULE and ASPHERE package.  See the "Making
+"USER-CGDNA"_#USER-CGDNA package and the MOLECULE and ASPHERE package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.
 
 [Related commands:]
 
-"fix nve"_fix_nve.html, "fix langevin"_fix_langevin.html, "fix nve/dot"_fix_nve_dot.html,
+"fix nve"_fix_nve.html, "fix langevin"_fix_langevin.html, "fix nve/dot"_fix_nve_dot.html, "bond_style oxdna/fene"_bond_oxdna.html, "bond_style oxdna2/fene"_bond_oxdna.html, "pair_style oxdna/excv"_pair_oxdna.html, "pair_style oxdna2/excv"_pair_oxdna2.html
 
 [Default:] none
 

doc/src/fix_rhok.txt

@@ -0,0 +1,56 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+fix rhok command :h3
+
+fix ID group-ID rhok nx ny nz K a :pre
+
+ID, group-ID are documented in "fix"_fix.html command
+nx, ny, nz = k-vektor of collective density field
+K = spring constant of bias potential
+a = anchor point of bias potential :ul
+
+[Examples:]
+
+fix bias all rhok 16 0 0 4.0 16.0
+fix 1 all npt temp 0.8 0.8 4.0 z 2.2 2.2 8.0
+# output of 4 values from fix rhok: U_bias rho_k_RE  rho_k_IM  |rho_k|
+thermo_style custom step temp pzz lz f_bias f_bias\[1\] f_bias\[2\] f_bias\[3\] :pre
+
+[Description:]
+
+The fix applies a force to atoms given by the potential
+
+:c,image(Eqs/fix_rhok.jpg)
+
+as described in "(Pedersen)"_#Pedersen.
+
+This field, which biases configurations with long-range order, can be
+used to study crystal-liquid interfaces and determine melting
+temperatures "(Pedersen)"_#Pedersen.
+
+An example of using the interface pinning method is located in the
+{examples/USER/misc/rhok} directory.
+
+[Restrictions:]
+
+This fix is part of the MISC package.  It is only enabled if LAMMPS
+was built with that package.  See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
+
+[Related commands:]
+
+"thermo_style"_thermo_style.html
+
+[Default:] none
+
+:line
+
+:link(Pedersen)
+[(Pedersen)] Pedersen, J. Chem. Phys., 139, 104102 (2013).
+

doc/src/fix_rigid.txt

@@ -26,6 +26,9 @@ style = {rigid} or {rigid/nve} or {rigid/nvt} or {rigid/npt} or {rigid/nph} or {
 bodystyle = {single} or {molecule} or {group} :l
   {single} args = none
   {molecule} args = none
+  {custom} args = {i_propname} or {v_varname}
+    i_propname = an integer property defined via fix property/atom
+    v_varname  = an atom-style or atomfile-style variable 
   {group} args = N groupID1 groupID2 ...
     N = # of groups
     groupID1, groupID2, ... = list of N group IDs :pre
@@ -80,6 +83,16 @@ fix 1 rods rigid/npt molecule temp 300.0 300.0 100.0 iso 0.5 0.5 10.0
 fix 1 particles rigid/npt molecule temp 1.0 1.0 5.0 x 0.5 0.5 1.0 z 0.5 0.5 1.0 couple xz
 fix 1 water rigid/nph molecule iso 0.5 0.5 1.0
 fix 1 particles rigid/npt/small molecule temp 1.0 1.0 1.0 iso 0.5 0.5 1.0 :pre
+
+variable bodyid atom 1.0*gmask(clump1)+2.0*gmask(clump2)+3.0*gmask(clump3)
+fix 1 clump rigid custom v_bodyid :pre
+
+variable bodyid atomfile bodies.txt
+fix 1 clump rigid custom v_bodyid :pre
+
+fix 0 all property/atom i_bodyid
+read_restart data.rigid fix 0 NULL Bodies
+fix 1 clump rigid/small custom i_bodyid :pre
 	
 [Description:]
 
@@ -100,7 +113,7 @@ of a biomolecule such as a protein.
 
 Example of small rigid bodies are patchy nanoparticles, such as those
 modeled in "this paper"_#Zhang1 by Sharon Glotzer's group, clumps of
-granular particles, lipid molecules consiting of one or more point
+granular particles, lipid molecules consisting of one or more point
 dipoles connected to other spheroids or ellipsoids, irregular
 particles built from line segments (2d) or triangles (3d), and
 coarse-grain models of nano or colloidal particles consisting of a
@@ -203,11 +216,11 @@ most one rigid body.  Which atoms are in which bodies can be defined
 via several options.
 
 NOTE: With the {rigid/small} styles, which require that {bodystyle} be
-specified as {molecule}, you can define a system that has no rigid
-bodies initially.  This is useful when you are using the {mol} keyword
-in conjunction with another fix that is adding rigid bodies on-the-fly
-as molecules, such as "fix deposit"_fix_deposit.html or "fix
-pour"_fix_pour.html.
+specified as {molecule} or {custom}, you can define a system that has
+no rigid bodies initially.  This is useful when you are using the {mol}
+keyword in conjunction with another fix that is adding rigid bodies
+on-the-fly as molecules, such as "fix deposit"_fix_deposit.html or
+"fix pour"_fix_pour.html.
 
 For bodystyle {single} the entire fix group of atoms is treated as one
 rigid body.  This option is only allowed for the {rigid} styles.
@@ -222,6 +235,15 @@ molecule ID = 0) surrounding rigid bodies, this may not be what you
 want.  Thus you should be careful to use a fix group that only
 includes atoms you want to be part of rigid bodies.
 
+Bodystyle {custom} is similar to bodystyle {molecule}, however some
+custom properties are used to group atoms into rigid bodies. The
+special case for molecule/body ID = 0 is not available. Possible
+custom properties are an integer property associated with atoms through
+"fix property/atom"_fix_property_atom.html or an atom style variable
+or an atomfile style variable. For the latter two, the variable value
+will be rounded to an integer and then rigid bodies defined from
+those values.
+
 For bodystyle {group}, each of the listed groups is treated as a
 separate rigid body.  Only atoms that are also in the fix group are
 included in each rigid body.  This option is only allowed for the
@@ -703,6 +725,11 @@ NVT, NPT, NPH rigid styles to add the energy change induced by the
 thermostatting to the system's potential energy as part of
 "thermodynamic output"_thermo_style.html.
 
+The "fix_modify"_fix_modify.html {virial} option is supported by this
+fix to add the contribution due to keeping the objects rigid to the
+system's virial as part of "thermodynamic output"_thermo_style.html.
+The default is {virial yes}
+
 The "fix_modify"_fix_modify.html {temp} and {press} options are
 supported by the 4 NPT and NPH rigid styles to change the computes
 used to calculate the instantaneous pressure tensor.  Note that the 2

doc/src/fix_rx.txt

@@ -7,6 +7,7 @@
 :line
 
 fix rx command :h3
+fix rx/kk command :h3
 
 [Syntax:]
 
@@ -182,6 +183,29 @@ read_data    data.dpd fix foo_SPECIES NULL Species
 
 :line
 
+Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in "Section 5"_Section_accelerate.html
+of the manual.  The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the "-suffix command-line
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
+use the "suffix"_suffix.html command in your input script.
+
+See "Section 5"_Section_accelerate.html of the manual for
+more instructions on how to use the accelerated styles effectively.
+
+:line
+
 [Restrictions:]
 
 This command is part of the USER-DPD package.  It is only enabled if

doc/src/fix_saed_vtk.txt

@@ -37,8 +37,8 @@ keyword = {file} or {ave} or {start} or {file} or {overwrite}:l
 compute 1 all saed 0.0251 Al O Kmax 1.70 Zone 0 0 1 dR_Ewald 0.01 c 0.5 0.5 0.5
 compute 2 all saed 0.0251 Ni Kmax 1.70 Zone 0 0 0 c 0.05 0.05 0.05 manual echo :pre
 
-fix saed/vtk 1 1 1 c_1 file Al2O3_001.saed
-fix saed/vtk 1 1 1 c_2 file Ni_000.saed :pre
+fix 1 all saed/vtk 1 1 1 c_1 file Al2O3_001.saed
+fix 2 all saed/vtk 1 1 1 c_2 file Ni_000.saed :pre
 
 [Description:]
 

doc/src/fix_shake.txt

@@ -186,6 +186,11 @@ to 1 and recompiling LAMMPS.
 
 [Restart, fix_modify, output, run start/stop, minimize info:]
 
+The "fix_modify"_fix_modify.html {virial} option is supported by this
+fix to add the contribution due to keeping the constraints to the
+system's virial as part of "thermodynamic output"_thermo_style.html.
+The default is {virial yes}
+
 No information about these fixes is written to "binary restart
 files"_restart.html.  None of the "fix_modify"_fix_modify.html options
 are relevant to these fixes.  No global or per-atom quantities are

doc/src/fix_shardlow.txt

@@ -7,6 +7,7 @@
 :line
 
 fix shardlow command :h3
+fix shardlow/kk command :h3
 
 [Syntax:]
 
@@ -52,6 +53,29 @@ examples/USER/dpd directory.
 
 :line
 
+Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in "Section 5"_Section_accelerate.html
+of the manual.  The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the "-suffix command-line
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
+use the "suffix"_suffix.html command in your input script.
+
+See "Section 5"_Section_accelerate.html of the manual for
+more instructions on how to use the accelerated styles effectively.
+
+:line
+
 [Restrictions:]
 
 This command is part of the USER-DPD package.  It is only enabled if

doc/src/fix_smd.txt

@@ -101,6 +101,11 @@ See the "read_restart"_read_restart.html command for info on how to
 re-specify a fix in an input script that reads a restart file, so that
 the operation of the fix continues in an uninterrupted fashion.
 
+The "fix_modify"_fix_modify.html {virial} option is supported by this
+fix to add the contribution due to the added forces on atoms to the
+system's virial as part of "thermodynamic output"_thermo_style.html.
+The default is {virial no}
+
 The "fix_modify"_fix_modify.html {respa} option is supported by
 this fix. This allows to set at which level of the "r-RESPA"_run_style.html
 integrator the fix is adding its forces. Default is the outermost level.

doc/src/fix_wall.txt

@@ -7,6 +7,7 @@
 :line
 
 fix wall/lj93 command :h3
+fix wall/lj93/kk command :h3
 fix wall/lj126 command :h3
 fix wall/lj1043 command :h3
 fix wall/colloid command :h3
@@ -251,6 +252,11 @@ fix to add the energy of interaction between atoms and each wall to
 the system's potential energy as part of "thermodynamic
 output"_thermo_style.html.
 
+The "fix_modify"_fix_modify.html {virial} option is supported by this
+fix to add the contribution due to the interaction between
+atoms and each wall to the system's virial as part of "thermodynamic
+output"_thermo_style.html. The default is {virial no}
+
 The "fix_modify"_fix_modify.html {respa} option is supported by this
 fix. This allows to set at which level of the "r-RESPA"_run_style.html
 integrator the fix is adding its forces. Default is the outermost level.
@@ -277,6 +283,31 @@ the total potential energy of the system (the quantity being
 minimized), you MUST enable the "fix_modify"_fix_modify.html {energy}
 option for this fix.
 
+:line
+
+Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in "Section 5"_Section_accelerate.html
+of the manual.  The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the "-suffix command-line
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
+use the "suffix"_suffix.html command in your input script.
+
+See "Section 5"_Section_accelerate.html of the manual for
+more instructions on how to use the accelerated styles effectively.
+
+:line
+
 [Restrictions:] none
 
 [Related commands:]

doc/src/fix_wall_region.txt

@@ -15,7 +15,7 @@ fix ID group-ID wall/region region-ID style epsilon sigma cutoff :pre
 ID, group-ID are documented in "fix"_fix.html command
 wall/region = style name of this fix command
 region-ID = region whose boundary will act as wall
-style = {lj93} or {lj126} or {colloid} or {harmonic}
+style = {lj93} or {lj126} or {lj1043} or {colloid} or {harmonic}
 epsilon = strength factor for wall-particle interaction (energy or energy/distance^2 units)
 sigma = size factor for wall-particle interaction (distance units)
 cutoff = distance from wall at which wall-particle interaction is cut off (distance units) :ul
@@ -112,6 +112,10 @@ For style {lj126}, the energy E is given by the 12/6 potential:
 
 :c,image(Eqs/pair_lj.jpg)
 
+For style {wall/lj1043}, the energy E is given by the 10/4/3 potential:
+
+:c,image(Eqs/fix_wall_lj1043.jpg)
+
 For style {colloid}, the energy E is given by an integrated form of
 the "pair_style colloid"_pair_colloid.html potential:
 
@@ -128,49 +132,8 @@ surface no longer interact.  The energy of the wall potential is
 shifted so that the wall-particle interaction energy is 0.0 at the
 cutoff distance.
 
-For the {lj93} and {lj126} styles, {epsilon} and {sigma} are the usual
-Lennard-Jones parameters, which determine the strength and size of the
-particle as it interacts with the wall.  Epsilon has energy units.
-Note that this {epsilon} and {sigma} may be different than any
-{epsilon} or {sigma} values defined for a pair style that computes
-particle-particle interactions.
-
-The {lj93} interaction is derived by integrating over a 3d
-half-lattice of Lennard-Jones 12/6 particles.  The {lj126} interaction
-is effectively a harder, more repulsive wall interaction.
-
-For the {colloid} style, {epsilon} is effectively a Hamaker constant
-with energy units for the colloid-wall interaction, {R} is the radius
-of the colloid particle, {D} is the distance from the surface of the
-colloid particle to the wall (r-R), and {sigma} is the size of a
-constituent LJ particle inside the colloid particle.  Note that the
-cutoff distance Rc in this case is the distance from the colloid
-particle center to the wall.
-
-The {colloid} interaction is derived by integrating over constituent
-LJ particles of size {sigma} within the colloid particle and a 3d
-half-lattice of Lennard-Jones 12/6 particles of size {sigma} in the
-wall.
-
-For the {wall/harmonic} style, {epsilon} is effectively the spring
-constant K, and has units (energy/distance^2).  The input parameter
-{sigma} is ignored.  The minimum energy position of the harmonic
-spring is at the {cutoff}.  This is a repulsive-only spring since the
-interaction is truncated at the {cutoff}
-
-NOTE: For all of the styles, you must insure that r is always > 0 for
-all particles in the group, or LAMMPS will generate an error.  This
-means you cannot start your simulation with particles on the region
-surface (r = 0) or with particles on the wrong side of the region
-surface (r < 0).  For the {wall/lj93} and {wall/lj126} styles, the
-energy of the wall/particle interaction (and hence the force on the
-particle) blows up as r -> 0.  The {wall/colloid} style is even more
-restrictive, since the energy blows up as D = r-R -> 0.  This means
-the finite-size particles of radius R must be a distance larger than R
-from the region surface.  The {harmonic} style is a softer potential
-and does not blow up as r -> 0, but you must use a large enough
-{epsilon} that particles always reamin on the correct side of the
-region surface (r > 0).
+For a full description of these wall styles, see fix_style
+"wall"_fix_wall.html
 
 [Restart, fix_modify, output, run start/stop, minimize info:]
 
@@ -182,6 +145,11 @@ fix to add the energy of interaction between atoms and the wall to the
 system's potential energy as part of "thermodynamic
 output"_thermo_style.html.
 
+The "fix_modify"_fix_modify.html {virial} option is supported by this
+fix to add the contribution due to the interaction between
+atoms and each wall to the system's virial as part of "thermodynamic
+output"_thermo_style.html. The default is {virial no}
+
 The "fix_modify"_fix_modify.html {respa} option is supported by this
 fix. This allows to set at which level of the "r-RESPA"_run_style.html
 integrator the fix is adding its forces. Default is the outermost level.

doc/src/fixes.txt

@@ -59,6 +59,7 @@ Fixes :h1
    fix_langevin
    fix_langevin_drude
    fix_langevin_eff
+   fix_latte
    fix_lb_fluid
    fix_lb_momentum
    fix_lb_pc
@@ -76,6 +77,7 @@ Fixes :h1
    fix_neb
    fix_nh
    fix_nh_eff
+   fix_nh_uef
    fix_nph_asphere
    fix_nph_body
    fix_nph_sphere
@@ -124,6 +126,7 @@ Fixes :h1
    fix_reaxc_species
    fix_recenter
    fix_restrain
+   fix_rhok
    fix_rigid
    fix_rx
    fix_saed_vtk

doc/src/lammps.book

@@ -62,6 +62,7 @@ dump_modify.html
 dump_molfile.html
 dump_netcdf.html
 dump_vtk.html
+dump_cfg_uef.html
 echo.html
 fix.html
 fix_modify.html
@@ -116,6 +117,7 @@ suffix.html
 tad.html
 temper.html
 temper_grem.html
+temper_npt.html
 thermo.html
 thermo_modify.html
 thermo_style.html
@@ -186,6 +188,7 @@ fix_ipi.html
 fix_langevin.html
 fix_langevin_drude.html
 fix_langevin_eff.html
+fix_latte.html
 fix_lb_fluid.html
 fix_lb_momentum.html
 fix_lb_pc.html
@@ -230,6 +233,7 @@ fix_nvt_manifold_rattle.html
 fix_nvt_sllod.html
 fix_nvt_sllod_eff.html
 fix_nvt_sphere.html
+fix_nh_uef.html
 fix_oneway.html
 fix_orient.html
 fix_phonon.html
@@ -252,6 +256,7 @@ fix_reaxc_species.html
 fix_recenter.html
 fix_restrain.html
 fix_rigid.html
+fix_rhok.html
 fix_rx.html
 fix_saed_vtk.html
 fix_setforce.html
@@ -353,6 +358,7 @@ compute_pe.html
 compute_pe_atom.html
 compute_plasticity_atom.html
 compute_pressure.html
+compute_pressure_uef.html
 compute_property_atom.html
 compute_property_chunk.html
 compute_property_local.html
@@ -402,6 +408,7 @@ compute_temp_region.html
 compute_temp_region_eff.html
 compute_temp_rotate.html
 compute_temp_sphere.html
+compute_temp_uef.html
 compute_ti.html
 compute_torque_chunk.html
 compute_vacf.html
@@ -513,7 +520,7 @@ pair_zero.html
 bond_class2.html
 bond_fene.html
 bond_fene_expand.html
-bond_oxdna.html
+bond_gromos.html
 bond_harmonic.html
 bond_harmonic_shift.html
 bond_harmonic_shift_cut.html
@@ -521,6 +528,7 @@ bond_hybrid.html
 bond_morse.html
 bond_none.html
 bond_nonlinear.html
+bond_oxdna.html
 bond_quartic.html
 bond_table.html
 bond_zero.html

doc/src/package.txt

@@ -62,7 +62,7 @@ args = arguments specific to the style :l
       {no_affinity} values = none
   {kokkos} args = keyword value ...
     zero or more keyword/value pairs may be appended
-    keywords = {neigh} or {neigh/qeq} or {newton} or {binsize} or {comm} or {comm/exchange} or {comm/forward}
+    keywords = {neigh} or {neigh/qeq} or {newton} or {binsize} or {comm} or {comm/exchange} or {comm/forward} or {comm/reverse}
       {neigh} value = {full} or {half}
         full = full neighbor list
         half = half neighbor list built in thread-safe manner
@@ -75,9 +75,10 @@ args = arguments specific to the style :l
       {binsize} value = size
         size = bin size for neighbor list construction (distance units)
       {comm} value = {no} or {host} or {device}
-        use value for both comm/exchange and comm/forward
+        use value for comm/exchange and comm/forward and comm/reverse
       {comm/exchange} value = {no} or {host} or {device}
       {comm/forward} value = {no} or {host} or {device}
+      {comm/reverse} value = {no} or {host} or {device}
         no = perform communication pack/unpack in non-KOKKOS mode
         host = perform pack/unpack on host (e.g. with OpenMP threading)
         device = perform pack/unpack on device (e.g. on GPU)
@@ -335,7 +336,8 @@ from the USER-INTEL package is not used, then the LRT setting is
 ignored and no extra threads are generated. Enabling LRT will replace
 the "run_style"_run_style.html with the {verlet/lrt/intel} style that
 is identical to the default {verlet} style aside from supporting the
-LRT feature.
+LRT feature. This feature requires setting the preprocessor flag
+-DLMP_INTEL_USELRT in the makefile when compiling LAMMPS.
 
 The {balance} keyword sets the fraction of "pair
 style"_pair_style.html work offloaded to the coprocessor for split
@@ -428,17 +430,18 @@ Coulombic solver"_kspace_style.html because the GPU is faster at
 performing pairwise interactions, then this rule of thumb may give too
 large a binsize.
 
-The {comm} and {comm/exchange} and {comm/forward} keywords determine
+The {comm} and {comm/exchange} and {comm/forward} and {comm/reverse} keywords determine
 whether the host or device performs the packing and unpacking of data
 when communicating per-atom data between processors.  "Exchange"
 communication happens only on timesteps that neighbor lists are
 rebuilt.  The data is only for atoms that migrate to new processors.
-"Forward" communication happens every timestep.  The data is for atom
+"Forward" communication happens every timestep. "Reverse" communication
+happens every timestep if the {newton} option is on.  The data is for atom
 coordinates and any other atom properties that needs to be updated for
 ghost atoms owned by each processor.
 
 The {comm} keyword is simply a short-cut to set the same value
-for both the {comm/exchange} and {comm/forward} keywords.
+for both the {comm/exchange} and {comm/forward} and {comm/reverse} keywords.
 
 The value options for all 3 keywords are {no} or {host} or {device}.
 A value of {no} means to use the standard non-KOKKOS method of

doc/src/pair_born.txt

@@ -17,6 +17,7 @@ pair_style born/coul/long/omp command :h3
 pair_style born/coul/msm command :h3
 pair_style born/coul/msm/omp command :h3
 pair_style born/coul/wolf command :h3
+pair_style born/coul/wolf/cs command :h3
 pair_style born/coul/wolf/gpu command :h3
 pair_style born/coul/wolf/omp command :h3
 pair_style born/coul/dsf command :h3
@@ -36,7 +37,7 @@ args = list of arguments for a particular style :ul
   {born/coul/msm} args = cutoff (cutoff2)
     cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units)
     cutoff2 = global cutoff for Coulombic (optional) (distance units)
-  {born/coul/wolf} args = alpha cutoff (cutoff2)
+  {born/coul/wolf} or {born/coul/wolf/cs} args = alpha cutoff (cutoff2)
     alpha = damping parameter (inverse distance units)
     cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units)
     cutoff2 = global cutoff for Coulombic (optional) (distance units)
@@ -65,6 +66,7 @@ pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 :pre
 
 pair_style born/coul/wolf 0.25 10.0
 pair_style born/coul/wolf 0.25 10.0 9.0
+pair_style born/coul/wolf/cs 0.25 10.0 9.0
 pair_coeff * * 6.08 0.317 2.340 24.18 11.51
 pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 :pre
 
@@ -106,8 +108,9 @@ damped shifted force model as in the "coul/dsf"_pair_coul.html style.
 Style {born/coul/long/cs} is identical to {born/coul/long} except that
 a term is added for the "core/shell model"_Section_howto.html#howto_25
 to allow charges on core and shell particles to be separated by r =
-0.0. The same correction is introduced for {born/coul/dsf/cs} style
-which is identical to {born/coul/dsf}.
+0.0.  The same correction is introduced for the {born/coul/dsf/cs}
+style which is identical to {born/coul/dsf}.  And likewise for
+{born/coul/wolf/cs} style which is identical to {born/coul/wolf}.
 
 Note that these potentials are related to the "Buckingham
 potential"_pair_buck.html.

doc/src/pair_coul.txt

@@ -29,6 +29,7 @@ pair_style coul/streitz command :h3
 pair_style coul/wolf command :h3
 pair_style coul/wolf/kk command :h3
 pair_style coul/wolf/omp command :h3
+pair_style coul/wolf/cs command :h3
 pair_style tip4p/cut command :h3
 pair_style tip4p/long command :h3
 pair_style tip4p/cut/omp command :h3
@@ -43,6 +44,7 @@ pair_style coul/long cutoff
 pair_style coul/long/cs cutoff
 pair_style coul/long/gpu cutoff
 pair_style coul/wolf alpha cutoff
+pair_style coul/wolf/cs alpha cutoff
 pair_style coul/streitz cutoff keyword alpha
 pair_style tip4p/cut otype htype btype atype qdist cutoff
 pair_style tip4p/long otype htype btype atype qdist cutoff :pre
@@ -72,6 +74,7 @@ pair_style coul/msm 10.0
 pair_coeff * * :pre
 
 pair_style coul/wolf 0.2 9.0
+pair_style coul/wolf/cs 0.2 9.0
 pair_coeff * * :pre
 
 pair_style coul/streitz 12.0 ewald
@@ -202,7 +205,9 @@ interactions outside that distance are computed in reciprocal space.
 
 Style {coul/long/cs} is identical to {coul/long} except that a term is
 added for the "core/shell model"_Section_howto.html#howto_25 to allow
-charges on core and shell particles to be separated by r = 0.0.
+charges on core and shell particles to be separated by r = 0.0.  The
+same correction is introduced for the {coul/wolf/cs} style which is
+identical to {coul/wolf}.
 
 Styles {tip4p/cut} and {tip4p/long} implement the coulomb part of
 the TIP4P water model of "(Jorgensen)"_#Jorgensen3, which introduces

doc/src/pair_cs.txt

@@ -9,12 +9,13 @@
 pair_style born/coul/long/cs command :h3
 pair_style buck/coul/long/cs command :h3
 pair_style born/coul/dsf/cs command :h3
+pair_style born/coul/wolf/cs command :h3
 
 [Syntax:]
 
 pair_style style args :pre
 
-style = {born/coul/long/cs} or {buck/coul/long/cs} or {born/coul/dsf/cs}
+style = {born/coul/long/cs} or {buck/coul/long/cs} or {born/coul/dsf/cs} or {born/coul/wolf/cs}
 args = list of arguments for a particular style :ul
   {born/coul/long/cs} args = cutoff (cutoff2)
     cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units)
@@ -26,6 +27,10 @@ args = list of arguments for a particular style :ul
     alpha = damping parameter (inverse distance units)
     cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units)
     cutoff2 = global cutoff for Coulombic (distance units) :pre
+  {born/coul/wolf/cs} args = alpha cutoff (cutoff2)
+    alpha = damping parameter (inverse distance units)
+    cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units)
+    cutoff2 = global cutoff for Coulombic (optional) (distance units)
 
 [Examples:]
 
@@ -41,6 +46,10 @@ pair_style born/coul/dsf/cs 0.1 10.0 12.0
 pair_coeff * *   0.0 1.00 0.00 0.00 0.00
 pair_coeff 1 1 480.0 0.25 0.00 1.05 0.50 :pre
 
+pair_style born/coul/wolf/cs 0.25 10.0 12.0
+pair_coeff * *   0.0 1.00 0.00 0.00 0.00
+pair_coeff 1 1 480.0 0.25 0.00 1.05 0.50 :pre
+
 [Description:]
 
 These pair styles are designed to be used with the adiabatic
@@ -73,13 +82,21 @@ the core and shell, epsilon is the dielectric constant and r_min is the
 minimal distance.
 
 The pair style {born/coul/dsf/cs} is identical to the
-"pair_style born/coul/dsf"_pair_born.html style, which uses the
+"pair_style born/coul/dsf"_pair_born.html style, which uses
 the damped shifted force model as in "coul/dsf"_pair_coul.html
 to compute the Coulomb contribution. This approach does not require
 a long-range solver, thus the only correction is the addition of a
 minimal distance to avoid the possible r = 0.0 case for a
 core/shell pair.
 
+The pair style {born/coul/wolf/cs} is identical to the
+"pair_style born/coul/wolf"_pair_born.html style, which uses
+the Wolf summation as in "coul/wolf"_pair_coul.html to compute
+the Coulomb contribution. This approach does not require
+a long-range solver, thus the only correction is the addition of a
+minimal distance to avoid the possible r = 0.0 case for a
+core/shell pair.
+
 [Restrictions:]
 
 These pair styles are part of the CORESHELL package.  They are only

doc/src/pair_dpd.txt

@@ -8,6 +8,7 @@
 
 pair_style dpd command :h3
 pair_style dpd/gpu command :h3
+pair_style dpd/intel command :h3
 pair_style dpd/omp command :h3
 pair_style dpd/tstat command :h3
 pair_style dpd/tstat/gpu command :h3

doc/src/pair_dpd_fdt.txt

@@ -8,6 +8,7 @@
 
 pair_style dpd/fdt command :h3
 pair_style dpd/fdt/energy command :h3
+pair_style dpd/fdt/energy/kk command :h3
 
 [Syntax:]
 
@@ -125,6 +126,29 @@ significantly larger timesteps to be taken.
 
 :line
 
+Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in "Section 5"_Section_accelerate.html
+of the manual.  The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the "-suffix command-line
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
+use the "suffix"_suffix.html command in your input script.
+
+See "Section 5"_Section_accelerate.html of the manual for
+more instructions on how to use the accelerated styles effectively.
+
+:line
+
 [Restrictions:]
 
 These commands are part of the USER-DPD package.  They are only

doc/src/pair_eam.txt

@@ -294,7 +294,7 @@ distribution have a ".cdeam" suffix.
 
 Style {eam/fs} computes pairwise interactions for metals and metal
 alloys using a generalized form of EAM potentials due to Finnis and
-Sinclair "(Finnis)"_#Finnis.  The total energy Ei of an atom I is
+Sinclair "(Finnis)"_#Finnis1.  The total energy Ei of an atom I is
 given by
 
 :c,image(Eqs/pair_eam_fs.jpg)
@@ -442,7 +442,7 @@ of Physics: Condensed Matter, 16, S2629 (2004).
 [(Daw)] Daw, Baskes, Phys Rev Lett, 50, 1285 (1983).
 Daw, Baskes, Phys Rev B, 29, 6443 (1984).
 
-:link(Finnis)
+:link(Finnis1)
 [(Finnis)] Finnis, Sinclair, Philosophical Magazine A, 50, 45 (1984).
 
 :link(Stukowski)

doc/src/pair_exp6_rx.txt

@@ -7,6 +7,7 @@
 :line
 
 pair_style exp6/rx command :h3
+pair_style exp6/rx/kk command :h3
 
 [Syntax:]
 
@@ -147,6 +148,31 @@ This style does not support the pair_modify tail option for adding long-range
 tail corrections to energy and pressure for the A,C terms in the
 pair interaction.
 
+:line
+
+Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in "Section 5"_Section_accelerate.html
+of the manual.  The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the "-suffix command-line
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
+use the "suffix"_suffix.html command in your input script.
+
+See "Section 5"_Section_accelerate.html of the manual for
+more instructions on how to use the accelerated styles effectively.
+
+:line
+
 [Restrictions:]
 
 This command is part of the USER-DPD package.  It is only enabled if

doc/src/pair_hybrid.txt

@@ -10,6 +10,7 @@ pair_style hybrid command :h3
 pair_style hybrid/omp command :h3
 pair_style hybrid/overlay command :h3
 pair_style hybrid/overlay/omp command :h3
+pair_style hybrid/overlay/kk command :h3
 
 [Syntax:]
 

doc/src/pair_multi_lucy_rx.txt

@@ -7,6 +7,7 @@
 :line
 
 pair_style multi/lucy/rx command :h3
+pair_style multi/lucy/rx/kk command :h3
 
 [Syntax:]
 
@@ -200,6 +201,29 @@ This pair style can only be used via the {pair} keyword of the
 
 :line
 
+Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in "Section 5"_Section_accelerate.html
+of the manual.  The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the "-suffix command-line
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
+use the "suffix"_suffix.html command in your input script.
+
+See "Section 5"_Section_accelerate.html of the manual for
+more instructions on how to use the accelerated styles effectively.
+
+:line
+
 [Restrictions:]
 
 This command is part of the USER-DPD package.  It is only enabled if

doc/src/pair_oxdna.txt

@@ -20,20 +20,24 @@ pair_coeff * * style2 args :pre
 
 style1 = {hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk} :ul
 
-style2 = {oxdna/stk}
-args = list of arguments for these two particular styles :ul
+style2 = {oxdna/excv} or {oxdna/stk} or {oxdna/hbond} or {oxdna/xstk} or {oxdna/coaxstk}
+args = list of arguments for these particular styles :ul
 
-  {oxdna2/stk} args = T 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
-    T = temperature (oxDNA units, 0.1 = 300 K) :pre
+  {oxdna/stk} args = seq T 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+    seq = seqav (for average sequence stacking strength) or seqdep (for sequence-dependent stacking strength)
+    T = temperature (oxDNA units, 0.1 = 300 K) 
+  {oxdna/hbond} args = seq eps 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+    seq = seqav (for average sequence base-pairing strength) or seqdep (for sequence-dependent base-pairing strength)
+    eps = 1.077 (between base pairs A-T and C-G) or 0 (all other pairs) :pre 
 
 [Examples:]
 
 pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
 pair_coeff * * oxdna/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
-pair_coeff * * oxdna/stk     0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
-pair_coeff * * oxdna/hbond   0.0   8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 1 4 oxdna/hbond   1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 2 3 oxdna/hbond   1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff * * oxdna/stk     seqdep 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna/hbond   seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 1 4 oxdna/hbond   seqdep 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 2 3 oxdna/hbond   seqdep 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
 pair_coeff * * oxdna/xstk    47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
 pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65 :pre
 
@@ -44,10 +48,11 @@ for coarse-grained modelling of DNA. The effective interaction between the nucle
 excluded volume interaction {oxdna/excv}, the stacking {oxdna/stk}, cross-stacking {oxdna/xstk}
 and coaxial stacking interaction {oxdna/coaxstk} as well
 as the hydrogen-bonding interaction {oxdna/hbond} between complementary pairs of nucleotides on
-opposite strands.
+opposite strands. Average sequence or sequence-dependent stacking and base-pairing strengths
+are supported "(Sulc)"_#Sulc1.
 
-The exact functional form of the pair styles is rather complex, which manifests itself in the 144 coefficients
-in the above example. The individual potentials consist of products of modulation factors,
+The exact functional form of the pair styles is rather complex.
+The individual potentials consist of products of modulation factors,
 which themselves are constructed from a number of more basic potentials
 (Morse, Lennard-Jones, harmonic angle and distance) as well as quadratic smoothing and modulation terms.
 We refer to "(Ouldridge-DPhil)"_#Ouldridge-DPhil1 and "(Ouldridge)"_#Ouldridge1
@@ -55,9 +60,10 @@ for a detailed description of the oxDNA force field.
 
 NOTE: These pair styles have to be used together with the related oxDNA bond style
 {oxdna/fene} for the connectivity of the phosphate backbone (see also documentation of
-"bond_style oxdna/fene"_bond_oxdna.html). With one exception the coefficients
+"bond_style oxdna/fene"_bond_oxdna.html). Most of the coefficients
 in the above example have to be kept fixed and cannot be changed without reparametrizing the entire model.
-The exception is the first coefficient after {oxdna/stk} (T=0.1 in the above example).
+Exceptions are the first and second coefficient after {oxdna/stk} (seq=seqdep and T=0.1 in the above example)
+and the first coefficient after {oxdna/hbond} (seq=seqdep in the above example).
 When using a Langevin thermostat, e.g. through "fix langevin"_fix_langevin.html
 or "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html
 the temperature coefficients have to be matched to the one used in the fix.
@@ -86,7 +92,11 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.
 
 :line
 
+:link(Sulc1)
+[(Sulc)] P. Sulc, F. Romano, T.E. Ouldridge, L. Rovigatti, J.P.K. Doye, A.A. Louis, J. Chem. Phys. 137, 135101 (2012).
+
 :link(Ouldridge-DPhil1)
 [(Ouldrigde-DPhil)] T.E. Ouldridge, Coarse-grained modelling of DNA and DNA self-assembly, DPhil. University of Oxford (2011).
+
 :link(Ouldridge1)
 [(Ouldridge)] T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011).

doc/src/pair_oxdna2.txt

@@ -21,11 +21,15 @@ pair_coeff * * style2 args :pre
 
 style1 = {hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh} :ul
 
-style2 = {oxdna2/stk} or {oxdna2/dh}
-args = list of arguments for these two particular styles :ul
+style2 = {oxdna2/excv} or {oxdna2/stk} or {oxdna2/hbond} or {oxdna2/xstk} or {oxdna2/coaxstk} or {oxdna2/dh}
+args = list of arguments for these particular styles :ul
 
-  {oxdna2/stk} args = T 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+  {oxdna2/stk} args = seq T 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+    seq = seqav (for average sequence stacking strength) or seqdep (for sequence-dependent stacking strength)
     T = temperature (oxDNA units, 0.1 = 300 K)
+  {oxdna/hbond} args = seq eps 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+    seq = seqav (for average sequence base-pairing strength) or seqdep (for sequence-dependent base-pairing strength)
+    eps = 1.0678 (between base pairs A-T and C-G) or 0 (all other pairs)
   {oxdna2/dh} args = T rhos qeff
     T = temperature (oxDNA units, 0.1 = 300 K)
     rhos = salt concentration (mole per litre)
@@ -35,10 +39,10 @@ args = list of arguments for these two particular styles :ul
 
 pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
 pair_coeff * * oxdna2/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
-pair_coeff * * oxdna2/stk     0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
-pair_coeff * * oxdna2/hbond   0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 1 4 oxdna2/hbond   1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 2 3 oxdna2/hbond   1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff * * oxdna2/stk     seqdep 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna2/hbond   seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 1 4 oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 2 3 oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
 pair_coeff * * oxdna2/xstk    47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
 pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
 pair_coeff * * oxdna2/dh      0.1 1.0 0.815 :pre
@@ -50,7 +54,8 @@ for coarse-grained modelling of DNA. The effective interaction between the nucle
 excluded volume interaction {oxdna2/excv}, the stacking {oxdna2/stk}, cross-stacking {oxdna2/xstk}
 and coaxial stacking interaction {oxdna2/coaxstk}, electrostatic Debye-Hueckel interaction {oxdna2/dh}
 as well as the hydrogen-bonding interaction {oxdna2/hbond} between complementary pairs of nucleotides on
-opposite strands.
+opposite strands. Average sequence or sequence-dependent stacking and base-pairing strengths
+are supported "(Sulc)"_#Sulc2.
 
 The exact functional form of the pair styles is rather complex.
 The individual potentials consist of products of modulation factors,
@@ -61,9 +66,10 @@ and  "(Ouldridge)"_#Ouldridge2 for a detailed description of the oxDNA2 force fi
 
 NOTE: These pair styles have to be used together with the related oxDNA2 bond style
 {oxdna2/fene} for the connectivity of the phosphate backbone (see also documentation of
-"bond_style oxdna2/fene"_bond_oxdna.html). Almost all coefficients
+"bond_style oxdna2/fene"_bond_oxdna.html). Most of the coefficients
 in the above example have to be kept fixed and cannot be changed without reparametrizing the entire model.
-Exceptions are the first coefficient after {oxdna2/stk} (T=0.1 in the above example) and the coefficients
+Exceptions are the first and the second coefficient after {oxdna2/stk} (seq=seqdep and T=0.1 in the above example),
+the first coefficient after {oxdna/hbond} (seq=seqdep in the above example) and the three coefficients 
 after {oxdna2/dh} (T=0.1, rhos=1.0, qeff=0.815 in the above example). When using a Langevin thermostat
 e.g. through "fix langevin"_fix_langevin.html or "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html
 the temperature coefficients have to be matched to the one used in the fix.
@@ -92,6 +98,9 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.
 
 :line
 
+:link(Sulc2)
+[(Sulc)] P. Sulc, F. Romano, T.E. Ouldridge, L. Rovigatti, J.P.K. Doye, A.A. Louis, J. Chem. Phys. 137, 135101 (2012).
+
 :link(Snodin)
 [(Snodin)] B.E. Snodin, F. Randisi, M. Mosayebi, et al., J. Chem. Phys. 142, 234901 (2015).
 

doc/src/pair_table_rx.txt

@@ -7,6 +7,7 @@
 :line
 
 pair_style table/rx command :h3
+pair_style table/rx/kk command :h3
 
 [Syntax:]
 
@@ -223,6 +224,29 @@ This pair style can only be used via the {pair} keyword of the
 
 :line
 
+Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in "Section 5"_Section_accelerate.html
+of the manual.  The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the "-suffix command-line
+switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can
+use the "suffix"_suffix.html command in your input script.
+
+See "Section 5"_Section_accelerate.html of the manual for
+more instructions on how to use the accelerated styles effectively.
+
+:line
+
 [Restrictions:]
 
 This command is part of the USER-DPD package.  It is only enabled if

doc/src/read_restart.txt

@@ -178,7 +178,7 @@ not the same and the current value is not the default.
 Note that some force field styles (pair, bond, angle, etc) do not
 store their coefficient info in restart files.  Typically these are
 many-body or tabulated potentials which read their parameters from
-separate files.  In these cases you will need to re-specify the "pair
+separate files.  In these cases you will need to re-specify the
 "pair_coeff"_pair_coeff.html, "bond_coeff"_bond_coeff.html, etc
 commands in your restart input script.  The doc pages for individual
 force field styles mention if this is the case.  This is also true of

doc/src/temper_npt.txt

@@ -0,0 +1,67 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+temper/npt command :h3
+
+[Syntax:]
+
+temper/npt  N M temp fix-ID seed1 seed2 pressure index :pre
+
+N = total # of timesteps to run
+M = attempt a tempering swap every this many steps
+temp = initial temperature for this ensemble
+fix-ID = ID of the fix that will control temperature and pressure during the run
+seed1 = random # seed used to decide on adjacent temperature to partner with
+seed2 = random # seed for Boltzmann factor in Metropolis swap
+pressure = setpoint pressure for the ensemble
+index = which temperature (0 to N-1) I am simulating (optional) :ul
+
+[Examples:]
+
+temper/npt 100000 100 $t nptfix 0 58728 1
+temper/npt 2500000 1000 300 nptfix  0 32285 $p 
+temper/npt 5000000 2000 $t nptfix 0 12523 1 $w :pre
+
+[Description:]
+
+Run a parallel tempering or replica exchange simulation using multiple
+replicas (ensembles) of a system in the isothermal-isobaric (NPT)
+ensemble.  The command temper/npt works like "temper"_temper.html but
+requires running replicas in the NPT ensemble instead of the canonical
+(NVT) ensemble and allows for pressure to be set in the ensembles.
+These multiple ensembles can run in parallel at different temperatures
+or different pressures.  The acceptance criteria for temper/npt is
+specific to the NPT ensemble and can be found in references
+"(Okabe)"_#Okabe2 and "(Mori)"_#Mori2.
+
+Apart from the difference in acceptance criteria and the specification
+of pressure, this command works much like the "temper"_temper.html
+command. See the documentation on "temper"_temper.html for information
+on how the parallel tempering is handled in general.
+
+:line 
+
+[Restrictions:]
+
+This command can only be used if LAMMPS was built with the USER-MISC
+package.  See the "Making LAMMPS"_Section_start.html#start_3 section
+for more info on packages.
+
+This command should be used with a fix that maintains the
+isothermal-isobaric (NPT) ensemble.
+
+[Related commands:]
+
+"temper"_temper.html, "variable"_variable.html, "fix_npt"_fix_nh.html
+
+[Default:] none
+
+:link(Okabe2)
+[(Okabe)] T. Okabe, M. Kawata, Y. Okamoto, M. Masuhiro, Chem. Phys. Lett., 335, 435-439 (2001).
+
+:link(Mori2)
+[(Mori)] Y. Mori, Y. Okamoto, J. Phys. Soc. Jpn., 7, 074003 (2010).

examples/README

@@ -79,6 +79,7 @@ granregion: use of fix wall/region/gran as boundary on granular particles
 hugoniostat: Hugoniostat shock dynamics
 indent:	  spherical indenter into a 2d solid
 kim:      use of potentials in Knowledge Base for Interatomic Models (KIM)
+latte:    use of LATTE density-functional tight-binding quantum code
 meam:	  MEAM test for SiC and shear (same as shear examples)
 melt:	  rapid melt of 3d LJ system
 micelle:  self-assembly of small lipid-like molecules into 2d bilayers

examples/USER/cgdna/examples/oxDNA/duplex1/input.duplex1

@@ -30,10 +30,10 @@ bond_coeff * 2.0 0.25 0.7525
 # oxDNA pair interactions
 pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
 pair_coeff * * oxdna/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
-pair_coeff * * oxdna/stk     0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
-pair_coeff * * oxdna/hbond   0.0   8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 1 4 oxdna/hbond   1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 2 3 oxdna/hbond   1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff * * oxdna/stk     seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna/hbond   seqav 0.0   8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 1 4 oxdna/hbond   seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 2 3 oxdna/hbond   seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
 pair_coeff * * oxdna/xstk    47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
 pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65
 

examples/USER/cgdna/examples/oxDNA/duplex1/log.24Mar17.duplex1.g++.1

@@ -48,10 +48,10 @@ bond_coeff * 2.0 0.25 0.7525
 # oxDNA pair interactions
 pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
 pair_coeff * * oxdna/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
-pair_coeff * * oxdna/stk     0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
-pair_coeff * * oxdna/hbond   0.0   8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 1 4 oxdna/hbond   1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 2 3 oxdna/hbond   1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff * * oxdna/stk     seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna/hbond   seqav 0.0   8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 1 4 oxdna/hbond   seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 2 3 oxdna/hbond   seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
 pair_coeff * * oxdna/xstk    47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
 pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65
 

examples/USER/cgdna/examples/oxDNA/duplex1/log.24Mar17.duplex1.g++.4

@@ -48,10 +48,10 @@ bond_coeff * 2.0 0.25 0.7525
 # oxDNA pair interactions
 pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
 pair_coeff * * oxdna/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
-pair_coeff * * oxdna/stk     0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
-pair_coeff * * oxdna/hbond   0.0   8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 1 4 oxdna/hbond   1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 2 3 oxdna/hbond   1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff * * oxdna/stk     seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna/hbond   seqav 0.0   8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 1 4 oxdna/hbond   seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 2 3 oxdna/hbond   seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
 pair_coeff * * oxdna/xstk    47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
 pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65
 

examples/USER/cgdna/examples/oxDNA/duplex2/input.duplex2

@@ -30,10 +30,10 @@ bond_coeff * 2.0 0.25 0.7525
 # oxDNA pair interactions
 pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
 pair_coeff * * oxdna/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
-pair_coeff * * oxdna/stk     0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
-pair_coeff * * oxdna/hbond   0.0   8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 1 4 oxdna/hbond   1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 2 3 oxdna/hbond   1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff * * oxdna/stk     seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna/hbond   seqav 0.0   8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 1 4 oxdna/hbond   seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 2 3 oxdna/hbond   seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
 pair_coeff * * oxdna/xstk    47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
 pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65
 

examples/USER/cgdna/examples/oxDNA/duplex2/log.24Mar17.duplex2.g++.1

@@ -48,10 +48,10 @@ bond_coeff * 2.0 0.25 0.7525
 # oxDNA pair interactions
 pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
 pair_coeff * * oxdna/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
-pair_coeff * * oxdna/stk     0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
-pair_coeff * * oxdna/hbond   0.0   8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 1 4 oxdna/hbond   1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 2 3 oxdna/hbond   1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff * * oxdna/stk     seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna/hbond   seqav 0.0   8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 1 4 oxdna/hbond   seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 2 3 oxdna/hbond   seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
 pair_coeff * * oxdna/xstk    47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
 pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65
 

examples/USER/cgdna/examples/oxDNA/duplex2/log.24Mar17.duplex2.g++.4

@@ -48,10 +48,10 @@ bond_coeff * 2.0 0.25 0.7525
 # oxDNA pair interactions
 pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
 pair_coeff * * oxdna/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
-pair_coeff * * oxdna/stk     0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
-pair_coeff * * oxdna/hbond   0.0   8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 1 4 oxdna/hbond   1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 2 3 oxdna/hbond   1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff * * oxdna/stk     seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna/hbond   seqav 0.0   8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 1 4 oxdna/hbond   seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 2 3 oxdna/hbond   seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
 pair_coeff * * oxdna/xstk    47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
 pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65
 

examples/USER/cgdna/examples/oxDNA2/duplex1/input.duplex1

@@ -30,10 +30,10 @@ bond_coeff * 2.0 0.25 0.7564
 # oxDNA pair interactions
 pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
 pair_coeff * * oxdna2/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
-pair_coeff * * oxdna2/stk     0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65   
-pair_coeff * * oxdna2/hbond   0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 1 4 oxdna2/hbond   1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 2 3 oxdna2/hbond   1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff * * oxdna2/stk     seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65   
+pair_coeff * * oxdna2/hbond   seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 1 4 oxdna2/hbond   seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 2 3 oxdna2/hbond   seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
 pair_coeff * * oxdna2/xstk    47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 
 pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
 pair_coeff * * oxdna2/dh      0.1 1.0 0.815

examples/USER/cgdna/examples/oxDNA2/duplex1/log.24Mar17.duplex1.g++.1

@@ -48,10 +48,10 @@ bond_coeff * 2.0 0.25 0.7564
 # oxDNA pair interactions
 pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
 pair_coeff * * oxdna2/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
-pair_coeff * * oxdna2/stk     0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
-pair_coeff * * oxdna2/hbond   0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 1 4 oxdna2/hbond   1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 2 3 oxdna2/hbond   1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff * * oxdna2/stk     seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna2/hbond   seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 1 4 oxdna2/hbond   seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 2 3 oxdna2/hbond   seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
 pair_coeff * * oxdna2/xstk    47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
 pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
 pair_coeff * * oxdna2/dh      0.1 1.0 0.815

examples/USER/cgdna/examples/oxDNA2/duplex1/log.24Mar17.duplex1.g++.4

@@ -48,10 +48,10 @@ bond_coeff * 2.0 0.25 0.7564
 # oxDNA pair interactions
 pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
 pair_coeff * * oxdna2/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
-pair_coeff * * oxdna2/stk     0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
-pair_coeff * * oxdna2/hbond   0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 1 4 oxdna2/hbond   1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 2 3 oxdna2/hbond   1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff * * oxdna2/stk     seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna2/hbond   seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 1 4 oxdna2/hbond   seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 2 3 oxdna2/hbond   seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
 pair_coeff * * oxdna2/xstk    47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
 pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
 pair_coeff * * oxdna2/dh      0.1 1.0 0.815

examples/USER/cgdna/examples/oxDNA2/duplex2/input.duplex2

@@ -30,10 +30,10 @@ bond_coeff * 2.0 0.25 0.7564
 # oxDNA pair interactions
 pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
 pair_coeff * * oxdna2/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
-pair_coeff * * oxdna2/stk     0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65   
-pair_coeff * * oxdna2/hbond   0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 1 4 oxdna2/hbond   1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 2 3 oxdna2/hbond   1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff * * oxdna2/stk     seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65   
+pair_coeff * * oxdna2/hbond   seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 1 4 oxdna2/hbond   seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 2 3 oxdna2/hbond   seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
 pair_coeff * * oxdna2/xstk    47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 
 pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
 pair_coeff * * oxdna2/dh      0.1 1.0 0.815

examples/USER/cgdna/examples/oxDNA2/duplex2/log.24Mar17.duplex2.g++.1

@@ -48,10 +48,10 @@ bond_coeff * 2.0 0.25 0.7564
 # oxDNA pair interactions
 pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
 pair_coeff * * oxdna2/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
-pair_coeff * * oxdna2/stk     0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
-pair_coeff * * oxdna2/hbond   0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 1 4 oxdna2/hbond   1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 2 3 oxdna2/hbond   1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff * * oxdna2/stk     seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna2/hbond   seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 1 4 oxdna2/hbond   seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 2 3 oxdna2/hbond   seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
 pair_coeff * * oxdna2/xstk    47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
 pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
 pair_coeff * * oxdna2/dh      0.1 1.0 0.815

examples/USER/cgdna/examples/oxDNA2/duplex2/log.24Mar17.duplex2.g++.4

@@ -48,10 +48,10 @@ bond_coeff * 2.0 0.25 0.7564
 # oxDNA pair interactions
 pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
 pair_coeff * * oxdna2/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
-pair_coeff * * oxdna2/stk     0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
-pair_coeff * * oxdna2/hbond   0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 1 4 oxdna2/hbond   1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 2 3 oxdna2/hbond   1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff * * oxdna2/stk     seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna2/hbond   seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 1 4 oxdna2/hbond   seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
+pair_coeff 2 3 oxdna2/hbond   seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
 pair_coeff * * oxdna2/xstk    47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
 pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
 pair_coeff * * oxdna2/dh      0.1 1.0 0.815

examples/USER/drude/README

@@ -6,8 +6,11 @@ Nosé-Hoover or Langevin thermostats.
 
 * `butane` -- simulation in NVT ensemble with Thole damping
 
+* `toluene` -- simulation in NVT ensemble with Thole damping and
+use of the `extra/special/per/atom` keyword
+
 * `ethanol` -- simulation in NpT ensemble with Thole damping
 
-* `swm4-ndp` -- 4-site rigid water model in NpT ensemble (no Thole 
+* `swm4-ndp` -- 4-site rigid water model in NpT ensemble (no Thole
 damping)
 

examples/USER/drude/toluene/in.toluene.lang

@@ -0,0 +1,116 @@
+# 250 toluene system for drude polarizability example (Langevin)
+
+units real
+boundary p p p
+
+atom_style full
+bond_style harmonic
+angle_style harmonic
+dihedral_style opls
+improper_style opls
+special_bonds lj/coul 0.0 0.0 0.5
+
+pair_style lj/cut/thole/long 2.600 8.0 8.0
+pair_modify mix geometric tail yes
+kspace_style pppm 1.0e-4
+
+read_data data.toluene extra/special/per/atom 1
+
+comm_modify vel yes
+
+group gTOLUENE molecule 1:250
+group gCORES type 1 2 3 4 5 6 7
+group gDRUDES type 8 9 10 11 12
+
+pair_coeff    1    1 0.069998 3.550000 1.620000 # CAT CAT
+pair_coeff    1    2 0.069998 3.550000 1.620000 # CAT CAO
+pair_coeff    1    3 0.069998 3.550000 1.620000 # CAT CAM
+pair_coeff    1    4 0.069998 3.550000 1.620000 # CAT CAP
+pair_coeff    1    5 0.067968 3.524911 1.620000 # CAT CTT
+pair_coeff    1    6 0.045825 2.931041 0.000000 # CAT HAT
+pair_coeff    1    7 0.045825 2.931041 0.000000 # CAT HT
+pair_coeff    2    2 0.069998 3.550000 1.620000 # CAO CAO
+pair_coeff    2    3 0.069998 3.550000 1.620000 # CAO CAM
+pair_coeff    2    4 0.069998 3.550000 1.620000 # CAO CAP
+pair_coeff    2    5 0.067968 3.524911 1.620000 # CAO CTT
+pair_coeff    2    6 0.045825 2.931041 0.000000 # CAO HAT
+pair_coeff    2    7 0.045825 2.931041 0.000000 # CAO HT
+pair_coeff    3    3 0.069998 3.550000 1.620000 # CAM CAM
+pair_coeff    3    4 0.069998 3.550000 1.620000 # CAM CAP
+pair_coeff    3    5 0.067968 3.524911 1.620000 # CAM CTT
+pair_coeff    3    6 0.045825 2.931041 0.000000 # CAM HAT
+pair_coeff    3    7 0.045825 2.931041 0.000000 # CAM HT
+pair_coeff    4    4 0.069998 3.550000 1.620000 # CAP CAP
+pair_coeff    4    5 0.067968 3.524911 1.620000 # CAP CTT
+pair_coeff    4    6 0.045825 2.931041 0.000000 # CAP HAT
+pair_coeff    4    7 0.045825 2.931041 0.000000 # CAP HT
+pair_coeff    5    5 0.065997 3.500000 1.620000 # CTT CTT
+pair_coeff    5    6 0.044496 2.910326 0.000000 # CTT HAT
+pair_coeff    5    7 0.044496 2.910326 0.000000 # CTT HT
+pair_coeff    6    6 0.029999 2.420000 0.000000 # HAT HAT
+pair_coeff    6    7 0.029999 2.420000 0.000000 # HAT HT
+pair_coeff    7    7 0.029999 2.420000 0.000000 # HT HT
+pair_coeff    1    8 0.000000 0.000000 1.620000 # CAT D_CAT
+pair_coeff    1    9 0.000000 0.000000 1.620000 # CAT D_CAO
+pair_coeff    1   10 0.000000 0.000000 1.620000 # CAT D_CAM
+pair_coeff    1   11 0.000000 0.000000 1.620000 # CAT D_CAP
+pair_coeff    1   12 0.000000 0.000000 1.620000 # CAT D_CTT
+pair_coeff    2    8 0.000000 0.000000 1.620000 # CAO D_CAT
+pair_coeff    2    9 0.000000 0.000000 1.620000 # CAO D_CAO
+pair_coeff    2   10 0.000000 0.000000 1.620000 # CAO D_CAM
+pair_coeff    2   11 0.000000 0.000000 1.620000 # CAO D_CAP
+pair_coeff    2   12 0.000000 0.000000 1.620000 # CAO D_CTT
+pair_coeff    3    8 0.000000 0.000000 1.620000 # CAM D_CAT
+pair_coeff    3    9 0.000000 0.000000 1.620000 # CAM D_CAO
+pair_coeff    3   10 0.000000 0.000000 1.620000 # CAM D_CAM
+pair_coeff    3   11 0.000000 0.000000 1.620000 # CAM D_CAP
+pair_coeff    3   12 0.000000 0.000000 1.620000 # CAM D_CTT
+pair_coeff    4    8 0.000000 0.000000 1.620000 # CAP D_CAT
+pair_coeff    4    9 0.000000 0.000000 1.620000 # CAP D_CAO
+pair_coeff    4   10 0.000000 0.000000 1.620000 # CAP D_CAM
+pair_coeff    4   11 0.000000 0.000000 1.620000 # CAP D_CAP
+pair_coeff    4   12 0.000000 0.000000 1.620000 # CAP D_CTT
+pair_coeff    5    8 0.000000 0.000000 1.620000 # CTT D_CAT
+pair_coeff    5    9 0.000000 0.000000 1.620000 # CTT D_CAO
+pair_coeff    5   10 0.000000 0.000000 1.620000 # CTT D_CAM
+pair_coeff    5   11 0.000000 0.000000 1.620000 # CTT D_CAP
+pair_coeff    5   12 0.000000 0.000000 1.620000 # CTT D_CTT
+pair_coeff    8    8 0.000000 0.000000 1.620000 # D_CAT D_CAT
+pair_coeff    8    9 0.000000 0.000000 1.620000 # D_CAT D_CAO
+pair_coeff    8   10 0.000000 0.000000 1.620000 # D_CAT D_CAM
+pair_coeff    8   11 0.000000 0.000000 1.620000 # D_CAT D_CAP
+pair_coeff    8   12 0.000000 0.000000 1.620000 # D_CAT D_CTT
+pair_coeff    9    9 0.000000 0.000000 1.620000 # D_CAO D_CAO
+pair_coeff    9   10 0.000000 0.000000 1.620000 # D_CAO D_CAM
+pair_coeff    9   11 0.000000 0.000000 1.620000 # D_CAO D_CAP
+pair_coeff    9   12 0.000000 0.000000 1.620000 # D_CAO D_CTT
+pair_coeff   10   10 0.000000 0.000000 1.620000 # D_CAM D_CAM
+pair_coeff   10   11 0.000000 0.000000 1.620000 # D_CAM D_CAP
+pair_coeff   10   12 0.000000 0.000000 1.620000 # D_CAM D_CTT
+pair_coeff   11   11 0.000000 0.000000 1.620000 # D_CAP D_CAP
+pair_coeff   11   12 0.000000 0.000000 1.620000 # D_CAP D_CTT
+pair_coeff   12   12 0.000000 0.000000 1.620000 # D_CTT D_CTT
+
+neighbor 2.0 bin
+
+variable vTEMP   equal 260.0
+variable vTEMP_D equal 1.0
+variable vPRESS  equal 1.0
+
+velocity gCORES  create ${vTEMP} 12345
+velocity gDRUDES create ${vTEMP_D} 12345
+
+fix fDRUDE all drude C C C C C N N D D D D D
+
+fix fSHAKE gCORES shake 0.0001 20 0 b 4 6 7 8
+
+fix fLANG all langevin/drude ${vTEMP} 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes
+fix fNPH all nve
+
+compute cTEMP all temp/drude
+
+thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2]
+thermo 50
+
+timestep 0.5
+run 2000

examples/USER/drude/toluene/in.toluene.nh

@@ -0,0 +1,122 @@
+# 250 toluene system for drude polarizability example (Nose-Hoover)
+
+units real
+boundary p p p
+
+atom_style full
+bond_style harmonic
+angle_style harmonic
+dihedral_style opls
+improper_style opls
+special_bonds lj/coul 0.0 0.0 0.5
+
+pair_style lj/cut/thole/long 2.600 8.0 8.0
+pair_modify mix geometric tail yes
+kspace_style pppm 1.0e-4
+
+read_data data.toluene extra/special/per/atom 1
+
+comm_modify vel yes
+
+group gTOLUENE molecule 1:250
+group gCORES type 1 2 3 4 5 6 7
+group gDRUDES type 8 9 10 11 12
+
+pair_coeff    1    1 0.069998 3.550000 1.620000 # CAT CAT
+pair_coeff    1    2 0.069998 3.550000 1.620000 # CAT CAO
+pair_coeff    1    3 0.069998 3.550000 1.620000 # CAT CAM
+pair_coeff    1    4 0.069998 3.550000 1.620000 # CAT CAP
+pair_coeff    1    5 0.067968 3.524911 1.620000 # CAT CTT
+pair_coeff    1    6 0.045825 2.931041 0.000000 # CAT HAT
+pair_coeff    1    7 0.045825 2.931041 0.000000 # CAT HT
+pair_coeff    2    2 0.069998 3.550000 1.620000 # CAO CAO
+pair_coeff    2    3 0.069998 3.550000 1.620000 # CAO CAM
+pair_coeff    2    4 0.069998 3.550000 1.620000 # CAO CAP
+pair_coeff    2    5 0.067968 3.524911 1.620000 # CAO CTT
+pair_coeff    2    6 0.045825 2.931041 0.000000 # CAO HAT
+pair_coeff    2    7 0.045825 2.931041 0.000000 # CAO HT
+pair_coeff    3    3 0.069998 3.550000 1.620000 # CAM CAM
+pair_coeff    3    4 0.069998 3.550000 1.620000 # CAM CAP
+pair_coeff    3    5 0.067968 3.524911 1.620000 # CAM CTT
+pair_coeff    3    6 0.045825 2.931041 0.000000 # CAM HAT
+pair_coeff    3    7 0.045825 2.931041 0.000000 # CAM HT
+pair_coeff    4    4 0.069998 3.550000 1.620000 # CAP CAP
+pair_coeff    4    5 0.067968 3.524911 1.620000 # CAP CTT
+pair_coeff    4    6 0.045825 2.931041 0.000000 # CAP HAT
+pair_coeff    4    7 0.045825 2.931041 0.000000 # CAP HT
+pair_coeff    5    5 0.065997 3.500000 1.620000 # CTT CTT
+pair_coeff    5    6 0.044496 2.910326 0.000000 # CTT HAT
+pair_coeff    5    7 0.044496 2.910326 0.000000 # CTT HT
+pair_coeff    6    6 0.029999 2.420000 0.000000 # HAT HAT
+pair_coeff    6    7 0.029999 2.420000 0.000000 # HAT HT
+pair_coeff    7    7 0.029999 2.420000 0.000000 # HT HT
+pair_coeff    1    8 0.000000 0.000000 1.620000 # CAT D_CAT
+pair_coeff    1    9 0.000000 0.000000 1.620000 # CAT D_CAO
+pair_coeff    1   10 0.000000 0.000000 1.620000 # CAT D_CAM
+pair_coeff    1   11 0.000000 0.000000 1.620000 # CAT D_CAP
+pair_coeff    1   12 0.000000 0.000000 1.620000 # CAT D_CTT
+pair_coeff    2    8 0.000000 0.000000 1.620000 # CAO D_CAT
+pair_coeff    2    9 0.000000 0.000000 1.620000 # CAO D_CAO
+pair_coeff    2   10 0.000000 0.000000 1.620000 # CAO D_CAM
+pair_coeff    2   11 0.000000 0.000000 1.620000 # CAO D_CAP
+pair_coeff    2   12 0.000000 0.000000 1.620000 # CAO D_CTT
+pair_coeff    3    8 0.000000 0.000000 1.620000 # CAM D_CAT
+pair_coeff    3    9 0.000000 0.000000 1.620000 # CAM D_CAO
+pair_coeff    3   10 0.000000 0.000000 1.620000 # CAM D_CAM
+pair_coeff    3   11 0.000000 0.000000 1.620000 # CAM D_CAP
+pair_coeff    3   12 0.000000 0.000000 1.620000 # CAM D_CTT
+pair_coeff    4    8 0.000000 0.000000 1.620000 # CAP D_CAT
+pair_coeff    4    9 0.000000 0.000000 1.620000 # CAP D_CAO
+pair_coeff    4   10 0.000000 0.000000 1.620000 # CAP D_CAM
+pair_coeff    4   11 0.000000 0.000000 1.620000 # CAP D_CAP
+pair_coeff    4   12 0.000000 0.000000 1.620000 # CAP D_CTT
+pair_coeff    5    8 0.000000 0.000000 1.620000 # CTT D_CAT
+pair_coeff    5    9 0.000000 0.000000 1.620000 # CTT D_CAO
+pair_coeff    5   10 0.000000 0.000000 1.620000 # CTT D_CAM
+pair_coeff    5   11 0.000000 0.000000 1.620000 # CTT D_CAP
+pair_coeff    5   12 0.000000 0.000000 1.620000 # CTT D_CTT
+pair_coeff    8    8 0.000000 0.000000 1.620000 # D_CAT D_CAT
+pair_coeff    8    9 0.000000 0.000000 1.620000 # D_CAT D_CAO
+pair_coeff    8   10 0.000000 0.000000 1.620000 # D_CAT D_CAM
+pair_coeff    8   11 0.000000 0.000000 1.620000 # D_CAT D_CAP
+pair_coeff    8   12 0.000000 0.000000 1.620000 # D_CAT D_CTT
+pair_coeff    9    9 0.000000 0.000000 1.620000 # D_CAO D_CAO
+pair_coeff    9   10 0.000000 0.000000 1.620000 # D_CAO D_CAM
+pair_coeff    9   11 0.000000 0.000000 1.620000 # D_CAO D_CAP
+pair_coeff    9   12 0.000000 0.000000 1.620000 # D_CAO D_CTT
+pair_coeff   10   10 0.000000 0.000000 1.620000 # D_CAM D_CAM
+pair_coeff   10   11 0.000000 0.000000 1.620000 # D_CAM D_CAP
+pair_coeff   10   12 0.000000 0.000000 1.620000 # D_CAM D_CTT
+pair_coeff   11   11 0.000000 0.000000 1.620000 # D_CAP D_CAP
+pair_coeff   11   12 0.000000 0.000000 1.620000 # D_CAP D_CTT
+pair_coeff   12   12 0.000000 0.000000 1.620000 # D_CTT D_CTT
+
+
+neighbor 2.0 bin
+
+variable vTEMP   equal 260.0
+variable vTEMP_D equal 1.0
+variable vPRESS  equal 1.0
+
+velocity gCORES  create ${vTEMP} 12345
+velocity gDRUDES create ${vTEMP_D} 12345
+
+fix fDRUDE all drude C C C C C N N D D D D D
+
+fix fSHAKE gCORES shake 0.0001 20 0 b 4 6 7 8
+
+compute cTEMP_CORE gCORES temp/com
+compute cTEMP all temp/drude
+
+fix fDIRECT all drude/transform/direct
+fix fNVT1 gCORES nvt temp ${vTEMP} ${vTEMP} 100.0
+fix fNVT2 gDRUDES nvt temp ${vTEMP_D} ${vTEMP_D} 20.0
+fix fINVERSE all drude/transform/inverse
+
+fix fMOMENTUM all momentum 100 linear 1 1 1
+
+thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2]
+thermo 50
+
+timestep 0.5
+run 2000

examples/USER/drude/toluene/log.toluene.lang.11Aug17.linux.1

@@ -0,0 +1,251 @@
+LAMMPS (11 Aug 2017)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+  using 1 OpenMP thread(s) per MPI task
+# 250 toluene system for drude polarizability example (Langevin)
+
+units real
+boundary p p p
+
+atom_style full
+bond_style harmonic
+angle_style harmonic
+dihedral_style opls
+improper_style opls
+special_bonds lj/coul 0.0 0.0 0.5
+
+pair_style lj/cut/thole/long 2.600 8.0 8.0
+pair_modify mix geometric tail yes
+kspace_style pppm 1.0e-4
+
+read_data data.toluene extra/special/per/atom 1
+  orthogonal box = (-18.2908 -18.1636 -18.223) to (18.3357 18.1621 18.3287)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  5500 atoms
+  scanning bonds ...
+  4 = max bonds/atom
+  scanning angles ...
+  6 = max angles/atom
+  scanning dihedrals ...
+  8 = max dihedrals/atom
+  scanning impropers ...
+  2 = max impropers/atom
+  reading bonds ...
+  5500 bonds
+  reading angles ...
+  6000 angles
+  reading dihedrals ...
+  6000 dihedrals
+  reading impropers ...
+  1500 impropers
+  5 = max # of 1-2 neighbors
+  10 = max # of 1-3 neighbors
+  16 = max # of 1-4 neighbors
+  20 = max # of special neighbors
+
+comm_modify vel yes
+
+group gTOLUENE molecule 1:250
+5500 atoms in group gTOLUENE
+group gCORES type 1 2 3 4 5 6 7
+3750 atoms in group gCORES
+group gDRUDES type 8 9 10 11 12
+1750 atoms in group gDRUDES
+
+pair_coeff    1    1 0.069998 3.550000 1.620000 # CAT CAT
+pair_coeff    1    2 0.069998 3.550000 1.620000 # CAT CAO
+pair_coeff    1    3 0.069998 3.550000 1.620000 # CAT CAM
+pair_coeff    1    4 0.069998 3.550000 1.620000 # CAT CAP
+pair_coeff    1    5 0.067968 3.524911 1.620000 # CAT CTT
+pair_coeff    1    6 0.045825 2.931041 0.000000 # CAT HAT
+pair_coeff    1    7 0.045825 2.931041 0.000000 # CAT HT
+pair_coeff    2    2 0.069998 3.550000 1.620000 # CAO CAO
+pair_coeff    2    3 0.069998 3.550000 1.620000 # CAO CAM
+pair_coeff    2    4 0.069998 3.550000 1.620000 # CAO CAP
+pair_coeff    2    5 0.067968 3.524911 1.620000 # CAO CTT
+pair_coeff    2    6 0.045825 2.931041 0.000000 # CAO HAT
+pair_coeff    2    7 0.045825 2.931041 0.000000 # CAO HT
+pair_coeff    3    3 0.069998 3.550000 1.620000 # CAM CAM
+pair_coeff    3    4 0.069998 3.550000 1.620000 # CAM CAP
+pair_coeff    3    5 0.067968 3.524911 1.620000 # CAM CTT
+pair_coeff    3    6 0.045825 2.931041 0.000000 # CAM HAT
+pair_coeff    3    7 0.045825 2.931041 0.000000 # CAM HT
+pair_coeff    4    4 0.069998 3.550000 1.620000 # CAP CAP
+pair_coeff    4    5 0.067968 3.524911 1.620000 # CAP CTT
+pair_coeff    4    6 0.045825 2.931041 0.000000 # CAP HAT
+pair_coeff    4    7 0.045825 2.931041 0.000000 # CAP HT
+pair_coeff    5    5 0.065997 3.500000 1.620000 # CTT CTT
+pair_coeff    5    6 0.044496 2.910326 0.000000 # CTT HAT
+pair_coeff    5    7 0.044496 2.910326 0.000000 # CTT HT
+pair_coeff    6    6 0.029999 2.420000 0.000000 # HAT HAT
+pair_coeff    6    7 0.029999 2.420000 0.000000 # HAT HT
+pair_coeff    7    7 0.029999 2.420000 0.000000 # HT HT
+pair_coeff    1    8 0.000000 0.000000 1.620000 # CAT D_CAT
+pair_coeff    1    9 0.000000 0.000000 1.620000 # CAT D_CAO
+pair_coeff    1   10 0.000000 0.000000 1.620000 # CAT D_CAM
+pair_coeff    1   11 0.000000 0.000000 1.620000 # CAT D_CAP
+pair_coeff    1   12 0.000000 0.000000 1.620000 # CAT D_CTT
+pair_coeff    2    8 0.000000 0.000000 1.620000 # CAO D_CAT
+pair_coeff    2    9 0.000000 0.000000 1.620000 # CAO D_CAO
+pair_coeff    2   10 0.000000 0.000000 1.620000 # CAO D_CAM
+pair_coeff    2   11 0.000000 0.000000 1.620000 # CAO D_CAP
+pair_coeff    2   12 0.000000 0.000000 1.620000 # CAO D_CTT
+pair_coeff    3    8 0.000000 0.000000 1.620000 # CAM D_CAT
+pair_coeff    3    9 0.000000 0.000000 1.620000 # CAM D_CAO
+pair_coeff    3   10 0.000000 0.000000 1.620000 # CAM D_CAM
+pair_coeff    3   11 0.000000 0.000000 1.620000 # CAM D_CAP
+pair_coeff    3   12 0.000000 0.000000 1.620000 # CAM D_CTT
+pair_coeff    4    8 0.000000 0.000000 1.620000 # CAP D_CAT
+pair_coeff    4    9 0.000000 0.000000 1.620000 # CAP D_CAO
+pair_coeff    4   10 0.000000 0.000000 1.620000 # CAP D_CAM
+pair_coeff    4   11 0.000000 0.000000 1.620000 # CAP D_CAP
+pair_coeff    4   12 0.000000 0.000000 1.620000 # CAP D_CTT
+pair_coeff    5    8 0.000000 0.000000 1.620000 # CTT D_CAT
+pair_coeff    5    9 0.000000 0.000000 1.620000 # CTT D_CAO
+pair_coeff    5   10 0.000000 0.000000 1.620000 # CTT D_CAM
+pair_coeff    5   11 0.000000 0.000000 1.620000 # CTT D_CAP
+pair_coeff    5   12 0.000000 0.000000 1.620000 # CTT D_CTT
+pair_coeff    8    8 0.000000 0.000000 1.620000 # D_CAT D_CAT
+pair_coeff    8    9 0.000000 0.000000 1.620000 # D_CAT D_CAO
+pair_coeff    8   10 0.000000 0.000000 1.620000 # D_CAT D_CAM
+pair_coeff    8   11 0.000000 0.000000 1.620000 # D_CAT D_CAP
+pair_coeff    8   12 0.000000 0.000000 1.620000 # D_CAT D_CTT
+pair_coeff    9    9 0.000000 0.000000 1.620000 # D_CAO D_CAO
+pair_coeff    9   10 0.000000 0.000000 1.620000 # D_CAO D_CAM
+pair_coeff    9   11 0.000000 0.000000 1.620000 # D_CAO D_CAP
+pair_coeff    9   12 0.000000 0.000000 1.620000 # D_CAO D_CTT
+pair_coeff   10   10 0.000000 0.000000 1.620000 # D_CAM D_CAM
+pair_coeff   10   11 0.000000 0.000000 1.620000 # D_CAM D_CAP
+pair_coeff   10   12 0.000000 0.000000 1.620000 # D_CAM D_CTT
+pair_coeff   11   11 0.000000 0.000000 1.620000 # D_CAP D_CAP
+pair_coeff   11   12 0.000000 0.000000 1.620000 # D_CAP D_CTT
+pair_coeff   12   12 0.000000 0.000000 1.620000 # D_CTT D_CTT
+
+neighbor 2.0 bin
+
+variable vTEMP   equal 260.0
+variable vTEMP_D equal 1.0
+variable vPRESS  equal 1.0
+
+velocity gCORES  create ${vTEMP} 12345
+velocity gCORES  create 260 12345
+velocity gDRUDES create ${vTEMP_D} 12345
+velocity gDRUDES create 1 12345
+
+fix fDRUDE all drude C C C C C N N D D D D D
+
+fix fSHAKE gCORES shake 0.0001 20 0 b 4 6 7 8
+  1250 = # of size 2 clusters
+  0 = # of size 3 clusters
+  250 = # of size 4 clusters
+  0 = # of frozen angles
+
+fix fLANG all langevin/drude ${vTEMP} 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes
+fix fLANG all langevin/drude 260 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes
+fix fLANG all langevin/drude 260 100.0 200611 1 20.0 260514 zero yes
+fix fNPH all nve
+
+compute cTEMP all temp/drude
+
+thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2]
+thermo 50
+
+timestep 0.5
+run 2000
+PPPM initialization ...
+WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+  G vector (1/distance) = 0.382011
+  grid = 40 40 40
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0325934
+  estimated relative force accuracy = 9.8154e-05
+  using double precision FFTs
+  3d grid and FFT values/proc = 103823 64000
+Rebuild special list taking Drude particles into account
+Old max number of 1-2 to 1-4 neighbors: 19
+New max number of 1-2 to 1-4 neighbors: 20 (+1)
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 10
+  ghost atom cutoff = 10
+  binsize = 5, bins = 8 8 8
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut/thole/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 42.06 | 42.06 | 42.06 Mbytes
+Step CPU TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume c_cTEMP[1] c_cTEMP[2] 
+       0            0    14386.197    2910.7282    202.07402    11475.469    6565.4851    20.333365 1.0706727e-06 1.3894617e-07    4972.8631    1306116.6   -1306199.8     40273.68    48631.318    314.89553    3.1777821 
+      50     4.311986    8083.3901    4729.9995    328.37487    3353.3906    1812.5186    685.40417    646.10358    50.083281    804.80656    1305984.8   -1306630.3    16960.287    48631.318    448.67988    116.22125 
+     100     8.756623    6206.7865     3683.944    255.75365    2522.8425    977.52675    777.45439    838.58809    68.086914    471.97862    1306097.1   -1306707.9    15657.142    48631.318    380.53159    35.760643 
+     150    13.134938    5386.0219     3582.482    248.70976    1803.5399    752.25928    803.04832    643.43249     49.76684    131.97853    1306139.2   -1306716.2    15140.102    48631.318    383.61303    10.880935 
+     200    17.508189    4846.4097    3254.3932    225.93257    1592.0166    700.43329    812.26722    657.52279    51.044716   -64.045174    1306160.5   -1306725.7    13844.277    48631.318    351.90677    3.8489009 
+     250    21.871676     4473.215    3091.5333     214.6262    1381.6817    688.24707    842.63267    590.45999     48.22798   -214.02425    1306156.6   -1306730.5    8808.7402    48631.318    335.32872    1.8372171 
+     300    26.226064    4191.8834    2883.8468     200.2078    1308.0367    734.36657    856.15482    584.87904    47.590787   -343.44615    1306163.4   -1306734.9    3389.3777    48631.318    313.03581    1.3011826 
+     350    30.568716    3972.0739    2756.8392    191.39044    1215.2347     664.4688    866.06348    580.13632    48.515297    -378.8729    1306173.3   -1306738.3    8458.1149    48631.318    299.31146    1.1345329 
+     400    34.845648    3838.3528    2731.3975    189.62419    1106.9552     684.0318    870.67752    548.93014    44.038787    -460.1537    1306160.4     -1306741    6697.9188    48631.318    296.54405    1.1332149 
+     450     39.17477      3731.18    2607.8585    181.04762    1123.3216    719.57572    894.99915    571.99504    47.625227   -537.60494    1306171.9   -1306745.2    2450.4224    48631.318    283.13713    1.0721818 
+     500    43.497489    3607.0055    2565.9469    178.13796    1041.0586    717.36452    841.34375    551.39834    45.985413   -542.47313    1306170.9   -1306743.4    3077.1849    48631.318    278.59462    1.0410963 
+     550    47.812038    3513.8132    2548.7259    176.94241    965.08736    673.81272    852.38161    522.99297    44.276434   -552.27379    1306171.2   -1306747.4    4659.7275    48631.318    276.70124    1.0757459 
+     600    52.124423    3386.9627    2471.0692    171.55118    915.89348    689.99732    833.61298    517.49343    43.023588   -594.96363    1306170.6   -1306743.8    2159.7328    48631.318    268.27854    1.0287605 
+     650    56.370068    3374.3191    2413.6719    167.56644    960.64717    703.32428    874.12028    535.41271    43.256032   -617.25815    1306168.6   -1306746.8    1262.4757    48631.318    261.99584    1.0950976 
+     700    60.667476    3342.9467    2412.9563    167.51676    929.99042    683.70355    882.22521    527.03932    43.661355   -616.70117      1306161     -1306751    2950.9009    48631.318    261.92814    1.0771869 
+     750    64.964696    3327.7938    2414.3547    167.61385    913.43902    695.12778    863.48248    542.99202    46.408369   -639.60076    1306160.7   -1306755.6    1583.0277    48631.318    262.09771    1.0464936 
+     800    69.256916     3391.689    2452.2049    170.24155    939.48407     694.2176    892.61592    557.53726    45.495129   -654.56675    1306155.2     -1306751    1232.1671    48631.318    266.20601    1.0640309 
+     850    73.527972    3386.8618    2486.6928    172.63584    900.16902     696.7684    880.27643    545.11446    46.474227   -665.90464    1306154.7   -1306757.3    1129.2062    48631.318    269.97945     1.027015 
+     900    77.775993    3368.0724    2416.7145    167.77767    951.35789    718.66654    893.18396    537.79136    46.404626   -641.29596    1306152.9   -1306756.3    1673.0743    48631.318    262.34697    1.0597091 
+     950    82.028341    3300.4793    2409.5613    167.28107      890.918    728.06888    890.51193    515.08456     44.36547   -671.13741    1306142.3   -1306758.2    1038.6579    48631.318    261.57036    1.0567234 
+    1000    86.189789    3333.2955    2452.2486    170.24458    881.04692     699.8414    915.33862    506.83261     41.77374   -665.68264    1306141.6   -1306758.7    467.42142    48631.318    266.19104    1.0987814 
+    1050    90.384168      3303.87    2376.9713    165.01854    926.89875    706.12941    930.65844    524.73304    42.644613   -657.19573    1306139.3   -1306759.4    1737.6624    48631.318    258.00246    1.0954432 
+    1100    94.549452     3367.668    2454.9154    170.42973    912.75259    715.68494     935.8363    516.52205    43.261761   -671.86101    1306137.9   -1306764.6    961.79199    48631.318      266.492    1.0797548 
+    1150     98.65493    3350.0898    2485.3993    172.54604    864.69051    699.23072    933.76405    510.60424    42.381362   -684.53513    1306127.1   -1306763.8   -272.48178    48631.318    269.82496    1.0512421 
+    1200    102.82045    3309.6871    2398.9577    166.54492    910.72944    705.58979    934.53183    531.90967    45.872142   -664.58495    1306126.9   -1306769.5    627.31931    48631.318    260.41866    1.0531639 
+    1250     106.9899     3304.504    2491.6998    172.98344    812.80426    710.83366    881.33764    494.90045     41.71618   -672.49264    1306123.8   -1306767.3    136.11723    48631.318    270.51026    1.0516137 
+    1300    111.16224    3318.9543    2462.0621    170.92588    856.89219    709.17314    932.87209    503.80373    43.426006    -680.2474    1306121.2   -1306773.3    1276.2503    48631.318    267.28591    1.0510113 
+    1350    115.27184    3314.8515    2434.8483    169.03659    880.00316    710.91641    922.28347    540.40795    44.753548   -686.09335    1306124.5   -1306776.7   -438.87694    48631.318    264.31236    1.0731666 
+    1400    119.44228    3349.0785    2457.7697    170.62788    891.30875    711.28064    936.58607    516.63511    42.396287   -653.09763    1306113.8   -1306776.3    350.79618    48631.318    266.80555    1.0745043 
+    1450    123.61267    3364.1486    2459.8741    170.77397    904.27455    696.57265    946.32098    538.55368     44.69075   -652.75091      1306111   -1306780.1    502.47466    48631.318    267.03201    1.0789056 
+    1500    127.72962    3341.9369    2454.3302     170.3891    887.60672    726.46979    903.40815    557.73064    47.536125   -667.65025    1306100.7   -1306780.6    -248.0975    48631.318    266.44821     1.044725 
+    1550    131.91041    3270.4282    2437.7916    169.24093    832.63655    691.49462    910.83807    523.17366     44.83093   -654.48655    1306100.5   -1306783.7    490.32965    48631.318    264.63652    1.0662604 
+    1600     136.0834    3252.0725    2429.6805    168.67782    822.39196    689.68155    898.22828    535.31963     43.84399   -660.93277    1306100.1   -1306783.9    1729.5956    48631.318    263.74523    1.0817172 
+    1650    140.26444     3239.748    2442.6258    169.57653    797.12222     671.1832     907.1659    507.03947    43.048028   -648.14001    1306103.3   -1306786.5    970.43988    48631.318    265.15987    1.0708872 
+    1700     144.3855    3202.9157     2410.267    167.33006    792.64869    686.40974    882.40791    527.02899    43.819792   -656.82001      1306096   -1306786.2   -107.50166    48631.318    261.64368     1.062837 
+    1750    148.56592    3214.6107    2366.3264    164.27953    848.28434    696.38228    915.58636     538.2236    47.852688    -652.7697    1306093.6   -1306790.6   -164.14366    48631.318    256.84519    1.0937744 
+    1800    152.74611    3209.5771    2421.4089    168.10357    788.16819    683.61816    869.45802    532.77927    45.708374   -658.39221    1306103.1   -1306788.1    277.61781    48631.318    262.83282    1.1036154 
+    1850    156.86567    3146.3973    2362.3333    164.00232      784.064    697.87032     875.8451    523.54452    43.851379   -665.83106    1306101.5   -1306792.7    497.88657    48631.318    256.42683    1.0654271 
+    1900     161.0419    3141.5496    2367.1077    164.33378    774.44186    693.39945    878.97447    515.65653    44.619392   -668.11692    1306103.8   -1306793.9   -1427.3998    48631.318    256.94212    1.0727903 
+    1950    165.22235    3134.6473     2295.577    159.36784    839.07025    699.62719    905.76937    519.32307    46.109334   -645.08933    1306104.9   -1306791.6    1744.2846    48631.318    249.19694    1.0064565 
+    2000        169.4     3146.866    2361.3821    163.93628    785.48386    682.24124     889.6864    534.94877    46.855983    -678.1614      1306104   -1306794.1     699.8735    48631.318    256.32873    1.0559143 
+Loop time of 169.4 on 1 procs for 2000 steps with 5500 atoms
+
+Performance: 0.510 ns/day, 47.056 hours/ns, 11.806 timesteps/s
+99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 107.93     | 107.93     | 107.93     |   0.0 | 63.71
+Bond    | 19.76      | 19.76      | 19.76      |   0.0 | 11.66
+Kspace  | 34.926     | 34.926     | 34.926     |   0.0 | 20.62
+Neigh   | 1.9932     | 1.9932     | 1.9932     |   0.0 |  1.18
+Comm    | 0.73555    | 0.73555    | 0.73555    |   0.0 |  0.43
+Output  | 0.0065863  | 0.0065863  | 0.0065863  |   0.0 |  0.00
+Modify  | 3.9135     | 3.9135     | 3.9135     |   0.0 |  2.31
+Other   |            | 0.133      |            |       |  0.08
+
+Nlocal:    5500 ave 5500 max 5500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    13219 ave 13219 max 13219 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    1.33739e+06 ave 1.33739e+06 max 1.33739e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1337388
+Ave neighs/atom = 243.161
+Ave special neighs/atom = 15.6364
+Neighbor list builds = 32
+Dangerous builds = 0
+Total wall time: 0:02:49

examples/USER/drude/toluene/log.toluene.lang.11Aug17.linux.4

@@ -0,0 +1,251 @@
+LAMMPS (11 Aug 2017)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+  using 1 OpenMP thread(s) per MPI task
+# 250 toluene system for drude polarizability example (Langevin)
+
+units real
+boundary p p p
+
+atom_style full
+bond_style harmonic
+angle_style harmonic
+dihedral_style opls
+improper_style opls
+special_bonds lj/coul 0.0 0.0 0.5
+
+pair_style lj/cut/thole/long 2.600 8.0 8.0
+pair_modify mix geometric tail yes
+kspace_style pppm 1.0e-4
+
+read_data data.toluene extra/special/per/atom 1
+  orthogonal box = (-18.2908 -18.1636 -18.223) to (18.3357 18.1621 18.3287)
+  2 by 1 by 2 MPI processor grid
+  reading atoms ...
+  5500 atoms
+  scanning bonds ...
+  4 = max bonds/atom
+  scanning angles ...
+  6 = max angles/atom
+  scanning dihedrals ...
+  8 = max dihedrals/atom
+  scanning impropers ...
+  2 = max impropers/atom
+  reading bonds ...
+  5500 bonds
+  reading angles ...
+  6000 angles
+  reading dihedrals ...
+  6000 dihedrals
+  reading impropers ...
+  1500 impropers
+  5 = max # of 1-2 neighbors
+  10 = max # of 1-3 neighbors
+  16 = max # of 1-4 neighbors
+  20 = max # of special neighbors
+
+comm_modify vel yes
+
+group gTOLUENE molecule 1:250
+5500 atoms in group gTOLUENE
+group gCORES type 1 2 3 4 5 6 7
+3750 atoms in group gCORES
+group gDRUDES type 8 9 10 11 12
+1750 atoms in group gDRUDES
+
+pair_coeff    1    1 0.069998 3.550000 1.620000 # CAT CAT
+pair_coeff    1    2 0.069998 3.550000 1.620000 # CAT CAO
+pair_coeff    1    3 0.069998 3.550000 1.620000 # CAT CAM
+pair_coeff    1    4 0.069998 3.550000 1.620000 # CAT CAP
+pair_coeff    1    5 0.067968 3.524911 1.620000 # CAT CTT
+pair_coeff    1    6 0.045825 2.931041 0.000000 # CAT HAT
+pair_coeff    1    7 0.045825 2.931041 0.000000 # CAT HT
+pair_coeff    2    2 0.069998 3.550000 1.620000 # CAO CAO
+pair_coeff    2    3 0.069998 3.550000 1.620000 # CAO CAM
+pair_coeff    2    4 0.069998 3.550000 1.620000 # CAO CAP
+pair_coeff    2    5 0.067968 3.524911 1.620000 # CAO CTT
+pair_coeff    2    6 0.045825 2.931041 0.000000 # CAO HAT
+pair_coeff    2    7 0.045825 2.931041 0.000000 # CAO HT
+pair_coeff    3    3 0.069998 3.550000 1.620000 # CAM CAM
+pair_coeff    3    4 0.069998 3.550000 1.620000 # CAM CAP
+pair_coeff    3    5 0.067968 3.524911 1.620000 # CAM CTT
+pair_coeff    3    6 0.045825 2.931041 0.000000 # CAM HAT
+pair_coeff    3    7 0.045825 2.931041 0.000000 # CAM HT
+pair_coeff    4    4 0.069998 3.550000 1.620000 # CAP CAP
+pair_coeff    4    5 0.067968 3.524911 1.620000 # CAP CTT
+pair_coeff    4    6 0.045825 2.931041 0.000000 # CAP HAT
+pair_coeff    4    7 0.045825 2.931041 0.000000 # CAP HT
+pair_coeff    5    5 0.065997 3.500000 1.620000 # CTT CTT
+pair_coeff    5    6 0.044496 2.910326 0.000000 # CTT HAT
+pair_coeff    5    7 0.044496 2.910326 0.000000 # CTT HT
+pair_coeff    6    6 0.029999 2.420000 0.000000 # HAT HAT
+pair_coeff    6    7 0.029999 2.420000 0.000000 # HAT HT
+pair_coeff    7    7 0.029999 2.420000 0.000000 # HT HT
+pair_coeff    1    8 0.000000 0.000000 1.620000 # CAT D_CAT
+pair_coeff    1    9 0.000000 0.000000 1.620000 # CAT D_CAO
+pair_coeff    1   10 0.000000 0.000000 1.620000 # CAT D_CAM
+pair_coeff    1   11 0.000000 0.000000 1.620000 # CAT D_CAP
+pair_coeff    1   12 0.000000 0.000000 1.620000 # CAT D_CTT
+pair_coeff    2    8 0.000000 0.000000 1.620000 # CAO D_CAT
+pair_coeff    2    9 0.000000 0.000000 1.620000 # CAO D_CAO
+pair_coeff    2   10 0.000000 0.000000 1.620000 # CAO D_CAM
+pair_coeff    2   11 0.000000 0.000000 1.620000 # CAO D_CAP
+pair_coeff    2   12 0.000000 0.000000 1.620000 # CAO D_CTT
+pair_coeff    3    8 0.000000 0.000000 1.620000 # CAM D_CAT
+pair_coeff    3    9 0.000000 0.000000 1.620000 # CAM D_CAO
+pair_coeff    3   10 0.000000 0.000000 1.620000 # CAM D_CAM
+pair_coeff    3   11 0.000000 0.000000 1.620000 # CAM D_CAP
+pair_coeff    3   12 0.000000 0.000000 1.620000 # CAM D_CTT
+pair_coeff    4    8 0.000000 0.000000 1.620000 # CAP D_CAT
+pair_coeff    4    9 0.000000 0.000000 1.620000 # CAP D_CAO
+pair_coeff    4   10 0.000000 0.000000 1.620000 # CAP D_CAM
+pair_coeff    4   11 0.000000 0.000000 1.620000 # CAP D_CAP
+pair_coeff    4   12 0.000000 0.000000 1.620000 # CAP D_CTT
+pair_coeff    5    8 0.000000 0.000000 1.620000 # CTT D_CAT
+pair_coeff    5    9 0.000000 0.000000 1.620000 # CTT D_CAO
+pair_coeff    5   10 0.000000 0.000000 1.620000 # CTT D_CAM
+pair_coeff    5   11 0.000000 0.000000 1.620000 # CTT D_CAP
+pair_coeff    5   12 0.000000 0.000000 1.620000 # CTT D_CTT
+pair_coeff    8    8 0.000000 0.000000 1.620000 # D_CAT D_CAT
+pair_coeff    8    9 0.000000 0.000000 1.620000 # D_CAT D_CAO
+pair_coeff    8   10 0.000000 0.000000 1.620000 # D_CAT D_CAM
+pair_coeff    8   11 0.000000 0.000000 1.620000 # D_CAT D_CAP
+pair_coeff    8   12 0.000000 0.000000 1.620000 # D_CAT D_CTT
+pair_coeff    9    9 0.000000 0.000000 1.620000 # D_CAO D_CAO
+pair_coeff    9   10 0.000000 0.000000 1.620000 # D_CAO D_CAM
+pair_coeff    9   11 0.000000 0.000000 1.620000 # D_CAO D_CAP
+pair_coeff    9   12 0.000000 0.000000 1.620000 # D_CAO D_CTT
+pair_coeff   10   10 0.000000 0.000000 1.620000 # D_CAM D_CAM
+pair_coeff   10   11 0.000000 0.000000 1.620000 # D_CAM D_CAP
+pair_coeff   10   12 0.000000 0.000000 1.620000 # D_CAM D_CTT
+pair_coeff   11   11 0.000000 0.000000 1.620000 # D_CAP D_CAP
+pair_coeff   11   12 0.000000 0.000000 1.620000 # D_CAP D_CTT
+pair_coeff   12   12 0.000000 0.000000 1.620000 # D_CTT D_CTT
+
+neighbor 2.0 bin
+
+variable vTEMP   equal 260.0
+variable vTEMP_D equal 1.0
+variable vPRESS  equal 1.0
+
+velocity gCORES  create ${vTEMP} 12345
+velocity gCORES  create 260 12345
+velocity gDRUDES create ${vTEMP_D} 12345
+velocity gDRUDES create 1 12345
+
+fix fDRUDE all drude C C C C C N N D D D D D
+
+fix fSHAKE gCORES shake 0.0001 20 0 b 4 6 7 8
+  1250 = # of size 2 clusters
+  0 = # of size 3 clusters
+  250 = # of size 4 clusters
+  0 = # of frozen angles
+
+fix fLANG all langevin/drude ${vTEMP} 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes
+fix fLANG all langevin/drude 260 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes
+fix fLANG all langevin/drude 260 100.0 200611 1 20.0 260514 zero yes
+fix fNPH all nve
+
+compute cTEMP all temp/drude
+
+thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2]
+thermo 50
+
+timestep 0.5
+run 2000
+PPPM initialization ...
+WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+  G vector (1/distance) = 0.382011
+  grid = 40 40 40
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0325934
+  estimated relative force accuracy = 9.8154e-05
+  using double precision FFTs
+  3d grid and FFT values/proc = 34263 16000
+Rebuild special list taking Drude particles into account
+Old max number of 1-2 to 1-4 neighbors: 19
+New max number of 1-2 to 1-4 neighbors: 20 (+1)
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 10
+  ghost atom cutoff = 10
+  binsize = 5, bins = 8 8 8
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut/thole/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 18 | 18 | 18 Mbytes
+Step CPU TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume c_cTEMP[1] c_cTEMP[2] 
+       0            0    14386.197    2910.7282    202.07402    11475.469    6565.4851    20.333365 1.0706727e-06 1.3894617e-07    4972.8631    1306116.6   -1306199.8     40273.68    48631.318    314.89553    3.1777821 
+      50    1.0658228    8014.6879    4671.7498    324.33095    3342.9381    1798.7991    670.22837    651.99307    50.352024    819.34616    1305984.9   -1306632.7    17255.952    48631.318    442.52888    116.12397 
+     100     2.136163    6185.5007    3697.0414    256.66292    2488.4593    974.42931    774.88353    840.46625    66.896007    427.27085    1306105.5     -1306701    15044.739    48631.318    381.93582    35.802658 
+     150     3.202647    5418.0644    3628.2714    251.88864    1789.7929    764.02696    804.61034    641.14915    47.995428    108.05084    1306138.9   -1306714.9    15258.194    48631.318    388.65363    10.777816 
+     200    4.2728949    4838.4235    3303.8964    229.36927    1534.5271    702.10438    772.85348    625.99718    52.299187   -63.792745    1306166.5   -1306721.4    13487.722    48631.318    357.35337    3.7423617 
+     250    5.3275268    4461.2438    3084.8973    214.16551    1376.3465    693.85145    823.23815    599.85313    48.280277   -230.56822    1306167.8   -1306726.1    8779.0061    48631.318    334.59262    1.8620294 
+     300    6.3794398    4179.6462    2885.0738    200.29299    1294.5724      739.337    868.84011    555.04912    44.838819   -354.73738    1306171.3     -1306730    4410.8735    48631.318    313.17473    1.2892347 
+     350     7.427706    3934.3968    2756.2421    191.34899    1178.1546    666.16877    877.32996    548.99846    45.087026   -404.32209      1306179   -1306734.1    8477.8828    48631.318    299.22663    1.1698531 
+     400    8.4820418    3800.4769    2674.8317    185.69716    1125.6452    693.29433    841.29833    579.61438    48.325361   -470.18802    1306170.5   -1306737.2    6265.7532    48631.318    290.39105    1.1303952 
+     450     9.528651      3685.28    2616.9074    181.67583    1068.3726    702.68328    886.66644    555.74511    46.160811   -557.70651    1306176.6   -1306741.7    2701.7737    48631.318    284.11064     1.091646 
+     500    10.579133    3582.6591    2517.6443    174.78461    1065.0148    701.82101     894.9429    554.06012    46.074357   -570.49878    1306181.8   -1306743.2    3643.7426    48631.318    273.31525    1.0831346 
+     550    11.629649    3542.0402    2527.0386     175.4368    1015.0016    688.73877     916.2381    521.69932    44.014375   -580.05437      1306171   -1306746.6    2928.6632    48631.318    274.34257    1.0740018 
+     600    12.684143    3507.0443    2519.9749    174.94641    987.06936    711.58734    894.63276    525.57884    42.944226   -603.24423    1306161.2   -1306745.7    2082.9907    48631.318    273.57124    1.0784841 
+     650    13.737965    3416.2001    2445.9361    169.80635    970.26394    706.95207    891.76446    540.90369    45.970985   -626.32832    1306160.2   -1306749.2    1912.8783    48631.318     265.5023    1.1021764 
+     700    14.777375    3419.7572     2446.117    169.81891    973.64019    664.17579    936.51992    551.67148    45.696531   -634.70926    1306159.6   -1306749.4    2215.7085    48631.318    265.53614    1.0774684 
+     750    15.795347    3418.6537     2449.343    170.04287    969.31069    706.12432    899.61553    553.21874    45.793213   -642.75298    1306158.1   -1306750.8    1022.2516    48631.318    265.89304    1.0681488 
+     800    16.835794    3385.2449    2465.4963    171.16429    919.74864    692.34918    888.91243    530.24204    45.132243   -638.54787    1306154.6     -1306753    1601.1391    48631.318    267.64361    1.0797553 
+     850     17.87536    3397.1124    2426.3129    168.44403    970.79951    717.48898    878.71057    580.26487    46.675101   -646.96926    1306150.9   -1306756.3    1048.7905    48631.318    263.38063    1.0785255 
+     900    18.899639    3324.2064    2447.5004    169.91495    876.70599    683.62339    881.77789    531.98758    43.646731   -648.59248    1306144.4   -1306760.2    2221.5859    48631.318    265.69596    1.0608373 
+     950    19.938468    3316.6329    2398.6988    166.52695    917.93405    702.84237    885.96473    540.35376    45.671318   -638.80334    1306144.4   -1306762.5    1955.2237    48631.318    260.38167    1.0687233 
+    1000    20.973543    3287.4205     2384.191    165.51976    903.22949    705.56988    889.96387    535.23674    44.902139   -661.28175    1306150.4   -1306761.6    90.200683    48631.318    258.81506    1.0477545 
+    1050    21.990961    3297.7806    2392.0372    166.06448    905.74339    697.33157    889.75086     537.2395    46.319713   -636.03286    1306135.9   -1306764.8    1893.8234    48631.318    259.67633    1.0344207 
+    1100    23.006456     3240.651    2370.2217    164.54996    870.42931    693.87289     897.0846    526.89184    43.778979   -657.83716    1306132.1   -1306765.5    799.62979    48631.318    257.28711    1.0618941 
+    1150    24.014558     3232.457    2377.9797    165.08855    854.47728    692.51558    897.77048     520.3269    43.903959   -657.38369    1306126.9   -1306769.6    178.21408    48631.318    258.13876    1.0479172 
+    1200    25.010178    3238.4266    2392.0623    166.06622    846.36427    695.98996      887.237    522.01974    42.355716   -660.92843    1306124.7     -1306765    1006.1877    48631.318    259.66037    1.0698925 
+    1250     26.01949    3198.3364    2332.7551    161.94888    865.58134    690.81786    897.35028    524.47996    44.421121   -640.92419    1306116.3   -1306766.8    2073.9672    48631.318      253.227    1.0326937 
+    1300    27.026911    3237.6809    2386.3739    165.67131    851.30706    672.11785    901.04813     530.2964    44.020263   -655.33033    1306125.7   -1306766.5    579.46013    48631.318    259.05838    1.0374113 
+    1350    28.033721    3285.9536     2371.155    164.61476    914.79862    718.12968    928.41764    524.02349     43.89896   -657.10221    1306127.3   -1306769.9    518.88041    48631.318    257.36737    1.0993197 
+    1400    29.026742    3272.2173    2391.4158    166.02134    880.80147    712.59883    896.13616    532.95785    45.989768   -658.37495    1306125.6   -1306774.1     961.2067    48631.318     259.5968    1.0557033 
+    1450    30.032566    3244.2627    2356.0955    163.56926    888.16727    714.72692    901.18382    534.59787    45.517573   -655.58258    1306124.5   -1306776.8    596.10558    48631.318    255.75173     1.058657 
+    1500     31.03878    3244.8598    2408.5382    167.21004    836.32161    695.63105    867.27743    527.37333    44.496971   -648.96393    1306125.2   -1306774.7    443.71088    48631.318    261.45495    1.0648973 
+    1550    32.041435    3239.3658    2367.1336    164.33557    872.23223    704.16965     884.5938    544.41685    46.110791   -654.61963    1306124.1   -1306776.5    -446.5562    48631.318    256.96289    1.0409003 
+    1600    33.058977    3221.4258    2334.2656    162.05375     887.1602     713.8296    885.80472    533.86753    45.413663   -633.58824    1306119.6   -1306777.8    1527.9489    48631.318    253.36367    1.0817678 
+    1650    34.080875    3224.4472    2385.9055    165.63879    838.54168    681.01628    879.88017    536.75983    43.884394   -643.24788      1306114   -1306773.8    1314.2208    48631.318    258.97106    1.1033457 
+    1700    35.095047    3178.6575    2352.4294    163.31475     826.2281    700.79494    854.06687    549.39826    46.155483   -662.57181    1306115.2   -1306776.9   -187.36898    48631.318    255.35015    1.0638209 
+    1750    36.093828     3219.473    2371.9421     164.6694    847.53093    699.44953    891.26068    541.91687    45.714235   -679.13432    1306120.3   -1306771.9   -618.32924    48631.318    257.48034    1.0512601 
+    1800    37.110101    3202.0094    2371.8909    164.66585    830.11842    698.44522    858.38216    550.82008    46.315893   -667.77838    1306119.2   -1306775.3   -9.4963278    48631.318    257.46873    1.0619052 
+    1850    38.121337    3202.0111    2366.6984    164.30536    835.31277    714.69988     849.6778    553.24258    46.502994   -667.44162    1306114.9   -1306776.3    131.11108    48631.318    256.90165    1.0656162 
+    1900    39.132607    3228.7805     2365.934    164.25229    862.84648    720.68418    890.65533    554.75943    45.736726   -685.52803    1306115.1   -1306778.5   -82.525994    48631.318    256.81451    1.0726218 
+    1950    40.127507    3218.4068    2443.0023    169.60267    775.40452    673.40001    874.63022    529.69964    43.166847   -680.57322    1306115.4   -1306780.3    622.76654    48631.318    265.20173    1.0693092 
+    2000    41.138176     3257.463    2375.6246    164.92505    881.83842    677.60747    933.47776    547.01076    46.507189   -665.56273    1306123.7   -1306780.9    1829.3477    48631.318    257.88171    1.0500311 
+Loop time of 41.1383 on 4 procs for 2000 steps with 5500 atoms
+
+Performance: 2.100 ns/day, 11.427 hours/ns, 48.617 timesteps/s
+99.8% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 21.082     | 22.483     | 24.145     |  26.6 | 54.65
+Bond    | 4.9992     | 5.0781     | 5.1544     |   2.7 | 12.34
+Kspace  | 9.1202     | 10.806     | 12.272     |  39.7 | 26.27
+Neigh   | 0.45045    | 0.45076    | 0.45094    |   0.0 |  1.10
+Comm    | 0.85982    | 0.87287    | 0.88725    |   1.2 |  2.12
+Output  | 0.0036495  | 0.004005   | 0.0049655  |   0.9 |  0.01
+Modify  | 1.4009     | 1.401      | 1.4013     |   0.0 |  3.41
+Other   |            | 0.04245    |            |       |  0.10
+
+Nlocal:    1375 ave 1398 max 1361 min
+Histogram: 1 0 2 0 0 0 0 0 0 1
+Nghost:    7745.75 ave 7788 max 7697 min
+Histogram: 1 0 0 1 0 0 0 0 1 1
+Neighs:    334374 ave 348629 max 319495 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+
+Total # of neighbors = 1337494
+Ave neighs/atom = 243.181
+Ave special neighs/atom = 15.6364
+Neighbor list builds = 31
+Dangerous builds = 0
+Total wall time: 0:00:41

examples/USER/drude/toluene/log.toluene.nh.11Aug17.linux.1

@@ -0,0 +1,259 @@
+LAMMPS (11 Aug 2017)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+  using 1 OpenMP thread(s) per MPI task
+# 250 toluene system for drude polarizability example (Nose-Hoover)
+
+units real
+boundary p p p
+
+atom_style full
+bond_style harmonic
+angle_style harmonic
+dihedral_style opls
+improper_style opls
+special_bonds lj/coul 0.0 0.0 0.5
+
+pair_style lj/cut/thole/long 2.600 8.0 8.0
+pair_modify mix geometric tail yes
+kspace_style pppm 1.0e-4
+
+read_data data.toluene extra/special/per/atom 1
+  orthogonal box = (-18.2908 -18.1636 -18.223) to (18.3357 18.1621 18.3287)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  5500 atoms
+  scanning bonds ...
+  4 = max bonds/atom
+  scanning angles ...
+  6 = max angles/atom
+  scanning dihedrals ...
+  8 = max dihedrals/atom
+  scanning impropers ...
+  2 = max impropers/atom
+  reading bonds ...
+  5500 bonds
+  reading angles ...
+  6000 angles
+  reading dihedrals ...
+  6000 dihedrals
+  reading impropers ...
+  1500 impropers
+  5 = max # of 1-2 neighbors
+  10 = max # of 1-3 neighbors
+  16 = max # of 1-4 neighbors
+  20 = max # of special neighbors
+
+comm_modify vel yes
+
+group gTOLUENE molecule 1:250
+5500 atoms in group gTOLUENE
+group gCORES type 1 2 3 4 5 6 7
+3750 atoms in group gCORES
+group gDRUDES type 8 9 10 11 12
+1750 atoms in group gDRUDES
+
+pair_coeff    1    1 0.069998 3.550000 1.620000 # CAT CAT
+pair_coeff    1    2 0.069998 3.550000 1.620000 # CAT CAO
+pair_coeff    1    3 0.069998 3.550000 1.620000 # CAT CAM
+pair_coeff    1    4 0.069998 3.550000 1.620000 # CAT CAP
+pair_coeff    1    5 0.067968 3.524911 1.620000 # CAT CTT
+pair_coeff    1    6 0.045825 2.931041 0.000000 # CAT HAT
+pair_coeff    1    7 0.045825 2.931041 0.000000 # CAT HT
+pair_coeff    2    2 0.069998 3.550000 1.620000 # CAO CAO
+pair_coeff    2    3 0.069998 3.550000 1.620000 # CAO CAM
+pair_coeff    2    4 0.069998 3.550000 1.620000 # CAO CAP
+pair_coeff    2    5 0.067968 3.524911 1.620000 # CAO CTT
+pair_coeff    2    6 0.045825 2.931041 0.000000 # CAO HAT
+pair_coeff    2    7 0.045825 2.931041 0.000000 # CAO HT
+pair_coeff    3    3 0.069998 3.550000 1.620000 # CAM CAM
+pair_coeff    3    4 0.069998 3.550000 1.620000 # CAM CAP
+pair_coeff    3    5 0.067968 3.524911 1.620000 # CAM CTT
+pair_coeff    3    6 0.045825 2.931041 0.000000 # CAM HAT
+pair_coeff    3    7 0.045825 2.931041 0.000000 # CAM HT
+pair_coeff    4    4 0.069998 3.550000 1.620000 # CAP CAP
+pair_coeff    4    5 0.067968 3.524911 1.620000 # CAP CTT
+pair_coeff    4    6 0.045825 2.931041 0.000000 # CAP HAT
+pair_coeff    4    7 0.045825 2.931041 0.000000 # CAP HT
+pair_coeff    5    5 0.065997 3.500000 1.620000 # CTT CTT
+pair_coeff    5    6 0.044496 2.910326 0.000000 # CTT HAT
+pair_coeff    5    7 0.044496 2.910326 0.000000 # CTT HT
+pair_coeff    6    6 0.029999 2.420000 0.000000 # HAT HAT
+pair_coeff    6    7 0.029999 2.420000 0.000000 # HAT HT
+pair_coeff    7    7 0.029999 2.420000 0.000000 # HT HT
+pair_coeff    1    8 0.000000 0.000000 1.620000 # CAT D_CAT
+pair_coeff    1    9 0.000000 0.000000 1.620000 # CAT D_CAO
+pair_coeff    1   10 0.000000 0.000000 1.620000 # CAT D_CAM
+pair_coeff    1   11 0.000000 0.000000 1.620000 # CAT D_CAP
+pair_coeff    1   12 0.000000 0.000000 1.620000 # CAT D_CTT
+pair_coeff    2    8 0.000000 0.000000 1.620000 # CAO D_CAT
+pair_coeff    2    9 0.000000 0.000000 1.620000 # CAO D_CAO
+pair_coeff    2   10 0.000000 0.000000 1.620000 # CAO D_CAM
+pair_coeff    2   11 0.000000 0.000000 1.620000 # CAO D_CAP
+pair_coeff    2   12 0.000000 0.000000 1.620000 # CAO D_CTT
+pair_coeff    3    8 0.000000 0.000000 1.620000 # CAM D_CAT
+pair_coeff    3    9 0.000000 0.000000 1.620000 # CAM D_CAO
+pair_coeff    3   10 0.000000 0.000000 1.620000 # CAM D_CAM
+pair_coeff    3   11 0.000000 0.000000 1.620000 # CAM D_CAP
+pair_coeff    3   12 0.000000 0.000000 1.620000 # CAM D_CTT
+pair_coeff    4    8 0.000000 0.000000 1.620000 # CAP D_CAT
+pair_coeff    4    9 0.000000 0.000000 1.620000 # CAP D_CAO
+pair_coeff    4   10 0.000000 0.000000 1.620000 # CAP D_CAM
+pair_coeff    4   11 0.000000 0.000000 1.620000 # CAP D_CAP
+pair_coeff    4   12 0.000000 0.000000 1.620000 # CAP D_CTT
+pair_coeff    5    8 0.000000 0.000000 1.620000 # CTT D_CAT
+pair_coeff    5    9 0.000000 0.000000 1.620000 # CTT D_CAO
+pair_coeff    5   10 0.000000 0.000000 1.620000 # CTT D_CAM
+pair_coeff    5   11 0.000000 0.000000 1.620000 # CTT D_CAP
+pair_coeff    5   12 0.000000 0.000000 1.620000 # CTT D_CTT
+pair_coeff    8    8 0.000000 0.000000 1.620000 # D_CAT D_CAT
+pair_coeff    8    9 0.000000 0.000000 1.620000 # D_CAT D_CAO
+pair_coeff    8   10 0.000000 0.000000 1.620000 # D_CAT D_CAM
+pair_coeff    8   11 0.000000 0.000000 1.620000 # D_CAT D_CAP
+pair_coeff    8   12 0.000000 0.000000 1.620000 # D_CAT D_CTT
+pair_coeff    9    9 0.000000 0.000000 1.620000 # D_CAO D_CAO
+pair_coeff    9   10 0.000000 0.000000 1.620000 # D_CAO D_CAM
+pair_coeff    9   11 0.000000 0.000000 1.620000 # D_CAO D_CAP
+pair_coeff    9   12 0.000000 0.000000 1.620000 # D_CAO D_CTT
+pair_coeff   10   10 0.000000 0.000000 1.620000 # D_CAM D_CAM
+pair_coeff   10   11 0.000000 0.000000 1.620000 # D_CAM D_CAP
+pair_coeff   10   12 0.000000 0.000000 1.620000 # D_CAM D_CTT
+pair_coeff   11   11 0.000000 0.000000 1.620000 # D_CAP D_CAP
+pair_coeff   11   12 0.000000 0.000000 1.620000 # D_CAP D_CTT
+pair_coeff   12   12 0.000000 0.000000 1.620000 # D_CTT D_CTT
+
+
+neighbor 2.0 bin
+
+variable vTEMP   equal 260.0
+variable vTEMP_D equal 1.0
+variable vPRESS  equal 1.0
+
+velocity gCORES  create ${vTEMP} 12345
+velocity gCORES  create 260 12345
+velocity gDRUDES create ${vTEMP_D} 12345
+velocity gDRUDES create 1 12345
+
+fix fDRUDE all drude C C C C C N N D D D D D
+
+fix fSHAKE gCORES shake 0.0001 20 0 b 4 6 7 8
+  1250 = # of size 2 clusters
+  0 = # of size 3 clusters
+  250 = # of size 4 clusters
+  0 = # of frozen angles
+
+compute cTEMP_CORE gCORES temp/com
+compute cTEMP all temp/drude
+
+fix fDIRECT all drude/transform/direct
+fix fNVT1 gCORES nvt temp ${vTEMP} ${vTEMP} 100.0
+fix fNVT1 gCORES nvt temp 260 ${vTEMP} 100.0
+fix fNVT1 gCORES nvt temp 260 260 100.0
+fix fNVT2 gDRUDES nvt temp ${vTEMP_D} ${vTEMP_D} 20.0
+fix fNVT2 gDRUDES nvt temp 1 ${vTEMP_D} 20.0
+fix fNVT2 gDRUDES nvt temp 1 1 20.0
+fix fINVERSE all drude/transform/inverse
+
+fix fMOMENTUM all momentum 100 linear 1 1 1
+
+thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2]
+thermo 50
+
+timestep 0.5
+run 2000
+PPPM initialization ...
+WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+  G vector (1/distance) = 0.382011
+  grid = 40 40 40
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0325934
+  estimated relative force accuracy = 9.8154e-05
+  using double precision FFTs
+  3d grid and FFT values/proc = 103823 64000
+Rebuild special list taking Drude particles into account
+Old max number of 1-2 to 1-4 neighbors: 19
+New max number of 1-2 to 1-4 neighbors: 20 (+1)
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 10
+  ghost atom cutoff = 10
+  binsize = 5, bins = 8 8 8
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut/thole/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 42.06 | 42.06 | 42.06 Mbytes
+Step CPU TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume c_cTEMP[1] c_cTEMP[2] 
+       0            0    14386.197    2910.7282    202.07402    11475.469    6565.4851    20.333365 1.0706727e-06 1.3894617e-07    4972.8631    1306116.6   -1306199.8     40273.68    48631.318    314.89553    3.1777821 
+      50     4.462481     6863.642    4633.9267    321.70512    2229.7153     735.2547     604.6946    648.35773    49.039129    824.06033    1306091.3   -1306722.9    17914.827    48631.318    504.18525 0.0086839843 
+     100    8.8666639    6628.0722    4376.1868    303.81182    2251.8853    598.11249    651.43051    919.41359    74.216826     589.6504    1306135.1     -1306716    17450.721    48631.318    476.14276 0.0075129702 
+     150    13.323556    6336.1884    4726.0692    328.10201    1610.1192    560.01225    621.30109    640.32475    45.531175    288.99128    1306173.9     -1306720    18303.624    48631.318    514.21215 0.0061921467 
+     200    17.710109    5997.6194    4565.6288    316.96362    1431.9906     524.2765    591.79843    718.11015    56.374558    88.660843      1306183   -1306730.3    17986.182    48631.318    496.75522   0.00681205 
+     250    22.154451    5648.1758    4433.1558    307.76682      1215.02    502.13687    578.85369    665.27326    49.096119   -19.019967    1306179.2   -1306740.5    11771.328    48631.318    482.34141 0.0071619539 
+     300    26.524393    5317.8584    4075.2077    282.91669    1242.6506    602.55113    637.40817    647.27074    44.769726   -123.22347    1306183.3   -1306749.5    3571.1867    48631.318     443.3952 0.0071733829 
+     350    30.881443     4996.709    3935.7988    273.23838    1060.9102    455.75196    634.36552    638.77826    45.831053    -157.6304    1306198.1   -1306754.3    13525.264    48631.318    428.22739 0.0063722044 
+     400    35.218285    4695.9297    3742.6585    259.82983    953.27122    457.49584    620.73047    591.94411    42.495713   -183.91838    1306186.7   -1306762.2    10901.217    48631.318    407.21326  0.005787501 
+     450    39.545502    4417.8027    3513.6374     243.9303    904.16528    519.61263    580.76003    624.06933    45.631271   -286.60025    1306184.3   -1306763.6    2956.9012    48631.318    382.29486 0.0057536613 
+     500    43.868895    4165.0012    3333.7203    231.43976    831.28089     465.5234    579.36085    580.60005     42.34515   -254.82269    1306183.9   -1306765.6    5818.5565    48631.318    362.71904 0.0059224891 
+     550    48.242395    3934.5209    3211.9362    222.98504    722.58462    431.14864    581.46511     517.2025    39.188196   -265.47041    1306182.7   -1306763.6    8537.9404    48631.318    349.46863 0.0055762504 
+     600    52.542171    3714.8655    3121.0494    216.67532    593.81611    425.12998    539.89496    490.30508    34.564566   -305.82069    1306175.2   -1306765.5    7402.7677    48631.318    339.57967 0.0057486673 
+     650    56.830079    3516.2452    2930.7498    203.46399    585.49537    511.91461    512.48859    521.40636    37.766801   -391.65392    1306163.5     -1306770    381.72879    48631.318    318.87447 0.0054629243 
+     700    61.119511    3342.7694    2864.1576     198.8409     478.6118    451.54683    498.82407    489.17207     35.23127   -375.78886    1306153.8   -1306774.2    3691.2716    48631.318    311.62801 0.0071278731 
+     750    65.401576    3181.7673    2786.7104    193.46422    395.05691    409.83192    508.19542    454.56182    32.890716   -379.80692      1306149   -1306779.6    7428.3698    48631.318    303.20195  0.006233194 
+     800    69.680899    3032.4158    2699.8707    187.43547    332.54509    453.40673    486.16575     441.1235    32.847786   -437.39338    1306144.4     -1306788    1701.7652    48631.318    293.75377 0.0056528223 
+     850     73.96463    2898.4928    2563.6959    177.98169     334.7969    463.66637    486.19929    453.38803    34.062233   -455.86062    1306144.2   -1306790.9   -285.03665    48631.318     278.9376 0.0052777781 
+     900    78.229548    2780.3555    2528.3241    175.52604    252.03136    396.92692    451.76463    435.59744    33.035257   -413.46176    1306142.9   -1306794.7    3836.4341    48631.318    275.08801 0.0070306435 
+     950    82.482848    2679.3417    2456.8817    170.56624    222.45998    385.66656     434.6516    418.37977    32.156722    -387.2201    1306136.9   -1306798.1    5510.2309    48631.318    267.31515 0.0064042654 
+    1000    86.722726    2593.4365    2367.4477    164.35738    225.98882     427.8524    453.27435    415.48809    31.097577   -436.62051    1306131.8   -1306796.9    1166.3909    48631.318    257.58464 0.0059160543 
+    1050    90.888482    2524.7788    2305.0253    160.02377    219.75349    432.90807    438.86657    412.79356    30.892593   -414.29436    1306119.4   -1306800.8    1698.2687    48631.318    250.79245 0.0065593259 
+    1100    95.024656    2471.8176    2311.0953    160.44518    160.72227    378.43572     453.3435    392.48525    29.012472   -409.64374    1306119.6   -1306802.5      4190.91    48631.318    251.45323 0.0059713432 
+    1150    99.165724    2433.9279    2279.0766    158.22231     154.8513    395.30434    436.87933    414.39389    31.118973   -428.90902    1306110.2   -1306804.2    3274.8924    48631.318    247.96893 0.0069039065 
+    1200    103.31062    2411.3777    2238.4638    155.40282    172.91381    453.61551    460.27693    408.59237    31.237062   -482.78549    1306110.2   -1306808.2   -523.10179    48631.318    243.55012 0.0068754631 
+    1250    107.40149    2402.1932    2286.0576    158.70696    116.13565    416.44979    462.75875    391.75373    29.446705   -477.67214    1306102.2   -1306808.8    484.04837    48631.318    248.72579  0.011679749 
+    1300    111.55448    2406.5029    2261.2729    156.98631    145.23005    408.68043    437.74725     400.4567    30.448106   -418.44274    1306096.8   -1306810.5    4490.4165    48631.318    245.99228  0.076574936 
+    1350    115.71244    2459.1398    2317.5855    160.89575    141.55434    651.84862    447.40877    400.66793    29.060967   -461.45124    1305884.3   -1306810.3    693.59782    48631.318    250.14098    3.5622064 
+    1400    119.88515    2479.5991    2285.6701    158.68006      193.929    582.54021    457.54475    430.29254    30.183876   -449.49979    1305955.6   -1306812.8    930.31169    48631.318    247.21826    2.5935077 
+    1450    124.05689    2498.3537    2286.4924    158.73715    211.86128    434.79588     477.9598    402.79356    31.070492   -406.60813    1306086.4   -1306814.5    2933.4418    48631.318    248.74646  0.058608522 
+    1500    128.29115      2546.66    2423.6257    168.25747    123.03432    392.07474    456.01536    385.97457    29.255586   -417.92459    1306089.9   -1306812.3    3333.3497    48631.318      263.694  0.011243575 
+    1550    132.46344    2596.5481    2325.2227    161.42596    271.32542    462.52464    469.53612    461.20308    34.616094   -423.51186    1306080.4   -1306813.4    2155.0566    48631.318    252.98739  0.011191115 
+    1600    136.64497    2646.7844    2387.8797    165.77585    258.90469     424.6071    484.95314    449.56642    33.318144   -395.67454      1306077   -1306814.8    1291.5449    48631.318    259.80403  0.012426122 
+    1650    140.83234    2700.2847    2387.3033    165.73584    312.98138    431.00741    496.39504    455.52303    32.724808   -357.63815    1306070.3   -1306815.3    5007.2365    48631.318    259.70198  0.081729799 
+    1700    145.02103    2777.9556    2386.7756     165.6992    391.18003    636.61544    523.12627    482.84847    35.186128   -391.10505    1305919.7   -1306815.2    2192.7076    48631.318    258.14043    2.7318649 
+    1750    149.22218    2829.5998    2559.2796    177.67509    270.32019      684.587    479.93609    446.30457    31.888933   -385.84966    1305832.5   -1306819.1    1683.1471    48631.318    276.95798    2.6465587 
+    1800    153.41978     2835.768    2465.6959    171.17815    370.07208    470.05934    508.38934    479.71489    37.826868    -369.0767    1306062.8   -1306819.6    3023.0762    48631.318    268.22249  0.097440318 
+    1850    157.62632    2857.7601    2504.3893    173.86439    353.37083    436.06841    516.10132    487.71301    36.514956   -385.43181    1306078.9   -1306816.5    2950.5189    48631.318    272.47825  0.016816883 
+    1900     161.8372     2867.791    2528.8957    175.56572    338.89527    446.38065    509.27013    485.03036    37.283587   -402.68445    1306076.6   -1306812.9    3161.5045    48631.318     275.1476  0.011615474 
+    1950    166.10858      2861.34    2513.9103    174.52538     347.4297     470.9855    536.84666     467.9604    36.049051   -430.05716    1306079.3   -1306813.6    738.77866    48631.318    273.51233  0.020075246 
+    2000    170.32286    2838.0367    2530.4481     175.6735    307.58858    423.18694    516.91384    454.72628    35.048394   -387.67176    1306074.6   -1306809.3    4321.7103    48631.318    275.24492   0.13775419 
+Loop time of 170.323 on 1 procs for 2000 steps with 5500 atoms
+
+Performance: 0.507 ns/day, 47.312 hours/ns, 11.742 timesteps/s
+99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 105.66     | 105.66     | 105.66     |   0.0 | 62.04
+Bond    | 19.802     | 19.802     | 19.802     |   0.0 | 11.63
+Kspace  | 35.029     | 35.029     | 35.029     |   0.0 | 20.57
+Neigh   | 2.7502     | 2.7502     | 2.7502     |   0.0 |  1.61
+Comm    | 0.62654    | 0.62654    | 0.62654    |   0.0 |  0.37
+Output  | 0.006705   | 0.006705   | 0.006705   |   0.0 |  0.00
+Modify  | 6.3072     | 6.3072     | 6.3072     |   0.0 |  3.70
+Other   |            | 0.1366     |            |       |  0.08
+
+Nlocal:    5500 ave 5500 max 5500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    15407 ave 15407 max 15407 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    1.30509e+06 ave 1.30509e+06 max 1.30509e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1305088
+Ave neighs/atom = 237.289
+Ave special neighs/atom = 15.6364
+Neighbor list builds = 44
+Dangerous builds = 0
+Total wall time: 0:02:50

examples/USER/drude/toluene/log.toluene.nh.11Aug17.linux.4

@@ -0,0 +1,259 @@
+LAMMPS (11 Aug 2017)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+  using 1 OpenMP thread(s) per MPI task
+# 250 toluene system for drude polarizability example (Nose-Hoover)
+
+units real
+boundary p p p
+
+atom_style full
+bond_style harmonic
+angle_style harmonic
+dihedral_style opls
+improper_style opls
+special_bonds lj/coul 0.0 0.0 0.5
+
+pair_style lj/cut/thole/long 2.600 8.0 8.0
+pair_modify mix geometric tail yes
+kspace_style pppm 1.0e-4
+
+read_data data.toluene extra/special/per/atom 1
+  orthogonal box = (-18.2908 -18.1636 -18.223) to (18.3357 18.1621 18.3287)
+  2 by 1 by 2 MPI processor grid
+  reading atoms ...
+  5500 atoms
+  scanning bonds ...
+  4 = max bonds/atom
+  scanning angles ...
+  6 = max angles/atom
+  scanning dihedrals ...
+  8 = max dihedrals/atom
+  scanning impropers ...
+  2 = max impropers/atom
+  reading bonds ...
+  5500 bonds
+  reading angles ...
+  6000 angles
+  reading dihedrals ...
+  6000 dihedrals
+  reading impropers ...
+  1500 impropers
+  5 = max # of 1-2 neighbors
+  10 = max # of 1-3 neighbors
+  16 = max # of 1-4 neighbors
+  20 = max # of special neighbors
+
+comm_modify vel yes
+
+group gTOLUENE molecule 1:250
+5500 atoms in group gTOLUENE
+group gCORES type 1 2 3 4 5 6 7
+3750 atoms in group gCORES
+group gDRUDES type 8 9 10 11 12
+1750 atoms in group gDRUDES
+
+pair_coeff    1    1 0.069998 3.550000 1.620000 # CAT CAT
+pair_coeff    1    2 0.069998 3.550000 1.620000 # CAT CAO
+pair_coeff    1    3 0.069998 3.550000 1.620000 # CAT CAM
+pair_coeff    1    4 0.069998 3.550000 1.620000 # CAT CAP
+pair_coeff    1    5 0.067968 3.524911 1.620000 # CAT CTT
+pair_coeff    1    6 0.045825 2.931041 0.000000 # CAT HAT
+pair_coeff    1    7 0.045825 2.931041 0.000000 # CAT HT
+pair_coeff    2    2 0.069998 3.550000 1.620000 # CAO CAO
+pair_coeff    2    3 0.069998 3.550000 1.620000 # CAO CAM
+pair_coeff    2    4 0.069998 3.550000 1.620000 # CAO CAP
+pair_coeff    2    5 0.067968 3.524911 1.620000 # CAO CTT
+pair_coeff    2    6 0.045825 2.931041 0.000000 # CAO HAT
+pair_coeff    2    7 0.045825 2.931041 0.000000 # CAO HT
+pair_coeff    3    3 0.069998 3.550000 1.620000 # CAM CAM
+pair_coeff    3    4 0.069998 3.550000 1.620000 # CAM CAP
+pair_coeff    3    5 0.067968 3.524911 1.620000 # CAM CTT
+pair_coeff    3    6 0.045825 2.931041 0.000000 # CAM HAT
+pair_coeff    3    7 0.045825 2.931041 0.000000 # CAM HT
+pair_coeff    4    4 0.069998 3.550000 1.620000 # CAP CAP
+pair_coeff    4    5 0.067968 3.524911 1.620000 # CAP CTT
+pair_coeff    4    6 0.045825 2.931041 0.000000 # CAP HAT
+pair_coeff    4    7 0.045825 2.931041 0.000000 # CAP HT
+pair_coeff    5    5 0.065997 3.500000 1.620000 # CTT CTT
+pair_coeff    5    6 0.044496 2.910326 0.000000 # CTT HAT
+pair_coeff    5    7 0.044496 2.910326 0.000000 # CTT HT
+pair_coeff    6    6 0.029999 2.420000 0.000000 # HAT HAT
+pair_coeff    6    7 0.029999 2.420000 0.000000 # HAT HT
+pair_coeff    7    7 0.029999 2.420000 0.000000 # HT HT
+pair_coeff    1    8 0.000000 0.000000 1.620000 # CAT D_CAT
+pair_coeff    1    9 0.000000 0.000000 1.620000 # CAT D_CAO
+pair_coeff    1   10 0.000000 0.000000 1.620000 # CAT D_CAM
+pair_coeff    1   11 0.000000 0.000000 1.620000 # CAT D_CAP
+pair_coeff    1   12 0.000000 0.000000 1.620000 # CAT D_CTT
+pair_coeff    2    8 0.000000 0.000000 1.620000 # CAO D_CAT
+pair_coeff    2    9 0.000000 0.000000 1.620000 # CAO D_CAO
+pair_coeff    2   10 0.000000 0.000000 1.620000 # CAO D_CAM
+pair_coeff    2   11 0.000000 0.000000 1.620000 # CAO D_CAP
+pair_coeff    2   12 0.000000 0.000000 1.620000 # CAO D_CTT
+pair_coeff    3    8 0.000000 0.000000 1.620000 # CAM D_CAT
+pair_coeff    3    9 0.000000 0.000000 1.620000 # CAM D_CAO
+pair_coeff    3   10 0.000000 0.000000 1.620000 # CAM D_CAM
+pair_coeff    3   11 0.000000 0.000000 1.620000 # CAM D_CAP
+pair_coeff    3   12 0.000000 0.000000 1.620000 # CAM D_CTT
+pair_coeff    4    8 0.000000 0.000000 1.620000 # CAP D_CAT
+pair_coeff    4    9 0.000000 0.000000 1.620000 # CAP D_CAO
+pair_coeff    4   10 0.000000 0.000000 1.620000 # CAP D_CAM
+pair_coeff    4   11 0.000000 0.000000 1.620000 # CAP D_CAP
+pair_coeff    4   12 0.000000 0.000000 1.620000 # CAP D_CTT
+pair_coeff    5    8 0.000000 0.000000 1.620000 # CTT D_CAT
+pair_coeff    5    9 0.000000 0.000000 1.620000 # CTT D_CAO
+pair_coeff    5   10 0.000000 0.000000 1.620000 # CTT D_CAM
+pair_coeff    5   11 0.000000 0.000000 1.620000 # CTT D_CAP
+pair_coeff    5   12 0.000000 0.000000 1.620000 # CTT D_CTT
+pair_coeff    8    8 0.000000 0.000000 1.620000 # D_CAT D_CAT
+pair_coeff    8    9 0.000000 0.000000 1.620000 # D_CAT D_CAO
+pair_coeff    8   10 0.000000 0.000000 1.620000 # D_CAT D_CAM
+pair_coeff    8   11 0.000000 0.000000 1.620000 # D_CAT D_CAP
+pair_coeff    8   12 0.000000 0.000000 1.620000 # D_CAT D_CTT
+pair_coeff    9    9 0.000000 0.000000 1.620000 # D_CAO D_CAO
+pair_coeff    9   10 0.000000 0.000000 1.620000 # D_CAO D_CAM
+pair_coeff    9   11 0.000000 0.000000 1.620000 # D_CAO D_CAP
+pair_coeff    9   12 0.000000 0.000000 1.620000 # D_CAO D_CTT
+pair_coeff   10   10 0.000000 0.000000 1.620000 # D_CAM D_CAM
+pair_coeff   10   11 0.000000 0.000000 1.620000 # D_CAM D_CAP
+pair_coeff   10   12 0.000000 0.000000 1.620000 # D_CAM D_CTT
+pair_coeff   11   11 0.000000 0.000000 1.620000 # D_CAP D_CAP
+pair_coeff   11   12 0.000000 0.000000 1.620000 # D_CAP D_CTT
+pair_coeff   12   12 0.000000 0.000000 1.620000 # D_CTT D_CTT
+
+
+neighbor 2.0 bin
+
+variable vTEMP   equal 260.0
+variable vTEMP_D equal 1.0
+variable vPRESS  equal 1.0
+
+velocity gCORES  create ${vTEMP} 12345
+velocity gCORES  create 260 12345
+velocity gDRUDES create ${vTEMP_D} 12345
+velocity gDRUDES create 1 12345
+
+fix fDRUDE all drude C C C C C N N D D D D D
+
+fix fSHAKE gCORES shake 0.0001 20 0 b 4 6 7 8
+  1250 = # of size 2 clusters
+  0 = # of size 3 clusters
+  250 = # of size 4 clusters
+  0 = # of frozen angles
+
+compute cTEMP_CORE gCORES temp/com
+compute cTEMP all temp/drude
+
+fix fDIRECT all drude/transform/direct
+fix fNVT1 gCORES nvt temp ${vTEMP} ${vTEMP} 100.0
+fix fNVT1 gCORES nvt temp 260 ${vTEMP} 100.0
+fix fNVT1 gCORES nvt temp 260 260 100.0
+fix fNVT2 gDRUDES nvt temp ${vTEMP_D} ${vTEMP_D} 20.0
+fix fNVT2 gDRUDES nvt temp 1 ${vTEMP_D} 20.0
+fix fNVT2 gDRUDES nvt temp 1 1 20.0
+fix fINVERSE all drude/transform/inverse
+
+fix fMOMENTUM all momentum 100 linear 1 1 1
+
+thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2]
+thermo 50
+
+timestep 0.5
+run 2000
+PPPM initialization ...
+WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+  G vector (1/distance) = 0.382011
+  grid = 40 40 40
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0325934
+  estimated relative force accuracy = 9.8154e-05
+  using double precision FFTs
+  3d grid and FFT values/proc = 34263 16000
+Rebuild special list taking Drude particles into account
+Old max number of 1-2 to 1-4 neighbors: 19
+New max number of 1-2 to 1-4 neighbors: 20 (+1)
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 10
+  ghost atom cutoff = 10
+  binsize = 5, bins = 8 8 8
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut/thole/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 18 | 18 | 18 Mbytes
+Step CPU TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume c_cTEMP[1] c_cTEMP[2] 
+       0            0    14386.197    2910.7282    202.07402    11475.469    6565.4851    20.333365 1.0706727e-06 1.3894617e-07    4972.8631    1306116.6   -1306199.8     40273.68    48631.318    314.89553    3.1777821 
+      50    1.1419601    6863.6417    4633.9267    321.70512     2229.715     735.2547    604.69459    648.35773    49.039129    824.06033    1306091.3   -1306722.9    17914.827    48631.318    504.18525 0.0086839775 
+     100    2.3001912    6628.0719    4376.1868    303.81182    2251.8851    598.11248    651.43051    919.41359    74.216825     589.6504    1306135.1     -1306716    17450.721    48631.318    476.14276 0.0075129701 
+     150     3.473469    6336.1884    4726.0692    328.10201    1610.1192    560.01225    621.30109    640.32474    45.531174    288.99129    1306173.9     -1306720    18303.624    48631.318    514.21215  0.006192153 
+     200    4.6296241    5997.6192    4565.6288    316.96362    1431.9903    524.27651    591.79844    718.11014    56.374557     88.66084      1306183   -1306730.3    17986.183    48631.318    496.75522 0.0068120542 
+     250    5.7982912    5648.1756    4433.1557    307.76682    1215.0199    502.13686     578.8537    665.27326    49.096119   -19.019961    1306179.2   -1306740.5    11771.328    48631.318    482.34141 0.0071619522 
+     300    6.9468622    5317.8583    4075.2077    282.91669    1242.6505    602.55113    637.40818    647.27073    44.769725   -123.22347    1306183.3   -1306749.5    3571.1872    48631.318     443.3952 0.0071733908 
+     350    8.0925181    4996.7094    3935.7988    273.23838    1060.9106    455.75195     634.3655    638.77824    45.831051   -157.63039    1306198.1   -1306754.3    13525.265    48631.318    428.22739 0.0063722017 
+     400    9.2309761    4695.9294    3742.6584    259.82983    953.27093    457.49585    620.73048    591.94413    42.495714   -183.91838    1306186.7   -1306762.2    10901.217    48631.318    407.21326    0.0057875 
+     450    10.363872    4417.8018    3513.6374     243.9303     904.1644    519.61261    580.76003    624.06933    45.631272   -286.60025    1306184.3   -1306763.6    2956.9021    48631.318    382.29485 0.0057536673 
+     500    11.493601    4165.0005    3333.7203    231.43976    831.28022    465.52341    579.36085    580.60004    42.345149   -254.82269    1306183.9   -1306765.6    5818.5549    48631.318    362.71904 0.0059224858 
+     550    12.636785    3934.5207    3211.9362    222.98504    722.58446    431.14864    581.46511    517.20249    39.188194    -265.4704    1306182.7   -1306763.6    8537.9415    48631.318    349.46863 0.0055762027 
+     600    13.759642    3714.8658    3121.0493    216.67532    593.81649    425.12998    539.89497    490.30506    34.564567   -305.82067    1306175.2   -1306765.5    7402.7688    48631.318    339.57967  0.005748668 
+     650    14.880794    3516.2453    2930.7499      203.464    585.49542    511.91457    512.48857    521.40634    37.766798   -391.65394    1306163.5     -1306770    381.72898    48631.318    318.87448 0.0054629381 
+     700     15.99791    3342.7693    2864.1576     198.8409    478.61174    451.54685    498.82406    489.17206    35.231269   -375.78888    1306153.8   -1306774.2    3691.2706    48631.318    311.62801 0.0071278792 
+     750    17.111346    3181.7665    2786.7104    193.46422    395.05608    409.83191    508.19537    454.56183    32.890719   -379.80694      1306149   -1306779.6    7428.3698    48631.318    303.20196 0.0062331873 
+     800    18.219225    3032.4162    2699.8707    187.43547    332.54543    453.40674    486.16573    441.12346    32.847783   -437.39291    1306144.4     -1306788    1701.7675    48631.318    293.75377 0.0056528077 
+     850    19.320825    2898.4936    2563.6961     177.9817    334.79757    463.66634    486.19928    453.38802    34.062236   -455.86081    1306144.2   -1306790.9   -285.04073    48631.318    278.93762 0.0052778244 
+     900     20.41979    2780.3551    2528.3241    175.52604    252.03099    396.92693     451.7645    435.59756    33.035261   -413.46181    1306142.9   -1306794.7    3836.4347    48631.318    275.08801 0.0070307677 
+     950    21.517533    2679.3418    2456.8821    170.56626    222.45967    385.66649     434.6516    418.37957    32.156706   -387.22039    1306136.9   -1306798.1    5510.2277    48631.318    267.31518 0.0064041284 
+    1000    22.614275     2593.435    2367.4471    164.35734    225.98798    427.85237    453.27432    415.48822    31.097611   -436.61808    1306131.8   -1306796.9    1166.3709    48631.318    257.58457 0.0059160188 
+    1050    23.688642    2524.7784    2305.0257     160.0238    219.75264    432.90797     438.8666    412.79338    30.892595   -414.29467    1306119.4   -1306800.8    1698.2602    48631.318     250.7925 0.0065595368 
+    1100    24.750163     2471.818     2311.095    160.44516    160.72297    378.43554     453.3434      392.485    29.012487   -409.64322    1306119.6   -1306802.5    4190.9174    48631.318     251.4532 0.0059713928 
+    1150    25.813605    2433.9311    2279.0768    158.22233    154.85433    395.30409    436.87935    414.39367    31.118959   -428.90913    1306110.2   -1306804.2    3274.9237    48631.318    247.96895 0.0069037916 
+    1200    26.876952    2411.3772    2238.4639    155.40283    172.91329    453.61525    460.27658    408.59192    31.237007   -482.78468    1306110.2   -1306808.2   -523.10237    48631.318    243.55013 0.0068752641 
+    1250    27.929701    2402.1937    2286.0559    158.70685    116.13778    416.44884    462.75935    391.75448    29.446777    -477.6718    1306102.2   -1306808.8     484.0561    48631.318    248.72561  0.011679662 
+    1300    29.000999    2406.5014     2261.274    156.98639    145.22737      408.678    437.74824    400.45662    30.448139   -418.44472    1306096.8   -1306810.5    4490.4105    48631.318     245.9924  0.076575975 
+    1350     30.07322     2459.141    2317.5852    160.89573    141.55579    651.85736    447.40791    400.66662    29.060882   -461.45016    1305884.3   -1306810.3     693.5247    48631.318    250.14112    3.5619231 
+    1400     31.14859    2479.6103    2285.6714    158.68015    193.93893    582.54135    457.54445    430.29301    30.184026   -449.49877    1305955.6   -1306812.8    930.44669    48631.318    247.21806    2.5941109 
+    1450    32.226914     2498.357    2286.4857    158.73668    211.87137    434.79636    477.95951    402.79572    31.070593   -406.60139    1306086.4   -1306814.5    2933.5045    48631.318    248.74572  0.058613153 
+    1500    33.410717    2546.6608    2423.6247    168.25741    123.03609    392.07322    456.01243    385.97344    29.255562   -417.91413    1306089.9   -1306812.3     3333.391    48631.318     263.6939  0.011242005 
+    1550    34.466176    2596.5534    2325.2208    161.42583    271.33259    462.52172    469.54241    461.20405    34.616224   -423.51068    1306080.4   -1306813.4    2155.1194    48631.318    252.98718  0.011190963 
+    1600    35.524206    2646.7837    2387.8846    165.77619     258.8991    424.60563    484.95051    449.57767    33.318683   -395.68293      1306077   -1306814.8      1291.42    48631.318    259.80456   0.01242131 
+    1650    36.582854    2700.2921    2387.3119    165.73643    312.98026    431.01369    496.39909    455.52591    32.725057   -357.65832    1306070.3   -1306815.3    5006.9348    48631.318    259.70291  0.081728845 
+    1700    37.641527    2777.9572    2386.7777    165.69934     391.1795    636.55763    523.11512     482.8483    35.185863    -391.0955    1305919.8   -1306815.2    2192.6733    48631.318     258.1403    2.7324891 
+    1750    38.722299    2829.6167    2559.2488    177.67295    270.36793    684.60746    479.95058    446.29664    31.887359   -385.83616    1305832.5     -1306819    1683.6061    48631.318      276.955    2.6459088 
+    1800    39.800548    2835.7772    2465.7031    171.17865    370.07414    470.05306    508.38361    479.70121    37.826988    -369.0694    1306062.8   -1306819.6    3022.9801    48631.318    268.22328  0.097437593 
+    1850    40.878327      2857.76    2504.4099    173.86582    353.35016    436.05857    516.10495    487.70907    36.514477   -385.43957    1306078.9   -1306816.5    2950.6415    48631.318    272.48049  0.016822774 
+    1900      41.9583    2867.7843    2528.8424    175.56202    338.94193    446.38058    509.30719    485.04661    37.284135   -402.67104    1306076.5   -1306812.9    3161.5835    48631.318     275.1418  0.011620333 
+    1950    43.058281    2861.3388    2513.8846     174.5236    347.45414    470.99292    536.81741    467.97736    36.047648   -430.00695    1306079.3   -1306813.6    739.25154    48631.318    273.50953  0.020089235 
+    2000    44.142059     2838.068    2530.3189    175.66453    307.74914    423.19157    516.85371    454.76945    35.048253   -387.49234    1306074.6   -1306809.3    4324.0966    48631.318    275.23081   0.13784772 
+Loop time of 44.1421 on 4 procs for 2000 steps with 5500 atoms
+
+Performance: 1.957 ns/day, 12.262 hours/ns, 45.308 timesteps/s
+99.7% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 21.008     | 22.592     | 23.892     |  21.7 | 51.18
+Bond    | 4.8951     | 5.1338     | 5.2542     |   6.4 | 11.63
+Kspace  | 9.1158     | 10.514     | 12.296     |  35.3 | 23.82
+Neigh   | 0.63826    | 0.63849    | 0.63875    |   0.0 |  1.45
+Comm    | 0.78008    | 0.80146    | 0.84186    |   2.7 |  1.82
+Output  | 0.0036852  | 0.0040929  | 0.0052037  |   1.0 |  0.01
+Modify  | 4.3966     | 4.4074     | 4.4147     |   0.3 |  9.98
+Other   |            | 0.05088    |            |       |  0.12
+
+Nlocal:    1375 ave 1415 max 1340 min
+Histogram: 2 0 0 0 0 0 0 0 1 1
+Nghost:    8101 ave 8147 max 8056 min
+Histogram: 2 0 0 0 0 0 0 0 1 1
+Neighs:    326274 ave 342552 max 306832 min
+Histogram: 1 0 0 0 1 0 1 0 0 1
+
+Total # of neighbors = 1305095
+Ave neighs/atom = 237.29
+Ave special neighs/atom = 15.6364
+Neighbor list builds = 44
+Dangerous builds = 0
+Total wall time: 0:00:44

examples/USER/misc/rhok/README.md

@@ -0,0 +1,74 @@
+# The Interface Pinning method for studying solid-liquid transitions
+
+In this example we will use the interface pinnig method to study a solid-liquid transition.
+This is done by adding a harmonic potential to the Hamiltonian 
+that bias the system towards two-phase configurations:
+
+  U_bias = 0.5*K*(Q-a)^2
+
+The bias field couple to an order-parameter of crystallinity Q. The implementation use long-range order:
+
+  Q=|rho_k|, 
+
+where rho_k is the collective density field of the wave-vector k. 
+For future reference we note that the structure factor S(k) is given by the variance of the collective density field: 
+
+  S(k)=|rho_k|^2.
+
+### About the method
+
+It is recommended to get familiar with the interface pinning method by reading:
+
+  [Ulf R. Pedersen, JCP 139, 104102 (2013)](http://dx.doi.org/10.1063/1.4818747)
+
+A detailed bibliography is provided at
+
+  <http://urp.dk/interface_pinning.htm>
+
+and a brief introduction can be found at YouTube:
+
+  [![Interface Pinning](http://img.youtube.com/vi/F_79JZNdyoQ/0.jpg)](http://www.youtube.com/watch?v=F_79JZNdyoQ)
+
+### Implimentation in LAMMPS
+
+For this example we will be using the rhok fix.
+
+   fix [name] [groupID] rhok [nx] [ny] [nz] [K] [a]
+
+This fix include a harmonic bias potential U_bias=0.5*K*(|rho_k|-a)^2 to the force calculation.
+The elements of the wave-vector k is given by the nx, ny and nz input: 
+
+  k_x = (2 pi / L_x) * n_x, k_y = (2 pi / L_y) * n_y and k_z = (2 pi / L_z) * n_z. 
+
+We will use a k vector that correspond to a Bragg peak.
+
+## Example: the Lennard-Jones (LJ) model
+
+We will use the interface pinning method to study melting of the LJ model
+at temperature 0.8 and pressure 2.185. This is a coexistence state-point, and the method
+can be used to show this. The present directory contains the input files that we will use:
+
+  in.crystal
+  in.setup
+  in.pinning
+
+1. First we will determine the density of the crystal with the LAMMPS input file in.crystal.
+  From the output we get that the average density after equilibration is 0.9731. 
+  We need this density to ensure hydrostatic pressure when in a two-phase simulation.
+
+2. Next, we setup a two-phase configuration using in.setup.
+
+3. Finally, we run a two-phase simulation with the bias-field applied using in.pinning.
+  The last column in the output show |rho_k|. We note that after a equilibration period
+  the value fluctuates around the anchor point (a) -- showing that this is indeed a coexistence
+  state point.
+
+The reference [JCP 139, 104102 (2013)](http://dx.doi.org/10.1063/1.4818747) gives details on using the method to find coexistence state points,
+and the reference [JCP 142, 044104 (2015)](http://dx.doi.org/10.1063/1.4818747) show how the crystal growth rate can be computed from fluctuations.
+That method have been experienced to be most effective in the slightly super-heated regime above the melting temperature.
+
+## Contact
+
+  Ulf R. Pedersen;
+  <http://www.urp.dk>;
+  ulf AT urp.dk

examples/USER/misc/rhok/in.crystal

@@ -0,0 +1,36 @@
+units		lj
+dimension	3
+boundary	p p p
+atom_style  atomic
+
+# truncated and shifted LJ potential
+pair_style	lj/cut 2.5
+pair_modify	shift yes
+lattice	fcc 0.9731
+region	my_box block 0 8.0   0 8.0   0 20.0
+create_box 1 my_box
+region particles block 0 8.0 0 8.0 0 20.0
+create_atoms 1 region particles
+pair_coeff 1 1 1.0 1.0 2.5
+pair_modify tail no
+pair_modify shift yes
+mass 1 1.0
+velocity all create 1.6 1 mom yes rot yes
+
+# simulation parameters
+neighbor	0.6 bin
+timestep	0.004
+run_style 	verlet
+fix ensemble all npt temp 0.8 0.8 4.0 aniso 2.185 2.185 8.0 pchain 32
+
+# computing long-range order (no bias is added since k=0)
+fix bias all rhok 16 0 0 0.0 0.0
+
+# output
+thermo 50
+thermo_style custom step temp press density f_bias[3]
+# dump dumpXYZ all xyz 2000 traj.xyz
+
+# NOTE: this is cut short to 5000 steps for demonstration purposes
+# run 100000
+run 5000