patch 22Sep17

Enhance Kokkos communication logic

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)
 
@@ -43,10 +41,14 @@ include(CheckCCompilerFlag)
 # 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 +60,15 @@ 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=${LAMMPS_MEMALIGN})
@@ -72,6 +76,13 @@ add_definitions(-DLAMMPS_MEMALIGN=${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)
@@ -85,11 +96,11 @@ 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-MOLFILE USER-NETCDF USER-PHONON USER-QTB USER-REAXC USER-SMD
   USER-SMTBQ USER-SPH USER-TALLY USER-VTK USER-QUIP USER-QMMM)
 set(ACCEL_PACKAGES USER-OMP KOKKOS OPT USER-INTEL GPU)
 foreach(PKG ${DEFAULT_PACKAGES})
@@ -120,8 +131,10 @@ 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 +169,22 @@ 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 +199,7 @@ 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 +238,29 @@ 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 +277,7 @@ 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 +286,6 @@ 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 +316,11 @@ 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 +346,7 @@ endforeach(FUNC)
 list(APPEND LAMMPS_LINK_LIBS ${MATH_LIBRARIES})
 
 ######################################
-# Generate Basic Style files 
+# Generate Basic Style files
 ######################################
 include(StyleHeaderUtils)
 RegisterStyles(${LAMMPS_SOURCE_DIR})
@@ -330,13 +355,27 @@ RegisterStyles(${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 +385,53 @@ 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 +528,130 @@ 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 +665,22 @@ 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)
+add_dependencies(lammps ${LAMMPS_DEPS})
+set_target_properties(lammps PROPERTIES OUTPUT_NAME lammps${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 +691,27 @@ 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/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="22 Sep 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
+22 Sep 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,
@@ -755,6 +757,7 @@ 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,

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
@@ -695,6 +696,65 @@ 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
+
+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 +2251,7 @@ 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
 

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

@@ -361,10 +361,14 @@ 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/commands.txt

@@ -92,6 +92,7 @@ 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/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_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"_#Finnis) 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(Finnis)
+[(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(Niklasson2014)
+[(Niklasson2017)] A. M. N. Niklasson, J. Chem. Phys., 147, 054103 (2017).
+
+:link(Niklasson2012)
+[(Niklasson2017)] 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_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_rigid.txt

@@ -703,6 +703,11 @@ 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/lammps.book

@@ -116,6 +116,7 @@ suffix.html
 tad.html
 temper.html
 temper_grem.html
+temper_npt.html
 thermo.html
 thermo_modify.html
 thermo_style.html

doc/src/package.txt

@@ -335,7 +335,8 @@ 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

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_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/temper_npt/in.temper_npt

@@ -0,0 +1,29 @@
+# Solvated 5-mer peptide
+# Demonstrating temper/npt
+units           real
+atom_style      full
+
+pair_style      lj/charmm/coul/long 8.0 10.0 10.0
+bond_style      harmonic
+angle_style     charmm
+dihedral_style  charmm
+improper_style  harmonic
+kspace_style    pppm 0.0001
+
+read_data       data.peptide
+
+neighbor        2.0 bin
+neigh_modify    delay 5
+
+timestep        2.0
+
+thermo_style    custom step temp epair emol etotal press density
+thermo          50
+
+variable        temper_T world 275 280 285 290 295 300 305 310
+variable        rep world 0 1 2 3 4 5 6 7
+fix             myfix all npt temp ${temper_T} ${temper_T} 100.0 iso 1 1 1000
+run             500
+temper/npt      2000 100 ${temper_T} myfix 0 58728 1
+fix             2 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
+group           peptide type <= 12

examples/USER/misc/temper_npt/log.temper_npt-17Aug17.g++.8

@@ -0,0 +1,24 @@
+LAMMPS (17 Aug 2017)
+Running on 8 partitions of processors
+Step T0 T1 T2 T3 T4 T5 T6 T7
+500 0 1 2 3 4 5 6 7
+600 0 1 2 3 5 4 7 6
+700 0 2 1 4 6 3 7 5
+800 0 2 1 4 6 3 7 5
+900 0 2 1 3 6 4 7 5
+1000 0 2 1 3 7 4 6 5
+1100 0 1 2 3 7 4 6 5
+1200 0 1 2 3 7 4 6 5
+1300 0 1 2 4 7 3 5 6
+1400 0 1 2 4 7 3 5 6
+1500 0 2 1 4 7 3 5 6
+1600 1 3 0 4 6 2 5 7
+1700 1 3 0 4 5 2 6 7
+1800 0 3 1 4 5 2 6 7
+1900 0 3 2 4 5 1 6 7
+2000 1 2 3 5 4 0 6 7
+2100 2 1 3 5 4 0 6 7
+2200 2 1 3 4 5 0 7 6
+2300 1 2 4 3 5 0 7 6
+2400 1 2 4 3 5 0 6 7
+2500 2 1 3 4 5 0 6 7

examples/USER/misc/temper_npt/log.temper_npt-17Aug17.g++.8.0

@@ -0,0 +1,211 @@
+LAMMPS (17 Aug 2017)
+Processor partition = 0
+  using 1 OpenMP thread(s) per MPI task
+# Solvated 5-mer peptide
+# Demonstrating temper/npt
+units           real
+atom_style      full
+
+pair_style      lj/charmm/coul/long 8.0 10.0 10.0
+bond_style      harmonic
+angle_style     charmm
+dihedral_style  charmm
+improper_style  harmonic
+kspace_style    pppm 0.0001
+
+read_data       data.peptide
+  orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
+  1 by 1 by 2 MPI processor grid
+  reading atoms ...
+  2004 atoms
+  reading velocities ...
+  2004 velocities
+  scanning bonds ...
+  3 = max bonds/atom
+  scanning angles ...
+  6 = max angles/atom
+  scanning dihedrals ...
+  14 = max dihedrals/atom
+  scanning impropers ...
+  1 = max impropers/atom
+  reading bonds ...
+  1365 bonds
+  reading angles ...
+  786 angles
+  reading dihedrals ...
+  207 dihedrals
+  reading impropers ...
+  12 impropers
+  4 = max # of 1-2 neighbors
+  7 = max # of 1-3 neighbors
+  14 = max # of 1-4 neighbors
+  18 = max # of special neighbors
+
+neighbor        2.0 bin
+neigh_modify    delay 5
+
+timestep        2.0
+
+thermo_style    custom step temp epair emol etotal press density
+thermo          50
+
+variable        temper_T world 275 280 285 290 295 300 305 310
+variable        rep world 0 1 2 3 4 5 6 7
+fix             myfix all npt temp ${temper_T} ${temper_T} 100.0 iso 1 1 1000
+fix             myfix all npt temp 275 ${temper_T} 100.0 iso 1 1 1000
+fix             myfix all npt temp 275 275 100.0 iso 1 1 1000
+run             500
+PPPM initialization ...
+WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+  G vector (1/distance) = 0.268725
+  grid = 15 15 15
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0228209
+  estimated relative force accuracy = 6.87243e-05
+  using double precision FFTs
+  3d grid and FFT values/proc = 6776 1800
+Neighbor list info ...
+  update every 1 steps, delay 5 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 12
+  ghost atom cutoff = 12
+  binsize = 6, bins = 5 5 5
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/charmm/coul/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) = 15.94 | 15.95 | 15.96 Mbytes
+Step Temp E_pair E_mol TotEng Press Density 
+       0     190.0857    -6442.768    70.391457   -5237.4579    20361.998   0.98480122 
+      50    221.73889   -7683.7524     1219.961   -5139.8856   -23756.591     0.996067 
+     100    253.40719   -6992.3405     479.6715   -4999.6856    12620.614    1.0124851 
+     150    273.60252   -6943.8714    474.24744   -4836.0631    6691.4146    1.0213937 
+     200    265.37126   -7274.7854    1059.7586   -4630.6111   -17765.088    1.0221471 
+     250     263.1769   -6503.9902    470.29014   -4462.3859    21936.742    1.0159924 
+     300    274.03852   -7026.6057    1021.3683   -4369.0734    -14847.42    1.0095778 
+     350    283.20032   -6715.3608     688.9769   -4335.5187    3430.7111    1.0045615 
+     400     282.2987   -6645.6692     598.6786   -4361.5086    6318.9525    1.0001513 
+     450    265.89091   -6977.5705    985.58718    -4404.465    -13261.32   0.99833097 
+     500    270.30038   -6683.7902     650.5748     -4419.37    10014.277     1.000501 
+Loop time of 11.0158 on 2 procs for 500 steps with 2004 atoms
+
+Performance: 7.843 ns/day, 3.060 hours/ns, 45.389 timesteps/s
+99.4% CPU use with 2 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 7.6893     | 7.8012     | 7.9131     |   4.0 | 70.82
+Bond    | 0.085948   | 0.089635   | 0.093322   |   1.2 |  0.81
+Kspace  | 1.1113     | 1.2333     | 1.3552     |  11.0 | 11.20
+Neigh   | 1.2316     | 1.2336     | 1.2356     |   0.2 | 11.20
+Comm    | 0.24281    | 0.24305    | 0.2433     |   0.0 |  2.21
+Output  | 0.00052857 | 0.00053537 | 0.00054216 |   0.0 |  0.00
+Modify  | 0.35968    | 0.38071    | 0.40175    |   3.4 |  3.46
+Other   |            | 0.03378    |            |       |  0.31
+
+Nlocal:    1002 ave 1012 max 992 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+Nghost:    8737.5 ave 8747 max 8728 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+Neighs:    359463 ave 359931 max 358995 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+
+Total # of neighbors = 718926
+Ave neighs/atom = 358.746
+Ave special neighs/atom = 2.34032
+Neighbor list builds = 50
+Dangerous builds = 0
+temper/npt      2000 100 ${temper_T} myfix 0 58728 1
+temper/npt      2000 100 275 myfix 0 58728 1
+PPPM initialization ...
+WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+  G vector (1/distance) = 0.269166
+  grid = 15 15 15
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0224625
+  estimated relative force accuracy = 6.76451e-05
+  using double precision FFTs
+  3d grid and FFT values/proc = 6776 1800
+Per MPI rank memory allocation (min/avg/max) = 15.94 | 15.95 | 15.96 Mbytes
+Step Temp E_pair E_mol TotEng Press Density 
+     500    270.30038   -6683.7883     650.5748   -4419.3682    10014.295     1.000501 
+     550    270.02511   -6875.5939    861.97452   -4401.4176   -7136.4285     1.005266 
+     600    278.94444    -6786.546    772.05516   -4349.0356    1262.4902    1.0110761 
+     650     283.8929   -6763.9691    734.90211   -4334.0667    3664.1311    1.0138933 
+     700    276.67406   -6889.5452    847.87041    -4389.775   -4754.9929    1.0145005 
+     750    266.09032   -6720.4921    700.27463   -4431.5085    5654.8094     1.013756 
+     800    277.69948   -6917.9358    860.12186   -4399.7918   -4729.7009    1.0124281 
+     850    278.00722   -6808.1267    798.69768   -4349.5695    1468.5155    1.0139727 
+     900    276.49266   -6784.5965    818.01248   -4315.7673    2510.6047    1.0158115 
+     950    270.36225   -6847.6403    901.97122   -4331.4544   -3448.3968    1.0175668 
+    1000    276.75533   -6809.4075    781.83481   -4375.1877    3379.8584    1.0173101 
+    1050    271.67172   -6913.3268    847.97269   -4443.3211   -2045.5605     1.016761 
+    1100    265.73149   -6867.7958    840.08439   -4441.1449   -323.23893    1.0170333 
+    1150    274.51451   -6834.9841    792.48751   -4403.4906    2604.0644    1.0175885 
+    1200    274.22914   -6919.9496    890.14423   -4392.5032   -3454.4418    1.0167016 
+    1250    274.13019   -6817.7256    825.11317    -4355.901    2067.3849    1.0181714 
+    1300    287.36094   -6906.5403    854.11016   -4336.7237   -438.01206    1.0180794 
+    1350    275.51763   -6911.8172    855.25923   -4411.5627   -742.96412    1.0180086 
+    1400    269.90457   -6919.4028    855.55485   -4452.3659    311.08918    1.0213368 
+    1450    276.99478   -6980.8317    913.69108    -4413.326   -1810.1051    1.0265437 
+    1500    282.20313    -6926.698    863.56525   -4378.2213     932.7594    1.0301769 
+    1550    276.82056    -6917.141    910.22058    -4354.146   -899.64097    1.0361201 
+    1600     278.2946   -6903.7351    893.14524   -4349.0145    1399.9679    1.0421849 
+    1650    270.12097   -6863.0844    879.81355   -4370.4967    1132.9864    1.0410741 
+    1700    274.02565   -6912.4818    893.37432   -4383.0202    -1359.393    1.0366624 
+    1750    276.77322   -6866.3214    899.18224   -4314.6474    887.47588    1.0332821 
+    1800    287.02945   -6961.9217    950.89476   -4297.2996   -1298.0904    1.0313542 
+    1850    279.37232     -6930.51    898.78906    -4363.711    397.74804    1.0309206 
+    1900    277.14727   -6978.8634    915.53145   -4408.6069    636.36898    1.0285813 
+    1950    275.14272    -7010.256    927.28727    -4440.212   -2352.6961    1.0241747 
+    2000    270.84972     -6967.52    913.42253   -4436.9722    1669.9637    1.0251906 
+    2050    276.70108   -6992.4582    993.37473   -4347.0223   -500.38379    1.0325714 
+    2100    278.49569   -6922.9266    939.43518   -4320.7155    700.24515    1.0385166 
+    2150    279.69822   -6896.5008    923.58805   -4302.9571    702.22759    1.0415681 
+    2200      284.136   -6951.6694    974.70903   -4280.5086    352.95043    1.0452009 
+    2250    292.01941   -6960.5848    964.01635   -4253.0483    2680.7007    1.0430517 
+    2300    277.58812   -6995.5006    1010.8176   -4327.3258   -1508.9961    1.0328658 
+    2350    270.61616     -6978.93    966.12478   -4397.0745   -1636.7434    1.0267664 
+    2400    279.36012   -6991.4739    957.43125   -4366.1056    432.00482    1.0260429 
+    2450    286.38546    -7074.807    1004.3206   -4360.6042     160.9109    1.0251585 
+    2500    269.98622   -6932.0456    957.35208    -4362.724    1748.1568    1.0186556 
+Loop time of 46.7361 on 2 procs for 2000 steps with 2004 atoms
+
+Performance: 7.395 ns/day, 3.246 hours/ns, 42.793 timesteps/s
+99.2% CPU use with 2 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 32.381     | 32.617     | 32.854     |   4.1 | 69.79
+Bond    | 0.3601     | 0.36578    | 0.37147    |   0.9 |  0.78
+Kspace  | 4.6658     | 4.933      | 5.2002     |  12.0 | 10.56
+Neigh   | 4.9833     | 4.9921     | 5.0009     |   0.4 | 10.68
+Comm    | 0.96477    | 0.96532    | 0.96587    |   0.1 |  2.07
+Output  | 0.0021896  | 0.0022331  | 0.0022767  |   0.1 |  0.00
+Modify  | 1.4424     | 1.5379     | 1.6334     |   7.7 |  3.29
+Other   |            | 1.322      |            |       |  2.83
+
+Nlocal:    1002 ave 1011 max 993 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+Nghost:    8835 ave 8847 max 8823 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+Neighs:    366395 ave 367166 max 365624 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+
+Total # of neighbors = 732790
+Ave neighs/atom = 365.664
+Ave special neighs/atom = 2.34032
+Neighbor list builds = 195
+Dangerous builds = 0
+fix             2 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
+  19 = # of size 2 clusters
+  6 = # of size 3 clusters
+  3 = # of size 4 clusters
+  640 = # of frozen angles
+group           peptide type <= 12
+84 atoms in group peptide
+Total wall time: 0:00:58

examples/USER/misc/temper_npt/log.temper_npt-17Aug17.g++.8.1

@@ -0,0 +1,211 @@
+LAMMPS (17 Aug 2017)
+Processor partition = 1
+  using 1 OpenMP thread(s) per MPI task
+# Solvated 5-mer peptide
+# Demonstrating temper/npt
+units           real
+atom_style      full
+
+pair_style      lj/charmm/coul/long 8.0 10.0 10.0
+bond_style      harmonic
+angle_style     charmm
+dihedral_style  charmm
+improper_style  harmonic
+kspace_style    pppm 0.0001
+
+read_data       data.peptide
+  orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
+  1 by 1 by 2 MPI processor grid
+  reading atoms ...
+  2004 atoms
+  reading velocities ...
+  2004 velocities
+  scanning bonds ...
+  3 = max bonds/atom
+  scanning angles ...
+  6 = max angles/atom
+  scanning dihedrals ...
+  14 = max dihedrals/atom
+  scanning impropers ...
+  1 = max impropers/atom
+  reading bonds ...
+  1365 bonds
+  reading angles ...
+  786 angles
+  reading dihedrals ...
+  207 dihedrals
+  reading impropers ...
+  12 impropers
+  4 = max # of 1-2 neighbors
+  7 = max # of 1-3 neighbors
+  14 = max # of 1-4 neighbors
+  18 = max # of special neighbors
+
+neighbor        2.0 bin
+neigh_modify    delay 5
+
+timestep        2.0
+
+thermo_style    custom step temp epair emol etotal press density
+thermo          50
+
+variable        temper_T world 275 280 285 290 295 300 305 310
+variable        rep world 0 1 2 3 4 5 6 7
+fix             myfix all npt temp ${temper_T} ${temper_T} 100.0 iso 1 1 1000
+fix             myfix all npt temp 280 ${temper_T} 100.0 iso 1 1 1000
+fix             myfix all npt temp 280 280 100.0 iso 1 1 1000
+run             500
+PPPM initialization ...
+WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+  G vector (1/distance) = 0.268725
+  grid = 15 15 15
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0228209
+  estimated relative force accuracy = 6.87243e-05
+  using double precision FFTs
+  3d grid and FFT values/proc = 6776 1800
+Neighbor list info ...
+  update every 1 steps, delay 5 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 12
+  ghost atom cutoff = 12
+  binsize = 6, bins = 5 5 5
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/charmm/coul/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) = 15.94 | 15.95 | 15.96 Mbytes
+Step Temp E_pair E_mol TotEng Press Density 
+       0     190.0857    -6442.768    70.391457   -5237.4579    20361.998   0.98480122 
+      50    222.19861   -7681.6246    1220.9355   -5134.0385   -23782.584   0.99586813 
+     100    254.66243   -6984.8813    480.32613   -4984.0772    12653.925    1.0120499 
+     150    275.28565   -6924.9875    473.42216   -4807.9551    6796.8759    1.0208676 
+     200    266.52981   -7245.4283    1066.0809   -4588.0144   -17643.106    1.0213699 
+     250    265.06051   -6458.7243    468.97999   -4407.1839    22476.585    1.0143215 
+     300    276.91573   -6986.8723    1020.9402   -4312.5895   -14559.244     1.005554 
+     350    284.26789   -6635.8191    681.27092   -4257.3089    2625.7849   0.99664411 
+     400    284.48799   -6543.0099    637.61352   -4206.8431    7901.0269   0.99079237 
+     450    271.30029   -6770.4441    1003.5624   -4147.0663    -13046.51    0.9856127 
+     500    292.02418   -6514.8219    628.56367   -4142.7096    9871.7492   0.98625432 
+Loop time of 11.1841 on 2 procs for 500 steps with 2004 atoms
+
+Performance: 7.725 ns/day, 3.107 hours/ns, 44.706 timesteps/s
+98.4% CPU use with 2 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 7.8072     | 7.9267     | 8.0463     |   4.2 | 70.88
+Bond    | 0.08858    | 0.091102   | 0.093624   |   0.8 |  0.81
+Kspace  | 1.1403     | 1.2665     | 1.3927     |  11.2 | 11.32
+Neigh   | 1.2478     | 1.2496     | 1.2514     |   0.2 | 11.17
+Comm    | 0.21574    | 0.23191    | 0.24809    |   3.4 |  2.07
+Output  | 0.00054431 | 0.00054872 | 0.00055313 |   0.0 |  0.00
+Modify  | 0.36159    | 0.38512    | 0.40864    |   3.8 |  3.44
+Other   |            | 0.03255    |            |       |  0.29
+
+Nlocal:    1002 ave 1026 max 978 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+Nghost:    8640.5 ave 8690 max 8591 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+Neighs:    354518 ave 367457 max 341580 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+
+Total # of neighbors = 709037
+Ave neighs/atom = 353.811
+Ave special neighs/atom = 2.34032
+Neighbor list builds = 49
+Dangerous builds = 0
+temper/npt      2000 100 ${temper_T} myfix 0 58728 1
+temper/npt      2000 100 280 myfix 0 58728 1
+PPPM initialization ...
+WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+  G vector (1/distance) = 0.268766
+  grid = 15 15 15
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0227872
+  estimated relative force accuracy = 6.8623e-05
+  using double precision FFTs
+  3d grid and FFT values/proc = 6776 1800
+Per MPI rank memory allocation (min/avg/max) = 15.94 | 15.95 | 15.96 Mbytes
+Step Temp E_pair E_mol TotEng Press Density 
+     500    292.02418   -6514.8215    628.56367   -4142.7092    9871.7534   0.98625432 
+     550    282.55729   -6813.6685    882.47773   -4244.1648   -5377.4053   0.98629839 
+     600    274.41644   -6737.0424    793.45027   -4305.1716   -306.54594   0.98725369 
+     650    274.38967   -6664.1973    722.25014   -4303.6865    4628.1283   0.99175575 
+     700    282.07693   -6819.1345    897.72476   -4237.2518   -7210.1942   0.99693402 
+     750    281.80476   -6580.3192    776.69527    -4121.091    5466.9616    1.0060075 
+     800    288.76507   -6726.7205    885.07773   -4117.5529   -2623.0756    1.0132495 
+     850    289.21519   -6755.4289    847.00353    -4181.648    776.75991    1.0160602 
+     900      280.679   -6694.3766    777.91069   -4240.6544    2272.2098    1.0170439 
+     950    280.93616   -6813.8865    910.52053   -4226.0191   -3872.8603    1.0202606 
+    1000    289.91762   -6710.0317    786.39268   -4192.6678    4456.0575    1.0222223 
+    1050     292.7318    -6830.313    882.85834   -4199.6812   -2434.3412    1.0214856 
+    1100    280.61029   -6789.3828    846.07872   -4267.9028    580.25027    1.0202095 
+    1150    277.27283   -6806.9599     852.2013   -4299.2838    18.428929    1.0180062 
+    1200    284.68488   -6849.8644    877.54803   -4272.5875   -1041.3591    1.0171686 
+    1250    290.47153   -6864.5918    827.15634   -4303.1571    2658.2245    1.0175104 
+    1300    279.84219   -6892.8497     884.4759   -4337.5586   -1800.8783    1.0176916 
+    1350    275.59818   -6848.0359    848.53171    -4354.028    1599.2311    1.0197901 
+    1400    276.67929    -6893.565    900.40614   -4341.2278    295.46659    1.0221449 
+    1450    281.18148   -6902.3901    931.40362   -4292.1748   -1585.1315    1.0243322 
+    1500    282.82339   -6846.4364     887.9988   -4269.8228    2142.9076    1.0291373 
+    1550    291.40537   -6898.3742    920.23257   -4238.2876   -355.99408    1.0308242 
+    1600     279.9548   -6863.2068    923.64788   -4268.0713    233.83555    1.0259922 
+    1650    282.90611   -6848.3952    903.97971   -4255.3069    369.65523    1.0200083 
+    1700    292.24099    -6884.346    965.54265   -4173.9603   -971.39092    1.0155909 
+    1750    285.95609   -6805.2486    955.25719   -4142.6727    646.23287     1.012031 
+    1800    293.50173   -6823.8152    919.24584    -4152.199    530.19678    1.0078324 
+    1850      300.737   -6918.3747    942.10944   -4180.6963   -949.67639    1.0061029 
+    1900    284.98969   -6913.5357    956.78373   -4255.2032   -163.02524    1.0095568 
+    1950    282.78589   -6905.1978    951.94384   -4264.8631   -891.31043    1.0177223 
+    2000    289.82463   -6977.0203    1022.9525   -4223.6518   -540.73403    1.0269481 
+    2050    292.13474   -6900.8375    924.54552   -4232.0833    2656.3028    1.0310097 
+    2100    284.54116     -6958.82    968.35681   -4291.5924   -286.70605    1.0264636 
+    2150    268.14376   -6966.2184    973.69354   -4391.5558   -1446.0052    1.0190957 
+    2200    275.09872     -6957.02    982.37472   -4332.1512   -1449.1984    1.0199163 
+    2250    285.69237   -7002.4814    1014.3438   -4282.3934   -1530.0347    1.0264012 
+    2300    282.59746   -6922.8242    980.57612   -4254.9822     381.8231    1.0332785 
+    2350    290.98138   -6993.8628     1022.527   -4234.0132    -559.9386    1.0396092 
+    2400    281.29903   -6963.5226    967.13898   -4316.8702    1438.7922    1.0452404 
+    2450    278.44605   -6968.5134    945.32295   -4360.7108    1102.9302    1.0498791 
+    2500    278.65789   -7034.3651    1032.8711   -4337.7496   -923.32414    1.0527955 
+Loop time of 46.7418 on 2 procs for 2000 steps with 2004 atoms
+
+Performance: 7.394 ns/day, 3.246 hours/ns, 42.788 timesteps/s
+98.3% CPU use with 2 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 33.141     | 33.146     | 33.152     |   0.1 | 70.91
+Bond    | 0.36441    | 0.36647    | 0.36853    |   0.3 |  0.78
+Kspace  | 4.9269     | 4.9539     | 4.9808     |   1.2 | 10.60
+Neigh   | 5.2154     | 5.223      | 5.2306     |   0.3 | 11.17
+Comm    | 0.90923    | 0.97305    | 1.0369     |   6.5 |  2.08
+Output  | 0.0021682  | 0.0027286  | 0.003289   |   1.1 |  0.01
+Modify  | 1.454      | 1.5534     | 1.6528     |   8.0 |  3.32
+Other   |            | 0.5229     |            |       |  1.12
+
+Nlocal:    1002 ave 1005 max 999 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+Nghost:    9059.5 ave 9084 max 9035 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+Neighs:    378277 ave 380641 max 375913 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+
+Total # of neighbors = 756554
+Ave neighs/atom = 377.522
+Ave special neighs/atom = 2.34032
+Neighbor list builds = 197
+Dangerous builds = 0
+fix             2 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
+  19 = # of size 2 clusters
+  6 = # of size 3 clusters
+  3 = # of size 4 clusters
+  640 = # of frozen angles
+group           peptide type <= 12
+84 atoms in group peptide
+Total wall time: 0:00:58

examples/USER/misc/temper_npt/log.temper_npt-17Aug17.g++.8.2

@@ -0,0 +1,211 @@
+LAMMPS (17 Aug 2017)
+Processor partition = 2
+  using 1 OpenMP thread(s) per MPI task
+# Solvated 5-mer peptide
+# Demonstrating temper/npt
+units           real
+atom_style      full
+
+pair_style      lj/charmm/coul/long 8.0 10.0 10.0
+bond_style      harmonic
+angle_style     charmm
+dihedral_style  charmm
+improper_style  harmonic
+kspace_style    pppm 0.0001
+
+read_data       data.peptide
+  orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
+  1 by 1 by 2 MPI processor grid
+  reading atoms ...
+  2004 atoms
+  reading velocities ...
+  2004 velocities
+  scanning bonds ...
+  3 = max bonds/atom
+  scanning angles ...
+  6 = max angles/atom
+  scanning dihedrals ...
+  14 = max dihedrals/atom
+  scanning impropers ...
+  1 = max impropers/atom
+  reading bonds ...
+  1365 bonds
+  reading angles ...
+  786 angles
+  reading dihedrals ...
+  207 dihedrals
+  reading impropers ...
+  12 impropers
+  4 = max # of 1-2 neighbors
+  7 = max # of 1-3 neighbors
+  14 = max # of 1-4 neighbors
+  18 = max # of special neighbors
+
+neighbor        2.0 bin
+neigh_modify    delay 5
+
+timestep        2.0
+
+thermo_style    custom step temp epair emol etotal press density
+thermo          50
+
+variable        temper_T world 275 280 285 290 295 300 305 310
+variable        rep world 0 1 2 3 4 5 6 7
+fix             myfix all npt temp ${temper_T} ${temper_T} 100.0 iso 1 1 1000
+fix             myfix all npt temp 285 ${temper_T} 100.0 iso 1 1 1000
+fix             myfix all npt temp 285 285 100.0 iso 1 1 1000
+run             500
+PPPM initialization ...
+WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+  G vector (1/distance) = 0.268725
+  grid = 15 15 15
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0228209
+  estimated relative force accuracy = 6.87243e-05
+  using double precision FFTs
+  3d grid and FFT values/proc = 6776 1800
+Neighbor list info ...
+  update every 1 steps, delay 5 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 12
+  ghost atom cutoff = 12
+  binsize = 6, bins = 5 5 5
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/charmm/coul/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) = 15.94 | 15.95 | 15.96 Mbytes
+Step Temp E_pair E_mol TotEng Press Density 
+       0     190.0857    -6442.768    70.391457   -5237.4579    20361.998   0.98480122 
+      50    222.63643     -7679.59    1221.8685   -5128.4568    -23807.78   0.99567623 
+     100    255.85049   -6977.7653    480.95894    -4969.235    12685.571    1.0116281 
+     150    276.83083   -6906.8603     472.9485    -4781.076    6899.3786    1.0203576 
+     200    267.19755    -7210.264    1068.2756   -4546.6687   -17521.505    1.0207097 
+     250     263.8837   -6392.2545     463.0506   -4353.6698    22886.964    1.0130132 
+     300    280.88953     -6919.81    1005.9833   -4236.7581   -14774.964    1.0024942 
+     350    289.59472   -6621.8351    734.60058   -4158.1911    2409.0738   0.99451628 
+     400    288.29076    -6495.283    634.61137   -4139.4136     6594.965   0.98796525 
+     450    281.92055   -6838.8449    1025.3043   -4130.3164   -12795.112   0.98591519 
+     500    298.25519   -6578.7232    652.75467   -4145.2172    10282.835   0.98902709 
+Loop time of 11.0965 on 2 procs for 500 steps with 2004 atoms
+
+Performance: 7.786 ns/day, 3.082 hours/ns, 45.059 timesteps/s
+99.1% CPU use with 2 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 7.9379     | 7.9449     | 7.952      |   0.2 | 71.60
+Bond    | 0.090588   | 0.090927   | 0.091265   |   0.1 |  0.82
+Kspace  | 1.1684     | 1.176      | 1.1837     |   0.7 | 10.60
+Neigh   | 1.2553     | 1.2556     | 1.256      |   0.0 | 11.32
+Comm    | 0.20599    | 0.21536    | 0.22474    |   2.0 |  1.94
+Output  | 0.00049877 | 0.00050557 | 0.00051236 |   0.0 |  0.00
+Modify  | 0.35224    | 0.37667    | 0.40111    |   4.0 |  3.39
+Other   |            | 0.03635    |            |       |  0.33
+
+Nlocal:    1002 ave 1007 max 997 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+Nghost:    8699.5 ave 8735 max 8664 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+Neighs:    355600 ave 363554 max 347647 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+
+Total # of neighbors = 711201
+Ave neighs/atom = 354.891
+Ave special neighs/atom = 2.34032
+Neighbor list builds = 50
+Dangerous builds = 0
+temper/npt      2000 100 ${temper_T} myfix 0 58728 1
+temper/npt      2000 100 285 myfix 0 58728 1
+PPPM initialization ...
+WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+  G vector (1/distance) = 0.268844
+  grid = 15 15 15
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0227233
+  estimated relative force accuracy = 6.84305e-05
+  using double precision FFTs
+  3d grid and FFT values/proc = 6776 1800
+Per MPI rank memory allocation (min/avg/max) = 15.94 | 15.95 | 15.96 Mbytes
+Step Temp E_pair E_mol TotEng Press Density 
+     500    298.25519   -6578.7239    652.75467    -4145.218     10282.81   0.98902709 
+     550    280.55812   -6800.9339    904.37474   -4221.4693   -6284.3677   0.99138729 
+     600    282.54117   -6736.9067    793.64464   -4256.3323    379.51956   0.99544144 
+     650      289.246   -6695.3988    727.43292   -4241.0045    3741.9292    1.0004679 
+     700    298.37935   -6898.8951    912.35329   -4205.0492   -5179.2622    1.0029455 
+     750    276.21453   -6657.3814    738.83164   -4269.3936    6422.8684     1.003042 
+     800    273.34049   -6770.7481    842.34057    -4296.411   -2699.1945    1.0011122 
+     850    279.30106   -6766.7842    807.51048   -4291.6893   -583.46522    1.0039015 
+     900    286.09076   -6808.4366    807.15205   -4293.1617    1405.0223    1.0062162 
+     950    283.04021   -6838.8107    869.45604   -4279.4454   -2826.6403     1.008228 
+    1000    278.36762   -6776.1595    827.04427    -4287.104    2510.6216    1.0123638 
+    1050    276.46194   -6858.6173    893.69758   -4314.2864   -1818.0617    1.0153108 
+    1100    270.91883   -6818.5634     864.2518   -4336.7738    1021.1432    1.0153455 
+    1150    274.70844   -6747.0957    849.98378    -4256.948    1453.2165    1.0141005 
+    1200    292.66211   -6864.4907    917.17522    -4199.958   -2889.5663    1.0130738 
+    1250     288.1024   -6814.0744    887.46443   -4206.4766    2384.4467    1.0139599 
+    1300    286.54446   -6864.9998      900.886   -4253.2821   -2397.0043    1.0140796 
+    1350    274.86169   -6804.6738    866.75191    -4296.843    1112.3802    1.0143892 
+    1400    275.30771   -6837.4182    904.04812   -4289.6282    136.99961    1.0170328 
+    1450    296.09129   -6868.8691    910.61078   -4190.4268   -1076.0085    1.0204782 
+    1500    292.50596   -6812.8248    889.10378   -4177.2959    1069.9919    1.0198406 
+    1550     284.3886    -6876.901    909.58572   -4269.3554   -1153.6899    1.0177539 
+    1600    276.41187   -6876.8574    907.69862   -4318.8244     114.8894    1.0158964 
+    1650    275.68967   -6919.4356    902.04604   -4371.3672   -1493.2092    1.0141832 
+    1700    271.20923   -6893.2373    912.27766    -4361.688   -563.23529    1.0157743 
+    1750    279.40649   -6842.0743    892.63677   -4281.2237    944.83039    1.0207184 
+    1800    282.84659   -6889.8537    934.73963   -4266.3608   -895.12942    1.0238833 
+    1850    279.58052   -6900.6624    951.17313   -4280.2364    648.68857     1.024366 
+    1900    276.44092   -6841.9805    881.15423   -4310.3185    1052.7352    1.0229576 
+    1950    289.89625    -6960.295     949.2514      -4280.2   -2500.9996    1.0210089 
+    2000    283.75058   -6908.6985    930.56698   -4283.9809     1529.221    1.0211902 
+    2050    284.00141   -6837.2348    943.57188   -4198.0147   -710.45695    1.0190262 
+    2100    294.53504   -6879.4583      983.431   -4137.4874   -496.16699    1.0172736 
+    2150    296.46029   -6854.8307    926.58211   -4158.2139    757.20038     1.017548 
+    2200    284.26196   -6896.5957     989.5222   -4209.8697   -1953.1733    1.0187998 
+    2250    284.51713   -6852.3924    938.51853   -4215.1465    210.72971    1.0208918 
+    2300    289.88921   -6867.2253    969.05163    -4167.372   -80.492209    1.0240397 
+    2350    296.17997   -6836.2421     954.2497   -4113.6314   -389.76698    1.0272081 
+    2400    309.56546   -6833.5714    970.44217   -4014.8493    610.57346    1.0294586 
+    2450    300.61402   -6827.9964    1025.4417   -4007.7199    1121.4824    1.0284326 
+    2500    298.82336   -6815.7862    945.53298   -4086.1097    -726.1131    1.0224541 
+Loop time of 46.7423 on 2 procs for 2000 steps with 2004 atoms
+
+Performance: 7.394 ns/day, 3.246 hours/ns, 42.788 timesteps/s
+99.3% CPU use with 2 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 32.492     | 32.625     | 32.758     |   2.3 | 69.80
+Bond    | 0.3584     | 0.36552    | 0.37265    |   1.2 |  0.78
+Kspace  | 4.7476     | 4.8898     | 5.0319     |   6.4 | 10.46
+Neigh   | 5.1461     | 5.1463     | 5.1464     |   0.0 | 11.01
+Comm    | 0.86246    | 0.89403    | 0.92559    |   3.3 |  1.91
+Output  | 0.0020437  | 0.0020902  | 0.0021367  |   0.1 |  0.00
+Modify  | 1.4279     | 1.5187     | 1.6095     |   7.4 |  3.25
+Other   |            | 1.301      |            |       |  2.78
+
+Nlocal:    1002 ave 1010 max 994 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+Nghost:    8922 ave 9009 max 8835 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+Neighs:    367689 ave 371637 max 363741 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+
+Total # of neighbors = 735378
+Ave neighs/atom = 366.955
+Ave special neighs/atom = 2.34032
+Neighbor list builds = 200
+Dangerous builds = 0
+fix             2 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
+  19 = # of size 2 clusters
+  6 = # of size 3 clusters
+  3 = # of size 4 clusters
+  640 = # of frozen angles
+group           peptide type <= 12
+84 atoms in group peptide
+Total wall time: 0:00:58

examples/USER/misc/temper_npt/log.temper_npt-17Aug17.g++.8.3

@@ -0,0 +1,211 @@
+LAMMPS (17 Aug 2017)
+Processor partition = 3
+  using 1 OpenMP thread(s) per MPI task
+# Solvated 5-mer peptide
+# Demonstrating temper/npt
+units           real
+atom_style      full
+
+pair_style      lj/charmm/coul/long 8.0 10.0 10.0
+bond_style      harmonic
+angle_style     charmm
+dihedral_style  charmm
+improper_style  harmonic
+kspace_style    pppm 0.0001
+
+read_data       data.peptide
+  orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
+  1 by 1 by 2 MPI processor grid
+  reading atoms ...
+  2004 atoms
+  reading velocities ...
+  2004 velocities
+  scanning bonds ...
+  3 = max bonds/atom
+  scanning angles ...
+  6 = max angles/atom
+  scanning dihedrals ...
+  14 = max dihedrals/atom
+  scanning impropers ...
+  1 = max impropers/atom
+  reading bonds ...
+  1365 bonds
+  reading angles ...
+  786 angles
+  reading dihedrals ...
+  207 dihedrals
+  reading impropers ...
+  12 impropers
+  4 = max # of 1-2 neighbors
+  7 = max # of 1-3 neighbors
+  14 = max # of 1-4 neighbors
+  18 = max # of special neighbors
+
+neighbor        2.0 bin
+neigh_modify    delay 5
+
+timestep        2.0
+
+thermo_style    custom step temp epair emol etotal press density
+thermo          50
+
+variable        temper_T world 275 280 285 290 295 300 305 310
+variable        rep world 0 1 2 3 4 5 6 7
+fix             myfix all npt temp ${temper_T} ${temper_T} 100.0 iso 1 1 1000
+fix             myfix all npt temp 290 ${temper_T} 100.0 iso 1 1 1000
+fix             myfix all npt temp 290 290 100.0 iso 1 1 1000
+run             500
+PPPM initialization ...
+WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+  G vector (1/distance) = 0.268725
+  grid = 15 15 15
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0228209
+  estimated relative force accuracy = 6.87243e-05
+  using double precision FFTs
+  3d grid and FFT values/proc = 6776 1800
+Neighbor list info ...
+  update every 1 steps, delay 5 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 12
+  ghost atom cutoff = 12
+  binsize = 6, bins = 5 5 5
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/charmm/coul/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) = 15.94 | 15.95 | 15.96 Mbytes
+Step Temp E_pair E_mol TotEng Press Density 
+       0     190.0857    -6442.768    70.391457   -5237.4579    20361.998   0.98480122 
+      50      223.053   -7677.6519    1222.7567   -5123.1433   -23832.135   0.99549097 
+     100    256.97829   -6970.9352    481.56411   -4955.0662    12716.194    1.0112202 
+     150    278.44824   -6890.5623    472.60764   -4755.4621    6994.6533    1.0198648 
+     200    271.15638   -7198.8095    1073.0275    -4506.826   -17647.735     1.020128 
+     250    271.19291   -6398.4699    477.07511   -4302.2206    23076.406    1.0123626 
+     300     295.5039   -6953.4923    1007.5309   -4181.6369   -15039.211    1.0007168 
+     350    297.29537   -6594.1646    707.50773   -4111.6362    1990.9893   0.99116796 
+     400    294.93533    -6450.921    630.83559   -4059.1555    6431.7427   0.98805162 
+     450    295.23265   -6781.3296    1002.9096    -4015.715   -12070.145   0.98722232 
+     500    284.70036   -6389.6524    668.83647   -4020.9946    10958.208   0.98502274 
+Loop time of 11.0942 on 2 procs for 500 steps with 2004 atoms
+
+Performance: 7.788 ns/day, 3.082 hours/ns, 45.069 timesteps/s
+99.3% CPU use with 2 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 7.7626     | 7.8378     | 7.913      |   2.7 | 70.65
+Bond    | 0.086271   | 0.08859    | 0.090909   |   0.8 |  0.80
+Kspace  | 1.1309     | 1.2146     | 1.2982     |   7.6 | 10.95
+Neigh   | 1.2958     | 1.2978     | 1.2999     |   0.2 | 11.70
+Comm    | 0.24052    | 0.24249    | 0.24445    |   0.4 |  2.19
+Output  | 0.00055242 | 0.00056267 | 0.00057292 |   0.0 |  0.01
+Modify  | 0.35597    | 0.3786     | 0.40124    |   3.7 |  3.41
+Other   |            | 0.03375    |            |       |  0.30
+
+Nlocal:    1002 ave 1015 max 989 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+Nghost:    8686.5 ave 8717 max 8656 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+Neighs:    354166 ave 365049 max 343283 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+
+Total # of neighbors = 708332
+Ave neighs/atom = 353.459
+Ave special neighs/atom = 2.34032
+Neighbor list builds = 52
+Dangerous builds = 0
+temper/npt      2000 100 ${temper_T} myfix 0 58728 1
+temper/npt      2000 100 290 myfix 0 58728 1
+PPPM initialization ...
+WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+  G vector (1/distance) = 0.268731
+  grid = 15 15 15
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0228157
+  estimated relative force accuracy = 6.87089e-05
+  using double precision FFTs
+  3d grid and FFT values/proc = 6776 1800
+Per MPI rank memory allocation (min/avg/max) = 15.94 | 15.95 | 15.96 Mbytes
+Step Temp E_pair E_mol TotEng Press Density 
+     500    284.70036   -6389.6523    668.83647   -4020.9946    10958.208   0.98502274 
+     550    290.90514   -6715.0579    911.30009   -4066.8904    -6474.803   0.98383517 
+     600    283.07652   -6555.4875    766.62589   -4098.7355    261.44315   0.98334866 
+     650    293.39943   -6543.5525    727.38701   -4064.4058    5298.0746   0.98688936 
+     700    295.77284   -6702.0803    912.68434   -4023.4658   -6806.6079   0.98957885 
+     750    302.19503   -6545.9025    745.53299   -3996.0952    4624.9549    0.9931176 
+     800    292.89947   -6664.6734    861.73293   -4054.1658   -1569.2753   0.99667377 
+     850    288.96376   -6637.9753    841.33585   -4071.3632    -864.6336    1.0003373 
+     900    291.22538   -6602.7272    806.80566   -4057.1422    2231.0477    1.0028411 
+     950    290.78982   -6720.7893    893.26995   -4091.3406   -3898.6743    1.0021058 
+    1000    285.74827   -6640.6252    810.15614   -4124.3911    558.53066    1.0051325 
+    1050     288.3183   -6717.0357     867.9383    -4127.675    355.99916    1.0122228 
+    1100    291.39421   -6746.7014    879.64717   -4127.2669   -736.99584     1.011619 
+    1150    290.47863   -6710.1637    836.85441   -4138.9885    1105.9666    1.0069336 
+    1200    288.94451   -6726.3595    867.56238   -4133.6359   -901.95525    1.0026837 
+    1250    290.75557   -6716.8398    867.19843   -4113.6671    1376.8368    1.0000807 
+    1300    289.52654   -6715.6758    904.46364   -4082.5758   -1400.2433   0.99935875 
+    1350    292.30663   -6661.0526    904.32661    -4011.491    196.73374   0.99704618 
+    1400    301.41479    -6661.807    880.88881   -3981.3023    1079.6673   0.99635503 
+    1450    301.10415   -6704.7089    950.31941   -3956.6283   -1083.4574   0.99740883 
+    1500    303.52341   -6687.1744    886.70817   -3988.2608    901.20455   0.99756877 
+    1550    290.70908   -6738.4941    931.37971   -4071.4177   -56.269366   0.99843015 
+    1600     289.8778    -6709.348    888.89193   -4089.7225    506.51952    1.0003118 
+    1650    288.12183   -6724.4008    896.24971   -4107.9017   -1229.6117     1.004563 
+    1700    297.81604   -6743.9356    906.62851   -4059.1778    1032.1913    1.0116813 
+    1750    304.22415   -6761.8681    932.14203   -4013.3368     1825.359     1.015764 
+    1800    286.62853   -6698.3527    911.17615    -4075.843   -1160.6136    1.0169905 
+    1850     292.7719   -6787.8009    918.61838   -4121.1696    1455.4151    1.0203418 
+    1900    290.87293   -6806.1448    960.43892   -4109.0309   -829.39096     1.022593 
+    1950     304.5232   -6848.8518    954.93165   -4075.7453    915.93096    1.0221703 
+    2000    286.15289    -6721.328    941.83273   -4071.0015     194.2717    1.0167052 
+    2050     305.2696   -6720.8244    968.69939   -3929.4938   -1154.2389    1.0114409 
+    2100    298.14935   -6678.8136    975.17824    -3923.516     794.1643    1.0070072 
+    2150    301.51333   -6734.6863    950.33572   -3984.1464   -537.44292    1.0048337 
+    2200    298.25074    -6736.277     945.4083    -4010.144    211.60185    1.0060101 
+    2250    297.20864   -6820.7924    941.75394   -4104.5356    772.05119    1.0087884 
+    2300    286.08552   -6853.0967    990.41746   -4154.5877   -760.47968    1.0110651 
+    2350    295.49972   -6888.1433    937.27703   -4186.5667    966.37988    1.0150101 
+    2400    289.60528   -6888.0768    967.74071   -4191.2297    1140.8847    1.0176507 
+    2450     290.7003    -6906.443    998.89141   -4171.9073   -363.47638    1.0151765 
+    2500    291.05855   -6817.2894    972.06896   -4107.4372    415.89846    1.0117849 
+Loop time of 46.7412 on 2 procs for 2000 steps with 2004 atoms
+
+Performance: 7.394 ns/day, 3.246 hours/ns, 42.789 timesteps/s
+99.3% CPU use with 2 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 31.884     | 32.272     | 32.659     |   6.8 | 69.04
+Bond    | 0.34239    | 0.35991    | 0.37742    |   2.9 |  0.77
+Kspace  | 4.6486     | 5.0781     | 5.5076     |  19.1 | 10.86
+Neigh   | 5.1657     | 5.1742     | 5.1828     |   0.4 | 11.07
+Comm    | 0.96743    | 0.96831    | 0.96918    |   0.1 |  2.07
+Output  | 0.0021966  | 0.0022568  | 0.002317   |   0.1 |  0.00
+Modify  | 1.4428     | 1.5251     | 1.6074     |   6.7 |  3.26
+Other   |            | 1.362      |            |       |  2.91
+
+Nlocal:    1002 ave 1004 max 1000 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+Nghost:    8824 ave 8848 max 8800 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+Neighs:    363564 ave 364653 max 362474 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+
+Total # of neighbors = 727127
+Ave neighs/atom = 362.838
+Ave special neighs/atom = 2.34032
+Neighbor list builds = 201
+Dangerous builds = 0
+fix             2 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
+  19 = # of size 2 clusters
+  6 = # of size 3 clusters
+  3 = # of size 4 clusters
+  640 = # of frozen angles
+group           peptide type <= 12
+84 atoms in group peptide
+Total wall time: 0:00:58

examples/USER/misc/temper_npt/log.temper_npt-17Aug17.g++.8.4

@@ -0,0 +1,211 @@
+LAMMPS (17 Aug 2017)
+Processor partition = 4
+  using 1 OpenMP thread(s) per MPI task
+# Solvated 5-mer peptide
+# Demonstrating temper/npt
+units           real
+atom_style      full
+
+pair_style      lj/charmm/coul/long 8.0 10.0 10.0
+bond_style      harmonic
+angle_style     charmm
+dihedral_style  charmm
+improper_style  harmonic
+kspace_style    pppm 0.0001
+
+read_data       data.peptide
+  orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
+  1 by 1 by 2 MPI processor grid
+  reading atoms ...
+  2004 atoms
+  reading velocities ...
+  2004 velocities
+  scanning bonds ...
+  3 = max bonds/atom
+  scanning angles ...
+  6 = max angles/atom
+  scanning dihedrals ...
+  14 = max dihedrals/atom
+  scanning impropers ...
+  1 = max impropers/atom
+  reading bonds ...
+  1365 bonds
+  reading angles ...
+  786 angles
+  reading dihedrals ...
+  207 dihedrals
+  reading impropers ...
+  12 impropers
+  4 = max # of 1-2 neighbors
+  7 = max # of 1-3 neighbors
+  14 = max # of 1-4 neighbors
+  18 = max # of special neighbors
+
+neighbor        2.0 bin
+neigh_modify    delay 5
+
+timestep        2.0
+
+thermo_style    custom step temp epair emol etotal press density
+thermo          50
+
+variable        temper_T world 275 280 285 290 295 300 305 310
+variable        rep world 0 1 2 3 4 5 6 7
+fix             myfix all npt temp ${temper_T} ${temper_T} 100.0 iso 1 1 1000
+fix             myfix all npt temp 295 ${temper_T} 100.0 iso 1 1 1000
+fix             myfix all npt temp 295 295 100.0 iso 1 1 1000
+run             500
+PPPM initialization ...
+WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+  G vector (1/distance) = 0.268725
+  grid = 15 15 15
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0228209
+  estimated relative force accuracy = 6.87243e-05
+  using double precision FFTs
+  3d grid and FFT values/proc = 6776 1800
+Neighbor list info ...
+  update every 1 steps, delay 5 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 12
+  ghost atom cutoff = 12
+  binsize = 6, bins = 5 5 5
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/charmm/coul/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) = 15.94 | 15.95 | 15.96 Mbytes
+Step Temp E_pair E_mol TotEng Press Density 
+       0     190.0857    -6442.768    70.391457   -5237.4579    20361.998   0.98480122 
+      50    223.44965   -7675.7636    1223.6082   -5118.0353   -23854.901   0.99531214 
+     100    258.05368   -6964.3986    482.14839   -4941.5246    12745.624     1.010825 
+     150    279.95689   -6874.6176    472.25664   -4730.8609    7091.9355    1.0193879 
+     200    275.57578   -7193.9232    1079.6288    -4468.952   -17877.542    1.0195441 
+     250    279.43717   -6402.2754    479.97988   -4253.8984    23273.809    1.0116181 
+     300    292.20824   -6863.5426    998.78846   -4120.1066   -14524.477   0.99985013 
+     350    297.83477   -6520.8204    705.46814   -4037.1112    1640.5321   0.99100268 
+     400    300.71476   -6441.8834    652.50284   -3993.9443    7052.2304   0.98787311 
+     450    298.04546   -6757.2898    986.07239   -3991.7184   -11211.612   0.98470906 
+     500    290.54704   -6432.0836    676.82263   -4020.5317    9503.0303   0.98022653 
+Loop time of 11.0411 on 2 procs for 500 steps with 2004 atoms
+
+Performance: 7.825 ns/day, 3.067 hours/ns, 45.286 timesteps/s
+99.2% CPU use with 2 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 7.7513     | 7.8142     | 7.8771     |   2.3 | 70.77
+Bond    | 0.087844   | 0.089858   | 0.091872   |   0.7 |  0.81
+Kspace  | 1.1507     | 1.2078     | 1.2649     |   5.2 | 10.94
+Neigh   | 1.2777     | 1.2798     | 1.282      |   0.2 | 11.59
+Comm    | 0.21883    | 0.2369     | 0.25497    |   3.7 |  2.15
+Output  | 0.00052476 | 0.00053084 | 0.00053692 |   0.0 |  0.00
+Modify  | 0.35187    | 0.38007    | 0.40828    |   4.6 |  3.44
+Other   |            | 0.03188    |            |       |  0.29
+
+Nlocal:    1002 ave 1018 max 986 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+Nghost:    8685.5 ave 8713 max 8658 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+Neighs:    352674 ave 363841 max 341507 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+
+Total # of neighbors = 705348
+Ave neighs/atom = 351.97
+Ave special neighs/atom = 2.34032
+Neighbor list builds = 51
+Dangerous builds = 0
+temper/npt      2000 100 ${temper_T} myfix 0 58728 1
+temper/npt      2000 100 295 myfix 0 58728 1
+PPPM initialization ...
+WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+  G vector (1/distance) = 0.268595
+  grid = 15 15 15
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0229274
+  estimated relative force accuracy = 6.90452e-05
+  using double precision FFTs
+  3d grid and FFT values/proc = 6776 1800
+Per MPI rank memory allocation (min/avg/max) = 15.94 | 15.95 | 15.96 Mbytes
+Step Temp E_pair E_mol TotEng Press Density 
+     500    290.54704   -6432.0826    676.82263   -4020.5307    9503.0509   0.98022653 
+     550    299.80307   -6732.1631    858.08424   -4084.0858   -5804.5234   0.97922483 
+     600    282.09517   -6605.4814    819.96587   -4101.2486   -819.40251   0.98081741 
+     650    294.53657   -6522.7525    767.04478   -3997.1588    4596.0585   0.98382352 
+     700      305.841   -6619.4153     905.5064   -3887.8662   -5973.5686   0.98622017 
+     750    307.23206    -6438.653    789.70387   -3814.6009    6681.8219   0.98950206 
+     800    307.87505   -6564.5918    887.75178   -3838.6527   -1917.6181   0.98688326 
+     850    298.61627   -6528.5749    847.91654   -3897.7513   -3785.6609    0.9806677 
+     900    300.37107   -6492.7964    828.13288   -3871.2792    3123.0873   0.97992098 
+     950    313.50832   -6648.6955    936.69562   -3840.1788   -3465.5075   0.97832705 
+    1000    300.79594   -6452.6853    828.10459   -3828.6598    2639.7489    0.9724972 
+    1050    316.04685   -6570.6422    935.04399   -3748.6208   -2434.9525   0.96835974 
+    1100     311.0203     -6489.14    897.50532   -3734.6686   -1557.8625   0.97044387 
+    1150    311.75575   -6489.2845    888.02191   -3739.9054    1954.7864   0.97411485 
+    1200    304.34674   -6521.7138    905.22814   -3799.3644   -1699.1298   0.98025305 
+    1250       305.82   -6594.6645    927.05285   -3841.6942    1061.9124   0.98818343 
+    1300    300.78043   -6566.1931    942.90743   -3827.4574   -864.10057   0.99107957 
+    1350    314.72676   -6545.9508    912.22446   -3754.6305    606.75529    0.9929135 
+    1400      315.913   -6551.4197      960.628   -3704.6134    1064.6728   0.99029667 
+    1450    309.18966   -6497.0696    918.08358   -3732.9498   -1325.2759   0.98343775 
+    1500    312.58526   -6494.4875    891.16465    -3737.013    1380.3782   0.98291945 
+    1550    317.55684   -6590.3216    970.14576   -3724.1828   -1866.6608    0.9847875 
+    1600    307.38151   -6552.4153      940.826   -3776.3487   -390.22458   0.98596757 
+    1650    295.78641    -6508.499    880.69089   -3861.7969   -1368.3717   0.98931642 
+    1700    306.06415   -6655.9157    976.17248   -3852.3681   -1599.4137   0.99512042 
+    1750    303.02767     -6625.01    920.50823   -3895.2561    2274.9319    1.0015941 
+    1800    295.63701   -6674.2337    928.57382   -3980.5406   -290.52041    1.0049878 
+    1850    302.04323   -6768.1711    959.29198   -4005.5112   -688.59334    1.0096755 
+    1900    299.41653   -6746.3896    940.56717   -4018.1373     1011.075    1.0170047 
+    1950    298.83395   -6766.5655    950.11421   -4032.2445   -187.97792    1.0202189 
+    2000    299.45823   -6824.2159    958.18625   -4078.0956   -715.67202    1.0223031 
+    2050    290.49349   -6835.2073    950.68063   -4150.1172   -345.43177    1.0232367 
+    2100    283.23103    -6798.203    936.42547    -4170.729    300.36081    1.0201704 
+    2150    295.58133   -6797.5304    933.21906   -4099.5245   -293.26979    1.0191458 
+    2200    287.12783   -6693.6112    942.32795   -4036.9686   -1430.1972    1.0191149 
+    2250    301.19592   -6762.0204    998.15337   -3965.5579   -956.39215    1.0207659 
+    2300    303.62433   -6716.6297    960.83467    -3942.987    77.237938    1.0202529 
+    2350    292.95455    -6741.789    993.45295   -3999.2326    1009.5683    1.0189011 
+    2400    295.01475    -6781.545    966.72586   -4053.4151    109.26284    1.0174852 
+    2450    300.36482   -6827.3015    978.76759    -4055.187    -395.9959    1.0168907 
+    2500    303.77029   -6833.9094    987.05071   -4033.1791    259.58796    1.0139892 
+Loop time of 46.7422 on 2 procs for 2000 steps with 2004 atoms
+
+Performance: 7.394 ns/day, 3.246 hours/ns, 42.788 timesteps/s
+99.3% CPU use with 2 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 31.75      | 32.061     | 32.372     |   5.5 | 68.59
+Bond    | 0.36191    | 0.36261    | 0.36331    |   0.1 |  0.78
+Kspace  | 4.6321     | 4.925      | 5.2179     |  13.2 | 10.54
+Neigh   | 5.3267     | 5.3348     | 5.3429     |   0.3 | 11.41
+Comm    | 0.88959    | 0.96174    | 1.0339     |   7.4 |  2.06
+Output  | 0.0022326  | 0.0022967  | 0.0023608  |   0.1 |  0.00
+Modify  | 1.4187     | 1.5349     | 1.6512     |   9.4 |  3.28
+Other   |            | 1.56       |            |       |  3.34
+
+Nlocal:    1002 ave 1009 max 995 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+Nghost:    8864 ave 8880 max 8848 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+Neighs:    364886 ave 365536 max 364236 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+
+Total # of neighbors = 729772
+Ave neighs/atom = 364.158
+Ave special neighs/atom = 2.34032
+Neighbor list builds = 206
+Dangerous builds = 0
+fix             2 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
+  19 = # of size 2 clusters
+  6 = # of size 3 clusters
+  3 = # of size 4 clusters
+  640 = # of frozen angles
+group           peptide type <= 12
+84 atoms in group peptide
+Total wall time: 0:00:58

examples/USER/misc/temper_npt/log.temper_npt-17Aug17.g++.8.5

@@ -0,0 +1,211 @@
+LAMMPS (17 Aug 2017)
+Processor partition = 5
+  using 1 OpenMP thread(s) per MPI task
+# Solvated 5-mer peptide
+# Demonstrating temper/npt
+units           real
+atom_style      full
+
+pair_style      lj/charmm/coul/long 8.0 10.0 10.0
+bond_style      harmonic
+angle_style     charmm
+dihedral_style  charmm
+improper_style  harmonic
+kspace_style    pppm 0.0001
+
+read_data       data.peptide
+  orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
+  1 by 1 by 2 MPI processor grid
+  reading atoms ...
+  2004 atoms
+  reading velocities ...
+  2004 velocities
+  scanning bonds ...
+  3 = max bonds/atom
+  scanning angles ...
+  6 = max angles/atom
+  scanning dihedrals ...
+  14 = max dihedrals/atom
+  scanning impropers ...
+  1 = max impropers/atom
+  reading bonds ...
+  1365 bonds
+  reading angles ...
+  786 angles
+  reading dihedrals ...
+  207 dihedrals
+  reading impropers ...
+  12 impropers
+  4 = max # of 1-2 neighbors
+  7 = max # of 1-3 neighbors
+  14 = max # of 1-4 neighbors
+  18 = max # of special neighbors
+
+neighbor        2.0 bin
+neigh_modify    delay 5
+
+timestep        2.0
+
+thermo_style    custom step temp epair emol etotal press density
+thermo          50
+
+variable        temper_T world 275 280 285 290 295 300 305 310
+variable        rep world 0 1 2 3 4 5 6 7
+fix             myfix all npt temp ${temper_T} ${temper_T} 100.0 iso 1 1 1000
+fix             myfix all npt temp 300 ${temper_T} 100.0 iso 1 1 1000
+fix             myfix all npt temp 300 300 100.0 iso 1 1 1000
+run             500
+PPPM initialization ...
+WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+  G vector (1/distance) = 0.268725
+  grid = 15 15 15
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0228209
+  estimated relative force accuracy = 6.87243e-05
+  using double precision FFTs
+  3d grid and FFT values/proc = 6776 1800
+Neighbor list info ...
+  update every 1 steps, delay 5 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 12
+  ghost atom cutoff = 12
+  binsize = 6, bins = 5 5 5
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/charmm/coul/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) = 15.94 | 15.95 | 15.96 Mbytes
+Step Temp E_pair E_mol TotEng Press Density 
+       0     190.0857    -6442.768    70.391457   -5237.4579    20361.998   0.98480122 
+      50    223.82864   -7673.9648    1224.4256   -5113.1564   -23877.062   0.99513919 
+     100    259.08234   -6958.1555    482.71038   -4928.5779    12773.331     1.010442 
+     150    281.33296   -6859.1832    472.14676   -4707.3204     7185.467    1.0189247 
+     200    278.97145   -7183.3765    1085.5768   -4432.1832   -18068.845    1.0189951 
+     250    279.03591   -6351.7829    479.41881   -4206.3627    23082.567    1.0112758 
+     300     300.6326   -6884.9027    1026.5309    -4063.426   -13809.886   0.99975981 
+     350     305.9627   -6542.2739    749.87415   -3965.6303     1365.919   0.98893682 
+     400    300.95813     -6356.16    664.78738   -3894.4833    7945.2634   0.98104761 
+     450    305.74067   -6698.3004    1016.1128   -3856.7437   -11928.509   0.97692928 
+     500    295.19123   -6343.4664    707.06763   -3873.9411    9895.6164   0.97622451 
+Loop time of 11.1232 on 2 procs for 500 steps with 2004 atoms
+
+Performance: 7.768 ns/day, 3.090 hours/ns, 44.951 timesteps/s
+99.0% CPU use with 2 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 7.8133     | 7.8368     | 7.8603     |   0.8 | 70.45
+Bond    | 0.088746   | 0.089125   | 0.089505   |   0.1 |  0.80
+Kspace  | 1.2047     | 1.2319     | 1.2591     |   2.5 | 11.07
+Neigh   | 1.3081     | 1.31       | 1.3119     |   0.2 | 11.78
+Comm    | 0.21978    | 0.23832    | 0.25687    |   3.8 |  2.14
+Output  | 0.00053644 | 0.00054514 | 0.00055385 |   0.0 |  0.00
+Modify  | 0.35216    | 0.38209    | 0.41202    |   4.8 |  3.44
+Other   |            | 0.03448    |            |       |  0.31
+
+Nlocal:    1002 ave 1003 max 1001 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+Nghost:    8664.5 ave 8679 max 8650 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+Neighs:    350634 ave 352508 max 348761 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+
+Total # of neighbors = 701269
+Ave neighs/atom = 349.935
+Ave special neighs/atom = 2.34032
+Neighbor list builds = 52
+Dangerous builds = 0
+temper/npt      2000 100 ${temper_T} myfix 0 58728 1
+temper/npt      2000 100 300 myfix 0 58728 1
+PPPM initialization ...
+WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+  G vector (1/distance) = 0.26848
+  grid = 15 15 15
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0230214
+  estimated relative force accuracy = 6.93284e-05
+  using double precision FFTs
+  3d grid and FFT values/proc = 6776 1800
+Per MPI rank memory allocation (min/avg/max) = 15.94 | 15.95 | 15.96 Mbytes
+Step Temp E_pair E_mol TotEng Press Density 
+     500    295.19123   -6343.4702    707.06763   -3873.9449    9895.5638   0.97622451 
+     550    302.94979   -6642.4394    911.36179   -3922.2969   -5410.8109   0.97461641 
+     600    297.33068   -6551.2919    805.26047      -3970.8   -646.78096   0.97348192 
+     650    294.80947   -6578.9544    780.59748   -4038.1786    3293.0695   0.97423526 
+     700     286.5511   -6718.4475    944.64841   -4062.9279   -5230.2518   0.97771554 
+     750    294.49463   -6602.2482    777.88337   -4066.0662     4142.887    0.9831379 
+     800    291.06018   -6664.3537    858.09465    -4068.466   -2624.3753   0.98991103 
+     850    293.82285   -6689.8325    860.75951   -4074.7853    -435.3378   0.99623629 
+     900    287.38111   -6671.9376    837.28605   -4118.8247    2185.0063   0.99906496 
+     950    288.54911   -6783.7293    916.92837   -4144.0005   -2644.9104   0.99578685 
+    1000    293.00277   -6687.2173    803.00518   -4134.8207     2220.968   0.98936787 
+    1050    301.16902   -6760.9066    892.18697   -4070.5711   -2974.6886   0.98583275 
+    1100    309.08554   -6738.1202    875.08899   -4017.6166    921.61791   0.98892607 
+    1150    298.58252   -6674.1083    871.86516   -4019.5376    944.64401   0.98978942 
+    1200    298.47184   -6760.3869    925.22004   -4053.1221    -798.3384   0.98947798 
+    1250    291.12935   -6703.3237    856.27457   -4108.8431    544.44438   0.98937896 
+    1300    293.02206   -6830.1194    917.90705   -4162.7058    432.93648   0.98837688 
+    1350    282.12152   -6775.1505    898.35169   -4192.3746   -968.85129   0.98738197 
+    1400    284.13008    -6684.782    848.15892   -4140.2066   -909.72792   0.98855422 
+    1450    283.07781   -6640.5698    889.19504    -4061.241    120.67624   0.99460963 
+    1500    299.32129   -6744.9956    896.07755   -4061.8016   -500.39827     1.002166 
+    1550    290.06547   -6763.7114    921.50981   -4110.3475    1970.1344    1.0045278 
+    1600    294.31127   -6824.5224    885.60385   -4181.7147   -1450.5522    1.0021664 
+    1650    289.14351   -6837.8321     902.7679   -4208.7148   -36.719886    1.0010127 
+    1700    284.10327   -6855.1076    903.75736   -4255.0939    984.04625    1.0006878 
+    1750    280.04385   -6904.9119    918.67229   -4314.2203   -1431.4015    1.0004286 
+    1800    281.68654   -6818.1122    846.72598   -4289.5591    520.17793    1.0021784 
+    1850    286.93593   -6902.5226    934.50057   -4254.8531   -793.77873    1.0057534 
+    1900    292.37295   -6876.9829    886.20947   -4245.1425    1563.8149    1.0119959 
+    1950    278.61219   -6897.2099    935.36125   -4298.3772   -498.09374    1.0139668 
+    2000    278.03754   -6936.4809    912.07762   -4364.3628    -475.0812    1.0140553 
+    2050    280.17142   -6999.6889    907.21584    -4419.692   -483.15119    1.0159549 
+    2100    275.01317   -7045.1909    966.49463   -4436.7129    516.29126    1.0192102 
+    2150    275.36286   -6985.3989    879.47784   -4461.8499   -33.602001    1.0183533 
+    2200    276.11062   -7026.4293     936.6898   -4441.2038   -1270.9384    1.0213402 
+    2250    283.79417   -7011.4884    977.04948   -4340.0281   -178.52826    1.0266779 
+    2300    276.26548   -6911.7259    909.12359    -4353.142    1380.5761    1.0284968 
+    2350     279.5692   -7056.2521    960.48747   -4426.5792    202.29669    1.0282733 
+    2400    270.18994   -6995.9308    932.57134   -4450.1735    -1921.755    1.0261097 
+    2450    273.41894   -6999.2367    955.71826   -4411.0536   -376.50236    1.0265598 
+    2500    279.53567   -6995.6096     941.2382   -4385.3862    300.84721    1.0300527 
+Loop time of 46.7426 on 2 procs for 2000 steps with 2004 atoms
+
+Performance: 7.394 ns/day, 3.246 hours/ns, 42.788 timesteps/s
+98.6% CPU use with 2 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 32.111     | 32.533     | 32.954     |   7.4 | 69.60
+Bond    | 0.36551    | 0.36836    | 0.3712     |   0.5 |  0.79
+Kspace  | 4.9203     | 5.3226     | 5.7249     |  17.4 | 11.39
+Neigh   | 5.2618     | 5.2695     | 5.2772     |   0.3 | 11.27
+Comm    | 0.89292    | 0.96319    | 1.0335     |   7.2 |  2.06
+Output  | 0.0021534  | 0.0022     | 0.0022466  |   0.1 |  0.00
+Modify  | 1.4108     | 1.5304     | 1.65       |   9.7 |  3.27
+Other   |            | 0.7537     |            |       |  1.61
+
+Nlocal:    1002 ave 1023 max 981 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+Nghost:    8955 ave 9060 max 8850 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+Neighs:    370398 ave 378514 max 362281 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+
+Total # of neighbors = 740795
+Ave neighs/atom = 369.658
+Ave special neighs/atom = 2.34032
+Neighbor list builds = 200
+Dangerous builds = 0
+fix             2 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
+  19 = # of size 2 clusters
+  6 = # of size 3 clusters
+  3 = # of size 4 clusters
+  640 = # of frozen angles
+group           peptide type <= 12
+84 atoms in group peptide
+Total wall time: 0:00:58

examples/USER/misc/temper_npt/log.temper_npt-17Aug17.g++.8.6

@@ -0,0 +1,211 @@
+LAMMPS (17 Aug 2017)
+Processor partition = 6
+  using 1 OpenMP thread(s) per MPI task
+# Solvated 5-mer peptide
+# Demonstrating temper/npt
+units           real
+atom_style      full
+
+pair_style      lj/charmm/coul/long 8.0 10.0 10.0
+bond_style      harmonic
+angle_style     charmm
+dihedral_style  charmm
+improper_style  harmonic
+kspace_style    pppm 0.0001
+
+read_data       data.peptide
+  orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
+  1 by 1 by 2 MPI processor grid
+  reading atoms ...
+  2004 atoms
+  reading velocities ...
+  2004 velocities
+  scanning bonds ...
+  3 = max bonds/atom
+  scanning angles ...
+  6 = max angles/atom
+  scanning dihedrals ...
+  14 = max dihedrals/atom
+  scanning impropers ...
+  1 = max impropers/atom
+  reading bonds ...
+  1365 bonds
+  reading angles ...
+  786 angles
+  reading dihedrals ...
+  207 dihedrals
+  reading impropers ...
+  12 impropers
+  4 = max # of 1-2 neighbors
+  7 = max # of 1-3 neighbors
+  14 = max # of 1-4 neighbors
+  18 = max # of special neighbors
+
+neighbor        2.0 bin
+neigh_modify    delay 5
+
+timestep        2.0
+
+thermo_style    custom step temp epair emol etotal press density
+thermo          50
+
+variable        temper_T world 275 280 285 290 295 300 305 310
+variable        rep world 0 1 2 3 4 5 6 7
+fix             myfix all npt temp ${temper_T} ${temper_T} 100.0 iso 1 1 1000
+fix             myfix all npt temp 305 ${temper_T} 100.0 iso 1 1 1000
+fix             myfix all npt temp 305 305 100.0 iso 1 1 1000
+run             500
+PPPM initialization ...
+WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+  G vector (1/distance) = 0.268725
+  grid = 15 15 15
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0228209
+  estimated relative force accuracy = 6.87243e-05
+  using double precision FFTs
+  3d grid and FFT values/proc = 6776 1800
+Neighbor list info ...
+  update every 1 steps, delay 5 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 12
+  ghost atom cutoff = 12
+  binsize = 6, bins = 5 5 5
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/charmm/coul/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) = 15.94 | 15.95 | 15.96 Mbytes
+Step Temp E_pair E_mol TotEng Press Density 
+       0     190.0857    -6442.768    70.391457   -5237.4579    20361.998   0.98480122 
+      50    224.19041   -7672.2342    1225.2069   -5108.4844   -23898.427    0.9949719 
+     100    260.06304   -6952.1103    483.25334   -4916.1343    12800.907      1.01007 
+     150    282.69922   -6844.8106     472.2939   -4684.6433    7274.1665    1.0184736 
+     200    283.07925   -7183.2915    1096.3999   -4396.7493   -18428.465    1.0184431 
+     250    283.61722   -6327.2943    475.82271   -4158.1172    23020.286    1.0107938 
+     300    301.71789   -6811.4188    1004.2807   -4005.7126   -14017.258   0.99889097 
+     350    311.03337   -6506.7477    765.85039   -3883.8531    763.04925   0.98860598 
+     400      317.775   -6392.1118    666.55754   -3828.2587    7828.8386   0.98148763 
+     450    303.51186   -6657.5211    1017.7742   -3827.6103   -12704.511   0.97662555 
+     500    296.45297   -6312.4144    719.53961   -3822.8838    8469.2935   0.97646495 
+Loop time of 10.8893 on 2 procs for 500 steps with 2004 atoms
+
+Performance: 7.934 ns/day, 3.025 hours/ns, 45.917 timesteps/s
+99.4% CPU use with 2 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 7.7295     | 7.7574     | 7.7852     |   1.0 | 71.24
+Bond    | 0.088436   | 0.089395   | 0.090353   |   0.3 |  0.82
+Kspace  | 1.1269     | 1.16       | 1.1931     |   3.1 | 10.65
+Neigh   | 1.2353     | 1.2377     | 1.2402     |   0.2 | 11.37
+Comm    | 0.21436    | 0.23339    | 0.25242    |   3.9 |  2.14
+Output  | 0.00055766 | 0.00056684 | 0.00057602 |   0.0 |  0.01
+Modify  | 0.34907    | 0.37832    | 0.40758    |   4.8 |  3.47
+Other   |            | 0.03245    |            |       |  0.30
+
+Nlocal:    1002 ave 1007 max 997 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+Nghost:    8685.5 ave 8750 max 8621 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+Neighs:    350698 ave 351936 max 349459 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+
+Total # of neighbors = 701395
+Ave neighs/atom = 349.998
+Ave special neighs/atom = 2.34032
+Neighbor list builds = 50
+Dangerous builds = 0
+temper/npt      2000 100 ${temper_T} myfix 0 58728 1
+temper/npt      2000 100 305 myfix 0 58728 1
+PPPM initialization ...
+WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+  G vector (1/distance) = 0.268487
+  grid = 15 15 15
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0230158
+  estimated relative force accuracy = 6.93113e-05
+  using double precision FFTs
+  3d grid and FFT values/proc = 6776 1800
+Per MPI rank memory allocation (min/avg/max) = 15.94 | 15.95 | 15.96 Mbytes
+Step Temp E_pair E_mol TotEng Press Density 
+     500    296.45297   -6312.4159    719.53961   -3822.8853    8469.2763   0.97646495 
+     550    303.89646   -6501.1353    863.14038   -3823.5621   -2928.2904   0.98030197 
+     600    309.76597   -6524.1714    843.08835    -3831.606   -871.10399   0.98376234 
+     650    299.00298   -6442.6354    805.96883   -3851.4506    3266.5866   0.98567102 
+     700    309.92953   -6599.5125    902.18135   -3846.8775   -4895.7743    0.9877618 
+     750    310.03453   -6432.9154    800.77648   -3781.0583    4312.9432   0.98939465 
+     800    313.79353   -6482.8645    876.10518   -3733.2354    459.73904    0.9883653 
+     850     308.0727   -6473.4666    891.51665   -3742.5826   -1645.1499    0.9829221 
+     900    312.68166    -6456.773     820.7786    -3769.109    2194.8957   0.97822936 
+     950    305.94065   -6546.0017    902.97469   -3816.3892   -2693.7918   0.97584317 
+    1000    298.40902   -6464.4155    886.05639   -3796.6893    592.46618    0.9764313 
+    1050    308.71394   -6480.6485    854.83864   -3782.6139    843.67793   0.97834087 
+    1100    309.34645   -6526.4283    897.66923   -3781.7868    -297.6956   0.98046791 
+    1150    303.65216    -6540.534    858.53216   -3869.0276    623.45838   0.98196819 
+    1200    298.33689   -6610.5403    897.10898   -3932.1923   -1107.1097   0.98263413 
+    1250    302.10596   -6587.4254    875.62056   -3908.0623    1244.7382   0.98273784 
+    1300    316.19456   -6618.7414    894.33747   -3836.5445   -1399.1921   0.98252654 
+    1350    302.28789   -6625.1555    938.19878   -3882.1279   -57.818071   0.98275084 
+    1400    301.42717   -6602.0706    858.72022   -3943.6606    1462.1175   0.97898596 
+    1450    299.43442   -6655.6584    893.68574   -3974.1807    383.13882   0.97462948 
+    1500    301.76848   -6653.4568    896.33172   -3955.3975   -756.22375   0.96978565 
+    1550    310.10887   -6664.8547    953.35222   -3859.9781   -1305.0786   0.96689812 
+    1600    297.16621   -6510.7805     907.3012   -3829.2299    992.41943   0.96413868 
+    1650    295.71413   -6598.1621    990.18935   -3842.3931   -2049.7934   0.96131396 
+    1700    303.88264   -6629.5417    931.13321   -3884.0582    -630.7683   0.96321179 
+    1750    300.85941   -6666.8007    941.42895   -3929.0719    357.85887   0.96822524 
+    1800    299.34518   -6674.9694    932.15075   -3955.5595   -914.97614   0.97074982 
+    1850    298.12166   -6610.2338    910.63353   -3919.6462    1390.5062   0.97402953 
+    1900    307.86527   -6647.8711    931.49082   -3878.2514   -1629.6931   0.97542316 
+    1950    305.04604   -6616.6069    937.35845    -3857.952    858.37861   0.97770539 
+    2000    305.41215   -6597.2293    916.75863   -3856.9883     763.6265   0.98001111 
+    2050    294.66502   -6632.9068     1035.729   -3837.8618   -2248.1496   0.98430681 
+    2100     300.5948   -6569.1213    956.22884   -3818.1724     291.3677   0.99188971 
+    2150    305.73836   -6623.7387    1021.1569   -3777.1519   -603.41468    1.0003649 
+    2200    316.63308   -6681.0402    972.23429   -3818.3283    948.97143    1.0073383 
+    2250    306.36381   -6653.5361    947.42424   -3876.9476    900.19264     1.010245 
+    2300     301.9961   -6699.2583    1022.4799   -3873.6918   -499.39887    1.0119712 
+    2350    307.25098   -6642.8345    970.32723   -3838.0461    366.40507    1.0118686 
+    2400    311.79941   -6675.2645    1030.8811   -3782.7656   -1083.5459    1.0113601 
+    2450    309.31064   -6630.1585    958.35981   -3825.0401    471.39091    1.0099697 
+    2500    301.87691   -6689.2603    967.59935   -3919.2859   -854.45149    1.0097679 
+Loop time of 46.7431 on 2 procs for 2000 steps with 2004 atoms
+
+Performance: 7.394 ns/day, 3.246 hours/ns, 42.787 timesteps/s
+99.4% CPU use with 2 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 31.029     | 31.472     | 31.916     |   7.9 | 67.33
+Bond    | 0.36154    | 0.36249    | 0.36343    |   0.2 |  0.78
+Kspace  | 4.7001     | 5.1269     | 5.5536     |  18.8 | 10.97
+Neigh   | 5.311      | 5.3205     | 5.33       |   0.4 | 11.38
+Comm    | 0.86766    | 0.94238    | 1.0171     |   7.7 |  2.02
+Output  | 0.0022194  | 0.0022837  | 0.0023479  |   0.1 |  0.00
+Modify  | 1.4059     | 1.5219     | 1.638      |   9.4 |  3.26
+Other   |            | 1.994      |            |       |  4.27
+
+Nlocal:    1002 ave 1012 max 992 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+Nghost:    8807.5 ave 8818 max 8797 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+Neighs:    363096 ave 369482 max 356711 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+
+Total # of neighbors = 726193
+Ave neighs/atom = 362.372
+Ave special neighs/atom = 2.34032
+Neighbor list builds = 207
+Dangerous builds = 0
+fix             2 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
+  19 = # of size 2 clusters
+  6 = # of size 3 clusters
+  3 = # of size 4 clusters
+  640 = # of frozen angles
+group           peptide type <= 12
+84 atoms in group peptide
+Total wall time: 0:00:58

examples/USER/misc/temper_npt/log.temper_npt-17Aug17.g++.8.7

@@ -0,0 +1,211 @@
+LAMMPS (17 Aug 2017)
+Processor partition = 7
+  using 1 OpenMP thread(s) per MPI task
+# Solvated 5-mer peptide
+# Demonstrating temper/npt
+units           real
+atom_style      full
+
+pair_style      lj/charmm/coul/long 8.0 10.0 10.0
+bond_style      harmonic
+angle_style     charmm
+dihedral_style  charmm
+improper_style  harmonic
+kspace_style    pppm 0.0001
+
+read_data       data.peptide
+  orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
+  1 by 1 by 2 MPI processor grid
+  reading atoms ...
+  2004 atoms
+  reading velocities ...
+  2004 velocities
+  scanning bonds ...
+  3 = max bonds/atom
+  scanning angles ...
+  6 = max angles/atom
+  scanning dihedrals ...
+  14 = max dihedrals/atom
+  scanning impropers ...
+  1 = max impropers/atom
+  reading bonds ...
+  1365 bonds
+  reading angles ...
+  786 angles
+  reading dihedrals ...
+  207 dihedrals
+  reading impropers ...
+  12 impropers
+  4 = max # of 1-2 neighbors
+  7 = max # of 1-3 neighbors
+  14 = max # of 1-4 neighbors
+  18 = max # of special neighbors
+
+neighbor        2.0 bin
+neigh_modify    delay 5
+
+timestep        2.0
+
+thermo_style    custom step temp epair emol etotal press density
+thermo          50
+
+variable        temper_T world 275 280 285 290 295 300 305 310
+variable        rep world 0 1 2 3 4 5 6 7
+fix             myfix all npt temp ${temper_T} ${temper_T} 100.0 iso 1 1 1000
+fix             myfix all npt temp 310 ${temper_T} 100.0 iso 1 1 1000
+fix             myfix all npt temp 310 310 100.0 iso 1 1 1000
+run             500
+PPPM initialization ...
+WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+  G vector (1/distance) = 0.268725
+  grid = 15 15 15
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0228209
+  estimated relative force accuracy = 6.87243e-05
+  using double precision FFTs
+  3d grid and FFT values/proc = 6776 1800
+Neighbor list info ...
+  update every 1 steps, delay 5 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 12
+  ghost atom cutoff = 12
+  binsize = 6, bins = 5 5 5
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/charmm/coul/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) = 15.94 | 15.95 | 15.96 Mbytes
+Step Temp E_pair E_mol TotEng Press Density 
+       0     190.0857    -6442.768    70.391457   -5237.4579    20361.998   0.98480122 
+      50     224.5362   -7670.5503    1225.9519   -5103.9909   -23918.514   0.99480995 
+     100    261.00419   -6946.2961    483.78483   -4904.1694    12827.309    1.0097087 
+     150    284.14624   -6832.0094    472.66187   -4662.8346    7354.8252    1.0180355 
+     200    284.05862   -7160.8537    1102.3553   -4362.5087   -18524.276    1.0178951 
+     250    290.82577   -6319.5357    471.77841   -4111.3638     22989.86    1.0099523 
+     300    306.50487   -6809.5465    1015.3715   -3964.1684   -13215.763   0.99625687 
+     350    319.20654   -6502.4307    761.98704    -3834.601   -965.94424   0.98284646 
+     400    316.81299   -6295.1539    646.79195   -3756.8102    8469.8917   0.97675631 
+     450    312.90373   -6639.6427    1048.7063   -3722.7251   -13014.646   0.97486033 
+     500    319.55848   -6335.5865    712.00927   -3715.6334    9980.2286   0.97468964 
+Loop time of 10.7877 on 2 procs for 500 steps with 2004 atoms
+
+Performance: 8.009 ns/day, 2.997 hours/ns, 46.349 timesteps/s
+99.1% CPU use with 2 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 7.6698     | 7.7211     | 7.7724     |   1.8 | 71.57
+Bond    | 0.085352   | 0.086755   | 0.088159   |   0.5 |  0.80
+Kspace  | 1.089      | 1.1417     | 1.1944     |   4.9 | 10.58
+Neigh   | 1.2554     | 1.2554     | 1.2554     |   0.0 | 11.64
+Comm    | 0.16438    | 0.17539    | 0.1864     |   2.6 |  1.63
+Output  | 0.00045967 | 0.0004642  | 0.00046873 |   0.0 |  0.00
+Modify  | 0.35006    | 0.37517    | 0.40028    |   4.1 |  3.48
+Other   |            | 0.0317     |            |       |  0.29
+
+Nlocal:    1002 ave 1004 max 1000 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+Nghost:    8709.5 ave 8714 max 8705 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+Neighs:    350398 ave 352725 max 348070 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+
+Total # of neighbors = 700795
+Ave neighs/atom = 349.698
+Ave special neighs/atom = 2.34032
+Neighbor list builds = 51
+Dangerous builds = 0
+temper/npt      2000 100 ${temper_T} myfix 0 58728 1
+temper/npt      2000 100 310 myfix 0 58728 1
+PPPM initialization ...
+WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+  G vector (1/distance) = 0.268436
+  grid = 15 15 15
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0230577
+  estimated relative force accuracy = 6.94376e-05
+  using double precision FFTs
+  3d grid and FFT values/proc = 6776 1800
+Per MPI rank memory allocation (min/avg/max) = 15.94 | 15.95 | 15.96 Mbytes
+Step Temp E_pair E_mol TotEng Press Density 
+     500    319.55848   -6335.5878    712.00927   -3715.6347    9980.2224   0.97468964 
+     550     312.3068   -6517.9692    882.51888   -3770.8031   -4737.1103   0.97368346 
+     600    306.74828   -6500.9408    860.97959   -3808.5014   -1687.6369   0.97333001 
+     650    309.25363   -6453.3615    753.23233    -3853.711    4484.0534   0.97330212 
+     700    305.22336   -6644.7434    922.38867   -3899.9996   -5823.8028   0.97262421 
+     750    297.24363   -6480.4086    771.41874   -3934.2782    5025.8889   0.97337406 
+     800    300.89643   -6587.4079    835.06282   -3955.8242   -1517.9426   0.97460241 
+     850    305.43206   -6685.1173    846.71999   -4014.7961    -1788.398   0.97836973 
+     900    289.95008   -6574.8681    806.12799    -4037.575     2604.847   0.98232784 
+     950    299.22424   -6671.7556    898.72395   -3986.4946    -2702.719   0.98919804 
+    1000     305.3932    -6576.089    826.21317   -3926.5066    2254.7456   0.99471125 
+    1050    304.62574    -6619.698    893.18161   -3907.7293   -1010.7916   0.99551385 
+    1100    304.13778   -6603.0961    846.91376   -3940.3087   -211.63132   0.99359493 
+    1150    285.80722   -6557.1116    859.12907   -3991.5526    1777.6534   0.99165538 
+    1200    295.20871   -6612.8101    855.05738   -3995.1906   -389.55216   0.98957199 
+    1250     301.4547   -6623.3355    907.78288   -3915.6984    1193.6428   0.98887879 
+    1300    302.29836   -6545.5769    862.86619   -3877.8194    443.76145    0.9853829 
+    1350    309.29624   -6539.3158    878.22476   -3814.4185   -769.46378   0.98002173 
+    1400    311.28962   -6582.4295    939.53596   -3784.3195   -239.11773   0.97952655 
+    1450    307.46833   -6597.7591    922.88062   -3839.1196    453.60414   0.98288752 
+    1500     308.8234   -6660.3138    910.39719   -3906.0672     356.0472   0.98507945 
+    1550    297.42322   -6596.3955    938.61921   -3881.9924   -883.10576   0.98730686 
+    1600      309.492   -6649.4174    963.57197   -3838.0041    470.91335   0.99194955 
+    1650    309.46921   -6602.6445    958.19972   -3796.7395    1417.6814   0.99437216 
+    1700    308.27043   -6575.0156    941.02926   -3793.4384   -445.78985   0.99171728 
+    1750    306.31262    -6515.703    929.60371   -3757.2406    944.20045   0.98661702 
+    1800    308.63008   -6484.7465    959.53268   -3682.5186    333.02755   0.98504191 
+    1850    316.69569   -6520.4677    975.02618   -3654.5901   -835.64735   0.98329409 
+    1900    316.03266   -6531.6456    948.03331   -3696.7196   -745.03047   0.98236945 
+    1950    308.97313   -6562.2733    955.48033   -3762.0496   -1147.5825     0.983921 
+    2000    305.67836   -6611.4675     991.3364   -3795.0594   -2361.1127   0.98852677 
+    2050    312.66709   -6687.3067    980.96042   -3839.5479   -244.80211   0.99714887 
+    2100    307.23751   -6664.4853    963.74125   -3866.3633    268.84485    1.0050595 
+    2150    296.36081   -6633.5455    966.74219   -3897.3626   -741.15958    1.0135557 
+    2200    306.79331   -6709.7668    989.09713   -3888.9411   -108.31295    1.0211476 
+    2250    310.62715   -6713.5021    973.14019   -3885.7431    1576.0539    1.0235204 
+    2300    304.34901   -6675.1811    1001.4509   -3856.5955   -481.96378    1.0180933 
+    2350    300.55584   -6592.7909    993.96783   -3804.3356    114.74351    1.0116595 
+    2400    307.16641   -6626.7049    984.70783   -3808.0408     620.2875    1.0087872 
+    2450    301.62279   -6643.7063    978.76012   -3864.0884    72.614095    1.0085247 
+    2500    307.17634   -6691.4794    975.63125   -3881.8326    495.45555    1.0099428 
+Loop time of 46.7465 on 2 procs for 2000 steps with 2004 atoms
+
+Performance: 7.393 ns/day, 3.246 hours/ns, 42.784 timesteps/s
+99.1% CPU use with 2 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 31.19      | 31.703     | 32.216     |   9.1 | 67.82
+Bond    | 0.35397    | 0.35463    | 0.35528    |   0.1 |  0.76
+Kspace  | 4.3783     | 4.8922     | 5.4062     |  23.2 | 10.47
+Neigh   | 5.2885     | 5.2889     | 5.2893     |   0.0 | 11.31
+Comm    | 0.67571    | 0.71687    | 0.75803    |   4.9 |  1.53
+Output  | 0.0019109  | 0.0019529  | 0.0019948  |   0.1 |  0.00
+Modify  | 1.4216     | 1.5185     | 1.6154     |   7.9 |  3.25
+Other   |            | 2.271      |            |       |  4.86
+
+Nlocal:    1002 ave 1010 max 994 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+Nghost:    8811.5 ave 8832 max 8791 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+Neighs:    363080 ave 367967 max 358193 min
+Histogram: 1 0 0 0 0 0 0 0 0 1
+
+Total # of neighbors = 726160
+Ave neighs/atom = 362.355
+Ave special neighs/atom = 2.34032
+Neighbor list builds = 207
+Dangerous builds = 0
+fix             2 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
+  19 = # of size 2 clusters
+  6 = # of size 3 clusters
+  3 = # of size 4 clusters
+  640 = # of frozen angles
+group           peptide type <= 12
+84 atoms in group peptide
+Total wall time: 0:00:58

examples/latte/TBparam/bondints.nonortho

@@ -0,0 +1,36 @@
+Noints= 34
+Element1 Element2  Kind     H0   B1      B2        B3           B4         B5  R1     Rcut H0   B1      B2        B3           B4         B5  R1     Rcut
+N O sss  -11.430028 -2.257346 -1.152844 0.000000 0.000000 1.200000 3.500000 4.000000 0.340064 -1.703613 -0.622348 0.036738 -0.040158 1.200000 3.500000 4.000000 
+N O sps  11.597479 -1.382001 -0.765170 0.000000 0.000000 1.200000 3.500000 4.000000 -0.370946 -1.040947 -0.931097 0.252441 -0.115450 1.200000 3.500000 4.000000 
+O N sps  12.143744 -0.822913 -0.676127 0.000000 0.000000 1.200000 3.500000 4.000000 -0.420014 -1.107918 -0.905594 0.188424 -0.088365 1.200000 3.500000 4.000000 
+N O pps  9.465191 -1.082032 -0.769214 0.000000 0.000000 1.200000 3.500000 4.000000 -0.314073 0.499050 -2.914288 2.067657 -0.738439 1.200000 3.500000 4.000000 
+N O ppp  -4.676789 -2.171480 -0.288002 0.000000 0.000000 1.200000 3.500000 4.000000 0.223937 -1.991867 -0.537630 -0.081270 -0.004130 1.200000 3.500000 4.000000 
+C O sss  -14.369472 -2.077439 -0.875471 0.000000 0.000000 1.200000 3.500000 4.000000 0.375339 -1.547372 -0.642492 0.020614 -0.026699 1.200000 3.500000 4.000000 
+C O sps  9.576296 -1.156217 -0.494803 0.000000 0.000000 1.200000 3.500000 4.000000 -0.373027 -0.776043 -1.019920 0.257539 -0.102838 1.200000 3.500000 4.000000 
+O C sps  14.037374 -1.192632 -0.654572 0.000000 0.000000 1.200000 3.500000 4.000000 -0.458068 -1.035067 -0.937868 0.190562 -0.077841 1.200000 3.500000 4.000000 
+C O pps  9.331152 -0.718120 -0.822100 0.000000 0.000000 1.200000 3.500000 4.000000 -0.322293 0.795473 -3.476601 2.589965 -0.897800 1.200000 3.500000 4.000000 
+C O ppp  -5.334367 -2.263939 -0.204910 0.000000 0.000000 1.200000 3.500000 4.000000 0.244570 -1.922717 -0.573671 -0.057280 -0.004108 1.200000 3.500000 4.000000 
+C N sss  -7.010061 -1.730597 -0.575559 0.000000 0.000000 1.500000 3.500000 4.000000 0.263438 -1.754525 -0.584215 -0.007801 -0.021729 1.500000 3.500000 4.000000 
+C N sps  7.543283 -1.293768 -0.624363 0.000000 0.000000 1.500000 3.500000 4.000000 -0.326609 -1.197485 -0.807786 0.134891 -0.084373 1.500000 3.500000 4.000000 
+N C sps  9.090970 -1.494255 -0.616711 0.000000 0.000000 1.500000 3.500000 4.000000 -0.337943 -1.335442 -0.769693 0.119373 -0.079493 1.500000 3.500000 4.000000 
+C N pps  6.892240 -0.931920 -0.769164 0.000000 0.000000 1.500000 3.500000 4.000000 -0.350240 -0.467439 -1.849316 1.854403 -0.988471 1.500000 3.500000 4.000000 
+C N ppp  -2.903346 -2.149349 -0.253006 0.000000 0.000000 1.500000 3.500000 4.000000 0.158424 -2.114409 -0.582346 -0.051076 -0.006183 1.500000 3.500000 4.000000 
+C C sss  -9.404207 -1.363297 -0.507128 0.000000 0.000000 1.400000 3.500000 4.000000 0.346977 -1.519820 -0.570812 -0.013518 -0.015829 1.400000 3.500000 4.000000 
+C C sps  8.662429 -1.047410 -0.661999 0.000000 0.000000 1.400000 3.500000 4.000000 -0.400467 -0.984048 -0.853949 0.157178 -0.073381 1.400000 3.500000 4.000000 
+C C pps  6.811512 -0.552299 -0.776890 0.000000 0.000000 1.400000 3.500000 4.000000 -0.382417 0.102889 -2.786680 2.646356 -1.134320 1.400000 3.500000 4.000000 
+C C ppp  -3.550127 -1.925572 -0.132715 0.000000 0.000000 1.400000 3.500000 4.000000 0.214357 -1.948923 -0.578323 -0.034356 -0.007257 1.400000 3.500000 4.000000 
+H C sss  -9.072577 -1.393093 -0.430611 0.000000 0.000000 1.100000 3.500000 4.000000 0.416003 -1.459596 -0.654874 0.009140 -0.012658 1.100000 3.500000 4.000000 
+H C sps  8.176008 -0.985177 -0.427403 0.000000 0.000000 1.100000 3.500000 4.000000 -0.495695 -0.901626 -1.007214 0.189808 -0.057087 1.100000 3.500000 4.000000 
+H H sss  -9.340000 -1.145903 -0.391777 0.000000 0.000000 0.750000 3.500000 4.000000 0.575007 -1.391261 -0.778831 0.080209 -0.017759 0.750000 3.500000 4.000000 
+O O sss  -12.737687 -1.851608 -0.666621 0.000000 0.000000 1.200000 3.500000 4.000000 0.296445 -1.911896 -0.663451 0.038054 -0.046608 1.200000 3.500000 4.000000 
+O O sps  13.683050 -1.684554 -0.468349 0.000000 0.000000 1.200000 3.500000 4.000000 -0.362143 -1.285274 -0.939591 0.204641 -0.106438 1.200000 3.500000 4.000000 
+O O pps  9.460772 -1.211748 -0.581016 0.000000 0.000000 1.200000 3.500000 4.000000 -0.312044 0.121814 -2.519352 1.681266 -0.644566 1.200000 3.500000 4.000000 
+O O ppp  -4.494595 -2.709223 -0.284124 0.000000 0.000000 1.200000 3.500000 4.000000 0.193010 -2.168462 -0.580629 -0.105104 0.004891 1.200000 3.500000 4.000000 
+H O sss  -12.230931 -1.808632 -0.421164 0.000000 0.000000 1.000000 3.500000 4.000000 0.404725 -1.702546 -0.707938 0.074904 -0.039922 1.000000 3.500000 4.000000 
+H O sps  9.466088 -1.321262 -0.386336 0.000000 0.000000 1.000000 3.500000 4.000000 -0.447660 -0.952979 -1.163537 0.400616 -0.156965 1.000000 3.500000 4.000000 
+N N sss  -7.710330 -2.365312 -0.525527 0.000000 0.000000 1.500000 3.500000 4.000000 0.231654 -1.879002 -0.572765 -0.004579 -0.031106 1.500000 3.500000 4.000000 
+N N sps  8.222314 -1.612118 -0.690081 0.000000 0.000000 1.500000 3.500000 4.000000 -0.305271 -1.385158 -0.751032 0.114531 -0.090839 1.500000 3.500000 4.000000 
+N N pps  7.178570 -1.176467 -0.571049 0.000000 0.000000 1.500000 3.500000 4.000000 -0.324668 -0.547805 -1.638658 1.495168 -0.827868 1.500000 3.500000 4.000000 
+N N ppp  -2.829344 -2.408049 -0.387709 0.000000 0.000000 1.500000 3.500000 4.000000 0.142909 -2.162036 -0.571942 -0.071640 -0.004682 1.500000 3.500000 4.000000 
+H N sss  -12.095890 -1.519057 -0.277247 0.000000 0.000000 1.000000 3.500000 4.000000 0.446693 -1.500463 -0.657448 0.065741 -0.037004 1.000000 3.500000 4.000000 
+H N sps  9.851338 -1.231616 -0.370836 0.000000 0.000000 1.000000 3.500000 4.000000 -0.501530 -0.785734 -1.123232 0.394878 -0.148501 1.000000 3.500000 4.000000 

examples/latte/TBparam/electrons.dat

@@ -0,0 +1,7 @@
+Noelem=  5
+Element   basis    Numel   Es          Ep        Ed          Ef    Mass     HubbardU  Wss        Wpp      Wdd        Wff
+N         sp       5.0    -18.58       -7.09     0.0         0.0   14.0067  15.93      0.0       -0.6950   0.0        0.0
+O         sp       6.0    -23.96       -9.02     0.0         0.0   15.9994  12.15      0.0       -0.7577   0.0        0.0
+H         s       1.0    -6.35        0.0       0.0         0.0    1.0079   12.85  -1.7937     0.0      0.0        0.0
+C         sp       4.0    -13.75       -5.28     0.0         0.0   12.01    10.0    0.0       -0.621    0.0        0.0
+Ti sd 4.0 -5.5 0.0 -3.0 0.0 47.867 10.0 0.0 0.0 0.0 0.0

examples/latte/TBparam/ppots.nonortho

@@ -0,0 +1,12 @@
+Nopps= 10
+Ele1  Ele2  A0        A1      A2      A3       A4      A5       A6      C    R1  Rcut
+N O 13.182426 20.050322 -46.806321 38.206953 -12.319656 0.000000 0.000000 0.000000 1.600000 1.700000 
+C N 88.953762 10.294988 -27.706877 22.101434 -6.836438 0.000000 0.000000 0.000000 1.600000 1.700000 
+C O 0.944093 30.116337 -59.608215 45.107654 -13.178839 0.000000 0.000000 0.000000 1.600000 1.700000 
+C H 104.889589 3.971095 -23.823043 26.408093 -11.317522 0.000000 0.000000 0.000000 1.200000 1.300000 
+C C 3.962931 24.467772 -51.156024 39.031644 -11.342979 0.000000 0.000000 0.000000 1.600000 1.700000 
+H H 38.512100 3.887860 -37.769100 57.083500 -34.512200 0.000000 0.000000 0.000000 0.900000 1.000000 
+N N 43.228899 15.004605 -36.621777 29.234888 -8.912743 0.000000 0.000000 0.000000 1.600000 1.700000 
+N H 0.625470 28.081241 -63.414297 53.286361 -17.352234 0.000000 0.000000 0.000000 1.300000 1.400000 
+O O 10.999870 19.303033 -45.747853 37.946431 -11.935755 0.000000 0.000000 0.000000 1.500000 1.600000 
+O H 0.481176 33.175383 -81.158683 74.935408 -26.792315 0.000000 0.000000 0.000000 1.200000 1.300000 

examples/latte/data.sucrose

@@ -0,0 +1,63 @@
+ LAMMPS Description
+ 
+          45 atoms
+ 
+           3 atom types
+ 
+   0.0000000000000000        17.202999999999999      xlo xhi
+   0.0000000000000000        18.009000000000000      ylo yhi
+   0.0000000000000000        21.643000000000001      zlo zhi
+ 
+ Masses
+ 
+              1   15.9994    
+              2   12.01
+              3   1.0079
+ 
+ Atoms
+ 
+    1    1    1   0.0   8.62700   8.66700  12.48600
+    2    1    1   0.0   9.11200   9.11800  10.27300
+    3    1    1   0.0   8.45700  11.33100  10.49000
+    4    1    1   0.0  11.72600   8.36500  10.66700
+    5    1    1   0.0   8.06500   8.99400   7.93600
+    6    1    2   0.0   9.62800   9.07200  11.59100
+    7    1    3   0.0   9.90900  10.08300  11.89200
+    8    1    2   0.0   9.07000  10.40400   9.64000
+    9    1    1   0.0   6.14600  11.61000   8.00500
+   10    1    1   0.0  11.07200  10.13000   8.37600
+   11    1    1   0.0   6.10200  10.00900  11.62100
+   12    1    2   0.0   8.14000  10.29100   8.45100
+   13    1    3   0.0   8.49000  10.91200   7.62300
+   14    1    1   0.0   7.41500   7.08400  14.43400
+   15    1    2   0.0  10.75100   8.07000  11.65100
+   16    1    3   0.0  11.24000   8.11800  12.63400
+   17    1    2   0.0   7.09000  11.63400  10.17000
+   18    1    3   0.0   7.06900  12.69800   9.91100
+   19    1    2   0.0   7.97200   7.44200  12.14000
+   20    1    3   0.0   7.54700   7.58300  11.13800
+   21    1    1   0.0  11.24900   5.73000  11.78600
+   22    1    2   0.0  10.26800   6.65900  11.37300
+   23    1    3   0.0  10.12300   6.53400  10.29200
+   24    1    2   0.0   6.78400  10.79500   8.95500
+   25    1    3   0.0   6.12100   9.95500   9.19600
+   26    1    2   0.0  10.47500  10.88300   9.39800
+   27    1    3   0.0  10.49500  11.92100   9.06900
+   28    1    3   0.0  11.09100  10.82000  10.30900
+   29    1    2   0.0   8.99100   6.32000  12.11700
+   30    1    3   0.0   9.23100   6.01100  13.14400
+   31    1    2   0.0   6.86600   7.25300  13.14500
+   32    1    3   0.0   6.17700   8.10100  13.15700
+   33    1    3   0.0   6.28900   6.35300  12.94300
+   34    1    2   0.0   6.24000  11.39400  11.39300
+   35    1    3   0.0   6.66500  11.86500  12.28300
+   36    1    3   0.0   5.23100  11.78100  11.26000
+   37    1    1   0.0   8.34300   5.24100  11.48000
+   38    1    3   0.0  12.00100   9.28600  10.78200
+   39    1    3   0.0  12.06300   5.97500  11.33000
+   40    1    3   0.0   6.99600   9.67600  11.79700
+   41    1    3   0.0   7.93700   7.87600  14.60900
+   42    1    3   0.0  10.95500   9.19800   8.60700
+   43    1    3   0.0   5.94400  11.05900   7.24100
+   44    1    3   0.0   7.94900   8.39500   8.68400
+   45    1    3   0.0   8.96400   4.50300  11.48800

examples/latte/data.water

@@ -0,0 +1,41 @@
+ LAMMPS Description
+ 
+          24 atoms
+ 
+           2 atom types
+ 
+   0.0000000000000000        6.2670000000000003      xlo xhi
+   0.0000000000000000        6.2670000000000003      ylo yhi
+   0.0000000000000000        6.2670000000000003      zlo zhi
+ 
+ Masses
+ 
+              1   15.994915008544922     
+              2   1.0078250169754028     
+ 
+ Atoms
+ 
+    1    1    1   0.0   3.08800   3.70000   3.12400
+    2    1    2   0.0   4.05800   3.70000   3.12400
+    3    1    2   0.0   2.76400   3.13200   3.84100
+    4    1    1   0.0   2.47000   0.39000   1.36000
+    5    1    2   0.0   1.54000   0.37000   1.73000
+    6    1    2   0.0   2.48000   0.00000   0.44000
+    7    1    1   0.0   1.99300   0.41700   5.25000
+    8    1    2   0.0   2.39300   1.32700   5.16000
+    9    1    2   0.0   0.99300   0.49700   5.31000
+   10    1    1   0.0   2.05300   6.09700   3.48000
+   11    1    2   0.0   2.12300   5.20700   3.02000
+   12    1    2   0.0   1.11300   0.17000   3.40000
+   13    1    1   0.0   4.90000   5.37700   2.14000
+   14    1    2   0.0   5.51000   6.17700   2.18000
+   15    1    2   0.0   3.95000   5.68700   2.21000
+   16    1    1   0.0   0.92000   3.82700   0.56000
+   17    1    2   0.0   0.00000   3.54700   0.27000
+   18    1    2   0.0   1.23000   4.59700   0.00000
+   19    1    1   0.0   0.89000   2.03700   3.41000
+   20    1    2   0.0   0.72000   2.86700   2.87000
+   21    1    2   0.0   1.79000   1.66700   3.19000
+   22    1    1   0.0   4.45000   4.61700   5.43000
+   23    1    2   0.0   4.75000   3.89700   4.81000
+   24    1    2   0.0   4.06000   4.21700   6.26000

examples/latte/in.latte.sucrose

@@ -0,0 +1,40 @@
+# simple sucrose model with LATTE
+
+units		metal
+atom_style	full
+atom_modify     sort 0 0.0    # turn off sorting of the coordinates
+
+read_data       data.sucrose
+
+# replicate system if requested
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+
+variable        nrep equal v_x*v_y*v_z
+if              "${nrep} > 1" then "replicate $x $y $z"
+
+# initialize system
+
+velocity	all create 0.0 87287 loop geom
+
+pair_style      zero 1.0
+pair_coeff	* *  
+
+neighbor	1.0 bin
+neigh_modify    every 1 delay 0 check yes 
+
+timestep        0.00025
+
+fix		1 all nve
+
+fix             2 all latte NULL
+fix_modify      2 energy yes
+
+thermo_style    custom step temp pe etotal press
+
+# dynamics
+
+thermo          10
+run		100

examples/latte/in.latte.water

@@ -0,0 +1,40 @@
+# simple water model with LATTE
+
+units		metal
+atom_style	full
+atom_modify     sort 0 0.0    # turn off sorting of the coordinates
+
+read_data       data.water
+
+# replicate system if requested
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+
+variable        nrep equal v_x*v_y*v_z
+if              "${nrep} > 1" then "replicate $x $y $z"
+
+# initialize system
+
+velocity	all create 0.0 87287 loop geom
+
+pair_style      zero 1.0
+pair_coeff	* *  
+
+neighbor	1.0 bin
+neigh_modify    every 1 delay 0 check yes 
+
+timestep        0.00025
+
+fix		1 all nve
+
+fix             2 all latte NULL
+fix_modify      2 energy yes
+
+thermo_style    custom step temp pe etotal press
+
+# dynamics
+
+thermo          10
+run		100

examples/latte/in.latte.water.min

@@ -0,0 +1,41 @@
+# simple water model with LATTE
+
+units		metal
+atom_style	full
+atom_modify     sort 0 0.0    # turn off sorting of the coordinates
+
+read_data       data.water
+
+# replicate system if requested
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+
+variable        nrep equal v_x*v_y*v_z
+if              "${nrep} > 1" then "replicate $x $y $z"
+
+# initialize system
+
+velocity	all create 0.0 87287 loop geom
+
+pair_style      zero 1.0
+pair_coeff	* *  
+
+neighbor	1.0 bin
+neigh_modify    every 1 delay 0 check yes 
+
+timestep        0.00025
+
+fix		1 all nve
+
+fix             2 all latte NULL
+fix_modify      2 energy yes
+
+thermo_style    custom step temp pe etotal press
+
+# minimization
+
+thermo          10
+min_style fire
+minimize        1.0e-9 1.0e-9 500 500

examples/latte/latte.in

@@ -0,0 +1,40 @@
+LATTE INPUT FILE
+================
+#This input file resumes the content of MDcontroller and TBparam/control.in
+#The parser will only read it is present inside the running folder. 
+#In case this file is not present Latte will read the two files as original.
+#The order of the keywords is not important in this file. 
+#To get a full description of these keywords please see: 
+## https://github.com/lanl/LATTE/blob/master/Manual/LATTE_manual.pdf
+
+#General controls
+CONTROL{
+  xControl= 1
+  BASISTYPE= NONORTHO
+  COORDSFILE= "./coords.dat"
+  PARAMPATH= "/home/user/LATTE/TBparam"
+  KBT= 0.0
+  ENTROPYKIND= 1
+  PPOTON= 1 
+  SPINON= 0 SPINTOL= 1.0e-4
+  ELECTRO= 1 ELECMETH= 0 ELEC_QTOL= 1.0e-8
+  MAXSCF= 450
+  BREAKTOL= 1.0E-6 MINSP2ITER= 22 SP2CONV= REL
+  FULLQCONV= 1 QITER= 3
+  QMIX= 0.25 SPINMIX= 0.25 MDMIX= 0.25
+  SPARSEON= 1 THRESHOLDON= 1 NUMTHRESH= 1.0e-6 FILLINSTOP= 100 BLKSZ= 4
+  MSPARSE= 1500
+  RELAX= 0 RELAXTYPE= SD MAXITER= 100000 RLXFTOL= 0.0000001
+  SKIN= 1.0
+  CHARGE= 0
+  XBO= 1
+  XBODISON= 1
+  XBODISORDER= 5
+  KON= 0
+}
+
+#Controls for QMD (if using lammps MAXITER must be set to -1)
+MDCONTROL{
+  MAXITER= -1
+}
+

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

@@ -0,0 +1,406 @@
+ The log file for latte_lib
+ 
+ CONTROL{                                          }                                                 
+  
+ WARNING: variable JobName= is missing. I will use a default value instead ...
+ WARNING: variable PARAMPATH= is missing. I will use a default value instead ...
+ WARNING: variable DEBUGON= is missing. I will use a default value instead ...
+ WARNING: variable FERMIM= is missing. I will use a default value instead ...
+ WARNING: variable CGORLIB= is missing. I will use a default value instead ...
+ WARNING: variable NORECS= is missing. I will use a default value instead ...
+ WARNING: variable VDWON= is missing. I will use a default value instead ...
+ WARNING: variable ORDERNMOL= is missing. I will use a default value instead ...
+ WARNING: variable LCNON= is missing. I will use a default value instead ...
+ WARNING: variable LCNITER= is missing. I will use a default value instead ...
+ WARNING: variable MDON= is missing. I will use a default value instead ...
+ WARNING: variable PBCON= is missing. I will use a default value instead ...
+ WARNING: variable RESTART= is missing. I will use a default value instead ...
+ WARNING: variable NGPU= is missing. I will use a default value instead ...
+ WARNING: variable COMPFORCE= is missing. I will use a default value instead ...
+ WARNING: variable DOSFIT= is missing. I will use a default value instead ...
+ WARNING: variable INTS2FIT= is missing. I will use a default value instead ...
+ WARNING: variable NFITSTEP= is missing. I will use a default value instead ...
+ WARNING: variable QFIT= is missing. I will use a default value instead ...
+ WARNING: variable PPFITON= is missing. I will use a default value instead ...
+ WARNING: variable ALLFITON= is missing. I will use a default value instead ...
+ WARNING: variable PPSTEP= is missing. I will use a default value instead ...
+ WARNING: variable BISTEP= is missing. I will use a default value instead ...
+ WARNING: variable PP2FIT= is missing. I will use a default value instead ...
+ WARNING: variable BINT2FIT= is missing. I will use a default value instead ...
+ WARNING: variable PPNMOL= is missing. I will use a default value instead ...
+ WARNING: variable PPNGEOM= is missing. I will use a default value instead ...
+ WARNING: variable PARREP= is missing. I will use a default value instead ...
+ WARNING: variable VERBOSE= is missing. I will use a default value instead ...
+ WARNING: variable MIXER= is missing. I will use a default value instead ...
+ WARNING: variable RESTARTLIB= is missing. I will use a default value instead ...
+ WARNING: variable CGTOL= is missing. I will use a default value instead ...
+ WARNING: variable ELEC_ETOL= is missing. I will use a default value instead ...
+ WARNING: variable COULACC= is missing. I will use a default value instead ...
+ WARNING: variable COULCUT= is missing. I will use a default value instead ...
+ WARNING: variable COULR1= is missing. I will use a default value instead ...
+ WARNING: variable CHTOL= is missing. I will use a default value instead ...
+ WARNING: variable BETA= is missing. I will use a default value instead ...
+ WARNING: variable MCSIGMA= is missing. I will use a default value instead ...
+ WARNING: variable PPBETA= is missing. I will use a default value instead ...
+ WARNING: variable PPSIGMA= is missing. I will use a default value instead ...
+ WARNING: variable ER= is missing. I will use a default value instead ...
+ WARNING: variable INITIALIZED= is missing. I will use a default value instead ...
+  
+  
+ ############### Parameters used for this run ################
+  CONTROL{                                          
+  xControl=           1
+  DEBUGON=           0
+  FERMIM=           6
+  CGORLIB=           1
+  NORECS=           1
+  ENTROPYKIND=           1
+  PPOTON=           1
+  VDWON=           0
+  SPINON=           0
+  ELECTRO=           1
+  ELECMETH=           0
+  MAXSCF=         450
+  MINSP2ITER=          22
+  FULLQCONV=           1
+  QITER=           3
+  ORDERNMOL=           0
+  SPARSEON=           1
+  THRESHOLDON=           1
+  FILLINSTOP=         100
+  BLKSZ=           4
+  MSPARSE=        1500
+  LCNON=           0
+  LCNITER=           4
+  RELAX=           0
+  MAXITER=      100000
+  MDON=           1
+  PBCON=           1
+  RESTART=           0
+  CHARGE=           0
+  XBO=           1
+  XBODISON=           1
+  XBODISORDER=           5
+  NGPU=           2
+  KON=           0
+  COMPFORCE=           1
+  DOSFIT=           0
+  INTS2FIT=           1
+  NFITSTEP=        5000
+  QFIT=           0
+  PPFITON=           0
+  ALLFITON=           0
+  PPSTEP=         500
+  BISTEP=         500
+  PP2FIT=           2
+  BINT2FIT=           6
+  PPNMOL=          10
+  PPNGEOM=         200
+  PARREP=           0
+  VERBOSE=           0
+  MIXER=           0
+  RESTARTLIB=           0
+  CGTOL=   9.9999999747524271E-007
+  KBT=   0.0000000000000000     
+  SPINTOL=   1.0000000000000000E-004
+  ELEC_ETOL=   1.0000000474974513E-003
+  ELEC_QTOL=   1.0000000000000000E-008
+  COULACC=   9.9999999747524271E-007
+  COULCUT=  -500.00000000000000     
+  COULR1=   500.00000000000000     
+  BREAKTOL=   9.9999999999999995E-007
+  QMIX=  0.25000000000000000     
+  SPINMIX=  0.25000000000000000     
+  MDMIX=  0.25000000000000000     
+  NUMTHRESH=   9.9999999999999995E-007
+  CHTOL=   9.9999997764825821E-003
+  SKIN=   1.0000000000000000     
+  RLXFTOL=   9.9999999999999995E-008
+  BETA=   1000.0000000000000     
+  MCSIGMA=  0.20000000298023224     
+  PPBETA=   1000.0000000000000     
+  PPSIGMA=   9.9999997764825821E-003
+  ER=   1.0000000000000000     
+  JobName=MyJob                                                                                               
+  BASISTYPE=NONORTHO                                                                                            
+  SP2CONV=REL                                                                                                 
+  RELAXTYPE=SD                                                                                                  
+  PARAMPATH=./TBparam                                                                                           
+  COORDSFILE=./coords.dat                                                                                        
+  INITIALIZED= F
+  }                                                 
+  
+ ./TBparam/electrons.dat
+ MDCONTROL{                                        }                                                 
+  
+ WARNING: variable RNDIST= is missing. I will use a default value instead ...
+ WARNING: variable SEEDINIT= is missing. I will use a default value instead ...
+ WARNING: variable NPTTYPE= is missing. I will use a default value instead ...
+ WARNING: variable UDNEIGH= is missing. I will use a default value instead ...
+ WARNING: variable DUMPFREQ= is missing. I will use a default value instead ...
+ WARNING: variable RSFREQ= is missing. I will use a default value instead ...
+ WARNING: variable WRTFREQ= is missing. I will use a default value instead ...
+ WARNING: variable TOINITTEMP5= is missing. I will use a default value instead ...
+ WARNING: variable THERMPER= is missing. I will use a default value instead ...
+ WARNING: variable THERMRUN= is missing. I will use a default value instead ...
+ WARNING: variable NVTON= is missing. I will use a default value instead ...
+ WARNING: variable NPTON= is missing. I will use a default value instead ...
+ WARNING: variable AVEPER= is missing. I will use a default value instead ...
+ WARNING: variable SEED= is missing. I will use a default value instead ...
+ WARNING: variable SHOCKON= is missing. I will use a default value instead ...
+ WARNING: variable SHOCKSTART= is missing. I will use a default value instead ...
+ WARNING: variable SHOCKDIR= is missing. I will use a default value instead ...
+ WARNING: variable MDADAPT= is missing. I will use a default value instead ...
+ WARNING: variable GETHUG= is missing. I will use a default value instead ...
+ WARNING: variable RSLEVEL= is missing. I will use a default value instead ...
+ WARNING: variable DT= is missing. I will use a default value instead ...
+ WARNING: variable TEMPERATURE= is missing. I will use a default value instead ...
+ WARNING: variable FRICTION= is missing. I will use a default value instead ...
+ WARNING: variable PTARGET= is missing. I will use a default value instead ...
+ WARNING: variable UPARTICLE= is missing. I will use a default value instead ...
+ WARNING: variable USHOCK= is missing. I will use a default value instead ...
+ WARNING: variable C0= is missing. I will use a default value instead ...
+ WARNING: variable E0= is missing. I will use a default value instead ...
+ WARNING: variable V0= is missing. I will use a default value instead ...
+ WARNING: variable P0= is missing. I will use a default value instead ...
+ WARNING: variable DUMMY= is missing. I will use a default value instead ...
+  
+  
+ ############### Parameters used for this run ################
+  MDCONTROL{                                        
+  MAXITER=          -1
+  UDNEIGH=           1
+  DUMPFREQ=         250
+  RSFREQ=         500
+  WRTFREQ=          25
+  TOINITTEMP5=           1
+  THERMPER=         500
+  THERMRUN=       50000
+  NVTON=           0
+  NPTON=           0
+  AVEPER=        1000
+  SEED=          54
+  SHOCKON=           0
+  SHOCKSTART=      100000
+  SHOCKDIR=           1
+  MDADAPT=           0
+  GETHUG=           0
+  RSLEVEL=           0
+  DT=  0.25000000000000000     
+  TEMPERATURE=   300.00000000000000     
+  FRICTION=   1000.0000000000000     
+  PTARGET=   0.0000000000000000     
+  UPARTICLE=   500.00000000000000     
+  USHOCK=  -4590.0000000000000     
+  C0=   1300.0000000000000     
+  E0=  -795.72497558593750     
+  V0=   896.98486328125000     
+  P0=   8.3149001002311707E-002
+  RNDIST=GAUSSIAN                                                                                            
+  SEEDINIT=UNIFORM                                                                                             
+  NPTTYPE=ISO                                                                                                 
+  DUMMY= F
+  }                                                 
+  
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+ Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -261.14423615166146        13.843167378892108        0.0000000000000000        3.9658364191978137     

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

@@ -0,0 +1,406 @@
+ The log file for latte_lib
+ 
+ CONTROL{                                          }                                                 
+  
+ WARNING: variable JobName= is missing. I will use a default value instead ...
+ WARNING: variable PARAMPATH= is missing. I will use a default value instead ...
+ WARNING: variable DEBUGON= is missing. I will use a default value instead ...
+ WARNING: variable FERMIM= is missing. I will use a default value instead ...
+ WARNING: variable CGORLIB= is missing. I will use a default value instead ...
+ WARNING: variable NORECS= is missing. I will use a default value instead ...
+ WARNING: variable VDWON= is missing. I will use a default value instead ...
+ WARNING: variable ORDERNMOL= is missing. I will use a default value instead ...
+ WARNING: variable LCNON= is missing. I will use a default value instead ...
+ WARNING: variable LCNITER= is missing. I will use a default value instead ...
+ WARNING: variable MDON= is missing. I will use a default value instead ...
+ WARNING: variable PBCON= is missing. I will use a default value instead ...
+ WARNING: variable RESTART= is missing. I will use a default value instead ...
+ WARNING: variable NGPU= is missing. I will use a default value instead ...
+ WARNING: variable COMPFORCE= is missing. I will use a default value instead ...
+ WARNING: variable DOSFIT= is missing. I will use a default value instead ...
+ WARNING: variable INTS2FIT= is missing. I will use a default value instead ...
+ WARNING: variable NFITSTEP= is missing. I will use a default value instead ...
+ WARNING: variable QFIT= is missing. I will use a default value instead ...
+ WARNING: variable PPFITON= is missing. I will use a default value instead ...
+ WARNING: variable ALLFITON= is missing. I will use a default value instead ...
+ WARNING: variable PPSTEP= is missing. I will use a default value instead ...
+ WARNING: variable BISTEP= is missing. I will use a default value instead ...
+ WARNING: variable PP2FIT= is missing. I will use a default value instead ...
+ WARNING: variable BINT2FIT= is missing. I will use a default value instead ...
+ WARNING: variable PPNMOL= is missing. I will use a default value instead ...
+ WARNING: variable PPNGEOM= is missing. I will use a default value instead ...
+ WARNING: variable PARREP= is missing. I will use a default value instead ...
+ WARNING: variable VERBOSE= is missing. I will use a default value instead ...
+ WARNING: variable MIXER= is missing. I will use a default value instead ...
+ WARNING: variable RESTARTLIB= is missing. I will use a default value instead ...
+ WARNING: variable CGTOL= is missing. I will use a default value instead ...
+ WARNING: variable ELEC_ETOL= is missing. I will use a default value instead ...
+ WARNING: variable COULACC= is missing. I will use a default value instead ...
+ WARNING: variable COULCUT= is missing. I will use a default value instead ...
+ WARNING: variable COULR1= is missing. I will use a default value instead ...
+ WARNING: variable CHTOL= is missing. I will use a default value instead ...
+ WARNING: variable BETA= is missing. I will use a default value instead ...
+ WARNING: variable MCSIGMA= is missing. I will use a default value instead ...
+ WARNING: variable PPBETA= is missing. I will use a default value instead ...
+ WARNING: variable PPSIGMA= is missing. I will use a default value instead ...
+ WARNING: variable ER= is missing. I will use a default value instead ...
+ WARNING: variable INITIALIZED= is missing. I will use a default value instead ...
+  
+  
+ ############### Parameters used for this run ################
+  CONTROL{                                          
+  xControl=           1
+  DEBUGON=           0
+  FERMIM=           6
+  CGORLIB=           1
+  NORECS=           1
+  ENTROPYKIND=           1
+  PPOTON=           1
+  VDWON=           0
+  SPINON=           0
+  ELECTRO=           1
+  ELECMETH=           0
+  MAXSCF=         450
+  MINSP2ITER=          22
+  FULLQCONV=           1
+  QITER=           3
+  ORDERNMOL=           0
+  SPARSEON=           1
+  THRESHOLDON=           1
+  FILLINSTOP=         100
+  BLKSZ=           4
+  MSPARSE=        1500
+  LCNON=           0
+  LCNITER=           4
+  RELAX=           0
+  MAXITER=      100000
+  MDON=           1
+  PBCON=           1
+  RESTART=           0
+  CHARGE=           0
+  XBO=           1
+  XBODISON=           1
+  XBODISORDER=           5
+  NGPU=           2
+  KON=           0
+  COMPFORCE=           1
+  DOSFIT=           0
+  INTS2FIT=           1
+  NFITSTEP=        5000
+  QFIT=           0
+  PPFITON=           0
+  ALLFITON=           0
+  PPSTEP=         500
+  BISTEP=         500
+  PP2FIT=           2
+  BINT2FIT=           6
+  PPNMOL=          10
+  PPNGEOM=         200
+  PARREP=           0
+  VERBOSE=           0
+  MIXER=           0
+  RESTARTLIB=           0
+  CGTOL=   9.9999999747524271E-007
+  KBT=   0.0000000000000000     
+  SPINTOL=   1.0000000000000000E-004
+  ELEC_ETOL=   1.0000000474974513E-003
+  ELEC_QTOL=   1.0000000000000000E-008
+  COULACC=   9.9999999747524271E-007
+  COULCUT=  -500.00000000000000     
+  COULR1=   500.00000000000000     
+  BREAKTOL=   9.9999999999999995E-007
+  QMIX=  0.25000000000000000     
+  SPINMIX=  0.25000000000000000     
+  MDMIX=  0.25000000000000000     
+  NUMTHRESH=   9.9999999999999995E-007
+  CHTOL=   9.9999997764825821E-003
+  SKIN=   1.0000000000000000     
+  RLXFTOL=   9.9999999999999995E-008
+  BETA=   1000.0000000000000     
+  MCSIGMA=  0.20000000298023224     
+  PPBETA=   1000.0000000000000     
+  PPSIGMA=   9.9999997764825821E-003
+  ER=   1.0000000000000000     
+  JobName=MyJob                                                                                               
+  BASISTYPE=NONORTHO                                                                                            
+  SP2CONV=REL                                                                                                 
+  RELAXTYPE=SD                                                                                                  
+  PARAMPATH=./TBparam                                                                                           
+  COORDSFILE=./coords.dat                                                                                        
+  INITIALIZED= F
+  }                                                 
+  
+ ./TBparam/electrons.dat
+ MDCONTROL{                                        }                                                 
+  
+ WARNING: variable RNDIST= is missing. I will use a default value instead ...
+ WARNING: variable SEEDINIT= is missing. I will use a default value instead ...
+ WARNING: variable NPTTYPE= is missing. I will use a default value instead ...
+ WARNING: variable UDNEIGH= is missing. I will use a default value instead ...
+ WARNING: variable DUMPFREQ= is missing. I will use a default value instead ...
+ WARNING: variable RSFREQ= is missing. I will use a default value instead ...
+ WARNING: variable WRTFREQ= is missing. I will use a default value instead ...
+ WARNING: variable TOINITTEMP5= is missing. I will use a default value instead ...
+ WARNING: variable THERMPER= is missing. I will use a default value instead ...
+ WARNING: variable THERMRUN= is missing. I will use a default value instead ...
+ WARNING: variable NVTON= is missing. I will use a default value instead ...
+ WARNING: variable NPTON= is missing. I will use a default value instead ...
+ WARNING: variable AVEPER= is missing. I will use a default value instead ...
+ WARNING: variable SEED= is missing. I will use a default value instead ...
+ WARNING: variable SHOCKON= is missing. I will use a default value instead ...
+ WARNING: variable SHOCKSTART= is missing. I will use a default value instead ...
+ WARNING: variable SHOCKDIR= is missing. I will use a default value instead ...
+ WARNING: variable MDADAPT= is missing. I will use a default value instead ...
+ WARNING: variable GETHUG= is missing. I will use a default value instead ...
+ WARNING: variable RSLEVEL= is missing. I will use a default value instead ...
+ WARNING: variable DT= is missing. I will use a default value instead ...
+ WARNING: variable TEMPERATURE= is missing. I will use a default value instead ...
+ WARNING: variable FRICTION= is missing. I will use a default value instead ...
+ WARNING: variable PTARGET= is missing. I will use a default value instead ...
+ WARNING: variable UPARTICLE= is missing. I will use a default value instead ...
+ WARNING: variable USHOCK= is missing. I will use a default value instead ...
+ WARNING: variable C0= is missing. I will use a default value instead ...
+ WARNING: variable E0= is missing. I will use a default value instead ...
+ WARNING: variable V0= is missing. I will use a default value instead ...
+ WARNING: variable P0= is missing. I will use a default value instead ...
+ WARNING: variable DUMMY= is missing. I will use a default value instead ...
+  
+  
+ ############### Parameters used for this run ################
+  MDCONTROL{                                        
+  MAXITER=          -1
+  UDNEIGH=           1
+  DUMPFREQ=         250
+  RSFREQ=         500
+  WRTFREQ=          25
+  TOINITTEMP5=           1
+  THERMPER=         500
+  THERMRUN=       50000
+  NVTON=           0
+  NPTON=           0
+  AVEPER=        1000
+  SEED=          54
+  SHOCKON=           0
+  SHOCKSTART=      100000
+  SHOCKDIR=           1
+  MDADAPT=           0
+  GETHUG=           0
+  RSLEVEL=           0
+  DT=  0.25000000000000000     
+  TEMPERATURE=   300.00000000000000     
+  FRICTION=   1000.0000000000000     
+  PTARGET=   0.0000000000000000     
+  UPARTICLE=   500.00000000000000     
+  USHOCK=  -4590.0000000000000     
+  C0=   1300.0000000000000     
+  E0=  -795.72497558593750     
+  V0=   896.98486328125000     
+  P0=   8.3149001002311707E-002
+  RNDIST=GAUSSIAN                                                                                            
+  SEEDINIT=UNIFORM                                                                                             
+  NPTTYPE=ISO                                                                                                 
+  DUMMY= F
+  }                                                 
+  
+ LIBCALLS           0
+ Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -110.94281402417451        9.3197859655447317        0.0000000000000000        3.3331152608769714     
+ LIBCALLS           1
+ Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -111.00875524736128        9.3653691493930946        0.0000000000000000        3.3307590218500454     
+ LIBCALLS           2
+ Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -111.20542679804305        9.5022104076319209        0.0000000000000000        3.3237269236958826     
+ LIBCALLS           3
+ Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -111.52938059528239        9.7304811436977623        0.0000000000000000        3.3121168872278743     
+ LIBCALLS           4
+ Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -111.97463249071366        10.050121693432235        0.0000000000000000        3.2961492065207088     
+ LIBCALLS           5
+ Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -112.53270518796754        10.460328095449432        0.0000000000000000        3.2761112890303719     
+ LIBCALLS           6
+ Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -113.19233973551384        10.958848347453728        0.0000000000000000        3.2524094948032394     
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+ Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -113.93936061504219        11.541120618354967        0.0000000000000000        3.2255715906285793     
+ LIBCALLS           8
+ Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -114.75657630591589        12.199315594286325        0.0000000000000000        3.1962412869596100     
+ LIBCALLS           9
+ Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -115.62363727592754        12.921383532128770        0.0000000000000000        3.1652236023838971     
+ LIBCALLS          10
+ Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -116.51738028417616        13.690253224922545        0.0000000000000000        3.1333864449223818     
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+ Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -117.41167836078414        14.483370804317431        0.0000000000000000        3.1018474945925432     
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+ Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -118.27888830961329        15.272791625586624        0.0000000000000000        3.0716022180609772     
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+ Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -119.09006809777934        16.026020995592610        0.0000000000000000        3.0437832241644842     
+ LIBCALLS          14
+ Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -119.81665859965702        16.707725410478066        0.0000000000000000        3.0194382402972129     
+ LIBCALLS          15
+ Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -120.43171665196000        17.282293509806884        0.0000000000000000        2.9995944159949395     
+ LIBCALLS          16
+ Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -120.91202932933264        17.717025741135480        0.0000000000000000        2.9850159611897484     
+ LIBCALLS          17
+ Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -121.23935305628714        17.985521384886379        0.0000000000000000        2.9763132734231292     
+ LIBCALLS          18
+ Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -121.40195013006486        18.070687763205626        0.0000000000000000        2.9738279411203812     
+ LIBCALLS          19
+ Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -121.39540873020161        17.966785565900089        0.0000000000000000        2.9776410698341418     
+ LIBCALLS          20
+ Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -121.22299732491055        17.680085363043698        0.0000000000000000        2.9875419962840417     
+ LIBCALLS          21
+ Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -120.89520311723561        17.228004261852682        0.0000000000000000        3.0030824758482719     
+ LIBCALLS          22
+ Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -120.42892991839108        16.636927104987372        0.0000000000000000        3.0235548851138652     
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+ Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -119.84603562384113        15.939176953031323        0.0000000000000000        3.0480682132279808     
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+ Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -115.35329645548983        11.329720850249741        0.0000000000000000        3.2241713466126849     
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+ Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -112.93101384064629        8.8018792766284140        0.0000000000000000        3.2893376450243901     
+ LIBCALLS          74
+ Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -113.01657988020818        8.8609123616606951        0.0000000000000000        3.2887786713823335     
+ LIBCALLS          75
+ Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -113.22122702505257        9.0105808374276855        0.0000000000000000        3.2838806809960044     
+ LIBCALLS          76
+ Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -113.54255812607462        9.2518619694254909        0.0000000000000000        3.2746170980725564     
+ LIBCALLS          77
+ Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -113.97595003796289        9.5854566564348804        0.0000000000000000        3.2610495238703536     
+ LIBCALLS          78
+ Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -114.51445216471619        10.011242264155852        0.0000000000000000        3.2433103887056101     
+ LIBCALLS          79
+ Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -115.14835871057100        10.527538366743359        0.0000000000000000        3.2217018278255036     
+ LIBCALLS          80
+ Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -115.86512618816471        11.130220642932718        0.0000000000000000        3.1966546818138903     
+ LIBCALLS          81
+ Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -116.64916580084807        11.811746817430592        0.0000000000000000        3.1687509169099037     
+ LIBCALLS          82
+ Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -117.48162972769103        12.560201275368994        0.0000000000000000        3.1387793445426220     
+ LIBCALLS          83
+ Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -118.34080112521505        13.358507776606700        0.0000000000000000        3.1076005013428842     
+ LIBCALLS          84
+ Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -119.20206255799097        14.183999576696523        0.0000000000000000        3.0762625451098367     
+ LIBCALLS          85
+ Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -120.03875955947012        15.008549885925623        0.0000000000000000        3.0458557745855401     
+ LIBCALLS          86
+ Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -120.82281065648482        15.799445052997022        0.0000000000000000        3.0175902569508040     
+ LIBCALLS          87
+ Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -121.52638053902615        16.521105731022047        0.0000000000000000        2.9925661691795984     
+ LIBCALLS          88
+ Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -122.12297505178334        17.137613862262167        0.0000000000000000        2.9718740800190462     
+ LIBCALLS          89
+ Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -122.58954501498538        17.615819283155187        0.0000000000000000        2.9563457612376758     
+ LIBCALLS          90
+ Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -122.90768650775293        17.928615619513138        0.0000000000000000        2.9466637669908935     
+ LIBCALLS          91
+ Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -123.06510359278838        18.057846294334183        0.0000000000000000        2.9432773288779130     
+ LIBCALLS          92
+ Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -123.05653995529889        17.996310208253615        0.0000000000000000        2.9463730237128352     
+ LIBCALLS          93
+ Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -122.88443709725219        17.748486968230267        0.0000000000000000        2.9557418006906766     
+ LIBCALLS          94
+ Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -122.55804625906457        17.329857520510558        0.0000000000000000        2.9710497340098647     
+ LIBCALLS          95
+ Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -122.09316916859144        16.764989519228550        0.0000000000000000        2.9916333369114647     
+ LIBCALLS          96
+ Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -121.51050736457847        16.084787212290774        0.0000000000000000        3.0167038701280053     
+ LIBCALLS          97
+ Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -120.83475656442954        15.323405512114466        0.0000000000000000        3.0451593241515909     
+ LIBCALLS          98
+ Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -120.09218577985371        14.515310319889227        0.0000000000000000        3.0759929793994090     
+ LIBCALLS          99
+ Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -119.30969482099719        13.692843612811791        0.0000000000000000        3.1081426979179545     
+ LIBCALLS         100
+ Energy Components (TRRHOH, EREP, ENTE, ECOUL)  -118.51358261827596        12.884492109393644        0.0000000000000000        3.1405428597121636     

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

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

examples/snap/Mo_Chen_PRM2017.snap

@@ -0,0 +1,7 @@
+
+# DATE: 2017-09-18 CONTRIBUTOR: Chi Chen <chc273@eng.ucsd.edu> CITATION: C. Chen, Z. Deng, R. Tran, H. Tang, I.-H. Chu, S. P. Ong, "Accurate force field for molybdenum by machine learning large materials data" Physical Review Materials 1, 04 3603 (2017)
+# Generated by Materials Virtual Lab
+# Definition of SNAP potential.
+pair_style snap
+pair_coeff * * Mo_Chen_PRM2017.snapcoeff Mo Mo_Chen_PRM2017.snapparam Mo
+

examples/snap/Mo_Chen_PRM2017.snapcoeff

@@ -0,0 +1,35 @@
+# DATE: 2017-09-18 CONTRIBUTOR: Chi Chen <chc273@eng.ucsd.edu> CITATION: C. Chen, Z. Deng, R. Tran, H. Tang, I.-H. Chu, S. P. Ong, "Accurate force field for molybdenum by machine learning large materials data" Physical Review Materials 1, 04 3603 (2017)
+# Generated by Materials Virtual Lab
+1 31
+Mo 0.5 1
+-17.2757958404
+0.00431015861472
+0.0657685117891
+0.477733335702
+0.0152688837211
+0.77559888196
+0.284846429566
+0.148804982644
+0.0573702179736
+0.19281989434
+0.323441703578
+0.101324335724
+0.0139639846514
+-0.0324444749083
+0.0349797952779
+0.0613023441282
+0.0881078513046
+0.118716074611
+0.0069662975532
+-0.0174658914685
+-0.0178902177779
+0.0195993756659
+0.0719238160707
+0.0344832661036
+-0.0358616891662
+-0.0292380783172
+-0.0334933909866
+0.00595462520243
+0.0754556638328
+-0.000972545258845
+-0.0100170422751

examples/snap/Mo_Chen_PRM2017.snapparam

@@ -0,0 +1,4 @@
+# DATE: 2017-09-18 CONTRIBUTOR: Chi Chen <chc273@eng.ucsd.edu> CITATION: C. Chen, Z. Deng, R. Tran, H. Tang, I.-H. Chu, S. P. Ong, "Accurate force field for molybdenum by machine learning large materials data" Physical Review Materials 1, 04 3603 (2017)
+# Generated by Materials Virtual Lab
+rcutfac 4.615858
+twojmax 6

examples/snap/in.snap.Mo_Chen

@@ -0,0 +1,45 @@
+# Demonstrate SNAP Ta potential
+
+# Initialize simulation
+
+variable nsteps index 100
+variable nrep equal 4
+variable a equal 3.160
+units		metal
+
+# generate the box and atom positions using a BCC lattice
+
+variable nx equal ${nrep}
+variable ny equal ${nrep}
+variable nz equal ${nrep}
+
+boundary	p p p
+
+lattice         bcc $a
+region		box block 0 ${nx} 0 ${ny} 0 ${nz}
+create_box	1 box
+create_atoms	1 box
+
+mass 1 183.84
+
+# choose potential
+
+include Mo_Chen_PRM2017.snap
+
+# Setup output
+
+thermo		10
+thermo_modify norm yes
+
+# Set up NVE run
+
+timestep 0.5e-3
+neighbor 1.0 bin
+neigh_modify once no every 1 delay 0 check yes
+
+# Run MD
+
+velocity all create 300.0 4928459
+fix 1 all nve
+run             ${nsteps}
+

lib/colvars/colvarbias_restraint.cpp

@@ -308,7 +308,7 @@ int colvarbias_restraint_centers_moving::update_centers(cvm::real lambda)
     colvarvalue const c_new = colvarvalue::interpolate(initial_centers[i],
                                                        target_centers[i],
                                                        lambda);
-    centers_incr[i] = (c_new).dist2_grad(colvar_centers[i]);
+    centers_incr[i] = 0.5 * c_new.dist2_grad(colvar_centers[i]);
     colvar_centers[i] = c_new;
     variables(i)->wrap(colvar_centers[i]);
   }

lib/gpu/.gitignore

@@ -4,3 +4,4 @@
 /nvc_get_devices
 /*.cubin
 /*_cubin.h
+/*_cl.h

lib/gpu/Makefile.linux

@@ -35,7 +35,7 @@ CUDA_PRECISION = -D_SINGLE_DOUBLE
 
 CUDA_INCLUDE = -I$(CUDA_HOME)/include
 CUDA_LIB = -L$(CUDA_HOME)/lib64
-CUDA_OPTS = -DUNIX -O3 -Xptxas -v --use_fast_math $(LMP_INC)
+CUDA_OPTS = -DUNIX -O3 -Xptxas -v --use_fast_math $(LMP_INC) -Xcompiler -fPIC
 
 CUDR_CPP = mpicxx -DMPI_GERYON -DUCL_NO_EXIT -DMPICH_IGNORE_CXX_SEEK -DOMPI_SKIP_MPICXX=1 -fPIC
 CUDR_OPTS = -O2 $(LMP_INC) # -xHost -no-prec-div -ansi-alias