diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS
index fdee6325d0f65c04fa76eec1cfa58ee90012c8c9..3d73ffc63ee4c719f751d19c9607e261acbabcc8 100644
--- a/.github/CODEOWNERS
+++ b/.github/CODEOWNERS
@@ -9,13 +9,37 @@ lib/kokkos/* @stanmoore1
lib/molfile/* @akohlmey
lib/qmmm/* @akohlmey
lib/vtk/* @rbberger
+lib/kim/* @ellio167
-# packages
-src/KOKKOS @stanmoore1
-src/USER-CGSDK @akohlmey
-src/USER-COLVARS @giacomofiorin
-src/USER-OMP @akohlmey
-src/USER-QMMM @akohlmey
+# whole packages
+src/COMPRESS/* @akohlmey
+src/GPU/* @ndtrung81
+src/KOKKOS/* @stanmoore1
+src/KIM/* @ellio167
+src/USER-CGDNA/* @ohenrich
+src/USER-CGSDK/* @akohlmey
+src/USER-COLVARS/* @giacomofiorin
+src/USER-DPD/* @timattox
+src/USER-INTEL/* @wmbrownintel
+src/USER-MANIFOLD/* @Pakketeretet2
+src/USER-MEAMC/* @martok
+src/USER-MOFFF/* @hheenen
+src/USER-MOLFILE/* @akohlmey
+src/USER-NETCDF/* @pastewka
+src/USER-PHONON/* @lingtikong
+src/USER-OMP/* @akohlmey
+src/USER-QMMM/* @akohlmey
+src/USER-REAXC/* @hasanmetin
+src/USER-TALLY/* @akohlmey
+src/USER-UEF/* @danicholson
+src/USER-VTK/* @rbberger
+
+# individual files in packages
+src/GPU/pair_vashishta_gpu.* @andeplane
+src/KOKKOS/pair_vashishta_kokkos.* @andeplane
+src/MANYBODY/pair_vashishta_table.* @andeplane
+src/USER-MISC/fix_bond_react.* @jrgissing
+src/USER-MISC/*_grem.* @dstelter92
# tools
tools/msi2lmp/* @akohlmey
diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt
index a4988611563ad8e681ae2ff39f3f7eeaad524ff6..7ce7ca23e16423be98be34edf51e4b4321931817 100644
--- a/cmake/CMakeLists.txt
+++ b/cmake/CMakeLists.txt
@@ -4,7 +4,7 @@
# Created by Christoph Junghans and Richard Berger
cmake_minimum_required(VERSION 3.1)
-project(lammps)
+project(lammps LANGUAGES CXX)
set(SOVERSION 0)
set(LAMMPS_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../src)
set(LAMMPS_LIB_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../lib)
@@ -23,14 +23,22 @@ if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CXX_FLAGS)
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)
-# 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})
+file(GLOB SRC_FILES ${LAMMPS_SOURCE_DIR}/*.cpp)
+list(SORT SRC_FILES)
+# check for files installed by make-based buildsystem
+# only run this time consuming check if there are new files
+if(NOT SRC_FILES STREQUAL SRC_FILES_CACHED)
+ file(GLOB SRC_PKG_FILES ${LAMMPS_SOURCE_DIR}/*/*.cpp)
+ message(STATUS "Running check for installed package (this might take a while)")
+ foreach(_SRC SRC_PKG_FILES)
+ get_filename_component(FILENAME "${_SRC}" NAME)
+ if(EXISTS ${LAMMPS_SOURCE_DIR}/${FILENAME})
+ message(FATAL_ERROR "Found packages installed by the make-based buildsystem, please run 'make -C ${LAMMPS_SOURCE_DIR} no-all purge'")
+ endif()
+ endforeach()
+ set(SRC_FILES_CACHED "${SRC_FILES}" CACHE INTERNAL "List of file in LAMMPS_SOURCE_DIR" FORCE)
endif()
-enable_language(CXX)
-
######################################################################
# compiler tests
# these need ot be done early (before further tests).
@@ -48,21 +56,27 @@ option(BUILD_SHARED_LIBS "Build shared libs" OFF)
if(BUILD_SHARED_LIBS) # for all pkg libs, mpi_stubs and linalg
set(CMAKE_POSITION_INDEPENDENT_CODE ON)
endif()
+option(DEVELOPER_MODE "Enable developer mode" OFF)
+mark_as_advanced(DEVELOPER_MODE)
+option(CMAKE_VERBOSE_MAKEFILE "Generate verbose Makefiles" OFF)
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 QUIET)
+option(BUILD_MPI "Build MPI version" ${MPI_FOUND})
+if(BUILD_MPI)
find_package(MPI REQUIRED)
- include_directories(${MPI_C_INCLUDE_PATH})
+ include_directories(${MPI_CXX_INCLUDE_PATH})
list(APPEND LAMMPS_LINK_LIBS ${MPI_CXX_LIBRARIES})
option(LAMMPS_LONGLONG_TO_LONG "Workaround if your system or MPI version does not recognize 'long long' data types" OFF)
if(LAMMPS_LONGLONG_TO_LONG)
add_definitions(-DLAMMPS_LONGLONG_TO_LONG)
endif()
else()
+ enable_language(C)
file(GLOB MPI_SOURCES ${LAMMPS_SOURCE_DIR}/STUBS/mpi.c)
add_library(mpi_stubs STATIC ${MPI_SOURCES})
include_directories(${LAMMPS_SOURCE_DIR}/STUBS)
@@ -101,21 +115,21 @@ set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GRANU
KSPACE MANYBODY MC MEAM MISC MOLECULE PERI QEQ
REAX REPLICA RIGID SHOCK SNAP SRD)
set(OTHER_PACKAGES KIM PYTHON MSCG MPIIO VORONOI POEMS LATTE
- USER-ATC USER-AWPMD USER-CGDNA USER-MESO
+ USER-ATC USER-AWPMD USER-BOCS 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-MOFFF USER-MOLFILE USER-NETCDF USER-PHONON USER-QTB USER-REAXC USER-SMD
USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM)
set(ACCEL_PACKAGES USER-OMP KOKKOS OPT USER-INTEL GPU)
foreach(PKG ${DEFAULT_PACKAGES})
- option(ENABLE_${PKG} "Build ${PKG} Package" ${ENABLE_ALL})
+ option(PKG_${PKG} "Build ${PKG} Package" ${ENABLE_ALL})
endforeach()
foreach(PKG ${ACCEL_PACKAGES} ${OTHER_PACKAGES})
- option(ENABLE_${PKG} "Build ${PKG} Package" OFF)
+ option(PKG_${PKG} "Build ${PKG} Package" OFF)
endforeach()
macro(pkg_depends PKG1 PKG2)
- if(ENABLE_${PKG1} AND NOT ENABLE_${PKG2})
+ if(PKG_${PKG1} AND NOT PKG_${PKG2})
message(FATAL_ERROR "${PKG1} package needs LAMMPS to be build with ${PKG2}")
endif()
endmacro()
@@ -128,38 +142,53 @@ pkg_depends(USER-LB MPI)
pkg_depends(USER-MISC MANYBODY)
pkg_depends(USER-PHONON KSPACE)
-if(ENABLE_BODY AND ENABLE_POEMS)
- message(FATAL_ERROR "BODY and POEMS cannot be enabled at the same time")
-endif()
-
######################################################
# packages with special compiler needs or external libs
######################################################
-if(ENABLE_REAX OR ENABLE_MEAM OR ENABLE_USER-QUIP OR ENABLE_USER-QMMM OR ENABLE_LATTE)
+if(PKG_REAX OR PKG_MEAM OR PKG_USER-QUIP OR PKG_USER-QMMM OR PKG_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)
+if(PKG_MEAM)
+ enable_language(C)
+endif()
+
+if(PKG_KOKKOS OR PKG_MSCG)
# starting with CMake 3.1 this is all you have to do to enforce C++11
set(CMAKE_CXX_STANDARD 11) # C++11...
set(CMAKE_CXX_STANDARD_REQUIRED ON) #...is required...
set(CMAKE_CXX_EXTENSIONS OFF) #...without compiler extensions like gnu++11
endif()
-if(ENABLE_USER-OMP OR ENABLE_KOKKOS OR ENABLE_USER-INTEL)
+find_package(OpenMP QUIET)
+option(BUILD_OMP "Build with OpenMP support" ${OpenMP_FOUND})
+if(BUILD_OMP OR PKG_USER-OMP OR PKG_KOKKOS OR PKG_USER-INTEL)
find_package(OpenMP REQUIRED)
set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")
set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
endif()
-if(ENABLE_KSPACE)
- set(FFT "KISSFFT" CACHE STRING "FFT library for KSPACE package")
- set_property(CACHE FFT PROPERTY STRINGS KISSFFT FFTW3 MKL FFTW2)
+if(PKG_KSPACE)
+ option(FFT_SINGLE "Use single precision FFT instead of double" OFF)
+ set(FFTW "FFTW3")
+ if(FFT_SINGLE)
+ set(FFTW "FFTW3F")
+ add_definitions(-DFFT_SINGLE)
+ endif()
+ find_package(${FFTW} QUIET)
+ if(${FFTW}_FOUND)
+ set(FFT "${FFTW}" CACHE STRING "FFT library for KSPACE package")
+ else()
+ set(FFT "KISSFFT" CACHE STRING "FFT library for KSPACE package")
+ endif()
+ set_property(CACHE FFT PROPERTY STRINGS KISSFFT ${FFTW} MKL)
if(NOT FFT STREQUAL "KISSFFT")
find_package(${FFT} REQUIRED)
- add_definitions(-DFFT_${FFT})
+ if(NOT FFT STREQUAL "FFTW3F")
+ add_definitions(-DFFT_FFTW)
+ else()
+ add_definitions(-DFFT_${FFT})
+ endif()
include_directories(${${FFT}_INCLUDE_DIRS})
list(APPEND LAMMPS_LINK_LIBS ${${FFT}_LIBRARIES})
endif()
@@ -170,22 +199,17 @@ if(ENABLE_KSPACE)
endif()
endif()
-if(ENABLE_MSCG OR ENABLE_USER-ATC OR ENABLE_USER-AWPMD OR ENABLE_USER-QUIP OR ENABLE_LATTE)
+if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE)
find_package(LAPACK)
if(NOT LAPACK_FOUND)
enable_language(Fortran)
file(GLOB LAPACK_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/linalg/*.f)
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()
-if(ENABLE_PYTHON)
+if(PKG_PYTHON)
find_package(PythonInterp REQUIRED)
find_package(PythonLibs REQUIRED)
add_definitions(-DLMP_PYTHON)
@@ -201,16 +225,25 @@ if(ENABLE_PYTHON)
endif()
endif()
-find_package(JPEG)
-if(JPEG_FOUND)
+find_package(JPEG QUIET)
+option(WITH_JPEG "Enable JPEG support" ${JPEG_FOUND})
+if(WITH_JPEG)
+ find_package(JPEG REQUIRED)
add_definitions(-DLAMMPS_JPEG)
include_directories(${JPEG_INCLUDE_DIR})
list(APPEND LAMMPS_LINK_LIBS ${JPEG_LIBRARIES})
endif()
-find_package(PNG)
-find_package(ZLIB)
+find_package(PNG QUIET)
+find_package(ZLIB QUIET)
if(PNG_FOUND AND ZLIB_FOUND)
+ option(WITH_PNG "Enable PNG support" ON)
+else()
+ option(WITH_PNG "Enable PNG support" OFF)
+endif()
+if(WITH_PNG)
+ find_package(PNG REQUIRED)
+ find_package(ZLIB REQUIRED)
include_directories(${PNG_INCLUDE_DIRS} ${ZLIB_INCLUDE_DIRS})
list(APPEND LAMMPS_LINK_LIBS ${PNG_LIBRARIES} ${ZLIB_LIBRARIES})
add_definitions(-DLAMMPS_PNG)
@@ -218,25 +251,50 @@ endif()
find_program(GZIP_EXECUTABLE gzip)
find_package_handle_standard_args(GZIP REQUIRED_VARS GZIP_EXECUTABLE)
-if(GZIP_FOUND)
+option(WITH_GZIP "Enable GZIP support" ${GZIP_FOUND})
+if(WITH_GZIP)
+ if(NOT GZIP_FOUND)
+ message(FATAL_ERROR "gzip executable not found")
+ endif()
add_definitions(-DLAMMPS_GZIP)
endif()
find_program(FFMPEG_EXECUTABLE ffmpeg)
find_package_handle_standard_args(FFMPEG REQUIRED_VARS FFMPEG_EXECUTABLE)
-if(FFMPEG_FOUND)
+option(WITH_FFMPEG "Enable FFMPEG support" ${FFMPEG_FOUND})
+if(WITH_FFMPEG)
+ if(NOT FFMPEG_FOUND)
+ message(FATAL_ERROR "ffmpeg executable not found")
+ endif()
add_definitions(-DLAMMPS_FFMPEG)
endif()
-if(ENABLE_VORONOI)
- find_package(VORO REQUIRED) #some distros
+if(PKG_VORONOI)
+ option(DOWNLOAD_VORO "Download voro++ (instead of using the system's one)" OFF)
+ if(DOWNLOAD_VORO)
+ include(ExternalProject)
+ ExternalProject_Add(voro_build
+ URL http://math.lbl.gov/voro++/download/dir/voro++-0.4.6.tar.gz
+ URL_MD5 2338b824c3b7b25590e18e8df5d68af9
+ CONFIGURE_COMMAND "" BUILD_IN_SOURCE 1 INSTALL_COMMAND ""
+ )
+ ExternalProject_get_property(voro_build SOURCE_DIR)
+ set(VORO_LIBRARIES ${SOURCE_DIR}/src/libvoro++.a)
+ set(VORO_INCLUDE_DIRS ${SOURCE_DIR}/src)
+ list(APPEND LAMMPS_DEPS voro_build)
+ else()
+ find_package(VORO)
+ if(NOT VORO_FOUND)
+ message(FATAL_ERROR "VORO not found, help CMake to find it by setting VORO_LIBRARY and VORO_INCLUDE_DIR, or set DOWNLOAD_VORO=ON to download it")
+ endif()
+ endif()
include_directories(${VORO_INCLUDE_DIRS})
list(APPEND LAMMPS_LINK_LIBS ${VORO_LIBRARIES})
endif()
-if(ENABLE_LATTE)
- find_package(LATTE QUIET)
- if(NOT LATTE_FOUND)
+if(PKG_LATTE)
+ option(DOWNLOAD_LATTE "Download latte (instead of using the system's one)" OFF)
+ if(DOWNLOAD_LATTE)
message(STATUS "LATTE not found - we will build our own")
include(ExternalProject)
ExternalProject_Add(latte_build
@@ -248,55 +306,79 @@ if(ENABLE_LATTE)
ExternalProject_get_property(latte_build INSTALL_DIR)
set(LATTE_LIBRARIES ${INSTALL_DIR}/${CMAKE_INSTALL_LIBDIR}/liblatte.a)
list(APPEND LAMMPS_DEPS latte_build)
+ else()
+ find_package(LATTE)
+ if(NOT LATTE_FOUND)
+ message(FATAL_ERROR "LATTE not found, help CMake to find it by setting LATTE_LIBRARY, or set DOWNLOAD_LATTE=ON to download it")
+ endif()
endif()
list(APPEND LAMMPS_LINK_LIBS ${LATTE_LIBRARIES} ${LAPACK_LIBRARIES} ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
endif()
-if(ENABLE_USER-MOLFILE)
+if(PKG_USER-MOLFILE)
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)
+if(PKG_USER-NETCDF)
find_package(NetCDF REQUIRED)
include_directories(NETCDF_INCLUDE_DIR)
list(APPEND LAMMPS_LINK_LIBS ${NETCDF_LIBRARY})
add_definitions(-DLMP_HAS_NETCDF -DNC_64BIT_DATA=0x0020)
endif()
-if(ENABLE_USER-SMD)
- find_package(Eigen3 REQUIRED)
+if(PKG_USER-SMD)
+ option(DOWNLOAD_Eigen3 "Download Eigen3 (instead of using the system's one)" OFF)
+ if(DOWNLOAD_Eigen3)
+ include(ExternalProject)
+ ExternalProject_Add(Eigen3_build
+ URL http://bitbucket.org/eigen/eigen/get/3.3.4.tar.gz
+ URL_MD5 1a47e78efe365a97de0c022d127607c3
+ CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR> -DEIGEN_TEST_NOQT=ON
+ -DCMAKE_DISABLE_FIND_PACKAGE_LAPACK=ON -DCMAKE_DISABLE_FIND_PACKAGE_Cholmod=ON -DCMAKE_DISABLE_FIND_PACKAGE_Umfpack=ON -DCMAKE_DISABLE_FIND_PACKAGE_SuperLU=ON
+ -DCMAKE_DISABLE_FIND_PACKAGE_PASTIX=ON -DCMAKE_DISABLE_FIND_PACKAGE_SPQR=ON -DCMAKE_DISABLE_FIND_PACKAGE_Boost=ON -DCMAKE_DISABLE_FIND_PACKAGE_CUDA=ON
+ -DCMAKE_DISABLE_FIND_PACKAGE_FFTW=ON -DCMAKE_DISABLE_FIND_PACKAGE_MPFR=ON -DCMAKE_DISABLE_FIND_PACKAGE_OpenGL=ON
+ )
+ ExternalProject_get_property(Eigen3_build INSTALL_DIR)
+ set(EIGEN3_INCLUDE_DIR ${INSTALL_DIR}/include/eigen3)
+ list(APPEND LAMMPS_DEPS Eigen3_build)
+ else()
+ find_package(Eigen3)
+ if(NOT Eigen3_FOUND)
+ message(FATAL_ERROR "Eigen3 not found, help CMake to find it by setting EIGEN3_INCLUDE_DIR, or set DOWNLOAD_Eigen3=ON to download it")
+ endif()
+ endif()
include_directories(${EIGEN3_INCLUDE_DIR})
endif()
-if(ENABLE_USER-QUIP)
+if(PKG_USER-QUIP)
find_package(QUIP REQUIRED)
list(APPEND LAMMPS_LINK_LIBS ${QUIP_LIBRARIES} ${LAPACK_LIBRARIES} ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
endif()
-if(ENABLE_USER-QMMM)
+if(PKG_USER-QMMM)
+ message(WARNING "Building QMMM with CMake is still experimental")
find_package(QE REQUIRED)
include_directories(${QE_INCLUDE_DIRS})
list(APPEND LAMMPS_LINK_LIBS ${QE_LIBRARIES} ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
endif()
-if(ENABLE_USER-VTK)
+if(PKG_USER-VTK)
find_package(VTK REQUIRED NO_MODULE)
include(${VTK_USE_FILE})
add_definitions(-DLAMMPS_VTK)
list(APPEND LAMMPS_LINK_LIBS ${VTK_LIBRARIES})
endif()
-if(ENABLE_KIM)
- find_package(KIM QUIET)
- if(NOT KIM_FOUND)
- message(STATUS "KIM not found - we will build our own")
+if(PKG_KIM)
+ option(DOWNLOAD_KIM "Download kim-api (instead of using the system's one)" OFF)
+ if(DOWNLOAD_KIM)
include(ExternalProject)
ExternalProject_Add(kim_build
- URL https://github.com/openkim/kim-api/archive/v1.9.4.tar.gz
- URL_MD5 f4d35a1705eed46d64c7c0ab448ff3e0
+ URL https://github.com/openkim/kim-api/archive/v1.9.5.tar.gz
+ URL_MD5 9f66efc128da33039e30659f36fc6d00
BUILD_IN_SOURCE 1
CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR>
)
@@ -304,12 +386,17 @@ if(ENABLE_KIM)
set(KIM_INCLUDE_DIRS ${INSTALL_DIR}/include/kim-api-v1)
set(KIM_LIBRARIES ${INSTALL_DIR}/lib/libkim-api-v1.so)
list(APPEND LAMMPS_DEPS kim_build)
+ else()
+ find_package(KIM)
+ if(NOT KIM_FOUND)
+ message(FATAL_ERROR "KIM not found, help CMake to find it by setting KIM_LIBRARY and KIM_INCLUDE_DIR, or set DOWNLOAD_KIM=ON to download it")
+ endif()
endif()
list(APPEND LAMMPS_LINK_LIBS ${KIM_LIBRARIES})
include_directories(${KIM_INCLUDE_DIRS})
endif()
-if(ENABLE_MSCG)
+if(PKG_MSCG)
find_package(GSL REQUIRED)
set(LAMMPS_LIB_MSCG_BIN_DIR ${LAMMPS_LIB_BINARY_DIR}/mscg)
set(MSCG_TARBALL ${LAMMPS_LIB_MSCG_BIN_DIR}/MS-CG-master.zip)
@@ -333,12 +420,18 @@ if(ENABLE_MSCG)
target_link_libraries(mscg ${GSL_LIBRARIES} ${LAPACK_LIBRARIES})
endif()
+if(PKG_COMPRESS)
+ find_package(ZLIB REQUIRED)
+ include_directories(${ZLIB_INCLUDE_DIRS})
+ list(APPEND LAMMPS_LINK_LIBS ${ZLIB_LIBRARIES})
+endif()
+
########################################################################
# Basic system tests (standard libraries, headers, functions, types) #
########################################################################
-include(CheckIncludeFile)
+include(CheckIncludeFileCXX)
foreach(HEADER math.h)
- check_include_file(${HEADER} FOUND_${HEADER})
+ check_include_file_cxx(${HEADER} FOUND_${HEADER})
if(NOT FOUND_${HEADER})
message(FATAL_ERROR "Could not find needed header - ${HEADER}")
endif(NOT FOUND_${HEADER})
@@ -382,7 +475,7 @@ foreach(PKG ${DEFAULT_PACKAGES} ${OTHER_PACKAGES})
DetectAndRemovePackageHeader(${LAMMPS_SOURCE_DIR}/${FNAME})
endforeach()
- if(ENABLE_${PKG})
+ if(PKG_${PKG})
# detects styles in package and adds them to global list
RegisterStyles(${${PKG}_SOURCES_DIR})
@@ -396,7 +489,7 @@ endforeach()
############################################
foreach(SIMPLE_LIB REAX MEAM POEMS USER-ATC USER-AWPMD USER-COLVARS USER-H5MD
USER-QMMM)
- if(ENABLE_${SIMPLE_LIB})
+ if(PKG_${SIMPLE_LIB})
string(REGEX REPLACE "^USER-" "" PKG_LIB "${SIMPLE_LIB}")
string(TOLOWER "${PKG_LIB}" PKG_LIB)
file(GLOB_RECURSE ${PKG_LIB}_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/*.F
@@ -417,40 +510,26 @@ foreach(SIMPLE_LIB REAX MEAM POEMS USER-ATC USER-AWPMD USER-COLVARS USER-H5MD
endif()
endforeach()
-if(ENABLE_USER-AWPMD)
+if(PKG_USER-AWPMD)
target_link_libraries(awpmd ${LAPACK_LIBRARIES})
endif()
-if(ENABLE_USER-ATC)
+if(PKG_USER-ATC)
target_link_libraries(atc ${LAPACK_LIBRARIES})
endif()
-if(ENABLE_USER-H5MD)
+if(PKG_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
######################################################################
-if(ENABLE_USER-OMP)
+if(PKG_USER-OMP)
set(USER-OMP_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/USER-OMP)
set(USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/thr_data.cpp
${USER-OMP_SOURCES_DIR}/thr_omp.cpp
@@ -467,7 +546,7 @@ if(ENABLE_USER-OMP)
include_directories(${USER-OMP_SOURCES_DIR})
endif()
-if(ENABLE_KOKKOS)
+if(PKG_KOKKOS)
set(LAMMPS_LIB_KOKKOS_SRC_DIR ${LAMMPS_LIB_SOURCE_DIR}/kokkos)
set(LAMMPS_LIB_KOKKOS_BIN_DIR ${LAMMPS_LIB_BINARY_DIR}/kokkos)
add_definitions(-DLMP_KOKKOS)
@@ -503,7 +582,7 @@ if(ENABLE_KOKKOS)
RegisterNBinStyle(${KOKKOS_PKG_SOURCES_DIR}/nbin_kokkos.h)
RegisterNPairStyle(${KOKKOS_PKG_SOURCES_DIR}/npair_kokkos.h)
- if(ENABLE_USER-DPD)
+ if(PKG_USER-DPD)
get_property(KOKKOS_PKG_SOURCES GLOBAL PROPERTY KOKKOS_PKG_SOURCES)
list(APPEND KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/npair_ssa_kokkos.cpp)
RegisterNPairStyle(${KOKKOS_PKG_SOURCES_DIR}/npair_ssa_kokkos.h)
@@ -516,7 +595,7 @@ if(ENABLE_KOKKOS)
include_directories(${KOKKOS_PKG_SOURCES_DIR})
endif()
-if(ENABLE_OPT)
+if(PKG_OPT)
set(OPT_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/OPT)
set(OPT_SOURCES)
set_property(GLOBAL PROPERTY "OPT_SOURCES" "${OPT_SOURCES}")
@@ -530,7 +609,30 @@ if(ENABLE_OPT)
include_directories(${OPT_SOURCES_DIR})
endif()
-if(ENABLE_USER-INTEL)
+if(PKG_USER-INTEL)
+ if(NOT DEVELOPER_MODE)
+ if(NOT CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
+ message(FATAL_ERROR "USER-INTEL is only useful together with intel compiler")
+ endif()
+ if(CMAKE_CXX_COMPILER_VERSION VERSION_LESS 16)
+ message(FATAL_ERROR "USER-INTEL is needed at least 2016 intel compiler, found ${CMAKE_CXX_COMPILER_VERSION}")
+ endif()
+ endif()
+ option(INJECT_INTEL_FLAG "Inject OMG fast flags for USER-INTEL" ON)
+ if(INJECT_INTEL_FLAG AND CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
+ if(CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.3 OR CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.4)
+ set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -xCOMMON-AVX512")
+ else()
+ set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -xHost")
+ endif()
+ include(CheckCXXCompilerFlag)
+ foreach(_FLAG -qopenmp -qno-offload -fno-alias -ansi-alias -restrict -DLMP_INTEL_USELRT -DLMP_USE_MKL_RNG -O2 "-fp-model fast=2" -no-prec-div -qoverride-limits -qopt-zmm-usage=high)
+ check_cxx_compiler_flag("${__FLAG}" COMPILER_SUPPORTS${_FLAG})
+ if(COMPILER_SUPPORTS${_FLAG})
+ set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${_FLAG}")
+ endif()
+ endforeach()
+ endif()
set(USER-INTEL_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/USER-INTEL)
set(USER-INTEL_SOURCES ${USER-INTEL_SOURCES_DIR}/intel_preprocess.h
${USER-INTEL_SOURCES_DIR}/intel_buffers.h
@@ -554,7 +656,7 @@ if(ENABLE_USER-INTEL)
include_directories(${USER-INTEL_SOURCES_DIR})
endif()
-if(ENABLE_GPU)
+if(PKG_GPU)
set(GPU_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/GPU)
set(GPU_SOURCES ${GPU_SOURCES_DIR}/gpu_extra.h
${GPU_SOURCES_DIR}/fix_gpu.h
@@ -691,6 +793,7 @@ include_directories(${LAMMPS_STYLE_HEADERS_DIR})
# Actually add executable and lib to build
############################################
add_library(lammps ${LIB_SOURCES})
+list(REMOVE_DUPLICATES LAMMPS_LINK_LIBS)
target_link_libraries(lammps ${LAMMPS_LINK_LIBS})
if(LAMMPS_DEPS)
add_dependencies(lammps ${LAMMPS_DEPS})
@@ -716,31 +819,60 @@ endif()
# Print package summary
##################################
foreach(PKG ${DEFAULT_PACKAGES} ${OTHER_PACKAGES} ${ACCEL_PACKAGES})
- if(ENABLE_${PKG})
+ if(PKG_${PKG})
message(STATUS "Building package: ${PKG}")
endif()
endforeach()
string(TOUPPER "${CMAKE_BUILD_TYPE}" BTYPE)
+get_directory_property(CPPFLAGS DIRECTORY ${CMAKE_SOURCE_DIR} COMPILE_DEFINITIONS)
+include(FeatureSummary)
+feature_summary(INCLUDE_QUIET_PACKAGES WHAT ALL)
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}}")
+ Version ${CMAKE_CXX_COMPILER_VERSION}
+ C++ Flags ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_${BTYPE}}
+ Defines ${CPPFLAGS}")
get_property(LANGUAGES GLOBAL PROPERTY ENABLED_LANGUAGES)
-if(LANGUAGES MATCHES ".*Fortran.*")
+list (FIND LANGUAGES "Fortran" _index)
+if (${_index} GREATER -1)
message(STATUS "Fortran Compiler ${CMAKE_Fortran_COMPILER}
Type ${CMAKE_Fortran_COMPILER_ID}
+ Version ${CMAKE_Fortran_COMPILER_VERSION}
Fortran Flags ${CMAKE_Fortran_FLAGS} ${CMAKE_Fortran_FLAGS_${BTYPE}}")
endif()
-message(STATUS "Linker flags:
+list (FIND LANGUAGES "C" _index)
+if (${_index} GREATER -1)
+ message(STATUS "C Compiler ${CMAKE_C_COMPILER}
+ Type ${CMAKE_C_COMPILER_ID}
+ Version ${CMAKE_C_COMPILER_VERSION}
+ C Flags ${CMAKE_C_FLAGS} ${CMAKE_C_FLAGS_${BTYPE}}")
+endif()
+if(CMAKE_EXE_LINKER_FLAGS)
+ message(STATUS "Linker flags:
Executable ${CMAKE_EXE_LINKER_FLAGS}")
+ endif()
if(BUILD_SHARED_LIBS)
- message(STATUS "Shared libries ${CMAKE_SHARED_LINKER_FLAGS}")
+ message(STATUS "Shared libraries ${CMAKE_SHARED_LINKER_FLAGS}")
else()
- message(STATUS "Static libries ${CMAKE_STATIC_LINKER_FLAGS}")
+ message(STATUS "Static libraries ${CMAKE_STATIC_LINKER_FLAGS}")
endif()
message(STATUS "Link libraries: ${LAMMPS_LINK_LIBS}")
-
+if(BUILD_MPI)
+ message(STATUS "Using mpi with headers in ${MPI_CXX_INCLUDE_PATH} and ${MPI_CXX_LIBRARIES}")
+endif()
+if(ENABLED_GPU)
+ message(STATUS "GPU Api: ${GPU_API}")
+ if(GPU_API STREQUAL "CUDA")
+ message(STATUS "GPU Arch: ${GPU_ARCH}")
+ elseif(GPU_API STREQUAL "OpenCL")
+ message(STATUS "OCL Tune: ${OCL_TUNE}")
+ endif()
+endif()
+if(PKG_KSPACE)
+ message(STATUS "Using ${FFT} as FFT")
+endif()
diff --git a/cmake/Modules/FindFFTW2.cmake b/cmake/Modules/FindFFTW2.cmake
deleted file mode 100644
index c77e6cf8e9d126d5ebb4223e6e7cf53ef25b60b2..0000000000000000000000000000000000000000
--- a/cmake/Modules/FindFFTW2.cmake
+++ /dev/null
@@ -1,22 +0,0 @@
-# - Find fftw2
-# Find the native FFTW2 headers and libraries.
-#
-# FFTW2_INCLUDE_DIRS - where to find fftw2.h, etc.
-# FFTW2_LIBRARIES - List of libraries when using fftw2.
-# FFTW2_FOUND - True if fftw2 found.
-#
-
-find_path(FFTW2_INCLUDE_DIR fftw.h)
-
-find_library(FFTW2_LIBRARY NAMES fftw)
-
-set(FFTW2_LIBRARIES ${FFTW2_LIBRARY})
-set(FFTW2_INCLUDE_DIRS ${FFTW2_INCLUDE_DIR})
-
-include(FindPackageHandleStandardArgs)
-# handle the QUIETLY and REQUIRED arguments and set FFTW2_FOUND to TRUE
-# if all listed variables are TRUE
-
-find_package_handle_standard_args(FFTW2 DEFAULT_MSG FFTW2_LIBRARY FFTW2_INCLUDE_DIR)
-
-mark_as_advanced(FFTW2_INCLUDE_DIR FFTW2_LIBRARY )
diff --git a/cmake/Modules/FindFFTW3F.cmake b/cmake/Modules/FindFFTW3F.cmake
new file mode 100644
index 0000000000000000000000000000000000000000..92d1e85e791ec362a15909bd09dccdc046efc2a5
--- /dev/null
+++ b/cmake/Modules/FindFFTW3F.cmake
@@ -0,0 +1,25 @@
+# - Find fftw3f
+# Find the native FFTW3F headers and libraries.
+#
+# FFTW3F_INCLUDE_DIRS - where to find fftw3f.h, etc.
+# FFTW3F_LIBRARIES - List of libraries when using fftw3f.
+# FFTW3F_FOUND - True if fftw3f found.
+#
+
+find_package(PkgConfig)
+
+pkg_check_modules(PC_FFTW3F fftw3f)
+find_path(FFTW3F_INCLUDE_DIR fftw3.h HINTS ${PC_FFTW3F_INCLUDE_DIRS})
+
+find_library(FFTW3F_LIBRARY NAMES fftw3f HINTS ${PC_FFTW3F_LIBRARY_DIRS})
+
+set(FFTW3F_LIBRARIES ${FFTW3F_LIBRARY})
+set(FFTW3F_INCLUDE_DIRS ${FFTW3F_INCLUDE_DIR})
+
+include(FindPackageHandleStandardArgs)
+# handle the QUIETLY and REQUIRED arguments and set FFTW3F_FOUND to TRUE
+# if all listed variables are TRUE
+
+find_package_handle_standard_args(FFTW3F DEFAULT_MSG FFTW3F_LIBRARY FFTW3F_INCLUDE_DIR)
+
+mark_as_advanced(FFTW3F_INCLUDE_DIR FFTW3F_LIBRARY )
diff --git a/doc/src/Eqs/dihedral_table_cut.jpg b/doc/src/Eqs/dihedral_table_cut.jpg
new file mode 100644
index 0000000000000000000000000000000000000000..c124184c1773c60fe2564d8cabce2f6c7d7883c0
Binary files /dev/null and b/doc/src/Eqs/dihedral_table_cut.jpg differ
diff --git a/doc/src/Eqs/dihedral_table_cut.tex b/doc/src/Eqs/dihedral_table_cut.tex
new file mode 100644
index 0000000000000000000000000000000000000000..3cc1d331a8978d76e668de3f83cf0d4264be3301
--- /dev/null
+++ b/doc/src/Eqs/dihedral_table_cut.tex
@@ -0,0 +1,11 @@
+\documentclass[12pt]{article}
+\pagestyle{empty}
+\begin{document}
+
+\begin{eqnarray*}
+ f(\theta) & = & K \qquad\qquad\qquad\qquad\qquad\qquad \theta < \theta_1 \\
+ f(\theta) & = & K \left(1-\frac{(\theta - \theta_1)^2}{(\theta_2 - \theta_1)^2}\right) \qquad \theta_1 < \theta < \theta_2
+\end{eqnarray*}
+
+\end{document}
+
diff --git a/doc/src/Manual.txt b/doc/src/Manual.txt
index 077927ccc7ac2a62d60b988480cde725187a2736..6b2c7daac7d682c05469e44db60b9e0aad02f5c5 100644
--- a/doc/src/Manual.txt
+++ b/doc/src/Manual.txt
@@ -1,7 +1,7 @@
<!-- HTML_ONLY -->
<HEAD>
<TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="20 Apr 2018 version">
+<META NAME="docnumber" CONTENT="11 May 2018 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>
@@ -19,7 +19,7 @@
:line
LAMMPS Documentation :c,h1
-20 Apr 2018 version :c,h2
+11 May 2018 version :c,h2
Version info: :h3
diff --git a/doc/src/PDF/USER-CGDNA-overview.pdf b/doc/src/PDF/USER-CGDNA-overview.pdf
deleted file mode 100644
index e329877bc2cc5953574ea8fbd65789158a050879..0000000000000000000000000000000000000000
Binary files a/doc/src/PDF/USER-CGDNA-overview.pdf and /dev/null differ
diff --git a/doc/src/PDF/USER-CGDNA.pdf b/doc/src/PDF/USER-CGDNA.pdf
new file mode 100644
index 0000000000000000000000000000000000000000..843bba00d5c5a707577d07dda1929ba4c8a07987
Binary files /dev/null and b/doc/src/PDF/USER-CGDNA.pdf differ
diff --git a/doc/src/PDF/colvars-refman-lammps.pdf b/doc/src/PDF/colvars-refman-lammps.pdf
index 2d28758819a9a7a0dac700cd4a8239f51257b8e1..7f52367c82eec09a0465b356b326e996482a9bc3 100644
Binary files a/doc/src/PDF/colvars-refman-lammps.pdf and b/doc/src/PDF/colvars-refman-lammps.pdf differ
diff --git a/doc/src/Section_commands.txt b/doc/src/Section_commands.txt
index 76051490e401b9ff5b9ac3c4aeb292a1b86b66b3..3dabdbeaa1e1091db35b798f19cf9f3b2b74848f 100644
--- a/doc/src/Section_commands.txt
+++ b/doc/src/Section_commands.txt
@@ -684,6 +684,7 @@ package"_Section_start.html#start_3.
"addtorque"_fix_addtorque.html,
"atc"_fix_atc.html,
"ave/correlate/long"_fix_ave_correlate_long.html,
+"bond/react"_fix_bond_react.html,
"colvars"_fix_colvars.html,
"dpd/energy (k)"_fix_dpd_energy.html,
"drude"_fix_drude.html,
@@ -1211,7 +1212,8 @@ package"_Section_start.html#start_3.
"nharmonic (o)"_dihedral_nharmonic.html,
"quadratic (o)"_dihedral_quadratic.html,
"spherical (o)"_dihedral_spherical.html,
-"table (o)"_dihedral_table.html :tb(c=4,ea=c)
+"table (o)"_dihedral_table.html,
+"table/cut"_dihedral_table_cut.html :tb(c=4,ea=c)
:line
diff --git a/doc/src/Section_packages.txt b/doc/src/Section_packages.txt
index ade75c588f071fc75fb85e35b9e28e304f693070..e9387fe35fb41758089081bed202e832029c25df 100644
--- a/doc/src/Section_packages.txt
+++ b/doc/src/Section_packages.txt
@@ -122,6 +122,7 @@ Package, Description, Doc page, Example, Library
Package, Description, Doc page, Example, Library
"USER-ATC"_#USER-ATC, atom-to-continuum coupling, "fix atc"_fix_atc.html, USER/atc, int
"USER-AWPMD"_#USER-AWPMD, wave-packet MD, "pair_style awpmd/cut"_pair_awpmd.html, USER/awpmd, int
+"USER-BOCS"_#USER-BOCS, BOCS bottom up coarse graining, "fix bocs"_fix_bocs.html, USER/bocs, -
"USER-CGDNA"_#USER-CGDNA, coarse-grained DNA force fields, src/USER-CGDNA/README, USER/cgdna, -
"USER-CGSDK"_#USER-CGSDK, SDK coarse-graining model, "pair_style lj/sdk"_pair_sdk.html, USER/cgsdk, -
"USER-COLVARS"_#USER-COLVARS, collective variables library, "fix colvars"_fix_colvars.html, USER/colvars, int
@@ -1625,6 +1626,43 @@ examples/USER/awpmd :ul
:line
+USER-BOCS package :link(USER-BOCS),h4
+
+[Contents:]
+
+This package provides "fix bocs"_fix_bocs.html, a modified version
+of "fix npt"_fix_nh.html which includes the pressure correction to
+the barostat as outlined in:
+
+N. J. H. Dunn and W. G. Noid, "Bottom-up coarse-grained models that
+accurately describe the structure, pressure, and compressibility of
+molecular liquids," J. Chem. Phys. 143, 243148 (2015).
+
+[Authors:] Nicholas J. H. Dunn and Michael R. DeLyser (The Pennsylvania State University)
+
+[Install or un-install:]
+
+make yes-user-bocs
+make machine :pre
+
+make no-user-bocs
+make machine :pre
+
+[Supporting info:]
+
+The USER-BOCS user package for LAMMPS is part of the BOCS software package:
+"https://github.com/noid-group/BOCS"_https://github.com/noid-group/BOCS
+
+See the following reference for information about the entire package:
+
+Dunn, NJH; Lebold, KM; DeLyser, MR; Rudzinski, JF; Noid, WG.
+"BOCS: Bottom-Up Open-Source Coarse-Graining Software."
+J. Phys. Chem. B. 122, 13, 3363-3377 (2018).
+
+Example inputs are in the examples/USER/bocs folder.
+
+:line
+
USER-CGDNA package :link(USER-CGDNA),h4
[Contents:]
diff --git a/doc/src/bond_oxdna.txt b/doc/src/bond_oxdna.txt
index 2add6f4c2f0fb1f31aabaccca596cddbb41c5687..927fea64031d5422615d1251b9332e4e66120d3a 100644
--- a/doc/src/bond_oxdna.txt
+++ b/doc/src/bond_oxdna.txt
@@ -51,9 +51,11 @@ The coefficients in the above example have to be kept fixed and cannot be change
Example input and data files for DNA duplexes can be found in examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/.
A simple python setup tool which creates single straight or helical DNA strands,
DNA duplexes or arrays of DNA duplexes can be found in examples/USER/cgdna/util/.
-A technical report with more information on the model, the structure of the input file,
-the setup tool and the performance of the LAMMPS-implementation of oxDNA
-can be found "here"_PDF/USER-CGDNA-overview.pdf.
+
+Please cite "(Henrich)"_#Henrich2 and the relevant oxDNA articles in any publication that uses this implementation.
+The article contains more information on the model, the structure of the input file, the setup tool
+and the performance of the LAMMPS-implementation of oxDNA.
+The preprint version of the article can be found "here"_PDF/USER-CGDNA.pdf.
:line
@@ -72,6 +74,9 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.
:line
+:link(Henrich2)
+[(Henrich)] O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
+
:link(oxdna_fene)
[(Ouldridge)] T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011).
diff --git a/doc/src/compute_ackland_atom.txt b/doc/src/compute_ackland_atom.txt
index b75d100112b9f3a9a5e49d1ec282f275e56a9014..3fd838d95775ae9e97f7ad8da792112b9890d80d 100644
--- a/doc/src/compute_ackland_atom.txt
+++ b/doc/src/compute_ackland_atom.txt
@@ -10,19 +10,29 @@ compute ackland/atom command :h3
[Syntax:]
-compute ID group-ID ackland/atom :pre
+compute ID group-ID ackland/atom keyword/value :pre
-ID, group-ID are documented in "compute"_compute.html command
-ackland/atom = style name of this compute command :ul
+ID, group-ID are documented in "compute"_compute.html command :ulb,l
+ackland/atom = style name of this compute command :l
+
+zero or more keyword/value pairs may be appended :l
+keyword = {legacy} :l
+ {legacy} yes/no = use ({yes}) or do not use ({no}) legacy ackland algorithm implementation :pre
+:ule
[Examples:]
-compute 1 all ackland/atom :pre
+compute 1 all ackland/atom
+compute 1 all ackland/atom legacy yes :pre
[Description:]
Defines a computation that calculates the local lattice structure
according to the formulation given in "(Ackland)"_#Ackland.
+Historically, LAMMPS had two, slightly different implementations of
+the algorithm from the paper. With the {legacy} keyword, it is
+possible to switch between the pre-2015 ({legacy yes}) and post-2015
+implemention ({legacy no}). The post-2015 variant is the default.
In contrast to the "centro-symmetry
parameter"_compute_centro_atom.html this method is stable against
@@ -66,7 +76,8 @@ integers defined above.
"compute centro/atom"_compute_centro_atom.html
-[Default:] none
+[Default:]
+The keyword {legacy} defaults to {no}.
:line
diff --git a/doc/src/compute_displace_atom.txt b/doc/src/compute_displace_atom.txt
index 39c301cf911a159089189ee02cef15a5ffae4d1e..00e5f696c118029431bf5a36395bcd906fe432ee 100644
--- a/doc/src/compute_displace_atom.txt
+++ b/doc/src/compute_displace_atom.txt
@@ -15,7 +15,7 @@ compute ID group-ID displace/atom :pre
ID, group-ID are documented in "compute"_compute.html command :ulb,l
displace/atom = style name of this compute command :l
zero or more keyword/arg pairs may be appended :l
-keyword = {refresh} :
+keyword = {refresh} :l
{replace} arg = name of per-atom variable :pre
:ule
diff --git a/doc/src/compute_sna_atom.txt b/doc/src/compute_sna_atom.txt
index 1c3787e696638191373d0b563f461c37d42dddad..268e23ac2808d82f8750b95bd652cd4d50f6b9d2 100644
--- a/doc/src/compute_sna_atom.txt
+++ b/doc/src/compute_sna_atom.txt
@@ -161,9 +161,9 @@ function.
The keyword {bzeroflag} determines whether or not {B0}, the bispectrum
components of an atom with no neighbors, are subtracted from
-the calculated bispectrum components. This optional keyword is only
-available for compute {sna/atom}, as {snad/atom} and {snav/atom}
-are unaffected by the removal of constant terms.
+the calculated bispectrum components. This optional keyword
+normally only affects compute {sna/atom}. However, when
+{quadraticflag} is on, it also affects {snad/atom} and {snav/atom}.
The keyword {quadraticflag} determines whether or not the
quadratic analogs to the bispectrum quantities are generated.
@@ -230,13 +230,18 @@ are 30, 90, and 180, respectively. With {quadratic} value=1,
the numbers of columns are 930, 2790, and 5580, respectively.
If the {quadratic} keyword value is set to 1, then additional
-columns are appended to each per-atom array, corresponding to
+columns are generated, corresponding to
the products of all distinct pairs of bispectrum components. If the
number of bispectrum components is {K}, then the number of distinct pairs
-is {K}({K}+1)/2. These are output in subblocks of {K}({K}+1)/2 columns, using the same
-ordering of sub-blocks as was used for the bispectrum
-components. Within each sub-block, the ordering is upper-triangular,
-(1,1),(1,2)...(1,{K}),(2,1)...({K}-1,{K}-1),({K}-1,{K}),({K},{K})
+is {K}({K}+1)/2.
+For compute {sna/atom} these columns are appended to existing {K} columns.
+The ordering of quadratic terms is upper-triangular,
+(1,1),(1,2)...(1,{K}),(2,1)...({K}-1,{K}-1),({K}-1,{K}),({K},{K}).
+For computes {snad/atom} and {snav/atom} each set of {K}({K}+1)/2
+additional columns is inserted directly after each of sub-block
+of linear terms i.e. linear and quadratic terms are contiguous.
+So the nesting order from inside to outside is bispectrum component,
+linear then quadratic, vector/tensor component, type.
These values can be accessed by any command that uses per-atom values
from a compute as input. See "Section
diff --git a/doc/src/dihedral_table_cut.txt b/doc/src/dihedral_table_cut.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1c83d4ffa09f7221ac8c3859594abc754b9b28c4
--- /dev/null
+++ b/doc/src/dihedral_table_cut.txt
@@ -0,0 +1,205 @@
+"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
+
+dihedral_style table/cut command :h3
+
+[Syntax:]
+
+dihedral_style table/cut style Ntable :pre
+
+style = {linear} or {spline} = method of interpolation
+Ntable = size of the internal lookup table :ul
+
+[Examples:]
+
+dihedral_style table/cut spline 400
+dihedral_style table/cut linear 1000
+dihedral_coeff 1 aat 1.0 177 180 file.table DIH_TABLE1
+dihedral_coeff 2 aat 0.5 170 180 file.table DIH_TABLE2 :pre
+
+[Description:]
+
+The {table/cut} dihedral style creates interpolation tables of length
+{Ntable} from dihedral potential and derivative values listed in a
+file(s) as a function of the dihedral angle "phi". In addition, an
+analytic cutoff that is quadratic in the bond-angle (theta) is applied
+in order to regularize the dihedral interaction. The dihedral table
+files are read by the "dihedral_coeff"_dihedral_coeff.html command.
+
+The interpolation tables are created by fitting cubic splines to the
+file values and interpolating energy and derivative values at each of
+{Ntable} dihedral angles. During a simulation, these tables are used
+to interpolate energy and force values on individual atoms as
+needed. The interpolation is done in one of 2 styles: {linear} or
+{spline}.
+
+For the {linear} style, the dihedral angle (phi) is used to find 2
+surrounding table values from which an energy or its derivative is
+computed by linear interpolation.
+
+For the {spline} style, cubic spline coefficients are computed and
+stored at each of the {Ntable} evenly-spaced values in the
+interpolated table. For a given dihedral angle (phi), the appropriate
+coefficients are chosen from this list, and a cubic polynomial is used
+to compute the energy and the derivative at this angle.
+
+The following coefficients must be defined for each dihedral type via
+the "dihedral_coeff"_dihedral_coeff.html command as in the example
+above.
+
+style (aat)
+cutoff prefactor
+cutoff angle1
+cutoff angle2
+filename
+keyword :ul
+
+The cutoff dihedral style uses a tabulated dihedral interaction with a
+cutoff function:
+
+:c,image(Eqs/dihedral_table_cut.jpg)
+
+The cutoff specifies an prefactor to the cutoff function. While this value
+would ordinarily equal 1 there may be situations where the value should change.
+
+The cutoff angle1 specifies the angle (in degrees) below which the dihedral
+interaction is unmodified, i.e. the cutoff function is 1.
+
+The cutoff function is applied between angle1 and angle2, which is the angle at
+which the cutoff function drops to zero. The value of zero effectively "turns
+off" the dihedral interaction.
+
+The filename specifies a file containing tabulated energy and
+derivative values. The keyword specifies a section of the file. The
+format of this file is described below.
+
+:line
+
+The format of a tabulated file is as follows (without the
+parenthesized comments). It can begin with one or more comment
+or blank lines.
+
+# Table of the potential and its negative derivative :pre
+
+DIH_TABLE1 (keyword is the first text on line)
+N 30 DEGREES (N, NOF, DEGREES, RADIANS, CHECKU/F)
+ (blank line)
+1 -168.0 -1.40351172223 0.0423346818422
+2 -156.0 -1.70447981034 0.00811786522531
+3 -144.0 -1.62956100432 -0.0184129719987
+...
+30 180.0 -0.707106781187 0.0719306095245 :pre
+
+# Example 2: table of the potential. Forces omitted :pre
+
+DIH_TABLE2
+N 30 NOF CHECKU testU.dat CHECKF testF.dat :pre
+
+1 -168.0 -1.40351172223
+2 -156.0 -1.70447981034
+3 -144.0 -1.62956100432
+...
+30 180.0 -0.707106781187 :pre
+
+A section begins with a non-blank line whose 1st character is not a
+"#"; blank lines or lines starting with "#" can be used as comments
+between sections. The first line begins with a keyword which
+identifies the section. The line can contain additional text, but the
+initial text must match the argument specified in the
+"dihedral_coeff"_dihedral_coeff.html command. The next line lists (in
+any order) one or more parameters for the table. Each parameter is a
+keyword followed by one or more numeric values.
+
+Following a blank line, the next N lines list the tabulated values. On
+each line, the 1st value is the index from 1 to N, the 2nd value is
+the angle value, the 3rd value is the energy (in energy units), and
+the 4th is -dE/d(phi) also in energy units). The 3rd term is the
+energy of the 4-atom configuration for the specified angle. The 4th
+term (when present) is the negative derivative of the energy with
+respect to the angle (in degrees, or radians depending on whether the
+user selected DEGREES or RADIANS). Thus the units of the last term
+are still energy, not force. The dihedral angle values must increase
+from one line to the next.
+
+Dihedral table splines are cyclic. There is no discontinuity at 180
+degrees (or at any other angle). Although in the examples above, the
+angles range from -180 to 180 degrees, in general, the first angle in
+the list can have any value (positive, zero, or negative). However
+the {range} of angles represented in the table must be {strictly} less
+than 360 degrees (2pi radians) to avoid angle overlap. (You may not
+supply entries in the table for both 180 and -180, for example.) If
+the user's table covers only a narrow range of dihedral angles,
+strange numerical behavior can occur in the large remaining gap.
+
+[Parameters:]
+
+The parameter "N" is required and its value is the number of table
+entries that follow. Note that this may be different than the N
+specified in the "dihedral_style table"_dihedral_style.html command.
+Let {Ntable} is the number of table entries requested dihedral_style
+command, and let {Nfile} be the parameter following "N" in the
+tabulated file ("30" in the sparse example above). What LAMMPS does
+is a preliminary interpolation by creating splines using the {Nfile}
+tabulated values as nodal points. It uses these to interpolate as
+needed to generate energy and derivative values at {Ntable} different
+points (which are evenly spaced over a 360 degree range, even if the
+angles in the file are not). The resulting tables of length {Ntable}
+are then used as described above, when computing energy and force for
+individual dihedral angles and their atoms. This means that if you
+want the interpolation tables of length {Ntable} to match exactly what
+is in the tabulated file (with effectively nopreliminary
+interpolation), you should set {Ntable} = {Nfile}. To insure the
+nodal points in the user's file are aligned with the interpolated
+table entries, the angles in the table should be integer multiples of
+360/{Ntable} degrees, or 2*PI/{Ntable} radians (depending on your
+choice of angle units).
+
+The optional "NOF" keyword allows the user to omit the forces
+(negative energy derivatives) from the table file (normally located in
+the 4th column). In their place, forces will be calculated
+automatically by differentiating the potential energy function
+indicated by the 3rd column of the table (using either linear or
+spline interpolation).
+
+The optional "DEGREES" keyword allows the user to specify angles in
+degrees instead of radians (default).
+
+The optional "RADIANS" keyword allows the user to specify angles in
+radians instead of degrees. (Note: This changes the way the forces
+are scaled in the 4th column of the data file.)
+
+The optional "CHECKU" keyword is followed by a filename. This allows
+the user to save all of the the {Ntable} different entries in the
+interpolated energy table to a file to make sure that the interpolated
+function agrees with the user's expectations. (Note: You can
+temporarily increase the {Ntable} parameter to a high value for this
+purpose. "{Ntable}" is explained above.)
+
+The optional "CHECKF" keyword is analogous to the "CHECKU" keyword.
+It is followed by a filename, and it allows the user to check the
+interpolated force table. This option is available even if the user
+selected the "NOF" option.
+
+Note that one file can contain many sections, each with a tabulated
+potential. LAMMPS reads the file section by section until it finds one
+that matches the specified keyword.
+
+[Restrictions:]
+
+This dihedral style 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.
+
+[Related commands:]
+
+"dihedral_coeff"_dihedral_coeff.html, "dihedral_style table"_dihedral_table.html
+
+[Default:] none
+
+:link(dihedralcut-Salerno)
+[(Salerno)] Salerno, Bernstein, J Chem Theory Comput, --, ---- (2018).
diff --git a/doc/src/dihedrals.txt b/doc/src/dihedrals.txt
index 500a6a52bf69b7beb641c414f6dee354d6ca6b7b..a862bf50a0a9c357ffeed1129e3b67423259447c 100644
--- a/doc/src/dihedrals.txt
+++ b/doc/src/dihedrals.txt
@@ -19,6 +19,7 @@ Dihedral Styles :h1
dihedral_quadratic
dihedral_spherical
dihedral_table
+ dihedral_table_cut
dihedral_zero
dihedral_charmm
dihedral_class2
diff --git a/doc/src/dump_modify.txt b/doc/src/dump_modify.txt
index 6de6de545e720d518316ea9d31c82fb825fd8c9c..3230507dc3eaebc8bce634acf6a7ac2e3c2c7707 100644
--- a/doc/src/dump_modify.txt
+++ b/doc/src/dump_modify.txt
@@ -15,7 +15,7 @@ dump_modify dump-ID keyword values ... :pre
dump-ID = ID of dump to modify :ulb,l
one or more keyword/value pairs may be appended :l
these keywords apply to various dump styles :l
-keyword = {append} or {at} or {buffer} or {delay} or {element} or {every} or {fileper} or {first} or {flush} or {format} or {image} or {label} or {nfile} or {pad} or {precision} or {region} or {scale} or {sort} or {thresh} or {unwrap} :l
+keyword = {append} or {at} or {buffer} or {delay} or {element} or {every} or {fileper} or {first} or {flush} or {format} or {image} or {label} or {maxfiles} or {nfile} or {pad} or {precision} or {region} or {scale} or {sort} or {thresh} or {unwrap} :l
{append} arg = {yes} or {no}
{at} arg = N
N = index of frame written upon first dump
@@ -37,6 +37,8 @@ keyword = {append} or {at} or {buffer} or {delay} or {element} or {every} or {fi
{image} arg = {yes} or {no}
{label} arg = string
string = character string (e.g. BONDS) to use in header of dump local file
+ {maxfiles} arg = Fmax
+ Fmax = keep only the most recent {Fmax} snapshots (one snapshot per file)
{nfile} arg = Nf
Nf = write this many files, one from each of Nf processors
{pad} arg = Nchar = # of characters to convert timestep to
@@ -364,6 +366,20 @@ e.g. BONDS or ANGLES.
:line
+The {maxfiles} keyword can only be used when a '*' wildcard is
+included in the dump file name, i.e. when writing a new file(s) for
+each snapshot. The specified {Fmax} is how many snapshots will be
+kept. Once this number is reached, the file(s) containing the oldest
+snapshot is deleted before a new dump file is written. If the
+specified {Fmax} <= 0, then all files are retained.
+
+This can be useful for debugging, especially if you don't know on what
+timestep something bad will happen, e.g. when LAMMPS will exit with an
+error. You can dump every timestep, and limit the number of dump
+files produced, even if you run for 1000s of steps.
+
+:line
+
The {nfile} or {fileper} keywords can be used in conjunction with the
"%" wildcard character in the specified dump file name, for all dump
styles except the {dcd}, {image}, {movie}, {xtc}, and {xyz} styles
@@ -901,6 +917,7 @@ flush = yes
format = %d and %g for each integer or floating point value
image = no
label = ENTRIES
+maxifiles = -1
nfile = 1
pad = 0
pbc = no
diff --git a/doc/src/fix_bocs.txt b/doc/src/fix_bocs.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f53b7c785c251240a0d325b820545f342ce21c06
--- /dev/null
+++ b/doc/src/fix_bocs.txt
@@ -0,0 +1,112 @@
+<"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 bocs command :h3
+
+[Syntax:]
+
+fix ID group-ID bocs keyword values ... :pre
+
+keyword = {temp} or {cgiso} or {analytic} or {linear_spline} or {cubic_spline}
+ {temp} values = Tstart Tstop Tdamp
+ {cgiso} values = Pstart Pstop Pdamp
+ {basis set}
+ {analytic} values = V_avg N_particles N_coeff Coeff_1 Coeff_2 ... Coeff_N
+ {linear_spline} values = input_filename
+ {cubic_spline} values = input_filename :pre
+:ule
+
+[Examples:]
+
+fix 1 all bocs temp 300.0 300.0 100.0 cgiso 0.986 0.986 1000.0 analytic 66476.015 968 2 245030.10 8962.20 :pre
+
+fix 1 all bocs temp 300.0 300.0 100.0 cgiso 0.986 0.986 1000.0 cubic_spline input_Fv.dat :pre
+
+thermo_modify press 1_press :pre
+
+
+[Description:]
+
+These commands incorporate a pressure correction as described by
+Dunn and Noid in "(Dunn1)"_#bocs-Dunn1 to the standard MTTK
+barostat by Martyna et. al. in "(Martyna)"_#bocs-Martyna .
+The first half of the command mimics a standard fix npt command:
+
+fix 1 all bocs temp Tstart Tstop Tcoupl cgiso Pstart Pstop Pdamp :pre
+
+The two differences are replacing {npt} with {bocs}, and replacing
+{iso}/{aniso}/{etc} with {cgiso}.
+The rest of the command details what form you would like to use for
+the pressure correction equation. The choices are: {analytic}, {linear_spline},
+or {cubic_spline}.
+
+With either spline method, the only argument that needs to follow it
+is the name of a file that contains the desired pressure correction
+as a function of volume. The file should be formatted so each line has:
+
+Volume_i, PressureCorrection_i :pre
+
+Note both the COMMA and the SPACE separating the volume's
+value and its corresponding pressure correction. The volumes in the file
+should be uniformly spaced. Both the volumes and the pressure corrections
+should be provided in the proper units, e.g. if you are using {units real},
+the volumes should all be in cubic angstroms, and the pressure corrections
+should all be in atomspheres. Furthermore, the table should start/end at a
+volume considerably smaller/larger than you expect your system to sample
+during the simulation. If the system ever reaches a volume outside of the
+range provided, the simulation will stop.
+
+With the {analytic} option, the arguments are as follows:
+
+... analytic V_avg N_particles N_coeff Coeff_1 Coeff_2 ... Coeff_N :pre
+
+Note that {V_avg} and {Coeff_i} should all be in the proper units, e.g. if you
+are using {units real}, {V_avg} should be in cubic angstroms, and the
+coefficients should all be in atmospheres * cubic angstroms.
+
+[Restrictions:]
+
+As this is computing a (modified) pressure, group-ID should be {all}.
+
+The pressure correction has only been tested for use with an isotropic
+pressure coupling in 3 dimensions.
+
+By default, LAMMPS will still report the normal value for the pressure
+if the pressure is printed via a {thermo} command, or if the pressures
+are written to a file every so often. In order to have LAMMPS report the
+modified pressure, you must include the {thermo_modify} command given in
+the examples. For the last argument in the command, you should put
+XXXX_press, where XXXX is the ID given to the fix bocs command (in the
+example, the ID of the fix bocs command is 1 ).
+
+This fix is part of the USER-BOCS package. It is only enabled if
+LAMMPS was built with that package. See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
+
+[Related:]
+
+For more details about the pressure correction and the entire BOCS software
+package, visit the "BOCS package on github"_bocsgithub and read the release
+paper by Dunn et. al. "(Dunn2)"_#bocs-Dunn2 .
+
+
+:link(bocsgithub,https://github.com/noid-group/BOCS)
+
+:line
+
+:link(bocs-Dunn1)
+[(Dunn1)] Dunn and Noid, J Chem Phys, 143, 243148 (2015).
+
+:link(bocs-Martyna)
+[(Martyna)] Martyna, Tobias, and Klein, J Chem Phys, 101, 4177 (1994).
+
+:link(bocs-Dunn2)
+[(Dunn2)] Dunn, Lebold, DeLyser, Rudzinski, and Noid, J. Phys. Chem. B, 122, 3363 (2018).
+
+
+
diff --git a/doc/src/fix_bond_react.txt b/doc/src/fix_bond_react.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f85ef9bc1aa6ea034364e5358ac1eafa2824f0d6
--- /dev/null
+++ b/doc/src/fix_bond_react.txt
@@ -0,0 +1,332 @@
+"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 bond/react command :h3
+
+[Syntax:]
+
+fix ID group-ID bond/react common_keyword values ...
+ react react-ID react-group-ID Nevery Rmin Rmax template-ID(pre-reacted) template-ID(post-reacted) map_file individual_keyword values ...
+ react react-ID react-group-ID Nevery Rmin Rmax template-ID(pre-reacted) template-ID(post-reacted) map_file individual_keyword values ...
+ react react-ID react-group-ID Nevery Rmin Rmax template-ID(pre-reacted) template-ID(post-reacted) map_file individual_keyword values ...
+ ... :pre
+
+ID, group-ID are documented in "fix"_fix.html command. Group-ID is ignored. :ulb,l
+bond/react = style name of this fix command :l
+zero or more common keyword/value pairs may be appended directly after 'bond/react' :l
+these apply to all reaction specifications (below) :l
+common_keyword = {stabilization} :l
+ {stabilization} values = {no} or {yes} {group-ID} {xmax}
+ {no} = no reaction site stabilization
+ {yes} = perform reaction site stabilization
+ {group-ID} = user-assigned ID for all non-reacting atoms (group created internally)
+ {xmax} = xmax value that is used by an internally created "nve/limit"_fix_nve_limit.html integrator :pre
+react = mandatory argument indicating new reaction specification :l
+ react-ID = user-assigned name for the reaction :l
+ react-group-ID = only atoms in this group are available for the reaction :l
+ Nevery = attempt reaction every this many steps :l
+ Rmin = bonding pair atoms must be separated by more than Rmin to initiate reaction (distance units) :l
+ Rmax = bonding pair atoms must be separated by less than Rmax to initiate reaction (distance units) :l
+ template-ID(pre-reacted) = ID of a molecule template containing pre-reaction topology :l
+ template-ID(post-reacted) = ID of a molecule template containing post-reaction topology :l
+ map_file = name of file specifying corresponding atomIDs in the pre- and post-reacted templates :l
+ zero or more individual keyword/value pairs may be appended to each react argument :l
+ individual_keyword = {prob} or {stabilize_steps} :l
+ {prob} values = fraction seed
+ fraction = initiate reaction with this probability if otherwise eligible
+ seed = random number seed (positive integer)
+ {stabilize_steps} value = timesteps
+ timesteps = number of timesteps to apply internally created nve/limit.html :pre
+:ule
+
+[Examples:]
+
+molecule mol1 pre_reacted_topology.txt
+molecule mol2 post_reacted_topology.txt
+fix 5 all bond/react stabilization no react myrxn1 all 1 0 3.25 mol1 mol2 map_file.txt :pre
+
+molecule mol1 pre_reacted_rxn1.txt
+molecule mol2 post_reacted_rxn1.txt
+molecule mol3 pre_reacted_rxn2.txt
+molecule mol4 post_reacted_rxn2.txt
+fix 5 all bond/react stabilization yes nvt_grp .03 &
+ react myrxn1 all 1 0 3.25 mol1 mol2 map_file_rxn1.txt prob 0.50 12345 &
+ react myrxn2 all 1 0 2.75 mol3 mol4 map_file_rxn2.txt prob 0.25 12345
+fix 6 nvt_grp nvt temp 300 300 100 # set thermostat after bond/react :pre
+
+[Description:]
+
+Initiate complex covalent bonding (topology) changes. These topology
+changes will be referred to as 'reactions' throughout this
+documentation. Topology changes are defined in pre- and post-reaction
+molecule templates and can include creation and deletion of bonds,
+angles, dihedrals, impropers, bond-types, angle-types, dihedral-types,
+atom-types, or atomic charges.
+
+Fix bond/react does not use quantum mechanical (eg. fix qmmm) or
+pairwise bond-order potential (eg. Tersoff or AIREBO) methods to
+determine bonding changes a priori. Rather, it uses a distance-based
+probabilistic criteria to effect predetermined topology changes in
+simulations using standard force fields.
+
+This fix was created to facilitate the dynamic creation of polymeric,
+amorphous or highly-crosslinked systems. A suggested workflow for
+using this fix is: 1) identify a reaction to be simulated 2) build a
+molecule template of the reaction site before the reaction has
+occurred 3) build a molecule template of the reaction site after the
+reaction has occurred 4) create a map that relates the
+template-atom-IDs of each atom between pre- and post-reaction molecule
+templates 5) fill a simulation box with molecules and run a simulation
+with fix bond/react.
+
+Only one 'fix bond/react' command can be used at a time. Multiple
+reactions can be simultaneously applied by specifying multiple {react}
+arguments to a single 'fix bond/react' command. This syntax is
+necessary because the 'common keywords' are applied to all reactions.
+
+The {stabilization} keyword enables reaction site stabilization.
+Reaction site stabilization is performed by including reacting atoms
+in an internally created fix "nve/limit"_fix_nve_limit.html time
+integrator for a set number of timesteps given by the
+{stabilize_steps} keyword. While reacting atoms are being time
+integrated by the internal nve/limit, they are prevented from being
+involved in any new reactions. The {xmax} value keyword should
+typically be set to the maximum distance that non-reacting atoms move
+during the simulation.
+
+The group-ID set using the {stabilization} keyword should be a
+previously unused group-ID. It cannot be specified as 'all'. The fix
+bond/react command creates a "dynamic group"_group.html of this name
+that includes all non-reacting atoms. This dynamic group-ID should
+then be used by a subsequent system-wide time integrator such as nvt,
+npt, or nve, as shown in the second example above. It is currently
+necessary to place the time integration command after the fix
+bond/react command due to the internal dynamic grouping performed by
+fix bond/react.
+
+NOTE: The internally created group currently applies to all atoms in
+the system, i.e. you should generally not have a separate thermostat
+which acts on the 'all' group.
+
+The following comments pertain to each {react} argument:
+
+A check for possible new reaction sites is performed every {Nevery}
+timesteps.
+
+Two conditions must be met for a reaction to occur. First a bonding
+atom pair must be identified. Second, the topology surrounding the
+bonding atom pair must match the topology of the pre-reaction
+template. If both these conditions are met, the reaction site is
+modified to match the post-reaction template.
+
+A bonding atom pair will be identified if several conditions are met.
+First, a pair of atoms within the specified react-group-ID of type
+typei and typej must separated by a distance between {Rmin} and
+{Rmax}. It is possible that multiple bonding atom pairs are
+identified: if the bonding atoms in the pre-reacted template are not
+1-2, 1-3, or 1-4 neighbors, the closest bonding atom partner is set as
+its bonding partner; otherwise, the farthest potential partner is
+chosen. Then, if both an atomi and atomj have each other as their
+nearest bonding partners, these two atoms are identified as the
+bonding atom pair of the reaction site. Once this unique bonding atom
+pair is identified for each reaction, there could two or more
+reactions that involve a given atom on the same timestep. If this is
+the case, only one such reaction is permitted to occur. This reaction
+is chosen randomly from all potential reactions. This capability
+allows e.g. for different reaction pathways to proceed from identical
+reaction sites with user-specified probabilities.
+
+The pre-reacted molecule template is specified by a molecule command.
+This molecule template file contains a sample reaction site and its
+surrounding topology. As described below, the bonding atom pairs of
+the pre-reacted template are specified by atom ID in the map file. The
+pre-reacted molecule template should contain as few atoms as possible
+while still completely describing the topology of all atoms affected
+by the reaction. For example, if the force field contains dihedrals,
+the pre-reacted template should contain any atom within three bonds of
+reacting atoms.
+
+Some atoms in the pre-reacted template that are not reacting may have
+missing topology with respect to the simulation. For example, the
+pre-reacted template may contain an atom that would connect to the
+rest of a long polymer chain. These are referred to as edge atoms, and
+are also specified in the map file.
+
+Note that some care must be taken when a building a molecule template
+for a given simulation. All atom types in the pre-reacted template
+must be the same as those of a potential reaction site in the
+simulation. A detailed discussion of matching molecule template atom
+types with the simulation is provided on the "molecule"_molecule.html
+command page.
+
+The post-reacted molecule template contains a sample of the reaction
+site and its surrounding topology after the reaction has occurred. It
+must contain the same number of atoms as the pre-reacted template. A
+one-to-one correspondence between the atom IDs in the pre- and
+post-reacted templates is specified in the map file as described
+below. Note that during a reaction, an atom, bond, etc. type may
+change to one that was previously not present in the simulation. These
+new types must also be defined during the setup of a given simulation.
+A discussion of correctly handling this is also provided on the
+"molecule"_molecule.html command page.
+
+The map file is a text document with the following format:
+
+A map file has a header and a body. The header of map file the
+contains one mandatory keyword and one optional keyword. The mandatory
+keyword is 'equivalences' and the optional keyword is 'edgeIDs':
+
+N {equivalences} = # of atoms N in the reaction molecule templates
+N {edgeIDs} = # of edge atoms N in the pre-reacted molecule template :pre
+
+The body of the map file contains two mandatory sections and one
+optional section. The first mandatory section begins with the keyword
+'BondingIDs' and lists the atom IDs of the bonding atom pair in the
+pre-reacted molecule template. The second mandatory section begins
+with the keyword 'Equivalences' and lists a one-to-one correspondence
+between atom IDs of the pre- and post-reacted templates. The first
+column is an atom ID of the pre-reacted molecule template, and the
+second column is the corresponding atom ID of the post-reacted
+molecule template. The optional section begins with the keyword
+'EdgeIDs' and lists the atom IDs of edge atoms in the pre-reacted
+molecule template.
+
+A sample map file is given below:
+
+:line
+
+# this is a map file :pre
+
+2 edgeIDs
+7 equivalences :pre
+
+BondingIDs :pre
+
+3
+5 :pre
+
+EdgeIDs :pre
+
+1
+7 :pre
+
+Equivalences :pre
+
+1 1
+2 2
+3 3
+4 4
+5 5
+6 6
+7 7 :pre
+
+:line
+
+Once a reaction site has been successfully identified, data structures
+within LAMMPS that store bond topology are updated to reflect the
+post-reacted molecule template. All force fields with fixed bonds,
+angles, dihedrals or impropers are supported.
+
+A few capabilities to note: 1) You may specify as many {react}
+arguments as desired. For example, you could break down a complicated
+reaction mechanism into several reaction steps, each defined by its
+own {react} argument. 2) While typically a bond is formed or removed
+between the bonding atom pairs specified in the pre-reacted molecule
+template, this is not required. 3) By reversing the order of the pre-
+and post- reacted molecule templates in another {react} argument, you
+can allow for the possibility of one or more reverse reactions.
+
+The optional keywords deal with the probability of a given reaction
+occurring as well as the stable equilibration of each reaction site as
+it occurs.
+
+The {prob} keyword can affect whether an eligible reaction actually
+occurs. The fraction setting must be a value between 0.0 and 1.0. A
+uniform random number between 0.0 and 1.0 is generated and the
+eligible reaction only occurs if the random number is less than the
+fraction.
+
+The {stabilize_steps} keyword allows for the specification of how many
+timesteps a reaction site is stabilized before being returned to the
+overall system thermostat.
+
+In order to produce the most physical behavior, this 'reaction site
+equilibration time' should be tuned to be as small as possible while
+retaining stability for a given system or reaction step. After a
+limited number of case studies, this number has been set to a default
+of 60 timesteps. Ideally, it should be individually tuned for each fix
+reaction step. Note that in some situations, decreasing rather than
+increasing this parameter will result in an increase in stability.
+
+A few other considerations:
+
+It may be beneficial to ensure reacting atoms are at a certain
+temperature before being released to the overall thermostat. For this,
+you can use the internally-created dynamic group named
+"bond_react_MASTER_group." For example, adding the following command
+would thermostat the group of all atoms currently involved in a
+reaction:
+
+fix 1 bond_react_MASTER_group temp/rescale 1 300 300 10 1 :pre
+
+NOTE: This command must be added after the fix bond/react command, and
+will apply to all reactions.
+
+Computationally, each timestep this fix operates, it loops over
+neighbor lists (for bond-forming reactions) and computes distances
+between pairs of atoms in the list. It also communicates between
+neighboring processors to coordinate which bonds are created and/or
+removed. All of these operations increase the cost of a timestep. Thus
+you should be cautious about invoking this fix too frequently.
+
+You can dump out snapshots of the current bond topology via the dump
+local command.
+
+:line
+
+[Restart, fix_modify, output, run start/stop, minimize info:]
+
+No information about this fix is written to "binary restart
+files"_restart.html, aside from internally-created per-atom
+properties. None of the "fix_modify"_fix_modify.html options are
+relevant to this fix.
+
+This fix computes one statistic for each {react} argument that it
+stores in a global vector, of length 'number of react arguments', that
+can be accessed by various "output
+commands"_Section_howto.html#howto_15. The vector values calculated by
+this fix are "intensive".
+
+These is 1 quantity for each react argument:
+
+(1) cumulative # of reactions occurred :ul
+
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command. This fix is not invoked during "energy
+minimization"_minimize.html.
+
+[Restrictions:]
+
+This fix is part of the USER-MISC package. It is only enabled if
+LAMMPS was built with that package. See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
+
+[Related commands:]
+
+"fix bond/create"_fix_bond_create.html, "fix
+bond/break"_fix_bond_break.html, "fix bond/swap"_fix_bond_swap.html,
+"dump local"_dump.html, "special_bonds"_special_bonds.html
+
+[Default:]
+
+The option defaults are stabilization = no, stabilize_steps = 60
+
+:line
+
+:link(Gissinger)
+[(Gissinger)] Gissinger, Jensen and Wise, Polymer, 128, 211 (2017).
diff --git a/doc/src/fix_langevin_drude.txt b/doc/src/fix_langevin_drude.txt
index afc9c5f257523646906966d89464da26a070023e..c85ff24c96d2982439d67c4ac52fd3bea5083044 100644
--- a/doc/src/fix_langevin_drude.txt
+++ b/doc/src/fix_langevin_drude.txt
@@ -154,7 +154,7 @@ Note: The temperature thermostating the core-Drude particle pairs
should be chosen low enough, so as to mimic as closely as possible the
self-consistent minimization. It must however be high enough, so that
the dipoles can follow the local electric field exerted by the
-neighbouring atoms. The optimal value probably depends on the
+neighboring atoms. The optimal value probably depends on the
temperature of the centers of mass and on the mass of the Drude
particles.
diff --git a/doc/src/fix_modify.txt b/doc/src/fix_modify.txt
index 1c7dcf77a5dd0c72db2dea22873e0728417e8048..308bba1ac31fdf9a7cbd45ec1da50122cd46bcb9 100644
--- a/doc/src/fix_modify.txt
+++ b/doc/src/fix_modify.txt
@@ -14,14 +14,16 @@ 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 {virial} or {respa} or {dynamic/dof} :l
+keyword = {temp} or {press} or {energy} or {virial} or {respa} or {dynamic/dof} or {bodyforces} :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
+ yes/no = do or do not recompute the number of degrees of freedom (DOF) contributing to the temperature
+ {bodyforces} value = {early} or {late}
+ early/late = compute rigid-body forces/torques early or late in the timestep :pre
:ule
[Examples:]
@@ -84,9 +86,8 @@ 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}.
+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}
@@ -120,6 +121,28 @@ compute to calculate temperature. See the "compute_modify
dynamic/dof"_compute_modify.html command for a similar way to insure
correct temperature normalization for those thermostats.
+The {bodyforces} keyword determines whether the forces and torques
+acting on rigid bodies are computed {early} at the post-force stage of
+each timestep (right after per-atom forces have been computed and
+communicated among processors), or {late} at the final-integrate stage
+of each timestep (after any other fixes have finished their post-force
+tasks). Only the rigid-body integration fixes use this option, which
+includes "fix rigid"_fix_rigid.html and "fix
+rigid/small"_fix_rigid.html, and their variants, and also "fix
+poems"_fix_poems.html.
+
+The default is {late}. If there are other fixes that add forces to
+individual atoms, then the rigid-body constraints will include these
+forces when time-integrating the rigid bodies. If {early} is
+specified, then new fixes can be written that use or modify the
+per-body force and torque, before time-integration of the rigid bodies
+occurs. Note however this has the side effect, that fixes such as
+"fix addforce"_fix_addforce.html, "fix setforce"_fix_setforce.html,
+"fix spring"_fix_spring.html, which add forces to individual atoms
+will have no effect on the motion of the rigid bodies if they are
+specified in the input script after the fix rigid command. LAMMPS
+will give a warning if that is the case.
+
[Restrictions:] none
[Related commands:]
@@ -130,4 +153,5 @@ 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, virial = different for each fix style, respa = 0.
+by fix, energy = no, virial = different for each fix style, respa = 0,
+bodyforce = late.
diff --git a/doc/src/fix_poems.txt b/doc/src/fix_poems.txt
index d90d832cb8e2deed341771ea00e9f0b294e55c8b..03abc058b8b0d6e982f6291e1fecbb887cf2ad9a 100644
--- a/doc/src/fix_poems.txt
+++ b/doc/src/fix_poems.txt
@@ -106,12 +106,18 @@ off, and there is only a single fix poems defined.
[Restart, fix_modify, output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
-files"_restart.html. None of the "fix_modify"_fix_modify.html options
-are relevant to this fix. No global or per-atom quantities are stored
-by this fix for access by various "output
-commands"_Section_howto.html#howto_15. No parameter of this fix can
-be used with the {start/stop} keywords of the "run"_run.html command.
-This fix is not invoked during "energy minimization"_minimize.html.
+files"_restart.html.
+
+The "fix_modify"_fix_modify.html {bodyforces} option is supported by
+this fix style to set whether per-body forces and torques are computed
+early or late in a timestep, i.e. at the post-force stage or at the
+final-integrate stage, respectively.
+
+No global or per-atom quantities are stored by this fix for access by
+various "output commands"_Section_howto.html#howto_15. No parameter
+of this fix can be used with the {start/stop} keywords of the
+"run"_run.html command. This fix is not invoked during "energy
+minimization"_minimize.html.
[Restrictions:]
diff --git a/doc/src/fix_reax_bonds.txt b/doc/src/fix_reax_bonds.txt
index 54aa7faef802f3061f795c54a7449d6d93265d0b..3f8f237de1c7d574bfc214b9dfec2892e11b3793 100644
--- a/doc/src/fix_reax_bonds.txt
+++ b/doc/src/fix_reax_bonds.txt
@@ -34,6 +34,8 @@ written to {filename} on timesteps that are multiples of {Nevery},
including timestep 0. For time-averaged chemical species analysis,
please see the "fix reaxc/c/species"_fix_reaxc_species.html command.
+The specified group-ID is ignored by this fix.
+
The format of the output file should be reasonably self-explanatory.
The meaning of the column header abbreviations is as follows:
diff --git a/doc/src/fix_restrain.txt b/doc/src/fix_restrain.txt
index c8ec20daaa4ae3953b2660a2770607b15610533e..9de63defb700fb0f713187d87f4077fd35b86e0f 100644
--- a/doc/src/fix_restrain.txt
+++ b/doc/src/fix_restrain.txt
@@ -24,10 +24,12 @@ keyword = {bond} or {angle} or {dihedral} :l
atom1,atom2,atom3 = IDs of 3 atoms in angle, atom2 = middle atom
Kstart,Kstop = restraint coefficients at start/end of run (energy units)
theta0 = equilibrium angle theta (degrees)
- {dihedral} args = atom1 atom2 atom3 atom4 Kstart Kstop phi0
+ {dihedral} args = atom1 atom2 atom3 atom4 Kstart Kstop phi0 keyword/value
atom1,atom2,atom3,atom4 = IDs of 4 atoms in dihedral in linear order
Kstart,Kstop = restraint coefficients at start/end of run (energy units)
- phi0 = equilibrium dihedral angle phi (degrees) :pre
+ phi0 = equilibrium dihedral angle phi (degrees)
+ keyword/value = optional keyword value pairs. supported keyword/value pairs:
+ {mult} n = dihedral multiplicity n (integer >= 0, default = 1) :pre
:ule
[Examples:]
@@ -155,11 +157,13 @@ associated with the restraint is
with the following coefficients:
K (energy)
-n = 1
+n (multiplicity, >= 0)
d (degrees) = phi0 + 180 :ul
-K and phi0 are specified with the fix. Note that the value of n is
-hard-wired to 1. Also note that the energy will be a minimum when the
+K and phi0 are specified with the fix. Note that the value of the
+dihedral multiplicity {n} is set by default to 1. You can use the
+optional {mult} keyword to set it to a different positive integer.
+Also note that the energy will be a minimum when the
current dihedral angle phi is equal to phi0.
:line
@@ -183,10 +187,17 @@ added 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.
-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 for all the restraints as discussed above. The scalar
-value calculated by this fix is "extensive".
+This fix computes a global scalar and a global vector of length 3, which
+can be accessed by various "output commands"_Section_howto.html#howto_15.
+The scalar is the total potential energy for {all} the restraints as
+discussed above. The vector values are the sum of contributions to the
+following individual categories:
+
+1 = bond energy
+2 = angle energy
+3 = dihedral energy :ul
+
+The scalar and vector values calculated by this fix are "extensive".
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command.
diff --git a/doc/src/fix_rigid.txt b/doc/src/fix_rigid.txt
index 24642a23acc4a04592a62e46d0a21132bb056136..63c7f8e9db4769a13cc0ff500e3954d9f481ecd5 100644
--- a/doc/src/fix_rigid.txt
+++ b/doc/src/fix_rigid.txt
@@ -223,10 +223,10 @@ via several options.
NOTE: With the {rigid/small} styles, which require that {bodystyle} be
specified as {molecule} or {custom}, you can define a system that has
-no rigid bodies initially. This is useful when you are using the {mol}
-keyword in conjunction with another fix that is adding rigid bodies
-on-the-fly as molecules, such as "fix deposit"_fix_deposit.html or
-"fix pour"_fix_pour.html.
+no rigid bodies initially. This is useful when you are using the
+{mol} keyword in conjunction with another fix that is adding rigid
+bodies on-the-fly as molecules, such as "fix deposit"_fix_deposit.html
+or "fix pour"_fix_pour.html.
For bodystyle {single} the entire fix group of atoms is treated as one
rigid body. This option is only allowed for the {rigid} styles.
@@ -742,6 +742,11 @@ used to calculate the instantaneous pressure tensor. Note that the 2
NVT rigid fixes do not use any external compute to compute
instantaneous temperature.
+The "fix_modify"_fix_modify.html {bodyforces} option is supported by
+all rigid styles to set whether per-body forces and torques are
+computed early or late in a timestep, i.e. at the post-force stage or
+at the final-integrate stage or the timestep, respectively.
+
The 2 NVE rigid fixes compute a global scalar which can be accessed by
various "output commands"_Section_howto.html#howto_15. The scalar
value calculated by these fixes is "intensive". The scalar is the
diff --git a/doc/src/fixes.txt b/doc/src/fixes.txt
index c3fcc06bf1c53e780b9b7bc3ce9885671fc9f690..79c2f75b8ba46f2924c2e34ed98c81edd6fe71b8 100644
--- a/doc/src/fixes.txt
+++ b/doc/src/fixes.txt
@@ -20,9 +20,11 @@ Fixes :h1
fix_ave_time
fix_aveforce
fix_balance
+ fix_bocs
fix_bond_break
fix_bond_create
fix_bond_swap
+ fix_bond_react
fix_box_relax
fix_cmap
fix_colvars
diff --git a/doc/src/lammps.book b/doc/src/lammps.book
index ec34f41872db2aa143628ce3f99c249a8641cda9..0764c593f7e56cc251588d800a53d06a11e232b4 100644
--- a/doc/src/lammps.book
+++ b/doc/src/lammps.book
@@ -135,8 +135,10 @@ fix_ave_histo.html
fix_ave_time.html
fix_aveforce.html
fix_balance.html
+fix_bocs.html
fix_bond_break.html
fix_bond_create.html
+fix_bond_react.html
fix_bond_swap.html
fix_box_relax.html
fix_cmap.html
@@ -580,6 +582,7 @@ dihedral_opls.html
dihedral_quadratic.html
dihedral_spherical.html
dihedral_table.html
+dihedral_table_cut.html
dihedral_zero.html
lammps_commands_improper.html
diff --git a/doc/src/pair_kolmogorov_crespi_z.txt b/doc/src/pair_kolmogorov_crespi_z.txt
index c7e005a591c04b712f0bb2ed3a640b1ea8e3e5e1..97f132eacd41e00cd4318cfde24b09e29b4a6ae1 100644
--- a/doc/src/pair_kolmogorov_crespi_z.txt
+++ b/doc/src/pair_kolmogorov_crespi_z.txt
@@ -38,7 +38,7 @@ This shift is achieved by the last term in the equation for {Vij} above.
This potential is intended for interactions between two layers of graphene.
Therefore, to avoid interaction between layers in multi-layered materials,
each layer should have a separate atom type and interactions should only
-be computed between atom types of neighbouring layers.
+be computed between atom types of neighboring layers.
The parameter file (e.g. CC.KC), is intended for use with metal
"units"_units.html, with energies in meV. An additional parameter, {S},
diff --git a/doc/src/pair_oxdna.txt b/doc/src/pair_oxdna.txt
index 26a205bcf9b449ee20eea88ce5aff6a3feca024b..f272d15a8680d6499df5f7164186789426589413 100644
--- a/doc/src/pair_oxdna.txt
+++ b/doc/src/pair_oxdna.txt
@@ -71,9 +71,11 @@ the temperature coefficients have to be matched to the one used in the fix.
Example input and data files for DNA duplexes can be found in examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/.
A simple python setup tool which creates single straight or helical DNA strands,
DNA duplexes or arrays of DNA duplexes can be found in examples/USER/cgdna/util/.
-A technical report with more information on the model, the structure of the input file,
-the setup tool and the performance of the LAMMPS-implementation of oxDNA
-can be found "here"_PDF/USER-CGDNA-overview.pdf.
+
+Please cite "(Henrich)"_#Henrich1 and the relevant oxDNA articles in any publication that uses this implementation.
+The article contains more information on the model, the structure of the input file, the setup tool
+and the performance of the LAMMPS-implementation of oxDNA.
+The preprint version of the article can be found "here"_PDF/USER-CGDNA.pdf.
:line
@@ -92,6 +94,9 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.
:line
+:link(Henrich1)
+[(Henrich)] O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
+
: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).
diff --git a/doc/src/pair_oxdna2.txt b/doc/src/pair_oxdna2.txt
index 2408c02d101135639561652db8f5e74dae7e037f..1b55031b2c97dc8c935c0ddb83a567f24d64ab6f 100644
--- a/doc/src/pair_oxdna2.txt
+++ b/doc/src/pair_oxdna2.txt
@@ -77,9 +77,11 @@ the temperature coefficients have to be matched to the one used in the fix.
Example input and data files for DNA duplexes can be found in examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/.
A simple python setup tool which creates single straight or helical DNA strands,
DNA duplexes or arrays of DNA duplexes can be found in examples/USER/cgdna/util/.
-A technical report with more information on the model, the structure of the input file,
-the setup tool and the performance of the LAMMPS-implementation of oxDNA
-can be found "here"_PDF/USER-CGDNA-overview.pdf.
+
+Please cite "(Henrich)"_#Henrich and the relevant oxDNA articles in any publication that uses this implementation.
+The article contains more information on the model, the structure of the input file, the setup tool
+and the performance of the LAMMPS-implementation of oxDNA.
+The preprint version of the article can be found "here"_PDF/USER-CGDNA.pdf.
:line
@@ -98,6 +100,9 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.
:line
+:link(Henrich)
+[(Henrich)] O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
+
: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).
diff --git a/examples/USER/bocs/README b/examples/USER/bocs/README
new file mode 100644
index 0000000000000000000000000000000000000000..ae1739f8c0378256a7232290ecdd6a3a238bc7e9
--- /dev/null
+++ b/examples/USER/bocs/README
@@ -0,0 +1,6 @@
+This folder contains the files to run a NPT simulation of 1 site CG methanol
+while employing a correction to the barostat.
+The pair force was computed via the Multi-Scale Coarse-Graining method.
+The resulting model was then iteratively pressure matched.
+The model accurately reproduces both structural (RDF) and thermodynamic
+(Pressure-Volume EoS) properties of the underlying OPLS-AA model of methanol.
diff --git a/examples/USER/bocs/in.methanol b/examples/USER/bocs/in.methanol
new file mode 100644
index 0000000000000000000000000000000000000000..e7c80e014d04de182615de67dd142c54034beccf
--- /dev/null
+++ b/examples/USER/bocs/in.methanol
@@ -0,0 +1,69 @@
+units real
+dimension 3
+boundary p p p
+atom_style atomic
+
+newton on
+timestep 1.0
+
+read_data methanol.data
+
+velocity all create 300.0 16802 dist gaussian
+
+pair_style table spline 15000
+
+pair_coeff 1 1 lammps_nb_MET-MET.table nb_METMET 12.0
+
+neigh_modify delay 0 every 1 check yes one 10000
+neighbor 12.0 bin
+
+thermo 500
+thermo_style custom step temp pe etotal press vol
+
+variable STEP equal step
+variable TEMP equal temp
+## volume from cubic angstroms to cubic nm
+variable VOL equal vol/1000.0
+## pressure from atm to bar
+variable PRESS equal press*1.01325
+variable PXX equal pxx*1.01325
+variable PYY equal pyy*1.01325
+variable PZZ equal pzz*1.01325
+variable PXY equal pxy*1.01325
+variable PXZ equal pxz*1.01325
+variable PYZ equal pyz*1.01325
+## energy from kcal/mol to kJ/mol
+variable KE equal ke*4.184
+variable PE equal pe*4.184
+variable UVDW equal evdwl*4.184
+
+
+##### SPECIAL COMMANDS FOR FIX_BOCS #####
+# ID group-ID style_name thermostat T_init T_end T_couple barostat P_start P_end P_couple pmatch_basis avg_vol N_sites N_coeffs coeff1 coeff2
+fix 1 all bocs temp 300.0 300.0 100.0 cgiso 0.986 0.986 1000.0 analytic 66476.015 968 2 245030.10 8962.20
+
+# Report the modified pressure
+thermo_modify press 1_press
+
+
+
+## Uncomment to save some data from simulation to files
+#fix print_temp all print 500 "${STEP} ${TEMP}" file temp.dat screen no
+#fix print_vol all print 500 "${STEP} ${VOL}" file vol.dat screen no
+#fix print_press all print 500 "${STEP} ${PRESS}" file press.dat screen no
+#fix print_ke all print 500 "${STEP} ${KE}" file kinetic_E.dat screen no
+#fix print_pe all print 500 "${STEP} ${PE}" file potential_E.dat screen no
+#fix print_ve all print 500 "${STEP} ${UVDW}" file vdw_E.dat screen no
+#fix print_press_tens all print 500 "${STEP} ${PXX} ${PYY} ${PZZ} ${PXY} ${PXZ} ${PYZ}" file press_tens.dat screen no
+#fix print_PV_eos all print 500 "${VOL} ${PRESS}" file pv_eos.dat screen no
+
+## Prints a configuration to dump.txt every 500 steps
+#dump 1 all custom 500 dump.txt id type x y z fx fy fz
+
+# Write restart files to continue simulations
+#restart 10000 state1.restart state2.restart
+
+## Run for this many steps
+run_style verlet
+run 10000
+
diff --git a/examples/USER/bocs/lammps_nb_MET-MET.table b/examples/USER/bocs/lammps_nb_MET-MET.table
new file mode 100644
index 0000000000000000000000000000000000000000..c6d9fc6ca251cd012c78f50b1e86bc03c72cc6be
--- /dev/null
+++ b/examples/USER/bocs/lammps_nb_MET-MET.table
@@ -0,0 +1,2505 @@
+#Converted from table.xvg
+
+nb_METMET
+N 2500
+
+1 0.010000 573.151769 380.122371
+2 0.020000 569.356836 378.855163
+3 0.030000 565.574570 377.588193
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diff --git a/examples/USER/bocs/log.20Apr18.methanol.g++.1 b/examples/USER/bocs/log.20Apr18.methanol.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..a94bd959c816c3cb1faa1b03ee9dc176b5301950
--- /dev/null
+++ b/examples/USER/bocs/log.20Apr18.methanol.g++.1
@@ -0,0 +1,143 @@
+LAMMPS (20 Apr 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+ using 1 OpenMP thread(s) per MPI task
+units real
+dimension 3
+boundary p p p
+atom_style atomic
+
+newton on
+timestep 1.0
+
+read_data methanol.data
+ orthogonal box = (0 0 0) to (40.4635 40.4635 40.4635)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 968 atoms
+
+velocity all create 300.0 16802 dist gaussian
+
+pair_style table spline 15000
+
+pair_coeff 1 1 lammps_nb_MET-MET.table nb_METMET 12.0
+WARNING: 78 of 2500 force values in table are inconsistent with -dE/dr.
+ Should only be flagged at inflection points (../pair_table.cpp:481)
+
+neigh_modify delay 0 every 1 check yes one 10000
+neighbor 12.0 bin
+
+thermo 500
+thermo_style custom step temp pe etotal press vol
+
+variable STEP equal step
+variable TEMP equal temp
+## volume from cubic angstroms to cubic nm
+variable VOL equal vol/1000.0
+## pressure from atm to bar
+variable PRESS equal press*1.01325
+variable PXX equal pxx*1.01325
+variable PYY equal pyy*1.01325
+variable PZZ equal pzz*1.01325
+variable PXY equal pxy*1.01325
+variable PXZ equal pxz*1.01325
+variable PYZ equal pyz*1.01325
+## energy from kcal/mol to kJ/mol
+variable KE equal ke*4.184
+variable PE equal pe*4.184
+variable UVDW equal evdwl*4.184
+
+
+##### SPECIAL COMMANDS FOR FIX_BOCS #####
+# ID group-ID style_name thermostat T_init T_end T_couple barostat P_start P_end P_couple pmatch_basis avg_vol N_sites N_coeffs coeff1 coeff2
+fix 1 all bocs temp 300.0 300.0 100.0 cgiso 0.986 0.986 1000.0 analytic 66476.015 968 2 245030.10 8962.20
+
+# Report the modified pressure
+thermo_modify press 1_press
+
+
+
+## Uncomment to save some data from simulation to files
+#fix print_temp all print 500 "${STEP} ${TEMP}" file temp.dat screen no
+#fix print_vol all print 500 "${STEP} ${VOL}" file vol.dat screen no
+#fix print_press all print 500 "${STEP} ${PRESS}" file press.dat screen no
+#fix print_ke all print 500 "${STEP} ${KE}" file kinetic_E.dat screen no
+#fix print_pe all print 500 "${STEP} ${PE}" file potential_E.dat screen no
+#fix print_ve all print 500 "${STEP} ${UVDW}" file vdw_E.dat screen no
+#fix print_press_tens all print 500 "${STEP} ${PXX} ${PYY} ${PZZ} ${PXY} ${PXZ} ${PYZ}" file press_tens.dat screen no
+#fix print_PV_eos all print 500 "${VOL} ${PRESS}" file pv_eos.dat screen no
+
+## Prints a configuration to dump.txt every 500 steps
+#dump 1 all custom 500 dump.txt id type x y z fx fy fz
+
+# Write restart files to continue simulations
+#restart 10000 state1.restart state2.restart
+
+## Run for this many steps
+run_style verlet
+run 10000
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 10000, page size: 100000
+ master list distance cutoff = 24
+ ghost atom cutoff = 24
+ binsize = 12, bins = 4 4 4
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair table, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 4.691 | 4.691 | 4.691 Mbytes
+Step Temp PotEng TotEng Press Volume
+ 0 300 1061.5961 1926.3291 107.006 66250.679
+ 500 314.54728 1034.1091 1940.7738 194.42689 65660.282
+ 1000 301.41603 1030.7027 1899.5173 -91.966709 66262.543
+ 1500 298.8308 1014.8276 1876.1905 -80.178606 67053.605
+ 2000 294.78476 1046.8207 1896.521 50.592942 66316.735
+ 2500 301.18564 1033.9214 1902.0719 40.48255 66607.667
+ 3000 301.06632 1022.0381 1889.8447 47.582344 66341.947
+ 3500 297.98361 989.80983 1848.7307 -204.69879 67462.078
+ 4000 299.03493 1034.6571 1896.6083 89.188888 66457.385
+ 4500 306.03351 985.4121 1867.5363 -51.102407 67519.446
+ 5000 305.6903 1013.8613 1894.9963 -141.13704 67240.467
+ 5500 292.23444 1029.5558 1871.905 20.764579 66683.876
+ 6000 287.87735 1017.7325 1847.5226 -35.288049 66630.031
+ 6500 305.26461 960.08118 1839.9891 -352.42596 67612.317
+ 7000 300.34449 1055.0664 1920.7923 22.04027 66187.27
+ 7500 305.48612 1038.6651 1919.2115 17.807254 66324.168
+ 8000 316.03232 1034.6809 1945.6262 27.482857 66502.198
+ 8500 294.28636 1038.8213 1887.085 -72.840559 66851.661
+ 9000 316.69029 1065.7481 1978.5899 245.61677 65678.385
+ 9500 297.46127 1034.5547 1891.97 54.23428 66892.627
+ 10000 301.24799 1036.5432 1904.8735 7.7134029 66150.506
+Loop time of 34.426 on 1 procs for 10000 steps with 968 atoms
+
+Performance: 25.097 ns/day, 0.956 hours/ns, 290.478 timesteps/s
+99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 33.324 | 33.324 | 33.324 | 0.0 | 96.80
+Neigh | 0.12198 | 0.12198 | 0.12198 | 0.0 | 0.35
+Comm | 0.42865 | 0.42865 | 0.42865 | 0.0 | 1.25
+Output | 0.00059938 | 0.00059938 | 0.00059938 | 0.0 | 0.00
+Modify | 0.42553 | 0.42553 | 0.42553 | 0.0 | 1.24
+Other | | 0.1252 | | | 0.36
+
+Nlocal: 968 ave 968 max 968 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 9112 ave 9112 max 9112 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 404392 ave 404392 max 404392 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 404392
+Ave neighs/atom = 417.76
+Neighbor list builds = 13
+Dangerous builds = 0
+
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:34
diff --git a/examples/USER/bocs/log.20Apr18.methanol.g++.4 b/examples/USER/bocs/log.20Apr18.methanol.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..cf5891f97cbf6fee1cc998fb40fb4e8e7cb04a24
--- /dev/null
+++ b/examples/USER/bocs/log.20Apr18.methanol.g++.4
@@ -0,0 +1,143 @@
+LAMMPS (20 Apr 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+ using 1 OpenMP thread(s) per MPI task
+units real
+dimension 3
+boundary p p p
+atom_style atomic
+
+newton on
+timestep 1.0
+
+read_data methanol.data
+ orthogonal box = (0 0 0) to (40.4635 40.4635 40.4635)
+ 1 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 968 atoms
+
+velocity all create 300.0 16802 dist gaussian
+
+pair_style table spline 15000
+
+pair_coeff 1 1 lammps_nb_MET-MET.table nb_METMET 12.0
+WARNING: 78 of 2500 force values in table are inconsistent with -dE/dr.
+ Should only be flagged at inflection points (../pair_table.cpp:481)
+
+neigh_modify delay 0 every 1 check yes one 10000
+neighbor 12.0 bin
+
+thermo 500
+thermo_style custom step temp pe etotal press vol
+
+variable STEP equal step
+variable TEMP equal temp
+## volume from cubic angstroms to cubic nm
+variable VOL equal vol/1000.0
+## pressure from atm to bar
+variable PRESS equal press*1.01325
+variable PXX equal pxx*1.01325
+variable PYY equal pyy*1.01325
+variable PZZ equal pzz*1.01325
+variable PXY equal pxy*1.01325
+variable PXZ equal pxz*1.01325
+variable PYZ equal pyz*1.01325
+## energy from kcal/mol to kJ/mol
+variable KE equal ke*4.184
+variable PE equal pe*4.184
+variable UVDW equal evdwl*4.184
+
+
+##### SPECIAL COMMANDS FOR FIX_BOCS #####
+# ID group-ID style_name thermostat T_init T_end T_couple barostat P_start P_end P_couple pmatch_basis avg_vol N_sites N_coeffs coeff1 coeff2
+fix 1 all bocs temp 300.0 300.0 100.0 cgiso 0.986 0.986 1000.0 analytic 66476.015 968 2 245030.10 8962.20
+
+# Report the modified pressure
+thermo_modify press 1_press
+
+
+
+## Uncomment to save some data from simulation to files
+#fix print_temp all print 500 "${STEP} ${TEMP}" file temp.dat screen no
+#fix print_vol all print 500 "${STEP} ${VOL}" file vol.dat screen no
+#fix print_press all print 500 "${STEP} ${PRESS}" file press.dat screen no
+#fix print_ke all print 500 "${STEP} ${KE}" file kinetic_E.dat screen no
+#fix print_pe all print 500 "${STEP} ${PE}" file potential_E.dat screen no
+#fix print_ve all print 500 "${STEP} ${UVDW}" file vdw_E.dat screen no
+#fix print_press_tens all print 500 "${STEP} ${PXX} ${PYY} ${PZZ} ${PXY} ${PXZ} ${PYZ}" file press_tens.dat screen no
+#fix print_PV_eos all print 500 "${VOL} ${PRESS}" file pv_eos.dat screen no
+
+## Prints a configuration to dump.txt every 500 steps
+#dump 1 all custom 500 dump.txt id type x y z fx fy fz
+
+# Write restart files to continue simulations
+#restart 10000 state1.restart state2.restart
+
+## Run for this many steps
+run_style verlet
+run 10000
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 10000, page size: 100000
+ master list distance cutoff = 24
+ ghost atom cutoff = 24
+ binsize = 12, bins = 4 4 4
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair table, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.37 | 3.37 | 3.371 Mbytes
+Step Temp PotEng TotEng Press Volume
+ 0 300 1061.5961 1926.3291 107.006 66250.679
+ 500 314.54728 1034.1091 1940.7738 194.42689 65660.282
+ 1000 301.41603 1030.7027 1899.5173 -91.966709 66262.543
+ 1500 298.8308 1014.8276 1876.1905 -80.178606 67053.605
+ 2000 294.78476 1046.8207 1896.521 50.592942 66316.735
+ 2500 301.18564 1033.9214 1902.0719 40.482557 66607.667
+ 3000 301.06631 1022.0381 1889.8447 47.582403 66341.947
+ 3500 297.98353 989.81011 1848.7308 -204.69823 67462.076
+ 4000 299.03465 1034.6603 1896.6108 89.196235 66457.338
+ 4500 306.04532 985.37017 1867.5285 -51.094929 67519.735
+ 5000 304.72903 1014.9543 1893.3184 -127.04402 67238.517
+ 5500 292.52622 1025.6599 1868.8502 -19.753932 66716.551
+ 6000 296.82719 1031.5184 1887.1059 -1.2609328 66368.611
+ 6500 298.63312 1018.4299 1879.2229 -24.75835 66524.898
+ 7000 303.25389 1005.9283 1880.0404 -96.273504 67349.674
+ 7500 292.45089 1068.2863 1911.2595 103.23295 65778.08
+ 8000 301.22765 1040.6294 1908.9011 -0.83635353 66831.038
+ 8500 300.19765 1047.5856 1912.8883 -31.582343 66316.305
+ 9000 295.1108 1023.8234 1874.4635 -88.165532 67192.344
+ 9500 302.1087 1003.6348 1874.4459 -18.707065 66369.361
+ 10000 296.3083 1004.126 1858.2178 -28.293045 66862.576
+Loop time of 28.8053 on 4 procs for 10000 steps with 968 atoms
+
+Performance: 29.994 ns/day, 0.800 hours/ns, 347.159 timesteps/s
+95.2% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 19.929 | 21.765 | 23.391 | 27.8 | 75.56
+Neigh | 0.067397 | 0.071231 | 0.077313 | 1.5 | 0.25
+Comm | 3.9226 | 5.5183 | 7.3214 | 53.7 | 19.16
+Output | 0.00069928 | 0.0016099 | 0.0043275 | 3.9 | 0.01
+Modify | 1.0874 | 1.1376 | 1.1888 | 4.2 | 3.95
+Other | | 0.3112 | | | 1.08
+
+Nlocal: 242 ave 244 max 239 min
+Histogram: 1 0 0 0 0 0 1 0 1 1
+Nghost: 5718.5 ave 5736 max 5702 min
+Histogram: 1 0 0 0 1 1 0 0 0 1
+Neighs: 100703 ave 108064 max 93454 min
+Histogram: 1 0 0 1 0 0 1 0 0 1
+
+Total # of neighbors = 402813
+Ave neighs/atom = 416.129
+Neighbor list builds = 14
+Dangerous builds = 0
+
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:28
diff --git a/examples/USER/bocs/methanol.data b/examples/USER/bocs/methanol.data
new file mode 100644
index 0000000000000000000000000000000000000000..01f66de6f62294929f87497522ae541b567596a0
--- /dev/null
+++ b/examples/USER/bocs/methanol.data
@@ -0,0 +1,991 @@
+LAMMPS Description
+
+ 968 atoms
+ 0 bonds
+ 0 angles
+ 0 dihedrals
+ 0 impropers
+
+ 1 atom types
+ 0 bond types
+ 0 angle types
+ 0 dihedral types
+
+ 0 40.4635 xlo xhi
+ 0 40.4635 ylo yhi
+ 0 40.4635 zlo zhi
+
+Masses
+
+ 1 32.0424
+
+Atoms
+
+1 1 36.39 8.05 27.55
+2 1 18.38 15.72 26.03
+3 1 3.52 1.77 23.57
+4 1 31.09 11.38 12.17
+5 1 13.3 34.8 2.89
+6 1 1.72 38.55 10.36
+7 1 38.6 23.16 6.19
+8 1 0.74 33.21 0.17
+9 1 26.97 9.53 11.24
+10 1 31.68 12.19 17.04
+11 1 15.19 9.06 0.2
+12 1 34.39 20.63 35.71
+13 1 21.79 4.93 6.49
+14 1 28.08 33.01 24.51
+15 1 37.03 20.52 32.9
+16 1 32.69 20 30.11
+17 1 23.77 38.59 18.79
+18 1 16.01 2.31 20.15
+19 1 5.65 15.5 28.5
+20 1 8.35 17.35 20.48
+21 1 31.24 24.68 27.4
+22 1 29.41 16.64 19.79
+23 1 37.42 31.93 26.68
+24 1 18.76 39.06 30.68
+25 1 22.97 35 20.81
+26 1 39.47 18.28 29.6
+27 1 34.37 19.4 0.17
+28 1 5.94 9.53 10.95
+29 1 11.45 38.44 14.64
+30 1 39.57 11.04 1.57
+31 1 25.91 20.97 12.79
+32 1 36.3 22.1 1.68
+33 1 21.87 22.49 3.43
+34 1 5.77 18.66 3.97
+35 1 7 7.59 18.42
+36 1 39.76 27.63 17.98
+37 1 10.26 23.18 5.11
+38 1 23.23 21.37 17.38
+39 1 7.47 37.37 5.57
+40 1 0.73 21.6 14.78
+41 1 2.27 30.22 14.93
+42 1 7.39 28.22 14.88
+43 1 27.48 1.11 25.02
+44 1 8.37 13.19 14.64
+45 1 7.11 33.57 0.65
+46 1 34.19 35.11 3.17
+47 1 7.52 3.2 20.33
+48 1 1.02 17.69 37.85
+49 1 8.59 6.21 10.26
+50 1 2.89 16.81 30.02
+51 1 27.05 9.07 32.8
+52 1 12.32 14.79 21.11
+53 1 26.63 22.69 16.75
+54 1 31.6 2.79 20.45
+55 1 35.11 0.74 12.16
+56 1 29.71 31.23 37.63
+57 1 38.22 19.02 18.12
+58 1 10.95 17.4 0.39
+59 1 1.65 19.87 6.67
+60 1 5.15 1.94 14.61
+61 1 8.2 31.43 15.72
+62 1 0.55 20.85 2.45
+63 1 15.27 31.74 0.33
+64 1 17.9 9.84 23.87
+65 1 1.46 8.39 19.24
+66 1 37.79 25.11 12.24
+67 1 14.11 27.19 30.7
+68 1 29.39 24.12 38.92
+69 1 39.15 20.32 39.86
+70 1 11.79 11.38 30.6
+71 1 29.87 30.18 32.5
+72 1 11.06 37.8 30.18
+73 1 20.11 4.59 35.57
+74 1 37.19 27.23 1.44
+75 1 18.83 26.13 35.26
+76 1 29.27 7.86 36.75
+77 1 34.83 29.59 37.82
+78 1 22.16 34.68 25.27
+79 1 5.95 14.65 25.55
+80 1 -0.04 3.48 29.91
+81 1 14.69 6.75 38.06
+82 1 16.8 23.69 3.14
+83 1 14.52 38.72 21.61
+84 1 37.36 15.13 27.98
+85 1 29.79 17.03 27.55
+86 1 21.01 0.39 0.9
+87 1 35.3 6.45 14.41
+88 1 13.74 34.69 10.01
+89 1 13.83 7.92 31.88
+90 1 26.88 37.81 22.36
+91 1 31.76 7.34 10.03
+92 1 11.98 37.49 19.61
+93 1 29.19 31.74 20.69
+94 1 39.15 10.97 21.06
+95 1 1.47 5 22.21
+96 1 -0.1 1.33 16.26
+97 1 34.74 34.78 30.66
+98 1 22.09 26.78 2.27
+99 1 36.58 34.8 16.19
+100 1 19.09 24.88 15.75
+101 1 2.21 31.42 38.32
+102 1 28.02 8.18 29.77
+103 1 15.99 16.78 17.61
+104 1 32.43 12.2 35.3
+105 1 26.54 38.8 30.88
+106 1 35.58 22.23 18.31
+107 1 28.3 30.81 2.96
+108 1 8.95 32.9 9.02
+109 1 28.51 30.02 29.39
+110 1 13 5.35 34.26
+111 1 37.9 36.79 1.37
+112 1 12.78 1.99 40.66
+113 1 21.19 34.55 17.45
+114 1 10.5 20 5.07
+115 1 16.19 21.64 18.49
+116 1 14.62 26.41 19.88
+117 1 27.97 2.89 28.03
+118 1 29.44 14.35 39.04
+119 1 2.29 24.16 33.8
+120 1 39.22 15.81 32.02
+121 1 7.31 19.66 18.18
+122 1 27.67 7.98 15.53
+123 1 31.23 4.04 33
+124 1 29.52 39.44 28.71
+125 1 30.86 20.28 15.84
+126 1 32.25 7.44 19.79
+127 1 34.68 15.68 1.18
+128 1 16.58 27.98 27.97
+129 1 32.27 24.24 15.82
+130 1 3.86 6.57 39.8
+131 1 9.1 2.88 13.12
+132 1 17.84 27.8 11.79
+133 1 4.77 10.88 6.75
+134 1 16.58 24.21 24.5
+135 1 10.17 19.31 38.32
+136 1 6.27 7.81 36.44
+137 1 34.76 37.89 29.76
+138 1 40.99 38.22 35.21
+139 1 25.04 21.79 36.88
+140 1 4.78 15.35 16.44
+141 1 19.24 5.77 40.18
+142 1 13.59 11.27 37.14
+143 1 1.61 23.83 39.61
+144 1 6.02 33.07 3.77
+145 1 0.85 7.4 35.42
+146 1 6.47 40.34 4.65
+147 1 16.45 36.52 15.44
+148 1 19.58 9.5 1.64
+149 1 1.36 1.72 35.53
+150 1 11.74 5.48 4.98
+151 1 25.45 40.36 15.44
+152 1 19.09 0.74 36.18
+153 1 31.78 37.98 1.84
+154 1 23.26 18.47 38.56
+155 1 7.29 22.87 25.86
+156 1 2.36 7.83 8.78
+157 1 39.61 25.94 21.12
+158 1 7.78 18.97 25.29
+159 1 36.56 19.61 26.7
+160 1 4.64 12.06 19.9
+161 1 21.05 33.08 0.87
+162 1 33.93 22.87 39.71
+163 1 33.62 29.48 20.83
+164 1 0.64 18.79 9.52
+165 1 27.53 16.7 22.51
+166 1 17.66 9.84 14.61
+167 1 31.23 22.44 24.98
+168 1 39.3 34.88 11.03
+169 1 24.01 10.56 0.09
+170 1 15.81 33.44 18.52
+171 1 19.92 30.61 19.25
+172 1 16.49 3.95 38.28
+173 1 18.6 38.87 24.98
+174 1 33.04 25.55 8.57
+175 1 16.9 35.09 22.94
+176 1 15.18 6.74 2.33
+177 1 40.54 12.58 31.65
+178 1 21.21 37.62 14.35
+179 1 33.52 38.19 14.89
+180 1 22.06 12.49 29.81
+181 1 19.49 29.03 2.52
+182 1 26.97 18.55 38.45
+183 1 24.1 11.86 17.22
+184 1 12.02 0.55 10.39
+185 1 3.8 35.94 19.94
+186 1 8.31 14.31 37.4
+187 1 29.03 8.28 22.92
+188 1 18.92 0.22 27.87
+189 1 26.79 24.9 24.62
+190 1 36.59 18.86 21.13
+191 1 33.06 13.58 30.17
+192 1 32.37 2.02 39.69
+193 1 22.65 25.97 32.59
+194 1 21.81 38.04 33.85
+195 1 36.82 37.68 19.22
+196 1 32.48 31.43 33.66
+197 1 8.75 36.66 20.34
+198 1 14.88 15.11 28.76
+199 1 22.83 28.55 29.5
+200 1 2.98 12.06 2.88
+201 1 3.01 37 6.91
+202 1 14.79 16.69 3.66
+203 1 12.62 38.28 0.97
+204 1 40.07 21.27 25.25
+205 1 34.58 6.14 39.48
+206 1 11.51 30.52 33.53
+207 1 32.22 9.28 30.52
+208 1 0.7 4.01 38.87
+209 1 32.66 39.86 36.84
+210 1 27.34 34.57 21.76
+211 1 13.7 23.12 8.34
+212 1 28 9.71 6.29
+213 1 31.69 26.39 38.19
+214 1 2.04 20.93 36.95
+215 1 30.31 26.61 12.31
+216 1 25.37 20.63 9.4
+217 1 16.29 5.62 14.04
+218 1 1.36 1.95 4.97
+219 1 38.75 26.8 5.62
+220 1 40.28 29.89 12.27
+221 1 0.52 31.22 7.58
+222 1 15.64 21.64 14.71
+223 1 10.11 28.8 9.67
+224 1 19.03 37.3 38.87
+225 1 12.07 6.46 19.25
+226 1 36.22 21.11 15.02
+227 1 12.49 15.69 7.21
+228 1 25.2 30.8 19.71
+229 1 8.24 35.22 23.02
+230 1 9.94 4.1 1.86
+231 1 4.31 19.07 26.23
+232 1 22.03 19.99 14.19
+233 1 30.84 5.24 2.75
+234 1 35.51 30.52 32.3
+235 1 3.88 20.41 39.48
+236 1 30.86 0.39 31.56
+237 1 25.91 27.12 39.04
+238 1 33.39 5.37 4.51
+239 1 20.58 28.33 37.53
+240 1 11.83 21.81 39.11
+241 1 39.94 5.2 5.73
+242 1 29.89 33.21 15.44
+243 1 23.42 15.38 30.98
+244 1 28.66 11.56 16.13
+245 1 16.74 20.43 21.72
+246 1 9.31 0.26 22.42
+247 1 4.38 37.78 14.12
+248 1 13.86 4.65 16.99
+249 1 6.72 27.43 8.14
+250 1 33.45 18.74 19.98
+251 1 17.34 14.55 35.57
+252 1 14.21 37.39 28.76
+253 1 26.29 29.06 22.26
+254 1 36.52 26.18 15.62
+255 1 17.6 8.81 10.14
+256 1 21.95 25.19 17.69
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+839 1 16.12 23.66 38.29
+840 1 8.67 4.79 31.8
+841 1 27.82 0.02 20.45
+842 1 4.46 2.44 29.46
+843 1 39.11 22.69 36.33
+844 1 4.26 2.45 34.43
+845 1 13.47 3.5 30.9
+846 1 26.92 22.55 26.54
+847 1 5.66 30.07 30.65
+848 1 31.58 35.68 25.46
+849 1 31.23 5.65 27.78
+850 1 8.76 19.49 28.61
+851 1 24.13 8.02 2.3
+852 1 8.27 6.8 4.93
+853 1 15.31 34.36 37.63
+854 1 3.96 35.82 26.97
+855 1 24.95 4.01 29.96
+856 1 26.54 25.95 19.15
+857 1 17.76 29.23 5.35
+858 1 16.95 21.79 0.78
+859 1 17.52 39.02 13.01
+860 1 20.5 22.86 10.41
+861 1 27.67 27.07 2.78
+862 1 37.1 31.02 2.03
+863 1 37.17 2.24 16.34
+864 1 24.51 34.69 10.28
+865 1 17.38 13.41 21.4
+866 1 38 9.37 17.94
+867 1 35.67 25.27 5.3
+868 1 22.66 4.47 0.97
+869 1 20.06 28.17 27.42
+870 1 27.33 2.38 9.79
+871 1 36.4 10.73 31.42
+872 1 0.53 9.45 6.96
+873 1 12.89 9.03 25.13
+874 1 37.5 23.54 21.33
+875 1 7.19 28.87 19.11
+876 1 21.45 32.81 22.71
+877 1 8.76 8.3 13.51
+878 1 10.24 31.46 3.73
+879 1 15.93 9.7 35.82
+880 1 14.92 19.46 39.91
+881 1 13.02 22.03 27.3
+882 1 34.57 1.59 34.73
+883 1 0.5 21.04 30.77
+884 1 24.84 32.67 4.97
+885 1 30.96 4.24 17.34
+886 1 23.63 8.84 32.7
+887 1 6.84 3.83 26.13
+888 1 31.57 9.23 27.06
+889 1 14.99 35.15 0.07
+890 1 36.29 40.01 8.22
+891 1 18 36.86 35.66
+892 1 11.5 29.22 0.37
+893 1 35.18 36.03 24.88
+894 1 14.49 9.41 27.73
+895 1 10.12 12.91 0.99
+896 1 11.91 29.4 27.3
+897 1 25.51 28.68 14.56
+898 1 29.32 12.95 35.59
+899 1 2.96 0.59 0.53
+900 1 5.47 5.35 9.88
+901 1 8.93 39.33 1.78
+902 1 39.68 38.49 12.33
+903 1 3.78 1.24 11.85
+904 1 29.54 33.76 11.99
+905 1 7.48 6.16 28.8
+906 1 10.83 33.63 36.96
+907 1 22.03 19.06 21.39
+908 1 31.68 31 3.71
+909 1 35.32 0.3 30.88
+910 1 9.93 35.42 14.85
+911 1 21.01 10.66 12.97
+912 1 22.54 21.62 33.81
+913 1 12.48 12.46 25.15
+914 1 0.64 27.93 39.01
+915 1 13.88 27.29 3.8
+916 1 13.03 20.93 19.25
+917 1 5.7 37.48 34.09
+918 1 2.27 35.08 14.29
+919 1 21.75 26.44 13.48
+920 1 10.66 11.35 17.49
+921 1 36.67 34.72 27.69
+922 1 8.23 22.8 33.36
+923 1 4.79 4.05 3.48
+924 1 35.61 35 35.21
+925 1 31.38 37.67 10.06
+926 1 26.44 35.58 27.52
+927 1 25.53 4.47 8.03
+928 1 38.81 33.08 31.55
+929 1 29.62 39.68 34.32
+930 1 0.76 3.88 10.61
+931 1 24.06 30.13 24.84
+932 1 18.77 8.38 37.02
+933 1 2.81 24.14 24.45
+934 1 11.33 1.25 19.69
+935 1 1.61 26.53 6.48
+936 1 9.52 29.81 35.98
+937 1 7.83 31.75 20.77
+938 1 9.67 23.93 20.57
+939 1 33.96 16.95 24.79
+940 1 37.55 37.31 37.17
+941 1 6.2 24.19 31.13
+942 1 17.79 4.35 30.56
+943 1 13.51 20.25 30.45
+944 1 14.76 12.48 13.13
+945 1 32.56 27.52 30.41
+946 1 35.81 40.1 4.85
+947 1 39.01 25.43 27.07
+948 1 22.8 5.53 32.22
+949 1 2.35 39.55 32.5
+950 1 3.31 31.51 34.19
+951 1 40.63 37.01 15.9
+952 1 18.43 35.86 30.77
+953 1 37.01 39.18 15.57
+954 1 6.74 6.26 21.64
+955 1 5.22 24.94 22.53
+956 1 25.2 11.08 13.98
+957 1 14.66 -0.14 5
+958 1 14.96 8.38 20.32
+959 1 1.89 23.03 10.1
+960 1 33.01 11.23 39.32
+961 1 32.68 6.79 32.04
+962 1 6.25 25.81 3.82
+963 1 18.37 31.97 14.57
+964 1 9.74 30.21 22.71
+965 1 3.09 1.52 19.38
+966 1 33.98 37.34 5.63
+967 1 32.19 28.35 15.8
+968 1 24.4 15.49 19.39
diff --git a/examples/USER/misc/bond_react/nylon,6-6_melt/in.large_nylon_melt b/examples/USER/misc/bond_react/nylon,6-6_melt/in.large_nylon_melt
new file mode 100644
index 0000000000000000000000000000000000000000..f2dc506ddef28d978d48eb90569302e0de27124b
--- /dev/null
+++ b/examples/USER/misc/bond_react/nylon,6-6_melt/in.large_nylon_melt
@@ -0,0 +1,52 @@
+# 35,000 atom nylon melt example
+
+units real
+
+boundary p p p
+
+atom_style full
+
+kspace_style pppm 1.0e-4
+
+pair_style lj/class2/coul/long 8.5
+
+angle_style class2
+
+bond_style class2
+
+dihedral_style class2
+
+improper_style class2
+
+read_data large_nylon_melt.data.gz
+
+velocity all create 800.0 4928459 dist gaussian
+
+molecule mol1 rxn1_stp1_unreacted.data_template
+molecule mol2 rxn1_stp1_reacted.data_template
+molecule mol3 rxn1_stp2_unreacted.data_template
+molecule mol4 rxn1_stp2_reacted.data_template
+
+thermo 50
+
+# dump 1 all xyz 100 test_vis.xyz
+
+fix myrxns all bond/react stabilization yes statted_grp .03 &
+ react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map &
+ react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
+
+# stable at 800K
+fix 1 statted_grp nvt temp 800 800 100
+
+# in order to customize behavior of reacting atoms,
+# you can use the internally created 'bond_react_MASTER_group', like so:
+# fix 2 bond_react_MASTER_group temp/rescale 1 800 800 10 1
+
+thermo_style custom step temp press density f_myrxns[1] f_myrxns[2] # cumulative reaction counts
+
+# restart 100 restart1 restart2
+
+run 200
+
+# write_restart restart_longrun
+# write_data restart_longrun.data
diff --git a/examples/USER/misc/bond_react/nylon,6-6_melt/large_nylon_melt.data.gz b/examples/USER/misc/bond_react/nylon,6-6_melt/large_nylon_melt.data.gz
new file mode 100644
index 0000000000000000000000000000000000000000..c620b879a883817b8eb7abe4495e585ecacfaf02
Binary files /dev/null and b/examples/USER/misc/bond_react/nylon,6-6_melt/large_nylon_melt.data.gz differ
diff --git a/examples/USER/misc/bond_react/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.1 b/examples/USER/misc/bond_react/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..653c7582f8d7aba4c8800e5fcfff5ebb22d44a15
--- /dev/null
+++ b/examples/USER/misc/bond_react/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.1
@@ -0,0 +1,175 @@
+LAMMPS (20 Apr 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+ using 1 OpenMP thread(s) per MPI task
+# 35,000 atom nylon melt example
+
+units real
+
+boundary p p p
+
+atom_style full
+
+kspace_style pppm 1.0e-4
+
+pair_style lj/class2/coul/long 8.5
+
+angle_style class2
+
+bond_style class2
+
+dihedral_style class2
+
+improper_style class2
+
+read_data large_nylon_melt.data.gz
+ orthogonal box = (-2.68344 -2.06791 -2.21988) to (73.4552 73.2448 73.4065)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 35200 atoms
+ reading velocities ...
+ 35200 velocities
+ scanning bonds ...
+ 9 = max bonds/atom
+ scanning angles ...
+ 21 = max angles/atom
+ scanning dihedrals ...
+ 31 = max dihedrals/atom
+ scanning impropers ...
+ 29 = max impropers/atom
+ reading bonds ...
+ 33600 bonds
+ reading angles ...
+ 59200 angles
+ reading dihedrals ...
+ 80000 dihedrals
+ reading impropers ...
+ 35200 impropers
+ 4 = max # of 1-2 neighbors
+ 6 = max # of 1-3 neighbors
+ 12 = max # of 1-4 neighbors
+ 41 = max # of special neighbors
+
+velocity all create 800.0 4928459 dist gaussian
+
+molecule mol1 rxn1_stp1_unreacted.data_template
+Read molecule mol1:
+ 18 atoms with max type 8
+ 16 bonds with max type 12
+ 25 angles with max type 24
+ 23 dihedrals with max type 33
+ 14 impropers with max type 9
+molecule mol2 rxn1_stp1_reacted.data_template
+Read molecule mol2:
+ 18 atoms with max type 9
+ 17 bonds with max type 11
+ 31 angles with max type 23
+ 39 dihedrals with max type 30
+ 20 impropers with max type 1
+molecule mol3 rxn1_stp2_unreacted.data_template
+Read molecule mol3:
+ 15 atoms with max type 9
+ 14 bonds with max type 11
+ 25 angles with max type 23
+ 30 dihedrals with max type 30
+ 16 impropers with max type 1
+molecule mol4 rxn1_stp2_reacted.data_template
+Read molecule mol4:
+ 15 atoms with max type 11
+ 13 bonds with max type 13
+ 19 angles with max type 25
+ 16 dihedrals with max type 29
+ 10 impropers with max type 11
+
+thermo 50
+
+# dump 1 all xyz 100 test_vis.xyz
+
+fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
+WARNING: An atom in 'react #1' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489)
+WARNING: An atom in 'react #2' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489)
+dynamic group bond_react_MASTER_group defined
+dynamic group statted_grp defined
+dynamic group bond_react_MASTER_group defined
+dynamic group statted_grp defined
+
+# stable at 800K
+fix 1 statted_grp nvt temp 800 800 100
+
+# in order to customize behavior of reacting atoms,
+# you can use the internally created 'bond_react_MASTER_group', like so:
+# fix 2 bond_react_MASTER_group temp/rescale 1 800 800 10 1
+
+thermo_style custom step temp press density f_myrxns[1] f_myrxns[2] # cumulative reaction counts
+
+# restart 100 restart1 restart2
+
+run 200
+PPPM initialization ...
+ using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+ G vector (1/distance) = 0.20765
+ grid = 18 18 18
+ stencil order = 5
+ estimated absolute RMS force accuracy = 0.0333156
+ estimated relative force accuracy = 0.000100329
+ using double precision FFTs
+ 3d grid and FFT values/proc = 12167 5832
+Neighbor list info ...
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 10.5
+ ghost atom cutoff = 10.5
+ binsize = 5.25, bins = 15 15 15
+ 2 neighbor lists, perpetual/occasional/extra = 1 1 0
+ (1) pair lj/class2/coul/long, perpetual
+ attributes: half, newton on
+ pair build: half/bin/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+ (2) fix bond/react, occasional, copy from (1)
+ attributes: half, newton on
+ pair build: copy
+ stencil: none
+ bin: none
+Per MPI rank memory allocation (min/avg/max) = 209.1 | 209.1 | 209.1 Mbytes
+Step Temp Press Density f_myrxns[1] f_myrxns[2]
+ 0 800 3666.3948 0.80366765 0 0
+ 50 673.95238 -9670.9169 0.80366765 31 0
+ 100 697.22819 -4624.0512 0.80366765 57 22
+ 150 723.60507 -17175.571 0.80366765 76 48
+ 200 736.71277 -12961.963 0.80366765 84 64
+Loop time of 102.825 on 1 procs for 200 steps with 35200 atoms
+
+Performance: 0.168 ns/day, 142.812 hours/ns, 1.945 timesteps/s
+99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 27.193 | 27.193 | 27.193 | 0.0 | 26.45
+Bond | 11.324 | 11.324 | 11.324 | 0.0 | 11.01
+Kspace | 4.1878 | 4.1878 | 4.1878 | 0.0 | 4.07
+Neigh | 54.724 | 54.724 | 54.724 | 0.0 | 53.22
+Comm | 0.40662 | 0.40662 | 0.40662 | 0.0 | 0.40
+Output | 0.0011101 | 0.0011101 | 0.0011101 | 0.0 | 0.00
+Modify | 4.9422 | 4.9422 | 4.9422 | 0.0 | 4.81
+Other | | 0.04545 | | | 0.04
+
+Nlocal: 35200 ave 35200 max 35200 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 38403 ave 38403 max 38403 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 6.9281e+06 ave 6.9281e+06 max 6.9281e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 6928101
+Ave neighs/atom = 196.821
+Ave special neighs/atom = 9.83727
+Neighbor list builds = 200
+Dangerous builds = 0
+
+# write_restart restart_longrun
+# write_data restart_longrun.data
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:01:43
diff --git a/examples/USER/misc/bond_react/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.4 b/examples/USER/misc/bond_react/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..cc0dda60c7dcec4b775d0d5cd6cdad4f6b751124
--- /dev/null
+++ b/examples/USER/misc/bond_react/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.4
@@ -0,0 +1,175 @@
+LAMMPS (20 Apr 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+ using 1 OpenMP thread(s) per MPI task
+# 35,000 atom nylon melt example
+
+units real
+
+boundary p p p
+
+atom_style full
+
+kspace_style pppm 1.0e-4
+
+pair_style lj/class2/coul/long 8.5
+
+angle_style class2
+
+bond_style class2
+
+dihedral_style class2
+
+improper_style class2
+
+read_data large_nylon_melt.data.gz
+ orthogonal box = (-2.68344 -2.06791 -2.21988) to (73.4552 73.2448 73.4065)
+ 2 by 1 by 2 MPI processor grid
+ reading atoms ...
+ 35200 atoms
+ reading velocities ...
+ 35200 velocities
+ scanning bonds ...
+ 9 = max bonds/atom
+ scanning angles ...
+ 21 = max angles/atom
+ scanning dihedrals ...
+ 31 = max dihedrals/atom
+ scanning impropers ...
+ 29 = max impropers/atom
+ reading bonds ...
+ 33600 bonds
+ reading angles ...
+ 59200 angles
+ reading dihedrals ...
+ 80000 dihedrals
+ reading impropers ...
+ 35200 impropers
+ 4 = max # of 1-2 neighbors
+ 6 = max # of 1-3 neighbors
+ 12 = max # of 1-4 neighbors
+ 41 = max # of special neighbors
+
+velocity all create 800.0 4928459 dist gaussian
+
+molecule mol1 rxn1_stp1_unreacted.data_template
+Read molecule mol1:
+ 18 atoms with max type 8
+ 16 bonds with max type 12
+ 25 angles with max type 24
+ 23 dihedrals with max type 33
+ 14 impropers with max type 9
+molecule mol2 rxn1_stp1_reacted.data_template
+Read molecule mol2:
+ 18 atoms with max type 9
+ 17 bonds with max type 11
+ 31 angles with max type 23
+ 39 dihedrals with max type 30
+ 20 impropers with max type 1
+molecule mol3 rxn1_stp2_unreacted.data_template
+Read molecule mol3:
+ 15 atoms with max type 9
+ 14 bonds with max type 11
+ 25 angles with max type 23
+ 30 dihedrals with max type 30
+ 16 impropers with max type 1
+molecule mol4 rxn1_stp2_reacted.data_template
+Read molecule mol4:
+ 15 atoms with max type 11
+ 13 bonds with max type 13
+ 19 angles with max type 25
+ 16 dihedrals with max type 29
+ 10 impropers with max type 11
+
+thermo 50
+
+# dump 1 all xyz 100 test_vis.xyz
+
+fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
+WARNING: An atom in 'react #1' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489)
+WARNING: An atom in 'react #2' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489)
+dynamic group bond_react_MASTER_group defined
+dynamic group statted_grp defined
+dynamic group bond_react_MASTER_group defined
+dynamic group statted_grp defined
+
+# stable at 800K
+fix 1 statted_grp nvt temp 800 800 100
+
+# in order to customize behavior of reacting atoms,
+# you can use the internally created 'bond_react_MASTER_group', like so:
+# fix 2 bond_react_MASTER_group temp/rescale 1 800 800 10 1
+
+thermo_style custom step temp press density f_myrxns[1] f_myrxns[2] # cumulative reaction counts
+
+# restart 100 restart1 restart2
+
+run 200
+PPPM initialization ...
+ using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+ G vector (1/distance) = 0.20765
+ grid = 18 18 18
+ stencil order = 5
+ estimated absolute RMS force accuracy = 0.0333156
+ estimated relative force accuracy = 0.000100329
+ using double precision FFTs
+ 3d grid and FFT values/proc = 4508 1620
+Neighbor list info ...
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 10.5
+ ghost atom cutoff = 10.5
+ binsize = 5.25, bins = 15 15 15
+ 2 neighbor lists, perpetual/occasional/extra = 1 1 0
+ (1) pair lj/class2/coul/long, perpetual
+ attributes: half, newton on
+ pair build: half/bin/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+ (2) fix bond/react, occasional, copy from (1)
+ attributes: half, newton on
+ pair build: copy
+ stencil: none
+ bin: none
+Per MPI rank memory allocation (min/avg/max) = 81.11 | 81.13 | 81.15 Mbytes
+Step Temp Press Density f_myrxns[1] f_myrxns[2]
+ 0 800 3666.3948 0.80366765 0 0
+ 50 673.95238 -9670.9169 0.80366765 31 0
+ 100 697.22819 -4624.0512 0.80366765 57 22
+ 150 724.40407 -17166.729 0.80366765 76 49
+ 200 737.28582 -12968.224 0.80366765 84 65
+Loop time of 51.171 on 4 procs for 200 steps with 35200 atoms
+
+Performance: 0.338 ns/day, 71.071 hours/ns, 3.908 timesteps/s
+98.4% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 12.926 | 13.247 | 13.493 | 6.7 | 25.89
+Bond | 5.2132 | 5.2733 | 5.3367 | 1.9 | 10.31
+Kspace | 2.3601 | 2.6534 | 3.0067 | 16.0 | 5.19
+Neigh | 25.93 | 25.934 | 25.937 | 0.1 | 50.68
+Comm | 0.73273 | 0.75464 | 0.78505 | 2.3 | 1.47
+Output | 0.00045228 | 0.00067407 | 0.0013323 | 0.0 | 0.00
+Modify | 3.2682 | 3.2686 | 3.2692 | 0.0 | 6.39
+Other | | 0.03995 | | | 0.08
+
+Nlocal: 8800 ave 8913 max 8652 min
+Histogram: 1 0 0 0 1 0 0 0 1 1
+Nghost: 18366 ave 18461 max 18190 min
+Histogram: 1 0 0 0 0 0 0 1 1 1
+Neighs: 1.73203e+06 ave 1.77261e+06 max 1.68165e+06 min
+Histogram: 1 0 1 0 0 0 0 0 0 2
+
+Total # of neighbors = 6928132
+Ave neighs/atom = 196.822
+Ave special neighs/atom = 9.83608
+Neighbor list builds = 200
+Dangerous builds = 0
+
+# write_restart restart_longrun
+# write_data restart_longrun.data
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:52
diff --git a/examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp1_map b/examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp1_map
new file mode 100644
index 0000000000000000000000000000000000000000..44f7ad8137549eaa375046e114c59a7aa09c0c65
--- /dev/null
+++ b/examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp1_map
@@ -0,0 +1,35 @@
+this is a nominal superimpose file
+
+2 edgeIDs
+18 equivalences
+
+BondingIDs
+
+10
+1
+
+EdgeIDs
+
+16
+8
+
+Equivalences
+
+1 1
+2 2
+3 3
+4 4
+5 5
+6 6
+7 7
+8 8
+9 9
+10 10
+11 11
+12 12
+13 13
+14 14
+15 15
+16 16
+17 17
+18 18
diff --git a/examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp1_reacted.data_template b/examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp1_reacted.data_template
new file mode 100644
index 0000000000000000000000000000000000000000..61c0408ce3e57955e736d15e77736b95dccf240b
--- /dev/null
+++ b/examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp1_reacted.data_template
@@ -0,0 +1,189 @@
+this is a molecule template for: initial nylon crosslink, post-reacting
+
+18 atoms
+17 bonds
+31 angles
+39 dihedrals
+20 impropers
+
+Types
+
+1 9
+2 1
+3 1
+4 4
+5 4
+6 3
+7 3
+8 1
+9 1
+10 5
+11 8
+12 6
+13 3
+14 3
+15 7
+16 1
+17 3
+18 3
+
+Charges
+
+1 -0.300000
+2 0.000000
+3 0.000000
+4 0.000000
+5 0.000000
+6 0.000000
+7 0.000000
+8 0.000000
+9 0.000000
+10 0.300000
+11 0.000000
+12 0.000000
+13 0.000000
+14 0.000000
+15 0.000000
+16 0.000000
+17 0.000000
+18 0.000000
+
+Coords
+
+1 -5.522237 -0.752722 1.631158
+2 -5.170398 -0.545733 0.178130
+3 -6.469695 -0.553072 -0.648889
+4 -6.052076 -1.721152 1.744648
+5 -6.183059 0.071387 1.971497
+6 -4.489340 -1.389197 -0.173156
+7 -4.637591 0.453703 0.051252
+8 -5.618658 0.138919 4.386107
+9 -4.669492 -0.989819 3.943591
+10 -4.270194 -0.766405 2.474102
+11 -3.348470 -1.875393 2.024289
+12 -3.569794 0.564183 2.345995
+13 -5.201079 -1.993301 4.044219
+14 -3.736682 -0.984819 4.598305
+15 -4.255402 1.370923 2.679069
+16 -6.136394 -0.339866 -2.136775
+17 -6.996331 -1.555519 -0.517408
+18 -7.153308 0.284949 -0.289930
+
+Bonds
+
+1 9 1 2
+2 10 1 4
+3 10 1 5
+4 11 1 10
+5 1 2 3
+6 2 2 6
+7 2 2 7
+8 1 3 16
+9 2 3 17
+10 2 3 18
+11 1 8 9
+12 6 9 10
+13 2 9 13
+14 2 9 14
+15 7 10 11
+16 5 10 12
+17 8 12 15
+
+Angles
+
+1 14 2 1 4
+2 14 2 1 5
+3 15 2 1 10
+4 16 4 1 5
+5 17 4 1 10
+6 17 5 1 10
+7 18 1 2 3
+8 19 1 2 6
+9 19 1 2 7
+10 1 3 2 6
+11 1 3 2 7
+12 3 6 2 7
+13 2 2 3 16
+14 1 2 3 17
+15 1 2 3 18
+16 1 16 3 17
+17 1 16 3 18
+18 3 17 3 18
+19 12 8 9 10
+20 1 8 9 13
+21 1 8 9 14
+22 13 13 9 10
+23 13 14 9 10
+24 3 13 9 14
+25 10 9 10 11
+26 8 9 10 12
+27 20 1 10 9
+28 21 11 10 12
+29 22 1 10 11
+30 23 1 10 12
+31 11 10 12 15
+
+Dihedrals
+
+1 16 4 1 2 3
+2 17 4 1 2 6
+3 17 4 1 2 7
+4 16 5 1 2 3
+5 17 5 1 2 6
+6 17 5 1 2 7
+7 18 10 1 2 3
+8 19 10 1 2 6
+9 19 10 1 2 7
+10 20 2 1 10 9
+11 21 2 1 10 11
+12 22 2 1 10 12
+13 23 4 1 10 9
+14 24 4 1 10 11
+15 25 4 1 10 12
+16 23 5 1 10 9
+17 24 5 1 10 11
+18 25 5 1 10 12
+19 26 1 2 3 16
+20 27 1 2 3 17
+21 27 1 2 3 18
+22 4 16 3 2 6
+23 2 6 2 3 17
+24 2 6 2 3 18
+25 4 16 3 2 7
+26 2 7 2 3 17
+27 2 7 2 3 18
+28 14 8 9 10 11
+29 12 8 9 10 12
+30 28 8 9 10 1
+31 15 13 9 10 11
+32 13 13 9 10 12
+33 29 13 9 10 1
+34 15 14 9 10 11
+35 13 14 9 10 12
+36 29 14 9 10 1
+37 10 9 10 12 15
+38 11 11 10 12 15
+39 30 1 10 12 15
+
+Impropers
+
+1 1 2 1 4 5
+2 1 2 1 4 10
+3 1 2 1 5 10
+4 1 4 1 5 10
+5 1 1 2 3 6
+6 1 1 2 3 7
+7 1 1 2 6 7
+8 1 3 2 6 7
+9 1 2 3 16 17
+10 1 2 3 16 18
+11 1 2 3 17 18
+12 1 16 3 17 18
+13 1 8 9 13 10
+14 1 8 9 14 10
+15 1 8 9 13 14
+16 1 13 9 14 10
+17 1 9 10 11 12
+18 1 1 10 9 11
+19 1 1 10 9 12
+20 1 1 10 11 12
diff --git a/examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp1_unreacted.data_template b/examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp1_unreacted.data_template
new file mode 100644
index 0000000000000000000000000000000000000000..944d6918c57e77d2d96b3a949efac38cfce1c5f6
--- /dev/null
+++ b/examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp1_unreacted.data_template
@@ -0,0 +1,160 @@
+this is a molecule template for: initial nylon crosslink, pre-reacting
+
+18 atoms
+16 bonds
+25 angles
+23 dihedrals
+14 impropers
+
+Types
+
+1 2
+2 1
+3 1
+4 4
+5 4
+6 3
+7 3
+8 1
+9 1
+10 5
+11 8
+12 6
+13 3
+14 3
+15 7
+16 1
+17 3
+18 3
+
+Charges
+
+1 -0.300000
+2 0.000000
+3 0.000000
+4 0.000000
+5 0.000000
+6 0.000000
+7 0.000000
+8 0.000000
+9 0.000000
+10 0.300000
+11 0.000000
+12 0.000000
+13 0.000000
+14 0.000000
+15 0.000000
+16 0.000000
+17 0.000000
+18 0.000000
+
+Coords
+
+1 -4.922858 -0.946982 1.146055
+2 -5.047195 -0.935267 -0.358173
+3 -6.526281 -0.755366 -0.743523
+4 -5.282604 0.020447 1.552710
+5 -3.860697 -1.095850 1.428305
+6 -4.662382 -1.920900 -0.781524
+7 -4.433977 -0.072765 -0.784071
+8 -5.506279 0.202610 4.825816
+9 -4.449177 -0.844592 4.423366
+10 -4.103916 -0.749629 2.925195
+11 -3.376249 -1.886171 2.245643
+12 -4.493235 0.477214 2.137199
+13 -4.849053 -1.888877 4.663994
+14 -3.491823 -0.662913 5.018510
+15 -5.020777 1.189745 2.805427
+16 -3.964987 2.900602 -1.551341
+17 -4.460694 2.836102 0.668882
+18 -4.828494 3.219656 -0.122111
+
+Bonds
+
+1 12 1 2
+2 4 1 4
+3 4 1 5
+4 1 2 3
+5 2 2 6
+6 2 2 7
+7 1 3 16
+8 2 3 17
+9 2 3 18
+10 1 8 9
+11 6 9 10
+12 2 9 13
+13 2 9 14
+14 7 10 11
+15 5 10 12
+16 8 12 15
+
+Angles
+
+1 6 2 1 4
+2 6 2 1 5
+3 7 4 1 5
+4 24 1 2 3
+5 5 1 2 6
+6 5 1 2 7
+7 1 3 2 6
+8 1 3 2 7
+9 3 6 2 7
+10 2 2 3 16
+11 1 2 3 17
+12 1 2 3 18
+13 1 16 3 17
+14 1 16 3 18
+15 3 17 3 18
+16 12 8 9 10
+17 1 8 9 13
+18 1 8 9 14
+19 13 13 9 10
+20 13 14 9 10
+21 3 13 9 14
+22 10 9 10 11
+23 8 9 10 12
+24 21 11 10 12
+25 11 10 12 15
+
+Dihedrals
+
+1 31 4 1 2 3
+2 32 4 1 2 6
+3 32 4 1 2 7
+4 31 5 1 2 3
+5 32 5 1 2 6
+6 32 5 1 2 7
+7 33 1 2 3 16
+8 1 1 2 3 17
+9 1 1 2 3 18
+10 4 16 3 2 6
+11 2 6 2 3 17
+12 2 6 2 3 18
+13 4 16 3 2 7
+14 2 7 2 3 17
+15 2 7 2 3 18
+16 14 8 9 10 11
+17 12 8 9 10 12
+18 15 13 9 10 11
+19 13 13 9 10 12
+20 15 14 9 10 11
+21 13 14 9 10 12
+22 10 9 10 12 15
+23 11 11 10 12 15
+
+Impropers
+
+1 1 2 1 4 5
+2 9 9 10 11 12
+3 1 1 2 3 6
+4 1 1 2 3 7
+5 1 1 2 6 7
+6 1 3 2 6 7
+7 1 2 3 16 17
+8 1 2 3 16 18
+9 1 2 3 17 18
+10 1 16 3 17 18
+11 1 8 9 13 10
+12 1 8 9 14 10
+13 1 8 9 13 14
+14 1 13 9 14 10
diff --git a/examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp2_map b/examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp2_map
new file mode 100644
index 0000000000000000000000000000000000000000..35fe47fdb3bdb0386d65b950d45cbfb39fbe6f7f
--- /dev/null
+++ b/examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp2_map
@@ -0,0 +1,32 @@
+this is a nominal superimpose file
+
+2 edgeIDs
+15 equivalences
+
+BondingIDs
+
+4
+12
+
+EdgeIDs
+
+8
+3
+
+Equivalences
+
+1 1
+2 2
+3 3
+4 4
+5 5
+6 6
+7 7
+8 8
+9 9
+10 10
+11 11
+12 12
+13 13
+14 14
+15 15
diff --git a/examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp2_reacted.data_template b/examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp2_reacted.data_template
new file mode 100644
index 0000000000000000000000000000000000000000..ffd3ef733c0ff4eb28c59ba4d8c657a2710dd8ad
--- /dev/null
+++ b/examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp2_reacted.data_template
@@ -0,0 +1,131 @@
+this is a molecule template for: water condensation, post-reacting
+
+15 atoms
+13 bonds
+19 angles
+16 dihedrals
+10 impropers
+
+Types
+
+1 9
+2 1
+3 1
+4 10
+5 4
+6 3
+7 3
+8 1
+9 1
+10 5
+11 8
+12 11
+13 3
+14 3
+15 10
+
+Charges
+
+1 -0.300000
+2 0.000000
+3 0.000000
+4 0.410000
+5 0.000000
+6 0.000000
+7 0.000000
+8 0.000000
+9 0.000000
+10 0.300000
+11 0.000000
+12 -0.820000
+13 0.000000
+14 0.000000
+15 0.410000
+
+Coords
+
+1 -4.856280 -1.050468 1.432625
+2 -5.047195 -0.935267 -0.358173
+3 -6.526281 -0.755366 -0.743523
+4 -5.282604 0.020447 1.552710
+5 -3.860697 -1.095850 1.428305
+6 -4.662382 -1.920900 -0.781524
+7 -4.433977 -0.072765 -0.784071
+8 -5.506279 0.202610 4.825816
+9 -4.449177 -0.844592 4.423366
+10 -4.103916 -0.749629 2.925195
+11 -3.376249 -1.886171 2.245643
+12 -4.493235 0.477214 2.137199
+13 -4.849053 -1.888877 4.663994
+14 -3.491823 -0.662913 5.018510
+15 -5.020777 1.189745 2.805427
+
+Bonds
+
+1 9 1 2
+2 10 1 5
+3 11 1 10
+4 1 2 3
+5 2 2 6
+6 2 2 7
+7 13 4 12
+8 1 8 9
+9 6 9 10
+10 2 9 13
+11 2 9 14
+12 7 10 11
+13 13 15 12
+
+Angles
+
+1 14 2 1 5
+2 15 2 1 10
+3 17 5 1 10
+4 18 1 2 3
+5 19 1 2 6
+6 19 1 2 7
+7 1 3 2 6
+8 1 3 2 7
+9 3 6 2 7
+10 12 8 9 10
+11 1 8 9 13
+12 1 8 9 14
+13 13 13 9 10
+14 13 14 9 10
+15 3 13 9 14
+16 10 9 10 11
+17 20 1 10 9
+18 22 1 10 11
+19 25 15 12 4
+
+Dihedrals
+
+1 16 5 1 2 3
+2 17 5 1 2 6
+3 17 5 1 2 7
+4 18 10 1 2 3
+5 19 10 1 2 6
+6 19 10 1 2 7
+7 20 2 1 10 9
+8 21 2 1 10 11
+9 23 5 1 10 9
+10 24 5 1 10 11
+11 14 8 9 10 11
+12 28 8 9 10 1
+13 15 13 9 10 11
+14 29 13 9 10 1
+15 15 14 9 10 11
+16 29 14 9 10 1
+
+Impropers
+
+1 10 2 1 5 10
+2 11 1 10 9 11
+3 1 1 2 3 6
+4 1 1 2 3 7
+5 1 1 2 6 7
+6 1 3 2 6 7
+7 1 8 9 13 10
+8 1 8 9 14 10
+9 1 8 9 13 14
+10 1 13 9 14 10
diff --git a/examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp2_unreacted.data_template b/examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp2_unreacted.data_template
new file mode 100644
index 0000000000000000000000000000000000000000..7abe15ada8d2372e4435ef82b5e60b7417865790
--- /dev/null
+++ b/examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp2_unreacted.data_template
@@ -0,0 +1,158 @@
+this is a molecule template for: water condensation, pre-reacting
+
+15 atoms
+14 bonds
+25 angles
+30 dihedrals
+16 impropers
+
+Types
+
+1 9
+2 1
+3 1
+4 4
+5 4
+6 3
+7 3
+8 1
+9 1
+10 5
+11 8
+12 6
+13 3
+14 3
+15 7
+
+Charges
+
+1 -0.300000
+2 0.000000
+3 0.000000
+4 0.000000
+5 0.000000
+6 0.000000
+7 0.000000
+8 0.000000
+9 0.000000
+10 0.300000
+11 0.000000
+12 0.000000
+13 0.000000
+14 0.000000
+15 0.000000
+
+Coords
+
+1 -4.922858 -0.946982 1.146055
+2 -5.047195 -0.935267 -0.358173
+3 -6.526281 -0.755366 -0.743523
+4 -5.282604 0.020447 1.552710
+5 -3.860697 -1.095850 1.428305
+6 -4.662382 -1.920900 -0.781524
+7 -4.433977 -0.072765 -0.784071
+8 -5.506279 0.202610 4.825816
+9 -4.449177 -0.844592 4.423366
+10 -4.103916 -0.749629 2.925195
+11 -3.376249 -1.886171 2.245643
+12 -4.493235 0.477214 2.137199
+13 -4.849053 -1.888877 4.663994
+14 -3.491823 -0.662913 5.018510
+15 -5.020777 1.189745 2.805427
+
+Bonds
+
+1 9 1 2
+2 10 1 4
+3 10 1 5
+4 11 1 10
+5 1 2 3
+6 2 2 6
+7 2 2 7
+8 1 8 9
+9 6 9 10
+10 2 9 13
+11 2 9 14
+12 7 10 11
+13 5 10 12
+14 8 12 15
+
+Angles
+
+1 14 2 1 4
+2 14 2 1 5
+3 15 2 1 10
+4 16 4 1 5
+5 17 4 1 10
+6 17 5 1 10
+7 18 1 2 3
+8 19 1 2 6
+9 19 1 2 7
+10 1 3 2 6
+11 1 3 2 7
+12 3 6 2 7
+13 12 8 9 10
+14 1 8 9 13
+15 1 8 9 14
+16 13 13 9 10
+17 13 14 9 10
+18 3 13 9 14
+19 10 9 10 11
+20 8 9 10 12
+21 20 1 10 9
+22 21 11 10 12
+23 22 1 10 11
+24 23 1 10 12
+25 11 10 12 15
+
+Dihedrals
+
+1 16 4 1 2 3
+2 17 4 1 2 6
+3 17 4 1 2 7
+4 16 5 1 2 3
+5 17 5 1 2 6
+6 17 5 1 2 7
+7 18 10 1 2 3
+8 19 10 1 2 6
+9 19 10 1 2 7
+10 20 2 1 10 9
+11 21 2 1 10 11
+12 22 2 1 10 12
+13 23 4 1 10 9
+14 24 4 1 10 11
+15 25 4 1 10 12
+16 23 5 1 10 9
+17 24 5 1 10 11
+18 25 5 1 10 12
+19 14 8 9 10 11
+20 12 8 9 10 12
+21 28 8 9 10 1
+22 15 13 9 10 11
+23 13 13 9 10 12
+24 29 13 9 10 1
+25 15 14 9 10 11
+26 13 14 9 10 12
+27 29 14 9 10 1
+28 10 9 10 12 15
+29 11 11 10 12 15
+30 30 1 10 12 15
+
+Impropers
+
+1 1 2 1 4 5
+2 1 2 1 4 10
+3 1 2 1 5 10
+4 1 4 1 5 10
+5 1 1 2 3 6
+6 1 1 2 3 7
+7 1 1 2 6 7
+8 1 3 2 6 7
+9 1 8 9 13 10
+10 1 8 9 14 10
+11 1 8 9 13 14
+12 1 13 9 14 10
+13 1 9 10 11 12
+14 1 1 10 9 11
+15 1 1 10 9 12
+16 1 1 10 11 12
diff --git a/examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon b/examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon
new file mode 100644
index 0000000000000000000000000000000000000000..1f7e9c42b7b4098fd355dec8afc696e42631321c
--- /dev/null
+++ b/examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon
@@ -0,0 +1,50 @@
+# two monomer nylon example
+# reaction produces a condensed water molecule
+
+units real
+
+boundary p p p
+
+atom_style full
+
+kspace_style pppm 1.0e-4
+
+pair_style lj/class2/coul/long 8.5
+
+angle_style class2
+
+bond_style class2
+
+dihedral_style class2
+
+improper_style class2
+
+read_data tiny_nylon.data
+
+velocity all create 300.0 4928459 dist gaussian
+
+molecule mol1 rxn1_stp1_unreacted.data_template
+molecule mol2 rxn1_stp1_reacted.data_template
+molecule mol3 rxn1_stp2_unreacted.data_template
+molecule mol4 rxn1_stp2_reacted.data_template
+
+thermo 50
+
+# dump 1 all xyz 1 test_vis.xyz
+
+fix myrxns all bond/react stabilization yes statted_grp .03 &
+ react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map &
+ react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
+
+fix 1 statted_grp nvt temp 300 300 100
+
+fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1
+
+thermo_style custom step temp press density f_myrxns[1] f_myrxns[2]
+
+# restart 100 restart1 restart2
+
+run 10000
+
+# write_restart restart_longrun
+# write_data restart_longrun.data
diff --git a/examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.1 b/examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..344439f94c5906e1fc7417921b89434ae0a7b8b5
--- /dev/null
+++ b/examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.1
@@ -0,0 +1,370 @@
+LAMMPS (20 Apr 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+ using 1 OpenMP thread(s) per MPI task
+# two monomer nylon example
+# reaction produces a condensed water molecule
+
+units real
+
+boundary p p p
+
+atom_style full
+
+kspace_style pppm 1.0e-4
+
+pair_style lj/class2/coul/long 8.5
+
+angle_style class2
+
+bond_style class2
+
+dihedral_style class2
+
+improper_style class2
+
+read_data tiny_nylon.data
+ orthogonal box = (-25 -25 -25) to (25 25 25)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 44 atoms
+ reading velocities ...
+ 44 velocities
+ scanning bonds ...
+ 9 = max bonds/atom
+ scanning angles ...
+ 21 = max angles/atom
+ scanning dihedrals ...
+ 29 = max dihedrals/atom
+ scanning impropers ...
+ 29 = max impropers/atom
+ reading bonds ...
+ 42 bonds
+ reading angles ...
+ 74 angles
+ reading dihedrals ...
+ 100 dihedrals
+ reading impropers ...
+ 44 impropers
+ 4 = max # of 1-2 neighbors
+ 6 = max # of 1-3 neighbors
+ 12 = max # of 1-4 neighbors
+ 41 = max # of special neighbors
+
+velocity all create 300.0 4928459 dist gaussian
+
+molecule mol1 rxn1_stp1_unreacted.data_template
+Read molecule mol1:
+ 18 atoms with max type 8
+ 16 bonds with max type 14
+ 25 angles with max type 28
+ 23 dihedrals with max type 36
+ 14 impropers with max type 11
+molecule mol2 rxn1_stp1_reacted.data_template
+Read molecule mol2:
+ 18 atoms with max type 9
+ 17 bonds with max type 13
+ 31 angles with max type 27
+ 39 dihedrals with max type 33
+ 20 impropers with max type 1
+molecule mol3 rxn1_stp2_unreacted.data_template
+Read molecule mol3:
+ 15 atoms with max type 9
+ 14 bonds with max type 13
+ 25 angles with max type 27
+ 30 dihedrals with max type 33
+ 16 impropers with max type 1
+molecule mol4 rxn1_stp2_reacted.data_template
+Read molecule mol4:
+ 15 atoms with max type 11
+ 13 bonds with max type 15
+ 19 angles with max type 29
+ 16 dihedrals with max type 32
+ 10 impropers with max type 13
+
+thermo 50
+
+# dump 1 all xyz 1 test_vis.xyz
+
+fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
+WARNING: An atom in 'react #1' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489)
+WARNING: An atom in 'react #2' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489)
+dynamic group bond_react_MASTER_group defined
+dynamic group statted_grp defined
+dynamic group bond_react_MASTER_group defined
+dynamic group statted_grp defined
+
+fix 1 statted_grp nvt temp 300 300 100
+
+fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1
+
+thermo_style custom step temp press density f_myrxns[1] f_myrxns[2]
+
+# restart 100 restart1 restart2
+
+run 10000
+PPPM initialization ...
+ using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+ G vector (1/distance) = 0.0534597
+ grid = 2 2 2
+ stencil order = 5
+ estimated absolute RMS force accuracy = 0.0402256
+ estimated relative force accuracy = 0.000121138
+ using double precision FFTs
+ 3d grid and FFT values/proc = 343 8
+Neighbor list info ...
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 10.5
+ ghost atom cutoff = 10.5
+ binsize = 5.25, bins = 10 10 10
+ 2 neighbor lists, perpetual/occasional/extra = 1 1 0
+ (1) pair lj/class2/coul/long, perpetual
+ attributes: half, newton on
+ pair build: half/bin/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+ (2) fix bond/react, occasional, copy from (1)
+ attributes: half, newton on
+ pair build: copy
+ stencil: none
+ bin: none
+WARNING: Inconsistent image flags (../domain.cpp:786)
+Per MPI rank memory allocation (min/avg/max) = 33.34 | 33.34 | 33.34 Mbytes
+Step Temp Press Density f_myrxns[1] f_myrxns[2]
+ 0 300 346.78165 0.0034851739 0 0
+ 50 296.70408 -51.30066 0.0034851739 1 0
+ 100 274.25324 46.715512 0.0034851739 1 1
+ 150 471.61579 31.321598 0.0034851739 1 1
+ 200 362.87766 42.061118 0.0034851739 1 1
+ 250 367.58058 65.303109 0.0034851739 1 1
+ 300 372.38236 -52.421725 0.0034851739 1 1
+ 350 297.69957 17.869945 0.0034851739 1 1
+ 400 258.30433 49.19156 0.0034851739 1 1
+ 450 253.34384 -5.8162637 0.0034851739 1 1
+ 500 269.96465 -43.337517 0.0034851739 1 1
+ 550 303.23718 10.180246 0.0034851739 1 1
+ 600 329.59579 -48.97461 0.0034851739 1 1
+ 650 350.42568 50.983183 0.0034851739 1 1
+ 700 342.03272 35.43465 0.0034851739 1 1
+ 750 269.23405 -41.873166 0.0034851739 1 1
+ 800 245.15025 13.953092 0.0034851739 1 1
+ 850 257.85421 -3.1492141 0.0034851739 1 1
+ 900 316.15644 7.7798301 0.0034851739 1 1
+ 950 299.9124 -15.77014 0.0034851739 1 1
+ 1000 302.89968 -17.049693 0.0034851739 1 1
+ 1050 308.91651 71.84632 0.0034851739 1 1
+ 1100 348.43932 -18.742012 0.0034851739 1 1
+ 1150 309.03036 50.536311 0.0034851739 1 1
+ 1200 318.9761 -16.905746 0.0034851739 1 1
+ 1250 320.42806 -0.057975092 0.0034851739 1 1
+ 1300 289.7824 18.200772 0.0034851739 1 1
+ 1350 284.79836 -9.1978427 0.0034851739 1 1
+ 1400 325.43292 42.082833 0.0034851739 1 1
+ 1450 261.5041 -37.823325 0.0034851739 1 1
+ 1500 298.88723 -5.1647385 0.0034851739 1 1
+ 1550 291.37403 -7.7764201 0.0034851739 1 1
+ 1600 293.83475 22.2458 0.0034851739 1 1
+ 1650 293.80611 24.202512 0.0034851739 1 1
+ 1700 291.70205 -23.397884 0.0034851739 1 1
+ 1750 292.32437 -10.671214 0.0034851739 1 1
+ 1800 302.01367 -11.671025 0.0034851739 1 1
+ 1850 322.1651 24.438331 0.0034851739 1 1
+ 1900 310.45076 45.343592 0.0034851739 1 1
+ 1950 325.91745 -19.847809 0.0034851739 1 1
+ 2000 276.89662 63.387098 0.0034851739 1 1
+ 2050 311.33783 -24.683247 0.0034851739 1 1
+ 2100 346.2336 -27.526891 0.0034851739 1 1
+ 2150 345.30604 -15.722411 0.0034851739 1 1
+ 2200 346.7718 -17.857633 0.0034851739 1 1
+ 2250 304.28676 -1.9965581 0.0034851739 1 1
+ 2300 322.56372 -31.786868 0.0034851739 1 1
+ 2350 282.64326 6.1982735 0.0034851739 1 1
+ 2400 286.65759 -63.207781 0.0034851739 1 1
+ 2450 257.05528 32.931491 0.0034851739 1 1
+ 2500 283.64386 26.912373 0.0034851739 1 1
+ 2550 299.54005 27.277039 0.0034851739 1 1
+ 2600 283.92503 14.660972 0.0034851739 1 1
+ 2650 321.93453 -18.977358 0.0034851739 1 1
+ 2700 376.7189 31.826935 0.0034851739 1 1
+ 2750 372.20075 -32.821697 0.0034851739 1 1
+ 2800 361.40604 83.035183 0.0034851739 1 1
+ 2850 332.27269 -23.927452 0.0034851739 1 1
+ 2900 331.14638 -0.12328446 0.0034851739 1 1
+ 2950 303.67489 -24.078857 0.0034851739 1 1
+ 3000 311.40462 21.563537 0.0034851739 1 1
+ 3050 284.72849 -23.849667 0.0034851739 1 1
+ 3100 303.48477 39.347763 0.0034851739 1 1
+ 3150 264.2739 -0.22299879 0.0034851739 1 1
+ 3200 300.03351 31.545323 0.0034851739 1 1
+ 3250 288.56663 5.7225228 0.0034851739 1 1
+ 3300 200.13238 -31.239655 0.0034851739 1 1
+ 3350 231.32512 16.631728 0.0034851739 1 1
+ 3400 260.57402 2.1717992 0.0034851739 1 1
+ 3450 301.47128 -42.210623 0.0034851739 1 1
+ 3500 321.77414 40.074365 0.0034851739 1 1
+ 3550 353.21858 28.387783 0.0034851739 1 1
+ 3600 331.45989 -57.800858 0.0034851739 1 1
+ 3650 303.88123 44.86596 0.0034851739 1 1
+ 3700 329.73833 -0.80615652 0.0034851739 1 1
+ 3750 297.55588 -0.49626039 0.0034851739 1 1
+ 3800 286.38794 -10.010003 0.0034851739 1 1
+ 3850 290.17417 -43.51187 0.0034851739 1 1
+ 3900 247.88933 51.23735 0.0034851739 1 1
+ 3950 332.31324 -18.194985 0.0034851739 1 1
+ 4000 325.56802 18.402825 0.0034851739 1 1
+ 4050 338.37593 36.430977 0.0034851739 1 1
+ 4100 370.95478 39.290285 0.0034851739 1 1
+ 4150 348.47859 -7.0779678 0.0034851739 1 1
+ 4200 241.30632 -33.371788 0.0034851739 1 1
+ 4250 242.17258 -9.986197 0.0034851739 1 1
+ 4300 300.85311 -7.9244294 0.0034851739 1 1
+ 4350 273.15684 -21.257283 0.0034851739 1 1
+ 4400 305.77463 -5.8720722 0.0034851739 1 1
+ 4450 314.97697 45.0373 0.0034851739 1 1
+ 4500 310.77723 16.958773 0.0034851739 1 1
+ 4550 302.1742 12.156862 0.0034851739 1 1
+ 4600 319.74799 6.84889 0.0034851739 1 1
+ 4650 270.86805 -13.767905 0.0034851739 1 1
+ 4700 249.81731 -31.197487 0.0034851739 1 1
+ 4750 285.86481 -9.8916364 0.0034851739 1 1
+ 4800 233.98321 7.1338571 0.0034851739 1 1
+ 4850 302.60551 49.262889 0.0034851739 1 1
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+ 4950 357.32741 11.583006 0.0034851739 1 1
+ 5000 400.21045 -8.1781061 0.0034851739 1 1
+ 5050 390.01845 -20.490275 0.0034851739 1 1
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+ 5150 324.02038 -15.023862 0.0034851739 1 1
+ 5200 262.08429 10.937354 0.0034851739 1 1
+ 5250 255.75508 16.381455 0.0034851739 1 1
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+ 5350 302.92832 9.1989494 0.0034851739 1 1
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+ 5450 300.71266 -4.7030295 0.0034851739 1 1
+ 5500 343.5499 -0.30550044 0.0034851739 1 1
+ 5550 369.51271 21.691649 0.0034851739 1 1
+ 5600 372.69789 -38.67994 0.0034851739 1 1
+ 5650 327.41266 11.352137 0.0034851739 1 1
+ 5700 278.98614 -23.827304 0.0034851739 1 1
+ 5750 308.30054 -20.756187 0.0034851739 1 1
+ 5800 341.45594 28.058441 0.0034851739 1 1
+ 5850 322.97844 -10.731921 0.0034851739 1 1
+ 5900 304.53591 32.825279 0.0034851739 1 1
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+ 6000 296.52681 18.781896 0.0034851739 1 1
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+ 6100 313.86576 3.4342714 0.0034851739 1 1
+ 6150 325.64196 32.392039 0.0034851739 1 1
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+ 6300 328.92285 -23.175157 0.0034851739 1 1
+ 6350 305.63077 4.9024453 0.0034851739 1 1
+ 6400 241.70341 -13.676629 0.0034851739 1 1
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+ 6550 294.53814 10.853462 0.0034851739 1 1
+ 6600 308.2025 18.995308 0.0034851739 1 1
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+ 6700 320.27344 11.336281 0.0034851739 1 1
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+ 6800 303.40388 7.6224553 0.0034851739 1 1
+ 6850 297.18966 51.52256 0.0034851739 1 1
+ 6900 284.18909 -8.4947203 0.0034851739 1 1
+ 6950 331.03663 13.233655 0.0034851739 1 1
+ 7000 311.37928 -43.265479 0.0034851739 1 1
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+ 7100 302.84119 12.048954 0.0034851739 1 1
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+ 7200 332.47359 26.048249 0.0034851739 1 1
+ 7250 262.70677 41.176242 0.0034851739 1 1
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+ 7350 296.91117 35.88133 0.0034851739 1 1
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+ 7450 272.28131 -23.322585 0.0034851739 1 1
+ 7500 209.04985 13.871239 0.0034851739 1 1
+ 7550 255.00955 4.9325621 0.0034851739 1 1
+ 7600 312.30937 -37.368274 0.0034851739 1 1
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+ 7700 325.09504 -18.347711 0.0034851739 1 1
+ 7750 363.28282 -22.479686 0.0034851739 1 1
+ 7800 350.17429 26.849547 0.0034851739 1 1
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+ 7900 272.66484 -11.701967 0.0034851739 1 1
+ 7950 298.60202 -12.765675 0.0034851739 1 1
+ 8000 274.58852 49.641532 0.0034851739 1 1
+ 8050 304.72347 -0.55414183 0.0034851739 1 1
+ 8100 328.30757 -39.861301 0.0034851739 1 1
+ 8150 406.67601 2.8999409 0.0034851739 1 1
+ 8200 332.20083 -51.217399 0.0034851739 1 1
+ 8250 354.50609 53.128769 0.0034851739 1 1
+ 8300 337.2758 20.68562 0.0034851739 1 1
+ 8350 361.89708 -54.185869 0.0034851739 1 1
+ 8400 305.63496 24.058529 0.0034851739 1 1
+ 8450 303.27461 4.304683 0.0034851739 1 1
+ 8500 253.53694 -10.909021 0.0034851739 1 1
+ 8550 277.03017 23.241479 0.0034851739 1 1
+ 8600 291.41844 -22.240665 0.0034851739 1 1
+ 8650 307.85368 31.919587 0.0034851739 1 1
+ 8700 309.19724 0.53529642 0.0034851739 1 1
+ 8750 354.6583 11.565515 0.0034851739 1 1
+ 8800 329.78598 19.5996 0.0034851739 1 1
+ 8850 240.79198 21.803515 0.0034851739 1 1
+ 8900 318.40749 -59.816923 0.0034851739 1 1
+ 8950 308.47211 -57.808635 0.0034851739 1 1
+ 9000 271.51207 50.943482 0.0034851739 1 1
+ 9050 249.4005 6.7529187 0.0034851739 1 1
+ 9100 221.8772 47.196092 0.0034851739 1 1
+ 9150 297.9351 4.0058184 0.0034851739 1 1
+ 9200 274.85051 -24.774393 0.0034851739 1 1
+ 9250 336.04757 5.3799028 0.0034851739 1 1
+ 9300 380.44956 -22.389381 0.0034851739 1 1
+ 9350 336.9824 23.050616 0.0034851739 1 1
+ 9400 304.46425 32.530218 0.0034851739 1 1
+ 9450 317.55591 -22.265425 0.0034851739 1 1
+ 9500 323.70901 -7.0159787 0.0034851739 1 1
+ 9550 316.07308 28.062131 0.0034851739 1 1
+ 9600 262.74608 -0.78519192 0.0034851739 1 1
+ 9650 271.55045 -21.430123 0.0034851739 1 1
+ 9700 239.6022 14.483637 0.0034851739 1 1
+ 9750 338.1437 -0.72765302 0.0034851739 1 1
+ 9800 334.50189 19.495144 0.0034851739 1 1
+ 9850 354.87554 19.272719 0.0034851739 1 1
+ 9900 334.02141 -22.393457 0.0034851739 1 1
+ 9950 293.63651 19.178873 0.0034851739 1 1
+ 10000 319.81736 21.904414 0.0034851739 1 1
+Loop time of 1.84987 on 1 procs for 10000 steps with 44 atoms
+
+Performance: 467.059 ns/day, 0.051 hours/ns, 5405.774 timesteps/s
+99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.26152 | 0.26152 | 0.26152 | 0.0 | 14.14
+Bond | 0.74069 | 0.74069 | 0.74069 | 0.0 | 40.04
+Kspace | 0.30505 | 0.30505 | 0.30505 | 0.0 | 16.49
+Neigh | 0.39991 | 0.39991 | 0.39991 | 0.0 | 21.62
+Comm | 0.02261 | 0.02261 | 0.02261 | 0.0 | 1.22
+Output | 0.0034585 | 0.0034585 | 0.0034585 | 0.0 | 0.19
+Modify | 0.099979 | 0.099979 | 0.099979 | 0.0 | 5.40
+Other | | 0.01666 | | | 0.90
+
+Nlocal: 44 ave 44 max 44 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 44 ave 44 max 44 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 823 ave 823 max 823 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 823
+Ave neighs/atom = 18.7045
+Ave special neighs/atom = 9.77273
+Neighbor list builds = 10000
+Dangerous builds = 0
+
+# write_restart restart_longrun
+# write_data restart_longrun.data
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:01
diff --git a/examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.4 b/examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..377781f48f7091dbc910d9ce1ab0f98723abb7bb
--- /dev/null
+++ b/examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.4
@@ -0,0 +1,370 @@
+LAMMPS (20 Apr 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+ using 1 OpenMP thread(s) per MPI task
+# two monomer nylon example
+# reaction produces a condensed water molecule
+
+units real
+
+boundary p p p
+
+atom_style full
+
+kspace_style pppm 1.0e-4
+
+pair_style lj/class2/coul/long 8.5
+
+angle_style class2
+
+bond_style class2
+
+dihedral_style class2
+
+improper_style class2
+
+read_data tiny_nylon.data
+ orthogonal box = (-25 -25 -25) to (25 25 25)
+ 1 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 44 atoms
+ reading velocities ...
+ 44 velocities
+ scanning bonds ...
+ 9 = max bonds/atom
+ scanning angles ...
+ 21 = max angles/atom
+ scanning dihedrals ...
+ 29 = max dihedrals/atom
+ scanning impropers ...
+ 29 = max impropers/atom
+ reading bonds ...
+ 42 bonds
+ reading angles ...
+ 74 angles
+ reading dihedrals ...
+ 100 dihedrals
+ reading impropers ...
+ 44 impropers
+ 4 = max # of 1-2 neighbors
+ 6 = max # of 1-3 neighbors
+ 12 = max # of 1-4 neighbors
+ 41 = max # of special neighbors
+
+velocity all create 300.0 4928459 dist gaussian
+
+molecule mol1 rxn1_stp1_unreacted.data_template
+Read molecule mol1:
+ 18 atoms with max type 8
+ 16 bonds with max type 14
+ 25 angles with max type 28
+ 23 dihedrals with max type 36
+ 14 impropers with max type 11
+molecule mol2 rxn1_stp1_reacted.data_template
+Read molecule mol2:
+ 18 atoms with max type 9
+ 17 bonds with max type 13
+ 31 angles with max type 27
+ 39 dihedrals with max type 33
+ 20 impropers with max type 1
+molecule mol3 rxn1_stp2_unreacted.data_template
+Read molecule mol3:
+ 15 atoms with max type 9
+ 14 bonds with max type 13
+ 25 angles with max type 27
+ 30 dihedrals with max type 33
+ 16 impropers with max type 1
+molecule mol4 rxn1_stp2_reacted.data_template
+Read molecule mol4:
+ 15 atoms with max type 11
+ 13 bonds with max type 15
+ 19 angles with max type 29
+ 16 dihedrals with max type 32
+ 10 impropers with max type 13
+
+thermo 50
+
+# dump 1 all xyz 1 test_vis.xyz
+
+fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
+WARNING: An atom in 'react #1' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489)
+WARNING: An atom in 'react #2' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489)
+dynamic group bond_react_MASTER_group defined
+dynamic group statted_grp defined
+dynamic group bond_react_MASTER_group defined
+dynamic group statted_grp defined
+
+fix 1 statted_grp nvt temp 300 300 100
+
+fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1
+
+thermo_style custom step temp press density f_myrxns[1] f_myrxns[2]
+
+# restart 100 restart1 restart2
+
+run 10000
+PPPM initialization ...
+ using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+ G vector (1/distance) = 0.0534597
+ grid = 2 2 2
+ stencil order = 5
+ estimated absolute RMS force accuracy = 0.0402256
+ estimated relative force accuracy = 0.000121138
+ using double precision FFTs
+ 3d grid and FFT values/proc = 252 2
+Neighbor list info ...
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 10.5
+ ghost atom cutoff = 10.5
+ binsize = 5.25, bins = 10 10 10
+ 2 neighbor lists, perpetual/occasional/extra = 1 1 0
+ (1) pair lj/class2/coul/long, perpetual
+ attributes: half, newton on
+ pair build: half/bin/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+ (2) fix bond/react, occasional, copy from (1)
+ attributes: half, newton on
+ pair build: copy
+ stencil: none
+ bin: none
+WARNING: Inconsistent image flags (../domain.cpp:786)
+Per MPI rank memory allocation (min/avg/max) = 33.34 | 33.69 | 34.37 Mbytes
+Step Temp Press Density f_myrxns[1] f_myrxns[2]
+ 0 300 346.78165 0.0034851739 0 0
+ 50 296.70408 -51.30066 0.0034851739 1 0
+ 100 274.25324 46.715512 0.0034851739 1 1
+ 150 471.61579 31.321598 0.0034851739 1 1
+ 200 362.87766 42.061118 0.0034851739 1 1
+ 250 367.58058 65.303109 0.0034851739 1 1
+ 300 372.38236 -52.421725 0.0034851739 1 1
+ 350 297.69957 17.869945 0.0034851739 1 1
+ 400 258.30433 49.19156 0.0034851739 1 1
+ 450 253.34384 -5.8162637 0.0034851739 1 1
+ 500 269.96465 -43.337517 0.0034851739 1 1
+ 550 303.23718 10.180246 0.0034851739 1 1
+ 600 329.59579 -48.97461 0.0034851739 1 1
+ 650 350.42568 50.983183 0.0034851739 1 1
+ 700 342.03272 35.43465 0.0034851739 1 1
+ 750 269.23405 -41.873166 0.0034851739 1 1
+ 800 245.15025 13.953092 0.0034851739 1 1
+ 850 257.85421 -3.1492141 0.0034851739 1 1
+ 900 316.15644 7.7798301 0.0034851739 1 1
+ 950 299.9124 -15.77014 0.0034851739 1 1
+ 1000 302.89968 -17.049693 0.0034851739 1 1
+ 1050 308.91651 71.84632 0.0034851739 1 1
+ 1100 348.43932 -18.742012 0.0034851739 1 1
+ 1150 309.03036 50.536311 0.0034851739 1 1
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+ 1300 289.7824 18.200772 0.0034851739 1 1
+ 1350 284.79836 -9.1978427 0.0034851739 1 1
+ 1400 325.43292 42.082833 0.0034851739 1 1
+ 1450 261.5041 -37.823325 0.0034851739 1 1
+ 1500 298.88723 -5.1647385 0.0034851739 1 1
+ 1550 291.37403 -7.7764201 0.0034851739 1 1
+ 1600 293.83475 22.2458 0.0034851739 1 1
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+ 1750 292.32437 -10.671214 0.0034851739 1 1
+ 1800 302.01367 -11.671025 0.0034851739 1 1
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+ 9900 330.93364 -28.292992 0.0034851739 1 1
+ 9950 291.25518 25.795948 0.0034851739 1 1
+ 10000 319.25565 25.323846 0.0034851739 1 1
+Loop time of 3.55353 on 4 procs for 10000 steps with 44 atoms
+
+Performance: 243.139 ns/day, 0.099 hours/ns, 2814.105 timesteps/s
+93.4% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.0030422 | 0.10454 | 0.35211 | 44.8 | 2.94
+Bond | 0.0063896 | 0.29222 | 0.94356 | 71.3 | 8.22
+Kspace | 0.88508 | 1.6486 | 1.979 | 35.1 | 46.39
+Neigh | 0.61154 | 0.62212 | 0.63307 | 1.0 | 17.51
+Comm | 0.18944 | 0.24549 | 0.29196 | 7.9 | 6.91
+Output | 0.0050066 | 0.011804 | 0.032134 | 10.8 | 0.33
+Modify | 0.52282 | 0.60522 | 0.69588 | 7.9 | 17.03
+Other | | 0.02359 | | | 0.66
+
+Nlocal: 11 ave 44 max 0 min
+Histogram: 3 0 0 0 0 0 0 0 0 1
+Nghost: 33 ave 44 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 3
+Neighs: 205.75 ave 823 max 0 min
+Histogram: 3 0 0 0 0 0 0 0 0 1
+
+Total # of neighbors = 823
+Ave neighs/atom = 18.7045
+Ave special neighs/atom = 9.77273
+Neighbor list builds = 10000
+Dangerous builds = 0
+
+# write_restart restart_longrun
+# write_data restart_longrun.data
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:03
diff --git a/examples/USER/misc/bond_react/tiny_nylon/rxn1_stp1_map b/examples/USER/misc/bond_react/tiny_nylon/rxn1_stp1_map
new file mode 100644
index 0000000000000000000000000000000000000000..44f7ad8137549eaa375046e114c59a7aa09c0c65
--- /dev/null
+++ b/examples/USER/misc/bond_react/tiny_nylon/rxn1_stp1_map
@@ -0,0 +1,35 @@
+this is a nominal superimpose file
+
+2 edgeIDs
+18 equivalences
+
+BondingIDs
+
+10
+1
+
+EdgeIDs
+
+16
+8
+
+Equivalences
+
+1 1
+2 2
+3 3
+4 4
+5 5
+6 6
+7 7
+8 8
+9 9
+10 10
+11 11
+12 12
+13 13
+14 14
+15 15
+16 16
+17 17
+18 18
diff --git a/examples/USER/misc/bond_react/tiny_nylon/rxn1_stp1_reacted.data_template b/examples/USER/misc/bond_react/tiny_nylon/rxn1_stp1_reacted.data_template
new file mode 100644
index 0000000000000000000000000000000000000000..d7256f43d2b3c659159ef23e3169dc6123d193ec
--- /dev/null
+++ b/examples/USER/misc/bond_react/tiny_nylon/rxn1_stp1_reacted.data_template
@@ -0,0 +1,189 @@
+this is a molecule template for: initial nylon crosslink, post-reacting
+
+18 atoms
+17 bonds
+31 angles
+39 dihedrals
+20 impropers
+
+Types
+
+1 9
+2 1
+3 1
+4 8
+5 8
+6 4
+7 4
+8 1
+9 1
+10 2
+11 6
+12 3
+13 4
+14 4
+15 5
+16 1
+17 4
+18 4
+
+Charges
+
+1 -0.300000
+2 0.000000
+3 0.000000
+4 0.000000
+5 0.000000
+6 0.000000
+7 0.000000
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+11 0.000000
+12 0.000000
+13 0.000000
+14 0.000000
+15 0.000000
+16 0.000000
+17 0.000000
+18 0.000000
+
+Coords
+
+1 -5.522237 -0.752722 1.631158
+2 -5.170398 -0.545733 0.178130
+3 -6.469695 -0.553072 -0.648889
+4 -6.052076 -1.721152 1.744648
+5 -6.183059 0.071387 1.971497
+6 -4.489340 -1.389197 -0.173156
+7 -4.637591 0.453703 0.051252
+8 -5.618658 0.138919 4.386107
+9 -4.669492 -0.989819 3.943591
+10 -4.270194 -0.766405 2.474102
+11 -3.348470 -1.875393 2.024289
+12 -3.569794 0.564183 2.345995
+13 -5.201079 -1.993301 4.044219
+14 -3.736682 -0.984819 4.598305
+15 -4.255402 1.370923 2.679069
+16 -6.136394 -0.339866 -2.136775
+17 -6.996331 -1.555519 -0.517408
+18 -7.153308 0.284949 -0.289930
+
+Bonds
+
+1 11 1 2
+2 12 1 4
+3 12 1 5
+4 13 1 10
+5 2 2 3
+6 1 2 6
+7 1 2 7
+8 2 3 16
+9 1 3 17
+10 1 3 18
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+12 4 9 10
+13 1 9 13
+14 1 9 14
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+16 3 10 12
+17 6 12 15
+
+Angles
+
+1 17 2 1 4
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+3 18 2 1 10
+4 19 4 1 5
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+6 20 5 1 10
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+25 6 9 10 11
+26 4 9 10 12
+27 24 1 10 9
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+29 26 1 10 11
+30 27 1 10 12
+31 7 10 12 15
+
+Dihedrals
+
+1 19 4 1 2 3
+2 20 4 1 2 6
+3 20 4 1 2 7
+4 19 5 1 2 3
+5 20 5 1 2 6
+6 20 5 1 2 7
+7 21 10 1 2 3
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+33 32 13 9 10 1
+34 11 14 9 10 11
+35 9 14 9 10 12
+36 32 14 9 10 1
+37 6 9 10 12 15
+38 7 11 10 12 15
+39 33 1 10 12 15
+
+Impropers
+
+1 1 2 1 4 5
+2 1 2 1 4 10
+3 1 2 1 5 10
+4 1 4 1 5 10
+5 1 1 2 3 6
+6 1 1 2 3 7
+7 1 1 2 6 7
+8 1 3 2 6 7
+9 1 2 3 16 17
+10 1 2 3 16 18
+11 1 2 3 17 18
+12 1 16 3 17 18
+13 1 8 9 13 10
+14 1 8 9 14 10
+15 1 8 9 13 14
+16 1 13 9 14 10
+17 1 9 10 11 12
+18 1 1 10 9 11
+19 1 1 10 9 12
+20 1 1 10 11 12
diff --git a/examples/USER/misc/bond_react/tiny_nylon/rxn1_stp1_unreacted.data_template b/examples/USER/misc/bond_react/tiny_nylon/rxn1_stp1_unreacted.data_template
new file mode 100644
index 0000000000000000000000000000000000000000..ec3f109d7b50c06c642635693f77257c4ce68c7e
--- /dev/null
+++ b/examples/USER/misc/bond_react/tiny_nylon/rxn1_stp1_unreacted.data_template
@@ -0,0 +1,160 @@
+this is a molecule template for: initial nylon crosslink, pre-reacting
+
+18 atoms
+16 bonds
+25 angles
+23 dihedrals
+14 impropers
+
+Types
+
+1 7
+2 1
+3 1
+4 8
+5 8
+6 4
+7 4
+8 1
+9 1
+10 2
+11 6
+12 3
+13 4
+14 4
+15 5
+16 1
+17 4
+18 4
+
+Charges
+
+1 -0.300000
+2 0.000000
+3 0.000000
+4 0.000000
+5 0.000000
+6 0.000000
+7 0.000000
+8 0.000000
+9 0.000000
+10 0.300000
+11 0.000000
+12 0.000000
+13 0.000000
+14 0.000000
+15 0.000000
+16 0.000000
+17 0.000000
+18 0.000000
+
+Coords
+
+1 -4.922858 -0.946982 1.146055
+2 -5.047195 -0.935267 -0.358173
+3 -6.526281 -0.755366 -0.743523
+4 -5.282604 0.020447 1.552710
+5 -3.860697 -1.095850 1.428305
+6 -4.662382 -1.920900 -0.781524
+7 -4.433977 -0.072765 -0.784071
+8 -5.506279 0.202610 4.825816
+9 -4.449177 -0.844592 4.423366
+10 -4.103916 -0.749629 2.925195
+11 -3.376249 -1.886171 2.245643
+12 -4.493235 0.477214 2.137199
+13 -4.849053 -1.888877 4.663994
+14 -3.491823 -0.662913 5.018510
+15 -5.020777 1.189745 2.805427
+16 -3.964987 2.900602 -1.551341
+17 -4.460694 2.836102 0.668882
+18 -4.828494 3.219656 -0.122111
+
+Bonds
+
+1 14 1 2
+2 10 1 4
+3 10 1 5
+4 2 2 3
+5 1 2 6
+6 1 2 7
+7 2 3 16
+8 1 3 17
+9 1 3 18
+10 2 8 9
+11 4 9 10
+12 1 9 13
+13 1 9 14
+14 5 10 11
+15 3 10 12
+16 6 12 15
+
+Angles
+
+1 15 2 1 4
+2 15 2 1 5
+3 16 4 1 5
+4 28 1 2 3
+5 14 1 2 6
+6 14 1 2 7
+7 2 3 2 6
+8 2 3 2 7
+9 1 6 2 7
+10 3 2 3 16
+11 2 2 3 17
+12 2 2 3 18
+13 2 16 3 17
+14 2 16 3 18
+15 1 17 3 18
+16 8 8 9 10
+17 2 8 9 13
+18 2 8 9 14
+19 23 13 9 10
+20 23 14 9 10
+21 1 13 9 14
+22 6 9 10 11
+23 4 9 10 12
+24 25 11 10 12
+25 7 10 12 15
+
+Dihedrals
+
+1 34 4 1 2 3
+2 35 4 1 2 6
+3 35 4 1 2 7
+4 34 5 1 2 3
+5 35 5 1 2 6
+6 35 5 1 2 7
+7 36 1 2 3 16
+8 12 1 2 3 17
+9 12 1 2 3 18
+10 4 16 3 2 6
+11 2 6 2 3 17
+12 2 6 2 3 18
+13 4 16 3 2 7
+14 2 7 2 3 17
+15 2 7 2 3 18
+16 10 8 9 10 11
+17 8 8 9 10 12
+18 11 13 9 10 11
+19 9 13 9 10 12
+20 11 14 9 10 11
+21 9 14 9 10 12
+22 6 9 10 12 15
+23 7 11 10 12 15
+
+Impropers
+
+1 6 2 1 4 5
+2 11 9 10 11 12
+3 1 1 2 3 6
+4 1 1 2 3 7
+5 1 1 2 6 7
+6 1 3 2 6 7
+7 1 2 3 16 17
+8 1 2 3 16 18
+9 1 2 3 17 18
+10 1 16 3 17 18
+11 1 8 9 13 10
+12 1 8 9 14 10
+13 1 8 9 13 14
+14 1 13 9 14 10
diff --git a/examples/USER/misc/bond_react/tiny_nylon/rxn1_stp2_map b/examples/USER/misc/bond_react/tiny_nylon/rxn1_stp2_map
new file mode 100644
index 0000000000000000000000000000000000000000..35fe47fdb3bdb0386d65b950d45cbfb39fbe6f7f
--- /dev/null
+++ b/examples/USER/misc/bond_react/tiny_nylon/rxn1_stp2_map
@@ -0,0 +1,32 @@
+this is a nominal superimpose file
+
+2 edgeIDs
+15 equivalences
+
+BondingIDs
+
+4
+12
+
+EdgeIDs
+
+8
+3
+
+Equivalences
+
+1 1
+2 2
+3 3
+4 4
+5 5
+6 6
+7 7
+8 8
+9 9
+10 10
+11 11
+12 12
+13 13
+14 14
+15 15
diff --git a/examples/USER/misc/bond_react/tiny_nylon/rxn1_stp2_reacted.data_template b/examples/USER/misc/bond_react/tiny_nylon/rxn1_stp2_reacted.data_template
new file mode 100644
index 0000000000000000000000000000000000000000..785363464696967b7938c142043868792546e3cf
--- /dev/null
+++ b/examples/USER/misc/bond_react/tiny_nylon/rxn1_stp2_reacted.data_template
@@ -0,0 +1,131 @@
+this is a molecule template for: water condensation, post-reacting
+
+15 atoms
+13 bonds
+19 angles
+16 dihedrals
+10 impropers
+
+Types
+
+1 9
+2 1
+3 1
+4 10
+5 8
+6 4
+7 4
+8 1
+9 1
+10 2
+11 6
+12 11
+13 4
+14 4
+15 10
+
+Charges
+
+1 -0.300000
+2 0.000000
+3 0.000000
+4 0.410000
+5 0.000000
+6 0.000000
+7 0.000000
+8 0.000000
+9 0.000000
+10 0.300000
+11 0.000000
+12 -0.820000
+13 0.000000
+14 0.000000
+15 0.410000
+
+Coords
+
+1 -4.856280 -1.050468 1.432625
+2 -5.047195 -0.935267 -0.358173
+3 -6.526281 -0.755366 -0.743523
+4 -5.282604 0.020447 1.552710
+5 -3.860697 -1.095850 1.428305
+6 -4.662382 -1.920900 -0.781524
+7 -4.433977 -0.072765 -0.784071
+8 -5.506279 0.202610 4.825816
+9 -4.449177 -0.844592 4.423366
+10 -4.103916 -0.749629 2.925195
+11 -3.376249 -1.886171 2.245643
+12 -4.493235 0.477214 2.137199
+13 -4.849053 -1.888877 4.663994
+14 -3.491823 -0.662913 5.018510
+15 -5.020777 1.189745 2.805427
+
+Bonds
+
+1 11 1 2
+2 12 1 5
+3 13 1 10
+4 2 2 3
+5 1 2 6
+6 1 2 7
+7 15 4 12
+8 2 8 9
+9 4 9 10
+10 1 9 13
+11 1 9 14
+12 5 10 11
+13 15 15 12
+
+Angles
+
+1 17 2 1 5
+2 18 2 1 10
+3 20 5 1 10
+4 21 1 2 3
+5 22 1 2 6
+6 22 1 2 7
+7 2 3 2 6
+8 2 3 2 7
+9 1 6 2 7
+10 8 8 9 10
+11 2 8 9 13
+12 2 8 9 14
+13 23 13 9 10
+14 23 14 9 10
+15 1 13 9 14
+16 6 9 10 11
+17 24 1 10 9
+18 26 1 10 11
+19 29 15 12 4
+
+Dihedrals
+
+1 19 5 1 2 3
+2 20 5 1 2 6
+3 20 5 1 2 7
+4 21 10 1 2 3
+5 22 10 1 2 6
+6 22 10 1 2 7
+7 23 2 1 10 9
+8 24 2 1 10 11
+9 26 5 1 10 9
+10 27 5 1 10 11
+11 10 8 9 10 11
+12 31 8 9 10 1
+13 11 13 9 10 11
+14 32 13 9 10 1
+15 11 14 9 10 11
+16 32 14 9 10 1
+
+Impropers
+
+1 12 2 1 5 10
+2 13 1 10 9 11
+3 1 1 2 3 6
+4 1 1 2 3 7
+5 1 1 2 6 7
+6 1 3 2 6 7
+7 1 8 9 13 10
+8 1 8 9 14 10
+9 1 8 9 13 14
+10 1 13 9 14 10
diff --git a/examples/USER/misc/bond_react/tiny_nylon/rxn1_stp2_unreacted.data_template b/examples/USER/misc/bond_react/tiny_nylon/rxn1_stp2_unreacted.data_template
new file mode 100644
index 0000000000000000000000000000000000000000..847f0622e506865117fbe542f89de35fb20ccede
--- /dev/null
+++ b/examples/USER/misc/bond_react/tiny_nylon/rxn1_stp2_unreacted.data_template
@@ -0,0 +1,158 @@
+this is a molecule template for: water condensation, pre-reacting
+
+15 atoms
+14 bonds
+25 angles
+30 dihedrals
+16 impropers
+
+Types
+
+1 9
+2 1
+3 1
+4 8
+5 8
+6 4
+7 4
+8 1
+9 1
+10 2
+11 6
+12 3
+13 4
+14 4
+15 5
+
+Charges
+
+1 -0.300000
+2 0.000000
+3 0.000000
+4 0.000000
+5 0.000000
+6 0.000000
+7 0.000000
+8 0.000000
+9 0.000000
+10 0.300000
+11 0.000000
+12 0.000000
+13 0.000000
+14 0.000000
+15 0.000000
+
+Coords
+
+1 -4.922858 -0.946982 1.146055
+2 -5.047195 -0.935267 -0.358173
+3 -6.526281 -0.755366 -0.743523
+4 -5.282604 0.020447 1.552710
+5 -3.860697 -1.095850 1.428305
+6 -4.662382 -1.920900 -0.781524
+7 -4.433977 -0.072765 -0.784071
+8 -5.506279 0.202610 4.825816
+9 -4.449177 -0.844592 4.423366
+10 -4.103916 -0.749629 2.925195
+11 -3.376249 -1.886171 2.245643
+12 -4.493235 0.477214 2.137199
+13 -4.849053 -1.888877 4.663994
+14 -3.491823 -0.662913 5.018510
+15 -5.020777 1.189745 2.805427
+
+Bonds
+
+1 11 1 2
+2 12 1 4
+3 12 1 5
+4 13 1 10
+5 2 2 3
+6 1 2 6
+7 1 2 7
+8 2 8 9
+9 4 9 10
+10 1 9 13
+11 1 9 14
+12 5 10 11
+13 3 10 12
+14 6 12 15
+
+Angles
+
+1 17 2 1 4
+2 17 2 1 5
+3 18 2 1 10
+4 19 4 1 5
+5 20 4 1 10
+6 20 5 1 10
+7 21 1 2 3
+8 22 1 2 6
+9 22 1 2 7
+10 2 3 2 6
+11 2 3 2 7
+12 1 6 2 7
+13 8 8 9 10
+14 2 8 9 13
+15 2 8 9 14
+16 23 13 9 10
+17 23 14 9 10
+18 1 13 9 14
+19 6 9 10 11
+20 4 9 10 12
+21 24 1 10 9
+22 25 11 10 12
+23 26 1 10 11
+24 27 1 10 12
+25 7 10 12 15
+
+Dihedrals
+
+1 19 4 1 2 3
+2 20 4 1 2 6
+3 20 4 1 2 7
+4 19 5 1 2 3
+5 20 5 1 2 6
+6 20 5 1 2 7
+7 21 10 1 2 3
+8 22 10 1 2 6
+9 22 10 1 2 7
+10 23 2 1 10 9
+11 24 2 1 10 11
+12 25 2 1 10 12
+13 26 4 1 10 9
+14 27 4 1 10 11
+15 28 4 1 10 12
+16 26 5 1 10 9
+17 27 5 1 10 11
+18 28 5 1 10 12
+19 10 8 9 10 11
+20 8 8 9 10 12
+21 31 8 9 10 1
+22 11 13 9 10 11
+23 9 13 9 10 12
+24 32 13 9 10 1
+25 11 14 9 10 11
+26 9 14 9 10 12
+27 32 14 9 10 1
+28 6 9 10 12 15
+29 7 11 10 12 15
+30 33 1 10 12 15
+
+Impropers
+
+1 1 2 1 4 5
+2 1 2 1 4 10
+3 1 2 1 5 10
+4 1 4 1 5 10
+5 1 1 2 3 6
+6 1 1 2 3 7
+7 1 1 2 6 7
+8 1 3 2 6 7
+9 1 8 9 13 10
+10 1 8 9 14 10
+11 1 8 9 13 14
+12 1 13 9 14 10
+13 1 9 10 11 12
+14 1 1 10 9 11
+15 1 1 10 9 12
+16 1 1 10 11 12
diff --git a/examples/USER/misc/bond_react/tiny_nylon/tiny_nylon.data b/examples/USER/misc/bond_react/tiny_nylon/tiny_nylon.data
new file mode 100644
index 0000000000000000000000000000000000000000..8466e68ea57fed2ddca9851724e4ea1509049435
--- /dev/null
+++ b/examples/USER/misc/bond_react/tiny_nylon/tiny_nylon.data
@@ -0,0 +1,795 @@
+this is LAMMPS data file containing two nylon monomers
+
+44 atoms
+11 atom types
+42 bonds
+15 bond types
+74 angles
+29 angle types
+100 dihedrals
+36 dihedral types
+44 impropers
+13 improper types
+5 extra bond per atom
+15 extra angle per atom
+15 extra dihedral per atom
+25 extra improper per atom
+25 extra special per atom
+
+-25 25 xlo xhi
+-25 25 ylo yhi
+-25 25 zlo zhi
+
+Masses
+
+1 12.0112
+2 12.0112
+3 15.9994
+4 1.00797
+5 1.00797
+6 15.9994
+7 14.0067
+8 1.00797
+9 14.0067
+10 1.00797
+11 15.9994
+
+Pair Coeffs # lj/class2/coul/cut
+
+1 0.054 4.01
+2 0.12 3.81
+3 0.24 3.535
+4 0.02 2.7
+5 0.013 1.098
+6 0.267 3.3
+7 0.065 4.07
+8 0.013 1.098
+9 0.106 4.07
+10 0.013 1.098
+11 0.26 3.61
+
+Bond Coeffs # class2
+
+1 1.101 345 -691.89 844.6
+2 1.53 299.67 -501.77 679.81
+3 1.3649 368.731 -832.478 1274.02
+4 1.5202 253.707 -423.037 396.9
+5 1.202 851.14 -1918.49 2160.77
+6 0.965 532.506 -1282.9 2004.77
+7 1.53 299.67 -501.77 679.81
+8 1.101 345 -691.89 844.6
+9 1.457 365.805 -699.637 998.484
+10 1.006 466.74 -1073.6 1251.11
+11 1.452 327.166 -547.899 526.5
+12 1.01 462.75 -1053.63 1545.76
+13 1.416 359.159 -558.473 1146.38
+14 1.457 365.805 -699.637 998.484
+15 0.97 563.28 -1428.22 1902.12
+
+Angle Coeffs # class2
+
+1 107.66 39.641 -12.921 -2.4318
+2 110.77 41.453 -10.604 5.129
+3 112.67 39.516 -7.443 -9.5583
+4 123.145 55.5431 -17.2123 0.1348
+5 118.986 98.6813 -22.2485 10.3673
+6 123.145 55.5431 -17.2123 0.1348
+7 111.254 53.5303 -11.8454 -11.5405
+8 108.53 51.9747 -9.4851 -10.9985
+9 107.734 40.6099 -28.8121 0
+10 110.77 41.453 -10.604 5.129
+11 112.67 39.516 -7.443 -9.5583
+12 107.66 39.641 -12.921 -2.4318
+13 111.91 60.7147 -13.3366 -13.0785
+14 110.62 51.3137 -6.7198 -2.6003
+15 110.954 50.8652 -4.4522 -10.0298
+16 107.067 45.252 -7.5558 -9.512
+17 113.868 45.9271 -20.0824 0
+18 111.037 31.8958 -6.6942 -6.837
+19 116.94 37.5749 -8.6676 0
+20 117.961 37.4964 -8.1837 0
+21 114.302 42.6589 -10.5464 -9.3243
+22 108.937 57.401 2.9374 0
+23 107.734 40.6099 -28.8121 0
+24 116.926 39.4193 -10.9945 -8.7733
+25 118.986 98.6813 -22.2485 10.3673
+26 125.542 92.572 -34.48 -11.1871
+27 0 0 0 0
+28 111.91 60.7147 -13.3366 -13.0785
+29 103.7 49.84 -11.6 -8
+
+BondBond Coeffs
+
+1 5.3316 1.101 1.101
+2 3.3872 1.53 1.101
+3 0 1.53 1.53
+4 0 1.5202 1.3649
+5 0 1.3649 1.202
+6 46.0685 1.5202 1.202
+7 0 1.3649 0.965
+8 5.4199 1.53 1.5202
+9 0.7115 1.5202 1.101
+10 3.3872 1.53 1.101
+11 0 1.53 1.53
+12 5.3316 1.101 1.101
+13 4.6217 1.53 1.457
+14 12.426 1.457 1.101
+15 -6.4168 1.457 1.006
+16 -1.8749 1.006 1.006
+17 -3.471 1.452 1.01
+18 12.1186 1.452 1.416
+19 -0.5655 1.01 1.01
+20 -4.3126 1.01 1.416
+21 3.5446 1.452 1.53
+22 15.2994 1.452 1.101
+23 0.7115 1.101 1.5202
+24 0 1.416 1.5202
+25 0 1.202 1.3649
+26 138.495 1.416 1.202
+27 0 1.416 1.3649
+28 4.6217 1.457 1.53
+29 -9.5 0.97 0.97
+
+BondAngle Coeffs
+
+1 18.103 18.103 1.101 1.101
+2 20.754 11.421 1.53 1.101
+3 8.016 8.016 1.53 1.53
+4 0 0 1.5202 1.3649
+5 0 0 1.3649 1.202
+6 34.9982 37.1298 1.5202 1.202
+7 0 0 1.3649 0.965
+8 18.1678 15.8758 1.53 1.5202
+9 12.4632 9.1765 1.5202 1.101
+10 20.754 11.421 1.53 1.101
+11 8.016 8.016 1.53 1.53
+12 18.103 18.103 1.101 1.101
+13 6.0876 16.5702 1.53 1.457
+14 42.4332 13.4582 1.457 1.101
+15 31.8096 20.5799 1.457 1.006
+16 28.0322 28.0322 1.006 1.006
+17 11.8828 5.9339 1.452 1.01
+18 3.7812 14.8633 1.452 1.416
+19 19.8125 19.8125 1.01 1.01
+20 10.8422 29.5743 1.01 1.416
+21 4.6031 -5.479 1.452 1.53
+22 34.8907 10.6917 1.452 1.101
+23 9.1765 12.4632 1.101 1.5202
+24 0 0 1.416 1.5202
+25 0 0 1.202 1.3649
+26 62.7124 52.4045 1.416 1.202
+27 0 0 1.416 1.3649
+28 16.5702 6.0876 1.457 1.53
+29 22.35 22.35 0.97 0.97
+
+Dihedral Coeffs # class2
+
+1 -0.0228 0 0.028 0 -0.1863 0
+2 -0.1432 0 0.0617 0 -0.1083 0
+3 0.0972 0 0.0722 0 -0.2581 0
+4 0 0 0.0316 0 -0.1681 0
+5 0 0 0.0514 0 -0.143 0
+6 0 0 0 0 0 0
+7 -2.7332 0 2.9646 0 -0.0155 0
+8 0 0 0 0 0 0
+9 0 0 0 0 0 0
+10 0.0442 0 0.0292 0 0.0562 0
+11 -0.1804 0 0.0012 0 0.0371 0
+12 -0.2428 0 0.4065 0 -0.3079 0
+13 -0.1432 0 0.0617 0 -0.1083 0
+14 0.1764 0 0.1766 0 -0.5206 0
+15 0 0 0.0316 0 -0.1681 0
+16 0 0 0.0514 0 -0.143 0
+17 -1.1506 0 -0.6344 0 -0.1845 0
+18 -0.5187 0 -0.4837 0 -0.1692 0
+19 -0.0483 0 -0.0077 0 -0.0014 0
+20 -0.0148 0 -0.0791 0 -0.0148 0
+21 0.0143 0 -0.0132 0 0.0091 0
+22 0.0219 0 -0.026 0 0.0714 0
+23 -0.7532 0 2.7392 0 0.0907 0
+24 0.8297 0 3.7234 0 -0.0495 0
+25 0 0 0 0 0 0
+26 0 0 0 0 0 0
+27 -1.6938 0 2.7386 0 -0.336 0
+28 0 0 0 0 0 0
+29 0.0972 0 0.0722 0 -0.2581 0
+30 -0.0228 0 0.028 0 -0.1863 0
+31 0.1693 0 -0.009 0 -0.0687 0
+32 0.1693 0 -0.009 0 -0.0687 0
+33 0 0 0 0 0 0
+34 -1.1506 0 -0.6344 0 -0.1845 0
+35 -0.5187 0 -0.4837 0 -0.1692 0
+36 0.1764 0 0.1766 0 -0.5206 0
+
+AngleAngleTorsion Coeffs
+
+1 -5.3624 108.53 110.77
+2 -12.564 110.77 110.77
+3 -0.3801 112.67 108.53
+4 -16.164 112.67 110.77
+5 -22.045 112.67 112.67
+6 0 0 111.254
+7 0 118.985 111.254
+8 0 108.53 0
+9 0 107.734 0
+10 -8.019 108.53 123.145
+11 -15.3496 107.734 123.145
+12 -15.7572 111.91 110.77
+13 -12.564 110.77 110.77
+14 -27.3953 112.67 111.91
+15 -16.164 112.67 110.77
+16 -22.045 112.67 112.67
+17 -7.5499 111.91 110.954
+18 -10.4258 110.62 110.954
+19 -4.6337 113.868 114.302
+20 -6.659 113.868 108.937
+21 -7.4314 111.037 114.302
+22 -8.1335 111.037 108.937
+23 -6.5335 111.037 116.926
+24 -15.5547 111.037 125.542
+25 0 111.037 0
+26 -1.3234 117.961 116.926
+27 -7.3186 117.961 125.542
+28 0 117.961 0
+29 -1.0631 114.302 112.67
+30 -12.7974 114.302 110.77
+31 -5.4514 108.53 116.926
+32 -12.2417 107.734 116.926
+33 0 0 111.254
+34 -7.5499 110.954 111.91
+35 -10.4258 110.954 110.62
+36 -27.3953 111.91 112.67
+
+EndBondTorsion Coeffs
+
+1 -0.0204 0.3628 -0.4426 -0.0097 -0.0315 -0.0755 1.5202 1.101
+2 0.213 0.312 0.0777 0.213 0.312 0.0777 1.101 1.101
+3 0.0062 -0.0002 0.0036 0.0055 0.006 -0.0009 1.53 1.5202
+4 0.2486 0.2422 -0.0925 0.0814 0.0591 0.2219 1.53 1.101
+5 -0.0732 0 0 -0.0732 0 0 1.53 1.53
+6 0 0 0 0 0 0 1.5202 0.965
+7 0 0 0 0 0 0 1.202 0.965
+8 0 0 0 0 0 0 1.53 1.3649
+9 0 0 0 0 0 0 1.101 1.3649
+10 0.2654 0.0503 0.1046 -0.281 0.0816 -0.1522 1.53 1.202
+11 1.2143 0.2831 0.3916 -0.2298 0.0354 0.3853 1.101 1.202
+12 0.1022 0.209 0.6433 0.196 0.7056 0.112 1.457 1.101
+13 0.213 0.312 0.0777 0.213 0.312 0.0777 1.101 1.101
+14 0.1032 0.5896 -0.4836 0.0579 -0.0043 -0.1906 1.53 1.457
+15 0.2486 0.2422 -0.0925 0.0814 0.0591 0.2219 1.53 1.101
+16 -0.0732 0 0 -0.0732 0 0 1.53 1.53
+17 -0.9466 0.9356 -0.5542 0.057 0.0625 0.4112 1.53 1.006
+18 -1.1685 0.9266 -0.0993 0.085 0.3061 0.2104 1.101 1.006
+19 -0.0992 -0.0727 -0.4139 0.132 0.0015 0.1324 1.01 1.53
+20 -0.4894 0.1644 0.3105 -0.8983 0.2826 0.0881 1.01 1.101
+21 -0.1245 -0.9369 0.7781 -0.2033 0.0035 0.056 1.416 1.53
+22 0.2292 1.1732 -0.058 -0.3667 0.8197 0.1335 1.416 1.101
+23 0.2299 -0.1141 -0.1424 0.0933 -0.4631 0.2883 1.452 1.5202
+24 0.1598 0.7253 -0.1007 0.1226 -2.1326 0.5581 1.452 1.202
+25 0 0 0 0 0 0 1.452 1.3649
+26 0.6413 0.1676 0.144 -0.6979 0.5619 0.4212 1.01 1.5202
+27 0.1214 0.1936 0.0816 -0.7604 -2.6431 1.2467 1.01 1.202
+28 0 0 0 0 0 0 1.01 1.3649
+29 -0.0797 -0.0406 0.0255 0.0742 0.0105 0.0518 1.452 1.53
+30 0.3022 0.2513 0.4641 -0.0601 -0.3763 -0.1876 1.452 1.101
+31 -0.2631 -0.0076 -0.1145 -0.2751 -0.3058 -0.1767 1.53 1.416
+32 -0.0268 0.7836 0.0035 0.3552 -0.2685 0.5834 1.101 1.416
+33 0 0 0 0 0 0 1.416 0.965
+34 0.057 0.0625 0.4112 -0.9466 0.9356 -0.5542 1.006 1.53
+35 0.085 0.3061 0.2104 -1.1685 0.9266 -0.0993 1.006 1.101
+36 0.0579 -0.0043 -0.1906 0.1032 0.5896 -0.4836 1.457 1.53
+
+MiddleBondTorsion Coeffs
+
+1 -3.5039 1.2458 -0.761 1.53
+2 -14.261 -0.5322 -0.4864 1.53
+3 -1.5945 0.2267 -0.6911 1.53
+4 -14.879 -3.6581 -0.3138 1.53
+5 -17.787 -7.1877 0 1.53
+6 0 0 0 1.3649
+7 0 0 0 1.3649
+8 0 0 0 1.5202
+9 0 0 0 1.5202
+10 0.3388 -0.1096 0.1219 1.5202
+11 0.2359 0.9139 0.9594 1.5202
+12 -10.4959 -0.7647 -0.0545 1.53
+13 -14.261 -0.5322 -0.4864 1.53
+14 -15.4174 -7.3055 -1.0749 1.53
+15 -14.879 -3.6581 -0.3138 1.53
+16 -17.787 -7.1877 0 1.53
+17 -2.2208 0.5479 -0.3527 1.457
+18 -3.4611 1.6996 -0.6007 1.457
+19 -3.5406 -3.3866 0.0352 1.452
+20 -1.1752 2.8058 0.8083 1.452
+21 -3.9501 -0.4002 -0.6798 1.452
+22 -0.6899 -2.2646 1.1579 1.452
+23 0 0 0 1.416
+24 -8.8301 14.3079 -1.7716 1.416
+25 0 0 0 1.416
+26 0 0 0 1.416
+27 -0.9084 6.1447 -0.4852 1.416
+28 0 0 0 1.416
+29 -4.2324 -3.3023 -1.3244 1.53
+30 -4.1028 -0.5941 -0.047 1.53
+31 0 0 0 1.5202
+32 0 0 0 1.5202
+33 0 0 0 1.3649
+34 -2.2208 0.5479 -0.3527 1.457
+35 -3.4611 1.6996 -0.6007 1.457
+36 -15.4174 -7.3055 -1.0749 1.53
+
+BondBond13 Coeffs
+
+1 0 1.5202 1.101
+2 0 1.101 1.101
+3 0 1.53 1.5202
+4 0 1.53 1.101
+5 0 1.53 1.53
+6 0 1.5202 0.965
+7 0 1.202 0.965
+8 0 1.53 1.3649
+9 0 1.101 1.3649
+10 0 1.53 1.202
+11 0 1.101 1.202
+12 0 1.457 1.101
+13 0 1.101 1.101
+14 0 1.53 1.457
+15 0 1.53 1.101
+16 0 1.53 1.53
+17 0 1.53 1.006
+18 0 1.101 1.006
+19 0 1.01 1.53
+20 0 1.01 1.101
+21 0 1.416 1.53
+22 0 1.416 1.101
+23 0 1.452 1.5202
+24 0 1.452 1.202
+25 0 1.452 1.3649
+26 0 1.01 1.5202
+27 0 1.01 1.202
+28 0 1.01 1.3649
+29 0 1.452 1.53
+30 0 1.452 1.101
+31 0 1.53 1.416
+32 0 1.101 1.416
+33 0 1.416 0.965
+34 0 1.006 1.53
+35 0 1.006 1.101
+36 0 1.457 1.53
+
+AngleTorsion Coeffs
+
+1 -0.7466 -0.9448 -0.6321 0.0162 1.4211 -1.4092 108.53 110.77
+2 -0.8085 0.5569 -0.2466 -0.8085 0.5569 -0.2466 110.77 110.77
+3 -0.2607 0.3203 -0.2283 0.0515 -0.0674 -0.0474 112.67 108.53
+4 -0.2454 0 -0.1136 0.3113 0.4516 -0.1988 112.67 110.77
+5 0.3886 -0.3139 0.1389 0.3886 -0.3139 0.1389 112.67 112.67
+6 0 0 0 0 0 0 0 111.254
+7 0 0 0 0 0 0 118.985 111.254
+8 0 0 0 0 0 0 108.53 0
+9 0 0 0 0 0 0 107.734 0
+10 0.0885 -1.3703 -0.5452 0.675 0.5965 0.6725 108.53 123.145
+11 9.1299 -0.4847 0.3582 -1.4946 0.7308 -0.2083 107.734 123.145
+12 -1.1075 0.282 0.8318 0.5111 1.6328 -1.0155 111.91 110.77
+13 -0.8085 0.5569 -0.2466 -0.8085 0.5569 -0.2466 110.77 110.77
+14 -1.9225 -1.345 0.221 2.0125 0.944 -2.7612 112.67 111.91
+15 -0.2454 0 -0.1136 0.3113 0.4516 -0.1988 112.67 110.77
+16 0.3886 -0.3139 0.1389 0.3886 -0.3139 0.1389 112.67 112.67
+17 -3.343 4.4558 -0.0346 0.2873 -0.8072 -0.096 111.91 110.954
+18 -3.9582 2.0063 0.3213 -0.4294 -0.4442 -0.6141 110.62 110.954
+19 -0.5807 0.2041 -0.1384 -2.8967 2.7084 -0.0375 113.868 114.302
+20 -0.3868 0.2041 0.0445 -3.7022 1.3876 0.2393 113.868 108.937
+21 -1.523 1.1296 0.7167 -0.7555 0.0564 1.2177 111.037 114.302
+22 0.0372 -0.3418 -0.0775 -1.5157 2.0781 0.5364 111.037 108.937
+23 5.916 1.7856 0.4052 4.2133 2.9302 3.2903 111.037 116.926
+24 7.4427 2.1505 -0.2206 4.4466 4.0317 1.7129 111.037 125.542
+25 0 0 0 0 0 0 111.037 0
+26 1.9306 0.2105 0.0557 -2.2134 1.2909 0.9726 117.961 116.926
+27 2.3848 0.703 0.1399 -2.6238 0.3606 0.5474 117.961 125.542
+28 0 0 0 0 0 0 117.961 0
+29 0.2039 0.1602 -0.7946 -0.5501 -1.6982 0.2485 114.302 112.67
+30 -1.982 0.2325 -0.3928 -1.2469 1.6933 -1.2081 114.302 110.77
+31 2.1802 -0.0335 -1.3816 2.1221 0.5032 -0.0767 108.53 116.926
+32 7.095 0.0075 0.691 2.0013 0.5068 0.8406 107.734 116.926
+33 0 0 0 0 0 0 0 111.254
+34 0.2873 -0.8072 -0.096 -3.343 4.4558 -0.0346 110.954 111.91
+35 -0.4294 -0.4442 -0.6141 -3.9582 2.0063 0.3213 110.954 110.62
+36 2.0125 0.944 -2.7612 -1.9225 -1.345 0.221 111.91 112.67
+
+Improper Coeffs # class2
+
+1 0 0
+2 0 0
+3 0 0
+4 0 0
+5 0 0
+6 0 0
+7 0 0
+8 0 0
+9 0 0
+10 0 0
+11 0 0
+12 0 0
+13 24.3329 0
+
+AngleAngle Coeffs
+
+1 0 0 0 0 118.985 123.145
+2 0.2738 -0.4825 0.2738 110.77 107.66 110.77
+3 -1.3199 -1.3199 0.1184 112.67 110.77 110.77
+4 2.0403 -1.8202 1.0827 108.53 107.734 110.77
+5 -3.3867 -3.4976 -3.3867 107.734 107.66 107.734
+6 0 0 0 110.954 107.067 110.954
+7 0.2738 -0.4825 0.2738 110.77 107.66 110.77
+8 -1.3199 -1.3199 0.1184 112.67 110.77 110.77
+9 -2.5301 0.5381 2.4286 111.91 110.62 110.77
+10 2.4321 -3.5496 2.4321 110.62 107.66 110.62
+11 0 0 0 123.145 118.985 0
+12 0 0 0 113.868 117.961 111.037
+13 0 0 0 116.926 123.145 125.542
+
+Atoms # full
+
+1 1 1 0.0000000000000000e+00 12.288168 0.738732 4.374280 0 0 0
+2 1 2 2.9999999999999999e-01 13.959928 -0.883144 5.090597 0 0 0
+3 1 3 0.0000000000000000e+00 14.411288 -1.994419 5.682160 0 0 0
+4 1 4 0.0000000000000000e+00 12.881083 0.872503 3.506176 0 0 0
+5 1 4 0.0000000000000000e+00 11.232775 0.801641 3.998777 0 0 0
+6 1 5 0.0000000000000000e+00 13.704366 -2.470396 6.130105 0 0 0
+7 1 1 0.0000000000000000e+00 12.489752 -0.793693 4.710639 0 0 0
+8 1 1 0.0000000000000000e+00 12.455071 1.866388 5.385870 0 0 0
+9 1 1 0.0000000000000000e+00 11.248961 1.901849 6.347664 0 0 0
+10 1 2 2.9999999999999999e-01 10.005971 2.466710 5.772840 -1 1 0
+11 1 6 0.0000000000000000e+00 14.795360 -0.034436 4.807367 0 0 0
+12 1 6 0.0000000000000000e+00 9.115239 1.654547 5.617002 -1 0 0
+13 1 3 0.0000000000000000e+00 9.745096 3.807654 5.573585 -1 1 0
+14 1 4 0.0000000000000000e+00 12.248215 -1.371492 3.808598 0 0 0
+15 1 4 0.0000000000000000e+00 11.715755 -1.036825 5.500449 0 0 0
+16 1 4 0.0000000000000000e+00 12.559724 2.807687 4.858452 0 1 0
+17 1 4 0.0000000000000000e+00 13.299968 1.616570 6.123781 0 0 0
+18 1 4 0.0000000000000000e+00 11.650505 2.330454 7.282410 0 1 0
+19 1 4 0.0000000000000000e+00 10.888420 0.913219 6.637162 -1 0 0
+20 1 5 0.0000000000000000e+00 10.550073 4.294209 5.758192 -1 1 0
+21 2 1 0.0000000000000000e+00 5.851425 1.929552 6.038335 0 0 0
+22 2 1 0.0000000000000000e+00 6.741509 3.160751 6.233074 0 0 0
+23 2 7 -2.9999999999999999e-01 7.957761 3.121780 5.252257 1 0 0
+24 2 7 -2.9999999999999999e-01 2.599653 -2.258940 5.985863 0 -1 0
+25 2 1 0.0000000000000000e+00 3.834337 -1.907078 5.441528 0 -1 0
+26 2 1 0.0000000000000000e+00 4.810793 -1.083699 6.310184 0 -1 0
+27 2 4 0.0000000000000000e+00 6.505912 1.182799 5.449104 0 0 0
+28 2 4 0.0000000000000000e+00 5.156429 2.256468 5.348423 0 0 0
+29 2 4 0.0000000000000000e+00 7.232782 3.178785 7.181911 0 0 0
+30 2 4 0.0000000000000000e+00 6.251671 4.103621 6.222913 0 0 0
+31 2 8 0.0000000000000000e+00 8.249909 4.070668 4.881297 1 0 0
+32 2 8 0.0000000000000000e+00 7.813025 2.623184 4.400744 1 0 0
+33 2 8 0.0000000000000000e+00 2.626695 -2.857547 6.817247 0 -1 0
+34 2 8 0.0000000000000000e+00 1.955281 -2.684319 5.328460 0 -1 0
+35 2 4 0.0000000000000000e+00 3.637708 -1.322842 4.469265 0 -1 0
+36 2 4 0.0000000000000000e+00 4.415570 -2.739689 4.997336 0 -1 0
+37 2 4 0.0000000000000000e+00 5.710714 -1.010014 5.642798 0 -1 0
+38 2 4 0.0000000000000000e+00 5.103831 -1.696423 7.160345 0 -1 0
+39 2 1 0.0000000000000000e+00 5.270763 1.286629 7.308822 0 0 0
+40 2 4 0.0000000000000000e+00 4.834381 2.168531 7.931687 0 0 1
+41 2 4 0.0000000000000000e+00 6.118354 0.786724 7.794709 0 0 1
+42 2 1 0.0000000000000000e+00 4.273849 0.167695 6.957862 0 -1 0
+43 2 4 0.0000000000000000e+00 3.792544 -0.081782 7.904418 0 -1 1
+44 2 4 0.0000000000000000e+00 3.527495 0.674238 6.348869 0 0 0
+
+Velocities
+
+1 -2.4626989626218821e-03 -1.5920230003311222e-03 -3.0621927786115238e-03
+2 9.5082416704385837e-03 -6.9903166167507250e-03 1.3702671335945608e-02
+3 2.3431518493187576e-03 -2.9261683108242173e-03 1.4269399726982105e-03
+4 -1.8184451408256214e-02 3.1103803691687960e-02 -1.3358827768357973e-02
+5 2.6084132471017967e-02 -1.0819576493517332e-02 3.0403384454794881e-02
+6 -4.7312115958218744e-03 -1.9111462399478338e-02 -3.6793354156497558e-02
+7 -7.5068797595949869e-03 6.5661422055962489e-03 1.3226575122695422e-03
+8 3.3807881380161281e-03 3.0458732663557089e-03 2.2368826795446284e-03
+9 -3.1113905793879316e-03 8.2908867720754773e-03 -1.7561238039496530e-03
+10 2.4685206571693056e-03 1.3194776209841030e-03 -2.8041877032800441e-03
+11 -3.4945605770565296e-03 3.2323777135621814e-03 1.6223017668450866e-03
+12 -6.1153483612847778e-03 -5.1534857074262185e-03 1.7735747357354274e-03
+13 2.1384296781859011e-04 -4.5398902942729667e-03 6.1649769894413760e-03
+14 2.5004619864373401e-03 -1.5709184283264888e-03 2.0837548254667757e-02
+15 6.0547939205643532e-03 -1.2650704436910937e-02 -5.4430753266962190e-03
+16 -1.0374605775698001e-02 9.1408658463889240e-03 -1.1306875858287088e-02
+17 -1.2736499128987409e-02 -9.1726811852506501e-03 5.1136502685461254e-03
+18 7.6741778607048112e-03 1.8629856635459279e-02 -1.1300096447670932e-02
+19 -1.8616138775281121e-02 1.0848388547730185e-03 -5.7118433687798576e-03
+20 5.4137572241479059e-03 -1.4564578166395727e-02 -1.2618420441909540e-02
+21 5.8473521452312256e-03 -4.0595286000332086e-03 -6.2517801580146415e-03
+22 3.6402033824753104e-03 -1.4629540504663154e-03 -4.0030712318898046e-03
+23 9.0266305019107689e-03 -2.7511425384659687e-03 4.5576402565437142e-03
+24 -1.3102302415548614e-02 -4.7286703965305791e-03 -1.8966887841189517e-03
+25 7.8621682621103171e-03 -4.2046313540949568e-03 9.6887957374751301e-04
+26 -4.7380176438337968e-03 9.6090441940775827e-03 -8.7592431387039336e-03
+27 5.4311658811632517e-03 2.0032224663495989e-02 -9.4952076489808503e-03
+28 -2.9056381493904374e-03 3.3317109723156875e-03 1.6650350064426677e-02
+29 -6.4569944033489122e-03 2.8423983541959541e-03 -2.6066912906505167e-02
+30 -2.2173867823429387e-02 1.4628839880961319e-02 -2.3330833961402380e-02
+31 9.1925713381983114e-03 -2.5697556639281928e-03 -1.2822203161488303e-02
+32 -8.3206975051927905e-03 -2.2538429924858707e-03 7.7620244118580314e-03
+33 1.9920685674825727e-02 5.0317764848494097e-03 -2.1106672824976403e-02
+34 1.4118463330250982e-02 1.7455545466840316e-02 -1.2482101375598437e-02
+35 -6.1116505640437966e-03 1.3353021777303568e-02 -2.5492434283827668e-02
+36 9.1001521565859649e-03 5.5737774505222404e-03 1.4573768978939985e-02
+37 1.6523593470528035e-03 -2.2107518020000917e-02 2.0311423445130115e-02
+38 -1.0346275393471860e-02 1.6055856586351790e-02 5.5489127019262424e-03
+39 -3.2054811383248638e-03 1.6779208962376315e-03 2.9390509537535661e-03
+40 1.9649219364916443e-02 4.0815776523222859e-03 -9.8422441166041274e-03
+41 5.6961697588160361e-04 7.1361132234741477e-04 4.6335764220256257e-03
+42 2.2221300208006252e-03 3.6217319632558197e-03 -6.3299398503455151e-03
+43 2.5710172734841170e-03 8.0029179814482924e-03 1.9992986928468189e-02
+44 -6.0827581822674656e-03 -1.1834273655641976e-02 2.0526923045885208e-02
+
+Bonds
+
+1 1 1 5
+2 1 1 4
+3 2 1 7
+4 2 1 8
+5 3 2 3
+6 5 2 11
+7 6 3 6
+8 4 7 2
+9 1 7 14
+10 1 7 15
+11 2 8 9
+12 1 8 16
+13 1 8 17
+14 4 9 10
+15 1 9 18
+16 1 9 19
+17 5 10 12
+18 3 10 13
+19 6 13 20
+20 7 21 22
+21 8 21 27
+22 8 21 28
+23 7 21 39
+24 9 22 23
+25 8 22 29
+26 8 22 30
+27 10 23 31
+28 10 23 32
+29 10 24 33
+30 10 24 34
+31 9 25 24
+32 7 25 26
+33 8 25 35
+34 8 25 36
+35 8 26 37
+36 8 26 38
+37 7 26 42
+38 8 39 40
+39 8 39 41
+40 7 39 42
+41 8 42 43
+42 8 42 44
+
+Angles
+
+1 1 5 1 4
+2 2 7 1 5
+3 2 8 1 5
+4 2 7 1 4
+5 2 8 1 4
+6 3 7 1 8
+7 4 7 2 3
+8 5 3 2 11
+9 6 7 2 11
+10 7 2 3 6
+11 8 1 7 2
+12 2 1 7 14
+13 2 1 7 15
+14 9 2 7 14
+15 9 2 7 15
+16 1 14 7 15
+17 3 1 8 9
+18 2 1 8 16
+19 2 1 8 17
+20 2 9 8 16
+21 2 9 8 17
+22 1 16 8 17
+23 8 8 9 10
+24 2 8 9 18
+25 2 8 9 19
+26 9 10 9 18
+27 9 10 9 19
+28 1 18 9 19
+29 6 9 10 12
+30 4 9 10 13
+31 5 13 10 12
+32 7 10 13 20
+33 10 22 21 27
+34 10 22 21 28
+35 11 22 21 39
+36 12 27 21 28
+37 10 39 21 27
+38 10 39 21 28
+39 13 21 22 23
+40 10 21 22 29
+41 10 21 22 30
+42 14 23 22 29
+43 14 23 22 30
+44 12 29 22 30
+45 15 22 23 31
+46 15 22 23 32
+47 16 31 23 32
+48 15 25 24 33
+49 15 25 24 34
+50 16 33 24 34
+51 13 26 25 24
+52 14 24 25 35
+53 14 24 25 36
+54 10 26 25 35
+55 10 26 25 36
+56 12 35 25 36
+57 10 25 26 37
+58 10 25 26 38
+59 11 25 26 42
+60 12 37 26 38
+61 10 42 26 37
+62 10 42 26 38
+63 10 21 39 40
+64 10 21 39 41
+65 11 21 39 42
+66 12 40 39 41
+67 10 42 39 40
+68 10 42 39 41
+69 11 26 42 39
+70 10 26 42 43
+71 10 26 42 44
+72 10 39 42 43
+73 10 39 42 44
+74 12 43 42 44
+
+Dihedrals
+
+1 2 5 1 7 14
+2 2 5 1 7 15
+3 2 4 1 7 14
+4 2 4 1 7 15
+5 3 8 1 7 2
+6 4 8 1 7 14
+7 4 8 1 7 15
+8 2 5 1 8 16
+9 2 5 1 8 17
+10 2 4 1 8 16
+11 2 4 1 8 17
+12 5 7 1 8 9
+13 4 7 1 8 16
+14 4 7 1 8 17
+15 6 7 2 3 6
+16 7 11 2 3 6
+17 1 2 7 1 5
+18 1 2 7 1 4
+19 8 1 7 2 3
+20 9 14 7 2 3
+21 9 15 7 2 3
+22 10 1 7 2 11
+23 11 14 7 2 11
+24 11 15 7 2 11
+25 4 9 8 1 5
+26 4 9 8 1 4
+27 3 1 8 9 10
+28 4 1 8 9 18
+29 4 1 8 9 19
+30 2 16 8 9 18
+31 2 16 8 9 19
+32 2 17 8 9 18
+33 2 17 8 9 19
+34 1 10 9 8 16
+35 1 10 9 8 17
+36 10 8 9 10 12
+37 8 8 9 10 13
+38 11 18 9 10 12
+39 9 18 9 10 13
+40 11 19 9 10 12
+41 9 19 9 10 13
+42 6 9 10 13 20
+43 7 12 10 13 20
+44 13 27 21 22 29
+45 13 27 21 22 30
+46 13 28 21 22 29
+47 13 28 21 22 30
+48 14 39 21 22 23
+49 15 39 21 22 29
+50 15 39 21 22 30
+51 15 22 21 39 40
+52 15 22 21 39 41
+53 16 22 21 39 42
+54 13 27 21 39 40
+55 13 27 21 39 41
+56 13 28 21 39 40
+57 13 28 21 39 41
+58 12 23 22 21 27
+59 12 23 22 21 28
+60 17 21 22 23 31
+61 17 21 22 23 32
+62 18 29 22 23 31
+63 18 29 22 23 32
+64 18 30 22 23 31
+65 18 30 22 23 32
+66 17 26 25 24 33
+67 18 35 25 24 33
+68 18 36 25 24 33
+69 17 26 25 24 34
+70 18 35 25 24 34
+71 18 36 25 24 34
+72 12 24 25 26 37
+73 12 24 25 26 38
+74 13 35 25 26 37
+75 13 35 25 26 38
+76 13 36 25 26 37
+77 13 36 25 26 38
+78 14 42 26 25 24
+79 15 42 26 25 35
+80 15 42 26 25 36
+81 16 25 26 42 39
+82 15 25 26 42 43
+83 15 25 26 42 44
+84 13 37 26 42 43
+85 13 37 26 42 44
+86 13 38 26 42 43
+87 13 38 26 42 44
+88 15 42 39 21 27
+89 15 42 39 21 28
+90 16 21 39 42 26
+91 15 21 39 42 43
+92 15 21 39 42 44
+93 13 40 39 42 43
+94 13 40 39 42 44
+95 13 41 39 42 43
+96 13 41 39 42 44
+97 15 39 42 26 37
+98 15 39 42 26 38
+99 15 26 42 39 40
+100 15 26 42 39 41
+
+Impropers
+
+1 2 7 1 4 5
+2 2 8 1 4 5
+3 3 7 1 8 5
+4 3 7 1 8 4
+5 1 7 2 3 11
+6 4 1 7 2 14
+7 4 1 7 2 15
+8 2 1 7 14 15
+9 5 2 7 14 15
+10 3 1 8 9 16
+11 3 1 8 9 17
+12 2 1 8 16 17
+13 2 9 8 16 17
+14 4 8 9 10 18
+15 4 8 9 10 19
+16 2 8 9 18 19
+17 5 10 9 18 19
+18 1 9 10 13 12
+19 7 22 21 27 28
+20 8 22 21 39 27
+21 8 22 21 39 28
+22 7 39 21 28 27
+23 9 21 22 23 29
+24 9 21 22 23 30
+25 7 21 22 29 30
+26 10 23 22 29 30
+27 6 22 23 31 32
+28 6 25 24 33 34
+29 9 26 25 24 35
+30 9 26 25 24 36
+31 10 24 25 35 36
+32 7 26 25 35 36
+33 7 25 26 37 38
+34 8 25 26 42 37
+35 8 25 26 42 38
+36 7 42 26 38 37
+37 7 21 39 40 41
+38 8 21 39 42 40
+39 8 21 39 42 41
+40 7 42 39 41 40
+41 8 26 42 39 43
+42 8 26 42 39 44
+43 7 26 42 43 44
+44 7 39 42 43 44
diff --git a/examples/rigid/in.rigid-atomfile b/examples/rigid/in.rigid.atomfile
similarity index 100%
rename from examples/rigid/in.rigid-atomfile
rename to examples/rigid/in.rigid.atomfile
diff --git a/examples/rigid/in.rigid-atomvar b/examples/rigid/in.rigid.atomvar
similarity index 100%
rename from examples/rigid/in.rigid-atomvar
rename to examples/rigid/in.rigid.atomvar
diff --git a/examples/rigid/in.rigid.early b/examples/rigid/in.rigid.early
new file mode 100644
index 0000000000000000000000000000000000000000..6f04ba40f4fb3ca879f9955c964cdc7716014656
--- /dev/null
+++ b/examples/rigid/in.rigid.early
@@ -0,0 +1,83 @@
+# Simple rigid body system
+
+units lj
+atom_style atomic
+
+pair_style lj/cut 2.5
+
+read_data data.rigid
+
+velocity all create 100.0 4928459
+
+# unconnected bodies
+
+group clump1 id <> 1 9
+group clump2 id <> 10 18
+group clump3 id <> 19 27
+group clump4 id <> 28 36
+group clump5 id <> 37 45
+group clump6 id <> 46 54
+group clump7 id <> 55 63
+group clump8 id <> 64 72
+group clump9 id <> 73 81
+
+fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 &
+ clump6 clump7 clump8 clump9
+
+fix_modify 1 bodyforces early
+
+# 1 chain of connected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 9 18
+#group clump3 id <> 18 27
+#group clump4 id <> 27 36
+#group clump5 id <> 36 45
+#group clump6 id <> 45 54
+#group clump7 id <> 54 63
+#group clump8 id <> 63 72
+#group clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 &
+# clump6 clump7 clump8 clump9
+
+# 2 chains of connected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 9 18
+#group clump3 id <> 18 27
+#group clump4 id <> 27 36
+#group clump5 id <> 37 45
+#group clump6 id <> 45 54
+#group clump7 id <> 54 63
+#group clump8 id <> 63 72
+#group clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4
+#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
+
+neigh_modify exclude group clump1 clump1
+neigh_modify exclude group clump2 clump2
+neigh_modify exclude group clump3 clump3
+neigh_modify exclude group clump4 clump4
+neigh_modify exclude group clump5 clump5
+neigh_modify exclude group clump6 clump6
+neigh_modify exclude group clump7 clump7
+neigh_modify exclude group clump8 clump8
+neigh_modify exclude group clump9 clump9
+
+thermo 100
+
+#dump 1 all atom 50 dump.rigid
+
+#dump 2 all image 100 image.*.jpg type type &
+# axes yes 0.8 0.02 view 60 -30
+#dump_modify 2 pad 5
+
+#dump 3 all movie 100 movie.mpg type type &
+# axes yes 0.8 0.02 view 60 -30
+#dump_modify 3 pad 5
+
+timestep 0.0001
+thermo 50
+run 10000
diff --git a/examples/rigid/in.rigid.nve b/examples/rigid/in.rigid.nve
new file mode 100644
index 0000000000000000000000000000000000000000..d61cdecfe8ac021110939746c5d908fe741d7523
--- /dev/null
+++ b/examples/rigid/in.rigid.nve
@@ -0,0 +1,81 @@
+# Simple rigid body system
+
+units lj
+atom_style atomic
+
+pair_style lj/cut 2.5
+
+read_data data.rigid
+
+velocity all create 100.0 4928459
+
+# unconnected bodies
+
+group clump1 id <> 1 9
+group clump2 id <> 10 18
+group clump3 id <> 19 27
+group clump4 id <> 28 36
+group clump5 id <> 37 45
+group clump6 id <> 46 54
+group clump7 id <> 55 63
+group clump8 id <> 64 72
+group clump9 id <> 73 81
+
+fix 1 all rigid/nve group 9 clump1 clump2 clump3 clump4 clump5 &
+ clump6 clump7 clump8 clump9
+
+# 1 chain of connected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 9 18
+#group clump3 id <> 18 27
+#group clump4 id <> 27 36
+#group clump5 id <> 36 45
+#group clump6 id <> 45 54
+#group clump7 id <> 54 63
+#group clump8 id <> 63 72
+#group clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 &
+# clump6 clump7 clump8 clump9
+
+# 2 chains of connected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 9 18
+#group clump3 id <> 18 27
+#group clump4 id <> 27 36
+#group clump5 id <> 37 45
+#group clump6 id <> 45 54
+#group clump7 id <> 54 63
+#group clump8 id <> 63 72
+#group clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4
+#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
+
+neigh_modify exclude group clump1 clump1
+neigh_modify exclude group clump2 clump2
+neigh_modify exclude group clump3 clump3
+neigh_modify exclude group clump4 clump4
+neigh_modify exclude group clump5 clump5
+neigh_modify exclude group clump6 clump6
+neigh_modify exclude group clump7 clump7
+neigh_modify exclude group clump8 clump8
+neigh_modify exclude group clump9 clump9
+
+thermo 100
+
+#dump 1 all atom 50 dump.rigid
+
+#dump 2 all image 100 image.*.jpg type type &
+# axes yes 0.8 0.02 view 60 -30
+#dump_modify 2 pad 5
+
+#dump 3 all movie 100 movie.mpg type type &
+# axes yes 0.8 0.02 view 60 -30
+#dump_modify 3 pad 5
+
+timestep 0.0001
+thermo 50
+run 10000
diff --git a/examples/rigid/in.rigid.nve.early b/examples/rigid/in.rigid.nve.early
new file mode 100644
index 0000000000000000000000000000000000000000..86e970ee75151de0d51f253585b80b9dc2a081f0
--- /dev/null
+++ b/examples/rigid/in.rigid.nve.early
@@ -0,0 +1,83 @@
+# Simple rigid body system
+
+units lj
+atom_style atomic
+
+pair_style lj/cut 2.5
+
+read_data data.rigid
+
+velocity all create 100.0 4928459
+
+# unconnected bodies
+
+group clump1 id <> 1 9
+group clump2 id <> 10 18
+group clump3 id <> 19 27
+group clump4 id <> 28 36
+group clump5 id <> 37 45
+group clump6 id <> 46 54
+group clump7 id <> 55 63
+group clump8 id <> 64 72
+group clump9 id <> 73 81
+
+fix 1 all rigid/nve group 9 clump1 clump2 clump3 clump4 clump5 &
+ clump6 clump7 clump8 clump9
+
+fix_modify 1 bodyforces early
+
+# 1 chain of connected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 9 18
+#group clump3 id <> 18 27
+#group clump4 id <> 27 36
+#group clump5 id <> 36 45
+#group clump6 id <> 45 54
+#group clump7 id <> 54 63
+#group clump8 id <> 63 72
+#group clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 &
+# clump6 clump7 clump8 clump9
+
+# 2 chains of connected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 9 18
+#group clump3 id <> 18 27
+#group clump4 id <> 27 36
+#group clump5 id <> 37 45
+#group clump6 id <> 45 54
+#group clump7 id <> 54 63
+#group clump8 id <> 63 72
+#group clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4
+#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
+
+neigh_modify exclude group clump1 clump1
+neigh_modify exclude group clump2 clump2
+neigh_modify exclude group clump3 clump3
+neigh_modify exclude group clump4 clump4
+neigh_modify exclude group clump5 clump5
+neigh_modify exclude group clump6 clump6
+neigh_modify exclude group clump7 clump7
+neigh_modify exclude group clump8 clump8
+neigh_modify exclude group clump9 clump9
+
+thermo 100
+
+#dump 1 all atom 50 dump.rigid
+
+#dump 2 all image 100 image.*.jpg type type &
+# axes yes 0.8 0.02 view 60 -30
+#dump_modify 2 pad 5
+
+#dump 3 all movie 100 movie.mpg type type &
+# axes yes 0.8 0.02 view 60 -30
+#dump_modify 3 pad 5
+
+timestep 0.0001
+thermo 50
+run 10000
diff --git a/examples/rigid/in.rigid-property b/examples/rigid/in.rigid.property
similarity index 100%
rename from examples/rigid/in.rigid-property
rename to examples/rigid/in.rigid.property
diff --git a/examples/rigid/log.20Apr18.rigid.atomfile.g++.1 b/examples/rigid/log.20Apr18.rigid.atomfile.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..c66711c41c26e15490051359a8990e3c6fbd402b
--- /dev/null
+++ b/examples/rigid/log.20Apr18.rigid.atomfile.g++.1
@@ -0,0 +1,338 @@
+LAMMPS (20 Apr 2018)
+ using 1 OpenMP thread(s) per MPI task
+# Simple rigid body system
+
+units lj
+atom_style atomic
+atom_modify map array
+
+pair_style lj/cut 2.5
+
+read_data data.rigid
+ orthogonal box = (-12 -12 -12) to (12 12 12)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 81 atoms
+
+velocity all create 100.0 4928459
+
+
+# unconnected bodies
+
+group clump1 id <> 1 9
+9 atoms in group clump1
+group clump2 id <> 10 18
+9 atoms in group clump2
+group clump3 id <> 19 27
+9 atoms in group clump3
+group clump4 id <> 28 36
+9 atoms in group clump4
+group clump5 id <> 37 45
+9 atoms in group clump5
+group clump6 id <> 46 54
+9 atoms in group clump6
+group clump7 id <> 55 63
+9 atoms in group clump7
+group clump8 id <> 64 72
+9 atoms in group clump8
+group clump9 id <> 73 81
+9 atoms in group clump9
+
+variable bodies atomfile bodies.txt
+fix 1 all rigid custom v_bodies
+9 rigid bodies with 81 atoms
+
+# 1 chain of connected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 9 18
+#group clump3 id <> 18 27
+#group clump4 id <> 27 36
+#group clump5 id <> 36 45
+#group clump6 id <> 45 54
+#group clump7 id <> 54 63
+#group clump8 id <> 63 72
+#group clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
+
+# 2 chains of connected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 9 18
+#group clump3 id <> 18 27
+#group clump4 id <> 27 36
+#group clump5 id <> 37 45
+#group clump6 id <> 45 54
+#group clump7 id <> 54 63
+#group clump8 id <> 63 72
+#group clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4
+#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
+
+neigh_modify exclude group clump1 clump1
+neigh_modify exclude group clump2 clump2
+neigh_modify exclude group clump3 clump3
+neigh_modify exclude group clump4 clump4
+neigh_modify exclude group clump5 clump5
+neigh_modify exclude group clump6 clump6
+neigh_modify exclude group clump7 clump7
+neigh_modify exclude group clump8 clump8
+neigh_modify exclude group clump9 clump9
+
+thermo 100
+
+#dump 1 all atom 50 dump.rigid
+
+#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 2 pad 5
+
+#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 3 pad 5
+
+timestep 0.0001
+thermo 50
+run 10000
+Neighbor list info ...
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 18 18 18
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 4.109 | 4.109 | 4.109 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 115.29439 5235.9179 0 5272.2142 -2.7403788
+ 50 14910.685 571.71558 0 5265.82 32.006171
+ 100 16298.442 136.66184 0 5267.653 16.444229
+ 150 16682.606 17.490511 0 5269.4219 14.900344
+ 200 16733.929 1.372872 0 5269.4617 14.569267
+ 250 16738.853 -0.15252816 0 5269.4864 14.496404
+ 300 16738.588 -0.055171335 0 5269.5002 14.496025
+ 350 16738.492 -0.017444677 0 5269.5077 14.496446
+ 400 16738.464 -0.0060102023 0 5269.5104 14.496618
+ 450 16738.455 -0.0012713351 0 5269.5124 14.496701
+ 500 16738.455 -0.00081068621 0 5269.5128 14.496709
+ 550 16738.455 -0.00083203497 0 5269.5129 14.496707
+ 600 16738.455 -0.00058355356 0 5269.5131 14.496709
+ 650 16738.455 -0.00047226704 0 5269.5131 14.496708
+ 700 16738.455 0 0 5269.5136 14.496713
+ 750 16738.455 0 0 5269.5136 14.49671
+ 800 16738.455 0 0 5269.5137 14.496709
+ 850 16738.455 0 0 5269.5137 14.49671
+ 900 16738.456 0 0 5269.5138 14.496713
+ 950 16738.462 -0.0035323872 0 5269.5122 14.496671
+ 1000 16738.586 -0.051135144 0 5269.5036 14.496229
+ 1050 16737.358 0.32995057 0 5269.4981 14.525763
+ 1100 16737.892 0.16210246 0 5269.4984 14.531983
+ 1150 16738.703 -0.089235095 0 5269.5025 14.509899
+ 1200 16738.466 -0.0075446243 0 5269.5096 14.510615
+ 1250 16738.456 0 0 5269.514 14.510704
+ 1300 16738.457 0 0 5269.5141 14.510701
+ 1350 16738.457 0 0 5269.5141 14.510699
+ 1400 16738.457 -0.00044736511 0 5269.5138 14.510693
+ 1450 16738.458 -0.0010971179 0 5269.5134 14.510687
+ 1500 16738.458 -0.00057885428 0 5269.5139 14.510698
+ 1550 16738.457 0 0 5269.5143 14.51071
+ 1600 16738.457 0 0 5269.5144 14.510712
+ 1650 16738.457 0 0 5269.5144 14.510712
+ 1700 16738.458 0 0 5269.5144 14.51071
+ 1750 16738.458 0 0 5269.5145 14.510708
+ 1800 16738.458 0 0 5269.5145 14.510706
+ 1850 16738.458 0 0 5269.5146 14.510705
+ 1900 16738.458 0 0 5269.5146 14.510706
+ 1950 16738.465 -0.0031733615 0 5269.5134 14.510659
+ 2000 16738.491 -0.013255268 0 5269.5117 14.510532
+ 2050 16738.556 -0.0365811 0 5269.5087 14.51029
+ 2100 16738.633 -0.063209659 0 5269.5065 14.510219
+ 2150 16738.607 -0.05601761 0 5269.5055 14.510231
+ 2200 16738.557 -0.038423032 0 5269.5072 14.510404
+ 2250 16738.515 -0.023709918 0 5269.5088 14.510539
+ 2300 16738.489 -0.013249035 0 5269.5111 14.510621
+ 2350 16738.468 -0.0045563719 0 5269.5131 14.510714
+ 2400 16738.46 -0.00052194273 0 5269.5146 14.510771
+ 2450 16738.464 -0.0023259756 0 5269.514 14.510746
+ 2500 16738.468 -0.0051929186 0 5269.5127 14.510731
+ 2550 16738.581 -0.044940117 0 5269.5085 14.510315
+ 2600 16738.427 -7.9722839e-05 0 5269.5046 14.510657
+ 2650 16733.017 1.705148 0 5269.5067 14.596295
+ 2700 16738.761 -0.10614946 0 5269.5038 14.499584
+ 2750 16733.973 1.4038179 0 5269.5064 14.598107
+ 2800 16738.585 -0.046813448 0 5269.5076 14.511073
+ 2850 16738.487 -0.012558719 0 5269.5111 14.510111
+ 2900 16738.465 -0.0026252725 0 5269.514 14.510277
+ 2950 16738.476 -0.0082220764 0 5269.512 14.510223
+ 3000 16738.66 -0.071284779 0 5269.507 14.509758
+ 3050 16715.332 7.2419351 0 5269.476 14.870305
+ 3100 16653.226 26.818761 0 5269.5009 14.496764
+ 3150 16739.351 -0.30690375 0 5269.4886 13.643904
+ 3200 16733.238 1.6025328 0 5269.4737 12.016934
+ 3250 16734.374 1.2554429 0 5269.4841 11.963561
+ 3300 16732.156 1.9585967 0 5269.4893 12.234024
+ 3350 16738.655 -0.079693236 0 5269.497 12.092757
+ 3400 16738.543 -0.042215005 0 5269.4991 12.092809
+ 3450 16738.591 -0.059327511 0 5269.4972 12.092536
+ 3500 16738.759 -0.11761245 0 5269.4918 12.09203
+ 3550 16713.405 7.846062 0 5269.4737 12.389816
+ 3600 16734.939 1.0821936 0 5269.4891 12.173591
+ 3650 16738.808 -0.13663194 0 5269.4882 12.027009
+ 3700 16738.602 -0.070934367 0 5269.4889 12.025288
+ 3750 16737.731 0.20706557 0 5269.4927 12.061948
+ 3800 16738.578 -0.05582043 0 5269.4965 12.035665
+ 3850 16738.471 -0.016307928 0 5269.5024 12.035302
+ 3900 16738.449 -0.0058182199 0 5269.5059 12.035401
+ 3950 16738.439 -0.0012027325 0 5269.5074 12.035461
+ 4000 16738.436 -0.00020698452 0 5269.5075 12.035469
+ 4050 16738.437 0 0 5269.5078 12.035454
+ 4100 16738.437 0 0 5269.508 12.035435
+ 4150 16738.438 0 0 5269.5081 12.035426
+ 4200 16738.438 0 0 5269.5083 12.035432
+ 4250 16738.439 0 0 5269.5085 12.035447
+ 4300 16738.439 0 0 5269.5086 12.035463
+ 4350 16738.44 0 0 5269.5087 12.035474
+ 4400 16738.44 0 0 5269.5088 12.035478
+ 4450 16738.44 0 0 5269.5089 12.035474
+ 4500 16738.44 0 0 5269.509 12.035462
+ 4550 16738.441 0 0 5269.5092 12.035449
+ 4600 16738.441 0 0 5269.5093 12.035445
+ 4650 16738.442 0 0 5269.5095 12.035451
+ 4700 16738.442 0 0 5269.5096 12.03546
+ 4750 16738.443 0 0 5269.5097 12.035465
+ 4800 16738.443 0 0 5269.5098 12.035466
+ 4850 16738.443 0 0 5269.51 12.035463
+ 4900 16738.444 0 0 5269.5101 12.035456
+ 4950 16738.444 0 0 5269.5102 12.035447
+ 5000 16738.445 0 0 5269.5104 12.03544
+ 5050 16738.445 0 0 5269.5105 12.035442
+ 5100 16738.446 0 0 5269.5107 12.035455
+ 5150 16738.446 0 0 5269.5108 12.03547
+ 5200 16738.446 0 0 5269.5109 12.035479
+ 5250 16738.447 0 0 5269.511 12.035479
+ 5300 16738.447 0 0 5269.5111 12.03547
+ 5350 16738.447 0 0 5269.5112 12.035454
+ 5400 16738.448 0 0 5269.5113 12.035434
+ 5450 16738.448 0 0 5269.5115 12.03542
+ 5500 16738.449 0 0 5269.5117 12.035422
+ 5550 16738.457 -0.0030919234 0 5269.5111 12.035383
+ 5600 16738.51 -0.021618357 0 5269.5092 12.035106
+ 5650 16738.622 -0.059214788 0 5269.507 12.035694
+ 5700 16395.28 108.06942 0 5269.5463 24.369038
+ 5750 16738.544 -0.033973429 0 5269.5077 12.011261
+ 5800 16738.456 -0.0037013529 0 5269.5102 12.011675
+ 5850 16738.451 0 0 5269.5123 12.011709
+ 5900 16738.451 -0.00022115871 0 5269.5122 12.011687
+ 5950 16738.452 -0.00024253349 0 5269.5124 12.011678
+ 6000 16738.452 0 0 5269.5128 12.011688
+ 6050 16738.453 0 0 5269.513 12.011702
+ 6100 16738.453 0 0 5269.5131 12.011716
+ 6150 16738.454 0 0 5269.5132 12.011725
+ 6200 16738.454 0 0 5269.5133 12.011728
+ 6250 16738.454 0 0 5269.5134 12.011723
+ 6300 16738.455 0 0 5269.5135 12.011712
+ 6350 16738.455 0 0 5269.5137 12.0117
+ 6400 16738.456 0 0 5269.5138 12.011697
+ 6450 16738.456 0 0 5269.514 12.011704
+ 6500 16738.456 0 0 5269.5141 12.011714
+ 6550 16738.457 0 0 5269.5142 12.011719
+ 6600 16738.457 0 0 5269.5143 12.011718
+ 6650 16738.458 0 0 5269.5144 12.011713
+ 6700 16738.458 0 0 5269.5146 12.011705
+ 6750 16738.459 0 0 5269.5147 12.011696
+ 6800 16738.459 0 0 5269.5149 12.01169
+ 6850 16738.46 0 0 5269.515 12.011695
+ 6900 16738.46 0 0 5269.5152 12.01171
+ 6950 16738.46 0 0 5269.5153 12.011726
+ 7000 16738.461 0 0 5269.5154 12.011736
+ 7050 16738.461 0 0 5269.5155 12.011737
+ 7100 16738.461 0 0 5269.5155 12.011728
+ 7150 16738.461 0 0 5269.5156 12.011712
+ 7200 16738.462 0 0 5269.5158 12.011691
+ 7250 16738.463 0 0 5269.516 12.011676
+ 7300 16738.463 0 0 5269.5162 12.011677
+ 7350 16738.464 0 0 5269.5164 12.011693
+ 7400 16738.464 0 0 5269.5165 12.011713
+ 7450 16738.465 0 0 5269.5166 12.011729
+ 7500 16738.465 0 0 5269.5167 12.011736
+ 7550 16738.465 0 0 5269.5168 12.011734
+ 7600 16738.465 0 0 5269.5168 12.011722
+ 7650 16738.466 0 0 5269.517 12.011704
+ 7700 16738.466 0 0 5269.5171 12.011687
+ 7750 16738.467 0 0 5269.5173 12.011681
+ 7800 16738.467 0 0 5269.5175 12.011687
+ 7850 16738.468 0 0 5269.5176 12.0117
+ 7900 16738.468 0 0 5269.5178 12.011712
+ 7950 16738.469 0 0 5269.5179 12.011721
+ 8000 16738.469 0 0 5269.518 12.011724
+ 8050 16738.469 0 0 5269.5181 12.01172
+ 8100 16738.47 0 0 5269.5182 12.011709
+ 8150 16738.47 0 0 5269.5183 12.0117
+ 8200 16738.47 0 0 5269.5185 12.0117
+ 8250 16738.471 0 0 5269.5186 12.011709
+ 8300 16738.471 0 0 5269.5187 12.011719
+ 8350 16738.472 0 0 5269.5189 12.011723
+ 8400 16738.472 0 0 5269.519 12.01172
+ 8450 16738.473 -0.00039690663 0 5269.5189 12.011706
+ 8500 16738.481 -0.0034646802 0 5269.5182 12.011643
+ 8550 16738.483 -0.0045307409 0 5269.5178 12.011621
+ 8600 16738.474 -0.00076532813 0 5269.5189 12.011681
+ 8650 16738.474 0 0 5269.5197 12.011699
+ 8700 16738.475 0 0 5269.5199 12.011715
+ 8750 16738.475 0 0 5269.52 12.011732
+ 8800 16738.475 0 0 5269.52 12.011743
+ 8850 16738.476 0 0 5269.5201 12.011744
+ 8900 16738.476 0 0 5269.5202 12.011735
+ 8950 16738.476 0 0 5269.5203 12.011719
+ 9000 16738.477 0 0 5269.5205 12.011698
+ 9050 16738.477 0 0 5269.5206 12.011683
+ 9100 16738.478 0 0 5269.5208 12.011684
+ 9150 16738.479 0 0 5269.521 12.011701
+ 9200 16738.479 0 0 5269.5212 12.011722
+ 9250 16738.479 0 0 5269.5213 12.011738
+ 9300 16738.48 0 0 5269.5214 12.011746
+ 9350 16738.48 0 0 5269.5214 12.011744
+ 9400 16738.48 0 0 5269.5215 12.011732
+ 9450 16738.48 0 0 5269.5216 12.011715
+ 9500 16738.481 -0.00037652438 0 5269.5216 12.011692
+ 9550 16738.493 -0.0053156162 0 5269.5203 12.011611
+ 9600 16738.549 -0.026814371 0 5269.5163 12.011415
+ 9650 16738.765 -0.10191523 0 5269.5092 12.011013
+ 9700 16735.041 1.0589893 0 5269.4979 12.062708
+ 9750 16738.013 0.13550102 0 5269.5101 11.407246
+ 9800 16738.512 -0.011620328 0 5269.5201 11.394974
+ 9850 16738.489 -0.00067270521 0 5269.5237 11.395098
+ 9900 16738.489 -0.00024984561 0 5269.5242 11.395085
+ 9950 16738.49 0 0 5269.5245 11.395076
+ 10000 16738.49 0 0 5269.5246 11.395075
+Loop time of 0.140447 on 1 procs for 10000 steps with 81 atoms
+
+Performance: 615179.112 tau/day, 71201.286 timesteps/s
+98.2% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.010351 | 0.010351 | 0.010351 | 0.0 | 7.37
+Neigh | 0.036597 | 0.036597 | 0.036597 | 0.0 | 26.06
+Comm | 0.0092356 | 0.0092356 | 0.0092356 | 0.0 | 6.58
+Output | 0.0023856 | 0.0023856 | 0.0023856 | 0.0 | 1.70
+Modify | 0.07586 | 0.07586 | 0.07586 | 0.0 | 54.01
+Other | | 0.006017 | | | 4.28
+
+Nlocal: 81 ave 81 max 81 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 84 ave 84 max 84 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 998
+Dangerous builds = 997
+Total wall time: 0:00:00
diff --git a/examples/rigid/log.20Apr18.rigid.atomfile.g++.4 b/examples/rigid/log.20Apr18.rigid.atomfile.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..70f86f32bbee23abe600df2cf540dd2624d5292e
--- /dev/null
+++ b/examples/rigid/log.20Apr18.rigid.atomfile.g++.4
@@ -0,0 +1,338 @@
+LAMMPS (20 Apr 2018)
+ using 1 OpenMP thread(s) per MPI task
+# Simple rigid body system
+
+units lj
+atom_style atomic
+atom_modify map array
+
+pair_style lj/cut 2.5
+
+read_data data.rigid
+ orthogonal box = (-12 -12 -12) to (12 12 12)
+ 1 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 81 atoms
+
+velocity all create 100.0 4928459
+
+
+# unconnected bodies
+
+group clump1 id <> 1 9
+9 atoms in group clump1
+group clump2 id <> 10 18
+9 atoms in group clump2
+group clump3 id <> 19 27
+9 atoms in group clump3
+group clump4 id <> 28 36
+9 atoms in group clump4
+group clump5 id <> 37 45
+9 atoms in group clump5
+group clump6 id <> 46 54
+9 atoms in group clump6
+group clump7 id <> 55 63
+9 atoms in group clump7
+group clump8 id <> 64 72
+9 atoms in group clump8
+group clump9 id <> 73 81
+9 atoms in group clump9
+
+variable bodies atomfile bodies.txt
+fix 1 all rigid custom v_bodies
+9 rigid bodies with 81 atoms
+
+# 1 chain of connected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 9 18
+#group clump3 id <> 18 27
+#group clump4 id <> 27 36
+#group clump5 id <> 36 45
+#group clump6 id <> 45 54
+#group clump7 id <> 54 63
+#group clump8 id <> 63 72
+#group clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
+
+# 2 chains of connected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 9 18
+#group clump3 id <> 18 27
+#group clump4 id <> 27 36
+#group clump5 id <> 37 45
+#group clump6 id <> 45 54
+#group clump7 id <> 54 63
+#group clump8 id <> 63 72
+#group clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4
+#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
+
+neigh_modify exclude group clump1 clump1
+neigh_modify exclude group clump2 clump2
+neigh_modify exclude group clump3 clump3
+neigh_modify exclude group clump4 clump4
+neigh_modify exclude group clump5 clump5
+neigh_modify exclude group clump6 clump6
+neigh_modify exclude group clump7 clump7
+neigh_modify exclude group clump8 clump8
+neigh_modify exclude group clump9 clump9
+
+thermo 100
+
+#dump 1 all atom 50 dump.rigid
+
+#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 2 pad 5
+
+#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 3 pad 5
+
+timestep 0.0001
+thermo 50
+run 10000
+Neighbor list info ...
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 18 18 18
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 4.08 | 4.174 | 4.455 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 115.29439 5235.9179 0 5272.2142 -2.7403788
+ 50 14910.685 571.71558 0 5265.82 32.006171
+ 100 16298.442 136.66184 0 5267.653 16.444229
+ 150 16682.606 17.490511 0 5269.4219 14.900344
+ 200 16733.929 1.372872 0 5269.4617 14.569267
+ 250 16738.853 -0.15252816 0 5269.4864 14.496404
+ 300 16738.588 -0.055171335 0 5269.5002 14.496025
+ 350 16738.492 -0.017444677 0 5269.5077 14.496446
+ 400 16738.464 -0.0060102023 0 5269.5104 14.496618
+ 450 16738.455 -0.0012713351 0 5269.5124 14.496701
+ 500 16738.455 -0.00081068621 0 5269.5128 14.496709
+ 550 16738.455 -0.00083203497 0 5269.5129 14.496707
+ 600 16738.455 -0.00058355356 0 5269.5131 14.496709
+ 650 16738.455 -0.00047226704 0 5269.5131 14.496708
+ 700 16738.455 0 0 5269.5136 14.496713
+ 750 16738.455 0 0 5269.5136 14.49671
+ 800 16738.455 0 0 5269.5137 14.496709
+ 850 16738.455 0 0 5269.5137 14.49671
+ 900 16738.456 0 0 5269.5138 14.496713
+ 950 16738.462 -0.0035323872 0 5269.5122 14.496671
+ 1000 16738.586 -0.051135144 0 5269.5036 14.496229
+ 1050 16737.358 0.32995057 0 5269.4981 14.525763
+ 1100 16737.892 0.16210246 0 5269.4984 14.531983
+ 1150 16738.703 -0.089235095 0 5269.5025 14.509899
+ 1200 16738.466 -0.0075446243 0 5269.5096 14.510615
+ 1250 16738.456 0 0 5269.514 14.510704
+ 1300 16738.457 0 0 5269.5141 14.510701
+ 1350 16738.457 0 0 5269.5141 14.510699
+ 1400 16738.457 -0.00044736511 0 5269.5138 14.510693
+ 1450 16738.458 -0.0010971179 0 5269.5134 14.510687
+ 1500 16738.458 -0.00057885428 0 5269.5139 14.510698
+ 1550 16738.457 0 0 5269.5143 14.51071
+ 1600 16738.457 0 0 5269.5144 14.510712
+ 1650 16738.457 0 0 5269.5144 14.510712
+ 1700 16738.458 0 0 5269.5144 14.51071
+ 1750 16738.458 0 0 5269.5145 14.510708
+ 1800 16738.458 0 0 5269.5145 14.510706
+ 1850 16738.458 0 0 5269.5146 14.510705
+ 1900 16738.458 0 0 5269.5146 14.510706
+ 1950 16738.465 -0.0031733615 0 5269.5134 14.510659
+ 2000 16738.491 -0.013255268 0 5269.5117 14.510532
+ 2050 16738.556 -0.0365811 0 5269.5087 14.51029
+ 2100 16738.633 -0.063209659 0 5269.5065 14.510219
+ 2150 16738.607 -0.05601761 0 5269.5055 14.510231
+ 2200 16738.557 -0.038423032 0 5269.5072 14.510404
+ 2250 16738.515 -0.023709918 0 5269.5088 14.510539
+ 2300 16738.489 -0.013249035 0 5269.5111 14.510621
+ 2350 16738.468 -0.0045563719 0 5269.5131 14.510714
+ 2400 16738.46 -0.00052194273 0 5269.5146 14.510771
+ 2450 16738.464 -0.0023259756 0 5269.514 14.510746
+ 2500 16738.468 -0.0051929186 0 5269.5127 14.510731
+ 2550 16738.581 -0.044940117 0 5269.5085 14.510315
+ 2600 16738.427 -7.9722854e-05 0 5269.5046 14.510657
+ 2650 16733.017 1.705148 0 5269.5067 14.596295
+ 2700 16738.761 -0.10614946 0 5269.5038 14.499584
+ 2750 16733.973 1.4038179 0 5269.5064 14.598107
+ 2800 16738.585 -0.046813448 0 5269.5076 14.511073
+ 2850 16738.487 -0.012558719 0 5269.5111 14.510111
+ 2900 16738.465 -0.0026252725 0 5269.514 14.510277
+ 2950 16738.476 -0.0082220764 0 5269.512 14.510223
+ 3000 16738.66 -0.071284779 0 5269.507 14.509758
+ 3050 16715.332 7.2419351 0 5269.476 14.870305
+ 3100 16653.226 26.818761 0 5269.5009 14.496764
+ 3150 16739.351 -0.30690375 0 5269.4886 13.643904
+ 3200 16733.238 1.6025328 0 5269.4737 12.016934
+ 3250 16734.374 1.2554429 0 5269.4841 11.963561
+ 3300 16732.156 1.9585967 0 5269.4893 12.234024
+ 3350 16738.655 -0.079693236 0 5269.497 12.092757
+ 3400 16738.543 -0.042215005 0 5269.4991 12.092809
+ 3450 16738.591 -0.059327511 0 5269.4972 12.092536
+ 3500 16738.759 -0.11761245 0 5269.4918 12.09203
+ 3550 16713.405 7.846062 0 5269.4737 12.389816
+ 3600 16734.939 1.0821936 0 5269.4891 12.173591
+ 3650 16738.808 -0.13663194 0 5269.4882 12.027009
+ 3700 16738.602 -0.070934368 0 5269.4889 12.025288
+ 3750 16737.731 0.20706558 0 5269.4927 12.061948
+ 3800 16738.578 -0.05582043 0 5269.4965 12.035665
+ 3850 16738.471 -0.016307928 0 5269.5024 12.035302
+ 3900 16738.449 -0.0058182199 0 5269.5059 12.035401
+ 3950 16738.439 -0.0012027325 0 5269.5074 12.035461
+ 4000 16738.436 -0.00020698452 0 5269.5075 12.035469
+ 4050 16738.437 0 0 5269.5078 12.035454
+ 4100 16738.437 0 0 5269.508 12.035435
+ 4150 16738.438 0 0 5269.5081 12.035426
+ 4200 16738.438 0 0 5269.5083 12.035432
+ 4250 16738.439 0 0 5269.5085 12.035447
+ 4300 16738.439 0 0 5269.5086 12.035463
+ 4350 16738.44 0 0 5269.5087 12.035474
+ 4400 16738.44 0 0 5269.5088 12.035478
+ 4450 16738.44 0 0 5269.5089 12.035474
+ 4500 16738.44 0 0 5269.509 12.035462
+ 4550 16738.441 0 0 5269.5092 12.035449
+ 4600 16738.441 0 0 5269.5093 12.035445
+ 4650 16738.442 0 0 5269.5095 12.035451
+ 4700 16738.442 0 0 5269.5096 12.03546
+ 4750 16738.443 0 0 5269.5097 12.035465
+ 4800 16738.443 0 0 5269.5098 12.035466
+ 4850 16738.443 0 0 5269.51 12.035463
+ 4900 16738.444 0 0 5269.5101 12.035456
+ 4950 16738.444 0 0 5269.5102 12.035447
+ 5000 16738.445 0 0 5269.5104 12.03544
+ 5050 16738.445 0 0 5269.5105 12.035442
+ 5100 16738.446 0 0 5269.5107 12.035455
+ 5150 16738.446 0 0 5269.5108 12.03547
+ 5200 16738.446 0 0 5269.5109 12.035479
+ 5250 16738.447 0 0 5269.511 12.035479
+ 5300 16738.447 0 0 5269.5111 12.03547
+ 5350 16738.447 0 0 5269.5112 12.035454
+ 5400 16738.448 0 0 5269.5113 12.035434
+ 5450 16738.448 0 0 5269.5115 12.03542
+ 5500 16738.449 0 0 5269.5117 12.035422
+ 5550 16738.457 -0.0030919234 0 5269.5111 12.035383
+ 5600 16738.51 -0.021618357 0 5269.5092 12.035106
+ 5650 16738.622 -0.059214788 0 5269.507 12.035694
+ 5700 16395.28 108.06942 0 5269.5463 24.369038
+ 5750 16738.544 -0.033973429 0 5269.5077 12.011261
+ 5800 16738.456 -0.0037013529 0 5269.5102 12.011675
+ 5850 16738.451 0 0 5269.5123 12.011709
+ 5900 16738.451 -0.0002211587 0 5269.5122 12.011687
+ 5950 16738.452 -0.00024253349 0 5269.5124 12.011678
+ 6000 16738.452 0 0 5269.5128 12.011688
+ 6050 16738.453 0 0 5269.513 12.011702
+ 6100 16738.453 0 0 5269.5131 12.011716
+ 6150 16738.454 0 0 5269.5132 12.011725
+ 6200 16738.454 0 0 5269.5133 12.011728
+ 6250 16738.454 0 0 5269.5134 12.011723
+ 6300 16738.455 0 0 5269.5135 12.011712
+ 6350 16738.455 0 0 5269.5137 12.0117
+ 6400 16738.456 0 0 5269.5138 12.011697
+ 6450 16738.456 0 0 5269.514 12.011704
+ 6500 16738.456 0 0 5269.5141 12.011714
+ 6550 16738.457 0 0 5269.5142 12.011719
+ 6600 16738.457 0 0 5269.5143 12.011718
+ 6650 16738.458 0 0 5269.5144 12.011713
+ 6700 16738.458 0 0 5269.5146 12.011705
+ 6750 16738.459 0 0 5269.5147 12.011696
+ 6800 16738.459 0 0 5269.5149 12.01169
+ 6850 16738.46 0 0 5269.515 12.011695
+ 6900 16738.46 0 0 5269.5152 12.01171
+ 6950 16738.46 0 0 5269.5153 12.011726
+ 7000 16738.461 0 0 5269.5154 12.011736
+ 7050 16738.461 0 0 5269.5155 12.011737
+ 7100 16738.461 0 0 5269.5155 12.011728
+ 7150 16738.461 0 0 5269.5156 12.011712
+ 7200 16738.462 0 0 5269.5158 12.011691
+ 7250 16738.463 0 0 5269.516 12.011676
+ 7300 16738.463 0 0 5269.5162 12.011677
+ 7350 16738.464 0 0 5269.5164 12.011693
+ 7400 16738.464 0 0 5269.5165 12.011713
+ 7450 16738.465 0 0 5269.5166 12.011729
+ 7500 16738.465 0 0 5269.5167 12.011736
+ 7550 16738.465 0 0 5269.5168 12.011734
+ 7600 16738.465 0 0 5269.5168 12.011722
+ 7650 16738.466 0 0 5269.517 12.011704
+ 7700 16738.466 0 0 5269.5171 12.011687
+ 7750 16738.467 0 0 5269.5173 12.011681
+ 7800 16738.467 0 0 5269.5175 12.011687
+ 7850 16738.468 0 0 5269.5176 12.0117
+ 7900 16738.468 0 0 5269.5178 12.011712
+ 7950 16738.469 0 0 5269.5179 12.011721
+ 8000 16738.469 0 0 5269.518 12.011724
+ 8050 16738.469 0 0 5269.5181 12.01172
+ 8100 16738.47 0 0 5269.5182 12.011709
+ 8150 16738.47 0 0 5269.5183 12.0117
+ 8200 16738.47 0 0 5269.5185 12.0117
+ 8250 16738.471 0 0 5269.5186 12.011709
+ 8300 16738.471 0 0 5269.5187 12.011719
+ 8350 16738.472 0 0 5269.5189 12.011723
+ 8400 16738.472 0 0 5269.519 12.01172
+ 8450 16738.473 -0.00039690664 0 5269.5189 12.011706
+ 8500 16738.481 -0.0034646803 0 5269.5182 12.011643
+ 8550 16738.483 -0.0045307409 0 5269.5178 12.011621
+ 8600 16738.474 -0.00076532811 0 5269.5189 12.011681
+ 8650 16738.474 0 0 5269.5197 12.011699
+ 8700 16738.475 0 0 5269.5199 12.011715
+ 8750 16738.475 0 0 5269.52 12.011732
+ 8800 16738.475 0 0 5269.52 12.011743
+ 8850 16738.476 0 0 5269.5201 12.011744
+ 8900 16738.476 0 0 5269.5202 12.011735
+ 8950 16738.476 0 0 5269.5203 12.011719
+ 9000 16738.477 0 0 5269.5205 12.011698
+ 9050 16738.477 0 0 5269.5206 12.011683
+ 9100 16738.478 0 0 5269.5208 12.011684
+ 9150 16738.479 0 0 5269.521 12.011701
+ 9200 16738.479 0 0 5269.5212 12.011722
+ 9250 16738.479 0 0 5269.5213 12.011738
+ 9300 16738.48 0 0 5269.5214 12.011746
+ 9350 16738.48 0 0 5269.5214 12.011744
+ 9400 16738.48 0 0 5269.5215 12.011732
+ 9450 16738.48 0 0 5269.5216 12.011715
+ 9500 16738.481 -0.00037652437 0 5269.5216 12.011692
+ 9550 16738.493 -0.0053156159 0 5269.5203 12.011611
+ 9600 16738.549 -0.026814369 0 5269.5163 12.011415
+ 9650 16738.765 -0.10191523 0 5269.5092 12.011013
+ 9700 16735.041 1.0589887 0 5269.4979 12.062708
+ 9750 16738.013 0.135501 0 5269.5101 11.407245
+ 9800 16738.512 -0.011620329 0 5269.5201 11.394973
+ 9850 16738.489 -0.00067270548 0 5269.5237 11.395098
+ 9900 16738.489 -0.00024984569 0 5269.5242 11.395084
+ 9950 16738.49 0 0 5269.5245 11.395076
+ 10000 16738.49 0 0 5269.5246 11.395075
+Loop time of 0.191483 on 4 procs for 10000 steps with 81 atoms
+
+Performance: 451214.099 tau/day, 52223.854 timesteps/s
+96.3% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.0024264 | 0.0036595 | 0.0042815 | 1.2 | 1.91
+Neigh | 0.011347 | 0.012011 | 0.013367 | 0.7 | 6.27
+Comm | 0.081701 | 0.083476 | 0.087947 | 0.9 | 43.59
+Output | 0.0042565 | 0.0045614 | 0.0053556 | 0.7 | 2.38
+Modify | 0.075719 | 0.078165 | 0.080737 | 0.7 | 40.82
+Other | | 0.009611 | | | 5.02
+
+Nlocal: 20.25 ave 38 max 3 min
+Histogram: 1 0 1 0 0 0 1 0 0 1
+Nghost: 27.25 ave 48 max 13 min
+Histogram: 1 0 1 1 0 0 0 0 0 1
+Neighs: 0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 998
+Dangerous builds = 997
+Total wall time: 0:00:00
diff --git a/examples/rigid/log.20Apr18.rigid.atomvar.g++.1 b/examples/rigid/log.20Apr18.rigid.atomvar.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..99098d04d21db9221011b9f511c469eb180e213f
--- /dev/null
+++ b/examples/rigid/log.20Apr18.rigid.atomvar.g++.1
@@ -0,0 +1,338 @@
+LAMMPS (20 Apr 2018)
+ using 1 OpenMP thread(s) per MPI task
+# Simple rigid body system
+
+units lj
+atom_style atomic
+atom_modify map array
+
+pair_style lj/cut 2.5
+
+read_data data.rigid
+ orthogonal box = (-12 -12 -12) to (12 12 12)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 81 atoms
+
+velocity all create 100.0 4928459
+
+
+# unconnected bodies
+
+group clump1 id <> 1 9
+9 atoms in group clump1
+group clump2 id <> 10 18
+9 atoms in group clump2
+group clump3 id <> 19 27
+9 atoms in group clump3
+group clump4 id <> 28 36
+9 atoms in group clump4
+group clump5 id <> 37 45
+9 atoms in group clump5
+group clump6 id <> 46 54
+9 atoms in group clump6
+group clump7 id <> 55 63
+9 atoms in group clump7
+group clump8 id <> 64 72
+9 atoms in group clump8
+group clump9 id <> 73 81
+9 atoms in group clump9
+
+variable bodies atom 1.0*gmask(clump1)+2.0*gmask(clump2)+3.0*gmask(clump3)+4.0*gmask(clump4)+5.0*gmask(clump5)+6.0*gmask(clump6)+7.0*gmask(clump7)+8.0*gmask(clump8)+9.0*gmask(clump9)
+fix 1 all rigid custom v_bodies
+9 rigid bodies with 81 atoms
+
+# 1 chain of connected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 9 18
+#group clump3 id <> 18 27
+#group clump4 id <> 27 36
+#group clump5 id <> 36 45
+#group clump6 id <> 45 54
+#group clump7 id <> 54 63
+#group clump8 id <> 63 72
+#group clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
+
+# 2 chains of connected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 9 18
+#group clump3 id <> 18 27
+#group clump4 id <> 27 36
+#group clump5 id <> 37 45
+#group clump6 id <> 45 54
+#group clump7 id <> 54 63
+#group clump8 id <> 63 72
+#group clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4
+#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
+
+neigh_modify exclude group clump1 clump1
+neigh_modify exclude group clump2 clump2
+neigh_modify exclude group clump3 clump3
+neigh_modify exclude group clump4 clump4
+neigh_modify exclude group clump5 clump5
+neigh_modify exclude group clump6 clump6
+neigh_modify exclude group clump7 clump7
+neigh_modify exclude group clump8 clump8
+neigh_modify exclude group clump9 clump9
+
+thermo 100
+
+#dump 1 all atom 50 dump.rigid
+
+#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 2 pad 5
+
+#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 3 pad 5
+
+timestep 0.0001
+thermo 50
+run 10000
+Neighbor list info ...
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 18 18 18
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.984 | 3.984 | 3.984 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 115.29439 5235.9179 0 5272.2142 -2.7403788
+ 50 14910.685 571.71558 0 5265.82 32.006171
+ 100 16298.442 136.66184 0 5267.653 16.444229
+ 150 16682.606 17.490511 0 5269.4219 14.900344
+ 200 16733.929 1.372872 0 5269.4617 14.569267
+ 250 16738.853 -0.15252816 0 5269.4864 14.496404
+ 300 16738.588 -0.055171335 0 5269.5002 14.496025
+ 350 16738.492 -0.017444677 0 5269.5077 14.496446
+ 400 16738.464 -0.0060102023 0 5269.5104 14.496618
+ 450 16738.455 -0.0012713351 0 5269.5124 14.496701
+ 500 16738.455 -0.00081068621 0 5269.5128 14.496709
+ 550 16738.455 -0.00083203497 0 5269.5129 14.496707
+ 600 16738.455 -0.00058355356 0 5269.5131 14.496709
+ 650 16738.455 -0.00047226704 0 5269.5131 14.496708
+ 700 16738.455 0 0 5269.5136 14.496713
+ 750 16738.455 0 0 5269.5136 14.49671
+ 800 16738.455 0 0 5269.5137 14.496709
+ 850 16738.455 0 0 5269.5137 14.49671
+ 900 16738.456 0 0 5269.5138 14.496713
+ 950 16738.462 -0.0035323872 0 5269.5122 14.496671
+ 1000 16738.586 -0.051135144 0 5269.5036 14.496229
+ 1050 16737.358 0.32995057 0 5269.4981 14.525763
+ 1100 16737.892 0.16210246 0 5269.4984 14.531983
+ 1150 16738.703 -0.089235095 0 5269.5025 14.509899
+ 1200 16738.466 -0.0075446243 0 5269.5096 14.510615
+ 1250 16738.456 0 0 5269.514 14.510704
+ 1300 16738.457 0 0 5269.5141 14.510701
+ 1350 16738.457 0 0 5269.5141 14.510699
+ 1400 16738.457 -0.00044736511 0 5269.5138 14.510693
+ 1450 16738.458 -0.0010971179 0 5269.5134 14.510687
+ 1500 16738.458 -0.00057885428 0 5269.5139 14.510698
+ 1550 16738.457 0 0 5269.5143 14.51071
+ 1600 16738.457 0 0 5269.5144 14.510712
+ 1650 16738.457 0 0 5269.5144 14.510712
+ 1700 16738.458 0 0 5269.5144 14.51071
+ 1750 16738.458 0 0 5269.5145 14.510708
+ 1800 16738.458 0 0 5269.5145 14.510706
+ 1850 16738.458 0 0 5269.5146 14.510705
+ 1900 16738.458 0 0 5269.5146 14.510706
+ 1950 16738.465 -0.0031733615 0 5269.5134 14.510659
+ 2000 16738.491 -0.013255268 0 5269.5117 14.510532
+ 2050 16738.556 -0.0365811 0 5269.5087 14.51029
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+ 9550 16738.493 -0.0053156162 0 5269.5203 12.011611
+ 9600 16738.549 -0.026814371 0 5269.5163 12.011415
+ 9650 16738.765 -0.10191523 0 5269.5092 12.011013
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+ 9750 16738.013 0.13550102 0 5269.5101 11.407246
+ 9800 16738.512 -0.011620328 0 5269.5201 11.394974
+ 9850 16738.489 -0.00067270521 0 5269.5237 11.395098
+ 9900 16738.489 -0.00024984561 0 5269.5242 11.395085
+ 9950 16738.49 0 0 5269.5245 11.395076
+ 10000 16738.49 0 0 5269.5246 11.395075
+Loop time of 0.139024 on 1 procs for 10000 steps with 81 atoms
+
+Performance: 621477.474 tau/day, 71930.263 timesteps/s
+99.0% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.010292 | 0.010292 | 0.010292 | 0.0 | 7.40
+Neigh | 0.036968 | 0.036968 | 0.036968 | 0.0 | 26.59
+Comm | 0.0091348 | 0.0091348 | 0.0091348 | 0.0 | 6.57
+Output | 0.0024047 | 0.0024047 | 0.0024047 | 0.0 | 1.73
+Modify | 0.074017 | 0.074017 | 0.074017 | 0.0 | 53.24
+Other | | 0.006207 | | | 4.46
+
+Nlocal: 81 ave 81 max 81 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 84 ave 84 max 84 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 998
+Dangerous builds = 997
+Total wall time: 0:00:00
diff --git a/examples/rigid/log.20Apr18.rigid.atomvar.g++.4 b/examples/rigid/log.20Apr18.rigid.atomvar.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..76344d09952c3346a80847688e6398edebf5d765
--- /dev/null
+++ b/examples/rigid/log.20Apr18.rigid.atomvar.g++.4
@@ -0,0 +1,338 @@
+LAMMPS (20 Apr 2018)
+ using 1 OpenMP thread(s) per MPI task
+# Simple rigid body system
+
+units lj
+atom_style atomic
+atom_modify map array
+
+pair_style lj/cut 2.5
+
+read_data data.rigid
+ orthogonal box = (-12 -12 -12) to (12 12 12)
+ 1 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 81 atoms
+
+velocity all create 100.0 4928459
+
+
+# unconnected bodies
+
+group clump1 id <> 1 9
+9 atoms in group clump1
+group clump2 id <> 10 18
+9 atoms in group clump2
+group clump3 id <> 19 27
+9 atoms in group clump3
+group clump4 id <> 28 36
+9 atoms in group clump4
+group clump5 id <> 37 45
+9 atoms in group clump5
+group clump6 id <> 46 54
+9 atoms in group clump6
+group clump7 id <> 55 63
+9 atoms in group clump7
+group clump8 id <> 64 72
+9 atoms in group clump8
+group clump9 id <> 73 81
+9 atoms in group clump9
+
+variable bodies atom 1.0*gmask(clump1)+2.0*gmask(clump2)+3.0*gmask(clump3)+4.0*gmask(clump4)+5.0*gmask(clump5)+6.0*gmask(clump6)+7.0*gmask(clump7)+8.0*gmask(clump8)+9.0*gmask(clump9)
+fix 1 all rigid custom v_bodies
+9 rigid bodies with 81 atoms
+
+# 1 chain of connected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 9 18
+#group clump3 id <> 18 27
+#group clump4 id <> 27 36
+#group clump5 id <> 36 45
+#group clump6 id <> 45 54
+#group clump7 id <> 54 63
+#group clump8 id <> 63 72
+#group clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
+
+# 2 chains of connected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 9 18
+#group clump3 id <> 18 27
+#group clump4 id <> 27 36
+#group clump5 id <> 37 45
+#group clump6 id <> 45 54
+#group clump7 id <> 54 63
+#group clump8 id <> 63 72
+#group clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4
+#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
+
+neigh_modify exclude group clump1 clump1
+neigh_modify exclude group clump2 clump2
+neigh_modify exclude group clump3 clump3
+neigh_modify exclude group clump4 clump4
+neigh_modify exclude group clump5 clump5
+neigh_modify exclude group clump6 clump6
+neigh_modify exclude group clump7 clump7
+neigh_modify exclude group clump8 clump8
+neigh_modify exclude group clump9 clump9
+
+thermo 100
+
+#dump 1 all atom 50 dump.rigid
+
+#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 2 pad 5
+
+#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 3 pad 5
+
+timestep 0.0001
+thermo 50
+run 10000
+Neighbor list info ...
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 18 18 18
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.955 | 4.049 | 4.33 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 115.29439 5235.9179 0 5272.2142 -2.7403788
+ 50 14910.685 571.71558 0 5265.82 32.006171
+ 100 16298.442 136.66184 0 5267.653 16.444229
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+ 9500 16738.481 -0.00037652437 0 5269.5216 12.011692
+ 9550 16738.493 -0.0053156159 0 5269.5203 12.011611
+ 9600 16738.549 -0.026814369 0 5269.5163 12.011415
+ 9650 16738.765 -0.10191523 0 5269.5092 12.011013
+ 9700 16735.041 1.0589887 0 5269.4979 12.062708
+ 9750 16738.013 0.135501 0 5269.5101 11.407245
+ 9800 16738.512 -0.011620329 0 5269.5201 11.394973
+ 9850 16738.489 -0.00067270548 0 5269.5237 11.395098
+ 9900 16738.489 -0.00024984569 0 5269.5242 11.395084
+ 9950 16738.49 0 0 5269.5245 11.395076
+ 10000 16738.49 0 0 5269.5246 11.395075
+Loop time of 0.202733 on 4 procs for 10000 steps with 81 atoms
+
+Performance: 426175.966 tau/day, 49325.922 timesteps/s
+96.3% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.0025222 | 0.0037088 | 0.0044038 | 1.2 | 1.83
+Neigh | 0.01135 | 0.012003 | 0.013654 | 0.9 | 5.92
+Comm | 0.088217 | 0.089948 | 0.091659 | 0.4 | 44.37
+Output | 0.0044014 | 0.0047023 | 0.0055132 | 0.7 | 2.32
+Modify | 0.080218 | 0.082638 | 0.084872 | 0.6 | 40.76
+Other | | 0.009733 | | | 4.80
+
+Nlocal: 20.25 ave 38 max 3 min
+Histogram: 1 0 1 0 0 0 1 0 0 1
+Nghost: 27.25 ave 48 max 13 min
+Histogram: 1 0 1 1 0 0 0 0 0 1
+Neighs: 0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 998
+Dangerous builds = 997
+Total wall time: 0:00:00
diff --git a/examples/rigid/log.20Apr18.rigid.early.g++.1 b/examples/rigid/log.20Apr18.rigid.early.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..5402647b9814753bbcfd831d54d12823586a59f1
--- /dev/null
+++ b/examples/rigid/log.20Apr18.rigid.early.g++.1
@@ -0,0 +1,337 @@
+LAMMPS (20 Apr 2018)
+ using 1 OpenMP thread(s) per MPI task
+# Simple rigid body system
+
+units lj
+atom_style atomic
+
+pair_style lj/cut 2.5
+
+read_data data.rigid
+ orthogonal box = (-12 -12 -12) to (12 12 12)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 81 atoms
+
+velocity all create 100.0 4928459
+
+# unconnected bodies
+
+group clump1 id <> 1 9
+9 atoms in group clump1
+group clump2 id <> 10 18
+9 atoms in group clump2
+group clump3 id <> 19 27
+9 atoms in group clump3
+group clump4 id <> 28 36
+9 atoms in group clump4
+group clump5 id <> 37 45
+9 atoms in group clump5
+group clump6 id <> 46 54
+9 atoms in group clump6
+group clump7 id <> 55 63
+9 atoms in group clump7
+group clump8 id <> 64 72
+9 atoms in group clump8
+group clump9 id <> 73 81
+9 atoms in group clump9
+
+fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
+9 rigid bodies with 81 atoms
+
+fix_modify 1 bodyforces early
+
+# 1 chain of connected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 9 18
+#group clump3 id <> 18 27
+#group clump4 id <> 27 36
+#group clump5 id <> 36 45
+#group clump6 id <> 45 54
+#group clump7 id <> 54 63
+#group clump8 id <> 63 72
+#group clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
+
+# 2 chains of connected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 9 18
+#group clump3 id <> 18 27
+#group clump4 id <> 27 36
+#group clump5 id <> 37 45
+#group clump6 id <> 45 54
+#group clump7 id <> 54 63
+#group clump8 id <> 63 72
+#group clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4
+#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
+
+neigh_modify exclude group clump1 clump1
+neigh_modify exclude group clump2 clump2
+neigh_modify exclude group clump3 clump3
+neigh_modify exclude group clump4 clump4
+neigh_modify exclude group clump5 clump5
+neigh_modify exclude group clump6 clump6
+neigh_modify exclude group clump7 clump7
+neigh_modify exclude group clump8 clump8
+neigh_modify exclude group clump9 clump9
+
+thermo 100
+
+#dump 1 all atom 50 dump.rigid
+
+#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 2 pad 5
+
+#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 3 pad 5
+
+timestep 0.0001
+thermo 50
+run 10000
+Neighbor list info ...
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 18 18 18
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.979 | 3.979 | 3.979 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 115.29439 5235.9179 0 5272.2142 -2.7403788
+ 50 14910.685 571.71558 0 5265.82 32.006171
+ 100 16298.442 136.66184 0 5267.653 16.444229
+ 150 16682.606 17.490511 0 5269.4219 14.900344
+ 200 16733.929 1.372872 0 5269.4617 14.569267
+ 250 16738.853 -0.15252816 0 5269.4864 14.496404
+ 300 16738.588 -0.055171335 0 5269.5002 14.496025
+ 350 16738.492 -0.017444677 0 5269.5077 14.496446
+ 400 16738.464 -0.0060102023 0 5269.5104 14.496618
+ 450 16738.455 -0.0012713351 0 5269.5124 14.496701
+ 500 16738.455 -0.00081068621 0 5269.5128 14.496709
+ 550 16738.455 -0.00083203497 0 5269.5129 14.496707
+ 600 16738.455 -0.00058355356 0 5269.5131 14.496709
+ 650 16738.455 -0.00047226704 0 5269.5131 14.496708
+ 700 16738.455 0 0 5269.5136 14.496713
+ 750 16738.455 0 0 5269.5136 14.49671
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+ 1100 16737.892 0.16210246 0 5269.4984 14.531983
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+ 3100 16653.226 26.818761 0 5269.5009 14.496764
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+ 5700 16395.28 108.06942 0 5269.5463 24.369038
+ 5750 16738.544 -0.033973429 0 5269.5077 12.011261
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+ 9350 16738.48 0 0 5269.5214 12.011744
+ 9400 16738.48 0 0 5269.5215 12.011732
+ 9450 16738.48 0 0 5269.5216 12.011715
+ 9500 16738.481 -0.00037652438 0 5269.5216 12.011692
+ 9550 16738.493 -0.0053156162 0 5269.5203 12.011611
+ 9600 16738.549 -0.026814371 0 5269.5163 12.011415
+ 9650 16738.765 -0.10191523 0 5269.5092 12.011013
+ 9700 16735.041 1.0589893 0 5269.4979 12.062708
+ 9750 16738.013 0.13550102 0 5269.5101 11.407246
+ 9800 16738.512 -0.011620328 0 5269.5201 11.394974
+ 9850 16738.489 -0.00067270521 0 5269.5237 11.395098
+ 9900 16738.489 -0.00024984561 0 5269.5242 11.395085
+ 9950 16738.49 0 0 5269.5245 11.395076
+ 10000 16738.49 0 0 5269.5246 11.395075
+Loop time of 0.142284 on 1 procs for 10000 steps with 81 atoms
+
+Performance: 607236.588 tau/day, 70282.013 timesteps/s
+99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.010693 | 0.010693 | 0.010693 | 0.0 | 7.52
+Neigh | 0.037908 | 0.037908 | 0.037908 | 0.0 | 26.64
+Comm | 0.0087049 | 0.0087049 | 0.0087049 | 0.0 | 6.12
+Output | 0.0025849 | 0.0025849 | 0.0025849 | 0.0 | 1.82
+Modify | 0.076329 | 0.076329 | 0.076329 | 0.0 | 53.65
+Other | | 0.006064 | | | 4.26
+
+Nlocal: 81 ave 81 max 81 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 84 ave 84 max 84 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 998
+Dangerous builds = 997
+Total wall time: 0:00:00
diff --git a/examples/rigid/log.20Apr18.rigid.early.g++.4 b/examples/rigid/log.20Apr18.rigid.early.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..c9513a211e9fbc42cfb70bea162e3791cbd98abc
--- /dev/null
+++ b/examples/rigid/log.20Apr18.rigid.early.g++.4
@@ -0,0 +1,337 @@
+LAMMPS (20 Apr 2018)
+ using 1 OpenMP thread(s) per MPI task
+# Simple rigid body system
+
+units lj
+atom_style atomic
+
+pair_style lj/cut 2.5
+
+read_data data.rigid
+ orthogonal box = (-12 -12 -12) to (12 12 12)
+ 1 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 81 atoms
+
+velocity all create 100.0 4928459
+
+# unconnected bodies
+
+group clump1 id <> 1 9
+9 atoms in group clump1
+group clump2 id <> 10 18
+9 atoms in group clump2
+group clump3 id <> 19 27
+9 atoms in group clump3
+group clump4 id <> 28 36
+9 atoms in group clump4
+group clump5 id <> 37 45
+9 atoms in group clump5
+group clump6 id <> 46 54
+9 atoms in group clump6
+group clump7 id <> 55 63
+9 atoms in group clump7
+group clump8 id <> 64 72
+9 atoms in group clump8
+group clump9 id <> 73 81
+9 atoms in group clump9
+
+fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
+9 rigid bodies with 81 atoms
+
+fix_modify 1 bodyforces early
+
+# 1 chain of connected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 9 18
+#group clump3 id <> 18 27
+#group clump4 id <> 27 36
+#group clump5 id <> 36 45
+#group clump6 id <> 45 54
+#group clump7 id <> 54 63
+#group clump8 id <> 63 72
+#group clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
+
+# 2 chains of connected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 9 18
+#group clump3 id <> 18 27
+#group clump4 id <> 27 36
+#group clump5 id <> 37 45
+#group clump6 id <> 45 54
+#group clump7 id <> 54 63
+#group clump8 id <> 63 72
+#group clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4
+#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
+
+neigh_modify exclude group clump1 clump1
+neigh_modify exclude group clump2 clump2
+neigh_modify exclude group clump3 clump3
+neigh_modify exclude group clump4 clump4
+neigh_modify exclude group clump5 clump5
+neigh_modify exclude group clump6 clump6
+neigh_modify exclude group clump7 clump7
+neigh_modify exclude group clump8 clump8
+neigh_modify exclude group clump9 clump9
+
+thermo 100
+
+#dump 1 all atom 50 dump.rigid
+
+#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 2 pad 5
+
+#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 3 pad 5
+
+timestep 0.0001
+thermo 50
+run 10000
+Neighbor list info ...
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 18 18 18
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.95 | 4.044 | 4.326 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 115.29439 5235.9179 0 5272.2142 -2.7403788
+ 50 14910.685 571.71558 0 5265.82 32.006171
+ 100 16298.442 136.66184 0 5267.653 16.444229
+ 150 16682.606 17.490511 0 5269.4219 14.900344
+ 200 16733.929 1.372872 0 5269.4617 14.569267
+ 250 16738.853 -0.15252816 0 5269.4864 14.496404
+ 300 16738.588 -0.055171335 0 5269.5002 14.496025
+ 350 16738.492 -0.017444677 0 5269.5077 14.496446
+ 400 16738.464 -0.0060102023 0 5269.5104 14.496618
+ 450 16738.455 -0.0012713351 0 5269.5124 14.496701
+ 500 16738.455 -0.00081068621 0 5269.5128 14.496709
+ 550 16738.455 -0.00083203497 0 5269.5129 14.496707
+ 600 16738.455 -0.00058355356 0 5269.5131 14.496709
+ 650 16738.455 -0.00047226704 0 5269.5131 14.496708
+ 700 16738.455 0 0 5269.5136 14.496713
+ 750 16738.455 0 0 5269.5136 14.49671
+ 800 16738.455 0 0 5269.5137 14.496709
+ 850 16738.455 0 0 5269.5137 14.49671
+ 900 16738.456 0 0 5269.5138 14.496713
+ 950 16738.462 -0.0035323872 0 5269.5122 14.496671
+ 1000 16738.586 -0.051135144 0 5269.5036 14.496229
+ 1050 16737.358 0.32995057 0 5269.4981 14.525763
+ 1100 16737.892 0.16210246 0 5269.4984 14.531983
+ 1150 16738.703 -0.089235095 0 5269.5025 14.509899
+ 1200 16738.466 -0.0075446243 0 5269.5096 14.510615
+ 1250 16738.456 0 0 5269.514 14.510704
+ 1300 16738.457 0 0 5269.5141 14.510701
+ 1350 16738.457 0 0 5269.5141 14.510699
+ 1400 16738.457 -0.00044736511 0 5269.5138 14.510693
+ 1450 16738.458 -0.0010971179 0 5269.5134 14.510687
+ 1500 16738.458 -0.00057885428 0 5269.5139 14.510698
+ 1550 16738.457 0 0 5269.5143 14.51071
+ 1600 16738.457 0 0 5269.5144 14.510712
+ 1650 16738.457 0 0 5269.5144 14.510712
+ 1700 16738.458 0 0 5269.5144 14.51071
+ 1750 16738.458 0 0 5269.5145 14.510708
+ 1800 16738.458 0 0 5269.5145 14.510706
+ 1850 16738.458 0 0 5269.5146 14.510705
+ 1900 16738.458 0 0 5269.5146 14.510706
+ 1950 16738.465 -0.0031733615 0 5269.5134 14.510659
+ 2000 16738.491 -0.013255268 0 5269.5117 14.510532
+ 2050 16738.556 -0.0365811 0 5269.5087 14.51029
+ 2100 16738.633 -0.063209659 0 5269.5065 14.510219
+ 2150 16738.607 -0.05601761 0 5269.5055 14.510231
+ 2200 16738.557 -0.038423032 0 5269.5072 14.510404
+ 2250 16738.515 -0.023709918 0 5269.5088 14.510539
+ 2300 16738.489 -0.013249035 0 5269.5111 14.510621
+ 2350 16738.468 -0.0045563719 0 5269.5131 14.510714
+ 2400 16738.46 -0.00052194273 0 5269.5146 14.510771
+ 2450 16738.464 -0.0023259756 0 5269.514 14.510746
+ 2500 16738.468 -0.0051929186 0 5269.5127 14.510731
+ 2550 16738.581 -0.044940117 0 5269.5085 14.510315
+ 2600 16738.427 -7.9722854e-05 0 5269.5046 14.510657
+ 2650 16733.017 1.705148 0 5269.5067 14.596295
+ 2700 16738.761 -0.10614946 0 5269.5038 14.499584
+ 2750 16733.973 1.4038179 0 5269.5064 14.598107
+ 2800 16738.585 -0.046813448 0 5269.5076 14.511073
+ 2850 16738.487 -0.012558719 0 5269.5111 14.510111
+ 2900 16738.465 -0.0026252725 0 5269.514 14.510277
+ 2950 16738.476 -0.0082220764 0 5269.512 14.510223
+ 3000 16738.66 -0.071284779 0 5269.507 14.509758
+ 3050 16715.332 7.2419351 0 5269.476 14.870305
+ 3100 16653.226 26.818761 0 5269.5009 14.496764
+ 3150 16739.351 -0.30690375 0 5269.4886 13.643904
+ 3200 16733.238 1.6025328 0 5269.4737 12.016934
+ 3250 16734.374 1.2554429 0 5269.4841 11.963561
+ 3300 16732.156 1.9585967 0 5269.4893 12.234024
+ 3350 16738.655 -0.079693236 0 5269.497 12.092757
+ 3400 16738.543 -0.042215005 0 5269.4991 12.092809
+ 3450 16738.591 -0.059327511 0 5269.4972 12.092536
+ 3500 16738.759 -0.11761245 0 5269.4918 12.09203
+ 3550 16713.405 7.846062 0 5269.4737 12.389816
+ 3600 16734.939 1.0821936 0 5269.4891 12.173591
+ 3650 16738.808 -0.13663194 0 5269.4882 12.027009
+ 3700 16738.602 -0.070934368 0 5269.4889 12.025288
+ 3750 16737.731 0.20706558 0 5269.4927 12.061948
+ 3800 16738.578 -0.05582043 0 5269.4965 12.035665
+ 3850 16738.471 -0.016307928 0 5269.5024 12.035302
+ 3900 16738.449 -0.0058182199 0 5269.5059 12.035401
+ 3950 16738.439 -0.0012027325 0 5269.5074 12.035461
+ 4000 16738.436 -0.00020698452 0 5269.5075 12.035469
+ 4050 16738.437 0 0 5269.5078 12.035454
+ 4100 16738.437 0 0 5269.508 12.035435
+ 4150 16738.438 0 0 5269.5081 12.035426
+ 4200 16738.438 0 0 5269.5083 12.035432
+ 4250 16738.439 0 0 5269.5085 12.035447
+ 4300 16738.439 0 0 5269.5086 12.035463
+ 4350 16738.44 0 0 5269.5087 12.035474
+ 4400 16738.44 0 0 5269.5088 12.035478
+ 4450 16738.44 0 0 5269.5089 12.035474
+ 4500 16738.44 0 0 5269.509 12.035462
+ 4550 16738.441 0 0 5269.5092 12.035449
+ 4600 16738.441 0 0 5269.5093 12.035445
+ 4650 16738.442 0 0 5269.5095 12.035451
+ 4700 16738.442 0 0 5269.5096 12.03546
+ 4750 16738.443 0 0 5269.5097 12.035465
+ 4800 16738.443 0 0 5269.5098 12.035466
+ 4850 16738.443 0 0 5269.51 12.035463
+ 4900 16738.444 0 0 5269.5101 12.035456
+ 4950 16738.444 0 0 5269.5102 12.035447
+ 5000 16738.445 0 0 5269.5104 12.03544
+ 5050 16738.445 0 0 5269.5105 12.035442
+ 5100 16738.446 0 0 5269.5107 12.035455
+ 5150 16738.446 0 0 5269.5108 12.03547
+ 5200 16738.446 0 0 5269.5109 12.035479
+ 5250 16738.447 0 0 5269.511 12.035479
+ 5300 16738.447 0 0 5269.5111 12.03547
+ 5350 16738.447 0 0 5269.5112 12.035454
+ 5400 16738.448 0 0 5269.5113 12.035434
+ 5450 16738.448 0 0 5269.5115 12.03542
+ 5500 16738.449 0 0 5269.5117 12.035422
+ 5550 16738.457 -0.0030919234 0 5269.5111 12.035383
+ 5600 16738.51 -0.021618357 0 5269.5092 12.035106
+ 5650 16738.622 -0.059214788 0 5269.507 12.035694
+ 5700 16395.28 108.06942 0 5269.5463 24.369038
+ 5750 16738.544 -0.033973429 0 5269.5077 12.011261
+ 5800 16738.456 -0.0037013529 0 5269.5102 12.011675
+ 5850 16738.451 0 0 5269.5123 12.011709
+ 5900 16738.451 -0.0002211587 0 5269.5122 12.011687
+ 5950 16738.452 -0.00024253349 0 5269.5124 12.011678
+ 6000 16738.452 0 0 5269.5128 12.011688
+ 6050 16738.453 0 0 5269.513 12.011702
+ 6100 16738.453 0 0 5269.5131 12.011716
+ 6150 16738.454 0 0 5269.5132 12.011725
+ 6200 16738.454 0 0 5269.5133 12.011728
+ 6250 16738.454 0 0 5269.5134 12.011723
+ 6300 16738.455 0 0 5269.5135 12.011712
+ 6350 16738.455 0 0 5269.5137 12.0117
+ 6400 16738.456 0 0 5269.5138 12.011697
+ 6450 16738.456 0 0 5269.514 12.011704
+ 6500 16738.456 0 0 5269.5141 12.011714
+ 6550 16738.457 0 0 5269.5142 12.011719
+ 6600 16738.457 0 0 5269.5143 12.011718
+ 6650 16738.458 0 0 5269.5144 12.011713
+ 6700 16738.458 0 0 5269.5146 12.011705
+ 6750 16738.459 0 0 5269.5147 12.011696
+ 6800 16738.459 0 0 5269.5149 12.01169
+ 6850 16738.46 0 0 5269.515 12.011695
+ 6900 16738.46 0 0 5269.5152 12.01171
+ 6950 16738.46 0 0 5269.5153 12.011726
+ 7000 16738.461 0 0 5269.5154 12.011736
+ 7050 16738.461 0 0 5269.5155 12.011737
+ 7100 16738.461 0 0 5269.5155 12.011728
+ 7150 16738.461 0 0 5269.5156 12.011712
+ 7200 16738.462 0 0 5269.5158 12.011691
+ 7250 16738.463 0 0 5269.516 12.011676
+ 7300 16738.463 0 0 5269.5162 12.011677
+ 7350 16738.464 0 0 5269.5164 12.011693
+ 7400 16738.464 0 0 5269.5165 12.011713
+ 7450 16738.465 0 0 5269.5166 12.011729
+ 7500 16738.465 0 0 5269.5167 12.011736
+ 7550 16738.465 0 0 5269.5168 12.011734
+ 7600 16738.465 0 0 5269.5168 12.011722
+ 7650 16738.466 0 0 5269.517 12.011704
+ 7700 16738.466 0 0 5269.5171 12.011687
+ 7750 16738.467 0 0 5269.5173 12.011681
+ 7800 16738.467 0 0 5269.5175 12.011687
+ 7850 16738.468 0 0 5269.5176 12.0117
+ 7900 16738.468 0 0 5269.5178 12.011712
+ 7950 16738.469 0 0 5269.5179 12.011721
+ 8000 16738.469 0 0 5269.518 12.011724
+ 8050 16738.469 0 0 5269.5181 12.01172
+ 8100 16738.47 0 0 5269.5182 12.011709
+ 8150 16738.47 0 0 5269.5183 12.0117
+ 8200 16738.47 0 0 5269.5185 12.0117
+ 8250 16738.471 0 0 5269.5186 12.011709
+ 8300 16738.471 0 0 5269.5187 12.011719
+ 8350 16738.472 0 0 5269.5189 12.011723
+ 8400 16738.472 0 0 5269.519 12.01172
+ 8450 16738.473 -0.00039690664 0 5269.5189 12.011706
+ 8500 16738.481 -0.0034646803 0 5269.5182 12.011643
+ 8550 16738.483 -0.0045307409 0 5269.5178 12.011621
+ 8600 16738.474 -0.00076532811 0 5269.5189 12.011681
+ 8650 16738.474 0 0 5269.5197 12.011699
+ 8700 16738.475 0 0 5269.5199 12.011715
+ 8750 16738.475 0 0 5269.52 12.011732
+ 8800 16738.475 0 0 5269.52 12.011743
+ 8850 16738.476 0 0 5269.5201 12.011744
+ 8900 16738.476 0 0 5269.5202 12.011735
+ 8950 16738.476 0 0 5269.5203 12.011719
+ 9000 16738.477 0 0 5269.5205 12.011698
+ 9050 16738.477 0 0 5269.5206 12.011683
+ 9100 16738.478 0 0 5269.5208 12.011684
+ 9150 16738.479 0 0 5269.521 12.011701
+ 9200 16738.479 0 0 5269.5212 12.011722
+ 9250 16738.479 0 0 5269.5213 12.011738
+ 9300 16738.48 0 0 5269.5214 12.011746
+ 9350 16738.48 0 0 5269.5214 12.011744
+ 9400 16738.48 0 0 5269.5215 12.011732
+ 9450 16738.48 0 0 5269.5216 12.011715
+ 9500 16738.481 -0.00037652437 0 5269.5216 12.011692
+ 9550 16738.493 -0.0053156159 0 5269.5203 12.011611
+ 9600 16738.549 -0.026814369 0 5269.5163 12.011415
+ 9650 16738.765 -0.10191523 0 5269.5092 12.011013
+ 9700 16735.041 1.0589887 0 5269.4979 12.062708
+ 9750 16738.013 0.135501 0 5269.5101 11.407245
+ 9800 16738.512 -0.011620329 0 5269.5201 11.394973
+ 9850 16738.489 -0.00067270548 0 5269.5237 11.395098
+ 9900 16738.489 -0.00024984569 0 5269.5242 11.395084
+ 9950 16738.49 0 0 5269.5245 11.395076
+ 10000 16738.49 0 0 5269.5246 11.395075
+Loop time of 0.170899 on 4 procs for 10000 steps with 81 atoms
+
+Performance: 505560.431 tau/day, 58513.939 timesteps/s
+96.4% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.0024047 | 0.0038016 | 0.0044513 | 1.3 | 2.22
+Neigh | 0.011313 | 0.012043 | 0.013355 | 0.7 | 7.05
+Comm | 0.066761 | 0.069035 | 0.071617 | 0.7 | 40.40
+Output | 0.0038884 | 0.0041398 | 0.0048923 | 0.7 | 2.42
+Modify | 0.071143 | 0.072567 | 0.074478 | 0.4 | 42.46
+Other | | 0.009313 | | | 5.45
+
+Nlocal: 20.25 ave 38 max 3 min
+Histogram: 1 0 1 0 0 0 1 0 0 1
+Nghost: 27.25 ave 48 max 13 min
+Histogram: 1 0 1 1 0 0 0 0 0 1
+Neighs: 0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 998
+Dangerous builds = 997
+Total wall time: 0:00:00
diff --git a/examples/rigid/log.5Oct16.rigid.g++.4 b/examples/rigid/log.20Apr18.rigid.g++.1
similarity index 91%
rename from examples/rigid/log.5Oct16.rigid.g++.4
rename to examples/rigid/log.20Apr18.rigid.g++.1
index 968f3a2d99bab33a911e22007e3ebc8548aba0ab..ca76376e320f83b2172b8d71b901e500c6b9314f 100644
--- a/examples/rigid/log.5Oct16.rigid.g++.4
+++ b/examples/rigid/log.20Apr18.rigid.g++.1
@@ -1,4 +1,5 @@
-LAMMPS (5 Oct 2016)
+LAMMPS (20 Apr 2018)
+ using 1 OpenMP thread(s) per MPI task
# Simple rigid body system
units lj
@@ -8,7 +9,7 @@ pair_style lj/cut 2.5
read_data data.rigid
orthogonal box = (-12 -12 -12) to (12 12 12)
- 1 by 2 by 2 MPI processor grid
+ 1 by 1 by 1 MPI processor grid
reading atoms ...
81 atoms
@@ -91,13 +92,18 @@ timestep 0.0001
thermo 50
run 10000
Neighbor list info ...
- 1 neighbor list requests
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
- binsize = 1.4 -> bins = 18 18 18
-Memory usage per processor = 3.62803 Mbytes
+ binsize = 1.4, bins = 18 18 18
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.979 | 3.979 | 3.979 Mbytes
Step Temp E_pair E_mol TotEng Press
0 115.29439 5235.9179 0 5272.2142 -2.7403788
50 14910.685 571.71558 0 5265.82 32.006171
@@ -151,7 +157,7 @@ Step Temp E_pair E_mol TotEng Press
2450 16738.464 -0.0023259756 0 5269.514 14.510746
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
2550 16738.581 -0.044940117 0 5269.5085 14.510315
- 2600 16738.427 -7.9722832e-05 0 5269.5046 14.510657
+ 2600 16738.427 -7.9722839e-05 0 5269.5046 14.510657
2650 16733.017 1.705148 0 5269.5067 14.596295
2700 16738.761 -0.10614946 0 5269.5038 14.499584
2750 16733.973 1.4038179 0 5269.5064 14.598107
@@ -173,7 +179,7 @@ Step Temp E_pair E_mol TotEng Press
3550 16713.405 7.846062 0 5269.4737 12.389816
3600 16734.939 1.0821936 0 5269.4891 12.173591
3650 16738.808 -0.13663194 0 5269.4882 12.027009
- 3700 16738.602 -0.070934368 0 5269.4889 12.025288
+ 3700 16738.602 -0.070934367 0 5269.4889 12.025288
3750 16737.731 0.20706557 0 5269.4927 12.061948
3800 16738.578 -0.05582043 0 5269.4965 12.035665
3850 16738.471 -0.016307928 0 5269.5024 12.035302
@@ -269,7 +275,7 @@ Step Temp E_pair E_mol TotEng Press
8350 16738.472 0 0 5269.5189 12.011723
8400 16738.472 0 0 5269.519 12.01172
8450 16738.473 -0.00039690663 0 5269.5189 12.011706
- 8500 16738.481 -0.0034646803 0 5269.5182 12.011643
+ 8500 16738.481 -0.0034646802 0 5269.5182 12.011643
8550 16738.483 -0.0045307409 0 5269.5178 12.011621
8600 16738.474 -0.00076532813 0 5269.5189 12.011681
8650 16738.474 0 0 5269.5197 12.011699
@@ -290,37 +296,37 @@ Step Temp E_pair E_mol TotEng Press
9400 16738.48 0 0 5269.5215 12.011732
9450 16738.48 0 0 5269.5216 12.011715
9500 16738.481 -0.00037652438 0 5269.5216 12.011692
- 9550 16738.493 -0.0053156163 0 5269.5203 12.011611
+ 9550 16738.493 -0.0053156162 0 5269.5203 12.011611
9600 16738.549 -0.026814371 0 5269.5163 12.011415
9650 16738.765 -0.10191523 0 5269.5092 12.011013
- 9700 16735.041 1.0589894 0 5269.4979 12.062708
- 9750 16738.013 0.13550109 0 5269.5101 11.407246
- 9800 16738.512 -0.011620327 0 5269.5201 11.394974
- 9850 16738.489 -0.00067270507 0 5269.5237 11.395098
- 9900 16738.489 -0.00024984555 0 5269.5242 11.395085
+ 9700 16735.041 1.0589893 0 5269.4979 12.062708
+ 9750 16738.013 0.13550102 0 5269.5101 11.407246
+ 9800 16738.512 -0.011620328 0 5269.5201 11.394974
+ 9850 16738.489 -0.00067270521 0 5269.5237 11.395098
+ 9900 16738.489 -0.00024984561 0 5269.5242 11.395085
9950 16738.49 0 0 5269.5245 11.395076
10000 16738.49 0 0 5269.5246 11.395075
-Loop time of 0.169479 on 4 procs for 10000 steps with 81 atoms
+Loop time of 0.155936 on 1 procs for 10000 steps with 81 atoms
-Performance: 509796.561 tau/day, 59004.232 timesteps/s
-98.1% CPU use with 4 MPI tasks x no OpenMP threads
+Performance: 554075.151 tau/day, 64129.068 timesteps/s
+98.3% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 0.0024633 | 0.0031875 | 0.0039403 | 0.9 | 1.88
-Neigh | 0.010975 | 0.011817 | 0.013459 | 0.9 | 6.97
-Comm | 0.072126 | 0.074024 | 0.076456 | 0.7 | 43.68
-Output | 0.0034711 | 0.0036327 | 0.0040615 | 0.4 | 2.14
-Modify | 0.069286 | 0.070574 | 0.073233 | 0.6 | 41.64
-Other | | 0.006244 | | | 3.68
+Pair | 0.013007 | 0.013007 | 0.013007 | 0.0 | 8.34
+Neigh | 0.041885 | 0.041885 | 0.041885 | 0.0 | 26.86
+Comm | 0.0094752 | 0.0094752 | 0.0094752 | 0.0 | 6.08
+Output | 0.002636 | 0.002636 | 0.002636 | 0.0 | 1.69
+Modify | 0.082249 | 0.082249 | 0.082249 | 0.0 | 52.75
+Other | | 0.006683 | | | 4.29
-Nlocal: 20.25 ave 38 max 3 min
-Histogram: 1 0 1 0 0 0 1 0 0 1
-Nghost: 27.25 ave 48 max 13 min
-Histogram: 1 0 1 1 0 0 0 0 0 1
+Nlocal: 81 ave 81 max 81 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 84 ave 84 max 84 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
-Histogram: 4 0 0 0 0 0 0 0 0 0
+Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
diff --git a/examples/rigid/log.5Oct16.rigid.g++.1 b/examples/rigid/log.20Apr18.rigid.g++.4
similarity index 89%
rename from examples/rigid/log.5Oct16.rigid.g++.1
rename to examples/rigid/log.20Apr18.rigid.g++.4
index 9b84f89c95e3182a0875dedd6ef0d13aa131af08..ff72c213edb53af7c1d29d67f70410453e144ca6 100644
--- a/examples/rigid/log.5Oct16.rigid.g++.1
+++ b/examples/rigid/log.20Apr18.rigid.g++.4
@@ -1,4 +1,5 @@
-LAMMPS (5 Oct 2016)
+LAMMPS (20 Apr 2018)
+ using 1 OpenMP thread(s) per MPI task
# Simple rigid body system
units lj
@@ -8,7 +9,7 @@ pair_style lj/cut 2.5
read_data data.rigid
orthogonal box = (-12 -12 -12) to (12 12 12)
- 1 by 1 by 1 MPI processor grid
+ 1 by 2 by 2 MPI processor grid
reading atoms ...
81 atoms
@@ -91,13 +92,18 @@ timestep 0.0001
thermo 50
run 10000
Neighbor list info ...
- 1 neighbor list requests
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
- binsize = 1.4 -> bins = 18 18 18
-Memory usage per processor = 3.65531 Mbytes
+ binsize = 1.4, bins = 18 18 18
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.95 | 4.044 | 4.326 Mbytes
Step Temp E_pair E_mol TotEng Press
0 115.29439 5235.9179 0 5272.2142 -2.7403788
50 14910.685 571.71558 0 5265.82 32.006171
@@ -151,8 +157,8 @@ Step Temp E_pair E_mol TotEng Press
2450 16738.464 -0.0023259756 0 5269.514 14.510746
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
2550 16738.581 -0.044940117 0 5269.5085 14.510315
- 2600 16738.427 -7.972284e-05 0 5269.5046 14.510657
- 2650 16733.017 1.7051479 0 5269.5067 14.596295
+ 2600 16738.427 -7.9722854e-05 0 5269.5046 14.510657
+ 2650 16733.017 1.705148 0 5269.5067 14.596295
2700 16738.761 -0.10614946 0 5269.5038 14.499584
2750 16733.973 1.4038179 0 5269.5064 14.598107
2800 16738.585 -0.046813448 0 5269.5076 14.511073
@@ -160,7 +166,7 @@ Step Temp E_pair E_mol TotEng Press
2900 16738.465 -0.0026252725 0 5269.514 14.510277
2950 16738.476 -0.0082220764 0 5269.512 14.510223
3000 16738.66 -0.071284779 0 5269.507 14.509758
- 3050 16715.332 7.2419352 0 5269.476 14.870305
+ 3050 16715.332 7.2419351 0 5269.476 14.870305
3100 16653.226 26.818761 0 5269.5009 14.496764
3150 16739.351 -0.30690375 0 5269.4886 13.643904
3200 16733.238 1.6025328 0 5269.4737 12.016934
@@ -170,7 +176,7 @@ Step Temp E_pair E_mol TotEng Press
3400 16738.543 -0.042215005 0 5269.4991 12.092809
3450 16738.591 -0.059327511 0 5269.4972 12.092536
3500 16738.759 -0.11761245 0 5269.4918 12.09203
- 3550 16713.405 7.8460621 0 5269.4737 12.389816
+ 3550 16713.405 7.846062 0 5269.4737 12.389816
3600 16734.939 1.0821936 0 5269.4891 12.173591
3650 16738.808 -0.13663194 0 5269.4882 12.027009
3700 16738.602 -0.070934368 0 5269.4889 12.025288
@@ -268,8 +274,8 @@ Step Temp E_pair E_mol TotEng Press
8300 16738.471 0 0 5269.5187 12.011719
8350 16738.472 0 0 5269.5189 12.011723
8400 16738.472 0 0 5269.519 12.01172
- 8450 16738.473 -0.00039690666 0 5269.5189 12.011706
- 8500 16738.481 -0.0034646804 0 5269.5182 12.011643
+ 8450 16738.473 -0.00039690664 0 5269.5189 12.011706
+ 8500 16738.481 -0.0034646803 0 5269.5182 12.011643
8550 16738.483 -0.0045307409 0 5269.5178 12.011621
8600 16738.474 -0.00076532811 0 5269.5189 12.011681
8650 16738.474 0 0 5269.5197 12.011699
@@ -289,38 +295,38 @@ Step Temp E_pair E_mol TotEng Press
9350 16738.48 0 0 5269.5214 12.011744
9400 16738.48 0 0 5269.5215 12.011732
9450 16738.48 0 0 5269.5216 12.011715
- 9500 16738.481 -0.00037652434 0 5269.5216 12.011692
- 9550 16738.493 -0.005315616 0 5269.5203 12.011611
- 9600 16738.549 -0.026814368 0 5269.5163 12.011415
+ 9500 16738.481 -0.00037652437 0 5269.5216 12.011692
+ 9550 16738.493 -0.0053156159 0 5269.5203 12.011611
+ 9600 16738.549 -0.026814369 0 5269.5163 12.011415
9650 16738.765 -0.10191523 0 5269.5092 12.011013
- 9700 16735.041 1.0589885 0 5269.4979 12.062708
- 9750 16738.013 0.13550123 0 5269.5101 11.407245
- 9800 16738.512 -0.011620328 0 5269.5201 11.394974
- 9850 16738.489 -0.00067270523 0 5269.5237 11.395098
- 9900 16738.489 -0.00024984554 0 5269.5242 11.395085
+ 9700 16735.041 1.0589887 0 5269.4979 12.062708
+ 9750 16738.013 0.135501 0 5269.5101 11.407245
+ 9800 16738.512 -0.011620329 0 5269.5201 11.394973
+ 9850 16738.489 -0.00067270548 0 5269.5237 11.395098
+ 9900 16738.489 -0.00024984569 0 5269.5242 11.395084
9950 16738.49 0 0 5269.5245 11.395076
10000 16738.49 0 0 5269.5246 11.395075
-Loop time of 0.125672 on 1 procs for 10000 steps with 81 atoms
+Loop time of 0.194532 on 4 procs for 10000 steps with 81 atoms
-Performance: 687503.421 tau/day, 79572.155 timesteps/s
-100.2% CPU use with 1 MPI tasks x no OpenMP threads
+Performance: 444142.918 tau/day, 51405.430 timesteps/s
+96.3% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 0.0097554 | 0.0097554 | 0.0097554 | 0.0 | 7.76
-Neigh | 0.038657 | 0.038657 | 0.038657 | 0.0 | 30.76
-Comm | 0.0074 | 0.0074 | 0.0074 | 0.0 | 5.89
-Output | 0.0010791 | 0.0010791 | 0.0010791 | 0.0 | 0.86
-Modify | 0.064604 | 0.064604 | 0.064604 | 0.0 | 51.41
-Other | | 0.004176 | | | 3.32
+Pair | 0.0025368 | 0.003831 | 0.0045376 | 1.2 | 1.97
+Neigh | 0.011299 | 0.012014 | 0.013005 | 0.6 | 6.18
+Comm | 0.081939 | 0.084112 | 0.087817 | 0.8 | 43.24
+Output | 0.0044608 | 0.0047221 | 0.0053811 | 0.6 | 2.43
+Modify | 0.078212 | 0.080219 | 0.082467 | 0.7 | 41.24
+Other | | 0.009634 | | | 4.95
-Nlocal: 81 ave 81 max 81 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 84 ave 84 max 84 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
+Nlocal: 20.25 ave 38 max 3 min
+Histogram: 1 0 1 0 0 0 1 0 0 1
+Nghost: 27.25 ave 48 max 13 min
+Histogram: 1 0 1 1 0 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
+Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
diff --git a/examples/rigid/log.20Apr18.rigid.nve.early.g++.1 b/examples/rigid/log.20Apr18.rigid.nve.early.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..7e92b4e6ef4efd96d7d3e1077f54cfc42e36a93c
--- /dev/null
+++ b/examples/rigid/log.20Apr18.rigid.nve.early.g++.1
@@ -0,0 +1,337 @@
+LAMMPS (20 Apr 2018)
+ using 1 OpenMP thread(s) per MPI task
+# Simple rigid body system
+
+units lj
+atom_style atomic
+
+pair_style lj/cut 2.5
+
+read_data data.rigid
+ orthogonal box = (-12 -12 -12) to (12 12 12)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 81 atoms
+
+velocity all create 100.0 4928459
+
+# unconnected bodies
+
+group clump1 id <> 1 9
+9 atoms in group clump1
+group clump2 id <> 10 18
+9 atoms in group clump2
+group clump3 id <> 19 27
+9 atoms in group clump3
+group clump4 id <> 28 36
+9 atoms in group clump4
+group clump5 id <> 37 45
+9 atoms in group clump5
+group clump6 id <> 46 54
+9 atoms in group clump6
+group clump7 id <> 55 63
+9 atoms in group clump7
+group clump8 id <> 64 72
+9 atoms in group clump8
+group clump9 id <> 73 81
+9 atoms in group clump9
+
+fix 1 all rigid/nve group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
+9 rigid bodies with 81 atoms
+
+fix_modify 1 bodyforces early
+
+# 1 chain of connected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 9 18
+#group clump3 id <> 18 27
+#group clump4 id <> 27 36
+#group clump5 id <> 36 45
+#group clump6 id <> 45 54
+#group clump7 id <> 54 63
+#group clump8 id <> 63 72
+#group clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
+
+# 2 chains of connected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 9 18
+#group clump3 id <> 18 27
+#group clump4 id <> 27 36
+#group clump5 id <> 37 45
+#group clump6 id <> 45 54
+#group clump7 id <> 54 63
+#group clump8 id <> 63 72
+#group clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4
+#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
+
+neigh_modify exclude group clump1 clump1
+neigh_modify exclude group clump2 clump2
+neigh_modify exclude group clump3 clump3
+neigh_modify exclude group clump4 clump4
+neigh_modify exclude group clump5 clump5
+neigh_modify exclude group clump6 clump6
+neigh_modify exclude group clump7 clump7
+neigh_modify exclude group clump8 clump8
+neigh_modify exclude group clump9 clump9
+
+thermo 100
+
+#dump 1 all atom 50 dump.rigid
+
+#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 2 pad 5
+
+#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 3 pad 5
+
+timestep 0.0001
+thermo 50
+run 10000
+Neighbor list info ...
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 18 18 18
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.979 | 3.979 | 3.979 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 115.29439 5235.9179 0 5272.2142 -2.7403788
+ 50 14910.69 571.70921 0 5265.8153 32.005816
+ 100 16298.128 136.75661 0 5267.6488 16.449029
+ 150 16682.532 17.504156 0 5269.4124 14.901186
+ 200 16733.906 1.3755079 0 5269.4571 14.571305
+ 250 16738.861 -0.15272039 0 5269.4886 14.498342
+ 300 16738.608 -0.055216883 0 5269.5066 14.498
+ 350 16738.5 -0.017457072 0 5269.5104 14.498392
+ 400 16738.451 -0.0060161309 0 5269.5063 14.49851
+ 450 16738.435 -0.001271965 0 5269.5059 14.498571
+ 500 16738.443 -0.00081074175 0 5269.509 14.498598
+ 550 16738.452 -0.00083208965 0 5269.5118 14.498618
+ 600 16738.45 -0.00058358431 0 5269.5116 14.498617
+ 650 16738.443 -0.00047228525 0 5269.5093 14.4986
+ 700 16738.444 0 0 5269.5102 14.498612
+ 750 16738.461 0 0 5269.5157 14.498654
+ 800 16738.479 0 0 5269.521 14.498697
+ 850 16738.473 0 0 5269.5192 14.498683
+ 900 16738.449 0 0 5269.5116 14.498624
+ 950 16738.438 -0.0035324203 0 5269.5046 14.498537
+ 1000 16738.562 -0.051134242 0 5269.4963 14.498093
+ 1050 16737.343 0.32970192 0 5269.4934 14.527634
+ 1100 16737.878 0.16213235 0 5269.4941 14.533864
+ 1150 16738.682 -0.089236256 0 5269.4959 14.511765
+ 1200 16738.444 -0.0075446558 0 5269.5025 14.512479
+ 1250 16738.45 0 0 5269.5119 14.512611
+ 1300 16738.475 0 0 5269.5199 14.512673
+ 1350 16738.484 0 0 5269.5228 14.512696
+ 1400 16738.469 -0.00044683992 0 5269.5175 14.512651
+ 1450 16738.45 -0.0010933363 0 5269.511 14.512595
+ 1500 16738.445 -0.00057484239 0 5269.51 14.512591
+ 1550 16738.451 0 0 5269.5123 14.512615
+ 1600 16738.452 0 0 5269.5127 14.512618
+ 1650 16738.443 0 0 5269.5099 14.512596
+ 1700 16738.433 0 0 5269.5068 14.512572
+ 1750 16738.438 0 0 5269.5084 14.512584
+ 1800 16738.459 0 0 5269.5149 14.512635
+ 1850 16738.473 0 0 5269.5193 14.51267
+ 1900 16738.462 0 0 5269.5159 14.512644
+ 1950 16738.446 -0.0032069962 0 5269.5076 14.512539
+ 2000 16738.463 -0.013425408 0 5269.5027 14.512382
+ 2050 16738.535 -0.036964311 0 5269.5017 14.512152
+ 2100 16738.621 -0.063490509 0 5269.5023 14.512108
+ 2150 16738.594 -0.056143934 0 5269.5012 14.512117
+ 2200 16738.536 -0.038486645 0 5269.5007 14.512277
+ 2250 16738.496 -0.023712406 0 5269.503 14.51242
+ 2300 16738.488 -0.013209094 0 5269.5109 14.51255
+ 2350 16738.486 -0.0045244524 0 5269.519 14.512693
+ 2400 16738.475 -0.00051678325 0 5269.5194 14.512743
+ 2450 16738.456 -0.0023209272 0 5269.5115 14.512659
+ 2500 16738.442 -0.0052101787 0 5269.5042 14.512594
+ 2550 16738.552 -0.04420046 0 5269.4998 14.512177
+ 2600 16738.42 -0.004347531 0 5269.4982 14.512783
+ 2650 16734.241 1.3131302 0 5269.5 14.577195
+ 2700 16738.737 -0.10612056 0 5269.4961 14.503874
+ 2750 16732.705 1.7939719 0 5269.4974 14.629294
+ 2800 16738.558 -0.042867033 0 5269.5032 14.519893
+ 2850 16738.499 -0.01271227 0 5269.5146 14.518524
+ 2900 16738.486 -0.0032778045 0 5269.52 14.518712
+ 2950 16738.482 -0.0089544631 0 5269.5133 14.518629
+ 3000 16738.647 -0.070862542 0 5269.5031 14.51803
+ 3050 16678.313 18.829038 0 5269.409 15.533426
+ 3100 16632.312 33.399217 0 5269.4975 14.588597
+ 3150 16739.318 -0.31388148 0 5269.4715 13.520782
+ 3200 16727.951 3.26736 0 5269.4741 12.288358
+ 3250 16686.364 16.353793 0 5269.4682 14.152517
+ 3300 16738.532 -0.031574462 0 5269.5064 13.310615
+ 3350 16738.454 -0.0062292918 0 5269.5071 13.308187
+ 3400 16738.445 -0.0049349125 0 5269.5055 13.308178
+ 3450 16738.489 -0.021623738 0 5269.5026 13.308001
+ 3500 16737.78 0.19719043 0 5269.4983 13.325999
+ 3550 16658.578 25.116206 0 5269.4834 13.778249
+ 3600 16738.51 -0.032864725 0 5269.4981 12.392389
+ 3650 16738.899 -0.15952703 0 5269.4938 12.383503
+ 3700 16738.879 -0.16025994 0 5269.487 12.382575
+ 3750 16738.878 -0.16608251 0 5269.4806 12.382765
+ 3800 16738.591 -0.078679341 0 5269.4776 12.383227
+ 3850 16738.429 -0.024729409 0 5269.4807 12.382942
+ 3900 16738.399 -0.0062729967 0 5269.4897 12.383192
+ 3950 16738.428 -0.002521266 0 5269.5027 12.383324
+ 4000 16738.467 -0.0002068506 0 5269.5173 12.383474
+ 4050 16738.488 0 0 5269.5241 12.383531
+ 4100 16738.468 0 0 5269.5178 12.383482
+ 4150 16738.422 0 0 5269.5033 12.383369
+ 4200 16738.387 0 0 5269.4921 12.383281
+ 4250 16738.383 0 0 5269.4908 12.38327
+ 4300 16738.4 0 0 5269.4964 12.383314
+ 4350 16738.423 0 0 5269.5036 12.38337
+ 4400 16738.441 0 0 5269.5092 12.383414
+ 4450 16738.45 0 0 5269.5121 12.383437
+ 4500 16738.45 0 0 5269.5122 12.383438
+ 4550 16738.442 0 0 5269.5095 12.383417
+ 4600 16738.425 0 0 5269.5042 12.383376
+ 4650 16738.404 -0.0014438316 0 5269.4961 12.383299
+ 4700 16738.444 -0.024020551 0 5269.4862 12.382975
+ 4750 16738.49 -0.048521421 0 5269.4761 12.385777
+ 4800 16735.057 1.0347219 0 5269.4786 12.43543
+ 4850 16735.441 0.92650928 0 5269.4913 12.418653
+ 4900 16723.839 4.5908971 0 5269.5033 13.410103
+ 4950 16738.531 -0.021537669 0 5269.5159 13.089982
+ 5000 16738.45 -0.0042589693 0 5269.5077 13.090062
+ 5050 16738.409 -0.00024692474 0 5269.4987 13.090038
+ 5100 16738.404 0 0 5269.4976 13.090032
+ 5150 16738.421 0 0 5269.5029 13.090073
+ 5200 16738.44 0 0 5269.5087 13.090119
+ 5250 16738.448 -0.0012793921 0 5269.5102 13.090114
+ 5300 16738.456 -0.0064376397 0 5269.5075 13.090026
+ 5350 16738.479 -0.020383842 0 5269.5007 13.089898
+ 5400 16735.845 0.79889481 0 5269.4909 13.136244
+ 5450 16735.558 0.87619898 0 5269.4778 12.324482
+ 5500 16711.494 8.47243 0 5269.4984 12.65658
+ 5550 16454.525 89.074845 0 5269.2031 16.996503
+ 5600 16713.084 7.9801091 0 5269.5065 13.774971
+ 5650 16738.676 -0.079987812 0 5269.5033 13.168292
+ 5700 16446.281 91.866085 0 5269.399 23.764658
+ 5750 16738.549 -0.039869082 0 5269.5034 13.378117
+ 5800 16738.487 -0.014994464 0 5269.5086 13.378394
+ 5850 16738.466 -0.0051267378 0 5269.512 13.378555
+ 5900 16738.462 -0.0043689966 0 5269.5113 13.378568
+ 5950 16738.528 -0.032727396 0 5269.5039 13.378192
+ 6000 16702.774 10.969422 0 5269.2502 13.788847
+ 6050 16682.271 17.483217 0 5269.3092 13.353098
+ 6100 16738.508 -0.028838289 0 5269.5016 12.521077
+ 6150 16738.425 -0.0067595568 0 5269.4974 12.521216
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+ 9400 16738.48 0 0 5269.5216 10.590528
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+ 9550 16738.484 0 0 5269.5226 10.590536
+ 9600 16738.483 0 0 5269.5223 10.590534
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+ 9700 16738.484 0 0 5269.5228 10.590537
+ 9750 16738.507 0 0 5269.53 10.590595
+ 9800 16738.482 0 0 5269.522 10.590532
+ 9850 16738.478 0 0 5269.5207 10.590521
+ 9900 16738.487 -0.00030979882 0 5269.5233 10.590538
+ 9950 16738.476 -0.00095967357 0 5269.5193 10.590496
+ 10000 16738.494 -0.00062714625 0 5269.5253 10.590548
+Loop time of 0.166298 on 1 procs for 10000 steps with 81 atoms
+
+Performance: 519549.516 tau/day, 60133.046 timesteps/s
+99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.011685 | 0.011685 | 0.011685 | 0.0 | 7.03
+Neigh | 0.038539 | 0.038539 | 0.038539 | 0.0 | 23.17
+Comm | 0.0086315 | 0.0086315 | 0.0086315 | 0.0 | 5.19
+Output | 0.0026531 | 0.0026531 | 0.0026531 | 0.0 | 1.60
+Modify | 0.098759 | 0.098759 | 0.098759 | 0.0 | 59.39
+Other | | 0.00603 | | | 3.63
+
+Nlocal: 81 ave 81 max 81 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 49 ave 49 max 49 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 3 ave 3 max 3 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 3
+Ave neighs/atom = 0.037037
+Neighbor list builds = 998
+Dangerous builds = 997
+Total wall time: 0:00:00
diff --git a/examples/rigid/log.20Apr18.rigid.nve.early.g++.4 b/examples/rigid/log.20Apr18.rigid.nve.early.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..1c3592990bbae7b9871d3557490358b33bd2dcb9
--- /dev/null
+++ b/examples/rigid/log.20Apr18.rigid.nve.early.g++.4
@@ -0,0 +1,337 @@
+LAMMPS (20 Apr 2018)
+ using 1 OpenMP thread(s) per MPI task
+# Simple rigid body system
+
+units lj
+atom_style atomic
+
+pair_style lj/cut 2.5
+
+read_data data.rigid
+ orthogonal box = (-12 -12 -12) to (12 12 12)
+ 1 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 81 atoms
+
+velocity all create 100.0 4928459
+
+# unconnected bodies
+
+group clump1 id <> 1 9
+9 atoms in group clump1
+group clump2 id <> 10 18
+9 atoms in group clump2
+group clump3 id <> 19 27
+9 atoms in group clump3
+group clump4 id <> 28 36
+9 atoms in group clump4
+group clump5 id <> 37 45
+9 atoms in group clump5
+group clump6 id <> 46 54
+9 atoms in group clump6
+group clump7 id <> 55 63
+9 atoms in group clump7
+group clump8 id <> 64 72
+9 atoms in group clump8
+group clump9 id <> 73 81
+9 atoms in group clump9
+
+fix 1 all rigid/nve group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
+9 rigid bodies with 81 atoms
+
+fix_modify 1 bodyforces early
+
+# 1 chain of connected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 9 18
+#group clump3 id <> 18 27
+#group clump4 id <> 27 36
+#group clump5 id <> 36 45
+#group clump6 id <> 45 54
+#group clump7 id <> 54 63
+#group clump8 id <> 63 72
+#group clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
+
+# 2 chains of connected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 9 18
+#group clump3 id <> 18 27
+#group clump4 id <> 27 36
+#group clump5 id <> 37 45
+#group clump6 id <> 45 54
+#group clump7 id <> 54 63
+#group clump8 id <> 63 72
+#group clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4
+#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
+
+neigh_modify exclude group clump1 clump1
+neigh_modify exclude group clump2 clump2
+neigh_modify exclude group clump3 clump3
+neigh_modify exclude group clump4 clump4
+neigh_modify exclude group clump5 clump5
+neigh_modify exclude group clump6 clump6
+neigh_modify exclude group clump7 clump7
+neigh_modify exclude group clump8 clump8
+neigh_modify exclude group clump9 clump9
+
+thermo 100
+
+#dump 1 all atom 50 dump.rigid
+
+#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 2 pad 5
+
+#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 3 pad 5
+
+timestep 0.0001
+thermo 50
+run 10000
+Neighbor list info ...
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 18 18 18
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.95 | 4.044 | 4.326 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 115.29439 5235.9179 0 5272.2142 -2.7403788
+ 50 14910.69 571.70921 0 5265.8153 32.005816
+ 100 16298.128 136.75661 0 5267.6488 16.449029
+ 150 16682.532 17.504156 0 5269.4124 14.901186
+ 200 16733.906 1.3755079 0 5269.4571 14.571305
+ 250 16738.861 -0.15272039 0 5269.4886 14.498342
+ 300 16738.608 -0.055216883 0 5269.5066 14.498
+ 350 16738.5 -0.017457072 0 5269.5104 14.498392
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+ 9900 16738.487 -0.00030979874 0 5269.5233 10.59032
+ 9950 16738.476 -0.00095967134 0 5269.5192 10.590278
+ 10000 16738.494 -0.00062714318 0 5269.5253 10.590329
+Loop time of 0.224811 on 4 procs for 10000 steps with 81 atoms
+
+Performance: 384323.005 tau/day, 44481.829 timesteps/s
+95.9% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.0032673 | 0.0039269 | 0.0048387 | 1.1 | 1.75
+Neigh | 0.010401 | 0.012159 | 0.015022 | 1.6 | 5.41
+Comm | 0.087584 | 0.08909 | 0.090645 | 0.4 | 39.63
+Output | 0.0042956 | 0.0045624 | 0.0052695 | 0.6 | 2.03
+Modify | 0.10208 | 0.10506 | 0.10697 | 0.6 | 46.73
+Other | | 0.01001 | | | 4.45
+
+Nlocal: 20.25 ave 34 max 9 min
+Histogram: 2 0 0 0 0 0 0 1 0 1
+Nghost: 38.5 ave 43 max 26 min
+Histogram: 1 0 0 0 0 0 0 0 0 3
+Neighs: 0.75 ave 2 max 0 min
+Histogram: 2 0 0 0 0 1 0 0 0 1
+
+Total # of neighbors = 3
+Ave neighs/atom = 0.037037
+Neighbor list builds = 998
+Dangerous builds = 997
+Total wall time: 0:00:00
diff --git a/examples/rigid/log.20Apr18.rigid.nve.g++.1 b/examples/rigid/log.20Apr18.rigid.nve.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..26fa4e7f680fb2a016cb0ea0c4ec195855ca4224
--- /dev/null
+++ b/examples/rigid/log.20Apr18.rigid.nve.g++.1
@@ -0,0 +1,335 @@
+LAMMPS (20 Apr 2018)
+ using 1 OpenMP thread(s) per MPI task
+# Simple rigid body system
+
+units lj
+atom_style atomic
+
+pair_style lj/cut 2.5
+
+read_data data.rigid
+ orthogonal box = (-12 -12 -12) to (12 12 12)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 81 atoms
+
+velocity all create 100.0 4928459
+
+# unconnected bodies
+
+group clump1 id <> 1 9
+9 atoms in group clump1
+group clump2 id <> 10 18
+9 atoms in group clump2
+group clump3 id <> 19 27
+9 atoms in group clump3
+group clump4 id <> 28 36
+9 atoms in group clump4
+group clump5 id <> 37 45
+9 atoms in group clump5
+group clump6 id <> 46 54
+9 atoms in group clump6
+group clump7 id <> 55 63
+9 atoms in group clump7
+group clump8 id <> 64 72
+9 atoms in group clump8
+group clump9 id <> 73 81
+9 atoms in group clump9
+
+fix 1 all rigid/nve group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
+9 rigid bodies with 81 atoms
+
+# 1 chain of connected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 9 18
+#group clump3 id <> 18 27
+#group clump4 id <> 27 36
+#group clump5 id <> 36 45
+#group clump6 id <> 45 54
+#group clump7 id <> 54 63
+#group clump8 id <> 63 72
+#group clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
+
+# 2 chains of connected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 9 18
+#group clump3 id <> 18 27
+#group clump4 id <> 27 36
+#group clump5 id <> 37 45
+#group clump6 id <> 45 54
+#group clump7 id <> 54 63
+#group clump8 id <> 63 72
+#group clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4
+#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
+
+neigh_modify exclude group clump1 clump1
+neigh_modify exclude group clump2 clump2
+neigh_modify exclude group clump3 clump3
+neigh_modify exclude group clump4 clump4
+neigh_modify exclude group clump5 clump5
+neigh_modify exclude group clump6 clump6
+neigh_modify exclude group clump7 clump7
+neigh_modify exclude group clump8 clump8
+neigh_modify exclude group clump9 clump9
+
+thermo 100
+
+#dump 1 all atom 50 dump.rigid
+
+#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 2 pad 5
+
+#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 3 pad 5
+
+timestep 0.0001
+thermo 50
+run 10000
+Neighbor list info ...
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 18 18 18
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.979 | 3.979 | 3.979 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 115.29439 5235.9179 0 5272.2142 -2.7403788
+ 50 14910.69 571.70921 0 5265.8153 32.005816
+ 100 16298.128 136.75661 0 5267.6488 16.449029
+ 150 16682.532 17.504156 0 5269.4124 14.901186
+ 200 16733.906 1.3755079 0 5269.4571 14.571305
+ 250 16738.861 -0.15272039 0 5269.4886 14.498342
+ 300 16738.608 -0.055216883 0 5269.5066 14.498
+ 350 16738.5 -0.017457072 0 5269.5104 14.498392
+ 400 16738.451 -0.0060161309 0 5269.5063 14.49851
+ 450 16738.435 -0.001271965 0 5269.5059 14.498571
+ 500 16738.443 -0.00081074175 0 5269.509 14.498598
+ 550 16738.452 -0.00083208965 0 5269.5118 14.498618
+ 600 16738.45 -0.00058358431 0 5269.5116 14.498617
+ 650 16738.443 -0.00047228525 0 5269.5093 14.4986
+ 700 16738.444 0 0 5269.5102 14.498612
+ 750 16738.461 0 0 5269.5157 14.498654
+ 800 16738.479 0 0 5269.521 14.498697
+ 850 16738.473 0 0 5269.5192 14.498683
+ 900 16738.449 0 0 5269.5116 14.498624
+ 950 16738.438 -0.0035324203 0 5269.5046 14.498537
+ 1000 16738.562 -0.051134242 0 5269.4963 14.498093
+ 1050 16737.343 0.32970192 0 5269.4934 14.527634
+ 1100 16737.878 0.16213235 0 5269.4941 14.533864
+ 1150 16738.682 -0.089236256 0 5269.4959 14.511765
+ 1200 16738.444 -0.0075446558 0 5269.5025 14.512479
+ 1250 16738.45 0 0 5269.5119 14.512611
+ 1300 16738.475 0 0 5269.5199 14.512673
+ 1350 16738.484 0 0 5269.5228 14.512696
+ 1400 16738.469 -0.00044683992 0 5269.5175 14.512651
+ 1450 16738.45 -0.0010933363 0 5269.511 14.512595
+ 1500 16738.445 -0.00057484239 0 5269.51 14.512591
+ 1550 16738.451 0 0 5269.5123 14.512615
+ 1600 16738.452 0 0 5269.5127 14.512618
+ 1650 16738.443 0 0 5269.5099 14.512596
+ 1700 16738.433 0 0 5269.5068 14.512572
+ 1750 16738.438 0 0 5269.5084 14.512584
+ 1800 16738.459 0 0 5269.5149 14.512635
+ 1850 16738.473 0 0 5269.5193 14.51267
+ 1900 16738.462 0 0 5269.5159 14.512644
+ 1950 16738.446 -0.0032069962 0 5269.5076 14.512539
+ 2000 16738.463 -0.013425408 0 5269.5027 14.512382
+ 2050 16738.535 -0.036964311 0 5269.5017 14.512152
+ 2100 16738.621 -0.063490509 0 5269.5023 14.512108
+ 2150 16738.594 -0.056143934 0 5269.5012 14.512117
+ 2200 16738.536 -0.038486645 0 5269.5007 14.512277
+ 2250 16738.496 -0.023712406 0 5269.503 14.51242
+ 2300 16738.488 -0.013209094 0 5269.5109 14.51255
+ 2350 16738.486 -0.0045244524 0 5269.519 14.512693
+ 2400 16738.475 -0.00051678325 0 5269.5194 14.512743
+ 2450 16738.456 -0.0023209272 0 5269.5115 14.512659
+ 2500 16738.442 -0.0052101787 0 5269.5042 14.512594
+ 2550 16738.552 -0.04420046 0 5269.4998 14.512177
+ 2600 16738.42 -0.004347531 0 5269.4982 14.512783
+ 2650 16734.241 1.3131302 0 5269.5 14.577195
+ 2700 16738.737 -0.10612056 0 5269.4961 14.503874
+ 2750 16732.705 1.7939719 0 5269.4974 14.629294
+ 2800 16738.558 -0.042867033 0 5269.5032 14.519893
+ 2850 16738.499 -0.01271227 0 5269.5146 14.518524
+ 2900 16738.486 -0.0032778045 0 5269.52 14.518712
+ 2950 16738.482 -0.0089544631 0 5269.5133 14.518629
+ 3000 16738.647 -0.070862542 0 5269.5031 14.51803
+ 3050 16678.313 18.829038 0 5269.409 15.533426
+ 3100 16632.312 33.399217 0 5269.4975 14.588597
+ 3150 16739.318 -0.31388148 0 5269.4715 13.520782
+ 3200 16727.951 3.26736 0 5269.4741 12.288358
+ 3250 16686.364 16.353793 0 5269.4682 14.152517
+ 3300 16738.532 -0.031574462 0 5269.5064 13.310615
+ 3350 16738.454 -0.0062292918 0 5269.5071 13.308187
+ 3400 16738.445 -0.0049349125 0 5269.5055 13.308178
+ 3450 16738.489 -0.021623738 0 5269.5026 13.308001
+ 3500 16737.78 0.19719043 0 5269.4983 13.325999
+ 3550 16658.578 25.116206 0 5269.4834 13.778249
+ 3600 16738.51 -0.032864725 0 5269.4981 12.392389
+ 3650 16738.899 -0.15952703 0 5269.4938 12.383503
+ 3700 16738.879 -0.16025994 0 5269.487 12.382575
+ 3750 16738.878 -0.16608251 0 5269.4806 12.382765
+ 3800 16738.591 -0.078679341 0 5269.4776 12.383227
+ 3850 16738.429 -0.024729409 0 5269.4807 12.382942
+ 3900 16738.399 -0.0062729967 0 5269.4897 12.383192
+ 3950 16738.428 -0.002521266 0 5269.5027 12.383324
+ 4000 16738.467 -0.0002068506 0 5269.5173 12.383474
+ 4050 16738.488 0 0 5269.5241 12.383531
+ 4100 16738.468 0 0 5269.5178 12.383482
+ 4150 16738.422 0 0 5269.5033 12.383369
+ 4200 16738.387 0 0 5269.4921 12.383281
+ 4250 16738.383 0 0 5269.4908 12.38327
+ 4300 16738.4 0 0 5269.4964 12.383314
+ 4350 16738.423 0 0 5269.5036 12.38337
+ 4400 16738.441 0 0 5269.5092 12.383414
+ 4450 16738.45 0 0 5269.5121 12.383437
+ 4500 16738.45 0 0 5269.5122 12.383438
+ 4550 16738.442 0 0 5269.5095 12.383417
+ 4600 16738.425 0 0 5269.5042 12.383376
+ 4650 16738.404 -0.0014438316 0 5269.4961 12.383299
+ 4700 16738.444 -0.024020551 0 5269.4862 12.382975
+ 4750 16738.49 -0.048521421 0 5269.4761 12.385777
+ 4800 16735.057 1.0347219 0 5269.4786 12.43543
+ 4850 16735.441 0.92650928 0 5269.4913 12.418653
+ 4900 16723.839 4.5908971 0 5269.5033 13.410103
+ 4950 16738.531 -0.021537669 0 5269.5159 13.089982
+ 5000 16738.45 -0.0042589693 0 5269.5077 13.090062
+ 5050 16738.409 -0.00024692474 0 5269.4987 13.090038
+ 5100 16738.404 0 0 5269.4976 13.090032
+ 5150 16738.421 0 0 5269.5029 13.090073
+ 5200 16738.44 0 0 5269.5087 13.090119
+ 5250 16738.448 -0.0012793921 0 5269.5102 13.090114
+ 5300 16738.456 -0.0064376397 0 5269.5075 13.090026
+ 5350 16738.479 -0.020383842 0 5269.5007 13.089898
+ 5400 16735.845 0.79889481 0 5269.4909 13.136244
+ 5450 16735.558 0.87619898 0 5269.4778 12.324482
+ 5500 16711.494 8.47243 0 5269.4984 12.65658
+ 5550 16454.525 89.074845 0 5269.2031 16.996503
+ 5600 16713.084 7.9801091 0 5269.5065 13.774971
+ 5650 16738.676 -0.079987812 0 5269.5033 13.168292
+ 5700 16446.281 91.866085 0 5269.399 23.764658
+ 5750 16738.549 -0.039869082 0 5269.5034 13.378117
+ 5800 16738.487 -0.014994464 0 5269.5086 13.378394
+ 5850 16738.466 -0.0051267378 0 5269.512 13.378555
+ 5900 16738.462 -0.0043689966 0 5269.5113 13.378568
+ 5950 16738.528 -0.032727396 0 5269.5039 13.378192
+ 6000 16702.774 10.969422 0 5269.2502 13.788847
+ 6050 16682.271 17.483217 0 5269.3092 13.353098
+ 6100 16738.508 -0.028838289 0 5269.5016 12.521077
+ 6150 16738.425 -0.0067595568 0 5269.4974 12.521216
+ 6200 16738.401 -0.0011499904 0 5269.4955 12.521247
+ 6250 16738.455 0 0 5269.5136 12.521403
+ 6300 16738.523 0 0 5269.5352 12.521573
+ 6350 16738.503 0 0 5269.5287 12.521525
+ 6400 16738.427 0 0 5269.5047 12.521337
+ 6450 16738.399 0 0 5269.496 12.521268
+ 6500 16738.425 0 0 5269.5042 12.521331
+ 6550 16738.441 0 0 5269.5093 12.521372
+ 6600 16738.42 0 0 5269.5025 12.521319
+ 6650 16738.398 0 0 5269.4957 12.521266
+ 6700 16738.435 0 0 5269.5074 12.521355
+ 6750 16738.505 0 0 5269.5293 12.521527
+ 6800 16738.508 0 0 5269.5303 12.521536
+ 6850 16738.446 0 0 5269.5108 12.521384
+ 6900 16738.414 0 0 5269.5009 12.521306
+ 6950 16738.432 0 0 5269.5063 12.521348
+ 7000 16738.444 0 0 5269.5102 12.521378
+ 7050 16738.421 0 0 5269.5029 12.521322
+ 7100 16738.393 0 0 5269.4941 12.521253
+ 7150 16738.419 0 0 5269.5022 12.521315
+ 7200 16738.489 0 0 5269.5244 12.521489
+ 7250 16738.505 0 0 5269.5293 12.521528
+ 7300 16738.443 0 0 5269.5098 12.521376
+ 7350 16738.404 0 0 5269.4976 12.521281
+ 7400 16738.43 0 0 5269.5058 12.521343
+ 7450 16738.461 0 0 5269.5156 12.521421
+ 7500 16738.447 0 0 5269.5109 12.521385
+ 7550 16738.407 0 0 5269.4986 12.521288
+ 7600 16738.412 0 0 5269.5002 12.5213
+ 7650 16738.478 0 0 5269.5208 12.52146
+ 7700 16738.51 0 0 5269.5309 12.521541
+ 7750 16738.454 0 0 5269.5135 12.521405
+ 7800 16738.398 0 0 5269.4958 12.521267
+ 7850 16738.407 -0.0002118068 0 5269.4982 12.521283
+ 7900 16738.441 -0.00021679441 0 5269.509 12.521366
+ 7950 16738.446 -0.00023847865 0 5269.5107 12.52138
+ 8000 16738.423 0 0 5269.5035 12.521326
+ 8050 16738.423 0 0 5269.5034 12.521325
+ 8100 16738.478 -0.00069624411 0 5269.52 12.521447
+ 8150 16738.523 -0.0040058094 0 5269.531 12.521494
+ 8200 16738.486 -0.0092298399 0 5269.5142 12.521327
+ 8250 16738.458 -0.023189572 0 5269.4914 12.521008
+ 8300 16738.513 -0.045847775 0 5269.4861 12.520773
+ 8350 16723.734 4.5722877 0 5269.4516 12.849562
+ 8400 16738.466 -0.020202622 0 5269.497 12.835807
+ 8450 16738.437 -0.012822209 0 5269.4952 12.829975
+ 8500 16738.408 -0.001683355 0 5269.4972 12.8301
+ 8550 16738.464 -0.00097382251 0 5269.5155 12.830254
+ 8600 16738.669 -0.050581166 0 5269.5304 12.829973
+ 8650 15918.256 250.07455 0 5261.3774 24.539208
+ 8700 16738.446 0.00084613367 0 5269.5116 10.591358
+ 8750 16738.472 -0.010145611 0 5269.5089 10.590277
+ 8800 16738.468 0 0 5269.5176 10.590497
+ 8850 16738.508 0 0 5269.5303 10.590596
+ 8900 16738.509 0 0 5269.5306 10.590599
+ 8950 16738.496 0 0 5269.5266 10.590568
+ 9000 16738.477 0 0 5269.5204 10.59052
+ 9050 16738.455 0 0 5269.5135 10.590465
+ 9100 16738.477 0 0 5269.5205 10.590519
+ 9150 16738.512 0 0 5269.5315 10.590606
+ 9200 16738.502 0 0 5269.5285 10.590583
+ 9250 16738.493 0 0 5269.5254 10.590559
+ 9300 16738.482 0 0 5269.522 10.590532
+ 9350 16738.46 0 0 5269.5151 10.590478
+ 9400 16738.48 0 0 5269.5216 10.590528
+ 9450 16738.509 0 0 5269.5306 10.590599
+ 9500 16738.49 0 0 5269.5247 10.590554
+ 9550 16738.484 0 0 5269.5226 10.590536
+ 9600 16738.483 0 0 5269.5223 10.590534
+ 9650 16738.464 0 0 5269.5165 10.590489
+ 9700 16738.484 0 0 5269.5228 10.590537
+ 9750 16738.507 0 0 5269.53 10.590595
+ 9800 16738.482 0 0 5269.522 10.590532
+ 9850 16738.478 0 0 5269.5207 10.590521
+ 9900 16738.487 -0.00030979882 0 5269.5233 10.590538
+ 9950 16738.476 -0.00095967357 0 5269.5193 10.590496
+ 10000 16738.494 -0.00062714625 0 5269.5253 10.590548
+Loop time of 0.166547 on 1 procs for 10000 steps with 81 atoms
+
+Performance: 518773.777 tau/day, 60043.261 timesteps/s
+99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.011439 | 0.011439 | 0.011439 | 0.0 | 6.87
+Neigh | 0.038572 | 0.038572 | 0.038572 | 0.0 | 23.16
+Comm | 0.0085464 | 0.0085464 | 0.0085464 | 0.0 | 5.13
+Output | 0.0025046 | 0.0025046 | 0.0025046 | 0.0 | 1.50
+Modify | 0.099479 | 0.099479 | 0.099479 | 0.0 | 59.73
+Other | | 0.006005 | | | 3.61
+
+Nlocal: 81 ave 81 max 81 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 49 ave 49 max 49 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 3 ave 3 max 3 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 3
+Ave neighs/atom = 0.037037
+Neighbor list builds = 998
+Dangerous builds = 997
+Total wall time: 0:00:00
diff --git a/examples/rigid/log.20Apr18.rigid.nve.g++.4 b/examples/rigid/log.20Apr18.rigid.nve.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..782457b42795a959c6a2dfbfcd003226e40bba24
--- /dev/null
+++ b/examples/rigid/log.20Apr18.rigid.nve.g++.4
@@ -0,0 +1,335 @@
+LAMMPS (20 Apr 2018)
+ using 1 OpenMP thread(s) per MPI task
+# Simple rigid body system
+
+units lj
+atom_style atomic
+
+pair_style lj/cut 2.5
+
+read_data data.rigid
+ orthogonal box = (-12 -12 -12) to (12 12 12)
+ 1 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 81 atoms
+
+velocity all create 100.0 4928459
+
+# unconnected bodies
+
+group clump1 id <> 1 9
+9 atoms in group clump1
+group clump2 id <> 10 18
+9 atoms in group clump2
+group clump3 id <> 19 27
+9 atoms in group clump3
+group clump4 id <> 28 36
+9 atoms in group clump4
+group clump5 id <> 37 45
+9 atoms in group clump5
+group clump6 id <> 46 54
+9 atoms in group clump6
+group clump7 id <> 55 63
+9 atoms in group clump7
+group clump8 id <> 64 72
+9 atoms in group clump8
+group clump9 id <> 73 81
+9 atoms in group clump9
+
+fix 1 all rigid/nve group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
+9 rigid bodies with 81 atoms
+
+# 1 chain of connected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 9 18
+#group clump3 id <> 18 27
+#group clump4 id <> 27 36
+#group clump5 id <> 36 45
+#group clump6 id <> 45 54
+#group clump7 id <> 54 63
+#group clump8 id <> 63 72
+#group clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
+
+# 2 chains of connected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 9 18
+#group clump3 id <> 18 27
+#group clump4 id <> 27 36
+#group clump5 id <> 37 45
+#group clump6 id <> 45 54
+#group clump7 id <> 54 63
+#group clump8 id <> 63 72
+#group clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4
+#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
+
+neigh_modify exclude group clump1 clump1
+neigh_modify exclude group clump2 clump2
+neigh_modify exclude group clump3 clump3
+neigh_modify exclude group clump4 clump4
+neigh_modify exclude group clump5 clump5
+neigh_modify exclude group clump6 clump6
+neigh_modify exclude group clump7 clump7
+neigh_modify exclude group clump8 clump8
+neigh_modify exclude group clump9 clump9
+
+thermo 100
+
+#dump 1 all atom 50 dump.rigid
+
+#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 2 pad 5
+
+#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 3 pad 5
+
+timestep 0.0001
+thermo 50
+run 10000
+Neighbor list info ...
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 18 18 18
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.95 | 4.044 | 4.326 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 115.29439 5235.9179 0 5272.2142 -2.7403788
+ 50 14910.69 571.70921 0 5265.8153 32.005816
+ 100 16298.128 136.75661 0 5267.6488 16.449029
+ 150 16682.532 17.504156 0 5269.4124 14.901186
+ 200 16733.906 1.3755079 0 5269.4571 14.571305
+ 250 16738.861 -0.15272039 0 5269.4886 14.498342
+ 300 16738.608 -0.055216883 0 5269.5066 14.498
+ 350 16738.5 -0.017457072 0 5269.5104 14.498392
+ 400 16738.451 -0.0060161309 0 5269.5063 14.49851
+ 450 16738.435 -0.001271965 0 5269.5059 14.498571
+ 500 16738.443 -0.00081074175 0 5269.509 14.498598
+ 550 16738.452 -0.00083208965 0 5269.5118 14.498618
+ 600 16738.45 -0.00058358431 0 5269.5116 14.498617
+ 650 16738.443 -0.00047228525 0 5269.5093 14.4986
+ 700 16738.444 0 0 5269.5102 14.498612
+ 750 16738.461 0 0 5269.5157 14.498654
+ 800 16738.479 0 0 5269.521 14.498697
+ 850 16738.473 0 0 5269.5192 14.498683
+ 900 16738.449 0 0 5269.5116 14.498624
+ 950 16738.438 -0.0035324203 0 5269.5046 14.498537
+ 1000 16738.562 -0.051134242 0 5269.4963 14.498093
+ 1050 16737.343 0.32970192 0 5269.4934 14.527634
+ 1100 16737.878 0.16213235 0 5269.4941 14.533864
+ 1150 16738.682 -0.089236256 0 5269.4959 14.511765
+ 1200 16738.444 -0.0075446558 0 5269.5025 14.512479
+ 1250 16738.45 0 0 5269.5119 14.512611
+ 1300 16738.475 0 0 5269.5199 14.512673
+ 1350 16738.484 0 0 5269.5228 14.512696
+ 1400 16738.469 -0.00044683992 0 5269.5175 14.512651
+ 1450 16738.45 -0.0010933363 0 5269.511 14.512595
+ 1500 16738.445 -0.00057484239 0 5269.51 14.512591
+ 1550 16738.451 0 0 5269.5123 14.512615
+ 1600 16738.452 0 0 5269.5127 14.512618
+ 1650 16738.443 0 0 5269.5099 14.512596
+ 1700 16738.433 0 0 5269.5068 14.512572
+ 1750 16738.438 0 0 5269.5084 14.512584
+ 1800 16738.459 0 0 5269.5149 14.512635
+ 1850 16738.473 0 0 5269.5193 14.51267
+ 1900 16738.462 0 0 5269.5159 14.512644
+ 1950 16738.446 -0.0032069962 0 5269.5076 14.512539
+ 2000 16738.463 -0.013425408 0 5269.5027 14.512382
+ 2050 16738.535 -0.036964311 0 5269.5017 14.512152
+ 2100 16738.621 -0.063490509 0 5269.5023 14.512108
+ 2150 16738.594 -0.056143934 0 5269.5012 14.512117
+ 2200 16738.536 -0.038486645 0 5269.5007 14.512277
+ 2250 16738.496 -0.023712406 0 5269.503 14.51242
+ 2300 16738.488 -0.013209094 0 5269.5109 14.51255
+ 2350 16738.486 -0.0045244524 0 5269.519 14.512693
+ 2400 16738.475 -0.00051678325 0 5269.5194 14.512743
+ 2450 16738.456 -0.0023209272 0 5269.5115 14.512659
+ 2500 16738.442 -0.0052101787 0 5269.5042 14.512594
+ 2550 16738.552 -0.04420046 0 5269.4998 14.512177
+ 2600 16738.42 -0.004347531 0 5269.4982 14.512783
+ 2650 16734.241 1.3131302 0 5269.5 14.577195
+ 2700 16738.737 -0.10612056 0 5269.4961 14.503874
+ 2750 16732.705 1.7939719 0 5269.4974 14.629294
+ 2800 16738.558 -0.042867033 0 5269.5032 14.519893
+ 2850 16738.499 -0.01271227 0 5269.5146 14.518524
+ 2900 16738.486 -0.0032778045 0 5269.52 14.518712
+ 2950 16738.482 -0.0089544631 0 5269.5133 14.518629
+ 3000 16738.647 -0.070862542 0 5269.5031 14.51803
+ 3050 16678.313 18.829038 0 5269.409 15.533426
+ 3100 16632.312 33.399217 0 5269.4975 14.588597
+ 3150 16739.318 -0.31388148 0 5269.4715 13.520782
+ 3200 16727.951 3.26736 0 5269.4741 12.288358
+ 3250 16686.364 16.353793 0 5269.4682 14.152517
+ 3300 16738.532 -0.031574462 0 5269.5064 13.310615
+ 3350 16738.454 -0.0062292918 0 5269.5071 13.308187
+ 3400 16738.445 -0.0049349125 0 5269.5055 13.308178
+ 3450 16738.489 -0.021623738 0 5269.5026 13.308001
+ 3500 16737.78 0.19719043 0 5269.4983 13.325999
+ 3550 16658.578 25.116206 0 5269.4834 13.778249
+ 3600 16738.51 -0.032864725 0 5269.4981 12.392389
+ 3650 16738.899 -0.15952703 0 5269.4938 12.383503
+ 3700 16738.879 -0.16025994 0 5269.487 12.382575
+ 3750 16738.878 -0.16608251 0 5269.4806 12.382765
+ 3800 16738.591 -0.078679341 0 5269.4776 12.383227
+ 3850 16738.429 -0.024729409 0 5269.4807 12.382942
+ 3900 16738.399 -0.0062729967 0 5269.4897 12.383192
+ 3950 16738.428 -0.002521266 0 5269.5027 12.383324
+ 4000 16738.467 -0.0002068506 0 5269.5173 12.383474
+ 4050 16738.488 0 0 5269.5241 12.383531
+ 4100 16738.468 0 0 5269.5178 12.383482
+ 4150 16738.422 0 0 5269.5033 12.383369
+ 4200 16738.387 0 0 5269.4921 12.383281
+ 4250 16738.383 0 0 5269.4908 12.38327
+ 4300 16738.4 0 0 5269.4964 12.383314
+ 4350 16738.423 0 0 5269.5036 12.38337
+ 4400 16738.441 0 0 5269.5092 12.383414
+ 4450 16738.45 0 0 5269.5121 12.383437
+ 4500 16738.45 0 0 5269.5122 12.383438
+ 4550 16738.442 0 0 5269.5095 12.383417
+ 4600 16738.425 0 0 5269.5042 12.383376
+ 4650 16738.404 -0.0014438316 0 5269.4961 12.383299
+ 4700 16738.444 -0.024020551 0 5269.4862 12.382975
+ 4750 16738.49 -0.048521424 0 5269.4761 12.385777
+ 4800 16735.057 1.0347218 0 5269.4786 12.43543
+ 4850 16735.441 0.92650925 0 5269.4913 12.418653
+ 4900 16723.839 4.5908973 0 5269.5033 13.410103
+ 4950 16738.531 -0.021537669 0 5269.5159 13.089982
+ 5000 16738.45 -0.0042589693 0 5269.5077 13.090062
+ 5050 16738.409 -0.00024692474 0 5269.4987 13.090038
+ 5100 16738.404 0 0 5269.4976 13.090032
+ 5150 16738.421 0 0 5269.5029 13.090073
+ 5200 16738.44 0 0 5269.5087 13.090119
+ 5250 16738.448 -0.0012793921 0 5269.5102 13.090114
+ 5300 16738.456 -0.0064376396 0 5269.5075 13.090026
+ 5350 16738.479 -0.020383843 0 5269.5007 13.089898
+ 5400 16735.845 0.79889489 0 5269.4909 13.136244
+ 5450 16735.558 0.87619907 0 5269.4778 12.324482
+ 5500 16711.494 8.4724273 0 5269.4984 12.656579
+ 5550 16454.525 89.074821 0 5269.2031 16.996502
+ 5600 16713.084 7.9801107 0 5269.5065 13.774972
+ 5650 16738.676 -0.079987805 0 5269.5033 13.168292
+ 5700 16446.281 91.866085 0 5269.399 23.764659
+ 5750 16738.549 -0.039869082 0 5269.5034 13.378118
+ 5800 16738.487 -0.014994465 0 5269.5086 13.378394
+ 5850 16738.466 -0.0051267396 0 5269.512 13.378555
+ 5900 16738.462 -0.004368998 0 5269.5113 13.378568
+ 5950 16738.528 -0.032727397 0 5269.5039 13.378192
+ 6000 16702.774 10.969422 0 5269.2502 13.788847
+ 6050 16682.271 17.483223 0 5269.3092 13.353098
+ 6100 16738.508 -0.028838294 0 5269.5016 12.521077
+ 6150 16738.425 -0.0067595586 0 5269.4974 12.521216
+ 6200 16738.401 -0.0011499906 0 5269.4955 12.521248
+ 6250 16738.455 0 0 5269.5136 12.521404
+ 6300 16738.523 0 0 5269.5352 12.521573
+ 6350 16738.503 0 0 5269.5287 12.521525
+ 6400 16738.427 0 0 5269.5047 12.521337
+ 6450 16738.399 0 0 5269.496 12.521268
+ 6500 16738.425 0 0 5269.5042 12.521331
+ 6550 16738.441 0 0 5269.5093 12.521372
+ 6600 16738.42 0 0 5269.5025 12.521319
+ 6650 16738.398 0 0 5269.4957 12.521266
+ 6700 16738.435 0 0 5269.5074 12.521355
+ 6750 16738.505 0 0 5269.5293 12.521527
+ 6800 16738.508 0 0 5269.5303 12.521536
+ 6850 16738.446 0 0 5269.5108 12.521384
+ 6900 16738.414 0 0 5269.5009 12.521306
+ 6950 16738.432 0 0 5269.5063 12.521348
+ 7000 16738.444 0 0 5269.5102 12.521379
+ 7050 16738.421 0 0 5269.5029 12.521322
+ 7100 16738.393 0 0 5269.4941 12.521253
+ 7150 16738.419 0 0 5269.5022 12.521315
+ 7200 16738.489 0 0 5269.5244 12.521489
+ 7250 16738.505 0 0 5269.5293 12.521528
+ 7300 16738.443 0 0 5269.5098 12.521377
+ 7350 16738.404 0 0 5269.4976 12.521281
+ 7400 16738.43 0 0 5269.5058 12.521344
+ 7450 16738.461 0 0 5269.5156 12.521421
+ 7500 16738.447 0 0 5269.5109 12.521385
+ 7550 16738.407 0 0 5269.4986 12.521288
+ 7600 16738.412 0 0 5269.5002 12.5213
+ 7650 16738.478 0 0 5269.5208 12.521461
+ 7700 16738.51 0 0 5269.5309 12.521541
+ 7750 16738.454 0 0 5269.5135 12.521406
+ 7800 16738.398 0 0 5269.4958 12.521267
+ 7850 16738.407 -0.00021180715 0 5269.4982 12.521283
+ 7900 16738.441 -0.0002167946 0 5269.509 12.521367
+ 7950 16738.446 -0.0002384787 0 5269.5107 12.52138
+ 8000 16738.423 0 0 5269.5035 12.521327
+ 8050 16738.423 0 0 5269.5034 12.521325
+ 8100 16738.478 -0.00069624484 0 5269.52 12.521448
+ 8150 16738.523 -0.0040058183 0 5269.531 12.521494
+ 8200 16738.486 -0.0092298512 0 5269.5142 12.521328
+ 8250 16738.458 -0.023189661 0 5269.4914 12.521008
+ 8300 16738.513 -0.045847765 0 5269.4861 12.520773
+ 8350 16723.735 4.5720344 0 5269.4516 12.849543
+ 8400 16738.466 -0.02019859 0 5269.497 12.835812
+ 8450 16738.437 -0.012822198 0 5269.4952 12.829979
+ 8500 16738.408 -0.0016833646 0 5269.4972 12.830104
+ 8550 16738.464 -0.00097382606 0 5269.5155 12.830258
+ 8600 16738.669 -0.050581176 0 5269.5304 12.829977
+ 8650 15918.073 250.131 0 5261.3761 24.542327
+ 8700 16738.446 0.00085039409 0 5269.5116 10.59114
+ 8750 16738.472 -0.010146632 0 5269.5089 10.590059
+ 8800 16738.468 0 0 5269.5176 10.590278
+ 8850 16738.508 0 0 5269.5303 10.590378
+ 8900 16738.509 0 0 5269.5306 10.590381
+ 8950 16738.496 0 0 5269.5266 10.590349
+ 9000 16738.477 0 0 5269.5204 10.590302
+ 9050 16738.455 0 0 5269.5135 10.590247
+ 9100 16738.477 0 0 5269.5205 10.590301
+ 9150 16738.512 0 0 5269.5315 10.590388
+ 9200 16738.502 0 0 5269.5285 10.590364
+ 9250 16738.493 0 0 5269.5254 10.59034
+ 9300 16738.482 0 0 5269.522 10.590314
+ 9350 16738.46 0 0 5269.5151 10.59026
+ 9400 16738.48 0 0 5269.5216 10.59031
+ 9450 16738.509 0 0 5269.5306 10.590381
+ 9500 16738.49 0 0 5269.5247 10.590335
+ 9550 16738.484 0 0 5269.5226 10.590318
+ 9600 16738.483 0 0 5269.5223 10.590316
+ 9650 16738.464 0 0 5269.5165 10.590271
+ 9700 16738.484 0 0 5269.5228 10.590319
+ 9750 16738.507 0 0 5269.53 10.590376
+ 9800 16738.482 0 0 5269.522 10.590314
+ 9850 16738.478 0 0 5269.5207 10.590303
+ 9900 16738.487 -0.00030979874 0 5269.5233 10.59032
+ 9950 16738.476 -0.00095967134 0 5269.5192 10.590278
+ 10000 16738.494 -0.00062714318 0 5269.5253 10.590329
+Loop time of 0.22441 on 4 procs for 10000 steps with 81 atoms
+
+Performance: 385008.767 tau/day, 44561.200 timesteps/s
+97.6% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.0032785 | 0.0039999 | 0.0052714 | 1.3 | 1.78
+Neigh | 0.010548 | 0.012524 | 0.016082 | 1.9 | 5.58
+Comm | 0.082771 | 0.087847 | 0.091037 | 1.1 | 39.15
+Output | 0.0042846 | 0.0045864 | 0.0054133 | 0.7 | 2.04
+Modify | 0.10401 | 0.10533 | 0.10736 | 0.4 | 46.94
+Other | | 0.01013 | | | 4.51
+
+Nlocal: 20.25 ave 34 max 9 min
+Histogram: 2 0 0 0 0 0 0 1 0 1
+Nghost: 38.5 ave 43 max 26 min
+Histogram: 1 0 0 0 0 0 0 0 0 3
+Neighs: 0.75 ave 2 max 0 min
+Histogram: 2 0 0 0 0 1 0 0 0 1
+
+Total # of neighbors = 3
+Ave neighs/atom = 0.037037
+Neighbor list builds = 998
+Dangerous builds = 997
+Total wall time: 0:00:00
diff --git a/examples/rigid/log.20Apr18.rigid.poems.g++.1 b/examples/rigid/log.20Apr18.rigid.poems.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..0cba72a2dd681d8b47f54984e93b6e8b280bbcd3
--- /dev/null
+++ b/examples/rigid/log.20Apr18.rigid.poems.g++.1
@@ -0,0 +1,338 @@
+LAMMPS (20 Apr 2018)
+ using 1 OpenMP thread(s) per MPI task
+# Simple rigid body system
+
+units lj
+atom_style atomic
+
+pair_style lj/cut 2.5
+
+read_data data.rigid
+ orthogonal box = (-12 -12 -12) to (12 12 12)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 81 atoms
+
+velocity all create 100.0 4928459
+
+# unconnected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 10 18
+#group clump3 id <> 19 27
+#group clump4 id <> 28 36
+#group clump5 id <> 37 45
+#group clump6 id <> 46 54
+#group clump7 id <> 55 63
+#group clump8 id <> 64 72
+#group clump9 id <> 73 81
+
+#fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
+
+# 1 chain of connected bodies
+
+group clump1 id <> 1 9
+9 atoms in group clump1
+group clump2 id <> 9 18
+10 atoms in group clump2
+group clump3 id <> 18 27
+10 atoms in group clump3
+group clump4 id <> 27 36
+10 atoms in group clump4
+group clump5 id <> 36 45
+10 atoms in group clump5
+group clump6 id <> 45 54
+10 atoms in group clump6
+group clump7 id <> 54 63
+10 atoms in group clump7
+group clump8 id <> 63 72
+10 atoms in group clump8
+group clump9 id <> 72 81
+10 atoms in group clump9
+
+fix 1 all poems group clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
+1 clusters, 9 bodies, 8 joints, 81 atoms
+
+# 2 chains of connected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 9 18
+#group clump3 id <> 18 27
+#group clump4 id <> 27 36
+#group clump5 id <> 37 45
+#group clump6 id <> 45 54
+#group clump7 id <> 54 63
+#group clump8 id <> 63 72
+#group clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4
+#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
+
+neigh_modify exclude group clump1 clump1
+neigh_modify exclude group clump2 clump2
+neigh_modify exclude group clump3 clump3
+neigh_modify exclude group clump4 clump4
+neigh_modify exclude group clump5 clump5
+neigh_modify exclude group clump6 clump6
+neigh_modify exclude group clump7 clump7
+neigh_modify exclude group clump8 clump8
+neigh_modify exclude group clump9 clump9
+
+thermo 100
+
+#dump 1 all atom 50 dump.rigid.poems
+
+#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 2 pad 5
+
+#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 3 pad 5
+
+timestep 0.0001
+thermo 50
+run 10000
+Neighbor list info ...
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 18 18 18
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.292 | 3.292 | 3.292 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 217.7783 3430.3907 0 3466.6871 -2.7403788
+ 50 13679.637 1404.2468 0 3684.1863 12.446066
+ 100 16777.225 888.87665 0 3685.0808 -31.828677
+ 150 19595.365 418.45042 0 3684.3446 40.709078
+ 200 18524.188 596.47273 0 3683.8375 -0.8159371
+ 250 21015.789 180.96521 0 3683.5967 -10.042469
+ 300 20785.513 219.25314 0 3683.5053 2.6452719
+ 350 21072.46 171.2554 0 3683.3321 7.0609024
+ 400 19956.414 356.36381 0 3682.4328 19.320259
+ 450 20724.42 227.73284 0 3681.8028 8.1259249
+ 500 20152.578 322.71466 0 3681.4777 5.4929878
+ 550 20017.022 345.29701 0 3681.4673 5.4661666
+ 600 17897.743 698.72196 0 3681.6791 3.2854742
+ 650 17297.758 796.60256 0 3679.5623 15.191113
+ 700 18581.934 584.29715 0 3681.2861 5.1588289
+ 750 21774.158 52.821062 0 3681.8474 -10.775664
+ 800 21604.055 81.188546 0 3681.8644 -3.2045743
+ 850 17821.483 711.53827 0 3681.7854 7.4384277
+ 900 21033.292 175.98127 0 3681.5299 -16.345167
+ 950 20968.166 186.59847 0 3681.2929 -2.330456
+ 1000 20490.66 266.19375 0 3681.3037 11.787983
+ 1050 20222.396 310.94072 0 3681.34 -8.3459539
+ 1100 21321.687 127.61533 0 3681.2299 -1.2184717
+ 1150 20849.582 206.01695 0 3680.9472 -0.86699146
+ 1200 21815.003 45.317414 0 3681.1512 1.5988314
+ 1250 18655.437 572.41453 0 3681.654 10.064078
+ 1300 20780.781 217.36506 0 3680.8286 6.0538615
+ 1350 20558.971 254.36482 0 3680.8601 -3.6773954
+ 1400 21485.029 99.812918 0 3680.6511 -16.185473
+ 1450 21771.107 52.159607 0 3680.6775 -2.4756675
+ 1500 21520.948 93.503927 0 3680.3286 2.1023577
+ 1550 21351.418 121.68138 0 3680.2511 5.515995
+ 1600 20778.805 216.92177 0 3680.0559 15.089187
+ 1650 21477.638 100.21836 0 3679.8247 -1.1045739
+ 1700 18501.339 596.47922 0 3680.0357 -15.679682
+ 1750 18563.642 587.3479 0 3681.2882 33.532211
+ 1800 19110.186 494.82336 0 3679.8543 18.024046
+ 1850 21364.191 119.23543 0 3679.9339 2.5291075
+ 1900 20146.627 322.14849 0 3679.9197 5.7313175
+ 1950 20692.671 231.25345 0 3680.0319 4.297772
+ 2000 20943.905 189.11218 0 3679.7629 -22.64509
+ 2050 19668.055 401.83025 0 3679.8394 3.6251438
+ 2100 20280.434 299.76289 0 3679.8353 7.4807805
+ 2150 19181.835 483.52621 0 3680.4987 22.62081
+ 2200 21300.18 130.7021 0 3680.7322 4.710193
+ 2250 20486.914 266.64414 0 3681.1299 -8.6458025
+ 2300 18653.082 572.25481 0 3681.1017 -5.2636982
+ 2350 21513.563 95.608298 0 3681.2021 -9.3624751
+ 2400 21466.205 103.57569 0 3681.2765 -29.559707
+ 2450 20100.204 332.25468 0 3682.2886 35.739592
+ 2500 20764.513 221.64794 0 3682.4001 -12.46688
+ 2550 20436.771 276.13128 0 3682.2598 -22.419404
+ 2600 21466.252 104.57185 0 3682.2806 -10.080362
+ 2650 20817.269 212.81674 0 3682.3615 5.1374497
+ 2700 18565.157 588.46125 0 3682.6541 22.283866
+ 2750 20780.743 218.76366 0 3682.2208 -8.0046411
+ 2800 21032.22 176.82368 0 3682.1936 -7.078895
+ 2850 16817.729 879.49153 0 3682.4464 33.140849
+ 2900 19309.511 463.89319 0 3682.145 7.9225025
+ 2950 20544.978 257.86831 0 3682.0314 2.0523059
+ 3000 20616.438 246.0975 0 3682.1706 -0.2824889
+ 3050 18648.596 574.37266 0 3682.4721 -5.8677065
+ 3100 19147.135 490.76826 0 3681.9574 -1.9922835
+ 3150 18568.022 587.36965 0 3682.0399 14.694505
+ 3200 19720.841 395.38315 0 3682.1899 5.9162402
+ 3250 19008.557 514.50687 0 3682.5998 -3.4702895
+ 3300 21708.937 64.231264 0 3682.3874 -5.4808611
+ 3350 20548.477 257.62974 0 3682.3759 9.7818301
+ 3400 20508.84 264.0153 0 3682.1553 -12.578182
+ 3450 18736.579 559.11222 0 3681.8754 21.920437
+ 3500 21444.82 107.82706 0 3681.9638 0.093050651
+ 3550 20439.241 275.31015 0 3681.8503 -3.0785302
+ 3600 21547.1 90.778361 0 3681.9617 -5.9189729
+ 3650 15623.305 1079.996 0 3683.8802 36.064752
+ 3700 19912.452 363.09483 0 3681.8368 5.4802367
+ 3750 21289.7 133.2258 0 3681.5091 -10.884642
+ 3800 20214.875 312.09245 0 3681.2382 8.6419893
+ 3850 19853.031 372.13835 0 3680.9769 2.6229234
+ 3900 17863.409 703.8716 0 3681.1064 -1.4250404
+ 3950 19926.351 359.87227 0 3680.9307 -14.60997
+ 4000 17595.665 747.85423 0 3680.4651 24.228859
+ 4050 18408.194 611.80934 0 3679.8416 4.4236034
+ 4100 17506.503 762.1286 0 3679.8792 5.0526379
+ 4150 18479.134 600.76034 0 3680.6159 -6.6523095
+ 4200 18475.322 601.95797 0 3681.1783 1.3292995
+ 4250 18301.378 630.34119 0 3680.5709 2.5387332
+ 4300 19384.541 449.98455 0 3680.7414 5.8750989
+ 4350 18717.888 561.31715 0 3680.9651 3.7948584
+ 4400 18893.773 532.20993 0 3681.172 10.963539
+ 4450 20269.613 302.15984 0 3680.4286 -10.145642
+ 4500 19151.762 489.32407 0 3681.2845 21.695364
+ 4550 19914.708 361.54065 0 3680.6587 -4.2298372
+ 4600 21153.44 154.99598 0 3680.5693 2.3172078
+ 4650 21021.611 176.81454 0 3680.4164 1.9128023
+ 4700 21707.966 62.767734 0 3680.762 -5.2080189
+ 4750 16517.674 927.53839 0 3680.484 17.329608
+ 4800 21654.604 71.574174 0 3680.6749 -6.0650166
+ 4850 18135.978 657.28622 0 3679.9493 5.4803307
+ 4900 20389.048 282.49215 0 3680.6668 -2.8570431
+ 4950 17159.074 820.81472 0 3680.6604 31.273877
+ 5000 20788.159 215.88415 0 3680.5773 4.6345196
+ 5050 21366.767 119.68693 0 3680.8148 -9.9482889
+ 5100 20668.21 236.17655 0 3680.8782 3.8118334
+ 5150 20468.573 269.83696 0 3681.2657 -26.625943
+ 5200 19493.142 432.49135 0 3681.3483 -7.6677112
+ 5250 19626.594 410.09767 0 3681.1967 7.3622341
+ 5300 20771.914 219.12484 0 3681.1105 -7.0871793
+ 5350 21152.459 155.26401 0 3680.6738 5.9030557
+ 5400 21376.189 117.91075 0 3680.6088 -1.2004513
+ 5450 21455.06 105.15166 0 3680.995 -9.1675471
+ 5500 21227.896 143.35739 0 3681.3401 -6.646305
+ 5550 21149.831 156.61404 0 3681.5858 -12.953136
+ 5600 21364.198 120.94695 0 3681.6466 1.0372254
+ 5650 20219.777 311.34588 0 3681.3088 6.5026316
+ 5700 21163.024 154.3001 0 3681.4708 -0.47587262
+ 5750 19583.077 418.40745 0 3682.2535 24.609517
+ 5800 18801.324 548.79742 0 3682.3515 -12.082631
+ 5850 20875.4 203.07604 0 3682.3093 -8.1191161
+ 5900 20737.053 226.2734 0 3682.4489 -7.6845943
+ 5950 21260.028 139.21888 0 3682.5568 -2.2977046
+ 6000 19823.84 378.71803 0 3682.6914 -1.1163373
+ 6050 20487.214 268.03474 0 3682.5704 4.313979
+ 6100 17853.211 707.10918 0 3682.6443 16.762322
+ 6150 21322.705 129.06 0 3682.8441 2.7500936
+ 6200 21609.008 81.580972 0 3683.0823 0.37062555
+ 6250 20364.115 289.30707 0 3683.3262 13.176034
+ 6300 20201.9 316.16558 0 3683.149 -1.6318339
+ 6350 21151.879 157.75018 0 3683.0634 -23.337621
+ 6400 21453.129 107.45563 0 3682.9772 -0.60776225
+ 6450 21105.382 165.1926 0 3682.7562 4.244932
+ 6500 20746.748 224.6945 0 3682.4859 0.2929158
+ 6550 20913.725 197.29847 0 3682.9194 -15.792862
+ 6600 17956.374 690.52623 0 3683.2552 15.445255
+ 6650 20270.609 303.60078 0 3682.0357 -0.26503277
+ 6700 21442.931 109.08904 0 3682.9109 -2.8409166
+ 6750 20907.994 198.30695 0 3682.9726 0.91664072
+ 6800 20431.208 277.98326 0 3683.1845 -1.8537161
+ 6850 20312.052 297.88656 0 3683.2285 3.1028547
+ 6900 19458.401 439.97157 0 3683.0385 -4.1856293
+ 6950 20507.759 264.99217 0 3682.952 -1.4597973
+ 7000 20782.356 219.47456 0 3683.2006 -7.1967021
+ 7050 20560.324 256.07109 0 3682.7917 -10.720013
+ 7100 21652.145 74.086415 0 3682.7772 -0.61455054
+ 7150 20134.823 326.40272 0 3682.2065 11.689827
+ 7200 20778.071 219.16459 0 3682.1765 -1.796567
+ 7250 20153.065 323.13721 0 3681.9814 -0.1215538
+ 7300 19524.938 427.99711 0 3682.1534 -3.1139903
+ 7350 20554.595 256.63855 0 3682.4044 10.023083
+ 7400 18778.53 552.29852 0 3682.0534 -1.7145222
+ 7450 18972.509 520.15393 0 3682.2388 1.4489874
+ 7500 17680.668 736.20139 0 3682.9794 15.096954
+ 7550 19070.785 504.65403 0 3683.1182 2.2707533
+ 7600 20805.541 214.54957 0 3682.1398 -3.4306308
+ 7650 18473.262 604.25322 0 3683.1301 2.2083367
+ 7700 19294.016 466.99211 0 3682.6615 2.2666382
+ 7750 20995.664 183.47108 0 3682.7484 -13.935938
+ 7800 21042.433 175.06619 0 3682.1384 0.49855811
+ 7850 19343.054 459.21955 0 3683.0618 7.9049312
+ 7900 18382.898 619.01969 0 3682.8361 1.7996366
+ 7950 16092.435 1000.6563 0 3682.7287 29.993154
+ 8000 17551.635 757.47719 0 3682.7498 8.1753011
+ 8050 20309.875 298.25877 0 3683.2379 -1.9545317
+ 8100 21746.174 59.002125 0 3683.3645 -2.6980678
+ 8150 21478.427 103.44202 0 3683.1799 -10.930392
+ 8200 20986.729 185.46995 0 3683.2581 -14.298403
+ 8250 20744.064 225.47546 0 3682.8194 -6.4982356
+ 8300 19887.982 368.35069 0 3683.0143 1.5899179
+ 8350 21871.414 37.899202 0 3683.1348 -2.0554107
+ 8400 20002.858 348.98887 0 3682.7985 8.2963084
+ 8450 21553.861 90.985193 0 3683.2953 2.8575186
+ 8500 21605.143 82.347635 0 3683.2048 -4.711565
+ 8550 20151.76 324.4703 0 3683.097 -8.5109459
+ 8600 20564.158 255.77814 0 3683.1378 -1.3815408
+ 8650 19316.602 463.61706 0 3683.0507 -2.6895635
+ 8700 18157.859 656.69518 0 3683.0051 19.428927
+ 8750 18752.43 557.67555 0 3683.0805 1.9765973
+ 8800 20903.812 199.07408 0 3683.0428 1.9011523
+ 8850 20132.963 327.56826 0 3683.0621 3.0389961
+ 8900 21667.171 71.80023 0 3682.9954 -2.0042246
+ 8950 20346.973 292.00907 0 3683.1712 7.5582361
+ 9000 17889.448 695.59406 0 3677.1688 7.5315391
+ 9050 19446.144 441.90609 0 3682.9302 5.9819228
+ 9100 20384.34 285.05862 0 3682.4486 9.8610378
+ 9150 20023.515 344.98587 0 3682.2384 -0.40175043
+ 9200 17786.795 718.76166 0 3683.2275 10.984317
+ 9250 20843.023 208.42263 0 3682.2597 -7.4709344
+ 9300 21670.622 70.503925 0 3682.2742 -6.2303366
+ 9350 20642.313 241.21277 0 3681.5983 4.7423898
+ 9400 19228.566 476.44753 0 3681.2085 10.836639
+ 9450 21215.705 146.40003 0 3682.3509 -9.091421
+ 9500 21543.685 91.725901 0 3682.3401 -1.0608492
+ 9550 20143.22 324.98532 0 3682.1887 -5.995164
+ 9600 21234.294 142.96512 0 3682.0142 0.004838125
+ 9650 21025.207 177.8801 0 3682.0813 -5.4857701
+ 9700 20638.235 242.46577 0 3682.1716 -1.6014085
+ 9750 18374.191 620.54322 0 3682.9084 13.864712
+ 9800 19730.262 393.89083 0 3682.2679 5.7601754
+ 9850 21547.855 91.283379 0 3682.5926 2.1989329
+ 9900 20959.935 189.28821 0 3682.6108 2.1174676
+ 9950 21191.026 150.79441 0 3682.6321 8.3829825
+ 10000 20776.574 220.03769 0 3682.8 -1.8404787
+Loop time of 3.0852 on 1 procs for 10000 steps with 81 atoms
+
+Performance: 28004.636 tau/day, 3241.277 timesteps/s
+99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.17336 | 0.17336 | 0.17336 | 0.0 | 5.62
+Neigh | 0.1094 | 0.1094 | 0.1094 | 0.0 | 3.55
+Comm | 0.010163 | 0.010163 | 0.010163 | 0.0 | 0.33
+Output | 0.0030687 | 0.0030687 | 0.0030687 | 0.0 | 0.10
+Modify | 2.7782 | 2.7782 | 2.7782 | 0.0 | 90.05
+Other | | 0.01105 | | | 0.36
+
+Nlocal: 81 ave 81 max 81 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 82 ave 82 max 82 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 887 ave 887 max 887 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 887
+Ave neighs/atom = 10.9506
+Neighbor list builds = 992
+Dangerous builds = 939
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:03
diff --git a/examples/rigid/log.20Apr18.rigid.poems.g++.4 b/examples/rigid/log.20Apr18.rigid.poems.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..e2fb6b65b6602bd72ac74b5d0719836f459cd25d
--- /dev/null
+++ b/examples/rigid/log.20Apr18.rigid.poems.g++.4
@@ -0,0 +1,338 @@
+LAMMPS (20 Apr 2018)
+ using 1 OpenMP thread(s) per MPI task
+# Simple rigid body system
+
+units lj
+atom_style atomic
+
+pair_style lj/cut 2.5
+
+read_data data.rigid
+ orthogonal box = (-12 -12 -12) to (12 12 12)
+ 1 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 81 atoms
+
+velocity all create 100.0 4928459
+
+# unconnected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 10 18
+#group clump3 id <> 19 27
+#group clump4 id <> 28 36
+#group clump5 id <> 37 45
+#group clump6 id <> 46 54
+#group clump7 id <> 55 63
+#group clump8 id <> 64 72
+#group clump9 id <> 73 81
+
+#fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
+
+# 1 chain of connected bodies
+
+group clump1 id <> 1 9
+9 atoms in group clump1
+group clump2 id <> 9 18
+10 atoms in group clump2
+group clump3 id <> 18 27
+10 atoms in group clump3
+group clump4 id <> 27 36
+10 atoms in group clump4
+group clump5 id <> 36 45
+10 atoms in group clump5
+group clump6 id <> 45 54
+10 atoms in group clump6
+group clump7 id <> 54 63
+10 atoms in group clump7
+group clump8 id <> 63 72
+10 atoms in group clump8
+group clump9 id <> 72 81
+10 atoms in group clump9
+
+fix 1 all poems group clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
+1 clusters, 9 bodies, 8 joints, 81 atoms
+
+# 2 chains of connected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 9 18
+#group clump3 id <> 18 27
+#group clump4 id <> 27 36
+#group clump5 id <> 37 45
+#group clump6 id <> 45 54
+#group clump7 id <> 54 63
+#group clump8 id <> 63 72
+#group clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4
+#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
+
+neigh_modify exclude group clump1 clump1
+neigh_modify exclude group clump2 clump2
+neigh_modify exclude group clump3 clump3
+neigh_modify exclude group clump4 clump4
+neigh_modify exclude group clump5 clump5
+neigh_modify exclude group clump6 clump6
+neigh_modify exclude group clump7 clump7
+neigh_modify exclude group clump8 clump8
+neigh_modify exclude group clump9 clump9
+
+thermo 100
+
+#dump 1 all atom 50 dump.rigid.poems
+
+#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 2 pad 5
+
+#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 3 pad 5
+
+timestep 0.0001
+thermo 50
+run 10000
+Neighbor list info ...
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 18 18 18
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.263 | 3.357 | 3.638 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 217.7783 3430.3907 0 3466.6871 -2.7403788
+ 50 13679.637 1404.2468 0 3684.1863 12.446066
+ 100 16777.225 888.87665 0 3685.0808 -31.828677
+ 150 19595.365 418.45042 0 3684.3446 40.709078
+ 200 18524.188 596.47273 0 3683.8375 -0.8159371
+ 250 21015.789 180.96521 0 3683.5967 -10.042469
+ 300 20785.513 219.25314 0 3683.5053 2.6452719
+ 350 21072.46 171.2554 0 3683.3321 7.0609024
+ 400 19956.414 356.36381 0 3682.4328 19.320259
+ 450 20724.42 227.73284 0 3681.8028 8.1259249
+ 500 20152.578 322.71466 0 3681.4777 5.4929878
+ 550 20017.022 345.29701 0 3681.4673 5.4661666
+ 600 17897.743 698.72196 0 3681.6791 3.2854742
+ 650 17297.758 796.60256 0 3679.5623 15.191113
+ 700 18581.934 584.29715 0 3681.2861 5.1588289
+ 750 21774.158 52.821062 0 3681.8474 -10.775664
+ 800 21604.055 81.188546 0 3681.8644 -3.2045743
+ 850 17821.483 711.53827 0 3681.7854 7.4384277
+ 900 21033.292 175.98127 0 3681.5299 -16.345167
+ 950 20968.166 186.59847 0 3681.2929 -2.330456
+ 1000 20490.66 266.19375 0 3681.3037 11.787983
+ 1050 20222.396 310.94072 0 3681.34 -8.3459539
+ 1100 21321.687 127.61533 0 3681.2299 -1.2184717
+ 1150 20849.582 206.01695 0 3680.9472 -0.86699147
+ 1200 21815.003 45.317414 0 3681.1512 1.5988314
+ 1250 18655.437 572.41453 0 3681.654 10.064078
+ 1300 20780.781 217.36506 0 3680.8286 6.0538614
+ 1350 20558.971 254.36483 0 3680.8601 -3.6773951
+ 1400 21485.029 99.812917 0 3680.6511 -16.185473
+ 1450 21771.107 52.15961 0 3680.6775 -2.4756673
+ 1500 21520.948 93.503926 0 3680.3286 2.1023576
+ 1550 21351.418 121.68137 0 3680.2511 5.5159947
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+ 1750 18563.642 587.34785 0 3681.2882 33.53221
+ 1800 19110.185 494.82342 0 3679.8543 18.024046
+ 1850 21364.191 119.23548 0 3679.9339 2.5291079
+ 1900 20146.626 322.14873 0 3679.9197 5.7313282
+ 1950 20692.672 231.2533 0 3680.0319 4.2977759
+ 2000 20943.904 189.11231 0 3679.7629 -22.645089
+ 2050 19668.052 401.83077 0 3679.8394 3.6251598
+ 2100 20280.434 299.76292 0 3679.8353 7.4807838
+ 2150 19181.841 483.52513 0 3680.4987 22.620829
+ 2200 21300.185 130.70136 0 3680.7321 4.7101928
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+ 2450 20100.274 332.24291 0 3682.2886 35.736349
+ 2500 20764.562 221.63964 0 3682.4 -12.465656
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+ 2700 18565.57 588.39438 0 3682.656 22.28768
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+ 2950 20558.495 255.61185 0 3682.0277 1.9151653
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+ 3100 19381.554 451.57712 0 3681.8361 -2.0887636
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+ 3200 20969.083 187.13559 0 3681.9828 12.156446
+ 3250 20474.81 269.6876 0 3682.156 1.4067779
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+ 3550 20627.979 244.69999 0 3682.6964 -0.33497747
+ 3600 19265.519 471.27582 0 3682.1956 2.3506222
+ 3650 20351.848 290.65727 0 3682.6319 3.5445062
+ 3700 18507.473 597.72931 0 3682.3082 -21.283074
+ 3750 20344.017 291.60622 0 3682.2757 6.5366987
+ 3800 20672.372 237.18966 0 3682.585 6.7310703
+ 3850 21366.943 122.07461 0 3683.2318 -3.5870721
+ 3900 20890.294 201.69901 0 3683.4147 -9.5644117
+ 3950 20684.181 235.91733 0 3683.2809 -4.8913079
+ 4000 21499.086 100.67563 0 3683.8566 1.1969651
+ 4050 18549.152 590.04529 0 3681.5707 -9.1914883
+ 4100 18436.457 604.2601 0 3677.003 3.6486137
+ 4150 19332.655 462.03124 0 3684.1404 -11.280758
+ 4200 21199.837 150.66602 0 3683.9722 0.14505208
+ 4250 19088.228 501.77395 0 3683.1453 1.6869973
+ 4300 16617.942 913.86736 0 3683.5244 9.1792322
+ 4350 19765.761 388.52744 0 3682.821 -4.1982973
+ 4400 20181.964 320.06096 0 3683.7216 5.3685715
+ 4450 20132.04 328.29106 0 3683.631 6.3340995
+ 4500 21026.359 179.13858 0 3683.5317 -15.365253
+ 4550 19273.765 471.36221 0 3683.6564 -0.71397595
+ 4600 20064.71 339.29348 0 3683.4117 -4.8121056
+ 4650 19821.01 380.27685 0 3683.7784 11.857115
+ 4700 18724.367 563.42963 0 3684.1575 13.250333
+ 4750 20467.467 273.2046 0 3684.449 -1.8076823
+ 4800 19630.315 412.48507 0 3684.2042 -9.0412254
+ 4850 19483.424 437.0206 0 3684.258 11.22465
+ 4900 18504.179 600.28485 0 3684.3146 -5.2345686
+ 4950 21436.13 111.62139 0 3684.3098 -5.8197915
+ 5000 18022.817 680.57727 0 3684.38 19.238942
+ 5050 20750.212 226.15635 0 3684.525 -0.73974419
+ 5100 20569.533 255.21358 0 3683.4691 -18.332775
+ 5150 21447.046 109.3048 0 3683.8124 -2.5745966
+ 5200 18985.753 519.77191 0 3684.0641 9.7821968
+ 5250 21334.568 128.16597 0 3683.9273 -0.61310451
+ 5300 18836.476 544.54018 0 3683.9528 -17.979429
+ 5350 18574.391 587.20088 0 3682.9327 40.990206
+ 5400 21003.047 183.40176 0 3683.9096 6.1115776
+ 5450 20693.875 234.62783 0 3683.607 5.4472209
+ 5500 17673.479 738.99306 0 3684.5729 -28.621738
+ 5550 19265.837 472.34663 0 3683.3195 -6.609151
+ 5600 20800.947 217.12409 0 3683.9486 2.6477049
+ 5650 21746.371 59.453265 0 3683.8485 1.5272163
+ 5700 20448.97 275.57425 0 3683.736 -7.9864104
+ 5750 19776.152 387.64417 0 3683.6695 -16.604848
+ 5800 15779.293 1055.4995 0 3685.3817 20.365883
+ 5850 21008.009 182.52093 0 3683.8557 -6.6727217
+ 5900 21566.123 89.588216 0 3683.9421 -7.8944316
+ 5950 21591.695 85.284975 0 3683.9009 -2.4895203
+ 6000 17737.17 726.79112 0 3682.9861 1.5643841
+ 6050 16648.524 907.73295 0 3682.487 3.0853478
+ 6100 19917.439 363.6324 0 3683.2056 4.358303
+ 6150 21767.004 56.152017 0 3683.986 -8.8722559
+ 6200 17654.098 742.15421 0 3684.5039 9.7673482
+ 6250 20125.754 329.65218 0 3683.9445 5.5050658
+ 6300 20160.047 323.44453 0 3683.4524 4.852504
+ 6350 20509.459 264.29515 0 3682.5383 2.5335834
+ 6400 17199.686 817.09171 0 3683.7061 8.3428304
+ 6450 18748.366 558.82243 0 3683.5501 0.23782614
+ 6500 19133.519 494.28383 0 3683.2037 8.1586096
+ 6550 20311.228 297.30741 0 3682.5122 -1.7015056
+ 6600 18879.49 536.62652 0 3683.2082 5.0874769
+ 6650 18189.35 651.42447 0 3682.9828 -15.223564
+ 6700 19925.861 361.90598 0 3682.8828 0.26811015
+ 6750 19420.312 445.30915 0 3682.0278 5.5725626
+ 6800 19925.024 361.87412 0 3682.7114 -3.9763013
+ 6850 16196.938 985.7242 0 3685.2138 2.8265047
+ 6900 19779.752 386.51634 0 3683.1416 16.798629
+ 6950 21043.144 176.83133 0 3684.0221 -4.193188
+ 7000 18555.362 589.47043 0 3682.0307 14.516315
+ 7050 21225.883 147.54974 0 3685.1969 -13.466586
+ 7100 21234.667 145.92615 0 3685.0373 -5.1951121
+ 7150 21483.472 104.62556 0 3685.2042 -5.6904048
+ 7200 21014.278 182.97687 0 3685.3566 1.044649
+ 7250 18588.789 587.96259 0 3686.094 22.707132
+ 7300 20202.932 318.14401 0 3685.2994 -10.795766
+ 7350 18304.22 634.7344 0 3685.4377 -1.6801482
+ 7400 20967.579 190.67822 0 3685.2747 -0.94800692
+ 7450 20991.588 186.07163 0 3684.6696 -1.411476
+ 7500 19056.583 507.18197 0 3683.2791 3.2026014
+ 7550 18542.455 594.92944 0 3685.3386 -27.908724
+ 7600 19895.73 367.08589 0 3683.0409 4.1334366
+ 7650 20384.942 285.88041 0 3683.3707 -7.515362
+ 7700 20683.189 235.46294 0 3682.6611 10.876437
+ 7750 20729.325 228.204 0 3683.0915 3.8844308
+ 7800 21667.475 71.752748 0 3682.9985 -15.457992
+ 7850 19043.652 508.96807 0 3682.9101 -5.8335792
+ 7900 21079.827 169.61123 0 3682.9158 -1.3216223
+ 7950 20713.266 230.43917 0 3682.6502 -0.20026535
+ 8000 20606.41 248.06357 0 3682.4652 4.2844844
+ 8050 20284.503 302.0469 0 3682.7973 6.3402329
+ 8100 21859.537 39.514865 0 3682.7711 -13.302141
+ 8150 18495.181 600.26329 0 3682.7934 9.9318242
+ 8200 21458.549 105.63828 0 3682.0631 -7.7419285
+ 8250 18704.511 564.30958 0 3681.728 14.680489
+ 8300 20689.366 233.57049 0 3681.7982 2.3067527
+ 8350 20692.974 232.67005 0 3681.499 4.2743386
+ 8400 20240.086 307.5395 0 3680.8872 1.9694217
+ 8450 19075.969 501.34689 0 3680.6751 11.056078
+ 8500 21456.727 103.36067 0 3679.4818 -3.4512371
+ 8550 20393.16 279.84781 0 3678.7078 6.3282998
+ 8600 20898.88 195.43751 0 3678.5842 -14.393947
+ 8650 20297.482 295.3169 0 3678.2306 -0.96829147
+ 8700 21079.56 164.72934 0 3677.9893 -8.339122
+ 8750 21142.519 154.18527 0 3677.9384 -4.6169442
+ 8800 20143.871 320.23161 0 3677.5435 6.5710426
+ 8850 21030.065 172.88831 0 3677.8992 1.3973883
+ 8900 19814.648 375.22097 0 3677.6624 2.6996208
+ 8950 17392.382 778.87517 0 3677.6055 11.963975
+ 9000 19209.163 476.44659 0 3677.9738 8.7050034
+ 9050 20143.824 320.17051 0 3677.4745 -5.8044332
+ 9100 21400.78 110.99404 0 3677.7908 -3.0027429
+ 9150 21834.471 38.970732 0 3678.0493 -2.5838117
+ 9200 21344.715 120.55831 0 3678.0108 4.8187829
+ 9250 20998.277 178.31959 0 3678.0324 -1.2009012
+ 9300 21141.788 154.4658 0 3678.0971 -21.693564
+ 9350 21439.398 105.00432 0 3678.2374 -16.113694
+ 9400 21296.282 128.83877 0 3678.2191 -2.9990284
+ 9450 19050.623 503.10319 0 3678.207 15.622525
+ 9500 20845.847 203.77117 0 3678.079 -1.7504827
+ 9550 18808.956 543.38757 0 3678.2135 -2.6611868
+ 9600 20612.559 242.57373 0 3678.0002 -0.1650541
+ 9650 20522.637 257.28926 0 3677.7288 6.8876074
+ 9700 20970.074 182.75754 0 3677.7699 -4.5350279
+ 9750 18297.505 625.06808 0 3674.6522 32.429153
+ 9800 21042.472 170.78969 0 3677.8684 5.4901963
+ 9850 20444.092 270.84839 0 3678.197 6.9444494
+ 9900 21597.787 78.901871 0 3678.533 2.3445932
+ 9950 18376.854 616.35469 0 3679.1636 -8.55063
+ 10000 21490.054 97.234379 0 3678.9101 -0.36115606
+Loop time of 3.38095 on 4 procs for 10000 steps with 81 atoms
+
+Performance: 25554.943 tau/day, 2957.748 timesteps/s
+98.7% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.015775 | 0.043664 | 0.1024 | 16.8 | 1.29
+Neigh | 0.012822 | 0.029038 | 0.061576 | 11.5 | 0.86
+Comm | 0.18256 | 0.2516 | 0.30898 | 10.5 | 7.44
+Output | 0.0063725 | 0.0069898 | 0.0081069 | 0.8 | 0.21
+Modify | 2.9608 | 3.0171 | 3.0947 | 2.8 | 89.24
+Other | | 0.03255 | | | 0.96
+
+Nlocal: 20.25 ave 81 max 0 min
+Histogram: 3 0 0 0 0 0 0 0 0 1
+Nghost: 45.5 ave 82 max 12 min
+Histogram: 2 0 0 0 0 0 0 0 1 1
+Neighs: 218.75 ave 875 max 0 min
+Histogram: 3 0 0 0 0 0 0 0 0 1
+
+Total # of neighbors = 875
+Ave neighs/atom = 10.8025
+Neighbor list builds = 993
+Dangerous builds = 945
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:03
diff --git a/examples/rigid/log.20Apr18.rigid.poems2.g++.1 b/examples/rigid/log.20Apr18.rigid.poems2.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..9062b78def3407178b062603c2a74207cac6e611
--- /dev/null
+++ b/examples/rigid/log.20Apr18.rigid.poems2.g++.1
@@ -0,0 +1,342 @@
+LAMMPS (20 Apr 2018)
+ using 1 OpenMP thread(s) per MPI task
+# Simple rigid body system
+
+units lj
+atom_style atomic
+
+pair_style lj/cut 2.5
+
+read_data data.rigid
+ orthogonal box = (-12 -12 -12) to (12 12 12)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 81 atoms
+
+velocity all create 100.0 4928459
+
+# unconnected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 10 18
+#group clump3 id <> 19 27
+#group clump4 id <> 28 36
+#group clump5 id <> 37 45
+#group clump6 id <> 46 54
+#group clump7 id <> 55 63
+#group clump8 id <> 64 72
+#group clump9 id <> 73 81
+
+#fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
+
+# 1 chain of connected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 9 18
+#group clump3 id <> 18 27
+#group clump4 id <> 27 36
+#group clump5 id <> 36 45
+#group clump6 id <> 45 54
+#group clump7 id <> 54 63
+#group clump8 id <> 63 72
+#group clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
+
+# 2 chains of connected bodies
+
+group clump1 id <> 1 9
+9 atoms in group clump1
+group clump2 id <> 9 18
+10 atoms in group clump2
+group clump3 id <> 18 27
+10 atoms in group clump3
+group clump4 id <> 27 36
+10 atoms in group clump4
+group clump5 id <> 37 45
+9 atoms in group clump5
+group clump6 id <> 45 54
+10 atoms in group clump6
+group clump7 id <> 54 63
+10 atoms in group clump7
+group clump8 id <> 63 72
+10 atoms in group clump8
+group clump9 id <> 72 81
+10 atoms in group clump9
+
+fix 1 all poems group clump1 clump2 clump3 clump4
+1 clusters, 4 bodies, 3 joints, 36 atoms
+fix 2 all poems group clump5 clump6 clump7 clump8 clump9
+1 clusters, 5 bodies, 4 joints, 45 atoms
+
+neigh_modify exclude group clump1 clump1
+neigh_modify exclude group clump2 clump2
+neigh_modify exclude group clump3 clump3
+neigh_modify exclude group clump4 clump4
+neigh_modify exclude group clump5 clump5
+neigh_modify exclude group clump6 clump6
+neigh_modify exclude group clump7 clump7
+neigh_modify exclude group clump8 clump8
+neigh_modify exclude group clump9 clump9
+
+thermo 100
+
+#dump 1 all atom 50 dump.rigid.poems2
+
+#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 2 pad 5
+
+#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 3 pad 5
+
+timestep 0.0001
+thermo 50
+run 10000
+WARNING: More than one fix poems (../fix_poems.cpp:363)
+WARNING: More than one fix poems (../fix_poems.cpp:363)
+WARNING: One or more atoms are time integrated more than once (../modify.cpp:279)
+Neighbor list info ...
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 18 18 18
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.854 | 3.854 | 3.854 Mbytes
+Step Temp E_pair E_mol TotEng Press
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+ 50 12167.633 1505.5478 0 3758.8133 35.125973
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+ 200 19757.51 105.30542 0 3764.1036 -0.030645317
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+ 300 19383.039 174.40688 0 3763.8586 5.7240693
+ 350 20125.986 36.972611 0 3764.0071 1.9559205
+ 400 18888.816 266.10975 0 3764.0386 9.6362168
+ 450 19307.656 188.2511 0 3763.743 1.9326206
+ 500 16331.197 738.56392 0 3762.8597 9.1715579
+ 550 19318.722 186.16172 0 3763.7027 3.0115336
+ 600 19455.268 161.20621 0 3764.0336 0.55208034
+ 650 18487.011 340.03216 0 3763.5528 -8.0359122
+ 700 17321.201 556.32471 0 3763.9545 -13.631751
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+ 9000 19117.66 222.84553 0 3763.153 5.2990011
+ 9050 19072.016 231.26038 0 3763.1152 -1.6513695
+ 9100 19284.933 191.73976 0 3763.0237 -3.932358
+ 9150 17356.576 548.61808 0 3762.7988 1.3659056
+ 9200 18939.549 255.43703 0 3762.761 3.3037106
+ 9250 19621.961 129.5012 0 3763.1976 1.667
+ 9300 16898.033 633.79921 0 3763.0647 7.5941845
+ 9350 19662.75 122.10836 0 3763.3584 -3.3144828
+ 9400 16118.338 778.70243 0 3763.5799 9.8684537
+ 9450 17362.374 548.18847 0 3763.443 6.8117548
+ 9500 17873.057 453.37389 0 3763.1993 9.5651746
+ 9550 19282.305 192.593 0 3763.3901 -4.987757
+ 9600 18236.48 386.36263 0 3763.4886 8.8658343
+ 9650 17695.571 486.6517 0 3763.6093 12.471421
+ 9700 19044.003 237.04652 0 3763.7138 0.84430497
+ 9750 17937.299 442.4372 0 3764.1592 3.981475
+ 9800 18179.761 396.86987 0 3763.4923 -11.397273
+ 9850 19157.292 215.8937 0 3763.5404 -7.7648682
+ 9900 19719.066 111.98124 0 3763.6602 5.5378968
+ 9950 18103.235 410.65473 0 3763.1056 28.201374
+ 10000 18479.903 341.32548 0 3763.5297 -5.0581298
+Loop time of 3.14341 on 1 procs for 10000 steps with 81 atoms
+
+Performance: 27486.104 tau/day, 3181.262 timesteps/s
+99.3% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.12201 | 0.12201 | 0.12201 | 0.0 | 3.88
+Neigh | 0.077269 | 0.077269 | 0.077269 | 0.0 | 2.46
+Comm | 0.012246 | 0.012246 | 0.012246 | 0.0 | 0.39
+Output | 0.0032048 | 0.0032048 | 0.0032048 | 0.0 | 0.10
+Modify | 2.9172 | 2.9172 | 2.9172 | 0.0 | 92.80
+Other | | 0.01151 | | | 0.37
+
+Nlocal: 81 ave 81 max 81 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 67 ave 67 max 67 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 599 ave 599 max 599 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 599
+Ave neighs/atom = 7.39506
+Neighbor list builds = 993
+Dangerous builds = 945
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:03
diff --git a/examples/rigid/log.20Apr18.rigid.poems2.g++.4 b/examples/rigid/log.20Apr18.rigid.poems2.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..812b101841c6a9260eb4fad1a39b26a07c2dd64a
--- /dev/null
+++ b/examples/rigid/log.20Apr18.rigid.poems2.g++.4
@@ -0,0 +1,342 @@
+LAMMPS (20 Apr 2018)
+ using 1 OpenMP thread(s) per MPI task
+# Simple rigid body system
+
+units lj
+atom_style atomic
+
+pair_style lj/cut 2.5
+
+read_data data.rigid
+ orthogonal box = (-12 -12 -12) to (12 12 12)
+ 1 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 81 atoms
+
+velocity all create 100.0 4928459
+
+# unconnected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 10 18
+#group clump3 id <> 19 27
+#group clump4 id <> 28 36
+#group clump5 id <> 37 45
+#group clump6 id <> 46 54
+#group clump7 id <> 55 63
+#group clump8 id <> 64 72
+#group clump9 id <> 73 81
+
+#fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
+
+# 1 chain of connected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 9 18
+#group clump3 id <> 18 27
+#group clump4 id <> 27 36
+#group clump5 id <> 36 45
+#group clump6 id <> 45 54
+#group clump7 id <> 54 63
+#group clump8 id <> 63 72
+#group clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
+
+# 2 chains of connected bodies
+
+group clump1 id <> 1 9
+9 atoms in group clump1
+group clump2 id <> 9 18
+10 atoms in group clump2
+group clump3 id <> 18 27
+10 atoms in group clump3
+group clump4 id <> 27 36
+10 atoms in group clump4
+group clump5 id <> 37 45
+9 atoms in group clump5
+group clump6 id <> 45 54
+10 atoms in group clump6
+group clump7 id <> 54 63
+10 atoms in group clump7
+group clump8 id <> 63 72
+10 atoms in group clump8
+group clump9 id <> 72 81
+10 atoms in group clump9
+
+fix 1 all poems group clump1 clump2 clump3 clump4
+1 clusters, 4 bodies, 3 joints, 36 atoms
+fix 2 all poems group clump5 clump6 clump7 clump8 clump9
+1 clusters, 5 bodies, 4 joints, 45 atoms
+
+neigh_modify exclude group clump1 clump1
+neigh_modify exclude group clump2 clump2
+neigh_modify exclude group clump3 clump3
+neigh_modify exclude group clump4 clump4
+neigh_modify exclude group clump5 clump5
+neigh_modify exclude group clump6 clump6
+neigh_modify exclude group clump7 clump7
+neigh_modify exclude group clump8 clump8
+neigh_modify exclude group clump9 clump9
+
+thermo 100
+
+#dump 1 all atom 50 dump.rigid.poems2
+
+#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 2 pad 5
+
+#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 3 pad 5
+
+timestep 0.0001
+thermo 50
+run 10000
+WARNING: More than one fix poems (../fix_poems.cpp:363)
+WARNING: More than one fix poems (../fix_poems.cpp:363)
+WARNING: One or more atoms are time integrated more than once (../modify.cpp:279)
+Neighbor list info ...
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 18 18 18
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.825 | 3.919 | 4.201 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 196.00047 3632.2347 0 3668.5311 -2.7403788
+ 50 12167.633 1505.5478 0 3758.8133 35.125973
+ 100 17556.978 512.66277 0 3763.9549 11.137534
+ 150 19579.586 138.04942 0 3763.8987 -29.953971
+ 200 19757.51 105.30542 0 3764.1036 -0.030645317
+ 250 18218.374 390.10747 0 3763.8804 13.711001
+ 300 19383.039 174.40688 0 3763.8586 5.7240693
+ 350 20125.986 36.972611 0 3764.0071 1.9559205
+ 400 18888.816 266.10975 0 3764.0386 9.6362168
+ 450 19307.656 188.2511 0 3763.743 1.9326206
+ 500 16331.197 738.56392 0 3762.8597 9.1715579
+ 550 19318.722 186.16172 0 3763.7027 3.0115336
+ 600 19455.268 161.20621 0 3764.0336 0.55208034
+ 650 18487.011 340.03216 0 3763.5528 -8.0359122
+ 700 17321.201 556.32471 0 3763.9545 -13.631751
+ 750 18979.187 249.04389 0 3763.7082 -2.6072455
+ 800 19342.456 181.85552 0 3763.7918 8.1918726
+ 850 19070.641 232.19342 0 3763.7936 7.3148472
+ 900 19478.873 156.65987 0 3763.8586 2.4284987
+ 950 19912.415 76.437437 0 3763.9216 -1.4667227
+ 1000 16003.749 802.39753 0 3766.0548 46.642188
+ 1050 19859.583 86.64176 0 3764.3424 -2.1961943
+ 1100 19229.575 203.61488 0 3764.6473 -10.632365
+ 1150 18821.6 279.15861 0 3764.64 -0.89495035
+ 1200 19392.695 173.59744 0 3764.8373 1.8508753
+ 1250 16459.624 717.32104 0 3765.3995 33.478127
+ 1300 19343.863 182.59043 0 3764.7874 0.75890736
+ 1350 20019.643 57.503573 0 3764.8448 0.31444671
+ 1400 18549.582 329.31436 0 3764.4221 10.738303
+ 1450 15163.926 957.47584 0 3765.6103 -17.923459
+ 1500 19223.688 204.15172 0 3764.0939 -1.6134536
+ 1550 18147.996 404.12676 0 3764.8668 8.4194774
+ 1600 18615.043 317.42466 0 3764.6548 -2.3288957
+ 1650 20120.654 38.887927 0 3764.935 -8.7620244
+ 1700 19450.906 162.98284 0 3765.0025 2.3254707
+ 1750 19374.632 177.37954 0 3765.2744 8.9328778
+ 1800 19424.403 167.93971 0 3765.0514 0.081234023
+ 1850 17936.311 442.83087 0 3764.3699 6.600894
+ 1900 19982.596 64.40607 0 3764.8868 -2.9530102
+ 1950 16215.95 761.89459 0 3764.8482 13.994238
+ 2000 18584.39 322.12621 0 3763.68 7.1654863
+ 2050 20107.966 41.025634 0 3764.723 -0.31093298
+ 2100 20002.346 60.590652 0 3764.7288 -6.7919499
+ 2150 16949.612 626.62391 0 3765.441 3.5094585
+ 2200 20010.952 58.808492 0 3764.5403 -10.862255
+ 2250 18982.727 247.00941 0 3762.3292 -0.53796622
+ 2300 18401.351 354.86992 0 3762.5275 1.0919209
+ 2350 19390.5 172.94589 0 3763.7793 -3.3526281
+ 2400 16081.648 786.23133 0 3764.3143 -16.197875
+ 2450 18870.722 268.69249 0 3763.2707 11.192419
+ 2500 19687.71 117.6898 0 3763.562 4.387789
+ 2550 18872.129 268.54506 0 3763.3838 -5.6577428
+ 2600 17017.179 612.11028 0 3763.4397 6.3187623
+ 2650 18766.343 288.63699 0 3763.8856 2.3968008
+ 2700 19737.998 108.02069 0 3763.2054 -0.30752024
+ 2750 19508.797 150.69812 0 3763.4384 -1.6171126
+ 2800 18394.822 355.73011 0 3762.1787 21.193311
+ 2850 18561.108 325.76417 0 3763.0065 3.9331499
+ 2900 20124.042 36.554163 0 3763.2286 0.54133121
+ 2950 15727.607 849.90471 0 3762.4245 13.885323
+ 3000 17991.206 431.32693 0 3763.0317 9.9953567
+ 3050 18834.86 275.34241 0 3763.2795 9.1519305
+ 3100 18986.272 247.38123 0 3763.3575 -1.8754521
+ 3150 19979.145 63.575968 0 3763.4177 -11.800026
+ 3200 19953.846 68.376593 0 3763.5332 -6.7719573
+ 3250 15646.02 867.19502 0 3764.6062 16.433911
+ 3300 16946.252 625.14854 0 3763.3433 4.3975456
+ 3350 19006.567 243.97026 0 3763.7048 5.3392405
+ 3400 18082.133 414.87059 0 3763.4138 15.143954
+ 3450 18273.719 379.36162 0 3763.3836 5.4465204
+ 3500 19783.17 100.06678 0 3763.6167 1.9588505
+ 3550 19794.99 97.904519 0 3763.6435 -3.0349395
+ 3600 18357.708 363.98291 0 3763.5585 -2.1229788
+ 3650 19647.179 125.48949 0 3763.8559 1.2967845
+ 3700 18806.632 281.78709 0 3764.4967 5.125718
+ 3750 18982.747 248.97053 0 3764.294 -0.72036085
+ 3800 19597.926 135.04805 0 3764.2935 -3.2129291
+ 3850 18914.042 261.7133 0 3764.3136 -12.163282
+ 3900 18646.326 311.16482 0 3764.1881 5.1808943
+ 3950 18589.554 321.36256 0 3763.8726 4.9554103
+ 4000 17877.615 453.02456 0 3763.694 9.8457113
+ 4050 19440.059 164.15739 0 3764.1684 -5.4054486
+ 4100 18505.545 337.36023 0 3764.313 4.8468985
+ 4150 19220.307 204.85944 0 3764.1755 -6.5040818
+ 4200 19058.915 234.79578 0 3764.2245 3.1852011
+ 4250 19867.025 85.136186 0 3764.2149 5.6156236
+ 4300 16989.857 616.86564 0 3763.1355 -3.4041875
+ 4350 19782.09 100.85847 0 3764.2085 3.2531098
+ 4400 19879.56 82.559198 0 3763.9593 1.6340828
+ 4450 19409.95 169.46676 0 3763.9019 -1.824265
+ 4500 19742.977 107.72786 0 3763.8347 -0.72711698
+ 4550 17166.529 585.04113 0 3764.028 -0.38806102
+ 4600 19604.596 133.61426 0 3764.0949 -5.2712214
+ 4650 18865.608 270.23956 0 3763.8707 1.5751363
+ 4700 20190.139 25.270932 0 3764.1855 -10.159924
+ 4750 20043.487 52.56327 0 3764.3201 -4.713579
+ 4800 19361.931 178.70311 0 3764.246 4.2460799
+ 4850 19460.365 160.29083 0 3764.0621 3.5079181
+ 4900 18252.89 384.16194 0 3764.3268 4.1870604
+ 4950 19516.947 150.07365 0 3764.3231 4.0238527
+ 5000 19041.145 238.27335 0 3764.4113 8.2280019
+ 5050 19519.408 149.66793 0 3764.3731 -0.088904966
+ 5100 18087.848 415.34004 0 3764.9416 8.9482852
+ 5150 19392.463 173.43121 0 3764.628 -6.6722716
+ 5200 19683.968 119.46663 0 3764.6458 -2.0330852
+ 5250 19675.404 121.09497 0 3764.6884 3.0627309
+ 5300 18627.53 314.96107 0 3764.5038 5.2692141
+ 5350 20022.616 56.725346 0 3764.6172 -7.7034469
+ 5400 19353.4 180.6482 0 3764.6112 -2.3897589
+ 5450 16966.649 622.29693 0 3764.2689 6.3601638
+ 5500 17584.292 508.42495 0 3764.7753 5.949219
+ 5550 19169.69 214.76864 0 3764.7113 3.3778997
+ 5600 19491.814 155.19149 0 3764.7866 -0.20031164
+ 5650 19079.585 231.70394 0 3764.9605 7.3017226
+ 5700 19686.564 119.34 0 3765 0.98980357
+ 5750 19639.909 127.89886 0 3764.919 2.3982612
+ 5800 19474.109 158.55418 0 3764.8706 3.4940447
+ 5850 16957.663 624.72623 0 3765.0342 10.739819
+ 5900 19950.579 70.027987 0 3764.5796 4.6925057
+ 5950 19759.601 105.38621 0 3764.5716 3.0958319
+ 6000 19129.749 221.96406 0 3764.5102 -1.0612997
+ 6050 16087.951 785.36134 0 3764.6115 -15.255986
+ 6100 18851.976 272.98306 0 3764.0896 4.9341766
+ 6150 19532.23 147.4113 0 3764.4909 1.3206073
+ 6200 18051.604 421.79367 0 3764.6833 2.587863
+ 6250 18922.77 259.81211 0 3764.0287 10.363589
+ 6300 18402.504 356.81518 0 3764.6864 8.3589218
+ 6350 19315.369 187.64457 0 3764.5647 1.0716382
+ 6400 19700.59 116.50438 0 3764.7618 2.165408
+ 6450 19596.362 135.79675 0 3764.7527 1.6466783
+ 6500 20217.677 20.884953 0 3764.8993 -3.5893732
+ 6550 18278.991 379.95981 0 3764.9582 7.0433091
+ 6600 20142.999 34.761283 0 3764.9462 1.7083655
+ 6650 20185.488 26.899017 0 3764.9524 -0.65741058
+ 6700 17942.962 441.72909 0 3764.4999 -3.691039
+ 6750 16435.681 720.9581 0 3764.6028 -9.4583249
+ 6800 17825.95 463.58979 0 3764.6916 6.1557503
+ 6850 19440.75 164.52796 0 3764.6669 -11.921703
+ 6900 18824.905 278.4897 0 3764.5832 -1.4668322
+ 6950 19069.14 233.25502 0 3764.5772 6.8149838
+ 7000 18983.209 249.29193 0 3764.701 15.140158
+ 7050 15623.103 872.33684 0 3765.5041 7.3268767
+ 7100 20090.283 44.006184 0 3764.429 2.6959947
+ 7150 15535.27 888.39683 0 3765.2987 -4.1285644
+ 7200 19425.575 167.19079 0 3764.5195 4.9190857
+ 7250 18684.497 304.24754 0 3764.3396 7.3927682
+ 7300 17632.518 498.82765 0 3764.1087 5.1101854
+ 7350 18969.793 251.66375 0 3764.5884 -3.7865508
+ 7400 17700.626 486.89931 0 3764.7931 -8.8531288
+ 7450 17897.361 450.31562 0 3764.6417 -3.6095062
+ 7500 18795.228 284.03842 0 3764.6361 8.3567203
+ 7550 18658.285 309.34015 0 3764.5781 0.4306691
+ 7600 19230.039 203.5385 0 3764.6567 0.80253549
+ 7650 19513.551 150.86999 0 3764.4906 0.32848159
+ 7700 19494.849 154.28788 0 3764.4452 -4.2498631
+ 7750 20011.058 58.832118 0 3764.5835 0.54896615
+ 7800 19241.055 201.57548 0 3764.7338 -0.26200786
+ 7850 19512.742 151.11436 0 3764.5851 2.7308876
+ 7900 19688.007 118.68023 0 3764.6075 0.80454178
+ 7950 16891.645 636.56823 0 3764.6507 -25.839253
+ 8000 19425.572 167.33746 0 3764.6657 -2.8744687
+ 8050 19444.916 163.57779 0 3764.4882 8.5388183
+ 8100 19540.338 145.77731 0 3764.3585 5.5606379
+ 8150 17997.991 429.85951 0 3762.8208 20.179487
+ 8200 19463.886 159.50302 0 3763.9264 0.19577123
+ 8250 19517.733 149.53457 0 3763.9295 2.3294314
+ 8300 19236.221 201.66041 0 3763.9236 5.8204747
+ 8350 18662.608 308.25544 0 3764.2939 5.4422482
+ 8400 19030.046 239.38211 0 3763.4647 3.7940188
+ 8450 18058.148 419.70672 0 3763.8081 4.4010713
+ 8500 16866.001 641.00564 0 3764.3392 -19.894815
+ 8550 19484.364 155.35821 0 3763.5737 4.2635496
+ 8600 18562.912 326.16323 0 3763.7395 11.288271
+ 8650 19256.188 197.67578 0 3763.6365 -4.1872666
+ 8700 19653.945 124.27148 0 3763.8909 -7.4888761
+ 8750 19590.834 136.12748 0 3764.0596 1.0605539
+ 8800 19065.424 233.46882 0 3764.1029 1.8432113
+ 8850 18961.297 252.69734 0 3764.0486 6.7414134
+ 8900 19879.711 82.777822 0 3764.2058 0.12631864
+ 8950 18689.712 302.80546 0 3763.8632 5.1584036
+ 9000 19114.403 224.23511 0 3763.9393 -4.5856366
+ 9050 17626.3 500.49518 0 3764.6248 -3.9436947
+ 9100 18552.501 328.86032 0 3764.5087 -0.32810034
+ 9150 15039.846 979.12961 0 3764.2862 16.571104
+ 9200 19146.923 218.64681 0 3764.3733 -4.6264398
+ 9250 17606.161 503.14852 0 3763.5487 13.13675
+ 9300 18002.328 430.47362 0 3764.2381 4.9326117
+ 9350 19980.452 64.168644 0 3764.2524 -5.6111349
+ 9400 18953.798 254.44926 0 3764.4118 2.3662302
+ 9450 17151.075 588.59472 0 3764.7197 4.3116983
+ 9500 19128.858 221.38199 0 3763.763 3.6641306
+ 9550 18217.322 390.53199 0 3764.1101 1.8537154
+ 9600 19094.478 227.98925 0 3764.0038 3.972665
+ 9650 19577.649 138.55507 0 3764.0456 4.0408247
+ 9700 19331.361 184.31942 0 3764.2011 -4.7996733
+ 9750 18999.798 245.87295 0 3764.3541 -0.26741334
+ 9800 18987.181 248.37105 0 3764.5157 6.1717595
+ 9850 20094.73 43.013036 0 3764.2593 -8.9770288
+ 9900 18988.815 247.63984 0 3764.087 -6.3990966
+ 9950 18290.808 377.34967 0 3764.5363 7.7453525
+ 10000 19558.326 142.47047 0 3764.3828 3.4110829
+Loop time of 3.53831 on 4 procs for 10000 steps with 81 atoms
+
+Performance: 24418.438 tau/day, 2826.208 timesteps/s
+98.7% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.0096724 | 0.035349 | 0.063574 | 10.3 | 1.00
+Neigh | 0.0091243 | 0.022333 | 0.037608 | 6.9 | 0.63
+Comm | 0.18063 | 0.2494 | 0.33202 | 12.6 | 7.05
+Output | 0.0060797 | 0.0065744 | 0.0074706 | 0.7 | 0.19
+Modify | 3.0943 | 3.1895 | 3.2828 | 4.0 | 90.14
+Other | | 0.0352 | | | 0.99
+
+Nlocal: 20.25 ave 36 max 0 min
+Histogram: 1 0 1 0 0 0 0 0 0 2
+Nghost: 17.5 ave 37 max 1 min
+Histogram: 2 0 0 0 0 0 0 0 1 1
+Neighs: 154.25 ave 393 max 0 min
+Histogram: 2 0 0 0 0 1 0 0 0 1
+
+Total # of neighbors = 617
+Ave neighs/atom = 7.61728
+Neighbor list builds = 993
+Dangerous builds = 948
+
+Please see the log.cite file for references relevant to this simulation
+
+Total wall time: 0:00:03
diff --git a/examples/rigid/log.20Apr18.rigid.property.g++.1 b/examples/rigid/log.20Apr18.rigid.property.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..76ef36825b00775073409ad7d4c97c9e9261e4c3
--- /dev/null
+++ b/examples/rigid/log.20Apr18.rigid.property.g++.1
@@ -0,0 +1,340 @@
+LAMMPS (20 Apr 2018)
+ using 1 OpenMP thread(s) per MPI task
+# Simple rigid body system
+
+units lj
+atom_style atomic
+atom_modify map array
+
+pair_style lj/cut 2.5
+
+fix 0 all property/atom i_bodies
+
+read_data data.rigid-property fix 0 NULL Bodies
+ orthogonal box = (-12 -12 -12) to (12 12 12)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 81 atoms
+
+velocity all create 100.0 4928459
+
+
+# unconnected bodies
+
+group clump1 id <> 1 9
+9 atoms in group clump1
+group clump2 id <> 10 18
+9 atoms in group clump2
+group clump3 id <> 19 27
+9 atoms in group clump3
+group clump4 id <> 28 36
+9 atoms in group clump4
+group clump5 id <> 37 45
+9 atoms in group clump5
+group clump6 id <> 46 54
+9 atoms in group clump6
+group clump7 id <> 55 63
+9 atoms in group clump7
+group clump8 id <> 64 72
+9 atoms in group clump8
+group clump9 id <> 73 81
+9 atoms in group clump9
+
+# assemble bodies from per-atom custom integer property bodies
+fix 1 all rigid custom i_bodies
+9 rigid bodies with 81 atoms
+
+# 1 chain of connected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 9 18
+#group clump3 id <> 18 27
+#group clump4 id <> 27 36
+#group clump5 id <> 36 45
+#group clump6 id <> 45 54
+#group clump7 id <> 54 63
+#group clump8 id <> 63 72
+#group clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
+
+# 2 chains of connected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 9 18
+#group clump3 id <> 18 27
+#group clump4 id <> 27 36
+#group clump5 id <> 37 45
+#group clump6 id <> 45 54
+#group clump7 id <> 54 63
+#group clump8 id <> 63 72
+#group clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4
+#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
+
+neigh_modify exclude group clump1 clump1
+neigh_modify exclude group clump2 clump2
+neigh_modify exclude group clump3 clump3
+neigh_modify exclude group clump4 clump4
+neigh_modify exclude group clump5 clump5
+neigh_modify exclude group clump6 clump6
+neigh_modify exclude group clump7 clump7
+neigh_modify exclude group clump8 clump8
+neigh_modify exclude group clump9 clump9
+
+thermo 100
+
+#dump 1 all atom 50 dump.rigid
+
+#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 2 pad 5
+
+#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 3 pad 5
+
+timestep 0.0001
+thermo 50
+run 10000
+Neighbor list info ...
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 18 18 18
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 4.046 | 4.046 | 4.046 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 115.29439 5235.9179 0 5272.2142 -2.7403788
+ 50 14910.685 571.71558 0 5265.82 32.006171
+ 100 16298.442 136.66184 0 5267.653 16.444229
+ 150 16682.606 17.490511 0 5269.4219 14.900344
+ 200 16733.929 1.372872 0 5269.4617 14.569267
+ 250 16738.853 -0.15252816 0 5269.4864 14.496404
+ 300 16738.588 -0.055171335 0 5269.5002 14.496025
+ 350 16738.492 -0.017444677 0 5269.5077 14.496446
+ 400 16738.464 -0.0060102023 0 5269.5104 14.496618
+ 450 16738.455 -0.0012713351 0 5269.5124 14.496701
+ 500 16738.455 -0.00081068621 0 5269.5128 14.496709
+ 550 16738.455 -0.00083203497 0 5269.5129 14.496707
+ 600 16738.455 -0.00058355356 0 5269.5131 14.496709
+ 650 16738.455 -0.00047226704 0 5269.5131 14.496708
+ 700 16738.455 0 0 5269.5136 14.496713
+ 750 16738.455 0 0 5269.5136 14.49671
+ 800 16738.455 0 0 5269.5137 14.496709
+ 850 16738.455 0 0 5269.5137 14.49671
+ 900 16738.456 0 0 5269.5138 14.496713
+ 950 16738.462 -0.0035323872 0 5269.5122 14.496671
+ 1000 16738.586 -0.051135144 0 5269.5036 14.496229
+ 1050 16737.358 0.32995057 0 5269.4981 14.525763
+ 1100 16737.892 0.16210246 0 5269.4984 14.531983
+ 1150 16738.703 -0.089235095 0 5269.5025 14.509899
+ 1200 16738.466 -0.0075446243 0 5269.5096 14.510615
+ 1250 16738.456 0 0 5269.514 14.510704
+ 1300 16738.457 0 0 5269.5141 14.510701
+ 1350 16738.457 0 0 5269.5141 14.510699
+ 1400 16738.457 -0.00044736511 0 5269.5138 14.510693
+ 1450 16738.458 -0.0010971179 0 5269.5134 14.510687
+ 1500 16738.458 -0.00057885428 0 5269.5139 14.510698
+ 1550 16738.457 0 0 5269.5143 14.51071
+ 1600 16738.457 0 0 5269.5144 14.510712
+ 1650 16738.457 0 0 5269.5144 14.510712
+ 1700 16738.458 0 0 5269.5144 14.51071
+ 1750 16738.458 0 0 5269.5145 14.510708
+ 1800 16738.458 0 0 5269.5145 14.510706
+ 1850 16738.458 0 0 5269.5146 14.510705
+ 1900 16738.458 0 0 5269.5146 14.510706
+ 1950 16738.465 -0.0031733615 0 5269.5134 14.510659
+ 2000 16738.491 -0.013255268 0 5269.5117 14.510532
+ 2050 16738.556 -0.0365811 0 5269.5087 14.51029
+ 2100 16738.633 -0.063209659 0 5269.5065 14.510219
+ 2150 16738.607 -0.05601761 0 5269.5055 14.510231
+ 2200 16738.557 -0.038423032 0 5269.5072 14.510404
+ 2250 16738.515 -0.023709918 0 5269.5088 14.510539
+ 2300 16738.489 -0.013249035 0 5269.5111 14.510621
+ 2350 16738.468 -0.0045563719 0 5269.5131 14.510714
+ 2400 16738.46 -0.00052194273 0 5269.5146 14.510771
+ 2450 16738.464 -0.0023259756 0 5269.514 14.510746
+ 2500 16738.468 -0.0051929186 0 5269.5127 14.510731
+ 2550 16738.581 -0.044940117 0 5269.5085 14.510315
+ 2600 16738.427 -7.9722839e-05 0 5269.5046 14.510657
+ 2650 16733.017 1.705148 0 5269.5067 14.596295
+ 2700 16738.761 -0.10614946 0 5269.5038 14.499584
+ 2750 16733.973 1.4038179 0 5269.5064 14.598107
+ 2800 16738.585 -0.046813448 0 5269.5076 14.511073
+ 2850 16738.487 -0.012558719 0 5269.5111 14.510111
+ 2900 16738.465 -0.0026252725 0 5269.514 14.510277
+ 2950 16738.476 -0.0082220764 0 5269.512 14.510223
+ 3000 16738.66 -0.071284779 0 5269.507 14.509758
+ 3050 16715.332 7.2419351 0 5269.476 14.870305
+ 3100 16653.226 26.818761 0 5269.5009 14.496764
+ 3150 16739.351 -0.30690375 0 5269.4886 13.643904
+ 3200 16733.238 1.6025328 0 5269.4737 12.016934
+ 3250 16734.374 1.2554429 0 5269.4841 11.963561
+ 3300 16732.156 1.9585967 0 5269.4893 12.234024
+ 3350 16738.655 -0.079693236 0 5269.497 12.092757
+ 3400 16738.543 -0.042215005 0 5269.4991 12.092809
+ 3450 16738.591 -0.059327511 0 5269.4972 12.092536
+ 3500 16738.759 -0.11761245 0 5269.4918 12.09203
+ 3550 16713.405 7.846062 0 5269.4737 12.389816
+ 3600 16734.939 1.0821936 0 5269.4891 12.173591
+ 3650 16738.808 -0.13663194 0 5269.4882 12.027009
+ 3700 16738.602 -0.070934367 0 5269.4889 12.025288
+ 3750 16737.731 0.20706557 0 5269.4927 12.061948
+ 3800 16738.578 -0.05582043 0 5269.4965 12.035665
+ 3850 16738.471 -0.016307928 0 5269.5024 12.035302
+ 3900 16738.449 -0.0058182199 0 5269.5059 12.035401
+ 3950 16738.439 -0.0012027325 0 5269.5074 12.035461
+ 4000 16738.436 -0.00020698452 0 5269.5075 12.035469
+ 4050 16738.437 0 0 5269.5078 12.035454
+ 4100 16738.437 0 0 5269.508 12.035435
+ 4150 16738.438 0 0 5269.5081 12.035426
+ 4200 16738.438 0 0 5269.5083 12.035432
+ 4250 16738.439 0 0 5269.5085 12.035447
+ 4300 16738.439 0 0 5269.5086 12.035463
+ 4350 16738.44 0 0 5269.5087 12.035474
+ 4400 16738.44 0 0 5269.5088 12.035478
+ 4450 16738.44 0 0 5269.5089 12.035474
+ 4500 16738.44 0 0 5269.509 12.035462
+ 4550 16738.441 0 0 5269.5092 12.035449
+ 4600 16738.441 0 0 5269.5093 12.035445
+ 4650 16738.442 0 0 5269.5095 12.035451
+ 4700 16738.442 0 0 5269.5096 12.03546
+ 4750 16738.443 0 0 5269.5097 12.035465
+ 4800 16738.443 0 0 5269.5098 12.035466
+ 4850 16738.443 0 0 5269.51 12.035463
+ 4900 16738.444 0 0 5269.5101 12.035456
+ 4950 16738.444 0 0 5269.5102 12.035447
+ 5000 16738.445 0 0 5269.5104 12.03544
+ 5050 16738.445 0 0 5269.5105 12.035442
+ 5100 16738.446 0 0 5269.5107 12.035455
+ 5150 16738.446 0 0 5269.5108 12.03547
+ 5200 16738.446 0 0 5269.5109 12.035479
+ 5250 16738.447 0 0 5269.511 12.035479
+ 5300 16738.447 0 0 5269.5111 12.03547
+ 5350 16738.447 0 0 5269.5112 12.035454
+ 5400 16738.448 0 0 5269.5113 12.035434
+ 5450 16738.448 0 0 5269.5115 12.03542
+ 5500 16738.449 0 0 5269.5117 12.035422
+ 5550 16738.457 -0.0030919234 0 5269.5111 12.035383
+ 5600 16738.51 -0.021618357 0 5269.5092 12.035106
+ 5650 16738.622 -0.059214788 0 5269.507 12.035694
+ 5700 16395.28 108.06942 0 5269.5463 24.369038
+ 5750 16738.544 -0.033973429 0 5269.5077 12.011261
+ 5800 16738.456 -0.0037013529 0 5269.5102 12.011675
+ 5850 16738.451 0 0 5269.5123 12.011709
+ 5900 16738.451 -0.00022115871 0 5269.5122 12.011687
+ 5950 16738.452 -0.00024253349 0 5269.5124 12.011678
+ 6000 16738.452 0 0 5269.5128 12.011688
+ 6050 16738.453 0 0 5269.513 12.011702
+ 6100 16738.453 0 0 5269.5131 12.011716
+ 6150 16738.454 0 0 5269.5132 12.011725
+ 6200 16738.454 0 0 5269.5133 12.011728
+ 6250 16738.454 0 0 5269.5134 12.011723
+ 6300 16738.455 0 0 5269.5135 12.011712
+ 6350 16738.455 0 0 5269.5137 12.0117
+ 6400 16738.456 0 0 5269.5138 12.011697
+ 6450 16738.456 0 0 5269.514 12.011704
+ 6500 16738.456 0 0 5269.5141 12.011714
+ 6550 16738.457 0 0 5269.5142 12.011719
+ 6600 16738.457 0 0 5269.5143 12.011718
+ 6650 16738.458 0 0 5269.5144 12.011713
+ 6700 16738.458 0 0 5269.5146 12.011705
+ 6750 16738.459 0 0 5269.5147 12.011696
+ 6800 16738.459 0 0 5269.5149 12.01169
+ 6850 16738.46 0 0 5269.515 12.011695
+ 6900 16738.46 0 0 5269.5152 12.01171
+ 6950 16738.46 0 0 5269.5153 12.011726
+ 7000 16738.461 0 0 5269.5154 12.011736
+ 7050 16738.461 0 0 5269.5155 12.011737
+ 7100 16738.461 0 0 5269.5155 12.011728
+ 7150 16738.461 0 0 5269.5156 12.011712
+ 7200 16738.462 0 0 5269.5158 12.011691
+ 7250 16738.463 0 0 5269.516 12.011676
+ 7300 16738.463 0 0 5269.5162 12.011677
+ 7350 16738.464 0 0 5269.5164 12.011693
+ 7400 16738.464 0 0 5269.5165 12.011713
+ 7450 16738.465 0 0 5269.5166 12.011729
+ 7500 16738.465 0 0 5269.5167 12.011736
+ 7550 16738.465 0 0 5269.5168 12.011734
+ 7600 16738.465 0 0 5269.5168 12.011722
+ 7650 16738.466 0 0 5269.517 12.011704
+ 7700 16738.466 0 0 5269.5171 12.011687
+ 7750 16738.467 0 0 5269.5173 12.011681
+ 7800 16738.467 0 0 5269.5175 12.011687
+ 7850 16738.468 0 0 5269.5176 12.0117
+ 7900 16738.468 0 0 5269.5178 12.011712
+ 7950 16738.469 0 0 5269.5179 12.011721
+ 8000 16738.469 0 0 5269.518 12.011724
+ 8050 16738.469 0 0 5269.5181 12.01172
+ 8100 16738.47 0 0 5269.5182 12.011709
+ 8150 16738.47 0 0 5269.5183 12.0117
+ 8200 16738.47 0 0 5269.5185 12.0117
+ 8250 16738.471 0 0 5269.5186 12.011709
+ 8300 16738.471 0 0 5269.5187 12.011719
+ 8350 16738.472 0 0 5269.5189 12.011723
+ 8400 16738.472 0 0 5269.519 12.01172
+ 8450 16738.473 -0.00039690663 0 5269.5189 12.011706
+ 8500 16738.481 -0.0034646802 0 5269.5182 12.011643
+ 8550 16738.483 -0.0045307409 0 5269.5178 12.011621
+ 8600 16738.474 -0.00076532813 0 5269.5189 12.011681
+ 8650 16738.474 0 0 5269.5197 12.011699
+ 8700 16738.475 0 0 5269.5199 12.011715
+ 8750 16738.475 0 0 5269.52 12.011732
+ 8800 16738.475 0 0 5269.52 12.011743
+ 8850 16738.476 0 0 5269.5201 12.011744
+ 8900 16738.476 0 0 5269.5202 12.011735
+ 8950 16738.476 0 0 5269.5203 12.011719
+ 9000 16738.477 0 0 5269.5205 12.011698
+ 9050 16738.477 0 0 5269.5206 12.011683
+ 9100 16738.478 0 0 5269.5208 12.011684
+ 9150 16738.479 0 0 5269.521 12.011701
+ 9200 16738.479 0 0 5269.5212 12.011722
+ 9250 16738.479 0 0 5269.5213 12.011738
+ 9300 16738.48 0 0 5269.5214 12.011746
+ 9350 16738.48 0 0 5269.5214 12.011744
+ 9400 16738.48 0 0 5269.5215 12.011732
+ 9450 16738.48 0 0 5269.5216 12.011715
+ 9500 16738.481 -0.00037652438 0 5269.5216 12.011692
+ 9550 16738.493 -0.0053156162 0 5269.5203 12.011611
+ 9600 16738.549 -0.026814371 0 5269.5163 12.011415
+ 9650 16738.765 -0.10191523 0 5269.5092 12.011013
+ 9700 16735.041 1.0589893 0 5269.4979 12.062708
+ 9750 16738.013 0.13550102 0 5269.5101 11.407246
+ 9800 16738.512 -0.011620328 0 5269.5201 11.394974
+ 9850 16738.489 -0.00067270521 0 5269.5237 11.395098
+ 9900 16738.489 -0.00024984561 0 5269.5242 11.395085
+ 9950 16738.49 0 0 5269.5245 11.395076
+ 10000 16738.49 0 0 5269.5246 11.395075
+Loop time of 0.140719 on 1 procs for 10000 steps with 81 atoms
+
+Performance: 613990.898 tau/day, 71063.761 timesteps/s
+97.1% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.010882 | 0.010882 | 0.010882 | 0.0 | 7.73
+Neigh | 0.037245 | 0.037245 | 0.037245 | 0.0 | 26.47
+Comm | 0.0092154 | 0.0092154 | 0.0092154 | 0.0 | 6.55
+Output | 0.0024879 | 0.0024879 | 0.0024879 | 0.0 | 1.77
+Modify | 0.074702 | 0.074702 | 0.074702 | 0.0 | 53.09
+Other | | 0.006187 | | | 4.40
+
+Nlocal: 81 ave 81 max 81 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 84 ave 84 max 84 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 998
+Dangerous builds = 997
+Total wall time: 0:00:00
diff --git a/examples/rigid/log.20Apr18.rigid.property.g++.4 b/examples/rigid/log.20Apr18.rigid.property.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..c34324b19c8d5928fd0bee8e128ff88555f65d92
--- /dev/null
+++ b/examples/rigid/log.20Apr18.rigid.property.g++.4
@@ -0,0 +1,340 @@
+LAMMPS (20 Apr 2018)
+ using 1 OpenMP thread(s) per MPI task
+# Simple rigid body system
+
+units lj
+atom_style atomic
+atom_modify map array
+
+pair_style lj/cut 2.5
+
+fix 0 all property/atom i_bodies
+
+read_data data.rigid-property fix 0 NULL Bodies
+ orthogonal box = (-12 -12 -12) to (12 12 12)
+ 1 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 81 atoms
+
+velocity all create 100.0 4928459
+
+
+# unconnected bodies
+
+group clump1 id <> 1 9
+9 atoms in group clump1
+group clump2 id <> 10 18
+9 atoms in group clump2
+group clump3 id <> 19 27
+9 atoms in group clump3
+group clump4 id <> 28 36
+9 atoms in group clump4
+group clump5 id <> 37 45
+9 atoms in group clump5
+group clump6 id <> 46 54
+9 atoms in group clump6
+group clump7 id <> 55 63
+9 atoms in group clump7
+group clump8 id <> 64 72
+9 atoms in group clump8
+group clump9 id <> 73 81
+9 atoms in group clump9
+
+# assemble bodies from per-atom custom integer property bodies
+fix 1 all rigid custom i_bodies
+9 rigid bodies with 81 atoms
+
+# 1 chain of connected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 9 18
+#group clump3 id <> 18 27
+#group clump4 id <> 27 36
+#group clump5 id <> 36 45
+#group clump6 id <> 45 54
+#group clump7 id <> 54 63
+#group clump8 id <> 63 72
+#group clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
+
+# 2 chains of connected bodies
+
+#group clump1 id <> 1 9
+#group clump2 id <> 9 18
+#group clump3 id <> 18 27
+#group clump4 id <> 27 36
+#group clump5 id <> 37 45
+#group clump6 id <> 45 54
+#group clump7 id <> 54 63
+#group clump8 id <> 63 72
+#group clump9 id <> 72 81
+
+#fix 1 all poems group clump1 clump2 clump3 clump4
+#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
+
+neigh_modify exclude group clump1 clump1
+neigh_modify exclude group clump2 clump2
+neigh_modify exclude group clump3 clump3
+neigh_modify exclude group clump4 clump4
+neigh_modify exclude group clump5 clump5
+neigh_modify exclude group clump6 clump6
+neigh_modify exclude group clump7 clump7
+neigh_modify exclude group clump8 clump8
+neigh_modify exclude group clump9 clump9
+
+thermo 100
+
+#dump 1 all atom 50 dump.rigid
+
+#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 2 pad 5
+
+#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
+#dump_modify 3 pad 5
+
+timestep 0.0001
+thermo 50
+run 10000
+Neighbor list info ...
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 18 18 18
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 4.017 | 4.111 | 4.392 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 115.29439 5235.9179 0 5272.2142 -2.7403788
+ 50 14910.685 571.71558 0 5265.82 32.006171
+ 100 16298.442 136.66184 0 5267.653 16.444229
+ 150 16682.606 17.490511 0 5269.4219 14.900344
+ 200 16733.929 1.372872 0 5269.4617 14.569267
+ 250 16738.853 -0.15252816 0 5269.4864 14.496404
+ 300 16738.588 -0.055171335 0 5269.5002 14.496025
+ 350 16738.492 -0.017444677 0 5269.5077 14.496446
+ 400 16738.464 -0.0060102023 0 5269.5104 14.496618
+ 450 16738.455 -0.0012713351 0 5269.5124 14.496701
+ 500 16738.455 -0.00081068621 0 5269.5128 14.496709
+ 550 16738.455 -0.00083203497 0 5269.5129 14.496707
+ 600 16738.455 -0.00058355356 0 5269.5131 14.496709
+ 650 16738.455 -0.00047226704 0 5269.5131 14.496708
+ 700 16738.455 0 0 5269.5136 14.496713
+ 750 16738.455 0 0 5269.5136 14.49671
+ 800 16738.455 0 0 5269.5137 14.496709
+ 850 16738.455 0 0 5269.5137 14.49671
+ 900 16738.456 0 0 5269.5138 14.496713
+ 950 16738.462 -0.0035323872 0 5269.5122 14.496671
+ 1000 16738.586 -0.051135144 0 5269.5036 14.496229
+ 1050 16737.358 0.32995057 0 5269.4981 14.525763
+ 1100 16737.892 0.16210246 0 5269.4984 14.531983
+ 1150 16738.703 -0.089235095 0 5269.5025 14.509899
+ 1200 16738.466 -0.0075446243 0 5269.5096 14.510615
+ 1250 16738.456 0 0 5269.514 14.510704
+ 1300 16738.457 0 0 5269.5141 14.510701
+ 1350 16738.457 0 0 5269.5141 14.510699
+ 1400 16738.457 -0.00044736511 0 5269.5138 14.510693
+ 1450 16738.458 -0.0010971179 0 5269.5134 14.510687
+ 1500 16738.458 -0.00057885428 0 5269.5139 14.510698
+ 1550 16738.457 0 0 5269.5143 14.51071
+ 1600 16738.457 0 0 5269.5144 14.510712
+ 1650 16738.457 0 0 5269.5144 14.510712
+ 1700 16738.458 0 0 5269.5144 14.51071
+ 1750 16738.458 0 0 5269.5145 14.510708
+ 1800 16738.458 0 0 5269.5145 14.510706
+ 1850 16738.458 0 0 5269.5146 14.510705
+ 1900 16738.458 0 0 5269.5146 14.510706
+ 1950 16738.465 -0.0031733615 0 5269.5134 14.510659
+ 2000 16738.491 -0.013255268 0 5269.5117 14.510532
+ 2050 16738.556 -0.0365811 0 5269.5087 14.51029
+ 2100 16738.633 -0.063209659 0 5269.5065 14.510219
+ 2150 16738.607 -0.05601761 0 5269.5055 14.510231
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+ 2550 16738.581 -0.044940117 0 5269.5085 14.510315
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+ 2650 16733.017 1.705148 0 5269.5067 14.596295
+ 2700 16738.761 -0.10614946 0 5269.5038 14.499584
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+ 2850 16738.487 -0.012558719 0 5269.5111 14.510111
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+ 3000 16738.66 -0.071284779 0 5269.507 14.509758
+ 3050 16715.332 7.2419351 0 5269.476 14.870305
+ 3100 16653.226 26.818761 0 5269.5009 14.496764
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+ 5700 16395.28 108.06942 0 5269.5463 24.369038
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+ 9000 16738.477 0 0 5269.5205 12.011698
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+ 9100 16738.478 0 0 5269.5208 12.011684
+ 9150 16738.479 0 0 5269.521 12.011701
+ 9200 16738.479 0 0 5269.5212 12.011722
+ 9250 16738.479 0 0 5269.5213 12.011738
+ 9300 16738.48 0 0 5269.5214 12.011746
+ 9350 16738.48 0 0 5269.5214 12.011744
+ 9400 16738.48 0 0 5269.5215 12.011732
+ 9450 16738.48 0 0 5269.5216 12.011715
+ 9500 16738.481 -0.00037652437 0 5269.5216 12.011692
+ 9550 16738.493 -0.0053156159 0 5269.5203 12.011611
+ 9600 16738.549 -0.026814369 0 5269.5163 12.011415
+ 9650 16738.765 -0.10191523 0 5269.5092 12.011013
+ 9700 16735.041 1.0589887 0 5269.4979 12.062708
+ 9750 16738.013 0.135501 0 5269.5101 11.407245
+ 9800 16738.512 -0.011620329 0 5269.5201 11.394973
+ 9850 16738.489 -0.00067270548 0 5269.5237 11.395098
+ 9900 16738.489 -0.00024984569 0 5269.5242 11.395084
+ 9950 16738.49 0 0 5269.5245 11.395076
+ 10000 16738.49 0 0 5269.5246 11.395075
+Loop time of 0.206235 on 4 procs for 10000 steps with 81 atoms
+
+Performance: 418940.303 tau/day, 48488.461 timesteps/s
+97.1% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.0026572 | 0.004187 | 0.0050838 | 1.5 | 2.03
+Neigh | 0.012115 | 0.012789 | 0.013634 | 0.5 | 6.20
+Comm | 0.084275 | 0.089969 | 0.095318 | 1.5 | 43.62
+Output | 0.0048559 | 0.0051559 | 0.0059836 | 0.7 | 2.50
+Modify | 0.077074 | 0.083586 | 0.088022 | 1.5 | 40.53
+Other | | 0.01055 | | | 5.11
+
+Nlocal: 20.25 ave 38 max 3 min
+Histogram: 1 0 1 0 0 0 1 0 0 1
+Nghost: 27.25 ave 48 max 13 min
+Histogram: 1 0 1 1 0 0 0 0 0 1
+Neighs: 0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 0
+Ave neighs/atom = 0
+Neighbor list builds = 998
+Dangerous builds = 997
+Total wall time: 0:00:00
diff --git a/examples/rigid/log.20Apr18.rigid.tnr.g++.1 b/examples/rigid/log.20Apr18.rigid.tnr.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..097fd132aa7c352d4ceac0735d1f9b455ec8e002
--- /dev/null
+++ b/examples/rigid/log.20Apr18.rigid.tnr.g++.1
@@ -0,0 +1,458 @@
+LAMMPS (20 Apr 2018)
+ using 1 OpenMP thread(s) per MPI task
+# Tethered nanorods
+
+atom_style molecular
+
+read_data data.rigid.tnr
+ orthogonal box = (-31.122 -31.122 -31.122) to (31.122 31.122 31.122)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 5600 atoms
+ scanning bonds ...
+ 1 = max bonds/atom
+ reading bonds ...
+ 1600 bonds
+ 2 = max # of 1-2 neighbors
+ 1 = max # of 1-3 neighbors
+ 1 = max # of 1-4 neighbors
+ 2 = max # of special neighbors
+
+# Specify bond parameters
+
+bond_style fene
+bond_coeff 1 30.0 1.5 1.0 1.0
+
+special_bonds fene
+ 2 = max # of 1-2 neighbors
+ 2 = max # of special neighbors
+
+# Specify initial velocities
+
+velocity all create 1.4 109345
+
+# Specify rigid components
+
+group rods type 2
+4000 atoms in group rods
+group tethers subtract all rods
+1600 atoms in group tethers
+
+neigh_modify exclude molecule/intra rods delay 0 every 1
+
+# Specify the pair potentials
+
+pair_style lj/cut 2.5
+pair_modify shift yes
+pair_coeff * * 1.0 1.0 1.122
+pair_coeff 2 2 1.0 1.0 2.5
+
+# Specify output
+
+thermo 100
+thermo_style custom step temp pe etotal press enthalpy lx ly lz pxx pyy pzz
+thermo_modify flush yes lost warn
+
+timestep 0.005
+
+fix 1 rods rigid molecule
+800 rigid bodies with 4000 atoms
+fix 2 tethers nve
+fix 3 all langevin 1.4 1.4 1.0 437624
+
+run 5000
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 45 45 45
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 7.769 | 7.769 | 7.769 Mbytes
+Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
+ 0 1.3963219 5.9478449 7.0445809 0.048565317 9.13595 62.244 62.244 62.244 0.0091983659 0.11850113 0.017996458
+ 100 1.3418512 5.9671777 7.0211299 0.025020362 8.0985822 62.244 62.244 62.244 0.02036076 0.038265078 0.016435248
+ 200 1.3730638 5.9750802 7.0535483 0.0053287535 7.2830205 62.244 62.244 62.244 -0.00054924195 0.0092396988 0.0072958036
+ 300 1.376262 5.9821642 7.0631443 0.0055536521 7.3023013 62.244 62.244 62.244 0.0033577704 0.0069111861 0.0063919998
+ 400 1.3782954 5.9983628 7.08094 0.0020507385 7.169251 62.244 62.244 62.244 -0.0060862717 0.0098998072 0.0023386801
+ 500 1.386863 6.0053312 7.0946377 -0.0009847031 7.0522334 62.244 62.244 62.244 -0.0038708372 0.0005697804 0.00034694745
+ 600 1.4069849 6.0035719 7.1086832 0.0047883912 7.3148858 62.244 62.244 62.244 0.001069365 0.0078059505 0.0054898581
+ 700 1.4423187 5.9982171 7.1310812 0.012141001 7.6539093 62.244 62.244 62.244 0.0094765272 0.011007593 0.015938883
+ 800 1.4303878 5.9968168 7.1203098 -0.00081349095 7.0852784 62.244 62.244 62.244 0.0011153812 0.00041597298 -0.0039718271
+ 900 1.4140538 5.9838168 7.0944803 0.00207609 7.183883 62.244 62.244 62.244 0.00043409671 0.0022778944 0.0035162788
+ 1000 1.3906567 5.988119 7.0804053 0.0022005856 7.1751692 62.244 62.244 62.244 0.0077268425 -0.0022042977 0.0010792119
+ 1100 1.3921992 5.9892203 7.0827181 0.0035041977 7.2336194 62.244 62.244 62.244 -0.0037576823 0.0040827951 0.01018748
+ 1200 1.3968803 5.9795846 7.0767592 -0.0031072146 6.9429532 62.244 62.244 62.244 -0.0077387449 0.0033056124 -0.0048885115
+ 1300 1.3755848 5.9739757 7.0544239 0.0092247106 7.4516677 62.244 62.244 62.244 0.0092788748 0.010737194 0.0076580625
+ 1400 1.3847985 5.9703631 7.0580481 0.0071703598 7.3668254 62.244 62.244 62.244 0.0080485848 0.012260474 0.001202021
+ 1500 1.4190051 5.956946 7.0714985 0.0035992903 7.2264948 62.244 62.244 62.244 -0.0055125437 0.01038369 0.0059267242
+ 1600 1.3980036 5.9671666 7.0652236 0.0061819851 7.3314385 62.244 62.244 62.244 0.0062429141 0.0035120077 0.0087910334
+ 1700 1.4276062 5.9610381 7.0823462 0.007832375 7.4196319 62.244 62.244 62.244 0.0083316819 0.0058394292 0.009326014
+ 1800 1.4112769 5.9630595 7.0715419 0.0068032101 7.3645087 62.244 62.244 62.244 0.0065502252 0.0062317255 0.0076276797
+ 1900 1.4276973 5.9489341 7.0703139 0.008397746 7.4319462 62.244 62.244 62.244 0.0148941 0.0032963108 0.0070028268
+ 2000 1.4056158 5.9564624 7.0604983 0.0090470732 7.4500926 62.244 62.244 62.244 0.011871718 0.0086681344 0.0066013673
+ 2100 1.3924778 5.9483611 7.0420778 0.0088893819 7.4248814 62.244 62.244 62.244 0.010247454 0.0097830093 0.0066376825
+ 2200 1.3760401 5.9435877 7.0243935 -0.0042972782 6.8393397 62.244 62.244 62.244 -0.0050064436 -0.0046216998 -0.0032636911
+ 2300 1.4191937 5.9334036 7.0481042 0.0047000032 7.2505006 62.244 62.244 62.244 0.0057709635 0.0044949165 0.0038341296
+ 2400 1.4213285 5.9472214 7.0635988 0.010197674 7.5027414 62.244 62.244 62.244 0.0083738261 0.0090537939 0.013165402
+ 2500 1.4153808 5.9421661 7.0538718 0.00015906308 7.0607216 62.244 62.244 62.244 0.0023516211 -0.0019814987 0.00010706678
+ 2600 1.4014223 5.9431386 7.0438807 0.0070733749 7.3484816 62.244 62.244 62.244 0.0054143871 0.010055843 0.0057498948
+ 2700 1.4138077 5.9369067 7.047377 0.0024268843 7.1518859 62.244 62.244 62.244 0.0052918436 0.0014960354 0.00049277379
+ 2800 1.432192 5.9347676 7.0596777 0.0077670448 7.3941501 62.244 62.244 62.244 0.012668421 0.0059113032 0.0047214106
+ 2900 1.3938659 5.921023 7.01583 0.0053751201 7.2472989 62.244 62.244 62.244 0.0020490372 0.0076566097 0.0064197134
+ 3000 1.390221 5.9205014 7.0124455 -0.0010750973 6.9661486 62.244 62.244 62.244 0.0019519817 -0.0041878875 -0.0009893861
+ 3100 1.4205722 5.9178284 7.0336117 0.0098735467 7.4587964 62.244 62.244 62.244 0.0040973349 0.012167268 0.013356037
+ 3200 1.398418 5.9150349 7.0134173 0.0061541837 7.278435 62.244 62.244 62.244 0.0067621825 0.011952562 -0.00025219321
+ 3300 1.4269859 5.9148727 7.0356937 0.006062387 7.2967584 62.244 62.244 62.244 0.012956233 -2.480748e-05 0.005255736
+ 3400 1.434286 5.9356705 7.0622253 0.0002731615 7.0739885 62.244 62.244 62.244 -0.00054959543 0.0052526331 -0.0038835532
+ 3500 1.4416808 5.9228153 7.0551783 0.0083383068 7.414251 62.244 62.244 62.244 0.0073994017 0.0030328023 0.014582716
+ 3600 1.4136063 5.9039442 7.0142562 0.0019711852 7.0991414 62.244 62.244 62.244 -0.00032317688 0.0035029725 0.0027337599
+ 3700 1.433382 5.91201 7.0378548 0.0071286927 7.3448378 62.244 62.244 62.244 0.0064768108 0.0046765006 0.010232767
+ 3800 1.3659481 5.9032872 6.9761663 -0.0054034056 6.7434793 62.244 62.244 62.244 -0.007394357 -0.0082833116 -0.00053254832
+ 3900 1.396322 5.9043001 7.0010362 0.005331024 7.2306062 62.244 62.244 62.244 0.0081855301 0.0048806234 0.0029269184
+ 4000 1.412548 5.906066 7.0155468 0.0028450132 7.1380616 62.244 62.244 62.244 0.0052588387 0.00072412871 0.0025520721
+ 4100 1.3943949 5.9040868 6.9993093 0.0058053193 7.2493039 62.244 62.244 62.244 0.0060583148 0.0024781972 0.0088794459
+ 4200 1.4249768 5.8906369 7.0098798 0.0030209006 7.1399689 62.244 62.244 62.244 0.0061742017 -0.0020795681 0.0049680681
+ 4300 1.3899827 5.8966327 6.9883897 0.0057278096 7.2350464 62.244 62.244 62.244 0.0049035059 0.0021868561 0.010093067
+ 4400 1.4414361 5.8986386 7.0308094 0.0050941357 7.2501783 62.244 62.244 62.244 0.0057971901 0.0037941986 0.0056910185
+ 4500 1.4093099 5.8922729 6.9992103 0.0012182325 7.0516711 62.244 62.244 62.244 0.0042896986 0.0014287789 -0.00206378
+ 4600 1.3779677 5.892894 6.9752138 0.002057623 7.0638213 62.244 62.244 62.244 0.0029271755 -0.0031752166 0.0064209102
+ 4700 1.4086418 5.9096898 7.0161024 -0.00052853259 6.9933422 62.244 62.244 62.244 -0.001862386 -0.0018129293 0.0020897176
+ 4800 1.4394 5.9146102 7.0451818 0.015326441 7.7051846 62.244 62.244 62.244 0.014754936 0.017967956 0.013256431
+ 4900 1.4496219 5.9074613 7.0460616 0.0075297868 7.370317 62.244 62.244 62.244 0.0092907193 0.0079794674 0.0053191736
+ 5000 1.4280291 5.9106136 7.032254 -0.0013249587 6.9751972 62.244 62.244 62.244 -0.0044875103 0.0020723667 -0.0015597324
+Loop time of 6.73744 on 1 procs for 5000 steps with 5600 atoms
+
+Performance: 320596.735 tau/day, 742.122 timesteps/s
+99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.52635 | 0.52635 | 0.52635 | 0.0 | 7.81
+Bond | 0.26628 | 0.26628 | 0.26628 | 0.0 | 3.95
+Neigh | 1.5927 | 1.5927 | 1.5927 | 0.0 | 23.64
+Comm | 0.16011 | 0.16011 | 0.16011 | 0.0 | 2.38
+Output | 0.0040634 | 0.0040634 | 0.0040634 | 0.0 | 0.06
+Modify | 4.0145 | 4.0145 | 4.0145 | 0.0 | 59.58
+Other | | 0.1735 | | | 2.57
+
+Nlocal: 5600 ave 5600 max 5600 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 1352 ave 1352 max 1352 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 5257 ave 5257 max 5257 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 5257
+Ave neighs/atom = 0.93875
+Ave special neighs/atom = 0.571429
+Neighbor list builds = 766
+Dangerous builds = 0
+
+# Replace fix rigid and fix langevin with new ones
+
+unfix 1
+unfix 3
+
+fix 3 tethers langevin 1.4 1.4 1.0 198450
+
+# Test different integrators for rods
+
+fix 1 rods rigid/nve molecule
+800 rigid bodies with 4000 atoms
+print "rigid/nve"
+rigid/nve
+run 1000
+Per MPI rank memory allocation (min/avg/max) = 7.77 | 7.77 | 7.77 Mbytes
+Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
+ 5000 1.4280291 5.9106136 7.032254 0.02814128 8.2441024 62.244 62.244 62.244 0.019873502 0.039656784 0.024893554
+ 5100 1.4435659 5.8998386 7.0336823 0.0063929319 7.3089813 62.244 62.244 62.244 0.0089837757 0.0052773116 0.0049177085
+ 5200 1.3970069 5.9117164 7.0089904 0.0065245686 7.289958 62.244 62.244 62.244 0.008502047 0.0043872479 0.0066844108
+ 5300 1.433167 5.8796669 7.0053428 0.0076478538 7.3346825 62.244 62.244 62.244 0.0061384889 0.0070193789 0.0097856935
+ 5400 1.4191626 5.8830864 6.9977626 0.0026371359 7.1113257 62.244 62.244 62.244 0.0024097043 -0.00082200506 0.0063237084
+ 5500 1.409376 5.8753367 6.982326 0.010180815 7.4207427 62.244 62.244 62.244 0.010429709 0.0081711083 0.011941628
+ 5600 1.4005678 5.882485 6.9825559 0.00036705268 6.9983623 62.244 62.244 62.244 -0.0034485466 0.0031079204 0.0014417843
+ 5700 1.4116833 5.8842566 6.9930582 0.00053413233 7.0160595 62.244 62.244 62.244 0.0016669624 -0.0030741941 0.0030096286
+ 5800 1.409035 5.894902 7.0016235 4.7080816e-05 7.003651 62.244 62.244 62.244 0.0018596854 -5.3937508e-05 -0.0016645054
+ 5900 1.4150353 5.8928576 7.004292 0.0063467985 7.2776043 62.244 62.244 62.244 0.0055755751 0.0090839847 0.0043808358
+ 6000 1.4374163 5.8778036 7.0068171 0.0031890481 7.1441472 62.244 62.244 62.244 0.0067647375 0.0015458579 0.0012565488
+Loop time of 1.41082 on 1 procs for 1000 steps with 5600 atoms
+
+Performance: 306205.780 tau/day, 708.810 timesteps/s
+99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.149 | 0.149 | 0.149 | 0.0 | 10.56
+Bond | 0.053873 | 0.053873 | 0.053873 | 0.0 | 3.82
+Neigh | 0.35532 | 0.35532 | 0.35532 | 0.0 | 25.19
+Comm | 0.032433 | 0.032433 | 0.032433 | 0.0 | 2.30
+Output | 0.00080752 | 0.00080752 | 0.00080752 | 0.0 | 0.06
+Modify | 0.78447 | 0.78447 | 0.78447 | 0.0 | 55.60
+Other | | 0.03491 | | | 2.47
+
+Nlocal: 5600 ave 5600 max 5600 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 1347 ave 1347 max 1347 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 5592 ave 5592 max 5592 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 5592
+Ave neighs/atom = 0.998571
+Ave special neighs/atom = 0.571429
+Neighbor list builds = 153
+Dangerous builds = 0
+unfix 1
+
+fix 1 rods rigid/nvt molecule temp 1.4 1.4 1.0
+800 rigid bodies with 4000 atoms
+print "rigid/nvt"
+rigid/nvt
+run 1000
+Per MPI rank memory allocation (min/avg/max) = 7.77 | 7.77 | 7.77 Mbytes
+Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
+ 6000 1.4374163 5.8778036 7.0068171 -0.0020672233 6.9177963 62.244 62.244 62.244 0.034504923 -0.030001164 -0.010705429
+ 6100 1.4393824 5.8852696 7.0158274 0.0055792227 7.2560855 62.244 62.244 62.244 0.0072602759 0.0074870643 0.0019903278
+ 6200 1.4265711 5.8853532 7.0058484 0.0019366613 7.0892468 62.244 62.244 62.244 -0.0035411799 0.0047319741 0.0046191897
+ 6300 1.4030198 5.8824874 6.9844843 0.0055760353 7.2246052 62.244 62.244 62.244 0.0031273033 0.0080002386 0.005600564
+ 6400 1.3592064 5.8924876 6.9600714 0.0051450348 7.1816321 62.244 62.244 62.244 0.0042848197 0.0044005693 0.0067497155
+ 6500 1.3946028 5.8798014 6.9751872 0.0051168754 7.1955353 62.244 62.244 62.244 0.0020473208 0.0038175566 0.0094857487
+ 6600 1.3652122 5.8985637 6.9708648 0.0065480579 7.2528439 62.244 62.244 62.244 0.0056940621 0.0062242398 0.0077258719
+ 6700 1.3808929 5.9047739 6.9893913 0.0074053719 7.308289 62.244 62.244 62.244 0.0049554161 0.012378296 0.0048824031
+ 6800 1.4140879 5.891133 7.0018233 0.001592636 7.070407 62.244 62.244 62.244 -9.4421917e-05 -0.00029455229 0.0051668821
+ 6900 1.4364121 5.8904988 7.0187235 0.00647853 7.2977086 62.244 62.244 62.244 0.0024458531 0.0073279625 0.0096617742
+ 7000 1.4370567 5.8900758 7.0188069 0.00098705898 7.0613127 62.244 62.244 62.244 0.0024436343 -0.0011032284 0.001620771
+Loop time of 1.44111 on 1 procs for 1000 steps with 5600 atoms
+
+Performance: 299769.942 tau/day, 693.912 timesteps/s
+99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.14928 | 0.14928 | 0.14928 | 0.0 | 10.36
+Bond | 0.053511 | 0.053511 | 0.053511 | 0.0 | 3.71
+Neigh | 0.35946 | 0.35946 | 0.35946 | 0.0 | 24.94
+Comm | 0.033026 | 0.033026 | 0.033026 | 0.0 | 2.29
+Output | 0.00081658 | 0.00081658 | 0.00081658 | 0.0 | 0.06
+Modify | 0.80995 | 0.80995 | 0.80995 | 0.0 | 56.20
+Other | | 0.03506 | | | 2.43
+
+Nlocal: 5600 ave 5600 max 5600 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 1351 ave 1351 max 1351 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 5541 ave 5541 max 5541 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 5541
+Ave neighs/atom = 0.989464
+Ave special neighs/atom = 0.571429
+Neighbor list builds = 153
+Dangerous builds = 0
+unfix 1
+
+compute myTemp all temp
+
+fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 iso 0.05 0.05 1.0 dilate all
+800 rigid bodies with 4000 atoms
+print "rigid/npt iso"
+rigid/npt iso
+fix_modify 1 temp myTemp
+
+run 1000
+Per MPI rank memory allocation (min/avg/max) = 7.77 | 7.77 | 7.77 Mbytes
+Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
+ 7000 1.4370567 5.8900758 7.0188069 -0.0033603557 6.8740999 62.244 62.244 62.244 -0.094745193 0.10894465 -0.024280521
+ 7100 1.485379 5.864626 7.0313116 0.018625962 7.6475425 57.008236 57.008236 57.008236 0.023222208 0.015549704 0.017105973
+ 7200 1.5367991 5.8157585 7.0228319 0.019179143 7.4580039 50.273593 50.273593 50.273593 0.019479917 0.008906575 0.029150938
+ 7300 1.5692285 5.785208 7.0177529 0.026450106 7.4560147 45.27218 45.27218 45.27218 0.029705272 0.019989987 0.029655059
+ 7400 1.5961415 5.7633541 7.0170377 0.049085262 7.6510208 41.665015 41.665015 41.665015 0.045248259 0.047932005 0.054075524
+ 7500 1.5805951 5.7223115 6.9637843 0.022024393 7.1962354 38.952791 38.952791 38.952791 0.017398546 0.0097043058 0.038970326
+ 7600 1.5679583 5.6928914 6.9244386 0.05023237 7.3717858 36.808633 36.808633 36.808633 0.029561593 0.080716323 0.040419195
+ 7700 1.5214637 5.661404 6.8564322 0.038992847 7.1614257 35.25044 35.25044 35.25044 0.013961981 0.064676103 0.038340457
+ 7800 1.5313649 5.6185256 6.8213307 0.053950562 7.1990319 33.971403 33.971403 33.971403 0.036690654 0.066107903 0.059053129
+ 7900 1.5272701 5.5732963 6.7728851 0.067896988 7.2131774 33.115109 33.115109 33.115109 0.046486851 0.073976177 0.083227936
+ 8000 1.4754162 5.5525858 6.7114461 0.036458901 6.9347086 32.48878 32.48878 32.48878 0.066065978 0.031260775 0.01204995
+Loop time of 3.09124 on 1 procs for 1000 steps with 5600 atoms
+
+Performance: 139749.554 tau/day, 323.494 timesteps/s
+99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.38334 | 0.38334 | 0.38334 | 0.0 | 12.40
+Bond | 0.079063 | 0.079063 | 0.079063 | 0.0 | 2.56
+Neigh | 1.3711 | 1.3711 | 1.3711 | 0.0 | 44.35
+Comm | 0.07249 | 0.07249 | 0.07249 | 0.0 | 2.35
+Output | 0.00079656 | 0.00079656 | 0.00079656 | 0.0 | 0.03
+Modify | 1.1412 | 1.1412 | 1.1412 | 0.0 | 36.92
+Other | | 0.04324 | | | 1.40
+
+Nlocal: 5600 ave 5600 max 5600 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 2922 ave 2922 max 2922 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 24639 ave 24639 max 24639 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 24639
+Ave neighs/atom = 4.39982
+Ave special neighs/atom = 0.571429
+Neighbor list builds = 335
+Dangerous builds = 0
+unfix 1
+
+fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 x 0.05 0.05 1.0 dilate all
+800 rigid bodies with 4000 atoms
+print "rigid/npt x"
+rigid/npt x
+run 1000
+Per MPI rank memory allocation (min/avg/max) = 7.784 | 7.784 | 7.784 Mbytes
+Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
+ 8000 1.4754162 5.5525858 6.7114461 -0.036273091 6.4893215 32.48878 32.48878 32.48878 -0.12886524 -0.13731772 0.15736368
+ 8100 1.4842494 5.5359706 6.701769 0.040754696 6.9494736 32.246136 32.48878 32.48878 0.0098547221 0.069850343 0.042559024
+ 8200 1.4385513 5.5252007 6.6551057 -0.0053954052 6.6228379 31.729684 32.48878 32.48878 0.029251386 -0.023427626 -0.022009975
+ 8300 1.4426011 5.5073818 6.6404676 0.034683453 6.8437384 31.093797 32.48878 32.48878 0.028287259 0.027455229 0.048307871
+ 8400 1.4194517 5.5015592 6.6164624 0.015869651 6.7074209 30.408624 32.48878 32.48878 0.020129982 0.00586219 0.021616782
+ 8500 1.4584335 5.4424151 6.5879365 0.025786252 6.7324275 29.728548 32.48878 32.48878 0.051564744 0.0046756434 0.021118368
+ 8600 1.4578973 5.4266016 6.5717019 0.061244725 6.9097759 29.286286 32.48878 32.48878 0.08652905 0.052448352 0.044756773
+ 8700 1.4158345 5.4199695 6.5320317 0.076133238 6.9466617 28.894001 32.48878 32.48878 0.078560655 0.077921379 0.071917679
+ 8800 1.4360707 5.3986549 6.5266116 0.05106059 6.7993343 28.337182 32.48878 32.48878 0.030158729 0.080651224 0.042371819
+ 8900 1.424778 5.386975 6.5060619 0.0023828771 6.5185272 27.75397 32.48878 32.48878 -0.026562751 0.0076340254 0.026077357
+ 9000 1.4273004 5.369067 6.490135 0.077698761 6.8879525 27.163833 32.48878 32.48878 0.056923916 0.050917329 0.12525504
+Loop time of 3.05599 on 1 procs for 1000 steps with 5600 atoms
+
+Performance: 141361.930 tau/day, 327.227 timesteps/s
+99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.60397 | 0.60397 | 0.60397 | 0.0 | 19.76
+Bond | 0.080384 | 0.080384 | 0.080384 | 0.0 | 2.63
+Neigh | 1.1078 | 1.1078 | 1.1078 | 0.0 | 36.25
+Comm | 0.057267 | 0.057267 | 0.057267 | 0.0 | 1.87
+Output | 0.0007937 | 0.0007937 | 0.0007937 | 0.0 | 0.03
+Modify | 1.1674 | 1.1674 | 1.1674 | 0.0 | 38.20
+Other | | 0.03837 | | | 1.26
+
+Nlocal: 5600 ave 5600 max 5600 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 3326 ave 3326 max 3326 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 31301 ave 31301 max 31301 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 31301
+Ave neighs/atom = 5.58946
+Ave special neighs/atom = 0.571429
+Neighbor list builds = 168
+Dangerous builds = 0
+unfix 1
+
+fix 1 rods rigid/nph molecule iso 0.05 0.05 1.0 dilate all
+800 rigid bodies with 4000 atoms
+print "rigid/nph iso"
+rigid/nph iso
+run 1000
+Per MPI rank memory allocation (min/avg/max) = 7.787 | 7.787 | 7.787 Mbytes
+Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
+ 9000 1.4273004 5.369067 6.490135 0.075024718 6.8742614 27.163833 32.48878 32.48878 0.020257355 0.083191009 0.12162579
+ 9100 1.425834 5.3711961 6.4911123 0.045582762 6.7236289 27.13015 32.448495 32.448495 0.047970965 0.045448278 0.043329042
+ 9200 1.4609827 5.3288319 6.4763555 0.072880923 6.8414166 26.96611 32.252298 32.252298 0.053774659 0.093193782 0.071674329
+ 9300 1.448717 5.3331013 6.4709909 0.048446002 6.7095138 26.811748 32.067676 32.067676 0.053340258 0.056657855 0.035339893
+ 9400 1.441683 5.326611 6.4589758 0.014571871 6.5288665 26.578822 31.789089 31.789089 0.043939432 -0.038654064 0.038430244
+ 9500 1.4651641 5.2943716 6.4451796 0.079668782 6.8205296 26.421077 31.600422 31.600422 0.10411792 0.075090335 0.059798087
+ 9600 1.4617024 5.2886327 6.4367216 0.01137432 6.4894218 26.274239 31.424799 31.424799 0.023318055 0.015516795 -0.0047118896
+ 9700 1.4381296 5.2798198 6.4093935 0.030371415 6.5484925 26.173039 31.303761 31.303761 0.05231569 0.025227191 0.013571362
+ 9800 1.4412744 5.2674085 6.3994523 0.076731911 6.7476559 26.092768 31.207754 31.207754 0.05712947 0.077029719 0.096036545
+ 9900 1.4427959 5.2666411 6.39988 0.034570225 6.5551479 26.003248 31.100686 31.100686 0.020955217 0.019879252 0.062876207
+ 10000 1.4337411 5.258442 6.3845688 0.011619021 6.4367617 26.004486 31.102166 31.102166 0.018666906 0.01076669 0.005423467
+Loop time of 3.23963 on 1 procs for 1000 steps with 5600 atoms
+
+Performance: 133348.758 tau/day, 308.678 timesteps/s
+99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.71266 | 0.71266 | 0.71266 | 0.0 | 22.00
+Bond | 0.0805 | 0.0805 | 0.0805 | 0.0 | 2.48
+Neigh | 1.2019 | 1.2019 | 1.2019 | 0.0 | 37.10
+Comm | 0.061646 | 0.061646 | 0.061646 | 0.0 | 1.90
+Output | 0.00080585 | 0.00080585 | 0.00080585 | 0.0 | 0.02
+Modify | 1.1436 | 1.1436 | 1.1436 | 0.0 | 35.30
+Other | | 0.03849 | | | 1.19
+
+Nlocal: 5600 ave 5600 max 5600 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 3617 ave 3617 max 3617 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 35834 ave 35834 max 35834 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 35834
+Ave neighs/atom = 6.39893
+Ave special neighs/atom = 0.571429
+Neighbor list builds = 162
+Dangerous builds = 0
+unfix 1
+
+fix 1 rods rigid/nph molecule x 0.05 0.05 1.0 y 0.05 0.05 1.0 couple xy dilate all
+800 rigid bodies with 4000 atoms
+print "rigid/nph xy couple"
+rigid/nph xy couple
+run 1000
+Per MPI rank memory allocation (min/avg/max) = 7.793 | 7.793 | 7.793 Mbytes
+Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
+ 10000 1.4337411 5.258442 6.3845688 0.26156311 7.559515 26.004486 31.102166 31.102166 0.31569183 0.56043401 -0.091436513
+ 10100 1.4450694 5.2429626 6.3779872 0.026397674 6.4966895 26.018016 31.118349 31.102166 0.012890725 0.035887426 0.030414871
+ 10200 1.4603735 5.2471262 6.3941713 0.041496848 6.5804213 25.993694 31.089259 31.102166 0.043043384 0.031851909 0.04959525
+ 10300 1.4434562 5.2268279 6.3605855 0.073867581 6.6874051 25.808018 30.867184 31.102166 0.049265569 0.084151743 0.08818543
+ 10400 1.4391471 5.209772 6.3401449 0.010656841 6.3865593 25.605881 30.625422 31.102166 -0.012411333 -0.014743822 0.059125677
+ 10500 1.4239127 5.2146206 6.3330277 0.08346505 6.689122 25.342982 30.310987 31.102166 0.15420896 0.040839126 0.055347067
+ 10600 1.4524651 5.1794989 6.3203324 -0.025909515 6.2120807 25.079294 29.995608 31.102166 -0.014573849 -0.056558124 -0.0065965719
+ 10700 1.4455577 5.1721256 6.3075337 0.084888991 6.6555495 24.842844 29.712806 31.102166 0.10063515 0.067972312 0.08605951
+ 10800 1.4598996 5.15251 6.2991829 0.11430526 6.7624231 24.700034 29.542001 31.102166 0.12408423 0.12316195 0.095669606
+ 10900 1.4149128 5.1641212 6.2754594 0.045495923 6.4584246 24.605124 29.428485 31.102166 0.10001213 0.053235051 -0.016759411
+ 11000 1.3909637 5.1566933 6.2492208 0.046382806 6.433354 24.446408 29.238657 31.102166 0.091440494 0.0046064525 0.043101472
+Loop time of 3.41971 on 1 procs for 1000 steps with 5600 atoms
+
+Performance: 126326.531 tau/day, 292.423 timesteps/s
+99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.78521 | 0.78521 | 0.78521 | 0.0 | 22.96
+Bond | 0.080655 | 0.080655 | 0.080655 | 0.0 | 2.36
+Neigh | 1.2846 | 1.2846 | 1.2846 | 0.0 | 37.57
+Comm | 0.064334 | 0.064334 | 0.064334 | 0.0 | 1.88
+Output | 0.00080228 | 0.00080228 | 0.00080228 | 0.0 | 0.02
+Modify | 1.1651 | 1.1651 | 1.1651 | 0.0 | 34.07
+Other | | 0.03903 | | | 1.14
+
+Nlocal: 5600 ave 5600 max 5600 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 3805 ave 3805 max 3805 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 40038 ave 40038 max 40038 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 40038
+Ave neighs/atom = 7.14964
+Ave special neighs/atom = 0.571429
+Neighbor list builds = 162
+Dangerous builds = 0
+
+Total wall time: 0:00:22
diff --git a/examples/rigid/log.20Apr18.rigid.tnr.g++.4 b/examples/rigid/log.20Apr18.rigid.tnr.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..28457f51ee4fef7fbc8db5d263e0abfa27bf8e61
--- /dev/null
+++ b/examples/rigid/log.20Apr18.rigid.tnr.g++.4
@@ -0,0 +1,458 @@
+LAMMPS (20 Apr 2018)
+ using 1 OpenMP thread(s) per MPI task
+# Tethered nanorods
+
+atom_style molecular
+
+read_data data.rigid.tnr
+ orthogonal box = (-31.122 -31.122 -31.122) to (31.122 31.122 31.122)
+ 1 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 5600 atoms
+ scanning bonds ...
+ 1 = max bonds/atom
+ reading bonds ...
+ 1600 bonds
+ 2 = max # of 1-2 neighbors
+ 1 = max # of 1-3 neighbors
+ 1 = max # of 1-4 neighbors
+ 2 = max # of special neighbors
+
+# Specify bond parameters
+
+bond_style fene
+bond_coeff 1 30.0 1.5 1.0 1.0
+
+special_bonds fene
+ 2 = max # of 1-2 neighbors
+ 2 = max # of special neighbors
+
+# Specify initial velocities
+
+velocity all create 1.4 109345
+
+# Specify rigid components
+
+group rods type 2
+4000 atoms in group rods
+group tethers subtract all rods
+1600 atoms in group tethers
+
+neigh_modify exclude molecule/intra rods delay 0 every 1
+
+# Specify the pair potentials
+
+pair_style lj/cut 2.5
+pair_modify shift yes
+pair_coeff * * 1.0 1.0 1.122
+pair_coeff 2 2 1.0 1.0 2.5
+
+# Specify output
+
+thermo 100
+thermo_style custom step temp pe etotal press enthalpy lx ly lz pxx pyy pzz
+thermo_modify flush yes lost warn
+
+timestep 0.005
+
+fix 1 rods rigid molecule
+800 rigid bodies with 4000 atoms
+fix 2 tethers nve
+fix 3 all langevin 1.4 1.4 1.0 437624
+
+run 5000
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 45 45 45
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 7.216 | 7.384 | 7.552 Mbytes
+Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
+ 0 1.3963219 5.9478449 7.0445809 0.048565317 9.13595 62.244 62.244 62.244 0.0091983659 0.11850113 0.017996458
+ 100 1.3999025 5.9707695 7.0703179 0.027293074 8.24564 62.244 62.244 62.244 0.017246307 0.04732529 0.017307624
+ 200 1.4245544 5.9878446 7.1067558 0.0072016369 7.41688 62.244 62.244 62.244 0.0071370801 0.0084066589 0.0060611719
+ 300 1.4212057 5.9942604 7.1105414 0.0023296933 7.210865 62.244 62.244 62.244 -0.0059197015 0.0040269953 0.008881786
+ 400 1.4030116 5.9953214 7.0973119 0.0055751834 7.3373961 62.244 62.244 62.244 -0.0026920847 0.013323321 0.0060943141
+ 500 1.4201338 5.9984777 7.1139168 -0.0018229523 7.035415 62.244 62.244 62.244 -0.0082217102 -0.00047319975 0.0032260529
+ 600 1.425173 5.9902537 7.1096508 0.013367744 7.6853062 62.244 62.244 62.244 0.012971415 0.016298595 0.010833222
+ 700 1.4181225 5.9840752 7.0979345 0.0014999758 7.1625279 62.244 62.244 62.244 -0.0015835387 0.0045967753 0.0014866907
+ 800 1.4084205 5.9778462 7.084085 0.0063728488 7.3585191 62.244 62.244 62.244 0.0036202744 0.005593586 0.0099046859
+ 900 1.3958301 5.9891019 7.0854517 0.0028974454 7.2102244 62.244 62.244 62.244 0.0087724642 0.0014508428 -0.001530971
+ 1000 1.3937374 5.9794855 7.0741916 0.0087158481 7.4495223 62.244 62.244 62.244 0.014424783 0.0034958881 0.0082268735
+ 1100 1.3729162 5.9916252 7.0699773 0.0030451966 7.2011127 62.244 62.244 62.244 0.00084635444 -0.00064448421 0.0089337195
+ 1200 1.4427374 5.9713589 7.1045519 0.0042680608 7.2883474 62.244 62.244 62.244 0.0030884628 0.0031576538 0.0065580658
+ 1300 1.3971469 5.9728674 7.0702514 0.0022809251 7.168475 62.244 62.244 62.244 0.00060902513 -0.00020572386 0.006439474
+ 1400 1.4194118 5.9672631 7.082135 0.012945844 7.6396221 62.244 62.244 62.244 0.0082418827 0.016256336 0.014339314
+ 1500 1.3866472 5.9728382 7.0619753 0.0010642438 7.1078049 62.244 62.244 62.244 0.0020316123 0.0020439035 -0.00088278431
+ 1600 1.4184955 5.9539591 7.0681113 0.0077605409 7.4023036 62.244 62.244 62.244 0.0033721722 0.0057827512 0.014126699
+ 1700 1.3612202 5.9676733 7.0368389 0.0001686213 7.0441002 62.244 62.244 62.244 0.0052525345 0.0007705269 -0.0055171975
+ 1800 1.3641041 5.9521837 7.0236144 0.0057884587 7.2728829 62.244 62.244 62.244 0.0038061044 0.0044032908 0.009155981
+ 1900 1.3594477 5.9646024 7.0323757 0.0044261926 7.2229809 62.244 62.244 62.244 0.0019417448 0.006871542 0.004465291
+ 2000 1.3776971 5.9431816 7.0252888 -0.0012460593 6.9716298 62.244 62.244 62.244 -0.0010913822 0.00098119435 -0.0036279901
+ 2100 1.3986245 5.9509735 7.0495181 0.007520633 7.3733792 62.244 62.244 62.244 0.008359824 0.0075919773 0.0066100978
+ 2200 1.4033594 5.9548158 7.0570794 0.0016804284 7.1294438 62.244 62.244 62.244 -0.001842641 0.0032876741 0.0035962521
+ 2300 1.4048926 5.9444129 7.0478808 0.0062444035 7.3167836 62.244 62.244 62.244 0.004383569 0.0065720464 0.007777595
+ 2400 1.4044043 5.9370822 7.0401666 0.0034562836 7.1890046 62.244 62.244 62.244 0.0068959298 0.0041111713 -0.00063825028
+ 2500 1.4200762 5.9359254 7.0513193 0.002831965 7.1732722 62.244 62.244 62.244 -0.00030414188 0.0039571831 0.0048428539
+ 2600 1.3876469 5.9249124 7.0148347 -0.0017777223 6.9382806 62.244 62.244 62.244 -0.00047616388 -0.0025484917 -0.0023085112
+ 2700 1.4099941 5.916763 7.0242378 0.0070716262 7.3287634 62.244 62.244 62.244 0.012628756 0.0053812867 0.0032048357
+ 2800 1.4444643 5.9283432 7.0628925 0.0019400019 7.1464348 62.244 62.244 62.244 0.0014895075 0.0046367395 -0.0003062412
+ 2900 1.3902832 5.9152516 7.0072446 -0.0021662211 6.9139606 62.244 62.244 62.244 -0.0012374413 -0.00056403267 -0.0046971892
+ 3000 1.3711706 5.922146 6.999127 0.011101505 7.4771914 62.244 62.244 62.244 0.011063833 0.012093025 0.010147658
+ 3100 1.3569137 5.9171753 6.9829583 -0.0028266781 6.861233 62.244 62.244 62.244 -0.0069507246 0.001008439 -0.0025377485
+ 3200 1.4004275 5.905939 7.0058998 0.005439464 7.2401395 62.244 62.244 62.244 0.010352181 0.0057594129 0.00020679783
+ 3300 1.3641217 5.9145275 6.985972 -0.0027212797 6.8687855 62.244 62.244 62.244 -0.00065933477 -0.0057712994 -0.0017332048
+ 3400 1.3868722 5.9059546 6.9952684 0.0092591181 7.3939939 62.244 62.244 62.244 0.010690872 0.01075251 0.0063339724
+ 3500 1.3939168 5.8992292 6.9940762 0.0074340103 7.3142071 62.244 62.244 62.244 0.010137319 0.0044252681 0.0077394433
+ 3600 1.3982507 5.921946 7.020197 0.0056794467 7.2647712 62.244 62.244 62.244 0.0023367139 0.0080592038 0.0066424225
+ 3700 1.4019908 5.9059954 7.007184 0.0065915246 7.291035 62.244 62.244 62.244 0.0049554227 0.010827006 0.0039921455
+ 3800 1.3960735 5.9020788 6.9986197 0.0027763543 7.1181779 62.244 62.244 62.244 -0.0015907599 0.0025861989 0.007333624
+ 3900 1.4352827 5.8986213 7.025959 0.0034983366 7.1766079 62.244 62.244 62.244 0.0030418079 0.002773833 0.0046793689
+ 4000 1.4121839 5.9079032 7.017098 0.0050464926 7.2344152 62.244 62.244 62.244 0.0045546986 0.0064116168 0.0041731626
+ 4100 1.3989613 5.9082377 7.0070468 0.00042898744 7.0255203 62.244 62.244 62.244 0.0025736361 0.0025182434 -0.0038049172
+ 4200 1.3998851 5.8998106 6.9993454 0.0042770066 7.1835262 62.244 62.244 62.244 0.0013728904 0.0064694548 0.0049886746
+ 4300 1.4076016 5.9044534 7.0100491 0.0066777871 7.2976147 62.244 62.244 62.244 0.0073579039 0.0048129651 0.0078624924
+ 4400 1.3948857 5.9101851 7.0057931 0.0013429373 7.063624 62.244 62.244 62.244 -0.00084288143 0.0061856571 -0.0013139638
+ 4500 1.4356157 5.8855608 7.01316 -0.0013707942 6.9541295 62.244 62.244 62.244 -0.0018523205 -0.0050195956 0.0027595334
+ 4600 1.4148397 5.8957564 7.0070372 0.0072212968 7.318008 62.244 62.244 62.244 0.011376867 0.0074399971 0.0028470263
+ 4700 1.3695106 5.8936708 6.969348 0.0017509017 7.0447471 62.244 62.244 62.244 -0.0061975951 0.0044076775 0.0070426225
+ 4800 1.4142735 5.8887578 6.9995939 0.0081923232 7.35238 62.244 62.244 62.244 0.013343877 0.0054560473 0.0057770449
+ 4900 1.4300042 5.8867398 7.0099315 0.0070875112 7.3151411 62.244 62.244 62.244 0.0080416381 0.0042409901 0.0089799056
+ 5000 1.4286039 5.8964609 7.0185527 -0.003158533 6.8825368 62.244 62.244 62.244 0.0024975808 -0.0097503027 -0.0022228771
+Loop time of 3.4608 on 4 procs for 5000 steps with 5600 atoms
+
+Performance: 624133.913 tau/day, 1444.754 timesteps/s
+98.0% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.083226 | 0.13336 | 0.18611 | 13.0 | 3.85
+Bond | 0.045169 | 0.066142 | 0.087486 | 7.8 | 1.91
+Neigh | 0.57772 | 0.57997 | 0.58211 | 0.3 | 16.76
+Comm | 0.19402 | 0.26217 | 0.32776 | 12.2 | 7.58
+Output | 0.0027087 | 0.0035715 | 0.0041978 | 0.9 | 0.10
+Modify | 2.1223 | 2.2156 | 2.2842 | 4.2 | 64.02
+Other | | 0.2 | | | 5.78
+
+Nlocal: 1400 ave 1844 max 907 min
+Histogram: 1 1 0 0 0 0 0 0 0 2
+Nghost: 642 ave 714 max 581 min
+Histogram: 1 1 0 0 0 0 1 0 0 1
+Neighs: 1307.25 ave 1883 max 682 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+
+Total # of neighbors = 5229
+Ave neighs/atom = 0.93375
+Ave special neighs/atom = 0.571429
+Neighbor list builds = 762
+Dangerous builds = 0
+
+# Replace fix rigid and fix langevin with new ones
+
+unfix 1
+unfix 3
+
+fix 3 tethers langevin 1.4 1.4 1.0 198450
+
+# Test different integrators for rods
+
+fix 1 rods rigid/nve molecule
+800 rigid bodies with 4000 atoms
+print "rigid/nve"
+rigid/nve
+run 1000
+Per MPI rank memory allocation (min/avg/max) = 7.217 | 7.395 | 7.573 Mbytes
+Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
+ 5000 1.4286039 5.8964609 7.0185527 -0.017900244 6.2477142 62.244 62.244 62.244 -0.017934885 -0.027283526 -0.0084823215
+ 5100 1.4251274 5.887521 7.0068821 0.0066290394 7.2923486 62.244 62.244 62.244 0.0033173534 0.0056467845 0.01092298
+ 5200 1.4246222 5.8928547 7.0118192 -0.00025763331 7.0007247 62.244 62.244 62.244 -0.001891953 -0.0031121381 0.0042311911
+ 5300 1.3905023 5.9024119 6.994577 0.0026824588 7.1100918 62.244 62.244 62.244 0.003106008 0.0040692376 0.00087213068
+ 5400 1.4139617 5.8906493 7.0012405 0.003175173 7.137973 62.244 62.244 62.244 0.0034546577 0.003858524 0.0022123373
+ 5500 1.4160473 5.8891813 7.0014106 0.0032907848 7.1431217 62.244 62.244 62.244 0.0014909385 0.0067546452 0.0016267707
+ 5600 1.4185962 5.8932473 7.0074786 0.013015823 7.5679792 62.244 62.244 62.244 0.011297248 0.011426835 0.016323387
+ 5700 1.4115847 5.892193 7.0009171 0.0080660065 7.3482637 62.244 62.244 62.244 0.0096534077 0.004127271 0.010417341
+ 5800 1.3920238 5.8874957 6.9808558 0.0087013878 7.3555639 62.244 62.244 62.244 0.0070865796 0.0093328615 0.0096847223
+ 5900 1.389416 5.8996657 6.9909775 0.0053218583 7.2201528 62.244 62.244 62.244 0.0050547275 0.0054113274 0.0054995198
+ 6000 1.4079053 5.8795437 6.9853779 0.0066005053 7.2696156 62.244 62.244 62.244 0.0087434104 0.0013589366 0.0096991689
+Loop time of 0.793224 on 4 procs for 1000 steps with 5600 atoms
+
+Performance: 544612.641 tau/day, 1260.677 timesteps/s
+98.6% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.018101 | 0.036068 | 0.051689 | 7.6 | 4.55
+Bond | 0.0083735 | 0.013206 | 0.017318 | 3.6 | 1.66
+Neigh | 0.12864 | 0.1293 | 0.13002 | 0.1 | 16.30
+Comm | 0.037184 | 0.056407 | 0.077999 | 7.4 | 7.11
+Output | 0.00048971 | 0.00072509 | 0.00083923 | 0.0 | 0.09
+Modify | 0.49526 | 0.51293 | 0.52997 | 2.2 | 64.66
+Other | | 0.04459 | | | 5.62
+
+Nlocal: 1400 ave 1844 max 884 min
+Histogram: 1 1 0 0 0 0 0 0 0 2
+Nghost: 713.5 ave 818 max 656 min
+Histogram: 1 1 1 0 0 0 0 0 0 1
+Neighs: 1315 ave 1956 max 573 min
+Histogram: 1 0 1 0 0 0 0 0 0 2
+
+Total # of neighbors = 5260
+Ave neighs/atom = 0.939286
+Ave special neighs/atom = 0.571429
+Neighbor list builds = 156
+Dangerous builds = 0
+unfix 1
+
+fix 1 rods rigid/nvt molecule temp 1.4 1.4 1.0
+800 rigid bodies with 4000 atoms
+print "rigid/nvt"
+rigid/nvt
+run 1000
+Per MPI rank memory allocation (min/avg/max) = 7.217 | 7.395 | 7.573 Mbytes
+Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
+ 6000 1.4079053 5.8795437 6.9853779 0.010184208 7.4239406 62.244 62.244 62.244 0.0015995549 0.064769849 -0.035816779
+ 6100 1.4031886 5.8721732 6.9743027 0.0039601 7.1448365 62.244 62.244 62.244 0.0019177243 0.0048575488 0.005105027
+ 6200 1.4078378 5.8813987 6.9871798 -0.0019043091 6.9051745 62.244 62.244 62.244 -0.0012543967 -0.0035545317 -0.00090399881
+ 6300 1.3898748 5.8818577 6.97353 0.0050781011 7.1922083 62.244 62.244 62.244 0.0037642013 0.0035169519 0.0079531499
+ 6400 1.3901345 5.8620878 6.953964 -0.0013161864 6.897285 62.244 62.244 62.244 0.0024166375 -0.0023907165 -0.0039744801
+ 6500 1.3990792 5.8647534 6.9636551 0.0025190902 7.0721348 62.244 62.244 62.244 0.003080505 -0.00072200043 0.0051987659
+ 6600 1.3802747 5.8639204 6.9480523 0.0030906745 7.0811461 62.244 62.244 62.244 0.0041979458 0.0059358092 -0.00086173155
+ 6700 1.392968 5.8692368 6.9633385 0.00060394401 6.9893462 62.244 62.244 62.244 0.0037955666 0.00058857296 -0.0025723075
+ 6800 1.4139599 5.8777321 6.9883218 0.0064457022 7.2658932 62.244 62.244 62.244 0.0066202313 0.0077537688 0.0049631066
+ 6900 1.3913822 5.8914016 6.9842578 0.0012411779 7.0377066 62.244 62.244 62.244 -0.0029791199 0.0027656154 0.0039370381
+ 7000 1.4203244 5.8676225 6.9832112 0.0053040447 7.2116194 62.244 62.244 62.244 0.0024159021 0.0053958945 0.0081003375
+Loop time of 0.812983 on 4 procs for 1000 steps with 5600 atoms
+
+Performance: 531376.713 tau/day, 1230.039 timesteps/s
+98.2% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.020489 | 0.038507 | 0.054352 | 7.9 | 4.74
+Bond | 0.0086164 | 0.013153 | 0.017908 | 3.5 | 1.62
+Neigh | 0.13205 | 0.13275 | 0.13353 | 0.1 | 16.33
+Comm | 0.039251 | 0.05774 | 0.079146 | 7.7 | 7.10
+Output | 0.00057149 | 0.00076026 | 0.00087905 | 0.0 | 0.09
+Modify | 0.51332 | 0.52873 | 0.54512 | 2.1 | 65.04
+Other | | 0.04134 | | | 5.09
+
+Nlocal: 1400 ave 1861 max 953 min
+Histogram: 2 0 0 0 0 0 0 0 1 1
+Nghost: 732.5 ave 799 max 634 min
+Histogram: 1 0 0 0 0 1 0 0 1 1
+Neighs: 1478.5 ave 2087 max 852 min
+Histogram: 1 1 0 0 0 0 0 0 0 2
+
+Total # of neighbors = 5914
+Ave neighs/atom = 1.05607
+Ave special neighs/atom = 0.571429
+Neighbor list builds = 154
+Dangerous builds = 0
+unfix 1
+
+compute myTemp all temp
+
+fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 iso 0.05 0.05 1.0 dilate all
+800 rigid bodies with 4000 atoms
+print "rigid/npt iso"
+rigid/npt iso
+fix_modify 1 temp myTemp
+
+run 1000
+Per MPI rank memory allocation (min/avg/max) = 7.217 | 7.395 | 7.573 Mbytes
+Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
+ 7000 1.4203244 5.8676225 6.9832112 -0.040722281 5.2295869 62.244 62.244 62.244 -0.12474488 0.041369653 -0.038791619
+ 7100 1.4820526 5.8454198 7.0094927 0.013935005 7.4687465 56.934813 56.934813 56.934813 0.011753675 0.011015866 0.019035475
+ 7200 1.5504398 5.8024995 7.0202869 0.023075447 7.5454178 50.323226 50.323226 50.323226 0.02128889 0.024383628 0.023553823
+ 7300 1.5422614 5.7803177 6.9916814 0.022398755 7.3670099 45.442117 45.442117 45.442117 0.011815608 0.027421849 0.027958808
+ 7400 1.5762224 5.7500188 6.988057 0.044637382 7.5673845 41.732187 41.732187 41.732187 0.045858714 0.035776277 0.052277154
+ 7500 1.5734284 5.7222605 6.9581042 0.029862564 7.2743396 38.996336 38.996336 38.996336 0.024440229 0.034455527 0.030691934
+ 7600 1.5572312 5.6929606 6.9160823 0.050216724 7.366563 36.898208 36.898208 36.898208 0.059366814 0.056376093 0.034907266
+ 7700 1.5225653 5.659289 6.8551824 0.042054552 7.1814902 35.15611 35.15611 35.15611 0.043735305 0.039349247 0.043079104
+ 7800 1.5081978 5.629903 6.8145116 0.057013188 7.2106251 33.885255 33.885255 33.885255 0.055017894 0.053733429 0.062288242
+ 7900 1.4721367 5.5821237 6.7384082 0.067262555 7.1645957 32.860322 32.860322 32.860322 0.097134972 0.066643481 0.03800921
+ 8000 1.4710105 5.5302806 6.6856805 0.054118027 7.0029681 32.020862 32.020862 32.020862 0.039052412 0.059044234 0.064257435
+Loop time of 1.47728 on 4 procs for 1000 steps with 5600 atoms
+
+Performance: 292430.022 tau/day, 676.921 timesteps/s
+98.1% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.064968 | 0.10073 | 0.1395 | 10.5 | 6.82
+Bond | 0.014031 | 0.019927 | 0.02572 | 3.7 | 1.35
+Neigh | 0.52043 | 0.52145 | 0.52214 | 0.1 | 35.30
+Comm | 0.069327 | 0.11344 | 0.15499 | 11.3 | 7.68
+Output | 0.00045276 | 0.00050163 | 0.00058174 | 0.0 | 0.03
+Modify | 0.65598 | 0.67559 | 0.69898 | 2.4 | 45.73
+Other | | 0.04563 | | | 3.09
+
+Nlocal: 1400 ave 1711 max 1074 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Nghost: 1617 ave 1748 max 1514 min
+Histogram: 1 0 0 2 0 0 0 0 0 1
+Neighs: 6221.75 ave 8875 max 3829 min
+Histogram: 2 0 0 0 0 0 0 0 1 1
+
+Total # of neighbors = 24887
+Ave neighs/atom = 4.44411
+Ave special neighs/atom = 0.571429
+Neighbor list builds = 340
+Dangerous builds = 0
+unfix 1
+
+fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 x 0.05 0.05 1.0 dilate all
+800 rigid bodies with 4000 atoms
+print "rigid/npt x"
+rigid/npt x
+run 1000
+Per MPI rank memory allocation (min/avg/max) = 7.227 | 7.408 | 7.596 Mbytes
+Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
+ 8000 1.4710105 5.5302806 6.6856805 0.19181859 7.81029 32.020862 32.020862 32.020862 0.26866704 0.14123342 0.16555531
+ 8100 1.47531 5.5300767 6.6888537 0.072844262 7.1138998 31.868578 32.020862 32.020862 0.090224787 0.062332105 0.065975895
+ 8200 1.448408 5.51143 6.6490768 0.069870568 7.0519422 31.491082 32.020862 32.020862 0.087940256 0.058037199 0.063634249
+ 8300 1.4057002 5.4923673 6.5964694 0.065508742 6.9688194 31.043742 32.020862 32.020862 0.079268242 0.048811269 0.068446714
+ 8400 1.3991297 5.4626242 6.5615657 -0.017027709 6.4660067 30.650474 32.020862 32.020862 0.0088006578 -0.001632039 -0.058251747
+ 8500 1.4126457 5.4676374 6.5771949 0.012615987 6.6471389 30.279686 32.020862 32.020862 0.010145607 0.017449486 0.010252867
+ 8600 1.4250925 5.4367644 6.5560982 0.057260287 6.8682646 29.775194 32.020862 32.020862 0.05660339 0.10551068 0.0096667873
+ 8700 1.4259617 5.431439 6.5514555 0.060058224 6.8743509 29.36374 32.020862 32.020862 0.059243843 0.040552126 0.080378702
+ 8800 1.4336545 5.3949149 6.5209738 0.052324111 6.7965365 28.763424 32.020862 32.020862 0.02607362 0.067534725 0.063363987
+ 8900 1.4228767 5.3718196 6.489413 0.04039784 6.6975045 28.133143 32.020862 32.020862 0.038493401 0.059136317 0.023563801
+ 9000 1.3840335 5.3851579 6.4722421 0.055356171 6.7513156 27.534332 32.020862 32.020862 0.067391117 0.061540537 0.03713686
+Loop time of 1.41644 on 4 procs for 1000 steps with 5600 atoms
+
+Performance: 304989.819 tau/day, 705.995 timesteps/s
+98.1% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.111 | 0.15928 | 0.20768 | 11.1 | 11.25
+Bond | 0.014816 | 0.020169 | 0.024592 | 3.1 | 1.42
+Neigh | 0.40146 | 0.40175 | 0.40221 | 0.0 | 28.36
+Comm | 0.063586 | 0.11635 | 0.16698 | 14.1 | 8.21
+Output | 0.00045538 | 0.00050312 | 0.00063586 | 0.0 | 0.04
+Modify | 0.66405 | 0.67875 | 0.69575 | 1.6 | 47.92
+Other | | 0.03963 | | | 2.80
+
+Nlocal: 1400 ave 1641 max 1120 min
+Histogram: 1 0 1 0 0 0 0 0 0 2
+Nghost: 1593.5 ave 1674 max 1480 min
+Histogram: 1 0 0 1 0 0 0 0 0 2
+Neighs: 7766.25 ave 10004 max 5618 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+
+Total # of neighbors = 31065
+Ave neighs/atom = 5.54732
+Ave special neighs/atom = 0.571429
+Neighbor list builds = 168
+Dangerous builds = 0
+unfix 1
+
+fix 1 rods rigid/nph molecule iso 0.05 0.05 1.0 dilate all
+800 rigid bodies with 4000 atoms
+print "rigid/nph iso"
+rigid/nph iso
+run 1000
+Per MPI rank memory allocation (min/avg/max) = 7.228 | 7.409 | 7.596 Mbytes
+Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
+ 9000 1.3840335 5.3851579 6.4722421 0.16503405 7.3042475 27.534332 32.020862 32.020862 0.18505216 0.10781406 0.20223595
+ 9100 1.3884253 5.3614209 6.4519546 -0.00091586458 6.4474179 27.373411 31.83372 31.83372 0.022761165 -0.0041100422 -0.021398716
+ 9200 1.420492 5.3303864 6.4461068 0.059143817 6.7274082 27.005021 31.405303 31.405303 0.083033013 0.062389471 0.032008967
+ 9300 1.4715513 5.2993502 6.4551749 -0.0012173753 6.4496031 26.66115 31.005402 31.005402 3.6757409e-05 -0.035942133 0.03225325
+ 9400 1.446323 5.2997487 6.4357579 0.089723486 6.8324557 26.355721 30.650205 30.650205 0.074549411 0.091827859 0.10279319
+ 9500 1.4429552 5.2778071 6.4111711 0.074185245 6.7328342 26.184941 30.451597 30.451597 0.081909739 0.072238574 0.068407422
+ 9600 1.4570864 5.2601352 6.4045984 0.0580315 6.6544318 26.122769 30.379295 30.379295 0.060115487 0.027228888 0.086750125
+ 9700 1.4421488 5.2741205 6.4068511 0.044711738 6.5981759 26.069954 30.317874 30.317874 0.093367845 0.025219144 0.015548226
+ 9800 1.4305027 5.2831767 6.4067599 0.064007051 6.6787519 26.009567 30.247648 30.247648 0.1207317 0.021857174 0.049432283
+ 9900 1.4457473 5.2513943 6.3869514 0.016264617 6.4551575 25.895064 30.114487 30.114487 0.055652525 0.015908352 -0.022767026
+ 10000 1.4739193 5.2108898 6.3685744 0.066079547 6.6416503 25.768894 29.967759 29.967759 0.059174033 0.048716715 0.090347892
+Loop time of 1.47405 on 4 procs for 1000 steps with 5600 atoms
+
+Performance: 293069.938 tau/day, 678.403 timesteps/s
+98.3% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.14109 | 0.19261 | 0.2429 | 10.7 | 13.07
+Bond | 0.015511 | 0.020164 | 0.023957 | 2.5 | 1.37
+Neigh | 0.43698 | 0.43723 | 0.43759 | 0.0 | 29.66
+Comm | 0.064379 | 0.1184 | 0.17429 | 14.5 | 8.03
+Output | 0.00053048 | 0.00056964 | 0.00067139 | 0.0 | 0.04
+Modify | 0.65413 | 0.66598 | 0.68039 | 1.3 | 45.18
+Other | | 0.0391 | | | 2.65
+
+Nlocal: 1400 ave 1629 max 1159 min
+Histogram: 1 1 0 0 0 0 0 0 0 2
+Nghost: 1760.25 ave 1871 max 1635 min
+Histogram: 1 0 0 1 0 0 0 1 0 1
+Neighs: 9467.75 ave 11967 max 6712 min
+Histogram: 1 1 0 0 0 0 0 0 0 2
+
+Total # of neighbors = 37871
+Ave neighs/atom = 6.76268
+Ave special neighs/atom = 0.571429
+Neighbor list builds = 163
+Dangerous builds = 0
+unfix 1
+
+fix 1 rods rigid/nph molecule x 0.05 0.05 1.0 y 0.05 0.05 1.0 couple xy dilate all
+800 rigid bodies with 4000 atoms
+print "rigid/nph xy couple"
+rigid/nph xy couple
+run 1000
+Per MPI rank memory allocation (min/avg/max) = 7.229 | 7.413 | 7.597 Mbytes
+Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
+ 10000 1.4739193 5.2108898 6.3685744 0.15675952 7.0163882 25.768894 29.967759 29.967759 0.15485552 -0.045372029 0.36079506
+ 10100 1.450711 5.2108741 6.3503298 0.0083383764 6.3849239 25.819477 30.026584 29.967759 0.0025039775 -0.0028716599 0.025382812
+ 10200 1.4627819 5.2187046 6.3676414 0.031215755 6.4961258 25.717327 29.907789 29.967759 0.04657158 0.0023172248 0.044758461
+ 10300 1.4689915 5.2231223 6.3769364 0.094530779 6.7645053 25.667024 29.84929 29.967759 0.10402187 0.089461211 0.090109255
+ 10400 1.465366 5.211321 6.3622875 0.057765151 6.5976168 25.585426 29.754396 29.967759 0.025724468 0.03148259 0.1160884
+ 10500 1.4206144 5.2096595 6.325476 0.029618225 6.4439115 25.348314 29.478648 29.967759 0.016757876 -0.021974627 0.094071428
+ 10600 1.4490516 5.1686358 6.3067882 0.10186675 6.705618 25.082174 29.169143 29.967759 0.13985672 0.13649813 0.029245401
+ 10700 1.42637 5.1516578 6.271995 0.12577606 6.7554051 24.851151 28.900476 29.967759 0.099699897 0.11678127 0.16084703
+ 10800 1.4675204 5.1334029 6.2860615 0.054610838 6.494291 24.752517 28.78577 29.967759 0.018006539 0.090588468 0.055237507
+ 10900 1.4312627 5.1332052 6.2573854 -0.0020120377 6.2496947 24.782913 28.821119 29.967759 -0.0035770106 0.047436898 -0.049896
+ 11000 1.3986074 5.1272068 6.225738 0.045641244 6.3993661 24.72401 28.752618 29.967759 0.052336235 0.073561738 0.011025759
+Loop time of 1.50406 on 4 procs for 1000 steps with 5600 atoms
+
+Performance: 287222.965 tau/day, 664.868 timesteps/s
+98.3% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.16856 | 0.21287 | 0.26569 | 9.4 | 14.15
+Bond | 0.016815 | 0.020397 | 0.023304 | 1.9 | 1.36
+Neigh | 0.44152 | 0.44161 | 0.44172 | 0.0 | 29.36
+Comm | 0.067729 | 0.1232 | 0.16886 | 13.0 | 8.19
+Output | 0.00045419 | 0.00048572 | 0.0005734 | 0.0 | 0.03
+Modify | 0.6568 | 0.66799 | 0.6841 | 1.3 | 44.41
+Other | | 0.0375 | | | 2.49
+
+Nlocal: 1400 ave 1605 max 1229 min
+Histogram: 1 1 0 0 0 0 0 1 0 1
+Nghost: 1859 ave 1964 max 1718 min
+Histogram: 1 0 0 0 0 1 0 1 0 1
+Neighs: 10208.2 ave 13091 max 7670 min
+Histogram: 1 1 0 0 0 0 1 0 0 1
+
+Total # of neighbors = 40833
+Ave neighs/atom = 7.29161
+Ave special neighs/atom = 0.571429
+Neighbor list builds = 160
+Dangerous builds = 0
+
+Total wall time: 0:00:10
diff --git a/examples/rigid/log.5Oct16.rigid.poems.g++.1 b/examples/rigid/log.5Oct16.rigid.poems.g++.1
deleted file mode 100644
index 8b5e47c00a078b92f4a66c0fb0a4cf30229c1949..0000000000000000000000000000000000000000
--- a/examples/rigid/log.5Oct16.rigid.poems.g++.1
+++ /dev/null
@@ -1,332 +0,0 @@
-LAMMPS (5 Oct 2016)
-# Simple rigid body system
-
-units lj
-atom_style atomic
-
-pair_style lj/cut 2.5
-
-read_data data.rigid
- orthogonal box = (-12 -12 -12) to (12 12 12)
- 1 by 1 by 1 MPI processor grid
- reading atoms ...
- 81 atoms
-
-velocity all create 100.0 4928459
-
-# unconnected bodies
-
-#group clump1 id <> 1 9
-#group clump2 id <> 10 18
-#group clump3 id <> 19 27
-#group clump4 id <> 28 36
-#group clump5 id <> 37 45
-#group clump6 id <> 46 54
-#group clump7 id <> 55 63
-#group clump8 id <> 64 72
-#group clump9 id <> 73 81
-
-#fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
-
-# 1 chain of connected bodies
-
-group clump1 id <> 1 9
-9 atoms in group clump1
-group clump2 id <> 9 18
-10 atoms in group clump2
-group clump3 id <> 18 27
-10 atoms in group clump3
-group clump4 id <> 27 36
-10 atoms in group clump4
-group clump5 id <> 36 45
-10 atoms in group clump5
-group clump6 id <> 45 54
-10 atoms in group clump6
-group clump7 id <> 54 63
-10 atoms in group clump7
-group clump8 id <> 63 72
-10 atoms in group clump8
-group clump9 id <> 72 81
-10 atoms in group clump9
-
-fix 1 all poems group clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
-1 clusters, 9 bodies, 8 joints, 81 atoms
-
-# 2 chains of connected bodies
-
-#group clump1 id <> 1 9
-#group clump2 id <> 9 18
-#group clump3 id <> 18 27
-#group clump4 id <> 27 36
-#group clump5 id <> 37 45
-#group clump6 id <> 45 54
-#group clump7 id <> 54 63
-#group clump8 id <> 63 72
-#group clump9 id <> 72 81
-
-#fix 1 all poems group clump1 clump2 clump3 clump4
-#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
-
-neigh_modify exclude group clump1 clump1
-neigh_modify exclude group clump2 clump2
-neigh_modify exclude group clump3 clump3
-neigh_modify exclude group clump4 clump4
-neigh_modify exclude group clump5 clump5
-neigh_modify exclude group clump6 clump6
-neigh_modify exclude group clump7 clump7
-neigh_modify exclude group clump8 clump8
-neigh_modify exclude group clump9 clump9
-
-thermo 100
-
-#dump 1 all atom 50 dump.rigid.poems
-
-#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
-#dump_modify 2 pad 5
-
-#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
-#dump_modify 3 pad 5
-
-timestep 0.0001
-thermo 50
-run 10000
-Neighbor list info ...
- 1 neighbor list requests
- update every 1 steps, delay 10 steps, check yes
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 2.8
- ghost atom cutoff = 2.8
- binsize = 1.4 -> bins = 18 18 18
-Memory usage per processor = 2.96781 Mbytes
-Step Temp E_pair E_mol TotEng Press
- 0 217.7783 3430.3907 0 3466.6871 -2.7403788
- 50 13679.637 1404.2468 0 3684.1863 12.446066
- 100 16777.225 888.87665 0 3685.0808 -31.828677
- 150 19595.365 418.45042 0 3684.3446 40.709078
- 200 18524.188 596.47273 0 3683.8375 -0.8159371
- 250 21015.789 180.96521 0 3683.5967 -10.042469
- 300 20785.513 219.25314 0 3683.5053 2.6452719
- 350 21072.46 171.2554 0 3683.3321 7.0609024
- 400 19956.414 356.36381 0 3682.4328 19.320259
- 450 20724.42 227.73284 0 3681.8028 8.1259249
- 500 20152.578 322.71466 0 3681.4777 5.4929878
- 550 20017.022 345.29701 0 3681.4673 5.4661666
- 600 17897.743 698.72196 0 3681.6791 3.2854742
- 650 17297.758 796.60256 0 3679.5623 15.191113
- 700 18581.934 584.29715 0 3681.2861 5.1588289
- 750 21774.158 52.821062 0 3681.8474 -10.775664
- 800 21604.055 81.188546 0 3681.8644 -3.2045743
- 850 17821.483 711.53827 0 3681.7854 7.4384277
- 900 21033.292 175.98127 0 3681.5299 -16.345167
- 950 20968.166 186.59847 0 3681.2929 -2.330456
- 1000 20490.66 266.19375 0 3681.3037 11.787983
- 1050 20222.396 310.94072 0 3681.34 -8.3459539
- 1100 21321.687 127.61533 0 3681.2299 -1.2184717
- 1150 20849.582 206.01695 0 3680.9472 -0.86699149
- 1200 21815.003 45.317414 0 3681.1512 1.5988314
- 1250 18655.437 572.41453 0 3681.654 10.064078
- 1300 20780.781 217.36506 0 3680.8286 6.0538616
- 1350 20558.971 254.36482 0 3680.8601 -3.6773952
- 1400 21485.029 99.812921 0 3680.6511 -16.185473
- 1450 21771.107 52.15961 0 3680.6775 -2.4756673
- 1500 21520.948 93.503927 0 3680.3286 2.1023576
- 1550 21351.418 121.68137 0 3680.2511 5.5159947
- 1600 20778.805 216.92177 0 3680.0559 15.089188
- 1650 21477.638 100.21836 0 3679.8247 -1.1045746
- 1700 18501.339 596.47914 0 3680.0357 -15.679679
- 1750 18563.642 587.34785 0 3681.2882 33.532209
- 1800 19110.185 494.8234 0 3679.8543 18.024046
- 1850 21364.191 119.23545 0 3679.9339 2.5291103
- 1900 20146.626 322.14867 0 3679.9197 5.7313218
- 1950 20692.672 231.25325 0 3680.0319 4.2977763
- 2000 20943.904 189.11235 0 3679.7629 -22.645121
- 2050 19668.057 401.82994 0 3679.8394 3.6251916
- 2100 20280.442 299.76155 0 3679.8353 7.4807949
- 2150 19181.86 483.522 0 3680.4987 22.620507
- 2200 21300.161 130.70534 0 3680.7322 4.7102665
- 2250 20486.943 266.63931 0 3681.1299 -8.6456512
- 2300 18653.122 572.24819 0 3681.1018 -5.2637122
- 2350 21513.523 95.614901 0 3681.2021 -9.3621767
- 2400 21466.272 103.56446 0 3681.2765 -29.561368
- 2450 20100.105 332.27123 0 3682.2887 35.744287
- 2500 20764.395 221.6677 0 3682.4001 -12.468906
- 2550 20435.699 276.31055 0 3682.2603 -22.413697
- 2600 21466.467 104.53618 0 3682.2807 -10.078508
- 2650 20814.737 213.23892 0 3682.3617 5.1390411
- 2700 18565.761 588.3578 0 3682.6513 22.27664
- 2750 20772.36 220.1607 0 3682.2206 -7.9448198
- 2800 21018.563 179.10058 0 3682.1945 -7.0717829
- 2850 16789.412 884.21472 0 3682.4501 33.279015
- 2900 19304.363 464.75282 0 3682.1466 7.947554
- 2950 20513.758 263.07578 0 3682.0355 2.2361434
- 3000 20617.309 245.95251 0 3682.1706 -0.75213689
- 3050 18567.52 587.90473 0 3682.4914 -4.0112006
- 3100 18696.577 566.20617 0 3682.3023 -1.4814167
- 3150 19864.606 371.56078 0 3682.3284 8.9362836
- 3200 18902.643 532.04614 0 3682.4867 0.76630303
- 3250 21110.454 163.86212 0 3682.271 -1.6253894
- 3300 19369.939 454.05833 0 3682.3816 4.9066544
- 3350 19082.603 501.69905 0 3682.133 3.5982292
- 3400 19527.779 426.918 0 3681.5478 6.9612143
- 3450 19892.953 366.19989 0 3681.6921 3.0050426
- 3500 19708.981 396.84552 0 3681.6756 7.0757635
- 3550 20256.096 306.23937 0 3682.2554 -1.752138
- 3600 21289.889 133.93823 0 3682.253 -3.7462615
- 3650 18333.877 627.18028 0 3682.8264 -15.276791
- 3700 19829.133 377.33753 0 3682.1931 -6.269648
- 3750 20771.635 220.07171 0 3682.0109 -28.479036
- 3800 18373.813 619.79253 0 3682.0947 29.594781
- 3850 19320.99 461.92786 0 3682.0928 -5.3212101
- 3900 16119.825 995.68064 0 3682.3182 -8.4683118
- 3950 15556.948 1091.3655 0 3684.1902 20.98273
- 4000 20000.464 348.24891 0 3681.6596 7.1589745
- 4050 18870.219 536.59924 0 3681.6358 -3.7997025
- 4100 19889.518 367.49253 0 3682.4122 -14.091266
- 4150 15789.623 1051.3399 0 3682.9438 -4.4152389
- 4200 20548.889 256.83493 0 3681.6498 0.92234153
- 4250 20681.925 235.46113 0 3682.4487 -11.515773
- 4300 19330.404 460.80975 0 3682.5437 -22.351775
- 4350 19369.443 453.35405 0 3681.5945 29.418242
- 4400 20762.165 222.24133 0 3682.6021 2.6627047
- 4450 19984.657 350.71294 0 3681.4891 28.88731
- 4500 21167.58 154.25344 0 3682.1834 -3.0784322
- 4550 18133.576 660.73671 0 3682.9995 2.5305835
- 4600 19935.069 360.36826 0 3682.8798 2.4575034
- 4650 21413.76 113.86464 0 3682.8246 -5.1271547
- 4700 21716.333 63.609419 0 3682.9982 -2.4708049
- 4750 21352.947 124.36961 0 3683.1941 -0.29026265
- 4800 19043.788 508.8617 0 3682.8264 14.797006
- 4850 20516.121 263.78758 0 3683.1411 7.1348281
- 4900 20624.5 245.81827 0 3683.235 0.34708051
- 4950 20317.197 296.68937 0 3682.8889 -0.55065946
- 5000 18346.865 625.37246 0 3683.1832 7.3371413
- 5050 18867.53 538.49153 0 3683.0799 1.9249866
- 5100 18790.276 551.17224 0 3682.885 2.2333017
- 5150 20241.365 311.84683 0 3685.4076 -3.998004
- 5200 17685.058 739.76418 0 3687.2739 3.2835025
- 5250 18496.626 604.58166 0 3687.3526 -10.185776
- 5300 18420.042 617.82026 0 3687.8273 -16.392458
- 5350 18767.338 559.0349 0 3686.9246 4.5320767
- 5400 20423.245 284.90517 0 3688.7794 -8.6356656
- 5450 21080.398 176.18494 0 3689.5846 -16.450038
- 5500 16684.424 909.12643 0 3689.8637 49.94555
- 5550 20132.31 335.03663 0 3690.4216 -16.018038
- 5600 20430.923 285.17562 0 3690.3295 -5.0773675
- 5650 20479.943 276.55962 0 3689.8834 5.4334564
- 5700 20061.532 345.95553 0 3689.5441 -16.230658
- 5750 20523.759 268.92217 0 3689.5487 -4.4128812
- 5800 18900.356 537.65462 0 3687.7139 13.605549
- 5850 20280.502 310.27193 0 3690.3556 -4.7884959
- 5900 19050.26 515.66087 0 3690.7042 7.8864722
- 5950 19566.917 430.2997 0 3691.4525 31.715268
- 6000 18878.118 544.75449 0 3691.1076 -4.2415329
- 6050 19308.682 471.70734 0 3689.821 -10.561614
- 6100 18776.194 560.04764 0 3689.4133 -7.7286747
- 6150 21475.064 110.1508 0 3689.3281 -3.6506391
- 6200 19975 360.82675 0 3689.9934 10.282021
- 6250 21396.341 123.5341 0 3689.5909 -5.7215163
- 6300 18533.423 600.87422 0 3689.778 15.408027
- 6350 20653.152 247.19253 0 3689.3846 8.5607784
- 6400 19716.537 403.41487 0 3689.5044 13.165575
- 6450 21120.66 168.79838 0 3688.9084 -0.50382728
- 6500 19700.345 404.7155 0 3688.1064 13.941375
- 6550 10818.393 1892.037 0 3695.1025 38.423155
- 6600 18684.478 574.84755 0 3688.9273 5.9176985
- 6650 19219.732 486.04269 0 3689.3314 18.287659
- 6700 20058.587 344.88255 0 3687.9804 6.5372086
- 6750 21279.318 142.77333 0 3689.3264 2.498188
- 6800 20671.545 244.25024 0 3689.5078 -4.1356416
- 6850 21203.598 155.82001 0 3689.753 -0.0083061182
- 6900 21699.344 73.301497 0 3689.8588 -8.0309898
- 6950 20951.212 197.19403 0 3689.0627 0.76668303
- 7000 20166.275 329.02869 0 3690.0746 2.0083318
- 7050 21554.944 97.465792 0 3689.9564 -3.2420086
- 7100 20817.494 220.25476 0 3689.8372 0.17206182
- 7150 21481.11 109.84029 0 3690.0253 -3.6814741
- 7200 21266.824 145.53099 0 3690.0016 -2.060543
- 7250 19434.684 450.81331 0 3689.9273 9.4822765
- 7300 21246.525 148.96573 0 3690.0532 3.3208839
- 7350 19749.269 398.60049 0 3690.1454 1.0929662
- 7400 20354.792 297.70261 0 3690.168 1.547159
- 7450 19996.859 357.16723 0 3689.977 -0.68412025
- 7500 20179.628 326.53243 0 3689.8038 -2.4805507
- 7550 18765.184 561.65039 0 3689.1811 -1.7976428
- 7600 19457.496 447.04428 0 3689.9603 -1.9055522
- 7650 18206.823 655.57276 0 3690.0433 1.2797964
- 7700 19152.344 497.77422 0 3689.8315 18.145069
- 7750 21387.484 125.48654 0 3690.0673 -2.9915772
- 7800 18127.052 668.61425 0 3689.7896 9.044869
- 7850 21419.557 120.08889 0 3690.015 6.2651717
- 7900 21817.182 53.739819 0 3689.9368 -4.2387416
- 7950 18215.195 654.15494 0 3690.0208 -54.628049
- 8000 21523.503 102.58018 0 3689.8307 -4.84236
- 8050 20720.799 236.28689 0 3689.7535 -9.3725225
- 8100 21196.483 157.3232 0 3690.0704 -7.7222497
- 8150 20869.667 211.65308 0 3689.9309 -6.8438295
- 8200 17790.052 725.72497 0 3690.7336 -25.697688
- 8250 19634.94 417.71929 0 3690.2094 8.861604
- 8300 19135.784 500.92443 0 3690.2218 -3.1245167
- 8350 20191.718 324.93312 0 3690.2195 6.5736107
- 8400 20695.239 241.02378 0 3690.2302 -14.592221
- 8450 21793.857 57.609525 0 3689.9191 -11.509747
- 8500 21271.088 144.43102 0 3689.6124 -0.091587085
- 8550 20064.337 345.21754 0 3689.2737 9.5058471
- 8600 20282.86 308.2307 0 3688.7074 2.265529
- 8650 21223.055 151.24306 0 3688.419 1.7296834
- 8700 18875.342 542.42055 0 3688.3108 6.367148
- 8750 20922.65 201.55122 0 3688.6595 3.4208578
- 8800 21406.54 120.8539 0 3688.6106 1.8253729
- 8850 19868.524 377.05623 0 3688.477 16.327796
- 8900 20025.322 348.94892 0 3686.5025 17.063406
- 8950 21224.374 151.3567 0 3688.7524 -0.11028753
- 9000 21318.309 135.862 0 3688.9135 -0.50826819
- 9050 17538.618 768.00136 0 3691.1043 37.978645
- 9100 21247.861 147.84641 0 3689.1566 -6.7773259
- 9150 18455.677 613.08767 0 3689.0339 -3.4844751
- 9200 19486.859 441.03829 0 3688.8482 -18.602827
- 9250 21774.926 59.710446 0 3688.8648 -13.379919
- 9300 17628.877 750.72321 0 3688.8694 27.797974
- 9350 19827.334 383.85708 0 3688.4128 6.5459021
- 9400 20020.126 351.61742 0 3688.3051 -14.332562
- 9450 21596.338 88.904175 0 3688.2939 1.5779716
- 9500 18981.418 524.60141 0 3688.1711 5.4352409
- 9550 18652.616 579.05144 0 3687.8208 25.600729
- 9600 21198.037 155.23097 0 3688.2371 -3.3586596
- 9650 19958.317 361.32544 0 3687.7115 4.2910178
- 9700 19129.101 499.5993 0 3687.7828 13.267102
- 9750 21913.967 35.689587 0 3688.0174 -7.3222905
- 9800 21314.694 135.43794 0 3687.8869 -9.5613518
- 9850 20899.743 204.82802 0 3688.1185 -2.6321428
- 9900 20288.244 306.5013 0 3687.8753 3.6196618
- 9950 19271.015 475.88527 0 3687.7211 -1.8196764
- 10000 21122.24 167.82714 0 3688.2005 -3.8464842
-Loop time of 3.6648 on 1 procs for 10000 steps with 81 atoms
-
-Performance: 23575.670 tau/day, 2728.665 timesteps/s
-99.9% CPU use with 1 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.15599 | 0.15599 | 0.15599 | 0.0 | 4.26
-Neigh | 0.099093 | 0.099093 | 0.099093 | 0.0 | 2.70
-Comm | 0.0088665 | 0.0088665 | 0.0088665 | 0.0 | 0.24
-Output | 0.0016377 | 0.0016377 | 0.0016377 | 0.0 | 0.04
-Modify | 3.392 | 3.392 | 3.392 | 0.0 | 92.56
-Other | | 0.007194 | | | 0.20
-
-Nlocal: 81 ave 81 max 81 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 95 ave 95 max 95 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 744 ave 744 max 744 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 744
-Ave neighs/atom = 9.18519
-Neighbor list builds = 992
-Dangerous builds = 941
-
-Please see the log.cite file for references relevant to this simulation
-
-Total wall time: 0:00:03
diff --git a/examples/rigid/log.5Oct16.rigid.poems.g++.4 b/examples/rigid/log.5Oct16.rigid.poems.g++.4
deleted file mode 100644
index 06610ea5c8e9ece3f154dc4c9d1730e592c7bc69..0000000000000000000000000000000000000000
--- a/examples/rigid/log.5Oct16.rigid.poems.g++.4
+++ /dev/null
@@ -1,332 +0,0 @@
-LAMMPS (5 Oct 2016)
-# Simple rigid body system
-
-units lj
-atom_style atomic
-
-pair_style lj/cut 2.5
-
-read_data data.rigid
- orthogonal box = (-12 -12 -12) to (12 12 12)
- 1 by 2 by 2 MPI processor grid
- reading atoms ...
- 81 atoms
-
-velocity all create 100.0 4928459
-
-# unconnected bodies
-
-#group clump1 id <> 1 9
-#group clump2 id <> 10 18
-#group clump3 id <> 19 27
-#group clump4 id <> 28 36
-#group clump5 id <> 37 45
-#group clump6 id <> 46 54
-#group clump7 id <> 55 63
-#group clump8 id <> 64 72
-#group clump9 id <> 73 81
-
-#fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
-
-# 1 chain of connected bodies
-
-group clump1 id <> 1 9
-9 atoms in group clump1
-group clump2 id <> 9 18
-10 atoms in group clump2
-group clump3 id <> 18 27
-10 atoms in group clump3
-group clump4 id <> 27 36
-10 atoms in group clump4
-group clump5 id <> 36 45
-10 atoms in group clump5
-group clump6 id <> 45 54
-10 atoms in group clump6
-group clump7 id <> 54 63
-10 atoms in group clump7
-group clump8 id <> 63 72
-10 atoms in group clump8
-group clump9 id <> 72 81
-10 atoms in group clump9
-
-fix 1 all poems group clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
-1 clusters, 9 bodies, 8 joints, 81 atoms
-
-# 2 chains of connected bodies
-
-#group clump1 id <> 1 9
-#group clump2 id <> 9 18
-#group clump3 id <> 18 27
-#group clump4 id <> 27 36
-#group clump5 id <> 37 45
-#group clump6 id <> 45 54
-#group clump7 id <> 54 63
-#group clump8 id <> 63 72
-#group clump9 id <> 72 81
-
-#fix 1 all poems group clump1 clump2 clump3 clump4
-#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
-
-neigh_modify exclude group clump1 clump1
-neigh_modify exclude group clump2 clump2
-neigh_modify exclude group clump3 clump3
-neigh_modify exclude group clump4 clump4
-neigh_modify exclude group clump5 clump5
-neigh_modify exclude group clump6 clump6
-neigh_modify exclude group clump7 clump7
-neigh_modify exclude group clump8 clump8
-neigh_modify exclude group clump9 clump9
-
-thermo 100
-
-#dump 1 all atom 50 dump.rigid.poems
-
-#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
-#dump_modify 2 pad 5
-
-#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
-#dump_modify 3 pad 5
-
-timestep 0.0001
-thermo 50
-run 10000
-Neighbor list info ...
- 1 neighbor list requests
- update every 1 steps, delay 10 steps, check yes
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 2.8
- ghost atom cutoff = 2.8
- binsize = 1.4 -> bins = 18 18 18
-Memory usage per processor = 2.94053 Mbytes
-Step Temp E_pair E_mol TotEng Press
- 0 217.7783 3430.3907 0 3466.6871 -2.7403788
- 50 13679.637 1404.2468 0 3684.1863 12.446066
- 100 16777.225 888.87665 0 3685.0808 -31.828677
- 150 19595.365 418.45042 0 3684.3446 40.709078
- 200 18524.188 596.47273 0 3683.8375 -0.8159371
- 250 21015.789 180.96521 0 3683.5967 -10.042469
- 300 20785.513 219.25314 0 3683.5053 2.6452719
- 350 21072.46 171.2554 0 3683.3321 7.0609024
- 400 19956.414 356.36381 0 3682.4328 19.320259
- 450 20724.42 227.73284 0 3681.8028 8.1259249
- 500 20152.578 322.71466 0 3681.4777 5.4929878
- 550 20017.022 345.29701 0 3681.4673 5.4661666
- 600 17897.743 698.72196 0 3681.6791 3.2854742
- 650 17297.758 796.60256 0 3679.5623 15.191113
- 700 18581.934 584.29715 0 3681.2861 5.1588289
- 750 21774.158 52.821062 0 3681.8474 -10.775664
- 800 21604.055 81.188546 0 3681.8644 -3.2045743
- 850 17821.483 711.53827 0 3681.7854 7.4384276
- 900 21033.292 175.98127 0 3681.5299 -16.345167
- 950 20968.166 186.59847 0 3681.2929 -2.330456
- 1000 20490.66 266.19375 0 3681.3037 11.787983
- 1050 20222.396 310.94072 0 3681.34 -8.3459539
- 1100 21321.687 127.61533 0 3681.2299 -1.2184718
- 1150 20849.582 206.01695 0 3680.9472 -0.8669916
- 1200 21815.003 45.317417 0 3681.1512 1.5988314
- 1250 18655.437 572.41453 0 3681.654 10.064076
- 1300 20780.781 217.36504 0 3680.8286 6.0538619
- 1350 20558.972 254.3648 0 3680.8601 -3.6773987
- 1400 21485.029 99.812949 0 3680.6511 -16.185471
- 1450 21771.108 52.15959 0 3680.6775 -2.4756681
- 1500 21520.948 93.503949 0 3680.3286 2.1023578
- 1550 21351.418 121.6814 0 3680.2511 5.5159978
- 1600 20778.805 216.92171 0 3680.0559 15.089182
- 1650 21477.639 100.2182 0 3679.8247 -1.1045944
- 1700 18501.343 596.47853 0 3680.0357 -15.67963
- 1750 18563.643 587.34767 0 3681.2882 33.532167
- 1800 19110.19 494.82264 0 3679.8543 18.024034
- 1850 21364.196 119.23454 0 3679.9339 2.5291491
- 1900 20146.643 322.14595 0 3679.9197 5.731152
- 1950 20692.67 231.25357 0 3680.0319 4.2977641
- 2000 20943.904 189.11223 0 3679.763 -22.645645
- 2050 19668.152 401.81407 0 3679.8394 3.6255896
- 2100 20280.572 299.73976 0 3679.8351 7.4809355
- 2150 19182.121 483.47905 0 3680.4992 22.615309
- 2200 21299.76 130.77281 0 3680.7327 4.7114154
- 2250 20487.784 266.4995 0 3681.1302 -8.6406776
- 2300 18655.125 571.91487 0 3681.1023 -5.2671669
- 2350 21512.614 95.766913 0 3681.2025 -9.3523428
- 2400 21467.773 103.31519 0 3681.2773 -29.600307
- 2450 20096.937 332.80159 0 3682.2911 35.890912
- 2500 20761.446 222.16118 0 3682.4022 -12.528127
- 2550 20409.6 280.67234 0 3682.2723 -22.277373
- 2600 21469.964 103.95529 0 3682.2826 -10.038267
- 2650 20708.138 231.00516 0 3682.3615 5.3659502
- 2700 18584.743 585.07862 0 3682.5357 21.785261
- 2750 20503.019 264.91491 0 3682.0847 -4.5583917
- 2800 20584.075 251.44664 0 3682.1258 -6.5084595
- 2850 17277.076 802.33356 0 3681.8462 15.519513
- 2900 19392.956 449.92915 0 3682.0885 -4.3829957
- 2950 18371.786 620.29835 0 3682.2626 7.2117592
- 3000 20412.015 280.25302 0 3682.2555 0.32492606
- 3050 20858.248 205.65269 0 3682.0273 4.5055715
- 3100 21561.094 88.438447 0 3681.9541 -3.7523733
- 3150 15471.278 1103.4497 0 3681.9961 -14.576367
- 3200 15386.973 1117.8815 0 3682.377 15.051163
- 3250 19741.037 392.04755 0 3682.2204 -2.6610995
- 3300 20870.191 203.58229 0 3681.9475 -4.7795545
- 3350 16648.228 907.66571 0 3682.3704 -8.9242511
- 3400 20104.016 331.58603 0 3682.2554 6.4783858
- 3450 21421.316 112.28228 0 3682.5015 -8.3484987
- 3500 19284.533 467.80739 0 3681.8962 -12.835452
- 3550 20160.125 322.4476 0 3682.4684 1.6574827
- 3600 16682.415 902.73752 0 3683.14 22.383296
- 3650 16762.19 890.14636 0 3683.8446 16.119412
- 3700 17858.568 707.37212 0 3683.8 -1.6582504
- 3750 20029.881 345.15986 0 3683.4733 -3.1415889
- 3800 20734 227.99158 0 3683.6582 -7.9580418
- 3850 20741.089 226.39408 0 3683.2423 8.3055765
- 3900 18671.251 571.42296 0 3683.2981 -3.7468858
- 3950 19547.209 423.14256 0 3681.0108 5.8312279
- 4000 19739.799 393.58799 0 3683.5544 18.604884
- 4050 20014.121 347.8176 0 3683.5044 9.93387
- 4100 20503.654 266.08691 0 3683.3626 8.1304118
- 4150 18309.702 632.29807 0 3683.9151 -0.0021480359
- 4200 20509.423 265.60353 0 3683.8408 -2.1658857
- 4250 21805.541 50.325935 0 3684.5828 1.082842
- 4300 21420.551 114.90431 0 3684.9962 -1.7985998
- 4350 20256.928 308.74187 0 3684.8966 -11.669472
- 4400 21633.488 79.629274 0 3685.2106 -0.96131785
- 4450 20793.327 219.66955 0 3685.2241 1.3752349
- 4500 18719.484 564.86754 0 3684.7816 2.6308699
- 4550 20966.335 190.68308 0 3685.0722 -18.587627
- 4600 19428.962 446.59618 0 3684.7565 -4.4051672
- 4650 18408.956 616.85009 0 3685.0095 2.777272
- 4700 19215.779 482.57562 0 3685.2054 19.441016
- 4750 20155.927 326.13401 0 3685.4553 6.1734993
- 4800 20918.085 199.31832 0 3685.6659 3.4407437
- 4850 20236.958 312.07276 0 3684.899 3.2612893
- 4900 21419.89 115.36879 0 3685.3505 -4.675951
- 4950 19707.901 401.14828 0 3685.7985 -10.730734
- 5000 19407.201 450.64394 0 3685.1775 17.518981
- 5050 21527.598 97.655186 0 3685.5882 -9.2294707
- 5100 21581.933 88.595517 0 3685.5843 -20.669485
- 5150 21161.214 158.48503 0 3685.3541 -2.7587502
- 5200 21166.679 157.24762 0 3685.0275 -18.180044
- 5250 20909.576 200.23507 0 3685.1644 -16.617303
- 5300 21911.746 33.236563 0 3685.1942 -5.8313967
- 5350 20857.303 208.87453 0 3685.0916 12.176312
- 5400 20958.96 191.96694 0 3685.1269 3.6116429
- 5450 20433.179 279.61178 0 3685.1415 13.324529
- 5500 19604.675 416.88499 0 3684.3308 21.536484
- 5550 18171.145 655.92915 0 3684.4534 -9.2269804
- 5600 19799.907 385.12116 0 3685.1056 22.202165
- 5650 19711.882 399.30581 0 3684.6194 15.93063
- 5700 17908.833 699.52405 0 3684.3295 0.35530356
- 5750 18606.518 583.538 0 3684.6243 -4.4540843
- 5800 21814.053 48.974627 0 3684.6501 -1.5206358
- 5850 18029.107 679.9357 0 3684.7868 12.137677
- 5900 21090.739 169.64502 0 3684.7682 -1.5051545
- 5950 21086.26 170.29075 0 3684.6674 -2.8164474
- 6000 21285.771 136.95608 0 3684.5846 -26.582739
- 6050 21203.994 150.87822 0 3684.8772 -2.6617226
- 6100 21481.553 104.57796 0 3684.8368 -16.524974
- 6150 20354.4 292.57675 0 3684.9767 2.7960207
- 6200 21326.591 130.75243 0 3685.1843 -1.5929194
- 6250 21505.087 101.07817 0 3685.2593 -3.7821931
- 6300 21296.273 135.6593 0 3685.0382 -0.55635908
- 6350 21295.389 135.86485 0 3685.0964 5.6614093
- 6400 16552.242 926.02655 0 3684.7336 14.177218
- 6450 20148.951 327.1151 0 3685.2736 7.4561085
- 6500 20962.151 191.79415 0 3685.486 -4.5436711
- 6550 21710.328 67.433972 0 3685.8219 -5.7678572
- 6600 20698.571 234.79099 0 3684.5528 -2.1984068
- 6650 17892.287 704.05484 0 3686.1026 11.525836
- 6700 21272.999 141.26589 0 3686.7657 0.44088069
- 6750 19558.993 426.46448 0 3686.2966 -16.907401
- 6800 20350.247 295.23951 0 3686.9474 1.1284348
- 6850 18665.05 573.5326 0 3684.3742 17.088712
- 6900 19769.199 392.1551 0 3687.0216 6.7562425
- 6950 19439.159 446.99138 0 3686.8512 -6.0105763
- 7000 19379.907 456.53471 0 3686.5192 -9.0505095
- 7050 19983.754 356.02523 0 3686.651 -5.6274314
- 7100 19867.737 375.47627 0 3686.7658 17.315482
- 7150 19258.794 477.47344 0 3687.2724 14.316676
- 7200 21282.428 139.96051 0 3687.0318 -0.77043459
- 7250 19828.603 381.98919 0 3686.7564 6.5142869
- 7300 20574.582 257.8245 0 3686.9215 -3.6547118
- 7350 21613.467 84.771568 0 3687.0161 -7.5188826
- 7400 21817.009 50.844944 0 3687.0131 -14.888864
- 7450 14937.538 1197.4257 0 3687.0154 1.7540499
- 7500 18326.914 632.40374 0 3686.8894 8.3397357
- 7550 13611.007 1418.4727 0 3686.9739 -19.379482
- 7600 19173.985 491.9482 0 3687.6123 17.229001
- 7650 16911.504 867.33649 0 3685.9204 -21.042834
- 7700 21752.116 61.143705 0 3686.4963 -10.344487
- 7750 20208.337 318.26355 0 3686.3197 13.385814
- 7800 21649.909 77.950987 0 3686.2692 -1.7911084
- 7850 20139.64 329.50319 0 3686.1098 -5.5805093
- 7900 21355.026 126.7642 0 3685.9352 -7.7062172
- 7950 21336.178 129.88925 0 3685.9188 -2.059298
- 8000 21047.596 177.71546 0 3685.6482 0.37963466
- 8050 19217.351 482.62331 0 3685.5152 6.5582595
- 8100 20499.057 268.7173 0 3685.2268 -1.1959737
- 8150 21494.301 102.83829 0 3685.2219 -1.6427647
- 8200 20074.928 339.19817 0 3685.0195 6.285123
- 8250 17335.157 793.47566 0 3682.6685 22.877381
- 8300 17340.544 794.62619 0 3684.7168 3.9147755
- 8350 20529.345 262.51162 0 3684.0691 4.031768
- 8400 18884.747 537.47827 0 3684.9361 22.853404
- 8450 20341.86 293.10484 0 3683.4148 0.33856656
- 8500 19300.282 467.58127 0 3684.2949 12.35507
- 8550 21631.936 78.254534 0 3683.5772 -10.992959
- 8600 20204.913 316.83233 0 3684.3178 20.74228
- 8650 21018.189 181.32054 0 3684.352 1.8412068
- 8700 20161.304 323.97907 0 3684.1964 -2.646629
- 8750 19081.79 504.00155 0 3684.2998 -10.088053
- 8800 20834.489 211.76247 0 3684.1773 14.896336
- 8850 20929.355 196.18335 0 3684.4092 -1.2602398
- 8900 21491.074 102.47788 0 3684.3235 -1.4696758
- 8950 20474.735 271.69461 0 3684.1504 -6.9489258
- 9000 21128.641 162.40732 0 3683.8474 -7.7928168
- 9050 18421.801 614.46442 0 3684.7646 24.40313
- 9100 19301.292 466.98873 0 3683.8707 4.4687046
- 9150 21575.705 88.213763 0 3684.1646 -0.94696984
- 9200 20004.776 350.05448 0 3684.1838 -7.3466605
- 9250 21384.079 120.14472 0 3684.1578 -8.3773844
- 9300 21980.599 20.702393 0 3684.1356 -12.666293
- 9350 21686.606 69.517984 0 3683.9524 -8.8366533
- 9400 20732.704 228.46247 0 3683.9131 -6.4080307
- 9450 19798.859 384.34696 0 3684.1568 7.6198484
- 9500 20270.695 305.22664 0 3683.6758 1.5862486
- 9550 16496.156 935.28481 0 3684.6441 15.001468
- 9600 20642.429 241.08853 0 3681.4934 -9.2159382
- 9650 21292.587 135.4474 0 3684.2119 -0.54770976
- 9700 18888.158 536.60518 0 3684.6315 5.3236926
- 9750 18750.018 559.35922 0 3684.3623 -9.9424949
- 9800 20544.772 259.71076 0 3683.8394 8.732202
- 9850 16698.125 901.90076 0 3684.9216 9.9553329
- 9900 21450.963 109.58687 0 3684.7474 -4.8001999
- 9950 20664.461 240.66995 0 3684.7468 -3.4840781
- 10000 18951.367 526.45428 0 3685.0155 21.512727
-Loop time of 3.89095 on 4 procs for 10000 steps with 81 atoms
-
-Performance: 22205.346 tau/day, 2570.063 timesteps/s
-99.6% CPU use with 4 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.012426 | 0.039516 | 0.089301 | 15.3 | 1.02
-Neigh | 0.012618 | 0.027118 | 0.055113 | 10.4 | 0.70
-Comm | 0.16629 | 0.21469 | 0.26329 | 8.2 | 5.52
-Output | 0.0051188 | 0.0053029 | 0.0055087 | 0.2 | 0.14
-Modify | 3.5241 | 3.5783 | 3.6729 | 3.0 | 91.96
-Other | | 0.02605 | | | 0.67
-
-Nlocal: 20.25 ave 81 max 0 min
-Histogram: 3 0 0 0 0 0 0 0 0 1
-Nghost: 46.25 ave 95 max 14 min
-Histogram: 2 0 0 0 0 1 0 0 0 1
-Neighs: 249.25 ave 997 max 0 min
-Histogram: 3 0 0 0 0 0 0 0 0 1
-
-Total # of neighbors = 997
-Ave neighs/atom = 12.3086
-Neighbor list builds = 993
-Dangerous builds = 943
-
-Please see the log.cite file for references relevant to this simulation
-
-Total wall time: 0:00:03
diff --git a/examples/rigid/log.5Oct16.rigid.poems2.g++.1 b/examples/rigid/log.5Oct16.rigid.poems2.g++.1
deleted file mode 100644
index edbef2d5b691d05bff1f665704301a72079aadc0..0000000000000000000000000000000000000000
--- a/examples/rigid/log.5Oct16.rigid.poems2.g++.1
+++ /dev/null
@@ -1,336 +0,0 @@
-LAMMPS (5 Oct 2016)
-# Simple rigid body system
-
-units lj
-atom_style atomic
-
-pair_style lj/cut 2.5
-
-read_data data.rigid
- orthogonal box = (-12 -12 -12) to (12 12 12)
- 1 by 1 by 1 MPI processor grid
- reading atoms ...
- 81 atoms
-
-velocity all create 100.0 4928459
-
-# unconnected bodies
-
-#group clump1 id <> 1 9
-#group clump2 id <> 10 18
-#group clump3 id <> 19 27
-#group clump4 id <> 28 36
-#group clump5 id <> 37 45
-#group clump6 id <> 46 54
-#group clump7 id <> 55 63
-#group clump8 id <> 64 72
-#group clump9 id <> 73 81
-
-#fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
-
-# 1 chain of connected bodies
-
-#group clump1 id <> 1 9
-#group clump2 id <> 9 18
-#group clump3 id <> 18 27
-#group clump4 id <> 27 36
-#group clump5 id <> 36 45
-#group clump6 id <> 45 54
-#group clump7 id <> 54 63
-#group clump8 id <> 63 72
-#group clump9 id <> 72 81
-
-#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
-
-# 2 chains of connected bodies
-
-group clump1 id <> 1 9
-9 atoms in group clump1
-group clump2 id <> 9 18
-10 atoms in group clump2
-group clump3 id <> 18 27
-10 atoms in group clump3
-group clump4 id <> 27 36
-10 atoms in group clump4
-group clump5 id <> 37 45
-9 atoms in group clump5
-group clump6 id <> 45 54
-10 atoms in group clump6
-group clump7 id <> 54 63
-10 atoms in group clump7
-group clump8 id <> 63 72
-10 atoms in group clump8
-group clump9 id <> 72 81
-10 atoms in group clump9
-
-fix 1 all poems group clump1 clump2 clump3 clump4
-1 clusters, 4 bodies, 3 joints, 36 atoms
-fix 2 all poems group clump5 clump6 clump7 clump8 clump9
-1 clusters, 5 bodies, 4 joints, 45 atoms
-
-neigh_modify exclude group clump1 clump1
-neigh_modify exclude group clump2 clump2
-neigh_modify exclude group clump3 clump3
-neigh_modify exclude group clump4 clump4
-neigh_modify exclude group clump5 clump5
-neigh_modify exclude group clump6 clump6
-neigh_modify exclude group clump7 clump7
-neigh_modify exclude group clump8 clump8
-neigh_modify exclude group clump9 clump9
-
-thermo 100
-
-#dump 1 all atom 50 dump.rigid.poems2
-
-#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
-#dump_modify 2 pad 5
-
-#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
-#dump_modify 3 pad 5
-
-timestep 0.0001
-thermo 50
-run 10000
-WARNING: More than one fix poems (../fix_poems.cpp:352)
-WARNING: More than one fix poems (../fix_poems.cpp:352)
-WARNING: One or more atoms are time integrated more than once (../modify.cpp:269)
-Neighbor list info ...
- 1 neighbor list requests
- update every 1 steps, delay 10 steps, check yes
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 2.8
- ghost atom cutoff = 2.8
- binsize = 1.4 -> bins = 18 18 18
-Memory usage per processor = 3.53031 Mbytes
-Step Temp E_pair E_mol TotEng Press
- 0 196.00047 3632.2347 0 3668.5311 -2.7403788
- 50 12167.633 1505.5478 0 3758.8133 35.125973
- 100 17556.978 512.66277 0 3763.9549 11.137534
- 150 19579.586 138.04942 0 3763.8987 -29.953971
- 200 19757.51 105.30542 0 3764.1036 -0.030645317
- 250 18218.374 390.10747 0 3763.8804 13.711001
- 300 19383.039 174.40688 0 3763.8586 5.7240693
- 350 20125.986 36.972611 0 3764.0071 1.9559205
- 400 18888.816 266.10975 0 3764.0386 9.6362168
- 450 19307.656 188.2511 0 3763.743 1.9326206
- 500 16331.197 738.56392 0 3762.8597 9.1715579
- 550 19318.722 186.16172 0 3763.7027 3.0115336
- 600 19455.268 161.20621 0 3764.0336 0.55208034
- 650 18487.011 340.03216 0 3763.5528 -8.0359122
- 700 17321.201 556.32471 0 3763.9545 -13.631751
- 750 18979.187 249.04389 0 3763.7082 -2.6072455
- 800 19342.456 181.85552 0 3763.7918 8.1918726
- 850 19070.641 232.19342 0 3763.7936 7.3148472
- 900 19478.873 156.65987 0 3763.8586 2.4284987
- 950 19912.415 76.437437 0 3763.9216 -1.4667227
- 1000 16003.749 802.39753 0 3766.0548 46.642188
- 1050 19859.583 86.64176 0 3764.3424 -2.1961943
- 1100 19229.575 203.61488 0 3764.6473 -10.632365
- 1150 18821.6 279.15861 0 3764.64 -0.89495035
- 1200 19392.695 173.59744 0 3764.8373 1.8508753
- 1250 16459.624 717.32104 0 3765.3995 33.478127
- 1300 19343.863 182.59043 0 3764.7874 0.75890736
- 1350 20019.643 57.503573 0 3764.8448 0.31444671
- 1400 18549.582 329.31436 0 3764.4221 10.738303
- 1450 15163.926 957.47585 0 3765.6103 -17.923459
- 1500 19223.688 204.15175 0 3764.0939 -1.6134531
- 1550 18147.996 404.12677 0 3764.8668 8.4194779
- 1600 18615.043 317.42467 0 3764.6548 -2.3288934
- 1650 20120.654 38.887913 0 3764.935 -8.7620277
- 1700 19450.907 162.98272 0 3765.0025 2.3254731
- 1750 19374.632 177.37966 0 3765.2744 8.9328774
- 1800 19424.404 167.93966 0 3765.0514 0.081230261
- 1850 17936.249 442.84231 0 3764.3699 6.6010636
- 1900 19982.595 64.406198 0 3764.8868 -2.9529813
- 1950 16215.852 761.91287 0 3764.8485 13.994708
- 2000 18584.422 322.12049 0 3763.68 7.1654003
- 2050 20107.965 41.025754 0 3764.723 -0.3109069
- 2100 20002.333 60.593017 0 3764.7288 -6.7919784
- 2150 16949.762 626.59623 0 3765.441 3.508941
- 2200 20010.953 58.808279 0 3764.5403 -10.862172
- 2250 18982.73 247.00892 0 3762.3292 -0.53807815
- 2300 18401.298 354.87973 0 3762.5274 1.0920554
- 2350 19390.524 172.9415 0 3763.7793 -3.3524932
- 2400 16080.801 786.38838 0 3764.3146 -16.200514
- 2450 18870.412 268.74976 0 3763.2705 11.197736
- 2500 19688.29 117.58223 0 3763.5618 4.382644
- 2550 18870.825 268.78678 0 3763.384 -5.6623656
- 2600 17019.35 611.70808 0 3763.4395 6.3109641
- 2650 18753.285 291.0596 0 3763.8902 2.4120296
- 2700 19742.456 107.20901 0 3763.2193 -0.33061303
- 2750 19522.438 148.16759 0 3763.4339 -1.6254851
- 2800 18304.801 372.55152 0 3762.3295 22.6368
- 2850 18465.36 343.48495 0 3762.9961 4.4169272
- 2900 20151.999 31.372926 0 3763.2245 1.2013699
- 2950 15498.143 892.80071 0 3762.8272 13.263724
- 3000 18728.301 294.65113 0 3762.855 8.1897838
- 3050 18538.466 330.25223 0 3763.3015 8.5865739
- 3100 19081.409 229.5907 0 3763.1849 -4.8573813
- 3150 18498.802 337.11548 0 3762.8195 1.0555321
- 3200 19925.897 73.358029 0 3763.339 -7.7325108
- 3250 19780.108 100.23785 0 3763.2209 -5.5974972
- 3300 19221.043 203.82387 0 3763.2763 4.2703251
- 3350 19025.292 240.11329 0 3763.3156 5.7708328
- 3400 18153.696 401.52086 0 3763.3164 21.076943
- 3450 18611.375 316.50396 0 3763.0548 -3.5484945
- 3500 19931.319 71.969274 0 3762.9543 1.8764978
- 3550 19747.562 106.05439 0 3763.0103 -2.5506186
- 3600 18491.39 338.4134 0 3762.7449 -4.0527808
- 3650 19757.998 104.19207 0 3763.0806 1.4865598
- 3700 20108.003 39.345514 0 3763.0498 0.062827129
- 3750 19222.505 203.28065 0 3763.0039 0.33719277
- 3800 19286.383 191.08831 0 3762.6406 -0.1826802
- 3850 19450.083 161.09138 0 3762.9587 -0.2708263
- 3900 18002.304 429.25655 0 3763.0166 -4.6832439
- 3950 17186.829 582.26502 0 3765.0111 55.816834
- 4000 16826.434 645.84974 0 3761.856 19.675962
- 4050 19227.526 202.18151 0 3762.8344 -0.2596098
- 4100 19908.792 76.084531 0 3762.8978 -2.796813
- 4150 17821.329 462.63065 0 3762.8768 13.069155
- 4200 19917.133 74.574998 0 3762.9329 -6.4181155
- 4250 19012.618 241.96787 0 3762.823 4.0847974
- 4300 19077.34 229.98133 0 3762.8221 4.324323
- 4350 19361.128 177.47406 0 3762.8681 -7.377974
- 4400 18565.044 324.95107 0 3762.9223 2.5229032
- 4450 19352.406 178.98756 0 3762.7665 0.10862717
- 4500 18482.218 340.15496 0 3762.788 12.518301
- 4550 18359.732 362.83749 0 3762.7879 3.7500902
- 4600 19623.618 128.71624 0 3762.7196 -1.1328521
- 4650 17565.707 509.99904 0 3762.9078 1.7135935
- 4700 19876.052 81.892814 0 3762.6431 0.32476108
- 4750 19022.676 239.92262 0 3762.6403 -0.24613022
- 4800 18862.685 269.24248 0 3762.3324 6.2733979
- 4850 19899.174 77.426145 0 3762.4584 0.42535238
- 4900 18250.865 382.72867 0 3762.5185 23.308462
- 4950 18895.847 263.22651 0 3762.4575 8.0634675
- 5000 19096.705 225.69358 0 3762.1204 3.6816481
- 5050 16546.294 698.91312 0 3763.0416 17.453618
- 5100 19501.208 151.20999 0 3762.5449 -1.1231291
- 5150 19479.879 155.00669 0 3762.3917 -3.983378
- 5200 17397.818 541.23039 0 3763.0485 6.1109992
- 5250 18564.869 324.10557 0 3762.0442 9.2244762
- 5300 16271.663 747.52374 0 3760.7947 -6.5256602
- 5350 19831.418 89.851887 0 3762.3367 -2.3453958
- 5400 18723.697 294.67435 0 3762.0256 4.6822081
- 5450 19547.28 142.21934 0 3762.086 -5.5243408
- 5500 19415.447 166.68729 0 3762.1404 -9.5658991
- 5550 18492.721 337.54773 0 3762.1256 6.5184903
- 5600 19391.389 171.14375 0 3762.1416 -0.53835361
- 5650 18503.465 334.62751 0 3761.1951 4.6580363
- 5700 18153.344 399.91064 0 3761.6409 12.851587
- 5750 18342.297 365.14769 0 3761.8694 2.7148176
- 5800 19583.241 135.64969 0 3762.1758 -1.089608
- 5850 15967.283 804.18382 0 3761.088 11.278762
- 5900 19040.271 235.35509 0 3761.3312 5.1352158
- 5950 17920.962 443.17951 0 3761.8762 4.9621366
- 6000 19100.92 224.3946 0 3761.602 -9.537589
- 6050 17982.119 432.3251 0 3762.3472 -2.851617
- 6100 16233.096 755.46191 0 3761.5908 25.113316
- 6150 18316.543 370.01118 0 3761.9635 -1.7445703
- 6200 18483.464 339.13282 0 3761.9966 -2.0857447
- 6250 18609.406 315.56032 0 3761.7467 -12.289208
- 6300 17167.919 582.68212 0 3761.9264 -3.8263397
- 6350 17870.329 452.58116 0 3761.9013 -3.3843134
- 6400 19309.717 186.11786 0 3761.9913 -4.9462739
- 6450 17964.073 435.39924 0 3762.0794 12.272972
- 6500 18772.847 285.61959 0 3762.0727 6.7928648
- 6550 18915.116 259.41365 0 3762.213 -4.1449761
- 6600 19446.628 161.18763 0 3762.415 -2.1906581
- 6650 16348.787 734.99282 0 3762.546 -9.9624546
- 6700 19066.684 231.43863 0 3762.3061 -5.362833
- 6750 14890.323 1004.547 0 3762.0143 37.373013
- 6800 18235.19 385.253 0 3762.1401 0.21012662
- 6850 16447.997 716.11276 0 3762.0382 -9.2095411
- 6900 18343.362 364.81902 0 3761.7379 10.417932
- 6950 16014.084 797.13348 0 3762.7046 6.7906777
- 7000 19120.393 221.29236 0 3762.1059 -1.3461375
- 7050 18055.409 418.30136 0 3761.8957 1.5772317
- 7100 18407.231 353.41868 0 3762.1652 0.61071769
- 7150 18728.136 293.64021 0 3761.8136 5.1649654
- 7200 17706.628 483.07628 0 3762.0815 18.000708
- 7250 19349.505 178.89673 0 3762.1385 2.540201
- 7300 20016.293 55.389159 0 3762.1101 -1.5793163
- 7350 19398.573 169.86661 0 3762.1949 -5.060123
- 7400 19466.526 157.37407 0 3762.2862 1.7158273
- 7450 18440.348 347.09196 0 3761.9712 12.781963
- 7500 19989.907 60.555934 0 3762.3906 -1.5033319
- 7550 19667.28 120.27403 0 3762.363 -3.3502366
- 7600 18497.707 336.15863 0 3761.66 1.7887539
- 7650 17901.957 447.17282 0 3762.3501 0.016725252
- 7700 19758.725 103.3129 0 3762.3361 -23.534448
- 7750 19443.957 161.6532 0 3762.386 -10.323924
- 7800 19776.178 100.1773 0 3762.4324 6.0854422
- 7850 19242.512 198.86705 0 3762.2952 5.2823659
- 7900 19499.929 151.30366 0 3762.4017 12.299911
- 7950 19630.317 127.19541 0 3762.4393 8.0799632
- 8000 19872.384 82.421129 0 3762.4923 2.2126691
- 8050 17747.038 476.27982 0 3762.7683 -7.7042786
- 8100 18832.654 274.78106 0 3762.3095 13.882157
- 8150 19949.814 68.09711 0 3762.5072 -0.54410896
- 8200 17555.866 511.02517 0 3762.1115 6.2471175
- 8250 17800.1 465.9992 0 3762.314 13.583485
- 8300 19755.224 103.89732 0 3762.2721 -1.487243
- 8350 17583.61 506.17539 0 3762.3995 -9.7819128
- 8400 18529.003 330.75623 0 3762.0532 14.731228
- 8450 20155.902 29.797078 0 3762.3716 -8.5711085
- 8500 18047.548 420.54645 0 3762.685 7.3875118
- 8550 19790.794 97.493375 0 3762.4553 -3.3427911
- 8600 19997.902 59.172074 0 3762.4874 3.3479688
- 8650 19987.319 61.148363 0 3762.5037 -1.889232
- 8700 19363.91 176.41833 0 3762.3276 -9.4291288
- 8750 18712.689 296.3979 0 3761.7107 5.9221369
- 8800 19783.17 98.860518 0 3762.4105 -3.5262066
- 8850 18796.049 281.60057 0 3762.3504 -8.2913002
- 8900 16738.277 662.62261 0 3762.3035 8.5838631
- 8950 17869.613 452.25006 0 3761.4377 11.561101
- 9000 18682.512 302.27997 0 3762.0043 3.8878724
- 9050 17513.759 518.50265 0 3761.7914 23.05778
- 9100 17500.686 521.57944 0 3762.4473 -2.8435751
- 9150 19645.683 124.43597 0 3762.5254 -3.0193092
- 9200 18898.897 262.76552 0 3762.5612 3.5891701
- 9250 20114.279 37.614866 0 3762.4813 -0.58120871
- 9300 19562.613 139.54073 0 3762.2468 -3.2630158
- 9350 19679.811 118.05865 0 3762.468 -3.4644363
- 9400 19297.384 188.84527 0 3762.4349 0.40498037
- 9450 18267.029 379.52581 0 3762.309 -0.13762867
- 9500 19951.072 67.63844 0 3762.2814 -7.575539
- 9550 19134.562 218.46835 0 3761.9057 -1.9626244
- 9600 19089.093 227.29178 0 3762.3089 -1.94158
- 9650 16964.603 620.71289 0 3762.3061 16.987042
- 9700 18846.881 271.3129 0 3761.4761 3.4458802
- 9750 19309.225 186.0142 0 3761.7966 9.4048627
- 9800 16359.704 733.51007 0 3763.0849 15.870164
- 9850 19958.532 66.203725 0 3762.2282 6.0043645
- 9900 19864.564 83.502384 0 3762.1253 -0.65360617
- 9950 18996.789 244.25101 0 3762.1749 -2.4961826
- 10000 17933.494 441.33587 0 3762.3532 -6.0731708
-Loop time of 3.80061 on 1 procs for 10000 steps with 81 atoms
-
-Performance: 22733.175 tau/day, 2631.155 timesteps/s
-100.0% CPU use with 1 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.11276 | 0.11276 | 0.11276 | 0.0 | 2.97
-Neigh | 0.075881 | 0.075881 | 0.075881 | 0.0 | 2.00
-Comm | 0.011113 | 0.011113 | 0.011113 | 0.0 | 0.29
-Output | 0.0016332 | 0.0016332 | 0.0016332 | 0.0 | 0.04
-Modify | 3.5918 | 3.5918 | 3.5918 | 0.0 | 94.51
-Other | | 0.007383 | | | 0.19
-
-Nlocal: 81 ave 81 max 81 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: 612 ave 612 max 612 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 612
-Ave neighs/atom = 7.55556
-Neighbor list builds = 989
-Dangerous builds = 906
-
-Please see the log.cite file for references relevant to this simulation
-
-Total wall time: 0:00:03
diff --git a/examples/rigid/log.5Oct16.rigid.poems2.g++.4 b/examples/rigid/log.5Oct16.rigid.poems2.g++.4
deleted file mode 100644
index b408fb6f098ec6b74d06d4b9f44cf19efdbf47fc..0000000000000000000000000000000000000000
--- a/examples/rigid/log.5Oct16.rigid.poems2.g++.4
+++ /dev/null
@@ -1,336 +0,0 @@
-LAMMPS (5 Oct 2016)
-# Simple rigid body system
-
-units lj
-atom_style atomic
-
-pair_style lj/cut 2.5
-
-read_data data.rigid
- orthogonal box = (-12 -12 -12) to (12 12 12)
- 1 by 2 by 2 MPI processor grid
- reading atoms ...
- 81 atoms
-
-velocity all create 100.0 4928459
-
-# unconnected bodies
-
-#group clump1 id <> 1 9
-#group clump2 id <> 10 18
-#group clump3 id <> 19 27
-#group clump4 id <> 28 36
-#group clump5 id <> 37 45
-#group clump6 id <> 46 54
-#group clump7 id <> 55 63
-#group clump8 id <> 64 72
-#group clump9 id <> 73 81
-
-#fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
-
-# 1 chain of connected bodies
-
-#group clump1 id <> 1 9
-#group clump2 id <> 9 18
-#group clump3 id <> 18 27
-#group clump4 id <> 27 36
-#group clump5 id <> 36 45
-#group clump6 id <> 45 54
-#group clump7 id <> 54 63
-#group clump8 id <> 63 72
-#group clump9 id <> 72 81
-
-#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
-
-# 2 chains of connected bodies
-
-group clump1 id <> 1 9
-9 atoms in group clump1
-group clump2 id <> 9 18
-10 atoms in group clump2
-group clump3 id <> 18 27
-10 atoms in group clump3
-group clump4 id <> 27 36
-10 atoms in group clump4
-group clump5 id <> 37 45
-9 atoms in group clump5
-group clump6 id <> 45 54
-10 atoms in group clump6
-group clump7 id <> 54 63
-10 atoms in group clump7
-group clump8 id <> 63 72
-10 atoms in group clump8
-group clump9 id <> 72 81
-10 atoms in group clump9
-
-fix 1 all poems group clump1 clump2 clump3 clump4
-1 clusters, 4 bodies, 3 joints, 36 atoms
-fix 2 all poems group clump5 clump6 clump7 clump8 clump9
-1 clusters, 5 bodies, 4 joints, 45 atoms
-
-neigh_modify exclude group clump1 clump1
-neigh_modify exclude group clump2 clump2
-neigh_modify exclude group clump3 clump3
-neigh_modify exclude group clump4 clump4
-neigh_modify exclude group clump5 clump5
-neigh_modify exclude group clump6 clump6
-neigh_modify exclude group clump7 clump7
-neigh_modify exclude group clump8 clump8
-neigh_modify exclude group clump9 clump9
-
-thermo 100
-
-#dump 1 all atom 50 dump.rigid.poems2
-
-#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
-#dump_modify 2 pad 5
-
-#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
-#dump_modify 3 pad 5
-
-timestep 0.0001
-thermo 50
-run 10000
-WARNING: More than one fix poems (../fix_poems.cpp:352)
-WARNING: More than one fix poems (../fix_poems.cpp:352)
-WARNING: One or more atoms are time integrated more than once (../modify.cpp:269)
-Neighbor list info ...
- 1 neighbor list requests
- update every 1 steps, delay 10 steps, check yes
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 2.8
- ghost atom cutoff = 2.8
- binsize = 1.4 -> bins = 18 18 18
-Memory usage per processor = 3.50303 Mbytes
-Step Temp E_pair E_mol TotEng Press
- 0 196.00047 3632.2347 0 3668.5311 -2.7403788
- 50 12167.633 1505.5478 0 3758.8133 35.125973
- 100 17556.978 512.66277 0 3763.9549 11.137534
- 150 19579.586 138.04942 0 3763.8987 -29.953971
- 200 19757.51 105.30542 0 3764.1036 -0.030645317
- 250 18218.374 390.10747 0 3763.8804 13.711001
- 300 19383.039 174.40688 0 3763.8586 5.7240693
- 350 20125.986 36.972611 0 3764.0071 1.9559205
- 400 18888.816 266.10975 0 3764.0386 9.6362168
- 450 19307.656 188.2511 0 3763.743 1.9326206
- 500 16331.197 738.56392 0 3762.8597 9.1715579
- 550 19318.722 186.16172 0 3763.7027 3.0115336
- 600 19455.268 161.20621 0 3764.0336 0.55208034
- 650 18487.011 340.03216 0 3763.5528 -8.0359122
- 700 17321.201 556.32471 0 3763.9545 -13.631751
- 750 18979.187 249.04389 0 3763.7082 -2.6072455
- 800 19342.456 181.85552 0 3763.7918 8.1918726
- 850 19070.641 232.19342 0 3763.7936 7.3148472
- 900 19478.873 156.65987 0 3763.8586 2.4284987
- 950 19912.415 76.437437 0 3763.9216 -1.4667227
- 1000 16003.749 802.39753 0 3766.0548 46.642188
- 1050 19859.583 86.64176 0 3764.3424 -2.1961943
- 1100 19229.575 203.61488 0 3764.6473 -10.632365
- 1150 18821.6 279.15861 0 3764.64 -0.89495035
- 1200 19392.695 173.59744 0 3764.8373 1.8508753
- 1250 16459.624 717.32104 0 3765.3995 33.478127
- 1300 19343.863 182.59043 0 3764.7874 0.75890736
- 1350 20019.643 57.503573 0 3764.8448 0.31444671
- 1400 18549.582 329.31436 0 3764.4221 10.738303
- 1450 15163.926 957.47585 0 3765.6103 -17.923459
- 1500 19223.688 204.15176 0 3764.0939 -1.6134529
- 1550 18147.996 404.12677 0 3764.8668 8.4194781
- 1600 18615.043 317.42468 0 3764.6548 -2.3288926
- 1650 20120.654 38.887908 0 3764.935 -8.7620288
- 1700 19450.907 162.98267 0 3765.0025 2.3254739
- 1750 19374.631 177.3797 0 3765.2744 8.9328773
- 1800 19424.404 167.93965 0 3765.0514 0.081228843
- 1850 17936.227 442.84645 0 3764.3699 6.6011251
- 1900 19982.595 64.406244 0 3764.8868 -2.952971
- 1950 16215.818 761.91942 0 3764.8486 13.994877
- 2000 18584.433 322.11846 0 3763.6801 7.1653695
- 2050 20107.965 41.025796 0 3764.723 -0.31089763
- 2100 20002.329 60.593879 0 3764.7288 -6.7919882
- 2150 16949.817 626.58598 0 3765.4409 3.5087505
- 2200 20010.954 58.8082 0 3764.5403 -10.862143
- 2250 18982.732 247.00854 0 3762.3293 -0.53812607
- 2300 18401.276 354.88369 0 3762.5274 1.0921058
- 2350 19390.535 172.93951 0 3763.7793 -3.3524354
- 2400 16080.475 786.44896 0 3764.3146 -16.201558
- 2450 18870.293 268.77171 0 3763.2704 11.199749
- 2500 19688.508 117.54164 0 3763.5617 4.3806994
- 2550 18870.328 268.87896 0 3763.3841 -5.6641099
- 2600 17020.211 611.54841 0 3763.4394 6.3081434
- 2650 18748.838 291.88478 0 3763.8917 2.4175163
- 2700 19743.991 106.92945 0 3763.224 -0.33916964
- 2750 19525.446 147.60906 0 3763.4324 -1.6251174
- 2800 18257.411 381.40184 0 3762.4038 23.39495
- 2850 18496.796 337.65425 0 3762.9868 4.3657735
- 2900 20163.418 29.253902 0 3763.2203 1.4431917
- 2950 16823.317 646.69817 0 3762.1273 4.9041552
- 3000 19223.007 203.2529 0 3763.069 4.0414458
- 3050 17391.02 542.93746 0 3763.4968 15.139863
- 3100 19205.6 206.57791 0 3763.1705 4.8519241
- 3150 19835.659 90.247763 0 3763.5179 -14.900053
- 3200 18962.776 251.5838 0 3763.2089 -13.706561
- 3250 19418.837 167.29058 0 3763.3716 -2.0866468
- 3300 18628.291 313.69067 0 3763.3742 5.9919715
- 3350 17465.974 529.14439 0 3763.5841 14.122593
- 3400 18488.661 339.6186 0 3763.4448 21.526798
- 3450 19163.152 214.26098 0 3762.9928 4.1888096
- 3500 18000.27 429.81789 0 3763.2011 5.4734485
- 3550 19582.423 136.71887 0 3763.0935 -2.5335675
- 3600 19634.325 127.2219 0 3763.208 -1.9728322
- 3650 19428.114 165.40707 0 3763.2059 -2.3318779
- 3700 19861.116 85.356944 0 3763.3414 -3.9097609
- 3750 19337.239 182.43992 0 3763.4102 -3.3559651
- 3800 19493.146 153.40349 0 3763.2453 -0.71089657
- 3850 18607.616 317.74889 0 3763.6037 3.475832
- 3900 19719.59 111.5553 0 3763.3313 0.58876668
- 3950 19756.661 104.5522 0 3763.1931 3.7526698
- 4000 17904.708 447.1673 0 3762.854 12.270654
- 4050 19588.087 135.80435 0 3763.2279 0.94578945
- 4100 19065.901 232.38235 0 3763.1048 -2.7495195
- 4150 18775.075 286.2257 0 3763.0915 -3.7039858
- 4200 18800.725 281.46601 0 3763.0817 0.15619543
- 4250 19732.687 108.90618 0 3763.1075 3.0865861
- 4300 18278.151 377.63653 0 3762.4794 1.5768601
- 4350 17915.757 445.4804 0 3763.2133 -3.7040484
- 4400 15987.794 802.41575 0 3763.1183 22.252078
- 4450 19302.37 188.69495 0 3763.2079 0.91081327
- 4500 20039.32 52.304099 0 3763.2893 -2.0828905
- 4550 19535.953 145.4374 0 3763.2064 -3.3804255
- 4600 19700.723 114.79823 0 3763.0803 -1.1761163
- 4650 17804.641 465.85788 0 3763.0136 7.5947192
- 4700 19913.881 75.240289 0 3762.996 -2.1100557
- 4750 19982.484 62.535995 0 3762.996 -4.5821237
- 4800 17400.76 540.21707 0 3762.58 -5.8418778
- 4850 19199.88 206.90989 0 3762.4433 3.4536341
- 4900 19173.92 212.11327 0 3762.8392 5.0387071
- 4950 19236.635 200.57537 0 3762.9152 -1.4932783
- 5000 19077.616 230.04967 0 3762.9415 4.3742655
- 5050 19893.763 78.909747 0 3762.94 -1.5796711
- 5100 18884.746 265.68301 0 3762.8583 2.2767949
- 5150 17417.096 537.54036 0 3762.9286 -2.8632555
- 5200 18247.844 383.60092 0 3762.8312 10.384179
- 5250 19494.107 152.60532 0 3762.6251 -4.7617287
- 5300 18739.781 292.46206 0 3762.7919 23.210048
- 5350 19310.938 186.62363 0 3762.7232 14.895327
- 5400 19540.39 144.14287 0 3762.7336 6.094624
- 5450 20074.459 45.247888 0 3762.7403 -2.0871835
- 5500 19986.377 61.668045 0 3762.849 -2.4551918
- 5550 19038.904 237.07578 0 3762.7987 5.4250813
- 5600 19439.124 163.1438 0 3762.9816 4.1291468
- 5650 19480.321 155.58325 0 3763.0501 -3.5308058
- 5700 19869.291 83.651379 0 3763.1497 -7.8661592
- 5750 19991.447 61.068554 0 3763.1884 -6.8473586
- 5800 19454.072 160.36805 0 3762.9739 1.527662
- 5850 17994.409 430.95597 0 3763.2539 -5.6078082
- 5900 19209.794 205.74997 0 3763.1193 8.4113055
- 5950 19046.427 236.06321 0 3763.1793 10.463356
- 6000 19409.899 168.95271 0 3763.3785 2.542067
- 6050 18068.174 417.35443 0 3763.3125 10.498199
- 6100 19549.253 143.21885 0 3763.4509 2.3075797
- 6150 18464.719 344.0303 0 3763.4228 0.46469762
- 6200 19811.205 94.62725 0 3763.3689 1.2382763
- 6250 18715.36 297.26445 0 3763.0718 -3.4541762
- 6300 17115.664 594.09913 0 3763.6666 4.2065564
- 6350 18155.927 400.71764 0 3762.9264 1.1521258
- 6400 19873.093 83.169067 0 3763.3716 0.16383592
- 6450 19991.88 61.13218 0 3763.3321 -1.3008128
- 6500 19434.416 164.40698 0 3763.3728 -13.593422
- 6550 19855.253 86.645329 0 3763.544 -0.85704037
- 6600 19251.141 198.41152 0 3763.4376 4.3027745
- 6650 19741.815 107.69047 0 3763.582 4.994835
- 6700 19633.466 127.69333 0 3763.5203 6.3677145
- 6750 16231.353 757.83705 0 3763.6431 -1.5978692
- 6800 18863.396 270.1114 0 3763.3329 -11.915909
- 6850 19644.779 125.29421 0 3763.2163 -1.151217
- 6900 18883.642 266.06889 0 3763.0397 -4.3950749
- 6950 19042.364 236.54144 0 3762.9052 5.5718878
- 7000 18351.868 364.38028 0 3762.8743 7.8958273
- 7050 19981.031 62.840667 0 3763.0316 -5.8572298
- 7100 19796.372 97.073665 0 3763.0685 -3.5178361
- 7150 19805.385 95.235221 0 3762.899 -2.5481726
- 7200 18722.055 295.86113 0 3762.9084 13.826356
- 7250 19537.304 144.54234 0 3762.5616 1.2288666
- 7300 18787.328 283.49504 0 3762.6299 9.0044469
- 7350 18886.005 265.52121 0 3762.9295 6.6791881
- 7400 19891.864 79.239278 0 3762.9178 -2.3882842
- 7450 18164.752 399.07065 0 3762.9137 3.9400481
- 7500 18702.612 299.582 0 3763.0286 4.7987316
- 7550 19884.986 80.231665 0 3762.6365 -0.75016515
- 7600 19549.059 142.16243 0 3762.3586 -2.1035756
- 7650 18223.668 387.9047 0 3762.658 -17.064339
- 7700 19428.4 164.79531 0 3762.6473 -2.8342541
- 7750 19239.584 199.93029 0 3762.8163 3.1746033
- 7800 19458.005 159.46176 0 3762.7961 1.714515
- 7850 18320.308 369.77051 0 3762.4202 2.1422976
- 7900 18817.415 278.04812 0 3762.7546 0.94492621
- 7950 19892.761 79.115928 0 3762.9606 1.4948501
- 8000 19592.344 134.7639 0 3762.9758 -1.8520224
- 8050 19316.109 185.70579 0 3762.7631 -4.8061205
- 8100 19867.017 83.850395 0 3762.9277 -3.496391
- 8150 19129.936 220.29802 0 3762.8789 -2.8357376
- 8200 18449.554 346.30415 0 3762.8883 1.4417837
- 8250 18405.197 354.49049 0 3762.8602 6.7020283
- 8300 18310.437 372.25376 0 3763.0755 3.9043508
- 8350 18842.702 273.55075 0 3762.94 -10.987272
- 8400 18574.308 323.33378 0 3763.0204 12.008785
- 8450 15368.628 918.21692 0 3764.2591 34.80292
- 8500 18432.887 349.54013 0 3763.0378 0.00064258465
- 8550 15777.73 841.79263 0 3763.5945 15.473699
- 8600 17205.381 576.4515 0 3762.6331 2.3985544
- 8650 19773.742 101.48276 0 3763.2869 2.3978892
- 8700 19059.824 232.99716 0 3762.5941 5.2611349
- 8750 19006.086 243.41125 0 3763.0568 4.7880403
- 8800 19492.691 153.0188 0 3762.7763 1.9118755
- 8850 19625.883 128.44474 0 3762.8675 3.4157389
- 8900 19916.97 74.635094 0 3762.9629 -10.157254
- 8950 16012.956 798.16801 0 3763.5302 16.904998
- 9000 19364.051 177.00354 0 3762.9389 -13.373346
- 9050 19133.929 219.61882 0 3762.9389 -7.3824392
- 9100 18657.168 307.85939 0 3762.8905 9.3071421
- 9150 17975.904 434.21548 0 3763.0867 6.9609506
- 9200 19075.282 230.41699 0 3762.8767 7.0961232
- 9250 20115.276 37.578674 0 3762.6298 1.8678552
- 9300 18195.486 393.20682 0 3762.7413 13.272552
- 9350 19617.155 129.85893 0 3762.6653 -2.0849447
- 9400 19276.325 193.03425 0 3762.724 -2.8963555
- 9450 18642.803 310.4759 0 3762.8467 3.407984
- 9500 19175.951 211.72785 0 3762.8298 -0.39025564
- 9550 17669.191 490.85942 0 3762.9319 5.3867954
- 9600 18481.199 340.29485 0 3762.7391 8.9004886
- 9650 20091.442 42.504743 0 3763.1422 -1.3206133
- 9700 19651.405 124.04835 0 3763.1975 1.4000525
- 9750 19138.245 219.03637 0 3763.1558 5.8352794
- 9800 19189.146 209.67958 0 3763.2251 6.214691
- 9850 19899.376 78.096337 0 3763.166 -0.75102404
- 9900 19447.247 161.27279 0 3762.6149 -6.4166376
- 9950 19807.083 95.152663 0 3763.1309 -0.88933698
- 10000 18972.157 249.56342 0 3762.9258 1.9189241
-Loop time of 3.99472 on 4 procs for 10000 steps with 81 atoms
-
-Performance: 21628.565 tau/day, 2503.306 timesteps/s
-99.7% CPU use with 4 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.0090363 | 0.029554 | 0.05092 | 8.8 | 0.74
-Neigh | 0.0090437 | 0.021045 | 0.034359 | 6.3 | 0.53
-Comm | 0.1326 | 0.17829 | 0.2132 | 7.3 | 4.46
-Output | 0.0044832 | 0.0048217 | 0.0053875 | 0.5 | 0.12
-Modify | 3.6632 | 3.7381 | 3.8211 | 2.9 | 93.58
-Other | | 0.02291 | | | 0.57
-
-Nlocal: 20.25 ave 37 max 0 min
-Histogram: 1 0 1 0 0 0 0 0 0 2
-Nghost: 17.75 ave 33 max 4 min
-Histogram: 2 0 0 0 0 0 0 0 1 1
-Neighs: 144.75 ave 356 max 0 min
-Histogram: 2 0 0 0 0 0 1 0 0 1
-
-Total # of neighbors = 579
-Ave neighs/atom = 7.14815
-Neighbor list builds = 994
-Dangerous builds = 958
-
-Please see the log.cite file for references relevant to this simulation
-
-Total wall time: 0:00:03
diff --git a/examples/rigid/log.5Oct16.rigid.tnr.g++.1 b/examples/rigid/log.5Oct16.rigid.tnr.g++.1
deleted file mode 100644
index 935b7eaf073db00214c230a128fc1e43153dad2e..0000000000000000000000000000000000000000
--- a/examples/rigid/log.5Oct16.rigid.tnr.g++.1
+++ /dev/null
@@ -1,452 +0,0 @@
-LAMMPS (5 Oct 2016)
-# Tethered nanorods
-
-atom_style molecular
-
-read_data data.rigid.tnr
- orthogonal box = (-31.122 -31.122 -31.122) to (31.122 31.122 31.122)
- 1 by 1 by 1 MPI processor grid
- reading atoms ...
- 5600 atoms
- scanning bonds ...
- 1 = max bonds/atom
- reading bonds ...
- 1600 bonds
- 2 = max # of 1-2 neighbors
- 1 = max # of 1-3 neighbors
- 1 = max # of 1-4 neighbors
- 2 = max # of special neighbors
-
-# Specify bond parameters
-
-bond_style fene
-bond_coeff 1 30.0 1.5 1.0 1.0
-
-special_bonds fene
- 2 = max # of 1-2 neighbors
- 2 = max # of special neighbors
-
-# Specify initial velocities
-
-velocity all create 1.4 109345
-
-# Specify rigid components
-
-group rods type 2
-4000 atoms in group rods
-group tethers subtract all rods
-1600 atoms in group tethers
-
-neigh_modify exclude molecule rods delay 0 every 1
-
-# Specify the pair potentials
-
-pair_style lj/cut 2.5
-pair_modify shift yes
-pair_coeff * * 1.0 1.0 1.122
-pair_coeff 2 2 1.0 1.0 2.5
-
-# Specify output
-
-thermo 100
-thermo_style custom step temp pe etotal press enthalpy lx ly lz pxx pyy pzz
-thermo_modify flush yes lost warn
-
-timestep 0.005
-
-fix 1 rods rigid molecule
-800 rigid bodies with 4000 atoms
-fix 2 tethers nve
-fix 3 all langevin 1.4 1.4 1.0 437624
-
-run 5000
-Neighbor list info ...
- 1 neighbor list requests
- update every 1 steps, delay 0 steps, check yes
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 2.8
- ghost atom cutoff = 2.8
- binsize = 1.4 -> bins = 45 45 45
-Memory usage per processor = 7.32042 Mbytes
-Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
- 0 1.3963219 5.9478449 7.0445809 0.048565317 9.13595 62.244 62.244 62.244 0.0091983659 0.11850113 0.017996458
- 100 1.3418512 5.9671777 7.0211299 0.025020362 8.0985822 62.244 62.244 62.244 0.02036076 0.038265078 0.016435248
- 200 1.3730638 5.9750802 7.0535483 0.0053287535 7.2830205 62.244 62.244 62.244 -0.00054924195 0.0092396988 0.0072958036
- 300 1.376262 5.9821642 7.0631443 0.0055536521 7.3023013 62.244 62.244 62.244 0.0033577704 0.0069111861 0.0063919998
- 400 1.3782954 5.9983628 7.08094 0.0020507385 7.169251 62.244 62.244 62.244 -0.0060862717 0.0098998072 0.0023386801
- 500 1.386863 6.0053312 7.0946377 -0.0009847031 7.0522334 62.244 62.244 62.244 -0.0038708372 0.0005697804 0.00034694745
- 600 1.4069849 6.0035719 7.1086832 0.0047883912 7.3148858 62.244 62.244 62.244 0.001069365 0.0078059505 0.0054898581
- 700 1.4423187 5.9982171 7.1310812 0.012141001 7.6539093 62.244 62.244 62.244 0.0094765272 0.011007593 0.015938883
- 800 1.4303878 5.9968168 7.1203098 -0.00081349095 7.0852784 62.244 62.244 62.244 0.0011153812 0.00041597298 -0.0039718271
- 900 1.4140538 5.9838168 7.0944803 0.00207609 7.183883 62.244 62.244 62.244 0.00043409671 0.0022778944 0.0035162788
- 1000 1.3906567 5.988119 7.0804053 0.0022005856 7.1751692 62.244 62.244 62.244 0.0077268425 -0.0022042977 0.0010792119
- 1100 1.3921992 5.9892203 7.0827181 0.0035041977 7.2336194 62.244 62.244 62.244 -0.0037576823 0.0040827951 0.01018748
- 1200 1.3968803 5.9795846 7.0767592 -0.0031072146 6.9429532 62.244 62.244 62.244 -0.0077387449 0.0033056124 -0.0048885115
- 1300 1.3755848 5.9739757 7.0544239 0.0092247106 7.4516677 62.244 62.244 62.244 0.0092788748 0.010737194 0.0076580625
- 1400 1.3847985 5.9703631 7.0580481 0.0071703598 7.3668254 62.244 62.244 62.244 0.0080485848 0.012260474 0.001202021
- 1500 1.4190051 5.956946 7.0714985 0.0035992903 7.2264948 62.244 62.244 62.244 -0.0055125437 0.01038369 0.0059267242
- 1600 1.3980036 5.9671666 7.0652236 0.0061819851 7.3314385 62.244 62.244 62.244 0.0062429141 0.0035120077 0.0087910334
- 1700 1.4276062 5.9610381 7.0823462 0.007832375 7.4196319 62.244 62.244 62.244 0.0083316819 0.0058394292 0.009326014
- 1800 1.4112769 5.9630595 7.0715419 0.0068032101 7.3645087 62.244 62.244 62.244 0.0065502252 0.0062317255 0.0076276797
- 1900 1.4276973 5.9489341 7.0703139 0.008397746 7.4319462 62.244 62.244 62.244 0.0148941 0.0032963108 0.0070028268
- 2000 1.4056158 5.9564624 7.0604983 0.0090470732 7.4500926 62.244 62.244 62.244 0.011871718 0.0086681344 0.0066013673
- 2100 1.3924778 5.9483611 7.0420778 0.0088893819 7.4248814 62.244 62.244 62.244 0.010247454 0.0097830093 0.0066376825
- 2200 1.3760401 5.9435877 7.0243935 -0.0042972782 6.8393397 62.244 62.244 62.244 -0.0050064436 -0.0046216999 -0.0032636911
- 2300 1.4191937 5.9334036 7.0481042 0.0047000032 7.2505006 62.244 62.244 62.244 0.0057709635 0.0044949165 0.0038341296
- 2400 1.4213285 5.9472214 7.0635988 0.010197674 7.5027414 62.244 62.244 62.244 0.008373826 0.0090537939 0.013165402
- 2500 1.4153808 5.9421661 7.0538718 0.00015906306 7.0607216 62.244 62.244 62.244 0.002351621 -0.0019814986 0.00010706677
- 2600 1.4014223 5.9431386 7.0438807 0.0070733749 7.3484816 62.244 62.244 62.244 0.0054143871 0.010055843 0.0057498948
- 2700 1.4138077 5.9369067 7.047377 0.0024268842 7.1518859 62.244 62.244 62.244 0.0052918436 0.0014960353 0.00049277371
- 2800 1.432192 5.9347676 7.0596777 0.0077670448 7.3941501 62.244 62.244 62.244 0.012668421 0.0059113033 0.0047214106
- 2900 1.3938659 5.921023 7.01583 0.0053751198 7.2472989 62.244 62.244 62.244 0.0020490372 0.0076566093 0.006419713
- 3000 1.390221 5.9205014 7.0124455 -0.0010750977 6.9661485 62.244 62.244 62.244 0.0019519817 -0.0041878885 -0.00098938611
- 3100 1.4205722 5.9178284 7.0336117 0.0098735475 7.4587965 62.244 62.244 62.244 0.0040973361 0.012167268 0.013356039
- 3200 1.398418 5.9150349 7.0134173 0.0061541841 7.2784351 62.244 62.244 62.244 0.0067621815 0.011952563 -0.00025219251
- 3300 1.4269859 5.9148727 7.0356937 0.0060623879 7.2967584 62.244 62.244 62.244 0.012956234 -2.4806661e-05 0.0052557362
- 3400 1.434286 5.9356705 7.0622253 0.00027315892 7.0739884 62.244 62.244 62.244 -0.00054959866 0.0052526278 -0.0038835524
- 3500 1.4416809 5.9228153 7.0551783 0.0083382977 7.4142506 62.244 62.244 62.244 0.007399393 0.0030328007 0.014582699
- 3600 1.4136063 5.9039442 7.0142562 0.0019712004 7.0991421 62.244 62.244 62.244 -0.00032316149 0.0035029874 0.0027337752
- 3700 1.4333819 5.9120101 7.0378548 0.0071287182 7.3448389 62.244 62.244 62.244 0.0064768218 0.0046765361 0.010232797
- 3800 1.3659481 5.9032873 6.9761663 -0.0054033416 6.7434821 62.244 62.244 62.244 -0.0073943479 -0.0082831992 -0.00053247772
- 3900 1.3963222 5.9042998 7.0010361 0.0053310264 7.2306062 62.244 62.244 62.244 0.0081855739 0.0048806019 0.0029269034
- 4000 1.4125482 5.9060665 7.0155474 0.0028450296 7.138063 62.244 62.244 62.244 0.0052588294 0.00072395285 0.0025523065
- 4100 1.3943951 5.9040875 6.9993102 0.0058050223 7.2492919 62.244 62.244 62.244 0.0060579697 0.0024782584 0.0088788387
- 4200 1.4249768 5.8906371 7.0098801 0.0030210669 7.1399763 62.244 62.244 62.244 0.006174431 -0.002079586 0.0049683557
- 4300 1.3899801 5.8966397 6.9883947 0.0057285402 7.2350829 62.244 62.244 62.244 0.0049048136 0.0021882328 0.010092574
- 4400 1.4414352 5.898628 7.0307981 0.0050932552 7.2501291 62.244 62.244 62.244 0.0057941393 0.0037951842 0.0056904421
- 4500 1.4092913 5.8922803 6.9992031 0.0012238869 7.0519073 62.244 62.244 62.244 0.0042907674 0.0014412643 -0.0020603711
- 4600 1.3779868 5.8928757 6.9752105 0.0020701322 7.0643566 62.244 62.244 62.244 0.0029283254 -0.0031683908 0.006450462
- 4700 1.4084635 5.9098782 7.0161508 -0.00052129502 6.9937023 62.244 62.244 62.244 -0.0018460523 -0.0018286314 0.0021107986
- 4800 1.4393258 5.9148464 7.0453597 0.015311954 7.7047386 62.244 62.244 62.244 0.014718813 0.01801777 0.013199278
- 4900 1.4500008 5.9076899 7.0465879 0.0075111779 7.3700419 62.244 62.244 62.244 0.0091865271 0.0080981174 0.0052488891
- 5000 1.4279632 5.9111567 7.0327453 -0.0014189553 6.9716408 62.244 62.244 62.244 -0.0046013754 0.0019937576 -0.001649248
-Loop time of 6.51777 on 1 procs for 5000 steps with 5600 atoms
-
-Performance: 331401.531 tau/day, 767.133 timesteps/s
-99.8% CPU use with 1 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.51894 | 0.51894 | 0.51894 | 0.0 | 7.96
-Bond | 0.24096 | 0.24096 | 0.24096 | 0.0 | 3.70
-Neigh | 1.8769 | 1.8769 | 1.8769 | 0.0 | 28.80
-Comm | 0.16548 | 0.16548 | 0.16548 | 0.0 | 2.54
-Output | 0.0032616 | 0.0032616 | 0.0032616 | 0.0 | 0.05
-Modify | 3.5349 | 3.5349 | 3.5349 | 0.0 | 54.23
-Other | | 0.1774 | | | 2.72
-
-Nlocal: 5600 ave 5600 max 5600 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 1351 ave 1351 max 1351 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 5254 ave 5254 max 5254 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 5254
-Ave neighs/atom = 0.938214
-Ave special neighs/atom = 0.571429
-Neighbor list builds = 766
-Dangerous builds = 0
-
-# Replace fix rigid and fix langevin with new ones
-
-unfix 1
-unfix 3
-
-fix 3 tethers langevin 1.4 1.4 1.0 198450
-
-# Test different integrators for rods
-
-fix 1 rods rigid/nve molecule
-800 rigid bodies with 4000 atoms
-print "rigid/nve"
-rigid/nve
-run 1000
-Memory usage per processor = 7.32042 Mbytes
-Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
- 5000 1.4279632 5.9111567 7.0327453 0.027874409 8.2331015 62.244 62.244 62.244 0.018992956 0.039655696 0.024974575
- 5100 1.439608 5.9052128 7.0359478 0.0060989863 7.2985885 62.244 62.244 62.244 0.0087364157 0.004022839 0.0055377041
- 5200 1.4120672 5.9102569 7.01936 0.0064301432 7.2962614 62.244 62.244 62.244 0.0082738077 0.0038925667 0.0071240551
- 5300 1.4452434 5.8842166 7.0193778 0.008172419 7.3713068 62.244 62.244 62.244 0.0077715647 0.0068924406 0.0098532518
- 5400 1.4170243 5.887522 7.0005186 0.0008656658 7.0377968 62.244 62.244 62.244 -9.1800583e-05 -0.0020237513 0.0047125493
- 5500 1.4209082 5.8758921 6.9919394 0.0093634084 7.395156 62.244 62.244 62.244 0.0088769348 0.0087092521 0.010504038
- 5600 1.4132978 5.8798939 6.9899636 0.0014877766 7.0540317 62.244 62.244 62.244 -0.0023427923 0.004559371 0.002246751
- 5700 1.4065053 5.887541 6.9922756 0.0028083452 7.1132114 62.244 62.244 62.244 0.0025188632 0.000510969 0.0053952035
- 5800 1.4079051 5.8940739 6.999908 0.0015946158 7.0685769 62.244 62.244 62.244 0.0037830287 0.00021751956 0.00078329927
- 5900 1.4076047 5.8941577 6.9997558 0.005189853 7.2232465 62.244 62.244 62.244 -0.00093244616 0.0096403542 0.0068616509
- 6000 1.4322772 5.8903539 7.0153309 0.00029752476 7.0281432 62.244 62.244 62.244 0.001913333 -0.00073790796 -0.00028285075
-Loop time of 1.37139 on 1 procs for 1000 steps with 5600 atoms
-
-Performance: 315008.398 tau/day, 729.186 timesteps/s
-100.0% CPU use with 1 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.1443 | 0.1443 | 0.1443 | 0.0 | 10.52
-Bond | 0.049211 | 0.049211 | 0.049211 | 0.0 | 3.59
-Neigh | 0.40564 | 0.40564 | 0.40564 | 0.0 | 29.58
-Comm | 0.033721 | 0.033721 | 0.033721 | 0.0 | 2.46
-Output | 0.00065017 | 0.00065017 | 0.00065017 | 0.0 | 0.05
-Modify | 0.70225 | 0.70225 | 0.70225 | 0.0 | 51.21
-Other | | 0.03562 | | | 2.60
-
-Nlocal: 5600 ave 5600 max 5600 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 1347 ave 1347 max 1347 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 5399 ave 5399 max 5399 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 5399
-Ave neighs/atom = 0.964107
-Ave special neighs/atom = 0.571429
-Neighbor list builds = 153
-Dangerous builds = 0
-unfix 1
-
-fix 1 rods rigid/nvt molecule temp 1.4 1.4 1.0
-800 rigid bodies with 4000 atoms
-print "rigid/nvt"
-rigid/nvt
-run 1000
-Memory usage per processor = 7.32042 Mbytes
-Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
- 6000 1.4322772 5.8903539 7.0153309 0.012980585 7.574314 62.244 62.244 62.244 0.058317363 0.0073619377 -0.026737547
- 6100 1.4199699 5.8764035 6.9917138 0.0054065567 7.2245364 62.244 62.244 62.244 0.0092276454 0.0019623806 0.005029644
- 6200 1.3976825 5.8924426 6.9902474 0.0004390082 7.0091524 62.244 62.244 62.244 -0.0023073118 -0.00049925474 0.0041235912
- 6300 1.4077283 5.8847362 6.9904313 0.0066398301 7.2763625 62.244 62.244 62.244 0.0058018933 0.0091933882 0.0049242089
- 6400 1.3749203 5.8817073 6.9616336 0.0074967166 7.2844648 62.244 62.244 62.244 0.012281889 0.0039781604 0.0062301007
- 6500 1.3467096 5.8881263 6.9458946 -0.00011926206 6.9407588 62.244 62.244 62.244 0.0030721983 -0.0013265855 -0.002103399
- 6600 1.3646558 5.8739857 6.9458497 0.0056064173 7.1872789 62.244 62.244 62.244 0.0059660118 0.0057680329 0.0050852071
- 6700 1.392725 5.8836119 6.9775228 0.0025583772 7.0876942 62.244 62.244 62.244 0.0030974509 0.0018499704 0.0027277104
- 6800 1.4017002 5.9015884 7.0025488 0.0039067256 7.1707842 62.244 62.244 62.244 0.0068315449 0.0020054024 0.0028832295
- 6900 1.4136756 5.8914708 7.0018372 0.005175385 7.2247049 62.244 62.244 62.244 0.0028462217 0.009405517 0.0032744161
- 7000 1.4286618 5.8935692 7.0157065 0.0062967875 7.2868652 62.244 62.244 62.244 0.0047257503 0.0093417536 0.0048228587
-Loop time of 1.38662 on 1 procs for 1000 steps with 5600 atoms
-
-Performance: 311550.061 tau/day, 721.181 timesteps/s
-99.9% CPU use with 1 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.14525 | 0.14525 | 0.14525 | 0.0 | 10.48
-Bond | 0.048966 | 0.048966 | 0.048966 | 0.0 | 3.53
-Neigh | 0.40266 | 0.40266 | 0.40266 | 0.0 | 29.04
-Comm | 0.033521 | 0.033521 | 0.033521 | 0.0 | 2.42
-Output | 0.00064969 | 0.00064969 | 0.00064969 | 0.0 | 0.05
-Modify | 0.71998 | 0.71998 | 0.71998 | 0.0 | 51.92
-Other | | 0.03559 | | | 2.57
-
-Nlocal: 5600 ave 5600 max 5600 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 1284 ave 1284 max 1284 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 5677 ave 5677 max 5677 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 5677
-Ave neighs/atom = 1.01375
-Ave special neighs/atom = 0.571429
-Neighbor list builds = 151
-Dangerous builds = 0
-unfix 1
-
-compute myTemp all temp
-
-fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 iso 0.05 0.05 1.0 dilate all
-800 rigid bodies with 4000 atoms
-print "rigid/npt iso"
-rigid/npt iso
-fix_modify 1 temp myTemp
-
-run 1000
-Memory usage per processor = 7.32042 Mbytes
-Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
- 7000 1.4286618 5.8935692 7.0157065 0.032107544 8.3983542 62.244 62.244 62.244 0.0040119822 0.040455544 0.051855105
- 7100 1.4709107 5.8870981 7.0424197 0.019698532 7.6954221 57.045709 57.045709 57.045709 0.012930036 0.020495433 0.025670125
- 7200 1.5163014 5.8421234 7.0330969 0.018918793 7.4624535 50.277182 50.277182 50.277182 0.017832308 0.02668088 0.012243191
- 7300 1.5675512 5.7752788 7.0065063 0.02287049 7.3825189 45.15491 45.15491 45.15491 0.019317818 0.024266569 0.025027083
- 7400 1.5432894 5.7512252 6.9633963 0.024351591 7.2723284 41.416611 41.416611 41.416611 0.032039305 0.022247464 0.018768005
- 7500 1.5510339 5.7073864 6.9256404 0.030706866 7.2413185 38.612893 38.612893 38.612893 0.04157713 0.012507079 0.038036388
- 7600 1.5435609 5.6657445 6.8781288 0.03187398 7.1535577 36.440727 36.440727 36.440727 0.036502896 0.022097075 0.037021969
- 7700 1.5862733 5.6141666 6.8600993 0.053474714 7.2612259 34.762178 34.762178 34.762178 0.035691782 0.06016314 0.064569222
- 7800 1.5106894 5.6005849 6.7871505 0.028896219 6.982719 33.59041 33.59041 33.59041 0.031167851 0.013090267 0.042430539
- 7900 1.472566 5.5634394 6.7200611 0.092340877 7.2955261 32.679168 32.679168 32.679168 0.060527481 0.10093222 0.11556293
- 8000 1.4805391 5.5132684 6.6761526 0.040035619 6.9105042 32.003919 32.003919 32.003919 0.04381615 0.023706176 0.052584532
-Loop time of 3.05773 on 1 procs for 1000 steps with 5600 atoms
-
-Performance: 141281.224 tau/day, 327.040 timesteps/s
-99.9% CPU use with 1 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.37231 | 0.37231 | 0.37231 | 0.0 | 12.18
-Bond | 0.07144 | 0.07144 | 0.07144 | 0.0 | 2.34
-Neigh | 1.3968 | 1.3968 | 1.3968 | 0.0 | 45.68
-Comm | 0.071773 | 0.071773 | 0.071773 | 0.0 | 2.35
-Output | 0.00065684 | 0.00065684 | 0.00065684 | 0.0 | 0.02
-Modify | 1.0951 | 1.0951 | 1.0951 | 0.0 | 35.82
-Other | | 0.04962 | | | 1.62
-
-Nlocal: 5600 ave 5600 max 5600 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 2963 ave 2963 max 2963 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 25797 ave 25797 max 25797 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 25797
-Ave neighs/atom = 4.60661
-Ave special neighs/atom = 0.571429
-Neighbor list builds = 334
-Dangerous builds = 0
-unfix 1
-
-fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 x 0.05 0.05 1.0 dilate all
-800 rigid bodies with 4000 atoms
-print "rigid/npt x"
-rigid/npt x
-run 1000
-Memory usage per processor = 7.32428 Mbytes
-Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
- 8000 1.4805391 5.5132684 6.6761526 0.10591497 7.2961342 32.003919 32.003919 32.003919 -0.0085253101 0.12196602 0.20430422
- 8100 1.4629588 5.5087415 6.6578173 0.080159269 7.1245058 31.831354 32.003919 32.003919 0.078046473 0.088201582 0.074229751
- 8200 1.4061729 5.5008938 6.6053673 0.038080967 6.8240633 31.398913 32.003919 32.003919 0.041554276 0.038085252 0.034603372
- 8300 1.4225542 5.4730766 6.5904167 0.071241779 6.992772 30.878537 32.003919 32.003919 0.068190354 0.076631686 0.068903297
- 8400 1.4344356 5.4772885 6.6039608 0.044141975 6.8495696 30.421029 32.003919 32.003919 0.031058774 0.039890974 0.061476178
- 8500 1.4377845 5.4485066 6.5778092 0.04242205 6.8099428 29.91769 32.003919 32.003919 0.053013546 0.050003453 0.02424915
- 8600 1.4339418 5.4280263 6.5543108 0.0048261176 6.58031 29.453954 32.003919 32.003919 -0.0020411927 0.005967365 0.010552181
- 8700 1.4284879 5.4273043 6.549305 0.058717611 6.8609844 29.021604 32.003919 32.003919 0.09927212 0.02309782 0.053782894
- 8800 1.3993066 5.4243917 6.5234721 0.030638337 6.683965 28.639961 32.003919 32.003919 0.08972583 0.0089328704 -0.0067436909
- 8900 1.4429241 5.3850352 6.5183748 0.0053167016 6.5458205 28.223699 32.003919 32.003919 0.052590681 -0.031563606 -0.0050769701
- 9000 1.41963 5.3772308 6.4922741 0.040105311 6.6961497 27.793622 32.003919 32.003919 0.070575176 0.0044551641 0.045285594
-Loop time of 2.94424 on 1 procs for 1000 steps with 5600 atoms
-
-Performance: 146727.069 tau/day, 339.646 timesteps/s
-99.9% CPU use with 1 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.57781 | 0.57781 | 0.57781 | 0.0 | 19.63
-Bond | 0.072705 | 0.072705 | 0.072705 | 0.0 | 2.47
-Neigh | 1.0768 | 1.0768 | 1.0768 | 0.0 | 36.57
-Comm | 0.052799 | 0.052799 | 0.052799 | 0.0 | 1.79
-Output | 0.00064921 | 0.00064921 | 0.00064921 | 0.0 | 0.02
-Modify | 1.1247 | 1.1247 | 1.1247 | 0.0 | 38.20
-Other | | 0.03878 | | | 1.32
-
-Nlocal: 5600 ave 5600 max 5600 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 3244 ave 3244 max 3244 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 30929 ave 30929 max 30929 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 30929
-Ave neighs/atom = 5.52304
-Ave special neighs/atom = 0.571429
-Neighbor list builds = 165
-Dangerous builds = 0
-unfix 1
-
-fix 1 rods rigid/nph molecule iso 0.05 0.05 1.0 dilate all
-800 rigid bodies with 4000 atoms
-print "rigid/nph iso"
-rigid/nph iso
-run 1000
-Memory usage per processor = 7.32428 Mbytes
-Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
- 9000 1.41963 5.3772308 6.4922741 0.054032922 6.7669508 27.793622 32.003919 32.003919 0.36183473 -0.1011685 -0.098567468
- 9100 1.468276 5.3693533 6.5226054 0.062009135 6.8364521 27.753087 31.957243 31.957243 0.072952506 0.067965393 0.045109506
- 9200 1.4790176 5.3498933 6.5115824 0.068306349 6.8531758 27.642255 31.829623 31.829623 0.057719204 0.083928825 0.063271019
- 9300 1.4685339 5.3439444 6.4973991 0.012381058 6.5578428 27.421331 31.575232 31.575232 0.018937907 0.0065076203 0.011697646
- 9400 1.4675871 5.3321417 6.4848528 0.056515448 6.7525582 27.146928 31.259261 31.259261 0.035834387 0.047161137 0.086550819
- 9500 1.4464119 5.3137665 6.4498455 0.043906827 6.6517871 26.881604 30.953745 30.953745 0.031891513 0.065507153 0.034321816
- 9600 1.4541889 5.284445 6.4266325 0.046471589 6.6332098 26.578003 30.604153 30.604153 0.0041035598 0.071274602 0.064036606
- 9700 1.4577034 5.2493866 6.3943346 0.045073503 6.5909605 26.41175 30.412715 30.412715 0.018293408 0.069031147 0.047895953
- 9800 1.4701089 5.2202499 6.3749417 0.055758411 6.6108197 26.142656 30.102857 30.102857 0.045171706 0.039488766 0.082614761
- 9900 1.4518855 5.2148116 6.3551898 0.011510897 6.4028899 25.963345 29.896384 29.896384 0.0060934464 0.010841773 0.017597473
- 10000 1.4445828 5.2098073 6.3444498 0.075197507 6.654918 25.931556 29.859779 29.859779 0.08350416 0.066240185 0.075848177
-Loop time of 3.13351 on 1 procs for 1000 steps with 5600 atoms
-
-Performance: 137864.384 tau/day, 319.131 timesteps/s
-99.9% CPU use with 1 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.68 | 0.68 | 0.68 | 0.0 | 21.70
-Bond | 0.073233 | 0.073233 | 0.073233 | 0.0 | 2.34
-Neigh | 1.1775 | 1.1775 | 1.1775 | 0.0 | 37.58
-Comm | 0.057102 | 0.057102 | 0.057102 | 0.0 | 1.82
-Output | 0.00068927 | 0.00068927 | 0.00068927 | 0.0 | 0.02
-Modify | 1.1058 | 1.1058 | 1.1058 | 0.0 | 35.29
-Other | | 0.03924 | | | 1.25
-
-Nlocal: 5600 ave 5600 max 5600 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 3635 ave 3635 max 3635 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 38235 ave 38235 max 38235 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 38235
-Ave neighs/atom = 6.82768
-Ave special neighs/atom = 0.571429
-Neighbor list builds = 165
-Dangerous builds = 0
-unfix 1
-
-fix 1 rods rigid/nph molecule x 0.05 0.05 1.0 y 0.05 0.05 1.0 couple xy dilate all
-800 rigid bodies with 4000 atoms
-print "rigid/nph xy couple"
-rigid/nph xy couple
-run 1000
-Memory usage per processor = 7.32811 Mbytes
-Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
- 10000 1.4445828 5.2098073 6.3444498 0.001962567 6.3525526 25.931556 29.859779 29.859779 0.18484796 -0.22902272 0.050062455
- 10100 1.4368894 5.2096239 6.3382235 0.10403552 6.7662753 25.886842 29.808292 29.859779 0.12565247 0.094955776 0.091498324
- 10200 1.4231669 5.2080497 6.3258711 0.086173671 6.682435 25.959905 29.892423 29.859779 0.11480457 0.12471881 0.018997629
- 10300 1.4334516 5.1992954 6.3251949 -0.0076414301 6.2932457 26.095439 30.048488 29.859779 0.00870511 -0.0049134764 -0.026715924
- 10400 1.4408912 5.1980613 6.3298041 0.070774329 6.6314048 26.345108 30.335978 29.859779 0.061559356 0.075929557 0.074834076
- 10500 1.4299517 5.1990298 6.3221802 0.077553868 6.6569567 26.515356 30.532016 29.859779 0.11568876 0.063812738 0.053160106
- 10600 1.439113 5.1937953 6.3241415 0.024333431 6.4286629 26.449816 30.456548 29.859779 0.035925567 0.023132021 0.013942706
- 10700 1.4379108 5.1704548 6.2998567 0.06126476 6.5597578 26.285754 30.267632 29.859779 0.074214186 0.040233796 0.069346299
- 10800 1.4358912 5.1798018 6.3076174 0.10549358 6.747456 26.058856 30.006363 29.859779 0.1992503 0.046346044 0.070884395
- 10900 1.4470038 5.1528383 6.2893823 0.045720444 6.4780533 25.92502 29.852253 29.859779 0.041394051 0.026837211 0.068930071
- 11000 1.437397 5.1841678 6.3131661 0.070020768 6.6023557 25.935798 29.864664 29.859779 0.11790932 0.072745235 0.019407746
-Loop time of 3.22377 on 1 procs for 1000 steps with 5600 atoms
-
-Performance: 134004.591 tau/day, 310.196 timesteps/s
-99.9% CPU use with 1 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.74959 | 0.74959 | 0.74959 | 0.0 | 23.25
-Bond | 0.073572 | 0.073572 | 0.073572 | 0.0 | 2.28
-Neigh | 1.1793 | 1.1793 | 1.1793 | 0.0 | 36.58
-Comm | 0.057446 | 0.057446 | 0.057446 | 0.0 | 1.78
-Output | 0.00065088 | 0.00065088 | 0.00065088 | 0.0 | 0.02
-Modify | 1.1241 | 1.1241 | 1.1241 | 0.0 | 34.87
-Other | | 0.03903 | | | 1.21
-
-Nlocal: 5600 ave 5600 max 5600 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost: 3799 ave 3799 max 3799 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs: 39646 ave 39646 max 39646 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 39646
-Ave neighs/atom = 7.07964
-Ave special neighs/atom = 0.571429
-Neighbor list builds = 158
-Dangerous builds = 0
-
-Total wall time: 0:00:21
diff --git a/examples/rigid/log.5Oct16.rigid.tnr.g++.4 b/examples/rigid/log.5Oct16.rigid.tnr.g++.4
deleted file mode 100644
index 2a27702446e57a6adc0b139c69592a1b3594b6ed..0000000000000000000000000000000000000000
--- a/examples/rigid/log.5Oct16.rigid.tnr.g++.4
+++ /dev/null
@@ -1,452 +0,0 @@
-LAMMPS (5 Oct 2016)
-# Tethered nanorods
-
-atom_style molecular
-
-read_data data.rigid.tnr
- orthogonal box = (-31.122 -31.122 -31.122) to (31.122 31.122 31.122)
- 1 by 2 by 2 MPI processor grid
- reading atoms ...
- 5600 atoms
- scanning bonds ...
- 1 = max bonds/atom
- reading bonds ...
- 1600 bonds
- 2 = max # of 1-2 neighbors
- 1 = max # of 1-3 neighbors
- 1 = max # of 1-4 neighbors
- 2 = max # of special neighbors
-
-# Specify bond parameters
-
-bond_style fene
-bond_coeff 1 30.0 1.5 1.0 1.0
-
-special_bonds fene
- 2 = max # of 1-2 neighbors
- 2 = max # of special neighbors
-
-# Specify initial velocities
-
-velocity all create 1.4 109345
-
-# Specify rigid components
-
-group rods type 2
-4000 atoms in group rods
-group tethers subtract all rods
-1600 atoms in group tethers
-
-neigh_modify exclude molecule rods delay 0 every 1
-
-# Specify the pair potentials
-
-pair_style lj/cut 2.5
-pair_modify shift yes
-pair_coeff * * 1.0 1.0 1.122
-pair_coeff 2 2 1.0 1.0 2.5
-
-# Specify output
-
-thermo 100
-thermo_style custom step temp pe etotal press enthalpy lx ly lz pxx pyy pzz
-thermo_modify flush yes lost warn
-
-timestep 0.005
-
-fix 1 rods rigid molecule
-800 rigid bodies with 4000 atoms
-fix 2 tethers nve
-fix 3 all langevin 1.4 1.4 1.0 437624
-
-run 5000
-Neighbor list info ...
- 1 neighbor list requests
- update every 1 steps, delay 0 steps, check yes
- max neighbors/atom: 2000, page size: 100000
- master list distance cutoff = 2.8
- ghost atom cutoff = 2.8
- binsize = 1.4 -> bins = 45 45 45
-Memory usage per processor = 6.96454 Mbytes
-Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
- 0 1.3963219 5.9478449 7.0445809 0.048565317 9.13595 62.244 62.244 62.244 0.0091983659 0.11850113 0.017996458
- 100 1.3999025 5.9707695 7.0703179 0.027293074 8.24564 62.244 62.244 62.244 0.017246307 0.04732529 0.017307624
- 200 1.4245544 5.9878446 7.1067558 0.0072016369 7.41688 62.244 62.244 62.244 0.0071370801 0.0084066589 0.0060611719
- 300 1.4212057 5.9942604 7.1105414 0.0023296933 7.210865 62.244 62.244 62.244 -0.0059197015 0.0040269953 0.008881786
- 400 1.4030116 5.9953214 7.0973119 0.0055751834 7.3373961 62.244 62.244 62.244 -0.0026920847 0.013323321 0.0060943141
- 500 1.4201338 5.9984777 7.1139168 -0.0018229523 7.035415 62.244 62.244 62.244 -0.0082217102 -0.00047319975 0.0032260529
- 600 1.425173 5.9902537 7.1096508 0.013367744 7.6853062 62.244 62.244 62.244 0.012971415 0.016298595 0.010833222
- 700 1.4181225 5.9840752 7.0979345 0.0014999758 7.1625279 62.244 62.244 62.244 -0.0015835387 0.0045967753 0.0014866907
- 800 1.4084205 5.9778462 7.084085 0.0063728488 7.3585191 62.244 62.244 62.244 0.0036202744 0.005593586 0.0099046859
- 900 1.3958301 5.9891019 7.0854517 0.0028974454 7.2102244 62.244 62.244 62.244 0.0087724642 0.0014508428 -0.001530971
- 1000 1.3937374 5.9794855 7.0741916 0.0087158481 7.4495223 62.244 62.244 62.244 0.014424783 0.0034958881 0.0082268735
- 1100 1.3729162 5.9916252 7.0699773 0.0030451966 7.2011127 62.244 62.244 62.244 0.00084635444 -0.00064448421 0.0089337195
- 1200 1.4427374 5.9713589 7.1045519 0.0042680608 7.2883474 62.244 62.244 62.244 0.0030884628 0.0031576538 0.0065580658
- 1300 1.3971469 5.9728674 7.0702514 0.0022809251 7.168475 62.244 62.244 62.244 0.00060902513 -0.00020572386 0.006439474
- 1400 1.4194118 5.9672631 7.082135 0.012945844 7.6396221 62.244 62.244 62.244 0.0082418827 0.016256336 0.014339314
- 1500 1.3866472 5.9728382 7.0619753 0.0010642438 7.1078049 62.244 62.244 62.244 0.0020316123 0.0020439035 -0.00088278432
- 1600 1.4184955 5.9539591 7.0681113 0.0077605409 7.4023036 62.244 62.244 62.244 0.0033721722 0.0057827512 0.014126699
- 1700 1.3612202 5.9676733 7.0368389 0.00016862131 7.0441002 62.244 62.244 62.244 0.0052525345 0.0007705269 -0.0055171975
- 1800 1.3641041 5.9521837 7.0236144 0.0057884587 7.2728829 62.244 62.244 62.244 0.0038061044 0.0044032908 0.009155981
- 1900 1.3594477 5.9646024 7.0323757 0.0044261926 7.2229809 62.244 62.244 62.244 0.0019417448 0.006871542 0.004465291
- 2000 1.3776971 5.9431816 7.0252888 -0.0012460593 6.9716298 62.244 62.244 62.244 -0.0010913822 0.00098119436 -0.0036279901
- 2100 1.3986245 5.9509735 7.0495181 0.007520633 7.3733792 62.244 62.244 62.244 0.008359824 0.0075919773 0.0066100978
- 2200 1.4033594 5.9548158 7.0570794 0.0016804284 7.1294438 62.244 62.244 62.244 -0.001842641 0.0032876741 0.0035962521
- 2300 1.4048926 5.9444129 7.0478808 0.0062444034 7.3167836 62.244 62.244 62.244 0.004383569 0.0065720464 0.007777595
- 2400 1.4044043 5.9370822 7.0401666 0.0034562836 7.1890046 62.244 62.244 62.244 0.0068959298 0.0041111713 -0.00063825026
- 2500 1.4200762 5.9359254 7.0513193 0.0028319649 7.1732722 62.244 62.244 62.244 -0.00030414203 0.0039571831 0.0048428538
- 2600 1.3876469 5.9249124 7.0148347 -0.0017777224 6.9382806 62.244 62.244 62.244 -0.00047616392 -0.0025484917 -0.0023085116
- 2700 1.4099941 5.916763 7.0242378 0.0070716263 7.3287634 62.244 62.244 62.244 0.012628756 0.0053812867 0.0032048359
- 2800 1.4444643 5.9283432 7.0628925 0.0019400024 7.1464349 62.244 62.244 62.244 0.0014895079 0.0046367397 -0.00030624055
- 2900 1.3902832 5.9152516 7.0072446 -0.002166221 6.9139606 62.244 62.244 62.244 -0.0012374412 -0.00056403267 -0.004697189
- 3000 1.3711706 5.922146 6.9991271 0.011101505 7.4771914 62.244 62.244 62.244 0.011063833 0.012093026 0.010147657
- 3100 1.3569137 5.9171753 6.9829583 -0.002826677 6.8612331 62.244 62.244 62.244 -0.0069507252 0.0010084399 -0.0025377458
- 3200 1.4004275 5.905939 7.0058998 0.005439467 7.2401397 62.244 62.244 62.244 0.010352184 0.0057594148 0.00020680265
- 3300 1.3641217 5.9145275 6.985972 -0.0027212811 6.8687855 62.244 62.244 62.244 -0.00065933677 -0.0057713008 -0.0017332057
- 3400 1.3868722 5.9059546 6.9952684 0.0092591256 7.3939943 62.244 62.244 62.244 0.010690877 0.010752519 0.006333981
- 3500 1.3939169 5.8992292 6.9940762 0.0074340028 7.3142068 62.244 62.244 62.244 0.010137307 0.0044252569 0.0077394447
- 3600 1.3982507 5.9219461 7.0201971 0.005679459 7.2647718 62.244 62.244 62.244 0.0023367243 0.008059221 0.0066424317
- 3700 1.4019908 5.9059957 7.0071843 0.0065915477 7.2910363 62.244 62.244 62.244 0.0049554109 0.010827005 0.0039922268
- 3800 1.3960736 5.902079 6.99862 0.0027763588 7.1181784 62.244 62.244 62.244 -0.0015907217 0.0025862003 0.0073335977
- 3900 1.4352825 5.8986215 7.025959 0.003498268 7.176605 62.244 62.244 62.244 0.0030416681 0.0027739509 0.0046791851
- 4000 1.4121845 5.907903 7.0170983 0.005046232 7.2344043 62.244 62.244 62.244 0.0045542682 0.0064113499 0.0041730779
- 4100 1.3989578 5.9082397 7.0070461 0.00042880001 7.0255115 62.244 62.244 62.244 0.0025735184 0.0025181486 -0.003805267
- 4200 1.3998829 5.8998147 6.9993477 0.0042777376 7.18356 62.244 62.244 62.244 0.0013744091 0.00646996 0.0049888436
- 4300 1.4076022 5.9044509 7.010047 0.0066789366 7.2976622 62.244 62.244 62.244 0.0073610616 0.0048139129 0.0078618353
- 4400 1.4161075 5.9064331 7.0187096 -0.0011844267 6.9677046 62.244 62.244 62.244 -0.0019088313 -0.0037556503 0.0021112015
- 4500 1.4292243 5.8980093 7.0205884 0.0018500416 7.1002567 62.244 62.244 62.244 0.0041144085 0.0010160497 0.00041966655
- 4600 1.3958775 5.8943133 6.9907003 0.0041485723 7.1693504 62.244 62.244 62.244 0.0033999287 0.0041620406 0.0048837475
- 4700 1.3856614 5.8886847 6.9770475 0.0013150314 7.0336767 62.244 62.244 62.244 -0.00051753674 0.0030875481 0.0013750828
- 4800 1.401683 5.9023505 7.0032974 0.002504877 7.1111649 62.244 62.244 62.244 0.0016543718 -0.0001813413 0.0060416007
- 4900 1.446628 5.9050553 7.0413042 -0.0026645902 6.9265589 62.244 62.244 62.244 -0.00069368076 -0.0073984763 9.8386402e-05
- 5000 1.4387091 5.9077604 7.0377893 0.0049468048 7.2508137 62.244 62.244 62.244 0.0042902506 0.0046715523 0.0058786114
-Loop time of 3.14543 on 4 procs for 5000 steps with 5600 atoms
-
-Performance: 686709.553 tau/day, 1589.605 timesteps/s
-99.2% CPU use with 4 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.081628 | 0.12747 | 0.17984 | 12.8 | 4.05
-Bond | 0.037502 | 0.057149 | 0.076595 | 7.6 | 1.82
-Neigh | 0.65705 | 0.6588 | 0.66084 | 0.2 | 20.94
-Comm | 0.1653 | 0.23616 | 0.29975 | 12.9 | 7.51
-Output | 0.0021076 | 0.0028133 | 0.003227 | 0.9 | 0.09
-Modify | 1.8231 | 1.8972 | 1.9713 | 5.2 | 60.32
-Other | | 0.1658 | | | 5.27
-
-Nlocal: 1400 ave 1868 max 905 min
-Histogram: 1 1 0 0 0 0 0 0 0 2
-Nghost: 648.25 ave 688 max 598 min
-Histogram: 1 0 0 1 0 0 0 0 1 1
-Neighs: 1202.5 ave 1821 max 698 min
-Histogram: 2 0 0 0 0 0 0 1 0 1
-
-Total # of neighbors = 4810
-Ave neighs/atom = 0.858929
-Ave special neighs/atom = 0.571429
-Neighbor list builds = 759
-Dangerous builds = 0
-
-# Replace fix rigid and fix langevin with new ones
-
-unfix 1
-unfix 3
-
-fix 3 tethers langevin 1.4 1.4 1.0 198450
-
-# Test different integrators for rods
-
-fix 1 rods rigid/nve molecule
-800 rigid bodies with 4000 atoms
-print "rigid/nve"
-rigid/nve
-run 1000
-Memory usage per processor = 6.98553 Mbytes
-Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
- 5000 1.4387091 5.9077604 7.0377893 0.0035977871 7.1927209 62.244 62.244 62.244 0.025518192 -0.016769871 0.0020450407
- 5100 1.4449405 5.8876257 7.022549 0.0023104502 7.122044 62.244 62.244 62.244 0.0045960664 0.0036845954 -0.0013493113
- 5200 1.4271652 5.9160022 7.036964 0.0020238904 7.1241189 62.244 62.244 62.244 -0.0022546188 0.00392213 0.0044041599
- 5300 1.4143299 5.9052666 7.016147 0.0064054214 7.2919838 62.244 62.244 62.244 0.0090997079 0.0026363579 0.0074801984
- 5400 1.4426441 5.9087558 7.0418754 0.0020465683 7.1300068 62.244 62.244 62.244 0.0043188307 3.0314417e-06 0.0018178427
- 5500 1.4281065 5.9038871 7.0255883 0.00058665945 7.0508516 62.244 62.244 62.244 0.005898925 0.00066013177 -0.0047990784
- 5600 1.4315628 5.902373 7.0267888 0.0096475978 7.4422435 62.244 62.244 62.244 0.0054175405 0.011780025 0.011745228
- 5700 1.4075482 5.9075587 7.0131124 0.0052150708 7.2376891 62.244 62.244 62.244 0.0030069124 0.0036690785 0.0089692215
- 5800 1.4215681 5.9048555 7.0214211 0.0015070444 7.086319 62.244 62.244 62.244 -5.6858344e-05 0.0023644208 0.0022135708
- 5900 1.3992461 5.8949367 6.9939696 0.0062425817 7.262794 62.244 62.244 62.244 0.0056972212 0.0095293238 0.0035012003
- 6000 1.385289 5.8972105 6.9852808 0.0043255163 7.1715506 62.244 62.244 62.244 0.0040215567 0.0026330714 0.0063219208
-Loop time of 0.74555 on 4 procs for 1000 steps with 5600 atoms
-
-Performance: 579437.739 tau/day, 1341.291 timesteps/s
-99.6% CPU use with 4 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.020915 | 0.033416 | 0.047822 | 6.7 | 4.48
-Bond | 0.0076883 | 0.011506 | 0.015239 | 3.3 | 1.54
-Neigh | 0.14225 | 0.14262 | 0.14297 | 0.1 | 19.13
-Comm | 0.030192 | 0.0485 | 0.064376 | 7.2 | 6.51
-Output | 0.00039148 | 0.0005275 | 0.00062299 | 0.4 | 0.07
-Modify | 0.46557 | 0.47773 | 0.49051 | 1.7 | 64.08
-Other | | 0.03125 | | | 4.19
-
-Nlocal: 1400 ave 1868 max 935 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-Nghost: 633.75 ave 695 max 541 min
-Histogram: 1 0 0 0 1 0 0 0 0 2
-Neighs: 1263 ave 1799 max 710 min
-Histogram: 1 1 0 0 0 0 0 0 0 2
-
-Total # of neighbors = 5052
-Ave neighs/atom = 0.902143
-Ave special neighs/atom = 0.571429
-Neighbor list builds = 153
-Dangerous builds = 0
-unfix 1
-
-fix 1 rods rigid/nvt molecule temp 1.4 1.4 1.0
-800 rigid bodies with 4000 atoms
-print "rigid/nvt"
-rigid/nvt
-run 1000
-Memory usage per processor = 6.98553 Mbytes
-Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
- 6000 1.385289 5.8972105 6.9852808 0.0029190017 7.1109818 62.244 62.244 62.244 0.026575922 -0.075631452 0.057812535
- 6100 1.3829575 5.9055308 6.9917699 0.0022904847 7.0904051 62.244 62.244 62.244 -0.00045870152 0.004055647 0.0032745086
- 6200 1.3942692 5.90506 7.0001838 0.0046406767 7.2000253 62.244 62.244 62.244 0.0042263478 0.0051632788 0.0045324035
- 6300 1.4009885 5.902399 7.0028005 0.0077682485 7.3373247 62.244 62.244 62.244 0.0071636925 0.0098268465 0.0063142066
- 6400 1.3627532 5.9075587 6.9779284 0.0093180812 7.3791931 62.244 62.244 62.244 0.0062401482 0.013022619 0.0086914761
- 6500 1.3341203 5.9012967 6.9491767 0.010108056 7.3844601 62.244 62.244 62.244 0.0031876333 0.011099549 0.016036984
- 6600 1.3572847 5.8915298 6.9576041 -0.00034416741 6.9427833 62.244 62.244 62.244 0.0025578983 -0.0011308804 -0.0024595201
- 6700 1.3663741 5.8985276 6.9717412 0.002947281 7.09866 62.244 62.244 62.244 0.0022469396 -0.00042872124 0.0070236245
- 6800 1.3816731 5.8909305 6.9761607 -9.1110394e-05 6.9722372 62.244 62.244 62.244 -0.0048195881 -0.00080983527 0.0053560922
- 6900 1.4011479 5.8881921 6.9887187 0.0010084642 7.0321462 62.244 62.244 62.244 0.0012132523 -0.0025918018 0.0044039422
- 7000 1.3973667 5.8867951 6.9843517 0.0070023833 7.2858955 62.244 62.244 62.244 0.0058928565 0.0076813429 0.0074329504
-Loop time of 0.761012 on 4 procs for 1000 steps with 5600 atoms
-
-Performance: 567665.504 tau/day, 1314.041 timesteps/s
-99.6% CPU use with 4 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.022122 | 0.034862 | 0.048912 | 6.6 | 4.58
-Bond | 0.0078702 | 0.011574 | 0.015191 | 3.2 | 1.52
-Neigh | 0.1398 | 0.14013 | 0.14044 | 0.1 | 18.41
-Comm | 0.029736 | 0.047586 | 0.064077 | 7.3 | 6.25
-Output | 0.00039291 | 0.00053465 | 0.00063396 | 0.4 | 0.07
-Modify | 0.48838 | 0.49907 | 0.50959 | 1.4 | 65.58
-Other | | 0.02726 | | | 3.58
-
-Nlocal: 1400 ave 1832 max 970 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-Nghost: 652.5 ave 749 max 561 min
-Histogram: 1 0 0 1 0 0 1 0 0 1
-Neighs: 1407.5 ave 2071 max 748 min
-Histogram: 1 1 0 0 0 0 0 0 1 1
-
-Total # of neighbors = 5630
-Ave neighs/atom = 1.00536
-Ave special neighs/atom = 0.571429
-Neighbor list builds = 149
-Dangerous builds = 0
-unfix 1
-
-compute myTemp all temp
-
-fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 iso 0.05 0.05 1.0 dilate all
-800 rigid bodies with 4000 atoms
-print "rigid/npt iso"
-rigid/npt iso
-fix_modify 1 temp myTemp
-
-run 1000
-Memory usage per processor = 6.98553 Mbytes
-Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
- 7000 1.3973667 5.8867951 6.9843517 0.0026559416 7.0987246 62.244 62.244 62.244 0.033713637 -0.0068647989 -0.018881013
- 7100 1.4639139 5.8611823 7.0110083 0.011521251 7.3924625 57.022152 57.022152 57.022152 0.010787531 0.0093708984 0.014405322
- 7200 1.4950463 5.8177011 6.9919798 0.023101297 7.5163969 50.281647 50.281647 50.281647 0.023242216 0.018105116 0.02795656
- 7300 1.5103331 5.7757714 6.9620571 0.022650056 7.3366292 45.243 45.243 45.243 0.023573421 0.022300241 0.022076507
- 7400 1.5582095 5.7578511 6.9817412 0.028508467 7.3477691 41.582392 41.582392 41.582392 0.02740467 0.030003113 0.028117619
- 7500 1.5992723 5.6927269 6.9488696 0.046538335 7.4419099 39.001967 39.001967 39.001967 0.057728057 0.030859627 0.05102732
- 7600 1.5572154 5.6717168 6.894826 0.032055597 7.184009 36.967405 36.967405 36.967405 0.034785798 0.033408508 0.027972486
- 7700 1.541013 5.6302838 6.840667 0.046629681 7.2052858 35.246953 35.246953 35.246953 0.051145184 0.022437926 0.066305932
- 7800 1.4922447 5.6135845 6.7856627 0.066398531 7.2467615 33.879827 33.879827 33.879827 0.05766722 0.07643975 0.065088623
- 7900 1.5126099 5.5498409 6.7379149 0.060758513 7.1190044 32.749346 32.749346 32.749346 0.045401188 0.069519167 0.067355184
- 8000 1.498932 5.5307653 6.708096 0.0068958389 6.7481394 31.918601 31.918601 31.918601 0.004934357 -0.0067897493 0.022542909
-Loop time of 1.40621 on 4 procs for 1000 steps with 5600 atoms
-
-Performance: 307209.818 tau/day, 711.134 timesteps/s
-99.5% CPU use with 4 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.057011 | 0.094542 | 0.13471 | 11.0 | 6.72
-Bond | 0.012043 | 0.017356 | 0.022935 | 3.8 | 1.23
-Neigh | 0.50655 | 0.50716 | 0.50781 | 0.1 | 36.07
-Comm | 0.060325 | 0.10627 | 0.14985 | 12.0 | 7.56
-Output | 0.0003705 | 0.00040978 | 0.00051475 | 0.3 | 0.03
-Modify | 0.60798 | 0.63453 | 0.65863 | 2.9 | 45.12
-Other | | 0.04594 | | | 3.27
-
-Nlocal: 1400 ave 1820 max 1010 min
-Histogram: 1 1 0 0 0 0 0 0 1 1
-Nghost: 1576 ave 1694 max 1470 min
-Histogram: 1 1 0 0 0 0 0 1 0 1
-Neighs: 6543 ave 9989 max 3497 min
-Histogram: 1 1 0 0 0 0 0 1 0 1
-
-Total # of neighbors = 26172
-Ave neighs/atom = 4.67357
-Ave special neighs/atom = 0.571429
-Neighbor list builds = 337
-Dangerous builds = 0
-unfix 1
-
-fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 x 0.05 0.05 1.0 dilate all
-800 rigid bodies with 4000 atoms
-print "rigid/npt x"
-rigid/npt x
-run 1000
-Memory usage per processor = 7.00192 Mbytes
-Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
- 8000 1.498932 5.5307653 6.708096 0.044418732 6.9660307 31.918601 31.918601 31.918601 0.033240642 0.090981355 0.0090341992
- 8100 1.4932748 5.5104122 6.6832996 0.078824127 7.1379335 31.703188 31.918601 31.918601 0.046668046 0.090499077 0.099305258
- 8200 1.4783774 5.4958482 6.6570345 0.024180825 6.7956092 31.500184 31.918601 31.918601 -0.01991799 0.022036912 0.070423554
- 8300 1.4699766 5.468569 6.6231569 0.050331767 6.9062762 30.919162 31.918601 31.918601 0.030889484 0.091318073 0.028787743
- 8400 1.4423945 5.4591749 6.5920985 0.034769472 6.7835475 30.266023 31.918601 31.918601 0.031838545 0.067297532 0.0051723374
- 8500 1.4478469 5.4405027 6.5777089 0.061608005 6.9111775 29.752136 31.918601 31.918601 0.056987338 0.064105062 0.063731616
- 8600 1.4216004 5.443144 6.5597349 0.031739807 6.7291722 29.343028 31.918601 31.918601 0.047008356 0.040197385 0.0080136813
- 8700 1.3993468 5.4199487 6.5190607 0.055753353 6.8130189 28.981104 31.918601 31.918601 0.038071725 0.050746074 0.078442261
- 8800 1.4272224 5.3956531 6.5166598 0.051937078 6.7855855 28.46133 31.918601 31.918601 0.038718856 0.054121272 0.062971108
- 8900 1.430201 5.3881483 6.5114945 0.042705385 6.728515 27.933053 31.918601 31.918601 0.053090216 0.033892798 0.04113314
- 9000 1.4147254 5.3571794 6.4683705 0.015474623 6.5454193 27.368213 31.918601 31.918601 0.018517547 0.023668345 0.0042379783
-Loop time of 1.3981 on 4 procs for 1000 steps with 5600 atoms
-
-Performance: 308990.110 tau/day, 715.255 timesteps/s
-99.4% CPU use with 4 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.090644 | 0.15054 | 0.22186 | 13.5 | 10.77
-Bond | 0.013196 | 0.017756 | 0.022439 | 2.9 | 1.27
-Neigh | 0.40253 | 0.40269 | 0.40288 | 0.0 | 28.80
-Comm | 0.057128 | 0.13282 | 0.1979 | 15.4 | 9.50
-Output | 0.00036597 | 0.00040632 | 0.0004673 | 0.2 | 0.03
-Modify | 0.62613 | 0.65125 | 0.67228 | 2.1 | 46.58
-Other | | 0.04265 | | | 3.05
-
-Nlocal: 1400 ave 1770 max 1095 min
-Histogram: 1 1 0 0 0 0 1 0 0 1
-Nghost: 1578.5 ave 1693 max 1493 min
-Histogram: 2 0 0 0 0 0 0 1 0 1
-Neighs: 7868 ave 12041 max 4579 min
-Histogram: 1 1 0 0 0 0 1 0 0 1
-
-Total # of neighbors = 31472
-Ave neighs/atom = 5.62
-Ave special neighs/atom = 0.571429
-Neighbor list builds = 167
-Dangerous builds = 0
-unfix 1
-
-fix 1 rods rigid/nph molecule iso 0.05 0.05 1.0 dilate all
-800 rigid bodies with 4000 atoms
-print "rigid/nph iso"
-rigid/nph iso
-run 1000
-Memory usage per processor = 7.00192 Mbytes
-Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
- 9000 1.4147254 5.3571794 6.4683705 0.026540417 6.6005164 27.368213 31.918601 31.918601 -0.25291277 0.19881452 0.1337195
- 9100 1.4143578 5.3349724 6.4458747 0.032533861 6.6070914 27.324726 31.867884 31.867884 0.031965858 0.023737907 0.041897818
- 9200 1.4489265 5.3126352 6.4506893 0.020125553 6.5486389 27.161226 31.6772 31.6772 0.024138053 0.045983015 -0.0097444101
- 9300 1.4434983 5.3100314 6.4438219 0.071722015 6.7864703 26.993744 31.481872 31.481872 0.081599435 0.059208723 0.074357889
- 9400 1.4179009 5.3170886 6.4307738 0.020348306 6.5262516 26.832169 31.293432 31.293432 0.070733237 -0.0042808269 -0.0054074919
- 9500 1.455947 5.2941589 6.4377273 0.0066330065 6.4680826 26.60963 31.033892 31.033892 -0.026145193 -0.017478757 0.06352297
- 9600 1.4322198 5.2747171 6.399649 0.079157317 6.755508 26.452091 30.85016 30.85016 0.09770091 0.095143096 0.044627945
- 9700 1.4366074 5.2650795 6.3934576 0.052444405 6.6264505 26.347873 30.728614 30.728614 0.043301655 0.043720535 0.070311026
- 9800 1.4311568 5.268838 6.392935 0.056161789 6.637248 26.163729 30.513853 30.513853 0.071096045 0.048086199 0.049303122
- 9900 1.4437347 5.2369801 6.3709564 0.11335968 6.8497267 25.907207 30.214681 30.214681 0.1259046 0.10149135 0.11268308
- 10000 1.4627878 5.2272205 6.376162 0.082077049 6.7164073 25.746677 30.02746 30.02746 0.060839015 0.13885619 0.046535946
-Loop time of 1.38185 on 4 procs for 1000 steps with 5600 atoms
-
-Performance: 312625.215 tau/day, 723.669 timesteps/s
-99.4% CPU use with 4 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.11291 | 0.17289 | 0.23942 | 12.0 | 12.51
-Bond | 0.013814 | 0.017709 | 0.022031 | 2.5 | 1.28
-Neigh | 0.40444 | 0.4048 | 0.40511 | 0.0 | 29.29
-Comm | 0.055045 | 0.12527 | 0.18875 | 14.9 | 9.07
-Output | 0.0003531 | 0.00038058 | 0.00045681 | 0.2 | 0.03
-Modify | 0.60769 | 0.62523 | 0.64283 | 1.7 | 45.25
-Other | | 0.03557 | | | 2.57
-
-Nlocal: 1400 ave 1669 max 1139 min
-Histogram: 1 0 1 0 0 0 0 1 0 1
-Nghost: 1761.5 ave 1898 max 1632 min
-Histogram: 2 0 0 0 0 0 0 0 1 1
-Neighs: 9311.75 ave 12525 max 5959 min
-Histogram: 1 0 1 0 0 0 0 1 0 1
-
-Total # of neighbors = 37247
-Ave neighs/atom = 6.65125
-Ave special neighs/atom = 0.571429
-Neighbor list builds = 165
-Dangerous builds = 0
-unfix 1
-
-fix 1 rods rigid/nph molecule x 0.05 0.05 1.0 y 0.05 0.05 1.0 couple xy dilate all
-800 rigid bodies with 4000 atoms
-print "rigid/nph xy couple"
-rigid/nph xy couple
-run 1000
-Memory usage per processor = 7.00192 Mbytes
-Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
- 10000 1.4627878 5.2272205 6.376162 0.087181735 6.7375684 25.746677 30.02746 30.02746 0.01077504 0.047196696 0.20357347
- 10100 1.461932 5.2277217 6.3759909 0.045218386 6.5623932 25.674625 29.943429 30.02746 0.029664553 0.034940919 0.071049687
- 10200 1.4394425 5.2183968 6.3490017 0.064139003 6.6129181 25.651225 29.916138 30.02746 0.063541799 0.099454655 0.029420554
- 10300 1.445679 5.2124787 6.3479821 0.073611235 6.6513251 25.670301 29.938385 30.02746 0.09678342 0.1092442 0.01480609
- 10400 1.4289478 5.2082727 6.3306346 -0.00091064043 6.3268902 25.642317 29.905748 30.02746 -0.021792005 0.043173882 -0.024113799
- 10500 1.4138512 5.191318 6.3018224 0.051274311 6.5114152 25.566672 29.817526 30.02746 0.087657762 0.022098862 0.04406631
- 10600 1.4101298 5.2048433 6.3124247 0.032021085 6.442127 25.450236 29.681731 30.02746 0.032483644 0.022737859 0.040841754
- 10700 1.4527253 5.1827275 6.3237654 0.045295082 6.5054661 25.327296 29.53835 30.02746 0.082847312 0.0364514 0.016586533
- 10800 1.4661732 5.1586918 6.3102923 0.084525247 6.6478976 25.272455 29.474391 30.02746 0.10699807 0.070825674 0.075751992
- 10900 1.4301511 5.1743273 6.2976344 0.014007746 6.3539547 25.356203 29.572064 30.02746 -0.015258276 -0.0047253148 0.06200683
- 11000 1.4346828 5.1625047 6.2893712 0.034027405 6.4273459 25.463687 29.697419 30.02746 0.041309225 0.014001823 0.046771165
-Loop time of 1.36647 on 4 procs for 1000 steps with 5600 atoms
-
-Performance: 316143.197 tau/day, 731.813 timesteps/s
-99.4% CPU use with 4 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section | min time | avg time | max time |%varavg| %total
----------------------------------------------------------------
-Pair | 0.13847 | 0.19365 | 0.24916 | 9.9 | 14.17
-Bond | 0.014236 | 0.017841 | 0.02132 | 2.2 | 1.31
-Neigh | 0.37634 | 0.37662 | 0.37685 | 0.0 | 27.56
-Comm | 0.057297 | 0.11588 | 0.17429 | 13.5 | 8.48
-Output | 0.00035167 | 0.00037664 | 0.00044203 | 0.2 | 0.03
-Modify | 0.61282 | 0.62929 | 0.64128 | 1.4 | 46.05
-Other | | 0.03282 | | | 2.40
-
-Nlocal: 1400 ave 1607 max 1199 min
-Histogram: 1 0 1 0 0 0 0 1 0 1
-Nghost: 1819.25 ave 1940 max 1712 min
-Histogram: 1 1 0 0 0 0 0 1 0 1
-Neighs: 9882 ave 12628 max 7201 min
-Histogram: 1 0 1 0 0 0 0 1 0 1
-
-Total # of neighbors = 39528
-Ave neighs/atom = 7.05857
-Ave special neighs/atom = 0.571429
-Neighbor list builds = 156
-Dangerous builds = 0
-
-Total wall time: 0:00:10
diff --git a/examples/snap/log.20Apr18.snap.Mo_Chen.g++.1 b/examples/snap/log.20Apr18.snap.Mo_Chen.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..c5e0f6abab7b7eb657e529096265fa9d3a9bfcff
--- /dev/null
+++ b/examples/snap/log.20Apr18.snap.Mo_Chen.g++.1
@@ -0,0 +1,127 @@
+LAMMPS (20 Apr 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+ using 1 OpenMP thread(s) per MPI task
+# 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 nx equal 4
+variable ny equal ${nrep}
+variable ny equal 4
+variable nz equal ${nrep}
+variable nz equal 4
+
+boundary p p p
+
+lattice bcc $a
+lattice bcc 3.16
+Lattice spacing in x,y,z = 3.16 3.16 3.16
+region box block 0 ${nx} 0 ${ny} 0 ${nz}
+region box block 0 4 0 ${ny} 0 ${nz}
+region box block 0 4 0 4 0 ${nz}
+region box block 0 4 0 4 0 4
+create_box 1 box
+Created orthogonal box = (0 0 0) to (12.64 12.64 12.64)
+ 1 by 1 by 1 MPI processor grid
+create_atoms 1 box
+Created 128 atoms
+ Time spent = 0.000223637 secs
+
+mass 1 183.84
+
+# choose potential
+
+include Mo_Chen_PRM2017.snap
+
+# 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
+Reading potential file Mo_Chen_PRM2017.snapcoeff with DATE: 2017-09-18
+SNAP Element = Mo, Radius 0.5, Weight 1
+Reading potential file Mo_Chen_PRM2017.snapparam with DATE: 2017-09-18
+SNAP keyword rcutfac 4.615858
+SNAP keyword twojmax 6
+
+
+# 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}
+run 100
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 5.61586
+ ghost atom cutoff = 5.61586
+ binsize = 2.80793, bins = 5 5 5
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair snap, perpetual
+ attributes: full, newton on
+ pair build: full/bin/atomonly
+ stencil: full/bin/3d
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.507 | 3.507 | 3.507 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 300 -22.405975 0 -22.3675 2575.7657
+ 10 294.77555 -22.405305 0 -22.3675 2756.6894
+ 20 279.53011 -22.40335 0 -22.3675 3285.8272
+ 30 255.52174 -22.40027 0 -22.3675 4122.8933
+ 40 224.7299 -22.396321 0 -22.367499 5204.3499
+ 50 189.67529 -22.391825 0 -22.367499 6449.1308
+ 60 153.18862 -22.387145 0 -22.367499 7765.911
+ 70 118.14998 -22.382652 0 -22.367499 9061.1616
+ 80 87.224916 -22.378685 0 -22.367499 10247.68
+ 90 62.623892 -22.37553 0 -22.367498 11250.067
+ 100 45.9103 -22.373386 0 -22.367498 12011.726
+Loop time of 3.3917 on 1 procs for 100 steps with 128 atoms
+
+Performance: 1.274 ns/day, 18.843 hours/ns, 29.484 timesteps/s
+99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 3.3906 | 3.3906 | 3.3906 | 0.0 | 99.97
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.00039721 | 0.00039721 | 0.00039721 | 0.0 | 0.01
+Output | 0.00023007 | 0.00023007 | 0.00023007 | 0.0 | 0.01
+Modify | 0.00021887 | 0.00021887 | 0.00021887 | 0.0 | 0.01
+Other | | 0.0002868 | | | 0.01
+
+Nlocal: 128 ave 128 max 128 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 727 ave 727 max 727 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs: 7424 ave 7424 max 7424 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 7424
+Ave neighs/atom = 58
+Neighbor list builds = 0
+Dangerous builds = 0
+
+Total wall time: 0:00:03
diff --git a/examples/snap/log.20Apr18.snap.Mo_Chen.g++.4 b/examples/snap/log.20Apr18.snap.Mo_Chen.g++.4
new file mode 100644
index 0000000000000000000000000000000000000000..c25f1f5530856ab7dc5492526aa168c9dafd6fad
--- /dev/null
+++ b/examples/snap/log.20Apr18.snap.Mo_Chen.g++.4
@@ -0,0 +1,127 @@
+LAMMPS (20 Apr 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+ using 1 OpenMP thread(s) per MPI task
+# 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 nx equal 4
+variable ny equal ${nrep}
+variable ny equal 4
+variable nz equal ${nrep}
+variable nz equal 4
+
+boundary p p p
+
+lattice bcc $a
+lattice bcc 3.16
+Lattice spacing in x,y,z = 3.16 3.16 3.16
+region box block 0 ${nx} 0 ${ny} 0 ${nz}
+region box block 0 4 0 ${ny} 0 ${nz}
+region box block 0 4 0 4 0 ${nz}
+region box block 0 4 0 4 0 4
+create_box 1 box
+Created orthogonal box = (0 0 0) to (12.64 12.64 12.64)
+ 1 by 2 by 2 MPI processor grid
+create_atoms 1 box
+Created 128 atoms
+ Time spent = 0.000277281 secs
+
+mass 1 183.84
+
+# choose potential
+
+include Mo_Chen_PRM2017.snap
+
+# 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
+Reading potential file Mo_Chen_PRM2017.snapcoeff with DATE: 2017-09-18
+SNAP Element = Mo, Radius 0.5, Weight 1
+Reading potential file Mo_Chen_PRM2017.snapparam with DATE: 2017-09-18
+SNAP keyword rcutfac 4.615858
+SNAP keyword twojmax 6
+
+
+# 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}
+run 100
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 5.61586
+ ghost atom cutoff = 5.61586
+ binsize = 2.80793, bins = 5 5 5
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair snap, perpetual
+ attributes: full, newton on
+ pair build: full/bin/atomonly
+ stencil: full/bin/3d
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.486 | 3.486 | 3.486 Mbytes
+Step Temp E_pair E_mol TotEng Press
+ 0 300 -22.405975 0 -22.3675 2575.7657
+ 10 294.63153 -22.405286 0 -22.3675 2753.4662
+ 20 278.98535 -22.40328 0 -22.3675 3272.416
+ 30 254.38916 -22.400125 0 -22.3675 4091.8933
+ 40 222.91191 -22.396088 0 -22.367499 5148.5505
+ 50 187.16984 -22.391504 0 -22.367499 6362.2454
+ 60 150.08253 -22.386747 0 -22.367499 7643.2732
+ 70 114.60307 -22.382197 0 -22.367499 8900.2448
+ 80 83.449257 -22.378201 0 -22.367499 10047.619
+ 90 58.862643 -22.375048 0 -22.367498 11012.233
+ 100 42.41931 -22.372939 0 -22.367498 11740.641
+Loop time of 1.91636 on 4 procs for 100 steps with 128 atoms
+
+Performance: 2.254 ns/day, 10.646 hours/ns, 52.182 timesteps/s
+97.9% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 1.8147 | 1.8411 | 1.8875 | 2.1 | 96.07
+Neigh | 0 | 0 | 0 | 0.0 | 0.00
+Comm | 0.022276 | 0.069629 | 0.095057 | 10.7 | 3.63
+Output | 0.00032496 | 0.00065821 | 0.0016179 | 0.0 | 0.03
+Modify | 0.00019503 | 0.00020915 | 0.00023341 | 0.0 | 0.01
+Other | | 0.00481 | | | 0.25
+
+Nlocal: 32 ave 32 max 32 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost: 431 ave 431 max 431 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs: 0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs: 1856 ave 1856 max 1856 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 7424
+Ave neighs/atom = 58
+Neighbor list builds = 0
+Dangerous builds = 0
+
+Total wall time: 0:00:01
diff --git a/examples/snap/log.5Oct16.snap.Ta06A.g++.1 b/examples/snap/log.20Apr18.snap.Ta06A.g++.1
similarity index 71%
rename from examples/snap/log.5Oct16.snap.Ta06A.g++.1
rename to examples/snap/log.20Apr18.snap.Ta06A.g++.1
index 647ffac8b4326efa8ce7f6fca6b4ee9e577d32f5..d2296852a051bc6d12c58924a802357574a47d6e 100644
--- a/examples/snap/log.5Oct16.snap.Ta06A.g++.1
+++ b/examples/snap/log.20Apr18.snap.Ta06A.g++.1
@@ -1,4 +1,6 @@
-LAMMPS (5 Oct 2016)
+LAMMPS (20 Apr 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+ using 1 OpenMP thread(s) per MPI task
# Demonstrate SNAP Ta potential
# Initialize simulation
@@ -31,12 +33,13 @@ Created orthogonal box = (0 0 0) to (13.264 13.264 13.264)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 128 atoms
+ Time spent = 0.000328064 secs
mass 1 180.88
# choose potential
-include Ta06A_pot.snap
+include Ta06A.snap
# DATE: 2014-09-05 CONTRIBUTOR: Aidan Thompson athomps@sandia.gov CITATION: Thompson, Swiler, Trott, Foiles and Tucker, arxiv.org, 1409.3880 (2014)
# Definition of SNAP potential Ta_Cand06A
@@ -48,10 +51,9 @@ variable zblz equal 73
# Specify hybrid with SNAP, ZBL
-pair_style hybrid/overlay snap zbl ${zblcutinner} ${zblcutouter}
-pair_style hybrid/overlay snap zbl 4 ${zblcutouter}
-pair_style hybrid/overlay snap zbl 4 4.8
-
+pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap
+pair_style hybrid/overlay zbl 4 ${zblcutouter} snap
+pair_style hybrid/overlay zbl 4 4.8 snap
pair_coeff 1 1 zbl ${zblz} ${zblz}
pair_coeff 1 1 zbl 73 ${zblz}
pair_coeff 1 1 zbl 73 73
@@ -61,10 +63,11 @@ SNAP Element = Ta, Radius 0.5, Weight 1
Reading potential file Ta06A.snapparam with DATE: 2014-09-05
SNAP keyword rcutfac 4.67637
SNAP keyword twojmax 6
-SNAP keyword gamma 1
SNAP keyword rfac0 0.99363
SNAP keyword rmin0 0
SNAP keyword diagonalstyle 3
+SNAP keyword bzeroflag 0
+SNAP keyword quadraticflag 0
# Setup output
@@ -85,13 +88,23 @@ fix 1 all nve
run ${nsteps}
run 100
Neighbor list info ...
- 2 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5.8
ghost atom cutoff = 5.8
- binsize = 2.9 -> bins = 5 5 5
-Memory usage per processor = 2.92823 Mbytes
+ binsize = 2.9, bins = 5 5 5
+ 2 neighbor lists, perpetual/occasional/extra = 2 0 0
+ (1) pair zbl, perpetual, half/full from (2)
+ attributes: half, newton on
+ pair build: halffull/newton
+ stencil: none
+ bin: none
+ (2) pair snap, perpetual
+ attributes: full, newton on
+ pair build: full/bin/atomonly
+ stencil: full/bin/3d
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 4.138 | 4.138 | 4.138 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -11.85157 0 -11.813095 2717.1661
10 295.96579 -11.851053 0 -11.813095 2696.1559
@@ -104,20 +117,20 @@ Step Temp E_pair E_mol TotEng Press
80 124.04276 -11.829003 0 -11.813094 1537.703
90 97.37622 -11.825582 0 -11.813094 1734.9662
100 75.007873 -11.822714 0 -11.813094 1930.8005
-Loop time of 3.43062 on 1 procs for 100 steps with 128 atoms
+Loop time of 2.53266 on 1 procs for 100 steps with 128 atoms
-Performance: 1.259 ns/day, 19.059 hours/ns, 29.149 timesteps/s
-99.9% CPU use with 1 MPI tasks x no OpenMP threads
+Performance: 1.706 ns/day, 14.070 hours/ns, 39.484 timesteps/s
+99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 3.4295 | 3.4295 | 3.4295 | 0.0 | 99.97
+Pair | 2.5313 | 2.5313 | 2.5313 | 0.0 | 99.95
Neigh | 0 | 0 | 0 | 0.0 | 0.00
-Comm | 0.00043988 | 0.00043988 | 0.00043988 | 0.0 | 0.01
-Output | 0.00010014 | 0.00010014 | 0.00010014 | 0.0 | 0.00
-Modify | 0.00024533 | 0.00024533 | 0.00024533 | 0.0 | 0.01
-Other | | 0.0002978 | | | 0.01
+Comm | 0.00051379 | 0.00051379 | 0.00051379 | 0.0 | 0.02
+Output | 0.00023317 | 0.00023317 | 0.00023317 | 0.0 | 0.01
+Modify | 0.00023675 | 0.00023675 | 0.00023675 | 0.0 | 0.01
+Other | | 0.0003583 | | | 0.01
Nlocal: 128 ave 128 max 128 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -133,4 +146,4 @@ Ave neighs/atom = 58
Neighbor list builds = 0
Dangerous builds = 0
-Total wall time: 0:00:03
+Total wall time: 0:00:02
diff --git a/examples/snap/log.5Oct16.snap.Ta06A.g++.4 b/examples/snap/log.20Apr18.snap.Ta06A.g++.4
similarity index 71%
rename from examples/snap/log.5Oct16.snap.Ta06A.g++.4
rename to examples/snap/log.20Apr18.snap.Ta06A.g++.4
index 19d64c557c33538c702da0ddfb4fa1b30c336f8e..4d26481d5de2ccb00bbc364d70af786f458ec2e2 100644
--- a/examples/snap/log.5Oct16.snap.Ta06A.g++.4
+++ b/examples/snap/log.20Apr18.snap.Ta06A.g++.4
@@ -1,4 +1,6 @@
-LAMMPS (5 Oct 2016)
+LAMMPS (20 Apr 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+ using 1 OpenMP thread(s) per MPI task
# Demonstrate SNAP Ta potential
# Initialize simulation
@@ -31,12 +33,13 @@ Created orthogonal box = (0 0 0) to (13.264 13.264 13.264)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 128 atoms
+ Time spent = 0.000288486 secs
mass 1 180.88
# choose potential
-include Ta06A_pot.snap
+include Ta06A.snap
# DATE: 2014-09-05 CONTRIBUTOR: Aidan Thompson athomps@sandia.gov CITATION: Thompson, Swiler, Trott, Foiles and Tucker, arxiv.org, 1409.3880 (2014)
# Definition of SNAP potential Ta_Cand06A
@@ -48,10 +51,9 @@ variable zblz equal 73
# Specify hybrid with SNAP, ZBL
-pair_style hybrid/overlay snap zbl ${zblcutinner} ${zblcutouter}
-pair_style hybrid/overlay snap zbl 4 ${zblcutouter}
-pair_style hybrid/overlay snap zbl 4 4.8
-
+pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap
+pair_style hybrid/overlay zbl 4 ${zblcutouter} snap
+pair_style hybrid/overlay zbl 4 4.8 snap
pair_coeff 1 1 zbl ${zblz} ${zblz}
pair_coeff 1 1 zbl 73 ${zblz}
pair_coeff 1 1 zbl 73 73
@@ -61,10 +63,11 @@ SNAP Element = Ta, Radius 0.5, Weight 1
Reading potential file Ta06A.snapparam with DATE: 2014-09-05
SNAP keyword rcutfac 4.67637
SNAP keyword twojmax 6
-SNAP keyword gamma 1
SNAP keyword rfac0 0.99363
SNAP keyword rmin0 0
SNAP keyword diagonalstyle 3
+SNAP keyword bzeroflag 0
+SNAP keyword quadraticflag 0
# Setup output
@@ -85,13 +88,23 @@ fix 1 all nve
run ${nsteps}
run 100
Neighbor list info ...
- 2 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5.8
ghost atom cutoff = 5.8
- binsize = 2.9 -> bins = 5 5 5
-Memory usage per processor = 2.91109 Mbytes
+ binsize = 2.9, bins = 5 5 5
+ 2 neighbor lists, perpetual/occasional/extra = 2 0 0
+ (1) pair zbl, perpetual, half/full from (2)
+ attributes: half, newton on
+ pair build: halffull/newton
+ stencil: none
+ bin: none
+ (2) pair snap, perpetual
+ attributes: full, newton on
+ pair build: full/bin/atomonly
+ stencil: full/bin/3d
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 4.118 | 4.118 | 4.118 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -11.85157 0 -11.813095 2717.1661
10 295.8664 -11.85104 0 -11.813095 2702.935
@@ -104,20 +117,20 @@ Step Temp E_pair E_mol TotEng Press
80 121.80051 -11.828715 0 -11.813094 1627.6911
90 95.262635 -11.825311 0 -11.813094 1812.9327
100 73.194645 -11.822481 0 -11.813094 1995.2199
-Loop time of 0.89193 on 4 procs for 100 steps with 128 atoms
+Loop time of 1.3621 on 4 procs for 100 steps with 128 atoms
-Performance: 4.843 ns/day, 4.955 hours/ns, 112.116 timesteps/s
-99.9% CPU use with 4 MPI tasks x no OpenMP threads
+Performance: 3.172 ns/day, 7.567 hours/ns, 73.416 timesteps/s
+98.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 0.84444 | 0.86772 | 0.88108 | 1.6 | 97.29
+Pair | 1.2867 | 1.309 | 1.35 | 2.1 | 96.10
Neigh | 0 | 0 | 0 | 0.0 | 0.00
-Comm | 0.009577 | 0.023049 | 0.046417 | 9.8 | 2.58
-Output | 0.00024009 | 0.00026137 | 0.00027895 | 0.1 | 0.03
-Modify | 8.2493e-05 | 9.352e-05 | 0.00010061 | 0.1 | 0.01
-Other | | 0.0008071 | | | 0.09
+Comm | 0.0096083 | 0.050652 | 0.072999 | 10.9 | 3.72
+Output | 0.00031447 | 0.00060236 | 0.0014303 | 0.0 | 0.04
+Modify | 0.00014234 | 0.00016212 | 0.00018811 | 0.0 | 0.01
+Other | | 0.001728 | | | 0.13
Nlocal: 32 ave 32 max 32 min
Histogram: 4 0 0 0 0 0 0 0 0 0
@@ -133,4 +146,4 @@ Ave neighs/atom = 58
Neighbor list builds = 0
Dangerous builds = 0
-Total wall time: 0:00:00
+Total wall time: 0:00:01
diff --git a/examples/snap/log.21Feb17.snap.W.2940.g++.1 b/examples/snap/log.20Apr18.snap.W.2940.g++.1
similarity index 79%
rename from examples/snap/log.21Feb17.snap.W.2940.g++.1
rename to examples/snap/log.20Apr18.snap.W.2940.g++.1
index 8c74380b8b7246dad9bf1079f17ad1ef8e56f7b8..19b2bfb40d88b1fd6dd62ab892dba1f463a48b03 100644
--- a/examples/snap/log.21Feb17.snap.W.2940.g++.1
+++ b/examples/snap/log.20Apr18.snap.W.2940.g++.1
@@ -1,4 +1,6 @@
-LAMMPS (13 Feb 2017)
+LAMMPS (20 Apr 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+ using 1 OpenMP thread(s) per MPI task
# Demonstrate SNAP Ta potential
# Initialize simulation
@@ -31,20 +33,21 @@ Created orthogonal box = (0 0 0) to (12.7212 12.7212 12.7212)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 128 atoms
+ Time spent = 0.000190258 secs
mass 1 183.84
# choose potential
-include W_2940_2017_2.pot.snap
-# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. to appear in arxiv Feb2017
+include W_2940_2017_2.snap
+# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph]
#
# Definition of SNAP+ZBL potential.
variable zblcutinner equal 4
variable zblcutouter equal 4.8
variable zblz equal 74
-# Specify hybrid with SNAP, ZBL, and long-range Coulomb
+# Specify hybrid with SNAP and ZBL
pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap
pair_style hybrid/overlay zbl 4 ${zblcutouter} snap
@@ -58,10 +61,11 @@ SNAP Element = W, Radius 0.5, Weight 1
Reading potential file W_2940_2017_2.snapparam with DATE: 2017-02-20
SNAP keyword rcutfac 4.73442
SNAP keyword twojmax 8
-SNAP keyword gamma 1
SNAP keyword rfac0 0.99363
SNAP keyword rmin0 0
SNAP keyword diagonalstyle 3
+SNAP keyword bzeroflag 0
+SNAP keyword quadraticflag 0
#Nomenclature on the snap files are Element_DakotaID_Year_Month
@@ -99,7 +103,7 @@ Neighbor list info ...
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
-Memory usage per processor = 5.14696 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 5.15 | 5.15 | 5.15 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -11.028325 0 -10.98985 3010.497
10 293.40666 -11.027479 0 -10.989849 3246.0559
@@ -112,20 +116,20 @@ Step Temp E_pair E_mol TotEng Press
80 58.605244 -10.997364 0 -10.989848 11289.914
90 39.754503 -10.994946 0 -10.989848 11824.945
100 32.524085 -10.994019 0 -10.989848 11932.118
-Loop time of 11.8271 on 1 procs for 100 steps with 128 atoms
+Loop time of 9.69738 on 1 procs for 100 steps with 128 atoms
-Performance: 0.365 ns/day, 65.706 hours/ns, 8.455 timesteps/s
-99.9% CPU use with 1 MPI tasks x no OpenMP threads
+Performance: 0.445 ns/day, 53.874 hours/ns, 10.312 timesteps/s
+99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 11.826 | 11.826 | 11.826 | 0.0 | 99.99
+Pair | 9.6961 | 9.6961 | 9.6961 | 0.0 | 99.99
Neigh | 0 | 0 | 0 | 0.0 | 0.00
-Comm | 0.00044084 | 0.00044084 | 0.00044084 | 0.0 | 0.00
-Output | 0.00013232 | 0.00013232 | 0.00013232 | 0.0 | 0.00
-Modify | 0.00021887 | 0.00021887 | 0.00021887 | 0.0 | 0.00
-Other | | 0.0002718 | | | 0.00
+Comm | 0.00044036 | 0.00044036 | 0.00044036 | 0.0 | 0.00
+Output | 0.00024843 | 0.00024843 | 0.00024843 | 0.0 | 0.00
+Modify | 0.00023937 | 0.00023937 | 0.00023937 | 0.0 | 0.00
+Other | | 0.0003347 | | | 0.00
Nlocal: 128 ave 128 max 128 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -141,4 +145,4 @@ Ave neighs/atom = 58
Neighbor list builds = 0
Dangerous builds = 0
-Total wall time: 0:00:11
+Total wall time: 0:00:09
diff --git a/examples/snap/log.21Feb17.snap.W.2940.g++.4 b/examples/snap/log.20Apr18.snap.W.2940.g++.4
similarity index 79%
rename from examples/snap/log.21Feb17.snap.W.2940.g++.4
rename to examples/snap/log.20Apr18.snap.W.2940.g++.4
index 97ed5cc8d12728a0e1d9fb2bc79729188ad7c569..dfa63fc6ea208d4552b8533a1a32fd73bc88d4fe 100644
--- a/examples/snap/log.21Feb17.snap.W.2940.g++.4
+++ b/examples/snap/log.20Apr18.snap.W.2940.g++.4
@@ -1,4 +1,6 @@
-LAMMPS (13 Feb 2017)
+LAMMPS (20 Apr 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+ using 1 OpenMP thread(s) per MPI task
# Demonstrate SNAP Ta potential
# Initialize simulation
@@ -31,20 +33,21 @@ Created orthogonal box = (0 0 0) to (12.7212 12.7212 12.7212)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 128 atoms
+ Time spent = 0.000309944 secs
mass 1 183.84
# choose potential
-include W_2940_2017_2.pot.snap
-# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. to appear in arxiv Feb2017
+include W_2940_2017_2.snap
+# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph]
#
# Definition of SNAP+ZBL potential.
variable zblcutinner equal 4
variable zblcutouter equal 4.8
variable zblz equal 74
-# Specify hybrid with SNAP, ZBL, and long-range Coulomb
+# Specify hybrid with SNAP and ZBL
pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap
pair_style hybrid/overlay zbl 4 ${zblcutouter} snap
@@ -58,10 +61,11 @@ SNAP Element = W, Radius 0.5, Weight 1
Reading potential file W_2940_2017_2.snapparam with DATE: 2017-02-20
SNAP keyword rcutfac 4.73442
SNAP keyword twojmax 8
-SNAP keyword gamma 1
SNAP keyword rfac0 0.99363
SNAP keyword rmin0 0
SNAP keyword diagonalstyle 3
+SNAP keyword bzeroflag 0
+SNAP keyword quadraticflag 0
#Nomenclature on the snap files are Element_DakotaID_Year_Month
@@ -99,7 +103,7 @@ Neighbor list info ...
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
-Memory usage per processor = 5.12833 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 5.13 | 5.13 | 5.13 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -11.028325 0 -10.98985 3010.497
10 293.22504 -11.027456 0 -10.989849 3258.275
@@ -112,20 +116,20 @@ Step Temp E_pair E_mol TotEng Press
80 56.127265 -10.997046 0 -10.989848 11551.687
90 38.025013 -10.994724 0 -10.989847 12069.936
100 31.768127 -10.993922 0 -10.989847 12145.648
-Loop time of 3.03545 on 4 procs for 100 steps with 128 atoms
+Loop time of 5.15615 on 4 procs for 100 steps with 128 atoms
-Performance: 1.423 ns/day, 16.864 hours/ns, 32.944 timesteps/s
-99.9% CPU use with 4 MPI tasks x no OpenMP threads
+Performance: 0.838 ns/day, 28.645 hours/ns, 19.394 timesteps/s
+98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 2.9594 | 2.9866 | 3.0319 | 1.6 | 98.39
+Pair | 5.0497 | 5.0762 | 5.092 | 0.8 | 98.45
Neigh | 0 | 0 | 0 | 0.0 | 0.00
-Comm | 0.0024238 | 0.047825 | 0.075032 | 12.5 | 1.58
-Output | 0.00021601 | 0.00024045 | 0.00027442 | 0.0 | 0.01
-Modify | 9.6798e-05 | 0.00011188 | 0.00011802 | 0.0 | 0.00
-Other | | 0.000698 | | | 0.02
+Comm | 0.060802 | 0.07661 | 0.10305 | 6.1 | 1.49
+Output | 0.00040722 | 0.00078458 | 0.0018959 | 0.0 | 0.02
+Modify | 0.0002389 | 0.00024962 | 0.00027442 | 0.0 | 0.00
+Other | | 0.002315 | | | 0.04
Nlocal: 32 ave 32 max 32 min
Histogram: 4 0 0 0 0 0 0 0 0 0
@@ -141,4 +145,4 @@ Ave neighs/atom = 58
Neighbor list builds = 0
Dangerous builds = 0
-Total wall time: 0:00:03
+Total wall time: 0:00:05
diff --git a/examples/snap/log.21Feb17.snap.hybrid.WSNAP.HePair.g++.1 b/examples/snap/log.20Apr18.snap.hybrid.WSNAP.HePair.g++.1
similarity index 83%
rename from examples/snap/log.21Feb17.snap.hybrid.WSNAP.HePair.g++.1
rename to examples/snap/log.20Apr18.snap.hybrid.WSNAP.HePair.g++.1
index 846eef269ce580ca63d730be0fb1ced38da1bf58..3f40936308b21d4e3d0ed1e8e83145c5cfd9d0f7 100644
--- a/examples/snap/log.21Feb17.snap.hybrid.WSNAP.HePair.g++.1
+++ b/examples/snap/log.20Apr18.snap.hybrid.WSNAP.HePair.g++.1
@@ -1,4 +1,6 @@
-LAMMPS (13 Feb 2017)
+LAMMPS (20 Apr 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+ using 1 OpenMP thread(s) per MPI task
# Demonstrate SNAP Ta potential
# Initialize simulation
@@ -31,6 +33,7 @@ Created orthogonal box = (0 0 0) to (12.7212 12.7212 12.7212)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 128 atoms
+ Time spent = 0.000431538 secs
mass 1 183.84
mass 2 4.0026
@@ -42,15 +45,15 @@ group helium type 2
5 atoms in group helium
# choose potential
-include W.SNAP_HePair.pot
-# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. to appear in arxiv Feb2017, W-He and He-He from Juslin, N. and Wirth, B. D. Journal of Nuclear Materials, 423, (2013) p61-63
+include W_2940_2017_2_He_JW2013.snap
+# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph]
#
# Definition of SNAP+ZBL+Tabulated potential.
variable zblcutinner equal 4
variable zblcutouter equal 4.8
variable zblz equal 74
-# Specify hybrid with SNAP, ZBL, and long-range Coulomb
+# Specify hybrid with SNAP and ZBL
pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap table spline 10000 table spline 10000
pair_style hybrid/overlay zbl 4 ${zblcutouter} snap table spline 10000 table spline 10000
@@ -64,18 +67,19 @@ SNAP Element = W, Radius 0.5, Weight 1
Reading potential file W_2940_2017_2.snapparam with DATE: 2017-02-20
SNAP keyword rcutfac 4.73442
SNAP keyword twojmax 8
-SNAP keyword gamma 1
SNAP keyword rfac0 0.99363
SNAP keyword rmin0 0
SNAP keyword diagonalstyle 3
+SNAP keyword bzeroflag 0
+SNAP keyword quadraticflag 0
pair_coeff 2 2 table 1 He_He_JW2013.table HeHe
Reading potential file He_He_JW2013.table with DATE: 2017-02-20
WARNING: 1 of 4999 force values in table are inconsistent with -dE/dr.
- Should only be flagged at inflection points (../pair_table.cpp:476)
+ Should only be flagged at inflection points (../pair_table.cpp:481)
pair_coeff 1 2 table 2 W_He_JW2013.table WHe
Reading potential file W_He_JW2013.table with DATE: 2017-02-20
WARNING: 3 of 325 force values in table are inconsistent with -dE/dr.
- Should only be flagged at inflection points (../pair_table.cpp:476)
+ Should only be flagged at inflection points (../pair_table.cpp:481)
#Hybrid/overlay will take all pair styles and add their contributions equally, order of pair_coeff doesnt matter here
#This is not the case for pair_style hybrid ... where only one pair_coeff is read for each type combination, order matters here.
@@ -134,7 +138,7 @@ Neighbor list info ...
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
-Memory usage per processor = 7.6729 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 7.676 | 7.676 | 7.676 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -10.438105 0 -10.39963 -5445.2808
10 290.48923 -10.436885 0 -10.399629 -5646.4813
@@ -147,20 +151,20 @@ Step Temp E_pair E_mol TotEng Press
80 85.903126 -10.410645 0 -10.399628 857.74986
90 65.223651 -10.407993 0 -10.399628 1494.2746
100 59.833542 -10.407302 0 -10.399628 1938.9164
-Loop time of 11.0736 on 1 procs for 100 steps with 128 atoms
+Loop time of 8.902 on 1 procs for 100 steps with 128 atoms
-Performance: 0.390 ns/day, 61.520 hours/ns, 9.030 timesteps/s
-99.9% CPU use with 1 MPI tasks x no OpenMP threads
+Performance: 0.485 ns/day, 49.456 hours/ns, 11.233 timesteps/s
+99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 11.072 | 11.072 | 11.072 | 0.0 | 99.99
-Neigh | 0.00041604 | 0.00041604 | 0.00041604 | 0.0 | 0.00
-Comm | 0.00046253 | 0.00046253 | 0.00046253 | 0.0 | 0.00
-Output | 0.0001657 | 0.0001657 | 0.0001657 | 0.0 | 0.00
-Modify | 0.0002265 | 0.0002265 | 0.0002265 | 0.0 | 0.00
-Other | | 0.0003119 | | | 0.00
+Pair | 8.9002 | 8.9002 | 8.9002 | 0.0 | 99.98
+Neigh | 0.00043058 | 0.00043058 | 0.00043058 | 0.0 | 0.00
+Comm | 0.00045776 | 0.00045776 | 0.00045776 | 0.0 | 0.01
+Output | 0.00025344 | 0.00025344 | 0.00025344 | 0.0 | 0.00
+Modify | 0.00022483 | 0.00022483 | 0.00022483 | 0.0 | 0.00
+Other | | 0.0003953 | | | 0.00
Nlocal: 128 ave 128 max 128 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -176,4 +180,4 @@ Ave neighs/atom = 53.5156
Neighbor list builds = 1
Dangerous builds = 0
-Total wall time: 0:00:11
+Total wall time: 0:00:09
diff --git a/examples/snap/log.21Feb17.snap.hybrid.WSNAP.HePair.g++.4 b/examples/snap/log.20Apr18.snap.hybrid.WSNAP.HePair.g++.4
similarity index 84%
rename from examples/snap/log.21Feb17.snap.hybrid.WSNAP.HePair.g++.4
rename to examples/snap/log.20Apr18.snap.hybrid.WSNAP.HePair.g++.4
index 9bcbd288aa664cf29025090e8c0937e2580d905a..4ec85a63d014085449367848dbfd2c6f787a41e4 100644
--- a/examples/snap/log.21Feb17.snap.hybrid.WSNAP.HePair.g++.4
+++ b/examples/snap/log.20Apr18.snap.hybrid.WSNAP.HePair.g++.4
@@ -1,4 +1,6 @@
-LAMMPS (13 Feb 2017)
+LAMMPS (20 Apr 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+ using 1 OpenMP thread(s) per MPI task
# Demonstrate SNAP Ta potential
# Initialize simulation
@@ -31,6 +33,7 @@ Created orthogonal box = (0 0 0) to (12.7212 12.7212 12.7212)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 128 atoms
+ Time spent = 0.000274658 secs
mass 1 183.84
mass 2 4.0026
@@ -42,15 +45,15 @@ group helium type 2
5 atoms in group helium
# choose potential
-include W.SNAP_HePair.pot
-# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. to appear in arxiv Feb2017, W-He and He-He from Juslin, N. and Wirth, B. D. Journal of Nuclear Materials, 423, (2013) p61-63
+include W_2940_2017_2_He_JW2013.snap
+# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph]
#
# Definition of SNAP+ZBL+Tabulated potential.
variable zblcutinner equal 4
variable zblcutouter equal 4.8
variable zblz equal 74
-# Specify hybrid with SNAP, ZBL, and long-range Coulomb
+# Specify hybrid with SNAP and ZBL
pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap table spline 10000 table spline 10000
pair_style hybrid/overlay zbl 4 ${zblcutouter} snap table spline 10000 table spline 10000
@@ -64,18 +67,19 @@ SNAP Element = W, Radius 0.5, Weight 1
Reading potential file W_2940_2017_2.snapparam with DATE: 2017-02-20
SNAP keyword rcutfac 4.73442
SNAP keyword twojmax 8
-SNAP keyword gamma 1
SNAP keyword rfac0 0.99363
SNAP keyword rmin0 0
SNAP keyword diagonalstyle 3
+SNAP keyword bzeroflag 0
+SNAP keyword quadraticflag 0
pair_coeff 2 2 table 1 He_He_JW2013.table HeHe
Reading potential file He_He_JW2013.table with DATE: 2017-02-20
WARNING: 1 of 4999 force values in table are inconsistent with -dE/dr.
- Should only be flagged at inflection points (../pair_table.cpp:476)
+ Should only be flagged at inflection points (../pair_table.cpp:481)
pair_coeff 1 2 table 2 W_He_JW2013.table WHe
Reading potential file W_He_JW2013.table with DATE: 2017-02-20
WARNING: 3 of 325 force values in table are inconsistent with -dE/dr.
- Should only be flagged at inflection points (../pair_table.cpp:476)
+ Should only be flagged at inflection points (../pair_table.cpp:481)
#Hybrid/overlay will take all pair styles and add their contributions equally, order of pair_coeff doesnt matter here
#This is not the case for pair_style hybrid ... where only one pair_coeff is read for each type combination, order matters here.
@@ -134,7 +138,7 @@ Neighbor list info ...
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
-Memory usage per processor = 7.65426 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 7.656 | 7.656 | 7.656 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -10.438105 0 -10.39963 -5445.2808
10 292.13979 -10.437097 0 -10.39963 -5516.3963
@@ -147,20 +151,20 @@ Step Temp E_pair E_mol TotEng Press
80 79.985938 -10.409886 0 -10.399628 2392.1106
90 62.568933 -10.407652 0 -10.399628 3141.7027
100 56.697933 -10.406899 0 -10.399628 3583.9538
-Loop time of 2.8757 on 4 procs for 100 steps with 128 atoms
+Loop time of 4.82103 on 4 procs for 100 steps with 128 atoms
-Performance: 1.502 ns/day, 15.976 hours/ns, 34.774 timesteps/s
-99.9% CPU use with 4 MPI tasks x no OpenMP threads
+Performance: 0.896 ns/day, 26.783 hours/ns, 20.742 timesteps/s
+99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 2.7363 | 2.8122 | 2.8636 | 2.9 | 97.79
+Pair | 4.4837 | 4.6734 | 4.7605 | 5.2 | 96.94
Neigh | 0 | 0 | 0 | 0.0 | 0.00
-Comm | 0.011014 | 0.062439 | 0.13842 | 19.3 | 2.17
-Output | 0.00023842 | 0.00025076 | 0.0002861 | 0.0 | 0.01
-Modify | 9.2506e-05 | 9.9301e-05 | 0.00010395 | 0.0 | 0.00
-Other | | 0.0006654 | | | 0.02
+Comm | 0.057389 | 0.14453 | 0.33421 | 29.4 | 3.00
+Output | 0.00038719 | 0.00073916 | 0.0017841 | 0.0 | 0.02
+Modify | 0.00018716 | 0.00022203 | 0.00026417 | 0.0 | 0.00
+Other | | 0.002119 | | | 0.04
Nlocal: 32 ave 32 max 32 min
Histogram: 4 0 0 0 0 0 0 0 0 0
@@ -176,4 +180,4 @@ Ave neighs/atom = 53.5156
Neighbor list builds = 0
Dangerous builds = 0
-Total wall time: 0:00:02
+Total wall time: 0:00:04
diff --git a/lib/atc/ATC_Method.cpp b/lib/atc/ATC_Method.cpp
index b1f3fa2545e74c68f882c434361c52b2091c8a95..5d61a7bed8ede5dfe033a952baf9d288e69a0054 100644
--- a/lib/atc/ATC_Method.cpp
+++ b/lib/atc/ATC_Method.cpp
@@ -2015,8 +2015,8 @@ pecified
LammpsInterface::instance()->int_allmax(&send_size,&max_size);
if (comm_rank == 0) {
- int intbuf[max_size];
- double buf[max_size];
+ int *intbuf = new int[max_size];
+ double *buf = new double[max_size];
for (int iproc = 1; iproc < nprocs; iproc++) {
LammpsInterface::instance()->int_recv(intbuf,max_size,iproc);
LammpsInterface::instance()->recv(buf,max_size,iproc);
@@ -2024,15 +2024,19 @@ pecified
out << intbuf[i] << " " << buf[i] << "\n";
}
}
+ delete[] intbuf;
+ delete[] buf;
} else {
- int intbuf[send_size];
- double buf[send_size];
+ int *intbuf = new int[send_size];
+ double *buf = new double[send_size];
for (int i = 0; i < send_size; i++) {
intbuf[i] = id2tag[i];
buf[i] = atomicVolumeMatrix(i,i);
}
LammpsInterface::instance()->int_send(intbuf,send_size);
LammpsInterface::instance()->send(buf,send_size);
+ delete[] intbuf;
+ delete[] buf;
}
}
diff --git a/lib/atc/Array.h b/lib/atc/Array.h
index 9df6cbbda245d1bc4730d124a1a6980bbad2dae4..21e66a95512b4b73b2e66e482312d8dd09110d19 100644
--- a/lib/atc/Array.h
+++ b/lib/atc/Array.h
@@ -4,7 +4,7 @@
#include <cstdlib>
#include <iostream>
#include <string>
-#include <stdio.h>
+#include <cstdio>
// for macros
#include "MatrixDef.h"
diff --git a/lib/atc/Array2D.h b/lib/atc/Array2D.h
index 8d3af47e12c14bea9e852928fea9b9cdee180009..25f895f72ccbaa82323ca1617d66f2fe8d519aba 100644
--- a/lib/atc/Array2D.h
+++ b/lib/atc/Array2D.h
@@ -2,10 +2,9 @@
#define ARRAY2D_H
#include <cstdlib>
+#include <cstdio>
#include <string>
#include <iostream>
-#include <cstdlib>
-#include <stdio.h>
#include "Array.h"
diff --git a/lib/atc/ElectronPhononExchange.cpp b/lib/atc/ElectronPhononExchange.cpp
index 2ed25fc557dd8494a9556a4fe86fa199fbc34d41..0ccc8ec67e1c70df9ff298eb0ee5b13b83afc006 100644
--- a/lib/atc/ElectronPhononExchange.cpp
+++ b/lib/atc/ElectronPhononExchange.cpp
@@ -5,7 +5,7 @@
#include <iostream>
#include <vector>
-#include <math.h>
+#include <cmath>
using ATC_Utility::command_line;
using ATC_Utility::str2dbl;
diff --git a/lib/atc/FE_Element.cpp b/lib/atc/FE_Element.cpp
index cfc59aa601d8b8019d5efdff63ffa3a6abc24a81..9eec08c483e971a4574c41ea653856a776841b41 100644
--- a/lib/atc/FE_Element.cpp
+++ b/lib/atc/FE_Element.cpp
@@ -8,7 +8,7 @@
#include "Utility.h"
// Other headers
-#include "math.h"
+#include <cmath>
using ATC_Utility::dbl_geq;
using ATC_Utility::det3;
diff --git a/lib/atc/FE_Engine.cpp b/lib/atc/FE_Engine.cpp
index d8d6e3e440b364c30a25f568d0ff076d729b3e06..efcde66d782fa9ce27bd596ad3418645c6b30b2f 100644
--- a/lib/atc/FE_Engine.cpp
+++ b/lib/atc/FE_Engine.cpp
@@ -7,8 +7,8 @@
#include "KernelFunction.h"
#include "Utility.h"
#include "MPI_Wrappers.h"
-#include <stdio.h>
-#include <stdlib.h>
+#include <cstdio>
+#include <cstdlib>
#include <map>
#include <string>
@@ -352,8 +352,9 @@ namespace ATC{
// each segment of the piecewise funcion is length-normalized separately
else if (strcmp(arg[argIdx],"position-number-density")==0) {
argIdx++;
- double y[nx],w[nx];
- int n[nx];
+ double *y = new double[nx];
+ double *w = new double[nx];
+ int *n = new int[nx];
int nn = 0;
while (argIdx < narg) {
if (! is_numeric(arg[argIdx])) break;
@@ -369,7 +370,7 @@ namespace ATC{
double w0 = w[i-1];
double dw = w[i]-w0;
double lx = 0;
- double l[dn];
+ double *l = new double[dn];
for (int j = 0; j < dn; ++j) {
double x = (j+0.5)/dn;
double dl = w0+x*dw;
@@ -380,7 +381,11 @@ namespace ATC{
for (int j = 0; j < dn; ++j) {
dx(k++) = scale*l[j];
}
+ delete[] l;
}
+ delete[] y;
+ delete[] w;
+ delete[] n;
}
// construct relative values from a density function
// evaluate for a domain (0,1)
diff --git a/lib/atc/FE_Interpolate.cpp b/lib/atc/FE_Interpolate.cpp
index 3f41e3002994db342561e2a5b8f2a6f5112ee9ec..19753a80079a6fe7e4e69d1cc624ef55c2ab56cb 100644
--- a/lib/atc/FE_Interpolate.cpp
+++ b/lib/atc/FE_Interpolate.cpp
@@ -5,7 +5,7 @@
#include "FE_Quadrature.h"
// Other headers
-#include "math.h"
+#include <cmath>
using std::map;
using std::vector;
diff --git a/lib/atc/FE_Mesh.cpp b/lib/atc/FE_Mesh.cpp
index 6225a1b192af060bdbccecd5d59ddd014414b1e8..b090bf2881bdbb9855c7098ccc7b5f2a6d4a4f7a 100644
--- a/lib/atc/FE_Mesh.cpp
+++ b/lib/atc/FE_Mesh.cpp
@@ -6,7 +6,7 @@
#include "OutputManager.h"
#include "Utility.h"
#include <sstream>
-#include <assert.h>
+#include <cassert>
#include <algorithm>
#include <cmath>
#include <functional>
diff --git a/lib/atc/FE_Mesh.h b/lib/atc/FE_Mesh.h
index b37cb1e8bad05ef6639e8aa83cb4b83327b844b7..be40d7cb28e21265646d5320a2ecce105eddb98c 100644
--- a/lib/atc/FE_Mesh.h
+++ b/lib/atc/FE_Mesh.h
@@ -12,7 +12,7 @@
#include <map>
#include <set>
#include <utility>
-#include <float.h>
+#include <cfloat>
#include <string>
#include <vector>
#include "mpi.h"
diff --git a/lib/atc/Function.cpp b/lib/atc/Function.cpp
index 0bd759695c0839db48d423dbe858a78b6de9c090..6004937a018ffe58fcc6f4c0ace6cf916b881f83 100644
--- a/lib/atc/Function.cpp
+++ b/lib/atc/Function.cpp
@@ -1,3 +1,6 @@
+#ifndef _WIN32
+#include <alloca.h>
+#endif
#include "Function.h"
#include "ATC_Error.h"
#include "LammpsInterface.h"
@@ -58,7 +61,11 @@ namespace ATC {
{
string type = args[0];
int narg = nargs -1;
- double dargs[narg];
+#ifdef _WIN32
+ double *dargs = (double *) _alloca(sizeof(double) * narg);
+#endif
+ double *dargs = (double *) alloca(sizeof(double) * narg);
+#endif
for (int i = 0; i < narg; ++i) dargs[i] = atof(args[i+1]);
return function(type, narg, dargs);
@@ -192,7 +199,11 @@ XT_Function_Mgr * XT_Function_Mgr::myInstance_ = NULL;
{
string type = args[0];
int narg = nargs -1;
- double dargs[narg];
+#ifdef _WIN32
+ double *dargs = (double *) _alloca(sizeof(double) * narg);
+#else
+ double *dargs = (double *) alloca(sizeof(double) * narg);
+#endif
for (int i = 0; i < narg; ++i) dargs[i] = atof(args[i+1]);
return function(type, narg, dargs);
diff --git a/lib/atc/Function.h b/lib/atc/Function.h
index 7368589e96ef65a958ce445040c3b92eaccd95e8..4572009f92a39729fb4b5342aaeb691b8099a76d 100644
--- a/lib/atc/Function.h
+++ b/lib/atc/Function.h
@@ -1,7 +1,7 @@
#ifndef XT_FUNCTION_H
#define XT_FUNCTION_H
-#include <math.h>
+#include <cmath>
#include <string>
#include <set>
#include <cstdlib>
diff --git a/lib/atc/GMRES.h b/lib/atc/GMRES.h
index 0cffe9837f952b59f0f29f260107b90e6739267c..a64fc70c009bfa5cd51766ca67c1dbe32bc5be75 100644
--- a/lib/atc/GMRES.h
+++ b/lib/atc/GMRES.h
@@ -19,7 +19,7 @@
//
//*****************************************************************
-#include <math.h>
+#include <cmath>
template<class Real>
diff --git a/lib/atc/InterscaleOperators.h b/lib/atc/InterscaleOperators.h
index 4681801e732dfacf1e2510cff8e09d70b08d9bd5..0ddca1dc67a08d4adb299a3648ddfad8a5f5b931 100644
--- a/lib/atc/InterscaleOperators.h
+++ b/lib/atc/InterscaleOperators.h
@@ -279,7 +279,7 @@ namespace ATC {
typename std::map<std::string,data * >::iterator it = list.find(tag);
if (it==list.end()) return NULL;
return it->second;
- };
+ }
/** helper function to add a data entry to a list */
template <typename data>
@@ -290,7 +290,7 @@ namespace ATC {
throw ATC_Error("Tried to add another Quantity with tag "+tag+" in InterscaleManager::add_quantity");
typename std::template pair<std::string,data * > myPair(tag,quantity);
list.insert(myPair);
- };
+ }
/** helper function to add a data entry to a list when it requires neighbor communication*/
template <typename data>
@@ -302,7 +302,7 @@ namespace ATC {
if (quantity->atom_type() == PROC_GHOST) {
commList.push_back(quantity);
}
- };
+ }
/** helper function to fina a data entry in a list */
template <typename data>
@@ -311,7 +311,7 @@ namespace ATC {
typename std::map<std::string,data * >::iterator it = list.find(tag);
if (it!=list.end()) return it->second;
return NULL;
- };
+ }
/** helper function to force the reset of all data in a list */
template <typename data>
@@ -319,7 +319,7 @@ namespace ATC {
{
for (typename std::map<std::string,data* >::iterator it = list.begin(); it != list.end(); ++it)
(it->second)->force_reset();
- };
+ }
/** helper function to set the memory type to temporary of a list */
template <typename data>
@@ -327,7 +327,7 @@ namespace ATC {
{
for (typename std::map<std::string,data* >::iterator it = list.begin(); it != list.end(); ++it)
(it->second)->set_memory_type(TEMPORARY);
- };
+ }
/** helper function to perform intialization for dfs of a list */
template <typename data>
@@ -336,7 +336,7 @@ namespace ATC {
for (typename std::map<std::string,data* >::iterator it = list.begin(); it != list.end(); ++it) {
(it->second)->dfsFound_ = false;
}
- };
+ }
/** helper function to start the dfs visit for list */
template <typename data>
@@ -349,7 +349,7 @@ namespace ATC {
if ((it->second)->memory_type()==TEMPORARY) list.erase(it++);
else ++it;
}
- };
+ }
// PAQ helper functions
/** helper function to adjust local atom count for all data in a list before exchange, only valid with quantities that do that are aware of atom counts */
@@ -359,7 +359,7 @@ namespace ATC {
for (typename std::map<std::string,data* >::iterator it = list.begin(); it != list.end(); ++it) {
(it->second)->reset_nlocal();
}
- };
+ }
/** helper function to indicate lammps data is stale for all data in a list before exchange, only valid with PAQs */
template <typename data>
@@ -367,7 +367,7 @@ namespace ATC {
{
for (typename std::map<std::string,data* >::iterator it = list.begin(); it != list.end(); ++it)
(it->second)->lammps_force_reset();
- };
+ }
/** helper function to size all data in a list, only valid with comm lists */
template <typename data>
@@ -375,7 +375,7 @@ namespace ATC {
{
for (typename std::vector<data* >::iterator it = list.begin(); it != list.end(); ++it)
(*it)->quantity();
- };
+ }
/** helper function to pack all data in a list before exchange, only valid with quantities that do work before parallel communication */
template <typename data>
@@ -384,7 +384,7 @@ namespace ATC {
for (typename std::map<std::string,data* >::iterator it = list.begin(); it != list.end(); ++it) {
(it->second)->prepare_exchange();
}
- };
+ }
/** helper function to extract all data in a list after exchange, only valid with quantities that do work after parallel communication */
template <typename data>
@@ -393,7 +393,7 @@ namespace ATC {
for (typename std::map<std::string,data* >::iterator it = list.begin(); it != list.end(); ++it) {
(it->second)->post_exchange();
}
- };
+ }
/** helper function to determine memory usage of all data in a list, only valid with PAQs */
template <typename data>
@@ -401,7 +401,7 @@ namespace ATC {
{
for (typename std::map<std::string,data* >::const_iterator it = list.begin(); it != list.end(); ++it)
usage += (it->second)->memory_usage();
- };
+ }
/** helper function to pack arrays of all data before exchange in a list, only valid with PAQs */
template <typename data>
@@ -410,7 +410,7 @@ namespace ATC {
for (typename std::map<std::string,data* >::iterator it = list.begin(); it != list.end(); ++it) {
index += (it->second)->pack_exchange(i,&buffer[index]);
}
- };
+ }
/** helper function to unpack arrays of all data after exchange in a list, only valid with PAQs */
template <typename data>
@@ -418,7 +418,7 @@ namespace ATC {
{
for (typename std::map<std::string,data* >::iterator it = list.begin(); it != list.end(); ++it)
index += (it->second)->unpack_exchange(i,&buffer[index]);
- };
+ }
/** helper function to pack arrays of all data in a list, only valid with comm lists */
template <typename data>
@@ -427,7 +427,7 @@ namespace ATC {
{
for (typename std::vector<data* >::iterator it = list.begin(); it != list.end(); ++it)
size += (*it)->pack_comm(index,&buf[size],pbc_flag,pbc);
- };
+ }
/** helper function to unpack arrays of all data in a list, only valid with comm lists */
template <typename data>
@@ -435,7 +435,7 @@ namespace ATC {
{
for (typename std::vector<data* >::iterator it = list.begin(); it != list.end(); ++it)
size += (*it)->unpack_comm(index,&buf[size]);
- };
+ }
/** helper function to grow arrays of all data in a list, only valid with PAQs */
template <typename data>
@@ -443,7 +443,7 @@ namespace ATC {
{
for (typename std::map<std::string,data* >::iterator it = list.begin(); it != list.end(); ++it)
(it->second)->grow_lammps_array(nmax,prefix_+it->first);
- };
+ }
/** helper function to copy arrays of all data in a list, only valid with PAQs */
template <typename data>
diff --git a/lib/atc/KD_Tree.cpp b/lib/atc/KD_Tree.cpp
index 362bd70d34bd35f8d94d18d7c52e36978dab0f03..1432663e8064b60b8862e707d99aa010fb0245c1 100644
--- a/lib/atc/KD_Tree.cpp
+++ b/lib/atc/KD_Tree.cpp
@@ -1,5 +1,5 @@
#include "KD_Tree.h"
-#include <assert.h>
+#include <cassert>
using std::vector;
diff --git a/lib/atc/KD_Tree.h b/lib/atc/KD_Tree.h
index 6c788c407112948bbcbbed4f3c8d2f612728fa69..3877cd40993bd910744b19b94b898842431af1b2 100644
--- a/lib/atc/KD_Tree.h
+++ b/lib/atc/KD_Tree.h
@@ -4,7 +4,7 @@
#include "Array2D.h"
#include "MatrixDef.h"
#include "MatrixLibrary.h"
-#include <math.h>
+#include <cmath>
#include <vector>
#include <utility>
diff --git a/lib/atc/KernelFunction.cpp b/lib/atc/KernelFunction.cpp
index 91f99a61494f185145af66f0d709dc209af7e6e0..80e41a15509bd1c4efd77f42e5d55e30e0a6f910 100644
--- a/lib/atc/KernelFunction.cpp
+++ b/lib/atc/KernelFunction.cpp
@@ -1,5 +1,5 @@
#include "KernelFunction.h"
-#include "math.h"
+#include <cmath>
#include <vector>
#include "ATC_Error.h"
#include "Quadrature.h"
diff --git a/lib/atc/LammpsInterface.cpp b/lib/atc/LammpsInterface.cpp
index d584d159eaade8822f93af0e92d05004e1032d14..2238d930f4d4fb3f5eb25fac636168743e35d0f3 100644
--- a/lib/atc/LammpsInterface.cpp
+++ b/lib/atc/LammpsInterface.cpp
@@ -131,15 +131,15 @@ void LammpsInterface::sparse_allsum(SparseMatrix<double> &toShare) const
if (error != MPI_SUCCESS) throw ATC_Error("error in sparse_allsum_numrows "+to_string(error));
// adjust row sendcounts because recRowsCRS is off by one
- int rowCounts[nProcs];
- int sizeCounts[nProcs];
+ int *rowCounts = new int[nProcs];
+ int *sizeCounts = new int[nProcs];
// set up total size of receive buffers for Allgatherv calls
int totalRowsCRS = 0;
int totalSize = 0;
// set up array of displacements for Allgatherv calls
- int rowOffsets[nProcs];
+ int *rowOffsets = new int[nProcs];
rowOffsets[0] = 0;
- int sizeOffsets[nProcs];
+ int *sizeOffsets = new int[nProcs];
sizeOffsets[0] = 0;
for (int i = 0; i < nProcs; i++) {
// find the total number of entries to share in the mpi calls below
@@ -156,8 +156,8 @@ void LammpsInterface::sparse_allsum(SparseMatrix<double> &toShare) const
// get actual rows
INDEX *rec_ia = new INDEX[totalRowsCRS];
if (toShare.size() == 0) {
- double dummy[0];
- error = MPI_Allgatherv(dummy, 0, MPI_INT,
+ double dummy;
+ error = MPI_Allgatherv(&dummy, 0, MPI_INT,
rec_ia, rowCounts, rowOffsets, MPI_INT, lammps_->world);
}
else
@@ -211,6 +211,10 @@ void LammpsInterface::sparse_allsum(SparseMatrix<double> &toShare) const
toShare += tempMat;
}
}
+ delete[] rowCounts;
+ delete[] sizeCounts;
+ delete[] rowOffsets;
+ delete[] sizeOffsets;
delete[] recInfo;
delete[] rec_ia;
diff --git a/lib/atc/LammpsInterface.h b/lib/atc/LammpsInterface.h
index ff2b4ba9b2696dfb270ba6e50191b73cea5ba1e7..2032571da5df99e642da3b761eb1464c176ed098 100644
--- a/lib/atc/LammpsInterface.h
+++ b/lib/atc/LammpsInterface.h
@@ -2,7 +2,7 @@
#define LAMMPS_INTERFACE_H
#include <iostream>
-#include <stdlib.h>
+#include <cstdlib>
#include <map>
#include <iostream>
#include <string>
@@ -315,7 +315,7 @@ class LammpsInterface {
}
else {
int commSize = comm_size();
- double recv[commSize];
+ double *recv = new double[commSize];
MPI_Wrappers::gather(lammps_->world,data,recv);
if (rank_zero()) {
full_msg << " ATC:" << tag;
@@ -324,6 +324,7 @@ class LammpsInterface {
}
full_msg << "\n";
}
+ delete[] recv;
}
if (rank_zero()) {
std::string mesg = full_msg.str();
@@ -577,13 +578,13 @@ class LammpsInterface {
void destroy_2d_int_array(int **i) const;
int ** grow_2d_int_array(int **array, int n1, int n2, const char *name) const;
template <typename T>
- T * grow_array(T *&array, int n, const char *name) const {return lammps_->memory->grow(array,n,name);};
+ T * grow_array(T *&array, int n, const char *name) const {return lammps_->memory->grow(array,n,name);}
template <typename T>
- void destroy_array(T * array) {lammps_->memory->destroy(array);};
+ void destroy_array(T * array) {lammps_->memory->destroy(array);}
template <typename T>
- T ** grow_array(T **&array, int n1, int n2, const char *name) const {return lammps_->memory->grow(array,n1,n2,name);};
+ T ** grow_array(T **&array, int n1, int n2, const char *name) const {return lammps_->memory->grow(array,n1,n2,name);}
template <typename T>
- void destroy_array(T ** array) const {lammps_->memory->destroy(array);};
+ void destroy_array(T ** array) const {lammps_->memory->destroy(array);}
/*@}*/
/** \name Methods that interface with Update class */
diff --git a/lib/atc/MPI_Wrappers.cpp b/lib/atc/MPI_Wrappers.cpp
index 9468644c53da762a871e64f7e569ab88605bc243..b8a8ab77b734d03442b30b0f3d8fadec53a3e886 100644
--- a/lib/atc/MPI_Wrappers.cpp
+++ b/lib/atc/MPI_Wrappers.cpp
@@ -94,7 +94,8 @@ namespace MPI_Wrappers {
{
int myRank;
MPI_Comm_rank(MPI_COMM_WORLD, &myRank);
- DOUBLE_RANK in[count],out[count];
+ DOUBLE_RANK *in = new DOUBLE_RANK[count];
+ DOUBLE_RANK *out = new DOUBLE_RANK[count];
for (int i = 0; i < count; i++) {
in[i].val = send_buf[i];
in[i].rank = myRank;
@@ -105,6 +106,8 @@ namespace MPI_Wrappers {
for (int i = 0; i < count; i++) {
rec_buf[i] = out[i].val;
}
+ delete[] in;
+ delete[] out;
return out[0].rank;
}
@@ -154,14 +157,16 @@ namespace MPI_Wrappers {
{
int error;
int numprocs = size(comm);
- int sizes[numprocs];
- int displacements[numprocs];
+ int *sizes = new int[numprocs];
+ int *displacements = new int[numprocs];
for (int i = 0; i < numprocs; ++i) {
sizes[i] = 1;
displacements[i] = i;
}
error = MPI_Scatterv(send_buf, sizes, displacements, MPI_INT, rec_buf, count, MPI_INT, 0, comm);
if (error != MPI_SUCCESS) throw ATC_Error("error in int_scatter "+to_string(error));
+ delete[] sizes;
+ delete[] displacements;
}
void allgatherv(MPI_Comm comm, double *send_buf, int send_count,
diff --git a/lib/atc/Makefile.mpi b/lib/atc/Makefile.mpi
index ec941efdcb6c0b0171440306653fa9522b8b65cf..c1ce0500ea5f717cec4d44f538127d330440312b 100644
--- a/lib/atc/Makefile.mpi
+++ b/lib/atc/Makefile.mpi
@@ -52,4 +52,4 @@ fastdep.exe: ../../src/DEPEND/fastdep.c
clean:
-rm -f *.o *~ .depend $(LIB) fastdep.exe
-sinclude $(DEPENDS)
+sinclude .depend
diff --git a/lib/atc/OutputManager.cpp b/lib/atc/OutputManager.cpp
index 414c5173e7b7cfb1bde38a5a263480eccec264d5..4340c8b8b0a3ca3c308be3838385a2b36a7b3c9a 100644
--- a/lib/atc/OutputManager.cpp
+++ b/lib/atc/OutputManager.cpp
@@ -1,6 +1,6 @@
#include <string>
#include <fstream>
-#include <stdio.h>
+#include <cstdio>
#include <sstream>
#include "OutputManager.h"
#include "ATC_Error.h"
diff --git a/lib/atc/PrescribedDataManager.h b/lib/atc/PrescribedDataManager.h
index 05f553ab2db9955c631c65ef122ae5768d213c92..738c34d593d5e9100422cd80622cc19dc2e7cc89 100644
--- a/lib/atc/PrescribedDataManager.h
+++ b/lib/atc/PrescribedDataManager.h
@@ -154,7 +154,7 @@ namespace ATC {
std::set<int> fluxes;
//list of nodes to insert.
//1 for nodes to insert, 0 for nodes not to insert.
- int toInsert[nNodes_];
+ int *toInsert = new int[nNodes_];
for (int i = 0; i < nNodes_; ++i) toInsert[i] = 0;
const std::map < std::pair <int, int>, Array < XT_Function * > > & sources = faceSources_.find(thisField)->second;
@@ -178,6 +178,7 @@ namespace ATC {
for (int node = 0; node < nNodes_; ++node) {
if (toInsert[node]) fluxes.insert(node);
}
+ delete[] toInsert;
return fluxes;
}
@@ -189,7 +190,7 @@ namespace ATC {
{
//list of nodes to insert.
//1 for nodes to insert, 0 for nodes not to insert.
- int toInsert[nNodes_];
+ int *toInsert = new int[nNodes_];
for (int i = 0; i < nNodes_; ++i) toInsert[i] = 0;
const std::map < std::pair <int, int>, Array < XT_Function * > > & sources = faceSources_.find(thisField)->second;
@@ -213,6 +214,7 @@ namespace ATC {
for (int node = 0; node < nNodes_; ++node) {
if (toInsert[node]) fluxes.insert(node);
}
+ delete[] toInsert;
}
/** */
@@ -223,7 +225,7 @@ namespace ATC {
std::set<int> fluxes;
//list of nodes to insert.
//1 for nodes to insert, 0 for nodes not to insert.
- int toInsert[nNodes_];
+ int *toInsert = new int[nNodes_];
for (int i = 0; i < nNodes_; ++i) toInsert[i] = 0;
const Array2D < XT_Function *> & sources = elementSources_.find(thisField)->second;
@@ -244,6 +246,7 @@ namespace ATC {
for (int node = 0; node < nNodes_; ++node) {
if (toInsert[node]) fluxes.insert(node);
}
+ delete[] toInsert;
return fluxes;
}
@@ -255,7 +258,7 @@ namespace ATC {
{
//list of nodes to insert.
//1 for nodes to insert, 0 for nodes not to insert.
- int toInsert[nNodes_];
+ int *toInsert = new int[nNodes_];
for (int i = 0; i < nNodes_; ++i) toInsert[i] = 0;
const Array2D < XT_Function *> & sources = elementSources_.find(thisField)->second;
@@ -276,6 +279,7 @@ namespace ATC {
for (int node = 0; node < nNodes_; ++node) {
if (toInsert[node]) fluxes.insert(node);
}
+ delete[] toInsert;
}
/** */
diff --git a/lib/atc/ShapeFunction.h b/lib/atc/ShapeFunction.h
index 724e66924feadf790deaf17bbda8b64e84edb44a..62b2138cd7fd7b994d7aaa5d7c071ec21c27966e 100644
--- a/lib/atc/ShapeFunction.h
+++ b/lib/atc/ShapeFunction.h
@@ -5,10 +5,10 @@
#include "DependencyManager.h"
#include "PaqAtcUtility.h"
-#include <map.h>
-#include <vector.h>
-#include <set.h>
-#include <pair.h>
+#include <map>
+#include <vector>
+#include <set>
+#include <pair>
namespace ATC {
diff --git a/lib/atc/SparseMatrix-inl.h b/lib/atc/SparseMatrix-inl.h
index 8d6aec78dca94f04503caf662761ff203d4e75e7..f70dd0361d3cf52e519fef06abc07f0518c86b21 100644
--- a/lib/atc/SparseMatrix-inl.h
+++ b/lib/atc/SparseMatrix-inl.h
@@ -67,9 +67,9 @@ void SparseMatrix<T>::_create(INDEX size, INDEX nrows)
// assign memory to hold matrix
try
{
- _val = (_size*nrows) ? new T [_size] : NULL;
- _ia = (_size*nrows) ? new INDEX [_nRowsCRS+1] : NULL;
- _ja = (_size*nrows) ? new INDEX [_size] : NULL;
+ _val = (_size && nrows) ? new T [_size] : NULL;
+ _ia = (_size && nrows) ? new INDEX [_nRowsCRS+1] : NULL;
+ _ja = (_size && nrows) ? new INDEX [_size] : NULL;
}
catch (std::exception &e)
{
diff --git a/lib/atc/Utility.h b/lib/atc/Utility.h
index f9e99ff194fb8245618c791858cd308208876a1d..d975d4804ae87ac5ee9043ae206bedbf1e815782 100644
--- a/lib/atc/Utility.h
+++ b/lib/atc/Utility.h
@@ -13,7 +13,7 @@
#include <sstream>
#include <iomanip>
#include <algorithm>
-#include "math.h"
+#include <cmath>
#include "ATC_Error.h"
diff --git a/lib/awpmd/ivutils/include/cerf.h b/lib/awpmd/ivutils/include/cerf.h
index 207fe8f4590b7e762c8c327340b69e6ee7d1d672..b094c4144f6d7dd49d023cc20669087871507625 100644
--- a/lib/awpmd/ivutils/include/cerf.h
+++ b/lib/awpmd/ivutils/include/cerf.h
@@ -42,11 +42,6 @@ Software Foundation, 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
//
-//#include <math.h>
-//#include <octave/oct.h>
-
-//#include "f77-fcn.h"
-
//
// Abramowitz and Stegun: (eqn: 7.1.14) gives this continued
// fraction for erfc(z)
@@ -242,4 +237,4 @@ const Complex cerf( const Complex z )
// 2.2 1.7 0.135021+0.153161i | 0.135021 +0.153161 1.65541359 -1.276707
// 2.2 2.7 0.127900+0.096330i | 0.127900 +0.096330 0.98619434 +0.000564
-# endif
\ No newline at end of file
+# endif
diff --git a/lib/awpmd/ivutils/include/logexc.h b/lib/awpmd/ivutils/include/logexc.h
index 0211a96034448869676e0a7739df88fcea3e2b6d..400b3fb7d2e970e1773ade440ff25ce1b295139f 100644
--- a/lib/awpmd/ivutils/include/logexc.h
+++ b/lib/awpmd/ivutils/include/logexc.h
@@ -1,9 +1,9 @@
# ifndef LOGEXC_H
# define LOGEXC_H
-#include <stdio.h>
-#include <stdlib.h>
-#include <stdarg.h>
+#include <cstdio>
+#include <cstdlib>
+#include <cstdarg>
#include <stdexcept>
#include <string>
diff --git a/lib/awpmd/ivutils/include/vector_3.h b/lib/awpmd/ivutils/include/vector_3.h
index 75ef801a2ea7a1194c1169b68ebb8d2ca4cb54b9..3e3d9e6e0b249a941e90ad34039a3de5fb03a998 100644
--- a/lib/awpmd/ivutils/include/vector_3.h
+++ b/lib/awpmd/ivutils/include/vector_3.h
@@ -84,7 +84,7 @@
# include <iostream>
# include <cmath>
# include <limits>
-# include <stdlib.h>
+# include <cstdlib>
// some compilers don't define PI!
# ifndef M_PI
diff --git a/lib/colvars/Makefile.deps b/lib/colvars/Makefile.deps
index 9a7de0647db57eeb3d62ee866e71f6e363b6c802..a0d8515bc104f985584d18726c79914c67227cdf 100644
--- a/lib/colvars/Makefile.deps
+++ b/lib/colvars/Makefile.deps
@@ -1,9 +1,9 @@
$(COLVARS_OBJ_DIR)colvaratoms.o: colvaratoms.cpp colvarmodule.h \
- colvars_version.h colvarproxy.h colvarvalue.h colvartypes.h \
+ colvars_version.h colvarproxy.h colvartypes.h colvarvalue.h \
colvarparse.h colvaratoms.h colvardeps.h
$(COLVARS_OBJ_DIR)colvarbias_abf.o: colvarbias_abf.cpp colvarmodule.h \
- colvars_version.h colvarproxy.h colvarvalue.h colvartypes.h colvar.h \
+ colvars_version.h colvarproxy.h colvartypes.h colvarvalue.h colvar.h \
colvarparse.h colvardeps.h lepton/include/Lepton.h \
lepton/include/lepton/CompiledExpression.h \
lepton/include/lepton/ExpressionTreeNode.h \
@@ -29,7 +29,7 @@ $(COLVARS_OBJ_DIR)colvarbias_alb.o: colvarbias_alb.cpp colvarmodule.h \
lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \
colvarbias_alb.h
$(COLVARS_OBJ_DIR)colvarbias.o: colvarbias.cpp colvarmodule.h \
- colvars_version.h colvarproxy.h colvarvalue.h colvartypes.h colvarbias.h \
+ colvars_version.h colvarproxy.h colvartypes.h colvarvalue.h colvarbias.h \
colvar.h colvarparse.h colvardeps.h lepton/include/Lepton.h \
lepton/include/lepton/CompiledExpression.h \
lepton/include/lepton/ExpressionTreeNode.h \
@@ -42,8 +42,8 @@ $(COLVARS_OBJ_DIR)colvarbias.o: colvarbias.cpp colvarmodule.h \
lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \
colvargrid.h
$(COLVARS_OBJ_DIR)colvarbias_histogram.o: colvarbias_histogram.cpp \
- colvarmodule.h colvars_version.h colvarproxy.h colvarvalue.h \
- colvartypes.h colvar.h colvarparse.h colvardeps.h \
+ colvarmodule.h colvars_version.h colvarproxy.h colvartypes.h \
+ colvarvalue.h colvar.h colvarparse.h colvardeps.h \
lepton/include/Lepton.h lepton/include/lepton/CompiledExpression.h \
lepton/include/lepton/ExpressionTreeNode.h \
lepton/include/lepton/windowsIncludes.h \
@@ -55,7 +55,7 @@ $(COLVARS_OBJ_DIR)colvarbias_histogram.o: colvarbias_histogram.cpp \
lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \
colvarbias_histogram.h colvarbias.h colvargrid.h
$(COLVARS_OBJ_DIR)colvarbias_meta.o: colvarbias_meta.cpp colvarmodule.h \
- colvars_version.h colvarproxy.h colvarvalue.h colvartypes.h colvar.h \
+ colvars_version.h colvarproxy.h colvartypes.h colvarvalue.h colvar.h \
colvarparse.h colvardeps.h lepton/include/Lepton.h \
lepton/include/lepton/CompiledExpression.h \
lepton/include/lepton/ExpressionTreeNode.h \
@@ -68,8 +68,8 @@ $(COLVARS_OBJ_DIR)colvarbias_meta.o: colvarbias_meta.cpp colvarmodule.h \
lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \
colvarbias_meta.h colvarbias.h colvargrid.h
$(COLVARS_OBJ_DIR)colvarbias_restraint.o: colvarbias_restraint.cpp \
- colvarmodule.h colvars_version.h colvarproxy.h colvarvalue.h \
- colvartypes.h colvarbias_restraint.h colvarbias.h colvar.h colvarparse.h \
+ colvarmodule.h colvars_version.h colvarproxy.h colvartypes.h \
+ colvarvalue.h colvarbias_restraint.h colvarbias.h colvar.h colvarparse.h \
colvardeps.h lepton/include/Lepton.h \
lepton/include/lepton/CompiledExpression.h \
lepton/include/lepton/ExpressionTreeNode.h \
@@ -171,7 +171,7 @@ $(COLVARS_OBJ_DIR)colvar.o: colvar.cpp colvarmodule.h colvars_version.h \
lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \
colvarcomp.h colvaratoms.h colvarproxy.h colvarscript.h colvarbias.h
$(COLVARS_OBJ_DIR)colvardeps.o: colvardeps.cpp colvarmodule.h \
- colvars_version.h colvarproxy.h colvarvalue.h colvartypes.h colvardeps.h \
+ colvars_version.h colvarproxy.h colvartypes.h colvarvalue.h colvardeps.h \
colvarparse.h
$(COLVARS_OBJ_DIR)colvargrid.o: colvargrid.cpp colvarmodule.h \
colvars_version.h colvarvalue.h colvartypes.h colvarparse.h colvar.h \
@@ -204,7 +204,7 @@ $(COLVARS_OBJ_DIR)colvarmodule.o: colvarmodule.cpp colvarmodule.h \
$(COLVARS_OBJ_DIR)colvarparse.o: colvarparse.cpp colvarmodule.h \
colvars_version.h colvarvalue.h colvartypes.h colvarparse.h
$(COLVARS_OBJ_DIR)colvarproxy.o: colvarproxy.cpp colvarmodule.h \
- colvars_version.h colvarproxy.h colvarvalue.h colvartypes.h \
+ colvars_version.h colvarproxy.h colvartypes.h colvarvalue.h \
colvarscript.h colvarbias.h colvar.h colvarparse.h colvardeps.h \
lepton/include/Lepton.h lepton/include/lepton/CompiledExpression.h \
lepton/include/lepton/ExpressionTreeNode.h \
diff --git a/lib/colvars/colvar.cpp b/lib/colvars/colvar.cpp
index 5a4e8b617a9007fff02e87233b8f8dfebb1e7a25..c5b6d906c1ec063fac7ee5e48b39a41c4e841e96 100644
--- a/lib/colvars/colvar.cpp
+++ b/lib/colvars/colvar.cpp
@@ -7,6 +7,10 @@
// If you wish to distribute your changes, please submit them to the
// Colvars repository at GitHub.
+#include <list>
+#include <vector>
+#include <algorithm>
+
#include "colvarmodule.h"
#include "colvarvalue.h"
#include "colvarparse.h"
@@ -14,15 +18,6 @@
#include "colvarcomp.h"
#include "colvarscript.h"
-// used in build_atom_list()
-#include <algorithm>
-
-
-/// Compare two cvcs using their names
-/// Used to sort CVC array in scripted coordinates
-bool compare(colvar::cvc *i, colvar::cvc *j) {
- return i->name < j->name;
-}
colvar::colvar()
@@ -34,6 +29,15 @@ colvar::colvar()
}
+namespace {
+ /// Compare two cvcs using their names
+ /// Used to sort CVC array in scripted coordinates
+ bool compare(colvar::cvc *i, colvar::cvc *j)
+ {
+ return i->name < j->name;
+ }
+}
+
int colvar::init(std::string const &conf)
{
cvm::log("Initializing a new collective variable.\n");
@@ -143,6 +147,9 @@ int colvar::init(std::string const &conf)
x.type(cvc_value);
x_reported.type(cvc_value);
}
+
+ set_enabled(f_cv_scalar, (value().type() == colvarvalue::type_scalar));
+
// If using scripted biases, any colvar may receive bias forces
// and will need its gradient
if (cvm::scripted_forces()) {
@@ -198,6 +205,7 @@ int colvar::init(std::string const &conf)
if (is_enabled(f_cv_homogeneous) && cvcs[0]->b_periodic) { // TODO make this a CVC feature
bool b_periodic = true;
period = cvcs[0]->period;
+ wrap_center = cvcs[0]->wrap_center;
for (i = 1; i < cvcs.size(); i++) {
if (!cvcs[i]->b_periodic || cvcs[i]->period != period) {
b_periodic = false;
@@ -211,6 +219,14 @@ int colvar::init(std::string const &conf)
set_enabled(f_cv_periodic, b_periodic);
}
+ // Allow scripted/custom functions to be defined as periodic
+ if ( (is_enabled(f_cv_scripted) || is_enabled(f_cv_custom_function)) && is_enabled(f_cv_scalar) ) {
+ if (get_keyval(conf, "period", period, 0.)) {
+ set_enabled(f_cv_periodic, true);
+ get_keyval(conf, "wrapAround", wrap_center, 0.);
+ }
+ }
+
// check that cvcs are compatible
for (i = 0; i < cvcs.size(); i++) {
@@ -443,8 +459,6 @@ int colvar::init_grid_parameters(std::string const &conf)
upper_boundary.type(value());
upper_wall.type(value());
- set_enabled(f_cv_scalar, (value().type() == colvarvalue::type_scalar));
-
if (is_enabled(f_cv_scalar)) {
if (get_keyval(conf, "lowerBoundary", lower_boundary, lower_boundary)) {
@@ -1503,7 +1517,7 @@ cvm::real colvar::update_forces_energy()
vr += (0.5 * dt) * f_ext / ext_mass;
xr += dt * vr;
xr.apply_constraints();
- if (this->is_enabled(f_cv_periodic)) this->wrap(xr);
+ this->wrap(xr);
}
// Now adding the force on the actual colvar (for those biases that
@@ -1714,9 +1728,18 @@ colvarvalue colvar::dist2_rgrad(colvarvalue const &x1,
void colvar::wrap(colvarvalue &x) const
{
- if (is_enabled(f_cv_homogeneous)) {
- (cvcs[0])->wrap(x);
+ if ( !is_enabled(f_cv_periodic) ) {
+ return;
+ }
+
+ if ( is_enabled(f_cv_scripted) || is_enabled(f_cv_custom_function) ) {
+ // Scripted functions do their own wrapping, as cvcs might not be periodic
+ cvm::real shift = std::floor((x.real_value - wrap_center) / period + 0.5);
+ x.real_value -= shift * period;
+ } else {
+ cvcs[0]->wrap(x);
}
+
return;
}
@@ -2244,7 +2267,7 @@ void colvar::calc_runave()
runave.type(value().type());
runave.reset();
- // first-step operations
+ // first-step operationsf
if (cvm::debug())
cvm::log("Colvar \""+this->name+
diff --git a/lib/colvars/colvar.h b/lib/colvars/colvar.h
index 32c329460d06cfa5ceba43e245aa08a0d0810100..271231fb2aa2c6c6404c2f19f752cb80edfc66bf 100644
--- a/lib/colvars/colvar.h
+++ b/lib/colvars/colvar.h
@@ -216,6 +216,7 @@ public:
/// Period, if this variable is periodic
cvm::real period;
+ cvm::real wrap_center;
/// \brief Expand the boundaries of multiples of width, to keep the
diff --git a/lib/colvars/colvar_UIestimator.h b/lib/colvars/colvar_UIestimator.h
index 36ed938119d41232dfdbdc42589cd35f8f67a735..759b8d54a034800bd9bebce1cb34753ca6bcef89 100644
--- a/lib/colvars/colvar_UIestimator.h
+++ b/lib/colvars/colvar_UIestimator.h
@@ -731,6 +731,6 @@ namespace UIestimator {
}
}
};
-};
+}
#endif
diff --git a/lib/colvars/colvaratoms.cpp b/lib/colvars/colvaratoms.cpp
index 1be6f42e594f86adf16a5b4702a631a6bef9c1e7..c8dcfc076619f881a3a217d4e794d52a9838c44e 100644
--- a/lib/colvars/colvaratoms.cpp
+++ b/lib/colvars/colvaratoms.cpp
@@ -7,6 +7,10 @@
// If you wish to distribute your changes, please submit them to the
// Colvars repository at GitHub.
+#include <list>
+#include <vector>
+#include <algorithm>
+
#include "colvarmodule.h"
#include "colvarproxy.h"
#include "colvarparse.h"
@@ -436,7 +440,7 @@ int cvm::atom_group::parse(std::string const &group_conf)
}
bool b_print_atom_ids = false;
- get_keyval(group_conf, "printAtomIDs", b_print_atom_ids, false, colvarparse::parse_silent);
+ get_keyval(group_conf, "printAtomIDs", b_print_atom_ids, false);
// Calculate all required properties (such as total mass)
setup();
@@ -715,13 +719,10 @@ int cvm::atom_group::parse_fitting_options(std::string const &group_conf)
"if provided, must be non-zero.\n", INPUT_ERROR);
return COLVARS_ERROR;
}
- } else {
- // if not, rely on existing atom indices for the group
- group_for_fit->create_sorted_ids();
- ref_pos.resize(group_for_fit->size());
}
- cvm::load_coords(ref_pos_file.c_str(), ref_pos, group_for_fit->sorted_ids,
+ ref_pos.resize(group_for_fit->size());
+ cvm::load_coords(ref_pos_file.c_str(), &ref_pos, group_for_fit,
ref_pos_col, ref_pos_col_value);
}
@@ -789,33 +790,39 @@ void cvm::atom_group::do_feature_side_effects(int id)
}
-int cvm::atom_group::create_sorted_ids(void)
+int cvm::atom_group::create_sorted_ids()
{
// Only do the work if the vector is not yet populated
- if (sorted_ids.size())
+ if (sorted_atoms_ids.size())
return COLVARS_OK;
- std::list<int> temp_id_list;
- for (cvm::atom_iter ai = this->begin(); ai != this->end(); ai++) {
- temp_id_list.push_back(ai->id);
- }
- temp_id_list.sort();
- temp_id_list.unique();
- if (temp_id_list.size() != this->size()) {
- cvm::error("Error: duplicate atom IDs in atom group? (found " +
- cvm::to_str(temp_id_list.size()) +
- " unique atom IDs instead of" +
- cvm::to_str(this->size()) + ").\n");
- return COLVARS_ERROR;
+ // Sort the internal IDs
+ std::list<int> sorted_atoms_ids_list;
+ for (size_t i = 0; i < this->size(); i++) {
+ sorted_atoms_ids_list.push_back(atoms_ids[i]);
}
- sorted_ids = std::vector<int> (temp_id_list.size());
- unsigned int id_i = 0;
- std::list<int>::iterator li;
- for (li = temp_id_list.begin(); li != temp_id_list.end(); ++li) {
- sorted_ids[id_i] = *li;
- id_i++;
+ sorted_atoms_ids_list.sort();
+ sorted_atoms_ids_list.unique();
+ if (sorted_atoms_ids_list.size() != this->size()) {
+ return cvm::error("Error: duplicate atom IDs in atom group? (found " +
+ cvm::to_str(sorted_atoms_ids_list.size()) +
+ " unique atom IDs instead of " +
+ cvm::to_str(this->size()) + ").\n", BUG_ERROR);
}
- return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
+
+ // Compute map between sorted and unsorted elements
+ sorted_atoms_ids.resize(this->size());
+ sorted_atoms_ids_map.resize(this->size());
+ std::list<int>::iterator lsii = sorted_atoms_ids_list.begin();
+ size_t ii = 0;
+ for ( ; ii < this->size(); lsii++, ii++) {
+ sorted_atoms_ids[ii] = *lsii;
+ size_t const pos = std::find(atoms_ids.begin(), atoms_ids.end(), *lsii) -
+ atoms_ids.begin();
+ sorted_atoms_ids_map[ii] = pos;
+ }
+
+ return COLVARS_OK;
}
diff --git a/lib/colvars/colvaratoms.h b/lib/colvars/colvaratoms.h
index 0dda6ab792d8ae20afcf6a9aeaa615675f332d1b..93ae594aae893e303fff493487c6b49e7cf09ae8 100644
--- a/lib/colvars/colvaratoms.h
+++ b/lib/colvars/colvaratoms.h
@@ -227,9 +227,16 @@ protected:
/// \brief Array of atom objects
std::vector<cvm::atom> atoms;
- /// \brief Array of atom identifiers for the MD program (0-based)
+ /// \brief Internal atom IDs for host code
std::vector<int> atoms_ids;
+ /// Sorted list of internal atom IDs (populated on-demand by
+ /// create_sorted_ids); used to read coordinate files
+ std::vector<int> sorted_atoms_ids;
+
+ /// Map entries of sorted_atoms_ids onto the original positions in the group
+ std::vector<int> sorted_atoms_ids_map;
+
/// \brief Dummy atom position
cvm::atom_pos dummy_atom_pos;
@@ -273,19 +280,34 @@ public:
return atoms.size();
}
- std::string const print_atom_ids() const;
-
/// \brief If this option is on, this group merely acts as a wrapper
/// for a fixed position; any calls to atoms within or to
/// functions that return disaggregated data will fail
bool b_dummy;
- /// Sorted list of zero-based (internal) atom ids
- /// (populated on-demand by create_sorted_ids)
- std::vector<int> sorted_ids;
+ /// Internal atom IDs (populated during initialization)
+ inline std::vector<int> const &ids() const
+ {
+ return atoms_ids;
+ }
+
+ std::string const print_atom_ids() const;
+
+ /// Allocates and populates sorted_ids and sorted_ids_map
+ int create_sorted_ids();
- /// Allocates and populates the sorted list of atom ids
- int create_sorted_ids(void);
+ /// Sorted internal atom IDs (populated on-demand by create_sorted_ids);
+ /// used to read coordinate files
+ inline std::vector<int> const &sorted_ids() const
+ {
+ return sorted_atoms_ids;
+ }
+
+ /// Map entries of sorted_atoms_ids onto the original positions in the group
+ inline std::vector<int> const &sorted_ids_map() const
+ {
+ return sorted_atoms_ids_map;
+ }
/// Detect whether two groups share atoms
/// If yes, returns 1-based number of a common atom; else, returns 0
diff --git a/lib/colvars/colvarbias_abf.cpp b/lib/colvars/colvarbias_abf.cpp
index b3b5b3eb1654df12992b2fafb206d82851d3788b..771955a4fa354222b300b2e3cefcfb71c81c2c12 100644
--- a/lib/colvars/colvarbias_abf.cpp
+++ b/lib/colvars/colvarbias_abf.cpp
@@ -17,17 +17,17 @@ colvarbias_abf::colvarbias_abf(char const *key)
: colvarbias(key),
b_UI_estimator(false),
b_CZAR_estimator(false),
+ pabf_freq(0),
system_force(NULL),
gradients(NULL),
- pmf(NULL),
samples(NULL),
+ pmf(NULL),
z_gradients(NULL),
z_samples(NULL),
czar_gradients(NULL),
czar_pmf(NULL),
last_gradients(NULL),
- last_samples(NULL),
- pabf_freq(0)
+ last_samples(NULL)
{
}
@@ -315,8 +315,6 @@ colvarbias_abf::~colvarbias_abf()
int colvarbias_abf::update()
{
- int iter;
-
if (cvm::debug()) cvm::log("Updating ABF bias " + this->name);
size_t i;
@@ -368,7 +366,12 @@ int colvarbias_abf::update()
if ( b_integrate ) {
if ( pabf_freq && cvm::step_relative() % pabf_freq == 0 ) {
cvm::real err;
- iter = pmf->integrate(integrate_steps, integrate_tol, err);
+ int iter = pmf->integrate(integrate_steps, integrate_tol, err);
+ if ( iter == integrate_steps ) {
+ cvm::log("Warning: PMF integration did not converge to " + cvm::to_str(integrate_tol)
+ + " in " + cvm::to_str(integrate_steps)
+ + " steps. Residual error: " + cvm::to_str(err));
+ }
pmf->set_zero_minimum(); // TODO: do this only when necessary
}
}
@@ -485,7 +488,6 @@ int colvarbias_abf::update()
int colvarbias_abf::replica_share() {
- int p;
if ( !cvm::replica_enabled() ) {
cvm::error("Error: shared ABF: No replicas.\n");
@@ -507,6 +509,7 @@ int colvarbias_abf::replica_share() {
char* msg_data = new char[msg_total];
if (cvm::replica_index() == 0) {
+ int p;
// Replica 0 collects the delta gradient and count from the others.
for (p = 1; p < cvm::replica_num(); p++) {
// Receive the deltas.
diff --git a/lib/colvars/colvarcomp.cpp b/lib/colvars/colvarcomp.cpp
index 589de1d32af44a82d8b6beb78e8ee3d5f5ec8fc3..39b84b26d195dc59eae8bbced3ef40ef14f4cbb9 100644
--- a/lib/colvars/colvarcomp.cpp
+++ b/lib/colvars/colvarcomp.cpp
@@ -21,6 +21,9 @@ colvar::cvc::cvc()
b_try_scalable(true)
{
init_cvc_requires();
+ sup_coeff = 1.0;
+ period = 0.0;
+ wrap_center = 0.0;
}
@@ -30,43 +33,52 @@ colvar::cvc::cvc(std::string const &conf)
b_periodic(false),
b_try_scalable(true)
{
+ init_cvc_requires();
+ sup_coeff = 1.0;
+ period = 0.0;
+ wrap_center = 0.0;
+ init(conf);
+}
+
+
+int colvar::cvc::init(std::string const &conf)
+{
+ int error_code = COLVARS_OK;
if (cvm::debug())
cvm::log("Initializing cvc base object.\n");
- init_cvc_requires();
-
- if (get_keyval(conf, "name", this->name, std::string(""), parse_silent)) {
+ get_keyval(conf, "name", this->name, this->name);
+ if (name.size() > 0) {
// Temporary description until child object is initialized
description = "cvc " + name;
} else {
description = "uninitialized cvc";
}
- get_keyval(conf, "componentCoeff", sup_coeff, 1.0);
- get_keyval(conf, "componentExp", sup_np, 1);
+ get_keyval(conf, "componentCoeff", sup_coeff, sup_coeff);
+ get_keyval(conf, "componentExp", sup_np, sup_np);
- get_keyval(conf, "period", period, 0.0);
- get_keyval(conf, "wrapAround", wrap_center, 0.0);
+ get_keyval(conf, "period", period, period);
+ get_keyval(conf, "wrapAround", wrap_center, wrap_center);
- get_keyval_feature((colvarparse *)this, conf, "debugGradients",
+ get_keyval_feature(dynamic_cast<colvarparse *>(this), conf, "debugGradients",
f_cvc_debug_gradient, false, parse_silent);
- {
- bool b_no_PBC = false;
- get_keyval(conf, "forceNoPBC", b_no_PBC, false);
- if (b_no_PBC) {
- disable(f_cvc_pbc_minimum_image);
- } else {
- enable(f_cvc_pbc_minimum_image);
- }
- // this does not use get_keyval_feature() only for backward compatibility
+ bool b_no_PBC = !is_enabled(f_cvc_pbc_minimum_image); // Enabled by default
+ get_keyval(conf, "forceNoPBC", b_no_PBC, b_no_PBC);
+ if (b_no_PBC) {
+ disable(f_cvc_pbc_minimum_image);
+ } else {
+ enable(f_cvc_pbc_minimum_image);
}
// Attempt scalable calculations when in parallel? (By default yes, if available)
- get_keyval(conf, "scalable", b_try_scalable, true);
+ get_keyval(conf, "scalable", b_try_scalable, b_try_scalable);
if (cvm::debug())
cvm::log("Done initializing cvc base object.\n");
+
+ return error_code;
}
diff --git a/lib/colvars/colvarcomp.h b/lib/colvars/colvarcomp.h
index 52078a3a3059cb91315ac9f52e62b2f06e1e55f3..b5c3b16098c94f3fa94140b1259f016ef6581187 100644
--- a/lib/colvars/colvarcomp.h
+++ b/lib/colvars/colvarcomp.h
@@ -98,12 +98,14 @@ public:
/// \brief Constructor
///
- /// At least one constructor which reads a string should be defined
- /// for every class inheriting from cvc \param conf Contents
- /// of the configuration file pertaining to this \link cvc
- /// \endlink
+ /// Calls the init() function of the class
cvc(std::string const &conf);
+ /// An init function should be defined for every class inheriting from cvc
+ /// \param conf Contents of the configuration file pertaining to this \link
+ /// cvc \endlink
+ virtual int init(std::string const &conf);
+
/// \brief Within the constructor, make a group parse its own
/// options from the provided configuration string
/// Returns reference to new group
@@ -231,7 +233,7 @@ public:
virtual colvarvalue dist2_rgrad(colvarvalue const &x1,
colvarvalue const &x2) const;
- /// \brief Wrapp value (for periodic/symmetric cvcs)
+ /// \brief Wrap value (for periodic/symmetric cvcs)
virtual void wrap(colvarvalue &x) const;
/// \brief Pointers to all atom groups, to let colvars collect info
diff --git a/lib/colvars/colvarcomp_distances.cpp b/lib/colvars/colvarcomp_distances.cpp
index 9911f4c87edef9c17605403f21a0ffc1a45826e9..57b2a9a625fa01c49a8301b34b7e5f688096f8b4 100644
--- a/lib/colvars/colvarcomp_distances.cpp
+++ b/lib/colvars/colvarcomp_distances.cpp
@@ -148,7 +148,7 @@ void colvar::distance_vec::apply_force(colvarvalue const &force)
cvm::real colvar::distance_vec::dist2(colvarvalue const &x1,
colvarvalue const &x2) const
{
- return cvm::position_dist2(x1.rvector_value, x2.rvector_value);
+ return (cvm::position_distance(x1.rvector_value, x2.rvector_value)).norm2();
}
@@ -192,7 +192,7 @@ colvar::distance_z::distance_z(std::string const &conf)
// this group is optional
ref2 = parse_group(conf, "ref2", true);
- if (ref2 && ref2->size()) {
+ if ( ref2 ) {
cvm::log("Using axis joining the centers of mass of groups \"ref\" and \"ref2\"");
fixed_axis = false;
if (key_lookup(conf, "axis"))
@@ -306,7 +306,7 @@ void colvar::distance_z::apply_force(colvarvalue const &force)
if (!ref1->noforce)
ref1->apply_colvar_force(force.real_value);
- if (ref2 && ref2->size() && !ref2->noforce)
+ if (ref2 && !ref2->noforce)
ref2->apply_colvar_force(force.real_value);
if (!main->noforce)
@@ -464,7 +464,7 @@ void colvar::distance_xy::apply_force(colvarvalue const &force)
if (!ref1->noforce)
ref1->apply_colvar_force(force.real_value);
- if (ref2 && ref2->size() && !ref2->noforce)
+ if (ref2 && !ref2->noforce)
ref2->apply_colvar_force(force.real_value);
if (!main->noforce)
@@ -979,14 +979,12 @@ colvar::rmsd::rmsd(std::string const &conf)
"if provided, must be non-zero.\n");
return;
}
- } else {
- // if not, rely on existing atom indices for the group
- atoms->create_sorted_ids();
- ref_pos.resize(atoms->size());
}
- cvm::load_coords(ref_pos_file.c_str(), ref_pos, atoms->sorted_ids,
- ref_pos_col, ref_pos_col_value);
+ ref_pos.resize(atoms->size());
+
+ cvm::load_coords(ref_pos_file.c_str(), &ref_pos, atoms,
+ ref_pos_col, ref_pos_col_value);
}
}
@@ -1172,13 +1170,11 @@ colvar::eigenvector::eigenvector(std::string const &conf)
"if provided, must be non-zero.\n");
return;
}
- } else {
- // if not, use atom indices
- atoms->create_sorted_ids();
}
ref_pos.resize(atoms->size());
- cvm::load_coords(file_name.c_str(), ref_pos, atoms->sorted_ids, file_col, file_col_value);
+ cvm::load_coords(file_name.c_str(), &ref_pos, atoms,
+ file_col, file_col_value);
}
}
@@ -1249,13 +1245,11 @@ colvar::eigenvector::eigenvector(std::string const &conf)
cvm::error("Error: vectorColValue, if provided, must be non-zero.\n");
return;
}
- } else {
- // if not, use atom indices
- atoms->create_sorted_ids();
}
eigenvec.resize(atoms->size());
- cvm::load_coords(file_name.c_str(), eigenvec, atoms->sorted_ids, file_col, file_col_value);
+ cvm::load_coords(file_name.c_str(), &eigenvec, atoms,
+ file_col, file_col_value);
}
}
diff --git a/lib/colvars/colvarcomp_rotations.cpp b/lib/colvars/colvarcomp_rotations.cpp
index 2650a9fe18efaaff66e6711d73be99a715d17ec1..498ef7c2f548f0cc6593725c52fb24d341c72822 100644
--- a/lib/colvars/colvarcomp_rotations.cpp
+++ b/lib/colvars/colvarcomp_rotations.cpp
@@ -50,12 +50,11 @@ colvar::orientation::orientation(std::string const &conf)
"if provided, must be non-zero.\n");
return;
}
- } else {
- // if not, use atom indices
- atoms->create_sorted_ids();
}
+
ref_pos.resize(atoms->size());
- cvm::load_coords(file_name.c_str(), ref_pos, atoms->sorted_ids, file_col, file_col_value);
+ cvm::load_coords(file_name.c_str(), &ref_pos, atoms,
+ file_col, file_col_value);
}
}
diff --git a/lib/colvars/colvardeps.cpp b/lib/colvars/colvardeps.cpp
index a058ad55c2a4911324c9cd07b4ea7bb1e1afb147..80bd6670d3f13317bdf10da43a48cee5b482ec61 100644
--- a/lib/colvars/colvardeps.cpp
+++ b/lib/colvars/colvardeps.cpp
@@ -549,7 +549,7 @@ void colvardeps::init_cv_requires() {
f_req_exclude(f_cv_custom_function, f_cv_scripted);
init_feature(f_cv_periodic, "periodic", f_type_static);
- f_req_self(f_cv_periodic, f_cv_homogeneous);
+ f_req_self(f_cv_periodic, f_cv_scalar);
init_feature(f_cv_scalar, "scalar", f_type_static);
init_feature(f_cv_linear, "linear", f_type_static);
init_feature(f_cv_homogeneous, "homogeneous", f_type_static);
diff --git a/lib/colvars/colvargrid.cpp b/lib/colvars/colvargrid.cpp
index 1ac4aae133c3a225aa8d4a8bb2dbdd1c3ac381cb..407b336afd7b09e49a05c1550096bf318f4f06f3 100644
--- a/lib/colvars/colvargrid.cpp
+++ b/lib/colvars/colvargrid.cpp
@@ -329,7 +329,6 @@ void integrate_potential::update_div_local(const std::vector<int> &ix0)
const int linear_index = address(ix0);
int i, j, k;
std::vector<int> ix = ix0;
- const cvm::real * g;
if (nd == 2) {
// gradients at grid points surrounding the current scalar grid point
@@ -783,7 +782,7 @@ void integrate_potential::atimes(const std::vector<cvm::real> &A, std::vector<cv
/// Inversion of preconditioner matrix (e.g. diagonal of the Laplacian)
void integrate_potential::asolve(const std::vector<cvm::real> &b, std::vector<cvm::real> &x)
{
- for (size_t i=0; i<nt; i++) {
+ for (size_t i=0; i<int(nt); i++) {
x[i] = b[i] * inv_lap_diag[i]; // Jacobi preconditioner - little benefit in tests so far
}
return;
@@ -803,7 +802,7 @@ void integrate_potential::nr_linbcg_sym(const std::vector<cvm::real> &b, std::ve
iter=0;
atimes(x,r);
- for (j=0;j<nt;j++) {
+ for (j=0;j<int(nt);j++) {
r[j]=b[j]-r[j];
}
bnrm=l2norm(b);
@@ -814,26 +813,26 @@ void integrate_potential::nr_linbcg_sym(const std::vector<cvm::real> &b, std::ve
bkden = 1.0;
while (iter < itmax) {
++iter;
- for (bknum=0.0,j=0;j<nt;j++) {
+ for (bknum=0.0,j=0;j<int(nt);j++) {
bknum += r[j]*r[j]; // precon: z[j]*r[j]
}
if (iter == 1) {
- for (j=0;j<nt;j++) {
+ for (j=0;j<int(nt);j++) {
p[j] = r[j]; // precon: p[j] = z[j]
}
} else {
bk=bknum/bkden;
- for (j=0;j<nt;j++) {
+ for (j=0;j<int(nt);j++) {
p[j] = bk*p[j] + r[j]; // precon: bk*p[j] + z[j]
}
}
bkden = bknum;
atimes(p,z);
- for (akden=0.0,j=0;j<nt;j++) {
+ for (akden=0.0,j=0;j<int(nt);j++) {
akden += z[j]*p[j];
}
ak = bknum/akden;
- for (j=0;j<nt;j++) {
+ for (j=0;j<int(nt);j++) {
x[j] += ak*p[j];
r[j] -= ak*z[j];
}
diff --git a/lib/colvars/colvarmodule.cpp b/lib/colvars/colvarmodule.cpp
index 9898e2d5e8264d96ba79d12aac5e70bf9dbfd67d..dc6242c5bc304069799af4c15fdde561a5e9e938 100644
--- a/lib/colvars/colvarmodule.cpp
+++ b/lib/colvars/colvarmodule.cpp
@@ -8,7 +8,7 @@
// Colvars repository at GitHub.
#include <sstream>
-#include <string.h>
+#include <cstring>
#include "colvarmodule.h"
#include "colvarparse.h"
@@ -30,10 +30,10 @@ colvarmodule::colvarmodule(colvarproxy *proxy_in)
depth_s = 0;
cv_traj_os = NULL;
- // pointer to the proxy object
if (proxy == NULL) {
- proxy = proxy_in;
- parse = new colvarparse();
+ proxy = proxy_in; // Pointer to the proxy object
+ parse = new colvarparse(); // Parsing object for global options
+ version_int = proxy->get_version_from_string(COLVARS_VERSION);
} else {
// TODO relax this error to handle multiple molecules in VMD
// once the module is not static anymore
@@ -58,22 +58,24 @@ colvarmodule::colvarmodule(colvarproxy *proxy_in)
// "it_restart" will be set by the input state file, if any;
// "it" should be updated by the proxy
colvarmodule::it = colvarmodule::it_restart = 0;
- colvarmodule::it_restart_from_state_file = true;
- colvarmodule::use_scripted_forces = false;
+ use_scripted_forces = false;
+ scripting_after_biases = false;
- colvarmodule::b_analysis = false;
+ b_analysis = false;
colvarmodule::debug_gradients_step_size = 1.0e-07;
colvarmodule::rotation::monitor_crossings = false;
colvarmodule::rotation::crossing_threshold = 1.0e-02;
- colvarmodule::cv_traj_freq = 100;
- colvarmodule::restart_out_freq = proxy->restart_frequency();
+ cv_traj_freq = 100;
+ restart_out_freq = proxy->restart_frequency();
// by default overwrite the existing trajectory file
- colvarmodule::cv_traj_append = false;
+ cv_traj_append = false;
+
+ cv_traj_write_labels = true;
}
@@ -189,26 +191,27 @@ int colvarmodule::parse_config(std::string &conf)
{
extra_conf.clear();
- // parse global options
+ // Parse global options
if (catch_input_errors(parse_global_params(conf))) {
return get_error();
}
- // parse the options for collective variables
+ // Parse the options for collective variables
if (catch_input_errors(parse_colvars(conf))) {
return get_error();
}
- // parse the options for biases
+ // Parse the options for biases
if (catch_input_errors(parse_biases(conf))) {
return get_error();
}
- // done parsing known keywords, check that all keywords found were valid ones
+ // Done parsing known keywords, check that all keywords found were valid ones
if (catch_input_errors(parse->check_keywords(conf, "colvarmodule"))) {
return get_error();
}
+ // Parse auto-generated configuration (e.g. for back-compatibility)
if (extra_conf.size()) {
catch_input_errors(parse_global_params(extra_conf));
catch_input_errors(parse_colvars(extra_conf));
@@ -222,13 +225,11 @@ int colvarmodule::parse_config(std::string &conf)
cvm::log("Collective variables module (re)initialized.\n");
cvm::log(cvm::line_marker);
- // update any necessary proxy data
+ // Update any necessary proxy data
proxy->setup();
- if (cv_traj_os != NULL) {
- // configuration might have changed, better redo the labels
- write_traj_label(*cv_traj_os);
- }
+ // configuration might have changed, better redo the labels
+ cv_traj_write_labels = true;
return get_error();
}
@@ -279,15 +280,18 @@ int colvarmodule::parse_global_params(std::string const &conf)
parse->get_keyval(conf, "colvarsTrajAppend",
cv_traj_append, cv_traj_append, colvarparse::parse_silent);
- parse->get_keyval(conf, "scriptedColvarForces", use_scripted_forces, false);
+ parse->get_keyval(conf, "scriptedColvarForces",
+ use_scripted_forces, use_scripted_forces);
- parse->get_keyval(conf, "scriptingAfterBiases", scripting_after_biases, true);
+ parse->get_keyval(conf, "scriptingAfterBiases",
+ scripting_after_biases, scripting_after_biases);
if (use_scripted_forces && !proxy->force_script_defined) {
- cvm::error("User script for scripted colvar forces not found.", INPUT_ERROR);
+ return cvm::error("User script for scripted colvar forces not found.",
+ INPUT_ERROR);
}
- return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
+ return cvm::get_error();
}
@@ -432,13 +436,13 @@ int colvarmodule::parse_biases(std::string const &conf)
}
-int colvarmodule::num_variables() const
+size_t colvarmodule::num_variables() const
{
return colvars.size();
}
-int colvarmodule::num_variables_feature(int feature_id) const
+size_t colvarmodule::num_variables_feature(int feature_id) const
{
size_t n = 0;
for (std::vector<colvar *>::const_iterator cvi = colvars.begin();
@@ -452,13 +456,13 @@ int colvarmodule::num_variables_feature(int feature_id) const
}
-int colvarmodule::num_biases() const
+size_t colvarmodule::num_biases() const
{
return biases.size();
}
-int colvarmodule::num_biases_feature(int feature_id) const
+size_t colvarmodule::num_biases_feature(int feature_id) const
{
size_t n = 0;
for (std::vector<colvarbias *>::const_iterator bi = biases.begin();
@@ -472,7 +476,7 @@ int colvarmodule::num_biases_feature(int feature_id) const
}
-int colvarmodule::num_biases_type(std::string const &type) const
+size_t colvarmodule::num_biases_type(std::string const &type) const
{
size_t n = 0;
for (std::vector<colvarbias *>::const_iterator bi = biases.begin();
@@ -971,13 +975,20 @@ int colvarmodule::write_restart_file(std::string const &out_name)
int colvarmodule::write_traj_files()
{
if (cv_traj_os == NULL) {
- open_traj_file(cv_traj_name);
+ if (open_traj_file(cv_traj_name) != COLVARS_OK) {
+ return cvm::get_error();
+ } else {
+ cv_traj_write_labels = true;
+ }
}
// write labels in the traj file every 1000 lines and at first timestep
- if ((cvm::step_absolute() % (cv_traj_freq * 1000)) == 0 || cvm::step_relative() == 0) {
+ if ((cvm::step_absolute() % (cv_traj_freq * 1000)) == 0 ||
+ cvm::step_relative() == 0 ||
+ cv_traj_write_labels) {
write_traj_label(*cv_traj_os);
}
+ cv_traj_write_labels = false;
if ((cvm::step_absolute() % cv_traj_freq) == 0) {
write_traj(*cv_traj_os);
@@ -1064,7 +1075,7 @@ int colvarmodule::reset()
{
parse->init();
- cvm::log("Resetting the Collective Variables Module.\n");
+ cvm::log("Resetting the Collective Variables module.\n");
// Iterate backwards because we are deleting the elements as we go
for (std::vector<colvarbias *>::reverse_iterator bi = biases.rbegin();
@@ -1073,6 +1084,7 @@ int colvarmodule::reset()
delete *bi; // the bias destructor updates the biases array
}
biases.clear();
+ biases_active_.clear();
// Iterate backwards because we are deleting the elements as we go
for (std::vector<colvar *>::reverse_iterator cvi = colvars.rbegin();
@@ -1088,7 +1100,7 @@ int colvarmodule::reset()
proxy->reset();
if (cv_traj_os != NULL) {
- // Do not close file here, as we might not be done with it yet.
+ // Do not close traj file here, as we might not be done with it yet.
proxy->flush_output_stream(cv_traj_os);
}
@@ -1188,12 +1200,10 @@ std::istream & colvarmodule::read_restart(std::istream &is)
// read global restart information
std::string restart_conf;
if (is >> colvarparse::read_block("configuration", restart_conf)) {
- if (it_restart_from_state_file) {
- parse->get_keyval(restart_conf, "step",
- it_restart, (size_t) 0,
- colvarparse::parse_silent);
+ parse->get_keyval(restart_conf, "step",
+ it_restart, (size_t) 0,
+ colvarparse::parse_silent);
it = it_restart;
- }
std::string restart_version;
parse->get_keyval(restart_conf, "version",
restart_version, std::string(""),
@@ -1688,40 +1698,59 @@ int cvm::read_index_file(char const *filename)
return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
}
+
int cvm::load_atoms(char const *file_name,
cvm::atom_group &atoms,
std::string const &pdb_field,
- double const pdb_field_value)
+ double pdb_field_value)
{
return proxy->load_atoms(file_name, atoms, pdb_field, pdb_field_value);
}
+
int cvm::load_coords(char const *file_name,
- std::vector<cvm::atom_pos> &pos,
- const std::vector<int> &indices,
+ std::vector<cvm::rvector> *pos,
+ cvm::atom_group *atoms,
std::string const &pdb_field,
- double const pdb_field_value)
+ double pdb_field_value)
{
- // Differentiate between PDB and XYZ files
- // for XYZ files, use CVM internal parser
- // otherwise call proxy function for PDB
+ int error_code = COLVARS_OK;
+
+ std::string const ext(strlen(file_name) > 4 ?
+ (file_name + (strlen(file_name) - 4)) :
+ file_name);
+
+ atoms->create_sorted_ids();
+
+ std::vector<cvm::rvector> sorted_pos(atoms->size(), cvm::rvector(0.0));
- std::string const ext(strlen(file_name) > 4 ? (file_name + (strlen(file_name) - 4)) : file_name);
+ // Differentiate between PDB and XYZ files
if (colvarparse::to_lower_cppstr(ext) == std::string(".xyz")) {
- if ( pdb_field.size() > 0 ) {
- cvm::error("Error: PDB column may not be specified for XYZ coordinate file.\n", INPUT_ERROR);
- return COLVARS_ERROR;
+ if (pdb_field.size() > 0) {
+ return cvm::error("Error: PDB column may not be specified "
+ "for XYZ coordinate files.\n", INPUT_ERROR);
}
- return cvm::load_coords_xyz(file_name, pos, indices);
+ // For XYZ files, use internal parser
+ error_code |= cvm::load_coords_xyz(file_name, &sorted_pos, atoms);
} else {
- return proxy->load_coords(file_name, pos, indices, pdb_field, pdb_field_value);
+ // Otherwise, call proxy function for PDB
+ error_code |= proxy->load_coords(file_name,
+ sorted_pos, atoms->sorted_ids(),
+ pdb_field, pdb_field_value);
}
+
+ std::vector<int> const &map = atoms->sorted_ids_map();
+ for (size_t i = 0; i < atoms->size(); i++) {
+ (*pos)[map[i]] = sorted_pos[i];
+ }
+
+ return error_code;
}
int cvm::load_coords_xyz(char const *filename,
- std::vector<atom_pos> &pos,
- const std::vector<int> &indices)
+ std::vector<rvector> *pos,
+ cvm::atom_group *atoms)
{
std::ifstream xyz_is(filename);
unsigned int natoms;
@@ -1736,12 +1765,12 @@ int cvm::load_coords_xyz(char const *filename,
cvm::getline(xyz_is, line);
cvm::getline(xyz_is, line);
xyz_is.width(255);
- std::vector<atom_pos>::iterator pos_i = pos.begin();
+ std::vector<atom_pos>::iterator pos_i = pos->begin();
- if (pos.size() != natoms) { // Use specified indices
+ if (pos->size() != natoms) { // Use specified indices
int next = 0; // indices are zero-based
- std::vector<int>::const_iterator index = indices.begin();
- for ( ; pos_i != pos.end() ; pos_i++, index++) {
+ std::vector<int>::const_iterator index = atoms->sorted_ids().begin();
+ for ( ; pos_i != pos->end() ; pos_i++, index++) {
while ( next < *index ) {
cvm::getline(xyz_is, line);
@@ -1751,7 +1780,7 @@ int cvm::load_coords_xyz(char const *filename,
xyz_is >> (*pos_i)[0] >> (*pos_i)[1] >> (*pos_i)[2];
}
} else { // Use all positions
- for ( ; pos_i != pos.end() ; pos_i++) {
+ for ( ; pos_i != pos->end() ; pos_i++) {
xyz_is >> symbol;
xyz_is >> (*pos_i)[0] >> (*pos_i)[1] >> (*pos_i)[2];
}
@@ -1792,17 +1821,13 @@ void cvm::request_total_force()
proxy->request_total_force(true);
}
-cvm::rvector cvm::position_distance(atom_pos const &pos1,
- atom_pos const &pos2)
+
+cvm::rvector cvm::position_distance(cvm::atom_pos const &pos1,
+ cvm::atom_pos const &pos2)
{
return proxy->position_distance(pos1, pos2);
}
-cvm::real cvm::position_dist2(cvm::atom_pos const &pos1,
- cvm::atom_pos const &pos2)
-{
- return proxy->position_dist2(pos1, pos2);
-}
cvm::real cvm::rand_gaussian(void)
{
diff --git a/lib/colvars/colvarmodule.h b/lib/colvars/colvarmodule.h
index 64a98b77a02d59eae598a3f223214fc103018263..f3d99a2b234baf4a72300b4c59c3c9595d318b12 100644
--- a/lib/colvars/colvarmodule.h
+++ b/lib/colvars/colvarmodule.h
@@ -73,8 +73,17 @@ private:
/// Impossible to initialize the main object without arguments
colvarmodule();
+ /// Integer representing the version string (allows comparisons)
+ int version_int;
+
public:
+ /// Get the version number (higher = more recent)
+ int version_number() const
+ {
+ return version_int;
+ }
+
friend class colvarproxy;
// TODO colvarscript should be unaware of colvarmodule's internals
friend class colvarscript;
@@ -158,10 +167,6 @@ public:
return it;
}
- /// If true, get it_restart from the state file; if set to false,
- /// the MD program is providing it
- bool it_restart_from_state_file;
-
/// \brief Finite difference step size (if there is no dynamics, or
/// if gradients need to be tested independently from the size of
/// dt)
@@ -306,19 +311,19 @@ private:
public:
/// Return how many variables are defined
- int num_variables() const;
+ size_t num_variables() const;
/// Return how many variables have this feature enabled
- int num_variables_feature(int feature_id) const;
+ size_t num_variables_feature(int feature_id) const;
/// Return how many biases are defined
- int num_biases() const;
+ size_t num_biases() const;
/// Return how many biases have this feature enabled
- int num_biases_feature(int feature_id) const;
+ size_t num_biases_feature(int feature_id) const;
/// Return how many biases of this type are defined
- int num_biases_type(std::string const &type) const;
+ size_t num_biases_type(std::string const &type) const;
/// Return the names of time-dependent biases with forces enabled (ABF,
/// metadynamics, etc)
@@ -479,9 +484,6 @@ public:
/// Print a message to the main log and set global error code
static int error(std::string const &message, int code = COLVARS_ERROR);
- /// Print a message to the main log and exit normally
- static void exit(std::string const &message);
-
// Replica exchange commands.
static bool replica_enabled();
static int replica_index();
@@ -495,15 +497,6 @@ public:
static rvector position_distance(atom_pos const &pos1,
atom_pos const &pos2);
- /// \brief Get the square distance between two positions (with
- /// periodic boundary conditions handled transparently)
- ///
- /// Note: in the case of periodic boundary conditions, this provides
- /// an analytical square distance (while taking the square of
- /// position_distance() would produce leads to a cusp)
- static real position_dist2(atom_pos const &pos1,
- atom_pos const &pos2);
-
/// \brief Names of groups from a Gromacs .ndx file to be read at startup
std::list<std::string> index_group_names;
@@ -513,29 +506,36 @@ public:
/// \brief Read a Gromacs .ndx file
int read_index_file(char const *filename);
-
- /// \brief Create atoms from a file \param filename name of the file
- /// (usually a PDB) \param atoms array of the atoms to be allocated
- /// \param pdb_field (optiona) if "filename" is a PDB file, use this
- /// field to determine which are the atoms to be set
+ /// \brief Select atom IDs from a file (usually PDB) \param filename name of
+ /// the file \param atoms array into which atoms read from "filename" will be
+ /// appended \param pdb_field (optional) if the file is a PDB and this
+ /// string is non-empty, select atoms for which this field is non-zero
+ /// \param pdb_field_value (optional) if non-zero, select only atoms whose
+ /// pdb_field equals this
static int load_atoms(char const *filename,
atom_group &atoms,
std::string const &pdb_field,
- double const pdb_field_value = 0.0);
-
- /// \brief Load the coordinates for a group of atoms from a file
- /// (PDB or XYZ)
+ double pdb_field_value = 0.0);
+
+ /// \brief Load coordinates for a group of atoms from a file (PDB or XYZ);
+ /// if "pos" is already allocated, the number of its elements must match the
+ /// number of entries in "filename" \param filename name of the file \param
+ /// pos array of coordinates \param atoms group containing the atoms (used
+ /// to obtain internal IDs) \param pdb_field (optional) if the file is a PDB
+ /// and this string is non-empty, select atoms for which this field is
+ /// non-zero \param pdb_field_value (optional) if non-zero, select only
+ /// atoms whose pdb_field equals this
static int load_coords(char const *filename,
- std::vector<atom_pos> &pos,
- const std::vector<int> &indices,
+ std::vector<rvector> *pos,
+ atom_group *atoms,
std::string const &pdb_field,
- double const pdb_field_value = 0.0);
+ double pdb_field_value = 0.0);
/// \brief Load the coordinates for a group of atoms from an
/// XYZ file
static int load_coords_xyz(char const *filename,
- std::vector<atom_pos> &pos,
- const std::vector<int> &indices);
+ std::vector<rvector> *pos,
+ atom_group *atoms);
/// Frequency for collective variables trajectory output
static size_t cv_traj_freq;
@@ -568,6 +568,9 @@ protected:
/// Appending to the existing trajectory file?
bool cv_traj_append;
+ /// Write labels at the next iteration
+ bool cv_traj_write_labels;
+
private:
/// Counter for the current depth in the object hierarchy (useg e.g. in output)
diff --git a/lib/colvars/colvarproxy.cpp b/lib/colvars/colvarproxy.cpp
index 8767d5f459090854cf19ad011f579e752c6d2230..86338dfd1b81768de686dfba86bfea964240eca0 100644
--- a/lib/colvars/colvarproxy.cpp
+++ b/lib/colvars/colvarproxy.cpp
@@ -8,7 +8,7 @@
// Colvars repository at GitHub.
#include <sstream>
-#include <string.h>
+#include <cstring>
#if defined(_OPENMP)
#include <omp.h>
@@ -26,7 +26,10 @@
-colvarproxy_system::colvarproxy_system() {}
+colvarproxy_system::colvarproxy_system()
+{
+ reset_pbc_lattice();
+}
colvarproxy_system::~colvarproxy_system() {}
@@ -55,10 +58,73 @@ bool colvarproxy_system::total_forces_same_step() const
}
-cvm::real colvarproxy_system::position_dist2(cvm::atom_pos const &pos1,
- cvm::atom_pos const &pos2)
+inline int round_to_integer(cvm::real x)
{
- return (position_distance(pos1, pos2)).norm2();
+ return std::floor(x+0.5);
+}
+
+
+void colvarproxy_system::update_pbc_lattice()
+{
+ // Periodicity is assumed in all directions
+
+ if (boundaries_type == boundaries_unsupported ||
+ boundaries_type == boundaries_non_periodic) {
+ cvm::error("Error: setting PBC lattice with unsupported boundaries.\n",
+ BUG_ERROR);
+ return;
+ }
+
+ {
+ cvm::rvector const v = cvm::rvector::outer(unit_cell_y, unit_cell_z);
+ reciprocal_cell_x = v/(v*unit_cell_x);
+ }
+ {
+ cvm::rvector const v = cvm::rvector::outer(unit_cell_z, unit_cell_x);
+ reciprocal_cell_y = v/(v*unit_cell_y);
+ }
+ {
+ cvm::rvector const v = cvm::rvector::outer(unit_cell_x, unit_cell_y);
+ reciprocal_cell_z = v/(v*unit_cell_z);
+ }
+}
+
+
+void colvarproxy_system::reset_pbc_lattice()
+{
+ unit_cell_x.reset();
+ unit_cell_y.reset();
+ unit_cell_z.reset();
+ reciprocal_cell_x.reset();
+ reciprocal_cell_y.reset();
+ reciprocal_cell_z.reset();
+}
+
+
+cvm::rvector colvarproxy_system::position_distance(cvm::atom_pos const &pos1,
+ cvm::atom_pos const &pos2)
+ const
+{
+ if (boundaries_type == boundaries_unsupported) {
+ cvm::error("Error: unsupported boundary conditions.\n", INPUT_ERROR);
+ }
+
+ cvm::rvector diff = (pos2 - pos1);
+
+ if (boundaries_type == boundaries_non_periodic) return diff;
+
+ cvm::real const x_shift = round_to_integer(reciprocal_cell_x*diff);
+ cvm::real const y_shift = round_to_integer(reciprocal_cell_y*diff);
+ cvm::real const z_shift = round_to_integer(reciprocal_cell_z*diff);
+
+ diff.x -= x_shift*unit_cell_x.x + y_shift*unit_cell_y.x +
+ z_shift*unit_cell_z.x;
+ diff.y -= x_shift*unit_cell_x.y + y_shift*unit_cell_y.y +
+ z_shift*unit_cell_z.y;
+ diff.z -= x_shift*unit_cell_x.z + y_shift*unit_cell_y.z +
+ z_shift*unit_cell_z.z;
+
+ return diff;
}
@@ -132,7 +198,7 @@ void colvarproxy_atoms::clear_atom(int index)
int colvarproxy_atoms::load_atoms(char const *filename,
cvm::atom_group &atoms,
std::string const &pdb_field,
- double const)
+ double)
{
return cvm::error("Error: loading atom identifiers from a file "
"is currently not implemented.\n",
@@ -142,9 +208,9 @@ int colvarproxy_atoms::load_atoms(char const *filename,
int colvarproxy_atoms::load_coords(char const *filename,
std::vector<cvm::atom_pos> &pos,
- const std::vector<int> &indices,
+ std::vector<int> const &sorted_ids,
std::string const &pdb_field,
- double const)
+ double)
{
return cvm::error("Error: loading atomic coordinates from a file "
"is currently not implemented.\n",
@@ -661,6 +727,7 @@ int colvarproxy_io::close_output_stream(std::string const &output_name)
for ( ; osi != output_files.end(); osi++, osni++) {
if (*osni == output_name) {
((std::ofstream *) (*osi))->close();
+ delete *osi;
output_files.erase(osi);
output_stream_names.erase(osni);
return COLVARS_OK;
@@ -729,3 +796,13 @@ size_t colvarproxy::restart_frequency()
return 0;
}
+
+int colvarproxy::get_version_from_string(char const *version_string)
+{
+ std::string const v(version_string);
+ std::istringstream is(v.substr(0, 4) + v.substr(5, 2) + v.substr(8, 2));
+ int newint;
+ is >> newint;
+ return newint;
+}
+
diff --git a/lib/colvars/colvarproxy.h b/lib/colvars/colvarproxy.h
index bf290482704af3204518c0ffae7daf5ad5d88c0b..845f93c9bcde6b2654b86fcc9b52baee998ec8a4 100644
--- a/lib/colvars/colvarproxy.h
+++ b/lib/colvars/colvarproxy.h
@@ -14,6 +14,7 @@
#include <list>
#include "colvarmodule.h"
+#include "colvartypes.h"
#include "colvarvalue.h"
@@ -29,7 +30,7 @@
/// To interface to a new MD engine, the simplest solution is to derive a new
/// class from \link colvarproxy \endlink. Currently implemented are: \link
/// colvarproxy_lammps, \endlink, \link colvarproxy_namd, \endlink, \link
-/// colvarproxy_vmd, \endlink.
+/// colvarproxy_vmd \endlink.
// forward declarations
@@ -68,14 +69,16 @@ public:
/// \brief Get the PBC-aware distance vector between two positions
virtual cvm::rvector position_distance(cvm::atom_pos const &pos1,
- cvm::atom_pos const &pos2) = 0;
+ cvm::atom_pos const &pos2) const;
- /// \brief Get the PBC-aware square distance between two positions;
- /// may need to be reimplemented independently from position_distance() for optimization purposes
- virtual cvm::real position_dist2(cvm::atom_pos const &pos1,
- cvm::atom_pos const &pos2);
+ /// Recompute PBC reciprocal lattice (assumes XYZ periodicity)
+ void update_pbc_lattice();
- /// Tell the proxy whether total forces are needed (may not always be available)
+ /// Set the lattice vectors to zero
+ void reset_pbc_lattice();
+
+ /// \brief Tell the proxy whether total forces are needed (they may not
+ /// always be available)
virtual void request_total_force(bool yesno);
/// Are total forces being used?
@@ -83,6 +86,29 @@ public:
/// Are total forces from the current step available?
virtual bool total_forces_same_step() const;
+
+protected:
+
+ /// \brief Type of boundary conditions
+ ///
+ /// Orthogonal and triclinic cells are made available to objects.
+ /// For any other conditions (mixed periodicity, triclinic cells in LAMMPS)
+ /// minimum-image distances are computed by the host engine regardless.
+ enum Boundaries_type {
+ boundaries_non_periodic,
+ boundaries_pbc_ortho,
+ boundaries_pbc_triclinic,
+ boundaries_unsupported
+ };
+
+ /// Type of boundary conditions
+ Boundaries_type boundaries_type;
+
+ /// Bravais lattice vectors
+ cvm::rvector unit_cell_x, unit_cell_y, unit_cell_z;
+
+ /// Reciprocal lattice vectors
+ cvm::rvector reciprocal_cell_x, reciprocal_cell_y, reciprocal_cell_z;
};
@@ -121,24 +147,30 @@ public:
/// (costly) set the corresponding atoms_ncopies to zero
virtual void clear_atom(int index);
- /// \brief Read atom identifiers from a file \param filename name of
- /// the file (usually a PDB) \param atoms array to which atoms read
- /// from "filename" will be appended \param pdb_field (optiona) if
- /// "filename" is a PDB file, use this field to determine which are
- /// the atoms to be set
+ /// \brief Select atom IDs from a file (usually PDB) \param filename name of
+ /// the file \param atoms array to which atoms read from "filename" will be
+ /// appended \param pdb_field (optional) if the file is a PDB and this
+ /// string is non-empty, select atoms for which this field is non-zero
+ /// \param pdb_field_value (optional) if non-zero, select only atoms whose
+ /// pdb_field equals this
virtual int load_atoms(char const *filename,
cvm::atom_group &atoms,
std::string const &pdb_field,
- double const pdb_field_value = 0.0);
-
- /// \brief Load the coordinates for a group of atoms from a file
- /// (usually a PDB); if "pos" is already allocated, the number of its
- /// elements must match the number of atoms in "filename"
+ double pdb_field_value = 0.0);
+
+ /// \brief Load a set of coordinates from a file (usually PDB); if "pos" is
+ /// already allocated, the number of its elements must match the number of
+ /// entries in "filename" \param filename name of the file \param pos array
+ /// of coordinates \param sorted_ids array of sorted internal IDs, used to
+ /// loop through the file only once \param pdb_field (optional) if the file
+ /// is a PDB and this string is non-empty, select atoms for which this field
+ /// is non-zero \param pdb_field_value (optional) if non-zero, select only
+ /// atoms whose pdb_field equals this
virtual int load_coords(char const *filename,
std::vector<cvm::atom_pos> &pos,
- const std::vector<int> &indices,
+ std::vector<int> const &sorted_ids,
std::string const &pdb_field,
- double const pdb_field_value = 0.0);
+ double pdb_field_value = 0.0);
/// Clear atomic data
int reset();
@@ -636,6 +668,15 @@ public:
return b_simulation_running;
}
+ /// Convert a version string "YYYY-MM-DD" into an integer
+ int get_version_from_string(char const *version_string);
+
+ /// Get the version number (higher = more recent)
+ int version_number() const
+ {
+ return version_int;
+ }
+
protected:
/// Whether a simulation is running (warn against irrecovarable errors)
@@ -644,6 +685,9 @@ protected:
/// Whether the entire module should be deallocated by the host engine
bool b_delete_requested;
+ /// Integer representing the version string (allows comparisons)
+ int version_int;
+
};
diff --git a/lib/colvars/colvars_version.h b/lib/colvars/colvars_version.h
index dc4b8bd07e420d83289b99f458ed2bf935ab210e..68f5cd13ab14eae1d71a47eba46d8729167966cd 100644
--- a/lib/colvars/colvars_version.h
+++ b/lib/colvars/colvars_version.h
@@ -1,5 +1,5 @@
#ifndef COLVARS_VERSION
-#define COLVARS_VERSION "2018-01-17"
+#define COLVARS_VERSION "2018-04-29"
// This file is part of the Collective Variables module (Colvars).
// The original version of Colvars and its updates are located at:
// https://github.com/colvars/colvars
diff --git a/lib/colvars/colvarscript.cpp b/lib/colvars/colvarscript.cpp
index 0977496b9e1c252e52c5670f44321796cfafd889..a55e4c65d921261c3f428cdef0f7211c8c5ad6a1 100644
--- a/lib/colvars/colvarscript.cpp
+++ b/lib/colvars/colvarscript.cpp
@@ -8,8 +8,7 @@
// Colvars repository at GitHub.
#include <cstdlib>
-#include <stdlib.h>
-#include <string.h>
+#include <cstring>
#define COLVARSCRIPT_CPP
#include "colvarscript.h"
diff --git a/lib/colvars/colvartypes.cpp b/lib/colvars/colvartypes.cpp
index b604606d4628911138f2553215db9d7b3c306630..2b45d77e078478e755b76194d2f39851e0c3881c 100644
--- a/lib/colvars/colvartypes.cpp
+++ b/lib/colvars/colvartypes.cpp
@@ -7,8 +7,8 @@
// If you wish to distribute your changes, please submit them to the
// Colvars repository at GitHub.
-#include <stdlib.h>
-#include <string.h>
+#include <cstdlib>
+#include <cstring>
#include "colvarmodule.h"
#include "colvartypes.h"
diff --git a/lib/colvars/colvartypes.h b/lib/colvars/colvartypes.h
index 97257d18ad66d1da99b0b74586190e735687850b..4ef9557dcbf400c2e7adfc846207874632b134ac 100644
--- a/lib/colvars/colvartypes.h
+++ b/lib/colvars/colvartypes.h
@@ -130,7 +130,7 @@ public:
}
}
- inline void operator *= (cvm::real const &a)
+ inline void operator *= (cvm::real a)
{
size_t i;
for (i = 0; i < this->size(); i++) {
@@ -138,7 +138,7 @@ public:
}
}
- inline void operator /= (cvm::real const &a)
+ inline void operator /= (cvm::real a)
{
size_t i;
for (i = 0; i < this->size(); i++) {
@@ -146,7 +146,8 @@ public:
}
}
- inline friend vector1d<T> operator + (vector1d<T> const &v1, vector1d<T> const &v2)
+ inline friend vector1d<T> operator + (vector1d<T> const &v1,
+ vector1d<T> const &v2)
{
check_sizes(v1.size(), v2.size());
vector1d<T> result(v1.size());
@@ -157,7 +158,8 @@ public:
return result;
}
- inline friend vector1d<T> operator - (vector1d<T> const &v1, vector1d<T> const &v2)
+ inline friend vector1d<T> operator - (vector1d<T> const &v1,
+ vector1d<T> const &v2)
{
check_sizes(v1.size(), v2.size());
vector1d<T> result(v1.size());
@@ -168,7 +170,7 @@ public:
return result;
}
- inline friend vector1d<T> operator * (vector1d<T> const &v, cvm::real const &a)
+ inline friend vector1d<T> operator * (vector1d<T> const &v, cvm::real a)
{
vector1d<T> result(v.size());
size_t i;
@@ -178,12 +180,12 @@ public:
return result;
}
- inline friend vector1d<T> operator * (cvm::real const &a, vector1d<T> const &v)
+ inline friend vector1d<T> operator * (cvm::real a, vector1d<T> const &v)
{
return v * a;
}
- inline friend vector1d<T> operator / (vector1d<T> const &v, cvm::real const &a)
+ inline friend vector1d<T> operator / (vector1d<T> const &v, cvm::real a)
{
vector1d<T> result(v.size());
size_t i;
@@ -246,7 +248,8 @@ public:
}
/// Assign a vector to a slice of this vector
- inline void sliceassign(size_t const i1, size_t const i2, vector1d<T> const &v)
+ inline void sliceassign(size_t const i1, size_t const i2,
+ vector1d<T> const &v)
{
if ((i2 < i1) || (i2 >= this->size())) {
cvm::error("Error: trying to slice a vector using incorrect boundaries.\n");
@@ -259,12 +262,13 @@ public:
/// Formatted output
- inline size_t output_width(size_t const &real_width) const
+ inline size_t output_width(size_t real_width) const
{
return real_width*(this->size()) + 3*(this->size()-1) + 4;
}
- inline friend std::istream & operator >> (std::istream &is, cvm::vector1d<T> &v)
+ inline friend std::istream & operator >> (std::istream &is,
+ cvm::vector1d<T> &v)
{
if (v.size() == 0) return is;
size_t const start_pos = is.tellg();
@@ -288,7 +292,8 @@ public:
return is;
}
- inline friend std::ostream & operator << (std::ostream &os, cvm::vector1d<T> const &v)
+ inline friend std::ostream & operator << (std::ostream &os,
+ cvm::vector1d<T> const &v)
{
std::streamsize const w = os.width();
std::streamsize const p = os.precision();
@@ -377,6 +382,15 @@ protected:
{
return vector1d<T>(length, data);
}
+ inline int set(cvm::vector1d<T> const &v) const
+ {
+ if (v.size() != length) {
+ return cvm::error("Error: setting a matrix row from a vector of "
+ "incompatible size.\n", BUG_ERROR);
+ }
+ for (size_t i = 0; i < length; i++) data[i] = v[i];
+ return COLVARS_OK;
+ }
};
std::vector<T> data;
@@ -515,9 +529,12 @@ public:
{
if ((m1.outer_length != m2.outer_length) ||
(m1.inner_length != m2.inner_length)) {
- cvm::error("Error: trying to perform an operation between matrices of different sizes, "+
- cvm::to_str(m1.outer_length)+"x"+cvm::to_str(m1.inner_length)+" and "+
- cvm::to_str(m2.outer_length)+"x"+cvm::to_str(m2.inner_length)+".\n");
+ cvm::error("Error: trying to perform an operation between "
+ "matrices of different sizes, "+
+ cvm::to_str(m1.outer_length)+"x"+
+ cvm::to_str(m1.inner_length)+" and "+
+ cvm::to_str(m2.outer_length)+"x"+
+ cvm::to_str(m2.inner_length)+".\n");
}
}
@@ -539,7 +556,7 @@ public:
}
}
- inline void operator *= (cvm::real const &a)
+ inline void operator *= (cvm::real a)
{
size_t i;
for (i = 0; i < data.size(); i++) {
@@ -547,7 +564,7 @@ public:
}
}
- inline void operator /= (cvm::real const &a)
+ inline void operator /= (cvm::real a)
{
size_t i;
for (i = 0; i < data.size(); i++) {
@@ -555,7 +572,8 @@ public:
}
}
- inline friend matrix2d<T> operator + (matrix2d<T> const &m1, matrix2d<T> const &m2)
+ inline friend matrix2d<T> operator + (matrix2d<T> const &m1,
+ matrix2d<T> const &m2)
{
check_sizes(m1, m2);
matrix2d<T> result(m1.outer_length, m1.inner_length);
@@ -566,7 +584,8 @@ public:
return result;
}
- inline friend matrix2d<T> operator - (matrix2d<T> const &m1, matrix2d<T> const &m2)
+ inline friend matrix2d<T> operator - (matrix2d<T> const &m1,
+ matrix2d<T> const &m2)
{
check_sizes(m1, m2);
matrix2d<T> result(m1.outer_length, m1.inner_length);
@@ -577,7 +596,7 @@ public:
return result;
}
- inline friend matrix2d<T> operator * (matrix2d<T> const &m, cvm::real const &a)
+ inline friend matrix2d<T> operator * (matrix2d<T> const &m, cvm::real a)
{
matrix2d<T> result(m.outer_length, m.inner_length);
size_t i;
@@ -587,12 +606,12 @@ public:
return result;
}
- inline friend matrix2d<T> operator * (cvm::real const &a, matrix2d<T> const &m)
+ inline friend matrix2d<T> operator * (cvm::real a, matrix2d<T> const &m)
{
return m * a;
}
- inline friend matrix2d<T> operator / (matrix2d<T> const &m, cvm::real const &a)
+ inline friend matrix2d<T> operator / (matrix2d<T> const &m, cvm::real a)
{
matrix2d<T> result(m.outer_length, m.inner_length);
size_t i;
@@ -602,34 +621,17 @@ public:
return result;
}
- /// Matrix multiplication
-// inline friend matrix2d<T> const & operator * (matrix2d<T> const &m1, matrix2d<T> const &m2)
-// {
-// matrix2d<T> result(m1.outer_length, m2.inner_length);
-// if (m1.inner_length != m2.outer_length) {
-// cvm::error("Error: trying to multiply two matrices of incompatible sizes, "+
-// cvm::to_str(m1.outer_length)+"x"+cvm::to_str(m1.inner_length)+" and "+
-// cvm::to_str(m2.outer_length)+"x"+cvm::to_str(m2.inner_length)+".\n");
-// } else {
-// size_t i, j, k;
-// for (i = 0; i < m1.outer_length; i++) {
-// for (j = 0; j < m2.inner_length; j++) {
-// for (k = 0; k < m1.inner_length; k++) {
-// result[i][j] += m1[i][k] * m2[k][j];
-// }
-// }
-// }
-// }
-// return result;
-// }
-
/// vector-matrix multiplication
- inline friend vector1d<T> operator * (vector1d<T> const &v, matrix2d<T> const &m)
+ inline friend vector1d<T> operator * (vector1d<T> const &v,
+ matrix2d<T> const &m)
{
vector1d<T> result(m.inner_length);
if (m.outer_length != v.size()) {
- cvm::error("Error: trying to multiply a vector and a matrix of incompatible sizes, "+
- cvm::to_str(v.size()) + " and " + cvm::to_str(m.outer_length)+"x"+cvm::to_str(m.inner_length) + ".\n");
+ cvm::error("Error: trying to multiply a vector and a matrix "
+ "of incompatible sizes, "+
+ cvm::to_str(v.size()) + " and " +
+ cvm::to_str(m.outer_length)+"x"+cvm::to_str(m.inner_length) +
+ ".\n");
} else {
size_t i, k;
for (i = 0; i < m.inner_length; i++) {
@@ -641,25 +643,6 @@ public:
return result;
}
-// /// matrix-vector multiplication (unused for now)
-// inline friend vector1d<T> const & operator * (matrix2d<T> const &m, vector1d<T> const &v)
-// {
-// vector1d<T> result(m.outer_length);
-// if (m.inner_length != v.size()) {
-// cvm::error("Error: trying to multiply a matrix and a vector of incompatible sizes, "+
-// cvm::to_str(m.outer_length)+"x"+cvm::to_str(m.inner_length)
-// + " and " + cvm::to_str(v.length) + ".\n");
-// } else {
-// size_t i, k;
-// for (i = 0; i < m.outer_length; i++) {
-// for (k = 0; k < m.inner_length; k++) {
-// result[i] += m[i][k] * v[k];
-// }
-// }
-// }
-// return result;
-// }
-
/// Formatted output
friend std::ostream & operator << (std::ostream &os,
matrix2d<T> const &m)
@@ -725,49 +708,52 @@ public:
cvm::real x, y, z;
inline rvector()
- : x(0.0), y(0.0), z(0.0)
- {}
+ {
+ reset();
+ }
- inline rvector(cvm::real const &x_i,
- cvm::real const &y_i,
- cvm::real const &z_i)
- : x(x_i), y(y_i), z(z_i)
- {}
+ /// \brief Set all components to zero
+ inline void reset()
+ {
+ set(0.0);
+ }
+
+ inline rvector(cvm::real x_i, cvm::real y_i, cvm::real z_i)
+ {
+ set(x_i, y_i, z_i);
+ }
inline rvector(cvm::vector1d<cvm::real> const &v)
- : x(v[0]), y(v[1]), z(v[2])
- {}
+ {
+ set(v[0], v[1], v[2]);
+ }
inline rvector(cvm::real t)
- : x(t), y(t), z(t)
- {}
+ {
+ set(t);
+ }
- /// \brief Set all components to a scalar value
- inline void set(cvm::real const &value) {
+ /// \brief Set all components to a scalar
+ inline void set(cvm::real value)
+ {
x = y = z = value;
}
/// \brief Assign all components
- inline void set(cvm::real const &x_i,
- cvm::real const &y_i,
- cvm::real const &z_i) {
+ inline void set(cvm::real x_i, cvm::real y_i, cvm::real z_i)
+ {
x = x_i;
y = y_i;
z = z_i;
}
- /// \brief Set all components to zero
- inline void reset() {
- x = y = z = 0.0;
- }
-
/// \brief Access cartesian components by index
- inline cvm::real & operator [] (int const &i) {
+ inline cvm::real & operator [] (int i) {
return (i == 0) ? x : (i == 1) ? y : (i == 2) ? z : x;
}
/// \brief Access cartesian components by index
- inline cvm::real const & operator [] (int const &i) const {
+ inline cvm::real operator [] (int i) const {
return (i == 0) ? x : (i == 1) ? y : (i == 2) ? z : x;
}
@@ -780,14 +766,6 @@ public:
return result;
}
- inline cvm::rvector & operator = (cvm::real const &v)
- {
- x = v;
- y = v;
- z = v;
- return *this;
- }
-
inline void operator += (cvm::rvector const &v)
{
x += v.x;
@@ -802,7 +780,7 @@ public:
z -= v.z;
}
- inline void operator *= (cvm::real const &v)
+ inline void operator *= (cvm::real v)
{
x *= v;
y *= v;
@@ -832,13 +810,14 @@ public:
return (n > 0. ? cvm::rvector(x, y, z)/n : cvm::rvector(1., 0., 0.));
}
- static inline size_t output_width(size_t const &real_width)
+ static inline size_t output_width(size_t real_width)
{
return 3*real_width + 10;
}
- static inline cvm::rvector outer(cvm::rvector const &v1, cvm::rvector const &v2)
+ static inline cvm::rvector outer(cvm::rvector const &v1,
+ cvm::rvector const &v2)
{
return cvm::rvector( v1.y*v2.z - v2.y*v1.z,
-v1.x*v2.z + v2.x*v1.z,
@@ -850,41 +829,35 @@ public:
return cvm::rvector(-v.x, -v.y, -v.z);
}
- friend inline int operator == (cvm::rvector const &v1, cvm::rvector const &v2)
- {
- return (v1.x == v2.x) && (v1.y == v2.y) && (v1.z == v2.z);
- }
-
- friend inline int operator != (cvm::rvector const &v1, cvm::rvector const &v2)
- {
- return (v1.x != v2.x) || (v1.y != v2.y) || (v1.z != v2.z);
- }
-
- friend inline cvm::rvector operator + (cvm::rvector const &v1, cvm::rvector const &v2)
+ friend inline cvm::rvector operator + (cvm::rvector const &v1,
+ cvm::rvector const &v2)
{
return cvm::rvector(v1.x + v2.x, v1.y + v2.y, v1.z + v2.z);
}
- friend inline cvm::rvector operator - (cvm::rvector const &v1, cvm::rvector const &v2)
+ friend inline cvm::rvector operator - (cvm::rvector const &v1,
+ cvm::rvector const &v2)
{
return cvm::rvector(v1.x - v2.x, v1.y - v2.y, v1.z - v2.z);
}
- friend inline cvm::real operator * (cvm::rvector const &v1, cvm::rvector const &v2)
+ /// Inner (dot) product
+ friend inline cvm::real operator * (cvm::rvector const &v1,
+ cvm::rvector const &v2)
{
return v1.x * v2.x + v1.y * v2.y + v1.z * v2.z;
}
- friend inline cvm::rvector operator * (cvm::real const &a, cvm::rvector const &v)
+ friend inline cvm::rvector operator * (cvm::real a, cvm::rvector const &v)
{
return cvm::rvector(a*v.x, a*v.y, a*v.z);
}
- friend inline cvm::rvector operator * (cvm::rvector const &v, cvm::real const &a)
+ friend inline cvm::rvector operator * (cvm::rvector const &v, cvm::real a)
{
return cvm::rvector(a*v.x, a*v.y, a*v.z);
}
- friend inline cvm::rvector operator / (cvm::rvector const &v, cvm::real const &a)
+ friend inline cvm::rvector operator / (cvm::rvector const &v, cvm::real a)
{
return cvm::rvector(v.x/a, v.y/a, v.z/a);
}
@@ -946,15 +919,9 @@ public:
{}
/// Constructor component by component
- inline rmatrix(cvm::real const &xxi,
- cvm::real const &xyi,
- cvm::real const &xzi,
- cvm::real const &yxi,
- cvm::real const &yyi,
- cvm::real const &yzi,
- cvm::real const &zxi,
- cvm::real const &zyi,
- cvm::real const &zzi)
+ inline rmatrix(cvm::real xxi, cvm::real xyi, cvm::real xzi,
+ cvm::real yxi, cvm::real yyi, cvm::real yzi,
+ cvm::real zxi, cvm::real zyi, cvm::real zzi)
: cvm::matrix2d<cvm::real>(3, 3)
{
this->xx() = xxi;
@@ -983,31 +950,13 @@ public:
inline cvm::rmatrix transpose() const
{
- return cvm::rmatrix(this->xx(),
- this->yx(),
- this->zx(),
- this->xy(),
- this->yy(),
- this->zy(),
- this->xz(),
- this->yz(),
- this->zz());
+ return cvm::rmatrix(this->xx(), this->yx(), this->zx(),
+ this->xy(), this->yy(), this->zy(),
+ this->xz(), this->yz(), this->zz());
}
friend cvm::rvector operator * (cvm::rmatrix const &m, cvm::rvector const &r);
- // friend inline cvm::rmatrix const operator * (cvm::rmatrix const &m1, cvm::rmatrix const &m2) {
- // return cvm::rmatrix (m1.xx()*m2.xx() + m1.xy()*m2.yx() + m1.xz()*m2.yz(),
- // m1.xx()*m2.xy() + m1.xy()*m2.yy() + m1.xz()*m2.zy(),
- // m1.xx()*m2.xz() + m1.xy()*m2.yz() + m1.xz()*m2.zz(),
- // m1.yx()*m2.xx() + m1.yy()*m2.yx() + m1.yz()*m2.yz(),
- // m1.yx()*m2.xy() + m1.yy()*m2.yy() + m1.yz()*m2.yy(),
- // m1.yx()*m2.xz() + m1.yy()*m2.yz() + m1.yz()*m2.yz(),
- // m1.zx()*m2.xx() + m1.zy()*m2.yx() + m1.zz()*m2.yz(),
- // m1.zx()*m2.xy() + m1.zy()*m2.yy() + m1.zz()*m2.yy(),
- // m1.zx()*m2.xz() + m1.zy()*m2.yz() + m1.zz()*m2.yz());
- // }
-
};
@@ -1031,7 +980,7 @@ public:
cvm::real q0, q1, q2, q3;
/// Constructor from a 3-d vector
- inline quaternion(cvm::real const &x, cvm::real const &y, cvm::real const &z)
+ inline quaternion(cvm::real x, cvm::real y, cvm::real z)
: q0(0.0), q1(x), q2(y), q3(z)
{}
@@ -1041,10 +990,10 @@ public:
{}
/// Constructor component by component
- inline quaternion(cvm::real const &q0i,
- cvm::real const &q1i,
- cvm::real const &q2i,
- cvm::real const &q3i)
+ inline quaternion(cvm::real q0i,
+ cvm::real q1i,
+ cvm::real q2i,
+ cvm::real q3i)
: q0(q0i), q1(q1i), q2(q2i), q3(q3i)
{}
@@ -1055,9 +1004,9 @@ public:
/// "Constructor" after Euler angles (in radians)
///
/// http://en.wikipedia.org/wiki/Conversion_between_quaternions_and_Euler_angles
- inline void set_from_euler_angles(cvm::real const &phi_in,
- cvm::real const &theta_in,
- cvm::real const &psi_in)
+ inline void set_from_euler_angles(cvm::real phi_in,
+ cvm::real theta_in,
+ cvm::real psi_in)
{
q0 = ( (std::cos(phi_in/2.0)) * (std::cos(theta_in/2.0)) * (std::cos(psi_in/2.0)) +
(std::sin(phi_in/2.0)) * (std::sin(theta_in/2.0)) * (std::sin(psi_in/2.0)) );
@@ -1079,7 +1028,7 @@ public:
}
/// \brief Set all components to a scalar
- inline void set(cvm::real const &value = 0.0)
+ inline void set(cvm::real value)
{
q0 = q1 = q2 = q3 = value;
}
@@ -1087,7 +1036,7 @@ public:
/// \brief Set all components to zero (null quaternion)
inline void reset()
{
- q0 = q1 = q2 = q3 = 0.0;
+ set(0.0);
}
/// \brief Set the q0 component to 1 and the others to 0 (quaternion
@@ -1099,7 +1048,7 @@ public:
}
/// Tell the number of characters required to print a quaternion, given that of a real number
- static inline size_t output_width(size_t const &real_width)
+ static inline size_t output_width(size_t real_width)
{
return 4*real_width + 13;
}
@@ -1113,7 +1062,7 @@ public:
friend std::istream & operator >> (std::istream &is, cvm::quaternion &q);
/// Access the quaternion as a 4-d array (return a reference)
- inline cvm::real & operator [] (int const &i) {
+ inline cvm::real & operator [] (int i) {
switch (i) {
case 0:
return this->q0;
@@ -1130,7 +1079,7 @@ public:
}
/// Access the quaternion as a 4-d array (return a value)
- inline cvm::real operator [] (int const &i) const {
+ inline cvm::real operator [] (int i) const {
switch (i) {
case 0:
return this->q0;
@@ -1175,12 +1124,12 @@ public:
return cvm::quaternion(q0, -q1, -q2, -q3);
}
- inline void operator *= (cvm::real const &a)
+ inline void operator *= (cvm::real a)
{
q0 *= a; q1 *= a; q2 *= a; q3 *= a;
}
- inline void operator /= (cvm::real const &a)
+ inline void operator /= (cvm::real a)
{
q0 /= a; q1 /= a; q2 /= a; q3 /= a;
}
@@ -1215,19 +1164,22 @@ public:
}
- friend inline cvm::quaternion operator + (cvm::quaternion const &h, cvm::quaternion const &q)
+ friend inline cvm::quaternion operator + (cvm::quaternion const &h,
+ cvm::quaternion const &q)
{
return cvm::quaternion(h.q0+q.q0, h.q1+q.q1, h.q2+q.q2, h.q3+q.q3);
}
- friend inline cvm::quaternion operator - (cvm::quaternion const &h, cvm::quaternion const &q)
+ friend inline cvm::quaternion operator - (cvm::quaternion const &h,
+ cvm::quaternion const &q)
{
return cvm::quaternion(h.q0-q.q0, h.q1-q.q1, h.q2-q.q2, h.q3-q.q3);
}
/// \brief Provides the quaternion product. \b NOTE: for the inner
/// product use: \code h.inner (q); \endcode
- friend inline cvm::quaternion operator * (cvm::quaternion const &h, cvm::quaternion const &q)
+ friend inline cvm::quaternion operator * (cvm::quaternion const &h,
+ cvm::quaternion const &q)
{
return cvm::quaternion(h.q0*q.q0 - h.q1*q.q1 - h.q2*q.q2 - h.q3*q.q3,
h.q0*q.q1 + h.q1*q.q0 + h.q2*q.q3 - h.q3*q.q2,
@@ -1235,18 +1187,18 @@ public:
h.q0*q.q3 + h.q3*q.q0 + h.q1*q.q2 - h.q2*q.q1);
}
- friend inline cvm::quaternion operator * (cvm::real const &c,
+ friend inline cvm::quaternion operator * (cvm::real c,
cvm::quaternion const &q)
{
return cvm::quaternion(c*q.q0, c*q.q1, c*q.q2, c*q.q3);
}
friend inline cvm::quaternion operator * (cvm::quaternion const &q,
- cvm::real const &c)
+ cvm::real c)
{
return cvm::quaternion(q.q0*c, q.q1*c, q.q2*c, q.q3*c);
}
friend inline cvm::quaternion operator / (cvm::quaternion const &q,
- cvm::real const &c)
+ cvm::real c)
{
return cvm::quaternion(q.q0/c, q.q1/c, q.q2/c, q.q3/c);
}
@@ -1407,7 +1359,7 @@ public:
std::vector< cvm::vector1d<cvm::rvector> > dQ0_1, dQ0_2;
/// Allocate space for the derivatives of the rotation
- inline void request_group1_gradients(size_t const &n)
+ inline void request_group1_gradients(size_t n)
{
dS_1.resize(n, cvm::matrix2d<cvm::rvector>(4, 4));
dL0_1.resize(n, cvm::rvector(0.0, 0.0, 0.0));
@@ -1415,7 +1367,7 @@ public:
}
/// Allocate space for the derivatives of the rotation
- inline void request_group2_gradients(size_t const &n)
+ inline void request_group2_gradients(size_t n)
{
dS_2.resize(n, cvm::matrix2d<cvm::rvector>(4, 4));
dL0_2.resize(n, cvm::rvector(0.0, 0.0, 0.0));
@@ -1448,7 +1400,7 @@ public:
}
/// Constructor after an axis of rotation and an angle (in radians)
- inline rotation(cvm::real const &angle, cvm::rvector const &axis)
+ inline rotation(cvm::real angle, cvm::rvector const &axis)
: b_debug_gradients(false)
{
cvm::rvector const axis_n = axis.unit();
@@ -1500,20 +1452,18 @@ public:
if (q.q0 != 0.0) {
- // cvm::real const x = iprod/q.q0;
-
- cvm::real const dspindx = (180.0/PI) * 2.0 * (1.0 / (1.0 + (iprod*iprod)/(q.q0*q.q0)));
+ cvm::real const dspindx =
+ (180.0/PI) * 2.0 * (1.0 / (1.0 + (iprod*iprod)/(q.q0*q.q0)));
- return
- cvm::quaternion( dspindx * (iprod * (-1.0) / (q.q0*q.q0)),
- dspindx * ((1.0/q.q0) * axis.x),
- dspindx * ((1.0/q.q0) * axis.y),
- dspindx * ((1.0/q.q0) * axis.z));
+ return cvm::quaternion( dspindx * (iprod * (-1.0) / (q.q0*q.q0)),
+ dspindx * ((1.0/q.q0) * axis.x),
+ dspindx * ((1.0/q.q0) * axis.y),
+ dspindx * ((1.0/q.q0) * axis.z));
} else {
// (1/(1+x^2)) ~ (1/x)^2
- return
- cvm::quaternion((180.0/PI) * 2.0 * ((-1.0)/iprod), 0.0, 0.0, 0.0);
- // XX TODO: What if iprod == 0? XX
+ // The documentation of spinAngle discourages its use when q_vec and
+ // axis are not close
+ return cvm::quaternion((180.0/PI) * 2.0 * ((-1.0)/iprod), 0.0, 0.0, 0.0);
}
}
diff --git a/lib/gpu/Makefile.linux_opencl b/lib/gpu/Makefile.linux_opencl
index e6358907785d1db0fb4c70c6e672ef33700956e4..640562dca535665d246d1b08e7350724309d3587 100644
--- a/lib/gpu/Makefile.linux_opencl
+++ b/lib/gpu/Makefile.linux_opencl
@@ -6,10 +6,10 @@
EXTRAMAKE = Makefile.lammps.opencl
-OCL_TUNE = -DFERMI_OCL # -- Uncomment for NVIDIA Fermi
+# OCL_TUNE = -DFERMI_OCL # -- Uncomment for NVIDIA Fermi
# OCL_TUNE = -DKEPLER_OCL # -- Uncomment for NVIDIA Kepler
# OCL_TUNE = -DCYPRESS_OCL # -- Uncomment for AMD Cypress
-# OCL_TUNE = -DGENERIC_OCL # -- Uncomment for generic device
+OCL_TUNE = -DGENERIC_OCL # -- Uncomment for generic device
# this setting should match LAMMPS Makefile
# one of LAMMPS_SMALLBIG (default), LAMMPS_BIGBIG and LAMMPS_SMALLSMALL
diff --git a/lib/gpu/cudpp_mini/cudpp.h b/lib/gpu/cudpp_mini/cudpp.h
index 088b560abc87bccd73604646a64df252b87a04fb..2f38d780a545a1881fd7b858cef1bd42d8727ea3 100644
--- a/lib/gpu/cudpp_mini/cudpp.h
+++ b/lib/gpu/cudpp_mini/cudpp.h
@@ -300,7 +300,7 @@
#ifndef __CUDPP_H__
#define __CUDPP_H__
-#include <stdlib.h> // for size_t
+#include <cstdlib> // for size_t
#ifdef __cplusplus
extern "C" {
diff --git a/lib/gpu/cudpp_mini/cudpp_plan.cpp b/lib/gpu/cudpp_mini/cudpp_plan.cpp
index b64b7b37ff5161832607b54d50aa2719ab35237b..e92a857dd1e195c4c656975a17dcef97e10405c6 100644
--- a/lib/gpu/cudpp_mini/cudpp_plan.cpp
+++ b/lib/gpu/cudpp_mini/cudpp_plan.cpp
@@ -16,7 +16,7 @@
//#include "cudpp_spmvmult.h"
#include "cudpp_radixsort.h"
-#include <assert.h>
+#include <cassert>
CUDPPPlanManager* CUDPPPlanManager::m_instance = NULL;
diff --git a/lib/gpu/cudpp_mini/cudpp_util.h b/lib/gpu/cudpp_mini/cudpp_util.h
index 5cff05e8182a9f5fb352e2303948f98128846be9..e1c21f3fe6d60074f6794ab82f7411caaa195765 100644
--- a/lib/gpu/cudpp_mini/cudpp_util.h
+++ b/lib/gpu/cudpp_mini/cudpp_util.h
@@ -25,7 +25,7 @@
#include <cuda.h>
#include <cudpp.h>
#include <limits.h>
-#include <float.h>
+#include <cfloat>
#if (CUDA_VERSION >= 3000)
#define LAUNCH_BOUNDS(x) __launch_bounds__((x))
diff --git a/lib/gpu/geryon/nvd_macros.h b/lib/gpu/geryon/nvd_macros.h
index e0e29b4c6f5d827231fcffb0dc57ca507dd70eac..08ff84991a914eda8deb24e23e5a5b65b52cfa13 100644
--- a/lib/gpu/geryon/nvd_macros.h
+++ b/lib/gpu/geryon/nvd_macros.h
@@ -1,7 +1,7 @@
#ifndef NVD_MACROS_H
#define NVD_MACROS_H
-#include <stdio.h>
+#include <cstdio>
#include <cassert>
#include <cuda.h>
diff --git a/lib/gpu/geryon/ocl_device.h b/lib/gpu/geryon/ocl_device.h
index 138b03c091c7ceac39e4ef4a2c2c54b702f967a7..584d04e616521056d11372e4b2e48291e2df04ab 100644
--- a/lib/gpu/geryon/ocl_device.h
+++ b/lib/gpu/geryon/ocl_device.h
@@ -353,7 +353,7 @@ int UCL_Device::set_platform(int pid) {
_num_devices=0;
return UCL_ERROR;
}
- cl_device_id device_list[_num_devices];
+ cl_device_id *device_list = new cl_device_id[_num_devices];
CL_SAFE_CALL(clGetDeviceIDs(_cl_platform,CL_DEVICE_TYPE_ALL,n,device_list,
&n));
@@ -362,7 +362,7 @@ int UCL_Device::set_platform(int pid) {
_cl_devices.push_back(device_list[i]);
add_properties(device_list[i]);
}
-
+ delete[] device_list;
return UCL_SUCCESS;
}
@@ -518,13 +518,14 @@ int UCL_Device::device_type(const int i) {
int UCL_Device::set(int num) {
clear();
- cl_device_id device_list[_num_devices];
+ cl_device_id *device_list = new cl_device_id[_num_devices];
cl_uint n;
CL_SAFE_CALL(clGetDeviceIDs(_cl_platform,CL_DEVICE_TYPE_ALL,_num_devices,
device_list,&n));
_device=num;
_cl_device=device_list[_device];
+ delete[] device_list;
return create_context();
}
diff --git a/lib/gpu/geryon/ocl_kernel.h b/lib/gpu/geryon/ocl_kernel.h
index e4c37b2a77b3b05975e9b0f46208621c09c349ec..b65049b9e698eaeab5a72eda799da39b1b820502 100644
--- a/lib/gpu/geryon/ocl_kernel.h
+++ b/lib/gpu/geryon/ocl_kernel.h
@@ -111,7 +111,7 @@ class UCL_Program {
size_t ms;
CL_SAFE_CALL(clGetProgramBuildInfo(_program,_device,CL_PROGRAM_BUILD_LOG,0,
NULL, &ms));
- char build_log[ms];
+ char *build_log = new char[ms];
CL_SAFE_CALL(clGetProgramBuildInfo(_program,_device,CL_PROGRAM_BUILD_LOG,ms,
build_log, NULL));
@@ -127,8 +127,9 @@ class UCL_Program {
<< "----------------------------------------------------------\n";
std::cerr << build_log << std::endl;
#endif
+ delete[] build_log;
return UCL_COMPILE_ERROR;
- }
+ } else delete[] build_log;
}
return UCL_SUCCESS;
diff --git a/lib/gpu/geryon/ocl_macros.h b/lib/gpu/geryon/ocl_macros.h
index d4e27b6e71d8e257b1b171e06f744ce3b4a9eccf..5fb7665817eb8166eeed750f1073dfbef8463f46 100644
--- a/lib/gpu/geryon/ocl_macros.h
+++ b/lib/gpu/geryon/ocl_macros.h
@@ -1,7 +1,7 @@
#ifndef OCL_MACROS_H
#define OCL_MACROS_H
-#include <stdio.h>
+#include <cstdio>
#include <cassert>
#ifdef __APPLE__
diff --git a/lib/gpu/geryon/ocl_memory.h b/lib/gpu/geryon/ocl_memory.h
index 28bb88941f7dbff83faffee954ed3c8500b1f7c7..9692f4dd7bd5b619565ba03d625ad5b6edb807d4 100644
--- a/lib/gpu/geryon/ocl_memory.h
+++ b/lib/gpu/geryon/ocl_memory.h
@@ -407,7 +407,7 @@ inline void _ocl_build(cl_program &program, cl_device_id &device,
size_t ms;
CL_SAFE_CALL(clGetProgramBuildInfo(program, device,CL_PROGRAM_BUILD_LOG, 0,
NULL, &ms));
- char build_log[ms];
+ char *build_log = new char[ms];
CL_SAFE_CALL(clGetProgramBuildInfo(program,device,CL_PROGRAM_BUILD_LOG,ms,
build_log, NULL));
@@ -416,6 +416,7 @@ inline void _ocl_build(cl_program &program, cl_device_id &device,
<< " Error compiling OpenCL Program...\n"
<< "----------------------------------------------------------\n";
std::cerr << build_log << std::endl;
+ delete[] build_log;
}
inline void _ocl_kernel_from_source(cl_context &context, cl_device_id &device,
diff --git a/lib/gpu/lal_answer.h b/lib/gpu/lal_answer.h
index 790d9c1f8d16ba95e14902bd6603fc0e23ca7285..557c69b4714bc8368ad13c6b4a031141efd16e7c 100644
--- a/lib/gpu/lal_answer.h
+++ b/lib/gpu/lal_answer.h
@@ -16,7 +16,7 @@
#ifndef LAL_ANSWER_H
#define LAL_ANSWER_H
-#include <math.h>
+#include <cmath>
#include "mpi.h"
#if defined(USE_OPENCL)
diff --git a/lib/gpu/lal_atom.h b/lib/gpu/lal_atom.h
index 1b4e17d972aeeca62d3a6bdc2bb2fb5dca823075..f6a0b109f2143889e5cde02f546de6e017d15561 100644
--- a/lib/gpu/lal_atom.h
+++ b/lib/gpu/lal_atom.h
@@ -16,7 +16,7 @@
#ifndef PAIR_GPU_ATOM_H
#define PAIR_GPU_ATOM_H
-#include <math.h>
+#include <cmath>
#include "mpi.h"
#if defined(USE_OPENCL)
diff --git a/lib/gpu/lal_balance.h b/lib/gpu/lal_balance.h
index e90e94bee1c974fcc3d8084bbd63f21157ab65ea..6aee5952ed00baa99637162b500dbe0ffd0ec083 100644
--- a/lib/gpu/lal_balance.h
+++ b/lib/gpu/lal_balance.h
@@ -17,7 +17,7 @@
#define LAL_BALANCE_H
#include "lal_device.h"
-#include <math.h>
+#include <cmath>
#define _HD_BALANCE_EVERY 25
#define _HD_BALANCE_WEIGHT 0.5
diff --git a/lib/gpu/lal_beck_ext.cpp b/lib/gpu/lal_beck_ext.cpp
index 226c2d477b53ebf444ea22eb1093efb194b6545d..dcba4e4f40b1ca65f5045e41d17a816f599ad906 100644
--- a/lib/gpu/lal_beck_ext.cpp
+++ b/lib/gpu/lal_beck_ext.cpp
@@ -15,7 +15,7 @@
#include <iostream>
#include <cassert>
-#include <math.h>
+#include <cmath>
#include "lal_beck.h"
diff --git a/lib/gpu/lal_born_coul_long_ext.cpp b/lib/gpu/lal_born_coul_long_ext.cpp
index feb7472e7446999ff0ba2b43496cbfcc38a2e361..d0825529b1bb8ed9bec9a2d858dce8f874dca116 100644
--- a/lib/gpu/lal_born_coul_long_ext.cpp
+++ b/lib/gpu/lal_born_coul_long_ext.cpp
@@ -15,7 +15,7 @@
#include <iostream>
#include <cassert>
-#include <math.h>
+#include <cmath>
#include "lal_born_coul_long.h"
diff --git a/lib/gpu/lal_born_coul_wolf_ext.cpp b/lib/gpu/lal_born_coul_wolf_ext.cpp
index 254b1c905b5c0991065bcc721bd3b770395040ba..d664f302128df2e33bfe873ed511276bbf756cc7 100644
--- a/lib/gpu/lal_born_coul_wolf_ext.cpp
+++ b/lib/gpu/lal_born_coul_wolf_ext.cpp
@@ -15,7 +15,7 @@
#include <iostream>
#include <cassert>
-#include <math.h>
+#include <cmath>
#include "lal_born_coul_wolf.h"
diff --git a/lib/gpu/lal_born_ext.cpp b/lib/gpu/lal_born_ext.cpp
index b1ebf5804c471d883761c89c8effc8a1969df4eb..63991889d90ee35dbeb5fb35ac686a8fa1a8745b 100644
--- a/lib/gpu/lal_born_ext.cpp
+++ b/lib/gpu/lal_born_ext.cpp
@@ -15,7 +15,7 @@
#include <iostream>
#include <cassert>
-#include <math.h>
+#include <cmath>
#include "lal_born.h"
diff --git a/lib/gpu/lal_buck_coul_ext.cpp b/lib/gpu/lal_buck_coul_ext.cpp
index e5a5e1315bbf845a770a92e97b7842ef156451db..2a089e20403d17f395cb135270919acbd608cc00 100644
--- a/lib/gpu/lal_buck_coul_ext.cpp
+++ b/lib/gpu/lal_buck_coul_ext.cpp
@@ -15,7 +15,7 @@
#include <iostream>
#include <cassert>
-#include <math.h>
+#include <cmath>
#include "lal_buck_coul.h"
diff --git a/lib/gpu/lal_buck_coul_long_ext.cpp b/lib/gpu/lal_buck_coul_long_ext.cpp
index 28a89746b3cdedaf44df8fa6907c2b6560d19d6e..c7e1cd1e35862d769ab135908670a69609865ac7 100644
--- a/lib/gpu/lal_buck_coul_long_ext.cpp
+++ b/lib/gpu/lal_buck_coul_long_ext.cpp
@@ -15,7 +15,7 @@
#include <iostream>
#include <cassert>
-#include <math.h>
+#include <cmath>
#include "lal_buck_coul_long.h"
diff --git a/lib/gpu/lal_buck_ext.cpp b/lib/gpu/lal_buck_ext.cpp
index 336aab6d4c5e72cffc63dc8d1f94f9194cc8b423..cc8b77c0a9f0e288d57cbc0ac762310ebac84b4e 100644
--- a/lib/gpu/lal_buck_ext.cpp
+++ b/lib/gpu/lal_buck_ext.cpp
@@ -15,7 +15,7 @@
#include <iostream>
#include <cassert>
-#include <math.h>
+#include <cmath>
#include "lal_buck.h"
diff --git a/lib/gpu/lal_charmm_long_ext.cpp b/lib/gpu/lal_charmm_long_ext.cpp
index e24c650be4dafb02a792f763406c3bebbdbdd8dc..743b510825515561bb110b4a42e01b82b43147a8 100644
--- a/lib/gpu/lal_charmm_long_ext.cpp
+++ b/lib/gpu/lal_charmm_long_ext.cpp
@@ -15,7 +15,7 @@
#include <iostream>
#include <cassert>
-#include <math.h>
+#include <cmath>
#include "lal_charmm_long.h"
diff --git a/lib/gpu/lal_colloid_ext.cpp b/lib/gpu/lal_colloid_ext.cpp
index 8e1b18e72f11bdefdbbb63ec6d74895047547c1c..961ad75925e5e0a18f585fd2e8f1a1cc17d72930 100644
--- a/lib/gpu/lal_colloid_ext.cpp
+++ b/lib/gpu/lal_colloid_ext.cpp
@@ -15,7 +15,7 @@
#include <iostream>
#include <cassert>
-#include <math.h>
+#include <cmath>
#include "lal_colloid.h"
diff --git a/lib/gpu/lal_coul_debye_ext.cpp b/lib/gpu/lal_coul_debye_ext.cpp
index af9156c24c8339089143310c751370072a38d186..af54746defca665a6a6a8ce0f98ff04028f55260 100644
--- a/lib/gpu/lal_coul_debye_ext.cpp
+++ b/lib/gpu/lal_coul_debye_ext.cpp
@@ -15,7 +15,7 @@
#include <iostream>
#include <cassert>
-#include <math.h>
+#include <cmath>
#include "lal_coul_debye.h"
diff --git a/lib/gpu/lal_coul_dsf_ext.cpp b/lib/gpu/lal_coul_dsf_ext.cpp
index 026dd924c9c49f786231088835bd4e7719ef9d7e..2d18f9f94d65c723aeb0833791659b72a374d9a6 100644
--- a/lib/gpu/lal_coul_dsf_ext.cpp
+++ b/lib/gpu/lal_coul_dsf_ext.cpp
@@ -15,7 +15,7 @@
#include <iostream>
#include <cassert>
-#include <math.h>
+#include <cmath>
#include "lal_coul_dsf.h"
diff --git a/lib/gpu/lal_coul_ext.cpp b/lib/gpu/lal_coul_ext.cpp
index f03d8fcdfcd91c063bba63713bbfbf3ec960bc9d..9779526d62aeac9b2a55d079d0ba3da296d689d6 100644
--- a/lib/gpu/lal_coul_ext.cpp
+++ b/lib/gpu/lal_coul_ext.cpp
@@ -15,7 +15,7 @@
#include <iostream>
#include <cassert>
-#include <math.h>
+#include <cmath>
#include "lal_coul.h"
diff --git a/lib/gpu/lal_coul_long_ext.cpp b/lib/gpu/lal_coul_long_ext.cpp
index 06c102b2d19f16917ca3d0f1a9ef86da47f4e0a0..653b4be4f322ec70bb1388aaa3cfa22498070ec9 100644
--- a/lib/gpu/lal_coul_long_ext.cpp
+++ b/lib/gpu/lal_coul_long_ext.cpp
@@ -15,7 +15,7 @@
#include <iostream>
#include <cassert>
-#include <math.h>
+#include <cmath>
#include "lal_coul_long.h"
diff --git a/lib/gpu/lal_device.cpp b/lib/gpu/lal_device.cpp
index e95f2b30efcc0356646fc0fdf5035034ccb8c996..c58b484e4ecbdf38e7a49609b5581a53c9fc7b69 100644
--- a/lib/gpu/lal_device.cpp
+++ b/lib/gpu/lal_device.cpp
@@ -16,7 +16,7 @@
#include "lal_device.h"
#include "lal_precision.h"
#include <map>
-#include <math.h>
+#include <cmath>
#ifdef _OPENMP
#include <omp.h>
#endif
@@ -78,7 +78,7 @@ int DeviceT::init_device(MPI_Comm world, MPI_Comm replica, const int first_gpu,
// Get the names of all nodes
int name_length;
char node_name[MPI_MAX_PROCESSOR_NAME];
- char node_names[MPI_MAX_PROCESSOR_NAME*_world_size];
+ char *node_names = new char[MPI_MAX_PROCESSOR_NAME*_world_size];
MPI_Get_processor_name(node_name,&name_length);
MPI_Allgather(&node_name,MPI_MAX_PROCESSOR_NAME,MPI_CHAR,&node_names,
MPI_MAX_PROCESSOR_NAME,MPI_CHAR,_comm_world);
@@ -104,6 +104,7 @@ int DeviceT::init_device(MPI_Comm world, MPI_Comm replica, const int first_gpu,
split_id=split_num;
split_num++;
}
+ delete[] node_names;
// Set up a per node communicator and find rank within
MPI_Comm node_comm;
diff --git a/lib/gpu/lal_device.h b/lib/gpu/lal_device.h
index 4f7b594c7c9ae7f86e059cee98ffa33b3711be4f..95e9f2a4309fa755bf10458f6c07ae12a8196191 100644
--- a/lib/gpu/lal_device.h
+++ b/lib/gpu/lal_device.h
@@ -22,7 +22,7 @@
#include "lal_pppm.h"
#include "mpi.h"
#include <sstream>
-#include "stdio.h"
+#include <cstdio>
#include <string>
#include <queue>
diff --git a/lib/gpu/lal_dipole_lj_ext.cpp b/lib/gpu/lal_dipole_lj_ext.cpp
index 76722a20b41c3b6992783ec80c5b141a184864ac..0a94969c8b3115952fa95b0f9b4cb7798854eecf 100644
--- a/lib/gpu/lal_dipole_lj_ext.cpp
+++ b/lib/gpu/lal_dipole_lj_ext.cpp
@@ -15,7 +15,7 @@
#include <iostream>
#include <cassert>
-#include <math.h>
+#include <cmath>
#include "lal_dipole_lj.h"
diff --git a/lib/gpu/lal_dipole_lj_sf_ext.cpp b/lib/gpu/lal_dipole_lj_sf_ext.cpp
index 68b935ff38f59add31f3a032a7907e629ec5a6f0..3626e8305ea36dd13844c7a9b9654c9d55bfac4a 100644
--- a/lib/gpu/lal_dipole_lj_sf_ext.cpp
+++ b/lib/gpu/lal_dipole_lj_sf_ext.cpp
@@ -15,7 +15,7 @@
#include <iostream>
#include <cassert>
-#include <math.h>
+#include <cmath>
#include "lal_dipole_lj_sf.h"
diff --git a/lib/gpu/lal_dpd_ext.cpp b/lib/gpu/lal_dpd_ext.cpp
index 26bbb660b840d48d2439dbf3963325cb65aa1e96..33b4beddb03849448943a96a0133d1489b1a11f1 100644
--- a/lib/gpu/lal_dpd_ext.cpp
+++ b/lib/gpu/lal_dpd_ext.cpp
@@ -15,7 +15,7 @@
#include <iostream>
#include <cassert>
-#include <math.h>
+#include <cmath>
#include "lal_dpd.h"
diff --git a/lib/gpu/lal_eam_alloy_ext.cpp b/lib/gpu/lal_eam_alloy_ext.cpp
index 9209ed5c2602769b034802a1ae26428abdec0d93..e5f1010e76dae225718deb446993183e69f846b7 100644
--- a/lib/gpu/lal_eam_alloy_ext.cpp
+++ b/lib/gpu/lal_eam_alloy_ext.cpp
@@ -15,7 +15,7 @@
#include <iostream>
#include <cassert>
-#include <math.h>
+#include <cmath>
#include "lal_eam.h"
diff --git a/lib/gpu/lal_eam_ext.cpp b/lib/gpu/lal_eam_ext.cpp
index 1b5602f808fc4a97f5fe6516d1cd01eb43f16cdc..78f2e3c1f834e5c6ed4bd53fb7dd777e70a14d0c 100644
--- a/lib/gpu/lal_eam_ext.cpp
+++ b/lib/gpu/lal_eam_ext.cpp
@@ -15,7 +15,7 @@
#include <iostream>
#include <cassert>
-#include <math.h>
+#include <cmath>
#include "lal_eam.h"
diff --git a/lib/gpu/lal_eam_fs_ext.cpp b/lib/gpu/lal_eam_fs_ext.cpp
index b9e25466aaa71c8c82a5b6511b96b0fea3c320c4..37208e54f8c4cf245bdcc4297455e03d72ed26e5 100644
--- a/lib/gpu/lal_eam_fs_ext.cpp
+++ b/lib/gpu/lal_eam_fs_ext.cpp
@@ -15,7 +15,7 @@
#include <iostream>
#include <cassert>
-#include <math.h>
+#include <cmath>
#include "lal_eam.h"
diff --git a/lib/gpu/lal_gauss_ext.cpp b/lib/gpu/lal_gauss_ext.cpp
index 7fa4b68870ea9ff4f6bb797e6904b99cd612e622..a2804ce3cf9b20994246c5077cc73de63c27dc55 100644
--- a/lib/gpu/lal_gauss_ext.cpp
+++ b/lib/gpu/lal_gauss_ext.cpp
@@ -15,7 +15,7 @@
#include <iostream>
#include <cassert>
-#include <math.h>
+#include <cmath>
#include "lal_gauss.h"
diff --git a/lib/gpu/lal_gayberne_ext.cpp b/lib/gpu/lal_gayberne_ext.cpp
index 451550e7efca8023f78397ca499dc459e4d3fb53..56aad61632f3c86a0531528ff6109d81f6edd973 100644
--- a/lib/gpu/lal_gayberne_ext.cpp
+++ b/lib/gpu/lal_gayberne_ext.cpp
@@ -15,7 +15,7 @@
#include <iostream>
#include <cassert>
-#include <math.h>
+#include <cmath>
#include "lal_gayberne.h"
diff --git a/lib/gpu/lal_lj96_ext.cpp b/lib/gpu/lal_lj96_ext.cpp
index 5c4a58c5e8a272541e8b95e80e4fad40c72dae5a..f68b35de57b283e9fb4039a3dacc1d13c9809909 100644
--- a/lib/gpu/lal_lj96_ext.cpp
+++ b/lib/gpu/lal_lj96_ext.cpp
@@ -15,7 +15,7 @@
#include <iostream>
#include <cassert>
-#include <math.h>
+#include <cmath>
#include "lal_lj96.h"
diff --git a/lib/gpu/lal_lj_class2_long_ext.cpp b/lib/gpu/lal_lj_class2_long_ext.cpp
index 6ed15126d99d08633f7b9677b69c24bf683a6cc7..f669a811898f9d06fc61be16bff3805434cde248 100644
--- a/lib/gpu/lal_lj_class2_long_ext.cpp
+++ b/lib/gpu/lal_lj_class2_long_ext.cpp
@@ -15,7 +15,7 @@
#include <iostream>
#include <cassert>
-#include <math.h>
+#include <cmath>
#include "lal_lj_class2_long.h"
diff --git a/lib/gpu/lal_lj_coul_debye_ext.cpp b/lib/gpu/lal_lj_coul_debye_ext.cpp
index 3a0a3593e7bf89a3e0ef83589251ecfda5a3f3f5..95588eb95ad6eb0442b9260ef7192304c4439d4c 100644
--- a/lib/gpu/lal_lj_coul_debye_ext.cpp
+++ b/lib/gpu/lal_lj_coul_debye_ext.cpp
@@ -15,7 +15,7 @@
#include <iostream>
#include <cassert>
-#include <math.h>
+#include <cmath>
#include "lal_lj_coul_debye.h"
diff --git a/lib/gpu/lal_lj_coul_ext.cpp b/lib/gpu/lal_lj_coul_ext.cpp
index b803101b9e49193ad7569205ce34d3da7fd5abf4..060088a7cbef707e275851f5701a1f671e784ce5 100644
--- a/lib/gpu/lal_lj_coul_ext.cpp
+++ b/lib/gpu/lal_lj_coul_ext.cpp
@@ -15,7 +15,7 @@
#include <iostream>
#include <cassert>
-#include <math.h>
+#include <cmath>
#include "lal_lj_coul.h"
diff --git a/lib/gpu/lal_lj_coul_long_ext.cpp b/lib/gpu/lal_lj_coul_long_ext.cpp
index 6f8b5c9fe12451773586e9b6c4b079adf9fa8bb6..33771af53c59e68dabf7e11857b0c744c88da7cc 100644
--- a/lib/gpu/lal_lj_coul_long_ext.cpp
+++ b/lib/gpu/lal_lj_coul_long_ext.cpp
@@ -15,7 +15,7 @@
#include <iostream>
#include <cassert>
-#include <math.h>
+#include <cmath>
#include "lal_lj_coul_long.h"
diff --git a/lib/gpu/lal_lj_coul_msm_ext.cpp b/lib/gpu/lal_lj_coul_msm_ext.cpp
index bf520e4dc55fd5a804e03cb6f454a24ed30e7a5b..d957cbe37670e449b18ec3db006531e1efe95c31 100644
--- a/lib/gpu/lal_lj_coul_msm_ext.cpp
+++ b/lib/gpu/lal_lj_coul_msm_ext.cpp
@@ -15,7 +15,7 @@
#include <iostream>
#include <cassert>
-#include <math.h>
+#include <cmath>
#include "lal_lj_coul_msm.h"
diff --git a/lib/gpu/lal_lj_cubic_ext.cpp b/lib/gpu/lal_lj_cubic_ext.cpp
index efbcee0a9f4db2dc78df16422c5f047b5c6344e7..f02ce0f184bca4fe1b507eb53f1541bf66d48661 100644
--- a/lib/gpu/lal_lj_cubic_ext.cpp
+++ b/lib/gpu/lal_lj_cubic_ext.cpp
@@ -15,7 +15,7 @@
#include <iostream>
#include <cassert>
-#include <math.h>
+#include <cmath>
#include "lal_lj_cubic.h"
diff --git a/lib/gpu/lal_lj_dsf_ext.cpp b/lib/gpu/lal_lj_dsf_ext.cpp
index 25802e75447d6b70c600495f069079e498ec57bc..6d53896a1181f32b33eb1f4f11a1def1159c83ad 100644
--- a/lib/gpu/lal_lj_dsf_ext.cpp
+++ b/lib/gpu/lal_lj_dsf_ext.cpp
@@ -15,7 +15,7 @@
#include <iostream>
#include <cassert>
-#include <math.h>
+#include <cmath>
#include "lal_lj_dsf.h"
diff --git a/lib/gpu/lal_lj_expand_ext.cpp b/lib/gpu/lal_lj_expand_ext.cpp
index a9c791803b11f3ff5343f10cfb433f0dd1d9924e..603e425d3f99c9f8b2927f2ea1f7e66e619eaa28 100644
--- a/lib/gpu/lal_lj_expand_ext.cpp
+++ b/lib/gpu/lal_lj_expand_ext.cpp
@@ -15,7 +15,7 @@
#include <iostream>
#include <cassert>
-#include <math.h>
+#include <cmath>
#include "lal_lj_expand.h"
diff --git a/lib/gpu/lal_lj_ext.cpp b/lib/gpu/lal_lj_ext.cpp
index 8124556d40394a5d2a2b3d78f61f41df9e5539ae..124cf46c8c18be346132e16f7603726eedc4c02b 100644
--- a/lib/gpu/lal_lj_ext.cpp
+++ b/lib/gpu/lal_lj_ext.cpp
@@ -15,7 +15,7 @@
#include <iostream>
#include <cassert>
-#include <math.h>
+#include <cmath>
#include "lal_lj.h"
diff --git a/lib/gpu/lal_lj_gromacs_ext.cpp b/lib/gpu/lal_lj_gromacs_ext.cpp
index 53b93bfdff306d8ad4eb993458ee6daad8ad8569..99d32ab09a5131681c909a162eabeb32c6a72acc 100644
--- a/lib/gpu/lal_lj_gromacs_ext.cpp
+++ b/lib/gpu/lal_lj_gromacs_ext.cpp
@@ -15,7 +15,7 @@
#include <iostream>
#include <cassert>
-#include <math.h>
+#include <cmath>
#include "lal_lj_gromacs.h"
diff --git a/lib/gpu/lal_lj_sdk_ext.cpp b/lib/gpu/lal_lj_sdk_ext.cpp
index 386106161e1b33a4ca11391e9470089d482ebeaf..de0c5fef4f224951e3533e48f20a8bfd91ec9430 100644
--- a/lib/gpu/lal_lj_sdk_ext.cpp
+++ b/lib/gpu/lal_lj_sdk_ext.cpp
@@ -15,7 +15,7 @@
#include <iostream>
#include <cassert>
-#include <math.h>
+#include <cmath>
#include "lal_lj_sdk.h"
diff --git a/lib/gpu/lal_lj_sdk_long_ext.cpp b/lib/gpu/lal_lj_sdk_long_ext.cpp
index 08390d3eeb8f1e011324e394f6b5b2281409746b..f29348728211644ee599f599380f0ac32c0cf472 100644
--- a/lib/gpu/lal_lj_sdk_long_ext.cpp
+++ b/lib/gpu/lal_lj_sdk_long_ext.cpp
@@ -15,7 +15,7 @@
#include <iostream>
#include <cassert>
-#include <math.h>
+#include <cmath>
#include "lal_lj_sdk_long.h"
diff --git a/lib/gpu/lal_mie_ext.cpp b/lib/gpu/lal_mie_ext.cpp
index 9b03903c4f027070a8048941beb42d69d3de3e45..f612de4336779c511ac3e5ef4f2013d0046ba3fb 100644
--- a/lib/gpu/lal_mie_ext.cpp
+++ b/lib/gpu/lal_mie_ext.cpp
@@ -15,7 +15,7 @@
#include <iostream>
#include <cassert>
-#include <math.h>
+#include <cmath>
#include "lal_mie.h"
diff --git a/lib/gpu/lal_morse_ext.cpp b/lib/gpu/lal_morse_ext.cpp
index 0338bc07a835a8716afd622b72563b3717c40aef..3b62d10305a2e6d1897846b70b87b52018a205fe 100644
--- a/lib/gpu/lal_morse_ext.cpp
+++ b/lib/gpu/lal_morse_ext.cpp
@@ -15,7 +15,7 @@
#include <iostream>
#include <cassert>
-#include <math.h>
+#include <cmath>
#include "lal_morse.h"
diff --git a/lib/gpu/lal_neighbor.cpp b/lib/gpu/lal_neighbor.cpp
index 0a9933a6c02982bce3a2521756d246341f826638..04e08c3e9c25d07b7a637b100b1d9ed4c3c3a01a 100644
--- a/lib/gpu/lal_neighbor.cpp
+++ b/lib/gpu/lal_neighbor.cpp
@@ -17,7 +17,7 @@
#include "lal_precision.h"
#include "lal_neighbor.h"
#include "lal_device.h"
-#include "math.h"
+#include <cmath>
using namespace LAMMPS_AL;
int Neighbor::bytes_per_atom(const int max_nbors) const {
diff --git a/lib/gpu/lal_pppm_ext.cpp b/lib/gpu/lal_pppm_ext.cpp
index 7e07d6c87b393190d3dbd342c0bc6ebfa1ead468..a75536eb19aa805a32c0fd307bc055896f7a80df 100644
--- a/lib/gpu/lal_pppm_ext.cpp
+++ b/lib/gpu/lal_pppm_ext.cpp
@@ -15,7 +15,7 @@
#include <iostream>
#include <cassert>
-#include <math.h>
+#include <cmath>
#include "lal_pppm.h"
diff --git a/lib/gpu/lal_re_squared_ext.cpp b/lib/gpu/lal_re_squared_ext.cpp
index b719dfe05f689ffcca81b7c8f93305b1b5998a41..e1eb8a45b01f7d2adc3bd7b8aad02aec03f2f2b6 100644
--- a/lib/gpu/lal_re_squared_ext.cpp
+++ b/lib/gpu/lal_re_squared_ext.cpp
@@ -15,7 +15,7 @@
#include <iostream>
#include <cassert>
-#include <math.h>
+#include <cmath>
#include "lal_re_squared.h"
diff --git a/lib/gpu/lal_soft_ext.cpp b/lib/gpu/lal_soft_ext.cpp
index d3b3fa25984cae7225ce70244771ee5a394ecb76..7c0cbe79731a9b204237ea6950a7020582d88662 100644
--- a/lib/gpu/lal_soft_ext.cpp
+++ b/lib/gpu/lal_soft_ext.cpp
@@ -15,7 +15,7 @@
#include <iostream>
#include <cassert>
-#include <math.h>
+#include <cmath>
#include "lal_soft.h"
diff --git a/lib/gpu/lal_sw_ext.cpp b/lib/gpu/lal_sw_ext.cpp
index 4959650c90887d7a5aaaba42fe94452b5b890d88..1935ed615b1acf41697c68ea848f01354b98c180 100644
--- a/lib/gpu/lal_sw_ext.cpp
+++ b/lib/gpu/lal_sw_ext.cpp
@@ -15,7 +15,7 @@
#include <iostream>
#include <cassert>
-#include <math.h>
+#include <cmath>
#include "lal_sw.h"
diff --git a/lib/gpu/lal_table_ext.cpp b/lib/gpu/lal_table_ext.cpp
index a2b5c61e74bb9ea6db513f17c3808b52a325088a..f067881b882f5c4321d05d8b3067bfc891fa050a 100644
--- a/lib/gpu/lal_table_ext.cpp
+++ b/lib/gpu/lal_table_ext.cpp
@@ -15,7 +15,7 @@
#include <iostream>
#include <cassert>
-#include <math.h>
+#include <cmath>
#include "lal_table.h"
diff --git a/lib/gpu/lal_tersoff_ext.cpp b/lib/gpu/lal_tersoff_ext.cpp
index e6dc5390354085e8b552a7eef683778795b8f2cc..749842864f958150170d534409d9fa12a03ac259 100644
--- a/lib/gpu/lal_tersoff_ext.cpp
+++ b/lib/gpu/lal_tersoff_ext.cpp
@@ -15,7 +15,7 @@
#include <iostream>
#include <cassert>
-#include <math.h>
+#include <cmath>
#include "lal_tersoff.h"
diff --git a/lib/gpu/lal_tersoff_mod_ext.cpp b/lib/gpu/lal_tersoff_mod_ext.cpp
index 7f0af3fce9f5a93ad7c22b84fce8d151a67466cb..cce9df8713ef112745a3e47f91073988253e46f6 100644
--- a/lib/gpu/lal_tersoff_mod_ext.cpp
+++ b/lib/gpu/lal_tersoff_mod_ext.cpp
@@ -15,7 +15,7 @@
#include <iostream>
#include <cassert>
-#include <math.h>
+#include <cmath>
#include "lal_tersoff_mod.h"
diff --git a/lib/gpu/lal_tersoff_zbl_ext.cpp b/lib/gpu/lal_tersoff_zbl_ext.cpp
index ccfcf6839d9d5510749fbc6f658c28745f81acb1..d1a9e090b64fece0ca181aa614ea7c7f35af2ee0 100644
--- a/lib/gpu/lal_tersoff_zbl_ext.cpp
+++ b/lib/gpu/lal_tersoff_zbl_ext.cpp
@@ -15,7 +15,7 @@
#include <iostream>
#include <cassert>
-#include <math.h>
+#include <cmath>
#include "lal_tersoff_zbl.h"
diff --git a/lib/gpu/lal_ufm_ext.cpp b/lib/gpu/lal_ufm_ext.cpp
index ae4a5fb8fc9fe11e658271154178610173541683..dd476ec3fa164c277716e431f08e77c1a31b8bec 100644
--- a/lib/gpu/lal_ufm_ext.cpp
+++ b/lib/gpu/lal_ufm_ext.cpp
@@ -17,7 +17,7 @@
#include <iostream>
#include <cassert>
-#include <math.h>
+#include <cmath>
#include "lal_ufm.h"
diff --git a/lib/gpu/lal_vashishta_ext.cpp b/lib/gpu/lal_vashishta_ext.cpp
index 22f530a7ed01dd580ad1122b06ac5785676f51a6..56dfd8a0ffb847c52baf7fd2108fc0e086df7a30 100644
--- a/lib/gpu/lal_vashishta_ext.cpp
+++ b/lib/gpu/lal_vashishta_ext.cpp
@@ -15,7 +15,7 @@
#include <iostream>
#include <cassert>
-#include <math.h>
+#include <cmath>
#include "lal_vashishta.h"
using namespace LAMMPS_AL;
diff --git a/lib/gpu/lal_yukawa_colloid_ext.cpp b/lib/gpu/lal_yukawa_colloid_ext.cpp
index e2b0354d1046497a338d684d81fa3ba11d82df5e..988d33bdd663448da64437b720f39d6a8c06f036 100644
--- a/lib/gpu/lal_yukawa_colloid_ext.cpp
+++ b/lib/gpu/lal_yukawa_colloid_ext.cpp
@@ -15,7 +15,7 @@
#include <iostream>
#include <cassert>
-#include <math.h>
+#include <cmath>
#include "lal_yukawa_colloid.h"
diff --git a/lib/gpu/lal_yukawa_ext.cpp b/lib/gpu/lal_yukawa_ext.cpp
index 9d38387bc1b5611c44e4a97a1c95ca99ebd88371..995694bdfd9f3a2e7b854267977bfffa14af7a39 100644
--- a/lib/gpu/lal_yukawa_ext.cpp
+++ b/lib/gpu/lal_yukawa_ext.cpp
@@ -15,7 +15,7 @@
#include <iostream>
#include <cassert>
-#include <math.h>
+#include <cmath>
#include "lal_yukawa.h"
diff --git a/lib/gpu/lal_zbl_ext.cpp b/lib/gpu/lal_zbl_ext.cpp
index 37aa74351b63897f9c0979a9401f64db833b94e5..f15e814a50ae1b0c95b9907e1570e83dc7486356 100644
--- a/lib/gpu/lal_zbl_ext.cpp
+++ b/lib/gpu/lal_zbl_ext.cpp
@@ -15,7 +15,7 @@
#include <iostream>
#include <cassert>
-#include <math.h>
+#include <cmath>
#include "lal_zbl.h"
diff --git a/lib/kim/Install.py b/lib/kim/Install.py
index 3f1d9fb19141e67be56a1fdeb898ce6853aba2f2..d098250906bfabd19e74db7ad2a657d92a4c4ead 100644
--- a/lib/kim/Install.py
+++ b/lib/kim/Install.py
@@ -21,7 +21,7 @@ Syntax from lib dir: python Install.py -b -v version -a kim-name
specify one or more options, order does not matter
-v = version of KIM API library to use
- default = kim-api-v1.9.4 (current as of Apr 2018)
+ default = kim-api-v1.9.5 (current as of May 2018)
-b = download and build base KIM API library with example Models
this will delete any previous installation in the current folder
-n = do NOT download and build base KIM API library.
@@ -109,7 +109,7 @@ nargs = len(args)
if nargs == 0: error()
thisdir = os.environ['PWD']
-version = "kim-api-v1.9.4"
+version = "kim-api-v1.9.5"
buildflag = False
everythingflag = False
diff --git a/lib/kokkos/core/src/impl/Kokkos_Atomic_Fetch_Sub.hpp b/lib/kokkos/core/src/impl/Kokkos_Atomic_Fetch_Sub.hpp
index 28aca0aeed25090ec2c6bb7655c9ead3757b841d..3f58c55396d5ca2f841b066f043ab8d0e6b9e660 100644
--- a/lib/kokkos/core/src/impl/Kokkos_Atomic_Fetch_Sub.hpp
+++ b/lib/kokkos/core/src/impl/Kokkos_Atomic_Fetch_Sub.hpp
@@ -70,6 +70,20 @@ __inline__ __device__
unsigned int atomic_fetch_sub( volatile unsigned int * const dest , const unsigned int val )
{ return atomicSub((unsigned int*)dest,val); }
+__inline__ __device__
+unsigned int atomic_fetch_sub( volatile int64_t * const dest , const int64_t val )
+{ return atomic_fetch_add(dest,-val); }
+
+__inline__ __device__
+unsigned int atomic_fetch_sub( volatile float * const dest , const float val )
+{ return atomicAdd((float*)dest,-val); }
+
+#if ( 600 <= __CUDA_ARCH__ )
+__inline__ __device__
+unsigned int atomic_fetch_sub( volatile double * const dest , const double val )
+{ return atomicAdd((double*)dest,-val); }
+#endif
+
template < typename T >
__inline__ __device__
T atomic_fetch_sub( volatile T * const dest ,
diff --git a/lib/latte/.gitignore b/lib/latte/.gitignore
index a4c2a2362e959e7672e6289f0b9cbade4b6156a5..2c9ff6be9e655db4bf7c02b5b639e398ac8781ad 100644
--- a/lib/latte/.gitignore
+++ b/lib/latte/.gitignore
@@ -2,4 +2,4 @@
/filelink
/liblink
/includelink
-/LATTE-master
+/LATTE-*
diff --git a/lib/poems/eulerparameters.cpp b/lib/poems/eulerparameters.cpp
index 61fcc5fcc2e07184f579866d2732a6b114e38808..032bc7da829aa9fc19cab2a95dc03173cfcb32bc 100644
--- a/lib/poems/eulerparameters.cpp
+++ b/lib/poems/eulerparameters.cpp
@@ -16,7 +16,7 @@
*_________________________________________________________________________*/
#include "eulerparameters.h"
-#include "math.h"
+#include <cmath>
using namespace std;
diff --git a/lib/poems/fastmatrixops.cpp b/lib/poems/fastmatrixops.cpp
index f65536ea68fb19860a2649d7e488939e3b43cc98..782381a7068c269b927d77c52ac55238bf353a7b 100644
--- a/lib/poems/fastmatrixops.cpp
+++ b/lib/poems/fastmatrixops.cpp
@@ -262,7 +262,7 @@ void FastLU(Matrix& A, Matrix& LU, int *indx){ // LU is the LU decomposition of
for (j=0;j<n;j++){
temp=fabs(LU.rows[i][j]);
if (temp > big) big=temp;
- }
+ }
vv[i]=1.0/big;
}
for (j=0;j<n;j++){
@@ -276,8 +276,8 @@ void FastLU(Matrix& A, Matrix& LU, int *indx){ // LU is the LU decomposition of
sum=LU.rows[i][j];
for (k=0;k<j;k++)
sum -= LU.rows[i][k]*LU.rows[k][j];
- LU.rows[i][j]=sum;
- if ((dum=vv[i]*fabs(sum)) >= big) {
+ LU.rows[i][j]=sum;
+ if ((dum=vv[i]*fabs(sum)) >= big) {
big=dum;
imax=i;
}
@@ -311,7 +311,7 @@ void FastLU(Mat3x3& A, Mat3x3& LU, int *indx){ // LU is the LU decomposition of
for (j=0;j<3;j++){
temp=fabs(LU.BasicGet(i,j));
if (temp > big) big=temp;
- }
+ }
vv[i]=1.0/big;
}
for (j=0;j<3;j++){
@@ -325,8 +325,8 @@ void FastLU(Mat3x3& A, Mat3x3& LU, int *indx){ // LU is the LU decomposition of
sum=LU.BasicGet(i,j);
for (k=0;k<j;k++)
sum -= LU.BasicGet(i,k)*LU.BasicGet(k,j);
- LU.BasicSet(i,j,sum);
- if ((dum=vv[i]*fabs(sum)) >= big) {
+ LU.BasicSet(i,j,sum);
+ if ((dum=vv[i]*fabs(sum)) >= big) {
big=dum;
imax=i;
}
@@ -373,8 +373,8 @@ void FastLU(Mat4x4& A, Mat4x4& LU, int *indx){ // LU is the LU decomposition of
sum=LU.BasicGet(i,j);
for (k=0;k<j;k++)
sum -= LU.BasicGet(i,k)*LU.BasicGet(k,j);
- LU.BasicSet(i,j,sum);
- if ((dum=vv[i]*fabs(sum)) >= big) {
+ LU.BasicSet(i,j,sum);
+ if ((dum=vv[i]*fabs(sum)) >= big) {
big=dum;
imax=i;
}
@@ -421,8 +421,8 @@ void FastLU(Mat6x6& A, Mat6x6& LU, int *indx){ // LU is the LU decomposition of
sum=LU.BasicGet(i,j);
for (k=0;k<j;k++)
sum -= LU.BasicGet(i,k)*LU.BasicGet(k,j);
- LU.BasicSet(i,j,sum);
- if ((dum=vv[i]*fabs(sum)) >= big) {
+ LU.BasicSet(i,j,sum);
+ if ((dum=vv[i]*fabs(sum)) >= big) {
big=dum;
imax=i;
}
@@ -1030,4 +1030,3 @@ void FastAssignT(Mat4x4& A, Mat4x4& C){
C.elements[2][3] = A.elements[3][2];
C.elements[3][2] = A.elements[2][3];
}
-
diff --git a/lib/poems/matrixfun.cpp b/lib/poems/matrixfun.cpp
index 84784436452a8098d407bc5204ffeb80e6ddc039..d193114679dbaf53e90f3e379f0dc31d79ad6691 100644
--- a/lib/poems/matrixfun.cpp
+++ b/lib/poems/matrixfun.cpp
@@ -16,7 +16,7 @@
*_________________________________________________________________________*/
#include "matrixfun.h"
-#include <math.h>
+#include <cmath>
#include "fastmatrixops.h"
#include <cstdlib>
diff --git a/lib/poems/system.cpp b/lib/poems/system.cpp
index d3702a6440fb0172374c8c332010b7b3e44ee23b..369213f7d0abdd59bf082eea910f293f19ad8121 100644
--- a/lib/poems/system.cpp
+++ b/lib/poems/system.cpp
@@ -19,7 +19,7 @@
#include "system.h"
#include "body.h"
#include "joint.h"
-#include <math.h>
+#include <cmath>
System::System(){
diff --git a/lib/poems/system.h b/lib/poems/system.h
index 39c1f518b31bec03d77a0203a83428ea0ead04a8..1b59395de701a45d87b2ec1a9187c69662b555e8 100644
--- a/lib/poems/system.h
+++ b/lib/poems/system.h
@@ -23,7 +23,7 @@
#include <iostream>
#include <fstream>
#include <string>
-#include <stdio.h>
+#include <cstdio>
#include <iomanip>
#include "poemslist.h"
diff --git a/lib/poems/workspace.h b/lib/poems/workspace.h
index 83af077832b9490bc1d71cfd66891e8dc1c398bb..5faaf904dc8c3804a41a4b9046835ee615b0216b 100644
--- a/lib/poems/workspace.h
+++ b/lib/poems/workspace.h
@@ -23,7 +23,7 @@
#include <iostream>
#include <fstream>
#include <string>
-#include <stdio.h>
+#include <cstdio>
#include <iomanip>
#include <vector>
diff --git a/lib/vtk/Makefile.lammps.fedora28_vtk7 b/lib/vtk/Makefile.lammps.fedora28_vtk7
new file mode 100644
index 0000000000000000000000000000000000000000..6919dd36b96c37cedd912ba5b0dad1f88dba0ded
--- /dev/null
+++ b/lib/vtk/Makefile.lammps.fedora28_vtk7
@@ -0,0 +1,8 @@
+# Settings that the LAMMPS build will import when this package library is used
+
+# settings for VTK 7.1.1 on Fedora 28. This seems to work with Fedora versions going back to at least 23 and VTK version 6.x.
+# You need to install vtk-devel and all its dependencies using "dnf install vtk-devel"
+vtk_SYSINC = -I/usr/include/vtk
+vtk_SYSLIB = -lvtkCommonCore -lvtkIOCore -lvtkCommonDataModel -lvtkIOXML -lvtkIOLegacy -lvtkIOParallelXML
+vtk_SYSPATH = -L/usr/lib64/vtk
+
diff --git a/python/lammps.py b/python/lammps.py
index e798ef60718d7cd9763641f799b0dd8330da1f53..417427eb4b715bb64cdabeceb65b93ae036f492c 100644
--- a/python/lammps.py
+++ b/python/lammps.py
@@ -5,7 +5,7 @@
#
# Copyright (2003) Sandia Corporation. Under the terms of Contract
# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
-# certain rights in this software. This software is distributed under
+# certain rights in this software. This software is distributed under
# the GNU General Public License.
#
# See the README file in the top-level LAMMPS directory.
@@ -37,7 +37,7 @@ def get_ctypes_int(size):
return c_int32
elif size == 8:
return c_int64
- return c_int
+ return c_int
class MPIAbortException(Exception):
def __init__(self, message):
@@ -47,7 +47,7 @@ class MPIAbortException(Exception):
return repr(self.message)
class lammps(object):
-
+
# detect if Python is using version of mpi4py that can pass a communicator
has_mpi4py = False
@@ -71,7 +71,7 @@ class lammps(object):
# if a pointer to a LAMMPS object is handed in,
# all symbols should already be available
-
+
try:
if ptr: self.lib = CDLL("",RTLD_GLOBAL)
except:
@@ -84,7 +84,7 @@ class lammps(object):
# so that LD_LIBRARY_PATH does not need to be set for regular install
# fall back to loading with a relative path,
# typically requires LD_LIBRARY_PATH to be set appropriately
-
+
if not self.lib:
try:
if not name: self.lib = CDLL(join(modpath,"liblammps.so"),RTLD_GLOBAL)
@@ -110,15 +110,15 @@ class lammps(object):
self.lib.lammps_gather_atoms.argtypes = \
[c_void_p,c_char_p,c_int,c_int,c_void_p]
self.lib.lammps_gather_atoms.restype = None
-
+
self.lib.lammps_gather_atoms_concat.argtypes = \
[c_void_p,c_char_p,c_int,c_int,c_void_p]
self.lib.lammps_gather_atoms_concat.restype = None
-
+
self.lib.lammps_gather_atoms_subset.argtypes = \
[c_void_p,c_char_p,c_int,c_int,c_int,POINTER(c_int),c_void_p]
self.lib.lammps_gather_atoms_subset.restype = None
-
+
self.lib.lammps_scatter_atoms.argtypes = \
[c_void_p,c_char_p,c_int,c_int,c_void_p]
self.lib.lammps_scatter_atoms.restype = None
@@ -137,7 +137,7 @@ class lammps(object):
# just convert it to ctypes ptr and store in self.lmp
if not ptr:
-
+
# with mpi4py v2, can pass MPI communicator to LAMMPS
# need to adjust for type of MPI communicator object
# allow for int (like MPICH) or void* (like OpenMPI)
@@ -211,7 +211,7 @@ class lammps(object):
self.c_imageint = get_ctypes_int(self.extract_setting("imageint"))
# shut-down LAMMPS instance
-
+
def __del__(self):
if self.lmp and self.opened:
self.lib.lammps_close(self.lmp)
@@ -230,7 +230,7 @@ class lammps(object):
self.lib.lammps_file(self.lmp,file)
# send a single command
-
+
def command(self,cmd):
if cmd: cmd = cmd.encode()
self.lib.lammps_command(self.lmp,cmd)
@@ -250,13 +250,13 @@ class lammps(object):
cmds = [x.encode() for x in cmdlist if type(x) is str]
args = (c_char_p * len(cmdlist))(*cmds)
self.lib.lammps_commands_list(self.lmp,len(cmdlist),args)
-
+
# send a string of commands
def commands_string(self,multicmd):
if type(multicmd) is str: multicmd = multicmd.encode()
self.lib.lammps_commands_string(self.lmp,c_char_p(multicmd))
-
+
# extract lammps type byte sizes
def extract_setting(self, name):
@@ -265,7 +265,7 @@ class lammps(object):
return int(self.lib.lammps_extract_setting(self.lmp,name))
# extract global info
-
+
def extract_global(self,name,type):
if name: name = name.encode()
if type == 0:
@@ -277,7 +277,7 @@ class lammps(object):
return ptr[0]
# extract global info
-
+
def extract_box(self):
boxlo = (3*c_double)()
boxhi = (3*c_double)()
@@ -286,11 +286,11 @@ class lammps(object):
xz = c_double()
periodicity = (3*c_int)()
box_change = c_int()
-
+
self.lib.lammps_extract_box(self.lmp,boxlo,boxhi,
byref(xy),byref(yz),byref(xz),
periodicity,byref(box_change))
-
+
boxlo = boxlo[:3]
boxhi = boxhi[:3]
xy = xy.value
@@ -298,9 +298,9 @@ class lammps(object):
xz = xz.value
periodicity = periodicity[:3]
box_change = box_change.value
-
+
return boxlo,boxhi,xy,yz,xz,periodicity,box_change
-
+
# extract per-atom info
# NOTE: need to insure are converting to/from correct Python type
# e.g. for Python list or NumPy or ctypes
@@ -318,7 +318,7 @@ class lammps(object):
else: return None
ptr = self.lib.lammps_extract_atom(self.lmp,name)
return ptr
-
+
@property
def numpy(self):
if not self._numpy:
@@ -371,7 +371,7 @@ class lammps(object):
return self._numpy
# extract compute info
-
+
def extract_compute(self,id,style,type):
if id: id = id.encode()
if type == 0:
@@ -384,9 +384,14 @@ class lammps(object):
ptr = self.lib.lammps_extract_compute(self.lmp,id,style,type)
return ptr
if type == 2:
- self.lib.lammps_extract_compute.restype = POINTER(POINTER(c_double))
- ptr = self.lib.lammps_extract_compute(self.lmp,id,style,type)
- return ptr
+ if style == 0:
+ self.lib.lammps_extract_compute.restype = POINTER(c_int)
+ ptr = self.lib.lammps_extract_compute(self.lmp,id,style,type)
+ return ptr[0]
+ else:
+ self.lib.lammps_extract_compute.restype = POINTER(POINTER(c_double))
+ ptr = self.lib.lammps_extract_compute(self.lmp,id,style,type)
+ return ptr
return None
# extract fix info
@@ -466,7 +471,7 @@ class lammps(object):
cboxlo = (3*c_double)(*boxlo)
cboxhi = (3*c_double)(*boxhi)
self.lib.lammps_reset_box(self.lmp,cboxlo,cboxhi,xy,yz,xz)
-
+
# return vector of atom properties gathered across procs
# 3 variants to match src/library.cpp
# name = atom property recognized by LAMMPS in atom->extract()
@@ -475,7 +480,7 @@ class lammps(object):
# returned data is a 1d vector - doc how it is ordered?
# NOTE: need to insure are converting to/from correct Python type
# e.g. for Python list or NumPy or ctypes
-
+
def gather_atoms(self,name,type,count):
if name: name = name.encode()
natoms = self.lib.lammps_get_natoms(self.lmp)
@@ -487,7 +492,7 @@ class lammps(object):
self.lib.lammps_gather_atoms(self.lmp,name,type,count,data)
else: return None
return data
-
+
def gather_atoms_concat(self,name,type,count):
if name: name = name.encode()
natoms = self.lib.lammps_get_natoms(self.lmp)
@@ -519,7 +524,7 @@ class lammps(object):
# assume data is of correct type and length, as created by gather_atoms()
# NOTE: need to insure are converting to/from correct Python type
# e.g. for Python list or NumPy or ctypes
-
+
def scatter_atoms(self,name,type,count,data):
if name: name = name.encode()
self.lib.lammps_scatter_atoms(self.lmp,name,type,count,data)
diff --git a/src/.gitignore b/src/.gitignore
index 94d55b87052fccae48f4d24b3db41695aa2f77a5..3ae05079d211d2c043615cf93be2013449090506 100644
--- a/src/.gitignore
+++ b/src/.gitignore
@@ -272,6 +272,8 @@
/compute_pe_tally.h
/compute_plasticity_atom.cpp
/compute_plasticity_atom.h
+/compute_pressure_bocs.cpp
+/compute_pressure_bocs.h
/compute_pressure_grem.cpp
/compute_pressure_grem.h
/compute_rigid_local.cpp
@@ -322,6 +324,8 @@
/dihedral_spherical.h
/dihedral_table.cpp
/dihedral_table.h
+/dihedral_table_cut.cpp
+/dihedral_table_cut.h
/dump_atom_gz.cpp
/dump_atom_gz.h
/dump_xyz_gz.cpp
@@ -370,10 +374,14 @@
/fix_atc.h
/fix_ave_correlate_long.cpp
/fix_ave_correlate_long.h
+/fix_bocs.cpp
+/fix_bocs.h
/fix_bond_break.cpp
/fix_bond_break.h
/fix_bond_create.cpp
/fix_bond_create.h
+/fix_bond_react.cpp
+/fix_bond_react.h
/fix_bond_swap.cpp
/fix_bond_swap.h
/fix_cmap.cpp
@@ -732,6 +740,8 @@
/pair_hbond_dreiding_morse.h
/pair_ilp_graphene_hbn.cpp
/pair_ilp_graphene_hbn.h
+/pair_kim.cpp
+/pair_kim.h
/pair_kolmogorov_crespi_full.cpp
/pair_kolmogorov_crespi_full.h
/pair_kolmogorov_crespi_z.cpp
diff --git a/src/ASPHERE/compute_temp_asphere.cpp b/src/ASPHERE/compute_temp_asphere.cpp
index b6d37db6ce91693d9c4592b8e501f37b33546df2..011d8cae80f662d668223f7f43af71fc162df413 100644
--- a/src/ASPHERE/compute_temp_asphere.cpp
+++ b/src/ASPHERE/compute_temp_asphere.cpp
@@ -16,7 +16,7 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <string.h>
+#include <cstring>
#include "compute_temp_asphere.h"
#include "math_extra.h"
#include "atom.h"
diff --git a/src/ASPHERE/fix_nh_asphere.cpp b/src/ASPHERE/fix_nh_asphere.cpp
index 2eee28dc1ce1ead9da818fb1e12832c06d8e5ef3..828c064a526cb3c8b0c3eb9c8e9341b7db3eed11 100644
--- a/src/ASPHERE/fix_nh_asphere.cpp
+++ b/src/ASPHERE/fix_nh_asphere.cpp
@@ -15,9 +15,9 @@
Contributing author: Mike Brown (SNL)
------------------------------------------------------------------------- */
-#include <string.h>
-#include <stdlib.h>
-#include <math.h>
+#include <cstring>
+#include <cstdlib>
+#include <cmath>
#include "math_extra.h"
#include "fix_nh_asphere.h"
#include "atom.h"
diff --git a/src/ASPHERE/fix_nph_asphere.cpp b/src/ASPHERE/fix_nph_asphere.cpp
index e0558ef4f24cd29af20311b03cfaef7528fb540a..5f201a8463e325c2ff9bdeae85a1e6687907fd77 100644
--- a/src/ASPHERE/fix_nph_asphere.cpp
+++ b/src/ASPHERE/fix_nph_asphere.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "fix_nph_asphere.h"
#include "modify.h"
#include "error.h"
diff --git a/src/ASPHERE/fix_npt_asphere.cpp b/src/ASPHERE/fix_npt_asphere.cpp
index 205630376af2d49b7ef5bf6d3a439f6f5ffd1e1a..5d528911698f2c045c763163ec2c8912ec1661c5 100644
--- a/src/ASPHERE/fix_npt_asphere.cpp
+++ b/src/ASPHERE/fix_npt_asphere.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "fix_npt_asphere.h"
#include "modify.h"
#include "error.h"
diff --git a/src/ASPHERE/fix_nve_asphere.cpp b/src/ASPHERE/fix_nve_asphere.cpp
index 2ac3f95c5398220c1d981844a82fd5d0a4b5ab3a..a33848f1a1dac5c143c411414a8eba0c8a50c683 100644
--- a/src/ASPHERE/fix_nve_asphere.cpp
+++ b/src/ASPHERE/fix_nve_asphere.cpp
@@ -15,9 +15,9 @@
Contributing author: Mike Brown (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstring>
#include "fix_nve_asphere.h"
#include "math_extra.h"
#include "atom.h"
diff --git a/src/ASPHERE/fix_nve_asphere_noforce.cpp b/src/ASPHERE/fix_nve_asphere_noforce.cpp
index 34fb57159c69612c19dacd5e1246f6a180532428..d944b68f35a425cceae1f6faec6ed3b5e70a68ac 100644
--- a/src/ASPHERE/fix_nve_asphere_noforce.cpp
+++ b/src/ASPHERE/fix_nve_asphere_noforce.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <string.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstring>
+#include <cstdlib>
#include "fix_nve_asphere_noforce.h"
#include "math_extra.h"
#include "atom.h"
diff --git a/src/ASPHERE/fix_nve_line.cpp b/src/ASPHERE/fix_nve_line.cpp
index 554242fb5b4209d797d91c0dbf1f61b6a0594e37..c145e99fcb1a608e540941eb2b6402a58e6a5a33 100644
--- a/src/ASPHERE/fix_nve_line.cpp
+++ b/src/ASPHERE/fix_nve_line.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstring>
#include "fix_nve_line.h"
#include "atom.h"
#include "atom_vec_line.h"
diff --git a/src/ASPHERE/fix_nve_tri.cpp b/src/ASPHERE/fix_nve_tri.cpp
index f859ce08c81b75b29adc72ddba388edd406931b6..d06063d905940276941a14f1d3f46e1f95a0ff5d 100644
--- a/src/ASPHERE/fix_nve_tri.cpp
+++ b/src/ASPHERE/fix_nve_tri.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstring>
#include "fix_nve_tri.h"
#include "math_extra.h"
#include "atom.h"
diff --git a/src/ASPHERE/fix_nvt_asphere.cpp b/src/ASPHERE/fix_nvt_asphere.cpp
index f43e731c23851520a03f4bd3775d410fff6660d8..5ef91923ebb396b008b07d274c90c625670713e7 100644
--- a/src/ASPHERE/fix_nvt_asphere.cpp
+++ b/src/ASPHERE/fix_nvt_asphere.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "fix_nvt_asphere.h"
#include "group.h"
#include "modify.h"
diff --git a/src/ASPHERE/pair_gayberne.cpp b/src/ASPHERE/pair_gayberne.cpp
index 9ff87326ed7a0f88d156a99e1c0123b48fe89d8b..857541957e6512ffad74bdccfb351c3a6a8acd0d 100644
--- a/src/ASPHERE/pair_gayberne.cpp
+++ b/src/ASPHERE/pair_gayberne.cpp
@@ -15,10 +15,10 @@
Contributing author: Mike Brown (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_gayberne.h"
#include "math_extra.h"
#include "atom.h"
diff --git a/src/ASPHERE/pair_line_lj.cpp b/src/ASPHERE/pair_line_lj.cpp
index 83a6f4ea8c998ccef44ac408d3d7b523dc9be061..963ff985c478e3c29a2e11ed8bf3fc37dd5fe536 100644
--- a/src/ASPHERE/pair_line_lj.cpp
+++ b/src/ASPHERE/pair_line_lj.cpp
@@ -11,10 +11,10 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_line_lj.h"
#include "atom.h"
#include "atom_vec_line.h"
diff --git a/src/ASPHERE/pair_resquared.cpp b/src/ASPHERE/pair_resquared.cpp
index caa031a1e83933f1e271216def61b81ee5355337..c477b1b8cfbfdf1a4faa721831874bcb009a7ae1 100644
--- a/src/ASPHERE/pair_resquared.cpp
+++ b/src/ASPHERE/pair_resquared.cpp
@@ -15,10 +15,10 @@
Contributing author: Mike Brown (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_resquared.h"
#include "math_extra.h"
#include "atom.h"
diff --git a/src/ASPHERE/pair_tri_lj.cpp b/src/ASPHERE/pair_tri_lj.cpp
index 4f30b40e9a8976d9abb98913c7d4b30c5ae78278..142caf376425b34bd5f0cad23b76a9436f4ea8be 100644
--- a/src/ASPHERE/pair_tri_lj.cpp
+++ b/src/ASPHERE/pair_tri_lj.cpp
@@ -11,10 +11,10 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_tri_lj.h"
#include "math_extra.h"
#include "atom.h"
diff --git a/src/BODY/body_nparticle.cpp b/src/BODY/body_nparticle.cpp
index 7e3e6f463cd44d5cea74317a7842a5f1aa87ef39..684e5768dae00176fa05eaacf75cf43c1cb60468 100644
--- a/src/BODY/body_nparticle.cpp
+++ b/src/BODY/body_nparticle.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <stdlib.h>
+#include <cstdlib>
#include "body_nparticle.h"
#include "math_extra.h"
#include "atom_vec_body.h"
diff --git a/src/BODY/compute_body_local.cpp b/src/BODY/compute_body_local.cpp
index e72dd59b25fb214cd6ae536333f2367dfdc1b3c4..df8a76d0fedc1f5951572999615ff9ae67ffbaf5 100644
--- a/src/BODY/compute_body_local.cpp
+++ b/src/BODY/compute_body_local.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <string.h>
+#include <cmath>
+#include <cstring>
#include "compute_body_local.h"
#include "atom.h"
#include "atom_vec_body.h"
diff --git a/src/BODY/compute_temp_body.cpp b/src/BODY/compute_temp_body.cpp
index ec992cea22490b5b05b455980636e48696c16a47..5446fb6d644497a2e9331c745f21e58bc5487644 100644
--- a/src/BODY/compute_temp_body.cpp
+++ b/src/BODY/compute_temp_body.cpp
@@ -17,7 +17,7 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <string.h>
+#include <cstring>
#include "compute_temp_body.h"
#include "math_extra.h"
#include "atom.h"
diff --git a/src/BODY/fix_nh_body.cpp b/src/BODY/fix_nh_body.cpp
index a1865dfd182af602bd63d26e778fa5c22f463869..97398424193f37d0b4f34e6268ec09b2ad5e60c4 100644
--- a/src/BODY/fix_nh_body.cpp
+++ b/src/BODY/fix_nh_body.cpp
@@ -16,9 +16,9 @@
based on FixNHAsphere
------------------------------------------------------------------------- */
-#include <string.h>
-#include <stdlib.h>
-#include <math.h>
+#include <cstring>
+#include <cstdlib>
+#include <cmath>
#include "math_extra.h"
#include "fix_nh_body.h"
#include "atom.h"
diff --git a/src/BODY/fix_nph_body.cpp b/src/BODY/fix_nph_body.cpp
index 99e33a3d22e90d814f9e92415e63024ee04e45dc..e647488bce9ae3de2cc3e232aa7a5bbb8c796679 100644
--- a/src/BODY/fix_nph_body.cpp
+++ b/src/BODY/fix_nph_body.cpp
@@ -15,7 +15,7 @@
Contributing author: Trung Dac Nguyen (ndactrung@gmail.com)
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "fix_nph_body.h"
#include "modify.h"
#include "error.h"
diff --git a/src/BODY/fix_npt_body.cpp b/src/BODY/fix_npt_body.cpp
index 077a7babd4866ad99e060723ae4cb503d6bc8194..3c30e9e4e92f3825cd3d89da1a46a6f3798f9130 100644
--- a/src/BODY/fix_npt_body.cpp
+++ b/src/BODY/fix_npt_body.cpp
@@ -15,7 +15,7 @@
Contributing author: Trung Dac Nguyen (ndactrung@gmail.com)
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "fix_npt_body.h"
#include "modify.h"
#include "error.h"
diff --git a/src/BODY/fix_nve_body.cpp b/src/BODY/fix_nve_body.cpp
index edc88ed3b4213fb5eae64a1283e5b1bb88bf14fa..0606723cb77d558c8500c5469e16d64773f962fd 100644
--- a/src/BODY/fix_nve_body.cpp
+++ b/src/BODY/fix_nve_body.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstring>
#include "fix_nve_body.h"
#include "math_extra.h"
#include "atom.h"
diff --git a/src/BODY/fix_nvt_body.cpp b/src/BODY/fix_nvt_body.cpp
index 464f42eae91d5cada1c2c0cf8c9b4f6eedce065b..273b5e7fffd2ac3bf0750ed6cfd2548b4f4f4465 100644
--- a/src/BODY/fix_nvt_body.cpp
+++ b/src/BODY/fix_nvt_body.cpp
@@ -15,7 +15,7 @@
Contributing author: Trung Dac Nguyen (ndactrung@gmail.com)
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "fix_nvt_body.h"
#include "group.h"
#include "modify.h"
diff --git a/src/BODY/pair_body.cpp b/src/BODY/pair_body.cpp
index b1be99731018e2f30ebaa4258a679abb93944472..8c12c0cf36aa0384c50e3745b45c969c8aa29cc2 100644
--- a/src/BODY/pair_body.cpp
+++ b/src/BODY/pair_body.cpp
@@ -11,10 +11,10 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_body.h"
#include "math_extra.h"
#include "atom.h"
diff --git a/src/CLASS2/angle_class2.cpp b/src/CLASS2/angle_class2.cpp
index 7dfdaa17f48dbca47b0dfa17bd4eeddf4b06eb85..24f41bfd587e00d1ec3ae121a9511c0dcf712641 100644
--- a/src/CLASS2/angle_class2.cpp
+++ b/src/CLASS2/angle_class2.cpp
@@ -15,9 +15,9 @@
Contributing author: Eric Simon (Cray)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <string.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstring>
+#include <cstdlib>
#include "angle_class2.h"
#include "atom.h"
#include "neighbor.h"
diff --git a/src/CLASS2/angle_class2.h b/src/CLASS2/angle_class2.h
index 1d595d5f6ac8737d58def4dff9109a4d13a09b26..d18f71e1eb74b9a8c852cebc8895b05195e9c90a 100644
--- a/src/CLASS2/angle_class2.h
+++ b/src/CLASS2/angle_class2.h
@@ -20,7 +20,7 @@ AngleStyle(class2,AngleClass2)
#ifndef LMP_ANGLE_CLASS2_H
#define LMP_ANGLE_CLASS2_H
-#include <stdio.h>
+#include <cstdio>
#include "angle.h"
namespace LAMMPS_NS {
diff --git a/src/CLASS2/bond_class2.cpp b/src/CLASS2/bond_class2.cpp
index b016de0206f5ae52ca61677512a44364d27e92e9..c3dc09715c9c341b57a73e274251cdc35bdeb0da 100644
--- a/src/CLASS2/bond_class2.cpp
+++ b/src/CLASS2/bond_class2.cpp
@@ -15,8 +15,8 @@
Contributing author: Eric Simon (Cray)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdlib>
#include "bond_class2.h"
#include "atom.h"
#include "neighbor.h"
diff --git a/src/CLASS2/bond_class2.h b/src/CLASS2/bond_class2.h
index 51e2c939a77432100f4833378d53e2dff652c826..f8e294e2b0dae71441151db5aa820db19e441c89 100644
--- a/src/CLASS2/bond_class2.h
+++ b/src/CLASS2/bond_class2.h
@@ -20,7 +20,7 @@ BondStyle(class2,BondClass2)
#ifndef LMP_BOND_CLASS2_H
#define LMP_BOND_CLASS2_H
-#include <stdio.h>
+#include <cstdio>
#include "bond.h"
namespace LAMMPS_NS {
diff --git a/src/CLASS2/dihedral_class2.cpp b/src/CLASS2/dihedral_class2.cpp
index b79f574829e3c40d3e4f4f2abdbe56a462d22612..c6360dd84643b95fc1996e4cd10e8005b5d3c8b8 100644
--- a/src/CLASS2/dihedral_class2.cpp
+++ b/src/CLASS2/dihedral_class2.cpp
@@ -15,9 +15,9 @@
Contributing author: Eric Simon (Cray)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <string.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstring>
+#include <cstdlib>
#include "dihedral_class2.h"
#include "atom.h"
#include "neighbor.h"
diff --git a/src/CLASS2/dihedral_class2.h b/src/CLASS2/dihedral_class2.h
index e8309dad7a94d2b1ebc91c08291185445006297c..9ccf6623a06533c40f823d9cbbdf04b6eda576d0 100644
--- a/src/CLASS2/dihedral_class2.h
+++ b/src/CLASS2/dihedral_class2.h
@@ -20,7 +20,7 @@ DihedralStyle(class2,DihedralClass2)
#ifndef LMP_DIHEDRAL_CLASS2_H
#define LMP_DIHEDRAL_CLASS2_H
-#include <stdio.h>
+#include <cstdio>
#include "dihedral.h"
namespace LAMMPS_NS {
diff --git a/src/CLASS2/improper_class2.cpp b/src/CLASS2/improper_class2.cpp
index e7c4aa94be8ae6c9fadf0b3938055234e0b694d3..3b3811584d07e4f71a53b986084cd735841decbd 100644
--- a/src/CLASS2/improper_class2.cpp
+++ b/src/CLASS2/improper_class2.cpp
@@ -15,9 +15,9 @@
Contributing author: Eric Simon (Cray)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <string.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstring>
+#include <cstdlib>
#include "improper_class2.h"
#include "atom.h"
#include "neighbor.h"
diff --git a/src/CLASS2/improper_class2.h b/src/CLASS2/improper_class2.h
index f814da96c545daee13babb3ca34f53bc03b235ca..f155f67c5c8169fa4125c3f6a19700a3e2ef2129 100644
--- a/src/CLASS2/improper_class2.h
+++ b/src/CLASS2/improper_class2.h
@@ -20,7 +20,7 @@ ImproperStyle(class2,ImproperClass2)
#ifndef LMP_IMPROPER_CLASS2_H
#define LMP_IMPROPER_CLASS2_H
-#include <stdio.h>
+#include <cstdio>
#include "improper.h"
namespace LAMMPS_NS {
diff --git a/src/CLASS2/pair_lj_class2.cpp b/src/CLASS2/pair_lj_class2.cpp
index 0b90b2717e314cda29d441465214b2767dff152d..e255807ab6a5f217f076892d9a695d5d5d4cd787 100644
--- a/src/CLASS2/pair_lj_class2.cpp
+++ b/src/CLASS2/pair_lj_class2.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
#include "pair_lj_class2.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/CLASS2/pair_lj_class2_coul_cut.cpp b/src/CLASS2/pair_lj_class2_coul_cut.cpp
index 395953e0a9c7a70fa9bb9d3cd8c4834c1923a714..5cd5ad0e32cc1ae4df4242144d4438c3f9996a7b 100644
--- a/src/CLASS2/pair_lj_class2_coul_cut.cpp
+++ b/src/CLASS2/pair_lj_class2_coul_cut.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
#include "pair_lj_class2_coul_cut.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/CLASS2/pair_lj_class2_coul_long.cpp b/src/CLASS2/pair_lj_class2_coul_long.cpp
index 9278703e2a4685898b97a4d0e1ebf3bca6a6b2ff..bf892bc894fd699a1d368a409b0c609bffef0134 100644
--- a/src/CLASS2/pair_lj_class2_coul_long.cpp
+++ b/src/CLASS2/pair_lj_class2_coul_long.cpp
@@ -11,10 +11,10 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_lj_class2_coul_long.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/COLLOID/fix_wall_colloid.cpp b/src/COLLOID/fix_wall_colloid.cpp
index 651e0da4f8e195f7f9abdec004acf44753ba2667..095d01eef3019b6a5735c93dfa5fb093feeca65d 100644
--- a/src/COLLOID/fix_wall_colloid.cpp
+++ b/src/COLLOID/fix_wall_colloid.cpp
@@ -15,8 +15,8 @@
Contributing authors: Jeremy Lechman (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <string.h>
+#include <cmath>
+#include <cstring>
#include "fix_wall_colloid.h"
#include "atom.h"
#include "atom_vec.h"
diff --git a/src/COLLOID/pair_brownian.cpp b/src/COLLOID/pair_brownian.cpp
index 2bf01303b44aa1193d9e885fc3f49e8ec27f5463..e532c06c863f28eba94c5b93cd8a8ef01dd78a23 100644
--- a/src/COLLOID/pair_brownian.cpp
+++ b/src/COLLOID/pair_brownian.cpp
@@ -15,10 +15,10 @@
Contributing authors: Amit Kumar and Michael Bybee (UIUC)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_brownian.h"
#include "atom.h"
#include "atom_vec.h"
diff --git a/src/COLLOID/pair_brownian_poly.cpp b/src/COLLOID/pair_brownian_poly.cpp
index 84c56109d13cbb6f788cd65135a8ca9a268ca853..c6d5def2fafd80be6e70052159ef9b6803effd74 100644
--- a/src/COLLOID/pair_brownian_poly.cpp
+++ b/src/COLLOID/pair_brownian_poly.cpp
@@ -16,10 +16,10 @@
Dave Heine (Corning), polydispersity
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_brownian_poly.h"
#include "atom.h"
#include "atom_vec.h"
diff --git a/src/COLLOID/pair_colloid.cpp b/src/COLLOID/pair_colloid.cpp
index 983b973e0e096e245d1b3eb9d3b1aae48888a165..4448d6e110ec8ca21840eab06258692e356ca650 100644
--- a/src/COLLOID/pair_colloid.cpp
+++ b/src/COLLOID/pair_colloid.cpp
@@ -15,10 +15,10 @@
Contributing author: Pieter in 't Veld (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_colloid.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/COLLOID/pair_lubricate.cpp b/src/COLLOID/pair_lubricate.cpp
index 93cb48a15db6355f79d25264a9dd0bed35681101..f0f7ce8c143f259c298e053ae1b509f1531837ce 100644
--- a/src/COLLOID/pair_lubricate.cpp
+++ b/src/COLLOID/pair_lubricate.cpp
@@ -16,10 +16,10 @@
Amit Kumar and Michael Bybee (UIUC)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_lubricate.h"
#include "atom.h"
#include "atom_vec.h"
@@ -43,10 +43,6 @@
using namespace LAMMPS_NS;
using namespace MathConst;
-// same as fix_deform.cpp
-
-enum{NO_REMAP,X_REMAP,V_REMAP};
-
// same as fix_wall.cpp
enum{EDGE,CONSTANT,VARIABLE};
@@ -570,7 +566,7 @@ void PairLubricate::init_style()
for (int i = 0; i < modify->nfix; i++){
if (strcmp(modify->fix[i]->style,"deform") == 0) {
shearing = flagdeform = 1;
- if (((FixDeform *) modify->fix[i])->remapflag != V_REMAP)
+ if (((FixDeform *) modify->fix[i])->remapflag != Domain::V_REMAP)
error->all(FLERR,"Using pair lubricate with inconsistent "
"fix deform remap option");
}
diff --git a/src/COLLOID/pair_lubricateU.cpp b/src/COLLOID/pair_lubricateU.cpp
index 5d0a4243a7fbb59e021dea3c9179146730c264c8..11fb2131577c6f32a20358fc9a769038d20e0075 100644
--- a/src/COLLOID/pair_lubricateU.cpp
+++ b/src/COLLOID/pair_lubricateU.cpp
@@ -16,10 +16,10 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_lubricateU.h"
#include "atom.h"
#include "atom_vec.h"
diff --git a/src/COLLOID/pair_lubricateU_poly.cpp b/src/COLLOID/pair_lubricateU_poly.cpp
index 428aa41cb6f9c2000549db290f45d813d6805d45..90ac848d2653479a34bcf2850d214fe8340b5a14 100644
--- a/src/COLLOID/pair_lubricateU_poly.cpp
+++ b/src/COLLOID/pair_lubricateU_poly.cpp
@@ -18,10 +18,10 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_lubricateU_poly.h"
#include "atom.h"
#include "atom_vec.h"
diff --git a/src/COLLOID/pair_lubricate_poly.cpp b/src/COLLOID/pair_lubricate_poly.cpp
index 2561ca3637317cfe1b640d070b866ece285566cd..5e5293336491ba2d78f15bea004eb6712ab76442 100644
--- a/src/COLLOID/pair_lubricate_poly.cpp
+++ b/src/COLLOID/pair_lubricate_poly.cpp
@@ -17,10 +17,10 @@
Dave Heine (Corning), polydispersity
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_lubricate_poly.h"
#include "atom.h"
#include "atom_vec.h"
@@ -44,11 +44,6 @@
using namespace LAMMPS_NS;
using namespace MathConst;
-// same as fix_deform.cpp
-
-enum{NO_REMAP,X_REMAP,V_REMAP};
-
-
// same as fix_wall.cpp
enum{EDGE,CONSTANT,VARIABLE};
@@ -474,7 +469,7 @@ void PairLubricatePoly::init_style()
for (int i = 0; i < modify->nfix; i++){
if (strcmp(modify->fix[i]->style,"deform") == 0) {
shearing = flagdeform = 1;
- if (((FixDeform *) modify->fix[i])->remapflag != V_REMAP)
+ if (((FixDeform *) modify->fix[i])->remapflag != Domain::V_REMAP)
error->all(FLERR,"Using pair lubricate with inconsistent "
"fix deform remap option");
}
@@ -550,7 +545,7 @@ void PairLubricatePoly::init_style()
for (int i = 0; i < modify->nfix; i++)
if (strcmp(modify->fix[i]->style,"deform") == 0) {
shearing = 1;
- if (((FixDeform *) modify->fix[i])->remapflag != V_REMAP)
+ if (((FixDeform *) modify->fix[i])->remapflag != Domain::V_REMAP)
error->all(FLERR,"Using pair lubricate/poly with inconsistent "
"fix deform remap option");
}
diff --git a/src/COLLOID/pair_yukawa_colloid.cpp b/src/COLLOID/pair_yukawa_colloid.cpp
index 87fa7f542285d4285e7229a0b61a893ea4d50eb8..5965fd3aa86913824e3a21be449d607a89f87e83 100644
--- a/src/COLLOID/pair_yukawa_colloid.cpp
+++ b/src/COLLOID/pair_yukawa_colloid.cpp
@@ -15,8 +15,8 @@
Contributing authors: Randy Schunk (Sandia)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdlib>
#include "pair_yukawa_colloid.h"
#include "atom.h"
#include "atom_vec.h"
diff --git a/src/COMPRESS/Install.sh b/src/COMPRESS/Install.sh
old mode 100644
new mode 100755
diff --git a/src/COMPRESS/dump_atom_gz.cpp b/src/COMPRESS/dump_atom_gz.cpp
index dfd23e2b4a8bc17d859f62a276591ebd28cb925e..ef7e6583be5e28d1af258aa636fa6c509816bc47 100644
--- a/src/COMPRESS/dump_atom_gz.cpp
+++ b/src/COMPRESS/dump_atom_gz.cpp
@@ -16,7 +16,7 @@
#include "error.h"
#include "update.h"
-#include <string.h>
+#include <cstring>
using namespace LAMMPS_NS;
@@ -71,6 +71,19 @@ void DumpAtomGZ::openfile()
sprintf(filecurrent,pad,filestar,update->ntimestep,ptr+1);
}
*ptr = '*';
+ if (maxfiles > 0) {
+ if (numfiles < maxfiles) {
+ nameslist[numfiles] = new char[strlen(filecurrent)+1];
+ strcpy(nameslist[numfiles],filecurrent);
+ ++numfiles;
+ } else {
+ remove(nameslist[fileidx]);
+ delete[] nameslist[fileidx];
+ nameslist[fileidx] = new char[strlen(filecurrent)+1];
+ strcpy(nameslist[fileidx],filecurrent);
+ fileidx = (fileidx + 1) % maxfiles;
+ }
+ }
}
// each proc with filewriter = 1 opens a file
diff --git a/src/COMPRESS/dump_cfg_gz.cpp b/src/COMPRESS/dump_cfg_gz.cpp
index 6f653e73ee2dcf545994c4e95d72a72c48115dd8..aaeb878584b0cca77110b1a7bbef58d8de6f6cab 100644
--- a/src/COMPRESS/dump_cfg_gz.cpp
+++ b/src/COMPRESS/dump_cfg_gz.cpp
@@ -17,7 +17,7 @@
#include "error.h"
#include "update.h"
-#include <string.h>
+#include <cstring>
using namespace LAMMPS_NS;
#define UNWRAPEXPAND 10.0
@@ -75,6 +75,19 @@ void DumpCFGGZ::openfile()
sprintf(filecurrent,pad,filestar,update->ntimestep,ptr+1);
}
*ptr = '*';
+ if (maxfiles > 0) {
+ if (numfiles < maxfiles) {
+ nameslist[numfiles] = new char[strlen(filecurrent)+1];
+ strcpy(nameslist[numfiles],filecurrent);
+ ++numfiles;
+ } else {
+ remove(nameslist[fileidx]);
+ delete[] nameslist[fileidx];
+ nameslist[fileidx] = new char[strlen(filecurrent)+1];
+ strcpy(nameslist[fileidx],filecurrent);
+ fileidx = (fileidx + 1) % maxfiles;
+ }
+ }
}
// each proc with filewriter = 1 opens a file
diff --git a/src/COMPRESS/dump_custom_gz.cpp b/src/COMPRESS/dump_custom_gz.cpp
index 1905577a12bbc5ca50decffa659bb300d6068160..9c30f4742f92de2dcf92c2c4c2e22f28b9c1ca02 100644
--- a/src/COMPRESS/dump_custom_gz.cpp
+++ b/src/COMPRESS/dump_custom_gz.cpp
@@ -16,7 +16,7 @@
#include "error.h"
#include "update.h"
-#include <string.h>
+#include <cstring>
using namespace LAMMPS_NS;
@@ -73,6 +73,19 @@ void DumpCustomGZ::openfile()
sprintf(filecurrent,pad,filestar,update->ntimestep,ptr+1);
}
*ptr = '*';
+ if (maxfiles > 0) {
+ if (numfiles < maxfiles) {
+ nameslist[numfiles] = new char[strlen(filecurrent)+1];
+ strcpy(nameslist[numfiles],filecurrent);
+ ++numfiles;
+ } else {
+ remove(nameslist[fileidx]);
+ delete[] nameslist[fileidx];
+ nameslist[fileidx] = new char[strlen(filecurrent)+1];
+ strcpy(nameslist[fileidx],filecurrent);
+ fileidx = (fileidx + 1) % maxfiles;
+ }
+ }
}
// each proc with filewriter = 1 opens a file
diff --git a/src/COMPRESS/dump_xyz_gz.cpp b/src/COMPRESS/dump_xyz_gz.cpp
index 1a4474cba2929ff918777bf3de04c8326425befc..7be1a10fe2b15b19daa5f3b93d0659d75959922f 100644
--- a/src/COMPRESS/dump_xyz_gz.cpp
+++ b/src/COMPRESS/dump_xyz_gz.cpp
@@ -16,7 +16,7 @@
#include "error.h"
#include "update.h"
-#include <string.h>
+#include <cstring>
using namespace LAMMPS_NS;
@@ -73,6 +73,19 @@ void DumpXYZGZ::openfile()
sprintf(filecurrent,pad,filestar,update->ntimestep,ptr+1);
}
*ptr = '*';
+ if (maxfiles > 0) {
+ if (numfiles < maxfiles) {
+ nameslist[numfiles] = new char[strlen(filecurrent)+1];
+ strcpy(nameslist[numfiles],filecurrent);
+ ++numfiles;
+ } else {
+ remove(nameslist[fileidx]);
+ delete[] nameslist[fileidx];
+ nameslist[fileidx] = new char[strlen(filecurrent)+1];
+ strcpy(nameslist[fileidx],filecurrent);
+ fileidx = (fileidx + 1) % maxfiles;
+ }
+ }
}
// each proc with filewriter = 1 opens a file
diff --git a/src/CORESHELL/Install.sh b/src/CORESHELL/Install.sh
old mode 100644
new mode 100755
diff --git a/src/CORESHELL/compute_temp_cs.cpp b/src/CORESHELL/compute_temp_cs.cpp
index d2345684dc61ff6dbb17c49286a77f9daf939a27..03ebfa154d5e2bf78dd6c0e731f5a6f4e2e92a8f 100644
--- a/src/CORESHELL/compute_temp_cs.cpp
+++ b/src/CORESHELL/compute_temp_cs.cpp
@@ -17,9 +17,9 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <stdlib.h>
-#include <string.h>
-#include <math.h>
+#include <cstdlib>
+#include <cstring>
+#include <cmath>
#include "compute_temp_cs.h"
#include "atom.h"
#include "atom_vec.h"
diff --git a/src/CORESHELL/pair_born_coul_dsf_cs.cpp b/src/CORESHELL/pair_born_coul_dsf_cs.cpp
index 4a5c9da07e0256f4c11ee44c7868b3785045e6a6..549c7c03481c6c4481085fe0a414780291687302 100644
--- a/src/CORESHELL/pair_born_coul_dsf_cs.cpp
+++ b/src/CORESHELL/pair_born_coul_dsf_cs.cpp
@@ -16,10 +16,10 @@
References: Fennell and Gezelter, JCP 124, 234104 (2006)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_born_coul_dsf_cs.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/CORESHELL/pair_born_coul_long_cs.cpp b/src/CORESHELL/pair_born_coul_long_cs.cpp
index 7d0d9c9416a4ad46ded5be36dbbaadd6a474ab38..76f6eb387df5f2df2ca8e7b4f3c05afc3ae78574 100644
--- a/src/CORESHELL/pair_born_coul_long_cs.cpp
+++ b/src/CORESHELL/pair_born_coul_long_cs.cpp
@@ -15,10 +15,10 @@
Contributing author: Hendrik Heenen (hendrik.heenen@mytum.de)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_born_coul_long_cs.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/CORESHELL/pair_born_coul_wolf_cs.cpp b/src/CORESHELL/pair_born_coul_wolf_cs.cpp
index f39e2ca81631b7ce85ce8b70b4649c1fcaf34f07..84179ce50ab7a8d20e27042480ccade65d331dd3 100644
--- a/src/CORESHELL/pair_born_coul_wolf_cs.cpp
+++ b/src/CORESHELL/pair_born_coul_wolf_cs.cpp
@@ -12,10 +12,10 @@
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_born_coul_wolf_cs.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/CORESHELL/pair_buck_coul_long_cs.cpp b/src/CORESHELL/pair_buck_coul_long_cs.cpp
index 822ec1049725ac2d2470b653ec9e68adc178702a..ea072d44a13d8a88fbc80e31f6339fdbe37e538d 100644
--- a/src/CORESHELL/pair_buck_coul_long_cs.cpp
+++ b/src/CORESHELL/pair_buck_coul_long_cs.cpp
@@ -15,10 +15,10 @@
Contributing author: Hendrik Heenen (hendrik.heenen@mytum.de)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_buck_coul_long_cs.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/CORESHELL/pair_coul_long_cs.cpp b/src/CORESHELL/pair_coul_long_cs.cpp
index 9177e9a0613ce7b61f3028fbad65d7076861664e..b21465384199c5a58a8fa3c03a700c29faadef17 100644
--- a/src/CORESHELL/pair_coul_long_cs.cpp
+++ b/src/CORESHELL/pair_coul_long_cs.cpp
@@ -15,10 +15,10 @@
Contributing author: Hendrik Heenen (hendrik.heenen@mytum.de)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_coul_long_cs.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/CORESHELL/pair_coul_wolf_cs.cpp b/src/CORESHELL/pair_coul_wolf_cs.cpp
index 5f277dcdd2e49e8b8bb37b639c4c9109c624388e..b50f14833e9664552022c3d54d36c4e2f953cc28 100644
--- a/src/CORESHELL/pair_coul_wolf_cs.cpp
+++ b/src/CORESHELL/pair_coul_wolf_cs.cpp
@@ -12,10 +12,10 @@
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_coul_wolf_cs.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/CORESHELL/pair_lj_cut_coul_long_cs.cpp b/src/CORESHELL/pair_lj_cut_coul_long_cs.cpp
index c660eee3bc19569578aae1aa5e661d2ca301d2cd..8caefc0e66096283ca363c207a6290bfcea5183d 100644
--- a/src/CORESHELL/pair_lj_cut_coul_long_cs.cpp
+++ b/src/CORESHELL/pair_lj_cut_coul_long_cs.cpp
@@ -15,10 +15,10 @@
Contributing author: Hendrik Heenen (hendrik.heenen@mytum.de)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_lj_cut_coul_long_cs.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/DIPOLE/atom_vec_dipole.cpp b/src/DIPOLE/atom_vec_dipole.cpp
index 5d69f03376b976fee756534660b8510bbe03162c..c304ae3bc660598eb421e2d67c4af4400886ec55 100644
--- a/src/DIPOLE/atom_vec_dipole.cpp
+++ b/src/DIPOLE/atom_vec_dipole.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdlib>
#include "atom_vec_dipole.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/DIPOLE/pair_lj_cut_dipole_cut.cpp b/src/DIPOLE/pair_lj_cut_dipole_cut.cpp
index af987bf2585f962d6c18f8fec4acd7306210cc8f..6af9b457246fb0bc446dfcc37ef1449806b745da 100644
--- a/src/DIPOLE/pair_lj_cut_dipole_cut.cpp
+++ b/src/DIPOLE/pair_lj_cut_dipole_cut.cpp
@@ -11,8 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "pair_lj_cut_dipole_cut.h"
#include "atom.h"
#include "neighbor.h"
@@ -22,7 +23,6 @@
#include "memory.h"
#include "error.h"
#include "update.h"
-#include <string.h>
using namespace LAMMPS_NS;
diff --git a/src/DIPOLE/pair_lj_cut_dipole_long.cpp b/src/DIPOLE/pair_lj_cut_dipole_long.cpp
index 63f48bea8116b026b29af9dee1d74d2726f21c08..817a120e3d084b9301095d2364e8402586a04b57 100644
--- a/src/DIPOLE/pair_lj_cut_dipole_long.cpp
+++ b/src/DIPOLE/pair_lj_cut_dipole_long.cpp
@@ -11,10 +11,10 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_lj_cut_dipole_long.h"
#include "atom.h"
#include "comm.h"
@@ -26,7 +26,6 @@
#include "memory.h"
#include "error.h"
#include "update.h"
-#include <string.h>
using namespace LAMMPS_NS;
diff --git a/src/DIPOLE/pair_lj_long_dipole_long.cpp b/src/DIPOLE/pair_lj_long_dipole_long.cpp
index 262727c5b600de8d2554a4a3ab9e673bf6137f2b..1635bd4f636f33d3b4f678aef45a4d2b4727fe2f 100644
--- a/src/DIPOLE/pair_lj_long_dipole_long.cpp
+++ b/src/DIPOLE/pair_lj_long_dipole_long.cpp
@@ -15,10 +15,10 @@
Contributing author: Pieter J. in 't Veld and Stan Moore (Sandia)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "math_const.h"
#include "math_vector.h"
#include "pair_lj_long_dipole_long.h"
diff --git a/src/Depend.sh b/src/Depend.sh
old mode 100644
new mode 100755
index a83a99ffb5da5bf320b8a28a151b33af4eb189f6..a3f4e496673f3b8c896e1675fe13608c0ddd8960
--- a/src/Depend.sh
+++ b/src/Depend.sh
@@ -87,6 +87,7 @@ if (test $1 = "MANYBODY") then
depend GPU
depend KOKKOS
depend OPT
+ depend QEQ
depend USER-MISC
depend USER-OMP
fi
@@ -95,9 +96,8 @@ if (test $1 = "MOLECULE") then
depend GPU
depend KOKKOS
depend USER-MISC
- depend USER-OMP
depend USER-FEP
- depend USER-CGDNA
+ depend USER-OMP
depend USER-INTEL
fi
@@ -134,6 +134,7 @@ fi
if (test $1 = "USER-MISC") then
depend GPU
depend USER-OMP
+ depend USER-INTEL
fi
if (test $1 = "USER-REAXC") then
diff --git a/src/GPU/Install.sh b/src/GPU/Install.sh
old mode 100644
new mode 100755
diff --git a/src/GPU/fix_gpu.cpp b/src/GPU/fix_gpu.cpp
index 87db73bd12d64bd792d684d3903c9b713f642b48..268a7410329176672eee4a6e8ca8a3428b77aa50 100644
--- a/src/GPU/fix_gpu.cpp
+++ b/src/GPU/fix_gpu.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
-#include <stdlib.h>
+#include <cstring>
+#include <cstdlib>
#include "fix_gpu.h"
#include "atom.h"
#include "force.h"
diff --git a/src/GPU/gpu_extra.h b/src/GPU/gpu_extra.h
index ddb0b5ceaa51cf1bae036d014f6aa24220bdc98d..56a4f15f1bff5a18ee050badf8acfb420c97b28b 100644
--- a/src/GPU/gpu_extra.h
+++ b/src/GPU/gpu_extra.h
@@ -61,13 +61,13 @@ namespace GPU_EXTRA {
else
error->all(FLERR,"Unknown error in GPU library");
}
- };
+ }
inline void gpu_ready(LAMMPS_NS::Modify *modify, LAMMPS_NS::Error *error) {
int ifix = modify->find_fix("package_gpu");
if (ifix < 0)
error->all(FLERR,"The package gpu command is required for gpu styles");
- };
+ }
}
#endif
diff --git a/src/GPU/pair_beck_gpu.cpp b/src/GPU/pair_beck_gpu.cpp
index c81318664086f895c7665d7bece4e25cd0ec40f8..f929dd437f8b808f4551850446ba7027b3d55799 100644
--- a/src/GPU/pair_beck_gpu.cpp
+++ b/src/GPU/pair_beck_gpu.cpp
@@ -15,9 +15,10 @@
Contributing author: Trung Dac Nguyen (ORNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_beck_gpu.h"
#include "atom.h"
#include "atom_vec.h"
@@ -32,7 +33,6 @@
#include "universe.h"
#include "update.h"
#include "domain.h"
-#include <string.h>
#include "gpu_extra.h"
#include "math_special.h"
diff --git a/src/GPU/pair_born_coul_long_gpu.cpp b/src/GPU/pair_born_coul_long_gpu.cpp
index b6a7e57038f6c217233768c265b513c124539f65..c3c3fee40c804314cb982db435a86731f2cb03f2 100644
--- a/src/GPU/pair_born_coul_long_gpu.cpp
+++ b/src/GPU/pair_born_coul_long_gpu.cpp
@@ -15,9 +15,10 @@
Contributing author: Trung Dac Nguyen (ORNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_born_coul_long_gpu.h"
#include "atom.h"
#include "atom_vec.h"
@@ -33,7 +34,6 @@
#include "universe.h"
#include "update.h"
#include "domain.h"
-#include <string.h>
#include "kspace.h"
#include "gpu_extra.h"
diff --git a/src/GPU/pair_born_coul_wolf_gpu.cpp b/src/GPU/pair_born_coul_wolf_gpu.cpp
index 931252be6bf92693a548fc9bc73aefb37d9a2ad7..df1922d76a00968b83490a639489faefb127b665 100644
--- a/src/GPU/pair_born_coul_wolf_gpu.cpp
+++ b/src/GPU/pair_born_coul_wolf_gpu.cpp
@@ -15,9 +15,10 @@
Contributing authors: Trung Dac Nguyen (ORNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_born_coul_wolf_gpu.h"
#include "atom.h"
#include "atom_vec.h"
@@ -33,7 +34,6 @@
#include "universe.h"
#include "update.h"
#include "domain.h"
-#include <string.h>
#include "gpu_extra.h"
using namespace LAMMPS_NS;
diff --git a/src/GPU/pair_born_gpu.cpp b/src/GPU/pair_born_gpu.cpp
index 46729ab77c577059c256d4ce7200079d4bf7fb54..92a7a85997fcaa6609e1f40a553accd0361affb8 100644
--- a/src/GPU/pair_born_gpu.cpp
+++ b/src/GPU/pair_born_gpu.cpp
@@ -15,9 +15,10 @@
Contributing author: Trung Dac Nguyen (ORNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_born_gpu.h"
#include "atom.h"
#include "atom_vec.h"
@@ -32,7 +33,6 @@
#include "universe.h"
#include "update.h"
#include "domain.h"
-#include <string.h>
#include "gpu_extra.h"
using namespace LAMMPS_NS;
diff --git a/src/GPU/pair_buck_coul_cut_gpu.cpp b/src/GPU/pair_buck_coul_cut_gpu.cpp
index e74020dd3a61f653cdaf008987480f1033cf2da7..6396e301e3f56e0fddcd040a4520b345bd34098f 100644
--- a/src/GPU/pair_buck_coul_cut_gpu.cpp
+++ b/src/GPU/pair_buck_coul_cut_gpu.cpp
@@ -15,9 +15,10 @@
Contributing authors: Trung Dac Nguyen (ORNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_buck_coul_cut_gpu.h"
#include "atom.h"
#include "atom_vec.h"
@@ -32,7 +33,6 @@
#include "universe.h"
#include "update.h"
#include "domain.h"
-#include <string.h>
#include "gpu_extra.h"
using namespace LAMMPS_NS;
diff --git a/src/GPU/pair_buck_coul_long_gpu.cpp b/src/GPU/pair_buck_coul_long_gpu.cpp
index c2a37fc3dc5fef8859aab5f8f2e84db58afdde23..73821cee8aaf826ac341655a2c48518bf9b0507f 100644
--- a/src/GPU/pair_buck_coul_long_gpu.cpp
+++ b/src/GPU/pair_buck_coul_long_gpu.cpp
@@ -15,9 +15,10 @@
Contributing author: Trung Dac Nguyen (ORNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_buck_coul_long_gpu.h"
#include "atom.h"
#include "atom_vec.h"
@@ -32,7 +33,6 @@
#include "universe.h"
#include "update.h"
#include "domain.h"
-#include <string.h>
#include "kspace.h"
#include "gpu_extra.h"
diff --git a/src/GPU/pair_buck_gpu.cpp b/src/GPU/pair_buck_gpu.cpp
index 1e9b838ec805301151c0f7fa892fa6f0bf4aded4..20302e4f1a14246b4e76037af59791cd380bd5c2 100644
--- a/src/GPU/pair_buck_gpu.cpp
+++ b/src/GPU/pair_buck_gpu.cpp
@@ -15,9 +15,10 @@
Contributing author: Trung Dac Nguyen (ORNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_buck_gpu.h"
#include "atom.h"
#include "atom_vec.h"
@@ -32,7 +33,6 @@
#include "universe.h"
#include "update.h"
#include "domain.h"
-#include <string.h>
#include "gpu_extra.h"
using namespace LAMMPS_NS;
diff --git a/src/GPU/pair_colloid_gpu.cpp b/src/GPU/pair_colloid_gpu.cpp
index d4e8224238375a1fd0b432a522c57c9370d48b9e..7bbac32ed3c287c13785fa31db863d48b33285ba 100644
--- a/src/GPU/pair_colloid_gpu.cpp
+++ b/src/GPU/pair_colloid_gpu.cpp
@@ -15,9 +15,10 @@
Contributing author: Trung Dac Nguyen (ORNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_colloid_gpu.h"
#include "atom.h"
#include "atom_vec.h"
@@ -32,7 +33,6 @@
#include "universe.h"
#include "update.h"
#include "domain.h"
-#include <string.h>
#include "gpu_extra.h"
using namespace LAMMPS_NS;
diff --git a/src/GPU/pair_coul_cut_gpu.cpp b/src/GPU/pair_coul_cut_gpu.cpp
index c66a0a8ef4b3891f82e96ad867d0382b4684cd7e..d5d9b10abba4d1a676cfcb804d2aaadafc9c80cc 100644
--- a/src/GPU/pair_coul_cut_gpu.cpp
+++ b/src/GPU/pair_coul_cut_gpu.cpp
@@ -15,9 +15,10 @@
Contributing author: Trung Dac Nguyen
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_coul_cut_gpu.h"
#include "atom.h"
#include "atom_vec.h"
@@ -32,7 +33,6 @@
#include "universe.h"
#include "update.h"
#include "domain.h"
-#include <string.h>
#include "gpu_extra.h"
using namespace LAMMPS_NS;
diff --git a/src/GPU/pair_coul_debye_gpu.cpp b/src/GPU/pair_coul_debye_gpu.cpp
index 2b5d608fc7f142d84270deae65e7cefc54e11f76..9fd28bf9c5f01863c6a6e28c999b5f4b9e2da97c 100644
--- a/src/GPU/pair_coul_debye_gpu.cpp
+++ b/src/GPU/pair_coul_debye_gpu.cpp
@@ -15,9 +15,10 @@
Contributing author: Trung Dac Nguyen (ndtrung@umich.edu)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_coul_debye_gpu.h"
#include "atom.h"
#include "atom_vec.h"
@@ -32,7 +33,6 @@
#include "universe.h"
#include "update.h"
#include "domain.h"
-#include <string.h>
#include "gpu_extra.h"
using namespace LAMMPS_NS;
diff --git a/src/GPU/pair_coul_dsf_gpu.cpp b/src/GPU/pair_coul_dsf_gpu.cpp
index d2d060281c23eeaf36f5fecae7ae5baecc7db906..75168c3cd96d3c2538d78e64de00d5a0dbb06206 100644
--- a/src/GPU/pair_coul_dsf_gpu.cpp
+++ b/src/GPU/pair_coul_dsf_gpu.cpp
@@ -15,9 +15,10 @@
Contributing author: Trung Dac Nguyen (ORNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_coul_dsf_gpu.h"
#include "atom.h"
#include "atom_vec.h"
@@ -32,7 +33,6 @@
#include "universe.h"
#include "update.h"
#include "domain.h"
-#include <string.h>
#include "gpu_extra.h"
#define MY_PIS 1.77245385090551602729
diff --git a/src/GPU/pair_coul_long_gpu.cpp b/src/GPU/pair_coul_long_gpu.cpp
index 465d82232f54da2ad4b5687a2c548530652764d0..2f12e41b0cc6af68cfe0a792357c88b9c19c3b87 100644
--- a/src/GPU/pair_coul_long_gpu.cpp
+++ b/src/GPU/pair_coul_long_gpu.cpp
@@ -15,9 +15,10 @@
Contributing author: Axel Kohlmeyer (Temple)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_coul_long_gpu.h"
#include "atom.h"
#include "atom_vec.h"
@@ -32,7 +33,6 @@
#include "universe.h"
#include "update.h"
#include "domain.h"
-#include <string.h>
#include "kspace.h"
#include "gpu_extra.h"
diff --git a/src/GPU/pair_dpd_gpu.cpp b/src/GPU/pair_dpd_gpu.cpp
index c82ed97485851fada7d1f71ab12c21c880d44664..293a82ffa9eaddd5aaf0dde87e468f35bcea0531 100644
--- a/src/GPU/pair_dpd_gpu.cpp
+++ b/src/GPU/pair_dpd_gpu.cpp
@@ -15,9 +15,10 @@
Contributing author: Trung Dac Nguyen (ORNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_dpd_gpu.h"
#include "atom.h"
#include "atom_vec.h"
@@ -33,7 +34,6 @@
#include "universe.h"
#include "update.h"
#include "domain.h"
-#include <string.h>
#include "gpu_extra.h"
using namespace LAMMPS_NS;
diff --git a/src/GPU/pair_dpd_tstat_gpu.cpp b/src/GPU/pair_dpd_tstat_gpu.cpp
index e051a13a0b2f947570d803a25bb584d69a5bb3f0..bf02570f439dbd8f06b786d5b89d112f2dceac06 100644
--- a/src/GPU/pair_dpd_tstat_gpu.cpp
+++ b/src/GPU/pair_dpd_tstat_gpu.cpp
@@ -15,9 +15,10 @@
Contributing author: Trung Dac Nguyen (ORNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_dpd_tstat_gpu.h"
#include "atom.h"
#include "atom_vec.h"
@@ -33,7 +34,6 @@
#include "universe.h"
#include "update.h"
#include "domain.h"
-#include <string.h>
#include "gpu_extra.h"
using namespace LAMMPS_NS;
diff --git a/src/GPU/pair_eam_alloy_gpu.cpp b/src/GPU/pair_eam_alloy_gpu.cpp
index 9b42b0a14fab56b44652942973fd122a7fe113da..3a8e440bdc0c88164e3e3f8c3ea17def4659bb4e 100644
--- a/src/GPU/pair_eam_alloy_gpu.cpp
+++ b/src/GPU/pair_eam_alloy_gpu.cpp
@@ -15,9 +15,9 @@
Contributing authors: Trung Dac Nguyen (ORNL), W. Michael Brown (ORNL)
------------------------------------------------------------------------- */
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_eam_alloy_gpu.h"
#include "atom.h"
#include "force.h"
diff --git a/src/GPU/pair_eam_fs_gpu.cpp b/src/GPU/pair_eam_fs_gpu.cpp
index c29b49631ce210121df7479b3fc60867bca31438..51681d563bc94894015219bb7d3dd5a69fbc436a 100644
--- a/src/GPU/pair_eam_fs_gpu.cpp
+++ b/src/GPU/pair_eam_fs_gpu.cpp
@@ -15,9 +15,9 @@
Contributing authors: Trung Dac Nguyen (ORNL), W. Michael Brown (ORNL)
------------------------------------------------------------------------- */
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_eam_fs_gpu.h"
#include "atom.h"
#include "force.h"
diff --git a/src/GPU/pair_eam_gpu.cpp b/src/GPU/pair_eam_gpu.cpp
index ea75ff8ca843637285083729e015f637063a3784..e2eb9dacedd2c5d7c95e9cbe029b4bb14dc4bc74 100644
--- a/src/GPU/pair_eam_gpu.cpp
+++ b/src/GPU/pair_eam_gpu.cpp
@@ -15,10 +15,10 @@
Contributing authors: Trung Dac Nguyen (ORNL), W. Michael Brown (ORNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_eam_gpu.h"
#include "atom.h"
#include "force.h"
diff --git a/src/GPU/pair_eam_gpu.h b/src/GPU/pair_eam_gpu.h
index 2c4731d9cf105b93a118756c4b62ee9062391b03..099529f3df90c766d0385dcb0319294b6f28c4b4 100644
--- a/src/GPU/pair_eam_gpu.h
+++ b/src/GPU/pair_eam_gpu.h
@@ -20,7 +20,7 @@ PairStyle(eam/gpu,PairEAMGPU)
#ifndef LMP_PAIR_EAM_GPU_H
#define LMP_PAIR_EAM_GPU_H
-#include <stdio.h>
+#include <cstdio>
#include "pair_eam.h"
namespace LAMMPS_NS {
diff --git a/src/GPU/pair_gauss_gpu.cpp b/src/GPU/pair_gauss_gpu.cpp
index 01cc63a9f9a49c378b7318cb36b9b6143269d853..f99a10a6809e5abbce5504dc2705650a3347ec7e 100644
--- a/src/GPU/pair_gauss_gpu.cpp
+++ b/src/GPU/pair_gauss_gpu.cpp
@@ -15,9 +15,10 @@
Contributing author: Trung Dac Nguyen (ORNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_gauss_gpu.h"
#include "atom.h"
#include "atom_vec.h"
@@ -32,7 +33,6 @@
#include "universe.h"
#include "update.h"
#include "domain.h"
-#include <string.h>
#include "gpu_extra.h"
using namespace LAMMPS_NS;
diff --git a/src/GPU/pair_gayberne_gpu.cpp b/src/GPU/pair_gayberne_gpu.cpp
index aae8fb2b7118e593edcf495e52229bfbfe5e4f8b..8bd5eb073fd6f18e9f6f4b4b7ce67539bf38fd53 100644
--- a/src/GPU/pair_gayberne_gpu.cpp
+++ b/src/GPU/pair_gayberne_gpu.cpp
@@ -15,9 +15,10 @@
Contributing author: Mike Brown (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_gayberne_gpu.h"
#include "math_extra.h"
#include "atom.h"
@@ -34,7 +35,6 @@
#include "universe.h"
#include "domain.h"
#include "update.h"
-#include <string.h>
#include "gpu_extra.h"
using namespace LAMMPS_NS;
diff --git a/src/GPU/pair_lj96_cut_gpu.cpp b/src/GPU/pair_lj96_cut_gpu.cpp
index 813daa4da24f33c4cf535146cd03a3d941fa866b..800f13ef60f3157eb55b08269f321abecce7228d 100644
--- a/src/GPU/pair_lj96_cut_gpu.cpp
+++ b/src/GPU/pair_lj96_cut_gpu.cpp
@@ -15,9 +15,10 @@
Contributing author: Mike Brown (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_lj96_cut_gpu.h"
#include "atom.h"
#include "atom_vec.h"
@@ -32,7 +33,6 @@
#include "universe.h"
#include "update.h"
#include "domain.h"
-#include <string.h>
#include "gpu_extra.h"
using namespace LAMMPS_NS;
diff --git a/src/GPU/pair_lj_charmm_coul_long_gpu.cpp b/src/GPU/pair_lj_charmm_coul_long_gpu.cpp
index b951567f45db68eb2a1699dfc4696bfcd6463e52..8c806053d4f2fb71a34047d1277c9bbd5956ec4b 100644
--- a/src/GPU/pair_lj_charmm_coul_long_gpu.cpp
+++ b/src/GPU/pair_lj_charmm_coul_long_gpu.cpp
@@ -15,9 +15,10 @@
Contributing author: Mike Brown (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_lj_charmm_coul_long_gpu.h"
#include "atom.h"
#include "atom_vec.h"
@@ -32,7 +33,6 @@
#include "universe.h"
#include "update.h"
#include "domain.h"
-#include <string.h>
#include "kspace.h"
#include "gpu_extra.h"
diff --git a/src/GPU/pair_lj_class2_coul_long_gpu.cpp b/src/GPU/pair_lj_class2_coul_long_gpu.cpp
index f7c874cb65e7ed50aa385be7da882e906acde79c..214ff306db0d8ac22903357f2bf20ac324963d6a 100644
--- a/src/GPU/pair_lj_class2_coul_long_gpu.cpp
+++ b/src/GPU/pair_lj_class2_coul_long_gpu.cpp
@@ -15,9 +15,10 @@
Contributing author: Mike Brown (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_lj_class2_coul_long_gpu.h"
#include "atom.h"
#include "atom_vec.h"
@@ -32,7 +33,6 @@
#include "universe.h"
#include "update.h"
#include "domain.h"
-#include <string.h>
#include "kspace.h"
#include "gpu_extra.h"
diff --git a/src/GPU/pair_lj_class2_gpu.cpp b/src/GPU/pair_lj_class2_gpu.cpp
index cc6866db1ca7a07bb79e05e1a5396db7211c5d97..61b0a8caf134695d96be363a4e90ed93396bfc5e 100644
--- a/src/GPU/pair_lj_class2_gpu.cpp
+++ b/src/GPU/pair_lj_class2_gpu.cpp
@@ -15,9 +15,10 @@
Contributing author: Mike Brown (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_lj_class2_gpu.h"
#include "atom.h"
#include "atom_vec.h"
@@ -32,7 +33,6 @@
#include "universe.h"
#include "update.h"
#include "domain.h"
-#include <string.h>
#include "gpu_extra.h"
using namespace LAMMPS_NS;
diff --git a/src/GPU/pair_lj_cubic_gpu.cpp b/src/GPU/pair_lj_cubic_gpu.cpp
index 516ac7d15432abfd7f3cd5d4fcb4bd774beb5153..366c33191b4f249afde0e133356783b3bac5d991 100644
--- a/src/GPU/pair_lj_cubic_gpu.cpp
+++ b/src/GPU/pair_lj_cubic_gpu.cpp
@@ -15,9 +15,10 @@
Contributing author: Trung Dac Nguyen (ndactrung@gmail.com)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_lj_cubic_gpu.h"
#include "atom.h"
#include "atom_vec.h"
@@ -32,7 +33,6 @@
#include "universe.h"
#include "update.h"
#include "domain.h"
-#include <string.h>
#include "gpu_extra.h"
using namespace LAMMPS_NS;
diff --git a/src/GPU/pair_lj_cut_coul_cut_gpu.cpp b/src/GPU/pair_lj_cut_coul_cut_gpu.cpp
index 840c07680f44a450a7beb240a1ec50223f64dfe2..baafcd2d62f936b8bc370ba96e99f8b1fd7ce4a3 100644
--- a/src/GPU/pair_lj_cut_coul_cut_gpu.cpp
+++ b/src/GPU/pair_lj_cut_coul_cut_gpu.cpp
@@ -15,9 +15,10 @@
Contributing author: Mike Brown (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_lj_cut_coul_cut_gpu.h"
#include "atom.h"
#include "atom_vec.h"
@@ -32,7 +33,6 @@
#include "universe.h"
#include "update.h"
#include "domain.h"
-#include <string.h>
#include "gpu_extra.h"
using namespace LAMMPS_NS;
diff --git a/src/GPU/pair_lj_cut_coul_debye_gpu.cpp b/src/GPU/pair_lj_cut_coul_debye_gpu.cpp
index 39108d8558f1bd5dca8549e1c7de5c979fc1ebd6..662375da2c6c6dc77872518f4a623e47133d2ec9 100644
--- a/src/GPU/pair_lj_cut_coul_debye_gpu.cpp
+++ b/src/GPU/pair_lj_cut_coul_debye_gpu.cpp
@@ -15,9 +15,10 @@
Contributing author: Trung Dac Nguyen (ORNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_lj_cut_coul_debye_gpu.h"
#include "atom.h"
#include "atom_vec.h"
@@ -32,7 +33,6 @@
#include "universe.h"
#include "update.h"
#include "domain.h"
-#include <string.h>
#include "gpu_extra.h"
using namespace LAMMPS_NS;
diff --git a/src/GPU/pair_lj_cut_coul_dsf_gpu.cpp b/src/GPU/pair_lj_cut_coul_dsf_gpu.cpp
index efca1a2c511d0ea45f521d2975a7337e603e7ec6..c8e68140a1a520c8efd3fe6b371d5833756faa04 100644
--- a/src/GPU/pair_lj_cut_coul_dsf_gpu.cpp
+++ b/src/GPU/pair_lj_cut_coul_dsf_gpu.cpp
@@ -15,9 +15,10 @@
Contributing author: Mike Brown (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_lj_cut_coul_dsf_gpu.h"
#include "atom.h"
#include "atom_vec.h"
@@ -32,7 +33,6 @@
#include "universe.h"
#include "update.h"
#include "domain.h"
-#include <string.h>
#include "gpu_extra.h"
#define MY_PIS 1.77245385090551602729
diff --git a/src/GPU/pair_lj_cut_coul_long_gpu.cpp b/src/GPU/pair_lj_cut_coul_long_gpu.cpp
index 0c09cb1d51a39beb952f85c4a29950d077df56f6..3cccb898cc4d57e6c5b565ca47f6dcdd77e4486a 100644
--- a/src/GPU/pair_lj_cut_coul_long_gpu.cpp
+++ b/src/GPU/pair_lj_cut_coul_long_gpu.cpp
@@ -15,9 +15,10 @@
Contributing author: Mike Brown (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_lj_cut_coul_long_gpu.h"
#include "atom.h"
#include "atom_vec.h"
@@ -32,7 +33,6 @@
#include "universe.h"
#include "update.h"
#include "domain.h"
-#include <string.h>
#include "kspace.h"
#include "gpu_extra.h"
diff --git a/src/GPU/pair_lj_cut_coul_msm_gpu.cpp b/src/GPU/pair_lj_cut_coul_msm_gpu.cpp
index 7d8be01e814398c630b4564ae44c79d0d469812a..04ffe245b24756dba88990345c625fa09b23b2f3 100644
--- a/src/GPU/pair_lj_cut_coul_msm_gpu.cpp
+++ b/src/GPU/pair_lj_cut_coul_msm_gpu.cpp
@@ -15,9 +15,10 @@
Contributing author: Trung Dac Nguyen (ORNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_lj_cut_coul_msm_gpu.h"
#include "atom.h"
#include "atom_vec.h"
@@ -33,7 +34,6 @@
#include "update.h"
#include "domain.h"
#include "kspace.h"
-#include <string.h>
#include "gpu_extra.h"
using namespace LAMMPS_NS;
diff --git a/src/GPU/pair_lj_cut_dipole_cut_gpu.cpp b/src/GPU/pair_lj_cut_dipole_cut_gpu.cpp
index 3b5f0c12830543ffa77f8914d063b92d4aa55ab9..1f4528cb88e4a73864553ed57506960595f8697d 100644
--- a/src/GPU/pair_lj_cut_dipole_cut_gpu.cpp
+++ b/src/GPU/pair_lj_cut_dipole_cut_gpu.cpp
@@ -15,9 +15,10 @@
Contributing author: Trung Dac Nguyen (ORNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_lj_cut_dipole_cut_gpu.h"
#include "atom.h"
#include "atom_vec.h"
@@ -32,7 +33,6 @@
#include "universe.h"
#include "update.h"
#include "domain.h"
-#include <string.h>
#include "gpu_extra.h"
using namespace LAMMPS_NS;
diff --git a/src/GPU/pair_lj_cut_gpu.cpp b/src/GPU/pair_lj_cut_gpu.cpp
index feba9ed88bb20a81e7ff3b016c36b636d8c4b388..af654bcc5dd0b09c90b0ac126b534d0f76d83aad 100644
--- a/src/GPU/pair_lj_cut_gpu.cpp
+++ b/src/GPU/pair_lj_cut_gpu.cpp
@@ -15,9 +15,10 @@
Contributing author: Mike Brown (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_lj_cut_gpu.h"
#include "atom.h"
#include "atom_vec.h"
@@ -32,7 +33,6 @@
#include "universe.h"
#include "update.h"
#include "domain.h"
-#include <string.h>
#include "gpu_extra.h"
using namespace LAMMPS_NS;
diff --git a/src/GPU/pair_lj_expand_gpu.cpp b/src/GPU/pair_lj_expand_gpu.cpp
index 43ec1ec45a0dc2ba63ba8b2b49d5755aaf711bcc..f0a9f67b10f3d1b4ee85163f66781871d24b96c3 100644
--- a/src/GPU/pair_lj_expand_gpu.cpp
+++ b/src/GPU/pair_lj_expand_gpu.cpp
@@ -15,9 +15,10 @@
Contributing author: Inderaj Bains (NVIDIA), ibains@nvidia.com
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_lj_expand_gpu.h"
#include "atom.h"
#include "atom_vec.h"
@@ -32,7 +33,6 @@
#include "universe.h"
#include "update.h"
#include "domain.h"
-#include <string.h>
#include "gpu_extra.h"
using namespace LAMMPS_NS;
diff --git a/src/GPU/pair_lj_gromacs_gpu.cpp b/src/GPU/pair_lj_gromacs_gpu.cpp
index d749eacba3301f07c8589d8968f586e625364e45..f2006798291751e5188406ec16e8e3f071844eac 100644
--- a/src/GPU/pair_lj_gromacs_gpu.cpp
+++ b/src/GPU/pair_lj_gromacs_gpu.cpp
@@ -15,9 +15,10 @@
Contributing author: Trung Dac Nguyen (ORNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_lj_gromacs_gpu.h"
#include "atom.h"
#include "atom_vec.h"
@@ -32,7 +33,6 @@
#include "universe.h"
#include "update.h"
#include "domain.h"
-#include <string.h>
#include "kspace.h"
#include "gpu_extra.h"
diff --git a/src/GPU/pair_lj_sdk_coul_long_gpu.cpp b/src/GPU/pair_lj_sdk_coul_long_gpu.cpp
index 77c0dc06601887f0d3451c9c3cd49480bb11e218..4dbd8874d65751c50da0398776f96389d7043860 100644
--- a/src/GPU/pair_lj_sdk_coul_long_gpu.cpp
+++ b/src/GPU/pair_lj_sdk_coul_long_gpu.cpp
@@ -15,9 +15,10 @@
Contributing author: Mike Brown (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_lj_sdk_coul_long_gpu.h"
#include "atom.h"
#include "atom_vec.h"
@@ -32,7 +33,6 @@
#include "universe.h"
#include "update.h"
#include "domain.h"
-#include <string.h>
#include "kspace.h"
#include "gpu_extra.h"
diff --git a/src/GPU/pair_lj_sdk_gpu.cpp b/src/GPU/pair_lj_sdk_gpu.cpp
index 67103181d53a852325a7c5ee8411fbb037695f52..84d224a8c4caca209b43828e2f9c8ab6ae4ddd03 100644
--- a/src/GPU/pair_lj_sdk_gpu.cpp
+++ b/src/GPU/pair_lj_sdk_gpu.cpp
@@ -15,9 +15,10 @@
Contributing author: Mike Brown (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_lj_sdk_gpu.h"
#include "atom.h"
#include "atom_vec.h"
@@ -32,7 +33,6 @@
#include "universe.h"
#include "update.h"
#include "domain.h"
-#include <string.h>
#include "gpu_extra.h"
using namespace LAMMPS_NS;
diff --git a/src/GPU/pair_lj_sf_dipole_sf_gpu.cpp b/src/GPU/pair_lj_sf_dipole_sf_gpu.cpp
index 5b22bebf7f357b0de570d8d15c29d821ddbab3a4..a5ebb1dbc1774234aacade666c565889b686f9ff 100644
--- a/src/GPU/pair_lj_sf_dipole_sf_gpu.cpp
+++ b/src/GPU/pair_lj_sf_dipole_sf_gpu.cpp
@@ -15,9 +15,10 @@
Contributing author: Trung Dac Nguyen (ORNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_lj_sf_dipole_sf_gpu.h"
#include "atom.h"
#include "atom_vec.h"
@@ -32,7 +33,6 @@
#include "universe.h"
#include "update.h"
#include "domain.h"
-#include <string.h>
#include "gpu_extra.h"
using namespace LAMMPS_NS;
diff --git a/src/GPU/pair_mie_cut_gpu.cpp b/src/GPU/pair_mie_cut_gpu.cpp
index 4857928a27c3d5b1d7aa23eb797669c341f81528..5919b054668e58b9c5dc497735207a0d4d335855 100644
--- a/src/GPU/pair_mie_cut_gpu.cpp
+++ b/src/GPU/pair_mie_cut_gpu.cpp
@@ -15,9 +15,10 @@
Contributing author: Trung Dac Nguyen (ORNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_mie_cut_gpu.h"
#include "atom.h"
#include "atom_vec.h"
@@ -32,7 +33,6 @@
#include "universe.h"
#include "update.h"
#include "domain.h"
-#include <string.h>
#include "gpu_extra.h"
using namespace LAMMPS_NS;
diff --git a/src/GPU/pair_morse_gpu.cpp b/src/GPU/pair_morse_gpu.cpp
index b72a6afaf4c72fcdf98b0dab1759e8bbe2cf2760..81ea7c818ae9fbfa625d5538e8e2860c14c30f70 100644
--- a/src/GPU/pair_morse_gpu.cpp
+++ b/src/GPU/pair_morse_gpu.cpp
@@ -15,9 +15,10 @@
Contributing author: Mike Brown (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_morse_gpu.h"
#include "atom.h"
#include "atom_vec.h"
@@ -32,7 +33,6 @@
#include "universe.h"
#include "update.h"
#include "domain.h"
-#include <string.h>
#include "gpu_extra.h"
using namespace LAMMPS_NS;
diff --git a/src/GPU/pair_resquared_gpu.cpp b/src/GPU/pair_resquared_gpu.cpp
index d83a63c467115af4b1df7427c5430715b85c98b1..34bd0ec22feb2f03c904330f50a5194ff7157ce2 100644
--- a/src/GPU/pair_resquared_gpu.cpp
+++ b/src/GPU/pair_resquared_gpu.cpp
@@ -15,9 +15,10 @@
Contributing author: Mike Brown (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_resquared_gpu.h"
#include "math_extra.h"
#include "atom.h"
@@ -34,7 +35,6 @@
#include "universe.h"
#include "domain.h"
#include "update.h"
-#include <string.h>
#include "gpu_extra.h"
using namespace LAMMPS_NS;
diff --git a/src/GPU/pair_soft_gpu.cpp b/src/GPU/pair_soft_gpu.cpp
index aa0268025c186100f0c6255e8a9efb336965c7a3..cc0ea7263353de6d62918d7ed3bb35657143a0d9 100644
--- a/src/GPU/pair_soft_gpu.cpp
+++ b/src/GPU/pair_soft_gpu.cpp
@@ -15,9 +15,10 @@
Contributing author: Trung Dac Nguyen (ORNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_soft_gpu.h"
#include "atom.h"
#include "atom_vec.h"
@@ -32,7 +33,6 @@
#include "universe.h"
#include "update.h"
#include "domain.h"
-#include <string.h>
#include "gpu_extra.h"
#include "math_const.h"
diff --git a/src/GPU/pair_sw_gpu.cpp b/src/GPU/pair_sw_gpu.cpp
index d2d21a131a2659d62a9336076e97ade12b318d78..5368bee95904ffd1cf805bfcc5936d4846b028f9 100644
--- a/src/GPU/pair_sw_gpu.cpp
+++ b/src/GPU/pair_sw_gpu.cpp
@@ -15,10 +15,10 @@
Contributing author: Mike Brown (ORNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_sw_gpu.h"
#include "atom.h"
#include "neighbor.h"
diff --git a/src/GPU/pair_table_gpu.cpp b/src/GPU/pair_table_gpu.cpp
index b0a38eb461e1a2826ada524a7ea70aaaf59b9567..c5aef996db4bbee0af580e9348fa1b4b0e69b20c 100644
--- a/src/GPU/pair_table_gpu.cpp
+++ b/src/GPU/pair_table_gpu.cpp
@@ -15,9 +15,10 @@
Contributing authors: Trung Dac Nguyen (ORNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_table_gpu.h"
#include "atom.h"
#include "atom_vec.h"
@@ -32,7 +33,6 @@
#include "universe.h"
#include "update.h"
#include "domain.h"
-#include <string.h>
#include "gpu_extra.h"
#define LOOKUP 0
diff --git a/src/GPU/pair_tersoff_gpu.cpp b/src/GPU/pair_tersoff_gpu.cpp
index 41d8e6b75145390a1e115fe844131393240a6054..535b56163ea2036e326f453cfcac254f139bad0d 100644
--- a/src/GPU/pair_tersoff_gpu.cpp
+++ b/src/GPU/pair_tersoff_gpu.cpp
@@ -15,10 +15,10 @@
Contributing author: Trung Dac Nguyen (ndactrung@gmail.com)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_tersoff_gpu.h"
#include "atom.h"
#include "neighbor.h"
diff --git a/src/GPU/pair_tersoff_mod_gpu.cpp b/src/GPU/pair_tersoff_mod_gpu.cpp
index 25ea2cb99f95f6514da5d721cdae9777ea5912ba..f8b6c50db5620853641d9bce6caad90df3b4f6b2 100644
--- a/src/GPU/pair_tersoff_mod_gpu.cpp
+++ b/src/GPU/pair_tersoff_mod_gpu.cpp
@@ -15,10 +15,10 @@
Contributing author: Trung Dac Nguyen (ndactrung@gmail.com)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_tersoff_mod_gpu.h"
#include "atom.h"
#include "neighbor.h"
diff --git a/src/GPU/pair_tersoff_zbl_gpu.cpp b/src/GPU/pair_tersoff_zbl_gpu.cpp
index b4b679b7d03e5a28722bab02180d8c981b9421aa..b45503d759e47931137e5892352c279d902fa197 100644
--- a/src/GPU/pair_tersoff_zbl_gpu.cpp
+++ b/src/GPU/pair_tersoff_zbl_gpu.cpp
@@ -15,10 +15,10 @@
Contributing author: Trung Dac Nguyen (ndactrung@gmail.com)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_tersoff_zbl_gpu.h"
#include "atom.h"
#include "neighbor.h"
diff --git a/src/GPU/pair_ufm_gpu.cpp b/src/GPU/pair_ufm_gpu.cpp
index ad66c3871fa5a2a03820ce60e344f1c222294655..40e8df33239bfeaeb2db9be4f7b63e416001971d 100644
--- a/src/GPU/pair_ufm_gpu.cpp
+++ b/src/GPU/pair_ufm_gpu.cpp
@@ -17,9 +17,10 @@
Maurice de Koning (Unicamp/Brazil) - dekoning@ifi.unicamp.br
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_ufm_gpu.h"
#include "atom.h"
#include "atom_vec.h"
@@ -34,7 +35,6 @@
#include "universe.h"
#include "update.h"
#include "domain.h"
-#include <string.h>
#include "gpu_extra.h"
using namespace LAMMPS_NS;
diff --git a/src/GPU/pair_vashishta_gpu.cpp b/src/GPU/pair_vashishta_gpu.cpp
index 7d21aaa581763d7da631cebf1dbb42cfbce8f098..00dbac5f1eac4942e9ccc4624047dd138c04dc3e 100644
--- a/src/GPU/pair_vashishta_gpu.cpp
+++ b/src/GPU/pair_vashishta_gpu.cpp
@@ -15,10 +15,10 @@
Contributing author: Anders Hafreager (UiO)
------------------------------------------------------------------------- */
#include <limits>
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_vashishta_gpu.h"
#include "atom.h"
#include "neighbor.h"
diff --git a/src/GPU/pair_yukawa_colloid_gpu.cpp b/src/GPU/pair_yukawa_colloid_gpu.cpp
index 4041bd2ebfb19e53343535e02a5f460f4862f5d7..0332e5f755f491bc34de0645d22994907306d8a3 100644
--- a/src/GPU/pair_yukawa_colloid_gpu.cpp
+++ b/src/GPU/pair_yukawa_colloid_gpu.cpp
@@ -15,9 +15,10 @@
Contributing author: Trung Dac Nguyen (ORNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_yukawa_colloid_gpu.h"
#include "atom.h"
#include "atom_vec.h"
@@ -32,7 +33,6 @@
#include "universe.h"
#include "update.h"
#include "domain.h"
-#include <string.h>
#include "gpu_extra.h"
using namespace LAMMPS_NS;
diff --git a/src/GPU/pair_yukawa_gpu.cpp b/src/GPU/pair_yukawa_gpu.cpp
index fcb0ae56bcc6376e62b77d9f80b1137ac4f5dd19..dda4250f0702ca71daba67519ad5dd22fcb3dec4 100644
--- a/src/GPU/pair_yukawa_gpu.cpp
+++ b/src/GPU/pair_yukawa_gpu.cpp
@@ -15,9 +15,10 @@
Contributing author: Trung Dac Nguyen (ORNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_yukawa_gpu.h"
#include "atom.h"
#include "atom_vec.h"
@@ -32,7 +33,6 @@
#include "universe.h"
#include "update.h"
#include "domain.h"
-#include <string.h>
#include "gpu_extra.h"
using namespace LAMMPS_NS;
diff --git a/src/GPU/pair_zbl_gpu.cpp b/src/GPU/pair_zbl_gpu.cpp
index f1f6bdd44bcdb2e8ad12a03ca21c5c3fe273de48..daca79c8e3454d812cf684365bd18db79b22387e 100644
--- a/src/GPU/pair_zbl_gpu.cpp
+++ b/src/GPU/pair_zbl_gpu.cpp
@@ -16,9 +16,10 @@
------------------------------------------------------------------------- */
#include "lmptype.h"
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_zbl_gpu.h"
#include "atom.h"
#include "atom_vec.h"
@@ -33,7 +34,6 @@
#include "universe.h"
#include "update.h"
#include "domain.h"
-#include <string.h>
#include "gpu_extra.h"
using namespace LAMMPS_NS;
diff --git a/src/GPU/pppm_gpu.cpp b/src/GPU/pppm_gpu.cpp
index b2b529f7ef1183494439c23c0c932ee11105bd2e..1f7c4239f8d5fff7793663440d460d536493d3bd 100644
--- a/src/GPU/pppm_gpu.cpp
+++ b/src/GPU/pppm_gpu.cpp
@@ -16,10 +16,10 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <string.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <math.h>
+#include <cstring>
+#include <cstdio>
+#include <cstdlib>
+#include <cmath>
#include "pppm_gpu.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/GRANULAR/fix_freeze.cpp b/src/GRANULAR/fix_freeze.cpp
index 3cfee675b26ec51f07d01f6e2a87f86f499a70ea..0f581be01c4718b52e6fa9b686329c2c26fc34b4 100644
--- a/src/GRANULAR/fix_freeze.cpp
+++ b/src/GRANULAR/fix_freeze.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "fix_freeze.h"
#include "atom.h"
#include "update.h"
diff --git a/src/GRANULAR/fix_pour.cpp b/src/GRANULAR/fix_pour.cpp
index c4e03a24a97609d6dffd22e43a72f3aea8b5b0f9..318c54c99a8844bea5f3f86d92c9ebd67f23abd3 100644
--- a/src/GRANULAR/fix_pour.cpp
+++ b/src/GRANULAR/fix_pour.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "fix_pour.h"
#include "atom.h"
#include "atom_vec.h"
@@ -39,7 +39,6 @@ using namespace MathConst;
enum{ATOM,MOLECULE};
enum{ONE,RANGE,POLY};
-enum{LAYOUT_UNIFORM,LAYOUT_NONUNIFORM,LAYOUT_TILED}; // several files
#define EPSILON 0.001
#define SMALL 1.0e-10
@@ -609,7 +608,7 @@ void FixPour::pre_exchange()
newcoord[1] >= sublo[1] && newcoord[1] < subhi[1] &&
newcoord[2] >= sublo[2] && newcoord[2] < subhi[2]) flag = 1;
else if (dimension == 3 && newcoord[2] >= domain->boxhi[2]) {
- if (comm->layout != LAYOUT_TILED) {
+ if (comm->layout != Comm::LAYOUT_TILED) {
if (comm->myloc[2] == comm->procgrid[2]-1 &&
newcoord[0] >= sublo[0] && newcoord[0] < subhi[0] &&
newcoord[1] >= sublo[1] && newcoord[1] < subhi[1]) flag = 1;
@@ -619,7 +618,7 @@ void FixPour::pre_exchange()
newcoord[1] >= sublo[1] && newcoord[1] < subhi[1]) flag = 1;
}
} else if (dimension == 2 && newcoord[1] >= domain->boxhi[1]) {
- if (comm->layout != LAYOUT_TILED) {
+ if (comm->layout != Comm::LAYOUT_TILED) {
if (comm->myloc[1] == comm->procgrid[1]-1 &&
newcoord[0] >= sublo[0] && newcoord[0] < subhi[0]) flag = 1;
} else {
diff --git a/src/GRANULAR/fix_wall_gran.cpp b/src/GRANULAR/fix_wall_gran.cpp
index 033c35dbacc0e96bb910cd1c3e6b2fa261eb815a..368ff99fb75929303f85b7a2bf8ffaaacc3a37ed 100644
--- a/src/GRANULAR/fix_wall_gran.cpp
+++ b/src/GRANULAR/fix_wall_gran.cpp
@@ -16,9 +16,9 @@
Dan Bolintineanu (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "fix_wall_gran.h"
#include "atom.h"
#include "domain.h"
diff --git a/src/GRANULAR/fix_wall_gran_region.cpp b/src/GRANULAR/fix_wall_gran_region.cpp
index d1c5d4c9c771f8a73bd0d95165ee362976f50509..12fa25714ccbbf8447cbda043ee8ba00d0d66c14 100644
--- a/src/GRANULAR/fix_wall_gran_region.cpp
+++ b/src/GRANULAR/fix_wall_gran_region.cpp
@@ -15,9 +15,9 @@
Contributing authors: Dan Bolintineanu (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "fix_wall_gran_region.h"
#include "region.h"
#include "atom.h"
diff --git a/src/GRANULAR/pair_gran_hertz_history.cpp b/src/GRANULAR/pair_gran_hertz_history.cpp
index 9723531625fdf44b81fa727538a394f9f24a157e..9d4f5c1a9b8a703d4dd83600e84186a6f140f5fe 100644
--- a/src/GRANULAR/pair_gran_hertz_history.cpp
+++ b/src/GRANULAR/pair_gran_hertz_history.cpp
@@ -15,10 +15,10 @@
Contributing authors: Leo Silbert (SNL), Gary Grest (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
-#include <stdio.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstdio>
+#include <cstring>
#include "pair_gran_hertz_history.h"
#include "atom.h"
#include "update.h"
diff --git a/src/GRANULAR/pair_gran_hooke.cpp b/src/GRANULAR/pair_gran_hooke.cpp
index 66e1c3dd7a8bc09a2b8649e388fce6ff832b0cdd..4937c2fe8b1142816d20c03f8548b208b594a860 100644
--- a/src/GRANULAR/pair_gran_hooke.cpp
+++ b/src/GRANULAR/pair_gran_hooke.cpp
@@ -15,9 +15,9 @@
Contributing authors: Leo Silbert (SNL), Gary Grest (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstring>
#include "pair_gran_hooke.h"
#include "atom.h"
#include "force.h"
diff --git a/src/GRANULAR/pair_gran_hooke_history.cpp b/src/GRANULAR/pair_gran_hooke_history.cpp
index 4f120150ded77ccfdaf5e839f2b5cc68a39ddfd7..d70c7391e2ba896961640895ce98e07acc6a0cd5 100644
--- a/src/GRANULAR/pair_gran_hooke_history.cpp
+++ b/src/GRANULAR/pair_gran_hooke_history.cpp
@@ -15,10 +15,10 @@
Contributing authors: Leo Silbert (SNL), Gary Grest (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_gran_hooke_history.h"
#include "atom.h"
#include "atom_vec.h"
diff --git a/src/Install.sh b/src/Install.sh
old mode 100644
new mode 100755
diff --git a/src/KIM/Install.sh b/src/KIM/Install.sh
old mode 100644
new mode 100755
diff --git a/src/KIM/pair_kim.cpp b/src/KIM/pair_kim.cpp
index 46e843158abe6649ba751b7480bba01e4ba94ebe..fe638214baabe8205172d78d898bd21ee75096e5 100644
--- a/src/KIM/pair_kim.cpp
+++ b/src/KIM/pair_kim.cpp
@@ -1264,15 +1264,15 @@ void *PairKIM::extract(const char *str, int &dim)
int ier;
int dummyint;
int isIndexed = 0;
- int maxLine = 1024;
+ const int MAXLINE = 1024;
int rank;
int validParam = 0;
int numParams;
- int *speciesIndex = new int[maxLine];
- char *paramStr = new char[maxLine];
+ int *speciesIndex = new int[MAXLINE];
+ char *paramStr = new char[MAXLINE];
char *paramName;
char *indexStr;
- char message[maxLine];
+ char message[MAXLINE];
int offset;
double* paramPtr;
@@ -1354,7 +1354,7 @@ void *PairKIM::extract(const char *str, int &dim)
}
kim_error(__LINE__,"get_rank",kimerror);
- int *shape = new int[maxLine];
+ int *shape = new int[MAXLINE];
dummyint = (*pkim).get_shape(paramName, shape, &kimerror);
if (kimerror == KIM_STATUS_FAIL)
{
diff --git a/src/KOKKOS/Install.sh b/src/KOKKOS/Install.sh
old mode 100644
new mode 100755
diff --git a/src/KOKKOS/angle_charmm_kokkos.cpp b/src/KOKKOS/angle_charmm_kokkos.cpp
index f048738489ea8efd7ce749c5477fdf1a391b3f6f..4a81f4f49436817027af36c6be411749d6a57a75 100644
--- a/src/KOKKOS/angle_charmm_kokkos.cpp
+++ b/src/KOKKOS/angle_charmm_kokkos.cpp
@@ -15,8 +15,8 @@
Contributing author: Stan Moore (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdlib>
#include "angle_charmm_kokkos.h"
#include "atom_kokkos.h"
#include "neighbor_kokkos.h"
diff --git a/src/KOKKOS/angle_class2_kokkos.cpp b/src/KOKKOS/angle_class2_kokkos.cpp
index 670cfa152d44ac7fe3b8e1e121d42354bf1bcd8b..870603791bd657d5d6e7157ae77bdd1002705c79 100644
--- a/src/KOKKOS/angle_class2_kokkos.cpp
+++ b/src/KOKKOS/angle_class2_kokkos.cpp
@@ -15,8 +15,8 @@
Contributing author: Ray Shan (Materials Design)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdlib>
#include "angle_class2_kokkos.h"
#include "atom_kokkos.h"
#include "neighbor_kokkos.h"
diff --git a/src/KOKKOS/angle_harmonic_kokkos.cpp b/src/KOKKOS/angle_harmonic_kokkos.cpp
index dd5a1e26c7c55d135a5e37a0619dace64b49dbb1..d8e5659e1efd9103c512163d9cd3c88868c84238 100644
--- a/src/KOKKOS/angle_harmonic_kokkos.cpp
+++ b/src/KOKKOS/angle_harmonic_kokkos.cpp
@@ -15,8 +15,8 @@
Contributing author: Stan Moore (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdlib>
#include "angle_harmonic_kokkos.h"
#include "atom_kokkos.h"
#include "neighbor_kokkos.h"
diff --git a/src/KOKKOS/atom_vec_angle_kokkos.cpp b/src/KOKKOS/atom_vec_angle_kokkos.cpp
index 8ff6d721a8a7b1fd4a8b06fdd7f534d0720530eb..352fec57fbbbff1c2510cabb0dda4aed7dc5082c 100644
--- a/src/KOKKOS/atom_vec_angle_kokkos.cpp
+++ b/src/KOKKOS/atom_vec_angle_kokkos.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <stdlib.h>
+#include <cstdlib>
#include "atom_vec_angle_kokkos.h"
#include "atom_kokkos.h"
#include "comm_kokkos.h"
diff --git a/src/KOKKOS/atom_vec_atomic_kokkos.cpp b/src/KOKKOS/atom_vec_atomic_kokkos.cpp
index 0b96d8dbadc98f8fcf3559e21464d6102b8af088..6aba49e5f3a5b9689b19ce109c5a2534d44c8fd8 100644
--- a/src/KOKKOS/atom_vec_atomic_kokkos.cpp
+++ b/src/KOKKOS/atom_vec_atomic_kokkos.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <stdlib.h>
+#include <cstdlib>
#include "atom_vec_atomic_kokkos.h"
#include "atom_kokkos.h"
#include "comm_kokkos.h"
diff --git a/src/KOKKOS/atom_vec_bond_kokkos.cpp b/src/KOKKOS/atom_vec_bond_kokkos.cpp
index adad4f767bb1d2e9a55021c32a71c3bb0b450d24..c884d23880504c533d7b9d545898a6a319c93149 100644
--- a/src/KOKKOS/atom_vec_bond_kokkos.cpp
+++ b/src/KOKKOS/atom_vec_bond_kokkos.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <stdlib.h>
+#include <cstdlib>
#include "atom_vec_bond_kokkos.h"
#include "atom_kokkos.h"
#include "comm_kokkos.h"
diff --git a/src/KOKKOS/atom_vec_charge_kokkos.cpp b/src/KOKKOS/atom_vec_charge_kokkos.cpp
index 3e50870c8f9db9a399355ef60724d6ac85f41ee2..11e46d1274165b4b58e509deb545dfc7848bf42a 100644
--- a/src/KOKKOS/atom_vec_charge_kokkos.cpp
+++ b/src/KOKKOS/atom_vec_charge_kokkos.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <stdlib.h>
+#include <cstdlib>
#include "atom_vec_charge_kokkos.h"
#include "atom_kokkos.h"
#include "comm_kokkos.h"
diff --git a/src/KOKKOS/atom_vec_dpd_kokkos.cpp b/src/KOKKOS/atom_vec_dpd_kokkos.cpp
index 06ca2083dce28372a6d9a05235ef224766420208..24b23c6ccf667f076c5fe6e51157a7fc4a555dc4 100644
--- a/src/KOKKOS/atom_vec_dpd_kokkos.cpp
+++ b/src/KOKKOS/atom_vec_dpd_kokkos.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <stdlib.h>
+#include <cstdlib>
#include "atom_vec_dpd_kokkos.h"
#include "atom_kokkos.h"
#include "comm_kokkos.h"
@@ -158,6 +158,7 @@ void AtomVecDPDKokkos::copy(int i, int j, int delflag)
{
sync(Host,X_MASK | V_MASK | TAG_MASK | TYPE_MASK |
MASK_MASK | IMAGE_MASK | DPDTHETA_MASK |
+ UCG_MASK | UCGNEW_MASK |
UCOND_MASK | UMECH_MASK | UCHEM_MASK | DVECTOR_MASK);
h_tag[j] = h_tag[i];
@@ -183,6 +184,7 @@ void AtomVecDPDKokkos::copy(int i, int j, int delflag)
modified(Host,X_MASK | V_MASK | TAG_MASK | TYPE_MASK |
MASK_MASK | IMAGE_MASK | DPDTHETA_MASK |
+ UCG_MASK | UCGNEW_MASK |
UCOND_MASK | UMECH_MASK | UCHEM_MASK | DVECTOR_MASK);
}
@@ -1029,7 +1031,7 @@ int AtomVecDPDKokkos::pack_comm_hybrid(int n, int *list, double *buf)
int i,j,m;
sync(Host,DPDTHETA_MASK | UCOND_MASK |
- UMECH_MASK | UCHEM_MASK | UCG_MASK | UCGNEW_MASK);
+ UMECH_MASK | UCHEM_MASK);
m = 0;
for (i = 0; i < n; i++) {
@@ -1234,7 +1236,7 @@ int AtomVecDPDKokkos::unpack_comm_hybrid(int n, int first, double *buf)
}
modified(Host,DPDTHETA_MASK | UCOND_MASK |
- UMECH_MASK | UCHEM_MASK | UCG_MASK | UCGNEW_MASK);
+ UMECH_MASK | UCHEM_MASK );
return m;
}
@@ -1645,6 +1647,8 @@ int AtomVecDPDKokkos::unpack_restart(double *buf)
h_uCond[nlocal] = buf[m++];
h_uMech[nlocal] = buf[m++];
h_uChem[nlocal] = buf[m++];
+ h_uCG[nlocal] = 0.0;
+ h_uCGnew[nlocal] = 0.0;
double **extra = atom->extra;
if (atom->nextra_store) {
@@ -1654,6 +1658,7 @@ int AtomVecDPDKokkos::unpack_restart(double *buf)
modified(Host,X_MASK | V_MASK | TAG_MASK | TYPE_MASK |
MASK_MASK | IMAGE_MASK | DPDTHETA_MASK |
+ UCG_MASK | UCGNEW_MASK |
UCOND_MASK | UMECH_MASK | UCHEM_MASK | DVECTOR_MASK);
atom->nlocal++;
diff --git a/src/KOKKOS/atom_vec_full_kokkos.cpp b/src/KOKKOS/atom_vec_full_kokkos.cpp
index 6492a264ac153d330c2d1670b67c790c7b163aa6..a6ae1e0cccebd8e87b9af5213e1583756c48347a 100644
--- a/src/KOKKOS/atom_vec_full_kokkos.cpp
+++ b/src/KOKKOS/atom_vec_full_kokkos.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <stdlib.h>
+#include <cstdlib>
#include "atom_vec_full_kokkos.h"
#include "atom_kokkos.h"
#include "comm_kokkos.h"
diff --git a/src/KOKKOS/atom_vec_hybrid_kokkos.cpp b/src/KOKKOS/atom_vec_hybrid_kokkos.cpp
index 67dce07b80d79323c0a822e64fcdc9847cb5bcac..7e1cc200d36bec7d4c9571fb403ca8f4dbd0c242 100644
--- a/src/KOKKOS/atom_vec_hybrid_kokkos.cpp
+++ b/src/KOKKOS/atom_vec_hybrid_kokkos.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <stdlib.h>
-#include <string.h>
+#include <cstdlib>
+#include <cstring>
#include "atom_vec_hybrid_kokkos.h"
#include "atom_kokkos.h"
#include "domain.h"
diff --git a/src/KOKKOS/atom_vec_hybrid_kokkos.h b/src/KOKKOS/atom_vec_hybrid_kokkos.h
index 988de7fa2124e452d8db4bafae5a3db3c6457317..1bbbd26319af9da9a7c90de4600d78fefe63f6c6 100644
--- a/src/KOKKOS/atom_vec_hybrid_kokkos.h
+++ b/src/KOKKOS/atom_vec_hybrid_kokkos.h
@@ -20,7 +20,7 @@ AtomStyle(hybrid/kk,AtomVecHybridKokkos)
#ifndef LMP_ATOM_VEC_HYBRID_KOKKOS_H
#define LMP_ATOM_VEC_HYBRID_KOKKOS_H
-#include <stdio.h>
+#include <cstdio>
#include "atom_vec_kokkos.h"
#include "kokkos_type.h"
diff --git a/src/KOKKOS/atom_vec_molecular_kokkos.cpp b/src/KOKKOS/atom_vec_molecular_kokkos.cpp
index 1a0c03cca5631ce58a86321757d5610323319336..9537320976298f4bf2a17cc0bd3bb6e93b703a76 100644
--- a/src/KOKKOS/atom_vec_molecular_kokkos.cpp
+++ b/src/KOKKOS/atom_vec_molecular_kokkos.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <stdlib.h>
+#include <cstdlib>
#include "atom_vec_molecular_kokkos.h"
#include "atom_kokkos.h"
#include "comm_kokkos.h"
diff --git a/src/KOKKOS/bond_class2_kokkos.cpp b/src/KOKKOS/bond_class2_kokkos.cpp
index 80f2a6dfbbe8b6e423d0b5fd7174f53f7eeb2da1..f5af93a22aaa666ae8ac03ec4c09d3f3a6530d92 100644
--- a/src/KOKKOS/bond_class2_kokkos.cpp
+++ b/src/KOKKOS/bond_class2_kokkos.cpp
@@ -15,8 +15,8 @@
Contributing author: Ray Shan (Materials Design)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdlib>
#include "bond_class2_kokkos.h"
#include "atom_kokkos.h"
#include "neighbor_kokkos.h"
diff --git a/src/KOKKOS/bond_fene_kokkos.cpp b/src/KOKKOS/bond_fene_kokkos.cpp
index 20c20542083b35c289d8efdab2f3dce5adc95077..30faf4cee03589161158e3bc9a58a09a6ea2d574 100644
--- a/src/KOKKOS/bond_fene_kokkos.cpp
+++ b/src/KOKKOS/bond_fene_kokkos.cpp
@@ -15,8 +15,8 @@
Contributing author: Stan Moore (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdlib>
#include "bond_fene_kokkos.h"
#include "atom_kokkos.h"
#include "neighbor_kokkos.h"
diff --git a/src/KOKKOS/bond_harmonic_kokkos.cpp b/src/KOKKOS/bond_harmonic_kokkos.cpp
index e277104ddb317217dfd5dcddeef9bac584b4dd6f..8aa71b9eb3ec2491ef6c710be6a6763fc776f218 100644
--- a/src/KOKKOS/bond_harmonic_kokkos.cpp
+++ b/src/KOKKOS/bond_harmonic_kokkos.cpp
@@ -15,8 +15,8 @@
Contributing author: Stan Moore (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdlib>
#include "bond_harmonic_kokkos.h"
#include "atom_kokkos.h"
#include "neighbor_kokkos.h"
diff --git a/src/KOKKOS/comm_kokkos.cpp b/src/KOKKOS/comm_kokkos.cpp
index d24fa8a536d56cbb550d5b7e547b32aef57bef0b..96d1c64d0d1aa389caca8c7ef8a635dd406fc2e9 100644
--- a/src/KOKKOS/comm_kokkos.cpp
+++ b/src/KOKKOS/comm_kokkos.cpp
@@ -36,8 +36,6 @@ using namespace LAMMPS_NS;
#define BUFMIN 10000
#define BUFEXTRA 1000
-enum{SINGLE,MULTI};
-
/* ----------------------------------------------------------------------
setup MPI and allocate buffer space
------------------------------------------------------------------------- */
@@ -709,7 +707,7 @@ void CommKokkos::borders()
if (!exchange_comm_classic) {
static int print = 1;
- if (style != SINGLE || bordergroup || ghost_velocity) {
+ if (style != Comm::SINGLE || bordergroup || ghost_velocity) {
if (print && comm->me==0) {
error->warning(FLERR,"Required border comm not yet implemented in Kokkos communication, "
"switching to classic communication");
@@ -817,7 +815,7 @@ void CommKokkos::borders_device() {
// store sent atom indices in list for use in future timesteps
x = atom->x;
- if (style == SINGLE) {
+ if (style == Comm::SINGLE) {
lo = slablo[iswap];
hi = slabhi[iswap];
} else {
@@ -846,7 +844,7 @@ void CommKokkos::borders_device() {
if (sendflag) {
if (!bordergroup || ineed >= 2) {
- if (style == SINGLE) {
+ if (style == Comm::SINGLE) {
k_total_send.h_view() = 0;
k_total_send.template modify<LMPHostType>();
k_total_send.template sync<LMPDeviceType>();
@@ -894,7 +892,7 @@ void CommKokkos::borders_device() {
} else {
error->all(FLERR,"Required border comm not yet "
"implemented with Kokkos");
- if (style == SINGLE) {
+ if (style == Comm::SINGLE) {
ngroup = atom->nfirst;
for (i = 0; i < ngroup; i++)
if (x[i][dim] >= lo && x[i][dim] <= hi) {
@@ -1099,7 +1097,7 @@ void CommKokkos::grow_swap(int n)
{
free_swap();
allocate_swap(n);
- if (style == MULTI) {
+ if (style == Comm::MULTI) {
free_multi();
allocate_multi(n);
}
diff --git a/src/KOKKOS/comm_tiled_kokkos.cpp b/src/KOKKOS/comm_tiled_kokkos.cpp
index 33cd8eaa6e9eabc518a163d1ffbe68bbe0cffc30..81cf1f0563ac799f801a2937afa481227c7d63c4 100644
--- a/src/KOKKOS/comm_tiled_kokkos.cpp
+++ b/src/KOKKOS/comm_tiled_kokkos.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "comm_tiled_kokkos.h"
#include "comm_brick.h"
#include "atom_kokkos.h"
@@ -39,9 +39,6 @@ using namespace LAMMPS_NS;
#define DELTA_PROCS 16
-enum{SINGLE,MULTI}; // same as in Comm
-enum{LAYOUT_UNIFORM,LAYOUT_NONUNIFORM,LAYOUT_TILED}; // several files
-
/* ---------------------------------------------------------------------- */
CommTiledKokkos::CommTiledKokkos(LAMMPS *lmp) : CommTiled(lmp)
diff --git a/src/KOKKOS/compute_temp_kokkos.cpp b/src/KOKKOS/compute_temp_kokkos.cpp
index 2ea67a1fb135a695a1e37b3c5d3e0de2ae82762e..fec3d89fffa8169e975373c3f20f258af3ee0b47 100644
--- a/src/KOKKOS/compute_temp_kokkos.cpp
+++ b/src/KOKKOS/compute_temp_kokkos.cpp
@@ -12,7 +12,7 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <string.h>
+#include <cstring>
#include "compute_temp_kokkos.h"
#include "atom_kokkos.h"
#include "update.h"
diff --git a/src/KOKKOS/dihedral_charmm_kokkos.cpp b/src/KOKKOS/dihedral_charmm_kokkos.cpp
index 13e3a6d2d1c600d62fd6cbeb56efa0f88b5553c1..41593ffbda6bebe72e4bf7d68bc250760c757d0c 100644
--- a/src/KOKKOS/dihedral_charmm_kokkos.cpp
+++ b/src/KOKKOS/dihedral_charmm_kokkos.cpp
@@ -15,8 +15,8 @@
Contributing author: Stan Moore (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdlib>
#include "dihedral_charmm_kokkos.h"
#include "atom_kokkos.h"
#include "comm.h"
diff --git a/src/KOKKOS/dihedral_class2_kokkos.cpp b/src/KOKKOS/dihedral_class2_kokkos.cpp
index b96e4c99af9893f644459e79b36b0bd87e90f865..f656fcf756ad5611985fb0739ff31136ef681971 100644
--- a/src/KOKKOS/dihedral_class2_kokkos.cpp
+++ b/src/KOKKOS/dihedral_class2_kokkos.cpp
@@ -15,8 +15,8 @@
Contributing author: Ray Shan (Materials Design)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdlib>
#include "dihedral_class2_kokkos.h"
#include "atom_kokkos.h"
#include "comm.h"
diff --git a/src/KOKKOS/dihedral_opls_kokkos.cpp b/src/KOKKOS/dihedral_opls_kokkos.cpp
index 4349aff48df93848f097bd1130c758ec6be91951..62c481fa9c3ee17ac92fbc17ec70fa6c1e833079 100644
--- a/src/KOKKOS/dihedral_opls_kokkos.cpp
+++ b/src/KOKKOS/dihedral_opls_kokkos.cpp
@@ -15,8 +15,8 @@
Contributing author: Stan Moore (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdlib>
#include "dihedral_opls_kokkos.h"
#include "atom_kokkos.h"
#include "comm.h"
diff --git a/src/KOKKOS/fix_deform_kokkos.cpp b/src/KOKKOS/fix_deform_kokkos.cpp
index 52953207340546890af19b6470f91f4b4b4c1f82..7b9336ed3b03822e78cfa91b4e1e920be550a02d 100644
--- a/src/KOKKOS/fix_deform_kokkos.cpp
+++ b/src/KOKKOS/fix_deform_kokkos.cpp
@@ -15,9 +15,9 @@
Contributing author: Pieter in 't Veld (SNL)
------------------------------------------------------------------------- */
-#include <string.h>
-#include <stdlib.h>
-#include <math.h>
+#include <cstring>
+#include <cstdlib>
+#include <cmath>
#include "fix_deform_kokkos.h"
#include "atom_kokkos.h"
#include "update.h"
@@ -41,10 +41,6 @@ using namespace MathConst;
enum{NONE,FINAL,DELTA,SCALE,VEL,ERATE,TRATE,VOLUME,WIGGLE,VARIABLE};
enum{ONE_FROM_ONE,ONE_FROM_TWO,TWO_FROM_ONE};
-// same as domain.cpp, fix_nvt_sllod.cpp, compute_temp_deform.cpp
-
-enum{NO_REMAP,X_REMAP,V_REMAP};
-
/* ---------------------------------------------------------------------- */
FixDeformKokkos::FixDeformKokkos(LAMMPS *lmp, int narg, char **arg) : FixDeform(lmp, narg, arg)
@@ -315,7 +311,7 @@ void FixDeformKokkos::end_of_step()
// convert atoms and rigid bodies to lamda coords
- if (remapflag == X_REMAP) {
+ if (remapflag == Domain::X_REMAP) {
int nlocal = atom->nlocal;
domainKK->x2lamda(nlocal);
@@ -355,7 +351,7 @@ void FixDeformKokkos::end_of_step()
// convert atoms and rigid bodies back to box coords
- if (remapflag == X_REMAP) {
+ if (remapflag == Domain::X_REMAP) {
int nlocal = atom->nlocal;
domainKK->lamda2x(nlocal);
diff --git a/src/KOKKOS/fix_dpd_energy_kokkos.cpp b/src/KOKKOS/fix_dpd_energy_kokkos.cpp
index e6878afed4ba44287e1efecb138b7f7c95272314..b12c6a476e0939d26da6c4d20a37cb56fe072e0c 100644
--- a/src/KOKKOS/fix_dpd_energy_kokkos.cpp
+++ b/src/KOKKOS/fix_dpd_energy_kokkos.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <stdio.h>
-#include <string.h>
+#include <cstdio>
+#include <cstring>
#include "fix_dpd_energy_kokkos.h"
#include "atom_masks.h"
#include "atom_kokkos.h"
diff --git a/src/KOKKOS/fix_eos_table_rx_kokkos.cpp b/src/KOKKOS/fix_eos_table_rx_kokkos.cpp
index fb4ca443a9dac49a9566733a0db474e2022b2fc7..39f612ec46e002fbaaab31ae42221b5b6fdf9e72 100644
--- a/src/KOKKOS/fix_eos_table_rx_kokkos.cpp
+++ b/src/KOKKOS/fix_eos_table_rx_kokkos.cpp
@@ -15,15 +15,15 @@
Contributing author: Stan Moore (Sandia)
------------------------------------------------------------------------- */
-#include <stdlib.h>
-#include <string.h>
+#include <cstdlib>
+#include <cstring>
#include "fix_eos_table_rx_kokkos.h"
#include "atom_kokkos.h"
#include "error.h"
#include "force.h"
#include "memory_kokkos.h"
#include "comm.h"
-#include <math.h>
+#include <cmath>
#include "modify.h"
#include "atom_masks.h"
@@ -387,7 +387,7 @@ void FixEOStableRXKokkos<DeviceType>::temperature_lookup(int id, double ui, doub
// Apply the Secant Method
for(it=0; it<maxit; it++){
if(fabs(f2-f1) < MY_EPSILON){
- if(isnan(f1) || isnan(f2)) k_error_flag.template view<DeviceType>()() = 2;
+ if(std::isnan(f1) || std::isnan(f2)) k_error_flag.template view<DeviceType>()() = 2;
temp = t1;
temp = MAX(temp,lo);
temp = MIN(temp,hi);
@@ -403,7 +403,7 @@ void FixEOStableRXKokkos<DeviceType>::temperature_lookup(int id, double ui, doub
f2 = u2 - ui;
}
if(it==maxit){
- if(isnan(f1) || isnan(f2) || isnan(ui) || isnan(thetai) || isnan(t1) || isnan(t2))
+ if(std::isnan(f1) || std::isnan(f2) || std::isnan(ui) || std::isnan(thetai) || std::isnan(t1) || std::isnan(t2))
k_error_flag.template view<DeviceType>()() = 2;
else
k_error_flag.template view<DeviceType>()() = 3;
diff --git a/src/KOKKOS/fix_langevin_kokkos.cpp b/src/KOKKOS/fix_langevin_kokkos.cpp
index 108c3b692ad7f4fcb176a407a558c5dca3685ca8..24d505e08d46854b3b72660436070ef1f9688a78 100644
--- a/src/KOKKOS/fix_langevin_kokkos.cpp
+++ b/src/KOKKOS/fix_langevin_kokkos.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstring>
#include "fix_langevin_kokkos.h"
#include "atom_masks.h"
#include "atom_kokkos.h"
diff --git a/src/KOKKOS/fix_momentum_kokkos.cpp b/src/KOKKOS/fix_momentum_kokkos.cpp
index 9ffe67a46ba7615efd9255f6a95500bcbe69af6e..9af7e79da88663490c30c31c494f0ca4ef49b86e 100644
--- a/src/KOKKOS/fix_momentum_kokkos.cpp
+++ b/src/KOKKOS/fix_momentum_kokkos.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <stdlib.h>
-#include <string.h>
+#include <cstdlib>
+#include <cstring>
#include "fix_momentum_kokkos.h"
#include "atom_kokkos.h"
#include "atom_masks.h"
diff --git a/src/KOKKOS/fix_nh_kokkos.cpp b/src/KOKKOS/fix_nh_kokkos.cpp
index 345259e35519b24a6b6b669c175fc9e5bdeaf746..679690ea82215c9a389ff9b417c74385a35a163e 100644
--- a/src/KOKKOS/fix_nh_kokkos.cpp
+++ b/src/KOKKOS/fix_nh_kokkos.cpp
@@ -15,9 +15,9 @@
Contributing author: Stan Moore (SNL)
------------------------------------------------------------------------- */
-#include <string.h>
-#include <stdlib.h>
-#include <math.h>
+#include <cstring>
+#include <cstdlib>
+#include <cmath>
#include "fix_nh_kokkos.h"
#include "math_extra.h"
#include "atom.h"
diff --git a/src/KOKKOS/fix_nph_kokkos.cpp b/src/KOKKOS/fix_nph_kokkos.cpp
index 34fc212c0f996adbed0597d479e63bcc929722f1..ed825ad9ee448a156ecf5e91b1fd329c94a79fa5 100644
--- a/src/KOKKOS/fix_nph_kokkos.cpp
+++ b/src/KOKKOS/fix_nph_kokkos.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "fix_nph_kokkos.h"
#include "modify.h"
#include "error.h"
diff --git a/src/KOKKOS/fix_npt_kokkos.cpp b/src/KOKKOS/fix_npt_kokkos.cpp
index c99a322a01679f0667c1de85d51c1d3afacc8ab3..b33e733aee707b8c4f572cc3ae93a14d09fc7eab 100644
--- a/src/KOKKOS/fix_npt_kokkos.cpp
+++ b/src/KOKKOS/fix_npt_kokkos.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "fix_npt_kokkos.h"
#include "modify.h"
#include "error.h"
diff --git a/src/KOKKOS/fix_nve_kokkos.cpp b/src/KOKKOS/fix_nve_kokkos.cpp
index c071447eb7872e72f51055e8ab5232a574f29545..cb3eadcd9009f8e7a4426dae6a2bc0c459592111 100644
--- a/src/KOKKOS/fix_nve_kokkos.cpp
+++ b/src/KOKKOS/fix_nve_kokkos.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <stdio.h>
-#include <string.h>
+#include <cstdio>
+#include <cstring>
#include "fix_nve_kokkos.h"
#include "atom_masks.h"
#include "atom_kokkos.h"
diff --git a/src/KOKKOS/fix_nvt_kokkos.cpp b/src/KOKKOS/fix_nvt_kokkos.cpp
index 9628ff023126b13286d3c5594050bf501c5e322d..8b2d9362745c98812b367b9df82054ac883158bf 100644
--- a/src/KOKKOS/fix_nvt_kokkos.cpp
+++ b/src/KOKKOS/fix_nvt_kokkos.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "fix_nvt_kokkos.h"
#include "group.h"
#include "modify.h"
diff --git a/src/KOKKOS/fix_property_atom_kokkos.cpp b/src/KOKKOS/fix_property_atom_kokkos.cpp
index fb3f5a3f341fbcf4f51ab555c1686a0f7de2d147..12f27f99322aaa863da3b77243715183dd951db6 100644
--- a/src/KOKKOS/fix_property_atom_kokkos.cpp
+++ b/src/KOKKOS/fix_property_atom_kokkos.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <stdlib.h>
-#include <string.h>
+#include <cstdlib>
+#include <cstring>
#include "fix_property_atom_kokkos.h"
#include "atom_kokkos.h"
#include "comm.h"
diff --git a/src/KOKKOS/fix_qeq_reax_kokkos.cpp b/src/KOKKOS/fix_qeq_reax_kokkos.cpp
index ca2525d4f0783f14851fe4c9c69b5fbd57fac32e..52822856ee014cbb5b13b09ef87e3f54186a4a53 100644
--- a/src/KOKKOS/fix_qeq_reax_kokkos.cpp
+++ b/src/KOKKOS/fix_qeq_reax_kokkos.cpp
@@ -15,10 +15,10 @@
Contributing author: Ray Shan (SNL), Stan Moore (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "fix_qeq_reax_kokkos.h"
#include "kokkos.h"
#include "atom.h"
diff --git a/src/KOKKOS/fix_reaxc_bonds_kokkos.cpp b/src/KOKKOS/fix_reaxc_bonds_kokkos.cpp
index 586daadd55e64c3922f52ee16faa454f7b723da5..9aed0b9ae4052490b798aad062c3856b0d225b81 100644
--- a/src/KOKKOS/fix_reaxc_bonds_kokkos.cpp
+++ b/src/KOKKOS/fix_reaxc_bonds_kokkos.cpp
@@ -15,8 +15,8 @@
Contributing author: Stan Moore (Sandia)
------------------------------------------------------------------------- */
-#include <stdlib.h>
-#include <string.h>
+#include <cstdlib>
+#include <cstring>
#include "fix_ave_atom.h"
#include "fix_reaxc_bonds_kokkos.h"
#include "atom.h"
diff --git a/src/KOKKOS/fix_reaxc_species_kokkos.cpp b/src/KOKKOS/fix_reaxc_species_kokkos.cpp
index a676c7ef27ae81cf7ec39e8467e7ecdceb816e06..bd92251960608a2bdfa6cb47c8a3180ae2356cec 100644
--- a/src/KOKKOS/fix_reaxc_species_kokkos.cpp
+++ b/src/KOKKOS/fix_reaxc_species_kokkos.cpp
@@ -15,10 +15,10 @@
Contributing authors: Stan Moore (Sandia)
------------------------------------------------------------------------- */
-#include <stdlib.h>
-#include <math.h>
+#include <cstdlib>
+#include <cmath>
#include "atom.h"
-#include <string.h>
+#include <cstring>
#include "fix_ave_atom.h"
#include "fix_reaxc_species_kokkos.h"
#include "domain.h"
diff --git a/src/KOKKOS/fix_rx_kokkos.cpp b/src/KOKKOS/fix_rx_kokkos.cpp
index 22450e19d948ac53a64837c021bf6c32c879968a..f636f6454d17874737a9e951bb271da0755328b9 100644
--- a/src/KOKKOS/fix_rx_kokkos.cpp
+++ b/src/KOKKOS/fix_rx_kokkos.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <stdio.h>
-#include <string.h>
+#include <cstdio>
+#include <cstring>
#include "fix_rx_kokkos.h"
#include "atom_masks.h"
#include "atom_kokkos.h"
@@ -30,7 +30,7 @@
#include "domain.h"
#include "kokkos.h"
-#include <float.h> // DBL_EPSILON
+#include <cfloat> // DBL_EPSILON
using namespace LAMMPS_NS;
using namespace FixConst;
diff --git a/src/KOKKOS/fix_setforce_kokkos.cpp b/src/KOKKOS/fix_setforce_kokkos.cpp
index e99160989497381ef63985fad512ec3e2d3af664..5150c71249dd7611e006241ba735de2176329ef9 100644
--- a/src/KOKKOS/fix_setforce_kokkos.cpp
+++ b/src/KOKKOS/fix_setforce_kokkos.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
-#include <stdlib.h>
+#include <cstring>
+#include <cstdlib>
#include "fix_setforce_kokkos.h"
#include "atom_kokkos.h"
#include "update.h"
diff --git a/src/KOKKOS/fix_shardlow_kokkos.cpp b/src/KOKKOS/fix_shardlow_kokkos.cpp
index e973e5c99f5d4035207689c297c0ba1bb4f92cd3..70055bf8c9df4fd0f70f32b83e012e9eec0132c9 100644
--- a/src/KOKKOS/fix_shardlow_kokkos.cpp
+++ b/src/KOKKOS/fix_shardlow_kokkos.cpp
@@ -33,9 +33,9 @@
135, 204105.
------------------------------------------------------------------------- */
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "fix_shardlow_kokkos.h"
#include "atom.h"
#include "atom_masks.h"
@@ -44,7 +44,7 @@
#include "update.h"
#include "respa.h"
#include "error.h"
-#include <math.h>
+#include <cmath>
#include "atom_vec.h"
#include "comm.h"
#include "neighbor.h"
diff --git a/src/KOKKOS/fix_shardlow_kokkos.h b/src/KOKKOS/fix_shardlow_kokkos.h
index 4e87de6910d7724a0bc1a736cb15b2b5d56c1049..0469f6033d33ad49d14282a61b9a16f008d55742 100644
--- a/src/KOKKOS/fix_shardlow_kokkos.h
+++ b/src/KOKKOS/fix_shardlow_kokkos.h
@@ -22,7 +22,6 @@ FixStyle(shardlow/kk/host,FixShardlowKokkos<LMPHostType>)
#ifndef LMP_FIX_SHARDLOW_KOKKOS_H
#define LMP_FIX_SHARDLOW_KOKKOS_H
-#include "float.h"
#include "fix_shardlow.h"
#include "kokkos_type.h"
#include "neigh_list_kokkos.h"
diff --git a/src/KOKKOS/fix_wall_lj93_kokkos.cpp b/src/KOKKOS/fix_wall_lj93_kokkos.cpp
index 602922d0ecae3426ba666dadf375ad26fd6adc99..3aaa45f8a8d0237be4cad83bd12d4f0ecfa81b8a 100644
--- a/src/KOKKOS/fix_wall_lj93_kokkos.cpp
+++ b/src/KOKKOS/fix_wall_lj93_kokkos.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "fix_wall_lj93_kokkos.h"
#include "atom_kokkos.h"
#include "error.h"
diff --git a/src/KOKKOS/fix_wall_reflect_kokkos.cpp b/src/KOKKOS/fix_wall_reflect_kokkos.cpp
index cd7a2c59b78ae84c3c0ae58f34c3998705b442d1..2516ac6577000b6f0c0de347b5e5dc60f0868b92 100644
--- a/src/KOKKOS/fix_wall_reflect_kokkos.cpp
+++ b/src/KOKKOS/fix_wall_reflect_kokkos.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <stdlib.h>
-#include <string.h>
+#include <cstdlib>
+#include <cstring>
#include "fix_wall_reflect_kokkos.h"
#include "atom_kokkos.h"
#include "comm.h"
diff --git a/src/KOKKOS/improper_class2_kokkos.cpp b/src/KOKKOS/improper_class2_kokkos.cpp
index 28f57608bbce990793b47b5f66f95d28dbec6ec5..fdb890be5481969c48b885b3f99f0b54d97e4f38 100644
--- a/src/KOKKOS/improper_class2_kokkos.cpp
+++ b/src/KOKKOS/improper_class2_kokkos.cpp
@@ -16,8 +16,8 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <math.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdlib>
#include "improper_class2_kokkos.h"
#include "atom_kokkos.h"
#include "comm.h"
diff --git a/src/KOKKOS/improper_harmonic_kokkos.cpp b/src/KOKKOS/improper_harmonic_kokkos.cpp
index f1a0ac3631c1a862dab0172b4f58dadcfeff8038..9f4e8b9440f52cbfa10262623544ac25bce78c4b 100644
--- a/src/KOKKOS/improper_harmonic_kokkos.cpp
+++ b/src/KOKKOS/improper_harmonic_kokkos.cpp
@@ -16,8 +16,8 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <math.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdlib>
#include "improper_harmonic_kokkos.h"
#include "atom_kokkos.h"
#include "comm.h"
diff --git a/src/KOKKOS/kokkos.cpp b/src/KOKKOS/kokkos.cpp
index 5f81078afdfb97f62404d9574f464afd3c8ab764..3bbff6be7e77c93930b23b1bf937c28c1a2afd04 100644
--- a/src/KOKKOS/kokkos.cpp
+++ b/src/KOKKOS/kokkos.cpp
@@ -11,11 +11,11 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <stdio.h>
-#include <string.h>
-#include <stdlib.h>
-#include <ctype.h>
-#include <signal.h>
+#include <cstdio>
+#include <cstring>
+#include <cstdlib>
+#include <cctype>
+#include <csignal>
#include <unistd.h>
#include "kokkos.h"
#include "lammps.h"
@@ -113,14 +113,15 @@ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
#ifdef KOKKOS_HAVE_CUDA
if (ngpu <= 0)
error->all(FLERR,"Kokkos has been compiled for CUDA but no GPUs are requested");
-
- Kokkos::HostSpace::execution_space::initialize(num_threads,numa);
- Kokkos::Cuda::SelectDevice select_device(device);
- Kokkos::Cuda::initialize(select_device);
-#else
- LMPHostType::initialize(num_threads,numa);
#endif
+ Kokkos::InitArguments args;
+ args.num_threads = num_threads;
+ args.num_numa = numa;
+ args.device_id = device;
+
+ Kokkos::initialize(args);
+
// default settings for package kokkos command
neighflag = FULL;
@@ -144,12 +145,7 @@ KokkosLMP::~KokkosLMP()
{
// finalize Kokkos
-#ifdef KOKKOS_HAVE_CUDA
- Kokkos::Cuda::finalize();
- Kokkos::HostSpace::execution_space::finalize();
-#else
- LMPHostType::finalize();
-#endif
+ Kokkos::finalize();
}
/* ----------------------------------------------------------------------
diff --git a/src/KOKKOS/math_special_kokkos.cpp b/src/KOKKOS/math_special_kokkos.cpp
index a8c35b12b8838ca3a83fe42c646851532523af89..127168ef8bae1bce35a2031fce6077e9d0020e1e 100644
--- a/src/KOKKOS/math_special_kokkos.cpp
+++ b/src/KOKKOS/math_special_kokkos.cpp
@@ -1,6 +1,6 @@
-#include <math.h>
-#include <stdint.h>
+#include <cmath>
+#include <cstdint>
#include "math_special_kokkos.h"
using namespace LAMMPS_NS;
diff --git a/src/KOKKOS/math_special_kokkos.h b/src/KOKKOS/math_special_kokkos.h
index 254b452eab786bc7dcac5255d7f98fec27bc31a7..d10d164bcfbc510cbe17c3f091c9ca1fb8d7b5f1 100644
--- a/src/KOKKOS/math_special_kokkos.h
+++ b/src/KOKKOS/math_special_kokkos.h
@@ -14,7 +14,7 @@
#ifndef LMP_MATH_SPECIAL_KOKKOS_H
#define LMP_MATH_SPECIAL_KOKKOS_H
-#include <math.h>
+#include <cmath>
#include "kokkos_type.h"
namespace LAMMPS_NS {
diff --git a/src/KOKKOS/nbin_kokkos.cpp b/src/KOKKOS/nbin_kokkos.cpp
index 2ca2a83b5ae5a7284ec5c65af956fdcf9fc131c3..c35c34967517291b67407a3f78f81773d7e9fe68 100644
--- a/src/KOKKOS/nbin_kokkos.cpp
+++ b/src/KOKKOS/nbin_kokkos.cpp
@@ -23,8 +23,6 @@
using namespace LAMMPS_NS;
-enum{NSQ,BIN,MULTI}; // also in Neighbor
-
#define SMALL 1.0e-6
#define CUT2BIN_RATIO 100
diff --git a/src/KOKKOS/neigh_bond_kokkos.cpp b/src/KOKKOS/neigh_bond_kokkos.cpp
index 3ecc8b5e516c8243a36a668fcdceb7b434e7145c..615dc94ee2faf6d2c690557909757b9a0525181d 100644
--- a/src/KOKKOS/neigh_bond_kokkos.cpp
+++ b/src/KOKKOS/neigh_bond_kokkos.cpp
@@ -28,7 +28,7 @@
#include "error.h"
#include "modify.h"
#include "fix.h"
-#include <string.h>
+#include <cstring>
#include "atom_masks.h"
#include "domain.h"
@@ -37,8 +37,6 @@ using namespace LAMMPS_NS;
#define BONDDELTA 10000
#define LB_FACTOR 1.5
-enum{IGNORE,WARN,ERROR}; // same as thermo.cpp
-
/* ---------------------------------------------------------------------- */
template<class DeviceType>
@@ -288,7 +286,7 @@ void NeighBondKokkos<DeviceType>::bond_all()
}
} while (h_fail_flag());
- if (nmissing && lostbond == ERROR) {
+ if (nmissing && lostbond == Thermo::ERROR) {
char str[128];
sprintf(str,"Bond atoms missing on proc %d at step " BIGINT_FORMAT,
me,update->ntimestep);
@@ -296,7 +294,7 @@ void NeighBondKokkos<DeviceType>::bond_all()
}
if (neighbor->cluster_check) bond_check();
- if (lostbond == IGNORE) return;
+ if (lostbond == Thermo::IGNORE) return;
int all;
MPI_Allreduce(&nmissing,&all,1,MPI_INT,MPI_SUM,world);
@@ -317,7 +315,7 @@ void NeighBondKokkos<DeviceType>::operator()(TagNeighBondBondAll, const int &i,
int atom1 = map_array(bond_atom(i,m));
if (atom1 == -1) {
nmissing++;
- if (lostbond == ERROR) return;
+ if (lostbond == Thermo::ERROR) return;
continue;
}
atom1 = closest_image(i,atom1);
@@ -383,7 +381,7 @@ void NeighBondKokkos<DeviceType>::bond_partial()
}
} while (h_fail_flag());
- if (nmissing && lostbond == ERROR) {
+ if (nmissing && lostbond == Thermo::ERROR) {
char str[128];
sprintf(str,"Bond atoms missing on proc %d at step " BIGINT_FORMAT,
me,update->ntimestep);
@@ -391,7 +389,7 @@ void NeighBondKokkos<DeviceType>::bond_partial()
}
if (neighbor->cluster_check) bond_check();
- if (lostbond == IGNORE) return;
+ if (lostbond == Thermo::IGNORE) return;
int all;
MPI_Allreduce(&nmissing,&all,1,MPI_INT,MPI_SUM,world);
@@ -413,7 +411,7 @@ void NeighBondKokkos<DeviceType>::operator()(TagNeighBondBondPartial, const int
int atom1 = map_array(bond_atom(i,m));
if (atom1 == -1) {
nmissing++;
- if (lostbond == ERROR) return;
+ if (lostbond == Thermo::ERROR) return;
continue;
}
atom1 = closest_image(i,atom1);
@@ -505,7 +503,7 @@ void NeighBondKokkos<DeviceType>::angle_all()
}
} while (h_fail_flag());
- if (nmissing && lostbond == ERROR) {
+ if (nmissing && lostbond == Thermo::ERROR) {
char str[128];
sprintf(str,"Angle atoms missing on proc %d at step " BIGINT_FORMAT,
me,update->ntimestep);
@@ -513,7 +511,7 @@ void NeighBondKokkos<DeviceType>::angle_all()
}
if (neighbor->cluster_check) angle_check();
- if (lostbond == IGNORE) return;
+ if (lostbond == Thermo::IGNORE) return;
int all;
MPI_Allreduce(&nmissing,&all,1,MPI_INT,MPI_SUM,world);
@@ -536,7 +534,7 @@ void NeighBondKokkos<DeviceType>::operator()(TagNeighBondAngleAll, const int &i,
int atom3 = map_array(angle_atom3(i,m));
if (atom1 == -1 || atom2 == -1 || atom3 == -1) {
nmissing++;
- if (lostbond == ERROR) return;
+ if (lostbond == Thermo::ERROR) return;
continue;
}
atom1 = closest_image(i,atom1);
@@ -607,7 +605,7 @@ void NeighBondKokkos<DeviceType>::angle_partial()
}
} while (h_fail_flag());
- if (nmissing && lostbond == ERROR) {
+ if (nmissing && lostbond == Thermo::ERROR) {
char str[128];
sprintf(str,"Angle atoms missing on proc %d at step " BIGINT_FORMAT,
me,update->ntimestep);
@@ -615,7 +613,7 @@ void NeighBondKokkos<DeviceType>::angle_partial()
}
if (neighbor->cluster_check) angle_check();
- if (lostbond == IGNORE) return;
+ if (lostbond == Thermo::IGNORE) return;
int all;
MPI_Allreduce(&nmissing,&all,1,MPI_INT,MPI_SUM,world);
@@ -639,7 +637,7 @@ void NeighBondKokkos<DeviceType>::operator()(TagNeighBondAnglePartial, const int
int atom3 = map_array(angle_atom3(i,m));
if (atom1 == -1 || atom2 == -1 || atom3 == -1) {
nmissing++;
- if (lostbond == ERROR) return;
+ if (lostbond == Thermo::ERROR) return;
continue;
}
atom1 = closest_image(i,atom1);
@@ -749,7 +747,7 @@ void NeighBondKokkos<DeviceType>::dihedral_all()
}
} while (h_fail_flag());
- if (nmissing && lostbond == ERROR) {
+ if (nmissing && lostbond == Thermo::ERROR) {
char str[128];
sprintf(str,"Dihedral atoms missing on proc %d at step " BIGINT_FORMAT,
me,update->ntimestep);
@@ -757,7 +755,7 @@ void NeighBondKokkos<DeviceType>::dihedral_all()
}
if (neighbor->cluster_check) dihedral_check(neighbor->ndihedrallist,v_dihedrallist);
- if (lostbond == IGNORE) return;
+ if (lostbond == Thermo::IGNORE) return;
int all;
MPI_Allreduce(&nmissing,&all,1,MPI_INT,MPI_SUM,world);
@@ -781,7 +779,7 @@ void NeighBondKokkos<DeviceType>::operator()(TagNeighBondDihedralAll, const int
int atom4 = map_array(dihedral_atom4(i,m));
if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1) {
nmissing++;
- if (lostbond == ERROR) return;
+ if (lostbond == Thermo::ERROR) return;
continue;
}
atom1 = closest_image(i,atom1);
@@ -856,7 +854,7 @@ void NeighBondKokkos<DeviceType>::dihedral_partial()
}
} while (h_fail_flag());
- if (nmissing && lostbond == ERROR) {
+ if (nmissing && lostbond == Thermo::ERROR) {
char str[128];
sprintf(str,"Dihedral atoms missing on proc %d at step " BIGINT_FORMAT,
me,update->ntimestep);
@@ -864,7 +862,7 @@ void NeighBondKokkos<DeviceType>::dihedral_partial()
}
if (neighbor->cluster_check) dihedral_check(neighbor->ndihedrallist,v_dihedrallist);
- if (lostbond == IGNORE) return;
+ if (lostbond == Thermo::IGNORE) return;
int all;
MPI_Allreduce(&nmissing,&all,1,MPI_INT,MPI_SUM,world);
@@ -889,7 +887,7 @@ void NeighBondKokkos<DeviceType>::operator()(TagNeighBondDihedralPartial, const
int atom4 = map_array(dihedral_atom4(i,m));
if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1) {
nmissing++;
- if (lostbond == ERROR) return;
+ if (lostbond == Thermo::ERROR) return;
continue;
}
atom1 = closest_image(i,atom1);
@@ -1020,7 +1018,7 @@ void NeighBondKokkos<DeviceType>::improper_all()
}
} while (h_fail_flag());
- if (nmissing && lostbond == ERROR) {
+ if (nmissing && lostbond == Thermo::ERROR) {
char str[128];
sprintf(str,"Improper atoms missing on proc %d at step " BIGINT_FORMAT,
me,update->ntimestep);
@@ -1028,7 +1026,7 @@ void NeighBondKokkos<DeviceType>::improper_all()
}
if (neighbor->cluster_check) dihedral_check(neighbor->nimproperlist,v_improperlist);
- if (lostbond == IGNORE) return;
+ if (lostbond == Thermo::IGNORE) return;
int all;
MPI_Allreduce(&nmissing,&all,1,MPI_INT,MPI_SUM,world);
@@ -1052,7 +1050,7 @@ void NeighBondKokkos<DeviceType>::operator()(TagNeighBondImproperAll, const int
int atom4 = map_array(improper_atom4(i,m));
if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1) {
nmissing++;
- if (lostbond == ERROR) return;
+ if (lostbond == Thermo::ERROR) return;
continue;
}
atom1 = closest_image(i,atom1);
@@ -1127,7 +1125,7 @@ void NeighBondKokkos<DeviceType>::improper_partial()
}
} while (h_fail_flag());
- if (nmissing && lostbond == ERROR) {
+ if (nmissing && lostbond == Thermo::ERROR) {
char str[128];
sprintf(str,"Improper atoms missing on proc %d at step " BIGINT_FORMAT,
me,update->ntimestep);
@@ -1135,7 +1133,7 @@ void NeighBondKokkos<DeviceType>::improper_partial()
}
if (neighbor->cluster_check) dihedral_check(neighbor->nimproperlist,v_improperlist);
- if (lostbond == IGNORE) return;
+ if (lostbond == Thermo::IGNORE) return;
int all;
MPI_Allreduce(&nmissing,&all,1,MPI_INT,MPI_SUM,world);
@@ -1160,7 +1158,7 @@ void NeighBondKokkos<DeviceType>::operator()(TagNeighBondImproperPartial, const
int atom4 = map_array(improper_atom4(i,m));
if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1) {
nmissing++;
- if (lostbond == ERROR) return;
+ if (lostbond == Thermo::ERROR) return;
continue;
}
atom1 = closest_image(i,atom1);
diff --git a/src/KOKKOS/neigh_list_kokkos.cpp b/src/KOKKOS/neigh_list_kokkos.cpp
index 98294a802aaa88e16a2c1ca8269cf235d149ff3a..93cf0af937a5e695e8f19f1d6bb18a12032deab7 100644
--- a/src/KOKKOS/neigh_list_kokkos.cpp
+++ b/src/KOKKOS/neigh_list_kokkos.cpp
@@ -17,8 +17,6 @@
using namespace LAMMPS_NS;
-enum{NSQ,BIN,MULTI};
-
/* ---------------------------------------------------------------------- */
template<class Device>
diff --git a/src/KOKKOS/neighbor_kokkos.cpp b/src/KOKKOS/neighbor_kokkos.cpp
index 72092aef0b17bfffaea8865c9156f010f9f829c0..6cd5c4e6e597c93c306156550bc7bd73787d6c28 100644
--- a/src/KOKKOS/neighbor_kokkos.cpp
+++ b/src/KOKKOS/neighbor_kokkos.cpp
@@ -33,8 +33,6 @@
using namespace LAMMPS_NS;
-enum{NSQ,BIN,MULTI}; // also in neigh_list.cpp
-
/* ---------------------------------------------------------------------- */
NeighborKokkos::NeighborKokkos(LAMMPS *lmp) : Neighbor(lmp),
@@ -98,7 +96,7 @@ void NeighborKokkos::init_cutneighsq_kokkos(int n)
void NeighborKokkos::create_kokkos_list(int i)
{
- if (style != BIN)
+ if (style != Neighbor::BIN)
error->all(FLERR,"KOKKOS package only supports 'bin' neighbor lists");
if (requests[i]->kokkos_device) {
@@ -300,7 +298,7 @@ void NeighborKokkos::build_kokkos(int topoflag)
// if bin then, atoms may have moved outside of proc domain & bin extent,
// leading to errors or even a crash
- if (style != NSQ) {
+ if (style != Neighbor::NSQ) {
for (int i = 0; i < nbin; i++) {
neigh_bin[i]->bin_atoms_setup(nall);
neigh_bin[i]->bin_atoms();
diff --git a/src/KOKKOS/neighbor_kokkos.h b/src/KOKKOS/neighbor_kokkos.h
index 137c071e87a7f078647f34ca43c73254c9ab916b..5c98c4d26db2d74b70747f705f0e9f755bae8edd 100644
--- a/src/KOKKOS/neighbor_kokkos.h
+++ b/src/KOKKOS/neighbor_kokkos.h
@@ -18,7 +18,7 @@
#include "neigh_list_kokkos.h"
#include "neigh_bond_kokkos.h"
#include "kokkos_type.h"
-#include <math.h>
+#include <cmath>
namespace LAMMPS_NS {
diff --git a/src/KOKKOS/pair_buck_coul_cut_kokkos.cpp b/src/KOKKOS/pair_buck_coul_cut_kokkos.cpp
index ba3eda64ddee4e389b771f5e47168c98c5a6fa08..9c12d2c978f7a385dfb11f82e34b55984cc0ec76 100644
--- a/src/KOKKOS/pair_buck_coul_cut_kokkos.cpp
+++ b/src/KOKKOS/pair_buck_coul_cut_kokkos.cpp
@@ -15,10 +15,10 @@
Contributing author: Ray Shan (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_buck_coul_cut_kokkos.h"
#include "kokkos.h"
#include "atom_kokkos.h"
diff --git a/src/KOKKOS/pair_buck_coul_long_kokkos.cpp b/src/KOKKOS/pair_buck_coul_long_kokkos.cpp
index 19af349a63588a464f4e1785be291510fd91acfa..4978d3d7fc3b210ecb98dbd55413014aff67ae8a 100644
--- a/src/KOKKOS/pair_buck_coul_long_kokkos.cpp
+++ b/src/KOKKOS/pair_buck_coul_long_kokkos.cpp
@@ -15,10 +15,10 @@
Contributing author: Ray Shan (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_buck_coul_long_kokkos.h"
#include "kokkos.h"
#include "atom_kokkos.h"
diff --git a/src/KOKKOS/pair_buck_kokkos.cpp b/src/KOKKOS/pair_buck_kokkos.cpp
index fcf14533dc991d469ad1c0e65951ca80d515b0b2..8785700186a94aa2a081873348c69b9712715e6c 100644
--- a/src/KOKKOS/pair_buck_kokkos.cpp
+++ b/src/KOKKOS/pair_buck_kokkos.cpp
@@ -15,10 +15,10 @@
Contributing author: Stan Moore (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_buck_kokkos.h"
#include "kokkos.h"
#include "atom_kokkos.h"
diff --git a/src/KOKKOS/pair_coul_cut_kokkos.cpp b/src/KOKKOS/pair_coul_cut_kokkos.cpp
index e20e243c09aefb7313cbe13ce50a498356ea405d..b6e36d4f0ddaae5d9db211607c0493623d0b76b7 100644
--- a/src/KOKKOS/pair_coul_cut_kokkos.cpp
+++ b/src/KOKKOS/pair_coul_cut_kokkos.cpp
@@ -11,10 +11,10 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_coul_cut_kokkos.h"
#include "kokkos.h"
#include "atom_kokkos.h"
diff --git a/src/KOKKOS/pair_coul_debye_kokkos.cpp b/src/KOKKOS/pair_coul_debye_kokkos.cpp
index 729b24ff29d2a8ca40e54ed0ad9c95d17ec8873a..5d15be7d769a16ff4185a8db0acb7c76d562538f 100644
--- a/src/KOKKOS/pair_coul_debye_kokkos.cpp
+++ b/src/KOKKOS/pair_coul_debye_kokkos.cpp
@@ -15,10 +15,10 @@
Contributing author: Ray Shan (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_coul_debye_kokkos.h"
#include "kokkos.h"
#include "atom_kokkos.h"
diff --git a/src/KOKKOS/pair_coul_dsf_kokkos.cpp b/src/KOKKOS/pair_coul_dsf_kokkos.cpp
index f77e63bbf0551b0412b21e0b7631c098ff082f78..a714f665f7f14e3424c66f5aadaf5b6c355a4c54 100644
--- a/src/KOKKOS/pair_coul_dsf_kokkos.cpp
+++ b/src/KOKKOS/pair_coul_dsf_kokkos.cpp
@@ -15,10 +15,10 @@
Contributing author: Stan Moore (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_coul_dsf_kokkos.h"
#include "kokkos.h"
#include "atom_kokkos.h"
diff --git a/src/KOKKOS/pair_coul_long_kokkos.cpp b/src/KOKKOS/pair_coul_long_kokkos.cpp
index f2ade3f367c0e01b8118d454a3d0259618cffddf..1e8c6c5f4e69f7f0f78ff927f9757c35b2046195 100644
--- a/src/KOKKOS/pair_coul_long_kokkos.cpp
+++ b/src/KOKKOS/pair_coul_long_kokkos.cpp
@@ -15,10 +15,10 @@
Contributing author: Ray Shan (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_coul_long_kokkos.h"
#include "kokkos.h"
#include "atom_kokkos.h"
diff --git a/src/KOKKOS/pair_coul_wolf_kokkos.cpp b/src/KOKKOS/pair_coul_wolf_kokkos.cpp
index 0f3e9b94290918dd78cb8940cc762d5e82494977..2bff824c3dd395e602d08243da7a5426805e9303 100644
--- a/src/KOKKOS/pair_coul_wolf_kokkos.cpp
+++ b/src/KOKKOS/pair_coul_wolf_kokkos.cpp
@@ -15,10 +15,10 @@
Contributing author: Stan Moore (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_coul_wolf_kokkos.h"
#include "kokkos.h"
#include "atom_kokkos.h"
diff --git a/src/KOKKOS/pair_dpd_fdt_energy_kokkos.cpp b/src/KOKKOS/pair_dpd_fdt_energy_kokkos.cpp
index 7d71719e0a115d99cf25a3a89a91487f9042edc2..7ff536f8dd792c77515ec0e0f55a569d1f4763ef 100644
--- a/src/KOKKOS/pair_dpd_fdt_energy_kokkos.cpp
+++ b/src/KOKKOS/pair_dpd_fdt_energy_kokkos.cpp
@@ -15,10 +15,10 @@
Contributing author: Stan Moore (Sandia)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "atom_kokkos.h"
#include "atom_vec.h"
#include "comm.h"
@@ -111,7 +111,10 @@ void PairDPDfdtEnergyKokkos<DeviceType>::init_style()
#ifdef DPD_USE_RAN_MARS
rand_pool.init(random,seed);
#else
- rand_pool.init(seed + comm->me,DeviceType::max_hardware_threads());
+ typedef Kokkos::Experimental::UniqueToken<
+ DeviceType, Kokkos::Experimental::UniqueTokenScope::Global> unique_token_type;
+ unique_token_type unique_token;
+ rand_pool.init(seed + comm->me,unique_token.size());
#endif
}
diff --git a/src/KOKKOS/pair_eam_alloy_kokkos.cpp b/src/KOKKOS/pair_eam_alloy_kokkos.cpp
index f263cbb6d90be1cd34d5f0f9abab2b4e04174794..f21ea2335dd36c00429064fd3924dd78055ce88f 100644
--- a/src/KOKKOS/pair_eam_alloy_kokkos.cpp
+++ b/src/KOKKOS/pair_eam_alloy_kokkos.cpp
@@ -15,10 +15,10 @@
Contributing authors: Stan Moore (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "kokkos.h"
#include "pair_kokkos.h"
#include "pair_eam_alloy_kokkos.h"
diff --git a/src/KOKKOS/pair_eam_alloy_kokkos.h b/src/KOKKOS/pair_eam_alloy_kokkos.h
index a962f559085d767f10c1b347a83b9d006c68a548..584839967218b3d8ea1079c9cbf7a2ea597436e4 100644
--- a/src/KOKKOS/pair_eam_alloy_kokkos.h
+++ b/src/KOKKOS/pair_eam_alloy_kokkos.h
@@ -23,7 +23,7 @@ PairStyle(eam/alloy/kk/host,PairEAMAlloyKokkos<LMPHostType>)
#ifndef LMP_PAIR_EAM_ALLOY_KOKKOS_H
#define LMP_PAIR_EAM_ALLOY_KOKKOS_H
-#include <stdio.h>
+#include <cstdio>
#include "kokkos_base.h"
#include "pair_kokkos.h"
#include "pair_eam.h"
diff --git a/src/KOKKOS/pair_eam_fs_kokkos.cpp b/src/KOKKOS/pair_eam_fs_kokkos.cpp
index 05ec1a644b829cc587ca30a4f99148d78dbeeb11..627b56b84ac10e76e9c189d80abde07fe2b8678f 100644
--- a/src/KOKKOS/pair_eam_fs_kokkos.cpp
+++ b/src/KOKKOS/pair_eam_fs_kokkos.cpp
@@ -15,10 +15,10 @@
Contributing authors: Stan Moore (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "kokkos.h"
#include "pair_kokkos.h"
#include "pair_eam_fs_kokkos.h"
diff --git a/src/KOKKOS/pair_eam_fs_kokkos.h b/src/KOKKOS/pair_eam_fs_kokkos.h
index ec87e44ece248f93f0193684311f3587be8ec5d3..ce0b572ea2054113b32064e748a970027b66ab35 100644
--- a/src/KOKKOS/pair_eam_fs_kokkos.h
+++ b/src/KOKKOS/pair_eam_fs_kokkos.h
@@ -23,7 +23,7 @@ PairStyle(eam/fs/kk/host,PairEAMFSKokkos<LMPHostType>)
#ifndef LMP_PAIR_EAM_FS_KOKKOS_H
#define LMP_PAIR_EAM_FS_KOKKOS_H
-#include <stdio.h>
+#include <cstdio>
#include "kokkos_base.h"
#include "pair_kokkos.h"
#include "pair_eam.h"
diff --git a/src/KOKKOS/pair_eam_kokkos.cpp b/src/KOKKOS/pair_eam_kokkos.cpp
index ffa65acb87db22116d32361ea1c049ae38c69e0a..1bfb8255dc68b089bc7362501691a577970d4af4 100644
--- a/src/KOKKOS/pair_eam_kokkos.cpp
+++ b/src/KOKKOS/pair_eam_kokkos.cpp
@@ -15,10 +15,10 @@
Contributing authors: Stan Moore (SNL), Christian Trott (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "kokkos.h"
#include "pair_kokkos.h"
#include "pair_eam_kokkos.h"
diff --git a/src/KOKKOS/pair_eam_kokkos.h b/src/KOKKOS/pair_eam_kokkos.h
index 34a4795ec54e97986b9cd39e0e79e7932d5d6bd4..c821750da54a0c2faf2eeb49ad0689f016bf1e41 100644
--- a/src/KOKKOS/pair_eam_kokkos.h
+++ b/src/KOKKOS/pair_eam_kokkos.h
@@ -23,7 +23,7 @@ PairStyle(eam/kk/host,PairEAMKokkos<LMPHostType>)
#ifndef LMP_PAIR_EAM_KOKKOS_H
#define LMP_PAIR_EAM_KOKKOS_H
-#include <stdio.h>
+#include <cstdio>
#include "kokkos_base.h"
#include "pair_kokkos.h"
#include "pair_eam.h"
diff --git a/src/KOKKOS/pair_exp6_rx_kokkos.cpp b/src/KOKKOS/pair_exp6_rx_kokkos.cpp
index 65b36635a34f88f1eb1ca6eaf6abfae2c1681086..810173d2195ad39c8715dcd6761691535bc85d72 100644
--- a/src/KOKKOS/pair_exp6_rx_kokkos.cpp
+++ b/src/KOKKOS/pair_exp6_rx_kokkos.cpp
@@ -15,10 +15,10 @@
Contributing author: Stan Moore (Sandia)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_exp6_rx_kokkos.h"
#include "atom.h"
#include "comm.h"
@@ -30,7 +30,7 @@
#include "error.h"
#include "modify.h"
#include "fix.h"
-#include <float.h>
+#include <cfloat>
#include "atom_masks.h"
#include "neigh_request.h"
#include "atom_kokkos.h"
@@ -815,7 +815,10 @@ void PairExp6rxKokkos<DeviceType>::operator()(TagPairExp6rxComputeNoAtomics<NEIG
int tid = 0;
#ifndef KOKKOS_HAVE_CUDA
- tid = DeviceType::hardware_thread_id();
+ typedef Kokkos::Experimental::UniqueToken<
+ DeviceType, Kokkos::Experimental::UniqueTokenScope::Global> unique_token_type;
+ unique_token_type unique_token;
+ tid = unique_token.acquire();
#endif
int i,jj,jnum,itype,jtype;
@@ -1152,6 +1155,10 @@ void PairExp6rxKokkos<DeviceType>::operator()(TagPairExp6rxComputeNoAtomics<NEIG
t_f(tid,i,2) += fz_i;
t_uCG(tid,i) += uCG_i;
t_uCGnew(tid,i) += uCGnew_i;
+
+#ifndef KOKKOS_HAVE_CUDA
+ unique_token.release(tid);
+#endif
}
// Experimental thread-safe approach using duplicated data instead of atomics and
@@ -1183,7 +1190,10 @@ void PairExp6rxKokkos<DeviceType>::vectorized_operator(const int &ii, EV_FLOAT&
int tid = 0;
#ifndef KOKKOS_HAVE_CUDA
- tid = DeviceType::hardware_thread_id();
+ typedef Kokkos::Experimental::UniqueToken<
+ DeviceType, Kokkos::Experimental::UniqueTokenScope::Global> unique_token_type;
+ unique_token_type unique_token;
+ tid = unique_token.acquire();
#endif
const int nRep = 12;
@@ -1612,6 +1622,10 @@ void PairExp6rxKokkos<DeviceType>::vectorized_operator(const int &ii, EV_FLOAT&
t_uCG(tid,i) += uCG_i;
t_uCGnew(tid,i) += uCGnew_i;
}
+
+#ifndef KOKKOS_HAVE_CUDA
+ unique_token.release(tid);
+#endif
}
template<class DeviceType>
diff --git a/src/KOKKOS/pair_hybrid_kokkos.cpp b/src/KOKKOS/pair_hybrid_kokkos.cpp
index db757f6ce1847806d266de13037d99b6489732a3..03ad77c34af8d0cc2b7760224ba7eac6814a9043 100644
--- a/src/KOKKOS/pair_hybrid_kokkos.cpp
+++ b/src/KOKKOS/pair_hybrid_kokkos.cpp
@@ -11,10 +11,10 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
-#include <ctype.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
+#include <cctype>
#include "pair_hybrid_kokkos.h"
#include "atom_kokkos.h"
#include "force.h"
diff --git a/src/KOKKOS/pair_hybrid_kokkos.h b/src/KOKKOS/pair_hybrid_kokkos.h
index 62d325925b87e188245feb813279c26871769caa..94e034f8757618105b8b64cf37af7ec2d0b13dd6 100644
--- a/src/KOKKOS/pair_hybrid_kokkos.h
+++ b/src/KOKKOS/pair_hybrid_kokkos.h
@@ -20,7 +20,7 @@ PairStyle(hybrid/kk,PairHybridKokkos)
#ifndef LMP_PAIR_HYBRID_KOKKOS_H
#define LMP_PAIR_HYBRID_KOKKOS_H
-#include <stdio.h>
+#include <cstdio>
#include "pair_hybrid.h"
#include "pair_kokkos.h"
#include "kokkos_type.h"
diff --git a/src/KOKKOS/pair_hybrid_overlay_kokkos.cpp b/src/KOKKOS/pair_hybrid_overlay_kokkos.cpp
index aa5d8951552889d492dba8405924d495eb2d63c4..a2c3edab6596061f39cda2e3fb4e1527e36dcd9c 100644
--- a/src/KOKKOS/pair_hybrid_overlay_kokkos.cpp
+++ b/src/KOKKOS/pair_hybrid_overlay_kokkos.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <stdlib.h>
-#include <string.h>
-#include <ctype.h>
+#include <cstdlib>
+#include <cstring>
+#include <cctype>
#include "pair_hybrid_overlay_kokkos.h"
#include "atom.h"
#include "force.h"
diff --git a/src/KOKKOS/pair_lj_charmm_coul_charmm_implicit_kokkos.cpp b/src/KOKKOS/pair_lj_charmm_coul_charmm_implicit_kokkos.cpp
index 70f0c3e00a639b532c236e62f9072e6e3c60e16a..d0d290d1f1c437df18718504e150b6a39f8fdf4c 100644
--- a/src/KOKKOS/pair_lj_charmm_coul_charmm_implicit_kokkos.cpp
+++ b/src/KOKKOS/pair_lj_charmm_coul_charmm_implicit_kokkos.cpp
@@ -15,10 +15,10 @@
Contributing author: Ray Shan (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_lj_charmm_coul_charmm_implicit_kokkos.h"
#include "kokkos.h"
#include "atom_kokkos.h"
diff --git a/src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.cpp b/src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.cpp
index 0316b65aedd6754dee21ace6cbc406a5c4ae00a7..2203dfa2a01821771943a3afa7c19ff32cb2ece2 100644
--- a/src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.cpp
+++ b/src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.cpp
@@ -15,10 +15,10 @@
Contributing author: Ray Shan (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_lj_charmm_coul_charmm_kokkos.h"
#include "kokkos.h"
#include "atom_kokkos.h"
diff --git a/src/KOKKOS/pair_lj_charmm_coul_long_kokkos.cpp b/src/KOKKOS/pair_lj_charmm_coul_long_kokkos.cpp
index 4d27373824b3ce4b778d54f31b9eb6ad3214f3db..e1ecfbac3c14ce9fe31151077a0ff99a58d8195b 100644
--- a/src/KOKKOS/pair_lj_charmm_coul_long_kokkos.cpp
+++ b/src/KOKKOS/pair_lj_charmm_coul_long_kokkos.cpp
@@ -15,10 +15,10 @@
Contributing author: Ray Shan (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_lj_charmm_coul_long_kokkos.h"
#include "kokkos.h"
#include "atom_kokkos.h"
diff --git a/src/KOKKOS/pair_lj_class2_coul_cut_kokkos.cpp b/src/KOKKOS/pair_lj_class2_coul_cut_kokkos.cpp
index 3f355b1b160bf34df464b833cf1c938e76f5a17e..abd0183e213b679560f8ea685b5da048d9c5580f 100644
--- a/src/KOKKOS/pair_lj_class2_coul_cut_kokkos.cpp
+++ b/src/KOKKOS/pair_lj_class2_coul_cut_kokkos.cpp
@@ -11,10 +11,10 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_lj_class2_coul_cut_kokkos.h"
#include "kokkos.h"
#include "atom_kokkos.h"
diff --git a/src/KOKKOS/pair_lj_class2_coul_long_kokkos.cpp b/src/KOKKOS/pair_lj_class2_coul_long_kokkos.cpp
index 47976ec610aecdef5d6c41bd9d612533e6bc16aa..5f850689d427154ddaeed02d0f23ae6650ca2cdb 100644
--- a/src/KOKKOS/pair_lj_class2_coul_long_kokkos.cpp
+++ b/src/KOKKOS/pair_lj_class2_coul_long_kokkos.cpp
@@ -11,10 +11,10 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_lj_class2_coul_long_kokkos.h"
#include "kokkos.h"
#include "atom_kokkos.h"
diff --git a/src/KOKKOS/pair_lj_class2_kokkos.cpp b/src/KOKKOS/pair_lj_class2_kokkos.cpp
index 5beb520c00feb1971f5248e4ab31a7442133faa7..063753f1f8ccba97326bb580cdd74dd83aab66df 100644
--- a/src/KOKKOS/pair_lj_class2_kokkos.cpp
+++ b/src/KOKKOS/pair_lj_class2_kokkos.cpp
@@ -15,10 +15,10 @@
Contributing author: Ray Shan (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_lj_class2_kokkos.h"
#include "kokkos.h"
#include "atom_kokkos.h"
diff --git a/src/KOKKOS/pair_lj_cut_coul_cut_kokkos.cpp b/src/KOKKOS/pair_lj_cut_coul_cut_kokkos.cpp
index 86e37bea77a6ffadf9ab082a36005ebca6da8aba..a2067f8cf90f4dac64a3d3dadd4be69ff8e51323 100644
--- a/src/KOKKOS/pair_lj_cut_coul_cut_kokkos.cpp
+++ b/src/KOKKOS/pair_lj_cut_coul_cut_kokkos.cpp
@@ -11,10 +11,10 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_lj_cut_coul_cut_kokkos.h"
#include "kokkos.h"
#include "atom_kokkos.h"
diff --git a/src/KOKKOS/pair_lj_cut_coul_debye_kokkos.cpp b/src/KOKKOS/pair_lj_cut_coul_debye_kokkos.cpp
index 76e488c68667e4ac7b19150ba70e876ebc81fe7e..277f1f658c2feabbdcff1ab678f4c8e08dc19d20 100644
--- a/src/KOKKOS/pair_lj_cut_coul_debye_kokkos.cpp
+++ b/src/KOKKOS/pair_lj_cut_coul_debye_kokkos.cpp
@@ -15,10 +15,10 @@
Contributing author: Ray Shan (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_lj_cut_coul_debye_kokkos.h"
#include "kokkos.h"
#include "atom_kokkos.h"
diff --git a/src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.cpp b/src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.cpp
index b64d9fa31a9101425b3b995c9ec711126b0e422f..165bd972763ef52019096ed66566af34ebb552fd 100644
--- a/src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.cpp
+++ b/src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.cpp
@@ -15,10 +15,10 @@
Contributing author: Ray Shan (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_lj_cut_coul_dsf_kokkos.h"
#include "kokkos.h"
#include "atom_kokkos.h"
diff --git a/src/KOKKOS/pair_lj_cut_coul_long_kokkos.cpp b/src/KOKKOS/pair_lj_cut_coul_long_kokkos.cpp
index 77a604534e2ae907a16db82ed013c26af2ec1042..d02e83eb116060f95ed7177a29e9424e8865d3e1 100644
--- a/src/KOKKOS/pair_lj_cut_coul_long_kokkos.cpp
+++ b/src/KOKKOS/pair_lj_cut_coul_long_kokkos.cpp
@@ -11,10 +11,10 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_lj_cut_coul_long_kokkos.h"
#include "kokkos.h"
#include "atom_kokkos.h"
diff --git a/src/KOKKOS/pair_lj_cut_kokkos.cpp b/src/KOKKOS/pair_lj_cut_kokkos.cpp
index 2a228fb168be97184fda12d80b012745b286fa80..daaab8d29ea45cc19c73f8c8b26a5ed8826684f6 100644
--- a/src/KOKKOS/pair_lj_cut_kokkos.cpp
+++ b/src/KOKKOS/pair_lj_cut_kokkos.cpp
@@ -11,10 +11,10 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_lj_cut_kokkos.h"
#include "kokkos.h"
#include "atom_kokkos.h"
diff --git a/src/KOKKOS/pair_lj_expand_kokkos.cpp b/src/KOKKOS/pair_lj_expand_kokkos.cpp
index aca7202b78be66a04ce7443e7eb4f34c34a6a6e0..55c8b200efc4c411b629503b47836b227ce9860e 100644
--- a/src/KOKKOS/pair_lj_expand_kokkos.cpp
+++ b/src/KOKKOS/pair_lj_expand_kokkos.cpp
@@ -15,10 +15,10 @@
Contributing author: Ray Shan (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_lj_expand_kokkos.h"
#include "kokkos.h"
#include "atom_kokkos.h"
diff --git a/src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.cpp b/src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.cpp
index 1cc8d9b3e2f042cd468afe8b4f151872e97215c7..b7fb5acccb7d147bc04e8498ae3a1808d9c2a169 100644
--- a/src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.cpp
+++ b/src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.cpp
@@ -15,10 +15,10 @@
Contributing author: Ray Shan (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_lj_gromacs_coul_gromacs_kokkos.h"
#include "kokkos.h"
#include "atom_kokkos.h"
diff --git a/src/KOKKOS/pair_lj_gromacs_kokkos.cpp b/src/KOKKOS/pair_lj_gromacs_kokkos.cpp
index f0ad9357694dc64b163f6a5d9c3307159a43ee48..5d2725ccddf7dd778271d7155b08b50a88af8754 100644
--- a/src/KOKKOS/pair_lj_gromacs_kokkos.cpp
+++ b/src/KOKKOS/pair_lj_gromacs_kokkos.cpp
@@ -15,10 +15,10 @@
Contributing author: Ray Shan (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_lj_gromacs_kokkos.h"
#include "kokkos.h"
#include "atom_kokkos.h"
diff --git a/src/KOKKOS/pair_lj_sdk_kokkos.cpp b/src/KOKKOS/pair_lj_sdk_kokkos.cpp
index aa579d5dc12995475731589da686ee4271867db9..8f719582fa981d4d856cabc4cc8b19740531a22f 100644
--- a/src/KOKKOS/pair_lj_sdk_kokkos.cpp
+++ b/src/KOKKOS/pair_lj_sdk_kokkos.cpp
@@ -11,10 +11,10 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_lj_sdk_kokkos.h"
#include "kokkos.h"
#include "atom_kokkos.h"
diff --git a/src/KOKKOS/pair_morse_kokkos.cpp b/src/KOKKOS/pair_morse_kokkos.cpp
index dd555b6eb9cf937be79a1377096a4687b026ca92..97c5f9be84ae10ecf3a1c98a8880701da08556d9 100644
--- a/src/KOKKOS/pair_morse_kokkos.cpp
+++ b/src/KOKKOS/pair_morse_kokkos.cpp
@@ -15,10 +15,10 @@
Contributing authors: Stefan Paquay (Eindhoven University of Technology)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_morse_kokkos.h"
#include "kokkos.h"
#include "atom_kokkos.h"
diff --git a/src/KOKKOS/pair_multi_lucy_rx_kokkos.cpp b/src/KOKKOS/pair_multi_lucy_rx_kokkos.cpp
index 7cb869a8a558bc524d172bf31b529554cfd0866d..a6af26cb0ffa891584ad622d2c6510e190f03b09 100644
--- a/src/KOKKOS/pair_multi_lucy_rx_kokkos.cpp
+++ b/src/KOKKOS/pair_multi_lucy_rx_kokkos.cpp
@@ -22,10 +22,10 @@
------------------------------------------------------------------------------------------- */
#include <mpi.h>
-#include <math.h>
+#include <cmath>
#include "math_const.h"
-#include <stdlib.h>
-#include <string.h>
+#include <cstdlib>
+#include <cstring>
#include "pair_multi_lucy_rx_kokkos.h"
#include "atom_kokkos.h"
#include "force.h"
diff --git a/src/KOKKOS/pair_reaxc_kokkos.cpp b/src/KOKKOS/pair_reaxc_kokkos.cpp
index 9352d8367c441919accde7f5a2c286f739ac26cb..bb9f8ab417fab2f659f17f18b58ad38b51861279 100644
--- a/src/KOKKOS/pair_reaxc_kokkos.cpp
+++ b/src/KOKKOS/pair_reaxc_kokkos.cpp
@@ -15,10 +15,10 @@
Contributing author: Ray Shan (SNL), Stan Moore (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_reaxc_kokkos.h"
#include "kokkos.h"
#include "atom_kokkos.h"
diff --git a/src/KOKKOS/pair_reaxc_kokkos.h b/src/KOKKOS/pair_reaxc_kokkos.h
index e69b80c2a7f5bcabdc982c2e133952def3910e1b..5175e274a8998f45ee6d8f40116f1bf47f671af3 100644
--- a/src/KOKKOS/pair_reaxc_kokkos.h
+++ b/src/KOKKOS/pair_reaxc_kokkos.h
@@ -23,7 +23,7 @@ PairStyle(reax/c/kk/host,PairReaxCKokkos<LMPHostType>)
#ifndef LMP_PAIR_REAXC_KOKKOS_H
#define LMP_PAIR_REAXC_KOKKOS_H
-#include <stdio.h>
+#include <cstdio>
#include "pair_kokkos.h"
#include "pair_reaxc.h"
#include "neigh_list_kokkos.h"
diff --git a/src/KOKKOS/pair_snap_kokkos_impl.h b/src/KOKKOS/pair_snap_kokkos_impl.h
index d79cfef24b599a2d347b17aeed9e2512b4249679..a024e5cbd19238a739663870c8e21fcabaea0a41 100644
--- a/src/KOKKOS/pair_snap_kokkos_impl.h
+++ b/src/KOKKOS/pair_snap_kokkos_impl.h
@@ -15,9 +15,9 @@
Contributing authors: Christian Trott (SNL), Stan Moore (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "pair_snap_kokkos.h"
#include "atom_kokkos.h"
#include "error.h"
diff --git a/src/KOKKOS/pair_sw_kokkos.cpp b/src/KOKKOS/pair_sw_kokkos.cpp
index a19e2fc271d0292e6e6c2d9d487c29a82c886135..8f4903c76794a4c7a1d38b5bbbf1b53894788bda 100644
--- a/src/KOKKOS/pair_sw_kokkos.cpp
+++ b/src/KOKKOS/pair_sw_kokkos.cpp
@@ -15,10 +15,10 @@
Contributing author: Stan Moore (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_sw_kokkos.h"
#include "kokkos.h"
#include "pair_kokkos.h"
diff --git a/src/KOKKOS/pair_table_kokkos.cpp b/src/KOKKOS/pair_table_kokkos.cpp
index e3e4ee01f397c750636fde67868fc7bf17f9555d..7b06f814bb4624874ca16f313f9faeda83cea9db 100644
--- a/src/KOKKOS/pair_table_kokkos.cpp
+++ b/src/KOKKOS/pair_table_kokkos.cpp
@@ -16,9 +16,9 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "pair_table_kokkos.h"
#include "kokkos.h"
#include "atom.h"
diff --git a/src/KOKKOS/pair_table_rx_kokkos.cpp b/src/KOKKOS/pair_table_rx_kokkos.cpp
index 0b1e0ee9e6f6adbaaef11d5011287269d8f4ed64..30ca54986b7d378d1ed88e26cf86597f8a775709 100644
--- a/src/KOKKOS/pair_table_rx_kokkos.cpp
+++ b/src/KOKKOS/pair_table_rx_kokkos.cpp
@@ -16,9 +16,9 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "pair_table_rx_kokkos.h"
#include "kokkos.h"
#include "atom.h"
diff --git a/src/KOKKOS/pair_tersoff_kokkos.cpp b/src/KOKKOS/pair_tersoff_kokkos.cpp
index 1fb97f913f8d560d7c9c3605fe577d08efffe711..cb4def2d373b4d3950334997b98ab09ffe0efe14 100644
--- a/src/KOKKOS/pair_tersoff_kokkos.cpp
+++ b/src/KOKKOS/pair_tersoff_kokkos.cpp
@@ -15,10 +15,10 @@
Contributing author: Ray Shan (SNL) and Christian Trott (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_tersoff_kokkos.h"
#include "kokkos.h"
#include "atom_kokkos.h"
diff --git a/src/KOKKOS/pair_tersoff_kokkos.h b/src/KOKKOS/pair_tersoff_kokkos.h
index f40d28b72bd96549f2fd53cd6ac191acda55d0fa..2dac2c5991fe1ba733b7ae1bedb7c9e640c1b645 100644
--- a/src/KOKKOS/pair_tersoff_kokkos.h
+++ b/src/KOKKOS/pair_tersoff_kokkos.h
@@ -23,7 +23,7 @@ PairStyle(tersoff/kk/host,PairTersoffKokkos<LMPHostType>)
#ifndef LMP_PAIR_TERSOFF_KOKKOS_H
#define LMP_PAIR_TERSOFF_KOKKOS_H
-#include <stdio.h>
+#include <cstdio>
#include "pair_kokkos.h"
#include "pair_tersoff.h"
#include "neigh_list_kokkos.h"
diff --git a/src/KOKKOS/pair_tersoff_mod_kokkos.cpp b/src/KOKKOS/pair_tersoff_mod_kokkos.cpp
index a30e1229f2a6959d35d462ff006e8ceabb07747b..0d150f83e4a084a8d92a24a79f806aecea3e34c3 100644
--- a/src/KOKKOS/pair_tersoff_mod_kokkos.cpp
+++ b/src/KOKKOS/pair_tersoff_mod_kokkos.cpp
@@ -15,10 +15,10 @@
Contributing author: Ray Shan (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_tersoff_mod_kokkos.h"
#include "kokkos.h"
#include "atom_kokkos.h"
diff --git a/src/KOKKOS/pair_tersoff_mod_kokkos.h b/src/KOKKOS/pair_tersoff_mod_kokkos.h
index c9995b2904349a03dffbe32bd7f234c2bf4f5225..dd5efb50f1da33e7743f6c8c4d51c5e1e9086dee 100644
--- a/src/KOKKOS/pair_tersoff_mod_kokkos.h
+++ b/src/KOKKOS/pair_tersoff_mod_kokkos.h
@@ -23,7 +23,7 @@ PairStyle(tersoff/mod/kk/host,PairTersoffMODKokkos<LMPHostType>)
#ifndef LMP_PAIR_TERSOFF_MOD_KOKKOS_H
#define LMP_PAIR_TERSOFF_MOD_KOKKOS_H
-#include <stdio.h>
+#include <cstdio>
#include "pair_kokkos.h"
#include "pair_tersoff_mod.h"
#include "neigh_list_kokkos.h"
diff --git a/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp b/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp
index aeefbf67f688caf403ca4e6a10d9a49ffc3e08cf..2fb9675db60efa9b5ebda7e81dee5e1271d021fd 100644
--- a/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp
+++ b/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp
@@ -15,10 +15,10 @@
Contributing author: Ray Shan (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_tersoff_zbl_kokkos.h"
#include "kokkos.h"
#include "atom_kokkos.h"
diff --git a/src/KOKKOS/pair_tersoff_zbl_kokkos.h b/src/KOKKOS/pair_tersoff_zbl_kokkos.h
index 92239532be72bae61ab223999f29a45d6ccab54d..45982bd420b5b860291a54e29ecf0f9f79581063 100644
--- a/src/KOKKOS/pair_tersoff_zbl_kokkos.h
+++ b/src/KOKKOS/pair_tersoff_zbl_kokkos.h
@@ -23,7 +23,7 @@ PairStyle(tersoff/zbl/kk/host,PairTersoffZBLKokkos<LMPHostType>)
#ifndef LMP_PAIR_TERSOFF_ZBL_KOKKOS_H
#define LMP_PAIR_TERSOFF_ZBL_KOKKOS_H
-#include <stdio.h>
+#include <cstdio>
#include "pair_kokkos.h"
#include "pair_tersoff_zbl.h"
#include "neigh_list_kokkos.h"
diff --git a/src/KOKKOS/pair_vashishta_kokkos.cpp b/src/KOKKOS/pair_vashishta_kokkos.cpp
index 2e4989356eab8b296f8ff87e882907101e82ae91..3d4bd22a3cb33913e7b8e96eb4bff020e7a27627 100644
--- a/src/KOKKOS/pair_vashishta_kokkos.cpp
+++ b/src/KOKKOS/pair_vashishta_kokkos.cpp
@@ -15,10 +15,10 @@
Contributing author: Anders Hafreager (UiO), andershaf@gmail.com
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_vashishta_kokkos.h"
#include "kokkos.h"
#include "pair_kokkos.h"
diff --git a/src/KOKKOS/pair_yukawa_kokkos.cpp b/src/KOKKOS/pair_yukawa_kokkos.cpp
index 6560ec9684b3f88abb0143aeb39ca791de02affb..8fc2fda1207a74c21ebda02a136348a796142b28 100644
--- a/src/KOKKOS/pair_yukawa_kokkos.cpp
+++ b/src/KOKKOS/pair_yukawa_kokkos.cpp
@@ -14,8 +14,8 @@
/* ----------------------------------------------------------------------
Contributing authors: Stefan Paquay (Brandeis University)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdlib>
#include "pair_yukawa_kokkos.h"
#include "kokkos.h"
#include "atom_kokkos.h"
diff --git a/src/KOKKOS/pair_zbl_kokkos.cpp b/src/KOKKOS/pair_zbl_kokkos.cpp
index 0ed9e62dfff2d496dde2d9cac65ab31423cb0982..f57d5eaad0cccf6751a839a96e3926270cfcb7a3 100644
--- a/src/KOKKOS/pair_zbl_kokkos.cpp
+++ b/src/KOKKOS/pair_zbl_kokkos.cpp
@@ -15,10 +15,10 @@
Contributing authors: Stan Moore (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_zbl_kokkos.h"
#include "atom_kokkos.h"
#include "comm.h"
diff --git a/src/KOKKOS/pppm_kokkos.cpp b/src/KOKKOS/pppm_kokkos.cpp
index a28e462044ac7a4f1b674b620c7c3102a846c9aa..13683d148f91d351dfe166da79925ebd20be9a35 100644
--- a/src/KOKKOS/pppm_kokkos.cpp
+++ b/src/KOKKOS/pppm_kokkos.cpp
@@ -16,10 +16,10 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <string.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <math.h>
+#include <cstring>
+#include <cstdio>
+#include <cstdlib>
+#include <cmath>
#include "pppm_kokkos.h"
#include "atom_kokkos.h"
#include "comm.h"
@@ -1579,7 +1579,7 @@ void PPPMKokkos<DeviceType>::particle_map()
k_flag.template modify<LMPHostType>();
k_flag.template sync<DeviceType>();
- if (!ISFINITE(boxlo[0]) || !ISFINITE(boxlo[1]) || !ISFINITE(boxlo[2]))
+ if (!std::isfinite(boxlo[0]) || !std::isfinite(boxlo[1]) || !std::isfinite(boxlo[2]))
error->one(FLERR,"Non-numeric box dimensions - simulation unstable");
copymode = 1;
diff --git a/src/KOKKOS/rand_pool_wrap_kokkos.h b/src/KOKKOS/rand_pool_wrap_kokkos.h
index 975ce0c89a41d9d4c866d673ddcba6a81c23851d..12255a8a62fc9f8eaabd520f29c9fe0ce1103b1e 100644
--- a/src/KOKKOS/rand_pool_wrap_kokkos.h
+++ b/src/KOKKOS/rand_pool_wrap_kokkos.h
@@ -55,11 +55,15 @@ class RandPoolWrap : protected Pointers {
#endif
RandWrap rand_wrap;
- int tid = 0;
-#ifndef KOKKOS_HAVE_CUDA
- tid = LMPDeviceType::hardware_thread_id();
-#endif
+
+ typedef Kokkos::Experimental::UniqueToken<
+ LMPHostType, Kokkos::Experimental::UniqueTokenScope::Global> unique_token_type;
+
+ unique_token_type unique_token;
+ int tid = (int) unique_token.acquire();
rand_wrap.rng = random_thr[tid];
+ unique_token.release(tid);
+
return rand_wrap;
}
diff --git a/src/KOKKOS/region_block_kokkos.cpp b/src/KOKKOS/region_block_kokkos.cpp
index eed4272f2302b7244be637409054ddac7a4d59f9..8ff6e8937d0919f905599c7b95bb6c01a9f7c0d6 100644
--- a/src/KOKKOS/region_block_kokkos.cpp
+++ b/src/KOKKOS/region_block_kokkos.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <stdlib.h>
-#include <string.h>
+#include <cstdlib>
+#include <cstring>
#include "region_block_kokkos.h"
#include "domain.h"
#include "force.h"
diff --git a/src/KOKKOS/sna_kokkos_impl.h b/src/KOKKOS/sna_kokkos_impl.h
index ccc4010f68af839e39f59a0277231e618b1d6d0e..25561fef5d0decf60f4ab6d74d3e8cf20693c9ff 100644
--- a/src/KOKKOS/sna_kokkos_impl.h
+++ b/src/KOKKOS/sna_kokkos_impl.h
@@ -16,9 +16,9 @@
------------------------------------------------------------------------- */
#include "sna_kokkos.h"
-#include <math.h>
-#include <string.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstring>
+#include <cstdlib>
using namespace LAMMPS_NS;
diff --git a/src/KOKKOS/verlet_kokkos.cpp b/src/KOKKOS/verlet_kokkos.cpp
index fe11e6b3fa4986459ad9847ec3f41b6d72ccd72e..136e543a2cd708501004d2f94290b21454dabe0a 100644
--- a/src/KOKKOS/verlet_kokkos.cpp
+++ b/src/KOKKOS/verlet_kokkos.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "verlet_kokkos.h"
#include "neighbor.h"
#include "domain.h"
diff --git a/src/KSPACE/ewald.cpp b/src/KSPACE/ewald.cpp
index 766520172b46e0c5103c7821bad3dc70c612ff3a..0ced09eb93610c42a13bdabe19f5067081735f25 100644
--- a/src/KSPACE/ewald.cpp
+++ b/src/KSPACE/ewald.cpp
@@ -19,10 +19,10 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <stdlib.h>
-#include <stdio.h>
-#include <string.h>
-#include <math.h>
+#include <cstdlib>
+#include <cstdio>
+#include <cstring>
+#include <cmath>
#include "ewald.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/KSPACE/ewald_disp.cpp b/src/KSPACE/ewald_disp.cpp
index e0424b0d932b7d4adbd50a5272695abe08da1fb9..8cdaa044aa737917ebfa9c04ff26391cbb2eb3eb 100644
--- a/src/KSPACE/ewald_disp.cpp
+++ b/src/KSPACE/ewald_disp.cpp
@@ -16,10 +16,10 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <string.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <math.h>
+#include <cstring>
+#include <cstdio>
+#include <cstdlib>
+#include <cmath>
#include "ewald_disp.h"
#include "math_vector.h"
#include "math_const.h"
@@ -39,8 +39,6 @@ using namespace MathSpecial;
#define SMALL 0.00001
-enum{GEOMETRIC,ARITHMETIC,SIXTHPOWER}; // same as in pair.h
-
//#define DEBUG
/* ---------------------------------------------------------------------- */
@@ -116,7 +114,7 @@ void EwaldDisp::init()
if (!(ptr||cutoff))
error->all(FLERR,"KSpace style is incompatible with Pair style");
int ewald_order = ptr ? *((int *) ptr) : 1<<1;
- int ewald_mix = ptr ? *((int *) pair->extract("ewald_mix",tmp)) : GEOMETRIC;
+ int ewald_mix = ptr ? *((int *) pair->extract("ewald_mix",tmp)) : Pair::GEOMETRIC;
memset(function, 0, EWALD_NFUNCS*sizeof(int));
for (int i=0; i<=EWALD_NORDER; ++i) // transcribe order
if (ewald_order&(1<<i)) { // from pair_style
@@ -127,8 +125,8 @@ void EwaldDisp::init()
case 3:
k = 3; break;
case 6:
- if (ewald_mix==GEOMETRIC) { k = 1; break; }
- else if (ewald_mix==ARITHMETIC) { k = 2; break; }
+ if (ewald_mix==Pair::GEOMETRIC) { k = 1; break; }
+ else if (ewald_mix==Pair::ARITHMETIC) { k = 2; break; }
error->all(FLERR,
"Unsupported mixing rule in kspace_style ewald/disp");
default:
diff --git a/src/KSPACE/fft3d.cpp b/src/KSPACE/fft3d.cpp
index 2a0d85bac655ff24000fb8755c4b531a47358763..6da7f197ee7024bb3a6457f33a21138ad24d0a73 100644
--- a/src/KSPACE/fft3d.cpp
+++ b/src/KSPACE/fft3d.cpp
@@ -20,9 +20,9 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <math.h>
+#include <cstdio>
+#include <cstdlib>
+#include <cmath>
#include "fft3d.h"
#include "remap.h"
diff --git a/src/KSPACE/fix_tune_kspace.cpp b/src/KSPACE/fix_tune_kspace.cpp
index 5ce867778d838eab52147a2edd55c76fd809048e..399e551b57dff8afea6a128bb88f6713572168a5 100644
--- a/src/KSPACE/fix_tune_kspace.cpp
+++ b/src/KSPACE/fix_tune_kspace.cpp
@@ -15,8 +15,8 @@
Contributing author: Paul Crozier (SNL)
------------------------------------------------------------------------- */
-#include <string.h>
-#include <stdlib.h>
+#include <cstring>
+#include <cstdlib>
#include "fix_tune_kspace.h"
#include "update.h"
#include "domain.h"
diff --git a/src/KSPACE/fix_tune_kspace.h b/src/KSPACE/fix_tune_kspace.h
index 3311bd1d430ee35c12c9c20aaa090d975efc8611..6f40fc8711e32f501237ef8f629dc3065beaea60 100644
--- a/src/KSPACE/fix_tune_kspace.h
+++ b/src/KSPACE/fix_tune_kspace.h
@@ -20,7 +20,7 @@ FixStyle(tune/kspace,FixTuneKspace)
#ifndef LMP_FIX_TUNE_KSPACE_H
#define LMP_FIX_TUNE_KSPACE_H
-#include <stdio.h>
+#include <cstdio>
#include "fix.h"
namespace LAMMPS_NS {
diff --git a/src/KSPACE/kissfft.h b/src/KSPACE/kissfft.h
index ec6ef97feab0eb3017fa15eae33c0a4d5a58a49d..4e15f494a972f817a23208d53b6d5c80e1f121ad 100644
--- a/src/KSPACE/kissfft.h
+++ b/src/KSPACE/kissfft.h
@@ -16,9 +16,9 @@
#ifndef LMP_FFT_KISSFFT
#define LMP_FFT_KISSFFT
-#include <stdlib.h>
-#include <string.h>
-#include <math.h>
+#include <cstdlib>
+#include <cstring>
+#include <cmath>
#if defined(_OPENMP)
#include <omp.h>
diff --git a/src/KSPACE/msm.cpp b/src/KSPACE/msm.cpp
index c151095a6724e827f101b057be6de2b9420517cb..9f3221449bb2329923cfa9ed987beb6f26e58e3f 100644
--- a/src/KSPACE/msm.cpp
+++ b/src/KSPACE/msm.cpp
@@ -16,10 +16,10 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <string.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <math.h>
+#include <cstring>
+#include <cstdio>
+#include <cstdlib>
+#include <cmath>
#include "msm.h"
#include "atom.h"
#include "comm.h"
@@ -1442,7 +1442,7 @@ void MSM::particle_map()
int flag = 0;
- if (!ISFINITE(boxlo[0]) || !ISFINITE(boxlo[1]) || !ISFINITE(boxlo[2]))
+ if (!std::isfinite(boxlo[0]) || !std::isfinite(boxlo[1]) || !std::isfinite(boxlo[2]))
error->one(FLERR,"Non-numeric box dimensions - simulation unstable");
for (int i = 0; i < nlocal; i++) {
@@ -2261,7 +2261,7 @@ void MSM::restriction(int n)
double ***qgrid2 = qgrid[n+1];
int k = 0;
- int index[p+2];
+ int *index = new int[p+2];
for (int nu=-p; nu<=p; nu++) {
if (nu%2 == 0 && nu != 0) continue;
phi1d[0][k] = compute_phi(nu*delxinv[n+1]/delxinv[n]);
@@ -2317,7 +2317,7 @@ void MSM::restriction(int n)
}
qgrid2[kp][jp][ip] += q2sum;
}
-
+ delete[] index;
}
/* ----------------------------------------------------------------------
@@ -2348,7 +2348,7 @@ void MSM::prolongation(int n)
double ***v5grid2 = v5grid[n+1];
int k = 0;
- int index[p+2];
+ int *index = new int[p+2];
for (int nu=-p; nu<=p; nu++) {
if (nu%2 == 0 && nu != 0) continue;
phi1d[0][k] = compute_phi(nu*delxinv[n+1]/delxinv[n]);
@@ -2420,7 +2420,7 @@ void MSM::prolongation(int n)
}
}
-
+ delete[] index;
}
/* ----------------------------------------------------------------------
diff --git a/src/KSPACE/msm_cg.cpp b/src/KSPACE/msm_cg.cpp
index 3354593ec86f58ad533427bf336ee2bd3df58b2f..3ae3d627251c02951bdf62c6653c535c87e6814f 100644
--- a/src/KSPACE/msm_cg.cpp
+++ b/src/KSPACE/msm_cg.cpp
@@ -16,10 +16,10 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "atom.h"
#include "gridcomm.h"
#include "domain.h"
@@ -314,7 +314,7 @@ void MSMCG::particle_map()
int flag = 0;
int i;
- if (!ISFINITE(boxlo[0]) || !ISFINITE(boxlo[1]) || !ISFINITE(boxlo[2]))
+ if (!std::isfinite(boxlo[0]) || !std::isfinite(boxlo[1]) || !std::isfinite(boxlo[2]))
error->one(FLERR,"Non-numeric box dimensions - simulation unstable");
for (int j = 0; j < num_charged; j++) {
diff --git a/src/KSPACE/pair_born_coul_long.cpp b/src/KSPACE/pair_born_coul_long.cpp
index 479128ef2b4ad070a5b567543652c6b93762d881..d55a5a3afe7e239480daa22f17712a020c44cc2f 100644
--- a/src/KSPACE/pair_born_coul_long.cpp
+++ b/src/KSPACE/pair_born_coul_long.cpp
@@ -15,10 +15,10 @@
Contributing author: Ahmed Ismail (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_born_coul_long.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/KSPACE/pair_born_coul_msm.cpp b/src/KSPACE/pair_born_coul_msm.cpp
index 6ed120cdc575341614e92e9d82ea2f2c654383a8..775d26df95e131fe812069c8124555739cee2f70 100644
--- a/src/KSPACE/pair_born_coul_msm.cpp
+++ b/src/KSPACE/pair_born_coul_msm.cpp
@@ -15,10 +15,10 @@
Contributing author: Stan Moore (SNL), Paul Crozier (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_born_coul_msm.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/KSPACE/pair_buck_coul_long.cpp b/src/KSPACE/pair_buck_coul_long.cpp
index 95496409b98fb21387c939da1dca06104445c3af..a37e4ab4e9429180b786d6d110512355ae3f4095 100644
--- a/src/KSPACE/pair_buck_coul_long.cpp
+++ b/src/KSPACE/pair_buck_coul_long.cpp
@@ -11,10 +11,10 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_buck_coul_long.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/KSPACE/pair_buck_coul_msm.cpp b/src/KSPACE/pair_buck_coul_msm.cpp
index e33bdc839c3dfaf4e97223381ba5121450170566..fc72f1a4d6886b275a8b195a162364f85ae50ddf 100644
--- a/src/KSPACE/pair_buck_coul_msm.cpp
+++ b/src/KSPACE/pair_buck_coul_msm.cpp
@@ -11,10 +11,10 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_buck_coul_msm.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/KSPACE/pair_buck_long_coul_long.cpp b/src/KSPACE/pair_buck_long_coul_long.cpp
index 7781e24a5ee8febd641a3af783bf9ede7ad47582..55825b56571c492eca8c3262a75916e29f82ae60 100644
--- a/src/KSPACE/pair_buck_long_coul_long.cpp
+++ b/src/KSPACE/pair_buck_long_coul_long.cpp
@@ -15,10 +15,10 @@
Contributing author: Pieter J. in 't Veld (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "math_vector.h"
#include "pair_buck_long_coul_long.h"
#include "atom.h"
diff --git a/src/KSPACE/pair_coul_long.cpp b/src/KSPACE/pair_coul_long.cpp
index 988694153afa952e71a403f859a0106860496a5a..4b10782ee646c23268fb5603cacb3f730336f1ba 100644
--- a/src/KSPACE/pair_coul_long.cpp
+++ b/src/KSPACE/pair_coul_long.cpp
@@ -15,10 +15,10 @@
Contributing author: Paul Crozier (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_coul_long.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/KSPACE/pair_coul_msm.cpp b/src/KSPACE/pair_coul_msm.cpp
index 62daee9a13695636aa3f10153bf7e4a2603f143d..f5cd9a04452a2a6c16a03e15527c47c331d11913 100644
--- a/src/KSPACE/pair_coul_msm.cpp
+++ b/src/KSPACE/pair_coul_msm.cpp
@@ -15,10 +15,10 @@
Contributing authors: Stan Moore (SNL), Paul Crozier (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_coul_msm.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/KSPACE/pair_lj_charmm_coul_long.cpp b/src/KSPACE/pair_lj_charmm_coul_long.cpp
index daa493cef06e6327966c9dfb490a33c071ff8a22..749d9657aacc6c0418ed04b059a737a031e3dfc0 100644
--- a/src/KSPACE/pair_lj_charmm_coul_long.cpp
+++ b/src/KSPACE/pair_lj_charmm_coul_long.cpp
@@ -15,10 +15,10 @@
Contributing author: Paul Crozier (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_lj_charmm_coul_long.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/KSPACE/pair_lj_charmm_coul_msm.cpp b/src/KSPACE/pair_lj_charmm_coul_msm.cpp
index 00617c0bf2331a51ba721cc9a8ba05ba5209f2ec..aecadcf127394e0b89dcbf56605e5e34ad7cfc81 100644
--- a/src/KSPACE/pair_lj_charmm_coul_msm.cpp
+++ b/src/KSPACE/pair_lj_charmm_coul_msm.cpp
@@ -15,10 +15,10 @@
Contributing authors: Paul Crozier (SNL), Stan Moore (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_lj_charmm_coul_msm.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp b/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp
index 4a37ddb81fa29989b06eb0934637ed77cf7931ff..614980117e4e8b9c45de65a80b8547a6b42f9d0b 100644
--- a/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp
+++ b/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp
@@ -19,10 +19,10 @@
additional assistance from Robert A. Latour, Clemson University
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_lj_charmmfsw_coul_long.h"
#include "atom.h"
#include "update.h"
diff --git a/src/KSPACE/pair_lj_cut_coul_long.cpp b/src/KSPACE/pair_lj_cut_coul_long.cpp
index 3096df2b01626e1fbfd255c176ed0803bf07817c..c9530fe157f5fcfa012b8fdb7ea49a9d2dc4c0aa 100644
--- a/src/KSPACE/pair_lj_cut_coul_long.cpp
+++ b/src/KSPACE/pair_lj_cut_coul_long.cpp
@@ -15,10 +15,10 @@
Contributing author: Paul Crozier (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_lj_cut_coul_long.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/KSPACE/pair_lj_cut_coul_msm.cpp b/src/KSPACE/pair_lj_cut_coul_msm.cpp
index 9f901db9fcfbb2375734877b0a918368cd49d5cb..78c364bd6aae4a416945e22e207bc28985ba0471 100644
--- a/src/KSPACE/pair_lj_cut_coul_msm.cpp
+++ b/src/KSPACE/pair_lj_cut_coul_msm.cpp
@@ -15,10 +15,10 @@
Contributing authors: Stan Moore (SNL), Paul Crozier (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_lj_cut_coul_msm.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/KSPACE/pair_lj_cut_tip4p_long.cpp b/src/KSPACE/pair_lj_cut_tip4p_long.cpp
index 588d21ac66be082e4bb9c8412bddd39261fc54fa..d622a83b394e95e48195cb037ba35ab67536e3b6 100644
--- a/src/KSPACE/pair_lj_cut_tip4p_long.cpp
+++ b/src/KSPACE/pair_lj_cut_tip4p_long.cpp
@@ -16,10 +16,10 @@
simpler force assignment added by Rolf Isele-Holder (Aachen University)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_lj_cut_tip4p_long.h"
#include "angle.h"
#include "atom.h"
diff --git a/src/KSPACE/pair_lj_long_coul_long.cpp b/src/KSPACE/pair_lj_long_coul_long.cpp
index f6f6ebd6a2988e1faa00495d348818d2579aea47..32d6d9e0a3e82e602d838beade4b656496e689b3 100644
--- a/src/KSPACE/pair_lj_long_coul_long.cpp
+++ b/src/KSPACE/pair_lj_long_coul_long.cpp
@@ -17,10 +17,10 @@
University New Orleans)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "math_vector.h"
#include "pair_lj_long_coul_long.h"
#include "atom.h"
diff --git a/src/KSPACE/pair_lj_long_tip4p_long.cpp b/src/KSPACE/pair_lj_long_tip4p_long.cpp
index 6dd552c819d2bbd918508240ae5fe2a03c2f7015..78316b9daad147c3fb7b236760c13a99a08c89dd 100644
--- a/src/KSPACE/pair_lj_long_tip4p_long.cpp
+++ b/src/KSPACE/pair_lj_long_tip4p_long.cpp
@@ -16,10 +16,10 @@
Rolf Isele-Holder (Aachen University)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_lj_long_tip4p_long.h"
#include "angle.h"
#include "atom.h"
diff --git a/src/KSPACE/pair_tip4p_long.cpp b/src/KSPACE/pair_tip4p_long.cpp
index 1dd57ce822c90751b523397f29ec636eaaffa49b..ac428d483af745221d89146d9de6f576c0923c8d 100644
--- a/src/KSPACE/pair_tip4p_long.cpp
+++ b/src/KSPACE/pair_tip4p_long.cpp
@@ -16,10 +16,10 @@
simpler force assignment added by Rolf Isele-Holder (Aachen University)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_tip4p_long.h"
#include "angle.h"
#include "atom.h"
diff --git a/src/KSPACE/pppm.cpp b/src/KSPACE/pppm.cpp
index bc82dce5320a7e8ea87d75dc6d29b18a86561263..132389b7d619b22d8f71cb0caf696e12498ab10c 100644
--- a/src/KSPACE/pppm.cpp
+++ b/src/KSPACE/pppm.cpp
@@ -19,10 +19,10 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <string.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <math.h>
+#include <cstring>
+#include <cstdio>
+#include <cstdlib>
+#include <cmath>
#include "pppm.h"
#include "atom.h"
#include "comm.h"
@@ -1913,7 +1913,7 @@ void PPPM::particle_map()
int flag = 0;
- if (!ISFINITE(boxlo[0]) || !ISFINITE(boxlo[1]) || !ISFINITE(boxlo[2]))
+ if (!std::isfinite(boxlo[0]) || !std::isfinite(boxlo[1]) || !std::isfinite(boxlo[2]))
error->one(FLERR,"Non-numeric box dimensions - simulation unstable");
for (int i = 0; i < nlocal; i++) {
diff --git a/src/KSPACE/pppm_cg.cpp b/src/KSPACE/pppm_cg.cpp
index 9489224e03031b8c279e05a5365a3ad9a58bb572..ca7abc9b5adc60454c4f7e4a24d501980005d679 100644
--- a/src/KSPACE/pppm_cg.cpp
+++ b/src/KSPACE/pppm_cg.cpp
@@ -16,9 +16,9 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "atom.h"
#include "gridcomm.h"
@@ -284,7 +284,7 @@ void PPPMCG::particle_map()
double **x = atom->x;
- if (!ISFINITE(boxlo[0]) || !ISFINITE(boxlo[1]) || !ISFINITE(boxlo[2]))
+ if (!std::isfinite(boxlo[0]) || !std::isfinite(boxlo[1]) || !std::isfinite(boxlo[2]))
error->one(FLERR,"Non-numeric box dimensions - simulation unstable");
int flag = 0;
diff --git a/src/KSPACE/pppm_disp.cpp b/src/KSPACE/pppm_disp.cpp
index 3e764cc3e7f6f3104f2d0a0722a4e72b5399ebe5..aea57da326e7f75b15a23ad3945a552f3eb56be9 100644
--- a/src/KSPACE/pppm_disp.cpp
+++ b/src/KSPACE/pppm_disp.cpp
@@ -17,10 +17,10 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <string.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <math.h>
+#include <cstring>
+#include <cstdio>
+#include <cstdlib>
+#include <cmath>
#include "pppm_disp.h"
#include "math_const.h"
#include "atom.h"
@@ -46,7 +46,6 @@ using namespace MathConst;
#define LARGE 10000.0
#define EPS_HOC 1.0e-7
-enum{GEOMETRIC,ARITHMETIC,SIXTHPOWER};
enum{REVERSE_RHO, REVERSE_RHO_G, REVERSE_RHO_A, REVERSE_RHO_NONE};
enum{FORWARD_IK, FORWARD_AD, FORWARD_IK_PERATOM, FORWARD_AD_PERATOM,
FORWARD_IK_G, FORWARD_AD_G, FORWARD_IK_PERATOM_G, FORWARD_AD_PERATOM_G,
@@ -304,7 +303,7 @@ void PPPMDisp::init()
// check out which types of potentials will have to be calculated
int ewald_order = ptr ? *((int *) ptr) : 1<<1;
- int ewald_mix = ptr ? *((int *) pair->extract("ewald_mix",tmp)) : GEOMETRIC;
+ int ewald_mix = ptr ? *((int *) pair->extract("ewald_mix",tmp)) : Pair::GEOMETRIC;
memset(function, 0, EWALD_FUNCS*sizeof(int));
for (int i=0; i<=EWALD_MAXORDER; ++i) // transcribe order
if (ewald_order&(1<<i)) { // from pair_style
@@ -314,9 +313,9 @@ void PPPMDisp::init()
case 1:
k = 0; break;
case 6:
- if ((ewald_mix==GEOMETRIC || ewald_mix==SIXTHPOWER ||
+ if ((ewald_mix==Pair::GEOMETRIC || ewald_mix==Pair::SIXTHPOWER ||
mixflag == 1) && mixflag!= 2) { k = 1; break; }
- else if (ewald_mix==ARITHMETIC && mixflag!=2) { k = 2; break; }
+ else if (ewald_mix==Pair::ARITHMETIC && mixflag!=2) { k = 2; break; }
else if (mixflag == 2) { k = 3; break; }
default:
sprintf(str, "Unsupported order in kspace_style "
@@ -4278,7 +4277,7 @@ void PPPMDisp::particle_map(double delx, double dely, double delz,
double **x = atom->x;
int nlocal = atom->nlocal;
- if (!ISFINITE(boxlo[0]) || !ISFINITE(boxlo[1]) || !ISFINITE(boxlo[2]))
+ if (!std::isfinite(boxlo[0]) || !std::isfinite(boxlo[1]) || !std::isfinite(boxlo[2]))
error->one(FLERR,"Non-numeric box dimensions - simulation unstable");
int flag = 0;
diff --git a/src/KSPACE/pppm_disp_tip4p.cpp b/src/KSPACE/pppm_disp_tip4p.cpp
index 686ed3df8ea0903979b2ef8e49289b46072d2507..1a25b300fc34b3db42bc5fb66342d2282704cb55 100644
--- a/src/KSPACE/pppm_disp_tip4p.cpp
+++ b/src/KSPACE/pppm_disp_tip4p.cpp
@@ -16,7 +16,7 @@
Rolf Isele-Holder (Aachen University)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pppm_disp_tip4p.h"
#include "pppm_disp.h"
#include "atom.h"
@@ -78,7 +78,7 @@ void PPPMDispTIP4P::particle_map_c(double delx, double dely, double delz,
double **x = atom->x;
int nlocal = atom->nlocal;
- if (!ISFINITE(boxlo[0]) || !ISFINITE(boxlo[1]) || !ISFINITE(boxlo[2]))
+ if (!std::isfinite(boxlo[0]) || !std::isfinite(boxlo[1]) || !std::isfinite(boxlo[2]))
error->one(FLERR,"Non-numeric box dimensions - simulation unstable");
int flag = 0;
diff --git a/src/KSPACE/pppm_stagger.cpp b/src/KSPACE/pppm_stagger.cpp
index 49c84e58c0b4f36c8be56d758fa2759a0c478c2b..6d3308a05b1d02d1db2344075577676f59d21fd6 100644
--- a/src/KSPACE/pppm_stagger.cpp
+++ b/src/KSPACE/pppm_stagger.cpp
@@ -16,10 +16,10 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <string.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <math.h>
+#include <cstring>
+#include <cstdio>
+#include <cstdlib>
+#include <cmath>
#include "pppm_stagger.h"
#include "atom.h"
#include "gridcomm.h"
@@ -680,7 +680,7 @@ void PPPMStagger::particle_map()
double **x = atom->x;
int nlocal = atom->nlocal;
- if (!ISFINITE(boxlo[0]) || !ISFINITE(boxlo[1]) || !ISFINITE(boxlo[2]))
+ if (!std::isfinite(boxlo[0]) || !std::isfinite(boxlo[1]) || !std::isfinite(boxlo[2]))
error->one(FLERR,"Non-numeric box dimensions - simulation unstable");
int flag = 0;
diff --git a/src/KSPACE/pppm_tip4p.cpp b/src/KSPACE/pppm_tip4p.cpp
index e807f7e2e98a8ecbddca91fdc6ddb0d29c3ff46d..08fc8c711cdb869e45dffefe6da6cae176d2ad69 100644
--- a/src/KSPACE/pppm_tip4p.cpp
+++ b/src/KSPACE/pppm_tip4p.cpp
@@ -15,7 +15,7 @@
Contributing authors: Amalie Frischknecht and Ahmed Ismail (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pppm_tip4p.h"
#include "atom.h"
#include "domain.h"
@@ -73,7 +73,7 @@ void PPPMTIP4P::particle_map()
double **x = atom->x;
int nlocal = atom->nlocal;
- if (!ISFINITE(boxlo[0]) || !ISFINITE(boxlo[1]) || !ISFINITE(boxlo[2]))
+ if (!std::isfinite(boxlo[0]) || !std::isfinite(boxlo[1]) || !std::isfinite(boxlo[2]))
error->one(FLERR,"Non-numeric box dimensions - simulation unstable");
int flag = 0;
diff --git a/src/KSPACE/remap.cpp b/src/KSPACE/remap.cpp
index 86522f3f2f7f166c6e34e6043047998d0178cc37..81dd692f4f91a44cebfdf68ab2ca79d8d37f0973 100644
--- a/src/KSPACE/remap.cpp
+++ b/src/KSPACE/remap.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <stdio.h>
-#include <stdlib.h>
+#include <cstdio>
+#include <cstdlib>
#include "remap.h"
#define PACK_DATA FFT_SCALAR
diff --git a/src/LATTE/Install.sh b/src/LATTE/Install.sh
old mode 100644
new mode 100755
index d034774e7aa3c06ad7885a9669949b4e21e2bcfb..73f8bc24cb02fa689591f97ca521f362cba7d277
--- a/src/LATTE/Install.sh
+++ b/src/LATTE/Install.sh
@@ -29,7 +29,7 @@ action () {
# all package files with no dependencies
for file in *.cpp *.h; do
- action $file
+ test -f ${file} && action $file
done
# edit 2 Makefile.package files to include/exclude package info
diff --git a/src/LATTE/fix_latte.cpp b/src/LATTE/fix_latte.cpp
index 4594f26f8f8c182901ed564895e5814d77cb5e06..c2bfa1a5a1f1ba6500b4da5baa4633833abb6d1b 100644
--- a/src/LATTE/fix_latte.cpp
+++ b/src/LATTE/fix_latte.cpp
@@ -15,8 +15,8 @@
Contributing author: Christian Negre (LANL)
------------------------------------------------------------------------- */
-#include <stdio.h>
-#include <string.h>
+#include <cstdio>
+#include <cstring>
#include "fix_latte.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/MANYBODY/fix_qeq_comb.cpp b/src/MANYBODY/fix_qeq_comb.cpp
index c0d36d8fac60f3df808ab251ac409c9c52457d44..b8d9c7e6dfb7b0c739f5195e538f7c4c399625db 100644
--- a/src/MANYBODY/fix_qeq_comb.cpp
+++ b/src/MANYBODY/fix_qeq_comb.cpp
@@ -16,9 +16,9 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "pair_comb.h"
#include "pair_comb3.h"
#include "fix_qeq_comb.h"
diff --git a/src/MANYBODY/fix_qeq_comb.h b/src/MANYBODY/fix_qeq_comb.h
index 384ea4bbccacd267300b1e8d36620f722affd0a5..dd4c9f729085ad8bc107b748036c57b57cc8c515 100644
--- a/src/MANYBODY/fix_qeq_comb.h
+++ b/src/MANYBODY/fix_qeq_comb.h
@@ -20,7 +20,7 @@ FixStyle(qeq/comb,FixQEQComb)
#ifndef LMP_FIX_QEQ_COMB_H
#define LMP_FIX_QEQ_COMB_H
-#include <stdio.h>
+#include <cstdio>
#include "fix.h"
namespace LAMMPS_NS {
diff --git a/src/MANYBODY/pair_adp.cpp b/src/MANYBODY/pair_adp.cpp
index 579675c4a020a1d08c60bb39b785a250e3edd8e8..d0b4d197583d260ccf42592dbb7b5921b0384d9d 100644
--- a/src/MANYBODY/pair_adp.cpp
+++ b/src/MANYBODY/pair_adp.cpp
@@ -16,10 +16,10 @@
Chandra Veer Singh (Cornell)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_adp.h"
#include "atom.h"
#include "force.h"
diff --git a/src/MANYBODY/pair_airebo.cpp b/src/MANYBODY/pair_airebo.cpp
index fd5691fecbc508cb7456e7885cac98db39f3a184..3be27354c15c46929e4700e8f453f2f1cce45c5e 100644
--- a/src/MANYBODY/pair_airebo.cpp
+++ b/src/MANYBODY/pair_airebo.cpp
@@ -20,10 +20,10 @@
Thomas C. O'Connor (JHU) 2014
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include <mpi.h>
#include "pair_airebo.h"
#include "atom.h"
diff --git a/src/MANYBODY/pair_airebo.h b/src/MANYBODY/pair_airebo.h
index d9628f3bb30893590c26d6260d1cb1e2da10acc7..c7c9b07357c2ae11bbd6a48ac427d6e435f1257e 100644
--- a/src/MANYBODY/pair_airebo.h
+++ b/src/MANYBODY/pair_airebo.h
@@ -22,7 +22,7 @@ PairStyle(airebo,PairAIREBO)
#include "pair.h"
#include "my_page.h"
-#include <math.h>
+#include <cmath>
#include "math_const.h"
namespace LAMMPS_NS {
diff --git a/src/MANYBODY/pair_bop.cpp b/src/MANYBODY/pair_bop.cpp
index 04d7cd41531a87dc4505a969dd14c69f9e974302..87a23dff99c4c16bd88fd68101f0b0103f08ab39 100644
--- a/src/MANYBODY/pair_bop.cpp
+++ b/src/MANYBODY/pair_bop.cpp
@@ -32,10 +32,10 @@
Rules"_http://lammps.sandia.gov/open_source.html
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include <mpi.h>
#include "pair_bop.h"
#include "atom.h"
@@ -49,7 +49,7 @@
#include "neigh_request.h"
#include "memory.h"
#include "error.h"
-#include <ctype.h>
+#include <cctype>
using namespace LAMMPS_NS;
diff --git a/src/MANYBODY/pair_bop.h b/src/MANYBODY/pair_bop.h
index ec6448db47c19cc53616a1945ecd74fff619c267..3bd9b8cea970da0ea9ede32c54c3290cf10c4644 100644
--- a/src/MANYBODY/pair_bop.h
+++ b/src/MANYBODY/pair_bop.h
@@ -26,7 +26,7 @@ PairStyle(bop,PairBOP)
#define LMP_PAIR_BOP_H
#include "pair.h"
-#include <time.h>
+#include <ctime>
#include "update.h"
namespace LAMMPS_NS {
diff --git a/src/MANYBODY/pair_comb.cpp b/src/MANYBODY/pair_comb.cpp
index 5a2b4c25403bb99d85c579640c663a312493c4e1..de686d4bcf5e68ebf9dedaf9aacc72dd3a3e8c65 100644
--- a/src/MANYBODY/pair_comb.cpp
+++ b/src/MANYBODY/pair_comb.cpp
@@ -18,10 +18,10 @@
and Aidan Thompson's Tersoff code in LAMMPS
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_comb.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/MANYBODY/pair_comb3.cpp b/src/MANYBODY/pair_comb3.cpp
index 743511e753201a7c7ee0afdd5e7b6f535ab05277..b4f9c02206f926d39307b19317bd7e00b9cd16eb 100644
--- a/src/MANYBODY/pair_comb3.cpp
+++ b/src/MANYBODY/pair_comb3.cpp
@@ -17,10 +17,10 @@
Dundar Yilmaz (dundar.yilmaz@zirve.edu.tr)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_comb3.h"
#include "atom.h"
#include "comm.h"
@@ -310,10 +310,10 @@ double PairComb3::init_one(int i, int j)
void PairComb3::read_lib()
{
- unsigned int maxlib = 1024;
+ const unsigned int MAXLIB = 1024;
int i,j,k,l,nwords,m;
int ii,jj,kk,ll,mm,iii;
- char s[maxlib];
+ char s[MAXLIB];
char **words = new char*[80];
// open libraray file on proc 0
@@ -327,8 +327,8 @@ void PairComb3::read_lib()
}
// read and store at the same time
- fgets(s,maxlib,fp);
- fgets(s,maxlib,fp);
+ fgets(s,MAXLIB,fp);
+ fgets(s,MAXLIB,fp);
nwords = 0;
words[nwords++] = strtok(s," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
@@ -339,7 +339,7 @@ void PairComb3::read_lib()
ccutoff[4] = atof(words[4]);
ccutoff[5] = atof(words[5]);
- fgets(s,maxlib,fp);
+ fgets(s,MAXLIB,fp);
nwords = 0;
words[nwords++] = strtok(s," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
@@ -351,7 +351,7 @@ void PairComb3::read_lib()
ch_a[5] = atof(words[5]);
ch_a[6] = atof(words[6]);
- fgets(s,maxlib,fp);
+ fgets(s,MAXLIB,fp);
nwords = 0;
words[nwords++] = strtok(s," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
@@ -359,7 +359,7 @@ void PairComb3::read_lib()
nsplrad = atoi(words[1]);
nspltor = atoi(words[2]);
- fgets(s,maxlib,fp);
+ fgets(s,MAXLIB,fp);
nwords = 0;
words[nwords++] = strtok(s," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
@@ -367,7 +367,7 @@ void PairComb3::read_lib()
maxy = atoi(words[1]);
maxz = atoi(words[2]);
- fgets(s,maxlib,fp);
+ fgets(s,MAXLIB,fp);
nwords = 0;
words[nwords++] = strtok(s," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
@@ -376,7 +376,7 @@ void PairComb3::read_lib()
maxconj = atoi(words[2]);
for (l=0; l<nsplpcn; l++) {
- fgets(s,maxlib,fp);
+ fgets(s,MAXLIB,fp);
nwords = 0;
words[nwords++] = strtok(s," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
@@ -385,14 +385,14 @@ void PairComb3::read_lib()
dvmaxxcn[l] = atof(words[3]);
}
- fgets(s,maxlib,fp);
+ fgets(s,MAXLIB,fp);
nwords = 0;
words[nwords++] = strtok(s," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
ntab = atoi(words[0]);
for (i=0; i<ntab+1; i++){
- fgets(s,maxlib,fp);
+ fgets(s,MAXLIB,fp);
nwords = 0;
words[nwords++] = strtok(s," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
@@ -405,7 +405,7 @@ void PairComb3::read_lib()
for (i=0; i<maxx+1; i++)
for (j=0; j<maxy+1; j++)
for (k=0; k<maxz+1; k++) {
- fgets(s,maxlib,fp);
+ fgets(s,MAXLIB,fp);
nwords = 0;
words[nwords++] = strtok(s," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
@@ -423,7 +423,7 @@ void PairComb3::read_lib()
for (i=0; i<maxx; i++)
for (j=0; j<maxy; j++)
for (k=0; k<maxz; k++) {
- fgets(s,maxlib,fp);
+ fgets(s,MAXLIB,fp);
nwords = 0;
words[nwords++] = strtok(s," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
@@ -432,7 +432,7 @@ void PairComb3::read_lib()
jj = atoi(words[2]);
kk = atoi(words[3]);
for(iii=0; iii<2; iii++) {
- fgets(s,maxlib,fp);
+ fgets(s,MAXLIB,fp);
nwords = 0;
words[nwords++] = strtok(s," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
@@ -447,7 +447,7 @@ void PairComb3::read_lib()
for (i=0; i<maxxc+1; i++)
for (j=0; j<maxyc+1; j++)
for (k=0; k<maxconj; k++) {
- fgets(s,maxlib,fp);
+ fgets(s,MAXLIB,fp);
nwords = 0;
words[nwords++] = strtok(s," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
@@ -465,7 +465,7 @@ void PairComb3::read_lib()
for (i=0; i<maxxc; i++)
for (j=0; j<maxyc; j++)
for (k=0; k<maxconj-1; k++) {
- fgets(s,maxlib,fp);
+ fgets(s,MAXLIB,fp);
nwords = 0;
words[nwords++] = strtok(s," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
@@ -474,7 +474,7 @@ void PairComb3::read_lib()
jj = atoi(words[2]);
kk = atoi(words[3])-1;
for (iii=0; iii<2; iii++) {
- fgets(s,maxlib,fp);
+ fgets(s,MAXLIB,fp);
nwords = 0;
words[nwords++] = strtok(s," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
@@ -489,7 +489,7 @@ void PairComb3::read_lib()
for (i=0; i<maxxc+1; i++)
for (j=0; j<maxyc+1; j++)
for (k=0; k<maxconj; k++) {
- fgets(s,maxlib,fp);
+ fgets(s,MAXLIB,fp);
nwords = 0;
words[nwords++] = strtok(s," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
@@ -507,7 +507,7 @@ void PairComb3::read_lib()
for (i=0; i<maxxc; i++)
for (j=0; j<maxyc; j++)
for (k=0; k<maxconj-1; k++) {
- fgets(s,maxlib,fp);
+ fgets(s,MAXLIB,fp);
nwords = 0;
words[nwords++] = strtok(s," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
@@ -516,7 +516,7 @@ void PairComb3::read_lib()
jj = atoi(words[2]);
kk = atoi(words[3])-1;
for(iii=0; iii<2; iii++) {
- fgets(s,maxlib,fp);
+ fgets(s,MAXLIB,fp);
nwords = 0;
words[nwords++] = strtok(s," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f")))continue;
diff --git a/src/MANYBODY/pair_eam.cpp b/src/MANYBODY/pair_eam.cpp
index 29a627e1d09b9406eb7372dfd33f28fb1110b355..9e70b19eea753ee8174808c5e063390123f6ba47 100644
--- a/src/MANYBODY/pair_eam.cpp
+++ b/src/MANYBODY/pair_eam.cpp
@@ -15,10 +15,10 @@
Contributing authors: Stephen Foiles (SNL), Murray Daw (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_eam.h"
#include "atom.h"
#include "force.h"
diff --git a/src/MANYBODY/pair_eam.h b/src/MANYBODY/pair_eam.h
index 63fdde9fc5a7a060e00ec704c2522fad0526a79a..234552157b305e7c439d0b04bf529c5c07a62934 100644
--- a/src/MANYBODY/pair_eam.h
+++ b/src/MANYBODY/pair_eam.h
@@ -20,7 +20,7 @@ PairStyle(eam,PairEAM)
#ifndef LMP_PAIR_EAM_H
#define LMP_PAIR_EAM_H
-#include <stdio.h>
+#include <cstdio>
#include "pair.h"
namespace LAMMPS_NS {
diff --git a/src/MANYBODY/pair_eam_alloy.cpp b/src/MANYBODY/pair_eam_alloy.cpp
index e22b4642a82d5609710c287fbabda4fe67792fd1..eed38f79e9f75c9a258dec18edff32307dbdfaf9 100644
--- a/src/MANYBODY/pair_eam_alloy.cpp
+++ b/src/MANYBODY/pair_eam_alloy.cpp
@@ -15,9 +15,9 @@
Contributing authors: Stephen Foiles (SNL), Murray Daw (SNL)
------------------------------------------------------------------------- */
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_eam_alloy.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/MANYBODY/pair_eam_fs.cpp b/src/MANYBODY/pair_eam_fs.cpp
index 2817e13f8a3b96d9121983e3710e0e29f64cb0eb..2b5d530d3a962e2c15b3e8dbc3d05ba2d59ac3f4 100644
--- a/src/MANYBODY/pair_eam_fs.cpp
+++ b/src/MANYBODY/pair_eam_fs.cpp
@@ -15,9 +15,9 @@
Contributing authors: Tim Lau (MIT)
------------------------------------------------------------------------- */
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_eam_fs.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/MANYBODY/pair_eim.cpp b/src/MANYBODY/pair_eim.cpp
index e2d8a88aee67c9ddb852865d29b095097145f14a..b810d444fc6483cde6a87733b9376557efce7739 100644
--- a/src/MANYBODY/pair_eim.cpp
+++ b/src/MANYBODY/pair_eim.cpp
@@ -15,10 +15,10 @@
Contributing author: Xiaowang Zhou (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_eim.h"
#include "atom.h"
#include "force.h"
diff --git a/src/MANYBODY/pair_eim.h b/src/MANYBODY/pair_eim.h
index 9b2d518a2a20d97af6ed3cc25cdb56c2ea10198f..50f9934c44b94ad6c74533bba1e9684ddfe15ade 100644
--- a/src/MANYBODY/pair_eim.h
+++ b/src/MANYBODY/pair_eim.h
@@ -20,7 +20,7 @@ PairStyle(eim,PairEIM)
#ifndef LMP_PAIR_EIM_H
#define LMP_PAIR_EIM_H
-#include <stdio.h>
+#include <cstdio>
#include "pair.h"
namespace LAMMPS_NS {
diff --git a/src/MANYBODY/pair_gw.cpp b/src/MANYBODY/pair_gw.cpp
index 8befa42d1c6ec5f022eb18ddf7c435253e9a0a1e..35f092b580e4693e45db8bbda6b0a12d20a094ac 100644
--- a/src/MANYBODY/pair_gw.cpp
+++ b/src/MANYBODY/pair_gw.cpp
@@ -16,10 +16,10 @@
based on PairTersoff by Aidan Thompson (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_gw.h"
#include "atom.h"
#include "neighbor.h"
diff --git a/src/MANYBODY/pair_gw_zbl.cpp b/src/MANYBODY/pair_gw_zbl.cpp
index a4e1ccb1f994b4a612b2eba8e9baf737891d6edb..81d4866e84f6a654dd057b9ea892ae9f6ce12505 100644
--- a/src/MANYBODY/pair_gw_zbl.cpp
+++ b/src/MANYBODY/pair_gw_zbl.cpp
@@ -16,10 +16,10 @@
Based on PairTersoffZBL by Aidan Thompson (SNL) and David Farrell (NWU)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_gw_zbl.h"
#include "atom.h"
#include "update.h"
diff --git a/src/MANYBODY/pair_lcbop.cpp b/src/MANYBODY/pair_lcbop.cpp
index 414f2adb741f4cbef4338eb2cbbec7eaee21bd4f..d334defcc607447a357b6a2da1d215d6dcd6cba5 100644
--- a/src/MANYBODY/pair_lcbop.cpp
+++ b/src/MANYBODY/pair_lcbop.cpp
@@ -16,10 +16,10 @@
based on pair_airebo by Ase Henry (MIT)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include <mpi.h>
#include "pair_lcbop.h"
#include "atom.h"
diff --git a/src/MANYBODY/pair_lcbop.h b/src/MANYBODY/pair_lcbop.h
index c099c7c4a1be2e64f5a664551b05c77fcaf718bf..0d7c7a51b17e220abc290d9d348398894c2dc08c 100644
--- a/src/MANYBODY/pair_lcbop.h
+++ b/src/MANYBODY/pair_lcbop.h
@@ -22,7 +22,7 @@ PairStyle(lcbop,PairLCBOP)
#include "pair.h"
#include "my_page.h"
-#include <math.h>
+#include <cmath>
#include "math_const.h"
namespace LAMMPS_NS {
diff --git a/src/MANYBODY/pair_nb3b_harmonic.cpp b/src/MANYBODY/pair_nb3b_harmonic.cpp
index 0b930c73608c1996a9e58f279332a19ac5f50bf9..36be9c2b90758b075a7566f6c469d038049c2f5d 100644
--- a/src/MANYBODY/pair_nb3b_harmonic.cpp
+++ b/src/MANYBODY/pair_nb3b_harmonic.cpp
@@ -16,10 +16,10 @@
(based on Stillinger-Weber pair style)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_nb3b_harmonic.h"
#include "atom.h"
#include "neighbor.h"
diff --git a/src/MANYBODY/pair_polymorphic.cpp b/src/MANYBODY/pair_polymorphic.cpp
index 9ceceed076825d4d81c4a90c85c9a40969a8def1..2afb08b7a1e6e56059a44c3e862d047bb95566be 100644
--- a/src/MANYBODY/pair_polymorphic.cpp
+++ b/src/MANYBODY/pair_polymorphic.cpp
@@ -16,10 +16,10 @@
This modifies from pair_tersoff.cpp by Aidan Thompson (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_polymorphic.h"
#include "atom.h"
#include "neighbor.h"
diff --git a/src/MANYBODY/pair_polymorphic.h b/src/MANYBODY/pair_polymorphic.h
index 3b5407f802938e4e78cf42e9a5669278ea92a402..32f1c5414a6714847f2877a643224d50544cf89f 100644
--- a/src/MANYBODY/pair_polymorphic.h
+++ b/src/MANYBODY/pair_polymorphic.h
@@ -21,7 +21,7 @@ PairStyle(polymorphic,PairPolymorphic)
#define LMP_PAIR_POLYMORPHIC_H
#include "pair.h"
-#include <math.h>
+#include <cmath>
namespace LAMMPS_NS {
diff --git a/src/MANYBODY/pair_sw.cpp b/src/MANYBODY/pair_sw.cpp
index da2f5da37e003119d2f77521f883bbb28630bc20..6fbc00204c3ba8e046262799357281d8730e4d22 100644
--- a/src/MANYBODY/pair_sw.cpp
+++ b/src/MANYBODY/pair_sw.cpp
@@ -15,10 +15,10 @@
Contributing author: Aidan Thompson (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_sw.h"
#include "atom.h"
#include "neighbor.h"
diff --git a/src/MANYBODY/pair_tersoff.cpp b/src/MANYBODY/pair_tersoff.cpp
index 047c59fc87797802531951c2f6abf81ca5c6e716..507b07e29a21fc1031b1c25269f35da942d19715 100644
--- a/src/MANYBODY/pair_tersoff.cpp
+++ b/src/MANYBODY/pair_tersoff.cpp
@@ -15,10 +15,10 @@
Contributing author: Aidan Thompson (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_tersoff.h"
#include "atom.h"
#include "neighbor.h"
diff --git a/src/MANYBODY/pair_tersoff_mod.cpp b/src/MANYBODY/pair_tersoff_mod.cpp
index a90cf3bb77fbcbce5f9609aa507ec3e44ffb023b..73297fb53451640d9cf105de3367d49b5cb78c82 100644
--- a/src/MANYBODY/pair_tersoff_mod.cpp
+++ b/src/MANYBODY/pair_tersoff_mod.cpp
@@ -16,10 +16,10 @@
Vitaly Dozhdikov (JIHT of RAS) - MOD addition
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_tersoff_mod.h"
#include "atom.h"
#include "neighbor.h"
diff --git a/src/MANYBODY/pair_tersoff_mod.h b/src/MANYBODY/pair_tersoff_mod.h
index 42a3a2b26c96ca2511ef0968b70177234bc88860..162603bc5ca42d16fe513e949b609583d74c83bd 100644
--- a/src/MANYBODY/pair_tersoff_mod.h
+++ b/src/MANYBODY/pair_tersoff_mod.h
@@ -21,7 +21,7 @@ PairStyle(tersoff/mod,PairTersoffMOD)
#define LMP_PAIR_TERSOFF_MOD_H
#include "pair_tersoff.h"
-#include <math.h>
+#include <cmath>
namespace LAMMPS_NS {
diff --git a/src/MANYBODY/pair_tersoff_mod_c.cpp b/src/MANYBODY/pair_tersoff_mod_c.cpp
index c0d6cb164a2d98dc13449c591e7e7e96cddaad7e..0d0016664a1dd93c1a981ae95af29958ef012c1f 100644
--- a/src/MANYBODY/pair_tersoff_mod_c.cpp
+++ b/src/MANYBODY/pair_tersoff_mod_c.cpp
@@ -15,10 +15,10 @@
Contributing author: Ganga P Purja Pun (George Mason University, Fairfax)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_tersoff_mod_c.h"
#include "atom.h"
#include "neighbor.h"
diff --git a/src/MANYBODY/pair_tersoff_zbl.cpp b/src/MANYBODY/pair_tersoff_zbl.cpp
index 15163c2bf9843607dde1f65d8e78d0abdef78957..1692c88a5087b1f970a63a3b4dce00705a5358f6 100644
--- a/src/MANYBODY/pair_tersoff_zbl.cpp
+++ b/src/MANYBODY/pair_tersoff_zbl.cpp
@@ -16,10 +16,10 @@
David Farrell (NWU) - ZBL addition
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_tersoff_zbl.h"
#include "atom.h"
#include "update.h"
diff --git a/src/MANYBODY/pair_vashishta.cpp b/src/MANYBODY/pair_vashishta.cpp
index bc594d9b4daf614bc0bc3afe835bb86bd0dfcd82..8506c9a69fd79f35f362f5f24f65854cf34e5537 100644
--- a/src/MANYBODY/pair_vashishta.cpp
+++ b/src/MANYBODY/pair_vashishta.cpp
@@ -16,10 +16,10 @@
Aidan Thompson (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_vashishta.h"
#include "atom.h"
#include "neighbor.h"
diff --git a/src/MANYBODY/pair_vashishta_table.cpp b/src/MANYBODY/pair_vashishta_table.cpp
index 88a7040d761d6127bd2f08a3e727dcbfd9b7f169..1055db99fa8b06df3e880280d839aafd19ef1650 100644
--- a/src/MANYBODY/pair_vashishta_table.cpp
+++ b/src/MANYBODY/pair_vashishta_table.cpp
@@ -15,10 +15,10 @@
Contributing author: Anders Hafreager (UiO), andershaf@gmail.com
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_vashishta_table.h"
#include "atom.h"
#include "neighbor.h"
diff --git a/src/MC/fix_atom_swap.cpp b/src/MC/fix_atom_swap.cpp
index 100600c0daeb2c169b6ed0a9ed66243315603e1e..4d9377022b265fe1488bf241e4ac69f3c1185252 100644
--- a/src/MC/fix_atom_swap.cpp
+++ b/src/MC/fix_atom_swap.cpp
@@ -16,10 +16,10 @@
Alexander Stukowski
------------------------------------------------------------------------- */
-#include <math.h>
-#include <float.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cfloat>
+#include <cstdlib>
+#include <cstring>
#include "fix_atom_swap.h"
#include "atom.h"
#include "atom_vec.h"
diff --git a/src/MC/fix_atom_swap.h b/src/MC/fix_atom_swap.h
index 74720d6222e1dcdf9cfc3a4d054c60a609cd9c43..19895704f186dd87325acfcefc56d6ad902863ff 100644
--- a/src/MC/fix_atom_swap.h
+++ b/src/MC/fix_atom_swap.h
@@ -20,7 +20,7 @@ FixStyle(atom/swap,FixAtomSwap)
#ifndef LMP_FIX_MCSWAP_H
#define LMP_FIX_MCSWAP_H
-#include <stdio.h>
+#include <cstdio>
#include "fix.h"
namespace LAMMPS_NS {
diff --git a/src/MC/fix_bond_break.cpp b/src/MC/fix_bond_break.cpp
index 711f764282b92737b6b98fda94c9cbd4ffe16fd2..9a5b59b60188b89d2cf671a1a3fbf1db1e265daa 100644
--- a/src/MC/fix_bond_break.cpp
+++ b/src/MC/fix_bond_break.cpp
@@ -11,10 +11,10 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include <mpi.h>
-#include <string.h>
-#include <stdlib.h>
+#include <cstring>
+#include <cstdlib>
#include "fix_bond_break.h"
#include "update.h"
#include "respa.h"
diff --git a/src/MC/fix_bond_create.cpp b/src/MC/fix_bond_create.cpp
index 789f1794f1864f1823def41669bb5250b452ce08..8e9db6a18b130819adbbf280fdbdae9ce2c9fea4 100644
--- a/src/MC/fix_bond_create.cpp
+++ b/src/MC/fix_bond_create.cpp
@@ -11,10 +11,10 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include <mpi.h>
-#include <string.h>
-#include <stdlib.h>
+#include <cstring>
+#include <cstdlib>
#include "fix_bond_create.h"
#include "update.h"
#include "respa.h"
diff --git a/src/MC/fix_bond_swap.cpp b/src/MC/fix_bond_swap.cpp
index d5b7394dd1e799ea32299f82233b29d641baf7df..d6df4d9a960343520e610280e5941600584b6050 100644
--- a/src/MC/fix_bond_swap.cpp
+++ b/src/MC/fix_bond_swap.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "fix_bond_swap.h"
#include "atom.h"
#include "force.h"
diff --git a/src/MC/fix_gcmc.cpp b/src/MC/fix_gcmc.cpp
index f2c41c9ccf0559ee3103c99d62994d95e2af907d..6221e6d52c26b359d9efd7d87460a1ed3ceacaf3 100644
--- a/src/MC/fix_gcmc.cpp
+++ b/src/MC/fix_gcmc.cpp
@@ -15,9 +15,9 @@
Contributing author: Paul Crozier, Aidan Thompson (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "fix_gcmc.h"
#include "atom.h"
#include "atom_vec.h"
@@ -1349,7 +1349,7 @@ void FixGCMC::attempt_molecule_insertion()
MathExtra::quat_to_mat(quat,rotmat);
double insertion_energy = 0.0;
- bool procflag[natoms_per_molecule];
+ bool *procflag = new bool[natoms_per_molecule];
for (int i = 0; i < natoms_per_molecule; i++) {
MathExtra::matvec(rotmat,onemols[imol]->x[i],molcoords[i]);
@@ -1472,6 +1472,7 @@ void FixGCMC::attempt_molecule_insertion()
update_gas_atoms_list();
ninsertion_successes += 1.0;
}
+ delete[] procflag;
}
/* ----------------------------------------------------------------------
@@ -1934,7 +1935,7 @@ void FixGCMC::attempt_molecule_deletion_full()
grow_molecule_arrays(nmolq);
int m = 0;
- int tmpmask[atom->nlocal];
+ int *tmpmask = new int[atom->nlocal];
for (int i = 0; i < atom->nlocal; i++) {
if (atom->molecule[i] == deletion_molecule) {
tmpmask[i] = atom->mask[i];
@@ -1982,6 +1983,7 @@ void FixGCMC::attempt_molecule_deletion_full()
if (force->kspace) force->kspace->qsum_qsq();
}
update_gas_atoms_list();
+ delete[] tmpmask;
}
/* ----------------------------------------------------------------------
@@ -2426,9 +2428,9 @@ void FixGCMC::update_gas_atoms_list()
for (int i = 0; i < nlocal; i++) maxmol = MAX(maxmol,molecule[i]);
tagint maxmol_all;
MPI_Allreduce(&maxmol,&maxmol_all,1,MPI_LMP_TAGINT,MPI_MAX,world);
- double comx[maxmol_all];
- double comy[maxmol_all];
- double comz[maxmol_all];
+ double *comx = new double[maxmol_all];
+ double *comy = new double[maxmol_all];
+ double *comz = new double[maxmol_all];
for (int imolecule = 0; imolecule < maxmol_all; imolecule++) {
for (int i = 0; i < nlocal; i++) {
if (molecule[i] == imolecule) {
@@ -2458,7 +2460,9 @@ void FixGCMC::update_gas_atoms_list()
}
}
}
-
+ delete[] comx;
+ delete[] comy;
+ delete[] comz;
} else {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
diff --git a/src/MC/fix_gcmc.h b/src/MC/fix_gcmc.h
index e8de53215fcd319bb0ecc62fb42c2ec11071c150..5d0b7aab8fab5377f2ec065110b76fce99816851 100644
--- a/src/MC/fix_gcmc.h
+++ b/src/MC/fix_gcmc.h
@@ -20,7 +20,7 @@ FixStyle(gcmc,FixGCMC)
#ifndef LMP_FIX_GCMC_H
#define LMP_FIX_GCMC_H
-#include <stdio.h>
+#include <cstdio>
#include "fix.h"
namespace LAMMPS_NS {
diff --git a/src/MC/fix_tfmc.cpp b/src/MC/fix_tfmc.cpp
index 60ded5fd4470edab95493552700d820111323b9c..b8217103535a2e08826fffa134c831e3856bdffe 100644
--- a/src/MC/fix_tfmc.cpp
+++ b/src/MC/fix_tfmc.cpp
@@ -17,9 +17,9 @@
#include "fix_tfmc.h"
#include <mpi.h>
-#include <string.h>
-#include <math.h>
-#include <float.h>
+#include <cstring>
+#include <cmath>
+#include <cfloat>
#include "atom.h"
#include "force.h"
#include "update.h"
diff --git a/src/MC/pair_dsmc.cpp b/src/MC/pair_dsmc.cpp
index d3327eea296b943a8c49e0bf57d270b6a7917944..02f9754c2a2fdd1a78565931d607010ca66e1a49 100644
--- a/src/MC/pair_dsmc.cpp
+++ b/src/MC/pair_dsmc.cpp
@@ -15,10 +15,11 @@
Contributing authors: Paul Crozier (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
+#include <climits>
#include "pair_dsmc.h"
#include "atom.h"
#include "comm.h"
@@ -28,7 +29,6 @@
#include "domain.h"
#include "update.h"
#include "random_mars.h"
-#include <limits.h>
using namespace LAMMPS_NS;
diff --git a/src/MEAM/Install.sh b/src/MEAM/Install.sh
old mode 100644
new mode 100755
diff --git a/src/MEAM/pair_meam.cpp b/src/MEAM/pair_meam.cpp
index fa47944cd50944c4e5c631b8088c42a51c519f86..687055aa6a6735fceb1749c4124ae73797dc8d9f 100644
--- a/src/MEAM/pair_meam.cpp
+++ b/src/MEAM/pair_meam.cpp
@@ -15,10 +15,10 @@
Contributing author: Greg Wagner (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_meam.h"
#include "atom.h"
#include "force.h"
diff --git a/src/MISC/compute_msd_nongauss.cpp b/src/MISC/compute_msd_nongauss.cpp
index 4639fa7916c116ef0f4786819c716b0cf91474b3..f6291f4204e0633921c69f63c3f0709922e7fe24 100644
--- a/src/MISC/compute_msd_nongauss.cpp
+++ b/src/MISC/compute_msd_nongauss.cpp
@@ -15,7 +15,7 @@
Contributing authors: Rob Hoy
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "compute_msd_nongauss.h"
#include "atom.h"
#include "update.h"
diff --git a/src/MISC/compute_ti.cpp b/src/MISC/compute_ti.cpp
index 9f1b2898bbe67ea3d3fc1f73bef1db7c46bd42bc..d2e43a9f69ffd417afd1668b983b2225960816b1 100644
--- a/src/MISC/compute_ti.cpp
+++ b/src/MISC/compute_ti.cpp
@@ -17,7 +17,7 @@
#include <mpi.h>
#include "atom.h"
-#include <string.h>
+#include <cstring>
#include "compute_ti.h"
#include "update.h"
#include "modify.h"
diff --git a/src/MISC/dump_xtc.cpp b/src/MISC/dump_xtc.cpp
index 674e480f9e697fd0b2049d208fa79094e2b99ff8..a82cba20bde3fd4e1c05bac4525abe898d61fbae 100644
--- a/src/MISC/dump_xtc.cpp
+++ b/src/MISC/dump_xtc.cpp
@@ -22,11 +22,11 @@
support for groups
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-#include <limits.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
+#include <climits>
#include "dump_xtc.h"
#include "domain.h"
#include "atom.h"
diff --git a/src/MISC/fix_deposit.cpp b/src/MISC/fix_deposit.cpp
index 023ec797df0099d3724beac106ebfdb5f8f39497..1428299eb7d8366446cff2323f7c5f7496311f5e 100644
--- a/src/MISC/fix_deposit.cpp
+++ b/src/MISC/fix_deposit.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "fix_deposit.h"
#include "atom.h"
#include "atom_vec.h"
@@ -37,7 +37,6 @@ using namespace FixConst;
using namespace MathConst;
enum{ATOM,MOLECULE};
-enum{LAYOUT_UNIFORM,LAYOUT_NONUNIFORM,LAYOUT_TILED}; // several files
enum{DIST_UNIFORM,DIST_GAUSSIAN};
#define EPSILON 1.0e6
@@ -506,7 +505,7 @@ void FixDeposit::pre_exchange()
newcoord[1] >= sublo[1] && newcoord[1] < subhi[1] &&
newcoord[2] >= sublo[2] && newcoord[2] < subhi[2]) flag = 1;
else if (dimension == 3 && newcoord[2] >= domain->boxhi[2]) {
- if (comm->layout != LAYOUT_TILED) {
+ if (comm->layout != Comm::LAYOUT_TILED) {
if (comm->myloc[2] == comm->procgrid[2]-1 &&
newcoord[0] >= sublo[0] && newcoord[0] < subhi[0] &&
newcoord[1] >= sublo[1] && newcoord[1] < subhi[1]) flag = 1;
@@ -516,7 +515,7 @@ void FixDeposit::pre_exchange()
newcoord[1] >= sublo[1] && newcoord[1] < subhi[1]) flag = 1;
}
} else if (dimension == 2 && newcoord[1] >= domain->boxhi[1]) {
- if (comm->layout != LAYOUT_TILED) {
+ if (comm->layout != Comm::LAYOUT_TILED) {
if (comm->myloc[1] == comm->procgrid[1]-1 &&
newcoord[0] >= sublo[0] && newcoord[0] < subhi[0]) flag = 1;
} else {
diff --git a/src/MISC/fix_deposit.h b/src/MISC/fix_deposit.h
index 46de781d8998f4c47a4bc0f75c8ff83afcee27ac..38958b80e7a2af9f0d2d088d5b716f4b575ebe19 100644
--- a/src/MISC/fix_deposit.h
+++ b/src/MISC/fix_deposit.h
@@ -20,7 +20,7 @@ FixStyle(deposit,FixDeposit)
#ifndef LMP_FIX_DEPOSIT_H
#define LMP_FIX_DEPOSIT_H
-#include <stdio.h>
+#include <cstdio>
#include "fix.h"
namespace LAMMPS_NS {
diff --git a/src/MISC/fix_efield.cpp b/src/MISC/fix_efield.cpp
index c0384adc410e64d6c8b337ca9e551bb5bcb5e753..1fa141e2bf3c9ea821436fc46a105dbbf034dd6b 100644
--- a/src/MISC/fix_efield.cpp
+++ b/src/MISC/fix_efield.cpp
@@ -16,9 +16,9 @@
Stan Moore (Sandia) for dipole terms
------------------------------------------------------------------------- */
-#include <math.h>
-#include <string.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstring>
+#include <cstdlib>
#include "fix_efield.h"
#include "atom.h"
#include "update.h"
diff --git a/src/MISC/fix_evaporate.cpp b/src/MISC/fix_evaporate.cpp
index 54d1090892eeb75cc84dd704e987489d14ba7c6e..1bf7a15f1fe02372998cad59e425529e7470a822 100644
--- a/src/MISC/fix_evaporate.cpp
+++ b/src/MISC/fix_evaporate.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "fix_evaporate.h"
#include "atom.h"
#include "atom_vec.h"
diff --git a/src/MISC/fix_gld.cpp b/src/MISC/fix_gld.cpp
index 90579388cc9cb953d6447d40cf2a95ea6514ef45..370730133ee1cc77eaa9dde98bb91ebb5e8bc01c 100644
--- a/src/MISC/fix_gld.cpp
+++ b/src/MISC/fix_gld.cpp
@@ -16,9 +16,9 @@
Andrew Baczewski (Michigan State/SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstring>
#include "fix_gld.h"
#include "math_extra.h"
#include "atom.h"
diff --git a/src/MISC/fix_oneway.cpp b/src/MISC/fix_oneway.cpp
index 758beed5536f273e331a2b814e2cc81b606d4593..73853775a30c2d8db9710101c366a6e714bd3903 100644
--- a/src/MISC/fix_oneway.cpp
+++ b/src/MISC/fix_oneway.cpp
@@ -15,7 +15,7 @@
Contributing author: Axel Kohlmeyer (ICTP, Italy)
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "fix_oneway.h"
#include "atom.h"
#include "domain.h"
diff --git a/src/MISC/fix_orient_bcc.cpp b/src/MISC/fix_orient_bcc.cpp
index 0cb0f96aa8d722bffed2edb04999cb7a36c41217..c5ba6514a90c566688e530f85d65415039586b22 100644
--- a/src/MISC/fix_orient_bcc.cpp
+++ b/src/MISC/fix_orient_bcc.cpp
@@ -18,9 +18,9 @@
(https://dx.doi.org/10.6084/m9.figshare.1488628.v1
------------------------------------------------------------------------- */
-#include <math.h>
-#include <string.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstring>
+#include <cstdlib>
#include <mpi.h>
#include "fix_orient_bcc.h"
#include "atom.h"
diff --git a/src/MISC/fix_orient_fcc.cpp b/src/MISC/fix_orient_fcc.cpp
index 6743132cfa2e0f1d862626e4b4a1de040f9d45b7..5786571a89e9a9ccb8445ee2bc4c5582af8c22f6 100644
--- a/src/MISC/fix_orient_fcc.cpp
+++ b/src/MISC/fix_orient_fcc.cpp
@@ -15,9 +15,9 @@
Contributing authors: Koenraad Janssens and David Olmsted (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <string.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstring>
+#include <cstdlib>
#include <mpi.h>
#include "fix_orient_fcc.h"
#include "atom.h"
diff --git a/src/MISC/fix_thermal_conductivity.cpp b/src/MISC/fix_thermal_conductivity.cpp
index b9e70e9c009cb4bdb57146a953ecaa43abfa8138..f1aec3ff6991a1adb129c54d90b0198dbee2831d 100644
--- a/src/MISC/fix_thermal_conductivity.cpp
+++ b/src/MISC/fix_thermal_conductivity.cpp
@@ -16,10 +16,10 @@
for swapping atoms of different masses
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include <mpi.h>
-#include <string.h>
-#include <stdlib.h>
+#include <cstring>
+#include <cstdlib>
#include "fix_thermal_conductivity.h"
#include "atom.h"
#include "force.h"
diff --git a/src/MISC/fix_ttm.cpp b/src/MISC/fix_ttm.cpp
index bb13b166fbcf4ceb7ea645a55e709067e5c2c075..7ffd979e5089ca391990427693276bc30c74b5a4 100644
--- a/src/MISC/fix_ttm.cpp
+++ b/src/MISC/fix_ttm.cpp
@@ -17,9 +17,9 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <math.h>
-#include <string.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstring>
+#include <cstdlib>
#include "fix_ttm.h"
#include "atom.h"
#include "force.h"
diff --git a/src/MISC/fix_viscosity.cpp b/src/MISC/fix_viscosity.cpp
index 3f6d5e33d1ac6eb3dea29b23ca693d7056a51fd3..8e33c1c6148ec4ca20fab9219cf7348722b65ddb 100644
--- a/src/MISC/fix_viscosity.cpp
+++ b/src/MISC/fix_viscosity.cpp
@@ -16,10 +16,10 @@
for swapping atoms of different masses
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include <mpi.h>
-#include <string.h>
-#include <stdlib.h>
+#include <cstring>
+#include <cstdlib>
#include "fix_viscosity.h"
#include "atom.h"
#include "domain.h"
diff --git a/src/MISC/pair_nm_cut.cpp b/src/MISC/pair_nm_cut.cpp
index b9bf6ac477052d400a1340620465d731ee3c5774..83d734de0f4e492f8ffdadf2c771aaaaf250b248 100644
--- a/src/MISC/pair_nm_cut.cpp
+++ b/src/MISC/pair_nm_cut.cpp
@@ -15,10 +15,10 @@
Contributing Author: Julien Devemy (ICCF)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_nm_cut.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/MISC/pair_nm_cut_coul_cut.cpp b/src/MISC/pair_nm_cut_coul_cut.cpp
index 78c77a648f906da56b38848436e0ec45aa485eb5..0c9a43f4dc94fc5b4a8e9d2c705be0bad3cc2438 100644
--- a/src/MISC/pair_nm_cut_coul_cut.cpp
+++ b/src/MISC/pair_nm_cut_coul_cut.cpp
@@ -15,10 +15,10 @@
Contributing Author: Julien Devemy (ICCF)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_nm_cut_coul_cut.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/MISC/pair_nm_cut_coul_long.cpp b/src/MISC/pair_nm_cut_coul_long.cpp
index 8e0da40eac78d4689e666325a27da008d4667b3e..3296f8fd92b62ae567c7790ffbf0d98c62cd021a 100644
--- a/src/MISC/pair_nm_cut_coul_long.cpp
+++ b/src/MISC/pair_nm_cut_coul_long.cpp
@@ -15,10 +15,10 @@
Contributing Author: Julien Devemy (ICCF)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_nm_cut_coul_long.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/MISC/xdr_compat.cpp b/src/MISC/xdr_compat.cpp
index 9483070fee919f50b14e1b2dd1f0b8384988bbda..3987aa02fc2e0252cdd1eff3ceaf0b2113cd72c1 100644
--- a/src/MISC/xdr_compat.cpp
+++ b/src/MISC/xdr_compat.cpp
@@ -1,6 +1,6 @@
-#include <stdlib.h>
-#include <limits.h>
-#include <string.h>
+#include <cstdlib>
+#include <climits>
+#include <cstring>
#include "xdr_compat.h"
/* This file is needed for systems, that do not provide XDR support
diff --git a/src/MISC/xdr_compat.h b/src/MISC/xdr_compat.h
index 605374c47fc7172f42dad2a89137628e2b8bc236..30622350807b7d871a9870e17b45cc4890e38646 100644
--- a/src/MISC/xdr_compat.h
+++ b/src/MISC/xdr_compat.h
@@ -1,9 +1,9 @@
#ifndef LMP_XDR_COMPAT_H
#define LMP_XDR_COMPAT_H
-#include <limits.h>
-#include <stdio.h>
-#include <stdlib.h>
+#include <climits>
+#include <cstdio>
+#include <cstdlib>
#ifdef __cplusplus
extern "C" {
diff --git a/src/MOLECULE/angle_charmm.cpp b/src/MOLECULE/angle_charmm.cpp
index c7284add8ccfa765b96a70e27d861b454de67cc2..3608601c1fdb73ccf0c20b9910ee3101c32bdbfe 100644
--- a/src/MOLECULE/angle_charmm.cpp
+++ b/src/MOLECULE/angle_charmm.cpp
@@ -15,8 +15,8 @@
Contributing author: Paul Crozier (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdlib>
#include "angle_charmm.h"
#include "atom.h"
#include "neighbor.h"
diff --git a/src/MOLECULE/angle_charmm.h b/src/MOLECULE/angle_charmm.h
index fa27866be38750ae04cf08ddaab0d6fed5ab479e..82c9e42fbabc92f6a1a4be186aeccfa095e5bcc2 100644
--- a/src/MOLECULE/angle_charmm.h
+++ b/src/MOLECULE/angle_charmm.h
@@ -20,7 +20,7 @@ AngleStyle(charmm,AngleCharmm)
#ifndef LMP_ANGLE_CHARMM_H
#define LMP_ANGLE_CHARMM_H
-#include <stdio.h>
+#include <cstdio>
#include "angle.h"
namespace LAMMPS_NS {
diff --git a/src/MOLECULE/angle_cosine.cpp b/src/MOLECULE/angle_cosine.cpp
index f064a34f20d17aa02f07c90ef152ab87246d8357..e3472dfd7a6b3050a0ab2690764efb8ffaece032 100644
--- a/src/MOLECULE/angle_cosine.cpp
+++ b/src/MOLECULE/angle_cosine.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdlib>
#include "angle_cosine.h"
#include "atom.h"
#include "neighbor.h"
diff --git a/src/MOLECULE/angle_cosine.h b/src/MOLECULE/angle_cosine.h
index a6581f11bde0bd01e2c5459000df9495c146a9da..ac50a67468ea875df965388fc1a52be35c8db2b7 100644
--- a/src/MOLECULE/angle_cosine.h
+++ b/src/MOLECULE/angle_cosine.h
@@ -20,7 +20,7 @@ AngleStyle(cosine,AngleCosine)
#ifndef LMP_ANGLE_COSINE_H
#define LMP_ANGLE_COSINE_H
-#include <stdio.h>
+#include <cstdio>
#include "angle.h"
namespace LAMMPS_NS {
diff --git a/src/MOLECULE/angle_cosine_delta.cpp b/src/MOLECULE/angle_cosine_delta.cpp
index fe482eb3ebef6fe18160c602c143ed3712747700..6f4f5c20d71198cb00b2b5469e43c0fefee0fe2f 100644
--- a/src/MOLECULE/angle_cosine_delta.cpp
+++ b/src/MOLECULE/angle_cosine_delta.cpp
@@ -15,8 +15,8 @@
Contributing author: Axel Kohlmeyer (Temple U), akohlmey at gmail.com
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdlib>
#include "angle_cosine_delta.h"
#include "atom.h"
#include "neighbor.h"
diff --git a/src/MOLECULE/angle_cosine_delta.h b/src/MOLECULE/angle_cosine_delta.h
index b29064e35eadbcb2d4fd6ad8efc6b4994fef5995..1e19ecaf7962e4883403a51e34d3707df5e1693e 100644
--- a/src/MOLECULE/angle_cosine_delta.h
+++ b/src/MOLECULE/angle_cosine_delta.h
@@ -20,7 +20,7 @@ AngleStyle(cosine/delta,AngleCosineDelta)
#ifndef LMP_ANGLE_COSINE_DELTA_H
#define LMP_ANGLE_COSINE_DELTA_H
-#include <stdio.h>
+#include <cstdio>
#include "angle_cosine_squared.h"
namespace LAMMPS_NS {
diff --git a/src/MOLECULE/angle_cosine_periodic.cpp b/src/MOLECULE/angle_cosine_periodic.cpp
index 77fb335b785c769c6494012e2e5798b29ca44555..4e620b436e4f0a3a505d683e792e1ea8fc5cc3a0 100644
--- a/src/MOLECULE/angle_cosine_periodic.cpp
+++ b/src/MOLECULE/angle_cosine_periodic.cpp
@@ -15,8 +15,8 @@
Contributing author: Tod A Pascal (Caltech)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdlib>
#include "angle_cosine_periodic.h"
#include "atom.h"
#include "neighbor.h"
diff --git a/src/MOLECULE/angle_cosine_periodic.h b/src/MOLECULE/angle_cosine_periodic.h
index 9b7f06227241f929095e0b00f153c413f98e05e3..e131e85101e8d452bca29cc4389bd268baf5a8d2 100644
--- a/src/MOLECULE/angle_cosine_periodic.h
+++ b/src/MOLECULE/angle_cosine_periodic.h
@@ -20,7 +20,7 @@ AngleStyle(cosine/periodic, AngleCosinePeriodic)
#ifndef LMP_ANGLE_PERIODIC_H
#define LMP_ANGLE_PERIODIC_H
-#include <stdio.h>
+#include <cstdio>
#include "angle.h"
namespace LAMMPS_NS {
diff --git a/src/MOLECULE/angle_cosine_squared.cpp b/src/MOLECULE/angle_cosine_squared.cpp
index bc38d76dcdb4fded224f9994d08f756c8532255b..c83ba90a60f35b1db16fde1c3a2cb53c31eafa82 100644
--- a/src/MOLECULE/angle_cosine_squared.cpp
+++ b/src/MOLECULE/angle_cosine_squared.cpp
@@ -15,8 +15,8 @@
Contributing author: Naveen Michaud-Agrawal (Johns Hopkins U)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdlib>
#include "angle_cosine_squared.h"
#include "atom.h"
#include "neighbor.h"
@@ -34,7 +34,11 @@ using namespace MathConst;
/* ---------------------------------------------------------------------- */
-AngleCosineSquared::AngleCosineSquared(LAMMPS *lmp) : Angle(lmp) {}
+AngleCosineSquared::AngleCosineSquared(LAMMPS *lmp) : Angle(lmp)
+{
+ k = NULL;
+ theta0 = NULL;
+}
/* ---------------------------------------------------------------------- */
diff --git a/src/MOLECULE/angle_cosine_squared.h b/src/MOLECULE/angle_cosine_squared.h
index b9f79f923fb794e5c4c0842c2da44023d9db18ec..8e8c84c0f99c98a107d8072cdfac53badf04c3b7 100644
--- a/src/MOLECULE/angle_cosine_squared.h
+++ b/src/MOLECULE/angle_cosine_squared.h
@@ -20,7 +20,7 @@ AngleStyle(cosine/squared,AngleCosineSquared)
#ifndef LMP_ANGLE_COSINE_SQUARED_H
#define LMP_ANGLE_COSINE_SQUARED_H
-#include <stdio.h>
+#include <cstdio>
#include "angle.h"
namespace LAMMPS_NS {
diff --git a/src/MOLECULE/angle_harmonic.cpp b/src/MOLECULE/angle_harmonic.cpp
index 7e8b57b04fad7748eeaf0ce0f1ee75a743992425..d28afd76d688ca2a0a1a8d39d0724dc84a5210b9 100644
--- a/src/MOLECULE/angle_harmonic.cpp
+++ b/src/MOLECULE/angle_harmonic.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdlib>
#include "angle_harmonic.h"
#include "atom.h"
#include "neighbor.h"
@@ -30,7 +30,11 @@ using namespace MathConst;
/* ---------------------------------------------------------------------- */
-AngleHarmonic::AngleHarmonic(LAMMPS *lmp) : Angle(lmp) {}
+AngleHarmonic::AngleHarmonic(LAMMPS *lmp) : Angle(lmp)
+{
+ k = NULL;
+ theta0 = NULL;
+}
/* ---------------------------------------------------------------------- */
diff --git a/src/MOLECULE/angle_harmonic.h b/src/MOLECULE/angle_harmonic.h
index 177e7cbadb7b404167bbdf91484a342c8ae6c211..ff8bd55fc00f217009ae3e606de45c18873cb796 100644
--- a/src/MOLECULE/angle_harmonic.h
+++ b/src/MOLECULE/angle_harmonic.h
@@ -20,7 +20,7 @@ AngleStyle(harmonic,AngleHarmonic)
#ifndef LMP_ANGLE_HARMONIC_H
#define LMP_ANGLE_HARMONIC_H
-#include <stdio.h>
+#include <cstdio>
#include "angle.h"
namespace LAMMPS_NS {
diff --git a/src/MOLECULE/angle_table.cpp b/src/MOLECULE/angle_table.cpp
index 6e145efa10850909b288d8e0941ecc27c641a979..235e9b4d5b379c480026b052e0fb63d7a175810a 100644
--- a/src/MOLECULE/angle_table.cpp
+++ b/src/MOLECULE/angle_table.cpp
@@ -15,9 +15,9 @@
Contributing author: Chuanfu Luo (luochuanfu@gmail.com)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "angle_table.h"
#include "atom.h"
#include "neighbor.h"
@@ -609,7 +609,7 @@ double AngleTable::splint(double *xa, double *ya, double *y2a, int n, double x)
void AngleTable::uf_lookup(int type, double x, double &u, double &f)
{
- if (!ISFINITE(x)) {
+ if (!std::isfinite(x)) {
error->one(FLERR,"Illegal angle in angle style table");
}
@@ -644,7 +644,7 @@ void AngleTable::uf_lookup(int type, double x, double &u, double &f)
void AngleTable::u_lookup(int type, double x, double &u)
{
- if (!ISFINITE(x)) {
+ if (!std::isfinite(x)) {
error->one(FLERR,"Illegal angle in angle style table");
}
diff --git a/src/MOLECULE/angle_table.h b/src/MOLECULE/angle_table.h
index 984c5dc640eafb82eacdcc85ef1e3842f2754c89..0088ace39b7a709a4da82d1a069c6a73d923956b 100644
--- a/src/MOLECULE/angle_table.h
+++ b/src/MOLECULE/angle_table.h
@@ -20,7 +20,7 @@ AngleStyle(table,AngleTable)
#ifndef LMP_ANGLE_TABLE_H
#define LMP_ANGLE_TABLE_H
-#include <stdio.h>
+#include <cstdio>
#include "angle.h"
namespace LAMMPS_NS {
diff --git a/src/MOLECULE/atom_vec_angle.cpp b/src/MOLECULE/atom_vec_angle.cpp
index 7053f0eb30b7b1976282bf16f49f5c87d0ae35a5..6eb5b50fd2265e0559b68637f2dafd58d1b0eae0 100644
--- a/src/MOLECULE/atom_vec_angle.cpp
+++ b/src/MOLECULE/atom_vec_angle.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <stdlib.h>
+#include <cstdlib>
#include "atom_vec_angle.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/MOLECULE/atom_vec_bond.cpp b/src/MOLECULE/atom_vec_bond.cpp
index bae924c28add23da39dc550f7c3ea1427607e1b6..6a7b3585b4a17d07bcd45a68a174f98ede2c486d 100644
--- a/src/MOLECULE/atom_vec_bond.cpp
+++ b/src/MOLECULE/atom_vec_bond.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <stdlib.h>
+#include <cstdlib>
#include "atom_vec_bond.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/MOLECULE/atom_vec_full.cpp b/src/MOLECULE/atom_vec_full.cpp
index ba85a1280b46545963ab5f700508ae433cd38621..d682abf7994705eb2ff93d4eeb25c170842d0f1e 100644
--- a/src/MOLECULE/atom_vec_full.cpp
+++ b/src/MOLECULE/atom_vec_full.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <stdlib.h>
+#include <cstdlib>
#include "atom_vec_full.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/MOLECULE/atom_vec_molecular.cpp b/src/MOLECULE/atom_vec_molecular.cpp
index 23786d7641a7464f63ddd93a910fa110fc50ee5a..6e903a936eb8177db81606880bd23655739f64dc 100644
--- a/src/MOLECULE/atom_vec_molecular.cpp
+++ b/src/MOLECULE/atom_vec_molecular.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <stdlib.h>
+#include <cstdlib>
#include "atom_vec_molecular.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/MOLECULE/atom_vec_template.cpp b/src/MOLECULE/atom_vec_template.cpp
index 5d3b0a326492fe1ca1aef37be2d20b2e2a762c1a..3172804b95b1009c2349192d10ffe2233744bfc3 100644
--- a/src/MOLECULE/atom_vec_template.cpp
+++ b/src/MOLECULE/atom_vec_template.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
-#include <stdlib.h>
+#include <cstring>
+#include <cstdlib>
#include "atom_vec_template.h"
#include "atom.h"
#include "molecule.h"
diff --git a/src/MOLECULE/bond_fene.cpp b/src/MOLECULE/bond_fene.cpp
index 5d58f2683a0a4969663776323761d101d50bb31b..b6da72bfaf6b6968609ed1670a14149b66cd5be3 100644
--- a/src/MOLECULE/bond_fene.cpp
+++ b/src/MOLECULE/bond_fene.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdlib>
#include "bond_fene.h"
#include "atom.h"
#include "neighbor.h"
diff --git a/src/MOLECULE/bond_fene.h b/src/MOLECULE/bond_fene.h
index 6124478567e8bfd550c1a90af645b800a2572660..678ae165d66ffd59347e8451d8f95fd8f1465e39 100644
--- a/src/MOLECULE/bond_fene.h
+++ b/src/MOLECULE/bond_fene.h
@@ -20,7 +20,7 @@ BondStyle(fene,BondFENE)
#ifndef LMP_BOND_FENE_H
#define LMP_BOND_FENE_H
-#include <stdio.h>
+#include <cstdio>
#include "bond.h"
namespace LAMMPS_NS {
diff --git a/src/MOLECULE/bond_fene_expand.cpp b/src/MOLECULE/bond_fene_expand.cpp
index 033f8d6502ef91d2fcb53b9b25a972bfa01eb391..26b699d7bfdcca6cdd8d1ecb2d87e0d610c4ac38 100644
--- a/src/MOLECULE/bond_fene_expand.cpp
+++ b/src/MOLECULE/bond_fene_expand.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdlib>
#include "bond_fene_expand.h"
#include "atom.h"
#include "neighbor.h"
diff --git a/src/MOLECULE/bond_fene_expand.h b/src/MOLECULE/bond_fene_expand.h
index 1971c6f428037558dace9aa741f85dcc0ad06d89..cb316ac5f2b366cd534e1429088eaffe6cce15e9 100644
--- a/src/MOLECULE/bond_fene_expand.h
+++ b/src/MOLECULE/bond_fene_expand.h
@@ -20,7 +20,7 @@ BondStyle(fene/expand,BondFENEExpand)
#ifndef LMP_BOND_FENE_EXPAND_H
#define LMP_BOND_FENE_EXPAND_H
-#include <stdio.h>
+#include <cstdio>
#include "bond.h"
namespace LAMMPS_NS {
diff --git a/src/MOLECULE/bond_gromos.cpp b/src/MOLECULE/bond_gromos.cpp
index 4e409b7a72d686a7c573801a7bdaba608548ffd7..8e989259afa750eabdf5f44ac2ef91ab8f943b58 100644
--- a/src/MOLECULE/bond_gromos.cpp
+++ b/src/MOLECULE/bond_gromos.cpp
@@ -15,9 +15,9 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "bond_gromos.h"
#include "atom.h"
#include "neighbor.h"
diff --git a/src/MOLECULE/bond_gromos.h b/src/MOLECULE/bond_gromos.h
index dafe85e92b2e671427d3c1e8e8e68e6ab38b0202..c26ad64b3d6ad5bcdeaaa3b8f94303299e7b0e82 100644
--- a/src/MOLECULE/bond_gromos.h
+++ b/src/MOLECULE/bond_gromos.h
@@ -20,7 +20,7 @@ BondStyle(gromos,BondGromos)
#ifndef LMP_BOND_GROMOS_H
#define LMP_BOND_GROMOS_H
-#include <stdio.h>
+#include <cstdio>
#include "bond.h"
namespace LAMMPS_NS {
diff --git a/src/MOLECULE/bond_harmonic.cpp b/src/MOLECULE/bond_harmonic.cpp
index 0763d7d3e24667be3c3d81adbd236c16c3a54c7b..e7f510d2de9c59607351eba0b80ac51ce19a7831 100644
--- a/src/MOLECULE/bond_harmonic.cpp
+++ b/src/MOLECULE/bond_harmonic.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "bond_harmonic.h"
#include "atom.h"
#include "neighbor.h"
diff --git a/src/MOLECULE/bond_harmonic.h b/src/MOLECULE/bond_harmonic.h
index a0fd24577a8988e18fcb7a676a0041c353c52191..73f6a9f774cbb373fa9161701cf6680822b23c29 100644
--- a/src/MOLECULE/bond_harmonic.h
+++ b/src/MOLECULE/bond_harmonic.h
@@ -20,7 +20,7 @@ BondStyle(harmonic,BondHarmonic)
#ifndef LMP_BOND_HARMONIC_H
#define LMP_BOND_HARMONIC_H
-#include <stdio.h>
+#include <cstdio>
#include "bond.h"
namespace LAMMPS_NS {
diff --git a/src/MOLECULE/bond_morse.cpp b/src/MOLECULE/bond_morse.cpp
index 3204a0ca6183b003e0ec012083a8cd817f6e6f2c..35be50e8df9b6eebd071933953b1298c9d6e8ad3 100644
--- a/src/MOLECULE/bond_morse.cpp
+++ b/src/MOLECULE/bond_morse.cpp
@@ -15,8 +15,8 @@
Contributing author: Jeff Greathouse (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdlib>
#include "bond_morse.h"
#include "atom.h"
#include "neighbor.h"
diff --git a/src/MOLECULE/bond_morse.h b/src/MOLECULE/bond_morse.h
index 74379c91ee766b50996ad32d97219bfbb7d31ecd..c4d60bc21768c1ffe3ddf806d26dfea6dd475a95 100644
--- a/src/MOLECULE/bond_morse.h
+++ b/src/MOLECULE/bond_morse.h
@@ -20,7 +20,7 @@ BondStyle(morse,BondMorse)
#ifndef LMP_BOND_MORSE_H
#define LMP_BOND_MORSE_H
-#include <stdio.h>
+#include <cstdio>
#include "bond.h"
namespace LAMMPS_NS {
diff --git a/src/MOLECULE/bond_nonlinear.cpp b/src/MOLECULE/bond_nonlinear.cpp
index edd9dcd4e5c9e8e8be20a2ea85c1ee5b3fb13a3a..3926c3494b3666e0a30af5b5c51bd00bc92476ca 100644
--- a/src/MOLECULE/bond_nonlinear.cpp
+++ b/src/MOLECULE/bond_nonlinear.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdlib>
#include "bond_nonlinear.h"
#include "atom.h"
#include "neighbor.h"
diff --git a/src/MOLECULE/bond_nonlinear.h b/src/MOLECULE/bond_nonlinear.h
index 5d2448b112b45d24229f5e1768911fe211b82f18..175421264b91e11b0f71453716bb11c774f00d34 100644
--- a/src/MOLECULE/bond_nonlinear.h
+++ b/src/MOLECULE/bond_nonlinear.h
@@ -20,7 +20,7 @@ BondStyle(nonlinear,BondNonlinear)
#ifndef LMP_BOND_NONLINEAR_H
#define LMP_BOND_NONLINEAR_H
-#include <stdio.h>
+#include <cstdio>
#include "bond.h"
namespace LAMMPS_NS {
diff --git a/src/MOLECULE/bond_quartic.cpp b/src/MOLECULE/bond_quartic.cpp
index 2a3e395a77f81f9c92b59f6137d0cfbdc6c13a26..f581c7f33155e6d0059d0925e6be5524680e2574 100644
--- a/src/MOLECULE/bond_quartic.cpp
+++ b/src/MOLECULE/bond_quartic.cpp
@@ -15,8 +15,8 @@
Contributing authors: Chris Lorenz and Mark Stevens (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdlib>
#include "bond_quartic.h"
#include "atom.h"
#include "neighbor.h"
diff --git a/src/MOLECULE/bond_quartic.h b/src/MOLECULE/bond_quartic.h
index 21bd7f00b4055a92e407fb0e4429b9de778f2e26..2aaa76e2c374e531637455f612af56ab30bcc3d8 100644
--- a/src/MOLECULE/bond_quartic.h
+++ b/src/MOLECULE/bond_quartic.h
@@ -20,7 +20,7 @@ BondStyle(quartic,BondQuartic)
#ifndef LMP_BOND_QUARTIC_H
#define LMP_BOND_QUARTIC_H
-#include <stdio.h>
+#include <cstdio>
#include "bond.h"
namespace LAMMPS_NS {
diff --git a/src/MOLECULE/bond_table.cpp b/src/MOLECULE/bond_table.cpp
index 4f8db66757c5b71fa392e3c84ee5d5d6f76ec946..7515f713df7db4d3e07fe0019f4fec10e93303a0 100644
--- a/src/MOLECULE/bond_table.cpp
+++ b/src/MOLECULE/bond_table.cpp
@@ -15,9 +15,9 @@
Contributing author: Chuanfu Luo (luochuanfu@gmail.com)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "bond_table.h"
#include "atom.h"
#include "neighbor.h"
@@ -590,7 +590,7 @@ double BondTable::splint(double *xa, double *ya, double *y2a, int n, double x)
void BondTable::uf_lookup(int type, double x, double &u, double &f)
{
- if (!ISFINITE(x)) {
+ if (!std::isfinite(x)) {
error->one(FLERR,"Illegal bond in bond style table");
}
@@ -633,7 +633,7 @@ void BondTable::uf_lookup(int type, double x, double &u, double &f)
void BondTable::u_lookup(int type, double x, double &u)
{
- if (!ISFINITE(x)) {
+ if (!std::isfinite(x)) {
error->one(FLERR,"Illegal bond in bond style table");
}
diff --git a/src/MOLECULE/bond_table.h b/src/MOLECULE/bond_table.h
index ee053d497bb4b2960b1ec174e86ae90b152aa05c..5766239167c26dbc80ef62e08d52da29b26bb50f 100644
--- a/src/MOLECULE/bond_table.h
+++ b/src/MOLECULE/bond_table.h
@@ -20,7 +20,7 @@ BondStyle(table,BondTable)
#ifndef LMP_BOND_TABLE_H
#define LMP_BOND_TABLE_H
-#include <stdio.h>
+#include <cstdio>
#include "bond.h"
namespace LAMMPS_NS {
diff --git a/src/MOLECULE/dihedral_charmm.cpp b/src/MOLECULE/dihedral_charmm.cpp
index 35953a6ac456185b8b87a49b5b7c5be772e2d3e5..2372fae38b696a01b61cdce87cc83c62e60ee50c 100644
--- a/src/MOLECULE/dihedral_charmm.cpp
+++ b/src/MOLECULE/dihedral_charmm.cpp
@@ -16,9 +16,9 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "dihedral_charmm.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/MOLECULE/dihedral_charmm.h b/src/MOLECULE/dihedral_charmm.h
index 2f8a6a667924473d0b8ecd0e3ec19f426355c13d..349bee73d8ae938f70a31ad13ff327ab25c95928 100644
--- a/src/MOLECULE/dihedral_charmm.h
+++ b/src/MOLECULE/dihedral_charmm.h
@@ -20,7 +20,7 @@ DihedralStyle(charmm,DihedralCharmm)
#ifndef LMP_DIHEDRAL_CHARMM_H
#define LMP_DIHEDRAL_CHARMM_H
-#include <stdio.h>
+#include <cstdio>
#include "dihedral.h"
namespace LAMMPS_NS {
diff --git a/src/MOLECULE/dihedral_charmmfsw.cpp b/src/MOLECULE/dihedral_charmmfsw.cpp
index d33db36fda302c9d01c88c9a3bcf23cc17322915..99a53336205f3b5f20623320dd8fa8b092a40073 100644
--- a/src/MOLECULE/dihedral_charmmfsw.cpp
+++ b/src/MOLECULE/dihedral_charmmfsw.cpp
@@ -19,9 +19,9 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "dihedral_charmmfsw.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/MOLECULE/dihedral_charmmfsw.h b/src/MOLECULE/dihedral_charmmfsw.h
index 3c93f8abcf127edc56cb8d8ba16b6374ed94a961..dd31067a8dba9bd39b01373fba5b3dc29da842d4 100644
--- a/src/MOLECULE/dihedral_charmmfsw.h
+++ b/src/MOLECULE/dihedral_charmmfsw.h
@@ -20,7 +20,7 @@ DihedralStyle(charmmfsw,DihedralCharmmfsw)
#ifndef LMP_DIHEDRAL_CHARMMFSW_H
#define LMP_DIHEDRAL_CHARMMFSW_H
-#include <stdio.h>
+#include <cstdio>
#include "dihedral.h"
namespace LAMMPS_NS {
diff --git a/src/MOLECULE/dihedral_harmonic.cpp b/src/MOLECULE/dihedral_harmonic.cpp
index 82c5fe31507d667359a208a00bb43056af1eef6a..cb122f4bc2b7166ae84a70f3199c0a042dfddcbd 100644
--- a/src/MOLECULE/dihedral_harmonic.cpp
+++ b/src/MOLECULE/dihedral_harmonic.cpp
@@ -16,8 +16,8 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <math.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdlib>
#include "dihedral_harmonic.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/MOLECULE/dihedral_harmonic.h b/src/MOLECULE/dihedral_harmonic.h
index db8789675d8c87f3e076ed9284d6c8cea69025ce..20312612568ae92681d8a79649069e9496028896 100644
--- a/src/MOLECULE/dihedral_harmonic.h
+++ b/src/MOLECULE/dihedral_harmonic.h
@@ -20,7 +20,7 @@ DihedralStyle(harmonic,DihedralHarmonic)
#ifndef LMP_DIHEDRAL_HARMONIC_H
#define LMP_DIHEDRAL_HARMONIC_H
-#include <stdio.h>
+#include <cstdio>
#include "dihedral.h"
namespace LAMMPS_NS {
diff --git a/src/MOLECULE/dihedral_helix.cpp b/src/MOLECULE/dihedral_helix.cpp
index 43794bd6aabfacca837f8b9a57e10452b46f2a70..ae23b77951dda47600972f86df05636db8757001 100644
--- a/src/MOLECULE/dihedral_helix.cpp
+++ b/src/MOLECULE/dihedral_helix.cpp
@@ -17,8 +17,8 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <math.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdlib>
#include "dihedral_helix.h"
#include "atom.h"
#include "neighbor.h"
@@ -332,3 +332,13 @@ void DihedralHelix::read_restart(FILE *fp)
for (int i = 1; i <= atom->ndihedraltypes; i++) setflag[i] = 1;
}
+
+/* ----------------------------------------------------------------------
+ proc 0 writes to data file
+------------------------------------------------------------------------- */
+
+void DihedralHelix::write_data(FILE *fp)
+{
+ for (int i = 1; i <= atom->ndihedraltypes; i++)
+ fprintf(fp,"%d %g %g %g\n",i,aphi[i],bphi[i],cphi[i]);
+}
diff --git a/src/MOLECULE/dihedral_helix.h b/src/MOLECULE/dihedral_helix.h
index 61aef1d2ecadeb27b892797b774847650ccb6e06..745ab841156164e095c0ffbc55f93705d83f7662 100644
--- a/src/MOLECULE/dihedral_helix.h
+++ b/src/MOLECULE/dihedral_helix.h
@@ -20,7 +20,7 @@ DihedralStyle(helix,DihedralHelix)
#ifndef LMP_DIHEDRAL_HELIX_H
#define LMP_DIHEDRAL_HELIX_H
-#include <stdio.h>
+#include <cstdio>
#include "dihedral.h"
namespace LAMMPS_NS {
@@ -33,6 +33,7 @@ class DihedralHelix : public Dihedral {
void coeff(int, char **);
void write_restart(FILE *);
void read_restart(FILE *);
+ void write_data(FILE *);
protected:
double *aphi,*bphi,*cphi;
diff --git a/src/MOLECULE/dihedral_multi_harmonic.cpp b/src/MOLECULE/dihedral_multi_harmonic.cpp
index 3a4be46fc7876360636365724968ca6fc007a710..f6461abb6e9fbf3ef84fbb82935755d73639c751 100644
--- a/src/MOLECULE/dihedral_multi_harmonic.cpp
+++ b/src/MOLECULE/dihedral_multi_harmonic.cpp
@@ -15,8 +15,8 @@
Contributing author: Mathias Puetz (SNL) and friends
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdlib>
#include "dihedral_multi_harmonic.h"
#include "atom.h"
#include "neighbor.h"
@@ -331,3 +331,13 @@ void DihedralMultiHarmonic::read_restart(FILE *fp)
for (int i = 1; i <= atom->ndihedraltypes; i++) setflag[i] = 1;
}
+
+/* ----------------------------------------------------------------------
+ proc 0 writes to data file
+------------------------------------------------------------------------- */
+
+void DihedralMultiHarmonic::write_data(FILE *fp)
+{
+ for (int i = 1; i <= atom->ndihedraltypes; i++)
+ fprintf(fp,"%d %g %g %g %g %g\n",i,a1[i],a2[i],a3[i],a4[i],a5[i]);
+}
diff --git a/src/MOLECULE/dihedral_multi_harmonic.h b/src/MOLECULE/dihedral_multi_harmonic.h
index 8f40b56a5ffb80ae428c8f059246173abb4b9d66..32f17e75ae4a79571a6cdca27e199405d25069c8 100644
--- a/src/MOLECULE/dihedral_multi_harmonic.h
+++ b/src/MOLECULE/dihedral_multi_harmonic.h
@@ -20,7 +20,7 @@ DihedralStyle(multi/harmonic,DihedralMultiHarmonic)
#ifndef LMP_DIHEDRAL_MULTI_HARMONIC_H
#define LMP_DIHEDRAL_MULTI_HARMONIC_H
-#include <stdio.h>
+#include <cstdio>
#include "dihedral.h"
namespace LAMMPS_NS {
@@ -33,6 +33,7 @@ class DihedralMultiHarmonic : public Dihedral {
void coeff(int, char **);
void write_restart(FILE *);
void read_restart(FILE *);
+ void write_data(FILE *);
protected:
double *a1,*a2,*a3,*a4,*a5;
diff --git a/src/MOLECULE/dihedral_opls.cpp b/src/MOLECULE/dihedral_opls.cpp
index c3a7ee6aa7f9a4388f058b39587b4e695702020b..b5103413b227d2402f4e9e3f563632ac2b914f9a 100644
--- a/src/MOLECULE/dihedral_opls.cpp
+++ b/src/MOLECULE/dihedral_opls.cpp
@@ -15,8 +15,8 @@
Contributing author: Mark Stevens (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdlib>
#include "dihedral_opls.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/MOLECULE/dihedral_opls.h b/src/MOLECULE/dihedral_opls.h
index 0a127d3ac178ebffb97a616dc64acb19abea91df..378dec1a6a930db5733fe20ee444f318fba81dfe 100644
--- a/src/MOLECULE/dihedral_opls.h
+++ b/src/MOLECULE/dihedral_opls.h
@@ -20,7 +20,7 @@ DihedralStyle(opls,DihedralOPLS)
#ifndef LMP_DIHEDRAL_OPLS_H
#define LMP_DIHEDRAL_OPLS_H
-#include <stdio.h>
+#include <cstdio>
#include "dihedral.h"
namespace LAMMPS_NS {
diff --git a/src/MOLECULE/fix_cmap.cpp b/src/MOLECULE/fix_cmap.cpp
index f4bc6c1ee645ee98fa9b77b680dc5c7fefe32b07..5ef2e662abfb6cc618cb8c377fef940385410b38 100644
--- a/src/MOLECULE/fix_cmap.cpp
+++ b/src/MOLECULE/fix_cmap.cpp
@@ -28,10 +28,10 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
-#include <stdio.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
+#include <cstdio>
#include "fix_cmap.h"
#include "atom.h"
#include "atom_vec.h"
diff --git a/src/MOLECULE/improper_cvff.cpp b/src/MOLECULE/improper_cvff.cpp
index 45740d7880f0b57409d8de9c73872d7176861cf7..641eea74a88f63aa40084d3d38b08f90c5a9c1c9 100644
--- a/src/MOLECULE/improper_cvff.cpp
+++ b/src/MOLECULE/improper_cvff.cpp
@@ -12,8 +12,8 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <math.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdlib>
#include "improper_cvff.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/MOLECULE/improper_cvff.h b/src/MOLECULE/improper_cvff.h
index 8e997e3ff4a5f8caf9f1ca75ed1661055f4ed9fc..d4c30cc2eead856bc70d8215add5d9a58b9942df 100644
--- a/src/MOLECULE/improper_cvff.h
+++ b/src/MOLECULE/improper_cvff.h
@@ -20,7 +20,7 @@ ImproperStyle(cvff,ImproperCvff)
#ifndef LMP_IMPROPER_CVFF_H
#define LMP_IMPROPER_CVFF_H
-#include <stdio.h>
+#include <cstdio>
#include "improper.h"
namespace LAMMPS_NS {
diff --git a/src/MOLECULE/improper_harmonic.cpp b/src/MOLECULE/improper_harmonic.cpp
index c482055c76f8c57b4acb7e1dee7af71066663d11..091bd463163488cba7a36dac2e114e1e272e6a0e 100644
--- a/src/MOLECULE/improper_harmonic.cpp
+++ b/src/MOLECULE/improper_harmonic.cpp
@@ -12,8 +12,8 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <math.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdlib>
#include "improper_harmonic.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/MOLECULE/improper_harmonic.h b/src/MOLECULE/improper_harmonic.h
index b5132ab7ffc636f6f0f0d411ab0a951ebd4c048c..be9b25f3b6929ced0877a647a2d561f9e864453c 100644
--- a/src/MOLECULE/improper_harmonic.h
+++ b/src/MOLECULE/improper_harmonic.h
@@ -20,7 +20,7 @@ ImproperStyle(harmonic,ImproperHarmonic)
#ifndef LMP_IMPROPER_HARMONIC_H
#define LMP_IMPROPER_HARMONIC_H
-#include <stdio.h>
+#include <cstdio>
#include "improper.h"
namespace LAMMPS_NS {
diff --git a/src/MOLECULE/improper_umbrella.cpp b/src/MOLECULE/improper_umbrella.cpp
index 8a9b0b44345711174b26c84799ac13b7793c5081..31d7cba54dca313ae2016fe477b9882e0787f515 100644
--- a/src/MOLECULE/improper_umbrella.cpp
+++ b/src/MOLECULE/improper_umbrella.cpp
@@ -16,8 +16,8 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <math.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdlib>
#include "improper_umbrella.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/MOLECULE/improper_umbrella.h b/src/MOLECULE/improper_umbrella.h
index f590a63c3277f7e2b4fe63988e0c06391eabb9bc..dc2262d01c31d48713c74bdcd1d347c7f8c98d15 100644
--- a/src/MOLECULE/improper_umbrella.h
+++ b/src/MOLECULE/improper_umbrella.h
@@ -20,7 +20,7 @@ ImproperStyle(umbrella,ImproperUmbrella)
#ifndef LMP_IMPROPER_UMBRELLA_H
#define LMP_IMPROPER_UMBRELLA_H
-#include <stdio.h>
+#include <cstdio>
#include "improper.h"
namespace LAMMPS_NS {
diff --git a/src/MOLECULE/pair_hbond_dreiding_lj.cpp b/src/MOLECULE/pair_hbond_dreiding_lj.cpp
index ecb4883cb364b07afbb56208e62c73afe91c50b2..26ff499dec6cd0dd2b6b8bb6ad15c95fb97032ca 100644
--- a/src/MOLECULE/pair_hbond_dreiding_lj.cpp
+++ b/src/MOLECULE/pair_hbond_dreiding_lj.cpp
@@ -15,10 +15,10 @@
Contributing author: Tod A Pascal (Caltech)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_hbond_dreiding_lj.h"
#include "atom.h"
#include "atom_vec.h"
diff --git a/src/MOLECULE/pair_hbond_dreiding_morse.cpp b/src/MOLECULE/pair_hbond_dreiding_morse.cpp
index 83b03f9a2fb9c6565c4cac14a685ea7e270d9a27..749053164cf5746602ac31e933ac533659e51609 100644
--- a/src/MOLECULE/pair_hbond_dreiding_morse.cpp
+++ b/src/MOLECULE/pair_hbond_dreiding_morse.cpp
@@ -15,10 +15,10 @@
Contributing author: Tod A Pascal (Caltech)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_hbond_dreiding_morse.h"
#include "atom.h"
#include "atom_vec.h"
diff --git a/src/MOLECULE/pair_lj_charmm_coul_charmm.cpp b/src/MOLECULE/pair_lj_charmm_coul_charmm.cpp
index 3700de00b0fe380a96abaf358ab0e06f0416ab5a..688c675815ad7efa3fa4bd6fec4e08a7e79108ca 100644
--- a/src/MOLECULE/pair_lj_charmm_coul_charmm.cpp
+++ b/src/MOLECULE/pair_lj_charmm_coul_charmm.cpp
@@ -15,10 +15,10 @@
Contributing author: Paul Crozier (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_lj_charmm_coul_charmm.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/MOLECULE/pair_lj_charmm_coul_charmm_implicit.cpp b/src/MOLECULE/pair_lj_charmm_coul_charmm_implicit.cpp
index 3421f88eb3c1edc1217f53da2f093ccde2aaa4e5..6c083a49b09ac84ca950abe8c4ca83d6f7e2123c 100644
--- a/src/MOLECULE/pair_lj_charmm_coul_charmm_implicit.cpp
+++ b/src/MOLECULE/pair_lj_charmm_coul_charmm_implicit.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <string.h>
+#include <cmath>
+#include <cstring>
#include "pair_lj_charmm_coul_charmm_implicit.h"
#include "atom.h"
#include "force.h"
diff --git a/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp b/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp
index 7da6d59d32f5ef2a1ae49b59226312968a6f080e..4b9147c1698a3a3eaab1ede1a648380ceb180dac 100644
--- a/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp
+++ b/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp
@@ -19,10 +19,10 @@
with additional assistance from Robert A. Latour, Clemson University
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_lj_charmmfsw_coul_charmmfsh.h"
#include "atom.h"
#include "update.h"
diff --git a/src/MOLECULE/pair_lj_cut_tip4p_cut.cpp b/src/MOLECULE/pair_lj_cut_tip4p_cut.cpp
index c616a9fa83af793eb095daff37b8e69ce20da915..92dead8435237b593d154d0f8337d8f1d6207240 100644
--- a/src/MOLECULE/pair_lj_cut_tip4p_cut.cpp
+++ b/src/MOLECULE/pair_lj_cut_tip4p_cut.cpp
@@ -15,9 +15,9 @@
Contributing author: Pavel Elkind (Gothenburg University)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "pair_lj_cut_tip4p_cut.h"
#include "atom.h"
#include "force.h"
diff --git a/src/MOLECULE/pair_tip4p_cut.cpp b/src/MOLECULE/pair_tip4p_cut.cpp
index 954bd35435604f118a77d05b70f25100cfa887a7..e9f52b87246c3ef076818253b160893d019c44b6 100644
--- a/src/MOLECULE/pair_tip4p_cut.cpp
+++ b/src/MOLECULE/pair_tip4p_cut.cpp
@@ -15,8 +15,8 @@
Contributing author: Pavel Elkind (Gothenburg University)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdlib>
#include "pair_tip4p_cut.h"
#include "atom.h"
#include "force.h"
diff --git a/src/MPIIO/Install.sh b/src/MPIIO/Install.sh
old mode 100644
new mode 100755
diff --git a/src/MPIIO/dump_atom_mpiio.cpp b/src/MPIIO/dump_atom_mpiio.cpp
index 75702ed9b0d7179aa1e9ee075d087be0b3ad9dc5..f2f299144261d9d6035e49db8e1f30dedeea38ac 100644
--- a/src/MPIIO/dump_atom_mpiio.cpp
+++ b/src/MPIIO/dump_atom_mpiio.cpp
@@ -15,7 +15,7 @@
Contributing author: Paul Coffman (IBM)
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "dump_atom_mpiio.h"
#include "domain.h"
#include "atom.h"
@@ -77,6 +77,19 @@ void DumpAtomMPIIO::openfile()
sprintf(filecurrent,pad,filestar,update->ntimestep,ptr+1);
}
*ptr = '*';
+ if (maxfiles > 0) {
+ if (numfiles < maxfiles) {
+ nameslist[numfiles] = new char[strlen(filecurrent)+1];
+ strcpy(nameslist[numfiles],filecurrent);
+ ++numfiles;
+ } else {
+ remove(nameslist[fileidx]);
+ delete[] nameslist[fileidx];
+ nameslist[fileidx] = new char[strlen(filecurrent)+1];
+ strcpy(nameslist[fileidx],filecurrent);
+ fileidx = (fileidx + 1) % maxfiles;
+ }
+ }
}
if (append_flag) { // append open
diff --git a/src/MPIIO/dump_atom_mpiio.h b/src/MPIIO/dump_atom_mpiio.h
index 265f9a3b0200c48249f0cdd0494453b7fe359d78..ad49fa11823a21354c0340b335a01129e20fd97b 100644
--- a/src/MPIIO/dump_atom_mpiio.h
+++ b/src/MPIIO/dump_atom_mpiio.h
@@ -21,7 +21,7 @@ DumpStyle(atom/mpiio,DumpAtomMPIIO)
#define LMP_DUMP_ATOM_MPIIO_H
#include "dump_atom.h"
-#include <stdlib.h>
+#include <cstdlib>
namespace LAMMPS_NS {
diff --git a/src/MPIIO/dump_cfg_mpiio.cpp b/src/MPIIO/dump_cfg_mpiio.cpp
index 1cca047bb2aaa3f055fcdf2257efc5eb7e73e8ac..c580d2e7af71cdb1b7ca037392e0e0656b6ac5b0 100644
--- a/src/MPIIO/dump_cfg_mpiio.cpp
+++ b/src/MPIIO/dump_cfg_mpiio.cpp
@@ -15,9 +15,9 @@
Contributing author: Paul Coffman (IBM)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "dump_cfg_mpiio.h"
#include "atom.h"
#include "domain.h"
@@ -34,7 +34,6 @@
#ifdef LMP_USER_IO_TIMER
#include <sys/times.h>
#include <hwi/include/bqc/A2_inlines.h>
-#include <stdlib.h>
long dumpCFGTimestamps[10];
#endif
@@ -48,8 +47,6 @@ using namespace LAMMPS_NS;
#define DUMP_BUF_CHUNK_SIZE 16384
#define DUMP_BUF_INCREMENT_SIZE 4096
-enum{INT,DOUBLE,STRING,BIGINT}; // same as in DumpCustom
-
#define UNWRAPEXPAND 10.0
#define ONEFIELD 32
#define DELTA 1048576
@@ -97,6 +94,19 @@ void DumpCFGMPIIO::openfile()
sprintf(filecurrent,pad,filestar,update->ntimestep,ptr+1);
}
*ptr = '*';
+ if (maxfiles > 0) {
+ if (numfiles < maxfiles) {
+ nameslist[numfiles] = new char[strlen(filecurrent)+1];
+ strcpy(nameslist[numfiles],filecurrent);
+ ++numfiles;
+ } else {
+ remove(nameslist[fileidx]);
+ delete[] nameslist[fileidx];
+ nameslist[fileidx] = new char[strlen(filecurrent)+1];
+ strcpy(nameslist[fileidx],filecurrent);
+ fileidx = (fileidx + 1) % maxfiles;
+ }
+ }
}
if (append_flag) { // append open
@@ -378,13 +388,13 @@ int DumpCFGMPIIO::convert_string_omp(int n, double *mybuf)
} else if (j == 1) {
mpifhStringCountPerThread[tid] += sprintf(&(mpifh_buffer_line_per_thread[tid][mpifhStringCountPerThread[tid]]),"%s \n",typenames[(int) mybuf[bufOffset[tid]+m]]);
} else if (j >= 2) {
- if (vtype[j] == INT)
+ if (vtype[j] == Dump::INT)
mpifhStringCountPerThread[tid] += sprintf(&(mpifh_buffer_line_per_thread[tid][mpifhStringCountPerThread[tid]]),vformat[j],static_cast<int> (mybuf[bufOffset[tid]+m]));
- else if (vtype[j] == DOUBLE)
+ else if (vtype[j] == Dump::DOUBLE)
mpifhStringCountPerThread[tid] += sprintf(&(mpifh_buffer_line_per_thread[tid][mpifhStringCountPerThread[tid]]),vformat[j],mybuf[bufOffset[tid]+m]);
- else if (vtype[j] == STRING)
+ else if (vtype[j] == Dump::STRING)
mpifhStringCountPerThread[tid] += sprintf(&(mpifh_buffer_line_per_thread[tid][mpifhStringCountPerThread[tid]]),vformat[j],typenames[(int) mybuf[bufOffset[tid]+m]]);
- else if (vtype[j] == BIGINT)
+ else if (vtype[j] == Dump::BIGINT)
mpifhStringCountPerThread[tid] += sprintf(&(mpifh_buffer_line_per_thread[tid][mpifhStringCountPerThread[tid]]),vformat[j],static_cast<bigint> (mybuf[bufOffset[tid]+m]));
}
m++;
@@ -411,18 +421,18 @@ int DumpCFGMPIIO::convert_string_omp(int n, double *mybuf)
//offset += sprintf(&sbuf[offset],vformat[j],unwrap_coord);
mpifhStringCountPerThread[tid] += sprintf(&(mpifh_buffer_line_per_thread[tid][mpifhStringCountPerThread[tid]]),vformat[j],unwrap_coord);
} else if (j >= 5 ) {
- if (vtype[j] == INT)
+ if (vtype[j] == Dump::INT)
//offset +=
// sprintf(&sbuf[offset],vformat[j],static_cast<int> (mybuf[m]));
mpifhStringCountPerThread[tid] += sprintf(&(mpifh_buffer_line_per_thread[tid][mpifhStringCountPerThread[tid]]),vformat[j],static_cast<int> (mybuf[bufOffset[tid]+m]));
- else if (vtype[j] == DOUBLE)
+ else if (vtype[j] == Dump::DOUBLE)
// offset += sprintf(&sbuf[offset],vformat[j],mybuf[m]);
mpifhStringCountPerThread[tid] += sprintf(&(mpifh_buffer_line_per_thread[tid][mpifhStringCountPerThread[tid]]),vformat[j],mybuf[bufOffset[tid]+m]);
- else if (vtype[j] == STRING)
+ else if (vtype[j] == Dump::STRING)
// offset +=
// sprintf(&sbuf[offset],vformat[j],typenames[(int) mybuf[m]]);
mpifhStringCountPerThread[tid] += sprintf(&(mpifh_buffer_line_per_thread[tid][mpifhStringCountPerThread[tid]]),vformat[j],typenames[(int) mybuf[bufOffset[tid]+m]]);
- else if (vtype[j] == BIGINT)
+ else if (vtype[j] == Dump::BIGINT)
// offset +=
// sprintf(&sbuf[offset],vformat[j],static_cast<bigint> (mybuf[m]));
mpifhStringCountPerThread[tid] += sprintf(&(mpifh_buffer_line_per_thread[tid][mpifhStringCountPerThread[tid]]),vformat[j],static_cast<bigint> (mybuf[bufOffset[tid]+m]));
diff --git a/src/MPIIO/dump_custom_mpiio.cpp b/src/MPIIO/dump_custom_mpiio.cpp
index 0b282b77efad41a25da336c34483ef51e098665e..3650ca994e4d519d319ae0d182cb9b2011afd764 100644
--- a/src/MPIIO/dump_custom_mpiio.cpp
+++ b/src/MPIIO/dump_custom_mpiio.cpp
@@ -15,9 +15,9 @@
Contributing author: Paul Coffman (IBM)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "dump_custom_mpiio.h"
#include "atom.h"
#include "force.h"
@@ -32,7 +32,6 @@
#include "fix.h"
#include "memory.h"
#include "error.h"
-#include <stdlib.h>
#if defined(_OPENMP)
#include <omp.h>
@@ -54,7 +53,6 @@ enum{ID,MOL,TYPE,ELEMENT,MASS,
TQX,TQY,TQZ,SPIN,ERADIUS,ERVEL,ERFORCE,
COMPUTE,FIX,VARIABLE};
enum{LT,LE,GT,GE,EQ,NEQ};
-enum{INT,DOUBLE,STRING,BIGINT}; // same as in DumpCustom
/* ---------------------------------------------------------------------- */
@@ -99,6 +97,19 @@ void DumpCustomMPIIO::openfile()
sprintf(filecurrent,pad,filestar,update->ntimestep,ptr+1);
}
*ptr = '*';
+ if (maxfiles > 0) {
+ if (numfiles < maxfiles) {
+ nameslist[numfiles] = new char[strlen(filecurrent)+1];
+ strcpy(nameslist[numfiles],filecurrent);
+ ++numfiles;
+ } else {
+ remove(nameslist[fileidx]);
+ delete[] nameslist[fileidx];
+ nameslist[fileidx] = new char[strlen(filecurrent)+1];
+ strcpy(nameslist[fileidx],filecurrent);
+ fileidx = (fileidx + 1) % maxfiles;
+ }
+ }
}
if (append_flag) { // append open
@@ -247,13 +258,13 @@ void DumpCustomMPIIO::init_style()
if (format_column_user[i]) {
vformat[i] = new char[strlen(format_column_user[i]) + 2];
strcpy(vformat[i],format_column_user[i]);
- } else if (vtype[i] == INT && format_int_user) {
+ } else if (vtype[i] == Dump::INT && format_int_user) {
vformat[i] = new char[strlen(format_int_user) + 2];
strcpy(vformat[i],format_int_user);
- } else if (vtype[i] == DOUBLE && format_float_user) {
+ } else if (vtype[i] == Dump::DOUBLE && format_float_user) {
vformat[i] = new char[strlen(format_float_user) + 2];
strcpy(vformat[i],format_float_user);
- } else if (vtype[i] == BIGINT && format_bigint_user) {
+ } else if (vtype[i] == Dump::BIGINT && format_bigint_user) {
vformat[i] = new char[strlen(format_bigint_user) + 2];
strcpy(vformat[i],format_bigint_user);
} else {
@@ -619,11 +630,11 @@ int DumpCustomMPIIO::convert_string_omp(int n, double *mybuf)
}
for (int j = 0; j < size_one; j++) {
- if (vtype[j] == INT)
+ if (vtype[j] == Dump::INT)
mpifhStringCountPerThread[tid] += sprintf(&(mpifh_buffer_line_per_thread[tid][mpifhStringCountPerThread[tid]]),vformat[j],static_cast<int> (mybuf[bufOffset[tid]+m]));
- else if (vtype[j] == DOUBLE)
+ else if (vtype[j] == Dump::DOUBLE)
mpifhStringCountPerThread[tid] += sprintf(&(mpifh_buffer_line_per_thread[tid][mpifhStringCountPerThread[tid]]),vformat[j],mybuf[bufOffset[tid]+m]);
- else if (vtype[j] == STRING)
+ else if (vtype[j] == Dump::STRING)
mpifhStringCountPerThread[tid] += sprintf(&(mpifh_buffer_line_per_thread[tid][mpifhStringCountPerThread[tid]]),vformat[j],typenames[(int) mybuf[bufOffset[tid]+m]]);
m ++;
}
diff --git a/src/MPIIO/dump_xyz_mpiio.cpp b/src/MPIIO/dump_xyz_mpiio.cpp
index cc87fe881c468ffbc84269558e96abd1b8c4d426..f15d340cd14f3f470ac981e80d29c7428c2f6e09 100644
--- a/src/MPIIO/dump_xyz_mpiio.cpp
+++ b/src/MPIIO/dump_xyz_mpiio.cpp
@@ -15,9 +15,9 @@
Contributing author: Paul Coffman (IBM)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "dump_xyz_mpiio.h"
#include "atom.h"
#include "force.h"
@@ -32,7 +32,6 @@
#include "fix.h"
#include "memory.h"
#include "error.h"
-#include <stdlib.h>
#if defined(_OPENMP)
#include <omp.h>
@@ -54,7 +53,6 @@ enum{ID,MOL,TYPE,ELEMENT,MASS,
TQX,TQY,TQZ,SPIN,ERADIUS,ERVEL,ERFORCE,
COMPUTE,FIX,VARIABLE};
enum{LT,LE,GT,GE,EQ,NEQ};
-enum{INT,DOUBLE,STRING}; // same as in DumpCFG
/* ---------------------------------------------------------------------- */
@@ -99,6 +97,19 @@ void DumpXYZMPIIO::openfile()
sprintf(filecurrent,pad,filestar,update->ntimestep,ptr+1);
}
*ptr = '*';
+ if (maxfiles > 0) {
+ if (numfiles < maxfiles) {
+ nameslist[numfiles] = new char[strlen(filecurrent)+1];
+ strcpy(nameslist[numfiles],filecurrent);
+ ++numfiles;
+ } else {
+ remove(nameslist[fileidx]);
+ delete[] nameslist[fileidx];
+ nameslist[fileidx] = new char[strlen(filecurrent)+1];
+ strcpy(nameslist[fileidx],filecurrent);
+ fileidx = (fileidx + 1) % maxfiles;
+ }
+ }
}
if (append_flag) { // append open
diff --git a/src/MPIIO/restart_mpiio.cpp b/src/MPIIO/restart_mpiio.cpp
index 8ad1dccdca9fe60fb5a29fdb2f5cf20d328eb4d2..804df211dc4579957b14fa1b3e94b0bcf36c73f6 100644
--- a/src/MPIIO/restart_mpiio.cpp
+++ b/src/MPIIO/restart_mpiio.cpp
@@ -16,9 +16,9 @@
------------------------------------------------------------------------- */
#include <mpi.h>
+#include <climits>
#include "restart_mpiio.h"
#include "error.h"
-#include <limits.h>
using namespace LAMMPS_NS;
diff --git a/src/MSCG/fix_mscg.cpp b/src/MSCG/fix_mscg.cpp
index fba198c814c77b2cf5585fd7e73f8311a271b4ae..b28259524071672463f17051e5a388e0d89d133d 100644
--- a/src/MSCG/fix_mscg.cpp
+++ b/src/MSCG/fix_mscg.cpp
@@ -16,11 +16,12 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <string.h>
-#include <stdlib.h>
+#include <cstring>
+#include <cstdlib>
#include "fix_mscg.h"
#include "mscg.h"
#include "atom.h"
+#include "comm.h"
#include "domain.h"
#include "error.h"
#include "force.h"
@@ -284,11 +285,9 @@ void FixMSCG::end_of_step()
if (domain->triclinic == 1)
error->all(FLERR,"Fix mscg does not yet support triclinic geometries");
- int natoms = atom->natoms;
int nlocal = atom->nlocal;
tagint *tag = atom->tag;
double **x = atom->x;
- double *prd_half = domain->prd_half;
int i,ii,j;
// trajectory information
diff --git a/src/Make.sh b/src/Make.sh
old mode 100644
new mode 100755
diff --git a/src/Makefile b/src/Makefile
index 03f40721324e8d1712d967481f7611484be0c558..d17a2ccbd99ecf0ff2c29b1626ebe1bdd3da39dc 100644
--- a/src/Makefile
+++ b/src/Makefile
@@ -57,10 +57,10 @@ PACKAGE = asphere body class2 colloid compress coreshell dipole gpu \
molecule mpiio mscg opt peri poems \
python qeq reax replica rigid shock snap srd voronoi
-PACKUSER = user-atc user-awpmd user-cgdna user-cgsdk user-colvars \
+PACKUSER = user-atc user-awpmd user-bocs user-cgdna user-cgsdk user-colvars \
user-diffraction user-dpd user-drude user-eff user-fep user-h5md \
user-intel user-lb user-manifold user-meamc user-meso \
- user-mgpt user-misc user-molfile \
+ user-mgpt user-misc user-mofff user-molfile \
user-netcdf user-omp user-phonon user-qmmm user-qtb \
user-quip user-reaxc user-smd user-smtbq user-sph user-tally \
user-uef user-vtk
@@ -267,7 +267,7 @@ package:
@echo 'make yes-all install all pgks in src dir'
@echo 'make no-all remove all pkgs from src dir'
@echo 'make yes-standard (yes-std) install all standard pkgs'
- @echo 'make no-standard (no-srd) remove all standard pkgs'
+ @echo 'make no-standard (no-std) remove all standard pkgs'
@echo 'make yes-user install all user pkgs'
@echo 'make no-user remove all user pkgs'
@echo 'make yes-lib install all pkgs with libs (included or ext)'
diff --git a/src/OPT/Install.sh b/src/OPT/Install.sh
old mode 100644
new mode 100755
diff --git a/src/OPT/pair_eam_opt.cpp b/src/OPT/pair_eam_opt.cpp
index 3afec5644a70bb12497163d8fd8174202f2d11b1..5345d7f8d6c40c41f56f1cc0b8df81a997a6c18e 100644
--- a/src/OPT/pair_eam_opt.cpp
+++ b/src/OPT/pair_eam_opt.cpp
@@ -19,8 +19,8 @@
Vincent Natoli, Stone Ridge Technology
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdlib>
#include "pair_eam_opt.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/OPT/pair_lj_charmm_coul_long_opt.cpp b/src/OPT/pair_lj_charmm_coul_long_opt.cpp
index b98dd36dd138fe7f93a60c2445decb3bd3f3736b..43f4ba7f5a9ae9fa29ae1d7c9c20220160cf96d1 100644
--- a/src/OPT/pair_lj_charmm_coul_long_opt.cpp
+++ b/src/OPT/pair_lj_charmm_coul_long_opt.cpp
@@ -18,8 +18,8 @@
Vincent Natoli, Stone Ridge Technology
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdlib>
#include "pair_lj_charmm_coul_long_opt.h"
#include "atom.h"
#include "force.h"
diff --git a/src/OPT/pair_lj_cut_coul_long_opt.cpp b/src/OPT/pair_lj_cut_coul_long_opt.cpp
index 140d4d023a688e52a2b65386442525a63d26570f..98683a67a4ccbfc537393c2aa55dcb758f1b0ee6 100644
--- a/src/OPT/pair_lj_cut_coul_long_opt.cpp
+++ b/src/OPT/pair_lj_cut_coul_long_opt.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_lj_cut_coul_long_opt.h"
#include "atom.h"
#include "force.h"
diff --git a/src/OPT/pair_lj_cut_opt.cpp b/src/OPT/pair_lj_cut_opt.cpp
index 0812a56f015cd1f888c1eee840f00484a645ce61..ed35178c1f9e60d6fd40cada3e5452f2b318a224 100644
--- a/src/OPT/pair_lj_cut_opt.cpp
+++ b/src/OPT/pair_lj_cut_opt.cpp
@@ -18,7 +18,7 @@
Vincent Natoli, Stone Ridge Technology
------------------------------------------------------------------------- */
-#include <stdlib.h>
+#include <cstdlib>
#include "pair_lj_cut_opt.h"
#include "atom.h"
#include "force.h"
diff --git a/src/OPT/pair_lj_cut_tip4p_long_opt.cpp b/src/OPT/pair_lj_cut_tip4p_long_opt.cpp
index db9402b521c902119e57fbe4dbdca27bb11e0a87..4842cc4fc00ea6725c5f683e010b1e58f55c5b21 100644
--- a/src/OPT/pair_lj_cut_tip4p_long_opt.cpp
+++ b/src/OPT/pair_lj_cut_tip4p_long_opt.cpp
@@ -15,7 +15,7 @@
OPT version: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_lj_cut_tip4p_long_opt.h"
#include "atom.h"
#include "domain.h"
diff --git a/src/OPT/pair_lj_long_coul_long_opt.cpp b/src/OPT/pair_lj_long_coul_long_opt.cpp
index c5756cbecc6de1613222e7163e43db7bf0885232..91ffc2c01ed20e96f317cf82cd48d778cb1233a0 100644
--- a/src/OPT/pair_lj_long_coul_long_opt.cpp
+++ b/src/OPT/pair_lj_long_coul_long_opt.cpp
@@ -15,7 +15,7 @@
OPT version: Wayne Mitchell (Loyola University New Orleans)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_lj_long_coul_long_opt.h"
#include "atom.h"
#include "force.h"
diff --git a/src/OPT/pair_morse_opt.cpp b/src/OPT/pair_morse_opt.cpp
index e63fbd0938c5cb235b22d10d92d86d84797513e9..6299136f46af21f358079429b8ed3981d4562589 100644
--- a/src/OPT/pair_morse_opt.cpp
+++ b/src/OPT/pair_morse_opt.cpp
@@ -18,8 +18,8 @@
Vincent Natoli, Stone Ridge Technology
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdlib>
#include "pair_morse_opt.h"
#include "atom.h"
#include "force.h"
diff --git a/src/OPT/pair_ufm_opt.cpp b/src/OPT/pair_ufm_opt.cpp
index f6f4c4ce3e7bc2a7a04a97db049c2a239e863288..85c76d624d7eaad82a27d319134642a0aee6724e 100644
--- a/src/OPT/pair_ufm_opt.cpp
+++ b/src/OPT/pair_ufm_opt.cpp
@@ -17,8 +17,8 @@
Maurice de Koning (Unicamp/Brazil) - dekoning@ifi.unicamp.br
------------------------------------------------------------------------- */
-#include <stdlib.h>
-#include <math.h>
+#include <cstdlib>
+#include <cmath>
#include "pair_ufm_opt.h"
#include "atom.h"
#include "force.h"
diff --git a/src/PERI/atom_vec_peri.cpp b/src/PERI/atom_vec_peri.cpp
index 3e6a72289a6d3afa7e6c4ccb7105f0f64d342221..d78fe27c94b62fa8d313b968cbc2fe55f54fb315 100644
--- a/src/PERI/atom_vec_peri.cpp
+++ b/src/PERI/atom_vec_peri.cpp
@@ -15,9 +15,9 @@
Contributing author: Mike Parks (SNL)
------------------------------------------------------------------------- */
-#include <float.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cfloat>
+#include <cstdlib>
+#include <cstring>
#include "atom_vec_peri.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/PERI/compute_damage_atom.cpp b/src/PERI/compute_damage_atom.cpp
index a3bc580f7ab72d0ddf7562eea2d858345578b803..4bf8fa17a57fd7ff034a46a15f64c713d741fc01 100644
--- a/src/PERI/compute_damage_atom.cpp
+++ b/src/PERI/compute_damage_atom.cpp
@@ -15,7 +15,7 @@
Contributing author: Mike Parks (SNL)
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "compute_damage_atom.h"
#include "atom.h"
#include "update.h"
diff --git a/src/PERI/compute_dilatation_atom.cpp b/src/PERI/compute_dilatation_atom.cpp
index d79b80f4d459ad3d60ee43d9795f898860024633..990731a227d30865c2dbba4a2566217cd94913d7 100644
--- a/src/PERI/compute_dilatation_atom.cpp
+++ b/src/PERI/compute_dilatation_atom.cpp
@@ -15,7 +15,7 @@
Contributing author: Rezwanur Rahman, John Foster (UTSA)
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "compute_dilatation_atom.h"
#include "atom.h"
#include "update.h"
diff --git a/src/PERI/compute_plasticity_atom.cpp b/src/PERI/compute_plasticity_atom.cpp
index 34fd23fe6a663bccb36257724ff09a4f46b146ab..d08fb98e07b84d1c893c5d05588cb1db4e4622a6 100644
--- a/src/PERI/compute_plasticity_atom.cpp
+++ b/src/PERI/compute_plasticity_atom.cpp
@@ -15,7 +15,7 @@
Contributing author: Rezwanur Rahman, John Foster (UTSA)
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "compute_plasticity_atom.h"
#include "atom.h"
#include "update.h"
diff --git a/src/PERI/fix_peri_neigh.cpp b/src/PERI/fix_peri_neigh.cpp
index d92f355c53866bf8e2f13d4e020b054a598e80a0..42d86e14b2b4eec17c78d95457c48647af0f7b86 100644
--- a/src/PERI/fix_peri_neigh.cpp
+++ b/src/PERI/fix_peri_neigh.cpp
@@ -15,7 +15,7 @@
Contributing authors: Mike Parks (SNL), Ezwanur Rahman, J.T. Foster (UTSA)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "fix_peri_neigh.h"
#include "pair_peri_pmb.h"
#include "pair_peri_lps.h"
diff --git a/src/PERI/pair_peri_eps.cpp b/src/PERI/pair_peri_eps.cpp
index 670e1d6937aaafce5962ca6f7a24bc2fb945f6fc..9950c36f41446ca28adbeb0162dd188adf0eb6e6 100644
--- a/src/PERI/pair_peri_eps.cpp
+++ b/src/PERI/pair_peri_eps.cpp
@@ -15,9 +15,9 @@
Contributing author: Rezwanur Rahman, John Foster (UTSA)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "pair_peri_eps.h"
#include "atom.h"
#include "domain.h"
diff --git a/src/PERI/pair_peri_lps.cpp b/src/PERI/pair_peri_lps.cpp
index 0fe8f29f387fee4513cb9dd1ad60305561b7f012..4c48223b0749e9ebc7b4cbe4e4d1345854da21b9 100644
--- a/src/PERI/pair_peri_lps.cpp
+++ b/src/PERI/pair_peri_lps.cpp
@@ -15,9 +15,9 @@
Contributing author: Mike Parks (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "pair_peri_lps.h"
#include "atom.h"
#include "domain.h"
diff --git a/src/PERI/pair_peri_pmb.cpp b/src/PERI/pair_peri_pmb.cpp
index 9e598289bd01842bb255a5501f5163fad9488d0e..81461f0b83f0c7c12df432046036a6003199397f 100644
--- a/src/PERI/pair_peri_pmb.cpp
+++ b/src/PERI/pair_peri_pmb.cpp
@@ -15,10 +15,10 @@
Contributing author: Mike Parks (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <float.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cfloat>
+#include <cstdlib>
+#include <cstring>
#include "pair_peri_pmb.h"
#include "atom.h"
#include "domain.h"
diff --git a/src/PERI/pair_peri_ves.cpp b/src/PERI/pair_peri_ves.cpp
index 87213b5b59c10de830ae0e131335f5f99779b0f9..a9f620ef4b7bcbc4b92b7881a6ebaf8e8ea0e8fc 100644
--- a/src/PERI/pair_peri_ves.cpp
+++ b/src/PERI/pair_peri_ves.cpp
@@ -15,9 +15,9 @@
Contributing authors: Rezwanur Rahman, J.T. Foster (UTSA)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "pair_peri_ves.h"
#include "atom.h"
#include "domain.h"
diff --git a/src/POEMS/Install.sh b/src/POEMS/Install.sh
old mode 100644
new mode 100755
diff --git a/src/POEMS/fix_poems.cpp b/src/POEMS/fix_poems.cpp
index 7ff9e91af8127ad76b0b7e661a00cbe47f1fbce1..2c2fefb250b14252fa31e88e489ea9f307e918a5 100644
--- a/src/POEMS/fix_poems.cpp
+++ b/src/POEMS/fix_poems.cpp
@@ -18,10 +18,10 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <math.h>
-#include <stdio.h>
-#include <string.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdio>
+#include <cstring>
+#include <cstdlib>
#include "workspace.h"
#include "fix_poems.h"
#include "atom.h"
@@ -267,6 +267,10 @@ FixPOEMS::FixPOEMS(LAMMPS *lmp, int narg, char **arg) :
poems = new Workspace;
+ // compute per body forces and torques inside final_integrate() by default
+
+ earlyflag = 0;
+
// print statistics
int nsum = 0;
@@ -351,12 +355,26 @@ void FixPOEMS::init()
int i,ibody;
// warn if more than one POEMS fix
+ // if earlyflag, warn if any post-force fixes come after POEMS fix
int count = 0;
for (int i = 0; i < modify->nfix; i++)
if (strcmp(modify->fix[i]->style,"poems") == 0) count++;
if (count > 1 && comm->me == 0) error->warning(FLERR,"More than one fix poems");
+ if (earlyflag) {
+ int pflag = 0;
+ for (i = 0; i < modify->nfix; i++) {
+ if (strcmp(modify->fix[i]->style,"poems") == 0) pflag = 1;
+ if (pflag && (modify->fmask[i] & POST_FORCE) &&
+ !modify->fix[i]->rigid_flag) {
+ char str[128];
+ sprintf(str,"Fix %s alters forces after fix poems",modify->fix[i]->id);
+ error->warning(FLERR,str);
+ }
+ }
+ }
+
// error if npt,nph fix comes before rigid fix
for (i = 0; i < modify->nfix; i++) {
@@ -696,7 +714,8 @@ void FixPOEMS::setup(int vflag)
// use post_force() to compute initial fcm & torque
- post_force(vflag);
+ compute_forces_and_torques();
+ //post_force(vflag);
// setup for POEMS
@@ -727,12 +746,29 @@ void FixPOEMS::initial_integrate(int vflag)
set_xv();
}
+/* ---------------------------------------------------------------------- */
+
+void FixPOEMS::post_force(int vflag)
+{
+ if (earlyflag) compute_forces_and_torques();
+
+ /*
+ for (int ibody = 0; ibody < nbody; ibody++) {
+ if (ibody == 0) {
+ printf("PFF %d %g %g %g\n",ibody,fcm[ibody][0],fcm[ibody][1],fcm[ibody][2]);
+ printf("PFT %d %g %g %g\n",ibody,
+ torque[ibody][0],torque[ibody][1],torque[ibody][2]);
+ }
+ }
+ */
+}
+
/* ----------------------------------------------------------------------
compute fcm,torque on each rigid body
only count joint atoms in 1st body
------------------------------------------------------------------------- */
-void FixPOEMS::post_force(int vflag)
+void FixPOEMS::compute_forces_and_torques()
{
int i,ibody;
int xbox,ybox,zbox;
@@ -790,6 +826,18 @@ void FixPOEMS::post_force(int vflag)
void FixPOEMS::final_integrate()
{
+ if (!earlyflag) compute_forces_and_torques();
+
+ /*
+ for (int ibody = 0; ibody < nbody; ibody++) {
+ if (ibody == 0) {
+ printf("FI %d %g %g %g\n",ibody,fcm[ibody][0],fcm[ibody][1],fcm[ibody][2]);
+ printf("TQ %d %g %g %g\n",ibody,
+ torque[ibody][0],torque[ibody][1],torque[ibody][2]);
+ }
+ }
+ */
+
// perform POEMS integration
poems->LobattoTwo(vcm,omega,torque,fcm);
@@ -1615,6 +1663,21 @@ int FixPOEMS::unpack_exchange(int nlocal, double *buf)
/* ---------------------------------------------------------------------- */
+int FixPOEMS::modify_param(int narg, char **arg)
+{
+ if (strcmp(arg[0],"bodyforces") == 0) {
+ if (narg < 2) error->all(FLERR,"Illegal fix_modify command");
+ if (strcmp(arg[1],"early") == 0) earlyflag = 1;
+ else if (strcmp(arg[1],"late") == 0) earlyflag = 0;
+ else error->all(FLERR,"Illegal fix_modify command");
+ return 2;
+ }
+
+ return 0;
+}
+
+/* ---------------------------------------------------------------------- */
+
void FixPOEMS::reset_dt()
{
dtv = update->dt;
diff --git a/src/POEMS/fix_poems.h b/src/POEMS/fix_poems.h
index 4d5e5c319861398f1c4e8f2f9d92f944dd4192e9..7b2c77a1bd78deec2d9ea0a62e3bc021d79b3e05 100644
--- a/src/POEMS/fix_poems.h
+++ b/src/POEMS/fix_poems.h
@@ -47,6 +47,7 @@ class FixPOEMS : public Fix {
void pre_neighbor();
int dof(int);
void deform(int);
+ int modify_param(int, char **);
void reset_dt();
private:
@@ -55,6 +56,7 @@ class FixPOEMS : public Fix {
double *step_respa;
int nlevels_respa;
double total_ke;
+ int earlyflag; // 1 if forces and torques are computed at post_force()
// atom assignment to rigid bodies
// double count joint atoms as being in multiple bodies
@@ -96,6 +98,7 @@ class FixPOEMS : public Fix {
// internal class functions
+ void compute_forces_and_torques();
void readfile(char *);
int readline(FILE *, char **, int *);
void jointbuild();
diff --git a/src/PYTHON/fix_python_invoke.cpp b/src/PYTHON/fix_python_invoke.cpp
index 9a4db51d99251a2e44d7101aeaa3530254b18a72..199dd94f3d1cd87cf9cc1fbbbdf15e161c2813fa 100644
--- a/src/PYTHON/fix_python_invoke.cpp
+++ b/src/PYTHON/fix_python_invoke.cpp
@@ -16,8 +16,8 @@
------------------------------------------------------------------------- */
#include <Python.h>
-#include <stdio.h>
-#include <string.h>
+#include <cstdio>
+#include <cstring>
#include "fix_python_invoke.h"
#include "atom.h"
#include "force.h"
diff --git a/src/PYTHON/fix_python_move.cpp b/src/PYTHON/fix_python_move.cpp
index 22d3bd065f5bc899eb89f2fc6359e399f6412306..b330ab79450b805e595e6b5d52710722d962ee32 100644
--- a/src/PYTHON/fix_python_move.cpp
+++ b/src/PYTHON/fix_python_move.cpp
@@ -16,9 +16,9 @@
------------------------------------------------------------------------- */
#include <Python.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "fix_python_move.h"
#include "atom.h"
#include "comm.h"
@@ -47,7 +47,7 @@ FixPythonMove::FixPythonMove(LAMMPS *lmp, int narg, char **arg) :
PyGILState_STATE gstate = PyGILState_Ensure();
// add current directory to PYTHONPATH
- PyObject * py_path = PySys_GetObject("path");
+ PyObject * py_path = PySys_GetObject((char *)"path");
PyList_Append(py_path, PY_STRING_FROM_STRING("."));
@@ -136,7 +136,7 @@ void FixPythonMove::init()
{
PyGILState_STATE gstate = PyGILState_Ensure();
PyObject *py_move_obj = (PyObject *) py_move;
- PyObject *py_init = PyObject_GetAttrString(py_move_obj,"init");
+ PyObject *py_init = PyObject_GetAttrString(py_move_obj,(char *)"init");
if (!py_init) {
PyErr_Print();
PyErr_Clear();
diff --git a/src/PYTHON/pair_python.cpp b/src/PYTHON/pair_python.cpp
index 0db987bb63d01c932f8e895218b1279ba01ceaf7..223129f7d662111de1f31573f3bf9f6a4945acb6 100644
--- a/src/PYTHON/pair_python.cpp
+++ b/src/PYTHON/pair_python.cpp
@@ -16,9 +16,9 @@
------------------------------------------------------------------------- */
#include <Python.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_python.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/Package.sh b/src/Package.sh
old mode 100644
new mode 100755
diff --git a/src/QEQ/Install.sh b/src/QEQ/Install.sh
new file mode 100755
index 0000000000000000000000000000000000000000..334be24e4bc0208b4640ca05829ef6e20ba39c03
--- /dev/null
+++ b/src/QEQ/Install.sh
@@ -0,0 +1,46 @@
+# Install/unInstall package files in LAMMPS
+# mode = 0/1/2 for uninstall/install/update
+
+# this is default Install.sh for all packages
+# if package has an auxiliary library or a file with a dependency,
+# then package dir has its own customized Install.sh
+
+mode=$1
+
+# enforce using portable C locale
+LC_ALL=C
+export LC_ALL
+
+# arg1 = file, arg2 = file it depends on
+
+action () {
+ if (test $mode = 0) then
+ rm -f ../$1
+ elif (! cmp -s $1 ../$1) then
+ if (test -z "$2" || test -e ../$2) then
+ cp $1 ..
+ if (test $mode = 2) then
+ echo " updating src/$1"
+ fi
+ fi
+ elif (test -n "$2") then
+ if (test ! -e ../$2) then
+ rm -f ../$1
+ fi
+ fi
+}
+
+# all package files with dependencies
+
+action fix_qeq.cpp
+action fix_qeq.h
+action fix_qeq_dynamic.cpp
+action fix_qeq_dynamic.h
+action fix_qeq_fire.cpp pair_comb.h
+action fix_qeq_fire.h pair_comb.h
+action fix_qeq_point.cpp
+action fix_qeq_point.h
+action fix_qeq_shielded.cpp
+action fix_qeq_shielded.h
+action fix_qeq_slater.cpp
+action fix_qeq_slater.h
diff --git a/src/QEQ/fix_qeq.cpp b/src/QEQ/fix_qeq.cpp
index afa2801831f0c677a979d4c49df7af2fe63bee75..8acf4498f5c6f67db6a1640d4872ff34efe2b746 100644
--- a/src/QEQ/fix_qeq.cpp
+++ b/src/QEQ/fix_qeq.cpp
@@ -16,10 +16,10 @@
Based on fix qeq/reax by H. Metin Aktulga
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "fix_qeq.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/QEQ/fix_qeq_dynamic.cpp b/src/QEQ/fix_qeq_dynamic.cpp
index 43e9a9c874c44c0ce1a421029992f7f1297f5417..aeb8dd2c59043d1c1852e8cd678074d19e51785c 100644
--- a/src/QEQ/fix_qeq_dynamic.cpp
+++ b/src/QEQ/fix_qeq_dynamic.cpp
@@ -15,10 +15,10 @@
Contributing author: Ray Shan (Sandia)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "fix_qeq_dynamic.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/QEQ/fix_qeq_fire.cpp b/src/QEQ/fix_qeq_fire.cpp
index 763a39e82e9d961d253c6085750270c891779245..db63bec2063f98de16b963be899e72b920d06023 100644
--- a/src/QEQ/fix_qeq_fire.cpp
+++ b/src/QEQ/fix_qeq_fire.cpp
@@ -15,10 +15,10 @@
Contributing author: Ray Shan (Sandia)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "fix_qeq_fire.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/QEQ/fix_qeq_point.cpp b/src/QEQ/fix_qeq_point.cpp
index 906f73799142fd0295b6096da6b2e0f6dc845169..bf7130c1d6704b334f05c227245082e61f107fd9 100644
--- a/src/QEQ/fix_qeq_point.cpp
+++ b/src/QEQ/fix_qeq_point.cpp
@@ -15,10 +15,10 @@
Contributing author: Ray Shan (Sandia)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "fix_qeq_point.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/QEQ/fix_qeq_shielded.cpp b/src/QEQ/fix_qeq_shielded.cpp
index e23384b1c92cdd1f945b93723b571245d4fa7e8d..70898fd96c68908ca4c74203a72c577883710ff0 100644
--- a/src/QEQ/fix_qeq_shielded.cpp
+++ b/src/QEQ/fix_qeq_shielded.cpp
@@ -15,10 +15,10 @@
Contributing author: Ray Shan (Sandia)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "fix_qeq_shielded.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/QEQ/fix_qeq_slater.cpp b/src/QEQ/fix_qeq_slater.cpp
index 544b9f037aeb9268d97603021078fe07372021ba..4ddcf06357b3e5c42e010a47c16f1fd8177a0a16 100644
--- a/src/QEQ/fix_qeq_slater.cpp
+++ b/src/QEQ/fix_qeq_slater.cpp
@@ -15,10 +15,10 @@
Contributing author: Ray Shan (Sandia)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "fix_qeq_slater.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/REAX/Install.sh b/src/REAX/Install.sh
old mode 100644
new mode 100755
diff --git a/src/REAX/fix_reax_bonds.cpp b/src/REAX/fix_reax_bonds.cpp
index 00cfb0937b93b1c03c8e23f9f258d80a54737df1..84e4a66e6cede6db5d347281df036486cc2efec9 100644
--- a/src/REAX/fix_reax_bonds.cpp
+++ b/src/REAX/fix_reax_bonds.cpp
@@ -19,8 +19,8 @@
#error LAMMPS_BIGBIG is not supported by the REAX package
#endif
-#include <stdlib.h>
-#include <string.h>
+#include <cstdlib>
+#include <cstring>
#include "fix_reax_bonds.h"
#include "pair_reax_fortran.h"
#include "atom.h"
diff --git a/src/REAX/fix_reax_bonds.h b/src/REAX/fix_reax_bonds.h
index 7246b836c1a2c693db3f0e8bf0b800503baf7688..03bad1ef16b3b0f45842ee709adef4e9be12868f 100644
--- a/src/REAX/fix_reax_bonds.h
+++ b/src/REAX/fix_reax_bonds.h
@@ -20,7 +20,7 @@ FixStyle(reax/bonds,FixReaxBonds)
#ifndef LMP_FIX_REAX_BONDS_H
#define LMP_FIX_REAX_BONDS_H
-#include <stdio.h>
+#include <cstdio>
#include "fix.h"
namespace LAMMPS_NS {
diff --git a/src/REAX/pair_reax.cpp b/src/REAX/pair_reax.cpp
index f6217c69a4aa7169d816e317cc508d75bae6761a..24083a288ab6ec3b5b66a771ca3a48a6b86d9cc2 100644
--- a/src/REAX/pair_reax.cpp
+++ b/src/REAX/pair_reax.cpp
@@ -21,10 +21,10 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_reax.h"
#include "pair_reax_fortran.h"
#include "atom.h"
diff --git a/src/REPLICA/compute_event_displace.cpp b/src/REPLICA/compute_event_displace.cpp
index 330e2ebca33a522267581e434a81b86cb627ba28..df142215863e73e13ab3448d95ef29f95c427bc6 100644
--- a/src/REPLICA/compute_event_displace.cpp
+++ b/src/REPLICA/compute_event_displace.cpp
@@ -16,9 +16,9 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "compute_event_displace.h"
#include "atom.h"
#include "domain.h"
diff --git a/src/REPLICA/fix_event.cpp b/src/REPLICA/fix_event.cpp
index f688550a6554c679432191817da5dd098254f26a..3b9b49ac57a24977766a144388a99b52cf3d8103 100644
--- a/src/REPLICA/fix_event.cpp
+++ b/src/REPLICA/fix_event.cpp
@@ -15,8 +15,8 @@
Contributing author: Mike Brown (SNL), Aidan Thompson (SNL)
------------------------------------------------------------------------- */
-#include <stdlib.h>
-#include <string.h>
+#include <cstdlib>
+#include <cstring>
#include "fix_event.h"
#include "atom.h"
#include "update.h"
diff --git a/src/REPLICA/fix_event_prd.cpp b/src/REPLICA/fix_event_prd.cpp
index 863caa64f240f999b920bf11ebe9bf7cf0e17ccd..a311a6444aad250d5b25454afabcf215a8be7fcc 100644
--- a/src/REPLICA/fix_event_prd.cpp
+++ b/src/REPLICA/fix_event_prd.cpp
@@ -15,8 +15,8 @@
Contributing author: Mike Brown (SNL)
------------------------------------------------------------------------- */
-#include <stdlib.h>
-#include <string.h>
+#include <cstdlib>
+#include <cstring>
#include "fix_event_prd.h"
#include "atom.h"
#include "update.h"
diff --git a/src/REPLICA/fix_event_tad.cpp b/src/REPLICA/fix_event_tad.cpp
index b2d74855faf08cb6001256be13e9a1caf894ce84..0916fdf493748a842a6ad84783d5dfa0f9960075 100644
--- a/src/REPLICA/fix_event_tad.cpp
+++ b/src/REPLICA/fix_event_tad.cpp
@@ -15,8 +15,8 @@
Contributing author: Mike Brown (SNL)
------------------------------------------------------------------------- */
-#include <stdlib.h>
-#include <string.h>
+#include <cstdlib>
+#include <cstring>
#include "fix_event_tad.h"
#include "atom.h"
#include "update.h"
diff --git a/src/REPLICA/fix_neb.cpp b/src/REPLICA/fix_neb.cpp
index 33f834a14069b42d4fa56379c35db41a2e102379..e5d24da392649fe1f8cecbd9bc20fea0e17194b9 100644
--- a/src/REPLICA/fix_neb.cpp
+++ b/src/REPLICA/fix_neb.cpp
@@ -17,9 +17,9 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "fix_neb.h"
#include "universe.h"
#include "update.h"
diff --git a/src/REPLICA/neb.cpp b/src/REPLICA/neb.cpp
index 692f9361258a847e51775cb1f451e1f04895ce11..c9aedf74018409a5913ed1055d554775e4704746 100644
--- a/src/REPLICA/neb.cpp
+++ b/src/REPLICA/neb.cpp
@@ -17,9 +17,9 @@
#include "lmptype.h"
#include <mpi.h>
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "neb.h"
#include "universe.h"
#include "atom.h"
@@ -303,7 +303,7 @@ void NEB::run()
update->minimize->setup();
if (me_universe == 0) {
- if (uscreen)
+ if (uscreen) {
if (verbose) {
fprintf(uscreen,"Step MaxReplicaForce MaxAtomForce "
"GradV0 GradV1 GradVc EBF EBR RDT "
@@ -317,7 +317,8 @@ void NEB::run()
"EBF EBR RDT "
"RD1 PE1 RD2 PE2 ... RDN PEN\n");
}
- if (ulogfile)
+ }
+ if (ulogfile) {
if (verbose) {
fprintf(ulogfile,"Step MaxReplicaForce MaxAtomForce "
"GradV0 GradV1 GradVc EBF EBR RDT "
@@ -331,6 +332,7 @@ void NEB::run()
"EBF EBR RDT "
"RD1 PE1 RD2 PE2 ... RDN PEN\n");
}
+ }
}
print_status();
@@ -588,7 +590,7 @@ void NEB::print_status()
MPI_Allgather(&fnorminf,1,MPI_DOUBLE,&fmaxatomInRepl[0],1,MPI_DOUBLE,roots);
}
- double one[numall];
+ double one[7];
one[0] = fneb->veng;
one[1] = fneb->plen;
one[2] = fneb->nlen;
diff --git a/src/REPLICA/neb.h b/src/REPLICA/neb.h
index 556ea22bbeb6ea0e25dd20ee16ee5927ffc432b7..9453c3c43bfb3786276094cf5dafc839daf8c0a1 100644
--- a/src/REPLICA/neb.h
+++ b/src/REPLICA/neb.h
@@ -20,7 +20,7 @@ CommandStyle(neb,NEB)
#ifndef LMP_NEB_H
#define LMP_NEB_H
-#include <stdio.h>
+#include <cstdio>
#include "pointers.h"
namespace LAMMPS_NS {
diff --git a/src/REPLICA/prd.cpp b/src/REPLICA/prd.cpp
index 684277a698b265f778864f5290325dffb232c21a..6d450f48e3ed6bac08bcef47f5666e4e06a3f283 100644
--- a/src/REPLICA/prd.cpp
+++ b/src/REPLICA/prd.cpp
@@ -21,9 +21,9 @@
#include "lmptype.h"
#include <mpi.h>
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "prd.h"
#include "universe.h"
#include "update.h"
diff --git a/src/REPLICA/tad.cpp b/src/REPLICA/tad.cpp
index 958a57e4e8936e895621fd4ec6fb5cf89baf153e..46073952fc6fe341f797364507b6d83fa392b59e 100644
--- a/src/REPLICA/tad.cpp
+++ b/src/REPLICA/tad.cpp
@@ -21,9 +21,9 @@
#include "lmptype.h"
#include <mpi.h>
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "tad.h"
#include "universe.h"
#include "update.h"
diff --git a/src/REPLICA/temper.cpp b/src/REPLICA/temper.cpp
index d7e8c981bb51a729595aeee17ae8c2c4b43fd71d..fe3e3fb993d43e0d88c8eb2dcc777ea621a482ef 100644
--- a/src/REPLICA/temper.cpp
+++ b/src/REPLICA/temper.cpp
@@ -15,9 +15,9 @@
Contributing author: Mark Sears (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "temper.h"
#include "universe.h"
#include "domain.h"
diff --git a/src/REPLICA/verlet_split.cpp b/src/REPLICA/verlet_split.cpp
index e47965d1c3c02a28f00351c5a8139caf4514915c..05ea0877ab1e84bd618ec125e1e287063344e5f3 100644
--- a/src/REPLICA/verlet_split.cpp
+++ b/src/REPLICA/verlet_split.cpp
@@ -15,7 +15,7 @@
Contributing authors: Yuxing Peng and Chris Knight (U Chicago)
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "verlet_split.h"
#include "universe.h"
#include "neighbor.h"
diff --git a/src/RIGID/compute_erotate_rigid.cpp b/src/RIGID/compute_erotate_rigid.cpp
index e31565cb6070844d8be629e49d4cd0b6ba99c3f1..a3ddffd9abed86427c1d06da997e7d5344676795 100644
--- a/src/RIGID/compute_erotate_rigid.cpp
+++ b/src/RIGID/compute_erotate_rigid.cpp
@@ -12,7 +12,7 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <string.h>
+#include <cstring>
#include "compute_erotate_rigid.h"
#include "update.h"
#include "force.h"
diff --git a/src/RIGID/compute_ke_rigid.cpp b/src/RIGID/compute_ke_rigid.cpp
index 2db756140fb7b35a2934ad9fb7d63aacfc4a21a2..4de13532b29856d7381f358d194d6554515983c6 100644
--- a/src/RIGID/compute_ke_rigid.cpp
+++ b/src/RIGID/compute_ke_rigid.cpp
@@ -12,7 +12,7 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <string.h>
+#include <cstring>
#include "compute_ke_rigid.h"
#include "update.h"
#include "force.h"
diff --git a/src/RIGID/compute_rigid_local.cpp b/src/RIGID/compute_rigid_local.cpp
index deca01f2aea749fa9cc82c075659fba711f13807..bcb778ab86b993c5391549b4040330bd424b651c 100644
--- a/src/RIGID/compute_rigid_local.cpp
+++ b/src/RIGID/compute_rigid_local.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <string.h>
+#include <cmath>
+#include <cstring>
#include "compute_rigid_local.h"
#include "atom.h"
#include "update.h"
diff --git a/src/RIGID/fix_ehex.cpp b/src/RIGID/fix_ehex.cpp
index 61b76b513f57f654268936711bfe535b2250b751..1476c71d3fa080912fbaa98ed44b09f410e43385 100644
--- a/src/RIGID/fix_ehex.cpp
+++ b/src/RIGID/fix_ehex.cpp
@@ -22,9 +22,9 @@
which implements the heat exchange (HEX) algorithm.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "fix_ehex.h"
#include "atom.h"
#include "domain.h"
diff --git a/src/RIGID/fix_rattle.cpp b/src/RIGID/fix_rattle.cpp
index 666561b462bb7011378e02e2d3bba776f723ff97..7ade8d6848f176e64456dd875c53768a69fe2fab 100644
--- a/src/RIGID/fix_rattle.cpp
+++ b/src/RIGID/fix_rattle.cpp
@@ -16,10 +16,10 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
-#include <stdio.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
+#include <cstdio>
#include "fix_rattle.h"
#include "atom.h"
#include "atom_vec.h"
diff --git a/src/RIGID/fix_rigid.cpp b/src/RIGID/fix_rigid.cpp
index e9f668dafdd4873d5c81f3ecd4275e0d470dd8a6..7104d3084994d2c7d9c4b4ff5d89d8aa387d6c00 100644
--- a/src/RIGID/fix_rigid.cpp
+++ b/src/RIGID/fix_rigid.cpp
@@ -11,10 +11,10 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "fix_rigid.h"
#include "math_extra.h"
#include "atom.h"
@@ -174,7 +174,8 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
MPI_Allreduce(&vmin,&minval,1,MPI_INT,MPI_MIN,world);
molecule = new tagint[nlocal];
for (i = 0; i < nlocal; i++)
- if (mask[i] & groupbit) molecule[i] = (tagint)((tagint)value[i] - minval + 1);
+ if (mask[i] & groupbit)
+ molecule[i] = (tagint)((tagint)value[i] - minval + 1);
delete[] value;
} else error->all(FLERR,"Unsupported fix rigid custom property");
} else {
@@ -624,6 +625,10 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
setupflag = 0;
+ // compute per body forces and torques at final_integrate() by default
+
+ earlyflag = 0;
+
// print statistics
int nsum = 0;
@@ -711,12 +716,26 @@ void FixRigid::init()
avec_tri = (AtomVecTri *) atom->style_match("tri");
// warn if more than one rigid fix
+ // if earlyflag, warn if any post-force fixes come after POEMS fix
int count = 0;
for (i = 0; i < modify->nfix; i++)
- if (strcmp(modify->fix[i]->style,"rigid") == 0) count++;
+ if (modify->fix[i]->rigid_flag) count++;
if (count > 1 && me == 0) error->warning(FLERR,"More than one fix rigid");
+ if (earlyflag) {
+ int rflag = 0;
+ for (i = 0; i < modify->nfix; i++) {
+ if (modify->fix[i]->rigid_flag) rflag = 1;
+ if (rflag && (modify->fmask[i] & POST_FORCE) &&
+ !modify->fix[i]->rigid_flag) {
+ char str[128];
+ sprintf(str,"Fix %s alters forces after fix rigid",modify->fix[i]->id);
+ error->warning(FLERR,str);
+ }
+ }
+ }
+
// error if npt,nph fix comes before rigid fix
for (i = 0; i < modify->nfix; i++) {
@@ -944,7 +963,7 @@ void FixRigid::initial_integrate(int vflag)
which are added in when final_integrate() calculates a new fcm/torque
------------------------------------------------------------------------- */
-void FixRigid::post_force(int vflag)
+void FixRigid::apply_langevin_thermostat()
{
if (me == 0) {
double gamma1,gamma2;
@@ -1008,7 +1027,7 @@ void FixRigid::enforce2d()
/* ---------------------------------------------------------------------- */
-void FixRigid::final_integrate()
+void FixRigid::compute_forces_and_torques()
{
int i,ibody;
double dtfm;
@@ -1062,9 +1081,7 @@ void FixRigid::final_integrate()
MPI_Allreduce(sum[0],all[0],6*nbody,MPI_DOUBLE,MPI_SUM,world);
- // update vcm and angmom
// include Langevin thermostat forces
- // fflag,tflag = 0 for some dimensions in 2d
for (ibody = 0; ibody < nbody; ibody++) {
fcm[ibody][0] = all[ibody][0] + langextra[ibody][0];
@@ -1073,6 +1090,31 @@ void FixRigid::final_integrate()
torque[ibody][0] = all[ibody][3] + langextra[ibody][3];
torque[ibody][1] = all[ibody][4] + langextra[ibody][4];
torque[ibody][2] = all[ibody][5] + langextra[ibody][5];
+ }
+}
+
+
+/* ---------------------------------------------------------------------- */
+
+void FixRigid::post_force(int vflag)
+{
+ if (langflag) apply_langevin_thermostat();
+ if (earlyflag) compute_forces_and_torques();
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixRigid::final_integrate()
+{
+ int ibody;
+ double dtfm;
+
+ if (!earlyflag) compute_forces_and_torques();
+
+ // update vcm and angmom
+ // fflag,tflag = 0 for some dimensions in 2d
+
+ for (ibody = 0; ibody < nbody; ibody++) {
// update vcm by 1/2 step
@@ -2342,7 +2384,7 @@ void FixRigid::write_restart_file(char *file)
sprintf(outfile,"%s.rigid",file);
FILE *fp = fopen(outfile,"w");
if (fp == NULL) {
- char str[128];
+ char str[192];
sprintf(str,"Cannot open fix rigid restart file %s",outfile);
error->one(FLERR,str);
}
@@ -2587,6 +2629,32 @@ void FixRigid::zero_rotation()
set_v();
}
+/* ---------------------------------------------------------------------- */
+
+int FixRigid::modify_param(int narg, char **arg)
+{
+ if (strcmp(arg[0],"bodyforces") == 0) {
+ if (narg < 2) error->all(FLERR,"Illegal fix_modify command");
+ if (strcmp(arg[1],"early") == 0) earlyflag = 1;
+ else if (strcmp(arg[1],"late") == 0) earlyflag = 0;
+ else error->all(FLERR,"Illegal fix_modify command");
+
+ // reset fix mask
+ // must do here and not in init,
+ // since modify.cpp::init() uses fix masks before calling fix::init()
+
+ for (int i = 0; i < modify->nfix; i++)
+ if (strcmp(modify->fix[i]->id,id) == 0) {
+ if (earlyflag) modify->fmask[i] |= POST_FORCE;
+ else if (!langflag) modify->fmask[i] &= ~POST_FORCE;
+ break;
+ }
+ return 2;
+ }
+
+ return 0;
+}
+
/* ----------------------------------------------------------------------
return temperature of collection of rigid bodies
non-active DOF are removed by fflag/tflag and in tfactor
diff --git a/src/RIGID/fix_rigid.h b/src/RIGID/fix_rigid.h
index 467ae56cf9e4ed88b83149064392c0fb910da475..507e4c755356686ae3b7a5f3f5c352e49932ae0f 100644
--- a/src/RIGID/fix_rigid.h
+++ b/src/RIGID/fix_rigid.h
@@ -38,7 +38,6 @@ class FixRigid : public Fix {
void final_integrate_respa(int, int);
void write_restart_file(char *);
virtual double compute_scalar();
- virtual int modify_param(int, char **) {return 0;}
double memory_usage();
void grow_arrays(int);
@@ -55,6 +54,7 @@ class FixRigid : public Fix {
void reset_dt();
void zero_momentum();
void zero_rotation();
+ virtual int modify_param(int, char **);
virtual void *extract(const char*, int &);
double extract_ke();
double extract_erotational();
@@ -70,6 +70,7 @@ class FixRigid : public Fix {
char *infile; // file to read rigid body attributes from
int rstyle; // SINGLE,MOLECULE,GROUP
int setupflag; // 1 if body properties are setup, else 0
+ int earlyflag; // 1 if forces/torques computed at post_force()
int dimension; // # of dimensions
int nbody; // # of rigid bodies
@@ -144,6 +145,8 @@ class FixRigid : public Fix {
void set_v();
void setup_bodies_static();
void setup_bodies_dynamic();
+ void apply_langevin_thermostat();
+ void compute_forces_and_torques();
void readfile(int, double *, double **, double **, double **,
imageint *, int *);
};
diff --git a/src/RIGID/fix_rigid_nh.cpp b/src/RIGID/fix_rigid_nh.cpp
index 0e05685dba4ac546c5e3d6b1f63844921309eddb..96c44d15b5b0e1861803203e4d20e0d0e052e891 100644
--- a/src/RIGID/fix_rigid_nh.cpp
+++ b/src/RIGID/fix_rigid_nh.cpp
@@ -17,9 +17,9 @@
Miller et al., J Chem Phys. 116, 8649-8659 (2002)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstring>
#include "fix_rigid_nh.h"
#include "math_extra.h"
#include "atom.h"
@@ -620,87 +620,14 @@ void FixRigidNH::final_integrate()
akin_t = akin_r = 0.0;
}
- // sum over atoms to get force and torque on rigid body
+ // late calculation of forces and torques (if requested)
- double **x = atom->x;
- double **f = atom->f;
- int nlocal = atom->nlocal;
-
- double xprd = domain->xprd;
- double yprd = domain->yprd;
- double zprd = domain->zprd;
- if (triclinic) {
- xy = domain->xy;
- xz = domain->xz;
- yz = domain->yz;
- }
-
- int xbox,ybox,zbox;
- double xunwrap,yunwrap,zunwrap,dx,dy,dz;
- for (ibody = 0; ibody < nbody; ibody++)
- for (i = 0; i < 6; i++) sum[ibody][i] = 0.0;
-
- for (i = 0; i < nlocal; i++) {
- if (body[i] < 0) continue;
- ibody = body[i];
-
- sum[ibody][0] += f[i][0];
- sum[ibody][1] += f[i][1];
- sum[ibody][2] += f[i][2];
-
- xbox = (xcmimage[i] & IMGMASK) - IMGMAX;
- ybox = (xcmimage[i] >> IMGBITS & IMGMASK) - IMGMAX;
- zbox = (xcmimage[i] >> IMG2BITS) - IMGMAX;
-
- if (triclinic == 0) {
- xunwrap = x[i][0] + xbox*xprd;
- yunwrap = x[i][1] + ybox*yprd;
- zunwrap = x[i][2] + zbox*zprd;
- } else {
- xunwrap = x[i][0] + xbox*xprd + ybox*xy + zbox*xz;
- yunwrap = x[i][1] + ybox*yprd + zbox*yz;
- zunwrap = x[i][2] + zbox*zprd;
- }
-
- dx = xunwrap - xcm[ibody][0];
- dy = yunwrap - xcm[ibody][1];
- dz = zunwrap - xcm[ibody][2];
-
- sum[ibody][3] += dy*f[i][2] - dz*f[i][1];
- sum[ibody][4] += dz*f[i][0] - dx*f[i][2];
- sum[ibody][5] += dx*f[i][1] - dy*f[i][0];
- }
-
- // extended particles add their torque to torque of body
-
- if (extended) {
- double **torque_one = atom->torque;
-
- for (i = 0; i < nlocal; i++) {
- if (body[i] < 0) continue;
- ibody = body[i];
-
- if (eflags[i] & TORQUE) {
- sum[ibody][3] += torque_one[i][0];
- sum[ibody][4] += torque_one[i][1];
- sum[ibody][5] += torque_one[i][2];
- }
- }
- }
-
- MPI_Allreduce(sum[0],all[0],6*nbody,MPI_DOUBLE,MPI_SUM,world);
+ if (!earlyflag) compute_forces_and_torques();
// update vcm and angmom
- // include Langevin thermostat forces
// fflag,tflag = 0 for some dimensions in 2d
for (ibody = 0; ibody < nbody; ibody++) {
- fcm[ibody][0] = all[ibody][0] + langextra[ibody][0];
- fcm[ibody][1] = all[ibody][1] + langextra[ibody][1];
- fcm[ibody][2] = all[ibody][2] + langextra[ibody][2];
- torque[ibody][0] = all[ibody][3] + langextra[ibody][3];
- torque[ibody][1] = all[ibody][4] + langextra[ibody][4];
- torque[ibody][2] = all[ibody][5] + langextra[ibody][5];
// update vcm by 1/2 step
@@ -1324,7 +1251,7 @@ int FixRigidNH::modify_param(int narg, char **arg)
return 2;
}
- return 0;
+ return FixRigid::modify_param(narg,arg);
}
/* ---------------------------------------------------------------------- */
diff --git a/src/RIGID/fix_rigid_nh_small.cpp b/src/RIGID/fix_rigid_nh_small.cpp
index 50777766fe33b2e6a38a13ea2fbb42b037785e58..135a1fb4bdb0e8ee37b8e958bb31e5b6117a1a33 100644
--- a/src/RIGID/fix_rigid_nh_small.cpp
+++ b/src/RIGID/fix_rigid_nh_small.cpp
@@ -17,9 +17,9 @@
Miller et al., J Chem Phys. 116, 8649-8659 (2002)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstring>
#include "fix_rigid_nh_small.h"
#include "math_extra.h"
#include "atom.h"
@@ -643,80 +643,9 @@ void FixRigidNHSmall::final_integrate()
scale_r *= exp(-dtq * (pdim * mtk_term2));
}
- // sum over atoms to get force and torque on rigid body
+ // late calculation of forces and torques (if requested)
- double **x = atom->x;
- double **f = atom->f;
- int nlocal = atom->nlocal;
-
- double dx,dy,dz;
- double unwrap[3];
- double *xcm,*fcm,*tcm;
-
- for (ibody = 0; ibody < nlocal_body+nghost_body; ibody++) {
- fcm = body[ibody].fcm;
- fcm[0] = fcm[1] = fcm[2] = 0.0;
- tcm = body[ibody].torque;
- tcm[0] = tcm[1] = tcm[2] = 0.0;
- }
-
- for (i = 0; i < nlocal; i++) {
- if (atom2body[i] < 0) continue;
- Body *b = &body[atom2body[i]];
-
- fcm = b->fcm;
- fcm[0] += f[i][0];
- fcm[1] += f[i][1];
- fcm[2] += f[i][2];
-
- domain->unmap(x[i],xcmimage[i],unwrap);
- xcm = b->xcm;
- dx = unwrap[0] - xcm[0];
- dy = unwrap[1] - xcm[1];
- dz = unwrap[2] - xcm[2];
-
- tcm = b->torque;
- tcm[0] += dy*f[i][2] - dz*f[i][1];
- tcm[1] += dz*f[i][0] - dx*f[i][2];
- tcm[2] += dx*f[i][1] - dy*f[i][0];
- }
-
- // extended particles add their torque to torque of body
-
- if (extended) {
- double **torque = atom->torque;
-
- for (i = 0; i < nlocal; i++) {
- if (atom2body[i] < 0) continue;
-
- if (eflags[i] & TORQUE) {
- tcm = body[atom2body[i]].torque;
- tcm[0] += torque[i][0];
- tcm[1] += torque[i][1];
- tcm[2] += torque[i][2];
- }
- }
- }
-
- // reverse communicate fcm, torque of all bodies
-
- commflag = FORCE_TORQUE;
- comm->reverse_comm_fix(this,6);
-
- // include Langevin thermostat forces and torques
-
- if (langflag) {
- for (int ibody = 0; ibody < nlocal_body; ibody++) {
- fcm = body[ibody].fcm;
- fcm[0] += langextra[ibody][0];
- fcm[1] += langextra[ibody][1];
- fcm[2] += langextra[ibody][2];
- tcm = body[ibody].torque;
- tcm[0] += langextra[ibody][3];
- tcm[1] += langextra[ibody][4];
- tcm[2] += langextra[ibody][5];
- }
- }
+ if (!earlyflag) compute_forces_and_torques();
// update vcm and angmom
// include Langevin thermostat forces
@@ -1440,7 +1369,7 @@ int FixRigidNHSmall::modify_param(int narg, char **arg)
return 2;
}
- return 0;
+ return FixRigidSmall::modify_param(narg,arg);
}
/* ---------------------------------------------------------------------- */
diff --git a/src/RIGID/fix_rigid_nph.cpp b/src/RIGID/fix_rigid_nph.cpp
index c0aa3b7040e0224a495af26dd7e934d2ab4b018f..45a4a8d09cd00dfa14abf23db64652a0ca5d4a12 100644
--- a/src/RIGID/fix_rigid_nph.cpp
+++ b/src/RIGID/fix_rigid_nph.cpp
@@ -17,7 +17,7 @@
Miller et al., J Chem Phys. 116, 8649-8659 (2002)
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "fix_rigid_nph.h"
#include "domain.h"
#include "modify.h"
diff --git a/src/RIGID/fix_rigid_nph_small.cpp b/src/RIGID/fix_rigid_nph_small.cpp
index 4e3e54766f7cbc8e7b179d63e0c5da394d51f956..d32e3043f45451b7ef9a07856f918b5b3deb2bf8 100644
--- a/src/RIGID/fix_rigid_nph_small.cpp
+++ b/src/RIGID/fix_rigid_nph_small.cpp
@@ -17,7 +17,7 @@
Miller et al., J Chem Phys. 116, 8649-8659 (2002)
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "fix_rigid_nph_small.h"
#include "domain.h"
#include "modify.h"
diff --git a/src/RIGID/fix_rigid_npt.cpp b/src/RIGID/fix_rigid_npt.cpp
index 24e12e41c235e37b26b9fa77b1f353d9c440223a..da5d5ffaa54837c0d54aa4830790ce98903a36cc 100644
--- a/src/RIGID/fix_rigid_npt.cpp
+++ b/src/RIGID/fix_rigid_npt.cpp
@@ -17,7 +17,7 @@
Miller et al., J Chem Phys. 116, 8649-8659 (2002)
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "fix_rigid_npt.h"
#include "domain.h"
#include "modify.h"
diff --git a/src/RIGID/fix_rigid_npt_small.cpp b/src/RIGID/fix_rigid_npt_small.cpp
index 551ef50ca91ce84b8d00dc1ed3e41c754bb18ad3..f1fd5470da68dfd80bdc15644952dcfd649dc160 100644
--- a/src/RIGID/fix_rigid_npt_small.cpp
+++ b/src/RIGID/fix_rigid_npt_small.cpp
@@ -17,7 +17,7 @@
Miller et al., J Chem Phys. 116, 8649-8659 (2002)
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "fix_rigid_npt_small.h"
#include "domain.h"
#include "modify.h"
diff --git a/src/RIGID/fix_rigid_small.cpp b/src/RIGID/fix_rigid_small.cpp
index 0cdec74fe86d3af2a675fd759badf913d2f95f3f..c1de89efc70da5221fd8c0ee6c75a0ec5312d450 100644
--- a/src/RIGID/fix_rigid_small.cpp
+++ b/src/RIGID/fix_rigid_small.cpp
@@ -11,10 +11,10 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "fix_rigid_small.h"
#include "math_extra.h"
#include "atom.h"
@@ -457,6 +457,10 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
avec_line = (AtomVecLine *) atom->style_match("line");
avec_tri = (AtomVecTri *) atom->style_match("tri");
+ // compute per body forces and torques inside final_integrate() by default
+
+ earlyflag = 0;
+
// print statistics
int one = 0;
@@ -555,9 +559,22 @@ void FixRigidSmall::init()
int count = 0;
for (i = 0; i < modify->nfix; i++)
- if (strcmp(modify->fix[i]->style,"rigid") == 0) count++;
+ if (modify->fix[i]->rigid_flag) count++;
if (count > 1 && me == 0) error->warning(FLERR,"More than one fix rigid");
+ if (earlyflag) {
+ int rflag = 0;
+ for (i = 0; i < modify->nfix; i++) {
+ if (modify->fix[i]->rigid_flag) rflag = 1;
+ if (rflag && (modify->fmask[i] & POST_FORCE) &&
+ !modify->fix[i]->rigid_flag) {
+ char str[128];
+ sprintf(str,"Fix %s alters forces after fix rigid",modify->fix[i]->id);
+ error->warning(FLERR,str);
+ }
+ }
+ }
+
// error if npt,nph fix comes before rigid fix
for (i = 0; i < modify->nfix; i++) {
@@ -770,10 +787,10 @@ void FixRigidSmall::initial_integrate(int vflag)
/* ----------------------------------------------------------------------
apply Langevin thermostat to all 6 DOF of rigid bodies I own
unlike fix langevin, this stores extra force in extra arrays,
- which are added in when final_integrate() calculates a new fcm/torque
+ which are added in when a new fcm/torque are calculated
------------------------------------------------------------------------- */
-void FixRigidSmall::post_force(int vflag)
+void FixRigidSmall::apply_langevin_thermostat()
{
double gamma1,gamma2;
@@ -850,10 +867,18 @@ void FixRigidSmall::enforce2d()
/* ---------------------------------------------------------------------- */
-void FixRigidSmall::final_integrate()
+void FixRigidSmall::post_force(int vflag)
+{
+ if (langflag) apply_langevin_thermostat();
+ if (earlyflag) compute_forces_and_torques();
+}
+
+
+/* ---------------------------------------------------------------------- */
+
+void FixRigidSmall::compute_forces_and_torques()
{
int i,ibody;
- double dtfm;
//check(3);
@@ -931,6 +956,18 @@ void FixRigidSmall::final_integrate()
tcm[2] += langextra[ibody][5];
}
}
+}
+
+
+/* ---------------------------------------------------------------------- */
+
+void FixRigidSmall::final_integrate()
+{
+ double dtfm;
+
+ //check(3);
+
+ if (!earlyflag) compute_forces_and_torques();
// update vcm and angmom, recompute omega
@@ -3384,6 +3421,33 @@ void FixRigidSmall::zero_rotation()
/* ---------------------------------------------------------------------- */
+int FixRigidSmall::modify_param(int narg, char **arg)
+{
+ if (strcmp(arg[0],"bodyforces") == 0) {
+ if (narg < 2) error->all(FLERR,"Illegal fix_modify command");
+ if (strcmp(arg[1],"early") == 0) earlyflag = 1;
+ else if (strcmp(arg[1],"late") == 0) earlyflag = 0;
+ else error->all(FLERR,"Illegal fix_modify command");
+
+ // reset fix mask
+ // must do here and not in init,
+ // since modify.cpp::init() uses fix masks before calling fix::init()
+
+ for (int i = 0; i < modify->nfix; i++)
+ if (strcmp(modify->fix[i]->id,id) == 0) {
+ if (earlyflag) modify->fmask[i] |= POST_FORCE;
+ else if (!langflag) modify->fmask[i] &= ~POST_FORCE;
+ break;
+ }
+
+ return 2;
+ }
+
+ return 0;
+}
+
+/* ---------------------------------------------------------------------- */
+
void *FixRigidSmall::extract(const char *str, int &dim)
{
if (strcmp(str,"body") == 0) {
diff --git a/src/RIGID/fix_rigid_small.h b/src/RIGID/fix_rigid_small.h
index 493185104f8b2d9fe4b7128303a7b5f0908c9ce8..3f6826f9bb140bf131d1ccb2a4c260fee6fd01e5 100644
--- a/src/RIGID/fix_rigid_small.h
+++ b/src/RIGID/fix_rigid_small.h
@@ -63,6 +63,7 @@ class FixRigidSmall : public Fix {
void reset_dt();
void zero_momentum();
void zero_rotation();
+ int modify_param(int, char **);
void *extract(const char*, int &);
double extract_ke();
double extract_erotational();
@@ -78,6 +79,7 @@ class FixRigidSmall : public Fix {
char *infile; // file to read rigid body attributes from
int setupflag; // 1 if body properties are setup, else 0
+ int earlyflag; // 1 if forces/torques are computed at post_force()
int commflag; // various modes of forward/reverse comm
int customflag; // 1 if custom property/variable define bodies
int nbody; // total # of rigid bodies
@@ -191,6 +193,8 @@ class FixRigidSmall : public Fix {
void create_bodies(tagint *);
void setup_bodies_static();
void setup_bodies_dynamic();
+ void apply_langevin_thermostat();
+ void compute_forces_and_torques();
void readfile(int, double **, int *);
void grow_body();
void reset_atom2body();
diff --git a/src/RIGID/fix_shake.cpp b/src/RIGID/fix_shake.cpp
index 35c8d7a91741432f04dd22ea46f3fa6939bd31c4..0beef3bfa24cec383ba2a5d29304aff1bb596366 100644
--- a/src/RIGID/fix_shake.cpp
+++ b/src/RIGID/fix_shake.cpp
@@ -12,10 +12,10 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
-#include <stdio.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
+#include <cstdio>
#include "fix_shake.h"
#include "fix_rattle.h"
#include "atom.h"
diff --git a/src/SHOCK/fix_append_atoms.cpp b/src/SHOCK/fix_append_atoms.cpp
index 80be74bee1634a0665c0a08fffde6b1197cd885e..d898d2a790d62a03c8451eaf9c564fe52334f3f1 100644
--- a/src/SHOCK/fix_append_atoms.cpp
+++ b/src/SHOCK/fix_append_atoms.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <string.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstring>
+#include <cstdlib>
#include "fix_append_atoms.h"
#include "atom.h"
#include "atom_vec.h"
@@ -29,8 +29,6 @@
using namespace LAMMPS_NS;
using namespace FixConst;
-enum{LAYOUT_UNIFORM,LAYOUT_NONUNIFORM,LAYOUT_TILED}; // several files
-
#define BIG 1.0e30
#define EPSILON 1.0e-6
@@ -417,7 +415,7 @@ void FixAppendAtoms::pre_exchange()
if (spatflag==1) if (get_spatial()==0) return;
int addflag = 0;
- if (comm->layout != LAYOUT_TILED) {
+ if (comm->layout != Comm::LAYOUT_TILED) {
if (comm->myloc[2] == comm->procgrid[2]-1) addflag = 1;
} else {
if (comm->mysplit[2][1] == 1.0) addflag = 1;
diff --git a/src/SHOCK/fix_msst.cpp b/src/SHOCK/fix_msst.cpp
index d7e5723980c647714836c561812f008d5daa561e..a7890c3afa4ab8825c585c06faae9cd4ef5135de 100644
--- a/src/SHOCK/fix_msst.cpp
+++ b/src/SHOCK/fix_msst.cpp
@@ -17,9 +17,9 @@
see Reed, Fried, Joannopoulos, Phys Rev Lett, 90, 235503 (2003)
------------------------------------------------------------------------- */
-#include <string.h>
-#include <stdlib.h>
-#include <math.h>
+#include <cstring>
+#include <cstdlib>
+#include <cmath>
#include "fix_msst.h"
#include "atom.h"
#include "force.h"
diff --git a/src/SHOCK/fix_nphug.cpp b/src/SHOCK/fix_nphug.cpp
index d28e9daf775e7bf85e8f20b52413f0e4ab7feeba..c6df6646cf44a436bc7f2622034add37c76d728e 100644
--- a/src/SHOCK/fix_nphug.cpp
+++ b/src/SHOCK/fix_nphug.cpp
@@ -11,8 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
-#include <stdlib.h>
+#include <cstring>
+#include <cstdlib>
+#include <cmath>
#include "fix_nphug.h"
#include "modify.h"
#include "error.h"
@@ -21,10 +22,8 @@
#include "force.h"
#include "domain.h"
#include "group.h"
-#include <math.h>
#include "memory.h"
#include "comm.h"
-#include <math.h>
using namespace LAMMPS_NS;
using namespace FixConst;
diff --git a/src/SHOCK/fix_wall_piston.cpp b/src/SHOCK/fix_wall_piston.cpp
index 7dff3d986ff136083566df2ab6988e904bf8fe9a..7146b46c1e12f4a021a71b9d4c1f0dd963975cd3 100644
--- a/src/SHOCK/fix_wall_piston.cpp
+++ b/src/SHOCK/fix_wall_piston.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <string.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstring>
+#include <cstdlib>
#include "fix_wall_piston.h"
#include "atom.h"
#include "modify.h"
diff --git a/src/SNAP/compute_sna_atom.cpp b/src/SNAP/compute_sna_atom.cpp
index 4b114d9ce777714ee305311398421979b99f69b7..0d8b0bae14c3f82ccac058b88c9e37757c8f1e12 100644
--- a/src/SNAP/compute_sna_atom.cpp
+++ b/src/SNAP/compute_sna_atom.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "sna.h"
-#include <string.h>
-#include <stdlib.h>
+#include <cstring>
+#include <cstdlib>
#include "compute_sna_atom.h"
#include "atom.h"
#include "update.h"
@@ -276,9 +276,13 @@ void ComputeSNAAtom::compute_peratom()
for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
double bi = snaptr[tid]->bvec[icoeff];
+ // diagonal element of quadratic matrix
+
+ sna[i][ncount++] = 0.5*bi*bi;
+
// upper-triangular elements of quadratic matrix
- for (int jcoeff = icoeff; jcoeff < ncoeff; jcoeff++)
+ for (int jcoeff = icoeff+1; jcoeff < ncoeff; jcoeff++)
sna[i][ncount++] = bi*snaptr[tid]->bvec[jcoeff];
}
}
diff --git a/src/SNAP/compute_snad_atom.cpp b/src/SNAP/compute_snad_atom.cpp
index 54a6ce761248c3ee6fcb2c4ab14fce16e5520e00..b0fef8e1e3fe5203f8c8d978b0f356671acbd97b 100644
--- a/src/SNAP/compute_snad_atom.cpp
+++ b/src/SNAP/compute_snad_atom.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "sna.h"
-#include <string.h>
-#include <stdlib.h>
+#include <cstring>
+#include <cstdlib>
#include "compute_snad_atom.h"
#include "atom.h"
#include "update.h"
@@ -95,6 +95,11 @@ ComputeSNADAtom::ComputeSNADAtom(LAMMPS *lmp, int narg, char **arg) :
error->all(FLERR,"Illegal compute snad/atom command");
rmin0 = atof(arg[iarg+1]);
iarg += 2;
+ } else if (strcmp(arg[iarg],"bzeroflag") == 0) {
+ if (iarg+2 > narg)
+ error->all(FLERR,"Illegal compute snad/atom command");
+ bzeroflag = atoi(arg[iarg+1]);
+ iarg += 2;
} else if (strcmp(arg[iarg],"switchflag") == 0) {
if (iarg+2 > narg)
error->all(FLERR,"Illegal compute snad/atom command");
@@ -121,16 +126,11 @@ ComputeSNADAtom::ComputeSNADAtom(LAMMPS *lmp, int narg, char **arg) :
}
ncoeff = snaptr[0]->ncoeff;
- twoncoeff = 2*ncoeff;
- threencoeff = 3*ncoeff;
- size_peratom_cols = threencoeff*atom->ntypes;
- if (quadraticflag) {
- ncoeffq = (ncoeff*(ncoeff+1))/2;
- twoncoeffq = 2*ncoeffq;
- threencoeffq = 3*ncoeffq;
- size_peratom_cols +=
- threencoeffq*atom->ntypes;
- }
+ nperdim = ncoeff;
+ if (quadraticflag) nperdim += (ncoeff*(ncoeff+1))/2;
+ yoffset = nperdim;
+ zoffset = 2*nperdim;
+ size_peratom_cols = 3*nperdim*atom->ntypes;
comm_reverse = size_peratom_cols;
peratom_flag = 1;
@@ -248,9 +248,10 @@ void ComputeSNADAtom::compute_peratom()
const int* const jlist = firstneigh[i];
const int jnum = numneigh[i];
- const int typeoffset = threencoeff*(atom->type[i]-1);
- const int quadraticoffset = threencoeff*atom->ntypes +
- threencoeffq*(atom->type[i]-1);
+ // const int typeoffset = threencoeff*(atom->type[i]-1);
+ // const int quadraticoffset = threencoeff*atom->ntypes +
+ // threencoeffq*(atom->type[i]-1);
+ const int typeoffset = 3*nperdim*(atom->type[i]-1);
// insure rij, inside, and typej are of size jnum
@@ -304,16 +305,17 @@ void ComputeSNADAtom::compute_peratom()
for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
snadi[icoeff] += snaptr[tid]->dbvec[icoeff][0];
- snadi[icoeff+ncoeff] += snaptr[tid]->dbvec[icoeff][1];
- snadi[icoeff+twoncoeff] += snaptr[tid]->dbvec[icoeff][2];
+ snadi[icoeff+yoffset] += snaptr[tid]->dbvec[icoeff][1];
+ snadi[icoeff+zoffset] += snaptr[tid]->dbvec[icoeff][2];
snadj[icoeff] -= snaptr[tid]->dbvec[icoeff][0];
- snadj[icoeff+ncoeff] -= snaptr[tid]->dbvec[icoeff][1];
- snadj[icoeff+twoncoeff] -= snaptr[tid]->dbvec[icoeff][2];
+ snadj[icoeff+yoffset] -= snaptr[tid]->dbvec[icoeff][1];
+ snadj[icoeff+zoffset] -= snaptr[tid]->dbvec[icoeff][2];
}
if (quadraticflag) {
- double *snadi = snad[i]+quadraticoffset;
- double *snadj = snad[j]+quadraticoffset;
+ const int quadraticoffset = ncoeff;
+ snadi += quadraticoffset;
+ snadj += quadraticoffset;
int ncount = 0;
for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
double bi = snaptr[tid]->bvec[icoeff];
@@ -321,21 +323,36 @@ void ComputeSNADAtom::compute_peratom()
double biy = snaptr[tid]->dbvec[icoeff][1];
double biz = snaptr[tid]->dbvec[icoeff][2];
+ // diagonal elements of quadratic matrix
+
+ double dbxtmp = bi*bix;
+ double dbytmp = bi*biy;
+ double dbztmp = bi*biz;
+
+ snadi[ncount] += dbxtmp;
+ snadi[ncount+yoffset] += dbytmp;
+ snadi[ncount+zoffset] += dbztmp;
+ snadj[ncount] -= dbxtmp;
+ snadj[ncount+yoffset] -= dbytmp;
+ snadj[ncount+zoffset] -= dbztmp;
+ ncount++;
+
// upper-triangular elements of quadratic matrix
- for (int jcoeff = icoeff; jcoeff < ncoeff; jcoeff++) {
+ for (int jcoeff = icoeff+1; jcoeff < ncoeff; jcoeff++) {
double dbxtmp = bi*snaptr[tid]->dbvec[jcoeff][0]
+ bix*snaptr[tid]->bvec[jcoeff];
double dbytmp = bi*snaptr[tid]->dbvec[jcoeff][1]
+ biy*snaptr[tid]->bvec[jcoeff];
double dbztmp = bi*snaptr[tid]->dbvec[jcoeff][2]
+ biz*snaptr[tid]->bvec[jcoeff];
- snadi[ncount] += dbxtmp;
- snadi[ncount+ncoeffq] += dbytmp;
- snadi[ncount+twoncoeffq] += dbztmp;
- snadj[ncount] -= dbxtmp;
- snadj[ncount+ncoeffq] -= dbytmp;
- snadj[ncount+twoncoeffq] -= dbztmp;
+
+ snadi[ncount] += dbxtmp;
+ snadi[ncount+yoffset] += dbytmp;
+ snadi[ncount+zoffset] += dbztmp;
+ snadj[ncount] -= dbxtmp;
+ snadj[ncount+yoffset] -= dbytmp;
+ snadj[ncount+zoffset] -= dbztmp;
ncount++;
}
}
@@ -361,7 +378,7 @@ int ComputeSNADAtom::pack_reverse_comm(int n, int first, double *buf)
for (i = first; i < last; i++)
for (icoeff = 0; icoeff < size_peratom_cols; icoeff++)
buf[m++] = snad[i][icoeff];
- return comm_reverse;
+ return m;
}
/* ---------------------------------------------------------------------- */
@@ -387,8 +404,7 @@ double ComputeSNADAtom::memory_usage()
double bytes = nmax*size_peratom_cols * sizeof(double);
bytes += 3*njmax*sizeof(double);
bytes += njmax*sizeof(int);
- bytes += threencoeff*atom->ntypes;
- if (quadraticflag) bytes += threencoeffq*atom->ntypes;
+ bytes += 3*nperdim*atom->ntypes;
bytes += snaptr[0]->memory_usage()*comm->nthreads;
return bytes;
}
diff --git a/src/SNAP/compute_snad_atom.h b/src/SNAP/compute_snad_atom.h
index 5e40632d8c5c61f7970428ce79ed1241c794c54c..a33e6047c2c2bd0fca6d25d8a2b948fef9f7d4f9 100644
--- a/src/SNAP/compute_snad_atom.h
+++ b/src/SNAP/compute_snad_atom.h
@@ -37,7 +37,7 @@ class ComputeSNADAtom : public Compute {
private:
int nmax, njmax, diagonalstyle;
- int ncoeff, twoncoeff, threencoeff, ncoeffq, twoncoeffq, threencoeffq;
+ int ncoeff, nperdim, yoffset, zoffset;
double **cutsq;
class NeighList *list;
double **snad;
diff --git a/src/SNAP/compute_snav_atom.cpp b/src/SNAP/compute_snav_atom.cpp
index 0278be5a97414f8dd9fb9ba681edd33255ecfbed..cf66b1c136ae8cbe32f1014005c49ce32f8d9d77 100644
--- a/src/SNAP/compute_snav_atom.cpp
+++ b/src/SNAP/compute_snav_atom.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "sna.h"
-#include <string.h>
-#include <stdlib.h>
+#include <cstring>
+#include <cstdlib>
#include "compute_snav_atom.h"
#include "atom.h"
#include "update.h"
@@ -96,6 +96,11 @@ ComputeSNAVAtom::ComputeSNAVAtom(LAMMPS *lmp, int narg, char **arg) :
error->all(FLERR,"Illegal compute snav/atom command");
switchflag = atoi(arg[iarg+1]);
iarg += 2;
+ } else if (strcmp(arg[iarg],"bzeroflag") == 0) {
+ if (iarg+2 > narg)
+ error->all(FLERR,"Illegal compute snav/atom command");
+ bzeroflag = atoi(arg[iarg+1]);
+ iarg += 2;
} else if (strcmp(arg[iarg],"quadraticflag") == 0) {
if (iarg+2 > narg)
error->all(FLERR,"Illegal compute snav/atom command");
@@ -117,22 +122,9 @@ ComputeSNAVAtom::ComputeSNAVAtom(LAMMPS *lmp, int narg, char **arg) :
}
ncoeff = snaptr[0]->ncoeff;
- twoncoeff = 2*ncoeff;
- threencoeff = 3*ncoeff;
- fourncoeff = 4*ncoeff;
- fivencoeff = 5*ncoeff;
- sixncoeff = 6*ncoeff;
- size_peratom_cols = sixncoeff*atom->ntypes;
- if (quadraticflag) {
- ncoeffq = ncoeff*ncoeff;
- twoncoeffq = 2*ncoeffq;
- threencoeffq = 3*ncoeffq;
- fourncoeffq = 4*ncoeffq;
- fivencoeffq = 5*ncoeffq;
- sixncoeffq = 6*ncoeffq;
- size_peratom_cols +=
- sixncoeffq*atom->ntypes;
- }
+ nperdim = ncoeff;
+ if (quadraticflag) nperdim += (ncoeff*(ncoeff+1))/2;
+ size_peratom_cols = 6*nperdim*atom->ntypes;
comm_reverse = size_peratom_cols;
peratom_flag = 1;
@@ -251,9 +243,7 @@ void ComputeSNAVAtom::compute_peratom()
const int* const jlist = firstneigh[i];
const int jnum = numneigh[i];
- const int typeoffset = sixncoeff*(atom->type[i]-1);
- const int quadraticoffset = sixncoeff*atom->ntypes +
- sixncoeffq*(atom->type[i]-1);
+ const int typeoffset = 6*nperdim*(atom->type[i]-1);
// insure rij, inside, and typej are of size jnum
@@ -307,23 +297,24 @@ void ComputeSNAVAtom::compute_peratom()
double *snavj = snav[j]+typeoffset;
for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
- snavi[icoeff] += snaptr[tid]->dbvec[icoeff][0]*xtmp;
- snavi[icoeff+ncoeff] += snaptr[tid]->dbvec[icoeff][1]*ytmp;
- snavi[icoeff+twoncoeff] += snaptr[tid]->dbvec[icoeff][2]*ztmp;
- snavi[icoeff+threencoeff] += snaptr[tid]->dbvec[icoeff][1]*ztmp;
- snavi[icoeff+fourncoeff] += snaptr[tid]->dbvec[icoeff][0]*ztmp;
- snavi[icoeff+fivencoeff] += snaptr[tid]->dbvec[icoeff][0]*ytmp;
- snavj[icoeff] -= snaptr[tid]->dbvec[icoeff][0]*x[j][0];
- snavj[icoeff+ncoeff] -= snaptr[tid]->dbvec[icoeff][1]*x[j][1];
- snavj[icoeff+twoncoeff] -= snaptr[tid]->dbvec[icoeff][2]*x[j][2];
- snavj[icoeff+threencoeff] -= snaptr[tid]->dbvec[icoeff][1]*x[j][2];
- snavj[icoeff+fourncoeff] -= snaptr[tid]->dbvec[icoeff][0]*x[j][2];
- snavj[icoeff+fivencoeff] -= snaptr[tid]->dbvec[icoeff][0]*x[j][1];
+ snavi[icoeff] += snaptr[tid]->dbvec[icoeff][0]*xtmp;
+ snavi[icoeff+nperdim] += snaptr[tid]->dbvec[icoeff][1]*ytmp;
+ snavi[icoeff+2*nperdim] += snaptr[tid]->dbvec[icoeff][2]*ztmp;
+ snavi[icoeff+3*nperdim] += snaptr[tid]->dbvec[icoeff][1]*ztmp;
+ snavi[icoeff+4*nperdim] += snaptr[tid]->dbvec[icoeff][0]*ztmp;
+ snavi[icoeff+5*nperdim] += snaptr[tid]->dbvec[icoeff][0]*ytmp;
+ snavj[icoeff] -= snaptr[tid]->dbvec[icoeff][0]*x[j][0];
+ snavj[icoeff+nperdim] -= snaptr[tid]->dbvec[icoeff][1]*x[j][1];
+ snavj[icoeff+2*nperdim] -= snaptr[tid]->dbvec[icoeff][2]*x[j][2];
+ snavj[icoeff+3*nperdim] -= snaptr[tid]->dbvec[icoeff][1]*x[j][2];
+ snavj[icoeff+4*nperdim] -= snaptr[tid]->dbvec[icoeff][0]*x[j][2];
+ snavj[icoeff+5*nperdim] -= snaptr[tid]->dbvec[icoeff][0]*x[j][1];
}
if (quadraticflag) {
- double *snavi = snav[i]+quadraticoffset;
- double *snavj = snav[j]+quadraticoffset;
+ const int quadraticoffset = ncoeff;
+ snavi += quadraticoffset;
+ snavj += quadraticoffset;
int ncount = 0;
for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
double bi = snaptr[tid]->bvec[icoeff];
@@ -331,27 +322,46 @@ void ComputeSNAVAtom::compute_peratom()
double biy = snaptr[tid]->dbvec[icoeff][1];
double biz = snaptr[tid]->dbvec[icoeff][2];
+ // diagonal element of quadratic matrix
+
+ double dbxtmp = bi*bix;
+ double dbytmp = bi*biy;
+ double dbztmp = bi*biz;
+ snavi[ncount] += dbxtmp*xtmp;
+ snavi[ncount+nperdim] += dbytmp*ytmp;
+ snavi[ncount+2*nperdim] += dbztmp*ztmp;
+ snavi[ncount+3*nperdim] += dbytmp*ztmp;
+ snavi[ncount+4*nperdim] += dbxtmp*ztmp;
+ snavi[ncount+5*nperdim] += dbxtmp*ytmp;
+ snavj[ncount] -= dbxtmp*x[j][0];
+ snavj[ncount+nperdim] -= dbytmp*x[j][1];
+ snavj[ncount+2*nperdim] -= dbztmp*x[j][2];
+ snavj[ncount+3*nperdim] -= dbytmp*x[j][2];
+ snavj[ncount+4*nperdim] -= dbxtmp*x[j][2];
+ snavj[ncount+5*nperdim] -= dbxtmp*x[j][1];
+ ncount++;
+
// upper-triangular elements of quadratic matrix
- for (int jcoeff = icoeff; jcoeff < ncoeff; jcoeff++) {
+ for (int jcoeff = icoeff+1; jcoeff < ncoeff; jcoeff++) {
double dbxtmp = bi*snaptr[tid]->dbvec[jcoeff][0]
+ bix*snaptr[tid]->bvec[jcoeff];
double dbytmp = bi*snaptr[tid]->dbvec[jcoeff][1]
+ biy*snaptr[tid]->bvec[jcoeff];
double dbztmp = bi*snaptr[tid]->dbvec[jcoeff][2]
+ biz*snaptr[tid]->bvec[jcoeff];
- snavi[ncount] += dbxtmp*xtmp;
- snavi[ncount+ncoeffq] += dbytmp*ytmp;
- snavi[ncount+twoncoeffq] += dbztmp*ztmp;
- snavi[ncount+threencoeffq] += dbytmp*ztmp;
- snavi[ncount+fourncoeffq] += dbxtmp*ztmp;
- snavi[ncount+fivencoeffq] += dbxtmp*ytmp;
- snavj[ncount] -= dbxtmp*x[j][0];
- snavj[ncount+ncoeffq] -= dbytmp*x[j][1];
- snavj[ncount+twoncoeffq] -= dbztmp*x[j][2];
- snavj[ncount+threencoeffq] -= dbytmp*x[j][2];
- snavj[ncount+fourncoeffq] -= dbxtmp*x[j][2];
- snavj[ncount+fivencoeffq] -= dbxtmp*x[j][1];
+ snavi[ncount] += dbxtmp*xtmp;
+ snavi[ncount+nperdim] += dbytmp*ytmp;
+ snavi[ncount+2*nperdim] += dbztmp*ztmp;
+ snavi[ncount+3*nperdim] += dbytmp*ztmp;
+ snavi[ncount+4*nperdim] += dbxtmp*ztmp;
+ snavi[ncount+5*nperdim] += dbxtmp*ytmp;
+ snavj[ncount] -= dbxtmp*x[j][0];
+ snavj[ncount+nperdim] -= dbytmp*x[j][1];
+ snavj[ncount+2*nperdim] -= dbztmp*x[j][2];
+ snavj[ncount+3*nperdim] -= dbytmp*x[j][2];
+ snavj[ncount+4*nperdim] -= dbxtmp*x[j][2];
+ snavj[ncount+5*nperdim] -= dbxtmp*x[j][1];
ncount++;
}
}
@@ -377,7 +387,7 @@ int ComputeSNAVAtom::pack_reverse_comm(int n, int first, double *buf)
for (i = first; i < last; i++)
for (icoeff = 0; icoeff < size_peratom_cols; icoeff++)
buf[m++] = snav[i][icoeff];
- return comm_reverse;
+ return m;
}
/* ---------------------------------------------------------------------- */
@@ -403,8 +413,8 @@ double ComputeSNAVAtom::memory_usage()
double bytes = nmax*size_peratom_cols * sizeof(double);
bytes += 3*njmax*sizeof(double);
bytes += njmax*sizeof(int);
- bytes += sixncoeff*atom->ntypes;
- if (quadraticflag) bytes += sixncoeffq*atom->ntypes;
+ bytes += 6*nperdim*atom->ntypes;
+ if (quadraticflag) bytes += 6*nperdim*atom->ntypes;
bytes += snaptr[0]->memory_usage()*comm->nthreads;
return bytes;
}
diff --git a/src/SNAP/compute_snav_atom.h b/src/SNAP/compute_snav_atom.h
index 35f1478393520dc9f2a687a0db86201b0ca5e52c..2eb9fb804f7420aab541b5995b81e39a2ca83766 100644
--- a/src/SNAP/compute_snav_atom.h
+++ b/src/SNAP/compute_snav_atom.h
@@ -37,8 +37,7 @@ class ComputeSNAVAtom : public Compute {
private:
int nmax, njmax, diagonalstyle;
- int ncoeff, twoncoeff, threencoeff, fourncoeff, fivencoeff, sixncoeff;
- int ncoeffq, twoncoeffq, threencoeffq, fourncoeffq, fivencoeffq, sixncoeffq;
+ int ncoeff, nperdim;
double **cutsq;
class NeighList *list;
double **snav;
diff --git a/src/SNAP/pair_snap.cpp b/src/SNAP/pair_snap.cpp
index 377235685cd0f052d2f51ab01967a63f6679707c..2b1816950c28c11c3b23c288aacb4fd33be5348f 100644
--- a/src/SNAP/pair_snap.cpp
+++ b/src/SNAP/pair_snap.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "pair_snap.h"
#include "atom.h"
#include "atom_vec.h"
@@ -278,14 +278,15 @@ void PairSNAP::compute_regular(int eflag, int vflag)
double bveci = snaptr->bvec[icoeff];
double fack = coeffi[k]*bveci;
double* dbveci = snaptr->dbvec[icoeff];
- fij[0] += fack*snaptr->dbvec[icoeff][0];
- fij[1] += fack*snaptr->dbvec[icoeff][1];
- fij[2] += fack*snaptr->dbvec[icoeff][2];
+ fij[0] += fack*dbveci[0];
+ fij[1] += fack*dbveci[1];
+ fij[2] += fack*dbveci[2];
k++;
for (int jcoeff = icoeff+1; jcoeff < ncoeff; jcoeff++) {
double facki = coeffi[k]*bveci;
double fackj = coeffi[k]*snaptr->bvec[jcoeff];
double* dbvecj = snaptr->dbvec[jcoeff];
+
fij[0] += facki*dbvecj[0]+fackj*dbveci[0];
fij[1] += facki*dbvecj[1]+fackj*dbveci[1];
fij[2] += facki*dbvecj[2]+fackj*dbveci[2];
@@ -1529,10 +1530,10 @@ void PairSNAP::coeff(int narg, char **arg)
}
if (comm->me == 0)
- printf("ncoeff = %d snancoeff = %d \n",ncoeff,sna[0]->ncoeff);
- if (ncoeff != sna[0]->ncoeff) {
- error->all(FLERR,"Incorrect SNAP parameter file");
- }
+ if (ncoeff != sna[0]->ncoeff) {
+ printf("ncoeff = %d snancoeff = %d \n",ncoeff,sna[0]->ncoeff);
+ error->all(FLERR,"Incorrect SNAP parameter file");
+ }
// Calculate maximum cutoff for all elements
diff --git a/src/SNAP/pair_snap.h b/src/SNAP/pair_snap.h
index d39cb0f8d44a73b37ff5c4688b4c3f690e52f232..b60ab3c3e42657fba6fff2f316aa6e93aa5056a5 100644
--- a/src/SNAP/pair_snap.h
+++ b/src/SNAP/pair_snap.h
@@ -37,11 +37,8 @@ public:
virtual double init_one(int, int);
virtual double memory_usage();
- double rcutfac, quadraticflag; // declared public to workaround gcc 4.9
- int ncoeff; // compiler bug, manifest in KOKKOS package
-
protected:
- int ncoeffq, ncoeffall;
+ int ncoeff, ncoeffq, ncoeffall;
double **bvec, ***dbvec;
class SNA** sna;
int nmax;
@@ -100,8 +97,8 @@ protected:
double *wjelem; // elements weights
double **coeffelem; // element bispectrum coefficients
int *map; // mapping from atom types to elements
- int twojmax, diagonalstyle, switchflag, bzeroflag;
- double rfac0, rmin0, wj1, wj2;
+ int twojmax, diagonalstyle, switchflag, bzeroflag, quadraticflag;
+ double rcutfac, rfac0, rmin0, wj1, wj2;
int rcutfacflag, twojmaxflag; // flags for required parameters
};
diff --git a/src/SNAP/sna.cpp b/src/SNAP/sna.cpp
index 16c382cc4ce34949e463d4b1bb8fae52512290ee..31505730433a4b00b2956c10afb5a272e94a0f55 100644
--- a/src/SNAP/sna.cpp
+++ b/src/SNAP/sna.cpp
@@ -16,11 +16,11 @@
------------------------------------------------------------------------- */
#include "sna.h"
-#include <math.h>
+#include <cmath>
#include "math_const.h"
#include "math_extra.h"
-#include <string.h>
-#include <stdlib.h>
+#include <cstring>
+#include <cstdlib>
#include "openmp_snap.h"
#include "memory.h"
diff --git a/src/SRD/fix_srd.cpp b/src/SRD/fix_srd.cpp
index 81ef2024203c0b858500466ecaab0500e828c955..564c1e98d7362a5947bc281a8b766ad5b6f4e479 100644
--- a/src/SRD/fix_srd.cpp
+++ b/src/SRD/fix_srd.cpp
@@ -15,9 +15,9 @@
Contributing authors: Jeremy Lechman (SNL), Pieter in 't Veld (BASF)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <string.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstring>
+#include <cstdlib>
#include "fix_srd.h"
#include "math_extra.h"
#include "atom.h"
@@ -52,8 +52,6 @@ enum{BIG_MOVE,SRD_MOVE,SRD_ROTATE};
enum{CUBIC_ERROR,CUBIC_WARN};
enum{SHIFT_NO,SHIFT_YES,SHIFT_POSSIBLE};
-enum{NO_REMAP,X_REMAP,V_REMAP}; // same as fix_deform.cpp
-
#define EINERTIA 0.2 // moment of inertia prefactor for ellipsoid
#define ATOMPERBIN 30
@@ -384,7 +382,7 @@ void FixSRD::init()
if (strcmp(modify->fix[i]->style,"deform") == 0) {
deformflag = 1;
FixDeform *deform = (FixDeform *) modify->fix[i];
- if (deform->box_change_shape && deform->remapflag != V_REMAP)
+ if (deform->box_change_shape && deform->remapflag != Domain::V_REMAP)
error->all(FLERR,"Using fix srd with inconsistent "
"fix deform remap option");
}
diff --git a/src/SRD/fix_wall_srd.cpp b/src/SRD/fix_wall_srd.cpp
index dbca9c5fc88adf49e47a024415bf3b1d9eb07ccb..24b0c3cec5c2d5210ed21a39450649ac16464485 100644
--- a/src/SRD/fix_wall_srd.cpp
+++ b/src/SRD/fix_wall_srd.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <stdlib.h>
-#include <string.h>
+#include <cstdlib>
+#include <cstring>
#include "fix_wall_srd.h"
#include "atom.h"
#include "modify.h"
diff --git a/src/USER-ATC/fix_atc.cpp b/src/USER-ATC/fix_atc.cpp
index 96ad93481d1aa4675eeb362cb6809ab35ad48b80..f53343ced1380ce59fe9a6b273e14fda3035335f 100644
--- a/src/USER-ATC/fix_atc.cpp
+++ b/src/USER-ATC/fix_atc.cpp
@@ -35,8 +35,8 @@
#include "ATC_CouplingMomentumEnergy.h"
#include "LammpsInterface.h"
// other
-#include <stdio.h>
-#include <string.h>
+#include <cstdio>
+#include <cstring>
#include <sstream>
using namespace LAMMPS_NS;
diff --git a/src/USER-AWPMD/Install.sh b/src/USER-AWPMD/Install.sh
old mode 100644
new mode 100755
diff --git a/src/USER-AWPMD/atom_vec_wavepacket.cpp b/src/USER-AWPMD/atom_vec_wavepacket.cpp
index 33048efba6d8c24f112dc36bc288179679165ff3..7556dd2c8e3ed968aa750620b58ce885debff2a5 100644
--- a/src/USER-AWPMD/atom_vec_wavepacket.cpp
+++ b/src/USER-AWPMD/atom_vec_wavepacket.cpp
@@ -15,9 +15,9 @@
Contributing author: Ilya Valuev (JIHT, Moscow, Russia)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "atom_vec_wavepacket.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-AWPMD/fix_nve_awpmd.cpp b/src/USER-AWPMD/fix_nve_awpmd.cpp
index 3ad425030d3d2ebfc81531f73e63e43b92dc68f6..7722c931218f3cc56c1a8acbf6fd0d4bcec97e78 100644
--- a/src/USER-AWPMD/fix_nve_awpmd.cpp
+++ b/src/USER-AWPMD/fix_nve_awpmd.cpp
@@ -15,16 +15,15 @@
Contributing author: Ilya Valuev (JIHT, Moscow, Russia)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstring>
#include "fix_nve_awpmd.h"
#include "atom.h"
#include "force.h"
#include "update.h"
#include "respa.h"
#include "error.h"
-#include <math.h>
#include "TCP/wpmd_split.h"
diff --git a/src/USER-AWPMD/pair_awpmd_cut.cpp b/src/USER-AWPMD/pair_awpmd_cut.cpp
index 2ce1a926845721c8fc10fe001585f99de5dae2b7..2dcb3e62962f43f6a1e9fc35aa75ffaa969557dc 100644
--- a/src/USER-AWPMD/pair_awpmd_cut.cpp
+++ b/src/USER-AWPMD/pair_awpmd_cut.cpp
@@ -15,10 +15,10 @@
Contributing author: Ilya Valuev (JIHT, Moscow, Russia)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_awpmd_cut.h"
#include "atom.h"
#include "update.h"
diff --git a/src/USER-BOCS/README b/src/USER-BOCS/README
new file mode 100644
index 0000000000000000000000000000000000000000..adeb34c38729a3614df738333bb64c6565c3dec7
--- /dev/null
+++ b/src/USER-BOCS/README
@@ -0,0 +1,19 @@
+This user package implements the pressure correction to the barostat as
+outlined in:
+
+N. J. H. Dunn and W. G. Noid, "Bottom-up coarse-grained models that
+accurately describe the structure, pressure, and compressibility of
+molecular liquids," J. Chem. Phys. 143, 243148 (2015).
+
+doi: 10.1063/1.4937383
+
+The USER-BOCS user package for LAMMPS is part of the BOCS software package:
+https://github.com/noid-group/BOCS
+
+See the following reference for information about the entire package:
+
+Dunn, NJH; Lebold, KM; DeLyser, MR; Rudzinski, JF; Noid, WG.
+"BOCS: Bottom-Up Open-Source Coarse-Graining Software."
+J. Phys. Chem. B. 122, 13, 3363-3377 (2018).
+
+Example inputs are in the examples/USER/bocs folder.
diff --git a/src/USER-BOCS/compute_pressure_bocs.cpp b/src/USER-BOCS/compute_pressure_bocs.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..fc24efab4c52e27529b225c67f37393d7c500b01
--- /dev/null
+++ b/src/USER-BOCS/compute_pressure_bocs.cpp
@@ -0,0 +1,444 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+-------------------------------------------------------------------------
+ USER-BOCS written by: Nicholas J. H. Dunn and Michael R. DeLyser
+ from The Pennsylvania State University
+------------------------------------------------------------------------- */
+
+#include <mpi.h>
+#include <cstring>
+#include <cstdlib>
+#include "compute_pressure_bocs.h"
+#include "atom.h"
+#include "update.h"
+#include "domain.h"
+#include "modify.h"
+#include "fix.h"
+#include "force.h"
+#include "pair.h"
+#include "bond.h"
+#include "angle.h"
+#include "dihedral.h"
+#include "improper.h"
+#include "kspace.h"
+#include "error.h"
+
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+ComputePressureBocs::ComputePressureBocs(LAMMPS *lmp, int narg, char **arg) :
+ Compute(lmp, narg, arg),
+ vptr(NULL), id_temp(NULL)
+{
+ if (narg < 4) error->all(FLERR,"Illegal compute pressure/bocs command");
+ if (igroup) error->all(FLERR,"Compute pressure/bocs must use group all");
+
+ scalar_flag = vector_flag = 1;
+ size_vector = 6;
+ extscalar = 0;
+ extvector = 0;
+ pressflag = 1;
+ timeflag = 1;
+
+ p_match_flag = 0;
+ phi_coeff = NULL;
+
+ // store temperature ID used by pressure computation
+ // insure it is valid for temperature computation
+
+ if (strcmp(arg[3],"NULL") == 0) id_temp = NULL;
+ else {
+ int n = strlen(arg[3]) + 1;
+ id_temp = new char[n];
+ strcpy(id_temp,arg[3]);
+
+ int icompute = modify->find_compute(id_temp);
+ if (icompute < 0)
+ error->all(FLERR,"Could not find compute pressure/bocs temperature ID");
+ if (modify->compute[icompute]->tempflag == 0)
+ error->all(FLERR,"Compute pressure/bocs temperature ID does not "
+ "compute temperature");
+ }
+
+ // process optional args
+
+ if (narg == 4) {
+ keflag = 1;
+ pairflag = 1;
+ bondflag = angleflag = dihedralflag = improperflag = 1;
+ kspaceflag = fixflag = 1;
+ } else {
+ keflag = 0;
+ pairflag = 0;
+ bondflag = angleflag = dihedralflag = improperflag = 0;
+ kspaceflag = fixflag = 0;
+ int iarg = 4;
+ while (iarg < narg) {
+ if (strcmp(arg[iarg],"ke") == 0) keflag = 1;
+ else if (strcmp(arg[iarg],"pair") == 0) pairflag = 1;
+ else if (strcmp(arg[iarg],"bond") == 0) bondflag = 1;
+ else if (strcmp(arg[iarg],"angle") == 0) angleflag = 1;
+ else if (strcmp(arg[iarg],"dihedral") == 0) dihedralflag = 1;
+ else if (strcmp(arg[iarg],"improper") == 0) improperflag = 1;
+ else if (strcmp(arg[iarg],"kspace") == 0) kspaceflag = 1;
+ else if (strcmp(arg[iarg],"fix") == 0) fixflag = 1;
+ else if (strcmp(arg[iarg],"virial") == 0) {
+ pairflag = 1;
+ bondflag = angleflag = dihedralflag = improperflag = 1;
+ kspaceflag = fixflag = 1;
+ } else error->all(FLERR,"Illegal compute pressure/bocs command");
+ iarg++;
+ }
+ }
+
+ // error check
+
+ if (keflag && id_temp == NULL)
+ error->all(FLERR,"Compute pressure/bocs requires temperature ID "
+ "to include kinetic energy");
+
+ vector = new double[6];
+ nvirial = 0;
+ vptr = NULL;
+}
+
+/* ---------------------------------------------------------------------- */
+
+ComputePressureBocs::~ComputePressureBocs()
+{
+ delete [] id_temp;
+ delete [] vector;
+ delete [] vptr;
+ if (phi_coeff) free(phi_coeff);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputePressureBocs::init()
+{
+ boltz = force->boltz;
+ nktv2p = force->nktv2p;
+ dimension = domain->dimension;
+
+ // set temperature compute, must be done in init()
+ // fixes could have changed or compute_modify could have changed it
+
+ if (keflag) {
+ int icompute = modify->find_compute(id_temp);
+ if (icompute < 0)
+ error->all(FLERR,"Could not find compute pressure/bocs temperature ID");
+ temperature = modify->compute[icompute];
+ }
+
+ // detect contributions to virial
+ // vptr points to all virial[6] contributions
+
+ delete [] vptr;
+ nvirial = 0;
+ vptr = NULL;
+
+ if (pairflag && force->pair) nvirial++;
+ if (bondflag && atom->molecular && force->bond) nvirial++;
+ if (angleflag && atom->molecular && force->angle) nvirial++;
+ if (dihedralflag && atom->molecular && force->dihedral) nvirial++;
+ if (improperflag && atom->molecular && force->improper) nvirial++;
+ if (fixflag)
+ for (int i = 0; i < modify->nfix; i++)
+ if (modify->fix[i]->virial_flag) nvirial++;
+
+ if (nvirial) {
+ vptr = new double*[nvirial];
+ nvirial = 0;
+ if (pairflag && force->pair) vptr[nvirial++] = force->pair->virial;
+ if (bondflag && force->bond) vptr[nvirial++] = force->bond->virial;
+ if (angleflag && force->angle) vptr[nvirial++] = force->angle->virial;
+ if (dihedralflag && force->dihedral)
+ vptr[nvirial++] = force->dihedral->virial;
+ if (improperflag && force->improper)
+ vptr[nvirial++] = force->improper->virial;
+ if (fixflag)
+ for (int i = 0; i < modify->nfix; i++)
+ if (modify->fix[i]->virial_flag)
+ vptr[nvirial++] = modify->fix[i]->virial;
+ }
+
+ // flag Kspace contribution separately, since not summed across procs
+
+ if (kspaceflag && force->kspace) kspace_virial = force->kspace->virial;
+ else kspace_virial = NULL;
+}
+
+/* Extra functions added for BOCS */
+
+/* ----------------------------------------------------------------------
+ Compute the pressure correction for the analytical basis set
+------------------------------------------------------------------------- */
+double ComputePressureBocs::get_cg_p_corr(int N_basis, double *phi_coeff,
+ int N_mol, double vavg, double vCG)
+{
+ double correction = 0.0;
+ for (int i = 1; i <= N_basis; ++i)
+ {
+ correction -= phi_coeff[i-1] * ( N_mol * i / vavg ) *
+ pow( ( 1 / vavg ) * ( vCG - vavg ),i-1);
+ }
+ return correction;
+}
+
+/* ----------------------------------------------------------------------
+ Find the relevant index position if using a spline basis set
+------------------------------------------------------------------------- */
+double ComputePressureBocs::find_index(double * grid, double value)
+{
+ int i;
+ double spacing = fabs(grid[1]-grid[0]);
+ int gridsize = spline_length;
+ for (i = 0; i < (gridsize-1); ++i)
+ {
+ if (value >= grid[i] && value <= grid[i+1]) { return i; }
+ }
+
+ if (value >= grid[i] && value <= (grid[i] + spacing)) { return i; }
+
+ for (int i = 0; i < gridsize; ++i)
+ {
+ fprintf(stderr, "grid %d: %f\n",i,grid[i]);
+ }
+ char * errmsg = (char *) calloc(100,sizeof(char));
+ sprintf(errmsg,"Value %f does not fall within spline grid.\n",value);
+ error->all(FLERR,errmsg);
+
+ exit(1);
+}
+
+/* ----------------------------------------------------------------------
+ Compute the pressure correction for a spline basis set
+------------------------------------------------------------------------- */
+
+double ComputePressureBocs::get_cg_p_corr(double ** grid, int basis_type,
+ double vCG)
+{
+ int i = find_index(grid[0],vCG);
+ double correction, deltax = vCG - grid[0][i];
+
+ if (basis_type == 1)
+ {
+ correction = grid[1][i] + (deltax) *
+ ( grid[1][i+1] - grid[1][i] ) / ( grid[0][i+1] - grid[0][i] );
+ }
+ else if (basis_type == 2)
+ {
+ correction = grid[1][i] + (grid[2][i] * deltax) +
+ (grid[3][i] * pow(deltax,2)) + (grid[4][i] * pow(deltax,3));
+ }
+ else
+ {
+ error->all(FLERR,"bad spline type passed to get_cg_p_corr()\n");
+ }
+ return correction;
+}
+
+/* ----------------------------------------------------------------------
+ send cg info from fix_bocs to compute_pressure_bocs for the analytical
+ basis set
+------------------------------------------------------------------------- */
+void ComputePressureBocs::send_cg_info(int basis_type, int sent_N_basis,
+ double *sent_phi_coeff, int sent_N_mol, double sent_vavg)
+{
+ if (basis_type == 0) { p_basis_type = 0; }
+ else
+ {
+ error->all(FLERR,"Incorrect basis type passed to ComputePressureBocs\n");
+ }
+
+ p_match_flag = 1;
+
+ N_basis = sent_N_basis;
+ if (phi_coeff) free(phi_coeff);
+ phi_coeff = ((double *) calloc(N_basis, sizeof(double)) );
+ for (int i=0; i<N_basis; i++) { phi_coeff[i] = sent_phi_coeff[i]; }
+
+ N_mol = sent_N_mol;
+ vavg = sent_vavg;
+}
+
+/* ----------------------------------------------------------------------
+ send cg info from fix_bocs to compute_pressure_bocs for a spline basis
+ set
+------------------------------------------------------------------------- */
+void ComputePressureBocs::send_cg_info(int basis_type,
+ double ** in_splines, int gridsize)
+{
+ if (basis_type == 1) { p_basis_type = 1; }
+ else if (basis_type == 2) { p_basis_type = 2; }
+ else
+ {
+ error->all(FLERR,"Incorrect basis type passed to ComputePressureBocs\n");
+ }
+ splines = in_splines;
+ spline_length = gridsize;
+ p_match_flag = 1;
+}
+
+/* End of new functions for BOCS */
+
+/* ----------------------------------------------------------------------
+ compute total pressure, averaged over Pxx, Pyy, Pzz
+------------------------------------------------------------------------- */
+double ComputePressureBocs::compute_scalar()
+{
+ invoked_scalar = update->ntimestep;
+ if (update->vflag_global != invoked_scalar)
+ error->all(FLERR,"Virial was not tallied on needed timestep");
+
+ // invoke temperature if it hasn't been already
+
+ double t;
+ double volume, correction = 0;
+ if (keflag) {
+ if (temperature->invoked_scalar != update->ntimestep)
+ t = temperature->compute_scalar();
+ else t = temperature->scalar;
+ }
+
+ if (dimension == 3) {
+ inv_volume = 1.0 / (domain->xprd * domain->yprd * domain->zprd);
+ volume = (domain->xprd * domain->yprd * domain->zprd);
+
+ /* MRD NJD if block */
+ if ( p_basis_type == 0 )
+ {
+ correction = get_cg_p_corr(N_basis,phi_coeff,N_mol,vavg,volume);
+ }
+ else if ( p_basis_type == 1 || p_basis_type == 2 )
+ {
+ correction = get_cg_p_corr(splines, p_basis_type, volume);
+ }
+
+ virial_compute(3,3);
+ if (keflag)
+ scalar = (temperature->dof * boltz * t +
+ virial[0] + virial[1] + virial[2]) / 3.0 *
+ inv_volume * nktv2p + (correction);
+ else
+ scalar = (virial[0] + virial[1] + virial[2]) / 3.0 *
+ inv_volume * nktv2p + (correction);
+ } else {
+ if (p_match_flag)
+ {
+ error->all(FLERR,"Pressure matching not implemented in 2-d.\n");
+ exit(1);
+ } // The rest of this can probably be deleted.
+ inv_volume = 1.0 / (domain->xprd * domain->yprd);
+ virial_compute(2,2);
+ if (keflag)
+ scalar = (temperature->dof * boltz * t +
+ virial[0] + virial[1]) / 2.0 * inv_volume * nktv2p;
+ else
+ scalar = (virial[0] + virial[1]) / 2.0 * inv_volume * nktv2p;
+ }
+
+ return scalar;
+}
+
+/* ----------------------------------------------------------------------
+ compute pressure tensor
+ assume KE tensor has already been computed
+------------------------------------------------------------------------- */
+
+void ComputePressureBocs::compute_vector()
+{
+ invoked_vector = update->ntimestep;
+ if (update->vflag_global != invoked_vector)
+ error->all(FLERR,"Virial was not tallied on needed timestep");
+
+ if (force->kspace && kspace_virial && force->kspace->scalar_pressure_flag)
+ error->all(FLERR,"Must use 'kspace_modify pressure/scalar no' for "
+ "tensor components with kspace_style msm");
+
+ // invoke temperature if it hasn't been already
+
+ double *ke_tensor;
+ if (keflag) {
+ if (temperature->invoked_vector != update->ntimestep)
+ temperature->compute_vector();
+ ke_tensor = temperature->vector;
+ }
+
+ if (dimension == 3) {
+ inv_volume = 1.0 / (domain->xprd * domain->yprd * domain->zprd);
+ virial_compute(6,3);
+ if (keflag) {
+ for (int i = 0; i < 6; i++)
+ vector[i] = (ke_tensor[i] + virial[i]) * inv_volume * nktv2p;
+ } else
+ for (int i = 0; i < 6; i++)
+ vector[i] = virial[i] * inv_volume * nktv2p;
+ } else {
+ inv_volume = 1.0 / (domain->xprd * domain->yprd);
+ virial_compute(4,2);
+ if (keflag) {
+ vector[0] = (ke_tensor[0] + virial[0]) * inv_volume * nktv2p;
+ vector[1] = (ke_tensor[1] + virial[1]) * inv_volume * nktv2p;
+ vector[3] = (ke_tensor[3] + virial[3]) * inv_volume * nktv2p;
+ vector[2] = vector[4] = vector[5] = 0.0;
+ } else {
+ vector[0] = virial[0] * inv_volume * nktv2p;
+ vector[1] = virial[1] * inv_volume * nktv2p;
+ vector[3] = virial[3] * inv_volume * nktv2p;
+ vector[2] = vector[4] = vector[5] = 0.0;
+ }
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputePressureBocs::virial_compute(int n, int ndiag)
+{
+ int i,j;
+ double v[6],*vcomponent;
+
+ for (i = 0; i < n; i++) v[i] = 0.0;
+
+ // sum contributions to virial from forces and fixes
+
+ for (j = 0; j < nvirial; j++) {
+ vcomponent = vptr[j];
+ for (i = 0; i < n; i++) v[i] += vcomponent[i];
+ }
+
+ // sum virial across procs
+
+ MPI_Allreduce(v,virial,n,MPI_DOUBLE,MPI_SUM,world);
+
+ // KSpace virial contribution is already summed across procs
+
+ if (kspace_virial)
+ for (i = 0; i < n; i++) virial[i] += kspace_virial[i];
+
+ // LJ long-range tail correction, only if pair contributions are included
+
+ if (force->pair && pairflag && force->pair->tail_flag)
+ for (i = 0; i < ndiag; i++) virial[i] += force->pair->ptail * inv_volume;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputePressureBocs::reset_extra_compute_fix(const char *id_new)
+{
+ delete [] id_temp;
+ int n = strlen(id_new) + 1;
+ id_temp = new char[n];
+ strcpy(id_temp,id_new);
+}
diff --git a/src/USER-BOCS/compute_pressure_bocs.h b/src/USER-BOCS/compute_pressure_bocs.h
new file mode 100644
index 0000000000000000000000000000000000000000..4fb932c5082473e2b3c111774dd78c1675ad6ec4
--- /dev/null
+++ b/src/USER-BOCS/compute_pressure_bocs.h
@@ -0,0 +1,114 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+-------------------------------------------------------------------------
+ USER-BOCS written by: Nicholas J. H. Dunn and Michael R. DeLyser
+ from The Pennsylvania State University
+------------------------------------------------------------------------- */
+
+#ifdef COMPUTE_CLASS
+
+ComputeStyle(PRESSURE/BOCS,ComputePressureBocs)
+
+#else
+
+
+#ifndef LMP_COMPUTE_PRESSURE_BOCS_H
+#define LMP_COMPUTE_PRESSURE_BOCS_H
+
+#include "compute.h"
+
+namespace LAMMPS_NS {
+// ComputePressure -> ComputePressureBocs MRD NJD
+class ComputePressureBocs : public Compute {
+ public:
+ ComputePressureBocs(class LAMMPS *, int, char **);
+ virtual ~ComputePressureBocs();
+ virtual void init();
+ virtual double compute_scalar();
+ virtual void compute_vector();
+ void reset_extra_compute_fix(const char *);
+
+ double compute_cg_scalar();
+ double get_cg_p_corr(int, double *, int, double, double);
+ double get_cg_fluct(double, double);
+ void send_cg_info(int, int, double*, int, double);
+ void send_cg_info(int, double **, int);
+ double get_cg_p_corr(double **, int, double);
+ double find_index(double* , double);
+
+ protected:
+ double boltz,nktv2p,inv_volume;
+ int nvirial,dimension;
+ double **vptr;
+ double *kspace_virial;
+ Compute *temperature;
+ char *id_temp;
+ double virial[6];
+ int keflag,pairflag,bondflag,angleflag,dihedralflag,improperflag;
+ int fixflag,kspaceflag;
+
+// NJD MRD
+ int p_basis_type;
+ int p_match_flag;
+ double vavg;
+ int N_mol;
+ int N_basis;
+ double *phi_coeff;
+ double ** splines;
+ int spline_length;
+
+ void virial_compute(int, int);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+E: Illegal ... command
+
+Self-explanatory. Check the input script syntax and compare to the
+documentation for the command. You can use -echo screen as a
+command-line option when running LAMMPS to see the offending line.
+
+E: Compute pressure must use group all
+
+Virial contributions computed by potentials (pair, bond, etc) are
+computed on all atoms.
+
+E: Could not find compute pressure temperature ID
+
+The compute ID for calculating temperature does not exist.
+
+E: Compute pressure temperature ID does not compute temperature
+
+The compute ID assigned to a pressure computation must compute
+temperature.
+
+E: Compute pressure requires temperature ID to include kinetic energy
+
+The keflag cannot be used unless a temperature compute is provided.
+
+E: Virial was not tallied on needed timestep
+
+You are using a thermo keyword that requires potentials to
+have tallied the virial, but they didn't on this timestep. See the
+variable doc page for ideas on how to make this work.
+
+E: Must use 'kspace_modify pressure/scalar no' for tensor components with kspace_style msm
+
+Otherwise MSM will compute only a scalar pressure. See the kspace_modify
+command for details on this setting.
+
+*/
diff --git a/src/USER-BOCS/fix_bocs.cpp b/src/USER-BOCS/fix_bocs.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..37e128f55662a6e6c9152abb518d3233845604fd
--- /dev/null
+++ b/src/USER-BOCS/fix_bocs.cpp
@@ -0,0 +1,2431 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+-------------------------------------------------------------------------
+ USER-BOCS written by: Nicholas J. H. Dunn and Michael R. DeLyser
+ from The Pennsylvania State University
+------------------------------------------------------------------------- */
+
+#include <cstring>
+#include <cstdlib>
+#include <cmath>
+#include "fix_bocs.h"
+#include "math_extra.h"
+#include "atom.h"
+#include "force.h"
+#include "group.h"
+#include "comm.h"
+#include "neighbor.h"
+#include "irregular.h"
+#include "modify.h"
+#include "fix_deform.h"
+#include "compute.h"
+#include "kspace.h"
+#include "update.h"
+#include "respa.h"
+#include "domain.h"
+#include "memory.h"
+#include "error.h"
+#include "citeme.h"
+
+#include "compute_pressure_bocs.h"
+
+using namespace LAMMPS_NS;
+using namespace FixConst;
+
+static const char cite_user_bocs_package[] =
+ "USER-BOCS package:\n\n"
+ "@Article{Dunn2018,\n"
+ " author = {NJH Dunn, KM Lebold, MR DeLyser, JF Rudzinski, WG Noid},\n"
+ " title = {BOCS: Bottom-Up Open-Source Coarse-Graining Software},\n"
+ " journal = {J. Phys. Chem. B},\n"
+ " year = 2018,\n"
+ " volume = 122,\n"
+ " pages = {3363--3377}\n"
+ "}\n\n";
+
+
+#define DELTAFLIP 0.1
+#define TILTMAX 1.5
+
+enum{NOBIAS,BIAS};
+enum{NONE,XYZ,XY,YZ,XZ};
+enum{ISO,ANISO,TRICLINIC};
+
+/* ----------------------------------------------------------------------
+ NVT,NPH,NPT integrators for improved Nose-Hoover equations of motion
+ ---------------------------------------------------------------------- */
+
+FixBocs::FixBocs(LAMMPS *lmp, int narg, char **arg) :
+ Fix(lmp, narg, arg),
+ rfix(NULL), id_dilate(NULL), irregular(NULL), id_temp(NULL), id_press(NULL),
+ eta(NULL), eta_dot(NULL), eta_dotdot(NULL),
+ eta_mass(NULL), etap(NULL), etap_dot(NULL), etap_dotdot(NULL),
+ etap_mass(NULL)
+{
+ if (lmp->citeme) lmp->citeme->add(cite_user_bocs_package);
+
+ if (narg < 4) error->all(FLERR,"Illegal fix bocs command");
+
+ restart_global = 1;
+ dynamic_group_allow = 1;
+ time_integrate = 1;
+ scalar_flag = 1;
+ vector_flag = 1;
+ global_freq = 1;
+ extscalar = 1;
+ extvector = 0;
+
+ // default values
+
+ pcouple = NONE;
+ drag = 0.0;
+ allremap = 1;
+ id_dilate = NULL;
+ mtchain = mpchain = 3;
+ nc_tchain = nc_pchain = 1;
+ mtk_flag = 1;
+ deviatoric_flag = 0;
+ nreset_h0 = 0;
+ eta_mass_flag = 1;
+ omega_mass_flag = 0;
+ etap_mass_flag = 0;
+ flipflag = 1;
+ dipole_flag = 0;
+ dlm_flag = 0;
+
+ tcomputeflag = 0;
+ pcomputeflag = 0;
+ id_temp = NULL;
+ id_press = NULL;
+
+ p_match_coeffs = NULL;
+
+ // turn on tilt factor scaling, whenever applicable
+
+ dimension = domain->dimension;
+
+ scaleyz = scalexz = scalexy = 0;
+ if (domain->yperiodic && domain->xy != 0.0) scalexy = 1;
+ if (domain->zperiodic && dimension == 3) {
+ if (domain->yz != 0.0) scaleyz = 1;
+ if (domain->xz != 0.0) scalexz = 1;
+ }
+
+ // set fixed-point to default = center of cell
+
+ fixedpoint[0] = 0.5*(domain->boxlo[0]+domain->boxhi[0]);
+ fixedpoint[1] = 0.5*(domain->boxlo[1]+domain->boxhi[1]);
+ fixedpoint[2] = 0.5*(domain->boxlo[2]+domain->boxhi[2]);
+
+ // used by FixNVTSllod to preserve non-default value
+
+ mtchain_default_flag = 1;
+
+ tstat_flag = 0;
+ double t_period = 0.0;
+
+ double p_period[6];
+ for (int i = 0; i < 6; i++) {
+ p_start[i] = p_stop[i] = p_period[i] = p_target[i] = 0.0;
+ p_flag[i] = 0;
+ }
+
+ // process keywords
+
+ int iarg = 3;
+
+ while (iarg < narg) {
+ if (strcmp(arg[iarg],"temp") == 0) {
+ if (iarg+4 > narg) error->all(FLERR,"Illegal fix bocs command");
+ tstat_flag = 1;
+ t_start = force->numeric(FLERR,arg[iarg+1]);
+ t_target = t_start;
+ t_stop = force->numeric(FLERR,arg[iarg+2]);
+ t_period = force->numeric(FLERR,arg[iarg+3]);
+ if (t_start <= 0.0 || t_stop <= 0.0)
+ error->all(FLERR,
+ "Target temperature for fix bocs cannot be 0.0");
+ iarg += 4;
+ } else if (strcmp(arg[iarg],"iso") == 0) {
+ error->all(FLERR,"Illegal fix bocs command. Pressure fix must be "
+ "cgiso . Use regular fix bocs for iso"); // MRD NJD
+ } else if (strcmp(arg[iarg],"cgiso") == 0) { // MRD NJD the whole else if
+ if (iarg+4 > narg)
+ error->all(FLERR,"Illegal fix bocs command. cgiso must be "
+ "followed by: P_0 P_f P_coupl");
+ p_match_flag = 1;
+ pcouple = XYZ;
+ p_start[0] = p_start[1] = p_start[2] =
+ force->numeric(FLERR,arg[iarg+1]);
+ p_stop[0] = p_stop[1] = p_stop[2] =
+ force->numeric(FLERR,arg[iarg+2]);
+ p_period[0] = p_period[1] = p_period[2] =
+ force->numeric(FLERR,arg[iarg+3]);
+
+ p_flag[0] = p_flag[1] = p_flag[2] = 1;
+ p_flag[3] = p_flag[4] = p_flag[5] = 0; // MRD
+ if (dimension == 2) { // Later I force 3D... MRD
+ p_start[2] = p_stop[2] = p_period[2] = 0.0;
+ p_flag[2] = 0;
+ }
+ iarg += 4;
+
+ if ( strcmp(arg[iarg], "analytic") == 0 ) {
+ if (iarg + 4 > narg) {
+ error->all(FLERR,"Illegal fix bocs command. basis type analytic"
+ " must be followed by: avg_vol n_mol n_pmatch_coeff");
+ }
+ p_basis_type = 0;
+ vavg = force->numeric(FLERR,arg[iarg+1]);
+ N_mol = force->inumeric(FLERR,arg[iarg+2]);
+ N_p_match = force->inumeric(FLERR,arg[iarg+3]);
+ p_match_coeffs = (double *) (calloc(N_p_match, sizeof(double)) );
+ iarg += 4;
+ if (iarg + N_p_match > narg)
+ error->all(FLERR,"Illegal fix bocs command. Missing coeffs.");
+ for (int pmatchi = 0; pmatchi < N_p_match; pmatchi++)
+ p_match_coeffs[pmatchi] = force->numeric(FLERR,arg[iarg+pmatchi]);
+ iarg += (N_p_match);
+ } else if (strcmp(arg[iarg], "linear_spline") == 0 ) {
+ if (iarg+2 > narg) error->all(FLERR,"Illegal fix bocs command. "
+ "Supply a file name after linear_spline.");
+ p_basis_type = 1;
+ spline_length = read_F_table( arg[iarg+1], p_basis_type );
+ iarg += 2;
+ } else if (strcmp(arg[iarg], "cubic_spline") == 0 ) {
+ if (iarg+2 > narg) error->all(FLERR,"Illegal fix bocs command. "
+ "Supply a file name after cubic_spline.");
+ p_basis_type = 2;
+ spline_length = read_F_table( arg[iarg+1], p_basis_type );
+ iarg += 2;
+ } else
+ {
+ char * errmsg = (char *) calloc(150,sizeof(char));
+ sprintf(errmsg,"CG basis type %s is not recognized\nSupported "
+ "basis types: analytic linear_spline cubic_spline",arg[iarg]);
+ error->all(FLERR,errmsg);
+ } // END NJD MRD
+ } else if (strcmp(arg[iarg],"tchain") == 0) {
+ if (iarg+2 > narg) error->all(FLERR,"Illegal fix bocs command");
+ mtchain = force->inumeric(FLERR,arg[iarg+1]);
+ // used by FixNVTSllod to preserve non-default value
+ mtchain_default_flag = 0;
+ if (mtchain < 1) error->all(FLERR,"Illegal fix bocs command");
+ iarg += 2;
+ } else if (strcmp(arg[iarg],"pchain") == 0) {
+ if (iarg+2 > narg) error->all(FLERR,"Illegal fix bocs command");
+ mpchain = force->inumeric(FLERR,arg[iarg+1]);
+ if (mpchain < 0) error->all(FLERR,"Illegal fix bocs command");
+ iarg += 2;
+ } else if (strcmp(arg[iarg],"mtk") == 0) {
+ if (iarg+2 > narg) error->all(FLERR,"Illegal fix bocs command");
+ if (strcmp(arg[iarg+1],"yes") == 0) mtk_flag = 1;
+ else if (strcmp(arg[iarg+1],"no") == 0) mtk_flag = 0;
+ else error->all(FLERR,"Illegal fix bocs command");
+ iarg += 2;
+ } else if (strcmp(arg[iarg],"tloop") == 0) {
+ if (iarg+2 > narg) error->all(FLERR,"Illegal fix bocs command");
+ nc_tchain = force->inumeric(FLERR,arg[iarg+1]);
+ if (nc_tchain < 0) error->all(FLERR,"Illegal fix bocs command");
+ iarg += 2;
+ } else if (strcmp(arg[iarg],"ploop") == 0) {
+ if (iarg+2 > narg) error->all(FLERR,"Illegal fix bocs command");
+ nc_pchain = force->inumeric(FLERR,arg[iarg+1]);
+ if (nc_pchain < 0) error->all(FLERR,"Illegal fix bocs command");
+ iarg += 2;
+ } else {
+ char * errmsg = (char *) calloc(80,sizeof(char));
+ sprintf(errmsg,"Illegal fix bocs command: unrecognized keyword %s"
+ ,arg[iarg]);
+ error->all(FLERR,errmsg);
+ }
+ }
+ // error checks
+
+ if (dimension != 3) // MRD NJD
+ error->all(FLERR,"Invalid fix bocs command. Must use 3 dimensions");
+
+// With cgiso, p_flag[0] = p_flag[1] = p_flag[2] = 1
+
+ // require periodicity in tensile dimension
+
+ if (p_flag[0] && domain->xperiodic == 0)
+ error->all(FLERR,"Cannot use fix bocs on a non-periodic dimension");
+ if (p_flag[1] && domain->yperiodic == 0)
+ error->all(FLERR,"Cannot use fix bocs on a non-periodic dimension");
+ if (p_flag[2] && domain->zperiodic == 0)
+ error->all(FLERR,"Cannot use fix bocs on a non-periodic dimension");
+
+ if (dipole_flag) {
+ if (!atom->sphere_flag)
+ error->all(FLERR,"Using update dipole flag requires atom style sphere");
+ if (!atom->mu_flag)
+ error->all(FLERR,"Using update dipole flag requires atom attribute mu");
+ }
+
+ if ((tstat_flag && t_period <= 0.0) ||
+ (p_flag[0] && p_period[0] <= 0.0) ||
+ (p_flag[1] && p_period[1] <= 0.0) ||
+ (p_flag[2] && p_period[2] <= 0.0) ||
+ (p_flag[3] && p_period[3] <= 0.0) ||
+ (p_flag[4] && p_period[4] <= 0.0) ||
+ (p_flag[5] && p_period[5] <= 0.0))
+ error->all(FLERR,"Fix bocs damping parameters must be > 0.0");
+
+ // set pstat_flag and box change and restart_pbc variables
+
+ pre_exchange_flag = 0;
+ pstat_flag = 0;
+ pstyle = ISO;
+
+ for (int i = 0; i < 6; i++)
+ if (p_flag[i]) pstat_flag = 1;
+
+ if (pstat_flag) {
+ if (p_flag[0] || p_flag[1] || p_flag[2]) box_change_size = 1;
+ if (p_flag[3] || p_flag[4] || p_flag[5]) box_change_shape = 1;
+ no_change_box = 1;
+ if (allremap == 0) restart_pbc = 1;
+
+ pstyle = ISO; // MRD this is the only one that can happen
+
+ // pre_exchange only required if flips can occur due to shape changes
+
+ if (flipflag && (p_flag[3] || p_flag[4] || p_flag[5]))
+ pre_exchange_flag = 1;
+ if (flipflag && (domain->yz != 0.0 || domain->xz != 0.0 ||
+ domain->xy != 0.0))
+ pre_exchange_flag = 1;
+ }
+
+ // convert input periods to frequencies
+
+ t_freq = 0.0;
+ p_freq[0] = p_freq[1] = p_freq[2] = p_freq[3] = p_freq[4] = p_freq[5] = 0.0;
+
+ if (tstat_flag) t_freq = 1.0 / t_period;
+ if (p_flag[0]) p_freq[0] = 1.0 / p_period[0];
+ if (p_flag[1]) p_freq[1] = 1.0 / p_period[1];
+ if (p_flag[2]) p_freq[2] = 1.0 / p_period[2];
+ if (p_flag[3]) p_freq[3] = 1.0 / p_period[3];
+ if (p_flag[4]) p_freq[4] = 1.0 / p_period[4];
+ if (p_flag[5]) p_freq[5] = 1.0 / p_period[5];
+
+ // Nose/Hoover temp and pressure init
+
+ size_vector = 0;
+
+ if (tstat_flag) {
+ int ich;
+ eta = new double[mtchain];
+
+ // add one extra dummy thermostat, set to zero
+
+ eta_dot = new double[mtchain+1];
+ eta_dot[mtchain] = 0.0;
+ eta_dotdot = new double[mtchain];
+ for (ich = 0; ich < mtchain; ich++) {
+ eta[ich] = eta_dot[ich] = eta_dotdot[ich] = 0.0;
+ }
+ eta_mass = new double[mtchain];
+ size_vector += 2*2*mtchain;
+ }
+
+ if (pstat_flag) {
+ omega[0] = omega[1] = omega[2] = 0.0;
+ omega_dot[0] = omega_dot[1] = omega_dot[2] = 0.0;
+ omega_mass[0] = omega_mass[1] = omega_mass[2] = 0.0;
+ omega[3] = omega[4] = omega[5] = 0.0;
+ omega_dot[3] = omega_dot[4] = omega_dot[5] = 0.0;
+ omega_mass[3] = omega_mass[4] = omega_mass[5] = 0.0;
+ if (pstyle == ISO) size_vector += 2*2*1;
+ else if (pstyle == ANISO) size_vector += 2*2*3;
+ else if (pstyle == TRICLINIC) size_vector += 2*2*6;
+
+ if (mpchain) {
+ int ich;
+ etap = new double[mpchain];
+
+ // add one extra dummy thermostat, set to zero
+
+ etap_dot = new double[mpchain+1];
+ etap_dot[mpchain] = 0.0;
+ etap_dotdot = new double[mpchain];
+ for (ich = 0; ich < mpchain; ich++) {
+ etap[ich] = etap_dot[ich] =
+ etap_dotdot[ich] = 0.0;
+ }
+ etap_mass = new double[mpchain];
+ size_vector += 2*2*mpchain;
+ }
+
+ if (deviatoric_flag) size_vector += 1;
+ }
+
+ nrigid = 0;
+ rfix = NULL;
+
+ if (pre_exchange_flag) irregular = new Irregular(lmp);
+ else irregular = NULL;
+
+ // initialize vol0,t0 to zero to signal uninitialized
+ // values then assigned in init(), if necessary
+
+ vol0 = t0 = 0.0;
+
+ /*~ MRD I copied this from fix_npt.cpp 8/17/17 ~*/
+
+ if (!tstat_flag)
+ error->all(FLERR,"Temperature control must be used with fix bocs");
+ if (!pstat_flag)
+ error->all(FLERR,"Pressure control must be used with fix bocs");
+
+ // create a new compute temp style
+ // id = fix-ID + temp
+ // compute group = all since pressure is always global (group all)
+ // and thus its KE/temperature contribution should use group all
+
+
+ int n = strlen(id) + 6;
+ id_temp = new char[n];
+ strcpy(id_temp,id);
+ strcat(id_temp,"_temp");
+
+ char **newarg = new char*[3];
+ newarg[0] = id_temp;
+ newarg[1] = (char *) "all";
+ newarg[2] = (char *) "temp";
+
+
+ modify->add_compute(3,newarg);
+ delete [] newarg;
+ tcomputeflag = 1;
+
+ // create a new compute pressure style
+ // id = fix-ID + press, compute group = all
+ // pass id_temp as 4th arg to pressure constructor
+
+ n = strlen(id) + 7;
+ id_press = new char[n];
+ strcpy(id_press,id);
+ strcat(id_press,"_press");
+
+ newarg = new char*[4];
+ newarg[0] = id_press;
+ newarg[1] = (char *) "all";
+ newarg[2] = (char *) "PRESSURE/BOCS";
+ newarg[3] = id_temp;
+ modify->add_compute(4,newarg);
+ delete [] newarg;
+ pcomputeflag = 1;
+
+/*~ MRD End of stuff copied from fix_npt.cpp~*/
+
+}
+
+/* ---------------------------------------------------------------------- */
+
+FixBocs::~FixBocs()
+{
+ if (copymode) return;
+
+ delete [] id_dilate;
+ delete [] rfix;
+
+ delete irregular;
+
+ // delete temperature and pressure if fix created them
+
+ if (tcomputeflag) modify->delete_compute(id_temp);
+ delete [] id_temp;
+
+ if (tstat_flag) {
+ delete [] eta;
+ delete [] eta_dot;
+ delete [] eta_dotdot;
+ delete [] eta_mass;
+ }
+
+ if (pstat_flag) {
+ if (pcomputeflag) modify->delete_compute(id_press);
+ delete [] id_press;
+ if (mpchain) {
+ delete [] etap;
+ delete [] etap_dot;
+ delete [] etap_dotdot;
+ delete [] etap_mass;
+ }
+ }
+ if (p_match_coeffs) free(p_match_coeffs);
+}
+
+/* ---------------------------------------------------------------------- */
+
+int FixBocs::setmask()
+{
+ int mask = 0;
+ mask |= INITIAL_INTEGRATE;
+ mask |= FINAL_INTEGRATE;
+ mask |= THERMO_ENERGY;
+ mask |= INITIAL_INTEGRATE_RESPA;
+ mask |= FINAL_INTEGRATE_RESPA;
+ if (pre_exchange_flag) mask |= PRE_EXCHANGE;
+ return mask;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixBocs::init()
+{
+ // recheck that dilate group has not been deleted
+ if (allremap == 0) {
+ int idilate = group->find(id_dilate);
+ if (idilate == -1)
+ error->all(FLERR,"Fix bocs dilate group ID does not exist");
+ dilate_group_bit = group->bitmask[idilate];
+ }
+
+ // ensure no conflict with fix deform
+
+ if (pstat_flag)
+ {
+ for (int i = 0; i < modify->nfix; i++)
+ if (strcmp(modify->fix[i]->style,"deform") == 0) {
+ int *dimflag = ((FixDeform *) modify->fix[i])->dimflag;
+ if ((p_flag[0] && dimflag[0]) || (p_flag[1] && dimflag[1]) ||
+ (p_flag[2] && dimflag[2]) || (p_flag[3] && dimflag[3]) ||
+ (p_flag[4] && dimflag[4]) || (p_flag[5] && dimflag[5]))
+ error->all(FLERR,"Cannot use fix bocs and fix deform on "
+ "same component of stress tensor");
+ }
+ }
+
+ // set temperature and pressure ptrs
+ int icompute = modify->find_compute(id_temp);
+ if (icompute < 0)
+ error->all(FLERR,"Temperature ID for fix bocs does not exist");
+ temperature = modify->compute[icompute];
+
+ if (temperature->tempbias) which = BIAS;
+ else which = NOBIAS;
+
+ if (pstat_flag) {
+ icompute = modify->find_compute(id_press);
+ if (icompute < 0)
+ error->all(FLERR,"Pressure ID for fix bocs does not exist");
+ pressure = modify->compute[icompute];
+ }
+
+
+ if (pstat_flag)
+ {
+ if (p_match_flag) // MRD NJD
+ {
+ if (pressure)
+ {
+ if (p_basis_type == 0)
+ {
+ ((ComputePressureBocs *)pressure)->send_cg_info(p_basis_type,
+ N_p_match, p_match_coeffs, N_mol, vavg);
+ }
+ else if ( p_basis_type == 1 || p_basis_type == 2 )
+ {
+ ((ComputePressureBocs *)pressure)->send_cg_info(p_basis_type,
+ splines, spline_length);
+ }
+ }
+ else
+ {
+ error->all(FLERR,"Unable to find pressure. Are you sure you included"
+ " the compute bocsPress and fix_modify commands?");
+ }
+ }
+ }
+
+
+ // set timesteps and frequencies
+
+ dtv = update->dt;
+ dtf = 0.5 * update->dt * force->ftm2v;
+ dthalf = 0.5 * update->dt;
+ dt4 = 0.25 * update->dt;
+ dt8 = 0.125 * update->dt;
+ dto = dthalf;
+
+ p_freq_max = 0.0;
+ if (pstat_flag) {
+ p_freq_max = MAX(p_freq[0],p_freq[1]);
+ p_freq_max = MAX(p_freq_max,p_freq[2]);
+ if (pstyle == TRICLINIC) {
+ p_freq_max = MAX(p_freq_max,p_freq[3]);
+ p_freq_max = MAX(p_freq_max,p_freq[4]);
+ p_freq_max = MAX(p_freq_max,p_freq[5]);
+ }
+ pdrag_factor = 1.0 - (update->dt * p_freq_max * drag / nc_pchain);
+ }
+
+ if (tstat_flag)
+ tdrag_factor = 1.0 - (update->dt * t_freq * drag / nc_tchain);
+
+ // tally the number of dimensions that are barostatted
+ // set initial volume and reference cell, if not already done
+
+ if (pstat_flag) {
+ pdim = p_flag[0] + p_flag[1] + p_flag[2];
+ if (vol0 == 0.0) {
+ if (dimension == 3) vol0 = domain->xprd * domain->yprd * domain->zprd;
+ else vol0 = domain->xprd * domain->yprd;
+ h0_inv[0] = domain->h_inv[0];
+ h0_inv[1] = domain->h_inv[1];
+ h0_inv[2] = domain->h_inv[2];
+ h0_inv[3] = domain->h_inv[3];
+ h0_inv[4] = domain->h_inv[4];
+ h0_inv[5] = domain->h_inv[5];
+ }
+ }
+
+ boltz = force->boltz;
+ nktv2p = force->nktv2p;
+
+ if (force->kspace) kspace_flag = 1;
+ else kspace_flag = 0;
+
+ if (strstr(update->integrate_style,"respa")) {
+ nlevels_respa = ((Respa *) update->integrate)->nlevels;
+ step_respa = ((Respa *) update->integrate)->step;
+ dto = 0.5*step_respa[0];
+ }
+
+ // detect if any rigid fixes exist so rigid bodies move when box is remapped
+ // rfix[] = indices to each fix rigid
+
+ delete [] rfix;
+ nrigid = 0;
+ rfix = NULL;
+
+ for (int i = 0; i < modify->nfix; i++)
+ if (modify->fix[i]->rigid_flag) nrigid++;
+ if (nrigid) {
+ rfix = new int[nrigid];
+ nrigid = 0;
+ for (int i = 0; i < modify->nfix; i++)
+ if (modify->fix[i]->rigid_flag) rfix[nrigid++] = i;
+ }
+}
+
+// NJD MRD 2 functions
+int FixBocs::read_F_table( char *filename, int p_basis_type )
+{
+ char separator = ',';
+ FILE *fpi;
+ int N_columns = 2, n_entries = 0, i;
+ float f1, f2;
+ double n1, n2;
+ int test_sscanf;
+ double **data = (double **) calloc(N_columns,sizeof(double *));
+ char * line = (char *) calloc(200,sizeof(char));
+
+ fpi = fopen(filename,"r");
+ if (fpi)
+ {
+ while (fgets(line,199,fpi)) { ++n_entries; }
+ fclose(fpi);
+ for (i = 0; i < N_columns; ++i)
+ {
+ data[i] = (double *) calloc(n_entries,sizeof(double));
+ }
+ }
+ else
+ {
+ char * errmsg = (char *) calloc(50,sizeof(char));
+ sprintf(errmsg,"Unable to open file: %s\n",filename);
+ error->all(FLERR,errmsg);
+ }
+
+ n_entries = 0;
+ fpi = fopen(filename,"r");
+ if (fpi)
+ {
+ while( fgets(line,199,fpi))
+ {
+ ++n_entries;
+ test_sscanf = sscanf(line," %f , %f ",&f1, &f2);
+ if (test_sscanf == 2)
+ {
+ data[0][n_entries-1] = (double) f1;
+ data[1][n_entries-1] = (double) f2;
+ }
+ else
+ {
+ fprintf(stderr,"WARNING: did not find 2 comma separated values in "
+ "line %d of file %s\n\tline: %s",n_entries,filename,line);
+ }
+ }
+ }
+ else
+ {
+ char * errmsg = (char *) calloc(50,sizeof(char));
+ sprintf(errmsg,"Unable to open file: %s\n",filename);
+ error->all(FLERR,errmsg);
+ }
+ fclose(fpi);
+
+ if (p_basis_type == 1)
+ {
+ splines = (double **) calloc(2,sizeof(double *));
+ splines[0] = (double *) calloc(n_entries,sizeof(double));
+ splines[1] = (double *) calloc(n_entries,sizeof(double));
+ int idxa, idxb;
+ for (idxa = 0; idxa < 2; ++idxa)
+ {
+ for (idxb = 0; idxb < n_entries; ++idxb)
+ {
+ splines[idxa][idxb] = data[idxa][idxb];
+ }
+ }
+ }
+ else if (p_basis_type == 2)
+ {
+ spline_length = n_entries;
+ build_cubic_splines(data);
+ n_entries -= 1;
+ }
+ else
+ {
+ char * errmsg = (char *) calloc(70,sizeof(char));
+ sprintf(errmsg,"ERROR: invalid p_basis_type value "
+ "of %d in read_F_table",p_basis_type);
+ error->all(FLERR,errmsg);
+ }
+ return n_entries;
+}
+
+void FixBocs::build_cubic_splines( double **data )
+{
+ double *a, *b, *d, *h, *alpha, *c, *l, *mu, *z;
+ int n = spline_length;
+ double alpha_i;
+ a = (double *) calloc(n,sizeof(double));
+ b = (double *) calloc(n+1,sizeof(double));
+ d = (double *) calloc(n+1,sizeof(double));
+ h = (double *) calloc(n,sizeof(double));
+ alpha = (double *) calloc(n,sizeof(double));
+ c = (double *) calloc(n+1,sizeof(double));
+ l = (double *) calloc(n,sizeof(double));
+ mu = (double *) calloc(n,sizeof(double));
+ z = (double *) calloc(n,sizeof(double));
+ int idx;
+ for (int i=0; i<n; i++)
+ {
+ a[i] = data[1][i];
+ b[i] = 0.0;
+ d[i] = 0.0;
+
+ if (i<(n-1))
+ {
+ h[i] = (data[0][i+1] - data[0][i]);
+ }
+
+ if (i>1 && i<(n-1))
+ {
+ alpha_i = (3.0 / h[i]) * ( data[1][i+1] - data[1][i]) - (3.0 / h[i-1] )
+ * ( data[1][i] - data[1][i-1] );
+ alpha[i-1] = alpha_i;
+ }
+ }
+ l[0] = 1.0;
+ mu[0] = 0.0;
+ z[0] = 0.0;
+
+ for (int i=1; i<n-1; i++)
+ {
+ l[i] = 2*(data[0][i+1] - data[0][i-1]) - h[i-1] * mu[i-1];
+ mu[i] = h[i]/l[i];
+ z[i] = (alpha[i] - h[i-1] * z[i-1]) / l[i];
+ }
+ l[n-1] = 1.0;
+ mu[n-1] = 0.0;
+ z[n-1] = 0.0;
+
+ c[n] = 0.0;
+ b[n] = 0.0;
+ d[n] = 0.0;
+
+ for(int j=n-1; j>=0; j--)
+ {
+ c[j] = z[j] - mu[j]*c[j+1];
+
+ b[j] = (a[j+1]-a[j])/h[j] - h[j]*(c[j+1] + 2.0 * c[j])/3.0;
+
+ d[j] = (c[j+1]-c[j])/(3.0 * h[j]);
+ }
+ splines = (double **) calloc(5,sizeof(double *));
+
+ for ( idx = 0; idx < 5; ++idx)
+ {
+ splines[idx] = (double *) calloc(n-1,sizeof(double));
+ }
+ idx = 0;
+ for ( idx = 0; idx < n - 1; ++idx)
+ {
+ splines[1][idx] = a[idx];
+ splines[2][idx] = b[idx];
+ splines[3][idx] = c[idx];
+ splines[4][idx] = d[idx];
+ splines[0][idx] = data[0][idx];
+ }
+}
+// END NJD MRD 2 functions
+
+/* ----------------------------------------------------------------------
+ compute T,P before integrator starts
+------------------------------------------------------------------------- */
+
+void FixBocs::setup(int vflag)
+{
+ // tdof needed by compute_temp_target()
+
+ t_current = temperature->compute_scalar();
+ tdof = temperature->dof;
+
+ // t_target is needed by NVT and NPT in compute_scalar()
+ // If no thermostat or using fix nphug,
+ // t_target must be defined by other means.
+
+ if (tstat_flag && strstr(style,"nphug") == NULL) {
+ compute_temp_target();
+ } else if (pstat_flag) {
+
+ // t0 = reference temperature for masses
+ // cannot be done in init() b/c temperature cannot be called there
+ // is b/c Modify::init() inits computes after fixes due to dof dependence
+ // guesstimate a unit-dependent t0 if actual T = 0.0
+ // if it was read in from a restart file, leave it be
+
+ if (t0 == 0.0) {
+ t0 = temperature->compute_scalar();
+ if (t0 == 0.0) {
+ if (strcmp(update->unit_style,"lj") == 0) t0 = 1.0;
+ else t0 = 300.0;
+ }
+ }
+ t_target = t0;
+ }
+
+ if (pstat_flag) compute_press_target();
+
+ if (pstat_flag) {
+ if (pstyle == ISO) pressure->compute_scalar();
+ else pressure->compute_vector();
+ couple();
+ pressure->addstep(update->ntimestep+1);
+ }
+
+ // masses and initial forces on thermostat variables
+
+ if (tstat_flag) {
+ eta_mass[0] = tdof * boltz * t_target / (t_freq*t_freq);
+ for (int ich = 1; ich < mtchain; ich++)
+ eta_mass[ich] = boltz * t_target / (t_freq*t_freq);
+ for (int ich = 1; ich < mtchain; ich++) {
+ eta_dotdot[ich] = (eta_mass[ich-1]*eta_dot[ich-1]*eta_dot[ich-1] -
+ boltz * t_target) / eta_mass[ich];
+ }
+ }
+
+ // masses and initial forces on barostat variables
+
+ if (pstat_flag) {
+ double kt = boltz * t_target;
+ double nkt = atom->natoms * kt;
+
+ for (int i = 0; i < 3; i++)
+ if (p_flag[i])
+ omega_mass[i] = nkt/(p_freq[i]*p_freq[i]);
+
+ if (pstyle == TRICLINIC) {
+ for (int i = 3; i < 6; i++)
+ if (p_flag[i]) omega_mass[i] = nkt/(p_freq[i]*p_freq[i]);
+ }
+
+ // masses and initial forces on barostat thermostat variables
+
+ if (mpchain) {
+ etap_mass[0] = boltz * t_target / (p_freq_max*p_freq_max);
+ for (int ich = 1; ich < mpchain; ich++)
+ etap_mass[ich] = boltz * t_target / (p_freq_max*p_freq_max);
+ for (int ich = 1; ich < mpchain; ich++)
+ etap_dotdot[ich] =
+ (etap_mass[ich-1]*etap_dot[ich-1]*etap_dot[ich-1] -
+ boltz * t_target) / etap_mass[ich];
+ }
+ }
+}
+
+/* ----------------------------------------------------------------------
+ 1st half of Verlet update
+------------------------------------------------------------------------- */
+
+void FixBocs::initial_integrate(int vflag)
+{
+ // update eta_press_dot
+
+ if (pstat_flag && mpchain) nhc_press_integrate();
+
+ // update eta_dot
+
+ if (tstat_flag) {
+ compute_temp_target();
+ nhc_temp_integrate();
+ }
+
+ // need to recompute pressure to account for change in KE
+ // t_current is up-to-date, but compute_temperature is not
+ // compute appropriately coupled elements of mvv_current
+
+ if (pstat_flag) {
+ if (pstyle == ISO) {
+ temperature->compute_scalar();
+ pressure->compute_scalar();
+ } else {
+ temperature->compute_vector();
+ pressure->compute_vector();
+ }
+ couple();
+ pressure->addstep(update->ntimestep+1);
+ }
+
+ if (pstat_flag) {
+ compute_press_target();
+ nh_omega_dot();
+ nh_v_press();
+ }
+
+ nve_v();
+
+ // remap simulation box by 1/2 step
+
+ if (pstat_flag) remap();
+
+ nve_x();
+
+ // remap simulation box by 1/2 step
+ // redo KSpace coeffs since volume has changed
+
+ if (pstat_flag) {
+ remap();
+ if (kspace_flag) force->kspace->setup();
+ }
+}
+
+/* ----------------------------------------------------------------------
+ 2nd half of Verlet update
+------------------------------------------------------------------------- */
+
+void FixBocs::final_integrate()
+{
+ nve_v();
+
+ // re-compute temp before nh_v_press()
+ // only needed for temperature computes with BIAS on reneighboring steps:
+ // b/c some biases store per-atom values (e.g. temp/profile)
+ // per-atom values are invalid if reneigh/comm occurred
+ // since temp->compute() in initial_integrate()
+
+ if (which == BIAS && neighbor->ago == 0)
+ t_current = temperature->compute_scalar();
+
+ if (pstat_flag) nh_v_press();
+
+ // compute new T,P after velocities rescaled by nh_v_press()
+ // compute appropriately coupled elements of mvv_current
+
+ t_current = temperature->compute_scalar();
+ tdof = temperature->dof;
+
+ if (pstat_flag) {
+ if (pstyle == ISO) pressure->compute_scalar();
+ else pressure->compute_vector();
+ couple();
+ pressure->addstep(update->ntimestep+1);
+ }
+
+ if (pstat_flag) nh_omega_dot();
+
+ // update eta_dot
+ // update eta_press_dot
+
+ if (tstat_flag) nhc_temp_integrate();
+ if (pstat_flag && mpchain) nhc_press_integrate();
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixBocs::initial_integrate_respa(int vflag, int ilevel, int iloop)
+{
+ // set timesteps by level
+
+ dtv = step_respa[ilevel];
+ dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
+ dthalf = 0.5 * step_respa[ilevel];
+
+ // outermost level - update eta_dot and omega_dot, apply to v
+ // all other levels - NVE update of v
+ // x,v updates only performed for atoms in group
+
+ if (ilevel == nlevels_respa-1) {
+
+ // update eta_press_dot
+
+ if (pstat_flag && mpchain) nhc_press_integrate();
+
+ // update eta_dot
+
+ if (tstat_flag) {
+ compute_temp_target();
+ nhc_temp_integrate();
+ }
+
+ // recompute pressure to account for change in KE
+ // t_current is up-to-date, but compute_temperature is not
+ // compute appropriately coupled elements of mvv_current
+
+ if (pstat_flag) {
+ if (pstyle == ISO) {
+ temperature->compute_scalar();
+ pressure->compute_scalar();
+ } else {
+ temperature->compute_vector();
+ pressure->compute_vector();
+ }
+ couple();
+ pressure->addstep(update->ntimestep+1);
+ }
+
+ if (pstat_flag) {
+ compute_press_target();
+ nh_omega_dot();
+ nh_v_press();
+ }
+
+ nve_v();
+
+ } else nve_v();
+
+ // innermost level - also update x only for atoms in group
+ // if barostat, perform 1/2 step remap before and after
+
+ if (ilevel == 0) {
+ if (pstat_flag) remap();
+ nve_x();
+ if (pstat_flag) remap();
+ }
+
+ // if barostat, redo KSpace coeffs at outermost level,
+ // since volume has changed
+
+ if (ilevel == nlevels_respa-1 && kspace_flag && pstat_flag)
+ force->kspace->setup();
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixBocs::final_integrate_respa(int ilevel, int iloop)
+{
+ // set timesteps by level
+
+ dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
+ dthalf = 0.5 * step_respa[ilevel];
+
+ // outermost level - update eta_dot and omega_dot, apply via final_integrate
+ // all other levels - NVE update of v
+
+ if (ilevel == nlevels_respa-1) final_integrate();
+ else nve_v();
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixBocs::couple()
+{
+ double *tensor = pressure->vector;
+
+ if (pstyle == ISO)
+ p_current[0] = p_current[1] = p_current[2] = pressure->scalar;
+ else if (pcouple == XYZ) {
+ double ave = 1.0/3.0 * (tensor[0] + tensor[1] + tensor[2]);
+ p_current[0] = p_current[1] = p_current[2] = ave;
+ } else if (pcouple == XY) {
+ double ave = 0.5 * (tensor[0] + tensor[1]);
+ p_current[0] = p_current[1] = ave;
+ p_current[2] = tensor[2];
+ } else if (pcouple == YZ) {
+ double ave = 0.5 * (tensor[1] + tensor[2]);
+ p_current[1] = p_current[2] = ave;
+ p_current[0] = tensor[0];
+ } else if (pcouple == XZ) {
+ double ave = 0.5 * (tensor[0] + tensor[2]);
+ p_current[0] = p_current[2] = ave;
+ p_current[1] = tensor[1];
+ } else {
+ p_current[0] = tensor[0];
+ p_current[1] = tensor[1];
+ p_current[2] = tensor[2];
+ }
+
+ if (!std::isfinite(p_current[0]) || !std::isfinite(p_current[1]) || !std::isfinite(p_current[2]))
+ error->all(FLERR,"Non-numeric pressure - simulation unstable");
+
+ // switch order from xy-xz-yz to Voigt
+
+ if (pstyle == TRICLINIC) {
+ p_current[3] = tensor[5];
+ p_current[4] = tensor[4];
+ p_current[5] = tensor[3];
+
+ if (!std::isfinite(p_current[3]) || !std::isfinite(p_current[4]) || !std::isfinite(p_current[5]))
+ error->all(FLERR,"Non-numeric pressure - simulation unstable");
+ }
+}
+
+/* ----------------------------------------------------------------------
+ change box size
+ remap all atoms or dilate group atoms depending on allremap flag
+ if rigid bodies exist, scale rigid body centers-of-mass
+------------------------------------------------------------------------- */
+
+void FixBocs::remap()
+{
+ int i;
+ double oldlo,oldhi;
+ double expfac;
+
+ double **x = atom->x;
+ int *mask = atom->mask;
+ int nlocal = atom->nlocal;
+ double *h = domain->h;
+
+ // omega is not used, except for book-keeping
+
+ for (int i = 0; i < 6; i++) omega[i] += dto*omega_dot[i];
+
+ // convert pertinent atoms and rigid bodies to lamda coords
+
+ if (allremap) domain->x2lamda(nlocal);
+ else {
+ for (i = 0; i < nlocal; i++)
+ if (mask[i] & dilate_group_bit)
+ domain->x2lamda(x[i],x[i]);
+ }
+
+ if (nrigid)
+ for (i = 0; i < nrigid; i++)
+ modify->fix[rfix[i]]->deform(0);
+
+ // reset global and local box to new size/shape
+
+ // this operation corresponds to applying the
+ // translate and scale operations
+ // corresponding to the solution of the following ODE:
+ //
+ // h_dot = omega_dot * h
+ //
+ // where h_dot, omega_dot and h are all upper-triangular
+ // 3x3 tensors. In Voigt notation, the elements of the
+ // RHS product tensor are:
+ // h_dot = [0*0, 1*1, 2*2, 1*3+3*2, 0*4+5*3+4*2, 0*5+5*1]
+ //
+ // Ordering of operations preserves time symmetry.
+
+ double dto2 = dto/2.0;
+ double dto4 = dto/4.0;
+ double dto8 = dto/8.0;
+
+ // off-diagonal components, first half
+
+ if (pstyle == TRICLINIC) {
+
+ if (p_flag[4]) {
+ expfac = exp(dto8*omega_dot[0]);
+ h[4] *= expfac;
+ h[4] += dto4*(omega_dot[5]*h[3]+omega_dot[4]*h[2]);
+ h[4] *= expfac;
+ }
+
+ if (p_flag[3]) {
+ expfac = exp(dto4*omega_dot[1]);
+ h[3] *= expfac;
+ h[3] += dto2*(omega_dot[3]*h[2]);
+ h[3] *= expfac;
+ }
+
+ if (p_flag[5]) {
+ expfac = exp(dto4*omega_dot[0]);
+ h[5] *= expfac;
+ h[5] += dto2*(omega_dot[5]*h[1]);
+ h[5] *= expfac;
+ }
+
+ if (p_flag[4]) {
+ expfac = exp(dto8*omega_dot[0]);
+ h[4] *= expfac;
+ h[4] += dto4*(omega_dot[5]*h[3]+omega_dot[4]*h[2]);
+ h[4] *= expfac;
+ }
+ }
+
+ // scale diagonal components
+ // scale tilt factors with cell, if set
+
+ if (p_flag[0]) {
+ oldlo = domain->boxlo[0];
+ oldhi = domain->boxhi[0];
+ expfac = exp(dto*omega_dot[0]);
+ domain->boxlo[0] = (oldlo-fixedpoint[0])*expfac + fixedpoint[0];
+ domain->boxhi[0] = (oldhi-fixedpoint[0])*expfac + fixedpoint[0];
+ }
+
+ if (p_flag[1]) {
+ oldlo = domain->boxlo[1];
+ oldhi = domain->boxhi[1];
+ expfac = exp(dto*omega_dot[1]);
+ domain->boxlo[1] = (oldlo-fixedpoint[1])*expfac + fixedpoint[1];
+ domain->boxhi[1] = (oldhi-fixedpoint[1])*expfac + fixedpoint[1];
+ if (scalexy) h[5] *= expfac;
+ }
+
+ if (p_flag[2]) {
+ oldlo = domain->boxlo[2];
+ oldhi = domain->boxhi[2];
+ expfac = exp(dto*omega_dot[2]);
+ domain->boxlo[2] = (oldlo-fixedpoint[2])*expfac + fixedpoint[2];
+ domain->boxhi[2] = (oldhi-fixedpoint[2])*expfac + fixedpoint[2];
+ if (scalexz) h[4] *= expfac;
+ if (scaleyz) h[3] *= expfac;
+ }
+
+ // off-diagonal components, second half
+
+ if (pstyle == TRICLINIC) {
+
+ if (p_flag[4]) {
+ expfac = exp(dto8*omega_dot[0]);
+ h[4] *= expfac;
+ h[4] += dto4*(omega_dot[5]*h[3]+omega_dot[4]*h[2]);
+ h[4] *= expfac;
+ }
+
+ if (p_flag[3]) {
+ expfac = exp(dto4*omega_dot[1]);
+ h[3] *= expfac;
+ h[3] += dto2*(omega_dot[3]*h[2]);
+ h[3] *= expfac;
+ }
+
+ if (p_flag[5]) {
+ expfac = exp(dto4*omega_dot[0]);
+ h[5] *= expfac;
+ h[5] += dto2*(omega_dot[5]*h[1]);
+ h[5] *= expfac;
+ }
+
+ if (p_flag[4]) {
+ expfac = exp(dto8*omega_dot[0]);
+ h[4] *= expfac;
+ h[4] += dto4*(omega_dot[5]*h[3]+omega_dot[4]*h[2]);
+ h[4] *= expfac;
+ }
+
+ }
+
+ domain->yz = h[3];
+ domain->xz = h[4];
+ domain->xy = h[5];
+
+ // tilt factor to cell length ratio can not exceed TILTMAX in one step
+
+ if (domain->yz < -TILTMAX*domain->yprd ||
+ domain->yz > TILTMAX*domain->yprd ||
+ domain->xz < -TILTMAX*domain->xprd ||
+ domain->xz > TILTMAX*domain->xprd ||
+ domain->xy < -TILTMAX*domain->xprd ||
+ domain->xy > TILTMAX*domain->xprd)
+ error->all(FLERR,"Fix bocs has tilted box too far in one step - "
+ "periodic cell is too far from equilibrium state");
+
+ domain->set_global_box();
+ domain->set_local_box();
+
+ // convert pertinent atoms and rigid bodies back to box coords
+
+ if (allremap) domain->lamda2x(nlocal);
+ else {
+ for (i = 0; i < nlocal; i++)
+ if (mask[i] & dilate_group_bit)
+ domain->lamda2x(x[i],x[i]);
+ }
+
+ if (nrigid)
+ for (i = 0; i < nrigid; i++)
+ modify->fix[rfix[i]]->deform(1);
+}
+
+/* ----------------------------------------------------------------------
+ pack entire state of Fix into one write
+------------------------------------------------------------------------- */
+
+void FixBocs::write_restart(FILE *fp)
+{
+ int nsize = size_restart_global();
+
+ double *list;
+ memory->create(list,nsize,"nh:list");
+
+ pack_restart_data(list);
+
+ if (comm->me == 0) {
+ int size = nsize * sizeof(double);
+ fwrite(&size,sizeof(int),1,fp);
+ fwrite(list,sizeof(double),nsize,fp);
+ }
+
+ memory->destroy(list);
+}
+
+/* ----------------------------------------------------------------------
+ calculate the number of data to be packed
+------------------------------------------------------------------------- */
+
+int FixBocs::size_restart_global()
+{
+ int nsize = 2;
+ if (tstat_flag) nsize += 1 + 2*mtchain;
+ if (pstat_flag) {
+ nsize += 16 + 2*mpchain;
+ if (deviatoric_flag) nsize += 6;
+ }
+
+ return nsize;
+}
+
+/* ----------------------------------------------------------------------
+ pack restart data
+------------------------------------------------------------------------- */
+
+int FixBocs::pack_restart_data(double *list)
+{
+ int n = 0;
+
+ list[n++] = tstat_flag;
+ if (tstat_flag) {
+ list[n++] = mtchain;
+ for (int ich = 0; ich < mtchain; ich++)
+ list[n++] = eta[ich];
+ for (int ich = 0; ich < mtchain; ich++)
+ list[n++] = eta_dot[ich];
+ }
+
+ list[n++] = pstat_flag;
+ if (pstat_flag) {
+ list[n++] = omega[0];
+ list[n++] = omega[1];
+ list[n++] = omega[2];
+ list[n++] = omega[3];
+ list[n++] = omega[4];
+ list[n++] = omega[5];
+ list[n++] = omega_dot[0];
+ list[n++] = omega_dot[1];
+ list[n++] = omega_dot[2];
+ list[n++] = omega_dot[3];
+ list[n++] = omega_dot[4];
+ list[n++] = omega_dot[5];
+ list[n++] = vol0;
+ list[n++] = t0;
+ list[n++] = mpchain;
+ if (mpchain) {
+ for (int ich = 0; ich < mpchain; ich++)
+ list[n++] = etap[ich];
+ for (int ich = 0; ich < mpchain; ich++)
+ list[n++] = etap_dot[ich];
+ }
+
+ list[n++] = deviatoric_flag;
+ if (deviatoric_flag) {
+ list[n++] = h0_inv[0];
+ list[n++] = h0_inv[1];
+ list[n++] = h0_inv[2];
+ list[n++] = h0_inv[3];
+ list[n++] = h0_inv[4];
+ list[n++] = h0_inv[5];
+ }
+ }
+
+ return n;
+}
+
+/* ----------------------------------------------------------------------
+ use state info from restart file to restart the Fix
+------------------------------------------------------------------------- */
+
+void FixBocs::restart(char *buf)
+{
+ int n = 0;
+ double *list = (double *) buf;
+ int flag = static_cast<int> (list[n++]);
+ if (flag) {
+ int m = static_cast<int> (list[n++]);
+ if (tstat_flag && m == mtchain) {
+ for (int ich = 0; ich < mtchain; ich++)
+ eta[ich] = list[n++];
+ for (int ich = 0; ich < mtchain; ich++)
+ eta_dot[ich] = list[n++];
+ } else n += 2*m;
+ }
+ flag = static_cast<int> (list[n++]);
+ if (flag) {
+ omega[0] = list[n++];
+ omega[1] = list[n++];
+ omega[2] = list[n++];
+ omega[3] = list[n++];
+ omega[4] = list[n++];
+ omega[5] = list[n++];
+ omega_dot[0] = list[n++];
+ omega_dot[1] = list[n++];
+ omega_dot[2] = list[n++];
+ omega_dot[3] = list[n++];
+ omega_dot[4] = list[n++];
+ omega_dot[5] = list[n++];
+ vol0 = list[n++];
+ t0 = list[n++];
+ int m = static_cast<int> (list[n++]);
+ if (pstat_flag && m == mpchain) {
+ for (int ich = 0; ich < mpchain; ich++)
+ etap[ich] = list[n++];
+ for (int ich = 0; ich < mpchain; ich++)
+ etap_dot[ich] = list[n++];
+ } else n+=2*m;
+ flag = static_cast<int> (list[n++]);
+ if (flag) {
+ h0_inv[0] = list[n++];
+ h0_inv[1] = list[n++];
+ h0_inv[2] = list[n++];
+ h0_inv[3] = list[n++];
+ h0_inv[4] = list[n++];
+ h0_inv[5] = list[n++];
+ }
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+int FixBocs::modify_param(int narg, char **arg)
+{
+ if (strcmp(arg[0],"temp") == 0) {
+ if (narg < 2) error->all(FLERR,"Illegal fix_modify command");
+ if (tcomputeflag) {
+ modify->delete_compute(id_temp);
+ tcomputeflag = 0;
+ }
+ delete [] id_temp;
+ int n = strlen(arg[1]) + 1;
+ id_temp = new char[n];
+ strcpy(id_temp,arg[1]);
+
+ int icompute = modify->find_compute(arg[1]);
+ if (icompute < 0)
+ error->all(FLERR,"Could not find fix_modify temperature ID");
+ temperature = modify->compute[icompute];
+
+ if (temperature->tempflag == 0)
+ error->all(FLERR,
+ "Fix_modify temperature ID does not compute temperature");
+ if (temperature->igroup != 0 && comm->me == 0)
+ error->warning(FLERR,"Temperature for fix modify is not for group all");
+
+ // reset id_temp of pressure to new temperature ID
+
+ if (pstat_flag) {
+ icompute = modify->find_compute(id_press);
+ if (icompute < 0)
+ error->all(FLERR,"Pressure ID for fix modify does not exist");
+ modify->compute[icompute]->reset_extra_compute_fix(id_temp);
+ }
+
+ return 2;
+
+ } else if (strcmp(arg[0],"press") == 0) {
+ if (narg < 2) error->all(FLERR,"Illegal fix_modify command");
+ if (!pstat_flag) error->all(FLERR,"Illegal fix_modify command");
+ if (pcomputeflag) {
+ modify->delete_compute(id_press);
+ pcomputeflag = 0;
+ }
+ delete [] id_press;
+ int n = strlen(arg[1]) + 1;
+ id_press = new char[n];
+ strcpy(id_press,arg[1]);
+
+ int icompute = modify->find_compute(arg[1]);
+ if (icompute < 0) error->all(FLERR,"Could not find fix_modify pressure ID");
+ pressure = modify->compute[icompute];
+
+ if (p_match_flag) // NJD MRD
+ {
+ if ( p_basis_type == 0 )
+ {
+ ((ComputePressureBocs *)pressure)->send_cg_info(p_basis_type, N_p_match,
+ p_match_coeffs, N_mol, vavg);
+ }
+ else if ( p_basis_type == 1 || p_basis_type == 2 )
+ {
+ ((ComputePressureBocs *)pressure)->send_cg_info(p_basis_type, splines,
+ spline_length );
+ }
+ }
+
+ if (pressure->pressflag == 0)
+ error->all(FLERR,"Fix_modify pressure ID does not compute pressure");
+ return 2;
+ }
+
+ return 0;
+}
+
+/* ---------------------------------------------------------------------- */
+
+double FixBocs::compute_scalar()
+{
+ int i;
+ double volume;
+ double energy;
+ double kt = boltz * t_target;
+ double lkt_press = kt;
+ int ich;
+ if (dimension == 3) volume = domain->xprd * domain->yprd * domain->zprd;
+ else volume = domain->xprd * domain->yprd;
+
+ energy = 0.0;
+
+ // thermostat chain energy is equivalent to Eq. (2) in
+ // Martyna, Tuckerman, Tobias, Klein, Mol Phys, 87, 1117
+ // Sum(0.5*p_eta_k^2/Q_k,k=1,M) + L*k*T*eta_1 + Sum(k*T*eta_k,k=2,M),
+ // where L = tdof
+ // M = mtchain
+ // p_eta_k = Q_k*eta_dot[k-1]
+ // Q_1 = L*k*T/t_freq^2
+ // Q_k = k*T/t_freq^2, k > 1
+
+ if (tstat_flag) {
+ energy += ke_target * eta[0] + 0.5*eta_mass[0]*eta_dot[0]*eta_dot[0];
+ for (ich = 1; ich < mtchain; ich++)
+ energy += kt * eta[ich] + 0.5*eta_mass[ich]*eta_dot[ich]*eta_dot[ich];
+ }
+
+ // barostat energy is equivalent to Eq. (8) in
+ // Martyna, Tuckerman, Tobias, Klein, Mol Phys, 87, 1117
+ // Sum(0.5*p_omega^2/W + P*V),
+ // where N = natoms
+ // p_omega = W*omega_dot
+ // W = N*k*T/p_freq^2
+ // sum is over barostatted dimensions
+
+ if (pstat_flag) {
+ for (i = 0; i < 3; i++)
+ if (p_flag[i])
+ energy += 0.5*omega_dot[i]*omega_dot[i]*omega_mass[i] +
+ p_hydro*(volume-vol0) / (pdim*nktv2p);
+
+ if (pstyle == TRICLINIC) {
+ for (i = 3; i < 6; i++)
+ if (p_flag[i])
+ energy += 0.5*omega_dot[i]*omega_dot[i]*omega_mass[i];
+ }
+
+ // extra contributions from thermostat chain for barostat
+
+ if (mpchain) {
+ energy += lkt_press * etap[0] + 0.5*etap_mass[0]*etap_dot[0]*etap_dot[0];
+ for (ich = 1; ich < mpchain; ich++)
+ energy += kt * etap[ich] +
+ 0.5*etap_mass[ich]*etap_dot[ich]*etap_dot[ich];
+ }
+
+ // extra contribution from strain energy
+
+ if (deviatoric_flag) energy += compute_strain_energy();
+ }
+
+ return energy;
+}
+
+/* ----------------------------------------------------------------------
+ return a single element of the following vectors, in this order:
+ eta[tchain], eta_dot[tchain], omega[ndof], omega_dot[ndof]
+ etap[pchain], etap_dot[pchain], PE_eta[tchain], KE_eta_dot[tchain]
+ PE_omega[ndof], KE_omega_dot[ndof], PE_etap[pchain], KE_etap_dot[pchain]
+ PE_strain[1]
+ if no thermostat exists, related quantities are omitted from the list
+ if no barostat exists, related quantities are omitted from the list
+ ndof = 1,3,6 degrees of freedom for pstyle = ISO,ANISO,TRI
+------------------------------------------------------------------------- */
+
+double FixBocs::compute_vector(int n)
+{
+ int ilen;
+
+ if (tstat_flag) {
+ ilen = mtchain;
+ if (n < ilen) return eta[n];
+ n -= ilen;
+ ilen = mtchain;
+ if (n < ilen) return eta_dot[n];
+ n -= ilen;
+ }
+
+ if (pstat_flag) {
+ if (pstyle == ISO) {
+ ilen = 1;
+ if (n < ilen) return omega[n];
+ n -= ilen;
+ } else if (pstyle == ANISO) {
+ ilen = 3;
+ if (n < ilen) return omega[n];
+ n -= ilen;
+ } else {
+ ilen = 6;
+ if (n < ilen) return omega[n];
+ n -= ilen;
+ }
+
+ if (pstyle == ISO) {
+ ilen = 1;
+ if (n < ilen) return omega_dot[n];
+ n -= ilen;
+ } else if (pstyle == ANISO) {
+ ilen = 3;
+ if (n < ilen) return omega_dot[n];
+ n -= ilen;
+ } else {
+ ilen = 6;
+ if (n < ilen) return omega_dot[n];
+ n -= ilen;
+ }
+
+ if (mpchain) {
+ ilen = mpchain;
+ if (n < ilen) return etap[n];
+ n -= ilen;
+ ilen = mpchain;
+ if (n < ilen) return etap_dot[n];
+ n -= ilen;
+ }
+ }
+
+ double volume;
+ double kt = boltz * t_target;
+ double lkt_press = kt;
+ int ich;
+ if (dimension == 3) volume = domain->xprd * domain->yprd * domain->zprd;
+ else volume = domain->xprd * domain->yprd;
+
+ if (tstat_flag) {
+ ilen = mtchain;
+ if (n < ilen) {
+ ich = n;
+ if (ich == 0)
+ return ke_target * eta[0];
+ else
+ return kt * eta[ich];
+ }
+ n -= ilen;
+ ilen = mtchain;
+ if (n < ilen) {
+ ich = n;
+ if (ich == 0)
+ return 0.5*eta_mass[0]*eta_dot[0]*eta_dot[0];
+ else
+ return 0.5*eta_mass[ich]*eta_dot[ich]*eta_dot[ich];
+ }
+ n -= ilen;
+ }
+
+ if (pstat_flag) {
+ if (pstyle == ISO) {
+ ilen = 1;
+ if (n < ilen)
+ return p_hydro*(volume-vol0) / nktv2p;
+ n -= ilen;
+ } else if (pstyle == ANISO) {
+ ilen = 3;
+ if (n < ilen) {
+ if (p_flag[n])
+ return p_hydro*(volume-vol0) / (pdim*nktv2p);
+ else
+ return 0.0;
+ }
+ n -= ilen;
+ } else {
+ ilen = 6;
+ if (n < ilen) {
+ if (n > 2) return 0.0;
+ else if (p_flag[n])
+ return p_hydro*(volume-vol0) / (pdim*nktv2p);
+ else
+ return 0.0;
+ }
+ n -= ilen;
+ }
+
+ if (pstyle == ISO) {
+ ilen = 1;
+ if (n < ilen)
+ return pdim*0.5*omega_dot[n]*omega_dot[n]*omega_mass[n];
+ n -= ilen;
+ } else if (pstyle == ANISO) {
+ ilen = 3;
+ if (n < ilen) {
+ if (p_flag[n])
+ return 0.5*omega_dot[n]*omega_dot[n]*omega_mass[n];
+ else return 0.0;
+ }
+ n -= ilen;
+ } else {
+ ilen = 6;
+ if (n < ilen) {
+ if (p_flag[n])
+ return 0.5*omega_dot[n]*omega_dot[n]*omega_mass[n];
+ else return 0.0;
+ }
+ n -= ilen;
+ }
+
+ if (mpchain) {
+ ilen = mpchain;
+ if (n < ilen) {
+ ich = n;
+ if (ich == 0) return lkt_press * etap[0];
+ else return kt * etap[ich];
+ }
+ n -= ilen;
+ ilen = mpchain;
+ if (n < ilen) {
+ ich = n;
+ if (ich == 0)
+ return 0.5*etap_mass[0]*etap_dot[0]*etap_dot[0];
+ else
+ return 0.5*etap_mass[ich]*etap_dot[ich]*etap_dot[ich];
+ }
+ n -= ilen;
+ }
+
+ if (deviatoric_flag) {
+ ilen = 1;
+ if (n < ilen)
+ return compute_strain_energy();
+ n -= ilen;
+ }
+ }
+
+ return 0.0;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixBocs::reset_target(double t_new)
+{
+ t_target = t_start = t_stop = t_new;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixBocs::reset_dt()
+{
+ dtv = update->dt;
+ dtf = 0.5 * update->dt * force->ftm2v;
+ dthalf = 0.5 * update->dt;
+ dt4 = 0.25 * update->dt;
+ dt8 = 0.125 * update->dt;
+ dto = dthalf;
+
+ // If using respa, then remap is performed in innermost level
+
+ if (strstr(update->integrate_style,"respa"))
+ dto = 0.5*step_respa[0];
+
+ if (pstat_flag)
+ pdrag_factor = 1.0 - (update->dt * p_freq_max * drag / nc_pchain);
+
+ if (tstat_flag)
+ tdrag_factor = 1.0 - (update->dt * t_freq * drag / nc_tchain);
+}
+
+/* ----------------------------------------------------------------------
+ extract thermostat properties
+------------------------------------------------------------------------- */
+
+void *FixBocs::extract(const char *str, int &dim)
+{
+ dim=0;
+ if (tstat_flag && strcmp(str,"t_target") == 0) {
+ return &t_target;
+ } else if (tstat_flag && strcmp(str,"t_start") == 0) {
+ return &t_start;
+ } else if (tstat_flag && strcmp(str,"t_stop") == 0) {
+ return &t_stop;
+ } else if (tstat_flag && strcmp(str,"mtchain") == 0) {
+ return &mtchain;
+ } else if (pstat_flag && strcmp(str,"mpchain") == 0) {
+ return &mtchain;
+ }
+ dim=1;
+ if (tstat_flag && strcmp(str,"eta") == 0) {
+ return η
+ } else if (pstat_flag && strcmp(str,"etap") == 0) {
+ return η
+ } else if (pstat_flag && strcmp(str,"p_flag") == 0) {
+ return &p_flag;
+ } else if (pstat_flag && strcmp(str,"p_start") == 0) {
+ return &p_start;
+ } else if (pstat_flag && strcmp(str,"p_stop") == 0) {
+ return &p_stop;
+ } else if (pstat_flag && strcmp(str,"p_target") == 0) {
+ return &p_target;
+ }
+ return NULL;
+}
+
+/* ----------------------------------------------------------------------
+ perform half-step update of chain thermostat variables
+------------------------------------------------------------------------- */
+
+void FixBocs::nhc_temp_integrate()
+{
+ int ich;
+ double expfac;
+ double kecurrent = tdof * boltz * t_current;
+
+ // Update masses, to preserve initial freq, if flag set
+
+ if (eta_mass_flag) {
+ eta_mass[0] = tdof * boltz * t_target / (t_freq*t_freq);
+ for (int ich = 1; ich < mtchain; ich++)
+ eta_mass[ich] = boltz * t_target / (t_freq*t_freq);
+ }
+
+ if (eta_mass[0] > 0.0)
+ eta_dotdot[0] = (kecurrent - ke_target)/eta_mass[0];
+ else eta_dotdot[0] = 0.0;
+
+ double ncfac = 1.0/nc_tchain;
+ for (int iloop = 0; iloop < nc_tchain; iloop++) {
+
+ for (ich = mtchain-1; ich > 0; ich--) {
+ expfac = exp(-ncfac*dt8*eta_dot[ich+1]);
+ eta_dot[ich] *= expfac;
+ eta_dot[ich] += eta_dotdot[ich] * ncfac*dt4;
+ eta_dot[ich] *= tdrag_factor;
+ eta_dot[ich] *= expfac;
+ }
+
+ expfac = exp(-ncfac*dt8*eta_dot[1]);
+ eta_dot[0] *= expfac;
+ eta_dot[0] += eta_dotdot[0] * ncfac*dt4;
+ eta_dot[0] *= tdrag_factor;
+ eta_dot[0] *= expfac;
+
+ factor_eta = exp(-ncfac*dthalf*eta_dot[0]);
+ nh_v_temp();
+
+ // rescale temperature due to velocity scaling
+ // should not be necessary to explicitly recompute the temperature
+
+ t_current *= factor_eta*factor_eta;
+ kecurrent = tdof * boltz * t_current;
+
+ if (eta_mass[0] > 0.0)
+ eta_dotdot[0] = (kecurrent - ke_target)/eta_mass[0];
+ else eta_dotdot[0] = 0.0;
+
+ for (ich = 0; ich < mtchain; ich++)
+ eta[ich] += ncfac*dthalf*eta_dot[ich];
+
+ eta_dot[0] *= expfac;
+ eta_dot[0] += eta_dotdot[0] * ncfac*dt4;
+ eta_dot[0] *= expfac;
+
+ for (ich = 1; ich < mtchain; ich++) {
+ expfac = exp(-ncfac*dt8*eta_dot[ich+1]);
+ eta_dot[ich] *= expfac;
+ eta_dotdot[ich] = (eta_mass[ich-1]*eta_dot[ich-1]*eta_dot[ich-1]
+ - boltz * t_target)/eta_mass[ich];
+ eta_dot[ich] += eta_dotdot[ich] * ncfac*dt4;
+ eta_dot[ich] *= expfac;
+ }
+ }
+}
+
+/* ----------------------------------------------------------------------
+ perform half-step update of chain thermostat variables for barostat
+ scale barostat velocities
+------------------------------------------------------------------------- */
+
+void FixBocs::nhc_press_integrate()
+{
+ int ich,i;
+ double expfac,factor_etap,kecurrent;
+ double kt = boltz * t_target;
+ double lkt_press = kt;
+
+ // Update masses, to preserve initial freq, if flag set
+
+ if (omega_mass_flag) {
+ double nkt = atom->natoms * kt;
+ for (int i = 0; i < 3; i++)
+ if (p_flag[i])
+ omega_mass[i] = nkt/(p_freq[i]*p_freq[i]);
+
+ if (pstyle == TRICLINIC) {
+ for (int i = 3; i < 6; i++)
+ if (p_flag[i]) omega_mass[i] = nkt/(p_freq[i]*p_freq[i]);
+ }
+ }
+
+ if (etap_mass_flag) {
+ if (mpchain) {
+ etap_mass[0] = boltz * t_target / (p_freq_max*p_freq_max);
+ for (int ich = 1; ich < mpchain; ich++)
+ etap_mass[ich] = boltz * t_target / (p_freq_max*p_freq_max);
+ for (int ich = 1; ich < mpchain; ich++)
+ etap_dotdot[ich] =
+ (etap_mass[ich-1]*etap_dot[ich-1]*etap_dot[ich-1] -
+ boltz * t_target) / etap_mass[ich];
+ }
+ }
+
+ kecurrent = 0.0;
+ for (i = 0; i < 3; i++)
+ if (p_flag[i]) kecurrent += omega_mass[i]*omega_dot[i]*omega_dot[i];
+
+ if (pstyle == TRICLINIC) {
+ for (i = 3; i < 6; i++)
+ if (p_flag[i]) kecurrent += omega_mass[i]*omega_dot[i]*omega_dot[i];
+ }
+
+ etap_dotdot[0] = (kecurrent - lkt_press)/etap_mass[0];
+
+ double ncfac = 1.0/nc_pchain;
+ for (int iloop = 0; iloop < nc_pchain; iloop++) {
+
+ for (ich = mpchain-1; ich > 0; ich--) {
+ expfac = exp(-ncfac*dt8*etap_dot[ich+1]);
+ etap_dot[ich] *= expfac;
+ etap_dot[ich] += etap_dotdot[ich] * ncfac*dt4;
+ etap_dot[ich] *= pdrag_factor;
+ etap_dot[ich] *= expfac;
+ }
+
+ expfac = exp(-ncfac*dt8*etap_dot[1]);
+ etap_dot[0] *= expfac;
+ etap_dot[0] += etap_dotdot[0] * ncfac*dt4;
+ etap_dot[0] *= pdrag_factor;
+ etap_dot[0] *= expfac;
+
+ for (ich = 0; ich < mpchain; ich++)
+ etap[ich] += ncfac*dthalf*etap_dot[ich];
+
+ factor_etap = exp(-ncfac*dthalf*etap_dot[0]);
+ for (i = 0; i < 3; i++)
+ if (p_flag[i]) omega_dot[i] *= factor_etap;
+
+ if (pstyle == TRICLINIC) {
+ for (i = 3; i < 6; i++)
+ if (p_flag[i]) omega_dot[i] *= factor_etap;
+ }
+
+ kecurrent = 0.0;
+ for (i = 0; i < 3; i++)
+ if (p_flag[i]) kecurrent += omega_mass[i]*omega_dot[i]*omega_dot[i];
+
+ if (pstyle == TRICLINIC) {
+ for (i = 3; i < 6; i++)
+ if (p_flag[i]) kecurrent += omega_mass[i]*omega_dot[i]*omega_dot[i];
+ }
+
+ etap_dotdot[0] = (kecurrent - lkt_press)/etap_mass[0];
+
+ etap_dot[0] *= expfac;
+ etap_dot[0] += etap_dotdot[0] * ncfac*dt4;
+ etap_dot[0] *= expfac;
+
+ for (ich = 1; ich < mpchain; ich++) {
+ expfac = exp(-ncfac*dt8*etap_dot[ich+1]);
+ etap_dot[ich] *= expfac;
+ etap_dotdot[ich] =
+ (etap_mass[ich-1]*etap_dot[ich-1]*etap_dot[ich-1] - boltz*t_target) /
+ etap_mass[ich];
+ etap_dot[ich] += etap_dotdot[ich] * ncfac*dt4;
+ etap_dot[ich] *= expfac;
+ }
+ }
+}
+
+/* ----------------------------------------------------------------------
+ perform half-step barostat scaling of velocities
+-----------------------------------------------------------------------*/
+
+void FixBocs::nh_v_press()
+{
+ double factor[3];
+ double **v = atom->v;
+ int *mask = atom->mask;
+ int nlocal = atom->nlocal;
+ if (igroup == atom->firstgroup) nlocal = atom->nfirst;
+
+ factor[0] = exp(-dt4*(omega_dot[0]+mtk_term2));
+ factor[1] = exp(-dt4*(omega_dot[1]+mtk_term2));
+ factor[2] = exp(-dt4*(omega_dot[2]+mtk_term2));
+
+ if (which == NOBIAS) {
+ for (int i = 0; i < nlocal; i++) {
+ if (mask[i] & groupbit) {
+ v[i][0] *= factor[0];
+ v[i][1] *= factor[1];
+ v[i][2] *= factor[2];
+ if (pstyle == TRICLINIC) {
+ v[i][0] += -dthalf*(v[i][1]*omega_dot[5] + v[i][2]*omega_dot[4]);
+ v[i][1] += -dthalf*v[i][2]*omega_dot[3];
+ }
+ v[i][0] *= factor[0];
+ v[i][1] *= factor[1];
+ v[i][2] *= factor[2];
+ }
+ }
+ } else if (which == BIAS) {
+ for (int i = 0; i < nlocal; i++) {
+ if (mask[i] & groupbit) {
+ temperature->remove_bias(i,v[i]);
+ v[i][0] *= factor[0];
+ v[i][1] *= factor[1];
+ v[i][2] *= factor[2];
+ if (pstyle == TRICLINIC) {
+ v[i][0] += -dthalf*(v[i][1]*omega_dot[5] + v[i][2]*omega_dot[4]);
+ v[i][1] += -dthalf*v[i][2]*omega_dot[3];
+ }
+ v[i][0] *= factor[0];
+ v[i][1] *= factor[1];
+ v[i][2] *= factor[2];
+ temperature->restore_bias(i,v[i]);
+ }
+ }
+ }
+}
+
+/* ----------------------------------------------------------------------
+ perform half-step update of velocities
+-----------------------------------------------------------------------*/
+
+void FixBocs::nve_v()
+{
+ double dtfm;
+ double **v = atom->v;
+ double **f = atom->f;
+ double *rmass = atom->rmass;
+ double *mass = atom->mass;
+ int *type = atom->type;
+ int *mask = atom->mask;
+ int nlocal = atom->nlocal;
+ if (igroup == atom->firstgroup) nlocal = atom->nfirst;
+
+ if (rmass) {
+ for (int i = 0; i < nlocal; i++) {
+ if (mask[i] & groupbit) {
+ dtfm = dtf / rmass[i];
+ v[i][0] += dtfm*f[i][0];
+ v[i][1] += dtfm*f[i][1];
+ v[i][2] += dtfm*f[i][2];
+ }
+ }
+ } else {
+ for (int i = 0; i < nlocal; i++) {
+ if (mask[i] & groupbit) {
+ dtfm = dtf / mass[type[i]];
+ v[i][0] += dtfm*f[i][0];
+ v[i][1] += dtfm*f[i][1];
+ v[i][2] += dtfm*f[i][2];
+ }
+ }
+ }
+}
+
+/* ----------------------------------------------------------------------
+ perform full-step update of positions
+-----------------------------------------------------------------------*/
+
+void FixBocs::nve_x()
+{
+ double **x = atom->x;
+ double **v = atom->v;
+ int *mask = atom->mask;
+ int nlocal = atom->nlocal;
+ if (igroup == atom->firstgroup) nlocal = atom->nfirst;
+
+ // x update by full step only for atoms in group
+
+ for (int i = 0; i < nlocal; i++) {
+ if (mask[i] & groupbit) {
+ x[i][0] += dtv * v[i][0];
+ x[i][1] += dtv * v[i][1];
+ x[i][2] += dtv * v[i][2];
+ }
+ }
+}
+
+/* ----------------------------------------------------------------------
+ perform half-step thermostat scaling of velocities
+-----------------------------------------------------------------------*/
+
+void FixBocs::nh_v_temp()
+{
+ double **v = atom->v;
+ int *mask = atom->mask;
+ int nlocal = atom->nlocal;
+ if (igroup == atom->firstgroup) nlocal = atom->nfirst;
+
+ if (which == NOBIAS) {
+ for (int i = 0; i < nlocal; i++) {
+ if (mask[i] & groupbit) {
+ v[i][0] *= factor_eta;
+ v[i][1] *= factor_eta;
+ v[i][2] *= factor_eta;
+ }
+ }
+ } else if (which == BIAS) {
+ for (int i = 0; i < nlocal; i++) {
+ if (mask[i] & groupbit) {
+ temperature->remove_bias(i,v[i]);
+ v[i][0] *= factor_eta;
+ v[i][1] *= factor_eta;
+ v[i][2] *= factor_eta;
+ temperature->restore_bias(i,v[i]);
+ }
+ }
+ }
+}
+
+/* ----------------------------------------------------------------------
+ compute sigma tensor
+ needed whenever p_target or h0_inv changes
+-----------------------------------------------------------------------*/
+
+void FixBocs::compute_sigma()
+{
+ // if nreset_h0 > 0, reset vol0 and h0_inv
+ // every nreset_h0 timesteps
+
+ if (nreset_h0 > 0) {
+ int delta = update->ntimestep - update->beginstep;
+ if (delta % nreset_h0 == 0) {
+ if (dimension == 3) vol0 = domain->xprd * domain->yprd * domain->zprd;
+ else vol0 = domain->xprd * domain->yprd;
+ h0_inv[0] = domain->h_inv[0];
+ h0_inv[1] = domain->h_inv[1];
+ h0_inv[2] = domain->h_inv[2];
+ h0_inv[3] = domain->h_inv[3];
+ h0_inv[4] = domain->h_inv[4];
+ h0_inv[5] = domain->h_inv[5];
+ }
+ }
+
+ // generate upper-triangular half of
+ // sigma = vol0*h0inv*(p_target-p_hydro)*h0inv^t
+ // units of sigma are are PV/L^2 e.g. atm.A
+ //
+ // [ 0 5 4 ] [ 0 5 4 ] [ 0 5 4 ] [ 0 - - ]
+ // [ 5 1 3 ] = [ - 1 3 ] [ 5 1 3 ] [ 5 1 - ]
+ // [ 4 3 2 ] [ - - 2 ] [ 4 3 2 ] [ 4 3 2 ]
+
+ sigma[0] =
+ vol0*(h0_inv[0]*((p_target[0]-p_hydro)*h0_inv[0] +
+ p_target[5]*h0_inv[5]+p_target[4]*h0_inv[4]) +
+ h0_inv[5]*(p_target[5]*h0_inv[0] +
+ (p_target[1]-p_hydro)*h0_inv[5]+p_target[3]*h0_inv[4]) +
+ h0_inv[4]*(p_target[4]*h0_inv[0]+p_target[3]*h0_inv[5] +
+ (p_target[2]-p_hydro)*h0_inv[4]));
+ sigma[1] =
+ vol0*(h0_inv[1]*((p_target[1]-p_hydro)*h0_inv[1] +
+ p_target[3]*h0_inv[3]) +
+ h0_inv[3]*(p_target[3]*h0_inv[1] +
+ (p_target[2]-p_hydro)*h0_inv[3]));
+ sigma[2] =
+ vol0*(h0_inv[2]*((p_target[2]-p_hydro)*h0_inv[2]));
+ sigma[3] =
+ vol0*(h0_inv[1]*(p_target[3]*h0_inv[2]) +
+ h0_inv[3]*((p_target[2]-p_hydro)*h0_inv[2]));
+ sigma[4] =
+ vol0*(h0_inv[0]*(p_target[4]*h0_inv[2]) +
+ h0_inv[5]*(p_target[3]*h0_inv[2]) +
+ h0_inv[4]*((p_target[2]-p_hydro)*h0_inv[2]));
+ sigma[5] =
+ vol0*(h0_inv[0]*(p_target[5]*h0_inv[1]+p_target[4]*h0_inv[3]) +
+ h0_inv[5]*((p_target[1]-p_hydro)*h0_inv[1]+p_target[3]*h0_inv[3]) +
+ h0_inv[4]*(p_target[3]*h0_inv[1]+(p_target[2]-p_hydro)*h0_inv[3]));
+}
+
+/* ----------------------------------------------------------------------
+ compute strain energy
+-----------------------------------------------------------------------*/
+
+double FixBocs::compute_strain_energy()
+{
+ // compute strain energy = 0.5*Tr(sigma*h*h^t) in energy units
+
+ double* h = domain->h;
+ double d0,d1,d2;
+
+ d0 =
+ sigma[0]*(h[0]*h[0]+h[5]*h[5]+h[4]*h[4]) +
+ sigma[5]*( h[1]*h[5]+h[3]*h[4]) +
+ sigma[4]*( h[2]*h[4]);
+ d1 =
+ sigma[5]*( h[5]*h[1]+h[4]*h[3]) +
+ sigma[1]*( h[1]*h[1]+h[3]*h[3]) +
+ sigma[3]*( h[2]*h[3]);
+ d2 =
+ sigma[4]*( h[4]*h[2]) +
+ sigma[3]*( h[3]*h[2]) +
+ sigma[2]*( h[2]*h[2]);
+
+ double energy = 0.5*(d0+d1+d2)/nktv2p;
+ return energy;
+}
+
+/* ----------------------------------------------------------------------
+ compute deviatoric barostat force = h*sigma*h^t
+-----------------------------------------------------------------------*/
+
+void FixBocs::compute_deviatoric()
+{
+ // generate upper-triangular part of h*sigma*h^t
+ // units of fdev are are PV, e.g. atm*A^3
+ // [ 0 5 4 ] [ 0 5 4 ] [ 0 5 4 ] [ 0 - - ]
+ // [ 5 1 3 ] = [ - 1 3 ] [ 5 1 3 ] [ 5 1 - ]
+ // [ 4 3 2 ] [ - - 2 ] [ 4 3 2 ] [ 4 3 2 ]
+
+ double* h = domain->h;
+
+ fdev[0] =
+ h[0]*(sigma[0]*h[0]+sigma[5]*h[5]+sigma[4]*h[4]) +
+ h[5]*(sigma[5]*h[0]+sigma[1]*h[5]+sigma[3]*h[4]) +
+ h[4]*(sigma[4]*h[0]+sigma[3]*h[5]+sigma[2]*h[4]);
+ fdev[1] =
+ h[1]*( sigma[1]*h[1]+sigma[3]*h[3]) +
+ h[3]*( sigma[3]*h[1]+sigma[2]*h[3]);
+ fdev[2] =
+ h[2]*( sigma[2]*h[2]);
+ fdev[3] =
+ h[1]*( sigma[3]*h[2]) +
+ h[3]*( sigma[2]*h[2]);
+ fdev[4] =
+ h[0]*( sigma[4]*h[2]) +
+ h[5]*( sigma[3]*h[2]) +
+ h[4]*( sigma[2]*h[2]);
+ fdev[5] =
+ h[0]*( sigma[5]*h[1]+sigma[4]*h[3]) +
+ h[5]*( sigma[1]*h[1]+sigma[3]*h[3]) +
+ h[4]*( sigma[3]*h[1]+sigma[2]*h[3]);
+}
+
+/* ----------------------------------------------------------------------
+ compute target temperature and kinetic energy
+-----------------------------------------------------------------------*/
+
+void FixBocs::compute_temp_target()
+{
+ double delta = update->ntimestep - update->beginstep;
+ if (delta != 0.0) delta /= update->endstep - update->beginstep;
+
+ t_target = t_start + delta * (t_stop-t_start);
+ ke_target = tdof * boltz * t_target;
+}
+
+/* ----------------------------------------------------------------------
+ compute hydrostatic target pressure
+-----------------------------------------------------------------------*/
+
+void FixBocs::compute_press_target()
+{
+ double delta = update->ntimestep - update->beginstep;
+ if (delta != 0.0) delta /= update->endstep - update->beginstep;
+
+ p_hydro = 0.0;
+ for (int i = 0; i < 3; i++)
+ if (p_flag[i]) {
+ p_target[i] = p_start[i] + delta * (p_stop[i]-p_start[i]);
+ p_hydro += p_target[i];
+ }
+ if (pdim > 0) p_hydro /= pdim;
+
+ if (pstyle == TRICLINIC)
+ for (int i = 3; i < 6; i++)
+ p_target[i] = p_start[i] + delta * (p_stop[i]-p_start[i]);
+
+ // if deviatoric, recompute sigma each time p_target changes
+
+ if (deviatoric_flag) compute_sigma();
+}
+
+/* ----------------------------------------------------------------------
+ update omega_dot, omega
+-----------------------------------------------------------------------*/
+
+void FixBocs::nh_omega_dot()
+{
+ double f_omega,volume;
+
+ if (dimension == 3) volume = domain->xprd*domain->yprd*domain->zprd;
+ else volume = domain->xprd*domain->yprd;
+
+ if (deviatoric_flag) compute_deviatoric();
+
+ mtk_term1 = 0.0;
+ if (mtk_flag) {
+ if (pstyle == ISO) {
+ mtk_term1 = tdof * boltz * t_current;
+ mtk_term1 /= pdim * atom->natoms;
+ } else {
+ double *mvv_current = temperature->vector;
+ for (int i = 0; i < 3; i++)
+ if (p_flag[i])
+ mtk_term1 += mvv_current[i];
+ mtk_term1 /= pdim * atom->natoms;
+ }
+ }
+
+ for (int i = 0; i < 3; i++)
+ if (p_flag[i]) {
+ f_omega = (p_current[i]-p_hydro)*volume /
+ (omega_mass[i] * nktv2p) + mtk_term1 / omega_mass[i];
+ if (deviatoric_flag) f_omega -= fdev[i]/(omega_mass[i] * nktv2p);
+ omega_dot[i] += f_omega*dthalf;
+ omega_dot[i] *= pdrag_factor;
+ }
+
+ mtk_term2 = 0.0;
+ if (mtk_flag) {
+ for (int i = 0; i < 3; i++)
+ if (p_flag[i])
+ mtk_term2 += omega_dot[i];
+ if (pdim > 0) mtk_term2 /= pdim * atom->natoms;
+ }
+
+ if (pstyle == TRICLINIC) {
+ for (int i = 3; i < 6; i++) {
+ if (p_flag[i]) {
+ f_omega = p_current[i]*volume/(omega_mass[i] * nktv2p);
+ if (deviatoric_flag)
+ f_omega -= fdev[i]/(omega_mass[i] * nktv2p);
+ omega_dot[i] += f_omega*dthalf;
+ omega_dot[i] *= pdrag_factor;
+ }
+ }
+ }
+}
+
+/* ----------------------------------------------------------------------
+ if any tilt ratios exceed limits, set flip = 1 and compute new tilt values
+ do not flip in x or y if non-periodic (can tilt but not flip)
+ this is b/c the box length would be changed (dramatically) by flip
+ if yz tilt exceeded, adjust C vector by one B vector
+ if xz tilt exceeded, adjust C vector by one A vector
+ if xy tilt exceeded, adjust B vector by one A vector
+ check yz first since it may change xz, then xz check comes after
+ if any flip occurs, create new box in domain
+ image_flip() adjusts image flags due to box shape change induced by flip
+ remap() puts atoms outside the new box back into the new box
+ perform irregular on atoms in lamda coords to migrate atoms to new procs
+ important that image_flip comes before remap, since remap may change
+ image flags to new values, making eqs in doc of Domain:image_flip incorrect
+------------------------------------------------------------------------- */
+
+void FixBocs::pre_exchange()
+{
+ double xprd = domain->xprd;
+ double yprd = domain->yprd;
+
+ // flip is only triggered when tilt exceeds 0.5 by DELTAFLIP
+ // this avoids immediate re-flipping due to tilt oscillations
+
+ double xtiltmax = (0.5+DELTAFLIP)*xprd;
+ double ytiltmax = (0.5+DELTAFLIP)*yprd;
+
+ int flipxy,flipxz,flipyz;
+ flipxy = flipxz = flipyz = 0;
+
+ if (domain->yperiodic) {
+ if (domain->yz < -ytiltmax) {
+ domain->yz += yprd;
+ domain->xz += domain->xy;
+ flipyz = 1;
+ } else if (domain->yz >= ytiltmax) {
+ domain->yz -= yprd;
+ domain->xz -= domain->xy;
+ flipyz = -1;
+ }
+ }
+
+ if (domain->xperiodic) {
+ if (domain->xz < -xtiltmax) {
+ domain->xz += xprd;
+ flipxz = 1;
+ } else if (domain->xz >= xtiltmax) {
+ domain->xz -= xprd;
+ flipxz = -1;
+ }
+ if (domain->xy < -xtiltmax) {
+ domain->xy += xprd;
+ flipxy = 1;
+ } else if (domain->xy >= xtiltmax) {
+ domain->xy -= xprd;
+ flipxy = -1;
+ }
+ }
+
+ int flip = 0;
+ if (flipxy || flipxz || flipyz) flip = 1;
+
+ if (flip) {
+ domain->set_global_box();
+ domain->set_local_box();
+
+ domain->image_flip(flipxy,flipxz,flipyz);
+
+ double **x = atom->x;
+ imageint *image = atom->image;
+ int nlocal = atom->nlocal;
+ for (int i = 0; i < nlocal; i++) domain->remap(x[i],image[i]);
+
+ domain->x2lamda(atom->nlocal);
+ irregular->migrate_atoms();
+ domain->lamda2x(atom->nlocal);
+ }
+}
+
+/* ----------------------------------------------------------------------
+ memory usage of Irregular
+------------------------------------------------------------------------- */
+
+double FixBocs::memory_usage()
+{
+ double bytes = 0.0;
+ if (irregular) bytes += irregular->memory_usage();
+ return bytes;
+}
diff --git a/src/USER-BOCS/fix_bocs.h b/src/USER-BOCS/fix_bocs.h
new file mode 100644
index 0000000000000000000000000000000000000000..34090e4f3ac5cfc624dbc22e1ae77b905c4ee153
--- /dev/null
+++ b/src/USER-BOCS/fix_bocs.h
@@ -0,0 +1,302 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+-------------------------------------------------------------------------
+ USER-BOCS written by: Nicholas J. H. Dunn and Michael R. DeLyser
+ from The Pennsylvania State University
+------------------------------------------------------------------------- */
+
+
+#ifdef FIX_CLASS
+
+FixStyle(bocs,FixBocs)
+
+#else
+
+#ifndef LMP_FIX_BOCS_H
+#define LMP_FIX_BOCS_H
+
+#include "fix.h"
+
+
+namespace LAMMPS_NS {
+
+class FixBocs : public Fix {
+ public:
+ FixBocs(class LAMMPS *, int, char **); // MRD NJD
+ virtual ~FixBocs(); // MRD NJD
+ int setmask();
+ virtual void init();
+ virtual void setup(int);
+ virtual void initial_integrate(int);
+ virtual void final_integrate();
+ void initial_integrate_respa(int, int, int);
+ void final_integrate_respa(int, int);
+ virtual void pre_exchange();
+ double compute_scalar();
+ virtual double compute_vector(int);
+ void write_restart(FILE *);
+ virtual int pack_restart_data(double *); // pack restart data
+ virtual void restart(char *);
+ int modify_param(int, char **);
+ void reset_target(double);
+ void reset_dt();
+ virtual void *extract(const char*,int &);
+ double memory_usage();
+
+
+ protected:
+ int dimension,which;
+ double dtv,dtf,dthalf,dt4,dt8,dto;
+ double boltz,nktv2p,tdof;
+ double vol0; // reference volume
+ double t0; // reference temperature
+ // used for barostat mass
+ double t_start,t_stop;
+ double t_current,t_target,ke_target;
+ double t_freq;
+
+ int tstat_flag; // 1 if control T
+ int pstat_flag; // 1 if control P
+
+ int pstyle,pcouple,allremap;
+ int p_flag[6]; // 1 if control P on this dim, 0 if not
+ double p_start[6],p_stop[6];
+ double p_freq[6],p_target[6];
+ double omega[6],omega_dot[6];
+ double omega_mass[6];
+ double p_current[6];
+ double drag,tdrag_factor; // drag factor on particle thermostat
+ double pdrag_factor; // drag factor on barostat
+ int kspace_flag; // 1 if KSpace invoked, 0 if not
+ int nrigid; // number of rigid fixes
+ int dilate_group_bit; // mask for dilation group
+ int *rfix; // indices of rigid fixes
+ char *id_dilate; // group name to dilate
+ class Irregular *irregular; // for migrating atoms after box flips
+
+// MRD NJD
+ int p_basis_type;
+ int p_match_flag;
+ double vavg;
+ int N_mol;
+ int N_p_match;
+ double *p_match_coeffs;
+ double ** splines;
+ int spline_length;
+
+
+ int nlevels_respa;
+ double *step_respa;
+
+ char *id_temp,*id_press;
+ class Compute *temperature,*pressure;
+ int tcomputeflag,pcomputeflag; // 1 = compute was created by fix
+ // 0 = created externally
+
+ double *eta,*eta_dot; // chain thermostat for particles
+ double *eta_dotdot;
+ double *eta_mass;
+ int mtchain; // length of chain
+ int mtchain_default_flag; // 1 = mtchain is default
+
+ double *etap; // chain thermostat for barostat
+ double *etap_dot;
+ double *etap_dotdot;
+ double *etap_mass;
+ int mpchain; // length of chain
+
+ int mtk_flag; // 0 if using Hoover barostat
+ int pdim; // number of barostatted dims
+ double p_freq_max; // maximum barostat frequency
+
+ double p_hydro; // hydrostatic target pressure
+
+ int nc_tchain,nc_pchain;
+ double factor_eta;
+ double sigma[6]; // scaled target stress
+ double fdev[6]; // deviatoric force on barostat
+ int deviatoric_flag; // 0 if target stress tensor is hydrostatic
+ double h0_inv[6]; // h_inv of reference (zero strain) box
+ int nreset_h0; // interval for resetting h0
+
+ double mtk_term1,mtk_term2; // Martyna-Tobias-Klein corrections
+
+ int eta_mass_flag; // 1 if eta_mass updated, 0 if not.
+ int omega_mass_flag; // 1 if omega_mass updated, 0 if not.
+ int etap_mass_flag; // 1 if etap_mass updated, 0 if not.
+ int dipole_flag; // 1 if dipole is updated, 0 if not.
+ int dlm_flag; // 1 if using the DLM rotational integrator, 0 if not
+
+ int scaleyz; // 1 if yz scaled with lz
+ int scalexz; // 1 if xz scaled with lz
+ int scalexy; // 1 if xy scaled with ly
+ int flipflag; // 1 if box flips are invoked as needed
+
+ int pre_exchange_flag; // set if pre_exchange needed for box flips
+
+ double fixedpoint[3]; // location of dilation fixed-point
+
+ void couple();
+ virtual void remap();
+ void nhc_temp_integrate();
+ void nhc_press_integrate();
+
+ int read_F_table(char *, int);
+ void build_cubic_splines(double **);
+
+ virtual void nve_x(); // may be overwritten by child classes
+ virtual void nve_v();
+ virtual void nh_v_press();
+ virtual void nh_v_temp();
+ virtual void compute_temp_target();
+ virtual int size_restart_global();
+
+ void compute_sigma();
+ void compute_deviatoric();
+ double compute_strain_energy();
+ void compute_press_target();
+ void nh_omega_dot();
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+E: Illegal ... command
+
+Self-explanatory. Check the input script syntax and compare to the
+documentation for the command. You can use -echo screen as a
+command-line option when running LAMMPS to see the offending line.
+
+E: Target temperature for fix bocs cannot be 0.0
+
+Self-explanatory.
+
+E: Invalid fix bocs command for a 2d simulation
+
+Cannot control z dimension in a 2d model.
+
+E: Fix bocs dilate group ID does not exist
+
+Self-explanatory.
+
+E: Invalid fix bocs command pressure settings
+
+If multiple dimensions are coupled, those dimensions must be
+specified.
+
+E: Cannot use fix bocs on a non-periodic dimension
+
+When specifying a diagonal pressure component, the dimension must be
+periodic.
+
+E: Cannot use fix bocs on a 2nd non-periodic dimension
+
+When specifying an off-diagonal pressure component, the 2nd of the two
+dimensions must be periodic. E.g. if the xy component is specified,
+then the y dimension must be periodic.
+
+E: Cannot use fix bocs with yz scaling when z is non-periodic dimension
+
+The 2nd dimension in the barostatted tilt factor must be periodic.
+
+E: Cannot use fix bocs with xz scaling when z is non-periodic dimension
+
+The 2nd dimension in the barostatted tilt factor must be periodic.
+
+E: Cannot use fix bocs with xy scaling when y is non-periodic dimension
+
+The 2nd dimension in the barostatted tilt factor must be periodic.
+
+E: Cannot use fix bocs with both yz dynamics and yz scaling
+
+Self-explanatory.
+
+E: Cannot use fix bocs with both xz dynamics and xz scaling
+
+Self-explanatory.
+
+E: Cannot use fix bocs with both xy dynamics and xy scaling
+
+Self-explanatory.
+
+E: Can not specify Pxy/Pxz/Pyz in fix bocs with non-triclinic box
+
+Only triclinic boxes can be used with off-diagonal pressure components.
+See the region prism command for details.
+
+E: Invalid fix bocs pressure settings
+
+Settings for coupled dimensions must be the same.
+
+E: Using update dipole flag requires atom style sphere
+
+Self-explanatory.
+
+E: Using update dipole flag requires atom attribute mu
+
+Self-explanatory.
+
+E: The dlm flag must be used with update dipole
+
+Self-explanatory.
+
+E: Fix bocs damping parameters must be > 0.0
+
+Self-explanatory.
+
+E: Cannot use fix npt and fix deform on same component of stress tensor
+
+This would be changing the same box dimension twice.
+
+E: Temperature ID for fix bocs does not exist
+
+Self-explanatory.
+
+E: Pressure ID for fix bocs does not exist
+
+Self-explanatory.
+
+E: Fix bocs has tilted box too far in one step - periodic cell is too far from equilibrium state
+
+Self-explanatory. The change in the box tilt is too extreme
+on a short timescale.
+
+E: Could not find fix_modify temperature ID
+
+The compute ID for computing temperature does not exist.
+
+E: Fix_modify temperature ID does not compute temperature
+
+The compute ID assigned to the fix must compute temperature.
+
+W: Temperature for fix modify is not for group all
+
+The temperature compute is being used with a pressure calculation
+which does operate on group all, so this may be inconsistent.
+
+E: Pressure ID for fix modify does not exist
+
+Self-explanatory.
+
+E: Could not find fix_modify pressure ID
+
+The compute ID for computing pressure does not exist.
+
+E: Fix_modify pressure ID does not compute pressure
+
+The compute ID assigned to the fix must compute pressure.
+
+*/
diff --git a/src/USER-CGDNA/Install.sh b/src/USER-CGDNA/Install.sh
old mode 100644
new mode 100755
diff --git a/src/USER-CGDNA/README b/src/USER-CGDNA/README
index 735f005f54e03e5024bdc51172453d986876f7c0..d71f3b7a43acc9df6f7c56f1077a991ce7e762e0 100644
--- a/src/USER-CGDNA/README
+++ b/src/USER-CGDNA/README
@@ -2,22 +2,29 @@ This package contains a LAMMPS implementation of coarse-grained
models of DNA, which can be used to model sequence-specific
DNA strands.
-See the doc pages and [1,2,3] for the individual bond and pair styles.
+Please cite [1] and the relevant oxDNA articles in any publication
+that uses this package.
+
+See the doc pages and [2,3,4] for the individual bond and pair styles.
The packages contains also a new Langevin-type rigid-body integrator,
-which has also its own doc page and is explained in [4].
+which has also its own doc page and is explained in [5].
+
+[1] O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge,
+"Coarse-grained simulation of DNA using LAMMPS",
+Eur. Phys. J. E 41, 57 (2018).
-[1] T. Ouldridge, A. Louis, J. Doye, "Structural, mechanical,
+[2] T. Ouldridge, A. Louis, J. Doye, "Structural, mechanical,
and thermodynamic properties of a coarse-grained DNA model",
J. Chem. Phys. 134, 085101 (2011).
-[2] T.E. Ouldridge, Coarse-grained modelling of DNA and DNA
+[3] T.E. Ouldridge, Coarse-grained modelling of DNA and DNA
self-assembly, DPhil. University of Oxford (2011).
-[3] B.E. Snodin, F. Randisi, M. Mosayebi, et al., Introducing
+[4] B.E. Snodin, F. Randisi, M. Mosayebi, et al., Introducing
Improved Structural Properties and Salt Dependence into a Coarse-Grained
Model of DNA, J. Chem. Phys. 142, 234901 (2015).
-[4] R. Davidchack, T. Ouldridge, M. Tretyakov, "New Langevin and
+[5] R. Davidchack, T. Ouldridge, M. Tretyakov, "New Langevin and
gradient thermostats for rigid body dynamics", J. Chem. Phys. 142,
144114 (2015).
@@ -28,7 +35,7 @@ well as DNA duplexes or arrays of duplexes can be found in
/examples/USER/cgdna/util/. A technical report with more information
on the models, the structure of the input and data file, the setup tool
and the performance of the LAMMPS-implementation of oxDNA can be found
-in /doc/src/PDF/USER-CGDNA-overview.pdf.
+in /doc/src/PDF/USER-CGDNA.pdf.
IMPORTANT NOTE: This package can only be used if LAMMPS is compiled
with the MOLECULE and ASPHERE packages. These should be included in
@@ -40,9 +47,8 @@ The creator of this package is:
Dr Oliver Henrich
University of Strathclyde, Glasgow, UK
-oliver.henrich at strath.ac.uk
-University of Edinburgh, UK
-ohenrich at staffmail.ed.ac.uk
+oliver d o t henrich a t strath d o t ac d o t uk
+
--------------------------------------------------------------------------
diff --git a/src/USER-CGDNA/bond_oxdna2_fene.cpp b/src/USER-CGDNA/bond_oxdna2_fene.cpp
index b2e1afb073d5af6a71a61428a2b64249d4af3166..39cbb04f88e1aad84a1b181757bf1b1b83d92f19 100644
--- a/src/USER-CGDNA/bond_oxdna2_fene.cpp
+++ b/src/USER-CGDNA/bond_oxdna2_fene.cpp
@@ -14,8 +14,8 @@
Contributing author: Oliver Henrich (University of Strathclyde, Glasgow)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdlib>
#include "bond_oxdna2_fene.h"
using namespace LAMMPS_NS;
diff --git a/src/USER-CGDNA/bond_oxdna_fene.cpp b/src/USER-CGDNA/bond_oxdna_fene.cpp
index e5d3a3e45242d29b21ba2c5683082d82f0e98f08..47d8d8f60b3854632e13bdf7358200f596fef98c 100644
--- a/src/USER-CGDNA/bond_oxdna_fene.cpp
+++ b/src/USER-CGDNA/bond_oxdna_fene.cpp
@@ -14,8 +14,8 @@
Contributing author: Oliver Henrich (University of Strathclyde, Glasgow)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdlib>
#include "bond_oxdna_fene.h"
#include "atom.h"
#include "neighbor.h"
@@ -242,7 +242,7 @@ void BondOxdnaFene::coeff(int narg, char **arg)
void BondOxdnaFene::init_style()
{
/* special bonds have to be lj = 0 1 1 and coul = 1 1 1 to exclude
- the ss excluded volume interaction between nearest neighbours */
+ the ss excluded volume interaction between nearest neighbors */
force->special_lj[1] = 0.0;
force->special_lj[2] = 1.0;
diff --git a/src/USER-CGDNA/fix_nve_dot.cpp b/src/USER-CGDNA/fix_nve_dot.cpp
index 5cdda597037e238de9da6d234d799728f04baf64..63f38a4e12af727939cb5848153315f44f43b662 100644
--- a/src/USER-CGDNA/fix_nve_dot.cpp
+++ b/src/USER-CGDNA/fix_nve_dot.cpp
@@ -14,9 +14,9 @@
Contributing author: Oliver Henrich (University of Strathclyde, Glasgow)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstring>
#include "fix_nve_dot.h"
#include "math_extra.h"
#include "atom.h"
diff --git a/src/USER-CGDNA/fix_nve_dotc_langevin.cpp b/src/USER-CGDNA/fix_nve_dotc_langevin.cpp
index fae515897c0ad4c07d019cf8c80284eec1d46f44..90f7b1caebbc56e5849e47b72895128b22afcbbb 100644
--- a/src/USER-CGDNA/fix_nve_dotc_langevin.cpp
+++ b/src/USER-CGDNA/fix_nve_dotc_langevin.cpp
@@ -15,9 +15,9 @@
Contributing author: Oliver Henrich (University of Strathclyde, Glasgow)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstring>
#include "fix_nve_dotc_langevin.h"
#include "math_extra.h"
#include "atom.h"
diff --git a/src/USER-CGDNA/mf_oxdna.h b/src/USER-CGDNA/mf_oxdna.h
index 56055d5facab082760d899473fec3cbe667b5f8f..c63a37cde2ab4b8a9fa07e6b556181e947e4c997 100644
--- a/src/USER-CGDNA/mf_oxdna.h
+++ b/src/USER-CGDNA/mf_oxdna.h
@@ -14,7 +14,7 @@
#ifndef MF_OXDNA_H
#define MF_OXDNA_H
-#include <stdio.h>
+#include <cstdio>
#include "math_extra.h"
namespace MFOxdna {
diff --git a/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp b/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp
index 8312d92bc06f788c8c87d76bb063fd6ad4ef1e67..151e7526924f508677c0c4648203b1091db9a4a0 100644
--- a/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp
+++ b/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp
@@ -14,10 +14,10 @@
Contributing author: Oliver Henrich (University of Strathclyde, Glasgow)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_oxdna2_coaxstk.h"
#include "mf_oxdna.h"
#include "atom.h"
@@ -157,7 +157,7 @@ void PairOxdna2Coaxstk::compute(int eflag, int vflag)
numneigh = list->numneigh;
firstneigh = list->firstneigh;
- // loop over pair interaction neighbours of my atoms
+ // loop over pair interaction neighbors of my atoms
for (ia = 0; ia < anum; ia++) {
@@ -183,7 +183,7 @@ void PairOxdna2Coaxstk::compute(int eflag, int vflag)
for (ib = 0; ib < bnum; ib++) {
b = blist[ib];
- factor_lj = special_lj[sbmask(b)]; // = 0 for nearest neighbours
+ factor_lj = special_lj[sbmask(b)]; // = 0 for nearest neighbors
b &= NEIGHMASK;
btype = type[b];
diff --git a/src/USER-CGDNA/pair_oxdna2_dh.cpp b/src/USER-CGDNA/pair_oxdna2_dh.cpp
index 48914239251e282239e8510a4355b31148e05dae..974ade89c1230b3e6fff154855cdf8c7d13513f3 100644
--- a/src/USER-CGDNA/pair_oxdna2_dh.cpp
+++ b/src/USER-CGDNA/pair_oxdna2_dh.cpp
@@ -14,10 +14,10 @@
Contributing author: Oliver Henrich (University of Strathclyde, Glasgow)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_oxdna2_dh.h"
#include "mf_oxdna.h"
#include "atom.h"
@@ -122,7 +122,7 @@ void PairOxdna2Dh::compute(int eflag, int vflag)
numneigh = list->numneigh;
firstneigh = list->firstneigh;
- // loop over pair interaction neighbours of my atoms
+ // loop over pair interaction neighbors of my atoms
for (ia = 0; ia < anum; ia++) {
@@ -145,7 +145,7 @@ void PairOxdna2Dh::compute(int eflag, int vflag)
for (ib = 0; ib < bnum; ib++) {
b = blist[ib];
- factor_lj = special_lj[sbmask(b)]; // = 0 for nearest neighbours
+ factor_lj = special_lj[sbmask(b)]; // = 0 for nearest neighbors
b &= NEIGHMASK;
btype = type[b];
@@ -186,7 +186,7 @@ void PairOxdna2Dh::compute(int eflag, int vflag)
}
- // knock out nearest-neighbour interaction between adjacent backbone sites
+ // knock out nearest-neighbor interaction between adjacent backbone sites
fpair *= factor_lj;
evdwl *= factor_lj;
diff --git a/src/USER-CGDNA/pair_oxdna2_excv.cpp b/src/USER-CGDNA/pair_oxdna2_excv.cpp
index e1b18e1487a0d41e079e4dc50fbaf1d1a2bf13aa..4329fbe0715a2e10d22302aa0b2b2e462047a299 100644
--- a/src/USER-CGDNA/pair_oxdna2_excv.cpp
+++ b/src/USER-CGDNA/pair_oxdna2_excv.cpp
@@ -14,10 +14,10 @@
Contributing author: Oliver Henrich (University of Strathclyde, Glasgow)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_oxdna2_excv.h"
using namespace LAMMPS_NS;
diff --git a/src/USER-CGDNA/pair_oxdna2_stk.cpp b/src/USER-CGDNA/pair_oxdna2_stk.cpp
index 3b98db32012d2cf4a99eafa3ef2a8545b8f7cbf7..f479572aa6ed5a070150cf2516a9012fbb96c471 100644
--- a/src/USER-CGDNA/pair_oxdna2_stk.cpp
+++ b/src/USER-CGDNA/pair_oxdna2_stk.cpp
@@ -14,10 +14,10 @@
Contributing author: Oliver Henrich (University of Strathclyde, Glasgow)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_oxdna2_stk.h"
using namespace LAMMPS_NS;
diff --git a/src/USER-CGDNA/pair_oxdna_coaxstk.cpp b/src/USER-CGDNA/pair_oxdna_coaxstk.cpp
index 4a1af83884d3a19fa10a82d905ae395b26a23639..0eb75fbb43b39b6bf29c460e2ebc0680d1cb66cb 100644
--- a/src/USER-CGDNA/pair_oxdna_coaxstk.cpp
+++ b/src/USER-CGDNA/pair_oxdna_coaxstk.cpp
@@ -14,10 +14,10 @@
Contributing author: Oliver Henrich (University of Strathclyde, Glasgow)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_oxdna_coaxstk.h"
#include "mf_oxdna.h"
#include "atom.h"
@@ -163,7 +163,7 @@ void PairOxdnaCoaxstk::compute(int eflag, int vflag)
numneigh = list->numneigh;
firstneigh = list->firstneigh;
- // loop over pair interaction neighbours of my atoms
+ // loop over pair interaction neighbors of my atoms
for (ia = 0; ia < anum; ia++) {
@@ -189,7 +189,7 @@ void PairOxdnaCoaxstk::compute(int eflag, int vflag)
for (ib = 0; ib < bnum; ib++) {
b = blist[ib];
- factor_lj = special_lj[sbmask(b)]; // = 0 for nearest neighbours
+ factor_lj = special_lj[sbmask(b)]; // = 0 for nearest neighbors
b &= NEIGHMASK;
btype = type[b];
diff --git a/src/USER-CGDNA/pair_oxdna_excv.cpp b/src/USER-CGDNA/pair_oxdna_excv.cpp
index 09ae13f1b2618fadf28b2f48bf6f7775ec56eea5..e2b8334078cc4c0fae3dc34dcceb6bdefc662657 100644
--- a/src/USER-CGDNA/pair_oxdna_excv.cpp
+++ b/src/USER-CGDNA/pair_oxdna_excv.cpp
@@ -14,10 +14,10 @@
Contributing author: Oliver Henrich (University of Strathclyde, Glasgow)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_oxdna_excv.h"
#include "mf_oxdna.h"
#include "atom.h"
@@ -152,7 +152,7 @@ void PairOxdnaExcv::compute(int eflag, int vflag)
numneigh = list->numneigh;
firstneigh = list->firstneigh;
- // loop over pair interaction neighbours of my atoms
+ // loop over pair interaction neighbors of my atoms
for (ia = 0; ia < anum; ia++) {
@@ -179,7 +179,7 @@ void PairOxdnaExcv::compute(int eflag, int vflag)
for (ib = 0; ib < bnum; ib++) {
b = blist[ib];
- factor_lj = special_lj[sbmask(b)]; // = 0 for nearest neighbours
+ factor_lj = special_lj[sbmask(b)]; // = 0 for nearest neighbors
b &= NEIGHMASK;
btype = type[b];
@@ -222,7 +222,7 @@ void PairOxdnaExcv::compute(int eflag, int vflag)
evdwl = F3(rsq_ss,cutsq_ss_ast[atype][btype],cut_ss_c[atype][btype],lj1_ss[atype][btype],
lj2_ss[atype][btype],epsilon_ss[atype][btype],b_ss[atype][btype],fpair);
- // knock out nearest-neighbour interaction between ss
+ // knock out nearest-neighbor interaction between ss
fpair *= factor_lj;
evdwl *= factor_lj;
diff --git a/src/USER-CGDNA/pair_oxdna_hbond.cpp b/src/USER-CGDNA/pair_oxdna_hbond.cpp
index 1caf320ef1b0105cc336cfa8c2125203bb4c3337..ce1bfe036a3842ae07ceb2baf3b42eef63bd3c7b 100644
--- a/src/USER-CGDNA/pair_oxdna_hbond.cpp
+++ b/src/USER-CGDNA/pair_oxdna_hbond.cpp
@@ -14,10 +14,10 @@
Contributing author: Oliver Henrich (University of Strathclyde, Glasgow)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_oxdna_hbond.h"
#include "mf_oxdna.h"
#include "atom.h"
@@ -168,7 +168,7 @@ void PairOxdnaHbond::compute(int eflag, int vflag)
numneigh = list->numneigh;
firstneigh = list->firstneigh;
- // loop over pair interaction neighbours of my atoms
+ // loop over pair interaction neighbors of my atoms
for (ia = 0; ia < anum; ia++) {
@@ -188,7 +188,7 @@ void PairOxdnaHbond::compute(int eflag, int vflag)
for (ib = 0; ib < bnum; ib++) {
b = blist[ib];
- factor_lj = special_lj[sbmask(b)]; // = 0 for nearest neighbours
+ factor_lj = special_lj[sbmask(b)]; // = 0 for nearest neighbors
b &= NEIGHMASK;
btype = type[b];
diff --git a/src/USER-CGDNA/pair_oxdna_stk.cpp b/src/USER-CGDNA/pair_oxdna_stk.cpp
index 9c3a11b9b712eef4dbaecf71c709fd0e9766d255..8c4498e627cfecb185289cf1834e74fab1f484a8 100644
--- a/src/USER-CGDNA/pair_oxdna_stk.cpp
+++ b/src/USER-CGDNA/pair_oxdna_stk.cpp
@@ -14,10 +14,10 @@
Contributing author: Oliver Henrich (University of Strathclyde, Glasgow)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_oxdna_stk.h"
#include "mf_oxdna.h"
#include "atom.h"
diff --git a/src/USER-CGDNA/pair_oxdna_xstk.cpp b/src/USER-CGDNA/pair_oxdna_xstk.cpp
index c14993dc36a4e8186e93d6f841b1697489edf386..e5b9de81c09c4450584434a8dfa006c826675c0a 100644
--- a/src/USER-CGDNA/pair_oxdna_xstk.cpp
+++ b/src/USER-CGDNA/pair_oxdna_xstk.cpp
@@ -14,10 +14,10 @@
Contributing author: Oliver Henrich (University of Strathclyde, Glasgow)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_oxdna_xstk.h"
#include "mf_oxdna.h"
#include "atom.h"
@@ -160,7 +160,7 @@ void PairOxdnaXstk::compute(int eflag, int vflag)
numneigh = list->numneigh;
firstneigh = list->firstneigh;
- // loop over pair interaction neighbours of my atoms
+ // loop over pair interaction neighbors of my atoms
for (ia = 0; ia < anum; ia++) {
@@ -180,7 +180,7 @@ void PairOxdnaXstk::compute(int eflag, int vflag)
for (ib = 0; ib < bnum; ib++) {
b = blist[ib];
- factor_lj = special_lj[sbmask(b)]; // = 0 for nearest neighbours
+ factor_lj = special_lj[sbmask(b)]; // = 0 for nearest neighbors
b &= NEIGHMASK;
btype = type[b];
diff --git a/src/USER-CGSDK/Install.sh b/src/USER-CGSDK/Install.sh
old mode 100644
new mode 100755
index 00f515b794bee82336ac36597bbbafe8a1c17de6..8e2432343dd74fec474044d06ed4ba0e0ca072c5
--- a/src/USER-CGSDK/Install.sh
+++ b/src/USER-CGSDK/Install.sh
@@ -28,8 +28,8 @@ action () {
# list of files with optional dependcies
-action angle_sdk.cpp angle_harmonic.cpp
-action angle_sdk.h angle_harmonic.cpp
+action angle_sdk.cpp
+action angle_sdk.h
action lj_sdk_common.h
action pair_lj_sdk.cpp
action pair_lj_sdk.h
diff --git a/src/USER-CGSDK/angle_sdk.cpp b/src/USER-CGSDK/angle_sdk.cpp
index a4f979961f2e3cdc6b91a9b42103427a088a4ec9..6b8245b4914447cab0426d9a3a95633105c119b2 100644
--- a/src/USER-CGSDK/angle_sdk.cpp
+++ b/src/USER-CGSDK/angle_sdk.cpp
@@ -18,8 +18,8 @@
lj/sdk potential for coarse grained MD simulations.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdlib>
#include "angle_sdk.h"
#include "atom.h"
#include "neighbor.h"
diff --git a/src/USER-CGSDK/angle_sdk.h b/src/USER-CGSDK/angle_sdk.h
index a5d917e57cfcc0e281d05b86335db9eb017709c8..293004ad4d51b4e159dce696cd8d7aea89caf063 100644
--- a/src/USER-CGSDK/angle_sdk.h
+++ b/src/USER-CGSDK/angle_sdk.h
@@ -20,7 +20,7 @@ AngleStyle(sdk,AngleSDK)
#ifndef LMP_ANGLE_SDK_H
#define LMP_ANGLE_SDK_H
-#include <stdio.h>
+#include <cstdio>
#include "angle.h"
namespace LAMMPS_NS {
diff --git a/src/USER-CGSDK/lj_sdk_common.h b/src/USER-CGSDK/lj_sdk_common.h
index f8f7a66ce9bd9570af5528b29aab1d4e627dbfef..c1f2cf215a68966884b90778bcd09319fe5e935b 100644
--- a/src/USER-CGSDK/lj_sdk_common.h
+++ b/src/USER-CGSDK/lj_sdk_common.h
@@ -19,7 +19,7 @@
#ifndef LMP_LJ_SDK_COMMON_H
#define LMP_LJ_SDK_COMMON_H
-#include <string.h>
+#include <cstring>
namespace LAMMPS_NS {
namespace LJSDKParms {
diff --git a/src/USER-CGSDK/pair_lj_sdk.cpp b/src/USER-CGSDK/pair_lj_sdk.cpp
index 56e56c9605cc82b3e20352dfc2303b948b486771..cbcba7f6b260dc777bd40433aaa5610d33be0800 100644
--- a/src/USER-CGSDK/pair_lj_sdk.cpp
+++ b/src/USER-CGSDK/pair_lj_sdk.cpp
@@ -16,10 +16,10 @@
This style is a simplified re-implementation of the CG/CMM pair style
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_lj_sdk.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-CGSDK/pair_lj_sdk_coul_long.cpp b/src/USER-CGSDK/pair_lj_sdk_coul_long.cpp
index 4c9e42f778431810a2c78af21ed4a7b702484c2d..1d93363e207f185d7460b3f038fb1042a82eb2b4 100644
--- a/src/USER-CGSDK/pair_lj_sdk_coul_long.cpp
+++ b/src/USER-CGSDK/pair_lj_sdk_coul_long.cpp
@@ -16,10 +16,10 @@
This style is a simplified re-implementation of the CG/CMM pair style
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_lj_sdk_coul_long.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-CGSDK/pair_lj_sdk_coul_msm.cpp b/src/USER-CGSDK/pair_lj_sdk_coul_msm.cpp
index ddca927a681bf94752825621698f0949bbd8112a..c4882fdbdb9e13b2ae953b5f666a8c95c92d4d63 100644
--- a/src/USER-CGSDK/pair_lj_sdk_coul_msm.cpp
+++ b/src/USER-CGSDK/pair_lj_sdk_coul_msm.cpp
@@ -16,10 +16,10 @@
This style is a simplified re-implementation of the CG/CMM pair style
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_lj_sdk_coul_msm.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-COLVARS/colvarproxy_lammps.cpp b/src/USER-COLVARS/colvarproxy_lammps.cpp
index c5b9e5a60c860355a4a5960089b8f288b9566841..ff74602b418e0bce8cfdfbc3f60692f4a8aeeebc 100644
--- a/src/USER-COLVARS/colvarproxy_lammps.cpp
+++ b/src/USER-COLVARS/colvarproxy_lammps.cpp
@@ -133,6 +133,8 @@ colvarproxy_lammps::colvarproxy_lammps(LAMMPS_NS::LAMMPS *lmp,
void colvarproxy_lammps::init(const char *conf_file)
{
+ version_int = get_version_from_string(COLVARPROXY_VERSION);
+
// create the colvarmodule instance
colvars = new colvarmodule(this);
@@ -203,6 +205,25 @@ double colvarproxy_lammps::compute()
}
previous_step = _lmp->update->ntimestep;
+ unit_cell_x.set(_lmp->domain->xprd, 0.0, 0.0);
+ unit_cell_y.set(0.0, _lmp->domain->yprd, 0.0);
+ unit_cell_z.set(0.0, 0.0, _lmp->domain->zprd);
+
+ if (_lmp->domain->xperiodic == 0 && _lmp->domain->yperiodic == 0 &&
+ _lmp->domain->zperiodic == 0) {
+ boundaries_type = boundaries_non_periodic;
+ reset_pbc_lattice();
+ } else if ((_lmp->domain->nonperiodic == 0) &&
+ (_lmp->domain->dimension == 3) &&
+ (_lmp->domain->triclinic == 0)) {
+ // Orthogonal unit cell
+ boundaries_type = boundaries_pbc_ortho;
+ colvarproxy_system::update_pbc_lattice();
+ // It is safer to let LAMMPS deal with high-tilt triclinic boxes
+ } else {
+ boundaries_type = boundaries_unsupported;
+ }
+
if (cvm::debug()) {
cvm::log(std::string(cvm::line_marker)+
"colvarproxy_lammps, step no. "+cvm::to_str(colvars->it)+"\n"+
@@ -263,8 +284,10 @@ bool colvarproxy_lammps::deserialize_status(std::string &rst)
}
}
+
cvm::rvector colvarproxy_lammps::position_distance(cvm::atom_pos const &pos1,
cvm::atom_pos const &pos2)
+ const
{
double xtmp = pos2.x - pos1.x;
double ytmp = pos2.y - pos1.y;
@@ -273,28 +296,6 @@ cvm::rvector colvarproxy_lammps::position_distance(cvm::atom_pos const &pos1,
return cvm::rvector(xtmp, ytmp, ztmp);
}
-cvm::real colvarproxy_lammps::position_dist2(cvm::atom_pos const &pos1,
- cvm::atom_pos const &pos2)
-{
- double xtmp = pos2.x - pos1.x;
- double ytmp = pos2.y - pos1.y;
- double ztmp = pos2.z - pos1.z;
- _lmp->domain->minimum_image(xtmp,ytmp,ztmp);
- return cvm::real(xtmp*xtmp + ytmp*ytmp + ztmp*ztmp);
-}
-
-
-void colvarproxy_lammps::select_closest_image(cvm::atom_pos &pos,
- cvm::atom_pos const &ref)
-{
- double xtmp = pos.x - ref.x;
- double ytmp = pos.y - ref.y;
- double ztmp = pos.z - ref.z;
- _lmp->domain->minimum_image(xtmp,ytmp,ztmp);
- pos.x = ref.x + xtmp;
- pos.y = ref.y + ytmp;
- pos.z = ref.z + ztmp;
-}
void colvarproxy_lammps::log(std::string const &message)
{
@@ -308,12 +309,14 @@ void colvarproxy_lammps::log(std::string const &message)
}
}
+
void colvarproxy_lammps::error(std::string const &message)
{
// In LAMMPS, all errors are fatal
fatal_error(message);
}
+
void colvarproxy_lammps::fatal_error(std::string const &message)
{
log(message);
@@ -321,13 +324,6 @@ void colvarproxy_lammps::fatal_error(std::string const &message)
"Fatal error in the collective variables module.\n");
}
-void colvarproxy_lammps::exit(std::string const &message)
-{
- log(message);
- log("Request to exit the simulation made.\n");
- do_exit=true;
-}
-
int colvarproxy_lammps::backup_file(char const *filename)
{
@@ -342,10 +338,12 @@ int colvarproxy_lammps::backup_file(char const *filename)
// multi-replica support
-void colvarproxy_lammps::replica_comm_barrier() {
+void colvarproxy_lammps::replica_comm_barrier()
+{
MPI_Barrier(inter_comm);
}
+
int colvarproxy_lammps::replica_comm_recv(char* msg_data,
int buf_len, int src_rep)
{
@@ -359,6 +357,7 @@ int colvarproxy_lammps::replica_comm_recv(char* msg_data,
return retval;
}
+
int colvarproxy_lammps::replica_comm_send(char* msg_data,
int msg_len, int dest_rep)
{
diff --git a/src/USER-COLVARS/colvarproxy_lammps.h b/src/USER-COLVARS/colvarproxy_lammps.h
index af2aa04dfc890a55443588435206279280581b6c..cdd86cbd16a04c50d176b720e676b36b0615d2a6 100644
--- a/src/USER-COLVARS/colvarproxy_lammps.h
+++ b/src/USER-COLVARS/colvarproxy_lammps.h
@@ -120,14 +120,9 @@ class colvarproxy_lammps : public colvarproxy {
void log(std::string const &message);
void error(std::string const &message);
void fatal_error(std::string const &message);
- void exit(std::string const &message);
cvm::rvector position_distance(cvm::atom_pos const &pos1,
- cvm::atom_pos const &pos2);
- cvm::real position_dist2(cvm::atom_pos const &pos1,
- cvm::atom_pos const &pos2);
- void select_closest_image(cvm::atom_pos &pos,
- cvm::atom_pos const &ref_pos);
+ cvm::atom_pos const &pos2) const;
int backup_file(char const *filename);
diff --git a/src/USER-COLVARS/colvarproxy_lammps_version.h b/src/USER-COLVARS/colvarproxy_lammps_version.h
index 79f77dad4e8284d4a7c0c771f0e464626a8f828d..0d451212b261cb07bb9aa2a66f9c8ad7e0918ce5 100644
--- a/src/USER-COLVARS/colvarproxy_lammps_version.h
+++ b/src/USER-COLVARS/colvarproxy_lammps_version.h
@@ -1,5 +1,5 @@
#ifndef COLVARPROXY_VERSION
-#define COLVARPROXY_VERSION "2017-12-01"
+#define COLVARPROXY_VERSION "2018-04-29"
// This file is part of the Collective Variables module (Colvars).
// The original version of Colvars and its updates are located at:
// https://github.com/colvars/colvars
diff --git a/src/USER-COLVARS/fix_colvars.cpp b/src/USER-COLVARS/fix_colvars.cpp
index 84b3ee07d62533c07c6cbc7cb68bb675a5b07d3a..0e4e151c3dcca2bc43e4033df9127480f46a1318 100644
--- a/src/USER-COLVARS/fix_colvars.cpp
+++ b/src/USER-COLVARS/fix_colvars.cpp
@@ -24,10 +24,10 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include <errno.h>
#include "fix_colvars.h"
diff --git a/src/USER-COLVARS/group_ndx.cpp b/src/USER-COLVARS/group_ndx.cpp
index 50769180390cec50f8f693444393506ca990522c..450c250ffa4fcbe23aef74fd10cda0887ecfb3dd 100644
--- a/src/USER-COLVARS/group_ndx.cpp
+++ b/src/USER-COLVARS/group_ndx.cpp
@@ -23,8 +23,8 @@
#include "memory.h"
#include "error.h"
-#include <stdio.h>
-#include <stdlib.h>
+#include <cstdio>
+#include <cstdlib>
using namespace LAMMPS_NS;
diff --git a/src/USER-COLVARS/ndx_group.cpp b/src/USER-COLVARS/ndx_group.cpp
index c7972e372ec940989ec58d2c727cf2ce4aba5a78..7b46364f189cc1e9ebef74bb965c8670affadbd2 100644
--- a/src/USER-COLVARS/ndx_group.cpp
+++ b/src/USER-COLVARS/ndx_group.cpp
@@ -24,9 +24,9 @@
#include "force.h"
#include "error.h"
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
using namespace LAMMPS_NS;
#define BUFLEN 4096
diff --git a/src/USER-DIFFRACTION/compute_saed.cpp b/src/USER-DIFFRACTION/compute_saed.cpp
index cc1dec96fa14872b1d792a5fab15847c796e825f..3d09955275c1b2de3aa7219b0a162151ce49de29 100644
--- a/src/USER-DIFFRACTION/compute_saed.cpp
+++ b/src/USER-DIFFRACTION/compute_saed.cpp
@@ -16,8 +16,10 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <math.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstdio>
+#include <cstring>
#include "math_const.h"
#include "compute_saed.h"
#include "compute_saed_consts.h"
@@ -29,8 +31,6 @@
#include "citeme.h"
#include "memory.h"
#include "error.h"
-#include <stdio.h>
-#include <string.h>
using namespace LAMMPS_NS;
using namespace MathConst;
diff --git a/src/USER-DIFFRACTION/compute_xrd.cpp b/src/USER-DIFFRACTION/compute_xrd.cpp
index 380629ffb9ea6c48f9c8113af305ea30b182a8ab..4d5cccdc504433afa39802bbd9d1a1ef1f5fd48b 100644
--- a/src/USER-DIFFRACTION/compute_xrd.cpp
+++ b/src/USER-DIFFRACTION/compute_xrd.cpp
@@ -17,8 +17,10 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <math.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstdio>
+#include <cstring>
#include "math_const.h"
#include "compute_xrd.h"
#include "compute_xrd_consts.h"
@@ -30,8 +32,6 @@
#include "citeme.h"
#include "memory.h"
#include "error.h"
-#include <stdio.h>
-#include <string.h>
using namespace LAMMPS_NS;
using namespace MathConst;
diff --git a/src/USER-DIFFRACTION/fix_saed_vtk.cpp b/src/USER-DIFFRACTION/fix_saed_vtk.cpp
index dfa63f630ad5537b7700a25b330d9e17af1d1185..45bfeca48bd2269d0579672994fca283d8495ae1 100644
--- a/src/USER-DIFFRACTION/fix_saed_vtk.cpp
+++ b/src/USER-DIFFRACTION/fix_saed_vtk.cpp
@@ -16,8 +16,9 @@
Incorporating SAED: Shawn Coleman (Arkansas)
------------------------------------------------------------------------- */
-#include <stdlib.h>
-#include <string.h>
+#include <cstdlib>
+#include <cstring>
+#include <cmath>
#include "fix_saed_vtk.h"
#include "update.h"
#include "modify.h"
@@ -29,7 +30,6 @@
#include "memory.h"
#include "error.h"
#include "force.h"
-#include <math.h>
#include "domain.h"
using namespace LAMMPS_NS;
diff --git a/src/USER-DIFFRACTION/fix_saed_vtk.h b/src/USER-DIFFRACTION/fix_saed_vtk.h
index fa379e7216ca9dfdb366969e3aca3c481559d3b4..2fc09c781c8da9644959fd5ddba30588556cf162 100644
--- a/src/USER-DIFFRACTION/fix_saed_vtk.h
+++ b/src/USER-DIFFRACTION/fix_saed_vtk.h
@@ -20,7 +20,7 @@ FixStyle(saed/vtk,FixSAEDVTK)
#ifndef LMP_FIX_SAED_VTK_H
#define LMP_FIX_SAED_VTK_H
-#include <stdio.h>
+#include <cstdio>
#include "fix.h"
namespace LAMMPS_NS {
diff --git a/src/USER-DPD/atom_vec_dpd.cpp b/src/USER-DPD/atom_vec_dpd.cpp
index 477ed05e3f04c85cd0ba864bb56b0bd76200df5b..4cf6356100c0bd4182bbc9f05eb95a0292876830 100644
--- a/src/USER-DPD/atom_vec_dpd.cpp
+++ b/src/USER-DPD/atom_vec_dpd.cpp
@@ -15,7 +15,7 @@
Contributing author: James Larentzos (U.S. Army Research Laboratory)
------------------------------------------------------------------------- */
-#include <stdlib.h>
+#include <cstdlib>
#include "atom_vec_dpd.h"
#include "atom.h"
#include "comm.h"
@@ -757,6 +757,8 @@ int AtomVecDPD::unpack_restart(double *buf)
uCond[nlocal] = buf[m++];
uMech[nlocal] = buf[m++];
uChem[nlocal] = buf[m++];
+ uCG[nlocal] = 0.0;
+ uCGnew[nlocal] = 0.0;
double **extra = atom->extra;
if (atom->nextra_store) {
diff --git a/src/USER-DPD/compute_dpd_atom.cpp b/src/USER-DPD/compute_dpd_atom.cpp
index c8231ddabc231cb806c7af2289168a8486826a1a..78f842a68f2f2b351c672ba68bf4dbd6f4628057 100644
--- a/src/USER-DPD/compute_dpd_atom.cpp
+++ b/src/USER-DPD/compute_dpd_atom.cpp
@@ -15,9 +15,9 @@
Contributing author: James Larentzos (U.S. Army Research Laboratory)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <string.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstring>
+#include <cstdlib>
#include "compute_dpd_atom.h"
#include "atom.h"
#include "update.h"
diff --git a/src/USER-DPD/fix_dpd_energy.cpp b/src/USER-DPD/fix_dpd_energy.cpp
index 475e12f02fb10a30acf23e5ed27ed4605b5995fc..d89ea7759a8fbae547aeb4d724b3b8c82ca73472 100644
--- a/src/USER-DPD/fix_dpd_energy.cpp
+++ b/src/USER-DPD/fix_dpd_energy.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <stdio.h>
-#include <string.h>
+#include <cstdio>
+#include <cstring>
#include "fix_dpd_energy.h"
#include "atom.h"
#include "force.h"
diff --git a/src/USER-DPD/fix_eos_cv.cpp b/src/USER-DPD/fix_eos_cv.cpp
index 7a2d278fe4766d73e20163704d3ffbcd23632fad..919e6829f30fd91d5a8d2580ac64c0b276f44ea0 100644
--- a/src/USER-DPD/fix_eos_cv.cpp
+++ b/src/USER-DPD/fix_eos_cv.cpp
@@ -15,8 +15,8 @@
Contributing author: James Larentzos (U.S. Army Research Laboratory)
------------------------------------------------------------------------- */
-#include <stdlib.h>
-#include <string.h>
+#include <cstdlib>
+#include <cstring>
#include "fix_eos_cv.h"
#include "atom.h"
#include "error.h"
diff --git a/src/USER-DPD/fix_eos_table.cpp b/src/USER-DPD/fix_eos_table.cpp
index c17a9721084d11968b5ae7ae9771fb1789c9fc97..e57a3788bf733f8f57ec12a54ea5b501eb0c0e4f 100644
--- a/src/USER-DPD/fix_eos_table.cpp
+++ b/src/USER-DPD/fix_eos_table.cpp
@@ -15,8 +15,8 @@
Contributing author: James Larentzos (U.S. Army Research Laboratory)
------------------------------------------------------------------------- */
-#include <stdlib.h>
-#include <string.h>
+#include <cstdlib>
+#include <cstring>
#include "fix_eos_table.h"
#include "atom.h"
#include "error.h"
diff --git a/src/USER-DPD/fix_eos_table_rx.cpp b/src/USER-DPD/fix_eos_table_rx.cpp
index c9a705446a0f6b54d2870590366a350b1a70ed04..73144c0a0f9423196b106ba67ebd917f56bf8c77 100644
--- a/src/USER-DPD/fix_eos_table_rx.cpp
+++ b/src/USER-DPD/fix_eos_table_rx.cpp
@@ -15,15 +15,15 @@
Contributing author: James Larentzos (U.S. Army Research Laboratory)
------------------------------------------------------------------------- */
-#include <stdlib.h>
-#include <string.h>
+#include <cstdlib>
+#include <cstring>
+#include <cmath>
#include "fix_eos_table_rx.h"
#include "atom.h"
#include "error.h"
#include "force.h"
#include "memory.h"
#include "comm.h"
-#include <math.h>
#include "modify.h"
#define MAXLINE 1024
@@ -774,7 +774,7 @@ void FixEOStableRX::temperature_lookup(int id, double ui, double &thetai)
// Apply the Secant Method
for(it=0; it<maxit; it++){
if(fabs(f2-f1) < MY_EPSILON){
- if(isnan(f1) || isnan(f2)) error->one(FLERR,"NaN detected in secant solver.");
+ if(std::isnan(f1) || std::isnan(f2)) error->one(FLERR,"NaN detected in secant solver.");
temp = t1;
temp = MAX(temp,tb->lo);
temp = MIN(temp,tb->hi);
@@ -794,7 +794,7 @@ void FixEOStableRX::temperature_lookup(int id, double ui, double &thetai)
if(it==maxit){
char str[256];
sprintf(str,"Maxit exceeded in secant solver: id=%d ui=%lf thetai=%lf t1=%lf t2=%lf f1=%lf f2=%lf\n",id,ui,thetai,t1,t2,f1,f2);
- if(isnan(f1) || isnan(f2) || isnan(ui) || isnan(thetai) || isnan(t1) || isnan(t2))
+ if(std::isnan(f1) || std::isnan(f2) || std::isnan(ui) || std::isnan(thetai) || std::isnan(t1) || std::isnan(t2))
error->one(FLERR,"NaN detected in secant solver.");
error->one(FLERR,str);
}
diff --git a/src/USER-DPD/fix_rx.cpp b/src/USER-DPD/fix_rx.cpp
index 0d0ec2a75b0ebba55b74162ac39fbcc71a517356..be78989bb5a81de1f686b10afd59d9989a9375dd 100644
--- a/src/USER-DPD/fix_rx.cpp
+++ b/src/USER-DPD/fix_rx.cpp
@@ -11,10 +11,11 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-#include <math.h>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
+#include <cmath>
+#include <cfloat> // DBL_EPSILON
#include "fix_rx.h"
#include "atom.h"
#include "error.h"
@@ -31,10 +32,8 @@
#include "math_special.h"
#include "pair_dpd_fdt_energy.h"
-#include <float.h> // DBL_EPSILON
#include <vector> // std::vector<>
#include <algorithm> // std::max
-#include <cmath> // std::fmod
using namespace LAMMPS_NS;
using namespace FixConst;
@@ -261,6 +260,7 @@ void FixRX::post_constructor()
error->all(FLERR,"fix rx cannot be combined with fix property/atom");
char **tmpspecies = new char*[maxspecies];
+ int tmpmaxstrlen = 0;
for(int jj=0; jj < maxspecies; jj++)
tmpspecies[jj] = NULL;
@@ -321,6 +321,7 @@ void FixRX::post_constructor()
error->all(FLERR,"Exceeded the maximum number of species permitted in fix rx.");
tmpspecies[nUniqueSpecies] = new char[strlen(word)+1];
strcpy(tmpspecies[nUniqueSpecies],word);
+ tmpmaxstrlen = MAX(tmpmaxstrlen,strlen(word));
nUniqueSpecies++;
}
word = strtok(NULL, " \t\n\r\f");
@@ -355,19 +356,21 @@ void FixRX::post_constructor()
newarg2[0] = id_fix_species_old;
newarg2[1] = group->names[igroup];
newarg2[2] = (char *) "property/atom";
+ char *str1 = new char[tmpmaxstrlen+3];
+ char *str2 = new char[tmpmaxstrlen+6];
for(int ii=0; ii<nspecies; ii++){
- char str1[2+strlen(tmpspecies[ii])+1];
- char str2[2+strlen(tmpspecies[ii])+4];
strcpy(str1,"d_");
strcpy(str2,"d_");
- strncat(str1,tmpspecies[ii],strlen(tmpspecies[ii]));
- strncat(str2,tmpspecies[ii],strlen(tmpspecies[ii]));
- strncat(str2,"Old",3);
+ strcat(str1,tmpspecies[ii]);
+ strcat(str2,tmpspecies[ii]);
+ strcat(str2,"Old");
newarg[ii+3] = new char[strlen(str1)+1];
newarg2[ii+3] = new char[strlen(str2)+1];
strcpy(newarg[ii+3],str1);
strcpy(newarg2[ii+3],str2);
}
+ delete[] str1;
+ delete[] str2;
newarg[nspecies+3] = (char *) "ghost";
newarg[nspecies+4] = (char *) "yes";
newarg2[nspecies+3] = (char *) "ghost";
diff --git a/src/USER-DPD/fix_shardlow.cpp b/src/USER-DPD/fix_shardlow.cpp
index cee67cfcf96ee84ec5752de69d09b3651157879d..06185dee7ec702d2dfb3a4686fa88c2c7e3b16f8 100644
--- a/src/USER-DPD/fix_shardlow.cpp
+++ b/src/USER-DPD/fix_shardlow.cpp
@@ -33,16 +33,16 @@
135, 204105.
------------------------------------------------------------------------- */
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
+#include <cmath>
#include "fix_shardlow.h"
#include "atom.h"
#include "force.h"
#include "update.h"
#include "respa.h"
#include "error.h"
-#include <math.h>
#include "atom_vec.h"
#include "comm.h"
#include "neighbor.h"
diff --git a/src/USER-DPD/fix_shardlow.h b/src/USER-DPD/fix_shardlow.h
index 21f7569a233de12032311d80b0144ef7fa8acf1e..67e4b8f32e8383ada4448c87434edaf5ea3a0b7a 100644
--- a/src/USER-DPD/fix_shardlow.h
+++ b/src/USER-DPD/fix_shardlow.h
@@ -22,7 +22,6 @@ FixStyle(shardlow,FixShardlow)
#include "fix.h"
#include "random_external_state.h"
-#include <math.h>
namespace LAMMPS_NS {
diff --git a/src/USER-DPD/nbin_ssa.h b/src/USER-DPD/nbin_ssa.h
index 12a572b94caab73125eb01887b89849189c11826..c738391d67f3cc0980b80dd8e275e1cb24c2ace4 100644
--- a/src/USER-DPD/nbin_ssa.h
+++ b/src/USER-DPD/nbin_ssa.h
@@ -22,8 +22,8 @@ NBinStyle(ssa,
#ifndef LMP_NBIN_SSA_H
#define LMP_NBIN_SSA_H
+#include <cmath>
#include "nbin_standard.h"
-#include "math.h"
#include "error.h"
namespace LAMMPS_NS {
@@ -54,7 +54,7 @@ class NBinSSA : public NBinStandard {
{
int ix,iy,iz;
- if (!ISFINITE(x) || !ISFINITE(y) || !ISFINITE(z))
+ if (!std::isfinite(x) || !std::isfinite(y) || !std::isfinite(z))
error->one(FLERR,"Non-numeric positions - simulation unstable");
if (x >= bboxhi_[0])
diff --git a/src/USER-DPD/pair_dpd_fdt.cpp b/src/USER-DPD/pair_dpd_fdt.cpp
index 95908c556d12156e3e8e0d14e8f672be66655890..aeade16e7cb0525a5e1ce75dba723832646b7ad4 100644
--- a/src/USER-DPD/pair_dpd_fdt.cpp
+++ b/src/USER-DPD/pair_dpd_fdt.cpp
@@ -15,10 +15,10 @@
Contributing author: James Larentzos (U.S. Army Research Laboratory)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "atom.h"
#include "atom_vec.h"
#include "comm.h"
diff --git a/src/USER-DPD/pair_dpd_fdt_energy.cpp b/src/USER-DPD/pair_dpd_fdt_energy.cpp
index 32ac456b0fffede0ea5b4551877f6d1e001bb511..d1f3cceed4ca14db73014d7e252770b007d8db95 100644
--- a/src/USER-DPD/pair_dpd_fdt_energy.cpp
+++ b/src/USER-DPD/pair_dpd_fdt_energy.cpp
@@ -15,10 +15,10 @@
Contributing author: James Larentzos (U.S. Army Research Laboratory)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "atom.h"
#include "atom_vec.h"
#include "comm.h"
diff --git a/src/USER-DPD/pair_exp6_rx.cpp b/src/USER-DPD/pair_exp6_rx.cpp
index 8b6fc9beed8e65836bb26350d1ecf8c48c02ed1d..057c8fa1190e00e61b718edc0f4d66f865cb43f0 100644
--- a/src/USER-DPD/pair_exp6_rx.cpp
+++ b/src/USER-DPD/pair_exp6_rx.cpp
@@ -11,10 +11,11 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
+#include <cfloat>
#include "pair_exp6_rx.h"
#include "atom.h"
#include "comm.h"
@@ -26,7 +27,6 @@
#include "error.h"
#include "modify.h"
#include "fix.h"
-#include <float.h>
using namespace LAMMPS_NS;
using namespace MathConst;
diff --git a/src/USER-DPD/pair_multi_lucy.cpp b/src/USER-DPD/pair_multi_lucy.cpp
index 6f4104e93d0d45705891ccbc09667e7fbc8c40c7..3d204a849e3bfe1d70497f0c2c2340f48b3dab47 100644
--- a/src/USER-DPD/pair_multi_lucy.cpp
+++ b/src/USER-DPD/pair_multi_lucy.cpp
@@ -22,10 +22,10 @@
------------------------------------------------------------------------------------------- */
#include <mpi.h>
-#include <math.h>
+#include <cmath>
#include "math_const.h"
-#include <stdlib.h>
-#include <string.h>
+#include <cstdlib>
+#include <cstring>
#include "pair_multi_lucy.h"
#include "atom.h"
#include "force.h"
diff --git a/src/USER-DPD/pair_multi_lucy_rx.cpp b/src/USER-DPD/pair_multi_lucy_rx.cpp
index 4628edbc127c41187ea750a5545b55f192c9592f..0070ca82d9c5eed5f07fa16defbf4b0da7944829 100644
--- a/src/USER-DPD/pair_multi_lucy_rx.cpp
+++ b/src/USER-DPD/pair_multi_lucy_rx.cpp
@@ -22,10 +22,10 @@
------------------------------------------------------------------------------------------- */
#include <mpi.h>
-#include <math.h>
+#include <cmath>
#include "math_const.h"
-#include <stdlib.h>
-#include <string.h>
+#include <cstdlib>
+#include <cstring>
#include "pair_multi_lucy_rx.h"
#include "atom.h"
#include "force.h"
diff --git a/src/USER-DPD/pair_table_rx.cpp b/src/USER-DPD/pair_table_rx.cpp
index 89d09e73227bd3ed0c6d9f3e86714237fc98ae3d..221944edc5170612b0ae7a246f3dd7bc61e6a26d 100644
--- a/src/USER-DPD/pair_table_rx.cpp
+++ b/src/USER-DPD/pair_table_rx.cpp
@@ -16,9 +16,9 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "pair_table_rx.h"
#include "atom.h"
#include "force.h"
diff --git a/src/USER-DPD/random_external_state.h b/src/USER-DPD/random_external_state.h
index 47288d77fd86ed4a13f8f3ff717903b6adecde29..de017ee8bdbe0e3ddb7e8ec714920ace97f2c49f 100644
--- a/src/USER-DPD/random_external_state.h
+++ b/src/USER-DPD/random_external_state.h
@@ -63,7 +63,7 @@
#ifndef LMP_RANDOM_EXTERNALSTATE_H
#define LMP_RANDOM_EXTERNALSTATE_H
-#include <math.h>
+#include <cmath>
#include "accelerator_kokkos.h"
diff --git a/src/USER-DRUDE/compute_temp_drude.cpp b/src/USER-DRUDE/compute_temp_drude.cpp
index 44b727f6b7b95660abc4cba3a0812edffe5ccecc..27b525c07d4393fc9cb4709b3a1c67f8d6351c97 100644
--- a/src/USER-DRUDE/compute_temp_drude.cpp
+++ b/src/USER-DRUDE/compute_temp_drude.cpp
@@ -12,8 +12,8 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cstdlib>
+#include <cstring>
#include "compute_temp_drude.h"
#include "atom.h"
#include "update.h"
diff --git a/src/USER-DRUDE/fix_drude.cpp b/src/USER-DRUDE/fix_drude.cpp
index a38f9f1e669716981174f6035089ff93eef571a5..19fd775715822d040edf8b3bf4621902fbafb71d 100644
--- a/src/USER-DRUDE/fix_drude.cpp
+++ b/src/USER-DRUDE/fix_drude.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
-#include <stdlib.h>
+#include <cstring>
+#include <cstdlib>
#include "fix_drude.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-DRUDE/fix_drude_transform.cpp b/src/USER-DRUDE/fix_drude_transform.cpp
index adbfd324df302a244189c7ea38495824d38ba4fc..34742a0683311a8e1286b4e122897434d845209b 100644
--- a/src/USER-DRUDE/fix_drude_transform.cpp
+++ b/src/USER-DRUDE/fix_drude_transform.cpp
@@ -12,7 +12,8 @@
------------------------------------------------------------------------- */
/** Fix Drude Transform ******************************************************/
-#include <math.h>
+#include <cmath>
+#include <cstring>
#include "fix_drude_transform.h"
#include "atom.h"
#include "domain.h"
@@ -21,8 +22,6 @@
#include "modify.h"
#include "force.h"
-#include <string.h>
-
using namespace LAMMPS_NS;
using namespace FixConst;
@@ -76,7 +75,7 @@ void FixDrudeTransform<inverse>::setup(int) {
if (!rmass) {
if (!mcoeff) mcoeff = new double[ntypes+1];
- double mcoeff_loc[ntypes+1];
+ double *mcoeff_loc = new double[ntypes+1];
for (int itype=0; itype<=ntypes; itype++) mcoeff_loc[itype] = 2.; // an impossible value: mcoeff is at most 1.
for (int i=0; i<nlocal; i++) {
if (drudetype[type[i]] == DRUDE_TYPE) {
@@ -96,6 +95,7 @@ void FixDrudeTransform<inverse>::setup(int) {
// mcoeff is 2 for non polarizable
// 0 < mcoeff < 1 for drude
// mcoeff < 0 for core
+ delete[] mcoeff_loc;
}
}
@@ -314,6 +314,6 @@ void FixDrudeTransform<inverse>::unpack_forward_comm(int n, int first, double *b
}
/* ---------------------------------------------------------------------- */
-template class FixDrudeTransform<false>;
-template class FixDrudeTransform<true>;
+template class LAMMPS_NS::FixDrudeTransform<false>;
+template class LAMMPS_NS::FixDrudeTransform<true>;
diff --git a/src/USER-DRUDE/fix_langevin_drude.cpp b/src/USER-DRUDE/fix_langevin_drude.cpp
index d04adb022327de0e3822f47b246e37c73d870513..235c5d224ba8e1914e201b95055cf072d3c9b64b 100644
--- a/src/USER-DRUDE/fix_langevin_drude.cpp
+++ b/src/USER-DRUDE/fix_langevin_drude.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
-#include <stdlib.h>
-#include <math.h>
+#include <cstring>
+#include <cstdlib>
+#include <cmath>
#include "fix_langevin_drude.h"
#include "atom.h"
#include "force.h"
diff --git a/src/USER-DRUDE/pair_lj_cut_thole_long.cpp b/src/USER-DRUDE/pair_lj_cut_thole_long.cpp
index f78ced3d8bd96caaa35798db21f1bce5f19a05e2..ce5d3a92a9002af04c1e3cbae013bc0c605424a9 100644
--- a/src/USER-DRUDE/pair_lj_cut_thole_long.cpp
+++ b/src/USER-DRUDE/pair_lj_cut_thole_long.cpp
@@ -15,10 +15,10 @@
Contributing author: Paul Crozier (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_lj_cut_thole_long.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-DRUDE/pair_thole.cpp b/src/USER-DRUDE/pair_thole.cpp
index ace119ce523892b0ad7a8d52c0288f0bc0f725b4..8c20ee8c4208e7cd59377d184b99662444bf35bd 100644
--- a/src/USER-DRUDE/pair_thole.cpp
+++ b/src/USER-DRUDE/pair_thole.cpp
@@ -11,10 +11,10 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_thole.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-EFF/atom_vec_electron.cpp b/src/USER-EFF/atom_vec_electron.cpp
index 56d61fd74f99ffb6c237ecfc2c0487bcd0d37569..1bc5387c9e20800a6c35809ed29a2587da6b2ed8 100644
--- a/src/USER-EFF/atom_vec_electron.cpp
+++ b/src/USER-EFF/atom_vec_electron.cpp
@@ -15,9 +15,9 @@
Contributing author: Andres Jaramillo-Botero (Caltech)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "atom_vec_electron.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-EFF/compute_ke_atom_eff.cpp b/src/USER-EFF/compute_ke_atom_eff.cpp
index 8d03e97b0af4d653d3d1d4809009d60b868c664a..b1b87cd3df18d10d9dd1e366d1ed8fc849fd7909 100644
--- a/src/USER-EFF/compute_ke_atom_eff.cpp
+++ b/src/USER-EFF/compute_ke_atom_eff.cpp
@@ -15,9 +15,9 @@
Contributing author: Andres Jaramillo-Botero
------------------------------------------------------------------------- */
-#include <math.h>
-#include <string.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstring>
+#include <cstdlib>
#include "compute_ke_atom_eff.h"
#include "atom.h"
#include "update.h"
diff --git a/src/USER-EFF/compute_ke_eff.cpp b/src/USER-EFF/compute_ke_eff.cpp
index 80c7192708fab9c6aebb39181cf4b27829ddd1e4..b4f571cb63718e8e425820961fb1ae62c4bea93c 100644
--- a/src/USER-EFF/compute_ke_eff.cpp
+++ b/src/USER-EFF/compute_ke_eff.cpp
@@ -16,8 +16,8 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <math.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdlib>
#include "compute_ke_eff.h"
#include "atom.h"
#include "update.h"
diff --git a/src/USER-EFF/compute_temp_deform_eff.cpp b/src/USER-EFF/compute_temp_deform_eff.cpp
index 40e8e529c0ea2baf1a0ada81edd5b0cbe06356bb..d3856e431d0d427e1f90c3435f99e63c37097c60 100644
--- a/src/USER-EFF/compute_temp_deform_eff.cpp
+++ b/src/USER-EFF/compute_temp_deform_eff.cpp
@@ -16,9 +16,9 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <math.h>
-#include <string.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstring>
+#include <cstdlib>
#include "compute_temp_deform_eff.h"
#include "domain.h"
#include "atom.h"
@@ -35,8 +35,6 @@
using namespace LAMMPS_NS;
-enum{NO_REMAP,X_REMAP,V_REMAP}; // same as fix_deform.cpp
-
/* ---------------------------------------------------------------------- */
ComputeTempDeformEff::ComputeTempDeformEff(LAMMPS *lmp, int narg, char **arg) :
@@ -76,7 +74,7 @@ void ComputeTempDeformEff::init()
int i;
for (i = 0; i < modify->nfix; i++)
if (strcmp(modify->fix[i]->style,"deform") == 0) {
- if (((FixDeform *) modify->fix[i])->remapflag == X_REMAP &&
+ if (((FixDeform *) modify->fix[i])->remapflag == Domain::X_REMAP &&
comm->me == 0)
error->warning(FLERR,"Using compute temp/deform/eff with inconsistent "
"fix deform remap option");
diff --git a/src/USER-EFF/compute_temp_eff.cpp b/src/USER-EFF/compute_temp_eff.cpp
index 251cdccaca7a83dc4cf2b866d075823d92b6892d..956461adf19489df4ad25c3c56812726c5a0a111 100644
--- a/src/USER-EFF/compute_temp_eff.cpp
+++ b/src/USER-EFF/compute_temp_eff.cpp
@@ -16,9 +16,9 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <math.h>
-#include <string.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstring>
+#include <cstdlib>
#include "compute_temp_eff.h"
#include "atom.h"
#include "update.h"
diff --git a/src/USER-EFF/compute_temp_region_eff.cpp b/src/USER-EFF/compute_temp_region_eff.cpp
index c0cd56f3a8d65c5b55d30108446cb3c58566e702..4548914ce13f5a349c0a6b00db726e5160c6cef3 100644
--- a/src/USER-EFF/compute_temp_region_eff.cpp
+++ b/src/USER-EFF/compute_temp_region_eff.cpp
@@ -16,9 +16,9 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <math.h>
-#include <string.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstring>
+#include <cstdlib>
#include "compute_temp_region_eff.h"
#include "atom.h"
#include "update.h"
diff --git a/src/USER-EFF/fix_langevin_eff.cpp b/src/USER-EFF/fix_langevin_eff.cpp
index 9584623fc3970e055ae9113d76b12e62cfccb1b9..2d0eef8e8573293af0ae480abb86898273d92a4a 100644
--- a/src/USER-EFF/fix_langevin_eff.cpp
+++ b/src/USER-EFF/fix_langevin_eff.cpp
@@ -16,9 +16,9 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <math.h>
-#include <string.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstring>
+#include <cstdlib>
#include "fix_langevin_eff.h"
#include "math_extra.h"
#include "atom.h"
diff --git a/src/USER-EFF/fix_nh_eff.cpp b/src/USER-EFF/fix_nh_eff.cpp
index 464498969ebf6ff0a23ba335e9f0842e1dc4f364..3e0a59612c2d0ccf4af8e64dd98f76e4dbfaa82c 100644
--- a/src/USER-EFF/fix_nh_eff.cpp
+++ b/src/USER-EFF/fix_nh_eff.cpp
@@ -15,8 +15,8 @@
Contributing author: Andres Jaramillo-Botero (Caltech)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdlib>
#include "fix_nh_eff.h"
#include "atom.h"
#include "atom_vec.h"
diff --git a/src/USER-EFF/fix_nph_eff.cpp b/src/USER-EFF/fix_nph_eff.cpp
index 0fe8c8e6dbd12116cbf5972e53c325de23aa00f9..28ebc620f9fe7aaf2c7425172385ae3c621fb97a 100644
--- a/src/USER-EFF/fix_nph_eff.cpp
+++ b/src/USER-EFF/fix_nph_eff.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "fix_nph_eff.h"
#include "modify.h"
#include "error.h"
diff --git a/src/USER-EFF/fix_npt_eff.cpp b/src/USER-EFF/fix_npt_eff.cpp
index 02f09839b182a7b7891d3f53f8e20619883c1b88..6aac7f373462daa1d290ed22b2b70a6dc6f944ee 100644
--- a/src/USER-EFF/fix_npt_eff.cpp
+++ b/src/USER-EFF/fix_npt_eff.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "fix_npt_eff.h"
#include "modify.h"
#include "error.h"
diff --git a/src/USER-EFF/fix_nve_eff.cpp b/src/USER-EFF/fix_nve_eff.cpp
index 09cd81a722165dfb9e9c7bacf39576f8707563bb..584714a44e7413e0eed09fedb95994a853b37811 100644
--- a/src/USER-EFF/fix_nve_eff.cpp
+++ b/src/USER-EFF/fix_nve_eff.cpp
@@ -15,17 +15,16 @@
Contributing author: Andres Jaramillo-Botero (Caltech)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <string.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdio>
+#include <cstring>
+#include <cstdlib>
#include "fix_nve_eff.h"
#include "atom.h"
#include "force.h"
#include "update.h"
#include "respa.h"
#include "error.h"
-#include <math.h>
#include "domain.h"
using namespace LAMMPS_NS;
diff --git a/src/USER-EFF/fix_nvt_eff.cpp b/src/USER-EFF/fix_nvt_eff.cpp
index ab82f9e0f8296f4008c44087f6ce0e5ad1a0b97b..9e23ee023be8702180190bae0bdf3d9e9f0e5ac2 100644
--- a/src/USER-EFF/fix_nvt_eff.cpp
+++ b/src/USER-EFF/fix_nvt_eff.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
-#include <math.h>
+#include <cstring>
+#include <cmath>
#include "fix_nvt_eff.h"
#include "group.h"
#include "modify.h"
diff --git a/src/USER-EFF/fix_nvt_sllod_eff.cpp b/src/USER-EFF/fix_nvt_sllod_eff.cpp
index 1b4ec1f3fbb25ecf565d19e4eed2ddbee72a1ab4..13cb34048c105d0e5a7f5b753bafbdcdab044eba 100644
--- a/src/USER-EFF/fix_nvt_sllod_eff.cpp
+++ b/src/USER-EFF/fix_nvt_sllod_eff.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdlib>
#include "fix_nvt_sllod_eff.h"
#include "math_extra.h"
#include "atom.h"
@@ -27,8 +27,6 @@
using namespace LAMMPS_NS;
using namespace FixConst;
-enum{NO_REMAP,X_REMAP,V_REMAP}; // same as fix_deform.cpp
-
/* ---------------------------------------------------------------------- */
FixNVTSllodEff::FixNVTSllodEff(LAMMPS *lmp, int narg, char **arg) :
@@ -78,7 +76,7 @@ void FixNVTSllodEff::init()
int i;
for (i = 0; i < modify->nfix; i++)
if (strcmp(modify->fix[i]->style,"deform") == 0) {
- if (((FixDeform *) modify->fix[i])->remapflag != V_REMAP)
+ if (((FixDeform *) modify->fix[i])->remapflag != Domain::V_REMAP)
error->all(FLERR,"Using fix nvt/sllod/eff with inconsistent fix deform "
"remap option");
break;
diff --git a/src/USER-EFF/fix_temp_rescale_eff.cpp b/src/USER-EFF/fix_temp_rescale_eff.cpp
index 774cd1f2e303782236613686a10d5eca3146a2bc..37f45b3c28ad45142262121a957787b5e8e43a8c 100644
--- a/src/USER-EFF/fix_temp_rescale_eff.cpp
+++ b/src/USER-EFF/fix_temp_rescale_eff.cpp
@@ -15,9 +15,9 @@
Contributing author: Andres Jaramillo-Botero
------------------------------------------------------------------------- */
-#include <string.h>
-#include <stdlib.h>
-#include <math.h>
+#include <cstring>
+#include <cstdlib>
+#include <cmath>
#include "fix_temp_rescale_eff.h"
#include "atom.h"
#include "force.h"
diff --git a/src/USER-EFF/pair_eff_cut.cpp b/src/USER-EFF/pair_eff_cut.cpp
index 850c52362967721bf00248aa0474d4a7d67efd18..0379c0264b5570f18ab1f8d401078c1abe700de9 100644
--- a/src/USER-EFF/pair_eff_cut.cpp
+++ b/src/USER-EFF/pair_eff_cut.cpp
@@ -15,10 +15,10 @@
Contributing author: Andres Jaramillo-Botero
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_eff_cut.h"
#include "pair_eff_inline.h"
#include "atom.h"
diff --git a/src/USER-FEP/Install.sh b/src/USER-FEP/Install.sh
old mode 100644
new mode 100755
diff --git a/src/USER-FEP/compute_fep.cpp b/src/USER-FEP/compute_fep.cpp
index bfa3bf7e2c91648cb08b74cca10e394da9a4a9e9..0e5f164f88d861b9614cd9e0bad8b93a3c4890e6 100644
--- a/src/USER-FEP/compute_fep.cpp
+++ b/src/USER-FEP/compute_fep.cpp
@@ -15,9 +15,9 @@
Contributing author: Agilio Padua (Univ Blaise Pascal & CNRS)
------------------------------------------------------------------------- */
-#include <stdlib.h>
-#include <string.h>
-#include <math.h>
+#include <cstdlib>
+#include <cstring>
+#include <cmath>
#include <mpi.h>
#include "comm.h"
#include "update.h"
diff --git a/src/USER-FEP/fix_adapt_fep.cpp b/src/USER-FEP/fix_adapt_fep.cpp
index 1b7fc559420f2ee6bd932d872c50524cebe208d9..3b8c9d4201f592343dff8d9e43c6a6b7ae9f1407 100644
--- a/src/USER-FEP/fix_adapt_fep.cpp
+++ b/src/USER-FEP/fix_adapt_fep.cpp
@@ -15,9 +15,9 @@
Charges by type and after option: Agilio Padua (Univ Blaise Pascal & CNRS)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <string.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstring>
+#include <cstdlib>
#include "fix_adapt_fep.h"
#include "atom.h"
#include "update.h"
diff --git a/src/USER-FEP/pair_coul_cut_soft.cpp b/src/USER-FEP/pair_coul_cut_soft.cpp
index a7ac8004fe631c576d9e5cc3b58106dd6d997356..5bcb5a752256a07ac83d4d74c2d044681b891b40 100644
--- a/src/USER-FEP/pair_coul_cut_soft.cpp
+++ b/src/USER-FEP/pair_coul_cut_soft.cpp
@@ -15,10 +15,10 @@
Soft-core version: Agilio Padua (Univ Blaise Pascal & CNRS)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_coul_cut_soft.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-FEP/pair_coul_long_soft.cpp b/src/USER-FEP/pair_coul_long_soft.cpp
index 3d24a997ddf0162af51b1a89a93dc0e525d4cf30..94bb3659fa3beea5a4025ace13b876ad6405375b 100644
--- a/src/USER-FEP/pair_coul_long_soft.cpp
+++ b/src/USER-FEP/pair_coul_long_soft.cpp
@@ -16,10 +16,10 @@
Soft-core version: Agilio Padua (Univ Blaise Pascal & CNRS)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_coul_long_soft.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-FEP/pair_lj_charmm_coul_long_soft.cpp b/src/USER-FEP/pair_lj_charmm_coul_long_soft.cpp
index 06285a58d3c3009e8ddb94fa7eb8402dc1ff8c3c..34758b159b34bcbf546b76add6e8329f28caaff1 100644
--- a/src/USER-FEP/pair_lj_charmm_coul_long_soft.cpp
+++ b/src/USER-FEP/pair_lj_charmm_coul_long_soft.cpp
@@ -16,10 +16,10 @@
Soft-core version: Agilio Padua (Univ Blaise Pascal & CNRS)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_lj_charmm_coul_long_soft.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-FEP/pair_lj_cut_coul_cut_soft.cpp b/src/USER-FEP/pair_lj_cut_coul_cut_soft.cpp
index 9e52a16a025d103a1c2ca95c60aac239e7b8c471..fc887fbec5cf2b8729bd6dc5f1cb433ed632209f 100644
--- a/src/USER-FEP/pair_lj_cut_coul_cut_soft.cpp
+++ b/src/USER-FEP/pair_lj_cut_coul_cut_soft.cpp
@@ -15,10 +15,10 @@
Soft-core version: Agilio Padua (Univ Blaise Pascal & CNRS)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_lj_cut_coul_cut_soft.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-FEP/pair_lj_cut_coul_long_soft.cpp b/src/USER-FEP/pair_lj_cut_coul_long_soft.cpp
index 7be2ebabea1fc434f5db0e920adc9f26fa70a875..a9032ab4d723d7e595b585f5ae910367107f7078 100644
--- a/src/USER-FEP/pair_lj_cut_coul_long_soft.cpp
+++ b/src/USER-FEP/pair_lj_cut_coul_long_soft.cpp
@@ -16,10 +16,10 @@
Soft-core version: Agilio Padua (Univ Blaise Pascal & CNRS)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_lj_cut_coul_long_soft.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-FEP/pair_lj_cut_soft.cpp b/src/USER-FEP/pair_lj_cut_soft.cpp
index 9ae108fa338849a37704e58b66e039fff49d09ee..4aaa5c292531f7cc0aee51712576de220fe56909 100644
--- a/src/USER-FEP/pair_lj_cut_soft.cpp
+++ b/src/USER-FEP/pair_lj_cut_soft.cpp
@@ -16,10 +16,10 @@
Soft-core version: Agilio Padua (Univ Blaise Pascal & CNRS)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_lj_cut_soft.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-FEP/pair_lj_cut_tip4p_long_soft.cpp b/src/USER-FEP/pair_lj_cut_tip4p_long_soft.cpp
index 8d9162e564097a44c68960ee2d28eb7746b856fc..8653800ee67f5f210e7a44db4789c571089cca08 100644
--- a/src/USER-FEP/pair_lj_cut_tip4p_long_soft.cpp
+++ b/src/USER-FEP/pair_lj_cut_tip4p_long_soft.cpp
@@ -17,10 +17,10 @@
Soft-core version: Agilio Padua (Univ Blaise Pascal & CNRS)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_lj_cut_tip4p_long_soft.h"
#include "angle.h"
#include "atom.h"
diff --git a/src/USER-FEP/pair_morse_soft.cpp b/src/USER-FEP/pair_morse_soft.cpp
index 1333bc28ca947075eeb439458db0870f53c5809a..7a897e1870ed96a0aad08671b5d031e7764557d7 100644
--- a/src/USER-FEP/pair_morse_soft.cpp
+++ b/src/USER-FEP/pair_morse_soft.cpp
@@ -11,10 +11,10 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_morse_soft.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-FEP/pair_tip4p_long_soft.cpp b/src/USER-FEP/pair_tip4p_long_soft.cpp
index 7ad654d95c3988e562d44829f5231f730b7e8303..5e8c5000f88e894bfc5ffd60224f26605a038dc6 100644
--- a/src/USER-FEP/pair_tip4p_long_soft.cpp
+++ b/src/USER-FEP/pair_tip4p_long_soft.cpp
@@ -17,10 +17,10 @@
Soft-core version: Agilio Padua (Univ Blaise Pascal & CNRS)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_tip4p_long_soft.h"
#include "angle.h"
#include "atom.h"
diff --git a/src/USER-H5MD/Install.sh b/src/USER-H5MD/Install.sh
old mode 100644
new mode 100755
diff --git a/src/USER-H5MD/dump_h5md.cpp b/src/USER-H5MD/dump_h5md.cpp
index 4e85b5c8b69175e98b374f53fc228ced6ab88998..393871ae0b9a7325d435f9a4f7f03f1fb2489090 100644
--- a/src/USER-H5MD/dump_h5md.cpp
+++ b/src/USER-H5MD/dump_h5md.cpp
@@ -15,11 +15,11 @@
Contributing author: Pierre de Buyl (KU Leuven)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-#include <limits.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
+#include <climits>
#include "ch5md.h"
#include "dump_h5md.h"
#include "domain.h"
diff --git a/src/USER-INTEL/Install.sh b/src/USER-INTEL/Install.sh
old mode 100644
new mode 100755
index da553d158ac24ff88ec9f86fd4e5b88ad7750191..8c291f0ae28da6090db92191e1ca48df7cebb8fd
--- a/src/USER-INTEL/Install.sh
+++ b/src/USER-INTEL/Install.sh
@@ -38,6 +38,8 @@ for file in *_intel.h; do
action $file $dep
done
+# step 2: handle cases and tasks not handled in step 1.
+
action intel_preprocess.h
action intel_buffers.h
action intel_buffers.cpp
@@ -50,8 +52,6 @@ action intel_simd.h
action intel_intrinsics.h pair_tersoff_intel.cpp
action intel_intrinsics_airebo.h pair_airebo_intel.cpp
-# step 2: handle cases and tasks not handled in step 1.
-
if (test $mode = 1) then
if (test -e ../Makefile.package) then
diff --git a/src/USER-INTEL/angle_charmm_intel.cpp b/src/USER-INTEL/angle_charmm_intel.cpp
index bcaecb4696fa1d93e277d473e931b268298c5153..672b70b6f68785256c67b694b58b8d8e741dce87 100644
--- a/src/USER-INTEL/angle_charmm_intel.cpp
+++ b/src/USER-INTEL/angle_charmm_intel.cpp
@@ -15,8 +15,8 @@
Contributing author: W. Michael Brown (Intel)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdlib>
#include "angle_charmm_intel.h"
#include "atom.h"
#include "neighbor.h"
diff --git a/src/USER-INTEL/angle_charmm_intel.h b/src/USER-INTEL/angle_charmm_intel.h
index 342af31b8c122a937ab156e71c5ef12a7290bd11..5d173ee6a982e834587d5d7bc908854ec3a538d8 100644
--- a/src/USER-INTEL/angle_charmm_intel.h
+++ b/src/USER-INTEL/angle_charmm_intel.h
@@ -24,7 +24,7 @@ AngleStyle(charmm/intel,AngleCharmmIntel)
#ifndef LMP_ANGLE_CHARMM_INTEL_H
#define LMP_ANGLE_CHARMM_INTEL_H
-#include <stdio.h>
+#include <cstdio>
#include "angle_charmm.h"
#include "fix_intel.h"
diff --git a/src/USER-INTEL/angle_harmonic_intel.cpp b/src/USER-INTEL/angle_harmonic_intel.cpp
index ffc81c496d77c654f35d6f0e1ad71a39a06844ee..74639f3aebddd8c705f622c2165edcf033617ea0 100644
--- a/src/USER-INTEL/angle_harmonic_intel.cpp
+++ b/src/USER-INTEL/angle_harmonic_intel.cpp
@@ -15,8 +15,8 @@
Contributing author: W. Michael Brown (Intel)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdlib>
#include "angle_harmonic_intel.h"
#include "atom.h"
#include "neighbor.h"
diff --git a/src/USER-INTEL/angle_harmonic_intel.h b/src/USER-INTEL/angle_harmonic_intel.h
index 301fc7cc066aabbb484f0c55b5065acbb93fd9b8..e7768542a1f1fbcb90692cf7f8afbad7f31d4ded 100644
--- a/src/USER-INTEL/angle_harmonic_intel.h
+++ b/src/USER-INTEL/angle_harmonic_intel.h
@@ -24,7 +24,7 @@ AngleStyle(harmonic/intel,AngleHarmonicIntel)
#ifndef LMP_ANGLE_HARMONIC_INTEL_H
#define LMP_ANGLE_HARMONIC_INTEL_H
-#include <stdio.h>
+#include <cstdio>
#include "angle_harmonic.h"
#include "fix_intel.h"
diff --git a/src/USER-INTEL/bond_fene_intel.cpp b/src/USER-INTEL/bond_fene_intel.cpp
index 004a2e5413d6d566cb536b9d4290e80540315e81..2d70049a89b705918589f6402e987f6eb3edff34 100644
--- a/src/USER-INTEL/bond_fene_intel.cpp
+++ b/src/USER-INTEL/bond_fene_intel.cpp
@@ -15,8 +15,8 @@
Contributing author: Stan Moore (Sandia)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdlib>
#include "bond_fene_intel.h"
#include "atom.h"
#include "modify.h"
diff --git a/src/USER-INTEL/bond_fene_intel.h b/src/USER-INTEL/bond_fene_intel.h
index 89c3033096e43eba27065220e2b77769cc831591..afe3b85470d6d81b0639a57a3ce7ade9a1ff0467 100644
--- a/src/USER-INTEL/bond_fene_intel.h
+++ b/src/USER-INTEL/bond_fene_intel.h
@@ -24,7 +24,7 @@ BondStyle(fene/intel,BondFENEIntel)
#ifndef LMP_BOND_FENE_INTEL_H
#define LMP_BOND_FENE_INTEL_H
-#include <stdio.h>
+#include <cstdio>
#include "bond_fene.h"
#include "fix_intel.h"
diff --git a/src/USER-INTEL/bond_harmonic_intel.cpp b/src/USER-INTEL/bond_harmonic_intel.cpp
index 0c714edc0959519621b624d19dd6e79b5b081977..ed9cab082ed5553c9afd38ddf12f2aabf98861fe 100644
--- a/src/USER-INTEL/bond_harmonic_intel.cpp
+++ b/src/USER-INTEL/bond_harmonic_intel.cpp
@@ -15,8 +15,8 @@
Contributing author: W. Michael Brown (Intel)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdlib>
#include "bond_harmonic_intel.h"
#include "atom.h"
#include "modify.h"
diff --git a/src/USER-INTEL/bond_harmonic_intel.h b/src/USER-INTEL/bond_harmonic_intel.h
index 8fc04f432a2a5994b08e9807f42161d36b933e62..b86a560d6e167e592aaee3cdfdc97b13fe906879 100644
--- a/src/USER-INTEL/bond_harmonic_intel.h
+++ b/src/USER-INTEL/bond_harmonic_intel.h
@@ -24,7 +24,7 @@ BondStyle(harmonic/intel,BondHarmonicIntel)
#ifndef LMP_BOND_HARMONIC_INTEL_H
#define LMP_BOND_HARMONIC_INTEL_H
-#include <stdio.h>
+#include <cstdio>
#include "bond_harmonic.h"
#include "fix_intel.h"
diff --git a/src/USER-INTEL/dihedral_charmm_intel.cpp b/src/USER-INTEL/dihedral_charmm_intel.cpp
index c8429dc8ff7079930f00459c33ad85674ebaf222..c9237e7309ea7b5f51a34fe86bcc13559119b7c7 100644
--- a/src/USER-INTEL/dihedral_charmm_intel.cpp
+++ b/src/USER-INTEL/dihedral_charmm_intel.cpp
@@ -16,7 +16,7 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <math.h>
+#include <cmath>
#include "dihedral_charmm_intel.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-INTEL/dihedral_fourier_intel.cpp b/src/USER-INTEL/dihedral_fourier_intel.cpp
index c46617bbc253ac9ac2bf3290d5a047ff456c0b95..6ad25f1ce49228f5f719cc21277b01a9bcfd26d8 100644
--- a/src/USER-INTEL/dihedral_fourier_intel.cpp
+++ b/src/USER-INTEL/dihedral_fourier_intel.cpp
@@ -16,7 +16,7 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <math.h>
+#include <cmath>
#include "dihedral_fourier_intel.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-INTEL/dihedral_harmonic_intel.cpp b/src/USER-INTEL/dihedral_harmonic_intel.cpp
index b35ea4e03a9b67a3b619028c0c559b304cbbaf07..b2bf54102c4b8cfb05d8cfbe949d4cca4261ead9 100644
--- a/src/USER-INTEL/dihedral_harmonic_intel.cpp
+++ b/src/USER-INTEL/dihedral_harmonic_intel.cpp
@@ -16,7 +16,7 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <math.h>
+#include <cmath>
#include "dihedral_harmonic_intel.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-INTEL/dihedral_opls_intel.cpp b/src/USER-INTEL/dihedral_opls_intel.cpp
index 6b7b2c81ebd75bace530cbde5dd9bee1f0981c57..832ce7ed50e482c787bd4e14e22d225b7b3be721 100644
--- a/src/USER-INTEL/dihedral_opls_intel.cpp
+++ b/src/USER-INTEL/dihedral_opls_intel.cpp
@@ -16,7 +16,7 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <math.h>
+#include <cmath>
#include "dihedral_opls_intel.h"
#include "atom.h"
#include "comm.h"
@@ -185,13 +185,6 @@ void DihedralOPLSIntel::eval(const int vflag,
const flt_t vb3y = x[i4].y - x[i3].y;
const flt_t vb3z = x[i4].z - x[i3].z;
- // 1-4
-
- const flt_t delx = x[i1].x - x[i4].x;
- const flt_t dely = x[i1].y - x[i4].y;
- const flt_t delz = x[i1].z - x[i4].z;
-
-
// c0 calculation
// 1st and 2nd angle
diff --git a/src/USER-INTEL/fix_intel.cpp b/src/USER-INTEL/fix_intel.cpp
index d05e05957844d37e1b100d04415632ffbbd0e05e..7a206f472a92eed49e814e9029d69a936b196daa 100644
--- a/src/USER-INTEL/fix_intel.cpp
+++ b/src/USER-INTEL/fix_intel.cpp
@@ -29,10 +29,10 @@
#include "update.h"
#include "fix_intel.h"
-#include <string.h>
-#include <stdlib.h>
-#include <stdio.h>
-#include <math.h>
+#include <cstring>
+#include <cstdlib>
+#include <cstdio>
+#include <cmath>
#ifdef LAMMPS_BIGBIG
#error "The USER-INTEL package is not compatible with -DLAMMPS_BIGBIG"
@@ -55,8 +55,6 @@ using namespace FixConst;
#endif
#endif
-enum{NSQ,BIN,MULTI};
-
/* ---------------------------------------------------------------------- */
FixIntel::FixIntel(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
@@ -353,7 +351,7 @@ void FixIntel::init()
void FixIntel::setup(int vflag)
{
- if (neighbor->style != BIN)
+ if (neighbor->style != Neighbor::BIN)
error->all(FLERR,
"Currently, neighbor style BIN must be used with Intel package.");
if (neighbor->exclude_setting() != 0)
diff --git a/src/USER-INTEL/fix_nh_intel.cpp b/src/USER-INTEL/fix_nh_intel.cpp
index 6e44b38ef17439d6c7080ad30c497e8efca6cd56..44253e8bb0b9c3b5750c6e0a46e2f3c3cf25a7ab 100644
--- a/src/USER-INTEL/fix_nh_intel.cpp
+++ b/src/USER-INTEL/fix_nh_intel.cpp
@@ -28,8 +28,8 @@
#include "update.h"
#include <cstring>
-#include <math.h>
-#include <stdio.h>
+#include <cmath>
+#include <cstdio>
using namespace LAMMPS_NS;
using namespace FixConst;
diff --git a/src/USER-INTEL/fix_npt_intel.cpp b/src/USER-INTEL/fix_npt_intel.cpp
index 56df3bba4bb3e999e12d49696c4f8e5dd162c2ce..bc0d297078a57adc0bfdf64a6431d2e6d20a1ade 100644
--- a/src/USER-INTEL/fix_npt_intel.cpp
+++ b/src/USER-INTEL/fix_npt_intel.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "fix_npt_intel.h"
#include "modify.h"
#include "error.h"
diff --git a/src/USER-INTEL/fix_nve_asphere_intel.cpp b/src/USER-INTEL/fix_nve_asphere_intel.cpp
index 8ad63f7326dfac6df7fa5f4e1e2cb36bb2368ee6..17bbcff77140de04b60b4cfdf8f79867d11f87d8 100644
--- a/src/USER-INTEL/fix_nve_asphere_intel.cpp
+++ b/src/USER-INTEL/fix_nve_asphere_intel.cpp
@@ -15,9 +15,9 @@
Contributing author: W. Michael Brown (Intel)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstring>
#include "fix_nve_asphere_intel.h"
#include "math_extra_intel.h"
#include "atom.h"
diff --git a/src/USER-INTEL/fix_nvt_intel.cpp b/src/USER-INTEL/fix_nvt_intel.cpp
index 3fe712c9ab812cf55bfbfab57d07e78c545a0559..547039ff23a10342a35c381e8ae6ef285d0e8d04 100644
--- a/src/USER-INTEL/fix_nvt_intel.cpp
+++ b/src/USER-INTEL/fix_nvt_intel.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "fix_nvt_intel.h"
#include "group.h"
#include "modify.h"
diff --git a/src/USER-INTEL/fix_nvt_sllod_intel.cpp b/src/USER-INTEL/fix_nvt_sllod_intel.cpp
index bab748ad748c72fdabbe11bf922731e595d5c95e..ad7e1384f06bd14d90dc241beb6ed1d25f465f49 100644
--- a/src/USER-INTEL/fix_nvt_sllod_intel.cpp
+++ b/src/USER-INTEL/fix_nvt_sllod_intel.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <string.h>
+#include <cmath>
+#include <cstring>
#include "fix_nvt_sllod_intel.h"
#include "math_extra.h"
#include "atom.h"
@@ -27,8 +27,6 @@
using namespace LAMMPS_NS;
using namespace FixConst;
-enum{NO_REMAP,X_REMAP,V_REMAP}; // same as fix_deform.cpp
-
/* ---------------------------------------------------------------------- */
FixNVTSllodIntel::FixNVTSllodIntel(LAMMPS *lmp, int narg, char **arg) :
@@ -79,7 +77,7 @@ void FixNVTSllodIntel::init()
int i;
for (i = 0; i < modify->nfix; i++)
if (strcmp(modify->fix[i]->style,"deform") == 0) {
- if (((FixDeform *) modify->fix[i])->remapflag != V_REMAP)
+ if (((FixDeform *) modify->fix[i])->remapflag != Domain::V_REMAP)
error->all(FLERR,"Using fix nvt/sllod with inconsistent fix deform "
"remap option");
break;
diff --git a/src/USER-INTEL/improper_cvff_intel.cpp b/src/USER-INTEL/improper_cvff_intel.cpp
index 39090e5a7420b3fd32598cbab2aca8a802e497b1..e0ef2162d1e72ce865cf080e5de9192c51247d6c 100644
--- a/src/USER-INTEL/improper_cvff_intel.cpp
+++ b/src/USER-INTEL/improper_cvff_intel.cpp
@@ -16,8 +16,8 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <math.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdlib>
#include "improper_cvff_intel.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-INTEL/improper_cvff_intel.h b/src/USER-INTEL/improper_cvff_intel.h
index cb5da25f992d26f95f365918f1a5691c0e3f0fe0..e815fa75c904e678f375af053c82ed2ea5a2a2b4 100644
--- a/src/USER-INTEL/improper_cvff_intel.h
+++ b/src/USER-INTEL/improper_cvff_intel.h
@@ -24,7 +24,7 @@ ImproperStyle(cvff/intel,ImproperCvffIntel)
#ifndef LMP_IMPROPER_CVFF_INTEL_H
#define LMP_IMPROPER_CVFF_INTEL_H
-#include <stdio.h>
+#include <cstdio>
#include "improper_cvff.h"
#include "fix_intel.h"
diff --git a/src/USER-INTEL/improper_harmonic_intel.cpp b/src/USER-INTEL/improper_harmonic_intel.cpp
index 3547061672cff079b53761f928761e746d637d8a..60cbe163586da454d9dd7d70710ad6551f0c89ff 100644
--- a/src/USER-INTEL/improper_harmonic_intel.cpp
+++ b/src/USER-INTEL/improper_harmonic_intel.cpp
@@ -16,8 +16,8 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <math.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdlib>
#include "improper_harmonic_intel.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-INTEL/improper_harmonic_intel.h b/src/USER-INTEL/improper_harmonic_intel.h
index 0b759b4e43e894d30d5a9ec5390b4259302a69a4..ce38e8fc317ed5dc996de47387baec910c40f71c 100644
--- a/src/USER-INTEL/improper_harmonic_intel.h
+++ b/src/USER-INTEL/improper_harmonic_intel.h
@@ -24,7 +24,7 @@ ImproperStyle(harmonic/intel,ImproperHarmonicIntel)
#ifndef LMP_IMPROPER_HARMONIC_INTEL_H
#define LMP_IMPROPER_HARMONIC_INTEL_H
-#include <stdio.h>
+#include <cstdio>
#include "improper_harmonic.h"
#include "fix_intel.h"
diff --git a/src/USER-INTEL/intel_buffers.cpp b/src/USER-INTEL/intel_buffers.cpp
index 8948abe1725ebe2547301591748523f021d81c5f..0f32cb48b201ca71c7181d512f241c0634db89ad 100644
--- a/src/USER-INTEL/intel_buffers.cpp
+++ b/src/USER-INTEL/intel_buffers.cpp
@@ -12,7 +12,7 @@
Contributing author: W. Michael Brown (Intel)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "intel_buffers.h"
#include "force.h"
#include "memory.h"
@@ -642,6 +642,6 @@ double IntelBuffers<flt_t, acc_t>::memory_usage(const int nthreads)
/* ---------------------------------------------------------------------- */
-template class IntelBuffers<float,float>;
-template class IntelBuffers<float,double>;
-template class IntelBuffers<double,double>;
+template class LAMMPS_NS::IntelBuffers<float,float>;
+template class LAMMPS_NS::IntelBuffers<float,double>;
+template class LAMMPS_NS::IntelBuffers<double,double>;
diff --git a/src/USER-INTEL/intel_intrinsics_airebo.h b/src/USER-INTEL/intel_intrinsics_airebo.h
index f17fd6985608307183aa7b69a36714a59be74dc5..4a86d8db290d096dff9ae1e16809176a6ce18930 100644
--- a/src/USER-INTEL/intel_intrinsics_airebo.h
+++ b/src/USER-INTEL/intel_intrinsics_airebo.h
@@ -744,7 +744,7 @@ struct intr_types<float,double> {
#include <cassert>
#include <immintrin.h>
-#include <stdint.h>
+#include <stdint.h> // <cstdint> requires C++-11
#define VEC_INLINE __attribute__((always_inline))
diff --git a/src/USER-INTEL/intel_simd.h b/src/USER-INTEL/intel_simd.h
index 4616f628e73a969b3aee3ba2e036d91ffa5f97f6..e9d5d929953682276884274fe6d90285a88bf5eb 100644
--- a/src/USER-INTEL/intel_simd.h
+++ b/src/USER-INTEL/intel_simd.h
@@ -29,7 +29,7 @@ authors for more details.
#ifndef INTEL_SIMD_H
#define INTEL_SIMD_H
-#include <stdio.h>
+#include <cstdio>
#include "intel_preprocess.h"
#include "immintrin.h"
diff --git a/src/USER-INTEL/pair_airebo_intel.cpp b/src/USER-INTEL/pair_airebo_intel.cpp
index 43e0bb7eedc9e64888d3e3ebbd5d4ecfab5ccc68..07f33f7ebe10bdfb1fac0511b768a9eba1fa3148 100644
--- a/src/USER-INTEL/pair_airebo_intel.cpp
+++ b/src/USER-INTEL/pair_airebo_intel.cpp
@@ -19,12 +19,13 @@
#pragma offload_attribute(push, target(mic))
#endif
#include <unistd.h>
-#include <stdlib.h>
-#include <math.h>
-#include <stdio.h>
-#include <stdint.h>
-#include <assert.h>
-#include <stddef.h>
+#include <cstdlib>
+#include <cstring>
+#include <cmath>
+#include <cstdio>
+#include <stdint.h> // <cstdint> requires C++-11
+#include <cassert>
+#include <cstddef>
#include "lmptype.h"
#include "intel_preprocess.h"
#include "intel_intrinsics_airebo.h"
@@ -35,7 +36,6 @@
#if defined(_OPENMP)
#include <omp.h>
#endif
-#include <string.h>
#include "pair_airebo_intel.h"
#include "atom.h"
#include "neighbor.h"
diff --git a/src/USER-INTEL/pair_buck_coul_cut_intel.cpp b/src/USER-INTEL/pair_buck_coul_cut_intel.cpp
index e32fd066607fff224be9bcf2d606c4472864220e..71aad95bc51016543352997c0ccba9e4b595ced3 100644
--- a/src/USER-INTEL/pair_buck_coul_cut_intel.cpp
+++ b/src/USER-INTEL/pair_buck_coul_cut_intel.cpp
@@ -15,10 +15,10 @@
Contributing author: Rodrigo Canales (RWTH Aachen University)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_buck_coul_cut_intel.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-INTEL/pair_buck_coul_long_intel.cpp b/src/USER-INTEL/pair_buck_coul_long_intel.cpp
index 2b9fea7a50f80c0298069d976c3211d47bffc12e..bba8a7b5e7e6a7f30133a0064bc5f102e7e5ea29 100644
--- a/src/USER-INTEL/pair_buck_coul_long_intel.cpp
+++ b/src/USER-INTEL/pair_buck_coul_long_intel.cpp
@@ -15,10 +15,10 @@
Contributing author: Rodrigo Canales (RWTH Aachen University)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_buck_coul_long_intel.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-INTEL/pair_buck_intel.cpp b/src/USER-INTEL/pair_buck_intel.cpp
index 05a28eb7f05b71e3df46b4403ae6971b70351295..f5dde26393d5878207df9b8775e2329cb19f272a 100644
--- a/src/USER-INTEL/pair_buck_intel.cpp
+++ b/src/USER-INTEL/pair_buck_intel.cpp
@@ -15,7 +15,7 @@
Contributing author: Rodrigo Canales (RWTH Aachen University)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_buck_intel.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-INTEL/pair_dpd_intel.cpp b/src/USER-INTEL/pair_dpd_intel.cpp
index 60361cac7953c17db45cde6683948499fb23dba2..cb8c06cacc258778ba944b02ccc4096600033ea1 100644
--- a/src/USER-INTEL/pair_dpd_intel.cpp
+++ b/src/USER-INTEL/pair_dpd_intel.cpp
@@ -13,7 +13,7 @@
Shun Xu (Computer Network Information Center, CAS)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_dpd_intel.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-INTEL/pair_eam_alloy_intel.cpp b/src/USER-INTEL/pair_eam_alloy_intel.cpp
index 4f47c7ee23967fd11c5042316b583b8157b3b19f..192b39b2e8c27ffd8a8cd3cffeee1de9969552e3 100644
--- a/src/USER-INTEL/pair_eam_alloy_intel.cpp
+++ b/src/USER-INTEL/pair_eam_alloy_intel.cpp
@@ -15,9 +15,9 @@
Contributing authors: Stephen Foiles (SNL), Murray Daw (SNL)
------------------------------------------------------------------------- */
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_eam_alloy_intel.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-INTEL/pair_eam_fs_intel.cpp b/src/USER-INTEL/pair_eam_fs_intel.cpp
index cfcc8200cc751a8f3aafde06e79d4a6827a59900..61bb6e0b4d17674a2602f7eddea08cc4b82fa0ce 100644
--- a/src/USER-INTEL/pair_eam_fs_intel.cpp
+++ b/src/USER-INTEL/pair_eam_fs_intel.cpp
@@ -15,9 +15,9 @@
Contributing authors: Tim Lau (MIT)
------------------------------------------------------------------------- */
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_eam_fs_intel.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-INTEL/pair_eam_intel.cpp b/src/USER-INTEL/pair_eam_intel.cpp
index ea4ee30d52602440b06b81603a3d93897b72cba3..94799cdba26b5b609aa2eb28e9966e03a23509f3 100644
--- a/src/USER-INTEL/pair_eam_intel.cpp
+++ b/src/USER-INTEL/pair_eam_intel.cpp
@@ -15,10 +15,10 @@
Contributing authors: W. Michael Brown (Intel)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_eam_intel.h"
#include "atom.h"
#include "force.h"
diff --git a/src/USER-INTEL/pair_eam_intel.h b/src/USER-INTEL/pair_eam_intel.h
index f34e740bdaaf83c9229239339d755dd0588dab55..83b1fbf6a13e76cffcd55e574cac81d4c4ac1d8a 100644
--- a/src/USER-INTEL/pair_eam_intel.h
+++ b/src/USER-INTEL/pair_eam_intel.h
@@ -20,7 +20,7 @@ PairStyle(eam/intel,PairEAMIntel)
#ifndef LMP_PAIR_EAM_INTEL_H
#define LMP_PAIR_EAM_INTEL_H
-#include <stdio.h>
+#include <cstdio>
#include "pair_eam.h"
#include "fix_intel.h"
diff --git a/src/USER-INTEL/pair_lj_charmm_coul_charmm_intel.cpp b/src/USER-INTEL/pair_lj_charmm_coul_charmm_intel.cpp
index b36e594f54e8ddb81a28ff0ea96671c99ba12ad1..7485395bef089c57338097d03145a5e3f435d2e3 100644
--- a/src/USER-INTEL/pair_lj_charmm_coul_charmm_intel.cpp
+++ b/src/USER-INTEL/pair_lj_charmm_coul_charmm_intel.cpp
@@ -12,7 +12,7 @@
Contributing author: W. Michael Brown (Intel)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_lj_charmm_coul_charmm_intel.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-INTEL/pair_lj_charmm_coul_long_intel.cpp b/src/USER-INTEL/pair_lj_charmm_coul_long_intel.cpp
index a2680cdff41bb964cf39e42f85c140837e08fca8..25cca59714c9f5bdadfbf19bd5cd8b64279afb25 100644
--- a/src/USER-INTEL/pair_lj_charmm_coul_long_intel.cpp
+++ b/src/USER-INTEL/pair_lj_charmm_coul_long_intel.cpp
@@ -12,7 +12,7 @@
Contributing author: W. Michael Brown (Intel)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_lj_charmm_coul_long_intel.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-INTEL/pair_lj_cut_coul_long_intel.cpp b/src/USER-INTEL/pair_lj_cut_coul_long_intel.cpp
index c0bf6f35c6e6b220f33d6d6bbb00232d8fcce3bd..cb7381270dd72d9dad1476645e901e13bc1998cb 100644
--- a/src/USER-INTEL/pair_lj_cut_coul_long_intel.cpp
+++ b/src/USER-INTEL/pair_lj_cut_coul_long_intel.cpp
@@ -12,7 +12,7 @@
Contributing author: W. Michael Brown (Intel)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_lj_cut_coul_long_intel.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-INTEL/pair_lj_cut_intel.cpp b/src/USER-INTEL/pair_lj_cut_intel.cpp
index f5a7999ee2e9cf13280167af8eecb008dbca59fe..b16f6230ccd5d30a6fc55eb239d8a5cc9f8c2cd2 100644
--- a/src/USER-INTEL/pair_lj_cut_intel.cpp
+++ b/src/USER-INTEL/pair_lj_cut_intel.cpp
@@ -12,7 +12,7 @@
Contributing author: W. Michael Brown (Intel)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_lj_cut_intel.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-INTEL/pair_lj_long_coul_long_intel.cpp b/src/USER-INTEL/pair_lj_long_coul_long_intel.cpp
index 86929d41ea3332db08e1a1295762b63884ac561d..8b9670f41917df66487a1b53dad343f96f59e9dc 100644
--- a/src/USER-INTEL/pair_lj_long_coul_long_intel.cpp
+++ b/src/USER-INTEL/pair_lj_long_coul_long_intel.cpp
@@ -15,7 +15,7 @@
Contributing authors: William McDoniel (RWTH Aachen University)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_lj_long_coul_long_intel.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-INTEL/pair_sw_intel.cpp b/src/USER-INTEL/pair_sw_intel.cpp
index 2c28fcfd94d2793b4338abb80024ec19722e261b..421de91ee938b1137ae546b0df36422c1b9ac5cb 100644
--- a/src/USER-INTEL/pair_sw_intel.cpp
+++ b/src/USER-INTEL/pair_sw_intel.cpp
@@ -25,9 +25,9 @@
#pragma offload_attribute(pop)
#endif
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "atom.h"
#include "neighbor.h"
#include "neigh_request.h"
diff --git a/src/USER-INTEL/pair_tersoff_intel.cpp b/src/USER-INTEL/pair_tersoff_intel.cpp
index a59fe12f5ba0ffcd9ee96145f37337cd4231e21a..c772546928dff386b5272d12a428553abe50f5eb 100644
--- a/src/USER-INTEL/pair_tersoff_intel.cpp
+++ b/src/USER-INTEL/pair_tersoff_intel.cpp
@@ -15,10 +15,10 @@
Contributing author: Markus Höhnerbach (RWTH)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_tersoff_intel.h"
#include "atom.h"
#include "neighbor.h"
diff --git a/src/USER-INTEL/pppm_disp_intel.cpp b/src/USER-INTEL/pppm_disp_intel.cpp
index 52e418c7138e1131919e90c0b434883982637233..0a41e5d8a5341c635853a2125ea2603ba6a9e64e 100644
--- a/src/USER-INTEL/pppm_disp_intel.cpp
+++ b/src/USER-INTEL/pppm_disp_intel.cpp
@@ -16,8 +16,8 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <stdlib.h>
-#include <math.h>
+#include <cstdlib>
+#include <cmath>
#include "pppm_disp_intel.h"
#include "atom.h"
#include "comm.h"
@@ -728,7 +728,7 @@ void PPPMDispIntel::particle_map(double delx, double dely, double delz,
int nlocal = atom->nlocal;
int nthr = comm->nthreads;
- if (!ISFINITE(boxlo[0]) || !ISFINITE(boxlo[1]) || !ISFINITE(boxlo[2]))
+ if (!std::isfinite(boxlo[0]) || !std::isfinite(boxlo[1]) || !std::isfinite(boxlo[2]))
error->one(FLERR,"Non-numeric box dimensions - simulation unstable");
int flag = 0;
diff --git a/src/USER-INTEL/pppm_intel.cpp b/src/USER-INTEL/pppm_intel.cpp
index 1fd267be51900d9c61d1112fb648f52491101ee6..46a55e558afbad5e408be10b24077430b53b65cc 100644
--- a/src/USER-INTEL/pppm_intel.cpp
+++ b/src/USER-INTEL/pppm_intel.cpp
@@ -19,8 +19,8 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <stdlib.h>
-#include <math.h>
+#include <cstdlib>
+#include <cmath>
#include "pppm_intel.h"
#include "atom.h"
#include "comm.h"
@@ -358,7 +358,7 @@ void PPPMIntel::particle_map(IntelBuffers<flt_t,acc_t> *buffers)
int flag = 0;
- if (!ISFINITE(boxlo[0]) || !ISFINITE(boxlo[1]) || !ISFINITE(boxlo[2]))
+ if (!std::isfinite(boxlo[0]) || !std::isfinite(boxlo[1]) || !std::isfinite(boxlo[2]))
error->one(FLERR,"Non-numeric box dimensions - simulation unstable");
#if defined(_OPENMP)
diff --git a/src/USER-INTEL/verlet_lrt_intel.cpp b/src/USER-INTEL/verlet_lrt_intel.cpp
index 1b9c305e9c69377906b0346de8b6803c37b307b9..962202e228f74bce7e9b8486c33d50b0a04d4da3 100644
--- a/src/USER-INTEL/verlet_lrt_intel.cpp
+++ b/src/USER-INTEL/verlet_lrt_intel.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "verlet_lrt_intel.h"
#include "neighbor.h"
#include "domain.h"
diff --git a/src/USER-LB/fix_lb_fluid.cpp b/src/USER-LB/fix_lb_fluid.cpp
index 638901d6b3d06199b56edc97ddf73624c84b01eb..7a0bd0572ed63f1df5cd51eb8bead57d5ec05349 100644
--- a/src/USER-LB/fix_lb_fluid.cpp
+++ b/src/USER-LB/fix_lb_fluid.cpp
@@ -17,11 +17,11 @@
------------------------------------------------------------------------- */
#include "fix_lb_fluid.h"
-#include <math.h>
+#include <cmath>
#include <mpi.h>
-#include <stdlib.h>
-#include <stdio.h>
-#include <string.h>
+#include <cstdlib>
+#include <cstdio>
+#include <cstring>
#include "comm.h"
#include "memory.h"
#include "error.h"
diff --git a/src/USER-LB/fix_lb_momentum.cpp b/src/USER-LB/fix_lb_momentum.cpp
index d604d8fed414240cedd96972d8b9ee08f882778d..490b95ef719a132448c2925ba2879c9f1874f163 100644
--- a/src/USER-LB/fix_lb_momentum.cpp
+++ b/src/USER-LB/fix_lb_momentum.cpp
@@ -18,8 +18,8 @@
Contributing author: Naveen Michaud-Agrawal (Johns Hopkins U)
------------------------------------------------------------------------- */
-#include <stdlib.h>
-#include <string.h>
+#include <cstdlib>
+#include <cstring>
#include "fix_lb_momentum.h"
#include "atom.h"
#include "domain.h"
@@ -102,8 +102,8 @@ void FixLbMomentum::end_of_step()
double masslb,masslbloc;
double momentumlbloc[3],momentumlb[3];
double vcmtotal[3];
- int numvel = fix_lb_fluid->numvel;
- double etacov[numvel];
+ const int numvel = fix_lb_fluid->numvel;
+ double etacov[19]; // = double etacov[numvel]; i.e. 15 or 19
double rho;
if (linear) {
diff --git a/src/USER-LB/fix_lb_pc.cpp b/src/USER-LB/fix_lb_pc.cpp
index c4d7cf70d3ae504f34a17418466533fdf7815396..9fd0dab51de39ec708cad06ac94202321d3bb59c 100644
--- a/src/USER-LB/fix_lb_pc.cpp
+++ b/src/USER-LB/fix_lb_pc.cpp
@@ -15,9 +15,9 @@
Contributing authors: Frances Mackay, Santtu Ollila, Colin Denniston (UWO)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstring>
#include "fix_lb_pc.h"
#include "atom.h"
#include "force.h"
diff --git a/src/USER-LB/fix_lb_rigid_pc_sphere.cpp b/src/USER-LB/fix_lb_rigid_pc_sphere.cpp
index 42e8eae3d225c36972d36a97c09b5d4c291a9b3c..dddd060fa4cd416bb3e97a77bfffedcb0a05da03 100644
--- a/src/USER-LB/fix_lb_rigid_pc_sphere.cpp
+++ b/src/USER-LB/fix_lb_rigid_pc_sphere.cpp
@@ -16,10 +16,10 @@
Based on fix_rigid (version from 2008).
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "fix_lb_rigid_pc_sphere.h"
#include "atom.h"
#include "atom_vec.h"
diff --git a/src/USER-LB/fix_lb_viscous.cpp b/src/USER-LB/fix_lb_viscous.cpp
index 0e156bc46ce957153bcbca2d2e68b5cbab4ebfd7..8ee4d8419e73e5a377fa65b2c8e40b13baef6b5a 100644
--- a/src/USER-LB/fix_lb_viscous.cpp
+++ b/src/USER-LB/fix_lb_viscous.cpp
@@ -15,9 +15,9 @@
Contributing authors: Frances Mackay, Santtu Ollila, Colin Denniston (UWO)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "fix_lb_viscous.h"
#include "atom.h"
#include "update.h"
diff --git a/src/USER-MANIFOLD/fix_manifoldforce.cpp b/src/USER-MANIFOLD/fix_manifoldforce.cpp
index e66b7c9fc2ac34bf80e197461b8ea9314c7320c4..ab33b5bc972627e1611bbc80bbbaa3f1e3c660b3 100644
--- a/src/USER-MANIFOLD/fix_manifoldforce.cpp
+++ b/src/USER-MANIFOLD/fix_manifoldforce.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <string.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstring>
+#include <cstdlib>
#include "atom.h"
#include "update.h"
#include "respa.h"
diff --git a/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp b/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp
index a8ce87ef111256b4eeb4c5bfa3c50c56c5ade443..4dcc3f9704aa3543aeaa62ed7a9202135218c801 100644
--- a/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp
+++ b/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp
@@ -32,16 +32,16 @@
------------------------------------------------------------------------- */
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "atom.h"
#include "force.h"
#include "update.h"
#include "respa.h"
#include "error.h"
#include "group.h"
-#include <math.h>
+#include <cmath>
#include "input.h"
#include "variable.h"
#include "citeme.h"
diff --git a/src/USER-MANIFOLD/fix_nvt_manifold_rattle.cpp b/src/USER-MANIFOLD/fix_nvt_manifold_rattle.cpp
index 38e8c6a26506b33c075a757e64ea29574fb09c64..973a5bcf43875d12af45655be1ff97f54c17e139 100644
--- a/src/USER-MANIFOLD/fix_nvt_manifold_rattle.cpp
+++ b/src/USER-MANIFOLD/fix_nvt_manifold_rattle.cpp
@@ -32,16 +32,16 @@
------------------------------------------------------------------------- */
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
+#include <cmath>
#include "atom.h"
#include "force.h"
#include "update.h"
#include "respa.h"
#include "error.h"
#include "group.h"
-#include <math.h>
#include "input.h"
#include "variable.h"
#include "citeme.h"
diff --git a/src/USER-MANIFOLD/manifold.h b/src/USER-MANIFOLD/manifold.h
index f0d56ffd82efd240526bbe204181206cbf2d2400..6eb09010efbb3022bed71c282744db7792140ba8 100644
--- a/src/USER-MANIFOLD/manifold.h
+++ b/src/USER-MANIFOLD/manifold.h
@@ -38,7 +38,7 @@
#define LMP_MANIFOLD_H
#include "pointers.h"
-#include <math.h>
+#include <cmath>
namespace LAMMPS_NS {
namespace user_manifold {
diff --git a/src/USER-MANIFOLD/manifold_cylinder_dent.cpp b/src/USER-MANIFOLD/manifold_cylinder_dent.cpp
index 687e311c9cd61d87fddf846e2af04f9418ed1cb1..21d4087d7c240722162b0eb556aa0b873c1a8896 100644
--- a/src/USER-MANIFOLD/manifold_cylinder_dent.cpp
+++ b/src/USER-MANIFOLD/manifold_cylinder_dent.cpp
@@ -1,7 +1,7 @@
#include "manifold_cylinder_dent.h"
#include "math_const.h"
-#include <math.h>
+#include <cmath>
using namespace LAMMPS_NS;
diff --git a/src/USER-MANIFOLD/manifold_dumbbell.cpp b/src/USER-MANIFOLD/manifold_dumbbell.cpp
index ed1583ac9af5cc0c74f73f7f558194a657d5909d..fa7edc6e4afa4fa345c283187d073365a05dedb7 100644
--- a/src/USER-MANIFOLD/manifold_dumbbell.cpp
+++ b/src/USER-MANIFOLD/manifold_dumbbell.cpp
@@ -1,6 +1,6 @@
#include "manifold_dumbbell.h"
-#include <math.h>
+#include <cmath>
using namespace LAMMPS_NS;
diff --git a/src/USER-MANIFOLD/manifold_factory.h b/src/USER-MANIFOLD/manifold_factory.h
index 7fdd0a6de555f23c146849d67909a9367d74c5ea..cc3e1245bfd11f0a4c46cdb55948f40c3810bffd 100644
--- a/src/USER-MANIFOLD/manifold_factory.h
+++ b/src/USER-MANIFOLD/manifold_factory.h
@@ -37,7 +37,7 @@
#include "manifold.h"
-#include <string.h>
+#include <cstring>
/*
* Defining USE_PHONY_LAMMPS makes sure that none of the LAMMPS classes are
diff --git a/src/USER-MANIFOLD/manifold_plane_wiggle.cpp b/src/USER-MANIFOLD/manifold_plane_wiggle.cpp
index 136c52ab361a2023ee2442fc038039a8d2c1a7d0..ccf0a794dadc28900dcee2a01cee1a6343d39b68 100644
--- a/src/USER-MANIFOLD/manifold_plane_wiggle.cpp
+++ b/src/USER-MANIFOLD/manifold_plane_wiggle.cpp
@@ -1,6 +1,6 @@
#include "manifold_plane_wiggle.h"
-#include <math.h>
+#include <cmath>
using namespace LAMMPS_NS;
using namespace user_manifold;
diff --git a/src/USER-MANIFOLD/manifold_spine.cpp b/src/USER-MANIFOLD/manifold_spine.cpp
index 1081ab673e2e493e8da40c8c1a1c41d2de58949c..308190c5288ea41ad9ceb689b9df1f849ffb8c08 100644
--- a/src/USER-MANIFOLD/manifold_spine.cpp
+++ b/src/USER-MANIFOLD/manifold_spine.cpp
@@ -1,6 +1,6 @@
#include "manifold_spine.h"
-#include <math.h>
+#include <cmath>
#include "math_special.h"
using namespace LAMMPS_NS;
diff --git a/src/USER-MANIFOLD/manifold_thylakoid.cpp b/src/USER-MANIFOLD/manifold_thylakoid.cpp
index 4bb2b71331ead05bc3a70c58d58a0f3378d36bf7..b7eb155ba27b5b40c4f4d1dafc87942839b887d4 100644
--- a/src/USER-MANIFOLD/manifold_thylakoid.cpp
+++ b/src/USER-MANIFOLD/manifold_thylakoid.cpp
@@ -1,5 +1,5 @@
#include "manifold_thylakoid.h"
-#include <math.h>
+#include <cmath>
#include "comm.h"
#include "domain.h" // For some checks regarding the simulation box.
@@ -85,7 +85,7 @@ double manifold_thylakoid::g( const double *x )
error->one(FLERR,msg);
}
double con_val = p->g(x);
- if( ISFINITE(con_val) ){
+ if( std::isfinite(con_val) ){
return con_val;
}else{
char msg[2048];
@@ -107,7 +107,7 @@ void manifold_thylakoid::n( const double *x, double *n )
error->one(FLERR,msg);
}
p->n(x,n);
- if( ISFINITE(n[0]) && ISFINITE(n[1]) && ISFINITE(n[2]) ){
+ if( std::isfinite(n[0]) && std::isfinite(n[1]) && std::isfinite(n[2]) ){
return;
}else{
char msg[2048];
diff --git a/src/USER-MANIFOLD/manifold_thylakoid.h b/src/USER-MANIFOLD/manifold_thylakoid.h
index 231525950d3324086f17b40508a77c35ebb8c7b4..5e5d3b9c4192a9c622c06da6daeee0722bf3cdff 100644
--- a/src/USER-MANIFOLD/manifold_thylakoid.h
+++ b/src/USER-MANIFOLD/manifold_thylakoid.h
@@ -3,7 +3,7 @@
#include "manifold.h"
#include <vector>
-#include <stdio.h>
+#include <cstdio>
#include "manifold_thylakoid_shared.h"
diff --git a/src/USER-MANIFOLD/manifold_thylakoid_shared.cpp b/src/USER-MANIFOLD/manifold_thylakoid_shared.cpp
index 5b87ba7c2b9eec67bff54e044450bcbfa2b3523f..4c4297f822ef2cfa7eb4113f4e61bb234dac6bf8 100644
--- a/src/USER-MANIFOLD/manifold_thylakoid_shared.cpp
+++ b/src/USER-MANIFOLD/manifold_thylakoid_shared.cpp
@@ -1,5 +1,5 @@
#include "manifold_thylakoid_shared.h"
-#include <math.h>
+#include <cmath>
using namespace LAMMPS_NS;
using namespace user_manifold;
diff --git a/src/USER-MANIFOLD/manifold_torus.cpp b/src/USER-MANIFOLD/manifold_torus.cpp
index b46998b28d7f04b61a8fee406d266a0d4d03ad43..44a17725b5e2230e4cbc2e2fb5809ef693d99c0a 100644
--- a/src/USER-MANIFOLD/manifold_torus.cpp
+++ b/src/USER-MANIFOLD/manifold_torus.cpp
@@ -1,4 +1,4 @@
-#include <math.h>
+#include <cmath>
#include "manifold_torus.h"
#include "error.h"
diff --git a/src/USER-MEAMC/meam.h b/src/USER-MEAMC/meam.h
index 4e86df62d5bad0b762db67a0e2cbf13a9a2ebebe..42fd722e016ce4dce882599cb1ff37fe24dd7422 100644
--- a/src/USER-MEAMC/meam.h
+++ b/src/USER-MEAMC/meam.h
@@ -2,8 +2,8 @@
#define LMP_MEAM_H
#include "memory.h"
-#include <math.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdlib>
#define maxelt 5
@@ -255,5 +255,5 @@ static inline double fdiv_zero(const double n, const double d) {
return n / d;
}
-};
+}
#endif
diff --git a/src/USER-MEAMC/meam_funcs.cpp b/src/USER-MEAMC/meam_funcs.cpp
index 3b7c114d5cc7e1e60baef248a9d220fc0a8200a7..599e9019d930aedac8a7c84ba45bfb8496f7a639 100644
--- a/src/USER-MEAMC/meam_funcs.cpp
+++ b/src/USER-MEAMC/meam_funcs.cpp
@@ -17,7 +17,7 @@
#include "meam.h"
#include "math_special.h"
-#include <math.h>
+#include <cmath>
using namespace LAMMPS_NS;
diff --git a/src/USER-MEAMC/meam_setup_global.cpp b/src/USER-MEAMC/meam_setup_global.cpp
index 7062d5ebca972c1a095222420926a189c335834e..7f8ad3d81f5f09fbff2224c28ee866ddf234686f 100644
--- a/src/USER-MEAMC/meam_setup_global.cpp
+++ b/src/USER-MEAMC/meam_setup_global.cpp
@@ -1,5 +1,5 @@
#include "meam.h"
-#include <math.h>
+#include <cmath>
using namespace LAMMPS_NS;
void
diff --git a/src/USER-MEAMC/pair_meamc.cpp b/src/USER-MEAMC/pair_meamc.cpp
index 2404005fdf695e9387b1a6d7a9ed5bc65262a23a..027e4c27a79ca000dd10a3b6383a97152f0a1bd1 100644
--- a/src/USER-MEAMC/pair_meamc.cpp
+++ b/src/USER-MEAMC/pair_meamc.cpp
@@ -15,10 +15,10 @@
Contributing author: Greg Wagner (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "meam.h"
#include "pair_meamc.h"
#include "atom.h"
diff --git a/src/USER-MESO/atom_vec_edpd.cpp b/src/USER-MESO/atom_vec_edpd.cpp
index c8f1421512f5e74211e5e768f0cc89e9a6f58f61..d956e914b5d851108a01f07019ffb606e82e9d0c 100644
--- a/src/USER-MESO/atom_vec_edpd.cpp
+++ b/src/USER-MESO/atom_vec_edpd.cpp
@@ -10,8 +10,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
-#include <stdlib.h>
+#include <cstring>
+#include <cstdlib>
#include "atom_vec_edpd.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-MESO/atom_vec_mdpd.cpp b/src/USER-MESO/atom_vec_mdpd.cpp
index 1d81bd2c39a0693d0becbf634800d1db32ec899f..5bc5e212ff62e5630da12864462ab901fbfca889 100644
--- a/src/USER-MESO/atom_vec_mdpd.cpp
+++ b/src/USER-MESO/atom_vec_mdpd.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
-#include <stdlib.h>
+#include <cstring>
+#include <cstdlib>
#include "atom_vec_mdpd.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-MESO/atom_vec_tdpd.cpp b/src/USER-MESO/atom_vec_tdpd.cpp
index 6733e3e4df51b3d1dddf7ee0691ba771929754f8..aa0dc93809f8d9b51065dfccc91306fac160a56b 100644
--- a/src/USER-MESO/atom_vec_tdpd.cpp
+++ b/src/USER-MESO/atom_vec_tdpd.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
-#include <stdlib.h>
+#include <cstring>
+#include <cstdlib>
#include "atom_vec_tdpd.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-MESO/compute_edpd_temp_atom.cpp b/src/USER-MESO/compute_edpd_temp_atom.cpp
index 15fdab2a69720102075f0c0b13c7ae1e11bc0345..119e0079d133dc50ba146952967cd99eb3dd3876 100644
--- a/src/USER-MESO/compute_edpd_temp_atom.cpp
+++ b/src/USER-MESO/compute_edpd_temp_atom.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "compute_edpd_temp_atom.h"
#include "atom.h"
#include "update.h"
diff --git a/src/USER-MESO/compute_tdpd_cc_atom.cpp b/src/USER-MESO/compute_tdpd_cc_atom.cpp
index b33550f5c164075a373fb1c4dce29de126d4da7d..6378ed5ef674eada4fea33594ffde53559fdc4a6 100644
--- a/src/USER-MESO/compute_tdpd_cc_atom.cpp
+++ b/src/USER-MESO/compute_tdpd_cc_atom.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "compute_tdpd_cc_atom.h"
#include "atom.h"
#include "update.h"
diff --git a/src/USER-MESO/fix_edpd_source.cpp b/src/USER-MESO/fix_edpd_source.cpp
index fb8fecdcdf470c3beb7edde514b2e2c187088b8e..8b03e051814ffe6f636f01d7c8e92f4b83950464 100644
--- a/src/USER-MESO/fix_edpd_source.cpp
+++ b/src/USER-MESO/fix_edpd_source.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <stdlib.h>
-#include <string.h>
+#include <cstdlib>
+#include <cstring>
#include "fix_edpd_source.h"
#include "atom.h"
#include "comm.h"
@@ -112,7 +112,7 @@ void FixEDPDSource::post_force(int vflag)
drx = x[i][0] - center[0];
dry = x[i][1] - center[1];
drz = x[i][2] - center[2];
- if(abs(drx) <= 0.5*dLx && abs(dry) <= 0.5*dLy && abs(drz) <= 0.5*dLz)
+ if(fabs(drx) <= 0.5*dLx && fabs(dry) <= 0.5*dLy && fabs(drz) <= 0.5*dLz)
edpd_flux[i] += value*edpd_cv[i];
}
}
diff --git a/src/USER-MESO/fix_mvv_dpd.cpp b/src/USER-MESO/fix_mvv_dpd.cpp
index c1c4f203f1cc0547fd87b4c46d7b822b0308e435..c97a2d779c0de1595e13a5e09f2a3809d4057fa1 100644
--- a/src/USER-MESO/fix_mvv_dpd.cpp
+++ b/src/USER-MESO/fix_mvv_dpd.cpp
@@ -20,8 +20,8 @@
Email: zhen_li@brown.edu
------------------------------------------------------------------------- */
-#include <stdio.h>
-#include <string.h>
+#include <cstdio>
+#include <cstring>
#include "fix_mvv_dpd.h"
#include "atom.h"
#include "force.h"
diff --git a/src/USER-MESO/fix_mvv_edpd.cpp b/src/USER-MESO/fix_mvv_edpd.cpp
index 12c8bbcafbbe0cb9e465ffc5cc9b5c50474023ea..89a831e121b9a37fbdb8271f9db554b2fa6d2d07 100644
--- a/src/USER-MESO/fix_mvv_edpd.cpp
+++ b/src/USER-MESO/fix_mvv_edpd.cpp
@@ -29,8 +29,8 @@
Communications, 2015, 51: 11038-11040.
------------------------------------------------------------------------- */
-#include <stdio.h>
-#include <string.h>
+#include <cstdio>
+#include <cstring>
#include "fix_mvv_edpd.h"
#include "atom.h"
#include "force.h"
diff --git a/src/USER-MESO/fix_mvv_tdpd.cpp b/src/USER-MESO/fix_mvv_tdpd.cpp
index 58832e084654f8b938350f0819389c0876bf067d..e16171800b1b61bc44899fc0895adff7a52637a3 100644
--- a/src/USER-MESO/fix_mvv_tdpd.cpp
+++ b/src/USER-MESO/fix_mvv_tdpd.cpp
@@ -25,8 +25,8 @@
-reaction problems". The Journal of Chemical Physics, 2015, 143: 014101.
------------------------------------------------------------------------- */
-#include <stdio.h>
-#include <string.h>
+#include <cstdio>
+#include <cstring>
#include "fix_mvv_tdpd.h"
#include "atom.h"
#include "force.h"
diff --git a/src/USER-MESO/fix_tdpd_source.cpp b/src/USER-MESO/fix_tdpd_source.cpp
index c58dff76be3915b8a5c313cf6e144cf351715bd5..64964a4c983ebb5ef8fb5cd27df15079f8860464 100644
--- a/src/USER-MESO/fix_tdpd_source.cpp
+++ b/src/USER-MESO/fix_tdpd_source.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <stdlib.h>
-#include <string.h>
+#include <cstdlib>
+#include <cstring>
#include "fix_tdpd_source.h"
#include "atom.h"
#include "comm.h"
@@ -112,7 +112,7 @@ void FixTDPDSource::post_force(int vflag)
drx = x[i][0] - center[0];
dry = x[i][1] - center[1];
drz = x[i][2] - center[2];
- if(abs(drx) <= 0.5*dLx && abs(dry) <= 0.5*dLy && abs(drz) <= 0.5*dLz)
+ if(fabs(drx) <= 0.5*dLx && fabs(dry) <= 0.5*dLy && fabs(drz) <= 0.5*dLz)
cc_flux[i][cc_index-1] += value;
}
}
diff --git a/src/USER-MESO/pair_edpd.cpp b/src/USER-MESO/pair_edpd.cpp
index 64d29cb65df27be31a658d5a4aeb5241090b9acf..351637a842018c6469c09a1929e5552487c20695 100644
--- a/src/USER-MESO/pair_edpd.cpp
+++ b/src/USER-MESO/pair_edpd.cpp
@@ -16,9 +16,11 @@
Email: zhen_li@brown.edu
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <ctime>
+#include <cstring>
#include "pair_edpd.h"
#include "atom.h"
#include "atom_vec.h"
@@ -31,8 +33,6 @@
#include "citeme.h"
#include "memory.h"
#include "error.h"
-#include <time.h>
-#include <string.h>
using namespace LAMMPS_NS;
@@ -59,7 +59,6 @@ static const char cite_pair_edpd[] =
" volume = {51},\n"
" pages = {11038--11040}\n"
"}\n\n";
-;
/* ---------------------------------------------------------------------- */
diff --git a/src/USER-MESO/pair_mdpd.cpp b/src/USER-MESO/pair_mdpd.cpp
index 1b8cd45be98d06900975243bf4aad62eaf2791f7..f9acd3dbe1eb3c74fa2d0f1af87e8ce4ae42e80f 100644
--- a/src/USER-MESO/pair_mdpd.cpp
+++ b/src/USER-MESO/pair_mdpd.cpp
@@ -16,9 +16,10 @@
Email: zhen_li@brown.edu
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <ctime>
#include "pair_mdpd.h"
#include "atom.h"
#include "atom_vec.h"
@@ -31,7 +32,6 @@
#include "citeme.h"
#include "memory.h"
#include "error.h"
-#include <time.h>
using namespace LAMMPS_NS;
diff --git a/src/USER-MESO/pair_mdpd_rhosum.cpp b/src/USER-MESO/pair_mdpd_rhosum.cpp
index ecfc9d5c00eb3d4f7ba4c86848d631b0805262f4..1264d03ed3b5dd9404fef9ba6a5eac0acb28b16d 100644
--- a/src/USER-MESO/pair_mdpd_rhosum.cpp
+++ b/src/USER-MESO/pair_mdpd_rhosum.cpp
@@ -19,8 +19,8 @@
Contributing author: Zhen Li (Brown University)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdlib>
#include "pair_mdpd_rhosum.h"
#include "atom.h"
#include "force.h"
diff --git a/src/USER-MESO/pair_tdpd.cpp b/src/USER-MESO/pair_tdpd.cpp
index 71dbaaba83e23bbe91f1404fb0422599adbb6851..b8bbf6d622f51e16f15813cbeb1af08a692adceb 100644
--- a/src/USER-MESO/pair_tdpd.cpp
+++ b/src/USER-MESO/pair_tdpd.cpp
@@ -16,9 +16,10 @@
Email: zhen_li@brown.edu
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <ctime>
#include "pair_tdpd.h"
#include "atom.h"
#include "atom_vec.h"
@@ -31,7 +32,6 @@
#include "citeme.h"
#include "memory.h"
#include "error.h"
-#include <time.h>
using namespace LAMMPS_NS;
@@ -280,7 +280,9 @@ void PairTDPD::coeff(int narg, char **arg)
double power_one = force->numeric(FLERR,arg[4]);
double cut_one = force->numeric(FLERR,arg[5]);
double cutcc_one = force->numeric(FLERR,arg[6]);
- double kappa_one[cc_species],epsilon_one[cc_species],powercc_one[cc_species];
+ double *kappa_one = new double[cc_species];
+ double *epsilon_one = new double[cc_species];
+ double *powercc_one = new double[cc_species];
for(int k=0; k<cc_species; k++) {
kappa_one[k] = force->numeric(FLERR,arg[7+3*k]);
epsilon_one[k] = force->numeric(FLERR,arg[8+3*k]);
@@ -304,6 +306,9 @@ void PairTDPD::coeff(int narg, char **arg)
setflag[i][j] = 1;
count++;
}
+ delete[] kappa_one;
+ delete[] epsilon_one;
+ delete[] powercc_one;
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
}
diff --git a/src/USER-MISC/Install.sh b/src/USER-MISC/Install.sh
old mode 100644
new mode 100755
diff --git a/src/USER-MISC/README b/src/USER-MISC/README
index a8c33fa38056454194ff2346c9bd2d4822019200..222c06b4c426ff1adf271dcccf7438921eb5e5ff 100644
--- a/src/USER-MISC/README
+++ b/src/USER-MISC/README
@@ -37,8 +37,10 @@ dihedral_style nharmonic, Loukas Peristeras, loukas.peristeras at scienomics.com
dihedral_style quadratic, Loukas Peristeras, loukas.peristeras at scienomics.com, 27 Oct 12
dihedral_style spherical, Andrew Jewett, jewett.aij@gmail.com, 15 Jul 16
dihedral_style table, Andrew Jewett, jewett.aij@gmail.com, 10 Jan 12
+dihedral_style table/cut, Mike Salerno, ksalerno@pha.jhu.edu, 11 May 18
fix addtorque, Laurent Joly (U Lyon), ljoly.ulyon at gmail.com, 8 Aug 11
fix ave/correlate/long, Jorge Ramirez (UPM Madrid), jorge.ramirez at upm.es, 21 Oct 2015
+fix bond/react, Jacob Gissinger (CU Boulder), info at disarmmd.org, 24 Feb 2018
fix filter/corotate, Lukas Fath (KIT), lukas.fath at kit.edu, 15 Mar 2017
fix flow/gauss, Joel Eaves (CU Boulder), Joel.Eaves@Colorado.edu, 23 Aug 2016
fix gle, Michele Ceriotti (EPFL Lausanne), michele.ceriotti at gmail.com, 24 Nov 2014
diff --git a/src/USER-MISC/angle_cosine_shift.cpp b/src/USER-MISC/angle_cosine_shift.cpp
index 66f5c82c8445185b07e618d77fcace93f03cba32..a361db497081441da026375482b8dcaef575bd4e 100644
--- a/src/USER-MISC/angle_cosine_shift.cpp
+++ b/src/USER-MISC/angle_cosine_shift.cpp
@@ -15,8 +15,8 @@
Contributing author: Carsten Svaneborg, science@zqex.dk
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdlib>
#include "angle_cosine_shift.h"
#include "atom.h"
#include "neighbor.h"
@@ -34,7 +34,10 @@ using namespace MathConst;
/* ---------------------------------------------------------------------- */
-AngleCosineShift::AngleCosineShift(LAMMPS *lmp) : Angle(lmp) {}
+AngleCosineShift::AngleCosineShift(LAMMPS *lmp) : Angle(lmp)
+{
+ kcost = NULL;
+}
/* ---------------------------------------------------------------------- */
diff --git a/src/USER-MISC/angle_cosine_shift.h b/src/USER-MISC/angle_cosine_shift.h
index b8ab74ee43d886a452ce542ba77c07244b4e529e..030709a0e20ba90a8a168fe11fcd1b53a33f72da 100644
--- a/src/USER-MISC/angle_cosine_shift.h
+++ b/src/USER-MISC/angle_cosine_shift.h
@@ -20,7 +20,7 @@ AngleStyle(cosine/shift,AngleCosineShift)
#ifndef LMP_ANGLE_COSINE_SHIFT_H
#define LMP_ANGLE_COSINE_SHIFT_H
-#include <stdio.h>
+#include <cstdio>
#include "angle.h"
namespace LAMMPS_NS {
diff --git a/src/USER-MISC/angle_cosine_shift_exp.cpp b/src/USER-MISC/angle_cosine_shift_exp.cpp
index 6d11c6894e0b7d1734b6393b582b8373c82f2c2d..c87c73171a9509fc8895ab9ac1caaa58f0b64dde 100644
--- a/src/USER-MISC/angle_cosine_shift_exp.cpp
+++ b/src/USER-MISC/angle_cosine_shift_exp.cpp
@@ -15,8 +15,8 @@
Contributing author: Carsten Svaneborg, science@zqex.dk
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdlib>
#include "angle_cosine_shift_exp.h"
#include "atom.h"
#include "neighbor.h"
@@ -34,7 +34,16 @@ using namespace MathConst;
/* ---------------------------------------------------------------------- */
-AngleCosineShiftExp::AngleCosineShiftExp(LAMMPS *lmp) : Angle(lmp) {}
+AngleCosineShiftExp::AngleCosineShiftExp(LAMMPS *lmp) : Angle(lmp)
+{
+ doExpansion = NULL;
+ umin = NULL;
+ a = NULL;
+ opt1 = NULL;
+ theta0 = NULL;
+ sint = NULL;
+ cost = NULL;
+}
/* ---------------------------------------------------------------------- */
diff --git a/src/USER-MISC/angle_cosine_shift_exp.h b/src/USER-MISC/angle_cosine_shift_exp.h
index 4db9e1f6960067df88249bc1ea5539594cf30f73..8b8e389380b7af7be8f1a2ce4816827c19000d29 100644
--- a/src/USER-MISC/angle_cosine_shift_exp.h
+++ b/src/USER-MISC/angle_cosine_shift_exp.h
@@ -18,7 +18,7 @@ AngleStyle(cosine/shift/exp,AngleCosineShiftExp)
#ifndef LMP_ANGLE_COSINE_SHIFT_EXP_H
#define LMP_ANGLE_COSINE_SHIFT_EXP_H
-#include <stdio.h>
+#include <cstdio>
#include "angle.h"
namespace LAMMPS_NS {
diff --git a/src/USER-MISC/angle_dipole.cpp b/src/USER-MISC/angle_dipole.cpp
index 1e8c0e18fb1ba99594e9ac19231364540dad6a6c..bcb631c61f065353cbb60761a4e693c28800693a 100644
--- a/src/USER-MISC/angle_dipole.cpp
+++ b/src/USER-MISC/angle_dipole.cpp
@@ -15,8 +15,8 @@
Contributing authors: Mario Orsi & Wei Ding (QMUL), m.orsi@qmul.ac.uk
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdlib>
#include "angle_dipole.h"
#include "atom.h"
#include "neighbor.h"
@@ -32,7 +32,11 @@ using namespace MathConst;
/* ---------------------------------------------------------------------- */
-AngleDipole::AngleDipole(LAMMPS *lmp) : Angle(lmp) {}
+AngleDipole::AngleDipole(LAMMPS *lmp) : Angle(lmp)
+{
+ k = NULL;
+ gamma0 = NULL;
+}
/* ---------------------------------------------------------------------- */
diff --git a/src/USER-MISC/angle_dipole.h b/src/USER-MISC/angle_dipole.h
index 347eecfca4a098477bf9a419a8fd6285fe51cdda..6c5dccb803677b274c7cd903549389b80befb986 100644
--- a/src/USER-MISC/angle_dipole.h
+++ b/src/USER-MISC/angle_dipole.h
@@ -20,7 +20,7 @@ AngleStyle(dipole,AngleDipole)
#ifndef LMP_ANGLE_DIPOLE_H
#define LMP_ANGLE_DIPOLE_H
-#include <stdio.h>
+#include <cstdio>
#include "angle.h"
namespace LAMMPS_NS {
diff --git a/src/USER-MISC/angle_fourier.cpp b/src/USER-MISC/angle_fourier.cpp
index 689caeaa5f457b6b3d6dcf4a6c1fe760aec2c47d..e6cc1f1a7e9945a55091002529051649f78186a9 100644
--- a/src/USER-MISC/angle_fourier.cpp
+++ b/src/USER-MISC/angle_fourier.cpp
@@ -16,8 +16,8 @@
[ based on angle_cosine_squared.cpp Naveen Michaud-Agrawal (Johns Hopkins U)]
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdlib>
#include "angle_fourier.h"
#include "atom.h"
#include "neighbor.h"
@@ -35,7 +35,13 @@ using namespace MathConst;
/* ---------------------------------------------------------------------- */
-AngleFourier::AngleFourier(LAMMPS *lmp) : Angle(lmp) {}
+AngleFourier::AngleFourier(LAMMPS *lmp) : Angle(lmp)
+{
+ k = NULL;
+ C0 = NULL;
+ C1 = NULL;
+ C2 = NULL;
+}
/* ---------------------------------------------------------------------- */
diff --git a/src/USER-MISC/angle_fourier.h b/src/USER-MISC/angle_fourier.h
index da5c96479f2febf30a9ca0f9f945980c216f69e6..14b4eedf57be4bee470b70243a9b30a5ec7e6554 100644
--- a/src/USER-MISC/angle_fourier.h
+++ b/src/USER-MISC/angle_fourier.h
@@ -20,7 +20,7 @@ AngleStyle(fourier,AngleFourier)
#ifndef ANGLE_FOURIER_H
#define ANGLE_FOURIER_H
-#include <stdio.h>
+#include <cstdio>
#include "angle.h"
namespace LAMMPS_NS {
diff --git a/src/USER-MISC/angle_fourier_simple.cpp b/src/USER-MISC/angle_fourier_simple.cpp
index bd4322fe78ca77e385d4c3668b1594408f9a55b9..8464fe815c9db0e9948ec9a0c7185a4409edf6e3 100644
--- a/src/USER-MISC/angle_fourier_simple.cpp
+++ b/src/USER-MISC/angle_fourier_simple.cpp
@@ -16,8 +16,8 @@
[ based on angle_cosine_squared.cpp Naveen Michaud-Agrawal (Johns Hopkins U)]
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdlib>
#include "angle_fourier_simple.h"
#include "atom.h"
#include "neighbor.h"
@@ -35,7 +35,12 @@ using namespace MathConst;
/* ---------------------------------------------------------------------- */
-AngleFourierSimple::AngleFourierSimple(LAMMPS *lmp) : Angle(lmp) {}
+AngleFourierSimple::AngleFourierSimple(LAMMPS *lmp) : Angle(lmp)
+{
+ k = NULL;
+ C = NULL;
+ N = NULL;
+}
/* ---------------------------------------------------------------------- */
diff --git a/src/USER-MISC/angle_fourier_simple.h b/src/USER-MISC/angle_fourier_simple.h
index ca160f185da7f393f9926a6f84a2e1aca232d6a5..3a7bd37750a93b029f0917a95dd5a7374c2a2e12 100644
--- a/src/USER-MISC/angle_fourier_simple.h
+++ b/src/USER-MISC/angle_fourier_simple.h
@@ -20,7 +20,7 @@ AngleStyle(fourier/simple,AngleFourierSimple)
#ifndef ANGLE_FOURIER_SIMPLE_H
#define ANGLE_FOURIER_SIMPLE_H
-#include <stdio.h>
+#include <cstdio>
#include "angle.h"
namespace LAMMPS_NS {
diff --git a/src/USER-MISC/angle_quartic.cpp b/src/USER-MISC/angle_quartic.cpp
index 5d990003a88ac063d1a6c108402a55fd5c3ecd9e..356f2df5d478683e4c0be128ff589f0de0a54047 100644
--- a/src/USER-MISC/angle_quartic.cpp
+++ b/src/USER-MISC/angle_quartic.cpp
@@ -16,8 +16,8 @@
[ based on angle_harmonic.cpp]
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdlib>
#include "angle_quartic.h"
#include "atom.h"
#include "neighbor.h"
diff --git a/src/USER-MISC/angle_quartic.h b/src/USER-MISC/angle_quartic.h
index 8844ad111de54d44d8f1c59828fc9cc9b056bfaa..7043cab06413dda4da43caa8baac0aa3a762cf6c 100644
--- a/src/USER-MISC/angle_quartic.h
+++ b/src/USER-MISC/angle_quartic.h
@@ -20,7 +20,7 @@ AngleStyle(quartic,AngleQuartic)
#ifndef LMP_ANGLE_QUARTIC_H
#define LMP_ANGLE_QUARTIC_H
-#include <stdio.h>
+#include <cstdio>
#include "angle.h"
namespace LAMMPS_NS {
diff --git a/src/USER-MISC/bond_harmonic_shift.cpp b/src/USER-MISC/bond_harmonic_shift.cpp
index 70db2cc2bd690f73ec687b9aeb9e616867853a33..7148c5438d1d4ff200915edbb5c1fda345bd3d01 100644
--- a/src/USER-MISC/bond_harmonic_shift.cpp
+++ b/src/USER-MISC/bond_harmonic_shift.cpp
@@ -15,8 +15,8 @@
Contributing author: Carsten Svaneborg, science@zqex.dk
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdlib>
#include "bond_harmonic_shift.h"
#include "atom.h"
#include "neighbor.h"
diff --git a/src/USER-MISC/bond_harmonic_shift.h b/src/USER-MISC/bond_harmonic_shift.h
index 95dc091a62926894c99417895050c7743a2c2b6f..ff0d358243a832c36e43333ce5707a4321fa9fcc 100644
--- a/src/USER-MISC/bond_harmonic_shift.h
+++ b/src/USER-MISC/bond_harmonic_shift.h
@@ -20,7 +20,7 @@ BondStyle(harmonic/shift,BondHarmonicShift)
#ifndef LMP_BOND_HARMONIC_SHIFT_H
#define LMP_BOND_HARMONIC_SHIFT_H
-#include <stdio.h>
+#include <cstdio>
#include "bond.h"
namespace LAMMPS_NS {
diff --git a/src/USER-MISC/bond_harmonic_shift_cut.cpp b/src/USER-MISC/bond_harmonic_shift_cut.cpp
index aa0091019dbc2509e83c86732c02c901ff66df85..20c8a1a30019fb5cb3bdb99b597e91c6fd116778 100644
--- a/src/USER-MISC/bond_harmonic_shift_cut.cpp
+++ b/src/USER-MISC/bond_harmonic_shift_cut.cpp
@@ -15,8 +15,8 @@
Contributing author: Carsten Svaneborg, science@zqex.dk
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdlib>
#include "bond_harmonic_shift_cut.h"
#include "atom.h"
#include "neighbor.h"
diff --git a/src/USER-MISC/bond_harmonic_shift_cut.h b/src/USER-MISC/bond_harmonic_shift_cut.h
index 9b2587936ec7012dfef6af00b715cc1a459bb4a2..5db76d51aa5fbde88bc2061a4b34c506bcd239c3 100644
--- a/src/USER-MISC/bond_harmonic_shift_cut.h
+++ b/src/USER-MISC/bond_harmonic_shift_cut.h
@@ -20,7 +20,7 @@ BondStyle(harmonic/shift/cut,BondHarmonicShiftCut)
#ifndef LMP_BOND_HARMONIC_SHIFT_CUT_H
#define LMP_BOND_HARMONIC_SHIFT_CUT_H
-#include <stdio.h>
+#include <cstdio>
#include "bond.h"
namespace LAMMPS_NS {
diff --git a/src/USER-MISC/compute_ackland_atom.cpp b/src/USER-MISC/compute_ackland_atom.cpp
index 285f64a5e94bec9678fcd9d57493fdf4d90902e0..a17aefe71b46b0dd435473c9d917eb6a74561365 100644
--- a/src/USER-MISC/compute_ackland_atom.cpp
+++ b/src/USER-MISC/compute_ackland_atom.cpp
@@ -12,11 +12,13 @@
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
- Contributing author: G. Ziegenhain, gerolf@ziegenhain.com
- Copyright (C) 2007
+ Contributing author: G. Ziegenhain, gerolf@ziegenhain.com
+ Copyright (C) 2007
+ Updated algorithm by: Brian Barnes, brian.c.barnes11.civ@mail.mil
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cmath>
+#include <cstring>
#include "compute_ackland_atom.h"
#include "atom.h"
#include "update.h"
@@ -29,7 +31,6 @@
#include "comm.h"
#include "memory.h"
#include "error.h"
-#include <math.h>
using namespace LAMMPS_NS;
@@ -40,7 +41,8 @@ enum{UNKNOWN,BCC,FCC,HCP,ICO};
ComputeAcklandAtom::ComputeAcklandAtom(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
- if (narg != 3) error->all(FLERR,"Illegal compute ackland/atom command");
+ if ((narg < 3) || (narg > 5))
+ error->all(FLERR,"Illegal compute ackland/atom command");
peratom_flag = 1;
size_peratom_cols = 0;
@@ -48,10 +50,26 @@ ComputeAcklandAtom::ComputeAcklandAtom(LAMMPS *lmp, int narg, char **arg) :
nmax = 0;
structure = NULL;
maxneigh = 0;
+ legacy = 0;
distsq = NULL;
nearest = NULL;
nearest_n0 = NULL;
nearest_n1 = NULL;
+
+ int iarg = 3;
+ while (narg > iarg) {
+ if (strcmp("legacy",arg[iarg]) == 0) {
+ ++iarg;
+ if (iarg >= narg)
+ error->all(FLERR,"Invalid compute ackland/atom command");
+ if (strcmp("yes",arg[iarg]) == 0)
+ legacy = 1;
+ else if (strcmp("no",arg[iarg]) == 0)
+ legacy = 0;
+ else error->all(FLERR,"Invalid compute ackland/atom command");
+ }
+ ++iarg;
+ }
}
/* ---------------------------------------------------------------------- */
@@ -140,13 +158,13 @@ void ComputeAcklandAtom::compute_peratom()
// ensure distsq and nearest arrays are long enough
if (jnum > maxneigh) {
- memory->destroy(distsq);
- memory->destroy(nearest);
+ memory->destroy(distsq);
+ memory->destroy(nearest);
memory->destroy(nearest_n0);
memory->destroy(nearest_n1);
- maxneigh = jnum;
- memory->create(distsq,maxneigh,"compute/ackland/atom:distsq");
- memory->create(nearest,maxneigh,"compute/ackland/atom:nearest");
+ maxneigh = jnum;
+ memory->create(distsq,maxneigh,"compute/ackland/atom:distsq");
+ memory->create(nearest,maxneigh,"compute/ackland/atom:nearest");
memory->create(nearest_n0,maxneigh,"compute/ackland/atom:nearest_n0");
memory->create(nearest_n1,maxneigh,"compute/ackland/atom:nearest_n1");
}
@@ -157,14 +175,14 @@ void ComputeAcklandAtom::compute_peratom()
n = 0;
for (jj = 0; jj < jnum; jj++) {
- j = jlist[jj];
+ j = jlist[jj];
j &= NEIGHMASK;
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
- if (rsq < cutsq) {
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+ if (rsq < cutsq) {
distsq[n] = rsq;
nearest[n++] = j;
}
@@ -188,12 +206,12 @@ void ComputeAcklandAtom::compute_peratom()
n1_dist_sq = 1.55*r0_sq;
int n0 = 0, n1 = 0;
for (j = 0; j < n; j++) {
- if (distsq[j] < n1_dist_sq) {
- nearest_n1[n1++] = nearest[j];
- if (distsq[j] < n0_dist_sq) {
- nearest_n0[n0++] = nearest[j];
- }
- }
+ if (distsq[j] < n1_dist_sq) {
+ nearest_n1[n1++] = nearest[j];
+ if (distsq[j] < n0_dist_sq) {
+ nearest_n0[n0++] = nearest[j];
+ }
+ }
}
// Evaluate all angles <(r_ij,rik) forall n0 particles with:
@@ -231,47 +249,98 @@ void ComputeAcklandAtom::compute_peratom()
else chi[7]++;
}
}
+ if (legacy) {
- if (chi[7] > 0 || n0 < 11) structure[i] = UNKNOWN;
- else if (chi[0] == 7) structure[i] = BCC;
- else if (chi[0] == 6) structure[i] = FCC;
- else if (chi[0] == 3) structure[i] = HCP;
- else {
+ // This is the original implementation by Gerolf Ziegenhain
// Deviations from the different lattice structures
+ double delta_bcc = 0.35*chi[4]/(double)(chi[5]+chi[6]-chi[4]);
double delta_cp = fabs(1.-(double)chi[6]/24.);
+ double delta_fcc = 0.61*(fabs((double)(chi[0]+chi[1]-6.))+
+ (double)chi[2])/6.0;
+ double delta_hcp = (fabs((double)chi[0]-3.)+
+ fabs((double)chi[0]+(double)chi[1]+
+ (double)chi[2]+(double)chi[3]-9.0))/12.0;
+
+ // Identification of the local structure according to the reference
+
+ if (chi[0] == 7) { delta_bcc = 0.; }
+ else if (chi[0] == 6) { delta_fcc = 0.; }
+ else if (chi[0] <= 3) { delta_hcp = 0.; }
+
+ if (chi[7] > 0.)
+ structure[i] = UNKNOWN;
+ else
+ if (chi[4] < 3.)
+ {
+ if (n1 > 13 || n1 < 11)
+ structure[i] = UNKNOWN;
+ else
+ structure[i] = ICO;
+ } else
+ if (delta_bcc <= delta_cp)
+ {
+ if (n1 < 11)
+ structure[i] = UNKNOWN;
+ else
+ structure[i] = BCC;
+ } else
+ if (n1 > 12 || n1 < 11)
+ structure[i] = UNKNOWN;
+ else
+ if (delta_fcc < delta_hcp)
+ structure[i] = FCC;
+ else
+ structure[i] = HCP;
- // ensure we do not get divide by zero
- // and if we will, make delta_bcc irrelevant
- double delta_bcc = delta_cp + 1.0;
- int chi56m4 = chi[5]+chi[6]-chi[4];
+ } else {
- // note that chi[7] presumed zero
- if (chi56m4 != 0) delta_bcc = 0.35*chi[4]/(double)chi56m4;
+ // This is the updated implementation by Brian Barnes
- double delta_fcc = 0.61*(fabs((double)(chi[0]+chi[1]-6))
- +(double)chi[2])/6.0;
+ if (chi[7] > 0 || n0 < 11) structure[i] = UNKNOWN;
+ else if (chi[0] == 7) structure[i] = BCC;
+ else if (chi[0] == 6) structure[i] = FCC;
+ else if (chi[0] == 3) structure[i] = HCP;
+ else {
+ // Deviations from the different lattice structures
- double delta_hcp = (fabs((double)chi[0]-3.)+fabs((double)chi[0]
- +(double)chi[1]+(double)chi[2]+(double)chi[3]
- -9.0))/12.0;
+ double delta_cp = fabs(1.-(double)chi[6]/24.);
- // Identification of the local structure according to the reference
+ // ensure we do not get divide by zero
+ // and if we will, make delta_bcc irrelevant
+ double delta_bcc = delta_cp + 1.0;
+ int chi56m4 = chi[5]+chi[6]-chi[4];
- if (delta_bcc >= 0.1 && delta_cp >= 0.1 && delta_fcc >= 0.1
- && delta_hcp >= 0.1) structure[i] = UNKNOWN;
+ // note that chi[7] presumed zero
+ if (chi56m4 != 0) delta_bcc = 0.35*chi[4]/(double)chi56m4;
- // not part of Ackland-Jones 2006; included for backward compatibility
- if (chi[4] < 3. && n1 == 12) structure[i] = ICO;
+ double delta_fcc = 0.61*(fabs((double)(chi[0]+chi[1]-6))
+ +(double)chi[2])/6.0;
+
+ double delta_hcp = (fabs((double)chi[0]-3.)
+ +fabs((double)chi[0]
+ +(double)chi[1]
+ +(double)chi[2]
+ +(double)chi[3]
+ -9.0))/12.0;
+
+ // Identification of the local structure according to the reference
+
+ if (delta_bcc >= 0.1 && delta_cp >= 0.1 && delta_fcc >= 0.1
+ && delta_hcp >= 0.1) structure[i] = UNKNOWN;
+
+ // not part of Ackland-Jones 2006; included for backward compatibility
+ if (chi[4] < 3. && n1 == 12) structure[i] = ICO;
- else {
- if (delta_bcc <= delta_cp && n1 > 10 && n1 < 13) structure[i] = BCC;
else {
- if (n0 > 12) structure[i] = UNKNOWN;
+ if (delta_bcc <= delta_cp && n1 > 10 && n1 < 13) structure[i] = BCC;
else {
- if (delta_fcc < delta_hcp) structure[i] = FCC;
- else
- structure[i] = HCP;
+ if (n0 > 12) structure[i] = UNKNOWN;
+ else {
+ if (delta_fcc < delta_hcp) structure[i] = FCC;
+ else
+ structure[i] = HCP;
+ }
}
}
}
diff --git a/src/USER-MISC/compute_ackland_atom.h b/src/USER-MISC/compute_ackland_atom.h
index 5464a10f872101fc5b07a85dab118d091ab2980e..dd70762627646080dace0fd75dfc94a11d98feaf 100644
--- a/src/USER-MISC/compute_ackland_atom.h
+++ b/src/USER-MISC/compute_ackland_atom.h
@@ -34,7 +34,7 @@ class ComputeAcklandAtom : public Compute {
double memory_usage();
private:
- int nmax,maxneigh;
+ int nmax,maxneigh,legacy;
double *distsq;
int *nearest, *nearest_n0, *nearest_n1;
double *structure;
diff --git a/src/USER-MISC/compute_basal_atom.cpp b/src/USER-MISC/compute_basal_atom.cpp
index cd393eb2acf81c6d2f14cc3516e87c24d6a3a906..4d8627a11fb66534b0e982413790156d4efaf524 100644
--- a/src/USER-MISC/compute_basal_atom.cpp
+++ b/src/USER-MISC/compute_basal_atom.cpp
@@ -16,7 +16,8 @@
Copyright (C) 2013
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cmath>
+#include <cstring>
#include "compute_basal_atom.h"
#include "atom.h"
#include "update.h"
@@ -29,7 +30,6 @@
#include "comm.h"
#include "memory.h"
#include "error.h"
-#include <math.h>
using namespace LAMMPS_NS;
@@ -204,8 +204,11 @@ void ComputeBasalAtom::compute_peratom()
double bond_angle;
double norm_j, norm_k;
chi[0] = chi[1] = chi[2] = chi[3] = chi[4] = chi[5] = chi[6] = chi[7] = 0;
- double x_ij, y_ij, z_ij, x_ik, y_ik, z_ik,x3[n0],y3[n0],z3[n0],
- xmean5, ymean5, zmean5, xmean6, ymean6, zmean6, xmean7, ymean7, zmean7;
+ double x_ij, y_ij, z_ij, x_ik, y_ik, z_ik, xmean5, ymean5, zmean5,
+ xmean6, ymean6, zmean6, xmean7, ymean7, zmean7;
+ double *x3 = new double[n0];
+ double *y3 = new double[n0];
+ double *z3 = new double[n0];
for (j = 0; j < n0; j++) {
x_ij = x[i][0]-x[nearest_n0[j]][0];
y_ij = x[i][1]-x[nearest_n0[j]][1];
@@ -411,9 +414,12 @@ void ComputeBasalAtom::compute_peratom()
}
}
}
- }
- //if there are less than two ~180 degree bond angles, the algorithm returns null
- else BPV[i][0] = BPV[i][1] = BPV[i][2] = 0.0;
+ //if there are less than two ~180 degree bond angles, the algorithm returns null
+ } else BPV[i][0] = BPV[i][1] = BPV[i][2] = 0.0;
+
+ delete[] x3;
+ delete[] y3;
+ delete[] z3;
//normalize BPV:
double Mag = sqrt(BPV[i][0]*BPV[i][0] +
diff --git a/src/USER-MISC/compute_cnp_atom.cpp b/src/USER-MISC/compute_cnp_atom.cpp
index f479486b79cc18f48fe7032f0c15ba3e9509f2df..51cf3ab07a43628ba454f708400d386bdffdb54f 100644
--- a/src/USER-MISC/compute_cnp_atom.cpp
+++ b/src/USER-MISC/compute_cnp_atom.cpp
@@ -21,9 +21,9 @@
branicio@usc.edu
------------------------------------------------------------------------- */
-#include <string.h>
-#include <stdlib.h>
-#include <math.h>
+#include <cstring>
+#include <cstdlib>
+#include <cmath>
#include "compute_cnp_atom.h"
#include "atom.h"
diff --git a/src/USER-MISC/compute_pressure_grem.cpp b/src/USER-MISC/compute_pressure_grem.cpp
index ae9179cc4313745ea248d606f1c4768e4fa86e82..087c01bd8e2ad8da526bf213609c8f7241377b0d 100644
--- a/src/USER-MISC/compute_pressure_grem.cpp
+++ b/src/USER-MISC/compute_pressure_grem.cpp
@@ -12,8 +12,8 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <string.h>
-#include <stdlib.h>
+#include <cstring>
+#include <cstdlib>
#include "compute_pressure_grem.h"
#include "atom.h"
#include "update.h"
diff --git a/src/USER-MISC/compute_temp_rotate.cpp b/src/USER-MISC/compute_temp_rotate.cpp
index b948738e0054dca0de40bde7481d678eb2bac198..66f1b8f5f75939d02092f5c1b9a7bf50a404c059 100644
--- a/src/USER-MISC/compute_temp_rotate.cpp
+++ b/src/USER-MISC/compute_temp_rotate.cpp
@@ -16,8 +16,8 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cstdlib>
+#include <cstring>
#include "compute_temp_rotate.h"
#include "atom.h"
#include "update.h"
diff --git a/src/USER-MISC/dihedral_cosine_shift_exp.cpp b/src/USER-MISC/dihedral_cosine_shift_exp.cpp
index 85ff4b27191e3b6d19bce335781f7bd715fbfff1..82da173f8e2c3d14bce6344f0f9d8080effd9594 100644
--- a/src/USER-MISC/dihedral_cosine_shift_exp.cpp
+++ b/src/USER-MISC/dihedral_cosine_shift_exp.cpp
@@ -16,8 +16,8 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <math.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdlib>
#include "dihedral_cosine_shift_exp.h"
#include "atom.h"
#include "comm.h"
@@ -26,6 +26,7 @@
#include "force.h"
#include "update.h"
#include "memory.h"
+#include "math_const.h"
#include "error.h"
using namespace LAMMPS_NS;
@@ -285,9 +286,9 @@ void DihedralCosineShiftExp::coeff(int narg, char **arg)
doExpansion[i]=(fabs(a_)<0.001);
umin[i] = umin_;
a[i] = a_;
- cost[i] = cos(theta0_*3.14159265/180);
- sint[i] = sin(theta0_*3.14159265/180);
- theta[i] = theta0_*3.14159265/180;
+ cost[i] = cos(theta0_*MathConst::MY_PI/180.0);
+ sint[i] = sin(theta0_*MathConst::MY_PI/180.0);
+ theta[i] = theta0_*MathConst::MY_PI/180.0;
if (!doExpansion[i]) opt1[i]=umin_/(exp(a_)-1);
@@ -338,3 +339,14 @@ void DihedralCosineShiftExp::read_restart(FILE *fp)
if (!doExpansion[i]) opt1[i]=umin[i]/(exp(a[i])-1);
}
}
+
+/* ----------------------------------------------------------------------
+ proc 0 writes to data file
+------------------------------------------------------------------------- */
+
+void DihedralCosineShiftExp::write_data(FILE *fp)
+{
+ for (int i = 1; i <= atom->ndihedraltypes; i++)
+ fprintf(fp,"%d %g %g %g\n",i,umin[i],
+ theta[i]*180.0/MathConst::MY_PI,a[i]);
+}
diff --git a/src/USER-MISC/dihedral_cosine_shift_exp.h b/src/USER-MISC/dihedral_cosine_shift_exp.h
index 819fd769cb13cb3fad446b9e4fd9faa9f79b93af..fc4be5049b49c920d40d4fe83995a3b89f2b87db 100644
--- a/src/USER-MISC/dihedral_cosine_shift_exp.h
+++ b/src/USER-MISC/dihedral_cosine_shift_exp.h
@@ -20,7 +20,7 @@ DihedralStyle(cosine/shift/exp,DihedralCosineShiftExp)
#ifndef LMP_DIHEDRAL_COSINE_SHIFT_EXP_H
#define LMP_DIHEDRAL_COSINE_SHIFT_EXP_H
-#include <stdio.h>
+#include <cstdio>
#include "dihedral.h"
namespace LAMMPS_NS {
@@ -33,6 +33,7 @@ class DihedralCosineShiftExp : public Dihedral {
void coeff(int, char **);
void write_restart(FILE *);
void read_restart(FILE *);
+ void write_data(FILE *);
protected:
bool *doExpansion;
diff --git a/src/USER-MISC/dihedral_fourier.cpp b/src/USER-MISC/dihedral_fourier.cpp
index fff10fde11b3c10b4c69294e9b0579869ff807a3..7c405ee28c3378c12a4ba6d28b44b366a1b2abb5 100644
--- a/src/USER-MISC/dihedral_fourier.cpp
+++ b/src/USER-MISC/dihedral_fourier.cpp
@@ -17,8 +17,8 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <math.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdlib>
#include "dihedral_fourier.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-MISC/dihedral_fourier.h b/src/USER-MISC/dihedral_fourier.h
index 4cdb7f222621666624816bcc89ab65d0562a3d58..c1ed843c3486348cd90d364f2d46453838f6d1fc 100644
--- a/src/USER-MISC/dihedral_fourier.h
+++ b/src/USER-MISC/dihedral_fourier.h
@@ -20,7 +20,7 @@ DihedralStyle(fourier,DihedralFourier)
#ifndef LMP_DIHEDRAL_FOURIER_H
#define LMP_DIHEDRAL_FOURIER_H
-#include <stdio.h>
+#include <cstdio>
#include "dihedral.h"
namespace LAMMPS_NS {
diff --git a/src/USER-MISC/dihedral_nharmonic.cpp b/src/USER-MISC/dihedral_nharmonic.cpp
index abb5904b6af55773b43a505263a457c2e92c0a6b..f8e885068070e3d7bbbf1601a7654e7331b5aa70 100644
--- a/src/USER-MISC/dihedral_nharmonic.cpp
+++ b/src/USER-MISC/dihedral_nharmonic.cpp
@@ -16,8 +16,8 @@
[ based on dihedral_multi_harmonic.cpp Mathias Puetz (SNL) and friends ]
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdlib>
#include "dihedral_nharmonic.h"
#include "atom.h"
#include "neighbor.h"
diff --git a/src/USER-MISC/dihedral_nharmonic.h b/src/USER-MISC/dihedral_nharmonic.h
index 2e8050feb9348307b0c21edaf5aa3a10aeaf44f1..7c6a35b200a3a6a8bb91cb21b9a5d9babc3cdfd8 100644
--- a/src/USER-MISC/dihedral_nharmonic.h
+++ b/src/USER-MISC/dihedral_nharmonic.h
@@ -20,7 +20,7 @@ DihedralStyle(nharmonic,DihedralNHarmonic)
#ifndef DIHEDRAL_NHARMONIC_H
#define DIHEDRAL_NHARMONIC_H
-#include <stdio.h>
+#include <cstdio>
#include "dihedral.h"
namespace LAMMPS_NS {
diff --git a/src/USER-MISC/dihedral_quadratic.cpp b/src/USER-MISC/dihedral_quadratic.cpp
index 6841492b2f077f5b2e875810b96c1a21a3761dd1..1b64b52faf34e50792105314277727edeb9efb1b 100644
--- a/src/USER-MISC/dihedral_quadratic.cpp
+++ b/src/USER-MISC/dihedral_quadratic.cpp
@@ -16,8 +16,8 @@
[ based on dihedral_helix.cpp Paul Crozier (SNL) ]
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdlib>
#include "dihedral_quadratic.h"
#include "atom.h"
#include "neighbor.h"
@@ -333,3 +333,12 @@ void DihedralQuadratic::read_restart(FILE *fp)
for (int i = 1; i <= atom->ndihedraltypes; i++) setflag[i] = 1;
}
+/* ----------------------------------------------------------------------
+ proc 0 writes to data file
+------------------------------------------------------------------------- */
+
+void DihedralQuadratic::write_data(FILE *fp)
+{
+ for (int i = 1; i <= atom->ndihedraltypes; i++)
+ fprintf(fp,"%d %g %g \n",i,k[i],phi0[i]*180.0/MY_PI);
+}
diff --git a/src/USER-MISC/dihedral_quadratic.h b/src/USER-MISC/dihedral_quadratic.h
index 638efac6687dc7f83754384d41c4cff0208a14b7..edc29c3cf8b5b87a84d291450dacdeb359d05ac1 100644
--- a/src/USER-MISC/dihedral_quadratic.h
+++ b/src/USER-MISC/dihedral_quadratic.h
@@ -20,7 +20,7 @@ DihedralStyle(quadratic,DihedralQuadratic)
#ifndef LMP_DIHEDRAL_QUADRATIC_H
#define LMP_DIHEDRAL_QUADRATIC_H
-#include <stdio.h>
+#include <cstdio>
#include "dihedral.h"
namespace LAMMPS_NS {
@@ -33,6 +33,7 @@ class DihedralQuadratic : public Dihedral {
void coeff(int, char **);
void write_restart(FILE *);
void read_restart(FILE *);
+ void write_data(FILE *);
protected:
double *k,*phi0;
diff --git a/src/USER-MISC/dihedral_spherical.h b/src/USER-MISC/dihedral_spherical.h
index 0067e5eca85058dc86d20b98cab2f5f716cd872b..ae0ece189a69118853c35b54ba74a00d7800a634 100644
--- a/src/USER-MISC/dihedral_spherical.h
+++ b/src/USER-MISC/dihedral_spherical.h
@@ -20,7 +20,7 @@ DihedralStyle(spherical,DihedralSpherical)
#ifndef LMP_DIHEDRAL_SPHERICAL_H
#define LMP_DIHEDRAL_SPHERICAL_H
-#include <stdio.h>
+#include <cstdio>
#include "dihedral.h"
namespace LAMMPS_NS {
diff --git a/src/USER-MISC/dihedral_table_cut.cpp b/src/USER-MISC/dihedral_table_cut.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..7345bcdad164c2df0cd598c8606b8f26cf1fc511
--- /dev/null
+++ b/src/USER-MISC/dihedral_table_cut.cpp
@@ -0,0 +1,1500 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+ Contributing author: K. Michael Salerno (NRL)
+ Based on tabulated dihedral (dihedral_table.cpp) by Andrew Jewett
+------------------------------------------------------------------------- */
+
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
+#include <cassert>
+#include <string>
+#include <fstream>
+#include <iostream>
+#include <sstream>
+
+#include "dihedral_table_cut.h"
+#include "atom.h"
+#include "neighbor.h"
+#include "update.h"
+#include "domain.h"
+#include "comm.h"
+#include "force.h"
+#include "citeme.h"
+#include "math_const.h"
+#include "math_extra.h"
+#include "memory.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+using namespace MathConst;
+using namespace std;
+using namespace MathExtra;
+
+
+static const char cite_dihedral_tablecut[] =
+ "dihedral_style tablecut command:\n\n"
+ "@Article{Salerno17,\n"
+ " author = {K. M. Salerno and N. Bernstein},\n"
+ " title = {Persistence Length, End-to-End Distance, and Structure of Coarse-Grained Polymers},\n"
+ " journal = {J.~Chem.~Theory Comput.},\n"
+ " year = 2018,\n"
+ " DOI = 10.1021/acs.jctc.7b01229"
+ "}\n\n";
+
+/* ---------------------------------------------------------------------- */
+
+#define TOLERANCE 0.05
+#define SMALL 0.0000001
+
+// ------------------------------------------------------------------------
+// The following auxiliary functions were left out of the
+// DihedralTable class either because they require template parameters,
+// or because they have nothing to do with dihedral angles.
+// ------------------------------------------------------------------------
+
+// -------------------------------------------------------------------
+// --------- The function was stolen verbatim from the ---------
+// --------- GNU Scientific Library (GSL, version 1.15) ---------
+// -------------------------------------------------------------------
+
+/* Author: Gerard Jungman */
+/* for description of method see [Engeln-Mullges + Uhlig, p. 96]
+ *
+ * diag[0] offdiag[0] 0 ..... offdiag[N-1]
+ * offdiag[0] diag[1] offdiag[1] .....
+ * 0 offdiag[1] diag[2]
+ * 0 0 offdiag[2] .....
+ * ... ...
+ * offdiag[N-1] ...
+ *
+ */
+// -- (A non-symmetric version of this function is also available.) --
+
+enum { //GSL status return codes.
+ GSL_FAILURE = -1,
+ GSL_SUCCESS = 0,
+ GSL_ENOMEM = 8,
+ GSL_EZERODIV = 12,
+ GSL_EBADLEN = 19
+};
+
+
+static int solve_cyc_tridiag( const double diag[], size_t d_stride,
+ const double offdiag[], size_t o_stride,
+ const double b[], size_t b_stride,
+ double x[], size_t x_stride,
+ size_t N, bool warn)
+{
+ int status = GSL_SUCCESS;
+ double * delta = (double *) malloc (N * sizeof (double));
+ double * gamma = (double *) malloc (N * sizeof (double));
+ double * alpha = (double *) malloc (N * sizeof (double));
+ double * c = (double *) malloc (N * sizeof (double));
+ double * z = (double *) malloc (N * sizeof (double));
+
+ if (delta == 0 || gamma == 0 || alpha == 0 || c == 0 || z == 0) {
+ if (warn)
+ fprintf(stderr,"Internal Cyclic Spline Error: failed to allocate working space\n");
+
+ if (delta) free(delta);
+ if (gamma) free(gamma);
+ if (alpha) free(alpha);
+ if (c) free(c);
+ if (z) free(z);
+ return GSL_ENOMEM;
+ }
+ else
+ {
+ size_t i, j;
+ double sum = 0.0;
+
+ /* factor */
+
+ if (N == 1)
+ {
+ x[0] = b[0] / diag[0];
+ free(delta);
+ free(gamma);
+ free(alpha);
+ free(c);
+ free(z);
+ return GSL_SUCCESS;
+ }
+
+ alpha[0] = diag[0];
+ gamma[0] = offdiag[0] / alpha[0];
+ delta[0] = offdiag[o_stride * (N-1)] / alpha[0];
+
+ if (alpha[0] == 0) {
+ status = GSL_EZERODIV;
+ }
+
+ for (i = 1; i < N - 2; i++)
+ {
+ alpha[i] = diag[d_stride * i] - offdiag[o_stride * (i-1)] * gamma[i - 1];
+ gamma[i] = offdiag[o_stride * i] / alpha[i];
+ delta[i] = -delta[i - 1] * offdiag[o_stride * (i-1)] / alpha[i];
+ if (alpha[i] == 0) {
+ status = GSL_EZERODIV;
+ }
+ }
+
+ for (i = 0; i < N - 2; i++)
+ {
+ sum += alpha[i] * delta[i] * delta[i];
+ }
+
+ alpha[N - 2] = diag[d_stride * (N - 2)] - offdiag[o_stride * (N - 3)] * gamma[N - 3];
+
+ gamma[N - 2] = (offdiag[o_stride * (N - 2)] - offdiag[o_stride * (N - 3)] * delta[N - 3]) / alpha[N - 2];
+
+ alpha[N - 1] = diag[d_stride * (N - 1)] - sum - alpha[(N - 2)] * gamma[N - 2] * gamma[N - 2];
+
+ /* update */
+ z[0] = b[0];
+ for (i = 1; i < N - 1; i++)
+ {
+ z[i] = b[b_stride * i] - z[i - 1] * gamma[i - 1];
+ }
+ sum = 0.0;
+ for (i = 0; i < N - 2; i++)
+ {
+ sum += delta[i] * z[i];
+ }
+ z[N - 1] = b[b_stride * (N - 1)] - sum - gamma[N - 2] * z[N - 2];
+ for (i = 0; i < N; i++)
+ {
+ c[i] = z[i] / alpha[i];
+ }
+
+ /* backsubstitution */
+ x[x_stride * (N - 1)] = c[N - 1];
+ x[x_stride * (N - 2)] = c[N - 2] - gamma[N - 2] * x[x_stride * (N - 1)];
+ if (N >= 3)
+ {
+ for (i = N - 3, j = 0; j <= N - 3; j++, i--)
+ {
+ x[x_stride * i] = c[i] - gamma[i] * x[x_stride * (i + 1)] - delta[i] * x[x_stride * (N - 1)];
+ }
+ }
+ }
+
+ free (z);
+ free (c);
+ free (alpha);
+ free (gamma);
+ free (delta);
+
+ if ((status == GSL_EZERODIV) && warn)
+ fprintf(stderr, "Internal Cyclic Spline Error: Matrix must be positive definite.\n");
+
+ return status;
+} //solve_cyc_tridiag()
+
+/* ----------------------------------------------------------------------
+ spline and splint routines modified from Numerical Recipes
+------------------------------------------------------------------------- */
+
+static int cyc_spline(double const *xa,
+ double const *ya,
+ int n,
+ double period,
+ double *y2a, bool warn)
+{
+
+ double *diag = new double[n];
+ double *offdiag = new double[n];
+ double *rhs = new double[n];
+ double xa_im1, xa_ip1;
+
+ // In the cyclic case, there are n equations with n unknows.
+ // The for loop sets up the equations we need to solve.
+ // Later we invoke the GSL tridiagonal matrix solver to solve them.
+
+ for(int i=0; i < n; i++) {
+
+ // I have to lookup xa[i+1] and xa[i-1]. This gets tricky because of
+ // periodic boundary conditions. We handle that now.
+ int im1 = i-1;
+ if (im1<0) {
+ im1 += n;
+ xa_im1 = xa[im1] - period;
+ }
+ else
+ xa_im1 = xa[im1];
+
+ int ip1 = i+1;
+ if (ip1>=n) {
+ ip1 -= n;
+ xa_ip1 = xa[ip1] + period;
+ }
+ else
+ xa_ip1 = xa[ip1];
+
+ // Recall that we want to find the y2a[] parameters (there are n of them).
+ // To solve for them, we have a linear equation with n unknowns
+ // (in the cyclic case that is). For details, the non-cyclic case is
+ // explained in equation 3.3.7 in Numerical Recipes in C, p. 115.
+ diag[i] = (xa_ip1 - xa_im1) / 3.0;
+ offdiag[i] = (xa_ip1 - xa[i]) / 6.0;
+ rhs[i] = ((ya[ip1] - ya[i]) / (xa_ip1 - xa[i])) -
+ ((ya[i] - ya[im1]) / (xa[i] - xa_im1));
+ }
+
+ // Because this matrix is tridiagonal (and cyclic), we can use the following
+ // cheap method to invert it.
+ if (solve_cyc_tridiag(diag, 1,
+ offdiag, 1,
+ rhs, 1,
+ y2a, 1,
+ n, warn) != GSL_SUCCESS) {
+ if (warn)
+ fprintf(stderr,"Error in inverting matrix for splines.\n");
+
+ delete [] diag;
+ delete [] offdiag;
+ delete [] rhs;
+ return 1;
+ }
+ delete [] diag;
+ delete [] offdiag;
+ delete [] rhs;
+ return 0;
+} // cyc_spline()
+
+/* ---------------------------------------------------------------------- */
+
+// cyc_splint(): Evaluates a spline at position x, with n control
+// points located at xa[], ya[], and with parameters y2a[]
+// The xa[] must be monotonically increasing and their
+// range should not exceed period (ie xa[n-1] < xa[0] + period).
+// x must lie in the range: [(xa[n-1]-period), (xa[0]+period)]
+// "period" is typically 2*PI.
+static double cyc_splint(double const *xa,
+ double const *ya,
+ double const *y2a,
+ int n,
+ double period,
+ double x)
+{
+ int klo = -1;
+ int khi = n;
+ int k;
+ double xlo = xa[n-1] - period;
+ double xhi = xa[0] + period;
+ while (khi-klo > 1) {
+ k = (khi+klo) >> 1; //(k=(khi+klo)/2)
+ if (xa[k] > x) {
+ khi = k;
+ xhi = xa[k];
+ }
+ else {
+ klo = k;
+ xlo = xa[k];
+ }
+ }
+
+ if (khi == n) khi = 0;
+ if (klo ==-1) klo = n-1;
+
+ double h = xhi-xlo;
+ double a = (xhi-x) / h;
+ double b = (x-xlo) / h;
+ double y = a*ya[klo] + b*ya[khi] +
+ ((a*a*a-a)*y2a[klo] + (b*b*b-b)*y2a[khi]) * (h*h)/6.0;
+
+ return y;
+
+} // cyc_splint()
+
+
+static double cyc_lin(double const *xa,
+ double const *ya,
+ int n,
+ double period,
+ double x)
+{
+ int klo = -1;
+ int khi = n;
+ int k;
+ double xlo = xa[n-1] - period;
+ double xhi = xa[0] + period;
+ while (khi-klo > 1) {
+ k = (khi+klo) >> 1; //(k=(khi+klo)/2)
+ if (xa[k] > x) {
+ khi = k;
+ xhi = xa[k];
+ }
+ else {
+ klo = k;
+ xlo = xa[k];
+ }
+ }
+
+ if (khi == n) khi = 0;
+ if (klo ==-1) klo = n-1;
+
+ double h = xhi-xlo;
+ double a = (xhi-x) / h;
+ double b = (x-xlo) / h;
+ double y = a*ya[klo] + b*ya[khi];
+
+ return y;
+
+} // cyc_lin()
+
+
+
+
+// cyc_splintD(): Evaluate the deriviative of a cyclic spline at position x,
+// with n control points at xa[], ya[], with parameters y2a[].
+// The xa[] must be monotonically increasing and their
+// range should not exceed period (ie xa[n-1] < xa[0] + period).
+// x must lie in the range: [(xa[n-1]-period), (xa[0]+period)]
+// "period" is typically 2*PI.
+static double cyc_splintD(double const *xa,
+ double const *ya,
+ double const *y2a,
+ int n,
+ double period,
+ double x)
+{
+ int klo = -1;
+ int khi = n; // (not n-1)
+ int k;
+ double xlo = xa[n-1] - period;
+ double xhi = xa[0] + period;
+ while (khi-klo > 1) {
+ k = (khi+klo) >> 1; //(k=(khi+klo)/2)
+ if (xa[k] > x) {
+ khi = k;
+ xhi = xa[k];
+ }
+ else {
+ klo = k;
+ xlo = xa[k];
+ }
+ }
+
+ if (khi == n) khi = 0;
+ if (klo ==-1) klo = n-1;
+
+ double yhi = ya[khi];
+ double ylo = ya[klo];
+ double h = xhi-xlo;
+ double g = yhi-ylo;
+ double a = (xhi-x) / h;
+ double b = (x-xlo) / h;
+ // Formula below taken from equation 3.3.5 of "numerical recipes in c"
+ // "yD" = the derivative of y
+ double yD = g/h - ( (3.0*a*a-1.0)*y2a[klo] - (3.0*b*b-1.0)*y2a[khi] ) * h/6.0;
+ // For rerefence: y = a*ylo + b*yhi +
+ // ((a*a*a-a)*y2a[klo] + (b*b*b-b)*y2a[khi]) * (h*h)/6.0;
+
+ return yD;
+
+} // cyc_splintD()
+
+
+/* ---------------------------------------------------------------------- */
+
+DihedralTableCut::DihedralTableCut(LAMMPS *lmp) : Dihedral(lmp)
+{
+ if (lmp->citeme) lmp->citeme->add(cite_dihedral_tablecut);
+ ntables = 0;
+ tables = NULL;
+ checkU_fname = checkF_fname = NULL;
+}
+
+/* ---------------------------------------------------------------------- */
+
+DihedralTableCut::~DihedralTableCut()
+{
+ if (allocated) {
+ memory->destroy(setflag);
+ memory->destroy(setflag_d);
+ memory->destroy(setflag_aat);
+
+ memory->destroy(k1);
+ memory->destroy(k2);
+ memory->destroy(k3);
+ memory->destroy(phi1);
+ memory->destroy(phi2);
+ memory->destroy(phi3);
+
+ memory->destroy(aat_k);
+ memory->destroy(aat_theta0_1);
+ memory->destroy(aat_theta0_2);
+
+ for (int m = 0; m < ntables; m++) free_table(&tables[m]);
+ memory->sfree(tables);
+ memory->sfree(checkU_fname);
+ memory->sfree(checkF_fname);
+
+ memory->destroy(setflag);
+ memory->destroy(tabindex);
+
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void DihedralTableCut::compute(int eflag, int vflag)
+{
+
+ int i1,i2,i3,i4,i,j,k,n,type;
+ double edihedral;
+ double vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,vb2xm,vb2ym,vb2zm;
+ double fphi,fpphi;
+ double r1mag2,r1,r2mag2,r2,r3mag2,r3;
+ double sb1,rb1,sb2,rb2,sb3,rb3,c0,r12c1;
+ double r12c2,costh12,costh13,costh23,sc1,sc2,s1,s2,c;
+ double phi,sinphi,a11,a22,a33,a12,a13,a23,sx1,sx2;
+ double sx12,sy1,sy2,sy12,sz1,sz2,sz12;
+ double t1,t2,t3,t4;
+ double da1,da2;
+ double s12,sin2;
+ double dcosphidr[4][3],dphidr[4][3],dthetadr[2][4][3];
+ double fabcd[4][3];
+
+ edihedral = 0.0;
+ if (eflag || vflag) ev_setup(eflag,vflag);
+ else evflag = 0;
+
+ double **x = atom->x;
+ double **f = atom->f;
+ int **dihedrallist = neighbor->dihedrallist;
+ int ndihedrallist = neighbor->ndihedrallist;
+ int nlocal = atom->nlocal;
+ int newton_bond = force->newton_bond;
+
+ for (n = 0; n < ndihedrallist; n++) {
+ i1 = dihedrallist[n][0];
+ i2 = dihedrallist[n][1];
+ i3 = dihedrallist[n][2];
+ i4 = dihedrallist[n][3];
+ type = dihedrallist[n][4];
+
+ // 1st bond
+
+ vb1x = x[i1][0] - x[i2][0];
+ vb1y = x[i1][1] - x[i2][1];
+ vb1z = x[i1][2] - x[i2][2];
+
+ // 2nd bond
+
+ vb2x = x[i3][0] - x[i2][0];
+ vb2y = x[i3][1] - x[i2][1];
+ vb2z = x[i3][2] - x[i2][2];
+
+ vb2xm = -vb2x;
+ vb2ym = -vb2y;
+ vb2zm = -vb2z;
+
+ // 3rd bond
+
+ vb3x = x[i4][0] - x[i3][0];
+ vb3y = x[i4][1] - x[i3][1];
+ vb3z = x[i4][2] - x[i3][2];
+
+ // distances
+
+ r1mag2 = vb1x*vb1x + vb1y*vb1y + vb1z*vb1z;
+ r1 = sqrt(r1mag2);
+ r2mag2 = vb2x*vb2x + vb2y*vb2y + vb2z*vb2z;
+ r2 = sqrt(r2mag2);
+ r3mag2 = vb3x*vb3x + vb3y*vb3y + vb3z*vb3z;
+ r3 = sqrt(r3mag2);
+
+ sb1 = 1.0/r1mag2;
+ rb1 = 1.0/r1;
+ sb2 = 1.0/r2mag2;
+ rb2 = 1.0/r2;
+ sb3 = 1.0/r3mag2;
+ rb3 = 1.0/r3;
+
+ c0 = (vb1x*vb3x + vb1y*vb3y + vb1z*vb3z) * rb1*rb3;
+
+ // angles
+
+ r12c1 = rb1*rb2;
+ r12c2 = rb2*rb3;
+ costh12 = (vb1x*vb2x + vb1y*vb2y + vb1z*vb2z) * r12c1;
+ costh13 = c0;
+ costh23 = (vb2xm*vb3x + vb2ym*vb3y + vb2zm*vb3z) * r12c2;
+
+ // cos and sin of 2 angles and final c
+
+ sin2 = MAX(1.0 - costh12*costh12,0.0);
+ sc1 = sqrt(sin2);
+ if (sc1 < SMALL) sc1 = SMALL;
+ sc1 = 1.0/sc1;
+
+ sin2 = MAX(1.0 - costh23*costh23,0.0);
+ sc2 = sqrt(sin2);
+ if (sc2 < SMALL) sc2 = SMALL;
+ sc2 = 1.0/sc2;
+
+ s1 = sc1 * sc1;
+ s2 = sc2 * sc2;
+ s12 = sc1 * sc2;
+ c = (c0 + costh12*costh23) * s12;
+
+ // error check
+
+ if (c > 1.0 + TOLERANCE || c < (-1.0 - TOLERANCE)) {
+ int me;
+ MPI_Comm_rank(world,&me);
+ if (screen) {
+ char str[128];
+ sprintf(str,"Dihedral problem: %d " BIGINT_FORMAT " "
+ TAGINT_FORMAT " " TAGINT_FORMAT " "
+ TAGINT_FORMAT " " TAGINT_FORMAT,
+ me,update->ntimestep,
+ atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
+ error->warning(FLERR,str,0);
+ fprintf(screen," 1st atom: %d %g %g %g\n",
+ me,x[i1][0],x[i1][1],x[i1][2]);
+ fprintf(screen," 2nd atom: %d %g %g %g\n",
+ me,x[i2][0],x[i2][1],x[i2][2]);
+ fprintf(screen," 3rd atom: %d %g %g %g\n",
+ me,x[i3][0],x[i3][1],x[i3][2]);
+ fprintf(screen," 4th atom: %d %g %g %g\n",
+ me,x[i4][0],x[i4][1],x[i4][2]);
+ }
+ }
+
+ if (c > 1.0) c = 1.0;
+ if (c < -1.0) c = -1.0;
+ double phil = acos(c);
+ phi = acos(c);
+
+ sinphi = sqrt(1.0 - c*c);
+ sinphi = MAX(sinphi,SMALL);
+
+ // n123 = vb1 x vb2
+
+ double n123x = vb1y*vb2z - vb1z*vb2y;
+ double n123y = vb1z*vb2x - vb1x*vb2z;
+ double n123z = vb1x*vb2y - vb1y*vb2x;
+ double n123_dot_vb3 = n123x*vb3x + n123y*vb3y + n123z*vb3z;
+ if (n123_dot_vb3 > 0.0) {
+ phil = -phil;
+ phi = -phi;
+ sinphi = -sinphi;
+ }
+
+ a11 = -c*sb1*s1;
+ a22 = sb2 * (2.0*costh13*s12 - c*(s1+s2));
+ a33 = -c*sb3*s2;
+ a12 = r12c1 * (costh12*c*s1 + costh23*s12);
+ a13 = rb1*rb3*s12;
+ a23 = r12c2 * (-costh23*c*s2 - costh12*s12);
+
+ sx1 = a11*vb1x + a12*vb2x + a13*vb3x;
+ sx2 = a12*vb1x + a22*vb2x + a23*vb3x;
+ sx12 = a13*vb1x + a23*vb2x + a33*vb3x;
+ sy1 = a11*vb1y + a12*vb2y + a13*vb3y;
+ sy2 = a12*vb1y + a22*vb2y + a23*vb3y;
+ sy12 = a13*vb1y + a23*vb2y + a33*vb3y;
+ sz1 = a11*vb1z + a12*vb2z + a13*vb3z;
+ sz2 = a12*vb1z + a22*vb2z + a23*vb3z;
+ sz12 = a13*vb1z + a23*vb2z + a33*vb3z;
+
+ // set up d(cos(phi))/d(r) and dphi/dr arrays
+
+ dcosphidr[0][0] = -sx1;
+ dcosphidr[0][1] = -sy1;
+ dcosphidr[0][2] = -sz1;
+ dcosphidr[1][0] = sx2 + sx1;
+ dcosphidr[1][1] = sy2 + sy1;
+ dcosphidr[1][2] = sz2 + sz1;
+ dcosphidr[2][0] = sx12 - sx2;
+ dcosphidr[2][1] = sy12 - sy2;
+ dcosphidr[2][2] = sz12 - sz2;
+ dcosphidr[3][0] = -sx12;
+ dcosphidr[3][1] = -sy12;
+ dcosphidr[3][2] = -sz12;
+
+ for (i = 0; i < 4; i++)
+ for (j = 0; j < 3; j++)
+ dphidr[i][j] = -dcosphidr[i][j] / sinphi;
+
+
+ for (i = 0; i < 4; i++)
+ for (j = 0; j < 3; j++)
+ fabcd[i][j] = 0;
+ edihedral = 0;
+
+
+ // set up d(theta)/d(r) array
+ // dthetadr(i,j,k) = angle i, atom j, coordinate k
+
+ for (i = 0; i < 2; i++)
+ for (j = 0; j < 4; j++)
+ for (k = 0; k < 3; k++)
+ dthetadr[i][j][k] = 0.0;
+
+ t1 = costh12 / r1mag2;
+ t2 = costh23 / r2mag2;
+ t3 = costh12 / r2mag2;
+ t4 = costh23 / r3mag2;
+
+ // angle12
+
+ dthetadr[0][0][0] = sc1 * ((t1 * vb1x) - (vb2x * r12c1));
+ dthetadr[0][0][1] = sc1 * ((t1 * vb1y) - (vb2y * r12c1));
+ dthetadr[0][0][2] = sc1 * ((t1 * vb1z) - (vb2z * r12c1));
+
+ dthetadr[0][1][0] = sc1 * ((-t1 * vb1x) + (vb2x * r12c1) +
+ (-t3 * vb2x) + (vb1x * r12c1));
+ dthetadr[0][1][1] = sc1 * ((-t1 * vb1y) + (vb2y * r12c1) +
+ (-t3 * vb2y) + (vb1y * r12c1));
+ dthetadr[0][1][2] = sc1 * ((-t1 * vb1z) + (vb2z * r12c1) +
+ (-t3 * vb2z) + (vb1z * r12c1));
+
+ dthetadr[0][2][0] = sc1 * ((t3 * vb2x) - (vb1x * r12c1));
+ dthetadr[0][2][1] = sc1 * ((t3 * vb2y) - (vb1y * r12c1));
+ dthetadr[0][2][2] = sc1 * ((t3 * vb2z) - (vb1z * r12c1));
+
+ // angle23
+
+ dthetadr[1][1][0] = sc2 * ((t2 * vb2x) + (vb3x * r12c2));
+ dthetadr[1][1][1] = sc2 * ((t2 * vb2y) + (vb3y * r12c2));
+ dthetadr[1][1][2] = sc2 * ((t2 * vb2z) + (vb3z * r12c2));
+
+ dthetadr[1][2][0] = sc2 * ((-t2 * vb2x) - (vb3x * r12c2) +
+ (t4 * vb3x) + (vb2x * r12c2));
+ dthetadr[1][2][1] = sc2 * ((-t2 * vb2y) - (vb3y * r12c2) +
+ (t4 * vb3y) + (vb2y * r12c2));
+ dthetadr[1][2][2] = sc2 * ((-t2 * vb2z) - (vb3z * r12c2) +
+ (t4 * vb3z) + (vb2z * r12c2));
+
+ dthetadr[1][3][0] = -sc2 * ((t4 * vb3x) + (vb2x * r12c2));
+ dthetadr[1][3][1] = -sc2 * ((t4 * vb3y) + (vb2y * r12c2));
+ dthetadr[1][3][2] = -sc2 * ((t4 * vb3z) + (vb2z * r12c2));
+
+ // angle/angle/torsion cutoff
+
+ da1 = acos(costh12) - aat_theta0_1[type] ;
+ da2 = acos(costh23) - aat_theta0_1[type] ;
+ double dtheta = aat_theta0_2[type]-aat_theta0_1[type];
+
+ fphi = 0.0;
+ fpphi = 0.0;
+ if (phil < 0) phil +=MY_2PI;
+ uf_lookup(type, phil, fphi, fpphi);
+
+ double gt = aat_k[type];
+ double gtt = aat_k[type];
+ double gpt = 0;
+ double gptt = 0;
+
+ if ( acos(costh12) > aat_theta0_1[type]) {
+ gt *= 1-da1*da1/dtheta/dtheta;
+ gpt = -aat_k[type]*2*da1/dtheta/dtheta;
+ }
+
+ if ( acos(costh23) > aat_theta0_1[type]) {
+ gtt *= 1-da2*da2/dtheta/dtheta;
+ gptt = -aat_k[type]*2*da2/dtheta/dtheta;
+ }
+
+ if (eflag) edihedral = gt*gtt*fphi;
+
+ for (i = 0; i < 4; i++)
+ for (j = 0; j < 3; j++)
+ fabcd[i][j] -= - gt*gtt*fpphi*dphidr[i][j]
+ - gt*gptt*fphi*dthetadr[1][i][j] + gpt*gtt*fphi*dthetadr[0][i][j];
+
+ // apply force to each of 4 atoms
+
+ if (newton_bond || i1 < nlocal) {
+ f[i1][0] += fabcd[0][0];
+ f[i1][1] += fabcd[0][1];
+ f[i1][2] += fabcd[0][2];
+ }
+
+ if (newton_bond || i2 < nlocal) {
+ f[i2][0] += fabcd[1][0];
+ f[i2][1] += fabcd[1][1];
+ f[i2][2] += fabcd[1][2];
+ }
+
+ if (newton_bond || i3 < nlocal) {
+ f[i3][0] += fabcd[2][0];
+ f[i3][1] += fabcd[2][1];
+ f[i3][2] += fabcd[2][2];
+ }
+
+ if (newton_bond || i4 < nlocal) {
+ f[i4][0] += fabcd[3][0];
+ f[i4][1] += fabcd[3][1];
+ f[i4][2] += fabcd[3][2];
+ }
+
+ if (evflag)
+ ev_tally(i1,i2,i3,i4,nlocal,newton_bond,edihedral,
+ fabcd[0],fabcd[2],fabcd[3],
+ vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z);
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void DihedralTableCut::allocate()
+{
+ allocated = 1;
+ int n = atom->ndihedraltypes;
+
+ memory->create(k1,n+1,"dihedral:k1");
+ memory->create(k2,n+1,"dihedral:k2");
+ memory->create(k3,n+1,"dihedral:k3");
+ memory->create(phi1,n+1,"dihedral:phi1");
+ memory->create(phi2,n+1,"dihedral:phi2");
+ memory->create(phi3,n+1,"dihedral:phi3");
+
+ memory->create(aat_k,n+1,"dihedral:aat_k");
+ memory->create(aat_theta0_1,n+1,"dihedral:aat_theta0_1");
+ memory->create(aat_theta0_2,n+1,"dihedral:aat_theta0_2");
+
+ memory->create(setflag,n+1,"dihedral:setflag");
+ memory->create(setflag_d,n+1,"dihedral:setflag_d");
+ memory->create(setflag_aat,n+1,"dihedral:setflag_aat");
+
+ memory->create(tabindex,n+1,"dihedral:tabindex");
+ //memory->create(phi0,n+1,"dihedral:phi0"); <-equilibrium angles not supported
+ memory->create(setflag,n+1,"dihedral:setflag");
+
+ for (int i = 1; i <= n; i++)
+ setflag[i] = setflag_d[i] = setflag_aat[i] = 0;
+}
+
+void DihedralTableCut::settings(int narg, char **arg)
+{
+ if (narg != 2) error->all(FLERR,"Illegal dihedral_style command");
+
+ if (strcmp(arg[0],"linear") == 0) tabstyle = LINEAR;
+ else if (strcmp(arg[0],"spline") == 0) tabstyle = SPLINE;
+ else error->all(FLERR,"Unknown table style in dihedral style table_cut");
+
+ tablength = force->inumeric(FLERR,arg[1]);
+ if (tablength < 3)
+ error->all(FLERR,"Illegal number of dihedral table entries");
+ // delete old tables, since cannot just change settings
+
+ for (int m = 0; m < ntables; m++) free_table(&tables[m]);
+ memory->sfree(tables);
+
+ if (allocated) {
+ memory->destroy(setflag);
+ memory->destroy(tabindex);
+ }
+ allocated = 0;
+
+ ntables = 0;
+ tables = NULL;
+}
+
+/* ----------------------------------------------------------------------
+ set coeffs for one or more types
+ arg1 = "aat" -> AngleAngleTorsion coeffs
+ arg1 -> Dihedral coeffs
+------------------------------------------------------------------------- */
+
+void DihedralTableCut::coeff(int narg, char **arg)
+{
+
+ if (narg != 7) error->all(FLERR,"Incorrect args for dihedral coefficients");
+ if (!allocated) allocate();
+ int ilo,ihi;
+ force->bounds(FLERR,arg[0],atom->ndihedraltypes,ilo,ihi);
+
+ int count = 0;
+
+
+ double k_one = force->numeric(FLERR,arg[2]);
+ double theta0_1_one = force->numeric(FLERR,arg[3]);
+ double theta0_2_one = force->numeric(FLERR,arg[4]);
+
+ // convert theta0's from degrees to radians
+
+ for (int i = ilo; i <= ihi; i++) {
+ aat_k[i] = k_one;
+ aat_theta0_1[i] = theta0_1_one/180.0 * MY_PI;
+ aat_theta0_2[i] = theta0_2_one/180.0 * MY_PI;
+ setflag_aat[i] = 1;
+ count++;
+ }
+
+ int me;
+ MPI_Comm_rank(world,&me);
+ tables = (Table *)
+ memory->srealloc(tables,(ntables+1)*sizeof(Table), "dihedral:tables");
+ Table *tb = &tables[ntables];
+ null_table(tb);
+ if (me == 0) read_table(tb,arg[5],arg[6]);
+ bcast_table(tb);
+
+ // --- check the angle data for range errors ---
+ // --- and resolve issues with periodicity ---
+
+ if (tb->ninput < 2) {
+ string err_msg;
+ err_msg = string("Invalid dihedral table length (")
+ + string(arg[5]) + string(").");
+ error->one(FLERR,err_msg.c_str());
+ }
+ else if ((tb->ninput == 2) && (tabstyle == SPLINE)) {
+ string err_msg;
+ err_msg = string("Invalid dihedral spline table length. (Try linear)\n (")
+ + string(arg[5]) + string(").");
+ error->one(FLERR,err_msg.c_str());
+ }
+
+ // check for monotonicity
+ for (int i=0; i < tb->ninput-1; i++) {
+ if (tb->phifile[i] >= tb->phifile[i+1]) {
+ stringstream i_str;
+ i_str << i+1;
+ string err_msg =
+ string("Dihedral table values are not increasing (") +
+ string(arg[5]) + string(", ")+i_str.str()+string("th entry)");
+ if (i==0)
+ err_msg += string("\n(This is probably a mistake with your table format.)\n");
+ error->all(FLERR,err_msg.c_str());
+ }
+ }
+
+ // check the range of angles
+ double philo = tb->phifile[0];
+ double phihi = tb->phifile[tb->ninput-1];
+ if (tb->use_degrees) {
+ if ((phihi - philo) >= 360) {
+ string err_msg;
+ err_msg = string("Dihedral table angle range must be < 360 degrees (")
+ +string(arg[5]) + string(").");
+ error->all(FLERR,err_msg.c_str());
+ }
+ }
+ else {
+ if ((phihi - philo) >= MY_2PI) {
+ string err_msg;
+ err_msg = string("Dihedral table angle range must be < 2*PI radians (")
+ + string(arg[5]) + string(").");
+ error->all(FLERR,err_msg.c_str());
+ }
+ }
+
+ // convert phi from degrees to radians
+ if (tb->use_degrees) {
+ for (int i=0; i < tb->ninput; i++) {
+ tb->phifile[i] *= MY_PI/180.0;
+ // I assume that if angles are in degrees, then the forces (f=dU/dphi)
+ // are specified with "phi" in degrees as well.
+ tb->ffile[i] *= 180.0/MY_PI;
+ }
+ }
+
+ // We want all the phi dihedral angles to lie in the range from 0 to 2*PI.
+ // But I don't want to restrict users to input their data in this range.
+ // We also want the angles to be sorted in increasing order.
+ // This messy code fixes these problems with the user's data:
+ {
+ double *phifile_tmp = new double [tb->ninput]; //temporary arrays
+ double *ffile_tmp = new double [tb->ninput]; //used for sorting
+ double *efile_tmp = new double [tb->ninput];
+
+ // After re-imaging, does the range of angles cross the 0 or 2*PI boundary?
+ // If so, find the discontinuity:
+ int i_discontinuity = tb->ninput;
+ for (int i=0; i < tb->ninput; i++) {
+ double phi = tb->phifile[i];
+ // Add a multiple of 2*PI to phi until it lies in the range [0, 2*PI).
+ phi -= MY_2PI * floor(phi/MY_2PI);
+ phifile_tmp[i] = phi;
+ efile_tmp[i] = tb->efile[i];
+ ffile_tmp[i] = tb->ffile[i];
+ if ((i>0) && (phifile_tmp[i] < phifile_tmp[i-1])) {
+ //There should only be at most one discontinuity, because we have
+ //insured that the data was sorted before imaging, and because the
+ //range of angle values does not exceed 2*PI.
+ i_discontinuity = i;
+ }
+ }
+
+ int I = 0;
+ for (int i = i_discontinuity; i < tb->ninput; i++) {
+ tb->phifile[I] = phifile_tmp[i];
+ tb->efile[I] = efile_tmp[i];
+ tb->ffile[I] = ffile_tmp[i];
+ I++;
+ }
+ for (int i = 0; i < i_discontinuity; i++) {
+ tb->phifile[I] = phifile_tmp[i];
+ tb->efile[I] = efile_tmp[i];
+ tb->ffile[I] = ffile_tmp[i];
+ I++;
+ }
+
+ // clean up temporary storage
+ delete[] phifile_tmp;
+ delete[] ffile_tmp;
+ delete[] efile_tmp;
+ }
+
+ // spline read-in and compute r,e,f vectors within table
+
+ spline_table(tb);
+ compute_table(tb);
+
+ // Optional: allow the user to print out the interpolated spline tables
+
+ if (me == 0) {
+ if (checkU_fname && (strlen(checkU_fname) != 0))
+ {
+ ofstream checkU_file;
+ checkU_file.open(checkU_fname, ios::out);
+ for (int i=0; i < tablength; i++) {
+ double phi = i*MY_2PI/tablength;
+ double u = tb->e[i];
+ if (tb->use_degrees)
+ phi *= 180.0/MY_PI;
+ checkU_file << phi << " " << u << "\n";
+ }
+ checkU_file.close();
+ }
+ if (checkF_fname && (strlen(checkF_fname) != 0))
+ {
+ ofstream checkF_file;
+ checkF_file.open(checkF_fname, ios::out);
+ for (int i=0; i < tablength; i++)
+ {
+ double phi = i*MY_2PI/tablength;
+ double f;
+ if ((tabstyle == SPLINE) && (tb->f_unspecified)) {
+ double dU_dphi =
+ // (If the user did not specify the forces now, AND the user
+ // selected the "spline" option, (as opposed to "linear")
+ // THEN the tb->f array is uninitialized, so there's
+ // no point to print out the contents of the tb->f[] array.
+ // Instead, later on, we will calculate the force using the
+ // -cyc_splintD() routine to calculate the derivative of the
+ // energy spline, using the energy data (tb->e[]).
+ // To be nice and report something, I do the same thing here.)
+ cyc_splintD(tb->phi, tb->e, tb->e2, tablength, MY_2PI,phi);
+ f = -dU_dphi;
+ }
+ else
+ // Otherwise we calculated the tb->f[] array. Report its contents.
+ f = tb->f[i];
+ if (tb->use_degrees) {
+ phi *= 180.0/MY_PI;
+ // If the user wants degree angle units, we should convert our
+ // internal force tables (in energy/radians) to (energy/degrees)
+ f *= MY_PI/180.0;
+ }
+ checkF_file << phi << " " << f << "\n";
+ }
+ checkF_file.close();
+ } // if (checkF_fname && (strlen(checkF_fname) != 0))
+ } // if (me == 0)
+
+ // store ptr to table in tabindex
+ count = 0;
+ for (int i = ilo; i <= ihi; i++)
+ {
+ tabindex[i] = ntables;
+ //phi0[i] = tb->phi0; <- equilibrium dihedral angles not supported
+ setflag[i] = 1;
+ count++;
+ }
+ ntables++;
+
+
+ if (count == 0) error->all(FLERR,"Incorrect args for dihedral coefficients");
+
+ for (int i = ilo; i <= ihi; i++)
+ if (setflag_d[i] == 1 && setflag_aat[i] == 1 )
+ setflag[i] = 1;
+}
+
+/* ----------------------------------------------------------------------
+ proc 0 writes out coeffs to restart file
+------------------------------------------------------------------------- */
+
+void DihedralTableCut::write_restart(FILE *fp)
+{
+ fwrite(&tabstyle,sizeof(int),1,fp);
+ fwrite(&tablength,sizeof(int),1,fp);
+ fwrite(&k1[1],sizeof(double),atom->ndihedraltypes,fp);
+ fwrite(&k2[1],sizeof(double),atom->ndihedraltypes,fp);
+ fwrite(&k3[1],sizeof(double),atom->ndihedraltypes,fp);
+ fwrite(&phi1[1],sizeof(double),atom->ndihedraltypes,fp);
+ fwrite(&phi2[1],sizeof(double),atom->ndihedraltypes,fp);
+ fwrite(&phi3[1],sizeof(double),atom->ndihedraltypes,fp);
+
+ fwrite(&aat_k[1],sizeof(double),atom->ndihedraltypes,fp);
+ fwrite(&aat_theta0_1[1],sizeof(double),atom->ndihedraltypes,fp);
+ fwrite(&aat_theta0_2[1],sizeof(double),atom->ndihedraltypes,fp);
+}
+
+/* ----------------------------------------------------------------------
+ proc 0 reads coeffs from restart file, bcasts them
+------------------------------------------------------------------------- */
+
+void DihedralTableCut::read_restart(FILE *fp)
+{
+ allocate();
+
+ if (comm->me == 0) {
+ fread(&tabstyle,sizeof(int),1,fp);
+ fread(&tablength,sizeof(int),1,fp);
+ fread(&k1[1],sizeof(double),atom->ndihedraltypes,fp);
+ fread(&k2[1],sizeof(double),atom->ndihedraltypes,fp);
+ fread(&k3[1],sizeof(double),atom->ndihedraltypes,fp);
+ fread(&phi1[1],sizeof(double),atom->ndihedraltypes,fp);
+ fread(&phi2[1],sizeof(double),atom->ndihedraltypes,fp);
+ fread(&phi3[1],sizeof(double),atom->ndihedraltypes,fp);
+
+ fread(&aat_k[1],sizeof(double),atom->ndihedraltypes,fp);
+ fread(&aat_theta0_1[1],sizeof(double),atom->ndihedraltypes,fp);
+ fread(&aat_theta0_2[1],sizeof(double),atom->ndihedraltypes,fp);
+ }
+
+ MPI_Bcast(&k1[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
+ MPI_Bcast(&k2[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
+ MPI_Bcast(&k3[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
+ MPI_Bcast(&phi1[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
+ MPI_Bcast(&phi2[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
+ MPI_Bcast(&phi3[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
+
+ MPI_Bcast(&aat_k[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
+ MPI_Bcast(&aat_theta0_1[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
+ MPI_Bcast(&aat_theta0_2[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
+ MPI_Bcast(&tabstyle,1,MPI_INT,0,world);
+ MPI_Bcast(&tablength,1,MPI_INT,0,world);
+
+ allocate();
+ for (int i = 1; i <= atom->ndihedraltypes; i++) setflag[i] = 1;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void DihedralTableCut::null_table(Table *tb)
+{
+ tb->phifile = tb->efile = tb->ffile = NULL;
+ tb->e2file = tb->f2file = NULL;
+ tb->phi = tb->e = tb->de = NULL;
+ tb->f = tb->df = tb->e2 = tb->f2 = NULL;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void DihedralTableCut::free_table(Table *tb)
+{
+ memory->destroy(tb->phifile);
+ memory->destroy(tb->efile);
+ memory->destroy(tb->ffile);
+ memory->destroy(tb->e2file);
+ memory->destroy(tb->f2file);
+
+ memory->destroy(tb->phi);
+ memory->destroy(tb->e);
+ memory->destroy(tb->de);
+ memory->destroy(tb->f);
+ memory->destroy(tb->df);
+ memory->destroy(tb->e2);
+ memory->destroy(tb->f2);
+}
+
+/* ----------------------------------------------------------------------
+ read table file, only called by proc 0
+------------------------------------------------------------------------- */
+
+static const int MAXLINE=2048;
+
+void DihedralTableCut::read_table(Table *tb, char *file, char *keyword)
+{
+ char line[MAXLINE];
+
+ // open file
+
+ FILE *fp = force->open_potential(file);
+ if (fp == NULL) {
+ string err_msg = string("Cannot open file ") + string(file);
+ error->one(FLERR,err_msg.c_str());
+ }
+
+ // loop until section found with matching keyword
+
+ while (1) {
+ if (fgets(line,MAXLINE,fp) == NULL) {
+ string err_msg=string("Did not find keyword \"")
+ +string(keyword)+string("\" in dihedral table file.");
+ error->one(FLERR, err_msg.c_str());
+ }
+ if (strspn(line," \t\n\r") == strlen(line)) continue; // blank line
+ if (line[0] == '#') continue; // comment
+ char *word = strtok(line," \t\n\r");
+ if (strcmp(word,keyword) == 0) break; // matching keyword
+ fgets(line,MAXLINE,fp); // no match, skip section
+ param_extract(tb,line);
+ fgets(line,MAXLINE,fp);
+ for (int i = 0; i < tb->ninput; i++)
+ fgets(line,MAXLINE,fp);
+ }
+
+ // read args on 2nd line of section
+ // allocate table arrays for file values
+
+ fgets(line,MAXLINE,fp);
+ param_extract(tb,line);
+ memory->create(tb->phifile,tb->ninput,"dihedral:phifile");
+ memory->create(tb->efile,tb->ninput,"dihedral:efile");
+ memory->create(tb->ffile,tb->ninput,"dihedral:ffile");
+
+ // read a,e,f table values from file
+
+ int itmp;
+ for (int i = 0; i < tb->ninput; i++) {
+ // Read the next line. Make sure the file is long enough.
+ if (! fgets(line,MAXLINE,fp))
+ error->one(FLERR, "Dihedral table does not contain enough entries.");
+ // Skip blank lines and delete text following a '#' character
+ char *pe = strchr(line, '#');
+ if (pe != NULL) *pe = '\0'; //terminate string at '#' character
+ char *pc = line;
+ while ((*pc != '\0') && isspace(*pc))
+ pc++;
+ if (*pc != '\0') { //If line is not a blank line
+ stringstream line_ss(line);
+ if (tb->f_unspecified) {
+ //sscanf(line,"%d %lg %lg",
+ // &itmp,&tb->phifile[i],&tb->efile[i]);
+ line_ss >> itmp;
+ line_ss >> tb->phifile[i];
+ line_ss >> tb->efile[i];
+ }
+ else {
+ //sscanf(line,"%d %lg %lg %lg",
+ // &itmp,&tb->phifile[i],&tb->efile[i],&tb->ffile[i]);
+ line_ss >> itmp;
+ line_ss >> tb->phifile[i];
+ line_ss >> tb->efile[i];
+ line_ss >> tb->ffile[i];
+ }
+ if (! line_ss) {
+ stringstream err_msg;
+ err_msg << "Read error in table "<< keyword<<", near line "<<i+1<<"\n"
+ << " (Check to make sure the number of colums is correct.)";
+ if ((! tb->f_unspecified) && (i==0))
+ err_msg << "\n (This sometimes occurs if users forget to specify the \"NOF\" option.)\n";
+ error->one(FLERR, err_msg.str().c_str());
+ }
+ }
+ else //if it is a blank line, then skip it.
+ i--;
+ } //for (int i = 0; (i < tb->ninput) && fp; i++) {
+
+ fclose(fp);
+}
+
+/* ----------------------------------------------------------------------
+ build spline representation of e,f over entire range of read-in table
+ this function sets these values in e2file,f2file.
+ I also perform a crude check for force & energy consistency.
+------------------------------------------------------------------------- */
+
+void DihedralTableCut::spline_table(Table *tb)
+{
+ memory->create(tb->e2file,tb->ninput,"dihedral:e2file");
+ memory->create(tb->f2file,tb->ninput,"dihedral:f2file");
+
+ if (cyc_spline(tb->phifile, tb->efile, tb->ninput,
+ MY_2PI,tb->e2file,comm->me == 0))
+ error->one(FLERR,"Error computing dihedral spline tables");
+
+ if (! tb->f_unspecified) {
+ if (cyc_spline(tb->phifile, tb->ffile, tb->ninput,
+ MY_2PI, tb->f2file, comm->me == 0))
+ error->one(FLERR,"Error computing dihedral spline tables");
+ }
+
+ // CHECK to help make sure the user calculated forces in a way
+ // which is grossly numerically consistent with the energy table.
+ if (! tb->f_unspecified) {
+ int num_disagreements = 0;
+ for (int i=0; i<tb->ninput; i++) {
+
+ // Calculate what the force should be at the control points
+ // by using linear interpolation of the derivatives of the energy:
+
+ double phi_i = tb->phifile[i];
+
+ // First deal with periodicity
+ double phi_im1, phi_ip1;
+ int im1 = i-1;
+ if (im1 < 0) {
+ im1 += tb->ninput;
+ phi_im1 = tb->phifile[im1] - MY_2PI;
+ }
+ else
+ phi_im1 = tb->phifile[im1];
+ int ip1 = i+1;
+ if (ip1 >= tb->ninput) {
+ ip1 -= tb->ninput;
+ phi_ip1 = tb->phifile[ip1] + MY_2PI;
+ }
+ else
+ phi_ip1 = tb->phifile[ip1];
+
+ // Now calculate the midpoints above and below phi_i = tb->phifile[i]
+ double phi_lo= 0.5*(phi_im1 + phi_i); //midpoint between phi_im1 and phi_i
+ double phi_hi= 0.5*(phi_i + phi_ip1); //midpoint between phi_i and phi_ip1
+
+ // Use a linear approximation to the derivative at these two midpoints
+ double dU_dphi_lo =
+ (tb->efile[i] - tb->efile[im1])
+ /
+ (phi_i - phi_im1);
+ double dU_dphi_hi =
+ (tb->efile[ip1] - tb->efile[i])
+ /
+ (phi_ip1 - phi_i);
+
+ // Now calculate the derivative at position
+ // phi_i (=tb->phifile[i]) using linear interpolation
+
+ double a = (phi_i - phi_lo) / (phi_hi - phi_lo);
+ double b = (phi_hi - phi_i) / (phi_hi - phi_lo);
+ double dU_dphi = a*dU_dphi_lo + b*dU_dphi_hi;
+ double f = -dU_dphi;
+ // Alternately, we could use spline interpolation instead:
+ // double f = - splintD(tb->phifile, tb->efile, tb->e2file,
+ // tb->ninput, MY_2PI, tb->phifile[i]);
+ // This is the way I originally did it, but I trust
+ // the ugly simple linear way above better.
+ // Recall this entire block of code doess not calculate
+ // anything important. It does not have to be perfect.
+ // We are only checking for stupid user errors here.
+
+ if ((f != 0.0) &&
+ (tb->ffile[i] != 0.0) &&
+ ((f/tb->ffile[i] < 0.5) || (f/tb->ffile[i] > 2.0))) {
+ num_disagreements++;
+ }
+ } // for (int i=0; i<tb->ninput; i++)
+
+ if ((num_disagreements > tb->ninput/2) && (num_disagreements > 2)) {
+ string msg("Dihedral table has inconsistent forces and energies. (Try \"NOF\".)\n");
+ error->all(FLERR,msg.c_str());
+ }
+
+ } // check for consistency if (! tb->f_unspecified)
+
+} // DihedralTable::spline_table()
+
+
+/* ----------------------------------------------------------------------
+ compute a,e,f vectors from splined values
+------------------------------------------------------------------------- */
+
+void DihedralTableCut::compute_table(Table *tb)
+{
+ //delta = table spacing in dihedral angle for tablength (cyclic) bins
+ tb->delta = MY_2PI / tablength;
+ tb->invdelta = 1.0/tb->delta;
+ tb->deltasq6 = tb->delta*tb->delta / 6.0;
+
+ // N evenly spaced bins in dihedral angle from 0 to 2*PI
+ // phi,e,f = value at lower edge of bin
+ // de,df values = delta values of e,f (cyclic, in this case)
+ // phi,e,f,de,df are arrays containing "tablength" number of entries
+
+ memory->create(tb->phi,tablength,"dihedral:phi");
+ memory->create(tb->e,tablength,"dihedral:e");
+ memory->create(tb->de,tablength,"dihedral:de");
+ memory->create(tb->f,tablength,"dihedral:f");
+ memory->create(tb->df,tablength,"dihedral:df");
+ memory->create(tb->e2,tablength,"dihedral:e2");
+ memory->create(tb->f2,tablength,"dihedral:f2");
+
+ if (tabstyle == SPLINE) {
+ // Use cubic spline interpolation to calculate the entries in the
+ // internal table. (This is true regardless...even if tabstyle!=SPLINE.)
+ for (int i = 0; i < tablength; i++) {
+ double phi = i*tb->delta;
+ tb->phi[i] = phi;
+ tb->e[i]= cyc_splint(tb->phifile,tb->efile,tb->e2file,tb->ninput,MY_2PI,phi);
+ if (! tb->f_unspecified)
+ tb->f[i] = cyc_splint(tb->phifile,tb->ffile,tb->f2file,tb->ninput,MY_2PI,phi);
+ }
+ } // if (tabstyle == SPLINE)
+ else if (tabstyle == LINEAR) {
+ if (! tb->f_unspecified) {
+ for (int i = 0; i < tablength; i++) {
+ double phi = i*tb->delta;
+ tb->phi[i] = phi;
+ tb->e[i]= cyc_lin(tb->phifile,tb->efile,tb->ninput,MY_2PI,phi);
+ tb->f[i]= cyc_lin(tb->phifile,tb->ffile,tb->ninput,MY_2PI,phi);
+ }
+ }
+ else {
+ for (int i = 0; i < tablength; i++) {
+ double phi = i*tb->delta;
+ tb->phi[i] = phi;
+ tb->e[i]= cyc_lin(tb->phifile,tb->efile,tb->ninput,MY_2PI,phi);
+ }
+ // In the linear case, if the user did not specify the forces, then we
+ // must generate the "f" array. Do this using linear interpolation
+ // of the e array (which itself was generated above)
+ for (int i = 0; i < tablength; i++) {
+ int im1 = i-1; if (im1 < 0) im1 += tablength;
+ int ip1 = i+1; if (ip1 >= tablength) ip1 -= tablength;
+ double dedx = (tb->e[ip1] - tb->e[im1]) / (2.0 * tb->delta);
+ // (This is the average of the linear slopes on either side of the node.
+ // Note that the nodes in the internal table are evenly spaced.)
+ tb->f[i] = -dedx;
+ }
+ }
+
+
+ // Fill the linear interpolation tables (de, df)
+ for (int i = 0; i < tablength; i++) {
+ int ip1 = i+1; if (ip1 >= tablength) ip1 -= tablength;
+ tb->de[i] = tb->e[ip1] - tb->e[i];
+ tb->df[i] = tb->f[ip1] - tb->f[i];
+ }
+ } // else if (tabstyle == LINEAR)
+
+
+
+ cyc_spline(tb->phi, tb->e, tablength, MY_2PI, tb->e2, comm->me == 0);
+ if (! tb->f_unspecified)
+ cyc_spline(tb->phi, tb->f, tablength, MY_2PI, tb->f2, comm->me == 0);
+}
+
+
+/* ----------------------------------------------------------------------
+ extract attributes from parameter line in table section
+ format of line: N value NOF DEGREES RADIANS
+ N is required, other params are optional
+------------------------------------------------------------------------- */
+
+void DihedralTableCut::param_extract(Table *tb, char *line)
+{
+ //tb->theta0 = 180.0; <- equilibrium angles not supported
+ tb->ninput = 0;
+ tb->f_unspecified = false; //default
+ tb->use_degrees = true; //default
+
+ char *word = strtok(line," \t\n\r\f");
+ while (word) {
+ if (strcmp(word,"N") == 0) {
+ word = strtok(NULL," \t\n\r\f");
+ tb->ninput = atoi(word);
+ }
+ else if (strcmp(word,"NOF") == 0) {
+ tb->f_unspecified = true;
+ }
+ else if ((strcmp(word,"DEGREES") == 0) || (strcmp(word,"degrees") == 0)) {
+ tb->use_degrees = true;
+ }
+ else if ((strcmp(word,"RADIANS") == 0) || (strcmp(word,"radians") == 0)) {
+ tb->use_degrees = false;
+ }
+ else if (strcmp(word,"CHECKU") == 0) {
+ word = strtok(NULL," \t\n\r\f");
+ memory->sfree(checkU_fname);
+ memory->create(checkU_fname,strlen(word)+1,"dihedral_table:checkU");
+ strcpy(checkU_fname, word);
+ }
+ else if (strcmp(word,"CHECKF") == 0) {
+ word = strtok(NULL," \t\n\r\f");
+ memory->sfree(checkF_fname);
+ memory->create(checkF_fname,strlen(word)+1,"dihedral_table:checkF");
+ strcpy(checkF_fname, word);
+ }
+ // COMMENTING OUT: equilibrium angles are not supported
+ //else if (strcmp(word,"EQ") == 0) {
+ // word = strtok(NULL," \t\n\r\f");
+ // tb->theta0 = atof(word);
+ //}
+ else {
+ string err_msg("Invalid keyword in dihedral angle table parameters");
+ err_msg += string(" (") + string(word) + string(")");
+ error->one(FLERR,err_msg.c_str());
+ }
+ word = strtok(NULL," \t\n\r\f");
+ }
+
+ if (tb->ninput == 0)
+ error->one(FLERR,"Dihedral table parameters did not set N");
+
+} // DihedralTable::param_extract()
+
+
+/* ----------------------------------------------------------------------
+ broadcast read-in table info from proc 0 to other procs
+ this function communicates these values in Table:
+ ninput,phifile,efile,ffile,
+ f_unspecified,use_degrees
+------------------------------------------------------------------------- */
+
+void DihedralTableCut::bcast_table(Table *tb)
+{
+ MPI_Bcast(&tb->ninput,1,MPI_INT,0,world);
+
+ int me;
+ MPI_Comm_rank(world,&me);
+ if (me > 0) {
+ memory->create(tb->phifile,tb->ninput,"dihedral:phifile");
+ memory->create(tb->efile,tb->ninput,"dihedral:efile");
+ memory->create(tb->ffile,tb->ninput,"dihedral:ffile");
+ }
+
+ MPI_Bcast(tb->phifile,tb->ninput,MPI_DOUBLE,0,world);
+ MPI_Bcast(tb->efile,tb->ninput,MPI_DOUBLE,0,world);
+ MPI_Bcast(tb->ffile,tb->ninput,MPI_DOUBLE,0,world);
+
+ MPI_Bcast(&tb->f_unspecified,1,MPI_INT,0,world);
+ MPI_Bcast(&tb->use_degrees,1,MPI_INT,0,world);
+
+ // COMMENTING OUT: equilibrium angles are not supported
+ //MPI_Bcast(&tb->theta0,1,MPI_DOUBLE,0,world);
+}
+
+
+
+/* ----------------------------------------------------------------------
+ proc 0 writes to data file
+------------------------------------------------------------------------- */
+
+void DihedralTableCut::write_data(FILE *fp)
+{
+ for (int i = 1; i <= atom->ndihedraltypes; i++)
+ fprintf(fp,"%d %g %g %g %g %g %g\n",i,
+ k1[i],phi1[i]*180.0/MY_PI,
+ k2[i],phi2[i]*180.0/MY_PI,
+ k3[i],phi3[i]*180.0/MY_PI);
+
+ fprintf(fp,"\nAngleAngleTorsion Coeffs\n\n");
+ for (int i = 1; i <= atom->ndihedraltypes; i++)
+ fprintf(fp,"%d %g %g %g\n",i,aat_k[i],
+ aat_theta0_1[i]*180.0/MY_PI,aat_theta0_2[i]*180.0/MY_PI);
+
+}
diff --git a/src/USER-MISC/dihedral_table_cut.h b/src/USER-MISC/dihedral_table_cut.h
new file mode 100644
index 0000000000000000000000000000000000000000..d01903c88b75d722aa2b5861a6cba4e00817ed87
--- /dev/null
+++ b/src/USER-MISC/dihedral_table_cut.h
@@ -0,0 +1,173 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef DIHEDRAL_CLASS
+
+DihedralStyle(table/cut,DihedralTableCut)
+
+#else
+
+#ifndef LMP_DIHEDRAL_TABLE_CUT_H
+#define LMP_DIHEDRAL_TABLE_CUT_H
+
+#include <stdio.h>
+#include "dihedral.h"
+
+namespace LAMMPS_NS {
+
+class DihedralTableCut : public Dihedral {
+ public:
+ DihedralTableCut(class LAMMPS *);
+ virtual ~DihedralTableCut();
+ virtual void compute(int, int);
+ void settings(int, char **);
+ void coeff(int, char **);
+ void write_restart(FILE *);
+ void read_restart(FILE *);
+ void write_data(FILE *);
+ double single(int type, int i1, int i2, int i3, int i4);
+
+ protected:
+ double *k1,*k2,*k3;
+ double *phi1,*phi2,*phi3;
+ double *aat_k,*aat_theta0_1,*aat_theta0_2;
+ int *setflag_d;
+ int *setflag_aat;
+
+ void allocate();
+
+ int tabstyle,tablength;
+ // double *phi0; <- equilibrium angles not supported
+ char *checkU_fname;
+ char *checkF_fname;
+
+ struct Table {
+ int ninput;
+ //double phi0; <-equilibrium angles not supported
+ int f_unspecified; // boolean (but MPI does not like type "bool")
+ int use_degrees; // boolean (but MPI does not like type "bool")
+ double *phifile,*efile,*ffile;
+ double *e2file,*f2file;
+ double delta,invdelta,deltasq6;
+ double *phi,*e,*de,*f,*df,*e2,*f2;
+ };
+
+ int ntables;
+ Table *tables;
+ int *tabindex;
+
+ void null_table(Table *);
+ void free_table(Table *);
+ void read_table(Table *, char *, char *);
+ void bcast_table(Table *);
+ void spline_table(Table *);
+ void compute_table(Table *);
+
+ void param_extract(Table *, char *);
+
+ // --------------------------------------------
+ // ------------ inline functions --------------
+ // --------------------------------------------
+
+ // -----------------------------------------------------------
+ // uf_lookup()
+ // quickly calculate the potential u and force f at angle x,
+ // using the internal tables tb->e and tb->f (evenly spaced)
+ // -----------------------------------------------------------
+ enum{LINEAR,SPLINE};
+
+ inline void uf_lookup(int type, double x, double &u, double &f)
+ {
+ Table *tb = &tables[tabindex[type]];
+ double x_over_delta = x*tb->invdelta;
+ int i = static_cast<int> (x_over_delta);
+ double a;
+ double b = x_over_delta - i;
+ // Apply periodic boundary conditions to indices i and i+1
+ if (i >= tablength) i -= tablength;
+ int ip1 = i+1; if (ip1 >= tablength) ip1 -= tablength;
+
+ switch(tabstyle) {
+ case LINEAR:
+ u = tb->e[i] + b * tb->de[i];
+ f = -(tb->f[i] + b * tb->df[i]); //<--works even if tb->f_unspecified==true
+ break;
+ case SPLINE:
+ a = 1.0 - b;
+ u = a * tb->e[i] + b * tb->e[ip1] +
+ ((a*a*a-a)*tb->e2[i] + (b*b*b-b)*tb->e2[ip1]) *
+ tb->deltasq6;
+ if (tb->f_unspecified)
+ //Formula below taken from equation3.3.5 of "numerical recipes in c"
+ //"f"=-derivative of e with respect to x (or "phi" in this case)
+ f = -((tb->e[i]-tb->e[ip1])*tb->invdelta +
+ ((3.0*a*a-1.0)*tb->e2[i]+(1.0-3.0*b*b)*tb->e2[ip1])*tb->delta/6.0);
+ else
+ f = -(a * tb->f[i] + b * tb->f[ip1] +
+ ((a*a*a-a)*tb->f2[i] + (b*b*b-b)*tb->f2[ip1]) *
+ tb->deltasq6);
+ break;
+ } // switch(tabstyle)
+ } // uf_lookup()
+
+
+ // ----------------------------------------------------------
+ // u_lookup()
+ // quickly calculate the potential u at angle x using tb->e
+ //-----------------------------------------------------------
+
+ inline void u_lookup(int type, double x, double &u)
+ {
+ Table *tb = &tables[tabindex[type]];
+ int N = tablength;
+
+ // i = static_cast<int> ((x - tb->lo) * tb->invdelta); <-general version
+ double x_over_delta = x*tb->invdelta;
+ int i = static_cast<int> (x_over_delta);
+ double b = x_over_delta - i;
+
+ // Apply periodic boundary conditions to indices i and i+1
+ if (i >= N) i -= N;
+ int ip1 = i+1; if (ip1 >= N) ip1 -= N;
+
+ if (tabstyle == LINEAR) {
+ u = tb->e[i] + b * tb->de[i];
+ }
+ else if (tabstyle == SPLINE) {
+ double a = 1.0 - b;
+ u = a * tb->e[i] + b * tb->e[ip1] +
+ ((a*a*a-a)*tb->e2[i] + (b*b*b-b)*tb->e2[ip1]) *
+ tb->deltasq6;
+ }
+ } // u_lookup()
+
+
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+W: Dihedral problem: %d %ld %d %d %d %d
+
+Conformation of the 4 listed dihedral atoms is extreme; you may want
+to check your simulation geometry.
+
+E: Incorrect args for dihedral coefficients
+
+Self-explanatory. Check the input script or data file.
+
+*/
diff --git a/src/USER-MISC/fix_addtorque.cpp b/src/USER-MISC/fix_addtorque.cpp
index 6c3bb5738d8daec03fa1e1dc9a1801d2b8a65297..654911769c271bce9c23c7488d5fa35ca88370e0 100644
--- a/src/USER-MISC/fix_addtorque.cpp
+++ b/src/USER-MISC/fix_addtorque.cpp
@@ -15,8 +15,8 @@
Contributing author: Laurent Joly (U Lyon, France), ljoly.ulyon@gmail.com
------------------------------------------------------------------------- */
-#include <string.h>
-#include <stdlib.h>
+#include <cstring>
+#include <cstdlib>
#include "fix_addtorque.h"
#include "atom.h"
#include "update.h"
diff --git a/src/USER-MISC/fix_ave_correlate_long.cpp b/src/USER-MISC/fix_ave_correlate_long.cpp
index e40447d859caf5cc890ccba60dec02dee30be9ba..da6d041287df6904548cd4fa0070ca2a58b7a86e 100644
--- a/src/USER-MISC/fix_ave_correlate_long.cpp
+++ b/src/USER-MISC/fix_ave_correlate_long.cpp
@@ -21,9 +21,9 @@
see J. Chem. Phys. 133, 154103 (2010)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include <unistd.h>
#include "fix_ave_correlate_long.h"
#include "update.h"
diff --git a/src/USER-MISC/fix_ave_correlate_long.h b/src/USER-MISC/fix_ave_correlate_long.h
index 2823a5beb398de0f2b680db01b5093a87b70e602..5b38f454eaebcab5a81bb7a23278ee8f63c099f1 100644
--- a/src/USER-MISC/fix_ave_correlate_long.h
+++ b/src/USER-MISC/fix_ave_correlate_long.h
@@ -20,7 +20,7 @@ FixStyle(ave/correlate/long,FixAveCorrelateLong)
#ifndef LMP_FIX_AVE_CORRELATE_LONG_H
#define LMP_FIX_AVE_CORRELATE_LONG_H
-#include <stdio.h>
+#include <cstdio>
#include "fix.h"
namespace LAMMPS_NS {
diff --git a/src/USER-MISC/fix_bond_react.cpp b/src/USER-MISC/fix_bond_react.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..4d4b536c36e2d53b4049d0fca54d78cf52e7b557
--- /dev/null
+++ b/src/USER-MISC/fix_bond_react.cpp
@@ -0,0 +1,2690 @@
+/* ----------------------------------------------------------------------
+LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+http://lammps.sandia.gov, Sandia National Laboratories
+Steve Plimpton, sjplimp@sandia.gov
+
+Copyright (2003) Sandia Corporation. Under the terms of Contract
+DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+certain rights in this software. This software is distributed under
+the GNU General Public License.
+
+See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+Contributing Author: Jacob Gissinger (jacob.gissinger@colorado.edu)
+------------------------------------------------------------------------- */
+
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
+#include <cstdlib>
+#include "fix_bond_react.h"
+#include "update.h"
+#include "modify.h"
+#include "respa.h"
+#include "atom.h"
+#include "atom_vec.h"
+#include "force.h"
+#include "pair.h"
+#include "comm.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "random_mars.h"
+#include "molecule.h"
+#include "group.h"
+#include "citeme.h"
+#include "memory.h"
+#include "error.h"
+
+#include <algorithm>
+
+using namespace LAMMPS_NS;
+using namespace FixConst;
+
+static const char cite_fix_bond_react[] =
+ "fix bond/react:\n\n"
+ "@Article{Gissinger17,\n"
+ " author = {J. R. Gissinger, B. D. Jensen, K. E. Wise},\n"
+ " title = {Modeling chemical reactions in classical molecular dynamics simulations},\n"
+ " journal = {Polymer},\n"
+ " year = 2017,\n"
+ " volume = 128,\n"
+ " pages = {211--217}\n"
+ "}\n\n";
+
+#define BIG 1.0e20
+#define DELTA 16
+#define MAXLINE 256
+#define MAXGUESS 20
+
+// various statuses of superimpose algorithm:
+// ACCEPT: site successfully matched to pre-reacted template
+// REJECT: site does not match pre-reacted template
+// PROCEED: normal execution (non-guessing mode)
+// CONTINUE: a neighbor has been assigned, skip to next neighbor
+// GUESSFAIL: a guess has failed (if no more restore points, status = 'REJECT')
+// RESTORE: restore mode, load most recent restore point
+enum{ACCEPT,REJECT,PROCEED,CONTINUE,GUESSFAIL,RESTORE};
+
+/* ---------------------------------------------------------------------- */
+
+FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
+ Fix(lmp, narg, arg)
+{
+ if (lmp->citeme) lmp->citeme->add(cite_fix_bond_react);
+
+ fix1 = NULL;
+ fix2 = NULL;
+
+ if (narg < 8) error->all(FLERR,"Illegal fix bond/react command 0.0");
+
+ MPI_Comm_rank(world,&me);
+ MPI_Comm_size(world,&nprocs);
+
+ attempted_rxn = 0;
+ force_reneighbor = 1;
+ next_reneighbor = -1;
+ vector_flag = 1;
+ global_freq = 1;
+ extvector = 0;
+ rxnID = 0;
+ status = PROCEED;
+
+ // these group names are reserved for use exclusively by bond/react
+ master_group = (char *) "bond_react_MASTER_group";
+
+ // by using fixed group names, only one instance of fix bond/react is allowed.
+ if (modify->find_fix_by_style("bond/react") != -1)
+ error->all(FLERR,"Only one instance of fix bond/react allowed at a time");
+
+ // let's find number of reactions specified
+ nreacts = 0;
+ for (int i = 3; i < narg; i++) {
+ if (strcmp(arg[i],"react") == 0) {
+ nreacts++;
+ i = i + 6; // skip past mandatory arguments
+ if (i > narg) error->all(FLERR,"Illegal fix bond/react command 0.1");
+ }
+ }
+
+ if (nreacts == 0) error->all(FLERR,"Illegal fix bond/react command: missing mandatory 'react' argument");
+
+ size_vector = nreacts;
+
+ int iarg = 3;
+ stabilization_flag = 0;
+ while (strcmp(arg[iarg],"react") != 0) {
+ if (strcmp(arg[iarg],"stabilization") == 0) {
+ if (strcmp(arg[iarg+1],"no") == 0) {
+ if (iarg+2 > narg) error->all(FLERR,"Illegal fix bond/react command 0.2");
+ iarg += 2;
+ }
+ if (strcmp(arg[iarg+1],"yes") == 0) {
+ if (iarg+4 > narg) error->all(FLERR,"Illegal fix bond/react command 0.21");
+ int n = strlen(arg[iarg+2]) + 1;
+ exclude_group = new char[n];
+ strcpy(exclude_group,arg[iarg+2]);
+ stabilization_flag = 1;
+ nve_limit_xmax = arg[iarg+3];
+ iarg += 4;
+ }
+ }
+ }
+
+ // set up common variables as vectors of length 'nreacts'
+ // nevery, cutoff, onemol, twomol, superimpose file
+
+ // this looks excessive
+ // the price of vectorization (all reactions in one command)?
+ memory->create(nevery,nreacts,"bond/react:nevery");
+ memory->create(cutsq,nreacts,2,"bond/react:cutsq");
+ memory->create(unreacted_mol,nreacts,"bond/react:unreacted_mol");
+ memory->create(reacted_mol,nreacts,"bond/react:reacted_mol");
+ memory->create(fraction,nreacts,"bond/react:fraction");
+ memory->create(seed,nreacts,"bond/react:seed");
+ memory->create(limit_duration,nreacts,"bond/react:limit_duration");
+ memory->create(stabilize_steps_flag,nreacts,"bond/react:stabilize_steps_flag");
+ memory->create(iatomtype,nreacts,"bond/react:iatomtype");
+ memory->create(jatomtype,nreacts,"bond/react:jatomtype");
+ memory->create(ibonding,nreacts,"bond/react:ibonding");
+ memory->create(jbonding,nreacts,"bond/react:jbonding");
+ memory->create(closeneigh,nreacts,"bond/react:closeneigh");
+ memory->create(groupbits,nreacts,"bond/react:groupbits");
+ memory->create(reaction_count,nreacts,"bond/react:reaction_count");
+ memory->create(local_rxn_count,nreacts,"bond/react:local_rxn_count");
+ memory->create(ghostly_rxn_count,nreacts,"bond/react:ghostly_rxn_count");
+ memory->create(reaction_count_total,nreacts,"bond/react:reaction_count_total");
+
+ for (int i = 0; i < nreacts; i++) {
+ fraction[i] = 1;
+ seed[i] = 12345;
+ stabilize_steps_flag[i] = 0;
+ // set default limit duration to 60 timesteps
+ limit_duration[i] = 60;
+ reaction_count[i] = 0;
+ local_rxn_count[i] = 0;
+ ghostly_rxn_count[i] = 0;
+ reaction_count_total[i] = 0;
+ }
+
+ char **files;
+ files = new char*[nreacts];
+
+ int rxn = 0;
+ while (iarg < narg && strcmp(arg[iarg],"react") == 0) {
+
+ iarg++;
+
+ iarg++; // read in reaction name here
+ //for example, rxn_name[rxn] = ...
+
+ int igroup = group->find(arg[iarg++]);
+ if (igroup == -1) error->all(FLERR,"Could not find fix group ID");
+ groupbits[rxn] = group->bitmask[igroup];
+
+ nevery[rxn] = force->inumeric(FLERR,arg[iarg++]);
+ if (nevery[rxn] <= 0) error->all(FLERR,"Illegal fix bond/react command 0.4");
+
+ double cutoff = force->numeric(FLERR,arg[iarg++]);
+ if (cutoff < 0.0) error->all(FLERR,"Illegal fix bond/react command 0.5");
+ cutsq[rxn][0] = cutoff*cutoff;
+
+ cutoff = force->numeric(FLERR,arg[iarg++]);
+ if (cutoff < 0.0) error->all(FLERR,"Illegal fix bond/react command 0.55");
+ cutsq[rxn][1] = cutoff*cutoff;
+
+ unreacted_mol[rxn] = atom->find_molecule(arg[iarg++]);
+ if (unreacted_mol[rxn] == -1) error->all(FLERR,"Unreacted molecule template ID for "
+ "fix bond/react does not exist");
+ reacted_mol[rxn] = atom->find_molecule(arg[iarg++]);
+ if (reacted_mol[rxn] == -1) error->all(FLERR,"Reacted molecule template ID for "
+ "fix bond/react does not exist");
+
+ //read superimpose file
+ files[rxn] = new char[strlen(arg[iarg])+1];
+ strcpy(files[rxn],arg[iarg]);
+ iarg++;
+
+ while (iarg < narg && strcmp(arg[iarg],"react") != 0 ) {
+ if (strcmp(arg[iarg],"prob") == 0) {
+ if (iarg+3 > narg) error->all(FLERR,"Illegal fix bond/react command 0.6");
+ fraction[rxn] = force->numeric(FLERR,arg[iarg+1]);
+ seed[rxn] = force->inumeric(FLERR,arg[iarg+2]);
+ if (fraction[rxn] < 0.0 || fraction[rxn] > 1.0)
+ error->all(FLERR,"Illegal fix bond/react command");
+ if (seed[rxn] <= 0) error->all(FLERR,"Illegal fix bond/react command 0.7");
+ iarg += 3;
+ } else if (strcmp(arg[iarg],"stabilize_steps") == 0) {
+ if (stabilization_flag == 0) error->all(FLERR,"Stabilize_steps keyword used without stabilization keyword");
+ if (iarg+2 > narg) error->all(FLERR,"Illegal fix bond/react command 0.8");
+ limit_duration[rxn] = force->numeric(FLERR,arg[iarg+1]);
+ stabilize_steps_flag[rxn] = 1;
+ iarg += 2;
+ } else error->all(FLERR,"Illegal fix bond/react command 0.9");
+ }
+ rxn++;
+ }
+
+ max_natoms = 0; // the number of atoms in largest molecule template
+ for (int myrxn = 0; myrxn < nreacts; myrxn++) {
+ twomol = atom->molecules[reacted_mol[myrxn]];
+ max_natoms = MAX(max_natoms,twomol->natoms);
+ }
+
+ memory->create(equivalences,max_natoms,2,nreacts,"bond/react:equivalences");
+ memory->create(reverse_equiv,max_natoms,2,nreacts,"bond/react:reverse_equiv");
+ memory->create(edge,max_natoms,nreacts,"bond/react:edge");
+ memory->create(landlocked_atoms,max_natoms,nreacts,"bond/react:landlocked_atoms");
+
+ // read all superimpose files afterward
+ for (int i = 0; i < nreacts; i++) {
+ open(files[i]);
+ onemol = atom->molecules[unreacted_mol[i]];
+ twomol = atom->molecules[reacted_mol[i]];
+ read(i);
+ fclose(fp);
+ iatomtype[i] = onemol->type[ibonding[i]-1];
+ jatomtype[i] = onemol->type[jbonding[i]-1];
+ find_landlocked_atoms(i);
+ }
+
+ for (int i = 0; i < nreacts; i++) {
+ delete [] files[i];
+ }
+ delete [] files;
+
+ if (atom->molecular != 1)
+ error->all(FLERR,"Cannot use fix bond/react with non-molecular systems");
+
+ // check if bonding atoms are 1-2, 1-3, or 1-4 bonded neighbors
+ // if so, we don't need non-bonded neighbor list
+ for (int myrxn = 0; myrxn < nreacts; myrxn++) {
+ closeneigh[myrxn] = -1; // indicates will search non-bonded neighbors
+ onemol = atom->molecules[unreacted_mol[myrxn]];
+ for (int k = 0; k < onemol->nspecial[ibonding[myrxn]-1][2]; k++) {
+ if (onemol->special[ibonding[myrxn]-1][k] == jbonding[myrxn]) {
+ closeneigh[myrxn] = 2; // index for 1-4 neighbor
+ if (k < onemol->nspecial[ibonding[myrxn]-1][1])
+ closeneigh[myrxn] = 1; // index for 1-3 neighbor
+ if (k < onemol->nspecial[ibonding[myrxn]-1][0])
+ closeneigh[myrxn] = 0; // index for 1-2 neighbor
+ break;
+ }
+ }
+ }
+
+ // initialize Marsaglia RNG with processor-unique seed
+
+ random = new class RanMars*[nreacts];
+ for (int i = 0; i < nreacts; i++) {
+ random[i] = new RanMars(lmp,seed[i] + me);
+ }
+
+ // set comm sizes needed by this fix
+ // forward is big due to comm of broken bonds and 1-2 neighbors
+
+ comm_forward = MAX(2,2+atom->maxspecial);
+ comm_reverse = 2;
+
+ // allocate arrays local to this fix
+
+ nmax = 0;
+ partner = finalpartner = NULL;
+ distsq = NULL;
+ probability = NULL;
+ maxcreate = 0;
+ created = NULL;
+ local_ncreate = NULL;
+ ncreate = NULL;
+ allncreate = 0;
+ local_num_mega = 0;
+ ghostly_num_mega = 0;
+ restore = NULL;
+
+ // zero out stats
+ global_megasize = 0;
+ avail_guesses = 0;
+ glove_counter = 0;
+ guess_branch = new int[MAXGUESS]();
+ pioneer_count = new int[max_natoms];
+ local_mega_glove = NULL;
+ ghostly_mega_glove = NULL;
+ global_mega_glove = NULL;
+
+ // these are merely loop indices that became important
+ pion = neigh = trace = 0;
+
+ id_fix1 = NULL;
+ id_fix2 = NULL;
+}
+
+/* ---------------------------------------------------------------------- */
+
+FixBondReact::~FixBondReact()
+{
+ // unregister callbacks to this fix from Atom class
+ atom->delete_callback(id,0);
+
+ for (int i = 0; i < nreacts; i++) {
+ delete random[i];
+ }
+ delete [] random;
+
+ memory->destroy(partner);
+ memory->destroy(finalpartner);
+ memory->destroy(local_ncreate);
+ memory->destroy(ncreate);
+ memory->destroy(distsq);
+ memory->destroy(probability);
+ memory->destroy(created);
+ memory->destroy(edge);
+ memory->destroy(equivalences);
+ memory->destroy(reverse_equiv);
+
+ memory->destroy(nevery);
+ memory->destroy(cutsq);
+ memory->destroy(unreacted_mol);
+ memory->destroy(reacted_mol);
+ memory->destroy(fraction);
+ memory->destroy(seed);
+ memory->destroy(limit_duration);
+ memory->destroy(stabilize_steps_flag);
+
+ memory->destroy(iatomtype);
+ memory->destroy(jatomtype);
+ memory->destroy(ibonding);
+ memory->destroy(jbonding);
+ memory->destroy(closeneigh);
+ memory->destroy(groupbits);
+ memory->destroy(reaction_count);
+ memory->destroy(local_rxn_count);
+ memory->destroy(ghostly_rxn_count);
+ memory->destroy(reaction_count_total);
+
+ if (attempted_rxn == 1) {
+ memory->destroy(restore_pt);
+ memory->destroy(restore);
+ memory->destroy(glove);
+ memory->destroy(pioneers);
+ memory->destroy(landlocked_atoms);
+ memory->destroy(local_mega_glove);
+ memory->destroy(ghostly_mega_glove);
+ }
+
+ memory->destroy(global_mega_glove);
+
+ if (stabilization_flag == 1) {
+ delete [] exclude_group;
+
+ // check nfix in case all fixes have already been deleted
+ if (id_fix1 == NULL && modify->nfix) modify->delete_fix(id_fix1);
+ delete [] id_fix1;
+ }
+
+ if (id_fix2 == NULL && modify->nfix) modify->delete_fix(id_fix2);
+ delete [] id_fix2;
+
+ delete [] guess_branch;
+ delete [] pioneer_count;
+}
+
+/* ---------------------------------------------------------------------- */
+
+int FixBondReact::setmask()
+{
+ int mask = 0;
+ mask |= POST_INTEGRATE;
+ mask |= POST_INTEGRATE_RESPA;
+ return mask;
+}
+
+/* ----------------------------------------------------------------------
+let's add an internal nve/limit fix for relaxation of reaction sites
+also let's add our per-atom property fix here!
+this per-atom property will state the timestep an atom was 'limited'
+it will have the name 'i_limit_tags' and will be intitialized to 0 (not in group)
+------------------------------------------------------------------------- */
+
+void FixBondReact::post_constructor()
+{
+ // let's add the limit_tags per-atom property fix
+ int len = strlen("bond_react_props_internal") + 1;
+ id_fix2 = new char[len];
+ strcpy(id_fix2,"bond_react_props_internal");
+
+ int ifix = modify->find_fix(id_fix2);
+ if (ifix == -1) {
+ char **newarg = new char*[8];
+ newarg[0] = (char *) "bond_react_props_internal";
+ newarg[1] = (char *) "all"; // group ID is ignored
+ newarg[2] = (char *) "property/atom";
+ newarg[3] = (char *) "i_limit_tags";
+ newarg[4] = (char *) "i_statted_tags";
+ newarg[5] = (char *) "i_react_tags";
+ newarg[6] = (char *) "ghost";
+ newarg[7] = (char *) "yes";
+ modify->add_fix(8,newarg);
+ fix2 = modify->fix[modify->nfix-1];
+ delete [] newarg;
+ }
+
+ // create master_group if not already existing
+ if (group->find(master_group) == -1) {
+ group->find_or_create(master_group);
+ char **newarg;
+ newarg = new char*[5];
+ newarg[0] = master_group;
+ newarg[1] = (char *) "dynamic";
+ newarg[2] = (char *) "all";
+ newarg[3] = (char *) "property";
+ newarg[4] = (char *) "limit_tags";
+ group->assign(5,newarg);
+ delete [] newarg;
+ }
+
+ // on to statted_tags (system-wide thermostat)
+ // intialize per-atom statted_flags to 1
+ // (only if not already initialized by restart)
+ // NOTE: limit_tags and react_tags automaticaly intitialized to zero (unless read from restart)
+ if (fix2->restart_reset != 1) {
+ int flag;
+ int index = atom->find_custom("statted_tags",flag);
+ int *i_statted_tags = atom->ivector[index];
+
+ for (int i = 0; i < atom->nlocal; i++)
+ i_statted_tags[i] = 1;
+ }
+
+ if (stabilization_flag == 1) {
+ // create exclude_group if not already existing
+ if (group->find(exclude_group) == -1) {
+ group->find_or_create(exclude_group);
+ char **newarg;
+ newarg = new char*[5];
+ newarg[0] = exclude_group;
+ newarg[1] = (char *) "dynamic";
+ newarg[2] = (char *) "all";
+ newarg[3] = (char *) "property";
+ newarg[4] = (char *) "statted_tags";
+ group->assign(5,newarg);
+ delete [] newarg;
+ }
+
+ // let's create a new nve/limit fix to limit newly reacted atoms
+ len = strlen("bond_react_MASTER_nve_limit") + 1;
+ id_fix1 = new char[len];
+ strcpy(id_fix1,"bond_react_MASTER_nve_limit");
+
+ ifix = modify->find_fix(id_fix1);
+
+ if (ifix == -1) {
+ char **newarg = new char*[4];
+ newarg[0] = id_fix1;
+ newarg[1] = master_group;
+ newarg[2] = (char *) "nve/limit";
+ newarg[3] = nve_limit_xmax;
+ modify->add_fix(4,newarg);
+ fix1 = modify->fix[modify->nfix-1];
+ delete [] newarg;
+ }
+
+ }
+
+ // currently must redefine dynamic groups so they are updated at proper time
+ // -> should double check as to why
+
+ int must_redefine_groups = 1;
+
+ if (must_redefine_groups) {
+ group->find_or_create(master_group);
+ char **newarg;
+ newarg = new char*[5];
+ newarg[0] = master_group;
+ newarg[1] = (char *) "dynamic";
+ newarg[2] = (char *) "all";
+ newarg[3] = (char *) "property";
+ newarg[4] = (char *) "limit_tags";
+ group->assign(5,newarg);
+ delete [] newarg;
+ }
+
+ if (stabilization_flag == 1) {
+ if (must_redefine_groups) {
+ group->find_or_create(exclude_group);
+ char **newarg;
+ newarg = new char*[5];
+ newarg[0] = exclude_group;
+ newarg[1] = (char *) "dynamic";
+ newarg[2] = (char *) "all";
+ newarg[3] = (char *) "property";
+ newarg[4] = (char *) "statted_tags";
+ group->assign(5,newarg);
+ delete [] newarg;
+ }
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixBondReact::init()
+{
+
+ // warn if more than one bond/react fix
+
+ int count = 0;
+ for (int i = 0; i < modify->nfix; i++)
+ if (strcmp(modify->fix[i]->style,"bond/react") == 0) count++;
+ if (count > 1 && comm->me == 0) error->warning(FLERR,"More than one fix bond/react");
+
+ if (force->newton_bond == 0 && comm->me == 0) error->warning(FLERR,"Fewer reactions may occur in some cases "
+ "when 'newton off' is set for bonded interactions. "
+ "The reccomended setting is 'newton on'.");
+
+ if (strstr(update->integrate_style,"respa"))
+ nlevels_respa = ((Respa *) update->integrate)->nlevels;
+
+ // check cutoff for iatomtype,jatomtype
+ for (int i = 0; i < nreacts; i++) {
+ if (force->pair == NULL || cutsq[i][1] > force->pair->cutsq[iatomtype[i]][jatomtype[i]])
+ error->all(FLERR,"Fix bond/react cutoff is longer than pairwise cutoff");
+ }
+
+ // need a half neighbor list, built every Nevery steps
+ int irequest = neighbor->request(this,instance_me);
+ neighbor->requests[irequest]->pair = 0;
+ neighbor->requests[irequest]->fix = 1;
+ neighbor->requests[irequest]->occasional = 1;
+
+ lastcheck = -1;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixBondReact::init_list(int id, NeighList *ptr)
+{
+ list = ptr;
+}
+
+/* ----------------------------------------------------------------------
+ Identify all pairs of potentially reactive atoms for this time step.
+ This function is modified from LAMMPS’ fix bond/create.
+---------------------------------------------------------------------- */
+
+void FixBondReact::post_integrate()
+{
+ // check if any reactions could occur on this timestep
+ int nevery_check = 1;
+ for (int i = 0; i < nreacts; i++) {
+ if (!(update->ntimestep % nevery[i])) {
+ nevery_check = 0;
+ break;
+ }
+ }
+
+ for (int i = 0; i < nreacts; i++) {
+ reaction_count[i] = 0;
+ local_rxn_count[i] = 0;
+ ghostly_rxn_count[i] = 0;
+ }
+
+ if (nevery_check) {
+ unlimit_bond();
+ return;
+ }
+
+ // acquire updated ghost atom positions
+ // necessary b/c are calling this after integrate, but before Verlet comm
+
+ comm->forward_comm();
+
+ // resize bond partner list and initialize it
+ // needs to be atom->nmax in length
+
+ if (atom->nmax > nmax) {
+ memory->destroy(partner);
+ memory->destroy(finalpartner);
+ memory->destroy(distsq);
+ memory->destroy(local_ncreate);
+ memory->destroy(ncreate);
+ memory->destroy(probability);
+ nmax = atom->nmax;
+ memory->create(partner,nmax,"bond/react:partner");
+ memory->create(finalpartner,nmax,"bond/react:finalpartner");
+ memory->create(distsq,nmax,2,"bond/react:distsq");
+ memory->create(local_ncreate,nreacts,"bond/react:local_ncreate");
+ memory->create(ncreate,nreacts,"bond/react:ncreate");
+ memory->create(probability,nmax,"bond/react:probability");
+ }
+
+ // reset create counts
+ for (int i = 0; i < nreacts; i++) {
+ local_ncreate[i] = 0;
+ ncreate[i] = 0;
+ }
+
+ int nlocal = atom->nlocal;
+ int nall = atom->nlocal + atom->nghost;
+
+ // loop over neighbors of my atoms
+ // each atom sets one closest eligible partner atom ID to bond with
+
+ tagint *tag = atom->tag;
+ int *type = atom->type;
+
+ neighbor->build_one(list,1);
+
+ int j;
+
+ for (rxnID = 0; rxnID < nreacts; rxnID++) {
+
+ for (int ii = 0; ii < nall; ii++) {
+ partner[ii] = 0;
+ finalpartner[ii] = 0;
+ distsq[ii][0] = 0.0;
+ distsq[ii][1] = BIG;
+ }
+
+ // fork between far and close_partner here
+ if (closeneigh[rxnID] < 0) far_partner();
+ else close_partner();
+
+ // reverse comm of distsq and partner
+ // not needed if newton_pair off since I,J pair was seen by both procs
+
+ commflag = 2;
+ if (force->newton_pair) comm->reverse_comm_fix(this);
+
+ // each atom now knows its winning partner
+ // for prob check, generate random value for each atom with a bond partner
+ // forward comm of partner and random value, so ghosts have it
+
+ if (fraction[rxnID] < 1.0) {
+ for (int i = 0; i < nlocal; i++)
+ if (partner[i]) probability[i] = random[rxnID]->uniform();
+ }
+
+ commflag = 2;
+ comm->forward_comm_fix(this,2);
+
+ // consider for reaction:
+ // only if both atoms list each other as winning bond partner
+ // and probability constraint is satisfied
+ // if other atom is owned by another proc, it should do same thing
+
+ int temp_ncreate = 0;
+ for (int i = 0; i < nlocal; i++) {
+ if (partner[i] == 0) {
+ continue;
+ }
+ j = atom->map(partner[i]);
+ if (partner[j] != tag[i]) {
+ continue;
+ }
+
+ // apply probability constraint using RN for atom with smallest ID
+
+ if (fraction[rxnID] < 1.0) {
+ if (tag[i] < tag[j]) {
+ if (probability[i] >= fraction[rxnID]) continue;
+ } else {
+ if (probability[j] >= fraction[rxnID]) continue;
+ }
+ }
+
+ // store final created bond partners and count the rxn possibility once
+
+ finalpartner[i] = tag[j];
+ finalpartner[j] = tag[i];
+
+ if (tag[i] < tag[j]) temp_ncreate++;
+ }
+
+ local_ncreate[rxnID] = temp_ncreate;
+ // break loop if no even eligible bonding atoms were found (on any proc)
+ int some_chance;
+ MPI_Allreduce(&temp_ncreate,&some_chance,1,MPI_INT,MPI_SUM,world);
+ if (!some_chance) continue;
+
+ // communicate final partner
+
+ commflag = 3;
+ comm->forward_comm_fix(this);
+
+ // add instance to 'created' only if this processor
+ // owns the atoms with smaller global ID
+ // NOTE: we no longer care about ghost-ghost instances as bond/create did
+ // this is because we take care of updating topology later (and differently)
+ for (int i = 0; i < nlocal; i++) {
+
+ if (finalpartner[i] == 0) continue;
+
+ j = atom->map(finalpartner[i]);
+ // if (j < 0 || tag[i] < tag[j]) {
+ if (tag[i] < tag[j]) { //atom->map(std::min(tag[i],tag[j])) <= nlocal &&
+ if (ncreate[rxnID] == maxcreate) {
+ maxcreate += DELTA;
+ // third column of 'created': bond/react integer ID
+ memory->grow(created,maxcreate,2,nreacts,"bond/react:created");
+ }
+ // to ensure types remain in same order
+ // unnecessary now taken from reaction map file
+ if (iatomtype[rxnID] == type[i]) {
+ created[ncreate[rxnID]][0][rxnID] = tag[i];
+ created[ncreate[rxnID]][1][rxnID] = finalpartner[i];
+ } else {
+ created[ncreate[rxnID]][0][rxnID] = finalpartner[i];
+ created[ncreate[rxnID]][1][rxnID] = tag[i];
+ }
+ ncreate[rxnID]++;
+ }
+ }
+ unlimit_bond(); //free atoms that have been relaxed
+ }
+
+ // break loop if no even eligible bonding atoms were found (on any proc)
+ int some_chance;
+
+ allncreate = 0;
+ for (int i = 0; i < nreacts; i++)
+ allncreate += ncreate[i];
+
+ MPI_Allreduce(&allncreate,&some_chance,1,MPI_INT,MPI_SUM,world);
+ if (!some_chance) {
+ unlimit_bond();
+ return;
+ }
+
+ // run through the superimpose algorithm
+ // this checks if simulation topology matches unreacted mol template
+ superimpose_algorithm();
+ // free atoms that have been limited after reacting
+ unlimit_bond();
+}
+
+/* ----------------------------------------------------------------------
+ Search non-bonded neighbor lists if bonding atoms are not in special list
+------------------------------------------------------------------------- */
+
+void FixBondReact::far_partner()
+{
+ int inum,jnum,itype,jtype,possible;
+ double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
+ int *ilist,*jlist,*numneigh,**firstneigh;
+
+ // loop over neighbors of my atoms
+ // each atom sets one closest eligible partner atom ID to bond with
+
+ double **x = atom->x;
+ tagint *tag = atom->tag;
+ int **nspecial = atom->nspecial;
+ tagint **special = atom->special;
+ int *mask = atom->mask;
+ int *type = atom->type;
+
+ inum = list->inum;
+ ilist = list->ilist;
+ numneigh = list->numneigh;
+ firstneigh = list->firstneigh;
+
+ // per-atom property indicating if in bond/react master group
+ int flag;
+ int index1 = atom->find_custom("limit_tags",flag);
+ int *i_limit_tags = atom->ivector[index1];
+
+ int i,j;
+
+ for (int ii = 0; ii < inum; ii++) {
+ i = ilist[ii];
+ if (!(mask[i] & groupbits[rxnID])) continue;
+ if (i_limit_tags[i] != 0) continue;
+ itype = type[i];
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+ jlist = firstneigh[i];
+ jnum = numneigh[i];
+
+ for (int jj = 0; jj < jnum; jj++) {
+ j = jlist[jj];
+ j &= NEIGHMASK;
+
+ if (!(mask[j] & groupbits[rxnID])) {
+ continue;
+}
+
+ if (i_limit_tags[j] != 0) {
+ continue;
+ }
+
+ jtype = type[j];
+ possible = 0;
+
+ if (itype == iatomtype[rxnID] && jtype == jatomtype[rxnID]) {
+ possible = 1;
+ } else if (itype == jatomtype[rxnID] && jtype == iatomtype[rxnID]) {
+ possible = 1;
+ }
+
+ if (possible == 0) continue;
+
+ // do not allow bonding atoms within special list
+ for (int k = 0; k < nspecial[i][2]; k++)
+ if (special[i][k] == tag[j]) possible = 0;
+ if (!possible) continue;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+
+ if (rsq >= cutsq[rxnID][1] || rsq <= cutsq[rxnID][0]) {
+ continue;
+ }
+ if (rsq < distsq[i][1]) {
+ partner[i] = tag[j];
+ distsq[i][1] = rsq;
+ }
+ if (rsq < distsq[j][1]) {
+ partner[j] = tag[i];
+ distsq[j][1] = rsq;
+ }
+ }
+ }
+}
+
+/* ----------------------------------------------------------------------
+ Slightly simpler to find bonding partner when a close neighbor
+------------------------------------------------------------------------- */
+
+void FixBondReact::close_partner()
+{
+ int n,i1,i2,itype,jtype;
+ double delx,dely,delz,rsq;
+
+ double **x = atom->x;
+ tagint *tag = atom->tag;
+ int *type = atom->type;
+ int *mask = atom->mask;
+ int **nspecial = atom->nspecial;
+ tagint **special = atom->special;
+
+ // per-atom property indicating if in bond/react master group
+ int flag;
+ int index1 = atom->find_custom("limit_tags",flag);
+ int *i_limit_tags = atom->ivector[index1];
+
+ // loop over special list
+ for (int ii = 0; ii < atom->nlocal; ii++) {
+ itype = type[ii];
+ n = 0;
+ if (closeneigh[rxnID] != 0)
+ n = nspecial[ii][closeneigh[rxnID]-1];
+ for (; n < nspecial[ii][closeneigh[rxnID]]; n++) {
+ i1 = ii;
+ i2 = atom->map(special[ii][n]);
+ jtype = type[i2];
+ if (!(mask[i1] & groupbits[rxnID])) continue;
+ if (!(mask[i2] & groupbits[rxnID])) continue;
+ if (i_limit_tags[i1] != 0) continue;
+ if (i_limit_tags[i2] != 0) continue;
+ if (itype != iatomtype[rxnID] || jtype != jatomtype[rxnID]) continue;
+
+ delx = x[i1][0] - x[i2][0];
+ dely = x[i1][1] - x[i2][1];
+ delz = x[i1][2] - x[i2][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+ if (rsq >= cutsq[rxnID][1] || rsq <= cutsq[rxnID][0]) continue;
+
+ if (rsq > distsq[i1][0]) {
+ partner[i1] = tag[i2];
+ distsq[i1][0] = rsq;
+ }
+ if (rsq > distsq[i2][0]) {
+ partner[i2] = tag[i1];
+ distsq[i2][0] = rsq;
+ }
+ }
+ }
+}
+
+/* ----------------------------------------------------------------------
+ Set up global variables. Loop through all pairs; loop through Pioneers
+ until Superimpose Algorithm is completed for each pair.
+------------------------------------------------------------------------- */
+
+void FixBondReact::superimpose_algorithm()
+{
+ local_num_mega = 0;
+ ghostly_num_mega = 0;
+
+ // quick description of important global indices you'll see floating about:
+ // 'pion' is the pioneer loop index
+ // 'neigh' in the first neighbor index
+ // 'trace' retraces the first nieghbors
+ // trace: once you choose a first neighbor, you then check for other nieghbors of same type
+
+ if (attempted_rxn == 1) {
+ memory->destroy(restore_pt);
+ memory->destroy(restore);
+ memory->destroy(glove);
+ memory->destroy(pioneers);
+ memory->destroy(local_mega_glove);
+ memory->destroy(ghostly_mega_glove);
+ }
+
+ memory->create(glove,max_natoms,2,"bond/react:glove");
+ memory->create(restore_pt,MAXGUESS,4,"bond/react:restore_pt");
+ memory->create(pioneers,max_natoms,"bond/react:pioneers");
+ memory->create(restore,max_natoms,MAXGUESS,"bond/react:restore");
+ memory->create(local_mega_glove,max_natoms+1,allncreate,"bond/react:local_mega_glove");
+ memory->create(ghostly_mega_glove,max_natoms+1,allncreate,"bond/react:ghostly_mega_glove");
+
+ attempted_rxn = 1;
+
+ for (int i = 0; i < max_natoms+1; i++) {
+ for (int j = 0; j < allncreate; j++) {
+ local_mega_glove[i][j] = 0;
+ ghostly_mega_glove[i][j] = 0;
+ }
+ }
+
+ //let's finally begin the superimpose loop
+ for (rxnID = 0; rxnID < nreacts; rxnID++) {
+ for (lcl_inst = 0; lcl_inst < ncreate[rxnID]; lcl_inst++) {
+
+ onemol = atom->molecules[unreacted_mol[rxnID]];
+ twomol = atom->molecules[reacted_mol[rxnID]];
+
+ status = PROCEED;
+
+ glove_counter = 0;
+ for (int i = 0; i < max_natoms; i++) {
+ for (int j = 0; j < 2; j++) {
+ glove[i][j] = 0;
+ }
+ }
+
+ for (int i = 0; i < MAXGUESS; i++) {
+ guess_branch[i] = 0;
+ }
+
+ int myibonding = ibonding[rxnID];
+ int myjbonding = jbonding[rxnID];
+
+ glove[myibonding-1][0] = myibonding;
+ glove[myibonding-1][1] = created[lcl_inst][0][rxnID];
+ glove_counter++;
+ glove[myjbonding-1][0] = myjbonding;
+ glove[myjbonding-1][1] = created[lcl_inst][1][rxnID];
+ glove_counter++;
+
+ avail_guesses = 0;
+
+ for (int i = 0; i < max_natoms; i++)
+ pioneer_count[i] = 0;
+
+ for (int i = 0; i < onemol->nspecial[myibonding-1][0]; i++)
+ pioneer_count[onemol->special[myibonding-1][i]-1]++;
+
+ for (int i = 0; i < onemol->nspecial[myjbonding-1][0]; i++)
+ pioneer_count[onemol->special[myjbonding-1][i]-1]++;
+
+
+ int hang_catch = 0;
+ while (!(status == ACCEPT || status == REJECT)) {
+
+ for (int i = 0; i < max_natoms; i++) {
+ pioneers[i] = 0;
+ }
+
+ for (int i = 0; i < onemol->natoms; i++) {
+ if (glove[i][0] !=0 && pioneer_count[i] < onemol->nspecial[i][0] && edge[i][rxnID] == 0) {
+ pioneers[i] = 1;
+ }
+ }
+
+ // run through the pioneers
+ // due to use of restore points, 'pion' index can change in loop
+ for (pion = 0; pion < onemol->natoms; pion++) {
+ if (pioneers[pion] || status == GUESSFAIL) {
+ make_a_guess();
+ if (status == ACCEPT || status == REJECT) break;
+ }
+ }
+
+ if (status == ACCEPT) { // reaction site found successfully!
+ glove_ghostcheck();
+ }
+ hang_catch++;
+ // let's go ahead and catch the simplest of hangs
+ //if (hang_catch > onemol->natoms*4)
+ if (hang_catch > atom->nlocal*3) {
+ error->all(FLERR,"Excessive iteration of superimpose algorithm");
+ }
+ }
+ }
+ }
+
+ global_megasize = 0;
+
+ ghost_glovecast(); // consolidate all mega_gloves to all processors
+ dedup_mega_gloves(0); // make sure atoms aren't added to more than one reaction
+
+ MPI_Allreduce(&local_rxn_count[0],&reaction_count[0],nreacts,MPI_INT,MPI_SUM,world);
+
+ for (int i = 0; i < nreacts; i++)
+ reaction_count_total[i] += reaction_count[i];
+
+ // this assumes compute_vector is called from process 0
+ // ...so doesn't bother to bcast ghostly_rxn_count
+ if (me == 0)
+ for (int i = 0; i < nreacts; i++)
+ reaction_count_total[i] += ghostly_rxn_count[i];
+
+ // this updates topology next step
+ next_reneighbor = update->ntimestep;
+
+ // call limit_bond in 'global_mega_glove mode.' oh, and local mode
+ limit_bond(0); // add reacting atoms to nve/limit
+ limit_bond(1);
+ update_everything(); // change topology
+}
+
+/* ----------------------------------------------------------------------
+ Screen for obvious algorithm fails. This is the return point when a guess
+ has failed: check for available restore points.
+------------------------------------------------------------------------- */
+
+void FixBondReact::make_a_guess()
+{
+ int **nspecial = atom->nspecial;
+ tagint **special = atom->special;
+ int *type = atom->type;
+ int nfirst_neighs = onemol->nspecial[pion][0];
+
+ // per-atom property indicating if in bond/react master group
+ int flag;
+ int index1 = atom->find_custom("limit_tags",flag);
+ int *i_limit_tags = atom->ivector[index1];
+
+ if (status == GUESSFAIL && avail_guesses == 0) {
+ status = REJECT;
+ return;
+ }
+
+ if (status == GUESSFAIL && avail_guesses > 0) {
+ // load restore point
+ for (int i = 0; i < onemol->natoms; i++) {
+ glove[i][0] = restore[i][(avail_guesses*4)-4];
+ glove[i][1] = restore[i][(avail_guesses*4)-3];
+ pioneer_count[i] = restore[i][(avail_guesses*4)-2];
+ pioneers[i] = restore[i][(avail_guesses*4)-1];
+ }
+ pion = restore_pt[avail_guesses-1][0];
+ neigh = restore_pt[avail_guesses-1][1];
+ trace = restore_pt[avail_guesses-1][2];
+ glove_counter = restore_pt[avail_guesses-1][3];
+ status = RESTORE;
+ neighbor_loop();
+ if (status != PROCEED) return;
+ }
+
+ nfirst_neighs = onemol->nspecial[pion][0];
+
+ // check if any of first neighbors are in bond_react_MASTER_group
+ // if so, this constitutes a fail
+ // because still undergoing a previous reaction!
+ // could technically fail unnecessarily during a wrong guess if near edge atoms
+ // we accept this temporary and infrequent decrease in reaction occurences
+
+ for (int i = 0; i < nspecial[atom->map(glove[pion][1])][0]; i++) {
+ if (atom->map(special[atom->map(glove[pion][1])][i]) < 0) {
+ error->all(FLERR,"Fix bond/react needs ghost atoms from further away1"); // parallel issues.
+ }
+ if (i_limit_tags[(int)atom->map(special[atom->map(glove[pion][1])][i])] != 0) {
+ status = GUESSFAIL;
+ return;
+ }
+ }
+
+ // check for same number of neighbors between unreacted mol and simulation
+ if (nfirst_neighs != nspecial[atom->map(glove[pion][1])][0]) {
+ status = GUESSFAIL;
+ return;
+ }
+
+ // make sure all neighbors aren't already assigned
+ // an issue discovered for coarse-grained example
+ int assigned_count = 0;
+ for (int i = 0; i < nfirst_neighs; i++)
+ for (int j = 0; j < onemol->natoms; j++)
+ if (special[atom->map(glove[pion][1])][i] == glove[j][1]) {
+ assigned_count++;
+ break;
+ }
+
+ if (assigned_count == nfirst_neighs) status = GUESSFAIL;
+
+ // check if all neigh atom types are the same between simulation and unreacted mol
+ int *mol_ntypes = new int[atom->ntypes];
+ int *lcl_ntypes = new int[atom->ntypes];
+
+ for (int i = 0; i < atom->ntypes; i++) {
+ mol_ntypes[i] = 0;
+ lcl_ntypes[i] = 0;
+ }
+
+ for (int i = 0; i < nfirst_neighs; i++) {
+ mol_ntypes[(int)onemol->type[(int)onemol->special[pion][i]-1]-1]++;
+ lcl_ntypes[(int)type[(int)atom->map(special[atom->map(glove[pion][1])][i])]-1]++; //added -1
+ }
+
+ for (int i = 0; i < atom->ntypes; i++) {
+ if (mol_ntypes[i] != lcl_ntypes[i]) {
+ status = GUESSFAIL;
+ delete [] mol_ntypes;
+ delete [] lcl_ntypes;
+ return;
+ }
+ }
+
+ delete [] mol_ntypes;
+ delete [] lcl_ntypes;
+
+ // okay everything seems to be in order. let's assign some ID pairs!!!
+ neighbor_loop();
+}
+
+/* ----------------------------------------------------------------------
+ Loop through all First Bonded Neighbors of the current Pioneer.
+ Prepare appropriately if we are in Restore Mode.
+------------------------------------------------------------------------- */
+
+void FixBondReact::neighbor_loop()
+{
+ int nfirst_neighs = onemol->nspecial[pion][0];
+
+ if (status == RESTORE) {
+ check_a_neighbor();
+ return;
+ }
+
+ for (neigh = 0; neigh < nfirst_neighs; neigh++) {
+ if (glove[(int)onemol->special[pion][neigh]-1][0] == 0) {
+ check_a_neighbor();
+ }
+ }
+ // status should still = PROCEED
+}
+
+/* ----------------------------------------------------------------------
+ Check if we can assign this First Neighbor to pre-reacted template
+ without guessing. If so, do it! If not, call crosscheck_the_nieghbor().
+------------------------------------------------------------------------- */
+
+void FixBondReact::check_a_neighbor()
+{
+ int **nspecial = atom->nspecial;
+ tagint **special = atom->special;
+ int *type = atom->type;
+ int nfirst_neighs = onemol->nspecial[pion][0];
+
+ if (status != RESTORE) {
+ // special consideration for hydrogen atoms (and all first neighbors bonded to no other atoms) (and aren't edge atoms)
+ if (onemol->nspecial[(int)onemol->special[pion][neigh]-1][0] == 1 && edge[(int)onemol->special[pion][neigh]-1][rxnID] == 0) {
+
+ for (int i = 0; i < nfirst_neighs; i++) {
+
+ if (type[(int)atom->map(special[(int)atom->map(glove[pion][1])][i])] == onemol->type[(int)onemol->special[pion][neigh]-1] &&
+ nspecial[(int)atom->map(special[(int)atom->map(glove[pion][1])][i])][0] == 1) {
+
+ int already_assigned = 0;
+ for (int j = 0; j < onemol->natoms; j++) {
+ if (glove[j][1] == special[atom->map(glove[pion][1])][i]) {
+ already_assigned = 1;
+ break;
+ }
+ }
+
+ if (already_assigned == 0) {
+ glove[(int)onemol->special[pion][neigh]-1][0] = onemol->special[pion][neigh];
+ glove[(int)onemol->special[pion][neigh]-1][1] = special[(int)atom->map(glove[pion][1])][i];
+
+ //another check for ghost atoms. perhaps remove the one in make_a_guess
+ if (atom->map(glove[(int)onemol->special[pion][neigh]-1][1]) < 0) {
+ error->all(FLERR,"Fix bond/react needs ghost atoms from further away2");
+ }
+
+ for (int j = 0; j < onemol->nspecial[onemol->special[pion][neigh]-1][0]; j++) {
+ pioneer_count[onemol->special[onemol->special[pion][neigh]-1][j]-1]++;
+ }
+
+ glove_counter++;
+ if (glove_counter == onemol->natoms) {
+ status = ACCEPT;
+ ring_check();
+ return;
+ }
+ // status should still == PROCEED
+ return;
+ }
+ }
+ }
+ // we are here if no matching atom found
+ status = GUESSFAIL;
+ return;
+ }
+ }
+
+ crosscheck_the_neighbor();
+ if (status != PROCEED) {
+ if (status == CONTINUE)
+ status = PROCEED;
+ return;
+ }
+
+ // finally ready to match non-duplicate, non-edge atom IDs!!
+
+ for (int i = 0; i < nfirst_neighs; i++) {
+
+ if (type[atom->map((int)special[(int)atom->map(glove[pion][1])][i])] == onemol->type[(int)onemol->special[pion][neigh]-1]) {
+ int already_assigned = 0;
+
+ //check if a first neighbor of the pioneer is already assigned to pre-reacted template
+ for (int j = 0; j < onemol->natoms; j++) {
+ if (glove[j][1] == special[atom->map(glove[pion][1])][i]) {
+ already_assigned = 1;
+ break;
+ }
+ }
+
+ if (already_assigned == 0) {
+ glove[(int)onemol->special[pion][neigh]-1][0] = onemol->special[pion][neigh];
+ glove[(int)onemol->special[pion][neigh]-1][1] = special[(int)atom->map(glove[pion][1])][i];
+
+ //another check for ghost atoms. perhaps remove the one in make_a_guess
+ if (atom->map(glove[(int)onemol->special[pion][neigh]-1][1]) < 0) {
+ error->all(FLERR,"Fix bond/react needs ghost atoms from further away3");
+ }
+
+ for (int ii = 0; ii < onemol->nspecial[onemol->special[pion][neigh]-1][0]; ii++) {
+ pioneer_count[onemol->special[onemol->special[pion][neigh]-1][ii]-1]++;
+ }
+
+ glove_counter++;
+ if (glove_counter == onemol->natoms) {
+ status = ACCEPT;
+ ring_check();
+ return;
+ // will never complete here when there are edge atoms
+ // ...actually that could be wrong if people get creative...shouldn't affect anything
+ }
+ // status should still = PROCEED
+ return;
+ }
+ }
+ }
+ // status is still 'PROCEED' if we are here!
+}
+
+/* ----------------------------------------------------------------------
+ Check if there a viable guess to be made. If so, prepare to make a
+ guess by recording a restore point.
+------------------------------------------------------------------------- */
+
+void FixBondReact::crosscheck_the_neighbor()
+{
+ int nfirst_neighs = onemol->nspecial[pion][0];
+
+ if (status == RESTORE) {
+ inner_crosscheck_loop();
+ return;
+ }
+
+ for (trace = 0; trace < nfirst_neighs; trace++) {
+ if (neigh!=trace && onemol->type[(int)onemol->special[pion][neigh]-1] == onemol->type[(int)onemol->special[pion][trace]-1] &&
+ glove[onemol->special[pion][trace]-1][0] == 0) {
+
+ if (avail_guesses == MAXGUESS) {
+ error->warning(FLERR,"Fix bond/react failed because MAXGUESS set too small. ask developer for info");
+ status = GUESSFAIL;
+ return;
+ }
+ avail_guesses++;
+ for (int i = 0; i < onemol->natoms; i++) {
+ restore[i][(avail_guesses*4)-4] = glove[i][0];
+ restore[i][(avail_guesses*4)-3] = glove[i][1];
+ restore[i][(avail_guesses*4)-2] = pioneer_count[i];
+ restore[i][(avail_guesses*4)-1] = pioneers[i];
+ restore_pt[avail_guesses-1][0] = pion;
+ restore_pt[avail_guesses-1][1] = neigh;
+ restore_pt[avail_guesses-1][2] = trace;
+ restore_pt[avail_guesses-1][3] = glove_counter;
+ }
+
+ inner_crosscheck_loop();
+ return;
+ }
+ }
+ // status is still 'PROCEED' if we are here!
+}
+
+/* ----------------------------------------------------------------------
+ We are ready to make a guess. If there are multiple possible choices
+ for this guess, keep track of these.
+------------------------------------------------------------------------- */
+
+void FixBondReact::inner_crosscheck_loop()
+{
+ tagint **special = atom->special;
+ int *type = atom->type;
+ // arbitrarily limited to 5 identical first neighbors
+ tagint tag_choices[5];
+ int nfirst_neighs = onemol->nspecial[pion][0];
+
+ int num_choices = 0;
+ for (int i = 0; i < nfirst_neighs; i++) {
+
+ int already_assigned = 0;
+ for (int j = 0; j < onemol->natoms; j++) {
+ if (glove[j][1] == special[atom->map(glove[pion][1])][i]) {
+ already_assigned = 1;
+ break;
+ }
+ }
+
+ if (already_assigned == 0 &&
+ type[(int)atom->map(special[atom->map(glove[pion][1])][i])] == onemol->type[(int)onemol->special[pion][neigh]-1]) {
+ if (num_choices > 5) { // here failed because too many identical first neighbors. but really no limit if situation arises
+ status = GUESSFAIL;
+ return;
+ }
+ tag_choices[num_choices++] = special[atom->map(glove[pion][1])][i];
+ }
+ }
+
+ // guess branch is for when multiple identical neighbors. then we guess each one in turn
+ // guess_branch must work even when avail_guesses = 0. so index accordingly!
+ // ...actually, avail_guesses should never be zero here anyway
+ if (guess_branch[avail_guesses-1] == 0) guess_branch[avail_guesses-1] = num_choices;
+
+ //std::size_t size = sizeof(tag_choices) / sizeof(tag_choices[0]);
+ std::sort(tag_choices, tag_choices + num_choices); //, std::greater<int>());
+ glove[onemol->special[pion][neigh]-1][0] = onemol->special[pion][neigh];
+ glove[onemol->special[pion][neigh]-1][1] = tag_choices[guess_branch[avail_guesses-1]-1];
+ guess_branch[avail_guesses-1]--;
+
+ //another check for ghost atoms. perhaps remove the one in make_a_guess
+ if (atom->map(glove[(int)onemol->special[pion][neigh]-1][1]) < 0) {
+ error->all(FLERR,"Fix bond/react needs ghost atoms from further away4");
+ }
+
+ if (guess_branch[avail_guesses-1] == 0) avail_guesses--;
+
+ for (int i = 0; i < onemol->nspecial[onemol->special[pion][neigh]-1][0]; i++) {
+ pioneer_count[onemol->special[onemol->special[pion][neigh]-1][i]-1]++;
+ }
+ glove_counter++;
+ if (glove_counter == onemol->natoms) {
+ status = ACCEPT;
+ ring_check();
+ return;
+ }
+ status = CONTINUE;
+}
+
+/* ----------------------------------------------------------------------
+ Check that newly assigned atoms have correct bonds
+ Necessary for certain ringed structures
+------------------------------------------------------------------------- */
+
+void FixBondReact::ring_check()
+{
+ // ring_check can be made more efficient by re-introducing 'frozen' atoms
+ // 'frozen' atoms have been assigned and also are no longer pioneers
+ int **nspecial = atom->nspecial;
+ tagint **special = atom->special;
+
+ for (int i = 0; i < onemol->natoms; i++) {
+ for (int j = 0; j < onemol->nspecial[i][0]; j++) {
+ int ring_fail = 1;
+ int ispecial = onemol->special[i][j];
+ for (int k = 0; k < nspecial[atom->map(glove[i][1])][0]; k++) {
+ if (special[atom->map(glove[i][1])][k] == glove[ispecial-1][1]) {
+ ring_fail = 0;
+ break;
+ }
+ }
+ if (ring_fail == 1) {
+ status = GUESSFAIL;
+ return;
+ }
+ }
+ }
+}
+
+/* ----------------------------------------------------------------------
+ Determine which pre-reacted template atoms are at least three bonds
+ away from edge atoms.
+------------------------------------------------------------------------- */
+
+void FixBondReact::find_landlocked_atoms(int myrxn)
+{
+ // landlocked_atoms are atoms for which all topology is contained in reacted template
+ // if dihedrals/impropers exist: this means that edge atoms are not in their 1-3 neighbor list
+ // note: due to various usage/defintions of impropers, treated same as dihedrals
+ // if angles exist: this means edge atoms not in their 1-2 neighbors list
+ // if just bonds: this just means that edge atoms are not landlocked
+ // Note: landlocked defined in terms of reacted template
+ // if no edge atoms (small reacting molecule), all atoms are landlocked
+ // we can delete all current topology of landlocked atoms and replace
+
+ // always remove edge atoms from landlocked list
+ for (int i = 0; i < twomol->natoms; i++) {
+ if (edge[equivalences[i][1][myrxn]-1][myrxn] == 1) landlocked_atoms[i][myrxn] = 0;
+ else landlocked_atoms[i][myrxn] = 1;
+ }
+ int nspecial_limit = -1;
+ if (force->angle && twomol->angleflag) nspecial_limit = 0;
+
+ if ((force->dihedral && twomol->dihedralflag) ||
+ (force->improper && twomol->improperflag)) nspecial_limit = 1;
+
+ if (nspecial_limit != -1) {
+ for (int i = 0; i < twomol->natoms; i++) {
+ for (int j = 0; j < twomol->nspecial[i][nspecial_limit]; j++) {
+ for (int k = 0; k < onemol->natoms; k++) {
+ if (equivalences[twomol->special[i][j]-1][1][myrxn] == k+1 && edge[k][myrxn] == 1) {
+ landlocked_atoms[i][myrxn] = 0;
+ }
+ }
+ }
+ }
+ }
+
+ // bad molecule templates check
+ // if atoms change types, but aren't landlocked, that's bad
+ for (int i = 0; i < twomol->natoms; i++) {
+ if (twomol->type[i] != onemol->type[equivalences[i][1][myrxn]-1] && landlocked_atoms[i][myrxn] == 0)
+ error->one(FLERR,"Atom affected by reaction too close to template edge");
+ }
+
+ // also, if atoms change number of bonds, but aren't landlocked, that could be bad
+ if (me == 0)
+ for (int i = 0; i < twomol->natoms; i++) {
+ if (twomol->nspecial[i][0] != onemol->nspecial[equivalences[i][1][myrxn]-1][0] && landlocked_atoms[i][myrxn] == 0) {
+ char str[128];
+ sprintf(str,"An atom in 'react #%d' changes bond connectivity but not atom type",myrxn+1);
+ error->warning(FLERR,str);
+ break;
+ }
+ }
+}
+
+/* ----------------------------------------------------------------------
+let's dedup global_mega_glove
+allows for same site undergoing different pathways, in parallel
+------------------------------------------------------------------------- */
+
+void FixBondReact::dedup_mega_gloves(int dedup_mode)
+{
+ // dedup_mode == 0 for local_dedup
+ // dedup_mode == 1 for global_mega_glove
+ for (int i = 0; i < nreacts; i++) {
+ if (dedup_mode == 0) local_rxn_count[i] = 0;
+ if (dedup_mode == 1) ghostly_rxn_count[i] = 0;
+ }
+
+ int dedup_size;
+ if (dedup_mode == 0) {
+ dedup_size = local_num_mega;
+ } else if (dedup_mode == 1) {
+ dedup_size = global_megasize;
+ }
+
+ tagint **dedup_glove;
+ memory->create(dedup_glove,max_natoms+1,dedup_size,"bond/react:dedup_glove");
+
+ if (dedup_mode == 0) {
+ for (int i = 0; i < dedup_size; i++) {
+ for (int j = 0; j < max_natoms+1; j++) {
+ dedup_glove[j][i] = local_mega_glove[j][i];
+ }
+ }
+ } else if (dedup_mode == 1) {
+ for (int i = 0; i < dedup_size; i++) {
+ for (int j = 0; j < max_natoms+1; j++) {
+ dedup_glove[j][i] = global_mega_glove[j][i];
+ }
+ }
+ }
+
+ // dedup_mask is size dedup_size and filters reactions that have been deleted
+ // a value of 1 means this reaction instance has been deleted
+ int *dedup_mask = new int[dedup_size];
+ int *dup_list = new int[dedup_size];
+
+ for (int i = 0; i < dedup_size; i++) {
+ dedup_mask[i] = 0;
+ dup_list[i] = 0;
+ }
+
+ // let's randomly mix up our reaction instances first
+ // then we can feel okay about ignoring ones we've already deleted (or accepted)
+ // based off std::shuffle
+ int *temp_rxn = new int[max_natoms+1];
+ for (int i = dedup_size-1; i > 0; --i) { //dedup_size
+ // choose random entry to swap current one with
+ int k = floor(random[0]->uniform()*(i+1));
+
+ // swap entries
+ for (int j = 0; j < max_natoms+1; j++)
+ temp_rxn[j] = dedup_glove[j][i];
+
+ for (int j = 0; j < max_natoms+1; j++) {
+ dedup_glove[j][i] = dedup_glove[j][k];
+ dedup_glove[j][k] = temp_rxn[j];
+ }
+ }
+ delete [] temp_rxn;
+
+ for (int i = 0; i < dedup_size; i++) {
+ if (dedup_mask[i] == 0) {
+ int num_dups = 0;
+ int myrxnid1 = dedup_glove[0][i];
+ onemol = atom->molecules[unreacted_mol[myrxnid1]];
+ for (int j = 0; j < onemol->natoms; j++) {
+ int check1 = dedup_glove[j+1][i];
+ for (int ii = i + 1; ii < dedup_size; ii++) {
+ int already_listed = 0;
+ for (int jj = 0; jj < num_dups; jj++) {
+ if (dup_list[jj] == ii) {
+ already_listed = 1;
+ break;
+ }
+ }
+ if (dedup_mask[ii] == 0 && already_listed == 0) {
+ int myrxnid2 = dedup_glove[0][ii];
+ twomol = atom->molecules[unreacted_mol[myrxnid2]];
+ for (int jj = 0; jj < twomol->natoms; jj++) {
+ int check2 = dedup_glove[jj+1][ii];
+ if (check2 == check1) {
+ // add this rxn instance as well
+ if (num_dups == 0) dup_list[num_dups++] = i;
+ dup_list[num_dups++] = ii;
+ break;
+ }
+ }
+ }
+ }
+ }
+ // here we choose random number and therefore reaction instance
+ int myrand = 1;
+ if (num_dups > 0) {
+ myrand = floor(random[0]->uniform()*num_dups);
+ for (int iii = 0; iii < num_dups; iii++) {
+ if (iii != myrand) dedup_mask[dup_list[iii]] = 1;
+ }
+ }
+ }
+ }
+
+ // we must update local_mega_glove and local_megasize
+ // we can simply overwrite local_mega_glove column by column
+ if (dedup_mode == 0) {
+ int new_local_megasize = 0;
+ for (int i = 0; i < local_num_mega; i++) {
+ if (dedup_mask[i] == 0) {
+ local_rxn_count[(int) dedup_glove[0][i]]++;
+ for (int j = 0; j < max_natoms+1; j++) {
+ local_mega_glove[j][new_local_megasize] = dedup_glove[j][i];
+ }
+ new_local_megasize++;
+ }
+ }
+
+ local_num_mega = new_local_megasize;
+ }
+
+ // we must update global_mega_glove and global_megasize
+ // we can simply overwrite global_mega_glove column by column
+ if (dedup_mode == 1) {
+ int new_global_megasize = 0;
+ for (int i = 0; i < global_megasize; i++) {
+ if (dedup_mask[i] == 0) {
+ ghostly_rxn_count[dedup_glove[0][i]]++;
+ for (int j = 0; j < max_natoms + 1; j++) {
+ global_mega_glove[j][new_global_megasize] = dedup_glove[j][i];
+ }
+ new_global_megasize++;
+ }
+ }
+ global_megasize = new_global_megasize;
+ }
+
+ memory->destroy(dedup_glove);
+ delete [] dedup_mask;
+ delete [] dup_list;
+}
+
+/* ----------------------------------------------------------------------
+let's limit movement of newly bonded atoms
+and exclude them from other thermostats via exclude_group
+------------------------------------------------------------------------- */
+
+void FixBondReact::limit_bond(int limit_bond_mode)
+{
+ //two types of passes: 1) while superimpose algorithm is iterating (only local atoms)
+ // 2) once more for global_mega_glove [after de-duplicating rxn instances]
+ //in second case, only add local atoms to group
+ //as with update_everything, we can pre-prepare these arrays, then run generic limit_bond code
+
+ //create local, generic variables for onemol->natoms and glove
+ //to be filled differently on respective passes
+
+ int nlocal = atom->nlocal;
+ int temp_limit_num = 0;
+ tagint *temp_limit_glove;
+ if (limit_bond_mode == 0) {
+ int max_temp = local_num_mega * (max_natoms + 1);
+ temp_limit_glove = new tagint[max_temp];
+ for (int j = 0; j < local_num_mega; j++) {
+ rxnID = local_mega_glove[0][j];
+ onemol = atom->molecules[unreacted_mol[rxnID]];
+ for (int i = 0; i < onemol->natoms; i++) {
+ temp_limit_glove[temp_limit_num++] = local_mega_glove[i+1][j];
+ }
+ }
+
+ } else if (limit_bond_mode == 1) {
+ int max_temp = global_megasize * (max_natoms + 1);
+ temp_limit_glove = new tagint[max_temp];
+ for (int j = 0; j < global_megasize; j++) {
+ rxnID = global_mega_glove[0][j];
+ onemol = atom->molecules[unreacted_mol[rxnID]];
+ for (int i = 0; i < onemol->natoms; i++) {
+ if (atom->map(global_mega_glove[i+1][j]) >= 0 &&
+ atom->map(global_mega_glove[i+1][j]) < nlocal)
+ temp_limit_glove[temp_limit_num++] = global_mega_glove[i+1][j];
+ }
+ }
+ }
+
+ if (temp_limit_num == 0) {
+ delete [] temp_limit_glove;
+ return;
+ }
+
+ // we must keep our own list of limited atoms
+ // this will be a new per-atom property!
+
+ int flag;
+ int index1 = atom->find_custom("limit_tags",flag);
+ int *i_limit_tags = atom->ivector[index1];
+
+ int index2 = atom->find_custom("statted_tags",flag);
+ int *i_statted_tags = atom->ivector[index2];
+
+ int index3 = atom->find_custom("react_tags",flag);
+ int *i_react_tags = atom->ivector[index3];
+
+ for (int i = 0; i < temp_limit_num; i++) {
+ // update->ntimestep could be 0. so add 1 throughout
+ i_limit_tags[atom->map(temp_limit_glove[i])] = update->ntimestep + 1;
+ i_statted_tags[atom->map(temp_limit_glove[i])] = 0;
+ i_react_tags[atom->map(temp_limit_glove[i])] = rxnID;
+ }
+
+ delete [] temp_limit_glove;
+}
+
+/* ----------------------------------------------------------------------
+let's unlimit movement of newly bonded atoms after n timesteps.
+we give them back to the system thermostat
+------------------------------------------------------------------------- */
+
+void FixBondReact::unlimit_bond()
+{
+ //let's now unlimit in terms of i_limit_tags
+ //we just run through all nlocal, looking for > limit_duration
+ //then we return i_limit_tag to 0 (which removes from dynamic group)
+ int flag;
+ int index1 = atom->find_custom("limit_tags",flag);
+ int *i_limit_tags = atom->ivector[index1];
+
+ int index2 = atom->find_custom("statted_tags",flag);
+ int *i_statted_tags = atom->ivector[index2];
+
+ int index3 = atom->find_custom("react_tags",flag);
+ int *i_react_tags = atom->ivector[index3];
+
+ for (int i = 0; i < atom->nlocal; i++) {
+ if (i_limit_tags[i] != 0 && (update->ntimestep + 1 - i_limit_tags[i]) > limit_duration[i_react_tags[i]]) {
+ i_limit_tags[i] = 0;
+ i_statted_tags[i] = 1;
+ i_react_tags[i] = 0;
+ }
+ }
+
+ //really should only communicate this per-atom property, not entire reneighboring
+ next_reneighbor = update->ntimestep;
+}
+
+/* ----------------------------------------------------------------------
+check mega_glove for ghosts
+if so, flag for broadcasting for perusal by all processors
+------------------------------------------------------------------------- */
+
+void FixBondReact::glove_ghostcheck()
+{
+ // it appears this little loop was deemed important enough for its own function!
+ // noteworthy: it's only relevant for parallel
+
+ // here we add glove to either local_mega_glove or ghostly_mega_glove
+ int ghostly = 0;
+ for (int i = 0; i < onemol->natoms; i++) {
+ if (atom->map(glove[i][1]) >= atom->nlocal) {
+ ghostly = 1;
+ break;
+ }
+ }
+
+ if (ghostly == 1) {
+ ghostly_mega_glove[0][ghostly_num_mega] = rxnID;
+ ghostly_rxn_count[rxnID]++; //for debuginng
+ for (int i = 0; i < onemol->natoms; i++) {
+ ghostly_mega_glove[i+1][ghostly_num_mega] = glove[i][1];
+ }
+ ghostly_num_mega++;
+ } else {
+ local_mega_glove[0][local_num_mega] = rxnID;
+ local_rxn_count[rxnID]++; //for debuginng
+ for (int i = 0; i < onemol->natoms; i++) {
+ local_mega_glove[i+1][local_num_mega] = glove[i][1];
+ }
+ local_num_mega++;
+ }
+}
+
+/* ----------------------------------------------------------------------
+broadcast entries of mega_glove which contain nonlocal atoms for perusal by all processors
+------------------------------------------------------------------------- */
+
+void FixBondReact::ghost_glovecast()
+{
+#if !defined(MPI_STUBS)
+
+ global_megasize = 0;
+
+ int *allncols = new int[nprocs];
+ for (int i = 0; i < nprocs; i++)
+ allncols[i] = 0;
+ MPI_Allgather(&ghostly_num_mega, 1, MPI_INT, allncols, 1, MPI_INT, world);
+ for (int i = 0; i < nprocs; i++)
+ global_megasize = global_megasize + allncols[i];
+
+ if (global_megasize == 0) {
+ delete [] allncols;
+ return;
+ }
+
+ int *allstarts = new int[nprocs];
+
+ int start = 0;
+ for (int i = 0; i < me; i++) {
+ start += allncols[i];
+ }
+ MPI_Allgather(&start, 1, MPI_INT, allstarts, 1, MPI_INT, world);
+ MPI_Datatype columnunsized, column;
+ int sizes[2] = {max_natoms+1, global_megasize};
+ int subsizes[2] = {max_natoms+1, 1};
+ int starts[2] = {0,0};
+ MPI_Type_create_subarray (2, sizes, subsizes, starts, MPI_ORDER_C,
+ MPI_LMP_TAGINT, &columnunsized);
+ MPI_Type_create_resized (columnunsized, 0, sizeof(tagint), &column);
+ MPI_Type_commit(&column);
+
+ memory->destroy(global_mega_glove);
+ memory->create(global_mega_glove,max_natoms+1,global_megasize,"bond/react:global_mega_glove");
+
+ for (int i = 0; i < max_natoms+1; i++)
+ for (int j = 0; j < global_megasize; j++)
+ global_mega_glove[i][j] = 0;
+
+ if (ghostly_num_mega > 0) {
+ for (int i = 0; i < max_natoms+1; i++) {
+ for (int j = 0; j < ghostly_num_mega; j++) {
+ global_mega_glove[i][j+start] = ghostly_mega_glove[i][j];
+ }
+ }
+ }
+ // let's send to root, dedup, then broadcast
+ if (me == 0) {
+ MPI_Gatherv(MPI_IN_PLACE, ghostly_num_mega, column, // Note: some values ignored for MPI_IN_PLACE
+ &(global_mega_glove[0][0]), allncols, allstarts,
+ column, 0, world);
+ } else {
+ MPI_Gatherv(&(global_mega_glove[0][start]), ghostly_num_mega, column,
+ &(global_mega_glove[0][0]), allncols, allstarts,
+ column, 0, world);
+ }
+
+ if (me == 0) dedup_mega_gloves(1); // global_mega_glove mode
+ MPI_Bcast(&global_megasize,1,MPI_INT,0,world);
+ MPI_Bcast(&(global_mega_glove[0][0]), global_megasize, column, 0, world);
+
+ delete [] allstarts;
+ delete [] allncols;
+
+ MPI_Type_free(&column);
+ MPI_Type_free(&columnunsized);
+#endif
+}
+
+/* ----------------------------------------------------------------------
+update charges, types, special lists and all topology
+------------------------------------------------------------------------- */
+
+void FixBondReact::update_everything()
+{
+ int *type = atom->type;
+
+ int nlocal = atom->nlocal;
+ int **nspecial = atom->nspecial;
+ tagint **special = atom->special;
+
+ int **bond_type = atom->bond_type;
+ tagint **bond_atom = atom->bond_atom;
+ int *num_bond = atom->num_bond;
+
+ // update atom->nbonds, etc.
+ // TODO: correctly tally with 'newton off'
+ int delta_bonds = 0;
+ int delta_angle = 0;
+ int delta_dihed = 0;
+ int delta_imprp = 0;
+
+ // pass through twice
+ // redefining 'update_num_mega' and 'update_mega_glove' each time
+ // first pass: when glove is all local atoms
+ // second pass: search for local atoms in global_mega_glove
+ // add check for local atoms as well
+
+ int update_num_mega;
+ tagint **update_mega_glove;
+ memory->create(update_mega_glove,max_natoms+1,MAX(local_num_mega,global_megasize),"bond/react:update_mega_glove");
+
+ for (int pass = 0; pass < 2; pass++) {
+
+ if (pass == 0) {
+ update_num_mega = local_num_mega;
+ for (int i = 0; i < update_num_mega; i++) {
+ for (int j = 0; j < max_natoms+1; j++)
+ update_mega_glove[j][i] = local_mega_glove[j][i];
+ }
+ } else if (pass == 1) {
+ update_num_mega = global_megasize;
+ for (int i = 0; i < global_megasize; i++) {
+ for (int j = 0; j < max_natoms+1; j++)
+ update_mega_glove[j][i] = global_mega_glove[j][i];
+ }
+ }
+
+ // update charges and types of landlocked atoms
+ // here, add check for charge instead of requiring it
+ for (int i = 0; i < update_num_mega; i++) {
+ rxnID = update_mega_glove[0][i];
+ twomol = atom->molecules[reacted_mol[rxnID]];
+ for (int j = 0; j < twomol->natoms; j++) {
+ int jj = equivalences[j][1][rxnID]-1;
+ if (landlocked_atoms[j][rxnID] == 1 && atom->map(update_mega_glove[jj+1][i]) >= 0 &&
+ atom->map(update_mega_glove[jj+1][i]) < nlocal) {
+ type[atom->map(update_mega_glove[jj+1][i])] = twomol->type[j];
+ if (twomol->qflag && atom->q_flag) {
+ double *q = atom->q;
+ q[atom->map(update_mega_glove[jj+1][i])] = twomol->q[j];
+ }
+ }
+ }
+ }
+
+ //maybe add check that all 1-3 neighbors of a local atoms are at least ghosts -> unneeded --jg
+ //okay, here goes:
+ for (int i = 0; i < update_num_mega; i++) {
+ rxnID = update_mega_glove[0][i];
+ twomol = atom->molecules[reacted_mol[rxnID]];
+ for (int j = 0; j < twomol->natoms; j++) {
+ int jj = equivalences[j][1][rxnID]-1;
+ if (atom->map(update_mega_glove[jj+1][i]) < nlocal && atom->map(update_mega_glove[jj+1][i]) >= 0) {
+ if (landlocked_atoms[j][rxnID] == 1) {
+ for (int k = 0; k < nspecial[atom->map(update_mega_glove[jj+1][i])][2]; k++) {
+ if (atom->map(special[atom->map(update_mega_glove[jj+1][i])][k]) < 0) {
+ error->all(FLERR,"Fix bond/react needs ghost atoms from further away - most likely too many processors");
+ }
+ }
+ }
+ }
+ }
+ }
+
+ int insert_num;
+ // very nice and easy to completely overwrite special bond info for landlocked atoms
+ for (int i = 0; i < update_num_mega; i++) {
+ rxnID = update_mega_glove[0][i];
+ twomol = atom->molecules[reacted_mol[rxnID]];
+ for (int j = 0; j < twomol->natoms; j++) {
+ int jj = equivalences[j][1][rxnID]-1;
+ if (atom->map(update_mega_glove[jj+1][i]) < nlocal && atom->map(update_mega_glove[jj+1][i]) >= 0) {
+ if (landlocked_atoms[j][rxnID] == 1) {
+ for (int k = 0; k < 3; k++) {
+ nspecial[atom->map(update_mega_glove[jj+1][i])][k] = twomol->nspecial[j][k];
+ }
+ for (int p = 0; p < twomol->nspecial[j][2]; p++) {
+ special[atom->map(update_mega_glove[jj+1][i])][p] = update_mega_glove[equivalences[twomol->special[j][p]-1][1][rxnID]][i];
+ }
+ }
+ // now delete and replace landlocked atoms from non-landlocked atoms' special info
+ if (landlocked_atoms[j][rxnID] == 0) {
+ for (int k = nspecial[atom->map(update_mega_glove[jj+1][i])][2]-1; k > -1; k--) {
+ for (int p = 0; p < twomol->natoms; p++) {
+ int pp = equivalences[p][1][rxnID]-1;
+ if (p!=j && special[atom->map(update_mega_glove[jj+1][i])][k] == update_mega_glove[pp+1][i]
+ && landlocked_atoms[p][rxnID] == 1 ) {
+ for (int n = k; n < nspecial[atom->map(update_mega_glove[jj+1][i])][2]-1; n++) {
+ special[atom->map(update_mega_glove[jj+1][i])][n] = special[atom->map(update_mega_glove[jj+1][i])][n+1];
+ }
+ if (k+1 > nspecial[atom->map(update_mega_glove[jj+1][i])][1]) {
+ nspecial[atom->map(update_mega_glove[jj+1][i])][2]--;
+ } else if (k+1 > nspecial[atom->map(update_mega_glove[jj+1][i])][0]) {
+ nspecial[atom->map(update_mega_glove[jj+1][i])][1]--;
+ nspecial[atom->map(update_mega_glove[jj+1][i])][2]--;
+ } else {
+ nspecial[atom->map(update_mega_glove[jj+1][i])][0]--;
+ nspecial[atom->map(update_mega_glove[jj+1][i])][1]--;
+ nspecial[atom->map(update_mega_glove[jj+1][i])][2]--;
+ }
+ break;
+ }
+ }
+ }
+ // now reassign from reacted template
+ for (int k = 0; k < twomol->nspecial[j][2]; k++) {
+ if (landlocked_atoms[twomol->special[j][k]-1][rxnID] == 1) {
+ if (k > twomol->nspecial[j][1] - 1) {
+ insert_num = nspecial[atom->map(update_mega_glove[jj+1][i])][2]++;
+ } else if (k > twomol->nspecial[j][0] - 1) {
+ insert_num = nspecial[atom->map(update_mega_glove[jj+1][i])][1]++;
+ nspecial[atom->map(update_mega_glove[jj+1][i])][2]++;
+ } else {
+ insert_num = nspecial[atom->map(update_mega_glove[jj+1][i])][0]++;
+ nspecial[atom->map(update_mega_glove[jj+1][i])][1]++;
+ nspecial[atom->map(update_mega_glove[jj+1][i])][2]++;
+ }
+ for (int n = nspecial[atom->map(update_mega_glove[jj+1][i])][2]; n > insert_num; n--) {
+ special[atom->map(update_mega_glove[jj+1][i])][n] = special[atom->map(update_mega_glove[jj+1][i])][n-1];
+ }
+ special[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->special[j][k]-1][1][rxnID]][i];
+ }
+ }
+ }
+ }
+ }
+ }
+
+ // next let's update bond info
+ // cool thing is, newton_bond issues are already taken care of in templates
+ // same with class2 improper issues, which is why this fix started in the first place
+ for (int i = 0; i < update_num_mega; i++) {
+ rxnID = update_mega_glove[0][i];
+ twomol = atom->molecules[reacted_mol[rxnID]];
+ // let's first delete all bond info about landlocked atoms
+ for (int j = 0; j < twomol->natoms; j++) {
+ int jj = equivalences[j][1][rxnID]-1;
+ if (atom->map(update_mega_glove[jj+1][i]) < nlocal && atom->map(update_mega_glove[jj+1][i]) >= 0) {
+ if (landlocked_atoms[j][rxnID] == 1) {
+ delta_bonds -= num_bond[atom->map(update_mega_glove[jj+1][i])];
+ num_bond[atom->map(update_mega_glove[jj+1][i])] = 0;
+ }
+ if (landlocked_atoms[j][rxnID] == 0) {
+ for (int p = num_bond[atom->map(update_mega_glove[jj+1][i])]-1; p > -1 ; p--) {
+ for (int n = 0; n < twomol->natoms; n++) {
+ int nn = equivalences[n][1][rxnID]-1;
+ if (n!=j && bond_atom[atom->map(update_mega_glove[jj+1][i])][p] == update_mega_glove[nn+1][i] && landlocked_atoms[n][rxnID] == 1) {
+ for (int m = p; m < num_bond[atom->map(update_mega_glove[jj+1][i])]-1; m++) {
+ bond_type[atom->map(update_mega_glove[jj+1][i])][m] = bond_type[atom->map(update_mega_glove[jj+1][i])][m+1];
+ bond_atom[atom->map(update_mega_glove[jj+1][i])][m] = bond_atom[atom->map(update_mega_glove[jj+1][i])][m+1];
+ }
+ num_bond[atom->map(update_mega_glove[jj+1][i])]--;
+ delta_bonds--;
+ }
+ }
+ }
+ }
+ }
+ }
+ // now let's add the new bond info.
+ for (int j = 0; j < twomol->natoms; j++) {
+ int jj = equivalences[j][1][rxnID]-1;
+ if (atom->map(update_mega_glove[jj+1][i]) < nlocal && atom->map(update_mega_glove[jj+1][i]) >= 0) {
+ if (landlocked_atoms[j][rxnID] == 1) {
+ num_bond[atom->map(update_mega_glove[jj+1][i])] = twomol->num_bond[j];
+ delta_bonds += twomol->num_bond[j];
+ for (int p = 0; p < twomol->num_bond[j]; p++) {
+ bond_type[atom->map(update_mega_glove[jj+1][i])][p] = twomol->bond_type[j][p];
+ bond_atom[atom->map(update_mega_glove[jj+1][i])][p] = update_mega_glove[equivalences[twomol->bond_atom[j][p]-1][1][rxnID]][i];
+ }
+ }
+ if (landlocked_atoms[j][rxnID] == 0) {
+ for (int p = 0; p < twomol->num_bond[j]; p++) {
+ if (landlocked_atoms[twomol->bond_atom[j][p]-1][rxnID] == 1) {
+ insert_num = num_bond[atom->map(update_mega_glove[jj+1][i])];
+ bond_type[atom->map(update_mega_glove[jj+1][i])][insert_num] = twomol->bond_type[j][p];
+ bond_atom[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->bond_atom[j][p]-1][1][rxnID]][i];
+ num_bond[atom->map(update_mega_glove[jj+1][i])]++;
+ delta_bonds++;
+ }
+ }
+ }
+ }
+ }
+ }
+
+ // Angles! First let's delete all angle info:
+ if (force->angle && twomol->angleflag) {
+ int *num_angle = atom->num_angle;
+ int **angle_type = atom->angle_type;
+ tagint **angle_atom1 = atom->angle_atom1;
+ tagint **angle_atom2 = atom->angle_atom2;
+ tagint **angle_atom3 = atom->angle_atom3;
+
+ for (int i = 0; i < update_num_mega; i++) {
+ rxnID = update_mega_glove[0][i];
+ twomol = atom->molecules[reacted_mol[rxnID]];
+ for (int j = 0; j < twomol->natoms; j++) {
+ int jj = equivalences[j][1][rxnID]-1;
+ if (atom->map(update_mega_glove[jj+1][i]) < nlocal && atom->map(update_mega_glove[jj+1][i]) >= 0) {
+ if (landlocked_atoms[j][rxnID] == 1) {
+ delta_angle -= num_angle[atom->map(update_mega_glove[jj+1][i])];
+ num_angle[atom->map(update_mega_glove[jj+1][i])] = 0;
+ }
+ if (landlocked_atoms[j][rxnID] == 0) {
+ for (int p = num_angle[atom->map(update_mega_glove[jj+1][i])]-1; p > -1; p--) {
+ for (int n = 0; n < twomol->natoms; n++) {
+ int nn = equivalences[n][1][rxnID]-1;
+ if (n!=j && landlocked_atoms[n][rxnID] == 1 &&
+ (angle_atom1[atom->map(update_mega_glove[jj+1][i])][p] == update_mega_glove[nn+1][i] ||
+ angle_atom2[atom->map(update_mega_glove[jj+1][i])][p] == update_mega_glove[nn+1][i] ||
+ angle_atom3[atom->map(update_mega_glove[jj+1][i])][p] == update_mega_glove[nn+1][i])) {
+ for (int m = p; m < num_angle[atom->map(update_mega_glove[jj+1][i])]-1; m++) {
+ angle_type[atom->map(update_mega_glove[jj+1][i])][m] = angle_type[atom->map(update_mega_glove[jj+1][i])][m+1];
+ angle_atom1[atom->map(update_mega_glove[jj+1][i])][m] = angle_atom1[atom->map(update_mega_glove[jj+1][i])][m+1];
+ angle_atom2[atom->map(update_mega_glove[jj+1][i])][m] = angle_atom2[atom->map(update_mega_glove[jj+1][i])][m+1];
+ angle_atom3[atom->map(update_mega_glove[jj+1][i])][m] = angle_atom3[atom->map(update_mega_glove[jj+1][i])][m+1];
+ }
+ num_angle[atom->map(update_mega_glove[jj+1][i])]--;
+ delta_angle--;
+ break;
+ }
+ }
+ }
+ }
+ }
+ }
+ // now let's add the new angle info.
+ for (int j = 0; j < twomol->natoms; j++) {
+ int jj = equivalences[j][1][rxnID]-1;
+ if (atom->map(update_mega_glove[jj+1][i]) < nlocal && atom->map(update_mega_glove[jj+1][i]) >= 0) {
+ if (landlocked_atoms[j][rxnID] == 1) {
+ num_angle[atom->map(update_mega_glove[jj+1][i])] = twomol->num_angle[j];
+ delta_angle += twomol->num_angle[j];
+ for (int p = 0; p < twomol->num_angle[j]; p++) {
+ angle_type[atom->map(update_mega_glove[jj+1][i])][p] = twomol->angle_type[j][p];
+ angle_atom1[atom->map(update_mega_glove[jj+1][i])][p] = update_mega_glove[equivalences[twomol->angle_atom1[j][p]-1][1][rxnID]][i];
+ angle_atom2[atom->map(update_mega_glove[jj+1][i])][p] = update_mega_glove[equivalences[twomol->angle_atom2[j][p]-1][1][rxnID]][i];
+ angle_atom3[atom->map(update_mega_glove[jj+1][i])][p] = update_mega_glove[equivalences[twomol->angle_atom3[j][p]-1][1][rxnID]][i];
+ }
+ }
+ if (landlocked_atoms[j][rxnID] == 0) {
+ for (int p = 0; p < twomol->num_angle[j]; p++) {
+ if (landlocked_atoms[twomol->angle_atom1[j][p]-1][rxnID] == 1 ||
+ landlocked_atoms[twomol->angle_atom2[j][p]-1][rxnID] == 1 ||
+ landlocked_atoms[twomol->angle_atom3[j][p]-1][rxnID] == 1) {
+ insert_num = num_angle[atom->map(update_mega_glove[jj+1][i])];
+ angle_type[atom->map(update_mega_glove[jj+1][i])][insert_num] = twomol->angle_type[j][p];
+ angle_atom1[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->angle_atom1[j][p]-1][1][rxnID]][i];
+ angle_atom2[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->angle_atom2[j][p]-1][1][rxnID]][i];
+ angle_atom3[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->angle_atom3[j][p]-1][1][rxnID]][i];
+ num_angle[atom->map(update_mega_glove[jj+1][i])]++;
+ delta_angle++;
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+
+ // Dihedrals! first let's delete all dihedral info for landlocked atoms
+ if (force->dihedral && twomol->dihedralflag) {
+ int *num_dihedral = atom->num_dihedral;
+ int **dihedral_type = atom->dihedral_type;
+ tagint **dihedral_atom1 = atom->dihedral_atom1;
+ tagint **dihedral_atom2 = atom->dihedral_atom2;
+ tagint **dihedral_atom3 = atom->dihedral_atom3;
+ tagint **dihedral_atom4 = atom->dihedral_atom4;
+
+ for (int i = 0; i < update_num_mega; i++) {
+ rxnID = update_mega_glove[0][i];
+ twomol = atom->molecules[reacted_mol[rxnID]];
+ for (int j = 0; j < twomol->natoms; j++) {
+ int jj = equivalences[j][1][rxnID]-1;
+ if (atom->map(update_mega_glove[jj+1][i]) < nlocal && atom->map(update_mega_glove[jj+1][i]) >= 0) {
+ if (landlocked_atoms[j][rxnID] == 1) {
+ delta_dihed -= num_dihedral[atom->map(update_mega_glove[jj+1][i])];
+ num_dihedral[atom->map(update_mega_glove[jj+1][i])] = 0;
+ }
+ if (landlocked_atoms[j][rxnID] == 0) {
+ for (int p = num_dihedral[atom->map(update_mega_glove[jj+1][i])]-1; p > -1; p--) {
+ for (int n = 0; n < twomol->natoms; n++) {
+ int nn = equivalences[n][1][rxnID]-1;
+ if (n!=j && landlocked_atoms[n][rxnID] == 1 &&
+ (dihedral_atom1[atom->map(update_mega_glove[jj+1][i])][p] == update_mega_glove[nn+1][i] ||
+ dihedral_atom2[atom->map(update_mega_glove[jj+1][i])][p] == update_mega_glove[nn+1][i] ||
+ dihedral_atom3[atom->map(update_mega_glove[jj+1][i])][p] == update_mega_glove[nn+1][i] ||
+ dihedral_atom4[atom->map(update_mega_glove[jj+1][i])][p] == update_mega_glove[nn+1][i])) {
+ for (int m = p; m < num_dihedral[atom->map(update_mega_glove[jj+1][i])]-1; m++) {
+ dihedral_type[atom->map(update_mega_glove[jj+1][i])][m] = dihedral_type[atom->map(update_mega_glove[jj+1][i])][m+1];
+ dihedral_atom1[atom->map(update_mega_glove[jj+1][i])][m] = dihedral_atom1[atom->map(update_mega_glove[jj+1][i])][m+1];
+ dihedral_atom2[atom->map(update_mega_glove[jj+1][i])][m] = dihedral_atom2[atom->map(update_mega_glove[jj+1][i])][m+1];
+ dihedral_atom3[atom->map(update_mega_glove[jj+1][i])][m] = dihedral_atom3[atom->map(update_mega_glove[jj+1][i])][m+1];
+ dihedral_atom4[atom->map(update_mega_glove[jj+1][i])][m] = dihedral_atom4[atom->map(update_mega_glove[jj+1][i])][m+1];
+ }
+ num_dihedral[atom->map(update_mega_glove[jj+1][i])]--;
+ delta_dihed--;
+ break;
+ }
+ }
+ }
+ }
+ }
+ }
+ // now let's add new dihedral info
+ for (int j = 0; j < twomol->natoms; j++) {
+ int jj = equivalences[j][1][rxnID]-1;
+ if (atom->map(update_mega_glove[jj+1][i]) < nlocal && atom->map(update_mega_glove[jj+1][i]) >= 0) {
+ if (landlocked_atoms[j][rxnID] == 1) {
+ num_dihedral[atom->map(update_mega_glove[jj+1][i])] = twomol->num_dihedral[j];
+ delta_dihed += twomol->num_dihedral[j];
+ for (int p = 0; p < twomol->num_dihedral[j]; p++) {
+ dihedral_type[atom->map(update_mega_glove[jj+1][i])][p] = twomol->dihedral_type[j][p];
+ dihedral_atom1[atom->map(update_mega_glove[jj+1][i])][p] = update_mega_glove[equivalences[twomol->dihedral_atom1[j][p]-1][1][rxnID]][i];
+ dihedral_atom2[atom->map(update_mega_glove[jj+1][i])][p] = update_mega_glove[equivalences[twomol->dihedral_atom2[j][p]-1][1][rxnID]][i];
+ dihedral_atom3[atom->map(update_mega_glove[jj+1][i])][p] = update_mega_glove[equivalences[twomol->dihedral_atom3[j][p]-1][1][rxnID]][i];
+ dihedral_atom4[atom->map(update_mega_glove[jj+1][i])][p] = update_mega_glove[equivalences[twomol->dihedral_atom4[j][p]-1][1][rxnID]][i];
+ }
+ }
+ if (landlocked_atoms[j][rxnID] == 0) {
+ for (int p = 0; p < twomol->num_dihedral[j]; p++) {
+ if (landlocked_atoms[twomol->dihedral_atom1[j][p]-1][rxnID] == 1 ||
+ landlocked_atoms[twomol->dihedral_atom2[j][p]-1][rxnID] == 1 ||
+ landlocked_atoms[twomol->dihedral_atom3[j][p]-1][rxnID] == 1 ||
+ landlocked_atoms[twomol->dihedral_atom4[j][p]-1][rxnID] == 1) {
+ insert_num = num_dihedral[atom->map(update_mega_glove[jj+1][i])];
+ dihedral_type[atom->map(update_mega_glove[jj+1][i])][insert_num] = twomol->dihedral_type[j][p];
+ dihedral_atom1[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->dihedral_atom1[j][p]-1][1][rxnID]][i];
+ dihedral_atom2[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->dihedral_atom2[j][p]-1][1][rxnID]][i];
+ dihedral_atom3[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->dihedral_atom3[j][p]-1][1][rxnID]][i];
+ dihedral_atom4[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->dihedral_atom4[j][p]-1][1][rxnID]][i];
+ num_dihedral[atom->map(update_mega_glove[jj+1][i])]++;
+ delta_dihed++;
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+
+ // finally IMPROPERS!!!! first let's delete all improper info for landlocked atoms
+ if (force->improper && twomol->improperflag) {
+ int *num_improper = atom->num_improper;
+ int **improper_type = atom->improper_type;
+ tagint **improper_atom1 = atom->improper_atom1;
+ tagint **improper_atom2 = atom->improper_atom2;
+ tagint **improper_atom3 = atom->improper_atom3;
+ tagint **improper_atom4 = atom->improper_atom4;
+
+ for (int i = 0; i < update_num_mega; i++) {
+ rxnID = update_mega_glove[0][i];
+ twomol = atom->molecules[reacted_mol[rxnID]];
+ for (int j = 0; j < twomol->natoms; j++) {
+ int jj = equivalences[j][1][rxnID]-1;
+ if (atom->map(update_mega_glove[jj+1][i]) < nlocal && atom->map(update_mega_glove[jj+1][i]) >= 0) {
+ if (landlocked_atoms[j][rxnID] == 1) {
+ delta_imprp -= num_improper[atom->map(update_mega_glove[jj+1][i])];
+ num_improper[atom->map(update_mega_glove[jj+1][i])] = 0;
+ }
+ if (landlocked_atoms[j][rxnID] == 0) {
+ for (int p = num_improper[atom->map(update_mega_glove[jj+1][i])]-1; p > -1; p--) {
+ for (int n = 0; n < twomol->natoms; n++) {
+ int nn = equivalences[n][1][rxnID]-1;
+ if (n!=j && landlocked_atoms[n][rxnID] == 1 &&
+ (improper_atom1[atom->map(update_mega_glove[jj+1][i])][p] == update_mega_glove[nn+1][i] ||
+ improper_atom2[atom->map(update_mega_glove[jj+1][i])][p] == update_mega_glove[nn+1][i] ||
+ improper_atom3[atom->map(update_mega_glove[jj+1][i])][p] == update_mega_glove[nn+1][i] ||
+ improper_atom4[atom->map(update_mega_glove[jj+1][i])][p] == update_mega_glove[nn+1][i])) {
+ for (int m = p; m < num_improper[atom->map(update_mega_glove[jj+1][i])]-1; m++) {
+ improper_type[atom->map(update_mega_glove[jj+1][i])][m] = improper_type[atom->map(update_mega_glove[jj+1][i])][m+1];
+ improper_atom1[atom->map(update_mega_glove[jj+1][i])][m] = improper_atom1[atom->map(update_mega_glove[jj+1][i])][m+1];
+ improper_atom2[atom->map(update_mega_glove[jj+1][i])][m] = improper_atom2[atom->map(update_mega_glove[jj+1][i])][m+1];
+ improper_atom3[atom->map(update_mega_glove[jj+1][i])][m] = improper_atom3[atom->map(update_mega_glove[jj+1][i])][m+1];
+ improper_atom4[atom->map(update_mega_glove[jj+1][i])][m] = improper_atom4[atom->map(update_mega_glove[jj+1][i])][m+1];
+ }
+ num_improper[atom->map(update_mega_glove[jj+1][i])]--;
+ delta_imprp--;
+ break;
+ }
+ }
+ }
+ }
+ }
+ }
+ // now let's add new improper info
+ for (int j = 0; j < twomol->natoms; j++) {
+ int jj = equivalences[j][1][rxnID]-1;
+ if (atom->map(update_mega_glove[jj+1][i]) < nlocal && atom->map(update_mega_glove[jj+1][i]) >= 0) {
+ if (landlocked_atoms[j][rxnID] == 1) {
+ num_improper[atom->map(update_mega_glove[jj+1][i])] = twomol->num_improper[j];
+ delta_imprp += twomol->num_improper[j];
+ for (int p = 0; p < twomol->num_improper[j]; p++) {
+ improper_type[atom->map(update_mega_glove[jj+1][i])][p] = twomol->improper_type[j][p];
+ improper_atom1[atom->map(update_mega_glove[jj+1][i])][p] = update_mega_glove[equivalences[twomol->improper_atom1[j][p]-1][1][rxnID]][i];
+ improper_atom2[atom->map(update_mega_glove[jj+1][i])][p] = update_mega_glove[equivalences[twomol->improper_atom2[j][p]-1][1][rxnID]][i];
+ improper_atom3[atom->map(update_mega_glove[jj+1][i])][p] = update_mega_glove[equivalences[twomol->improper_atom3[j][p]-1][1][rxnID]][i];
+ improper_atom4[atom->map(update_mega_glove[jj+1][i])][p] = update_mega_glove[equivalences[twomol->improper_atom4[j][p]-1][1][rxnID]][i];
+ }
+ }
+ if (landlocked_atoms[j][rxnID] == 0) {
+ for (int p = 0; p < twomol->num_improper[j]; p++) {
+ if (landlocked_atoms[twomol->improper_atom1[j][p]-1][rxnID] == 1 ||
+ landlocked_atoms[twomol->improper_atom2[j][p]-1][rxnID] == 1 ||
+ landlocked_atoms[twomol->improper_atom3[j][p]-1][rxnID] == 1 ||
+ landlocked_atoms[twomol->improper_atom4[j][p]-1][rxnID] == 1) {
+ insert_num = num_improper[atom->map(update_mega_glove[jj+1][i])];
+ improper_type[atom->map(update_mega_glove[jj+1][i])][insert_num] = twomol->improper_type[j][p];
+ improper_atom1[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->improper_atom1[j][p]-1][1][rxnID]][i];
+ improper_atom2[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->improper_atom2[j][p]-1][1][rxnID]][i];
+ improper_atom3[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->improper_atom3[j][p]-1][1][rxnID]][i];
+ improper_atom4[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->improper_atom4[j][p]-1][1][rxnID]][i];
+ num_improper[atom->map(update_mega_glove[jj+1][i])]++;
+ delta_imprp++;
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+
+ }
+
+ memory->destroy(update_mega_glove);
+
+ // something to think about: this could done much more concisely if
+ // all atom-level info (bond,angles, etc...) were kinda inherited from a common data struct --JG
+
+ int Tdelta_bonds;
+ MPI_Allreduce(&delta_bonds,&Tdelta_bonds,1,MPI_INT,MPI_SUM,world);
+ atom->nbonds += Tdelta_bonds;
+
+ int Tdelta_angle;
+ MPI_Allreduce(&delta_angle,&Tdelta_angle,1,MPI_INT,MPI_SUM,world);
+ atom->nangles += Tdelta_angle;
+
+ int Tdelta_dihed;
+ MPI_Allreduce(&delta_dihed,&Tdelta_dihed,1,MPI_INT,MPI_SUM,world);
+ atom->ndihedrals += Tdelta_dihed;
+
+ int Tdelta_imprp;
+ MPI_Allreduce(&delta_imprp,&Tdelta_imprp,1,MPI_INT,MPI_SUM,world);
+ atom->nimpropers += Tdelta_imprp;
+}
+
+/* ----------------------------------------------------------------------
+read superimpose file
+------------------------------------------------------------------------- */
+
+void FixBondReact::read(int myrxn)
+{
+ char line[MAXLINE],keyword[MAXLINE];
+ char *eof,*ptr;
+
+ // skip 1st line of file
+ eof = fgets(line,MAXLINE,fp);
+ if (eof == NULL) error->one(FLERR,"Unexpected end of superimpose file");
+
+ // read header lines
+ // skip blank lines or lines that start with "#"
+ // stop when read an unrecognized line
+
+ while (1) {
+
+ readline(line);
+
+ // trim anything from '#' onward
+ // if line is blank, continue
+
+ if ((ptr = strchr(line,'#'))) *ptr = '\0';
+ if (strspn(line," \t\n\r") == strlen(line)) continue;
+
+ if (strstr(line,"edgeIDs")) sscanf(line,"%d",&nedge);
+ else if (strstr(line,"equivalences")) sscanf(line,"%d",&nequivalent);
+ else break;
+ }
+
+ //count = NULL;
+
+ // grab keyword and skip next line
+
+ parse_keyword(0,line,keyword);
+ readline(line);
+
+ // loop over sections of superimpose file
+
+ int equivflag = 0, edgeflag = 0, bondflag = 0;
+ while (strlen(keyword)) {
+ if (strcmp(keyword,"BondingIDs") == 0) {
+ bondflag = 1;
+ readline(line);
+ sscanf(line,"%d",&ibonding[myrxn]);
+ readline(line);
+ sscanf(line,"%d",&jbonding[myrxn]);
+ } else if (strcmp(keyword,"EdgeIDs") == 0) {
+ edgeflag = 1;
+ for (int i = 0; i < onemol->natoms; i++) edge[i][myrxn] = 0;
+ EdgeIDs(line, myrxn);
+ } else if (strcmp(keyword,"Equivalences") == 0) {
+ equivflag = 1;
+ Equivalences(line, myrxn);
+ } else error->one(FLERR,"Unknown section in superimpose file");
+
+ parse_keyword(1,line,keyword);
+
+ }
+
+ // error check
+ if (bondflag == 0 || equivflag == 0 || edgeflag == 0)
+ error->all(FLERR,"Superimpose file missing BondingIDs, EdgeIDs, or Equivalences section\n");
+}
+
+void FixBondReact::EdgeIDs(char *line, int myrxn)
+{
+ // puts a 1 at edge(edgeID)
+
+ int tmp;
+ for (int i = 0; i < nedge; i++) {
+ readline(line);
+ sscanf(line,"%d",&tmp);
+ edge[tmp-1][myrxn] = 1;
+ }
+}
+
+void FixBondReact::Equivalences(char *line, int myrxn)
+{
+ int tmp1;
+ int tmp2;
+ for (int i = 0; i < nequivalent; i++) {
+ readline(line);
+ sscanf(line,"%d %d",&tmp1,&tmp2);
+ //equivalences is-> clmn 1: post-reacted, clmn 2: pre-reacted
+ equivalences[tmp2-1][0][myrxn] = tmp2;
+ equivalences[tmp2-1][1][myrxn] = tmp1;
+ //reverse_equiv is-> clmn 1: pre-reacted, clmn 2: post-reacted
+ reverse_equiv[tmp1-1][0][myrxn] = tmp1;
+ reverse_equiv[tmp1-1][1][myrxn] = tmp2;
+ }
+}
+
+void FixBondReact::open(char *file)
+{
+ fp = fopen(file,"r");
+ if (fp == NULL) {
+ char str[128];
+ sprintf(str,"Cannot open superimpose file %s",file);
+ error->one(FLERR,str);
+ }
+}
+
+void FixBondReact::readline(char *line)
+{
+ int n;
+ if (me == 0) {
+ if (fgets(line,MAXLINE,fp) == NULL) n = 0;
+ else n = strlen(line) + 1;
+ }
+ MPI_Bcast(&n,1,MPI_INT,0,world);
+ if (n == 0) error->all(FLERR,"Unexpected end of superimpose file");
+ MPI_Bcast(line,n,MPI_CHAR,0,world);
+}
+
+void FixBondReact::parse_keyword(int flag, char *line, char *keyword)
+{
+ if (flag) {
+
+ // read upto non-blank line plus 1 following line
+ // eof is set to 1 if any read hits end-of-file
+
+ int eof = 0;
+ if (me == 0) {
+ if (fgets(line,MAXLINE,fp) == NULL) eof = 1;
+ while (eof == 0 && strspn(line," \t\n\r") == strlen(line)) {
+ if (fgets(line,MAXLINE,fp) == NULL) eof = 1;
+ }
+ if (fgets(keyword,MAXLINE,fp) == NULL) eof = 1;
+ }
+
+ // if eof, set keyword empty and return
+
+ MPI_Bcast(&eof,1,MPI_INT,0,world);
+ if (eof) {
+ keyword[0] = '\0';
+ return;
+ }
+
+ // bcast keyword line to all procs
+
+ int n;
+ if (me == 0) n = strlen(line) + 1;
+ MPI_Bcast(&n,1,MPI_INT,0,world);
+ MPI_Bcast(line,n,MPI_CHAR,0,world);
+ }
+
+ // copy non-whitespace portion of line into keyword
+
+ int start = strspn(line," \t\n\r");
+ int stop = strlen(line) - 1;
+ while (line[stop] == ' ' || line[stop] == '\t'
+ || line[stop] == '\n' || line[stop] == '\r') stop--;
+ line[stop+1] = '\0';
+ strcpy(keyword,&line[start]);
+}
+
+
+void FixBondReact::skip_lines(int n, char *line)
+{
+ for (int i = 0; i < n; i++) readline(line);
+}
+
+int FixBondReact::parse(char *line, char **words, int max)
+{
+ char *ptr;
+
+ int nwords = 0;
+ words[nwords++] = strtok(line," \t\n\r\f");
+
+ while ((ptr = strtok(NULL," \t\n\r\f"))) {
+ if (nwords < max) words[nwords] = ptr;
+ nwords++;
+ }
+
+ return nwords;
+}
+
+/* ---------------------------------------------------------------------- */
+
+double FixBondReact::compute_vector(int n)
+{
+ // now we print just the totals for each reaction instance
+ return (double) reaction_count_total[n];
+
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixBondReact::post_integrate_respa(int ilevel, int iloop)
+{
+ if (ilevel == nlevels_respa-1) post_integrate();
+}
+
+/* ---------------------------------------------------------------------- */
+
+int FixBondReact::pack_forward_comm(int n, int *list, double *buf,
+ int pbc_flag, int *pbc)
+{
+ int i,j,k,m,ns;
+
+ m = 0;
+
+ if (commflag == 1) {
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ printf("hello you shouldn't be here\n");
+ //buf[m++] = ubuf(bondcount[j]).d;
+ }
+ return m;
+ }
+
+ if (commflag == 2) {
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = ubuf(partner[j]).d;
+ buf[m++] = probability[j];
+ }
+ return m;
+ }
+
+ int **nspecial = atom->nspecial;
+ tagint **special = atom->special;
+
+ m = 0;
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = ubuf(finalpartner[j]).d;
+ ns = nspecial[j][0];
+ buf[m++] = ubuf(ns).d;
+ for (k = 0; k < ns; k++)
+ buf[m++] = ubuf(special[j][k]).d;
+ }
+ return m;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixBondReact::unpack_forward_comm(int n, int first, double *buf)
+{
+ int i,j,m,ns,last;
+
+ m = 0;
+ last = first + n;
+
+ if (commflag == 1) {
+ for (i = first; i < last; i++)
+ printf("hello you shouldn't be here\n");
+ // bondcount[i] = (int) ubuf(buf[m++]).i;
+
+ } else if (commflag == 2) {
+ for (i = first; i < last; i++) {
+ partner[i] = (tagint) ubuf(buf[m++]).i;
+ probability[i] = buf[m++];
+ }
+
+ } else {
+ int **nspecial = atom->nspecial;
+ tagint **special = atom->special;
+
+ m = 0;
+ last = first + n;
+ for (i = first; i < last; i++) {
+ finalpartner[i] = (tagint) ubuf(buf[m++]).i;
+ ns = (int) ubuf(buf[m++]).i;
+ nspecial[i][0] = ns;
+ for (j = 0; j < ns; j++)
+ special[i][j] = (tagint) ubuf(buf[m++]).i;
+ }
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+int FixBondReact::pack_reverse_comm(int n, int first, double *buf)
+{
+ int i,m,last;
+
+ m = 0;
+ last = first + n;
+
+ for (i = first; i < last; i++) {
+ buf[m++] = ubuf(partner[i]).d;
+ if (closeneigh[rxnID] < 0)
+ buf[m++] = distsq[i][1];
+ else
+ buf[m++] = distsq[i][0];
+ }
+ return m;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixBondReact::unpack_reverse_comm(int n, int *list, double *buf)
+{
+ int i,j,m;
+
+ m = 0;
+
+ if (commflag != 1) {
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ if (closeneigh[rxnID] < 0)
+ if (buf[m+1] < distsq[j][1]) {
+ partner[j] = (tagint) ubuf(buf[m++]).i;
+ distsq[j][1] = buf[m++];
+ } else m += 2;
+ else
+ if (buf[m+1] > distsq[j][0]) {
+ partner[j] = (tagint) ubuf(buf[m++]).i;
+ distsq[j][0] = buf[m++];
+ } else m += 2;
+ }
+ }
+}
+
+/* ----------------------------------------------------------------------
+memory usage of local atom-based arrays
+------------------------------------------------------------------------- */
+
+double FixBondReact::memory_usage()
+{
+ int nmax = atom->nmax;
+ double bytes = nmax * sizeof(int);
+ bytes = 2*nmax * sizeof(tagint);
+ bytes += nmax * sizeof(double);
+ return bytes;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixBondReact::print_bb()
+{
+
+ //fix bond/create cargo code. eg nbonds needs to be added
+ /*
+for (int i = 0; i < atom->nlocal; i++) {
+ // printf("TAG " TAGINT_FORMAT ": %d nbonds: ",atom->tag[i],atom->num_bond[i]);
+ for (int j = 0; j < atom->num_bond[i]; j++) {
+ // printf(" " TAGINT_FORMAT,atom->bond_atom[i][j]);
+ }
+ // printf("\n");
+ // printf("TAG " TAGINT_FORMAT ": %d nangles: ",atom->tag[i],atom->num_angle[i]);
+ for (int j = 0; j < atom->num_angle[i]; j++) {
+ // printf(" " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT ",",
+ atom->angle_atom1[i][j], atom->angle_atom2[i][j],
+ atom->angle_atom3[i][j]);
+ }
+ // printf("\n");
+ // printf("TAG " TAGINT_FORMAT ": %d ndihedrals: ",atom->tag[i],atom->num_dihedral[i]);
+ for (int j = 0; j < atom->num_dihedral[i]; j++) {
+ // printf(" " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT " "
+ TAGINT_FORMAT ",", atom->dihedral_atom1[i][j],
+ atom->dihedral_atom2[i][j],atom->dihedral_atom3[i][j],
+ atom->dihedral_atom4[i][j]);
+ }
+ // printf("\n");
+ // printf("TAG " TAGINT_FORMAT ": %d nimpropers: ",atom->tag[i],atom->num_improper[i]);
+ for (int j = 0; j < atom->num_improper[i]; j++) {
+ // printf(" " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT " "
+ TAGINT_FORMAT ",",atom->improper_atom1[i][j],
+ atom->improper_atom2[i][j],atom->improper_atom3[i][j],
+ atom->improper_atom4[i][j]);
+ }
+ // printf("\n");
+ // printf("TAG " TAGINT_FORMAT ": %d %d %d nspecial: ",atom->tag[i],
+ atom->nspecial[i][0],atom->nspecial[i][1],atom->nspecial[i][2]);
+ for (int j = 0; j < atom->nspecial[i][2]; j++) {
+ // printf(" " TAGINT_FORMAT,atom->special[i][j]);
+ }
+ // printf("\n");
+}
+*/
+}
diff --git a/src/USER-MISC/fix_bond_react.h b/src/USER-MISC/fix_bond_react.h
new file mode 100644
index 0000000000000000000000000000000000000000..e60fff37fbaa93f6e4e09136a57282cd883d9fe3
--- /dev/null
+++ b/src/USER-MISC/fix_bond_react.h
@@ -0,0 +1,217 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+ Contributing Author: Jacob Gissinger (jacob.gissinger@colorado.edu)
+------------------------------------------------------------------------- */
+
+#ifdef FIX_CLASS
+
+FixStyle(bond/react,FixBondReact)
+
+#else
+
+#ifndef LMP_FIX_BOND_REACT_H
+#define LMP_FIX_BOND_REACT_H
+
+#include "fix.h"
+
+namespace LAMMPS_NS {
+
+class FixBondReact : public Fix {
+ public:
+ FixBondReact(class LAMMPS *, int, char **);
+ ~FixBondReact();
+ int setmask();
+ void post_constructor();
+ void init();
+ void init_list(int, class NeighList *);
+ void post_integrate();
+ void post_integrate_respa(int, int);
+
+ int pack_forward_comm(int, int *, double *, int, int *);
+ void unpack_forward_comm(int, int, double *);
+ int pack_reverse_comm(int, int, double *);
+ void unpack_reverse_comm(int, int *, double *);
+ double compute_vector(int);
+ double memory_usage();
+
+ private:
+ int me,nprocs;
+ int nreacts;
+ int *nevery;
+ FILE *fp;
+ int *iatomtype,*jatomtype;
+ int *seed;
+ double **cutsq,*fraction;
+ tagint lastcheck;
+ int stabilization_flag;
+ int *stabilize_steps_flag;
+ int status;
+ int *groupbits;
+
+ int rxnID; // integer ID for identifying current bond/react
+ int *reaction_count;
+ int *reaction_count_total;
+ int nmax; // max num local atoms
+ int max_natoms; // max natoms in a molecule template
+ tagint *partner,*finalpartner;
+ double **distsq,*probability;
+ int *ncreate;
+ int maxcreate;
+ int allncreate;
+ tagint ***created;
+ int *local_ncreate;
+
+ class Molecule *onemol; // pre-reacted molecule template
+ class Molecule *twomol; // post-reacted molecule template
+ Fix *fix1; // nve/limit used to relax reaction sites
+ Fix *fix2; // properties/atom used to indicate 1) indicate relaxing atoms
+ // 2) system-wide thermostat
+ // 3) to which 'react' atom belongs
+ class RanMars **random;
+ class NeighList *list;
+
+ int *reacted_mol,*unreacted_mol;
+ int *limit_duration; // indicates how long to relax
+ char *nve_limit_xmax; // indicates max distance allowed to move when relaxing
+ char *id_fix1; // id of internally created fix nve/limit
+ char *id_fix2; // id of internally created fix per-atom properties
+ char *master_group; // group containing relaxing atoms from all fix rxns
+ char *exclude_group; // group for system-wide thermostat
+
+ int countflag,commflag;
+ int nlevels_respa;
+
+ void superimpose_algorithm(); // main function of the superimpose algorithm
+
+ int *ibonding,*jbonding;
+ int *closeneigh; // indicates if bonding atoms of a rxn are 1-2, 1-3, or 1-4 neighbors
+ int nedge,nequivalent; // number of edge, equivalent atoms in mapping file
+ int attempted_rxn; // there was an attempt!
+ int *local_rxn_count;
+ int *ghostly_rxn_count;
+ int avail_guesses; // num of restore points available
+ int *guess_branch; // used when there is more than two choices when guessing
+ int **restore_pt; // contains info about restore points
+ tagint **restore; // contaings info about restore points
+ int *pioneer_count; // counts pioneers
+
+ int **edge; // atoms in molecule templates with incorrect valences
+ int ***equivalences; // relation between pre- and post-reacted templates
+ int ***reverse_equiv; // re-ordered equivalences
+ int **landlocked_atoms; // all atoms at least three bonds away from edge atoms
+
+ int pion,neigh,trace; // important indices for various loops. required for restore points
+ int lcl_inst; // reaction instance
+ tagint **glove; // 1st colmn: pre-reacted template, 2nd colmn: global IDs
+ // for all mega_gloves and global_mega_glove: first row is the ID of bond/react
+ tagint **local_mega_glove; // consolidation local of reaction instances
+ tagint **ghostly_mega_glove; // consolidation nonlocal of reaction instances
+ tagint **global_mega_glove; // consolidation (inter-processor) of gloves containing nonlocal atoms
+ int local_num_mega; // num of local reaction instances
+ int ghostly_num_mega; // num of ghostly reaction instances
+ int global_megasize; // num of reaction instances in global_mega_glove
+ int *pioneers; // during Superimpose Algorithm, atoms which have been assigned, but whose first neighbors haven't
+ int glove_counter; // used to determine when to terminate Superimpose Algorithm
+
+ void read(int);
+ void EdgeIDs(char *,int);
+ void Equivalences(char *,int);
+
+ void make_a_guess ();
+ void neighbor_loop();
+ void check_a_neighbor();
+ void crosscheck_the_neighbor();
+ void inner_crosscheck_loop();
+ void ring_check();
+
+ void open(char *);
+ void readline(char *);
+ void parse_keyword(int, char *, char *);
+ void skip_lines(int, char *);
+ int parse(char *, char **, int);
+
+ void far_partner();
+ void close_partner();
+ void find_landlocked_atoms(int);
+ void glove_ghostcheck();
+ void ghost_glovecast();
+ void update_everything();
+ void unlimit_bond();
+ void limit_bond(int);
+ void dedup_mega_gloves(int); //dedup global mega_glove
+
+ // DEBUG (currently obsolete)
+
+ void print_bb();
+
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+E: Illegal ... command
+
+Self-explanatory. Check the input script syntax and compare to the
+documentation for the command. You can use -echo screen as a
+command-line option when running LAMMPS to see the offending line.
+
+E: Invalid exclude group name
+
+Exclude group name should not previously be defined.
+
+E: Cannot use fix bond/react with non-molecular systems
+
+Only systems with bonds that can be changed can be used. Atom_style
+template does not qualify.
+
+E: Fix bond/react cutoff is longer than pairwise cutoff
+
+This is not allowed because bond creation is done using the
+pairwise neighbor list.
+
+E: Molecule template ID for fix bond/react does not exist
+
+A valid molecule template must have been created with the molecule command.
+
+E: Superimpose file errors:
+
+Please ensure superimpose file is properly formatted.
+
+E: Atom affected by reaction too close to template edge
+
+This means an atom which changes type during the reaction is too close
+to an 'edge' atom defined in the superimpose file. This could cause incorrect
+assignment of bonds, angle, etc. Generally, this means you must include
+more atoms in your templates, such that there are at least two atoms
+between each atom involved in the reaction and an edge atom.
+
+E: Fix bond/react needs ghost atoms from farther away
+
+This is because a processor needs to superimpose the entire unreacted
+molecule template onto simulation atoms it can 'see.' The comm_modify cutoff
+command can be used to extend the communication range.
+
+E: Excessive iteration of superimpose algorithm
+
+You may have discovered a bug! But first, please double check that your
+molecule template atom types, bond types, etc. are consistent with your simulation,
+and that all atoms affected by a reaction are sufficently separated from edge atoms.
+If this issue persists, please contact the developer.
+
+*/
diff --git a/src/USER-MISC/fix_filter_corotate.cpp b/src/USER-MISC/fix_filter_corotate.cpp
index 7ada3aeb99e0d582bda2048e4dddb576ba53fc4e..91c70335133e4fdf6a37c0ec212d5d38dc9501fb 100644
--- a/src/USER-MISC/fix_filter_corotate.cpp
+++ b/src/USER-MISC/fix_filter_corotate.cpp
@@ -17,8 +17,8 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <string.h>
-#include <stdlib.h>
+#include <cstring>
+#include <cstdlib>
#include "fix_filter_corotate.h"
#include "atom.h"
#include "atom_vec.h"
@@ -1527,7 +1527,10 @@ void FixFilterCorotate::general_cluster(int index, int index_in_list)
//derivative:
//dn1dx:
- double sum1[3][3*N];
+
+ double **sum1;
+ memory->create(sum1,3,3*N,"filter_corotate:sum1");
+
for (int i=0; i<3; i++)
for (int j=0; j<3*N; j++)
sum1[i][j] = 0;
@@ -1564,10 +1567,12 @@ void FixFilterCorotate::general_cluster(int index, int index_in_list)
dn1dx[i][j] = norm1*sum;
}
}
+ memory->destroy(sum1);
//dn2dx: norm2 * I3mn2n2T * (I3mn1n1T*sum2 - rkn1pn1rk*dn1dx)
- double sum2[3][3*N];
+ double **sum2;
+ memory->create(sum2,3,3*N,"filter_corotate:sum2");
for (int i=0; i<3; i++)
for (int j=0; j<3*N; j++)
sum2[i][j] = 0;
@@ -1618,7 +1623,8 @@ void FixFilterCorotate::general_cluster(int index, int index_in_list)
//dn2dx: norm2 * I3mn2n2T * (I3mn1n1T*sum2 - rkn1pn1rk*dn1dx)
//sum3 = (I3mn1n1T*sum2 - rkn1pn1rk*dn1dx)
- double sum3[3][3*N];
+ double **sum3;
+ memory->create(sum3,3,3*N,"filter_corotate:sum3");
for (int i=0; i<3; i++)
for (int j=0; j<3*N; j++) {
double sum = 0;
@@ -1627,6 +1633,7 @@ void FixFilterCorotate::general_cluster(int index, int index_in_list)
sum3[i][j] = sum;
}
+ memory->destroy(sum2);
//dn2dx = norm2 * I3mn2n2T * sum3
for (int i=0; i<3; i++)
for (int j=0; j<3*N; j++) {
@@ -1636,6 +1643,7 @@ void FixFilterCorotate::general_cluster(int index, int index_in_list)
dn2dx[i][j] = norm2*sum;
}
+ memory->destroy(sum3);
//dn3dx = norm3 * I3mn3n3T * cross
double I3mn3n3T[3][3]; //(I_3 - n3n3T)
for (int i=0; i<3; i++) {
@@ -1644,7 +1652,8 @@ void FixFilterCorotate::general_cluster(int index, int index_in_list)
I3mn3n3T[i][i] += 1.0;
}
- double cross[3][3*N];
+ double **cross;
+ memory->create(cross,3,3*N,"filter_corotate:cross");
for (int j=0; j<3*N; j++) {
cross[0][j] = dn1dx[1][j]*n2[2] -dn1dx[2][j]*n2[1] +
@@ -1663,6 +1672,7 @@ void FixFilterCorotate::general_cluster(int index, int index_in_list)
dn3dx[i][j] = norm3*sum;
}
+ memory->destroy(cross);
for (int l=0; l<N; l++)
for (int i=0; i<3; i++)
for (int j=0; j<3*N; j++)
diff --git a/src/USER-MISC/fix_flow_gauss.cpp b/src/USER-MISC/fix_flow_gauss.cpp
index 435e3972c8da83e03e3b6e80c989f85a3789b904..6a1e508030c16857aa282e0089c920bfdbbe8796 100644
--- a/src/USER-MISC/fix_flow_gauss.cpp
+++ b/src/USER-MISC/fix_flow_gauss.cpp
@@ -16,8 +16,8 @@
Joel.Eaves@Colorado.edu
------------------------------------------------------------------------- */
-#include <stdlib.h>
-#include <string.h>
+#include <cstdlib>
+#include <cstring>
#include "fix_flow_gauss.h"
#include "atom.h"
#include "force.h"
diff --git a/src/USER-MISC/fix_gle.cpp b/src/USER-MISC/fix_gle.cpp
index ecb3390e5ee6ecce55f64f2d3ee22516ba2a219b..584b33bfe7da1bc93d041ee15388d7e72ebe36d5 100644
--- a/src/USER-MISC/fix_gle.cpp
+++ b/src/USER-MISC/fix_gle.cpp
@@ -17,9 +17,9 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <math.h>
-#include <string.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstring>
+#include <cstdlib>
#include "fix_gle.h"
#include "math_extra.h"
#include "atom.h"
@@ -44,6 +44,7 @@ using namespace FixConst;
enum{NOBIAS,BIAS};
enum{CONSTANT,EQUAL,ATOM};
+
//#define GLE_DEBUG 1
#define MAXLINE 1024
@@ -62,35 +63,37 @@ namespace GLE {
//"stabilized" cholesky decomposition. does a LDL^t decomposition, then sets to zero the negative diagonal elements and gets MM^t
void StabCholesky(int n, const double* MMt, double* M)
{
- double L[n*n], D[n];
-
- int i,j,k;
- for(i=0; i<n; ++i) D[i]=0.;
- for(i=0; i<n*n; ++i) L[i]=0.;
-
- for(i=0; i<n; ++i)
- {
- L[midx(n,i,i)]=1.;
- for (j=0; j<i; j++)
- {
- L[midx(n,i,j)]=MMt[midx(n,i,j)];
- for (k=0; k<j; ++k) L[midx(n,i,j)]-=L[midx(n,i,k)]*L[midx(n,j,k)]*D[k];
- if (D[j]!=0.) L[midx(n,i,j)]/=D[j];
- else L[midx(n,i,j)]=0.0;
- }
- D[i]=MMt[midx(n,i,i)];
- for (k=0; k<i; ++k) D[i]-=L[midx(n,i,k)]*L[midx(n,i,k)]*D[k];
+ double *L = new double[n*n];
+ double *D = new double[n];
+
+ int i,j,k;
+ for (i=0; i<n; ++i) D[i]=0.0;
+ for (i=0; i<n*n; ++i) L[i]=0.0;
+
+ for (i=0; i<n; ++i) {
+ L[midx(n,i,i)]=1.0;
+ for (j=0; j<i; j++) {
+ L[midx(n,i,j)]=MMt[midx(n,i,j)];
+ for (k=0; k<j; ++k) L[midx(n,i,j)]-=L[midx(n,i,k)]*L[midx(n,j,k)]*D[k];
+ if (D[j]!=0.) L[midx(n,i,j)]/=D[j];
+ else L[midx(n,i,j)]=0.0;
}
+ D[i]=MMt[midx(n,i,i)];
+ for (k=0; k<i; ++k) D[i]-=L[midx(n,i,k)]*L[midx(n,i,k)]*D[k];
+ }
- for(i=0; i<n; ++i)
- {
+ for (i=0; i<n; ++i) {
#ifdef GLE_DEBUG
- if (D[i]<0) fprintf(stderr,"GLE Cholesky: Negative diagonal term %le, has been set to zero.\n", D[i]);
+ if (D[i]<0) fprintf(stderr,"GLE Cholesky: Negative diagonal term %le, has been set to zero.\n", D[i]);
#endif
- D[i]=(D[i]>0.?sqrt(D[i]):0.);
- }
+ D[i]=(D[i]>0.0) ? sqrt(D[i]):0.0;
+ }
+
+ for (i=0; i<n; ++i)
+ for (j=0; j<n; j++) M[midx(n,i,j)]=L[midx(n,i,j)]*D[j];
- for(i=0; i<n; ++i) for (j=0; j<n; j++) M[midx(n,i,j)]=L[midx(n,i,j)]*D[j];
+ delete[] D;
+ delete[] L;
}
void MyMult(int n, int m, int r, const double* A, const double* B, double* C, double cf=0.0)
@@ -162,26 +165,32 @@ void MyPrint(int n, const double* A)
//matrix exponential by scaling and squaring.
void MatrixExp(int n, const double* M, double* EM, int j=8, int k=8)
{
- double tc[j+1], SM[n*n], TMP[n*n];
- double onetotwok=pow(0.5,1.0*k);
+ double *tc = new double[j+1];
+ double *SM = new double[n*n];
+ double *TMP = new double[n*n];
+ double onetotwok=pow(0.5,1.0*k);
- tc[0]=1;
- for (int i=0; i<j; ++i) tc[i+1]=tc[i]/(i+1.0);
+ tc[0]=1;
+ for (int i=0; i<j; ++i) tc[i+1]=tc[i]/(i+1.0);
- for (int i=0; i<n*n; ++i) { SM[i]=M[i]*onetotwok; EM[i]=0.0; TMP[i]=0.0; }
+ for (int i=0; i<n*n; ++i) { SM[i]=M[i]*onetotwok; EM[i]=0.0; TMP[i]=0.0; }
- for (int i=0; i<n; ++i) EM[midx(n,i,i)]=tc[j];
+ for (int i=0; i<n; ++i) EM[midx(n,i,i)]=tc[j];
- //taylor exp of scaled matrix
- for (int p=j-1; p>=0; p--)
- {
- MyMult(n, n, n, SM, EM, TMP); for (int i=0; i<n*n; ++i) EM[i]=TMP[i];
- for (int i=0; i<n; ++i) EM[midx(n,i,i)]+=tc[p];
- }
+ //taylor exp of scaled matrix
+ for (int p=j-1; p>=0; p--) {
+ MyMult(n, n, n, SM, EM, TMP); for (int i=0; i<n*n; ++i) EM[i]=TMP[i];
+ for (int i=0; i<n; ++i) EM[midx(n,i,i)]+=tc[p];
+ }
- for (int p=0; p<k; p++)
- { MyMult(n, n, n, EM, EM, TMP); for (int i=0; i<n*n; ++i) EM[i]=TMP[i]; }
+ for (int p=0; p<k; p++) {
+ MyMult(n, n, n, EM, EM, TMP);
+ for (int i=0; i<n*n; ++i) EM[i]=TMP[i];
+ }
+ delete[] tc;
+ delete[] SM;
+ delete[] TMP;
}
}
diff --git a/src/USER-MISC/fix_grem.cpp b/src/USER-MISC/fix_grem.cpp
index 5a4e149316e38b16186ed5bd7f8cd06c94c20aa1..a5f8c344488864f80eb160d44c26c21b9ae7890a 100644
--- a/src/USER-MISC/fix_grem.cpp
+++ b/src/USER-MISC/fix_grem.cpp
@@ -22,9 +22,9 @@
Tom Keyes (Boston University)
------------------------------------------------------------------------- */
-#include <string.h>
-#include <stdlib.h>
-#include <math.h>
+#include <cstring>
+#include <cstdlib>
+#include <cmath>
#include "comm.h"
#include "fix_grem.h"
#include "atom.h"
diff --git a/src/USER-MISC/fix_imd.cpp b/src/USER-MISC/fix_imd.cpp
index b5bd8caf0b2bc5b2668c8f2590fbcd48891922cc..abf9e7cb0ba59629d5d1f65524dbea82b2f0db74 100644
--- a/src/USER-MISC/fix_imd.cpp
+++ b/src/USER-MISC/fix_imd.cpp
@@ -58,10 +58,10 @@ negotiate an appropriate license for such distribution."
#include "group.h"
#include "memory.h"
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#if defined(_MSC_VER) || defined(__MINGW32__)
#include <winsock2.h>
@@ -350,7 +350,7 @@ static void id_sort(tagint *idmap, tagint left, tagint right)
/* part 1: Interactive MD (IMD) API */
-#include <limits.h>
+#include <climits>
#if ( INT_MAX == 2147483647 )
typedef int int32;
diff --git a/src/USER-MISC/fix_ipi.cpp b/src/USER-MISC/fix_ipi.cpp
index bacce679019beca073158a3f6a215134b2d0dfaa..c4750ce49e211b22c6f3b1ddc8e8d812f1843402 100644
--- a/src/USER-MISC/fix_ipi.cpp
+++ b/src/USER-MISC/fix_ipi.cpp
@@ -16,9 +16,9 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <stdio.h>
-#include <string.h>
-#include <stdlib.h>
+#include <cstdio>
+#include <cstring>
+#include <cstdlib>
#include "fix_ipi.h"
#include "atom.h"
#include "force.h"
@@ -50,7 +50,7 @@ using namespace FixConst;
// socket interface
#ifndef _WIN32
-#include <stdlib.h>
+#include <cstdlib>
#include <unistd.h>
#include <sys/types.h>
#include <sys/socket.h>
@@ -428,7 +428,7 @@ void FixIPI::final_integrate()
int nat=bsize/3;
double **f= atom->f;
- double lbuf[bsize];
+ double *lbuf = new double[bsize];
// reassembles the force vector from the local arrays
int nlocal = atom->nlocal;
@@ -440,6 +440,7 @@ void FixIPI::final_integrate()
lbuf[3*(atom->tag[i]-1)+2]=f[i][2]*forceconv;
}
MPI_Allreduce(lbuf,buffer,bsize,MPI_DOUBLE,MPI_SUM,world);
+ delete[] lbuf;
for (int i = 0; i < 9; ++i) vir[i]=0.0;
diff --git a/src/USER-MISC/fix_nvk.cpp b/src/USER-MISC/fix_nvk.cpp
index 5dcfe53e788c5f23539cd7f4fbfb764933112e2a..dbf7b56fe22048745d10b71dad15e8def74fa30e 100644
--- a/src/USER-MISC/fix_nvk.cpp
+++ b/src/USER-MISC/fix_nvk.cpp
@@ -15,9 +15,9 @@
Contributing author: Efrem Braun (UC Berkeley)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstring>
#include "fix_nvk.h"
#include "atom.h"
#include "force.h"
diff --git a/src/USER-MISC/fix_pimd.cpp b/src/USER-MISC/fix_pimd.cpp
index 2c89ddda57e9a0a5d9a0f77e05e53f6f09f5049b..e65ae6ae28168acf3a766798f4028f5c7fca700a 100644
--- a/src/USER-MISC/fix_pimd.cpp
+++ b/src/USER-MISC/fix_pimd.cpp
@@ -21,9 +21,9 @@
Version 1.0
------------------------------------------------------------------------- */
-#include <math.h>
-#include <string.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstring>
+#include <cstdlib>
#include "fix_pimd.h"
#include "universe.h"
#include "comm.h"
diff --git a/src/USER-MISC/fix_rhok.cpp b/src/USER-MISC/fix_rhok.cpp
index 58b0e95a97e0abe10ac7d48e1e93807a0c5a16ab..bbc4ce417a460d194bf3014b61cadc802c763a8d 100644
--- a/src/USER-MISC/fix_rhok.cpp
+++ b/src/USER-MISC/fix_rhok.cpp
@@ -13,10 +13,10 @@
Contributing author: Ulf R. Pedersen, ulf@urp.dk
------------------------------------------------------------------------- */
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-#include <math.h>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
+#include <cmath>
#include "fix_rhok.h"
#include "atom.h"
diff --git a/src/USER-MISC/fix_smd.cpp b/src/USER-MISC/fix_smd.cpp
index b2d3ee0779ded92b42e020d9ba9794b6890981c5..fb22483a073d327e188c62ac9bc782c74000ae26 100644
--- a/src/USER-MISC/fix_smd.cpp
+++ b/src/USER-MISC/fix_smd.cpp
@@ -16,9 +16,9 @@
based on fix spring by: Paul Crozier (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "fix_smd.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-MISC/fix_srp.cpp b/src/USER-MISC/fix_srp.cpp
index 90935e482af3715e585b2e4f1249aea7a0969b43..e4d85e867418b3d3173b1883d79aa567d7129278 100644
--- a/src/USER-MISC/fix_srp.cpp
+++ b/src/USER-MISC/fix_srp.cpp
@@ -15,8 +15,8 @@
Contributing authors: Timothy Sirk (ARL), Pieter in't Veld (BASF)
------------------------------------------------------------------------- */
-#include <string.h>
-#include <stdlib.h>
+#include <cstring>
+#include <cstdlib>
#include "fix_srp.h"
#include "atom.h"
#include "force.h"
diff --git a/src/USER-MISC/fix_srp.h b/src/USER-MISC/fix_srp.h
index aaeea2f03a1ff9c7b1bc5ba10b5a6090a28b2c5b..7dbf044bdadcd14562d99ecd0b56d1f046cc9aed 100644
--- a/src/USER-MISC/fix_srp.h
+++ b/src/USER-MISC/fix_srp.h
@@ -20,7 +20,7 @@ FixStyle(SRP,FixSRP)
#ifndef LMP_FIX_SRP_H
#define LMP_FIX_SRP_H
-#include <stdio.h>
+#include <cstdio>
#include "fix.h"
namespace LAMMPS_NS {
diff --git a/src/USER-MISC/fix_ti_spring.cpp b/src/USER-MISC/fix_ti_spring.cpp
index fbbc747c38c91a88efaa148b5e723707a5a6a994..5812142763f82c44e9b9cab16595d579e5483701 100644
--- a/src/USER-MISC/fix_ti_spring.cpp
+++ b/src/USER-MISC/fix_ti_spring.cpp
@@ -18,8 +18,8 @@
Maurice de Koning (Unicamp/Brazil) - dekoning@ifi.unicamp.br
------------------------------------------------------------------------- */
-#include <stdlib.h>
-#include <string.h>
+#include <cstdlib>
+#include <cstring>
#include "fix_ti_spring.h"
#include "atom.h"
#include "update.h"
diff --git a/src/USER-MISC/fix_ttm_mod.cpp b/src/USER-MISC/fix_ttm_mod.cpp
index b7261b85d4103a63cbdf186f7d1d16d32b59c4ed..1e1e62b638595c9e2aabcb3e690c2d64517dab80 100644
--- a/src/USER-MISC/fix_ttm_mod.cpp
+++ b/src/USER-MISC/fix_ttm_mod.cpp
@@ -19,9 +19,9 @@
#include "lmptype.h"
#include <mpi.h>
-#include <math.h>
-#include <string.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstring>
+#include <cstdlib>
#include "fix_ttm_mod.h"
#include "atom.h"
#include "force.h"
diff --git a/src/USER-MISC/fix_wall_ees.cpp b/src/USER-MISC/fix_wall_ees.cpp
index 9b65d1e30f37b74dd226d19956ee1d7e57864a0d..5ca16ebdadd26706a3cdbcdb26d6ed3f4def9b0f 100644
--- a/src/USER-MISC/fix_wall_ees.cpp
+++ b/src/USER-MISC/fix_wall_ees.cpp
@@ -15,7 +15,7 @@
Contributing author: Abdoreza Ershadinia, a.ershadinia at gmail.com
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "math_extra.h"
#include "fix_wall_ees.h"
#include "atom.h"
diff --git a/src/USER-MISC/fix_wall_region_ees.cpp b/src/USER-MISC/fix_wall_region_ees.cpp
index e070e2a2216e81c63e897fc99bafc771ecadf1fb..82a78d3e73bc2d757ca2399c6a3ebc8726ad99af 100644
--- a/src/USER-MISC/fix_wall_region_ees.cpp
+++ b/src/USER-MISC/fix_wall_region_ees.cpp
@@ -15,9 +15,9 @@
Contributing author: Abdoreza Ershadinia, a.ershadinia at gmail.com
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "fix_wall_region_ees.h"
#include "atom.h"
#include "atom_vec.h"
diff --git a/src/USER-MISC/improper_cossq.cpp b/src/USER-MISC/improper_cossq.cpp
index 223df4a76d064abcfead348518d17f1034bbd1a9..2483840e4234f37c14636937e4d1efe4d0498ced 100644
--- a/src/USER-MISC/improper_cossq.cpp
+++ b/src/USER-MISC/improper_cossq.cpp
@@ -17,8 +17,8 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <math.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdlib>
#include "improper_cossq.h"
#include "atom.h"
#include "comm.h"
@@ -312,3 +312,13 @@ void ImproperCossq::read_restart(FILE *fp)
for (int i = 1; i <= atom->nimpropertypes; i++) setflag[i] = 1;
}
+
+/* ----------------------------------------------------------------------
+ proc 0 writes to data file
+------------------------------------------------------------------------- */
+
+void ImproperCossq::write_data(FILE *fp)
+{
+ for (int i = 1; i <= atom->nimpropertypes; i++)
+ fprintf(fp,"%d %g %g\n",i,k[i],chi[i]/MY_PI*180.0);
+}
diff --git a/src/USER-MISC/improper_cossq.h b/src/USER-MISC/improper_cossq.h
index 266e31797781ab10cc4cd4ba0f28f3dc7f25fab2..ea880adfaf40845d301893abeb63849fb13a93e6 100644
--- a/src/USER-MISC/improper_cossq.h
+++ b/src/USER-MISC/improper_cossq.h
@@ -20,7 +20,7 @@ ImproperStyle(cossq,ImproperCossq)
#ifndef LMP_IMPROPER_COSSQ_H
#define LMP_IMPROPER_COSSQ_H
-#include <stdio.h>
+#include <cstdio>
#include "improper.h"
namespace LAMMPS_NS {
@@ -33,6 +33,7 @@ class ImproperCossq : public Improper {
void coeff(int, char **);
void write_restart(FILE *);
void read_restart(FILE *);
+ void write_data(FILE *);
protected:
double *k, *chi;
diff --git a/src/USER-MISC/improper_distance.cpp b/src/USER-MISC/improper_distance.cpp
index ce6441d6746e3d4946bb8e21eaff27c39844cbe5..2edf37ec5c7b712c3c46a3da330ed4482edcd91d 100644
--- a/src/USER-MISC/improper_distance.cpp
+++ b/src/USER-MISC/improper_distance.cpp
@@ -16,8 +16,8 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <math.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdlib>
#include "improper_distance.h"
#include "atom.h"
#include "comm.h"
@@ -223,7 +223,6 @@ void ImproperDistance::coeff(int narg, char **arg)
int count = 0;
for (int i = ilo; i <= ihi; i++) {
k[i] = k_one;
- //chi[i] = chi_one/180.0 * PI;
chi[i] = chi_one;
setflag[i] = 1;
count++;
@@ -259,3 +258,13 @@ void ImproperDistance::read_restart(FILE *fp)
for (int i = 1; i <= atom->nimpropertypes; i++) setflag[i] = 1;
}
+
+/* ----------------------------------------------------------------------
+ proc 0 writes to data file
+------------------------------------------------------------------------- */
+
+void ImproperDistance::write_data(FILE *fp)
+{
+ for (int i = 1; i <= atom->nimpropertypes; i++)
+ fprintf(fp,"%d %g %g\n",i,k[i],chi[i]);
+}
diff --git a/src/USER-MISC/improper_distance.h b/src/USER-MISC/improper_distance.h
index cff96c6d9d7b096f3481730d23e354ad31cd6190..57e4d671e94320503bd1497ed18849366cd983b3 100644
--- a/src/USER-MISC/improper_distance.h
+++ b/src/USER-MISC/improper_distance.h
@@ -20,7 +20,7 @@ ImproperStyle(distance,ImproperDistance)
#ifndef LMP_IMPROPER_DISTANCE_H
#define LMP_IMPROPER_DISTANCE_H
-#include <stdio.h>
+#include <cstdio>
#include "improper.h"
namespace LAMMPS_NS {
@@ -33,6 +33,7 @@ class ImproperDistance : public Improper {
void coeff(int, char **);
void write_restart(FILE *);
void read_restart(FILE *);
+ void write_data(FILE *);
private:
double *k,*chi;
diff --git a/src/USER-MISC/improper_fourier.cpp b/src/USER-MISC/improper_fourier.cpp
index b139fdad569dc14d67560301c1550fb867204d16..11478d08eab135f70baa9ab6d69a762b4a302672 100644
--- a/src/USER-MISC/improper_fourier.cpp
+++ b/src/USER-MISC/improper_fourier.cpp
@@ -17,9 +17,9 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "improper_fourier.h"
#include "atom.h"
#include "comm.h"
@@ -343,3 +343,13 @@ void ImproperFourier::read_restart(FILE *fp)
for (int i = 1; i <= atom->nimpropertypes; i++) setflag[i] = 1;
}
+
+/* ----------------------------------------------------------------------
+ proc 0 writes to data file
+------------------------------------------------------------------------- */
+
+void ImproperFourier::write_data(FILE *fp)
+{
+ for (int i = 1; i <= atom->nimpropertypes; i++)
+ fprintf(fp,"%d %g %g %g %g %d\n",i,k[i],C0[i],C1[i],C2[i],all[i]);
+}
diff --git a/src/USER-MISC/improper_fourier.h b/src/USER-MISC/improper_fourier.h
index 903b9a12b652f50d0a3163c02934bb3982ae044e..0525c45494b56741b100d2e545c21364f5e8955a 100644
--- a/src/USER-MISC/improper_fourier.h
+++ b/src/USER-MISC/improper_fourier.h
@@ -20,7 +20,7 @@ ImproperStyle(fourier,ImproperFourier)
#ifndef LMP_IMPROPER_FOURIER_H
#define LMP_IMPROPER_FOURIER_H
-#include <stdio.h>
+#include <cstdio>
#include "improper.h"
namespace LAMMPS_NS {
@@ -33,6 +33,7 @@ class ImproperFourier : public Improper {
void coeff(int, char **);
void write_restart(FILE *);
void read_restart(FILE *);
+ void write_data(FILE *);
protected:
double *k, *C0, *C1, *C2;
diff --git a/src/USER-MISC/improper_ring.cpp b/src/USER-MISC/improper_ring.cpp
index adf17ed1d566e26dcd759914c9f46c8409c91552..70124b2ed1d91de9d900aacdea1c0c828303c7fc 100644
--- a/src/USER-MISC/improper_ring.cpp
+++ b/src/USER-MISC/improper_ring.cpp
@@ -37,8 +37,8 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <math.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdlib>
#include "improper_ring.h"
#include "atom.h"
#include "comm.h"
@@ -337,3 +337,13 @@ void ImproperRing::read_restart(FILE *fp)
for (int i = 1; i <= atom->nimpropertypes; i++) setflag[i] = 1;
}
+
+/* ----------------------------------------------------------------------
+ proc 0 writes to data file
+------------------------------------------------------------------------- */
+
+void ImproperRing::write_data(FILE *fp)
+{
+ for (int i = 1; i <= atom->nimpropertypes; i++)
+ fprintf(fp,"%d %g %g\n",i,k[i],acos(chi[i])/MY_PI*180.0);
+}
diff --git a/src/USER-MISC/improper_ring.h b/src/USER-MISC/improper_ring.h
index cdb2907c6578de27620e41a4d7107c8a709b0fb2..c31329816f806f573a044f77962eeab0c1cd418d 100644
--- a/src/USER-MISC/improper_ring.h
+++ b/src/USER-MISC/improper_ring.h
@@ -20,7 +20,7 @@ ImproperStyle(ring,ImproperRing)
#ifndef LMP_IMPROPER_RING_H
#define LMP_IMPROPER_RING_H
-#include <stdio.h>
+#include <cstdio>
#include "improper.h"
namespace LAMMPS_NS {
@@ -33,6 +33,7 @@ class ImproperRing : public Improper {
void coeff(int, char **);
void write_restart(FILE *);
void read_restart(FILE *);
+ void write_data(FILE *);
protected:
double *k,*chi;
diff --git a/src/USER-MISC/pair_agni.cpp b/src/USER-MISC/pair_agni.cpp
index 9cd2cf57b883175f5f8b50a1439f8fbed7bd9b8e..11bf2ae01ed2790cc65b62afe79c7bb2f392ee44 100644
--- a/src/USER-MISC/pair_agni.cpp
+++ b/src/USER-MISC/pair_agni.cpp
@@ -15,10 +15,10 @@
Contributing authors: Axel Kohlmeyer (Temple U), Venkatesh Botu
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_agni.h"
#include "atom.h"
#include "neighbor.h"
diff --git a/src/USER-MISC/pair_buck_mdf.cpp b/src/USER-MISC/pair_buck_mdf.cpp
index 372fbaf8c0f4d9eebec30238f9052009c6c560ab..457d75bc7712907bd06caab711216947e2bcc270 100644
--- a/src/USER-MISC/pair_buck_mdf.cpp
+++ b/src/USER-MISC/pair_buck_mdf.cpp
@@ -15,10 +15,10 @@
Contributing author: Paolo Raiteri (Curtin University)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_buck_mdf.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-MISC/pair_cdeam.cpp b/src/USER-MISC/pair_cdeam.cpp
index b5607012ce16789056b4afed345ffcfe54d1ca7e..53d9036a61d44da205f921c3272ccf41b9075cde 100644
--- a/src/USER-MISC/pair_cdeam.cpp
+++ b/src/USER-MISC/pair_cdeam.cpp
@@ -17,10 +17,10 @@
Germany Department of Materials Science
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_cdeam.h"
#include "atom.h"
#include "force.h"
diff --git a/src/USER-MISC/pair_coul_diel.cpp b/src/USER-MISC/pair_coul_diel.cpp
index c653e9abb23c6bfbe410d78f1691cf63a173ad7e..3f07df3d9861dbc0cb5af1bf6a3766d5ccebb38d 100644
--- a/src/USER-MISC/pair_coul_diel.cpp
+++ b/src/USER-MISC/pair_coul_diel.cpp
@@ -14,10 +14,10 @@
Contributiong authors: Arben Jusufi, Axel Kohlmeyer (Temple U.)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_coul_diel.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-MISC/pair_coul_shield.cpp b/src/USER-MISC/pair_coul_shield.cpp
index 0f7852163c1cd696867699e4e6bd8fec38133928..deec7da81faaa4a2557f7e40bd21c1389c6aa0e2 100644
--- a/src/USER-MISC/pair_coul_shield.cpp
+++ b/src/USER-MISC/pair_coul_shield.cpp
@@ -18,10 +18,10 @@
[Maaravi et al, J. Phys. Chem. C 121, 22826-22835 (2017)]
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_coul_shield.h"
#include "atom.h"
#include "comm.h"
@@ -231,6 +231,8 @@ void PairCoulShield::init_style()
{
if (!atom->q_flag)
error->all(FLERR,"Pair style coul/shield requires atom attribute q");
+ if (!atom->molecule_flag)
+ error->all(FLERR,"Pair style coul/shield requires atom attribute molecule");
neighbor->request(this,instance_me);
}
diff --git a/src/USER-MISC/pair_edip.cpp b/src/USER-MISC/pair_edip.cpp
index 5f83af7f497809fd18c686dbcd6fc38fde7a098f..f556a099c97370ddd350196a613e31f524d9087f 100644
--- a/src/USER-MISC/pair_edip.cpp
+++ b/src/USER-MISC/pair_edip.cpp
@@ -21,11 +21,11 @@
Phys. Rev. B 58, 2539 (1998)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <float.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cfloat>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_edip.h"
#include "atom.h"
#include "neighbor.h"
diff --git a/src/USER-MISC/pair_edip_multi.cpp b/src/USER-MISC/pair_edip_multi.cpp
index bcef1b013b67aae593ed44e7143c34335b0c2291..7a4193f55cbebb25944b8266a71444d3b265af0c 100644
--- a/src/USER-MISC/pair_edip_multi.cpp
+++ b/src/USER-MISC/pair_edip_multi.cpp
@@ -17,11 +17,11 @@
Contributing author: Chao Jiang
------------------------------------------------------------------------- */
-#include <math.h>
-#include <float.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cfloat>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_edip_multi.h"
#include "atom.h"
#include "neighbor.h"
diff --git a/src/USER-MISC/pair_extep.cpp b/src/USER-MISC/pair_extep.cpp
index cf859a28f8380fbfb65dd2b72092486f7d5941f3..5a8cdf28841cf2f7fa61b4f184867a2f8465ff7f 100644
--- a/src/USER-MISC/pair_extep.cpp
+++ b/src/USER-MISC/pair_extep.cpp
@@ -15,10 +15,10 @@
Contributing author: Jan Los
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_extep.h"
#include "atom.h"
#include "neighbor.h"
diff --git a/src/USER-MISC/pair_gauss_cut.cpp b/src/USER-MISC/pair_gauss_cut.cpp
index c1daf9c923f7b356f7a94ab330f1f353988ff7b1..85f7c02887a1d0c1a9a6841d69df6c17a754b5e6 100644
--- a/src/USER-MISC/pair_gauss_cut.cpp
+++ b/src/USER-MISC/pair_gauss_cut.cpp
@@ -15,10 +15,10 @@
Contributing authors: Arben Jusufi, Axel Kohlmeyer (Temple U.)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_gauss_cut.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-MISC/pair_ilp_graphene_hbn.cpp b/src/USER-MISC/pair_ilp_graphene_hbn.cpp
index 02c33c7e86926d8581a513a267d81bce278475c1..30ee2e7a5ae3c3aa42843f2ba07c1c8f36b7dbb9 100644
--- a/src/USER-MISC/pair_ilp_graphene_hbn.cpp
+++ b/src/USER-MISC/pair_ilp_graphene_hbn.cpp
@@ -21,10 +21,10 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_ilp_graphene_hbn.h"
#include "atom.h"
#include "comm.h"
@@ -636,7 +636,9 @@ void PairILPGrapheneHBN::calc_normal()
void PairILPGrapheneHBN::init_style()
{
if (force->newton_pair == 0)
- error->all(FLERR,"Pair style ILP requires newton pair on");
+ error->all(FLERR,"Pair style ilp/graphene/hbn requires newton pair on");
+ if (!atom->molecule_flag)
+ error->all(FLERR,"Pair style ilp/graphene/hbn requires atom attribute molecule");
// need a full neighbor list, including neighbors of ghosts
diff --git a/src/USER-MISC/pair_ilp_graphene_hbn.h b/src/USER-MISC/pair_ilp_graphene_hbn.h
index 3ced305429ad647387721672010ef7df5b0d356a..07c3b2e97b12c39224656eca4fa69cad6cc9a3dc 100644
--- a/src/USER-MISC/pair_ilp_graphene_hbn.h
+++ b/src/USER-MISC/pair_ilp_graphene_hbn.h
@@ -22,7 +22,7 @@ PairStyle(ilp/graphene/hbn,PairILPGrapheneHBN)
#include "pair.h"
#include "my_page.h"
-#include <math.h>
+#include <cmath>
namespace LAMMPS_NS {
diff --git a/src/USER-MISC/pair_kolmogorov_crespi_full.cpp b/src/USER-MISC/pair_kolmogorov_crespi_full.cpp
index a7eebe0b3f3162a210b63ba4a11a6a9179749d55..be0e81d48d9e986e38247aae32bb60b0ac4fb377 100644
--- a/src/USER-MISC/pair_kolmogorov_crespi_full.cpp
+++ b/src/USER-MISC/pair_kolmogorov_crespi_full.cpp
@@ -20,10 +20,10 @@
[Kolmogorov & Crespi, Phys. Rev. B 71, 235415 (2005)]
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include <mpi.h>
#include "pair_kolmogorov_crespi_full.h"
#include "atom.h"
@@ -640,7 +640,9 @@ void PairKolmogorovCrespiFull::calc_normal()
void PairKolmogorovCrespiFull::init_style()
{
if (force->newton_pair == 0)
- error->all(FLERR,"Pair style KC requires newton pair on");
+ error->all(FLERR,"Pair style kolmolgorov/crespi/full requires newton pair on");
+ if (!atom->molecule_flag)
+ error->all(FLERR,"Pair style kolmolgorov/crespi/full requires atom attribute molecule");
// need a full neighbor list, including neighbors of ghosts
diff --git a/src/USER-MISC/pair_kolmogorov_crespi_full.h b/src/USER-MISC/pair_kolmogorov_crespi_full.h
index 3078a7601a4053f2428c16400dd88701e6589e24..9923b409a7de490ce2717bf80aebfe010d34110d 100644
--- a/src/USER-MISC/pair_kolmogorov_crespi_full.h
+++ b/src/USER-MISC/pair_kolmogorov_crespi_full.h
@@ -22,7 +22,7 @@ PairStyle(kolmogorov/crespi/full,PairKolmogorovCrespiFull)
#include "pair.h"
#include "my_page.h"
-#include <math.h>
+#include <cmath>
namespace LAMMPS_NS {
diff --git a/src/USER-MISC/pair_kolmogorov_crespi_z.cpp b/src/USER-MISC/pair_kolmogorov_crespi_z.cpp
index dc1f56a318602b4792118d16673e2369e97849f0..fb7d5ae40eda1bc857c5c29f6f9955973e358f43 100644
--- a/src/USER-MISC/pair_kolmogorov_crespi_z.cpp
+++ b/src/USER-MISC/pair_kolmogorov_crespi_z.cpp
@@ -21,10 +21,10 @@
The simplification is that all normals are taken along the z-direction
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_kolmogorov_crespi_z.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-MISC/pair_lennard_mdf.cpp b/src/USER-MISC/pair_lennard_mdf.cpp
index b959f513c0cec33e496b4c324eacb85ad50c9501..f6e7f7f56b0084b8fe5115e0424fce3909bde8c4 100644
--- a/src/USER-MISC/pair_lennard_mdf.cpp
+++ b/src/USER-MISC/pair_lennard_mdf.cpp
@@ -16,10 +16,10 @@
Contributing author: Paolo Raiteri (Curtin University)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_lennard_mdf.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-MISC/pair_list.cpp b/src/USER-MISC/pair_list.cpp
index 6bb71d05c8cfb1239ce4e6d4ad66431c887d6e6b..aaeb586c1d544dca1916e9d1d0aceae7581c586c 100644
--- a/src/USER-MISC/pair_list.cpp
+++ b/src/USER-MISC/pair_list.cpp
@@ -24,10 +24,10 @@
#include "error.h"
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-#include <math.h>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
+#include <cmath>
using namespace LAMMPS_NS;
diff --git a/src/USER-MISC/pair_lj_mdf.cpp b/src/USER-MISC/pair_lj_mdf.cpp
index ebec1f80e1f75dd827fc6a9fb2f5cf10238db084..d43a6c30862165ea7cd6d0a801e7e285902feb0c 100644
--- a/src/USER-MISC/pair_lj_mdf.cpp
+++ b/src/USER-MISC/pair_lj_mdf.cpp
@@ -16,10 +16,10 @@
Contributing author: Paolo Raiteri (Curtin University)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_lj_mdf.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-MISC/pair_lj_sf_dipole_sf.cpp b/src/USER-MISC/pair_lj_sf_dipole_sf.cpp
index ab342fd055c5a6f2291d2dad357483a7c0723079..523b2ca71a7b466f35939a67c7b5e9ac77501cac 100644
--- a/src/USER-MISC/pair_lj_sf_dipole_sf.cpp
+++ b/src/USER-MISC/pair_lj_sf_dipole_sf.cpp
@@ -16,8 +16,9 @@
Samuel Genheden (University of Southampton)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "pair_lj_sf_dipole_sf.h"
#include "atom.h"
#include "neighbor.h"
@@ -27,7 +28,6 @@
#include "memory.h"
#include "error.h"
#include "update.h"
-#include <string.h>
using namespace LAMMPS_NS;
@@ -539,7 +539,7 @@ double PairLJSFDipoleSF::single(int i, int j, int itype, int jtype, double rsq,
double &fforce)
{
double r2inv,r6inv;
- double pdotp,pidotr,pjdotr,pre1,delx,dely,delz;
+ double pdotp,pidotr,pjdotr,delx,dely,delz;
double rinv, r3inv,r5inv, rcutlj2inv, rcutcoul2inv,rcutlj6inv;
double qtmp,xtmp,ytmp,ztmp,bfac,pqfac,qpfac, ecoul, evdwl;
diff --git a/src/USER-MISC/pair_meam_spline.cpp b/src/USER-MISC/pair_meam_spline.cpp
index 10659e86547e1de37b9a8eea241c0d546e43ca68..750f6ac5bbaee20ffcdffbaf8dccecf28576701b 100644
--- a/src/USER-MISC/pair_meam_spline.cpp
+++ b/src/USER-MISC/pair_meam_spline.cpp
@@ -31,10 +31,10 @@
conform with pairing, updated to LAMMPS style
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_meam_spline.h"
#include "atom.h"
#include "force.h"
diff --git a/src/USER-MISC/pair_meam_sw_spline.cpp b/src/USER-MISC/pair_meam_sw_spline.cpp
index 3eda3ea45d65dba61a454541f3e41d34e5c30a45..f6b7212f9cfd9ee124eed653d2cf588b77d502a0 100644
--- a/src/USER-MISC/pair_meam_sw_spline.cpp
+++ b/src/USER-MISC/pair_meam_sw_spline.cpp
@@ -23,10 +23,10 @@
* 01-Aug-12 - RER: First code version.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_meam_sw_spline.h"
#include "atom.h"
#include "force.h"
diff --git a/src/USER-MISC/pair_momb.cpp b/src/USER-MISC/pair_momb.cpp
index b69b8b86ccd066359667a8a161319ddd7bcb7919..12a40bb08beb6ce981920f5dbba5dc041564deb8 100644
--- a/src/USER-MISC/pair_momb.cpp
+++ b/src/USER-MISC/pair_momb.cpp
@@ -16,9 +16,9 @@
Ya Zhou (Penn State University)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
#include "pair_momb.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-MISC/pair_morse_smooth_linear.cpp b/src/USER-MISC/pair_morse_smooth_linear.cpp
index 37a880762079eb71885fa4c1286812c923abf997..8a9c89cf6945afbba59a7509d936f0ecf526c4a8 100644
--- a/src/USER-MISC/pair_morse_smooth_linear.cpp
+++ b/src/USER-MISC/pair_morse_smooth_linear.cpp
@@ -11,10 +11,10 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_morse_smooth_linear.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-MISC/pair_srp.cpp b/src/USER-MISC/pair_srp.cpp
index 69c7e6b0be377270492521515561c7985b669541..7297b545f967ca3901d5918327b3d69e3331e942 100644
--- a/src/USER-MISC/pair_srp.cpp
+++ b/src/USER-MISC/pair_srp.cpp
@@ -25,7 +25,8 @@ There is an example script for this package in examples/USER/srp.
Please contact Timothy Sirk for questions (tim.sirk@us.army.mil).
------------------------------------------------------------------------- */
-#include <stdlib.h>
+#include <cstdlib>
+#include <cstring>
#include "pair_srp.h"
#include "atom.h"
#include "comm.h"
@@ -40,7 +41,6 @@ Please contact Timothy Sirk for questions (tim.sirk@us.army.mil).
#include "fix_srp.h"
#include "thermo.h"
#include "output.h"
-#include <string.h>
#include "citeme.h"
using namespace LAMMPS_NS;
diff --git a/src/USER-MISC/pair_tersoff_table.cpp b/src/USER-MISC/pair_tersoff_table.cpp
index 1c96b3d002b2d3b57a84db51612825174a57b8b5..c2362b8de9ce0c186636d91d324f406b5bdadfd4 100644
--- a/src/USER-MISC/pair_tersoff_table.cpp
+++ b/src/USER-MISC/pair_tersoff_table.cpp
@@ -20,10 +20,10 @@
1) Tersoff, Phys. Rev. B 39, 5566 (1988)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_tersoff_table.h"
#include "atom.h"
#include "neighbor.h"
diff --git a/src/USER-MISC/temper_grem.cpp b/src/USER-MISC/temper_grem.cpp
index 9e5a4c5c3b95aed6cec87ea62e88d000874d9cc8..031a449689150ffe24d6413213d2183dd5ac5521 100644
--- a/src/USER-MISC/temper_grem.cpp
+++ b/src/USER-MISC/temper_grem.cpp
@@ -15,9 +15,9 @@
Contributing author: David Stelter (BU)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "temper_grem.h"
#include "fix_grem.h"
#include "universe.h"
diff --git a/src/USER-MISC/temper_npt.cpp b/src/USER-MISC/temper_npt.cpp
index 66ab92a43b6758497883accc4439d1b45d7339d2..7cf8fbab9b76d86e46c54ebfd9c17b77fc873d0e 100644
--- a/src/USER-MISC/temper_npt.cpp
+++ b/src/USER-MISC/temper_npt.cpp
@@ -17,9 +17,9 @@
Contact Email: amulyapervaje@gmail.com
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "temper_npt.h"
#include "universe.h"
#include "domain.h"
diff --git a/src/USER-MOFFF/angle_class2_p6.cpp b/src/USER-MOFFF/angle_class2_p6.cpp
index d173669771f4fbbdadd1b87732ccf2c5acc9cb61..c821c9d883ed611661dffb1ddeefea86c6d0ba77 100644
--- a/src/USER-MOFFF/angle_class2_p6.cpp
+++ b/src/USER-MOFFF/angle_class2_p6.cpp
@@ -16,9 +16,9 @@
and Rochus Schmid (Ruhr-Universitaet Bochum)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <string.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstring>
+#include <cstdlib>
#include "angle_class2_p6.h"
#include "atom.h"
#include "neighbor.h"
diff --git a/src/USER-MOFFF/angle_class2_p6.h b/src/USER-MOFFF/angle_class2_p6.h
index aa0bdea6d6d3f7643690dbfdcffb4966040b1168..b583a45b191d17b79f3f7537967331635c757c09 100644
--- a/src/USER-MOFFF/angle_class2_p6.h
+++ b/src/USER-MOFFF/angle_class2_p6.h
@@ -20,7 +20,7 @@ AngleStyle(class2/p6,AngleClass2P6)
#ifndef LMP_ANGLE_CLASS2_P6_H
#define LMP_ANGLE_CLASS2_P6_H
-#include <stdio.h>
+#include <cstdio>
#include "angle.h"
namespace LAMMPS_NS {
diff --git a/src/USER-MOFFF/angle_cosine_buck6d.cpp b/src/USER-MOFFF/angle_cosine_buck6d.cpp
index 493807dbdca9f34a3eca831403b4e81e2ae5f521..b5800db2beb9a398eaa2fd8d314a8ae5566df1a9 100644
--- a/src/USER-MOFFF/angle_cosine_buck6d.cpp
+++ b/src/USER-MOFFF/angle_cosine_buck6d.cpp
@@ -16,8 +16,8 @@
and Rochus Schmid (Ruhr-Universitaet Bochum)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdlib>
#include "angle_cosine_buck6d.h"
#include "atom.h"
#include "neighbor.h"
diff --git a/src/USER-MOFFF/angle_cosine_buck6d.h b/src/USER-MOFFF/angle_cosine_buck6d.h
index e021992b94565e04e7dda5e0146df006b6677ad5..689b1634e02c935c126380682fcbcbea0f573633 100644
--- a/src/USER-MOFFF/angle_cosine_buck6d.h
+++ b/src/USER-MOFFF/angle_cosine_buck6d.h
@@ -20,7 +20,7 @@ AngleStyle(cosine/buck6d, AngleCosineBuck6d)
#ifndef LMP_ANGLE_COSINE_BUCK6D_H
#define LMP_ANGLE_COSINE_BUCK6D_H
-#include <stdio.h>
+#include <cstdio>
#include "angle.h"
namespace LAMMPS_NS {
diff --git a/src/USER-MOFFF/improper_inversion_harmonic.cpp b/src/USER-MOFFF/improper_inversion_harmonic.cpp
index 3a7c0272aa31f21706f315646f29208ce3f6a148..53a7b4729a990c6adacf7b69c8a57558e586e465 100644
--- a/src/USER-MOFFF/improper_inversion_harmonic.cpp
+++ b/src/USER-MOFFF/improper_inversion_harmonic.cpp
@@ -20,9 +20,9 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <math.h>
-#include <stdlib.h>
-#include "string.h"
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "improper_inversion_harmonic.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-MOFFF/improper_inversion_harmonic.h b/src/USER-MOFFF/improper_inversion_harmonic.h
index 1b46c7489a9dafba9a569ad2bd2c5f3dca86a8a0..201c9e358d3d2d392dd856c9468595d2c9d53090 100644
--- a/src/USER-MOFFF/improper_inversion_harmonic.h
+++ b/src/USER-MOFFF/improper_inversion_harmonic.h
@@ -20,7 +20,7 @@ ImproperStyle(inversion/harmonic,ImproperInversionHarmonic)
#ifndef LMP_IMPROPER_INVERSION_HARMONIC_H
#define LMP_IMPROPER_INVERSION_HARMONIC_H
-#include <stdio.h>
+#include <cstdio>
#include "improper.h"
namespace LAMMPS_NS {
diff --git a/src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.cpp b/src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.cpp
index baa42a4bc0d7abf0b0e4efb85f50cdbc0de0673d..f434d03858b3d370c63e03a2b911e9554d9763e9 100644
--- a/src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.cpp
+++ b/src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.cpp
@@ -18,10 +18,10 @@
Fennell and Gezelter, JCP 124, 234104 (2006)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_buck6d_coul_gauss_dsf.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-MOFFF/pair_buck6d_coul_gauss_long.cpp b/src/USER-MOFFF/pair_buck6d_coul_gauss_long.cpp
index 36018613a2614d753564d403a5fc41ccf5c92493..9902896d18ece26a6e49f461e613182b4440b0b5 100644
--- a/src/USER-MOFFF/pair_buck6d_coul_gauss_long.cpp
+++ b/src/USER-MOFFF/pair_buck6d_coul_gauss_long.cpp
@@ -17,10 +17,10 @@
References: Bureekaew and Schmid, Phys. Status Solidi B 250, 1128 (2013)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_buck6d_coul_gauss_long.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-MOLFILE/Install.sh b/src/USER-MOLFILE/Install.sh
old mode 100644
new mode 100755
diff --git a/src/USER-MOLFILE/dump_molfile.cpp b/src/USER-MOLFILE/dump_molfile.cpp
index 54e86f3bc577fdfcc3c942fb40351b9cc4a685ba..732fea74bde61ae3a3fd4ba5bd6779cbeb1711db 100644
--- a/src/USER-MOLFILE/dump_molfile.cpp
+++ b/src/USER-MOLFILE/dump_molfile.cpp
@@ -15,9 +15,9 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <stdio.h>
-#include <string.h>
-#include <math.h>
+#include <cstdio>
+#include <cstring>
+#include <cmath>
#include "dump_molfile.h"
#include "domain.h"
#include "atom.h"
diff --git a/src/USER-MOLFILE/molfile_interface.cpp b/src/USER-MOLFILE/molfile_interface.cpp
index 9c0c15f1ee3d6524cfe1c01b3aaa3cf155c12c5d..798beaee096a68a0b4200219e81e7373532c3ba0 100644
--- a/src/USER-MOLFILE/molfile_interface.cpp
+++ b/src/USER-MOLFILE/molfile_interface.cpp
@@ -18,11 +18,11 @@
#include "molfile_interface.h"
#include <sys/types.h>
-#include <stdio.h>
+#include <cstdio>
#include <dirent.h>
-#include <string.h>
-#include <stdlib.h>
-#include <ctype.h>
+#include <cstring>
+#include <cstdlib>
+#include <cctype>
#if defined(_WIN32)
#include <windows.h>
diff --git a/src/USER-MOLFILE/reader_molfile.cpp b/src/USER-MOLFILE/reader_molfile.cpp
index 15735ab92a25bc47937a3b1de64089364b525fb0..6348009d8fd9ca866909f0994920a42a1a997258 100644
--- a/src/USER-MOLFILE/reader_molfile.cpp
+++ b/src/USER-MOLFILE/reader_molfile.cpp
@@ -15,9 +15,9 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <string.h>
-#include <stdlib.h>
-#include <math.h>
+#include <cstring>
+#include <cstdlib>
+#include <cmath>
#include "reader_molfile.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-NETCDF/Install.sh b/src/USER-NETCDF/Install.sh
old mode 100644
new mode 100755
diff --git a/src/USER-NETCDF/dump_netcdf.cpp b/src/USER-NETCDF/dump_netcdf.cpp
index 4147b3897d26df8a13086f43197ee8988de01248..c08bc89d04fd86215be6ecce3f6355a504fbad4a 100644
--- a/src/USER-NETCDF/dump_netcdf.cpp
+++ b/src/USER-NETCDF/dump_netcdf.cpp
@@ -18,8 +18,8 @@
#if defined(LMP_HAS_NETCDF)
#include <unistd.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cstdlib>
+#include <cstring>
#include <netcdf.h>
#include "dump_netcdf.h"
#include "atom.h"
diff --git a/src/USER-NETCDF/dump_netcdf_mpiio.cpp b/src/USER-NETCDF/dump_netcdf_mpiio.cpp
index 129f9cccbb9978dc77968b9c673bc4e7b639b6a0..0a292d4721b5e5c909375b3e56b7ac991ee01795 100644
--- a/src/USER-NETCDF/dump_netcdf_mpiio.cpp
+++ b/src/USER-NETCDF/dump_netcdf_mpiio.cpp
@@ -18,8 +18,8 @@
#if defined(LMP_HAS_PNETCDF)
#include <unistd.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cstdlib>
+#include <cstring>
#include <pnetcdf.h>
#include "dump_netcdf_mpiio.h"
#include "atom.h"
diff --git a/src/USER-OMP/Install.sh b/src/USER-OMP/Install.sh
old mode 100644
new mode 100755
diff --git a/src/USER-OMP/angle_charmm_omp.cpp b/src/USER-OMP/angle_charmm_omp.cpp
index 228ca94dee718796389e785f5388acfdb54eae0a..1f24438df3e44fb274f4e458fc4a873c96c5bdd6 100644
--- a/src/USER-OMP/angle_charmm_omp.cpp
+++ b/src/USER-OMP/angle_charmm_omp.cpp
@@ -24,7 +24,7 @@
#include "math_const.h"
-#include <math.h>
+#include <cmath>
#include "suffix.h"
using namespace LAMMPS_NS;
diff --git a/src/USER-OMP/angle_class2_omp.cpp b/src/USER-OMP/angle_class2_omp.cpp
index 8f958b477cb8443a9378b2ebe94668c947cd5c17..bd13e20bcc5827ef547370999b1654de4304942b 100644
--- a/src/USER-OMP/angle_class2_omp.cpp
+++ b/src/USER-OMP/angle_class2_omp.cpp
@@ -24,7 +24,7 @@
#include "math_const.h"
-#include <math.h>
+#include <cmath>
#include "suffix.h"
using namespace LAMMPS_NS;
diff --git a/src/USER-OMP/angle_cosine_delta_omp.cpp b/src/USER-OMP/angle_cosine_delta_omp.cpp
index f9891dbb3d7bbe0721509a67cb7d0b5ef3ffa5a4..b3bb3e1f8a7e0f42c792929f962d8be05fc8ef0d 100644
--- a/src/USER-OMP/angle_cosine_delta_omp.cpp
+++ b/src/USER-OMP/angle_cosine_delta_omp.cpp
@@ -24,7 +24,7 @@
#include "math_const.h"
-#include <math.h>
+#include <cmath>
#include "suffix.h"
using namespace LAMMPS_NS;
diff --git a/src/USER-OMP/angle_cosine_omp.cpp b/src/USER-OMP/angle_cosine_omp.cpp
index 39ae3ce698f9ab14705c775826d59d07cf04b0dd..04b3870bc4e0220f631511a0d48d0e483f9878a9 100644
--- a/src/USER-OMP/angle_cosine_omp.cpp
+++ b/src/USER-OMP/angle_cosine_omp.cpp
@@ -24,7 +24,7 @@
#include "math_const.h"
-#include <math.h>
+#include <cmath>
#include "suffix.h"
using namespace LAMMPS_NS;
diff --git a/src/USER-OMP/angle_cosine_periodic_omp.cpp b/src/USER-OMP/angle_cosine_periodic_omp.cpp
index 3bd4ef1212cc0edbf06ee7528490007ab7cb8033..8060ebec7b0ef1fbad1c3a896009ec8fdd9dc56c 100644
--- a/src/USER-OMP/angle_cosine_periodic_omp.cpp
+++ b/src/USER-OMP/angle_cosine_periodic_omp.cpp
@@ -25,7 +25,7 @@
#include "math_const.h"
#include "math_special.h"
-#include <math.h>
+#include <cmath>
#include "suffix.h"
using namespace LAMMPS_NS;
diff --git a/src/USER-OMP/angle_cosine_shift_exp_omp.cpp b/src/USER-OMP/angle_cosine_shift_exp_omp.cpp
index 3a3c31d62582db4f81b170a858bc3c7bf67f2d22..3e00681ec930aef234a266d803bc3fb22ee95147 100644
--- a/src/USER-OMP/angle_cosine_shift_exp_omp.cpp
+++ b/src/USER-OMP/angle_cosine_shift_exp_omp.cpp
@@ -24,7 +24,7 @@
#include "math_const.h"
-#include <math.h>
+#include <cmath>
#include "suffix.h"
using namespace LAMMPS_NS;
diff --git a/src/USER-OMP/angle_cosine_shift_omp.cpp b/src/USER-OMP/angle_cosine_shift_omp.cpp
index f9f538e55388b03fe4388d3c859cf7cef1a8caf8..0ab3df43594cc5caceeb0b760651bdc2e064f415 100644
--- a/src/USER-OMP/angle_cosine_shift_omp.cpp
+++ b/src/USER-OMP/angle_cosine_shift_omp.cpp
@@ -24,7 +24,7 @@
#include "math_const.h"
-#include <math.h>
+#include <cmath>
#include "suffix.h"
using namespace LAMMPS_NS;
diff --git a/src/USER-OMP/angle_cosine_squared_omp.cpp b/src/USER-OMP/angle_cosine_squared_omp.cpp
index c7d14468f5addd2614b7caf7e39a084987dd0f34..a1b1ffdf1a9ee121f1aa3b0dce09a78bd5ded27c 100644
--- a/src/USER-OMP/angle_cosine_squared_omp.cpp
+++ b/src/USER-OMP/angle_cosine_squared_omp.cpp
@@ -24,7 +24,7 @@
#include "math_const.h"
-#include <math.h>
+#include <cmath>
#include "suffix.h"
using namespace LAMMPS_NS;
diff --git a/src/USER-OMP/angle_dipole_omp.cpp b/src/USER-OMP/angle_dipole_omp.cpp
index ee2af539183d514a7c38b8273e8bf12dbbde64f9..92a5ba092edf1d5ad3c0ce0e19b1ef033a12c246 100644
--- a/src/USER-OMP/angle_dipole_omp.cpp
+++ b/src/USER-OMP/angle_dipole_omp.cpp
@@ -25,7 +25,7 @@
#include "math_const.h"
-#include <math.h>
+#include <cmath>
#include "suffix.h"
using namespace LAMMPS_NS;
diff --git a/src/USER-OMP/angle_fourier_omp.cpp b/src/USER-OMP/angle_fourier_omp.cpp
index 275eab29f1d7778d9c4d3cef6fa9432a57c29b20..dfc713c3728be3795ca98576666c89e69cf0f29d 100644
--- a/src/USER-OMP/angle_fourier_omp.cpp
+++ b/src/USER-OMP/angle_fourier_omp.cpp
@@ -24,7 +24,7 @@
#include "math_const.h"
-#include <math.h>
+#include <cmath>
#include "suffix.h"
using namespace LAMMPS_NS;
diff --git a/src/USER-OMP/angle_fourier_simple_omp.cpp b/src/USER-OMP/angle_fourier_simple_omp.cpp
index 5bdbfce05d38a28d53cad0c8e8eaf0aaf1a35449..dea7a8872340a655c14929543ae39af665197b70 100644
--- a/src/USER-OMP/angle_fourier_simple_omp.cpp
+++ b/src/USER-OMP/angle_fourier_simple_omp.cpp
@@ -24,7 +24,7 @@
#include "math_const.h"
-#include <math.h>
+#include <cmath>
#include "suffix.h"
using namespace LAMMPS_NS;
diff --git a/src/USER-OMP/angle_harmonic_omp.cpp b/src/USER-OMP/angle_harmonic_omp.cpp
index 917bc2d5b0b61412cca6c39c923d841f3aad06e4..0a71e5c9dd2ca645c59bf8166bdd48055350440a 100644
--- a/src/USER-OMP/angle_harmonic_omp.cpp
+++ b/src/USER-OMP/angle_harmonic_omp.cpp
@@ -24,7 +24,7 @@
#include "math_const.h"
-#include <math.h>
+#include <cmath>
#include "suffix.h"
using namespace LAMMPS_NS;
diff --git a/src/USER-OMP/angle_quartic_omp.cpp b/src/USER-OMP/angle_quartic_omp.cpp
index 70383fd50a56cd62b057cf1f1bac8cdf19d7f0fa..97a9b14f1dac16c87ab681fac72fc0c4e8ef1037 100644
--- a/src/USER-OMP/angle_quartic_omp.cpp
+++ b/src/USER-OMP/angle_quartic_omp.cpp
@@ -24,7 +24,7 @@
#include "math_const.h"
-#include <math.h>
+#include <cmath>
#include "suffix.h"
using namespace LAMMPS_NS;
diff --git a/src/USER-OMP/angle_sdk_omp.cpp b/src/USER-OMP/angle_sdk_omp.cpp
index 9b4a967bf32644979d7f9fe5fbb49ffdfab4e635..9383a9af83cda57631cf88fe77434461c5802000 100644
--- a/src/USER-OMP/angle_sdk_omp.cpp
+++ b/src/USER-OMP/angle_sdk_omp.cpp
@@ -23,7 +23,7 @@
#include "force.h"
#include "math_const.h"
-#include <math.h>
+#include <cmath>
#include "lj_sdk_common.h"
diff --git a/src/USER-OMP/angle_table_omp.cpp b/src/USER-OMP/angle_table_omp.cpp
index 465f4370fcce2b40946f3ae8bba77e7b2254c398..c3d2307489087fd412e67c94a238122aeea0194c 100644
--- a/src/USER-OMP/angle_table_omp.cpp
+++ b/src/USER-OMP/angle_table_omp.cpp
@@ -24,7 +24,7 @@
#include "math_const.h"
-#include <math.h>
+#include <cmath>
#include "suffix.h"
using namespace LAMMPS_NS;
diff --git a/src/USER-OMP/bond_class2_omp.cpp b/src/USER-OMP/bond_class2_omp.cpp
index 69decfb32acfd8d60bfc8693363403996fc5db75..1f9bcaa3204b054595664a027ef477c920374adc 100644
--- a/src/USER-OMP/bond_class2_omp.cpp
+++ b/src/USER-OMP/bond_class2_omp.cpp
@@ -22,7 +22,7 @@
#include "neighbor.h"
#include "domain.h"
-#include <math.h>
+#include <cmath>
#include "suffix.h"
using namespace LAMMPS_NS;
diff --git a/src/USER-OMP/bond_fene_expand_omp.cpp b/src/USER-OMP/bond_fene_expand_omp.cpp
index 37cb8b403e479e6b6402d1b869217731b5a666a0..d002d454dd912612cf777f680adede7547d95654 100644
--- a/src/USER-OMP/bond_fene_expand_omp.cpp
+++ b/src/USER-OMP/bond_fene_expand_omp.cpp
@@ -24,7 +24,7 @@
#include "error.h"
#include "update.h"
-#include <math.h>
+#include <cmath>
#include "suffix.h"
using namespace LAMMPS_NS;
diff --git a/src/USER-OMP/bond_fene_omp.cpp b/src/USER-OMP/bond_fene_omp.cpp
index e92dae999c41ac5e90fc30ad89b7b3a168bab4e7..ba958e1d6f3fc52f97bf3ea2adb60fde9b19121b 100644
--- a/src/USER-OMP/bond_fene_omp.cpp
+++ b/src/USER-OMP/bond_fene_omp.cpp
@@ -24,7 +24,7 @@
#include "error.h"
#include "update.h"
-#include <math.h>
+#include <cmath>
#include "suffix.h"
using namespace LAMMPS_NS;
diff --git a/src/USER-OMP/bond_gromos_omp.cpp b/src/USER-OMP/bond_gromos_omp.cpp
index 7904c4683b4c5526a99b2e4fa56049cc43be2dbf..bcfde436d5338e4d7e93fd20e2fc02b167f2989a 100644
--- a/src/USER-OMP/bond_gromos_omp.cpp
+++ b/src/USER-OMP/bond_gromos_omp.cpp
@@ -22,7 +22,7 @@
#include "neighbor.h"
#include "domain.h"
-#include <math.h>
+#include <cmath>
#include "suffix.h"
using namespace LAMMPS_NS;
diff --git a/src/USER-OMP/bond_harmonic_omp.cpp b/src/USER-OMP/bond_harmonic_omp.cpp
index b62fd531939bc572b820e3c668ad69aae9c2286e..46a93cbbdd60f089b2952acab2e395bf7a39c672 100644
--- a/src/USER-OMP/bond_harmonic_omp.cpp
+++ b/src/USER-OMP/bond_harmonic_omp.cpp
@@ -22,7 +22,7 @@
#include "neighbor.h"
#include "domain.h"
-#include <math.h>
+#include <cmath>
#include "suffix.h"
using namespace LAMMPS_NS;
diff --git a/src/USER-OMP/bond_harmonic_shift_cut_omp.cpp b/src/USER-OMP/bond_harmonic_shift_cut_omp.cpp
index db2518e9a9ba23d768f56d6b9cbf89e36c699b9d..5f39bb1b64beeeb977689da7ab31884ae05f7793 100644
--- a/src/USER-OMP/bond_harmonic_shift_cut_omp.cpp
+++ b/src/USER-OMP/bond_harmonic_shift_cut_omp.cpp
@@ -22,7 +22,7 @@
#include "neighbor.h"
#include "domain.h"
-#include <math.h>
+#include <cmath>
#include "suffix.h"
using namespace LAMMPS_NS;
diff --git a/src/USER-OMP/bond_harmonic_shift_omp.cpp b/src/USER-OMP/bond_harmonic_shift_omp.cpp
index 632db873012e45e5f8cd20b0fbbe6ac08fe01f70..8c260bfc9b12558670f1528f482ca8199da3ce7e 100644
--- a/src/USER-OMP/bond_harmonic_shift_omp.cpp
+++ b/src/USER-OMP/bond_harmonic_shift_omp.cpp
@@ -22,7 +22,7 @@
#include "neighbor.h"
#include "domain.h"
-#include <math.h>
+#include <cmath>
#include "suffix.h"
using namespace LAMMPS_NS;
diff --git a/src/USER-OMP/bond_morse_omp.cpp b/src/USER-OMP/bond_morse_omp.cpp
index d03783920b230529a41023ac8079be9050c45487..0c3cded71aa2ec6fab7ea44e8e3c5aa33c92b8d7 100644
--- a/src/USER-OMP/bond_morse_omp.cpp
+++ b/src/USER-OMP/bond_morse_omp.cpp
@@ -22,7 +22,7 @@
#include "neighbor.h"
#include "domain.h"
-#include <math.h>
+#include <cmath>
#include "suffix.h"
using namespace LAMMPS_NS;
diff --git a/src/USER-OMP/bond_nonlinear_omp.cpp b/src/USER-OMP/bond_nonlinear_omp.cpp
index 2bc77de85c0ea9a8062d8224b12c1c9bec55d6d6..cdc70eac8d18947f585902ee74dce696e0c3da57 100644
--- a/src/USER-OMP/bond_nonlinear_omp.cpp
+++ b/src/USER-OMP/bond_nonlinear_omp.cpp
@@ -22,7 +22,7 @@
#include "neighbor.h"
#include "domain.h"
-#include <math.h>
+#include <cmath>
#include "suffix.h"
using namespace LAMMPS_NS;
diff --git a/src/USER-OMP/bond_quartic_omp.cpp b/src/USER-OMP/bond_quartic_omp.cpp
index c0ddfd0b9267d888fd8bd3c4e623cfd80c08d51d..b2b1696bb41853b1205e143effa55972aa5d6328 100644
--- a/src/USER-OMP/bond_quartic_omp.cpp
+++ b/src/USER-OMP/bond_quartic_omp.cpp
@@ -23,7 +23,7 @@
#include "domain.h"
#include "pair.h"
-#include <math.h>
+#include <cmath>
#include "suffix.h"
using namespace LAMMPS_NS;
diff --git a/src/USER-OMP/bond_table_omp.cpp b/src/USER-OMP/bond_table_omp.cpp
index 53226df4f70368842a36310dc161f22b4e3ef4fc..71dc23749655e558a82ce2a0990518ecb994debb 100644
--- a/src/USER-OMP/bond_table_omp.cpp
+++ b/src/USER-OMP/bond_table_omp.cpp
@@ -22,7 +22,7 @@
#include "neighbor.h"
#include "domain.h"
-#include <math.h>
+#include <cmath>
#include "suffix.h"
using namespace LAMMPS_NS;
diff --git a/src/USER-OMP/dihedral_charmm_omp.cpp b/src/USER-OMP/dihedral_charmm_omp.cpp
index 95cab754c3b7465671f1c9e77d71ad6b0d99e2e6..1bed4497740c111386ec027469c04204662528f0 100644
--- a/src/USER-OMP/dihedral_charmm_omp.cpp
+++ b/src/USER-OMP/dihedral_charmm_omp.cpp
@@ -16,7 +16,7 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <math.h>
+#include <cmath>
#include "dihedral_charmm_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/dihedral_class2_omp.cpp b/src/USER-OMP/dihedral_class2_omp.cpp
index edf3e972d296c546bb808a2beb9b93911eae8d14..c7ae1572c766c2aaf0ad2c0ac036628049f9fd4e 100644
--- a/src/USER-OMP/dihedral_class2_omp.cpp
+++ b/src/USER-OMP/dihedral_class2_omp.cpp
@@ -15,7 +15,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "dihedral_class2_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/dihedral_cosine_shift_exp_omp.cpp b/src/USER-OMP/dihedral_cosine_shift_exp_omp.cpp
index fe99d52cb7e7d274873b85584443d2658231d03f..c43b9900281e54009ddf790a7b0c5bf6a895d540 100644
--- a/src/USER-OMP/dihedral_cosine_shift_exp_omp.cpp
+++ b/src/USER-OMP/dihedral_cosine_shift_exp_omp.cpp
@@ -15,7 +15,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "dihedral_cosine_shift_exp_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/dihedral_fourier_omp.cpp b/src/USER-OMP/dihedral_fourier_omp.cpp
index 9c93f2ad30651b4d498df9bf53e8a52b11eb0a6f..319acb0beb038eddb13384dc0cad10c5108fc00d 100644
--- a/src/USER-OMP/dihedral_fourier_omp.cpp
+++ b/src/USER-OMP/dihedral_fourier_omp.cpp
@@ -15,7 +15,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "dihedral_fourier_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/dihedral_harmonic_omp.cpp b/src/USER-OMP/dihedral_harmonic_omp.cpp
index 2e0a1cf5545694f24de16699e82fc5ee6f68d5cd..bb659cf2621a2929692fb0bed6cd076dda68cf25 100644
--- a/src/USER-OMP/dihedral_harmonic_omp.cpp
+++ b/src/USER-OMP/dihedral_harmonic_omp.cpp
@@ -15,7 +15,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "dihedral_harmonic_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/dihedral_helix_omp.cpp b/src/USER-OMP/dihedral_helix_omp.cpp
index 7dd1e8f8a4c59d5266a50fef0ac7757723254ca5..e40f084e547be390b30136135da554ada43b9deb 100644
--- a/src/USER-OMP/dihedral_helix_omp.cpp
+++ b/src/USER-OMP/dihedral_helix_omp.cpp
@@ -15,7 +15,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "dihedral_helix_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/dihedral_multi_harmonic_omp.cpp b/src/USER-OMP/dihedral_multi_harmonic_omp.cpp
index 06565e7b502a09217381e0b4e690ea685d30e765..e10fc7b94a0bcac42abd3350f4dbe320aeed1b10 100644
--- a/src/USER-OMP/dihedral_multi_harmonic_omp.cpp
+++ b/src/USER-OMP/dihedral_multi_harmonic_omp.cpp
@@ -15,7 +15,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "dihedral_multi_harmonic_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/dihedral_nharmonic_omp.cpp b/src/USER-OMP/dihedral_nharmonic_omp.cpp
index c698f7c109d1d9e88b1aa6c15f9e27bdf19a661a..ad758fc89231cd71cb8797cfb069081acde252ff 100644
--- a/src/USER-OMP/dihedral_nharmonic_omp.cpp
+++ b/src/USER-OMP/dihedral_nharmonic_omp.cpp
@@ -15,7 +15,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "dihedral_nharmonic_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/dihedral_opls_omp.cpp b/src/USER-OMP/dihedral_opls_omp.cpp
index 069d6d2dd203482adb62e7f6002d68c6fabeb128..53fddf51cbd6fe01fc236812b7b4d0db80d4d3cb 100644
--- a/src/USER-OMP/dihedral_opls_omp.cpp
+++ b/src/USER-OMP/dihedral_opls_omp.cpp
@@ -15,7 +15,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "dihedral_opls_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/dihedral_quadratic_omp.cpp b/src/USER-OMP/dihedral_quadratic_omp.cpp
index 3fa580defc20cd1027833d63f0655738f790b7d3..f6110cd5050ec580749530da13d699d74307d5b8 100644
--- a/src/USER-OMP/dihedral_quadratic_omp.cpp
+++ b/src/USER-OMP/dihedral_quadratic_omp.cpp
@@ -15,7 +15,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "dihedral_quadratic_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/ewald_omp.cpp b/src/USER-OMP/ewald_omp.cpp
index ad6b0bf80573f990616b53f0195ae092fa4f7e70..a26d5cf27d9be4f2e08103f7f9e0d36ed3156009 100644
--- a/src/USER-OMP/ewald_omp.cpp
+++ b/src/USER-OMP/ewald_omp.cpp
@@ -22,7 +22,7 @@
#include "force.h"
#include "memory.h"
-#include <math.h>
+#include <cmath>
#include "math_const.h"
diff --git a/src/USER-OMP/fix_gravity_omp.cpp b/src/USER-OMP/fix_gravity_omp.cpp
index 1e65d1f7641abd558040f8cc27f74788ea2f435f..ef1a07aa5ad909f0017bf58d3d304d610d9557e9 100644
--- a/src/USER-OMP/fix_gravity_omp.cpp
+++ b/src/USER-OMP/fix_gravity_omp.cpp
@@ -15,10 +15,10 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "fix_gravity_omp.h"
#include "atom.h"
#include "update.h"
diff --git a/src/USER-OMP/fix_neigh_history_omp.cpp b/src/USER-OMP/fix_neigh_history_omp.cpp
index a7ee18257f30ba43e90a137fa67808ba8940304d..efa7f5a3f1697499824d93a1b62a74b251b46bdc 100644
--- a/src/USER-OMP/fix_neigh_history_omp.cpp
+++ b/src/USER-OMP/fix_neigh_history_omp.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
-#include <stdio.h>
+#include <cstring>
+#include <cstdio>
#include "fix_neigh_history_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/fix_nh_asphere_omp.cpp b/src/USER-OMP/fix_nh_asphere_omp.cpp
index e710e6f12e4d86c427c4df84a7a75fb6272c9ccb..b0967bf7f78c7a2ca8f883c92c7b3558ddc2936d 100644
--- a/src/USER-OMP/fix_nh_asphere_omp.cpp
+++ b/src/USER-OMP/fix_nh_asphere_omp.cpp
@@ -15,9 +15,9 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <string.h>
-#include <stdlib.h>
-#include <math.h>
+#include <cstring>
+#include <cstdlib>
+#include <cmath>
#include "math_extra.h"
#include "fix_nh_asphere_omp.h"
#include "atom.h"
diff --git a/src/USER-OMP/fix_nh_omp.cpp b/src/USER-OMP/fix_nh_omp.cpp
index ccb6090378faf3da1990499b2ff87217c5338f52..76a47b71fdf7c86b0ead410c639e82050523ef44 100644
--- a/src/USER-OMP/fix_nh_omp.cpp
+++ b/src/USER-OMP/fix_nh_omp.cpp
@@ -22,8 +22,8 @@
#include "error.h"
#include "modify.h"
-#include <math.h>
-#include <stdio.h>
+#include <cmath>
+#include <cstdio>
using namespace LAMMPS_NS;
using namespace FixConst;
diff --git a/src/USER-OMP/fix_nh_sphere_omp.cpp b/src/USER-OMP/fix_nh_sphere_omp.cpp
index dd0530dcfa3c2da91e3ef566ecb6eaa97a38acf9..a32f0f8b51e3d4a91e3d866cd04afbe5e1520223 100644
--- a/src/USER-OMP/fix_nh_sphere_omp.cpp
+++ b/src/USER-OMP/fix_nh_sphere_omp.cpp
@@ -15,7 +15,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "fix_nh_sphere_omp.h"
#include "atom.h"
#include "atom_vec.h"
diff --git a/src/USER-OMP/fix_nph_asphere_omp.cpp b/src/USER-OMP/fix_nph_asphere_omp.cpp
index dfcbc87e6f9df5b0afa524b8484f2ca5142cfac3..c012583fda2a8a922aa2b3bac145cbb1de6c9b51 100644
--- a/src/USER-OMP/fix_nph_asphere_omp.cpp
+++ b/src/USER-OMP/fix_nph_asphere_omp.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "fix_nph_asphere_omp.h"
#include "modify.h"
#include "error.h"
diff --git a/src/USER-OMP/fix_nph_omp.cpp b/src/USER-OMP/fix_nph_omp.cpp
index f2a4e66f55a481ee4f371a3d621c989b46206ee9..c11a64cd47949009969c6bdb1e612888071b7947 100644
--- a/src/USER-OMP/fix_nph_omp.cpp
+++ b/src/USER-OMP/fix_nph_omp.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "fix_nph_omp.h"
#include "modify.h"
#include "error.h"
diff --git a/src/USER-OMP/fix_nph_sphere_omp.cpp b/src/USER-OMP/fix_nph_sphere_omp.cpp
index 670009de2fd29e44d3ca893b9a270712976c1696..21db6a3aaa8fc673498ff375eba913a903422f20 100644
--- a/src/USER-OMP/fix_nph_sphere_omp.cpp
+++ b/src/USER-OMP/fix_nph_sphere_omp.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "fix_nph_sphere_omp.h"
#include "modify.h"
#include "error.h"
diff --git a/src/USER-OMP/fix_nphug_omp.cpp b/src/USER-OMP/fix_nphug_omp.cpp
index 75ff393e288efb55863ed7354945bb4370bfc9f0..a2ed8eb7aae023ff0e74ca1e986932843076c696 100644
--- a/src/USER-OMP/fix_nphug_omp.cpp
+++ b/src/USER-OMP/fix_nphug_omp.cpp
@@ -11,8 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstring>
+#include <cstdlib>
#include "fix_nphug_omp.h"
#include "modify.h"
#include "error.h"
@@ -21,10 +22,8 @@
#include "force.h"
#include "domain.h"
#include "group.h"
-#include <math.h>
#include "memory.h"
#include "comm.h"
-#include <math.h>
using namespace LAMMPS_NS;
using namespace FixConst;
diff --git a/src/USER-OMP/fix_npt_asphere_omp.cpp b/src/USER-OMP/fix_npt_asphere_omp.cpp
index 1db62d40c091da4e1a2889e2f540a89bf74d51b4..f1fbe27d8397b4daa83cfa4c5bd924bc39bc2243 100644
--- a/src/USER-OMP/fix_npt_asphere_omp.cpp
+++ b/src/USER-OMP/fix_npt_asphere_omp.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "fix_npt_asphere_omp.h"
#include "modify.h"
#include "error.h"
diff --git a/src/USER-OMP/fix_npt_omp.cpp b/src/USER-OMP/fix_npt_omp.cpp
index 5610f62f368978788b2b4dc913514f1b0575d2e9..9244aa16068e0d5bd40014968e89588c8e529a5d 100644
--- a/src/USER-OMP/fix_npt_omp.cpp
+++ b/src/USER-OMP/fix_npt_omp.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "fix_npt_omp.h"
#include "modify.h"
#include "error.h"
diff --git a/src/USER-OMP/fix_npt_sphere_omp.cpp b/src/USER-OMP/fix_npt_sphere_omp.cpp
index d71d1380b9c73c370e1504215a91b7fd1d48779f..b12bafecdd50eac66bb1b19b38f217165812ba1a 100644
--- a/src/USER-OMP/fix_npt_sphere_omp.cpp
+++ b/src/USER-OMP/fix_npt_sphere_omp.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "fix_npt_sphere_omp.h"
#include "modify.h"
#include "error.h"
diff --git a/src/USER-OMP/fix_nve_sphere_omp.cpp b/src/USER-OMP/fix_nve_sphere_omp.cpp
index 43ecc998681992e0c061b2d336db88c81d888e4c..dd13e58d7cc2d0b37fc58368a59f57b51a7d3c73 100644
--- a/src/USER-OMP/fix_nve_sphere_omp.cpp
+++ b/src/USER-OMP/fix_nve_sphere_omp.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstring>
#include "fix_nve_sphere_omp.h"
#include "atom.h"
#include "atom_vec.h"
diff --git a/src/USER-OMP/fix_nvt_asphere_omp.cpp b/src/USER-OMP/fix_nvt_asphere_omp.cpp
index bb1e784a3799ce64813d14b5d69b50d8fe67a782..d0ef28f4deba8cf34272230c7be826a00df12139 100644
--- a/src/USER-OMP/fix_nvt_asphere_omp.cpp
+++ b/src/USER-OMP/fix_nvt_asphere_omp.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "fix_nvt_asphere_omp.h"
#include "group.h"
#include "modify.h"
diff --git a/src/USER-OMP/fix_nvt_omp.cpp b/src/USER-OMP/fix_nvt_omp.cpp
index f8f3c15b761384cb45e6f429ed353cecc8a56521..d4dbd4c8f0521be2ab4bf137c641886da1fb1d25 100644
--- a/src/USER-OMP/fix_nvt_omp.cpp
+++ b/src/USER-OMP/fix_nvt_omp.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "fix_nvt_omp.h"
#include "group.h"
#include "modify.h"
diff --git a/src/USER-OMP/fix_nvt_sllod_omp.cpp b/src/USER-OMP/fix_nvt_sllod_omp.cpp
index a829d49c0f9e126459d3d33755c4e4d9a67f774f..6ef1188d53c7fc650377432d11d5b320e3f27352 100644
--- a/src/USER-OMP/fix_nvt_sllod_omp.cpp
+++ b/src/USER-OMP/fix_nvt_sllod_omp.cpp
@@ -15,8 +15,8 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <string.h>
+#include <cmath>
+#include <cstring>
#include "fix_nvt_sllod_omp.h"
#include "math_extra.h"
#include "atom.h"
@@ -31,8 +31,6 @@
using namespace LAMMPS_NS;
using namespace FixConst;
-enum{NO_REMAP,X_REMAP,V_REMAP}; // same as fix_deform.cpp
-
typedef struct { double x,y,z; } dbl3_t;
/* ---------------------------------------------------------------------- */
@@ -85,7 +83,7 @@ void FixNVTSllodOMP::init()
int i;
for (i = 0; i < modify->nfix; i++)
if (strcmp(modify->fix[i]->style,"deform") == 0) {
- if (((FixDeform *) modify->fix[i])->remapflag != V_REMAP)
+ if (((FixDeform *) modify->fix[i])->remapflag != Domain::V_REMAP)
error->all(FLERR,"Using fix nvt/sllod/omp with inconsistent fix "
"deform remap option");
break;
diff --git a/src/USER-OMP/fix_nvt_sphere_omp.cpp b/src/USER-OMP/fix_nvt_sphere_omp.cpp
index 22eda99883a28a9d309f32bf54ceed9ccb7ecc96..33ea949fcb34e7135ef06e26397fb09fae55210a 100644
--- a/src/USER-OMP/fix_nvt_sphere_omp.cpp
+++ b/src/USER-OMP/fix_nvt_sphere_omp.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "fix_nvt_sphere_omp.h"
#include "group.h"
#include "modify.h"
diff --git a/src/USER-OMP/fix_omp.cpp b/src/USER-OMP/fix_omp.cpp
index 2a3717da0dcfa49036e8669da30aaa2017d63ecc..8d54d5b4516f109c2202868d985ca47e62893ce2 100644
--- a/src/USER-OMP/fix_omp.cpp
+++ b/src/USER-OMP/fix_omp.cpp
@@ -39,9 +39,9 @@
#include "improper_hybrid.h"
#include "kspace.h"
-#include <string.h>
-#include <stdlib.h>
-#include <stdio.h>
+#include <cstring>
+#include <cstdlib>
+#include <cstdio>
#include "suffix.h"
diff --git a/src/USER-OMP/fix_qeq_comb_omp.cpp b/src/USER-OMP/fix_qeq_comb_omp.cpp
index 351003b6685098390cab8525b20eeaa31629d63d..b898fe3fe4e90d17eb0b9847d5a49beef22b4b92 100644
--- a/src/USER-OMP/fix_qeq_comb_omp.cpp
+++ b/src/USER-OMP/fix_qeq_comb_omp.cpp
@@ -16,7 +16,8 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <math.h>
+#include <cmath>
+#include <cstring>
#include "fix_qeq_comb_omp.h"
#include "fix_omp.h"
#include "atom.h"
@@ -33,8 +34,6 @@
#include "update.h"
#include "pair_comb_omp.h"
-#include <string.h>
-
using namespace LAMMPS_NS;
using namespace FixConst;
diff --git a/src/USER-OMP/fix_qeq_reax_omp.cpp b/src/USER-OMP/fix_qeq_reax_omp.cpp
index d89c9627fe30a79d2b6d3ee2e3052fe322becf35..a9ffb32d9094277e2e7770c75ef0a129aa9f8042 100644
--- a/src/USER-OMP/fix_qeq_reax_omp.cpp
+++ b/src/USER-OMP/fix_qeq_reax_omp.cpp
@@ -31,10 +31,10 @@
High Performance Computing Applications, to appear.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "fix_qeq_reax_omp.h"
#include "pair_reaxc_omp.h"
#include "atom.h"
diff --git a/src/USER-OMP/fix_rigid_nh_omp.cpp b/src/USER-OMP/fix_rigid_nh_omp.cpp
index 9341f83079f8ad9fb3efb8492fa8908f74e51d7b..53d013474104725d33b9f5ad8a4e83d33cd0d140 100644
--- a/src/USER-OMP/fix_rigid_nh_omp.cpp
+++ b/src/USER-OMP/fix_rigid_nh_omp.cpp
@@ -29,7 +29,7 @@
#include "modify.h"
#include "update.h"
-#include <string.h>
+#include <cstring>
#if defined(_OPENMP)
#include <omp.h>
@@ -235,29 +235,9 @@ void FixRigidNHOMP::initial_integrate(int vflag)
/* ---------------------------------------------------------------------- */
-void FixRigidNHOMP::final_integrate()
+void FixRigidNHOMP::compute_forces_and_torques()
{
- double scale_t[3],scale_r;
-
- // compute scale variables
-
- scale_t[0] = scale_t[1] = scale_t[2] = 1.0;
- scale_r = 1.0;
-
- if (tstat_flag) {
- double tmp = exp(-1.0 * dtq * eta_dot_t[0]);
- scale_t[0] = scale_t[1] = scale_t[2] = tmp;
- scale_r = exp(-1.0 * dtq * eta_dot_r[0]);
- }
-
- if (pstat_flag) {
- scale_t[0] *= exp(-dtq * (epsilon_dot[0] + mtk_term2));
- scale_t[1] *= exp(-dtq * (epsilon_dot[1] + mtk_term2));
- scale_t[2] *= exp(-dtq * (epsilon_dot[2] + mtk_term2));
- scale_r *= exp(-dtq * (pdim * mtk_term2));
-
- akin_t = akin_r = 0.0;
- }
+ int ibody;
double * const * _noalias const x = atom->x;
const dbl3_t * _noalias const f = (dbl3_t *) atom->f[0];
@@ -395,12 +375,53 @@ void FixRigidNHOMP::final_integrate()
MPI_Allreduce(sum[0],all[0],6*nbody,MPI_DOUBLE,MPI_SUM,world);
+#if defined(_OPENMP)
+#pragma omp parallel for default(none) private(ibody) schedule(static)
+#endif
+ for (ibody = 0; ibody < nbody; ibody++) {
+ fcm[ibody][0] = all[ibody][0] + langextra[ibody][0];
+ fcm[ibody][1] = all[ibody][1] + langextra[ibody][1];
+ fcm[ibody][2] = all[ibody][2] + langextra[ibody][2];
+ torque[ibody][0] = all[ibody][3] + langextra[ibody][3];
+ torque[ibody][1] = all[ibody][4] + langextra[ibody][4];
+ torque[ibody][2] = all[ibody][5] + langextra[ibody][5];
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixRigidNHOMP::final_integrate()
+{
+ int ibody;
+ double scale_t[3],scale_r;
+
+ // compute scale variables
+
+ scale_t[0] = scale_t[1] = scale_t[2] = 1.0;
+ scale_r = 1.0;
+
+ if (tstat_flag) {
+ double tmp = exp(-1.0 * dtq * eta_dot_t[0]);
+ scale_t[0] = scale_t[1] = scale_t[2] = tmp;
+ scale_r = exp(-1.0 * dtq * eta_dot_r[0]);
+ }
+
+ if (pstat_flag) {
+ scale_t[0] *= exp(-dtq * (epsilon_dot[0] + mtk_term2));
+ scale_t[1] *= exp(-dtq * (epsilon_dot[1] + mtk_term2));
+ scale_t[2] *= exp(-dtq * (epsilon_dot[2] + mtk_term2));
+ scale_r *= exp(-dtq * (pdim * mtk_term2));
+
+ akin_t = akin_r = 0.0;
+ }
+
+ if (!earlyflag) compute_forces_and_torques();
+
// update vcm and angmom
// include Langevin thermostat forces
// fflag,tflag = 0 for some dimensions in 2d
double akt=0.0,akr=0.0;
const double dtf2 = dtf * 2.0;
- int ibody;
#if defined(_OPENMP)
#pragma omp parallel for default(none) private(ibody) shared(scale_t,scale_r) schedule(static) reduction(+:akt,akr)
@@ -408,13 +429,6 @@ void FixRigidNHOMP::final_integrate()
for (ibody = 0; ibody < nbody; ibody++) {
double mbody[3],tbody[3],fquat[4];
- fcm[ibody][0] = all[ibody][0] + langextra[ibody][0];
- fcm[ibody][1] = all[ibody][1] + langextra[ibody][1];
- fcm[ibody][2] = all[ibody][2] + langextra[ibody][2];
- torque[ibody][0] = all[ibody][3] + langextra[ibody][3];
- torque[ibody][1] = all[ibody][4] + langextra[ibody][4];
- torque[ibody][2] = all[ibody][5] + langextra[ibody][5];
-
// update vcm by 1/2 step
const double dtfm = dtf / masstotal[ibody];
diff --git a/src/USER-OMP/fix_rigid_nh_omp.h b/src/USER-OMP/fix_rigid_nh_omp.h
index 9210d7e5dc88f1a412f047f3d3eab5d19dc90c47..2f57b2723b8515dfb23606c45057ad742b4157e8 100644
--- a/src/USER-OMP/fix_rigid_nh_omp.h
+++ b/src/USER-OMP/fix_rigid_nh_omp.h
@@ -28,6 +28,9 @@ class FixRigidNHOMP : public FixRigidNH {
virtual void final_integrate();
virtual void remap();
+ protected:
+ virtual void compute_forces_and_torques();
+
private: // copied from FixRigidOMP
template <int, int> void set_xv_thr();
template <int, int> void set_v_thr();
diff --git a/src/USER-OMP/fix_rigid_nph_omp.cpp b/src/USER-OMP/fix_rigid_nph_omp.cpp
index 6aca84c30973566ef1b58e7954d667144277d7ef..7db45ed9bf414a4b0c417a47b08945c8f9ba1a91 100644
--- a/src/USER-OMP/fix_rigid_nph_omp.cpp
+++ b/src/USER-OMP/fix_rigid_nph_omp.cpp
@@ -17,7 +17,7 @@
Miller et al., J Chem Phys. 116, 8649-8659 (2002)
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "fix_rigid_nph_omp.h"
#include "domain.h"
#include "modify.h"
diff --git a/src/USER-OMP/fix_rigid_npt_omp.cpp b/src/USER-OMP/fix_rigid_npt_omp.cpp
index 23f16c61556034bd208dda6d20f941ba87045d23..a041706f388890decd8c834021553e9eb18ddec2 100644
--- a/src/USER-OMP/fix_rigid_npt_omp.cpp
+++ b/src/USER-OMP/fix_rigid_npt_omp.cpp
@@ -17,7 +17,7 @@
Miller et al., J Chem Phys. 116, 8649-8659 (2002)
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "fix_rigid_npt_omp.h"
#include "domain.h"
#include "modify.h"
diff --git a/src/USER-OMP/fix_rigid_omp.cpp b/src/USER-OMP/fix_rigid_omp.cpp
index 6f084c628cb7e6b3538b74d4d462e909b93b6440..12c6362ed8bd4803e76e07c1b8e54dec5a74f8d5 100644
--- a/src/USER-OMP/fix_rigid_omp.cpp
+++ b/src/USER-OMP/fix_rigid_omp.cpp
@@ -24,7 +24,7 @@
#include "comm.h"
#include "domain.h"
-#include <string.h>
+#include <cstring>
#if defined(_OPENMP)
#include <omp.h>
@@ -108,7 +108,7 @@ void FixRigidOMP::initial_integrate(int vflag)
/* ---------------------------------------------------------------------- */
-void FixRigidOMP::final_integrate()
+void FixRigidOMP::compute_forces_and_torques()
{
double * const * _noalias const x = atom->x;
const dbl3_t * _noalias const f = (dbl3_t *) atom->f[0];
@@ -261,6 +261,23 @@ void FixRigidOMP::final_integrate()
torque[ibody][0] = all[ibody][3] + langextra[ibody][3];
torque[ibody][1] = all[ibody][4] + langextra[ibody][4];
torque[ibody][2] = all[ibody][5] + langextra[ibody][5];
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixRigidOMP::final_integrate()
+{
+ int ibody;
+
+ if (!earlyflag) compute_forces_and_torques();
+
+ // update vcm and angmom
+
+#if defined(_OPENMP)
+#pragma omp parallel for default(none) private(ibody) schedule(static)
+#endif
+ for (ibody = 0; ibody < nbody; ibody++) {
// update vcm by 1/2 step
diff --git a/src/USER-OMP/fix_rigid_omp.h b/src/USER-OMP/fix_rigid_omp.h
index 2b7b9461d2adee1b4ba327d6903e2b7f476ba845..b666a173a87c0a949ba8e8aba33f81da493f345a 100644
--- a/src/USER-OMP/fix_rigid_omp.h
+++ b/src/USER-OMP/fix_rigid_omp.h
@@ -33,6 +33,9 @@ class FixRigidOMP : public FixRigid {
virtual void initial_integrate(int);
virtual void final_integrate();
+ protected:
+ virtual void compute_forces_and_torques();
+
private:
template <int, int> void set_xv_thr();
template <int, int> void set_v_thr();
@@ -42,4 +45,3 @@ class FixRigidOMP : public FixRigid {
#endif
#endif
-
diff --git a/src/USER-OMP/fix_rigid_small_omp.cpp b/src/USER-OMP/fix_rigid_small_omp.cpp
index 156ef8a2d7a04876fd186ae4ec70c2a00fad2a3a..a0495b3b933a4fa5a852b079dfd5936cb8b10088 100644
--- a/src/USER-OMP/fix_rigid_small_omp.cpp
+++ b/src/USER-OMP/fix_rigid_small_omp.cpp
@@ -24,7 +24,7 @@
#include "comm.h"
#include "domain.h"
-#include <string.h>
+#include <cstring>
#if defined(_OPENMP)
#include <omp.h>
@@ -112,7 +112,7 @@ void FixRigidSmallOMP::initial_integrate(int vflag)
/* ---------------------------------------------------------------------- */
-void FixRigidSmallOMP::final_integrate()
+void FixRigidSmallOMP::compute_forces_and_torques()
{
double * const * _noalias const x = atom->x;
const dbl3_t * _noalias const f = (dbl3_t *) atom->f[0];
@@ -201,6 +201,15 @@ void FixRigidSmallOMP::final_integrate()
tcm[2] += langextra[ibody][5];
}
}
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixRigidSmallOMP::final_integrate()
+{
+ int ibody;
+
+ if (!earlyflag) compute_forces_and_torques();
// update vcm and angmom, recompute omega
diff --git a/src/USER-OMP/fix_rigid_small_omp.h b/src/USER-OMP/fix_rigid_small_omp.h
index ffc4bee660ab3683498df38c9bd235cbf1522d95..298a1aa9de2ed8bc733840f4708608da9a9638a1 100644
--- a/src/USER-OMP/fix_rigid_small_omp.h
+++ b/src/USER-OMP/fix_rigid_small_omp.h
@@ -33,6 +33,9 @@ class FixRigidSmallOMP : public FixRigidSmall {
virtual void initial_integrate(int);
virtual void final_integrate();
+ protected:
+ virtual void compute_forces_and_torques();
+
private:
template <int, int> void set_xv_thr();
template <int, int> void set_v_thr();
diff --git a/src/USER-OMP/fix_wall_gran_omp.cpp b/src/USER-OMP/fix_wall_gran_omp.cpp
index 55ae8593a761d62d3cbfc1c136bb4ed611d8d2d5..d45e748b6a1100691fc7e46f246c08330913a870 100644
--- a/src/USER-OMP/fix_wall_gran_omp.cpp
+++ b/src/USER-OMP/fix_wall_gran_omp.cpp
@@ -15,7 +15,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "fix_wall_gran_omp.h"
#include "atom.h"
#include "memory.h"
diff --git a/src/USER-OMP/hack_openmp_for_pgi.sh b/src/USER-OMP/hack_openmp_for_pgi.sh
old mode 100644
new mode 100755
diff --git a/src/USER-OMP/improper_class2_omp.cpp b/src/USER-OMP/improper_class2_omp.cpp
index 3beeb41a2626d5f9b52d52a348d69cda07111c90..7184cbeb69b7800cc7477803b29df83e2af5fc10 100644
--- a/src/USER-OMP/improper_class2_omp.cpp
+++ b/src/USER-OMP/improper_class2_omp.cpp
@@ -15,7 +15,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "improper_class2_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/improper_cossq_omp.cpp b/src/USER-OMP/improper_cossq_omp.cpp
index f34941d6245b28f94d34d151225115c6b37976ad..022cfa6adf8216c80ce8ffd78068241ae35061be 100644
--- a/src/USER-OMP/improper_cossq_omp.cpp
+++ b/src/USER-OMP/improper_cossq_omp.cpp
@@ -15,7 +15,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "improper_cossq_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/improper_cvff_omp.cpp b/src/USER-OMP/improper_cvff_omp.cpp
index cba14226ac870029c3e6971155b5a6250eef3ba7..78c5a55e054da887354dc8707a026c9ddc9cb0da 100644
--- a/src/USER-OMP/improper_cvff_omp.cpp
+++ b/src/USER-OMP/improper_cvff_omp.cpp
@@ -15,7 +15,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "improper_cvff_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/improper_fourier_omp.cpp b/src/USER-OMP/improper_fourier_omp.cpp
index c1699baf02a5429c83ba561ea996fe632429975e..aed04003a5eff70550f4d98830145a7557cc22b5 100644
--- a/src/USER-OMP/improper_fourier_omp.cpp
+++ b/src/USER-OMP/improper_fourier_omp.cpp
@@ -15,7 +15,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "improper_fourier_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/improper_harmonic_omp.cpp b/src/USER-OMP/improper_harmonic_omp.cpp
index 8c1f91ecabb6213fe884cccfb7ecde71bedd9ada..3f1895142df47ebc6a6cfd532ff53e12a2517cff 100644
--- a/src/USER-OMP/improper_harmonic_omp.cpp
+++ b/src/USER-OMP/improper_harmonic_omp.cpp
@@ -15,7 +15,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "improper_harmonic_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/improper_ring_omp.cpp b/src/USER-OMP/improper_ring_omp.cpp
index 4eadc831833b9f2b3f9e26fd24a545ecafa962c4..7970de3839a8c98b92a68f65b8655110c3eda320 100644
--- a/src/USER-OMP/improper_ring_omp.cpp
+++ b/src/USER-OMP/improper_ring_omp.cpp
@@ -15,7 +15,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "improper_ring_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/improper_umbrella_omp.cpp b/src/USER-OMP/improper_umbrella_omp.cpp
index 9ea94c57050e3ba15555df231aaf94095228f8e9..dc11f24a4de084b07b666c08b76271d135218115 100644
--- a/src/USER-OMP/improper_umbrella_omp.cpp
+++ b/src/USER-OMP/improper_umbrella_omp.cpp
@@ -15,7 +15,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "improper_umbrella_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/msm_cg_omp.cpp b/src/USER-OMP/msm_cg_omp.cpp
index fb64bc5644683f1490bd8e90b9d5f64cc91cb871..226083deb48489ecb5cd6bedc56265185c506630 100644
--- a/src/USER-OMP/msm_cg_omp.cpp
+++ b/src/USER-OMP/msm_cg_omp.cpp
@@ -17,10 +17,10 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "atom.h"
#include "gridcomm.h"
@@ -331,7 +331,7 @@ void MSMCGOMP::particle_map()
int flag = 0;
int i;
- if (!ISFINITE(boxlo[0]) || !ISFINITE(boxlo[1]) || !ISFINITE(boxlo[2]))
+ if (!std::isfinite(boxlo[0]) || !std::isfinite(boxlo[1]) || !std::isfinite(boxlo[2]))
error->one(FLERR,"Non-numeric box dimensions - simulation unstable");
// XXX: O(N). is it worth to add OpenMP here?
diff --git a/src/USER-OMP/msm_omp.cpp b/src/USER-OMP/msm_omp.cpp
index 7a79dc865b7d28f6110d62823f9f259465e7f5fa..3bc7ddb1cdc28fc9851d12432422db994b3cbff7 100644
--- a/src/USER-OMP/msm_omp.cpp
+++ b/src/USER-OMP/msm_omp.cpp
@@ -24,7 +24,7 @@
#include "memory.h"
#include "math_const.h"
-#include <string.h>
+#include <cstring>
#if defined(_OPENMP)
#include <omp.h>
diff --git a/src/USER-OMP/npair_half_size_bin_newtoff_omp.cpp b/src/USER-OMP/npair_half_size_bin_newtoff_omp.cpp
index fc101a33d21ce88b683df8835b5d083af287cbd5..dff2a762d51dd71b96fc84d98aa26d618acd2750 100644
--- a/src/USER-OMP/npair_half_size_bin_newtoff_omp.cpp
+++ b/src/USER-OMP/npair_half_size_bin_newtoff_omp.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "npair_half_size_bin_newtoff_omp.h"
#include "npair_omp.h"
#include "neighbor.h"
diff --git a/src/USER-OMP/npair_half_size_bin_newton_omp.cpp b/src/USER-OMP/npair_half_size_bin_newton_omp.cpp
index 1f0dca79ac1b072b05176254577b3954bcb390e3..3053b815946f59ffa07b2943da022374083f1c14 100644
--- a/src/USER-OMP/npair_half_size_bin_newton_omp.cpp
+++ b/src/USER-OMP/npair_half_size_bin_newton_omp.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "npair_half_size_bin_newton_omp.h"
#include "npair_omp.h"
#include "neighbor.h"
diff --git a/src/USER-OMP/npair_half_size_nsq_newtoff_omp.cpp b/src/USER-OMP/npair_half_size_nsq_newtoff_omp.cpp
index 1615effad3864afbec6ee9633580bd754c44a834..717012b226e3dfb08292b40e029bdb65592450ce 100644
--- a/src/USER-OMP/npair_half_size_nsq_newtoff_omp.cpp
+++ b/src/USER-OMP/npair_half_size_nsq_newtoff_omp.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "npair_half_size_nsq_newtoff_omp.h"
#include "npair_omp.h"
#include "neighbor.h"
diff --git a/src/USER-OMP/npair_half_size_nsq_newton_omp.cpp b/src/USER-OMP/npair_half_size_nsq_newton_omp.cpp
index e5de57aa5112698f7bc069914eef8d5d9256401d..5a55029d30fd77e50349f2aa6214a38009588a86 100644
--- a/src/USER-OMP/npair_half_size_nsq_newton_omp.cpp
+++ b/src/USER-OMP/npair_half_size_nsq_newton_omp.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "npair_half_size_nsq_newton_omp.h"
#include "npair_omp.h"
#include "neighbor.h"
diff --git a/src/USER-OMP/pair_adp_omp.cpp b/src/USER-OMP/pair_adp_omp.cpp
index 658ef365a37c7948d36f8aea27feaa3b1f1b680a..264169773b9af8cb988377ebef73b187583013d2 100644
--- a/src/USER-OMP/pair_adp_omp.cpp
+++ b/src/USER-OMP/pair_adp_omp.cpp
@@ -12,8 +12,8 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <string.h>
+#include <cmath>
+#include <cstring>
#include "pair_adp_omp.h"
#include "atom.h"
diff --git a/src/USER-OMP/pair_agni_omp.cpp b/src/USER-OMP/pair_agni_omp.cpp
index 72e8331718c3461c1d33a147a41b63b2a1636af0..e8f003ea881674165d42e15053c2766b9be8a27e 100644
--- a/src/USER-OMP/pair_agni_omp.cpp
+++ b/src/USER-OMP/pair_agni_omp.cpp
@@ -12,9 +12,9 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <string.h>
-#include <stdint.h>
+#include <cmath>
+#include <cstring>
+#include <stdint.h> // <cstdint> requires C++-11
#include "pair_agni_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_airebo_omp.cpp b/src/USER-OMP/pair_airebo_omp.cpp
index 3e8f6d6df3ba242bc5d47249d8563bdc5136e03b..8decda7cabc86ef3096d806d03b101b3891afefa 100644
--- a/src/USER-OMP/pair_airebo_omp.cpp
+++ b/src/USER-OMP/pair_airebo_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_airebo_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_beck_omp.cpp b/src/USER-OMP/pair_beck_omp.cpp
index e56a0dc7faf1ac4b3ae8fa5442142b56d998b336..1494ec2987e09864b7b69f01cec12b59197d5bd5 100644
--- a/src/USER-OMP/pair_beck_omp.cpp
+++ b/src/USER-OMP/pair_beck_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_beck_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_born_coul_long_omp.cpp b/src/USER-OMP/pair_born_coul_long_omp.cpp
index cbb71dfeb54e65c728d6f22b2f493c3186c03247..f1981844066c3eab95133ef67957a8b9786414a7 100644
--- a/src/USER-OMP/pair_born_coul_long_omp.cpp
+++ b/src/USER-OMP/pair_born_coul_long_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_born_coul_long_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_born_coul_msm_omp.cpp b/src/USER-OMP/pair_born_coul_msm_omp.cpp
index 8ce564ccfabd10c2f8c3be2748822f430728327f..1b4757359f6a84b027a7e18078b8d7576993c64d 100644
--- a/src/USER-OMP/pair_born_coul_msm_omp.cpp
+++ b/src/USER-OMP/pair_born_coul_msm_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_born_coul_msm_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_born_coul_wolf_omp.cpp b/src/USER-OMP/pair_born_coul_wolf_omp.cpp
index bd3e539dd65dd030858b590754eed655fd3c6165..7904181ba594994be359c77c72dcf0be97d77082 100644
--- a/src/USER-OMP/pair_born_coul_wolf_omp.cpp
+++ b/src/USER-OMP/pair_born_coul_wolf_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_born_coul_wolf_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_born_omp.cpp b/src/USER-OMP/pair_born_omp.cpp
index 35669cb53955f3f9aca601efbafcda37b501998a..f75d4b9f35a6ba81467c382f6ce43f9052e0d4c6 100644
--- a/src/USER-OMP/pair_born_omp.cpp
+++ b/src/USER-OMP/pair_born_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_born_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_brownian_omp.cpp b/src/USER-OMP/pair_brownian_omp.cpp
index 9ea6a9187b75c0422043e7161a5c8d909618d32a..b1af821bba876a95dd27919c5d4abef736aa4af0 100644
--- a/src/USER-OMP/pair_brownian_omp.cpp
+++ b/src/USER-OMP/pair_brownian_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_brownian_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_brownian_poly_omp.cpp b/src/USER-OMP/pair_brownian_poly_omp.cpp
index d8cb3bf06e158454212026bd6d980cbae1dadcdf..2e677ed535220e11bf13ccbe4068a5bffebb91f8 100644
--- a/src/USER-OMP/pair_brownian_poly_omp.cpp
+++ b/src/USER-OMP/pair_brownian_poly_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_brownian_poly_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_buck_coul_cut_omp.cpp b/src/USER-OMP/pair_buck_coul_cut_omp.cpp
index ead60d70acc76e2fb650aa840a4550a716d93ded..8fa6be06b2ef595fd6d029e101d07e98e298632e 100644
--- a/src/USER-OMP/pair_buck_coul_cut_omp.cpp
+++ b/src/USER-OMP/pair_buck_coul_cut_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_buck_coul_cut_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_buck_coul_long_omp.cpp b/src/USER-OMP/pair_buck_coul_long_omp.cpp
index 48750f83181049664dd52618bf4ebb8aff3a0393..4d30eb3e82d991be28bf00ba4fc7ec67b4216bc8 100644
--- a/src/USER-OMP/pair_buck_coul_long_omp.cpp
+++ b/src/USER-OMP/pair_buck_coul_long_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_buck_coul_long_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_buck_coul_msm_omp.cpp b/src/USER-OMP/pair_buck_coul_msm_omp.cpp
index df94efc81232cc9547d01f9fabadfb30d6fda81e..a8bca36394bd5b4415ce840a238cdaaa195ab8df 100644
--- a/src/USER-OMP/pair_buck_coul_msm_omp.cpp
+++ b/src/USER-OMP/pair_buck_coul_msm_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_buck_coul_msm_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_buck_long_coul_long_omp.cpp b/src/USER-OMP/pair_buck_long_coul_long_omp.cpp
index dbcef106d2571f3a439a635be5f8417e3d105937..4a67cf9544fda593f82862e976498f1537d3a3c5 100644
--- a/src/USER-OMP/pair_buck_long_coul_long_omp.cpp
+++ b/src/USER-OMP/pair_buck_long_coul_long_omp.cpp
@@ -12,7 +12,7 @@
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "math_vector.h"
#include "pair_buck_long_coul_long_omp.h"
#include "atom.h"
diff --git a/src/USER-OMP/pair_buck_omp.cpp b/src/USER-OMP/pair_buck_omp.cpp
index 826fd78deb3368a0745b3f6ee2717c10e1376c58..f3fa32a5ea231fc772c3edd6596c43e85a644ded 100644
--- a/src/USER-OMP/pair_buck_omp.cpp
+++ b/src/USER-OMP/pair_buck_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_buck_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_cdeam_omp.cpp b/src/USER-OMP/pair_cdeam_omp.cpp
index 3bfe74e129d391af143d3301a06f1b1e6f91326c..c3a9454567cccc0cb0c075f635e61c247ef9c476 100644
--- a/src/USER-OMP/pair_cdeam_omp.cpp
+++ b/src/USER-OMP/pair_cdeam_omp.cpp
@@ -12,8 +12,8 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <string.h>
+#include <cmath>
+#include <cstring>
#include "pair_cdeam_omp.h"
#include "atom.h"
diff --git a/src/USER-OMP/pair_colloid_omp.cpp b/src/USER-OMP/pair_colloid_omp.cpp
index 4c6411f1509f86973731a699d241836571a14ea7..536b7644bd4f12efcd0818ae18f57cdf656b0b6d 100644
--- a/src/USER-OMP/pair_colloid_omp.cpp
+++ b/src/USER-OMP/pair_colloid_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_colloid_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_comb_omp.cpp b/src/USER-OMP/pair_comb_omp.cpp
index 2a0e6ceb2354ea0361a540b824c18f1cecbdbc9f..8a77ab955fdeba423203938e0bd50012b4228621 100644
--- a/src/USER-OMP/pair_comb_omp.cpp
+++ b/src/USER-OMP/pair_comb_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_comb_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_coul_cut_omp.cpp b/src/USER-OMP/pair_coul_cut_omp.cpp
index 381e7f83c208c97980f11c0fec8be31d2b7b5782..b9ac72421ef874728a22ad24279840210fdefb7a 100644
--- a/src/USER-OMP/pair_coul_cut_omp.cpp
+++ b/src/USER-OMP/pair_coul_cut_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_coul_cut_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_coul_cut_soft_omp.cpp b/src/USER-OMP/pair_coul_cut_soft_omp.cpp
index af9c9472fa788b827ac0eaf18f09d2db782e3d90..c7e8c5e5603a0765e4911f5d34357cd1181089e3 100644
--- a/src/USER-OMP/pair_coul_cut_soft_omp.cpp
+++ b/src/USER-OMP/pair_coul_cut_soft_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_coul_cut_soft_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_coul_debye_omp.cpp b/src/USER-OMP/pair_coul_debye_omp.cpp
index 0d9b1179674495710e42c4a8a578d71f8c0b44ea..cb7a9025ce718bf297bc83b1e718c20a32fd4a34 100644
--- a/src/USER-OMP/pair_coul_debye_omp.cpp
+++ b/src/USER-OMP/pair_coul_debye_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_coul_debye_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_coul_diel_omp.cpp b/src/USER-OMP/pair_coul_diel_omp.cpp
index 577ba6bf65a9b49e0a22e1dcd04257cc0bde947b..c75e36b55ee842c05c8f9ca8de58875fa8c08ae8 100644
--- a/src/USER-OMP/pair_coul_diel_omp.cpp
+++ b/src/USER-OMP/pair_coul_diel_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_coul_diel_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_coul_dsf_omp.cpp b/src/USER-OMP/pair_coul_dsf_omp.cpp
index 4707fad733520cca8fca7e02f87753e543f085c0..740e3242ad2bcf3c0db313f3f2989dac2e32867a 100644
--- a/src/USER-OMP/pair_coul_dsf_omp.cpp
+++ b/src/USER-OMP/pair_coul_dsf_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_coul_dsf_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_coul_long_omp.cpp b/src/USER-OMP/pair_coul_long_omp.cpp
index dc619913d6ef82c9c2e141ac5128617b7c25744c..eb74bb9615cf2a5ac2f9d1118f3b1fb6a7263d92 100644
--- a/src/USER-OMP/pair_coul_long_omp.cpp
+++ b/src/USER-OMP/pair_coul_long_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_coul_long_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_coul_long_soft_omp.cpp b/src/USER-OMP/pair_coul_long_soft_omp.cpp
index f44f95717d10e5fcef2f12dd32a94f6e492d17f2..4e65483a17c7f4a6b7d9759781df748dcdc89561 100644
--- a/src/USER-OMP/pair_coul_long_soft_omp.cpp
+++ b/src/USER-OMP/pair_coul_long_soft_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_coul_long_soft_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_coul_msm_omp.cpp b/src/USER-OMP/pair_coul_msm_omp.cpp
index baf9ceefb5b4957e83d7408243c791d0ff67b3cd..f4bc279532fe96386de8344d0797bd925e6104c9 100644
--- a/src/USER-OMP/pair_coul_msm_omp.cpp
+++ b/src/USER-OMP/pair_coul_msm_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_coul_msm_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_coul_wolf_omp.cpp b/src/USER-OMP/pair_coul_wolf_omp.cpp
index c5080bc7de2185f860530235e48f496da1a8dd34..bc86cdbf5dae8e5d3378458ec11df65117c94a20 100644
--- a/src/USER-OMP/pair_coul_wolf_omp.cpp
+++ b/src/USER-OMP/pair_coul_wolf_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_coul_wolf_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_dpd_omp.cpp b/src/USER-OMP/pair_dpd_omp.cpp
index 98e5af0d814cdeb429057ae23dc8837a6efec27b..29b5568defa983e9393358331dfb75fffc459b94 100644
--- a/src/USER-OMP/pair_dpd_omp.cpp
+++ b/src/USER-OMP/pair_dpd_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_dpd_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_dpd_tstat_omp.cpp b/src/USER-OMP/pair_dpd_tstat_omp.cpp
index ee697a2e96f687b404091b5055a3de4bc4e4d791..0a9e96fa0cca4478b5364528f3d0a16f1fefecc6 100644
--- a/src/USER-OMP/pair_dpd_tstat_omp.cpp
+++ b/src/USER-OMP/pair_dpd_tstat_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_dpd_tstat_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_eam_alloy_omp.cpp b/src/USER-OMP/pair_eam_alloy_omp.cpp
index eea7383eac3ee19edf12f32314c9866464bd0fee..bbb3b03b020cffdf39327c6b556b26e165983699 100644
--- a/src/USER-OMP/pair_eam_alloy_omp.cpp
+++ b/src/USER-OMP/pair_eam_alloy_omp.cpp
@@ -15,9 +15,9 @@
Contributing authors: Stephen Foiles (SNL), Murray Daw (SNL)
------------------------------------------------------------------------- */
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_eam_alloy_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_eam_fs_omp.cpp b/src/USER-OMP/pair_eam_fs_omp.cpp
index c646632224a213762eb50ae81868b65c5ebf217e..a678c887a0726ce23d3c5e9468cf8e77581ae5af 100644
--- a/src/USER-OMP/pair_eam_fs_omp.cpp
+++ b/src/USER-OMP/pair_eam_fs_omp.cpp
@@ -15,9 +15,9 @@
Contributing authors: Tim Lau (MIT)
------------------------------------------------------------------------- */
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_eam_fs_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_eam_omp.cpp b/src/USER-OMP/pair_eam_omp.cpp
index 9c28477af03053b28a4ecde21daab5f370bbae49..492ff797692d19fba1de48296b98f4450037fc00 100644
--- a/src/USER-OMP/pair_eam_omp.cpp
+++ b/src/USER-OMP/pair_eam_omp.cpp
@@ -12,8 +12,8 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <string.h>
+#include <cmath>
+#include <cstring>
#include "pair_eam_omp.h"
#include "atom.h"
diff --git a/src/USER-OMP/pair_edip_omp.cpp b/src/USER-OMP/pair_edip_omp.cpp
index 7c503ea8aa13057c9149a3116c92336c0b7aa0a0..5ad8c808ba5e39a0ce728f1375065f296b247048 100644
--- a/src/USER-OMP/pair_edip_omp.cpp
+++ b/src/USER-OMP/pair_edip_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_edip_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_eim_omp.cpp b/src/USER-OMP/pair_eim_omp.cpp
index e98c035860c74289548fbc2ee17333875093c5ad..6a3e0bc529d99f2201a6d0df25535acddffa08f5 100644
--- a/src/USER-OMP/pair_eim_omp.cpp
+++ b/src/USER-OMP/pair_eim_omp.cpp
@@ -12,8 +12,8 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <string.h>
+#include <cmath>
+#include <cstring>
#include "pair_eim_omp.h"
#include "atom.h"
diff --git a/src/USER-OMP/pair_gauss_cut_omp.cpp b/src/USER-OMP/pair_gauss_cut_omp.cpp
index ad0eb77963448d92a2a7e3c9c9b491c99b7c638c..9a41dcc87ef3a4024b1a4a1a19f6f87f8a6b41ca 100644
--- a/src/USER-OMP/pair_gauss_cut_omp.cpp
+++ b/src/USER-OMP/pair_gauss_cut_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_gauss_cut_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_gauss_omp.cpp b/src/USER-OMP/pair_gauss_omp.cpp
index 062da924e32b2f3b4f63560b093db792dac99caf..059c77c677aded43c3bfe1dcf4ca0cdedd15c851 100644
--- a/src/USER-OMP/pair_gauss_omp.cpp
+++ b/src/USER-OMP/pair_gauss_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_gauss_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_gayberne_omp.cpp b/src/USER-OMP/pair_gayberne_omp.cpp
index 54e4496f22efcb5954fdee9c83c91024e1d48a01..5b0ff67afed9a8d5e3dfbb858a68c4f4e08ec477 100644
--- a/src/USER-OMP/pair_gayberne_omp.cpp
+++ b/src/USER-OMP/pair_gayberne_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_gayberne_omp.h"
#include "math_extra.h"
#include "atom.h"
diff --git a/src/USER-OMP/pair_gran_hertz_history_omp.cpp b/src/USER-OMP/pair_gran_hertz_history_omp.cpp
index 046b71a73aee49f91222b0b787f1c1ea4551f434..9854b8f9ff5261cc5d2a2609a1e146971298a03d 100644
--- a/src/USER-OMP/pair_gran_hertz_history_omp.cpp
+++ b/src/USER-OMP/pair_gran_hertz_history_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_gran_hertz_history_omp.h"
#include "fix_neigh_history.h"
#include "atom.h"
diff --git a/src/USER-OMP/pair_gran_hooke_history_omp.cpp b/src/USER-OMP/pair_gran_hooke_history_omp.cpp
index 2e7d55aff059c1e7867cb35edd03bd3d19cf7eb6..2327fc815ac218709b28ad358c4d124f4393a3e5 100644
--- a/src/USER-OMP/pair_gran_hooke_history_omp.cpp
+++ b/src/USER-OMP/pair_gran_hooke_history_omp.cpp
@@ -12,7 +12,8 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
+#include <cstring>
#include "pair_gran_hooke_history_omp.h"
#include "fix_neigh_history.h"
#include "atom.h"
@@ -24,8 +25,6 @@
#include "neigh_list.h"
#include "update.h"
-#include <string.h>
-
#include "suffix.h"
using namespace LAMMPS_NS;
diff --git a/src/USER-OMP/pair_gran_hooke_omp.cpp b/src/USER-OMP/pair_gran_hooke_omp.cpp
index 3197b7076e8c09740ea75d1bd84950b4d8a67777..876fe9c4de5eb997a4c58b892a99f16728f87c6b 100644
--- a/src/USER-OMP/pair_gran_hooke_omp.cpp
+++ b/src/USER-OMP/pair_gran_hooke_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_gran_hooke_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_hbond_dreiding_lj_omp.cpp b/src/USER-OMP/pair_hbond_dreiding_lj_omp.cpp
index c22efffb5a8edca99cdfb486de5cfaab76dbcd26..ec9da78b16dc06d14135ade0263f635ecc39f25e 100644
--- a/src/USER-OMP/pair_hbond_dreiding_lj_omp.cpp
+++ b/src/USER-OMP/pair_hbond_dreiding_lj_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_hbond_dreiding_lj_omp.h"
#include "atom.h"
#include "atom_vec.h"
diff --git a/src/USER-OMP/pair_hbond_dreiding_morse_omp.cpp b/src/USER-OMP/pair_hbond_dreiding_morse_omp.cpp
index 7debe5a68a6f41ecbce2680e9c6671178af43288..4965be43b84a6f1dd3809c2cd90a5816adf14124 100644
--- a/src/USER-OMP/pair_hbond_dreiding_morse_omp.cpp
+++ b/src/USER-OMP/pair_hbond_dreiding_morse_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_hbond_dreiding_morse_omp.h"
#include "atom.h"
#include "atom_vec.h"
diff --git a/src/USER-OMP/pair_lj96_cut_omp.cpp b/src/USER-OMP/pair_lj96_cut_omp.cpp
index e502a93acfb1d711426b0660c401cdd16413eeb3..1cca6743690756f4e5f7300f425b4718999356ec 100644
--- a/src/USER-OMP/pair_lj96_cut_omp.cpp
+++ b/src/USER-OMP/pair_lj96_cut_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_lj96_cut_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_lj_charmm_coul_charmm_implicit_omp.cpp b/src/USER-OMP/pair_lj_charmm_coul_charmm_implicit_omp.cpp
index 1333ae27613e15beead53eac127fed836b52e28e..2f72f3851e244552b8b465ef05e7aca23a731872 100644
--- a/src/USER-OMP/pair_lj_charmm_coul_charmm_implicit_omp.cpp
+++ b/src/USER-OMP/pair_lj_charmm_coul_charmm_implicit_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_lj_charmm_coul_charmm_implicit_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_lj_charmm_coul_charmm_omp.cpp b/src/USER-OMP/pair_lj_charmm_coul_charmm_omp.cpp
index 9fd41e61dd48f4c92e925b5aeebbd4f0dbd6c7a0..b61a80a178b77c0b56ee696b30141b45f5b3e6eb 100644
--- a/src/USER-OMP/pair_lj_charmm_coul_charmm_omp.cpp
+++ b/src/USER-OMP/pair_lj_charmm_coul_charmm_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_lj_charmm_coul_charmm_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_lj_charmm_coul_long_omp.cpp b/src/USER-OMP/pair_lj_charmm_coul_long_omp.cpp
index acbf61d9fd717dfc403c219e180ca01fe88983b2..5351ab9aeaa95571a0fbb59f057c7b5d27ad6a06 100644
--- a/src/USER-OMP/pair_lj_charmm_coul_long_omp.cpp
+++ b/src/USER-OMP/pair_lj_charmm_coul_long_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_lj_charmm_coul_long_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_lj_charmm_coul_long_soft_omp.cpp b/src/USER-OMP/pair_lj_charmm_coul_long_soft_omp.cpp
index 4953c89a4d55142adade87e72685e5380f2085a4..ea5d739e49d2614f003571bc6128bca2c75d785c 100644
--- a/src/USER-OMP/pair_lj_charmm_coul_long_soft_omp.cpp
+++ b/src/USER-OMP/pair_lj_charmm_coul_long_soft_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_lj_charmm_coul_long_soft_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_lj_charmm_coul_msm_omp.cpp b/src/USER-OMP/pair_lj_charmm_coul_msm_omp.cpp
index c603f0dd3a01aa78d2c8b9d5cb29e0d8f1393f6c..3baa9597a8e28c3619fe1184c6fe937f0fd2012a 100644
--- a/src/USER-OMP/pair_lj_charmm_coul_msm_omp.cpp
+++ b/src/USER-OMP/pair_lj_charmm_coul_msm_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_lj_charmm_coul_msm_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_lj_class2_coul_cut_omp.cpp b/src/USER-OMP/pair_lj_class2_coul_cut_omp.cpp
index 98c2b0d578eaf153ee44d271b4db4cd1c82e03a0..38390918c7da9644f10193d362300d7c34324a54 100644
--- a/src/USER-OMP/pair_lj_class2_coul_cut_omp.cpp
+++ b/src/USER-OMP/pair_lj_class2_coul_cut_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_lj_class2_coul_cut_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_lj_class2_coul_long_omp.cpp b/src/USER-OMP/pair_lj_class2_coul_long_omp.cpp
index 3038332c905e7e69b4730816b1457519e632d19d..f47672c9bc39d3f01f8af5733f923d38578359f4 100644
--- a/src/USER-OMP/pair_lj_class2_coul_long_omp.cpp
+++ b/src/USER-OMP/pair_lj_class2_coul_long_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_lj_class2_coul_long_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_lj_class2_omp.cpp b/src/USER-OMP/pair_lj_class2_omp.cpp
index ffb0ceaa0a0f762ee63d8384b015bd2c4a1400fc..7ab4626c3e420ddf0e6dd633b8b8ca704568ae0e 100644
--- a/src/USER-OMP/pair_lj_class2_omp.cpp
+++ b/src/USER-OMP/pair_lj_class2_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_lj_class2_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_lj_cubic_omp.cpp b/src/USER-OMP/pair_lj_cubic_omp.cpp
index 1cea0f454a7199fbe54e6193b4ed75285b7cc1b5..3e8adb33b85df9fda3fcee37f875971713166661 100644
--- a/src/USER-OMP/pair_lj_cubic_omp.cpp
+++ b/src/USER-OMP/pair_lj_cubic_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_lj_cubic_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_lj_cut_coul_cut_omp.cpp b/src/USER-OMP/pair_lj_cut_coul_cut_omp.cpp
index 1f48b4245ec7f53b73807fe5f9ad5481e15674fa..ea560a09bf30382158a22fa5fadb575677ceb407 100644
--- a/src/USER-OMP/pair_lj_cut_coul_cut_omp.cpp
+++ b/src/USER-OMP/pair_lj_cut_coul_cut_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_lj_cut_coul_cut_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_lj_cut_coul_cut_soft_omp.cpp b/src/USER-OMP/pair_lj_cut_coul_cut_soft_omp.cpp
index f6ba7236a03f1700836098f2fd7dd5c19155f903..4ef12bb1bbe198439a2033ff8c5b9b5fdbcd8300 100644
--- a/src/USER-OMP/pair_lj_cut_coul_cut_soft_omp.cpp
+++ b/src/USER-OMP/pair_lj_cut_coul_cut_soft_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_lj_cut_coul_cut_soft_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_lj_cut_coul_debye_omp.cpp b/src/USER-OMP/pair_lj_cut_coul_debye_omp.cpp
index 9fc64cf38cdd6ea40564e09779f2958118d92f68..9163e98eddeae433ca7d360518d4197d51cf5c80 100644
--- a/src/USER-OMP/pair_lj_cut_coul_debye_omp.cpp
+++ b/src/USER-OMP/pair_lj_cut_coul_debye_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_lj_cut_coul_debye_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_lj_cut_coul_dsf_omp.cpp b/src/USER-OMP/pair_lj_cut_coul_dsf_omp.cpp
index d0b6c1b2dc3d108d24de94d2a0ebc9680baed248..9d9c098f8744afa5817f91b2fce97aed0fb213f3 100644
--- a/src/USER-OMP/pair_lj_cut_coul_dsf_omp.cpp
+++ b/src/USER-OMP/pair_lj_cut_coul_dsf_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_lj_cut_coul_dsf_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_lj_cut_coul_long_omp.cpp b/src/USER-OMP/pair_lj_cut_coul_long_omp.cpp
index 6746cf97015500e894a6c0bbf7f5a362a0856452..d2eaae4ca4f640282ad2c6d6ef885db228fdf1f5 100644
--- a/src/USER-OMP/pair_lj_cut_coul_long_omp.cpp
+++ b/src/USER-OMP/pair_lj_cut_coul_long_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_lj_cut_coul_long_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_lj_cut_coul_long_soft_omp.cpp b/src/USER-OMP/pair_lj_cut_coul_long_soft_omp.cpp
index 5f0a3d57c4cd940d3bd3db8a408942e633a8d4c0..725bfe4724020e70298a9d7fe955f04ae624cd71 100644
--- a/src/USER-OMP/pair_lj_cut_coul_long_soft_omp.cpp
+++ b/src/USER-OMP/pair_lj_cut_coul_long_soft_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_lj_cut_coul_long_soft_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_lj_cut_coul_msm_omp.cpp b/src/USER-OMP/pair_lj_cut_coul_msm_omp.cpp
index fba8f552db565aa9df09c1e9eb176f31111ea5c1..234204af93f362a5d81ecbf888b9cffa587d0aab 100644
--- a/src/USER-OMP/pair_lj_cut_coul_msm_omp.cpp
+++ b/src/USER-OMP/pair_lj_cut_coul_msm_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_lj_cut_coul_msm_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_lj_cut_coul_wolf_omp.cpp b/src/USER-OMP/pair_lj_cut_coul_wolf_omp.cpp
index 51574b2ee7d884f768ddd8635116bd0df842829a..36ef9d54f970741f0ab6638ca6d5d57c5b19528f 100644
--- a/src/USER-OMP/pair_lj_cut_coul_wolf_omp.cpp
+++ b/src/USER-OMP/pair_lj_cut_coul_wolf_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_lj_cut_coul_wolf_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_lj_cut_dipole_cut_omp.cpp b/src/USER-OMP/pair_lj_cut_dipole_cut_omp.cpp
index d9fd7ac72e1473389642ae650a77a480d794e1a9..d4145d98350c1890ca15ff869a880062471eb3ca 100644
--- a/src/USER-OMP/pair_lj_cut_dipole_cut_omp.cpp
+++ b/src/USER-OMP/pair_lj_cut_dipole_cut_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_lj_cut_dipole_cut_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_lj_cut_omp.cpp b/src/USER-OMP/pair_lj_cut_omp.cpp
index 34754975fb53f14de1997ebabfe165c05f86425c..319257b56b7f1800fd32c3624468b8cbaa08cb45 100644
--- a/src/USER-OMP/pair_lj_cut_omp.cpp
+++ b/src/USER-OMP/pair_lj_cut_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_lj_cut_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_lj_cut_soft_omp.cpp b/src/USER-OMP/pair_lj_cut_soft_omp.cpp
index 9147b9aa1c9e811d7fae59dc6bcdd3af1d1950be..7698f19b9512400e06c726be454c62c7df58805f 100644
--- a/src/USER-OMP/pair_lj_cut_soft_omp.cpp
+++ b/src/USER-OMP/pair_lj_cut_soft_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_lj_cut_soft_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_lj_cut_thole_long_omp.cpp b/src/USER-OMP/pair_lj_cut_thole_long_omp.cpp
index 110b8917cf07366b02aa0eeda1b99daeaffbe99a..536d5bcb863d7a0bfe2413caa750c59b9f7129fd 100644
--- a/src/USER-OMP/pair_lj_cut_thole_long_omp.cpp
+++ b/src/USER-OMP/pair_lj_cut_thole_long_omp.cpp
@@ -15,10 +15,10 @@
Contributing author: Paul Crozier (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_lj_cut_thole_long_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_lj_cut_tip4p_cut_omp.cpp b/src/USER-OMP/pair_lj_cut_tip4p_cut_omp.cpp
index 45797b289742084081cc6c874450859c48f3c441..619e970bb0035231a8e7a02dab09dd74ad22d09d 100644
--- a/src/USER-OMP/pair_lj_cut_tip4p_cut_omp.cpp
+++ b/src/USER-OMP/pair_lj_cut_tip4p_cut_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_lj_cut_tip4p_cut_omp.h"
#include "atom.h"
#include "domain.h"
diff --git a/src/USER-OMP/pair_lj_cut_tip4p_long_omp.cpp b/src/USER-OMP/pair_lj_cut_tip4p_long_omp.cpp
index d05b13cd10765b977adfbeff070f42a8e0e8ba63..ca8f450dc6b4f8371ad6e24bf0504890869ae6bf 100644
--- a/src/USER-OMP/pair_lj_cut_tip4p_long_omp.cpp
+++ b/src/USER-OMP/pair_lj_cut_tip4p_long_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_lj_cut_tip4p_long_omp.h"
#include "atom.h"
#include "domain.h"
diff --git a/src/USER-OMP/pair_lj_cut_tip4p_long_soft_omp.cpp b/src/USER-OMP/pair_lj_cut_tip4p_long_soft_omp.cpp
index b31c1c109b632d45e4a572000cc41d97bd0d6007..80b17fba96e6e81e0ba9ba34cb1450c37b478efc 100644
--- a/src/USER-OMP/pair_lj_cut_tip4p_long_soft_omp.cpp
+++ b/src/USER-OMP/pair_lj_cut_tip4p_long_soft_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_lj_cut_tip4p_long_soft_omp.h"
#include "atom.h"
#include "domain.h"
diff --git a/src/USER-OMP/pair_lj_expand_omp.cpp b/src/USER-OMP/pair_lj_expand_omp.cpp
index e0f64e471e46285511b3ac403a64ec02c12a0b36..064ea97809a791ccf77089ee9dba75b63c18d226 100644
--- a/src/USER-OMP/pair_lj_expand_omp.cpp
+++ b/src/USER-OMP/pair_lj_expand_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_lj_expand_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_lj_gromacs_coul_gromacs_omp.cpp b/src/USER-OMP/pair_lj_gromacs_coul_gromacs_omp.cpp
index 954fbe7cce751ce4036b022ae18c9b2c35994077..c87f369d115b499565ba3efd32f05a79627510a9 100644
--- a/src/USER-OMP/pair_lj_gromacs_coul_gromacs_omp.cpp
+++ b/src/USER-OMP/pair_lj_gromacs_coul_gromacs_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_lj_gromacs_coul_gromacs_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_lj_gromacs_omp.cpp b/src/USER-OMP/pair_lj_gromacs_omp.cpp
index 84c46886e10ec43c4dba2e3ed10508dca5c1cdfc..1d7cec5eef768425ed4d44ffb8d45d4e52b84af6 100644
--- a/src/USER-OMP/pair_lj_gromacs_omp.cpp
+++ b/src/USER-OMP/pair_lj_gromacs_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_lj_gromacs_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_lj_long_coul_long_omp.cpp b/src/USER-OMP/pair_lj_long_coul_long_omp.cpp
index 8cc4c95fc24f2cbd8584b816e5f6cc061a8810b8..0afc230e92c54c40f1a7578353ee367a80ef82b2 100644
--- a/src/USER-OMP/pair_lj_long_coul_long_omp.cpp
+++ b/src/USER-OMP/pair_lj_long_coul_long_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_lj_long_coul_long_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_lj_long_tip4p_long_omp.cpp b/src/USER-OMP/pair_lj_long_tip4p_long_omp.cpp
index f4b5071afbfe8eaadad74691d2bc113023223e02..8c0d72c74180a5dc61a32f6da8576196c5ee825e 100644
--- a/src/USER-OMP/pair_lj_long_tip4p_long_omp.cpp
+++ b/src/USER-OMP/pair_lj_long_tip4p_long_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_lj_long_tip4p_long_omp.h"
#include "atom.h"
#include "domain.h"
diff --git a/src/USER-OMP/pair_lj_sdk_coul_long_omp.cpp b/src/USER-OMP/pair_lj_sdk_coul_long_omp.cpp
index f388009bd808d12d6c6243bd6862fa38f1ec2328..c87f26204e8610114d5c6221278ec437b0ced1cd 100644
--- a/src/USER-OMP/pair_lj_sdk_coul_long_omp.cpp
+++ b/src/USER-OMP/pair_lj_sdk_coul_long_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_lj_sdk_coul_long_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_lj_sdk_coul_msm_omp.cpp b/src/USER-OMP/pair_lj_sdk_coul_msm_omp.cpp
index 9d991d5812ea7a1f88d929be5d2ac3b03c9dbf64..8ff0cfe9211f0221c106715ed4d6e264b64c7f50 100644
--- a/src/USER-OMP/pair_lj_sdk_coul_msm_omp.cpp
+++ b/src/USER-OMP/pair_lj_sdk_coul_msm_omp.cpp
@@ -13,7 +13,7 @@
This style is a simplified re-implementation of the CG/CMM pair style
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_lj_sdk_coul_msm_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_lj_sdk_omp.cpp b/src/USER-OMP/pair_lj_sdk_omp.cpp
index 36e170046dbe45512fc843b4ec0ae69b802391a2..e107399316bdc80b0288f96cdcc943c41f00395e 100644
--- a/src/USER-OMP/pair_lj_sdk_omp.cpp
+++ b/src/USER-OMP/pair_lj_sdk_omp.cpp
@@ -13,7 +13,7 @@
This style is a simplified re-implementation of the CG/CMM pair style
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_lj_sdk_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_lj_sf_dipole_sf_omp.cpp b/src/USER-OMP/pair_lj_sf_dipole_sf_omp.cpp
index 29250b09f4682b04ebe07720f9e9d7a19406b61f..250f6ff27214b4412935af0579c532165a504484 100644
--- a/src/USER-OMP/pair_lj_sf_dipole_sf_omp.cpp
+++ b/src/USER-OMP/pair_lj_sf_dipole_sf_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_lj_sf_dipole_sf_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_lj_smooth_linear_omp.cpp b/src/USER-OMP/pair_lj_smooth_linear_omp.cpp
index 9017ac740fb8d6ac6070b6295089898643bf31ca..b06de641f5b58337ec5d3e41f05ff4d61cd241e4 100644
--- a/src/USER-OMP/pair_lj_smooth_linear_omp.cpp
+++ b/src/USER-OMP/pair_lj_smooth_linear_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_lj_smooth_linear_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_lj_smooth_omp.cpp b/src/USER-OMP/pair_lj_smooth_omp.cpp
index 9bf15035bdce3604c09739d3cd0a4c43de434cf9..36935616bfdc5952cc77ef36fbc0958d80705f82 100644
--- a/src/USER-OMP/pair_lj_smooth_omp.cpp
+++ b/src/USER-OMP/pair_lj_smooth_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_lj_smooth_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_lubricate_omp.cpp b/src/USER-OMP/pair_lubricate_omp.cpp
index 1c622f5641035b743b3be6c08f6b7cebf13ea160..a7f9fc65b59589dfad8df2362184b31727b70f3a 100644
--- a/src/USER-OMP/pair_lubricate_omp.cpp
+++ b/src/USER-OMP/pair_lubricate_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_lubricate_omp.h"
#include "atom.h"
#include "comm.h"
@@ -32,10 +32,6 @@
using namespace LAMMPS_NS;
using namespace MathConst;
-// same as fix_deform.cpp
-
-enum{NO_REMAP,X_REMAP,V_REMAP};
-
// same as fix_wall.cpp
enum{EDGE,CONSTANT,VARIABLE};
diff --git a/src/USER-OMP/pair_lubricate_poly_omp.cpp b/src/USER-OMP/pair_lubricate_poly_omp.cpp
index 2e7140e32bc96eee7d92c579865eab434bb1c094..3f0ef1dba6ca6b51d651691031a5a4137577ebf7 100644
--- a/src/USER-OMP/pair_lubricate_poly_omp.cpp
+++ b/src/USER-OMP/pair_lubricate_poly_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_lubricate_poly_omp.h"
#include "atom.h"
#include "comm.h"
@@ -32,11 +32,6 @@
using namespace LAMMPS_NS;
using namespace MathConst;
-// same as fix_deform.cpp
-
-enum{NO_REMAP,X_REMAP,V_REMAP};
-
-
// same as fix_wall.cpp
enum{EDGE,CONSTANT,VARIABLE};
diff --git a/src/USER-OMP/pair_meam_spline_omp.cpp b/src/USER-OMP/pair_meam_spline_omp.cpp
index 4333d3b2a94ef8bc30d2aa2abef069041c07f584..dfc3b978a29f0a06665cfe4bbbbd35ef64dc03be 100644
--- a/src/USER-OMP/pair_meam_spline_omp.cpp
+++ b/src/USER-OMP/pair_meam_spline_omp.cpp
@@ -12,8 +12,8 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <string.h>
+#include <cmath>
+#include <cstring>
#include "pair_meam_spline_omp.h"
#include "atom.h"
diff --git a/src/USER-OMP/pair_morse_omp.cpp b/src/USER-OMP/pair_morse_omp.cpp
index 8aca4ef98f6c1ba0f939e54e198ad66134523fa3..922b67b46344335df4daad06d332ab973da72fb2 100644
--- a/src/USER-OMP/pair_morse_omp.cpp
+++ b/src/USER-OMP/pair_morse_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_morse_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_morse_smooth_linear_omp.cpp b/src/USER-OMP/pair_morse_smooth_linear_omp.cpp
index 113f6f2a02d57d081a31c43dbd800c7c330394a4..61cef69c377f3b706d59537c61d123a2640a2c43 100644
--- a/src/USER-OMP/pair_morse_smooth_linear_omp.cpp
+++ b/src/USER-OMP/pair_morse_smooth_linear_omp.cpp
@@ -13,7 +13,7 @@
Most code borrowed from pair_morse_omp.cpp
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_morse_smooth_linear_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_nb3b_harmonic_omp.cpp b/src/USER-OMP/pair_nb3b_harmonic_omp.cpp
index 199cbc93371b464c80626eef1b3b9d1438ff9ffa..2ab96c43a0c8d2e6c056365ea771f5a6392d7e30 100644
--- a/src/USER-OMP/pair_nb3b_harmonic_omp.cpp
+++ b/src/USER-OMP/pair_nb3b_harmonic_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_nb3b_harmonic_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_nm_cut_coul_cut_omp.cpp b/src/USER-OMP/pair_nm_cut_coul_cut_omp.cpp
index 38af84d1f73775b6de427ee960f7d7097c653632..fcbf5dbabbab67f3a8c8117f31e36928d9c911ca 100644
--- a/src/USER-OMP/pair_nm_cut_coul_cut_omp.cpp
+++ b/src/USER-OMP/pair_nm_cut_coul_cut_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_nm_cut_coul_cut_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_nm_cut_coul_long_omp.cpp b/src/USER-OMP/pair_nm_cut_coul_long_omp.cpp
index bbcdfb26c3c20c377002ae553a1eae47ec8d43c3..b31387dbfe0104fca9e582c6f169be4dab3c0b71 100644
--- a/src/USER-OMP/pair_nm_cut_coul_long_omp.cpp
+++ b/src/USER-OMP/pair_nm_cut_coul_long_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_nm_cut_coul_long_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_nm_cut_omp.cpp b/src/USER-OMP/pair_nm_cut_omp.cpp
index ea2d0fa7f5c7a368f3c117d1dfe91037e77b0ade..79cd0463114d5291bdcaa4c961f704c7ffe24428 100644
--- a/src/USER-OMP/pair_nm_cut_omp.cpp
+++ b/src/USER-OMP/pair_nm_cut_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_nm_cut_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_peri_lps_omp.cpp b/src/USER-OMP/pair_peri_lps_omp.cpp
index a471b47750ee7416ee494bee23fefba69554db20..7b174face743fedae1e6e6ef0949e39e4d1d60ee 100644
--- a/src/USER-OMP/pair_peri_lps_omp.cpp
+++ b/src/USER-OMP/pair_peri_lps_omp.cpp
@@ -12,8 +12,8 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <float.h>
+#include <cmath>
+#include <cfloat>
#include "pair_peri_lps_omp.h"
#include "fix.h"
#include "fix_peri_neigh.h"
diff --git a/src/USER-OMP/pair_peri_pmb_omp.cpp b/src/USER-OMP/pair_peri_pmb_omp.cpp
index 1c14ff753cf8e57820f04642bb0659b9798a960b..8199d8aa47a0d474aa558402b7e462f3c994ec9a 100644
--- a/src/USER-OMP/pair_peri_pmb_omp.cpp
+++ b/src/USER-OMP/pair_peri_pmb_omp.cpp
@@ -12,8 +12,8 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <float.h>
+#include <cmath>
+#include <cfloat>
#include "pair_peri_pmb_omp.h"
#include "fix.h"
#include "fix_peri_neigh.h"
diff --git a/src/USER-OMP/pair_resquared_omp.cpp b/src/USER-OMP/pair_resquared_omp.cpp
index a1364133d005b1ac51368a0ee4726c12e6c39e58..1736e794f55b7621f29d852e867307581238a38b 100644
--- a/src/USER-OMP/pair_resquared_omp.cpp
+++ b/src/USER-OMP/pair_resquared_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_resquared_omp.h"
#include "math_extra.h"
#include "atom.h"
diff --git a/src/USER-OMP/pair_soft_omp.cpp b/src/USER-OMP/pair_soft_omp.cpp
index 9a926652a853d12a0e2fef51ddfb03c19b889359..a860ad97d96af326aa602bf8dd7c06ee4eea9132 100644
--- a/src/USER-OMP/pair_soft_omp.cpp
+++ b/src/USER-OMP/pair_soft_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_soft_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_sw_omp.cpp b/src/USER-OMP/pair_sw_omp.cpp
index 9a63b4f4394846b09988a22ab2f55e00cb05d049..e323fc4c373a4882f586297d19b56b9e92e63f11 100644
--- a/src/USER-OMP/pair_sw_omp.cpp
+++ b/src/USER-OMP/pair_sw_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_sw_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_table_omp.cpp b/src/USER-OMP/pair_table_omp.cpp
index d584061648a2188530003bac065c27a06886c8b9..d27456e1b58f834193924cb70adb64dc5db66d4d 100644
--- a/src/USER-OMP/pair_table_omp.cpp
+++ b/src/USER-OMP/pair_table_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_table_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_tersoff_mod_c_omp.cpp b/src/USER-OMP/pair_tersoff_mod_c_omp.cpp
index 340eb3ebc5aa1f098cf87c84a87e72ac2f99ce79..fad077ca125a69617372f1b53eac0e2c013adf7e 100644
--- a/src/USER-OMP/pair_tersoff_mod_c_omp.cpp
+++ b/src/USER-OMP/pair_tersoff_mod_c_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_tersoff_mod_c_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_tersoff_mod_omp.cpp b/src/USER-OMP/pair_tersoff_mod_omp.cpp
index 403a61147beab5136ca5ff773061cb5948aeefcf..04e54c6e698707431c1ed80ae4d8d795a0158fd2 100644
--- a/src/USER-OMP/pair_tersoff_mod_omp.cpp
+++ b/src/USER-OMP/pair_tersoff_mod_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_tersoff_mod_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_tersoff_omp.cpp b/src/USER-OMP/pair_tersoff_omp.cpp
index db249b4ba907cd3afb78333141b2137a084504ff..a5afdc7509ab4944ad4b3a7e7a46ef70716f2cc0 100644
--- a/src/USER-OMP/pair_tersoff_omp.cpp
+++ b/src/USER-OMP/pair_tersoff_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_tersoff_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_tersoff_table_omp.cpp b/src/USER-OMP/pair_tersoff_table_omp.cpp
index 9de9ee57086c03d411c83c5be8ec684b6c6f1375..de045f9c622c63de9db428170a476f6543816529 100644
--- a/src/USER-OMP/pair_tersoff_table_omp.cpp
+++ b/src/USER-OMP/pair_tersoff_table_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_tersoff_table_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_tersoff_zbl_omp.cpp b/src/USER-OMP/pair_tersoff_zbl_omp.cpp
index f53778d1a13fe7d46b1fcfd7659cdc0e52fc1e83..ce3e6fea75320dcae3e5884df13a1b23efd8661f 100644
--- a/src/USER-OMP/pair_tersoff_zbl_omp.cpp
+++ b/src/USER-OMP/pair_tersoff_zbl_omp.cpp
@@ -16,10 +16,10 @@
David Farrell (NWU) - ZBL addition
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_tersoff_zbl_omp.h"
#include "atom.h"
#include "update.h"
diff --git a/src/USER-OMP/pair_tip4p_cut_omp.cpp b/src/USER-OMP/pair_tip4p_cut_omp.cpp
index c3662ad642a1f1883012e5189d32b09931eef662..85589cf043c231c24f0b4a69092f69d994fc8128 100644
--- a/src/USER-OMP/pair_tip4p_cut_omp.cpp
+++ b/src/USER-OMP/pair_tip4p_cut_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_tip4p_cut_omp.h"
#include "atom.h"
#include "domain.h"
diff --git a/src/USER-OMP/pair_tip4p_long_omp.cpp b/src/USER-OMP/pair_tip4p_long_omp.cpp
index bcd8659a54ce50e2b65a6406954e665fbe5c4801..c6c4bfe5fc953294db71ed8ea5d476e1d3855e0a 100644
--- a/src/USER-OMP/pair_tip4p_long_omp.cpp
+++ b/src/USER-OMP/pair_tip4p_long_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_tip4p_long_omp.h"
#include "atom.h"
#include "domain.h"
diff --git a/src/USER-OMP/pair_tip4p_long_soft_omp.cpp b/src/USER-OMP/pair_tip4p_long_soft_omp.cpp
index 2f16a28b8c00ad5cedd94f84fe859da7c1cd27e8..7e9d3b6dff84c37f556f4ee6980a009bc6f3dc1b 100644
--- a/src/USER-OMP/pair_tip4p_long_soft_omp.cpp
+++ b/src/USER-OMP/pair_tip4p_long_soft_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_tip4p_long_soft_omp.h"
#include "atom.h"
#include "domain.h"
diff --git a/src/USER-OMP/pair_ufm_omp.cpp b/src/USER-OMP/pair_ufm_omp.cpp
index b2e2cd29ee9026a9647bc825ef9dd63a1825dc79..ff258b5b3b8af8404f693c02ce452e2d5917d653 100644
--- a/src/USER-OMP/pair_ufm_omp.cpp
+++ b/src/USER-OMP/pair_ufm_omp.cpp
@@ -14,7 +14,7 @@
Maurice de Koning (Unicamp/Brazil) - dekoning@ifi.unicamp.br
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_ufm_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_vashishta_omp.cpp b/src/USER-OMP/pair_vashishta_omp.cpp
index c432738f6239e5079e2298b3055efdf5be0be217..194a3e2d86acb67b99ed0cdab2e644d3b936637b 100644
--- a/src/USER-OMP/pair_vashishta_omp.cpp
+++ b/src/USER-OMP/pair_vashishta_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_vashishta_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_vashishta_table_omp.cpp b/src/USER-OMP/pair_vashishta_table_omp.cpp
index d2298dca09d1a6bcec326c7eb4638ecd8a2038c2..e0d96d8bb6573a1bf00652996ed62e8fd07c0d3b 100644
--- a/src/USER-OMP/pair_vashishta_table_omp.cpp
+++ b/src/USER-OMP/pair_vashishta_table_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_vashishta_table_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_yukawa_colloid_omp.cpp b/src/USER-OMP/pair_yukawa_colloid_omp.cpp
index cc05fc91559893e02418f4e902317ebba82117c5..c1d2133a1ca585fc42650f17ae1005ec8a47570b 100644
--- a/src/USER-OMP/pair_yukawa_colloid_omp.cpp
+++ b/src/USER-OMP/pair_yukawa_colloid_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_yukawa_colloid_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_yukawa_omp.cpp b/src/USER-OMP/pair_yukawa_omp.cpp
index c705446f052710f3468139c9c7dba5fac709e10a..cbfd627f9789bdbfaba49b7c2226ec189b292735 100644
--- a/src/USER-OMP/pair_yukawa_omp.cpp
+++ b/src/USER-OMP/pair_yukawa_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_yukawa_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pair_zbl_omp.cpp b/src/USER-OMP/pair_zbl_omp.cpp
index 1d69487eb2d65639993ea0005764e6cc0e3393cd..788679434bd60b28e0dea8e1f5368e2b1936e31d 100644
--- a/src/USER-OMP/pair_zbl_omp.cpp
+++ b/src/USER-OMP/pair_zbl_omp.cpp
@@ -12,7 +12,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_zbl_omp.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-OMP/pppm_cg_omp.cpp b/src/USER-OMP/pppm_cg_omp.cpp
index eb230a3bb479c8314b80b11fab6284ff415f6809..990c50932ea9a5ae86824a35142d0870de233f65 100644
--- a/src/USER-OMP/pppm_cg_omp.cpp
+++ b/src/USER-OMP/pppm_cg_omp.cpp
@@ -15,6 +15,8 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
+#include <cstring>
+#include <cmath>
#include "pppm_cg_omp.h"
#include "atom.h"
#include "comm.h"
@@ -27,9 +29,6 @@
#include "math_const.h"
#include "math_special.h"
-#include <string.h>
-#include <math.h>
-
#include "suffix.h"
using namespace LAMMPS_NS;
using namespace MathConst;
diff --git a/src/USER-OMP/pppm_disp_omp.cpp b/src/USER-OMP/pppm_disp_omp.cpp
index 74881c9a8ad75ff7f084e07f291125a31c797ade..97bb909a2c546263d248ba9e62cd4637921b7f7e 100644
--- a/src/USER-OMP/pppm_disp_omp.cpp
+++ b/src/USER-OMP/pppm_disp_omp.cpp
@@ -16,6 +16,8 @@
Rolf Isele-Holder (RWTH Aachen University)
------------------------------------------------------------------------- */
+#include <cstring>
+#include <cmath>
#include "pppm_disp_omp.h"
#include "atom.h"
#include "comm.h"
@@ -24,9 +26,6 @@
#include "memory.h"
#include "math_const.h"
-#include <string.h>
-#include <math.h>
-
#include "suffix.h"
using namespace LAMMPS_NS;
using namespace MathConst;
@@ -358,7 +357,7 @@ void PPPMDispOMP::particle_map(double dxinv, double dyinv,
const int nyhi_out = nyhi_o;
const int nzhi_out = nzhi_o;
- if (!ISFINITE(boxlo[0]) || !ISFINITE(boxlo[1]) || !ISFINITE(boxlo[2]))
+ if (!std::isfinite(boxlo[0]) || !std::isfinite(boxlo[1]) || !std::isfinite(boxlo[2]))
error->one(FLERR,"Non-numeric box dimensions. Simulation unstable.");
int i, flag = 0;
diff --git a/src/USER-OMP/pppm_disp_tip4p_omp.cpp b/src/USER-OMP/pppm_disp_tip4p_omp.cpp
index 49e3681f6ee63357ca1bab5cebf1a86cd988e3e7..2f7fbbea550f3dcf373a8878d2d2b0ab8eb74820 100644
--- a/src/USER-OMP/pppm_disp_tip4p_omp.cpp
+++ b/src/USER-OMP/pppm_disp_tip4p_omp.cpp
@@ -15,6 +15,8 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
+#include <cstring>
+#include <cmath>
#include "pppm_disp_tip4p_omp.h"
#include "atom.h"
#include "comm.h"
@@ -26,9 +28,6 @@
#include "math_const.h"
#include "math_special.h"
-#include <string.h>
-#include <math.h>
-
#include "suffix.h"
using namespace LAMMPS_NS;
using namespace MathConst;
@@ -355,7 +354,7 @@ void PPPMDispTIP4POMP::particle_map_c(double dxinv, double dyinv,
const int nyhi_out = nyhi_o;
const int nzhi_out = nzhi_o;
- if (!ISFINITE(boxlo[0]) || !ISFINITE(boxlo[1]) || !ISFINITE(boxlo[2]))
+ if (!std::isfinite(boxlo[0]) || !std::isfinite(boxlo[1]) || !std::isfinite(boxlo[2]))
error->one(FLERR,"Non-numeric box dimensions - simulation unstable");
int i, flag = 0;
diff --git a/src/USER-OMP/pppm_omp.cpp b/src/USER-OMP/pppm_omp.cpp
index ef03ef1bba65473739af3404a922a22425655dda..e9c24a000c7727247807ca36a995de47146afb3d 100644
--- a/src/USER-OMP/pppm_omp.cpp
+++ b/src/USER-OMP/pppm_omp.cpp
@@ -15,6 +15,8 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
+#include <cstring>
+#include <cmath>
#include "pppm_omp.h"
#include "atom.h"
#include "comm.h"
@@ -26,9 +28,6 @@
#include "math_const.h"
#include "math_special.h"
-#include <string.h>
-#include <math.h>
-
#include "suffix.h"
using namespace LAMMPS_NS;
using namespace MathConst;
diff --git a/src/USER-OMP/pppm_tip4p_omp.cpp b/src/USER-OMP/pppm_tip4p_omp.cpp
index f9733ed95b9827430b459e9fc6742bf54a26477a..29966216da633de31c2d92537f778553647bf785 100644
--- a/src/USER-OMP/pppm_tip4p_omp.cpp
+++ b/src/USER-OMP/pppm_tip4p_omp.cpp
@@ -15,6 +15,8 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
+#include <cstring>
+#include <cmath>
#include "pppm_tip4p_omp.h"
#include "atom.h"
#include "comm.h"
@@ -26,9 +28,6 @@
#include "math_const.h"
#include "math_special.h"
-#include <string.h>
-#include <math.h>
-
#include "suffix.h"
using namespace LAMMPS_NS;
using namespace MathConst;
@@ -348,7 +347,7 @@ void PPPMTIP4POMP::particle_map()
const double boxloz = boxlo[2];
const int nlocal = atom->nlocal;
- if (!ISFINITE(boxlo[0]) || !ISFINITE(boxlo[1]) || !ISFINITE(boxlo[2]))
+ if (!std::isfinite(boxlo[0]) || !std::isfinite(boxlo[1]) || !std::isfinite(boxlo[2]))
error->one(FLERR,"Non-numeric box dimensions - simulation unstable");
int i, flag = 0;
diff --git a/src/USER-OMP/respa_omp.cpp b/src/USER-OMP/respa_omp.cpp
index d4fa529b1c22efbc1d64a69577c86e66a1dbd143..9c8555c66d6d12dfe2c0ca448d3b90a19bc5b332 100644
--- a/src/USER-OMP/respa_omp.cpp
+++ b/src/USER-OMP/respa_omp.cpp
@@ -15,8 +15,8 @@
Contributing authors: Mark Stevens (SNL), Paul Crozier (SNL)
------------------------------------------------------------------------- */
-#include <stdlib.h>
-#include <string.h>
+#include <cstdlib>
+#include <cstring>
#include "respa_omp.h"
#include "neighbor.h"
#include "domain.h"
diff --git a/src/USER-OMP/thr_data.cpp b/src/USER-OMP/thr_data.cpp
index 9d0b657b302452a290fba1d3437b705823c651c9..612c36053cd9a12b66155fe1d9951106dd6b1f2a 100644
--- a/src/USER-OMP/thr_data.cpp
+++ b/src/USER-OMP/thr_data.cpp
@@ -16,10 +16,10 @@
per-thread data management for LAMMPS
------------------------------------------------------------------------- */
-#include "thr_data.h"
+#include <cstring>
+#include <cstdio>
-#include <string.h>
-#include <stdio.h>
+#include "thr_data.h"
#include "memory.h"
#include "timer.h"
diff --git a/src/USER-OMP/thr_omp.cpp b/src/USER-OMP/thr_omp.cpp
index 4eaf09fb9a9568209778131e1ea22ca96502b0cb..22f751e6c0f99fb839632e25e8b72f08d60aacfb 100644
--- a/src/USER-OMP/thr_omp.cpp
+++ b/src/USER-OMP/thr_omp.cpp
@@ -16,6 +16,8 @@
OpenMP based threading support for LAMMPS
------------------------------------------------------------------------- */
+#include <cstring>
+
#include "atom.h"
#include "comm.h"
#include "error.h"
@@ -37,8 +39,6 @@
#include "math_const.h"
-#include <string.h>
-
using namespace LAMMPS_NS;
using namespace MathConst;
diff --git a/src/USER-PHONON/Install.sh b/src/USER-PHONON/Install.sh
old mode 100644
new mode 100755
index cfa369bb055ee2679b873535221244839cce9094..3428415443f5bc59c8486dd1e6327a50265c34e4
--- a/src/USER-PHONON/Install.sh
+++ b/src/USER-PHONON/Install.sh
@@ -26,6 +26,16 @@ action () {
fi
}
+# USER-PHONON uses the parallel FFT wrapper used in PPPM,
+# so we must require the KSPACE package to be installed.
+
+if (test $1 = 1) then
+ if (test ! -e ../fft3d_wrap.h) then
+ echo "Must install KSPACE package with USER-PHONON"
+ exit 1
+ fi
+fi
+
# list of files with optional dependcies
action fix_phonon.cpp fft3d_wrap.h
diff --git a/src/USER-PHONON/fix_phonon.cpp b/src/USER-PHONON/fix_phonon.cpp
index a0fa614eca8eba0dec0d404c2c5dbb75ec65d965..3a37c67a3871f1e044ba568e256c8c57a56620c8 100644
--- a/src/USER-PHONON/fix_phonon.cpp
+++ b/src/USER-PHONON/fix_phonon.cpp
@@ -23,9 +23,9 @@
konglt@sjtu.edu.cn; konglt@gmail.com
------------------------------------------------------------------------- */
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "fix_phonon.h"
#include "fft3d_wrap.h"
#include "atom.h"
@@ -668,7 +668,8 @@ void FixPhonon::postprocess( )
}
// to get Phi = KT.G^-1; normalization of FFTW data is done here
- double boltz = force->boltz, kbtsqrt[sysdim], TempAve = 0.;
+ double boltz = force->boltz, TempAve = 0.;
+ double *kbtsqrt = new double[sysdim];
double TempFac = inv_neval * inv_nTemp;
double NormFac = TempFac * double(ntotal);
@@ -692,7 +693,7 @@ void FixPhonon::postprocess( )
MPI_Gatherv(Phi_q[0],mynq*fft_dim2*2,MPI_DOUBLE,Phi_all[0],recvcnts,displs,MPI_DOUBLE,0,world);
// to collect all basis info and averaged it on root
- double basis_root[fft_dim];
+ double *basis_root = new double[fft_dim];
if (fft_dim > sysdim) MPI_Reduce(&basis[1][0], &basis_root[sysdim], fft_dim-sysdim, MPI_DOUBLE, MPI_SUM, 0, world);
if (me == 0){ // output dynamic matrix by root
@@ -772,7 +773,8 @@ void FixPhonon::postprocess( )
}
fflush(flog);
}
-
+ delete[] kbtsqrt;
+ delete[] basis_root;
} // end of postprocess
/* ----------------------------------------------------------------------
diff --git a/src/USER-QMMM/fix_qmmm.cpp b/src/USER-QMMM/fix_qmmm.cpp
index 7fae85f7df4aecfc2b1ed2197388ff14a0f8c82d..f1a34d95380b751e437d052ca13dc25e099856f9 100644
--- a/src/USER-QMMM/fix_qmmm.cpp
+++ b/src/USER-QMMM/fix_qmmm.cpp
@@ -15,6 +15,8 @@
Contributing author: Axel Kohlmeyer (ICTP)
------------------------------------------------------------------------- */
+#include <cstdlib>
+#include <cstring>
#include "fix_qmmm.h"
#include "atom.h"
#include "domain.h"
@@ -25,9 +27,6 @@
#include "group.h"
#include "memory.h"
-#include <stdlib.h>
-#include <string.h>
-
#include "libqmmm.h"
// message tags for QM/MM inter communicator communication
diff --git a/src/USER-QTB/fix_qbmsst.cpp b/src/USER-QTB/fix_qbmsst.cpp
index 21ae464e10ede952c5eaf7d0f32ef0adb08b415a..fa5ee75bcb8852fb6ea3e24f229d0ffdd1bb8812 100644
--- a/src/USER-QTB/fix_qbmsst.cpp
+++ b/src/USER-QTB/fix_qbmsst.cpp
@@ -17,9 +17,9 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <math.h>
-#include <string.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstring>
+#include <cstdlib>
#include "fix_qbmsst.h"
#include "math_extra.h"
#include "atom.h"
diff --git a/src/USER-QTB/fix_qtb.cpp b/src/USER-QTB/fix_qtb.cpp
index 98dd498088ef93d49d7d5a6142ecda88013ed018..7f9a6510bed1d6223d5afa71863f14fb24c91664 100644
--- a/src/USER-QTB/fix_qtb.cpp
+++ b/src/USER-QTB/fix_qtb.cpp
@@ -17,9 +17,9 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <math.h>
-#include <string.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstring>
+#include <cstdlib>
#include "fix_qtb.h"
#include "math_extra.h"
#include "atom.h"
diff --git a/src/USER-QUIP/Install.sh b/src/USER-QUIP/Install.sh
old mode 100644
new mode 100755
diff --git a/src/USER-QUIP/pair_quip.cpp b/src/USER-QUIP/pair_quip.cpp
index 6bbbcdb8e62375dac19f5d4b6489ac21e11bccd9..3bf12d19d2ab3217e44bea084f53523706328425 100644
--- a/src/USER-QUIP/pair_quip.cpp
+++ b/src/USER-QUIP/pair_quip.cpp
@@ -17,10 +17,10 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_quip.h"
#include "atom.h"
#include "update.h"
@@ -303,7 +303,7 @@ void PairQUIP::init_style()
if (force->newton_pair != 1)
error->all(FLERR,"Pair style quip requires newton pair on");
- // Initialise neighbour list
+ // Initialise neighbor list
int irequest_full = neighbor->request(this);
neighbor->requests[irequest_full]->id = 1;
neighbor->requests[irequest_full]->half = 0;
diff --git a/src/USER-REAXC/compute_spec_atom.cpp b/src/USER-REAXC/compute_spec_atom.cpp
index e913225492a08bcf545f4ed43ba9861a33478022..77b82b3e5514cf75a7e15f3a26f9a01ba2b63a85 100644
--- a/src/USER-REAXC/compute_spec_atom.cpp
+++ b/src/USER-REAXC/compute_spec_atom.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <string.h>
+#include <cmath>
+#include <cstring>
#include "compute_spec_atom.h"
#include "math_extra.h"
#include "atom.h"
diff --git a/src/USER-REAXC/fix_qeq_reax.cpp b/src/USER-REAXC/fix_qeq_reax.cpp
index 326af7505abaf10ccde5f82be949ff7a93e5aff6..a2f4d3d0e936c70674d1340e2c883cbb3a0c79be 100644
--- a/src/USER-REAXC/fix_qeq_reax.cpp
+++ b/src/USER-REAXC/fix_qeq_reax.cpp
@@ -18,10 +18,10 @@
Hybrid and sub-group capabilities: Ray Shan (Sandia)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "fix_qeq_reax.h"
#include "pair_reaxc.h"
#include "atom.h"
diff --git a/src/USER-REAXC/fix_reaxc_bonds.cpp b/src/USER-REAXC/fix_reaxc_bonds.cpp
index 09ca132635e83fde5bd95608a37db3fa71838d86..b38d137412b16d18130ed32dcaf82cd0ead7ab94 100644
--- a/src/USER-REAXC/fix_reaxc_bonds.cpp
+++ b/src/USER-REAXC/fix_reaxc_bonds.cpp
@@ -15,8 +15,8 @@
Contributing author: Ray Shan (Sandia, tnshan@sandia.gov)
------------------------------------------------------------------------- */
-#include <stdlib.h>
-#include <string.h>
+#include <cstdlib>
+#include <cstring>
#include "fix_ave_atom.h"
#include "fix_reaxc_bonds.h"
#include "atom.h"
diff --git a/src/USER-REAXC/fix_reaxc_bonds.h b/src/USER-REAXC/fix_reaxc_bonds.h
index e1dcd82c0e43ed96323668a918dfd9259e05939e..d72f5446b5141a7c701f527cc0f67c1e32524a8e 100644
--- a/src/USER-REAXC/fix_reaxc_bonds.h
+++ b/src/USER-REAXC/fix_reaxc_bonds.h
@@ -20,7 +20,7 @@ FixStyle(reax/c/bonds,FixReaxCBonds)
#ifndef LMP_FIX_REAXC_BONDS_H
#define LMP_FIX_REAXC_BONDS_H
-#include <stdio.h>
+#include <cstdio>
#include "fix.h"
#include "pointers.h"
diff --git a/src/USER-REAXC/fix_reaxc_species.cpp b/src/USER-REAXC/fix_reaxc_species.cpp
index 181c9bcd31763b1366c311d71d962c0c6367ed22..61b4cebf966592ff2a8a73ce708647d639ac8951 100644
--- a/src/USER-REAXC/fix_reaxc_species.cpp
+++ b/src/USER-REAXC/fix_reaxc_species.cpp
@@ -16,12 +16,12 @@
Oleg Sergeev (VNIIA, sergeev@vniia.ru)
------------------------------------------------------------------------- */
-#include <stdlib.h>
-#include <math.h>
-#include "atom.h"
-#include <string.h>
+#include <cstdlib>
+#include <cmath>
+#include <cstring>
#include "fix_ave_atom.h"
#include "fix_reaxc_species.h"
+#include "atom.h"
#include "domain.h"
#include "update.h"
#include "pair_reaxc.h"
diff --git a/src/USER-REAXC/reaxc_types.h b/src/USER-REAXC/reaxc_types.h
index fb1a9a853a7cc908347813a9d34336a82984a775..2666fcf85c80290f72fdca63921479448f488549 100644
--- a/src/USER-REAXC/reaxc_types.h
+++ b/src/USER-REAXC/reaxc_types.h
@@ -27,20 +27,20 @@
#ifndef __REAX_TYPES_H_
#define __REAX_TYPES_H_
+#include <mpi.h>
#include "lmptype.h"
-#include <ctype.h>
-#include <math.h>
-#include <mpi.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-#include "sys/time.h"
-#include <time.h>
+#include <cctype>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
+#include <ctime>
+#include <sys/time.h>
#include "accelerator_kokkos.h"
#if defined LMP_USER_OMP
-#define OMP_TIMING 1
+#define OMP_TIMING 0
#ifdef OMP_TIMING
// pkcoff timing fields
diff --git a/src/USER-SMD/Install.sh b/src/USER-SMD/Install.sh
old mode 100644
new mode 100755
diff --git a/src/USER-SMD/atom_vec_smd.cpp b/src/USER-SMD/atom_vec_smd.cpp
index ca38ca7ab5d1b2c6bde35c9468a7cdbcbabac6cb..e99f3c51694eb609944461f44a495bca88187e1e 100644
--- a/src/USER-SMD/atom_vec_smd.cpp
+++ b/src/USER-SMD/atom_vec_smd.cpp
@@ -22,9 +22,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "atom_vec_smd.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-SMD/compute_smd_contact_radius.cpp b/src/USER-SMD/compute_smd_contact_radius.cpp
index 991b1a2e674316d4b832aafaa60d620e40e8012d..8193ad6ccf4cf1e92c3875ed8276e1ad0cfb010b 100644
--- a/src/USER-SMD/compute_smd_contact_radius.cpp
+++ b/src/USER-SMD/compute_smd_contact_radius.cpp
@@ -23,7 +23,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "compute_smd_contact_radius.h"
#include "atom.h"
#include "update.h"
diff --git a/src/USER-SMD/compute_smd_damage.cpp b/src/USER-SMD/compute_smd_damage.cpp
index 7cb4d2b4b8dac1608091c72789d4456b404641d7..9603fd5c64c299ef1c89a48e66da913913328d2e 100644
--- a/src/USER-SMD/compute_smd_damage.cpp
+++ b/src/USER-SMD/compute_smd_damage.cpp
@@ -23,7 +23,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "compute_smd_damage.h"
#include "atom.h"
#include "update.h"
diff --git a/src/USER-SMD/compute_smd_hourglass_error.cpp b/src/USER-SMD/compute_smd_hourglass_error.cpp
index 1502f7ccb5ab8aa6d73840788d1c0f20c86cde7e..3b6b9000048b84ec3637e3325d27c9f58b34ce11 100644
--- a/src/USER-SMD/compute_smd_hourglass_error.cpp
+++ b/src/USER-SMD/compute_smd_hourglass_error.cpp
@@ -23,7 +23,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "compute_smd_hourglass_error.h"
#include "atom.h"
#include "update.h"
diff --git a/src/USER-SMD/compute_smd_internal_energy.cpp b/src/USER-SMD/compute_smd_internal_energy.cpp
index aabaa8906cb1bf8c7ca5a2be75f9963d98230af2..d937aa98a42a1d3e1079fd54b9bfe36ec5a98ec4 100644
--- a/src/USER-SMD/compute_smd_internal_energy.cpp
+++ b/src/USER-SMD/compute_smd_internal_energy.cpp
@@ -23,7 +23,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "compute_smd_internal_energy.h"
#include "atom.h"
#include "update.h"
diff --git a/src/USER-SMD/compute_smd_plastic_strain.cpp b/src/USER-SMD/compute_smd_plastic_strain.cpp
index 86a5c6329f3a351e51f880473b7443dfb6446416..67466ebb72cd97ea1769d81849fdc56de5457c88 100644
--- a/src/USER-SMD/compute_smd_plastic_strain.cpp
+++ b/src/USER-SMD/compute_smd_plastic_strain.cpp
@@ -23,7 +23,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "compute_smd_plastic_strain.h"
#include "atom.h"
#include "update.h"
diff --git a/src/USER-SMD/compute_smd_plastic_strain_rate.cpp b/src/USER-SMD/compute_smd_plastic_strain_rate.cpp
index 899e456c8883623f2812de8a207dadb60e69d2e9..20dfa64edd2c3762c067c54799a70746d5727354 100644
--- a/src/USER-SMD/compute_smd_plastic_strain_rate.cpp
+++ b/src/USER-SMD/compute_smd_plastic_strain_rate.cpp
@@ -23,7 +23,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "compute_smd_plastic_strain_rate.h"
#include "atom.h"
#include "update.h"
diff --git a/src/USER-SMD/compute_smd_rho.cpp b/src/USER-SMD/compute_smd_rho.cpp
index cb97755aca6c8547c73027696adddca12414ffba..5c78e604b6639428ca6d088a19e661ac28c6d5a1 100644
--- a/src/USER-SMD/compute_smd_rho.cpp
+++ b/src/USER-SMD/compute_smd_rho.cpp
@@ -22,7 +22,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "compute_smd_rho.h"
#include "atom.h"
#include "update.h"
diff --git a/src/USER-SMD/compute_smd_tlsph_defgrad.cpp b/src/USER-SMD/compute_smd_tlsph_defgrad.cpp
index 3ba66a656c6f3224960d0d1d6cfe366c5f1e3343..37ad78dcea2a532af82fc097307328a585e3366d 100644
--- a/src/USER-SMD/compute_smd_tlsph_defgrad.cpp
+++ b/src/USER-SMD/compute_smd_tlsph_defgrad.cpp
@@ -22,7 +22,11 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
+#include <iostream>
+#include <Eigen/Eigen>
#include "compute_smd_tlsph_defgrad.h"
#include "atom.h"
#include "update.h"
@@ -32,11 +36,6 @@
#include "memory.h"
#include "error.h"
#include "pair.h"
-#include <iostream>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-#include <Eigen/Eigen>
using namespace Eigen;
using namespace std;
using namespace LAMMPS_NS;
diff --git a/src/USER-SMD/compute_smd_tlsph_dt.cpp b/src/USER-SMD/compute_smd_tlsph_dt.cpp
index 6d573775fa2cf6d773bea02e44038603d200bcc2..7752436b8a40f67734d5e4596aec3fc0800e5545 100644
--- a/src/USER-SMD/compute_smd_tlsph_dt.cpp
+++ b/src/USER-SMD/compute_smd_tlsph_dt.cpp
@@ -22,7 +22,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "compute_smd_tlsph_dt.h"
#include "atom.h"
#include "update.h"
diff --git a/src/USER-SMD/compute_smd_tlsph_num_neighs.cpp b/src/USER-SMD/compute_smd_tlsph_num_neighs.cpp
index d0df4ff3d7051d74874ef6c2b50901126321ef39..347b1384123b180570ec2e48692f633c3692db19 100644
--- a/src/USER-SMD/compute_smd_tlsph_num_neighs.cpp
+++ b/src/USER-SMD/compute_smd_tlsph_num_neighs.cpp
@@ -23,7 +23,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "compute_smd_tlsph_num_neighs.h"
#include "atom.h"
#include "update.h"
diff --git a/src/USER-SMD/compute_smd_tlsph_shape.cpp b/src/USER-SMD/compute_smd_tlsph_shape.cpp
index d9dc070f6b67c4f061a9cf2c7920ff337ad563a6..bbab274b5cca0dd4d785ea0be2044df1e6c2cef9 100644
--- a/src/USER-SMD/compute_smd_tlsph_shape.cpp
+++ b/src/USER-SMD/compute_smd_tlsph_shape.cpp
@@ -22,7 +22,12 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
+#include <iostream>
+#include <Eigen/Eigen>
+#include <Eigen/Geometry>
#include "compute_smd_tlsph_shape.h"
#include "atom.h"
#include "update.h"
@@ -32,12 +37,7 @@
#include "memory.h"
#include "error.h"
#include "pair.h"
-#include <iostream>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-#include <Eigen/Eigen>
-#include <Eigen/Geometry>
+
using namespace Eigen;
using namespace std;
using namespace LAMMPS_NS;
diff --git a/src/USER-SMD/compute_smd_tlsph_strain.cpp b/src/USER-SMD/compute_smd_tlsph_strain.cpp
index ea137d5b2a718253b8f528891fe8d42fa186b574..a94a3cd51158defab103323d007c7662efafbeac 100644
--- a/src/USER-SMD/compute_smd_tlsph_strain.cpp
+++ b/src/USER-SMD/compute_smd_tlsph_strain.cpp
@@ -23,7 +23,11 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
+#include <iostream>
+#include <Eigen/Eigen>
#include "compute_smd_tlsph_strain.h"
#include "atom.h"
#include "update.h"
@@ -33,11 +37,7 @@
#include "memory.h"
#include "error.h"
#include "pair.h"
-#include <iostream>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-#include <Eigen/Eigen>
+
using namespace Eigen;
using namespace std;
using namespace LAMMPS_NS;
diff --git a/src/USER-SMD/compute_smd_tlsph_strain_rate.cpp b/src/USER-SMD/compute_smd_tlsph_strain_rate.cpp
index ed3525f4ad2c934d9b9191b8de903f525147ea80..895a973f6a1863c4faacbe59aa33d8fd18044211 100644
--- a/src/USER-SMD/compute_smd_tlsph_strain_rate.cpp
+++ b/src/USER-SMD/compute_smd_tlsph_strain_rate.cpp
@@ -23,7 +23,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
+#include <Eigen/Eigen>
#include "compute_smd_tlsph_strain_rate.h"
#include "atom.h"
#include "update.h"
@@ -33,7 +34,7 @@
#include "memory.h"
#include "error.h"
#include "pair.h"
-#include <Eigen/Eigen>
+
using namespace Eigen;
using namespace LAMMPS_NS;
diff --git a/src/USER-SMD/compute_smd_tlsph_stress.cpp b/src/USER-SMD/compute_smd_tlsph_stress.cpp
index cbcb4c45af60454e3d0afecccf7c85246d7ced3f..a54b07dd1ef5b007c9f7d9ede03bd6b8b6583c67 100644
--- a/src/USER-SMD/compute_smd_tlsph_stress.cpp
+++ b/src/USER-SMD/compute_smd_tlsph_stress.cpp
@@ -22,7 +22,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
+#include <Eigen/Eigen>
#include "compute_smd_tlsph_stress.h"
#include "atom.h"
#include "update.h"
@@ -32,7 +33,7 @@
#include "memory.h"
#include "error.h"
#include "pair.h"
-#include <Eigen/Eigen>
+
using namespace Eigen;
using namespace LAMMPS_NS;
diff --git a/src/USER-SMD/compute_smd_triangle_mesh_vertices.cpp b/src/USER-SMD/compute_smd_triangle_mesh_vertices.cpp
index e43dadb47ad99ba7652589710e5c32e9727835fb..67ec27778a692008a870b3af3728b0cfdcebfced 100644
--- a/src/USER-SMD/compute_smd_triangle_mesh_vertices.cpp
+++ b/src/USER-SMD/compute_smd_triangle_mesh_vertices.cpp
@@ -23,7 +23,11 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
+#include <iostream>
+#include <Eigen/Eigen>
#include "compute_smd_triangle_mesh_vertices.h"
#include "atom.h"
#include "update.h"
@@ -33,11 +37,7 @@
#include "memory.h"
#include "error.h"
#include "pair.h"
-#include <iostream>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-#include <Eigen/Eigen>
+
using namespace Eigen;
using namespace std;
using namespace LAMMPS_NS;
diff --git a/src/USER-SMD/compute_smd_ulsph_effm.cpp b/src/USER-SMD/compute_smd_ulsph_effm.cpp
index 9453d8cfa6a5cd474f85843adeef44d53cb19207..fc8637bbf01506114b0602d525fd52a79260458d 100644
--- a/src/USER-SMD/compute_smd_ulsph_effm.cpp
+++ b/src/USER-SMD/compute_smd_ulsph_effm.cpp
@@ -22,7 +22,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "compute_smd_ulsph_effm.h"
#include "atom.h"
#include "update.h"
diff --git a/src/USER-SMD/compute_smd_ulsph_num_neighs.cpp b/src/USER-SMD/compute_smd_ulsph_num_neighs.cpp
index efe6bba47ea16232af896ddd45092e75f682f69e..4ef339db9812d91ac32eb85187612c263eba1300 100644
--- a/src/USER-SMD/compute_smd_ulsph_num_neighs.cpp
+++ b/src/USER-SMD/compute_smd_ulsph_num_neighs.cpp
@@ -23,7 +23,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "compute_smd_ulsph_num_neighs.h"
#include "atom.h"
#include "update.h"
diff --git a/src/USER-SMD/compute_smd_ulsph_strain.cpp b/src/USER-SMD/compute_smd_ulsph_strain.cpp
index c7fcc909f37b71da4a97cc67e7e52d8e20481d11..89b85f7bc1cafc299fc45b55a5c88f5757b3d616 100644
--- a/src/USER-SMD/compute_smd_ulsph_strain.cpp
+++ b/src/USER-SMD/compute_smd_ulsph_strain.cpp
@@ -23,7 +23,11 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
+#include <iostream>
+#include <Eigen/Eigen>
#include "compute_smd_ulsph_strain.h"
#include "atom.h"
#include "update.h"
@@ -33,11 +37,7 @@
#include "memory.h"
#include "error.h"
#include "pair.h"
-#include <iostream>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-#include <Eigen/Eigen>
+
using namespace Eigen;
using namespace std;
using namespace LAMMPS_NS;
diff --git a/src/USER-SMD/compute_smd_ulsph_strain_rate.cpp b/src/USER-SMD/compute_smd_ulsph_strain_rate.cpp
index 0d472a368a0830bedf7861ebe4dfce384ea9719c..f5ff4fef98fc6ec308855be74c635b4d03465c87 100644
--- a/src/USER-SMD/compute_smd_ulsph_strain_rate.cpp
+++ b/src/USER-SMD/compute_smd_ulsph_strain_rate.cpp
@@ -22,7 +22,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
+#include <Eigen/Eigen>
#include "compute_smd_ulsph_strain_rate.h"
#include "atom.h"
#include "update.h"
@@ -32,7 +33,7 @@
#include "memory.h"
#include "error.h"
#include "pair.h"
-#include <Eigen/Eigen>
+
using namespace Eigen;
using namespace LAMMPS_NS;
diff --git a/src/USER-SMD/compute_smd_ulsph_stress.cpp b/src/USER-SMD/compute_smd_ulsph_stress.cpp
index 7069feced3f7e7801ec459b70d0909654c4c6987..7f1bbc4c29fadf300623ae243ae0ed97047ec220 100644
--- a/src/USER-SMD/compute_smd_ulsph_stress.cpp
+++ b/src/USER-SMD/compute_smd_ulsph_stress.cpp
@@ -22,7 +22,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
+#include <Eigen/Eigen>
#include "compute_smd_ulsph_stress.h"
#include "atom.h"
#include "update.h"
@@ -32,7 +33,7 @@
#include "memory.h"
#include "error.h"
#include "pair.h"
-#include <Eigen/Eigen>
+
using namespace Eigen;
using namespace LAMMPS_NS;
diff --git a/src/USER-SMD/compute_smd_vol.cpp b/src/USER-SMD/compute_smd_vol.cpp
index 3573ee6a6cc8d4b09c8dd53a21a0c8b3ecb9dd9d..17a6b556e8ac352eab0703e4d19744d51933905d 100644
--- a/src/USER-SMD/compute_smd_vol.cpp
+++ b/src/USER-SMD/compute_smd_vol.cpp
@@ -22,7 +22,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "compute_smd_vol.h"
#include "atom.h"
#include "update.h"
diff --git a/src/USER-SMD/fix_smd_adjust_dt.cpp b/src/USER-SMD/fix_smd_adjust_dt.cpp
index d2570b6bdc3f1b64a482732b45b1f26945e06f0e..3685248d5e556fa7aa08f09b1f5fa42d252e08e7 100644
--- a/src/USER-SMD/fix_smd_adjust_dt.cpp
+++ b/src/USER-SMD/fix_smd_adjust_dt.cpp
@@ -22,9 +22,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "fix_smd_adjust_dt.h"
#include "atom.h"
#include "update.h"
diff --git a/src/USER-SMD/fix_smd_integrate_tlsph.cpp b/src/USER-SMD/fix_smd_integrate_tlsph.cpp
index 2744211d87d8f3045741fe73dda514cff6d84c1e..4668e673fca68d72dd4c1ece19fecacc8ed94228 100644
--- a/src/USER-SMD/fix_smd_integrate_tlsph.cpp
+++ b/src/USER-SMD/fix_smd_integrate_tlsph.cpp
@@ -22,9 +22,11 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
+#include <iostream>
+#include <Eigen/Eigen>
#include "fix_smd_integrate_tlsph.h"
#include "atom.h"
#include "force.h"
@@ -32,13 +34,10 @@
#include "error.h"
#include "pair.h"
#include "neigh_list.h"
-#include <Eigen/Eigen>
#include "domain.h"
#include "neighbor.h"
#include "comm.h"
#include "modify.h"
-#include <stdio.h>
-#include <iostream>
using namespace Eigen;
using namespace LAMMPS_NS;
diff --git a/src/USER-SMD/fix_smd_integrate_ulsph.cpp b/src/USER-SMD/fix_smd_integrate_ulsph.cpp
index 9b892bf25976f5507663c9171a3616ddfdcf7a64..a145deeb61ce90733aafd5d54c32d1aadaca5dd5 100644
--- a/src/USER-SMD/fix_smd_integrate_ulsph.cpp
+++ b/src/USER-SMD/fix_smd_integrate_ulsph.cpp
@@ -22,12 +22,12 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <stdio.h>
-#include <string.h>
+#include <cstdio>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
+#include <Eigen/Eigen>
#include "fix_smd_integrate_ulsph.h"
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
#include "atom.h"
#include "comm.h"
#include "force.h"
@@ -41,7 +41,6 @@
#include "error.h"
#include "pair.h"
#include "domain.h"
-#include <Eigen/Eigen>
using namespace Eigen;
using namespace LAMMPS_NS;
diff --git a/src/USER-SMD/fix_smd_integrate_ulsph.h b/src/USER-SMD/fix_smd_integrate_ulsph.h
index ea4f46ce530ea0d40606c1c3aa157707f2a91e5a..9d954bf529aaf00ddf1df307d7f3a0b1d012538f 100644
--- a/src/USER-SMD/fix_smd_integrate_ulsph.h
+++ b/src/USER-SMD/fix_smd_integrate_ulsph.h
@@ -48,7 +48,7 @@ class FixSMDIntegrateUlsph : public Fix {
private:
class NeighList *list;
protected:
- double dtv,dtf, vlimit, vlimitsq;;
+ double dtv,dtf, vlimit, vlimitsq;
int mass_require;
bool xsphFlag;
bool adjust_radius_flag;
diff --git a/src/USER-SMD/fix_smd_move_triangulated_surface.cpp b/src/USER-SMD/fix_smd_move_triangulated_surface.cpp
index d8a0bda4d07629f49980c61d6aab84c17cf80cd3..d4afbe0535e4445709914d7ea71a9d1867a1eee5 100644
--- a/src/USER-SMD/fix_smd_move_triangulated_surface.cpp
+++ b/src/USER-SMD/fix_smd_move_triangulated_surface.cpp
@@ -22,12 +22,12 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <stdio.h>
-#include <string.h>
+#include <cstdio>
+#include <cstring>
+#include <cmath>
+#include <cstdlib>
+#include <Eigen/Eigen>
#include "fix_smd_move_triangulated_surface.h"
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
#include "atom.h"
#include "comm.h"
#include "force.h"
@@ -41,7 +41,6 @@
#include "error.h"
#include "pair.h"
#include "domain.h"
-#include <Eigen/Eigen>
#include "math_const.h"
using namespace Eigen;
diff --git a/src/USER-SMD/fix_smd_setvel.cpp b/src/USER-SMD/fix_smd_setvel.cpp
index 0c2dc31f45269af6abdcde5981003724c81c8719..5e7cdbad3807dc15e1a535bb81b6db24d331ced8 100644
--- a/src/USER-SMD/fix_smd_setvel.cpp
+++ b/src/USER-SMD/fix_smd_setvel.cpp
@@ -23,8 +23,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
-#include <stdlib.h>
+#include <cstring>
+#include <cstdlib>
#include "fix_smd_setvel.h"
#include "atom.h"
#include "update.h"
diff --git a/src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp b/src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp
index da0533c88bcbb15e0adc56a6345558823ad91bed..3e2812aa12e29a1f3e6d57ff3867d987676b361c 100644
--- a/src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp
+++ b/src/USER-SMD/fix_smd_tlsph_reference_configuration.cpp
@@ -24,15 +24,16 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "lattice.h"
#include <mpi.h>
-#include <string.h>
-#include <stdio.h>
+#include <cstring>
+#include <cstdio>
+#include <Eigen/Eigen>
#include "fix_smd_tlsph_reference_configuration.h"
#include "atom.h"
#include "comm.h"
#include "neighbor.h"
#include "neigh_list.h"
+#include "lattice.h"
#include "force.h"
#include "pair.h"
#include "update.h"
@@ -40,7 +41,6 @@
#include "memory.h"
#include "error.h"
#include "domain.h"
-#include <Eigen/Eigen>
#include "smd_kernels.h"
#include "smd_math.h"
diff --git a/src/USER-SMD/fix_smd_wall_surface.cpp b/src/USER-SMD/fix_smd_wall_surface.cpp
index 53232af0012af87ad8e813c8fbddaea59dcdb333..97c2ead5fc79d8b913173d09d709a34294888120 100644
--- a/src/USER-SMD/fix_smd_wall_surface.cpp
+++ b/src/USER-SMD/fix_smd_wall_surface.cpp
@@ -15,7 +15,10 @@
Contributing authors: Mike Parks (SNL), Ezwanur Rahman, J.T. Foster (UTSA)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
+#include <cstring>
+#include <cstdio>
+#include <Eigen/Eigen>
#include "fix_smd_wall_surface.h"
#include "atom.h"
#include "domain.h"
@@ -29,10 +32,7 @@
#include "lattice.h"
#include "memory.h"
#include "error.h"
-#include <Eigen/Eigen>
-#include <stdio.h>
#include "atom_vec.h"
-#include <string.h>
using namespace LAMMPS_NS;
using namespace FixConst;
@@ -40,10 +40,6 @@ using namespace Eigen;
using namespace std;
#define DELTA 16384
#define EPSILON 1.0e-6
-enum {
- LAYOUT_UNIFORM, LAYOUT_NONUNIFORM, LAYOUT_TILED
-};
-// several files
/* ---------------------------------------------------------------------- */
@@ -151,7 +147,7 @@ void FixSMDWallSurface::setup(int vflag) {
subhi[2] = domain->subhi_lamda[2];
}
- if (comm->layout != LAYOUT_TILED) {
+ if (comm->layout != Comm::LAYOUT_TILED) {
if (domain->xperiodic) {
if (comm->myloc[0] == 0)
sublo[0] -= epsilon[0];
diff --git a/src/USER-SMD/pair_smd_hertz.cpp b/src/USER-SMD/pair_smd_hertz.cpp
index 9b2638296587fd714cc562f898b25668fcae8379..815db4a4508a297d779a8a4499f21aa073fa17d4 100644
--- a/src/USER-SMD/pair_smd_hertz.cpp
+++ b/src/USER-SMD/pair_smd_hertz.cpp
@@ -26,10 +26,10 @@
Contributing author: Mike Parks (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <float.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cfloat>
+#include <cstdlib>
+#include <cstring>
#include "pair_smd_hertz.h"
#include "atom.h"
#include "domain.h"
diff --git a/src/USER-SMD/pair_smd_tlsph.cpp b/src/USER-SMD/pair_smd_tlsph.cpp
index 1a600b393e933e6abd431bb8740aa3dc31917ca1..4dd16c4d83a4ee212491da430dc37f34fe49b751 100644
--- a/src/USER-SMD/pair_smd_tlsph.cpp
+++ b/src/USER-SMD/pair_smd_tlsph.cpp
@@ -22,15 +22,19 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include "group.h"
-#include <math.h>
-#include <float.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cfloat>
+#include <cstdlib>
+#include <cstring>
+#include <cstdio>
+#include <iostream>
+#include <map>
+#include <Eigen/Eigen>
#include "pair_smd_tlsph.h"
#include "fix_smd_tlsph_reference_configuration.h"
#include "atom.h"
#include "domain.h"
+#include "group.h"
#include "force.h"
#include "update.h"
#include "modify.h"
@@ -41,15 +45,12 @@
#include "neigh_request.h"
#include "memory.h"
#include "error.h"
-#include <stdio.h>
-#include <iostream>
#include "math_special.h"
-#include <map>
#include "update.h"
-#include <Eigen/Eigen>
#include "smd_material_models.h"
#include "smd_kernels.h"
#include "smd_math.h"
+
using namespace SMD_Kernels;
using namespace Eigen;
using namespace std;
diff --git a/src/USER-SMD/pair_smd_triangulated_surface.cpp b/src/USER-SMD/pair_smd_triangulated_surface.cpp
index a62e262b7ac0036fdb33d1095b3ce34957ce228c..b8bff7e799948c73a47ecc71c44da5c15e068dd3 100644
--- a/src/USER-SMD/pair_smd_triangulated_surface.cpp
+++ b/src/USER-SMD/pair_smd_triangulated_surface.cpp
@@ -26,10 +26,13 @@
Contributing author: Mike Parks (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <float.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cfloat>
+#include <cstdlib>
+#include <cstring>
+#include <cstdio>
+#include <iostream>
+#include <Eigen/Eigen>
#include "pair_smd_triangulated_surface.h"
#include "atom.h"
#include "domain.h"
@@ -43,9 +46,6 @@
#include "neigh_request.h"
#include "memory.h"
#include "error.h"
-#include <Eigen/Eigen>
-#include <stdio.h>
-#include <iostream>
using namespace std;
using namespace LAMMPS_NS;
diff --git a/src/USER-SMD/pair_smd_ulsph.cpp b/src/USER-SMD/pair_smd_ulsph.cpp
index fcb5e7eeb0689ae785ca17f7ef2c19523f8699a7..96eb912faec26a2e7b18a888eebd359f68771fa2 100644
--- a/src/USER-SMD/pair_smd_ulsph.cpp
+++ b/src/USER-SMD/pair_smd_ulsph.cpp
@@ -22,10 +22,12 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <float.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cfloat>
+#include <cstdlib>
+#include <cstring>
+#include <cstdio>
+#include <iostream>
#include "pair_smd_ulsph.h"
#include "atom.h"
#include "domain.h"
@@ -39,8 +41,6 @@
#include "neigh_request.h"
#include "memory.h"
#include "error.h"
-#include <stdio.h>
-#include <iostream>
#include "smd_material_models.h"
#include "smd_math.h"
#include "smd_kernels.h"
diff --git a/src/USER-SMD/smd_material_models.cpp b/src/USER-SMD/smd_material_models.cpp
index 93228f3724d816c0ff1ff041bbabc5bef074fe5e..e3deb199b650be86b37fc7998152a57cfa6c22e1 100644
--- a/src/USER-SMD/smd_material_models.cpp
+++ b/src/USER-SMD/smd_material_models.cpp
@@ -22,8 +22,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include <iostream>
+#include <cstdio>
#include "math_special.h"
-#include <stdio.h>
#include <Eigen/Eigen>
diff --git a/src/USER-SMTBQ/pair_smtbq.cpp b/src/USER-SMTBQ/pair_smtbq.cpp
index 937b9e511736e6e4bbadc7f8d66f251383daa2d0..1028d8a8972117568e8670f101296a1db25703db 100644
--- a/src/USER-SMTBQ/pair_smtbq.cpp
+++ b/src/USER-SMTBQ/pair_smtbq.cpp
@@ -38,10 +38,10 @@
<http://www.gnu.org/licenses/>.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_smtbq.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-SPH/atom_vec_meso.cpp b/src/USER-SPH/atom_vec_meso.cpp
index daa7c10740d66c608e4d331f9fb11bd421eebc51..7dc6c6f7bd9382fa85496d96a448979751743d4e 100644
--- a/src/USER-SPH/atom_vec_meso.cpp
+++ b/src/USER-SPH/atom_vec_meso.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
-#include <stdlib.h>
+#include <cstring>
+#include <cstdlib>
#include "atom_vec_meso.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/USER-SPH/compute_meso_e_atom.cpp b/src/USER-SPH/compute_meso_e_atom.cpp
index dc8d0b55ad32f32d27f1bb14da002cfe57b359ec..e39dee2b5fb83e883e1bb8e4e8ff02892399d29a 100644
--- a/src/USER-SPH/compute_meso_e_atom.cpp
+++ b/src/USER-SPH/compute_meso_e_atom.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "compute_meso_e_atom.h"
#include "atom.h"
#include "update.h"
diff --git a/src/USER-SPH/compute_meso_rho_atom.cpp b/src/USER-SPH/compute_meso_rho_atom.cpp
index 9b4da8b339f55b53b07bcc0b4de11fa1b1098287..eeb3f987bc7d82aad15a09a11b7cb3532e0ce8c3 100644
--- a/src/USER-SPH/compute_meso_rho_atom.cpp
+++ b/src/USER-SPH/compute_meso_rho_atom.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "compute_meso_rho_atom.h"
#include "atom.h"
#include "update.h"
diff --git a/src/USER-SPH/compute_meso_t_atom.cpp b/src/USER-SPH/compute_meso_t_atom.cpp
index d901f73eff5feaba1490d349e6c3757e26113b69..dc4f3407f143ff7c75acdcee7ea7290aacf41503 100644
--- a/src/USER-SPH/compute_meso_t_atom.cpp
+++ b/src/USER-SPH/compute_meso_t_atom.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "compute_meso_t_atom.h"
#include "atom.h"
#include "update.h"
diff --git a/src/USER-SPH/fix_meso.cpp b/src/USER-SPH/fix_meso.cpp
index 665c9e0f3f866413924e617ee6b45f988daf5b9f..d7a5d81517600583101303174793d37f29ec27ae 100644
--- a/src/USER-SPH/fix_meso.cpp
+++ b/src/USER-SPH/fix_meso.cpp
@@ -11,12 +11,11 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <stdio.h>
-#include <string.h>
+#include <cstdio>
+#include <cstring>
+#include <cmath>
+#include <cstdlib>
#include "fix_meso.h"
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
#include "atom.h"
#include "comm.h"
#include "force.h"
diff --git a/src/USER-SPH/fix_meso_stationary.cpp b/src/USER-SPH/fix_meso_stationary.cpp
index 0607f2f3d0f51d9ff58548ca36dae65be937bd38..f5fc306320d1951078cd122500705898a30f6262 100644
--- a/src/USER-SPH/fix_meso_stationary.cpp
+++ b/src/USER-SPH/fix_meso_stationary.cpp
@@ -11,12 +11,11 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <stdio.h>
-#include <string.h>
+#include <cstdio>
+#include <cstring>
+#include <cmath>
+#include <cstdlib>
#include "fix_meso_stationary.h"
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
#include "atom.h"
#include "comm.h"
#include "force.h"
diff --git a/src/USER-SPH/pair_sph_heatconduction.cpp b/src/USER-SPH/pair_sph_heatconduction.cpp
index 02e667e437a2d2ff96c1f85600273954dff5af62..6f0cf7eca2f734b4e19bb3c69246aeae71996874 100644
--- a/src/USER-SPH/pair_sph_heatconduction.cpp
+++ b/src/USER-SPH/pair_sph_heatconduction.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdlib>
#include "pair_sph_heatconduction.h"
#include "atom.h"
#include "force.h"
diff --git a/src/USER-SPH/pair_sph_idealgas.cpp b/src/USER-SPH/pair_sph_idealgas.cpp
index 2ba0d9bfbe6a970bcffd36e17aa412e7d9df0e4f..99fba05917ae35dbf71836cf10c5c568c10a5278 100644
--- a/src/USER-SPH/pair_sph_idealgas.cpp
+++ b/src/USER-SPH/pair_sph_idealgas.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdlib>
#include "pair_sph_idealgas.h"
#include "atom.h"
#include "force.h"
diff --git a/src/USER-SPH/pair_sph_lj.cpp b/src/USER-SPH/pair_sph_lj.cpp
index 98752ac126aa6385c3bb1bc4f2df5b91d34d73bd..5cefdf87c43645e32be21de131ce1d8ec2046ee7 100644
--- a/src/USER-SPH/pair_sph_lj.cpp
+++ b/src/USER-SPH/pair_sph_lj.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdlib>
#include "pair_sph_lj.h"
#include "atom.h"
#include "force.h"
diff --git a/src/USER-SPH/pair_sph_rhosum.cpp b/src/USER-SPH/pair_sph_rhosum.cpp
index 4bff0ec27c6e75e33e904627d06c6336581a3627..605187d3a733115254fe3a74967442c63de0afa2 100644
--- a/src/USER-SPH/pair_sph_rhosum.cpp
+++ b/src/USER-SPH/pair_sph_rhosum.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdlib>
#include "pair_sph_rhosum.h"
#include "atom.h"
#include "force.h"
diff --git a/src/USER-SPH/pair_sph_taitwater.cpp b/src/USER-SPH/pair_sph_taitwater.cpp
index b1887c6164ac1e0d9528c8fec71d864a447d5e2c..00500b940de1803c47982e2b4936ddbd005cc915 100644
--- a/src/USER-SPH/pair_sph_taitwater.cpp
+++ b/src/USER-SPH/pair_sph_taitwater.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdlib>
#include "pair_sph_taitwater.h"
#include "atom.h"
#include "force.h"
diff --git a/src/USER-SPH/pair_sph_taitwater_morris.cpp b/src/USER-SPH/pair_sph_taitwater_morris.cpp
index 76b538e46bd38fb0037a412ae2203adaa15f0d98..80607cb333b2cd882c1b276c703e4c5d173c9b94 100644
--- a/src/USER-SPH/pair_sph_taitwater_morris.cpp
+++ b/src/USER-SPH/pair_sph_taitwater_morris.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdlib>
#include "pair_sph_taitwater_morris.h"
#include "atom.h"
#include "force.h"
diff --git a/src/USER-TALLY/compute_force_tally.cpp b/src/USER-TALLY/compute_force_tally.cpp
index 3ec6c188fc385026ce3fd93383fa87e38559b15f..0ec1d332a4ea91daf86330f7c51e33e980bc1553 100644
--- a/src/USER-TALLY/compute_force_tally.cpp
+++ b/src/USER-TALLY/compute_force_tally.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
-#include <math.h>
+#include <cstring>
+#include <cmath>
#include "compute_force_tally.h"
#include "atom.h"
#include "group.h"
diff --git a/src/USER-TALLY/compute_heat_flux_tally.cpp b/src/USER-TALLY/compute_heat_flux_tally.cpp
index 43b663b27a580495943b5d4835650ae01811b0cd..f8db92a730e320905d488e45d74c26ab1636d836 100644
--- a/src/USER-TALLY/compute_heat_flux_tally.cpp
+++ b/src/USER-TALLY/compute_heat_flux_tally.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "compute_heat_flux_tally.h"
#include "atom.h"
#include "group.h"
diff --git a/src/USER-TALLY/compute_pe_mol_tally.cpp b/src/USER-TALLY/compute_pe_mol_tally.cpp
index 0328740e0395bc6ca7914ee8d7b7b88e212e0000..264ddca270af4f7956b50ceb2da75ec380c57295 100644
--- a/src/USER-TALLY/compute_pe_mol_tally.cpp
+++ b/src/USER-TALLY/compute_pe_mol_tally.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "compute_pe_mol_tally.h"
#include "atom.h"
#include "group.h"
diff --git a/src/USER-TALLY/compute_pe_tally.cpp b/src/USER-TALLY/compute_pe_tally.cpp
index caa4cf134a89dd10d73169eae5ba02510a8bf2dd..3031915ebe54f76c51d409b36455cdccee9bdff0 100644
--- a/src/USER-TALLY/compute_pe_tally.cpp
+++ b/src/USER-TALLY/compute_pe_tally.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "compute_pe_tally.h"
#include "atom.h"
#include "group.h"
diff --git a/src/USER-TALLY/compute_stress_tally.cpp b/src/USER-TALLY/compute_stress_tally.cpp
index e44313d695c46959b87ddb89bbf50ec99078bd7c..8ed40ae8e24dad64c313563f5c157f8f7d0794cf 100644
--- a/src/USER-TALLY/compute_stress_tally.cpp
+++ b/src/USER-TALLY/compute_stress_tally.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "compute_stress_tally.h"
#include "atom.h"
#include "group.h"
diff --git a/src/USER-UEF/compute_pressure_uef.cpp b/src/USER-UEF/compute_pressure_uef.cpp
index 43054d7d3f9652f1770361596fa8c62d954ff898..8b6285304228970aaceb014bee9446990703ecad 100644
--- a/src/USER-UEF/compute_pressure_uef.cpp
+++ b/src/USER-UEF/compute_pressure_uef.cpp
@@ -14,8 +14,8 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <string.h>
-#include <stdlib.h>
+#include <cstring>
+#include <cstdlib>
#include "compute_pressure_uef.h"
#include "fix_nh_uef.h"
#include "update.h"
diff --git a/src/USER-UEF/compute_temp_uef.cpp b/src/USER-UEF/compute_temp_uef.cpp
index 605552405611711327b9fd0a7409b7edbec70eca..999296ec7e73f54bcb664cd6bc1492826ed4ce0c 100644
--- a/src/USER-UEF/compute_temp_uef.cpp
+++ b/src/USER-UEF/compute_temp_uef.cpp
@@ -13,8 +13,8 @@
Contributing author: David Nicholson (MIT)
------------------------------------------------------------------------- */
-#include <string.h>
-#include <stdlib.h>
+#include <cstring>
+#include <cstdlib>
#include "compute_temp_uef.h"
#include "fix_nh_uef.h"
#include "update.h"
diff --git a/src/USER-UEF/dump_cfg_uef.cpp b/src/USER-UEF/dump_cfg_uef.cpp
index 4b0c08275a62a7bb78132fd2ab6a138a0670d11d..44af823332c156d6ed520a460f277ae1a25e2bbe 100644
--- a/src/USER-UEF/dump_cfg_uef.cpp
+++ b/src/USER-UEF/dump_cfg_uef.cpp
@@ -14,9 +14,9 @@
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "dump_cfg.h"
#include "atom.h"
#include "domain.h"
@@ -30,8 +30,6 @@
using namespace LAMMPS_NS;
-enum{INT,DOUBLE,STRING,BIGINT}; // same as in DumpCustom
-
#define UNWRAPEXPAND 10.0
#define ONEFIELD 32
#define DELTA 1048576
diff --git a/src/USER-UEF/fix_nh_uef.cpp b/src/USER-UEF/fix_nh_uef.cpp
index 36494b0d493809c4ae10e9314bc58765a19ee674..cd0b2ba2683742ab1140ce3a41e0e7c506a40a33 100644
--- a/src/USER-UEF/fix_nh_uef.cpp
+++ b/src/USER-UEF/fix_nh_uef.cpp
@@ -13,9 +13,9 @@
Contributing author: David Nicholson (MIT)
------------------------------------------------------------------------- */
-#include <string.h>
-#include <stdlib.h>
-#include <math.h>
+#include <cstring>
+#include <cstdlib>
+#include <cmath>
#include "fix_nh_uef.h"
#include "atom.h"
#include "force.h"
diff --git a/src/USER-UEF/fix_nh_uef.h b/src/USER-UEF/fix_nh_uef.h
index 43f5bb46a9f2c97c6f3a5f784506d3c9839aed56..0629db5aa176c96e74271aef1b43e08383e0279b 100644
--- a/src/USER-UEF/fix_nh_uef.h
+++ b/src/USER-UEF/fix_nh_uef.h
@@ -23,7 +23,7 @@ namespace LAMMPS_NS {
// forward declaration
namespace UEF_utils {
class UEFBox;
- };
+ }
class FixNHUef : public FixNH {
public:
diff --git a/src/USER-UEF/uef_utils.cpp b/src/USER-UEF/uef_utils.cpp
index f270fe1d8b41760aa1236c1e4b478f79a24203ca..a5498d605f3d28291d91dcc320a4cd41dd999ce2 100644
--- a/src/USER-UEF/uef_utils.cpp
+++ b/src/USER-UEF/uef_utils.cpp
@@ -22,7 +22,7 @@
http://link.springer.com/chapter/10.1007%2F3-540-44670-2_13
*/
-#include <math.h>
+#include <cmath>
#include "uef_utils.h"
namespace LAMMPS_NS {
diff --git a/src/USER-VTK/Install.sh b/src/USER-VTK/Install.sh
old mode 100644
new mode 100755
diff --git a/src/USER-VTK/dump_vtk.cpp b/src/USER-VTK/dump_vtk.cpp
index 78be5668cfebb8954b58c3be6df6bd7149c43521..5f2e3d62ec433e4cd77e80852aa1e3f5e88ad913 100644
--- a/src/USER-VTK/dump_vtk.cpp
+++ b/src/USER-VTK/dump_vtk.cpp
@@ -22,9 +22,9 @@
Richard Berger (JKU)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "dump_vtk.h"
#include "atom.h"
#include "force.h"
@@ -87,7 +87,6 @@ enum{X,Y,Z, // required for vtk, must come first
VARIABLE,COMPUTE,FIX,INAME,DNAME,
ATTRIBUTES}; // must come last
enum{LT,LE,GT,GE,EQ,NEQ};
-enum{INT,DOUBLE,STRING,BIGINT}; // same as in DumpCFG
enum{VTK,VTP,VTU,PVTP,PVTU}; // file formats
#define INVOKED_PERATOM 8
@@ -1091,7 +1090,7 @@ void DumpVTK::buf2arrays(int n, double *mybuf)
vtkAbstractArray *paa = it->second;
if (it->second->GetNumberOfComponents() == 3) {
switch (vtype[it->first]) {
- case INT:
+ case Dump::INT:
{
int iv3[3] = { static_cast<int>(mybuf[iatom*size_one+j ]),
static_cast<int>(mybuf[iatom*size_one+j+1]),
@@ -1100,7 +1099,7 @@ void DumpVTK::buf2arrays(int n, double *mybuf)
pia->InsertNextTupleValue(iv3);
break;
}
- case DOUBLE:
+ case Dump::DOUBLE:
{
vtkDoubleArray *pda = static_cast<vtkDoubleArray*>(paa);
pda->InsertNextTupleValue(&mybuf[iatom*size_one+j]);
@@ -1110,19 +1109,19 @@ void DumpVTK::buf2arrays(int n, double *mybuf)
j+=3;
} else {
switch (vtype[it->first]) {
- case INT:
+ case Dump::INT:
{
vtkIntArray *pia = static_cast<vtkIntArray*>(paa);
pia->InsertNextValue(mybuf[iatom*size_one+j]);
break;
}
- case DOUBLE:
+ case Dump::DOUBLE:
{
vtkDoubleArray *pda = static_cast<vtkDoubleArray*>(paa);
pda->InsertNextValue(mybuf[iatom*size_one+j]);
break;
}
- case STRING:
+ case Dump::STRING:
{
vtkStringArray *psa = static_cast<vtkStringArray*>(paa);
psa->InsertNextValue(typenames[static_cast<int>(mybuf[iatom*size_one+j])]);
@@ -1482,13 +1481,13 @@ void DumpVTK::reset_vtk_data_containers()
++it; ++it; ++it;
for (; it!=vtype.end(); ++it) {
switch(vtype[it->first]) {
- case INT:
+ case Dump::INT:
myarrays[it->first] = vtkSmartPointer<vtkIntArray>::New();
break;
- case DOUBLE:
+ case Dump::DOUBLE:
myarrays[it->first] = vtkSmartPointer<vtkDoubleArray>::New();
break;
- case STRING:
+ case Dump::STRING:
myarrays[it->first] = vtkSmartPointer<vtkStringArray>::New();
break;
}
@@ -1509,13 +1508,13 @@ int DumpVTK::parse_fields(int narg, char **arg)
{
pack_choice[X] = &DumpVTK::pack_x;
- vtype[X] = DOUBLE;
+ vtype[X] = Dump::DOUBLE;
name[X] = "x";
pack_choice[Y] = &DumpVTK::pack_y;
- vtype[Y] = DOUBLE;
+ vtype[Y] = Dump::DOUBLE;
name[Y] = "y";
pack_choice[Z] = &DumpVTK::pack_z;
- vtype[Z] = DOUBLE;
+ vtype[Z] = Dump::DOUBLE;
name[Z] = "z";
// customize by adding to if statement
@@ -1525,33 +1524,33 @@ int DumpVTK::parse_fields(int narg, char **arg)
if (strcmp(arg[iarg],"id") == 0) {
pack_choice[ID] = &DumpVTK::pack_id;
- vtype[ID] = INT;
+ vtype[ID] = Dump::INT;
name[ID] = arg[iarg];
} else if (strcmp(arg[iarg],"mol") == 0) {
if (!atom->molecule_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[MOL] = &DumpVTK::pack_molecule;
- vtype[MOL] = INT;
+ vtype[MOL] = Dump::INT;
name[MOL] = arg[iarg];
} else if (strcmp(arg[iarg],"proc") == 0) {
pack_choice[PROC] = &DumpVTK::pack_proc;
- vtype[PROC] = INT;
+ vtype[PROC] = Dump::INT;
name[PROC] = arg[iarg];
} else if (strcmp(arg[iarg],"procp1") == 0) {
pack_choice[PROCP1] = &DumpVTK::pack_procp1;
- vtype[PROCP1] = INT;
+ vtype[PROCP1] = Dump::INT;
name[PROCP1] = arg[iarg];
} else if (strcmp(arg[iarg],"type") == 0) {
pack_choice[TYPE] = &DumpVTK::pack_type;
- vtype[TYPE] = INT;
+ vtype[TYPE] = Dump::INT;
name[TYPE] =arg[iarg];
} else if (strcmp(arg[iarg],"element") == 0) {
pack_choice[ELEMENT] = &DumpVTK::pack_type;
- vtype[ELEMENT] = STRING;
+ vtype[ELEMENT] = Dump::STRING;
name[ELEMENT] = arg[iarg];
} else if (strcmp(arg[iarg],"mass") == 0) {
pack_choice[MASS] = &DumpVTK::pack_mass;
- vtype[MASS] = DOUBLE;
+ vtype[MASS] = Dump::DOUBLE;
name[MASS] = arg[iarg];
} else if (strcmp(arg[iarg],"x") == 0) {
@@ -1563,181 +1562,181 @@ int DumpVTK::parse_fields(int narg, char **arg)
} else if (strcmp(arg[iarg],"xs") == 0) {
if (domain->triclinic) pack_choice[XS] = &DumpVTK::pack_xs_triclinic;
else pack_choice[XS] = &DumpVTK::pack_xs;
- vtype[XS] = DOUBLE;
+ vtype[XS] = Dump::DOUBLE;
name[XS] = arg[iarg];
} else if (strcmp(arg[iarg],"ys") == 0) {
if (domain->triclinic) pack_choice[YS] = &DumpVTK::pack_ys_triclinic;
else pack_choice[YS] = &DumpVTK::pack_ys;
- vtype[YS] = DOUBLE;
+ vtype[YS] = Dump::DOUBLE;
name[YS] = arg[iarg];
} else if (strcmp(arg[iarg],"zs") == 0) {
if (domain->triclinic) pack_choice[ZS] = &DumpVTK::pack_zs_triclinic;
else pack_choice[ZS] = &DumpVTK::pack_zs;
- vtype[ZS] = DOUBLE;
+ vtype[ZS] = Dump::DOUBLE;
name[ZS] = arg[iarg];
} else if (strcmp(arg[iarg],"xu") == 0) {
if (domain->triclinic) pack_choice[XU] = &DumpVTK::pack_xu_triclinic;
else pack_choice[XU] = &DumpVTK::pack_xu;
- vtype[XU] = DOUBLE;
+ vtype[XU] = Dump::DOUBLE;
name[XU] = arg[iarg];
} else if (strcmp(arg[iarg],"yu") == 0) {
if (domain->triclinic) pack_choice[YU] = &DumpVTK::pack_yu_triclinic;
else pack_choice[YU] = &DumpVTK::pack_yu;
- vtype[YU] = DOUBLE;
+ vtype[YU] = Dump::DOUBLE;
name[YU] = arg[iarg];
} else if (strcmp(arg[iarg],"zu") == 0) {
if (domain->triclinic) pack_choice[ZU] = &DumpVTK::pack_zu_triclinic;
else pack_choice[ZU] = &DumpVTK::pack_zu;
- vtype[ZU] = DOUBLE;
+ vtype[ZU] = Dump::DOUBLE;
name[ZU] = arg[iarg];
} else if (strcmp(arg[iarg],"xsu") == 0) {
if (domain->triclinic) pack_choice[XSU] = &DumpVTK::pack_xsu_triclinic;
else pack_choice[XSU] = &DumpVTK::pack_xsu;
- vtype[XSU] = DOUBLE;
+ vtype[XSU] = Dump::DOUBLE;
name[XSU] = arg[iarg];
} else if (strcmp(arg[iarg],"ysu") == 0) {
if (domain->triclinic) pack_choice[YSU] = &DumpVTK::pack_ysu_triclinic;
else pack_choice[YSU] = &DumpVTK::pack_ysu;
- vtype[YSU] = DOUBLE;
+ vtype[YSU] = Dump::DOUBLE;
name[YSU] = arg[iarg];
} else if (strcmp(arg[iarg],"zsu") == 0) {
if (domain->triclinic) pack_choice[ZSU] = &DumpVTK::pack_zsu_triclinic;
else pack_choice[ZSU] = &DumpVTK::pack_zsu;
- vtype[ZSU] = DOUBLE;
+ vtype[ZSU] = Dump::DOUBLE;
name[ZSU] = arg[iarg];
} else if (strcmp(arg[iarg],"ix") == 0) {
pack_choice[IX] = &DumpVTK::pack_ix;
- vtype[IX] = INT;
+ vtype[IX] = Dump::INT;
name[IX] = arg[iarg];
} else if (strcmp(arg[iarg],"iy") == 0) {
pack_choice[IY] = &DumpVTK::pack_iy;
- vtype[IY] = INT;
+ vtype[IY] = Dump::INT;
name[IY] = arg[iarg];
} else if (strcmp(arg[iarg],"iz") == 0) {
pack_choice[IZ] = &DumpVTK::pack_iz;
- vtype[IZ] = INT;
+ vtype[IZ] = Dump::INT;
name[IZ] = arg[iarg];
} else if (strcmp(arg[iarg],"vx") == 0) {
pack_choice[VX] = &DumpVTK::pack_vx;
- vtype[VX] = DOUBLE;
+ vtype[VX] = Dump::DOUBLE;
name[VX] = arg[iarg];
} else if (strcmp(arg[iarg],"vy") == 0) {
pack_choice[VY] = &DumpVTK::pack_vy;
- vtype[VY] = DOUBLE;
+ vtype[VY] = Dump::DOUBLE;
name[VY] = arg[iarg];
} else if (strcmp(arg[iarg],"vz") == 0) {
pack_choice[VZ] = &DumpVTK::pack_vz;
- vtype[VZ] = DOUBLE;
+ vtype[VZ] = Dump::DOUBLE;
name[VZ] = arg[iarg];
} else if (strcmp(arg[iarg],"fx") == 0) {
pack_choice[FX] = &DumpVTK::pack_fx;
- vtype[FX] = DOUBLE;
+ vtype[FX] = Dump::DOUBLE;
name[FX] = arg[iarg];
} else if (strcmp(arg[iarg],"fy") == 0) {
pack_choice[FY] = &DumpVTK::pack_fy;
- vtype[FY] = DOUBLE;
+ vtype[FY] = Dump::DOUBLE;
name[FY] = arg[iarg];
} else if (strcmp(arg[iarg],"fz") == 0) {
pack_choice[FZ] = &DumpVTK::pack_fz;
- vtype[FZ] = DOUBLE;
+ vtype[FZ] = Dump::DOUBLE;
name[FZ] = arg[iarg];
} else if (strcmp(arg[iarg],"q") == 0) {
if (!atom->q_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[Q] = &DumpVTK::pack_q;
- vtype[Q] = DOUBLE;
+ vtype[Q] = Dump::DOUBLE;
name[Q] = arg[iarg];
} else if (strcmp(arg[iarg],"mux") == 0) {
if (!atom->mu_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[MUX] = &DumpVTK::pack_mux;
- vtype[MUX] = DOUBLE;
+ vtype[MUX] = Dump::DOUBLE;
name[MUX] = arg[iarg];
} else if (strcmp(arg[iarg],"muy") == 0) {
if (!atom->mu_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[MUY] = &DumpVTK::pack_muy;
- vtype[MUY] = DOUBLE;
+ vtype[MUY] = Dump::DOUBLE;
name[MUY] = arg[iarg];
} else if (strcmp(arg[iarg],"muz") == 0) {
if (!atom->mu_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[MUZ] = &DumpVTK::pack_muz;
- vtype[MUZ] = DOUBLE;
+ vtype[MUZ] = Dump::DOUBLE;
name[MUZ] = arg[iarg];
} else if (strcmp(arg[iarg],"mu") == 0) {
if (!atom->mu_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[MU] = &DumpVTK::pack_mu;
- vtype[MU] = DOUBLE;
+ vtype[MU] = Dump::DOUBLE;
name[MU] = arg[iarg];
} else if (strcmp(arg[iarg],"radius") == 0) {
if (!atom->radius_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[RADIUS] = &DumpVTK::pack_radius;
- vtype[RADIUS] = DOUBLE;
+ vtype[RADIUS] = Dump::DOUBLE;
name[RADIUS] = arg[iarg];
} else if (strcmp(arg[iarg],"diameter") == 0) {
if (!atom->radius_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[DIAMETER] = &DumpVTK::pack_diameter;
- vtype[DIAMETER] = DOUBLE;
+ vtype[DIAMETER] = Dump::DOUBLE;
name[DIAMETER] = arg[iarg];
} else if (strcmp(arg[iarg],"omegax") == 0) {
if (!atom->omega_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[OMEGAX] = &DumpVTK::pack_omegax;
- vtype[OMEGAX] = DOUBLE;
+ vtype[OMEGAX] = Dump::DOUBLE;
name[OMEGAX] = arg[iarg];
} else if (strcmp(arg[iarg],"omegay") == 0) {
if (!atom->omega_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[OMEGAY] = &DumpVTK::pack_omegay;
- vtype[OMEGAY] = DOUBLE;
+ vtype[OMEGAY] = Dump::DOUBLE;
name[OMEGAY] = arg[iarg];
} else if (strcmp(arg[iarg],"omegaz") == 0) {
if (!atom->omega_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[OMEGAZ] = &DumpVTK::pack_omegaz;
- vtype[OMEGAZ] = DOUBLE;
+ vtype[OMEGAZ] = Dump::DOUBLE;
name[OMEGAZ] = arg[iarg];
} else if (strcmp(arg[iarg],"angmomx") == 0) {
if (!atom->angmom_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[ANGMOMX] = &DumpVTK::pack_angmomx;
- vtype[ANGMOMX] = DOUBLE;
+ vtype[ANGMOMX] = Dump::DOUBLE;
name[ANGMOMX] = arg[iarg];
} else if (strcmp(arg[iarg],"angmomy") == 0) {
if (!atom->angmom_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[ANGMOMY] = &DumpVTK::pack_angmomy;
- vtype[ANGMOMY] = DOUBLE;
+ vtype[ANGMOMY] = Dump::DOUBLE;
name[ANGMOMY] = arg[iarg];
} else if (strcmp(arg[iarg],"angmomz") == 0) {
if (!atom->angmom_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[ANGMOMZ] = &DumpVTK::pack_angmomz;
- vtype[ANGMOMZ] = DOUBLE;
+ vtype[ANGMOMZ] = Dump::DOUBLE;
name[ANGMOMZ] = arg[iarg];
} else if (strcmp(arg[iarg],"tqx") == 0) {
if (!atom->torque_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[TQX] = &DumpVTK::pack_tqx;
- vtype[TQX] = DOUBLE;
+ vtype[TQX] = Dump::DOUBLE;
name[TQX] = arg[iarg];
} else if (strcmp(arg[iarg],"tqy") == 0) {
if (!atom->torque_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[TQY] = &DumpVTK::pack_tqy;
- vtype[TQY] = DOUBLE;
+ vtype[TQY] = Dump::DOUBLE;
name[TQY] = arg[iarg];
} else if (strcmp(arg[iarg],"tqz") == 0) {
if (!atom->torque_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[TQZ] = &DumpVTK::pack_tqz;
- vtype[TQZ] = DOUBLE;
+ vtype[TQZ] = Dump::DOUBLE;
name[TQZ] = arg[iarg];
// compute value = c_ID
@@ -1745,7 +1744,7 @@ int DumpVTK::parse_fields(int narg, char **arg)
} else if (strncmp(arg[iarg],"c_",2) == 0) {
pack_choice[ATTRIBUTES+i] = &DumpVTK::pack_compute;
- vtype[ATTRIBUTES+i] = DOUBLE;
+ vtype[ATTRIBUTES+i] = Dump::DOUBLE;
int n = strlen(arg[iarg]);
char *suffix = new char[n];
@@ -1782,7 +1781,7 @@ int DumpVTK::parse_fields(int narg, char **arg)
} else if (strncmp(arg[iarg],"f_",2) == 0) {
pack_choice[ATTRIBUTES+i] = &DumpVTK::pack_fix;
- vtype[ATTRIBUTES+i] = DOUBLE;
+ vtype[ATTRIBUTES+i] = Dump::DOUBLE;
int n = strlen(arg[iarg]);
char *suffix = new char[n];
@@ -1816,7 +1815,7 @@ int DumpVTK::parse_fields(int narg, char **arg)
} else if (strncmp(arg[iarg],"v_",2) == 0) {
pack_choice[ATTRIBUTES+i] = &DumpVTK::pack_variable;
- vtype[ATTRIBUTES+i] = DOUBLE;
+ vtype[ATTRIBUTES+i] = Dump::DOUBLE;
int n = strlen(arg[iarg]);
char *suffix = new char[n];
@@ -1837,7 +1836,7 @@ int DumpVTK::parse_fields(int narg, char **arg)
} else if (strncmp(arg[iarg],"d_",2) == 0) {
pack_choice[ATTRIBUTES+i] = &DumpVTK::pack_custom;
- vtype[ATTRIBUTES+i] = DOUBLE;
+ vtype[ATTRIBUTES+i] = Dump::DOUBLE;
int n = strlen(arg[iarg]);
char *suffix = new char[n];
@@ -1860,7 +1859,7 @@ int DumpVTK::parse_fields(int narg, char **arg)
} else if (strncmp(arg[iarg],"i_",2) == 0) {
pack_choice[ATTRIBUTES+i] = &DumpVTK::pack_custom;
- vtype[ATTRIBUTES+i] = INT;
+ vtype[ATTRIBUTES+i] = Dump::INT;
int n = strlen(arg[iarg]);
char *suffix = new char[n];
diff --git a/src/VORONOI/compute_voronoi_atom.cpp b/src/VORONOI/compute_voronoi_atom.cpp
index d55db85ef8624501183cecc238fa9c9ae598e8e8..ea6158bfa225dcf9ccf75b21ce93ed0eb55c33c5 100644
--- a/src/VORONOI/compute_voronoi_atom.cpp
+++ b/src/VORONOI/compute_voronoi_atom.cpp
@@ -16,9 +16,9 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <math.h>
-#include <string.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstring>
+#include <cstdlib>
#include "compute_voronoi_atom.h"
#include "atom.h"
#include "group.h"
diff --git a/src/angle.cpp b/src/angle.cpp
index 1366c48865b5daa516b58bba254aa0171eaf3da0..2a297990ac83046595212b2819d621bfa6ab2b1a 100644
--- a/src/angle.cpp
+++ b/src/angle.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "angle.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/angle.h b/src/angle.h
index 000c3fe916d84c1766eeb4dd09dbd082fba61387..0247fa0ff83eb24204d01908577e60dab67883d4 100644
--- a/src/angle.h
+++ b/src/angle.h
@@ -14,7 +14,7 @@
#ifndef LMP_ANGLE_H
#define LMP_ANGLE_H
-#include <stdio.h>
+#include <cstdio>
#include "pointers.h"
namespace LAMMPS_NS {
diff --git a/src/angle_hybrid.cpp b/src/angle_hybrid.cpp
index 9b3af1856e67a33ae14eafd674b38d57782fb052..c29eaac2ae9e694c6eb3198099c04bcd9fb9122e 100644
--- a/src/angle_hybrid.cpp
+++ b/src/angle_hybrid.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <string.h>
-#include <ctype.h>
+#include <cmath>
+#include <cstring>
+#include <cctype>
#include "angle_hybrid.h"
#include "atom.h"
#include "neighbor.h"
diff --git a/src/angle_hybrid.h b/src/angle_hybrid.h
index 4ae34c176f9574ca013b4f8075157c8e155e9fa5..4fde71e43f1251822355823dab06e941d8f33f31 100644
--- a/src/angle_hybrid.h
+++ b/src/angle_hybrid.h
@@ -20,7 +20,7 @@ AngleStyle(hybrid,AngleHybrid)
#ifndef LMP_ANGLE_HYBRID_H
#define LMP_ANGLE_HYBRID_H
-#include <stdio.h>
+#include <cstdio>
#include "angle.h"
namespace LAMMPS_NS {
diff --git a/src/angle_zero.cpp b/src/angle_zero.cpp
index ba84295ca76a997a956991c35e6b0b194f925cdc..e5191c4fb22d6ceaaa0f4a562abe5b103364cefe 100644
--- a/src/angle_zero.cpp
+++ b/src/angle_zero.cpp
@@ -15,9 +15,9 @@
Contributing author: Carsten Svaneborg (SDU)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "angle_zero.h"
#include "atom.h"
#include "force.h"
diff --git a/src/angle_zero.h b/src/angle_zero.h
index e40fc8355ce2be6aad4723f147455dc028c5cd82..b91be5c8d72a5330cabd8b3dca8d0cb8c450ab69 100644
--- a/src/angle_zero.h
+++ b/src/angle_zero.h
@@ -20,7 +20,7 @@ AngleStyle(zero,AngleZero)
#ifndef LMP_ANGLE_ZERO_H
#define LMP_ANGLE_ZERO_H
-#include <stdio.h>
+#include <cstdio>
#include "angle.h"
namespace LAMMPS_NS {
diff --git a/src/atom.cpp b/src/atom.cpp
index 69475f75a77d33adda5379b0b0c1d42a5ce1e136..51b48f3e1b3bb11eaf57e6ef152e2a05baaecd5f 100644
--- a/src/atom.cpp
+++ b/src/atom.cpp
@@ -12,11 +12,11 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-#include <limits.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
+#include <climits>
#include "atom.h"
#include "style_atom.h"
#include "atom_vec.h"
@@ -51,8 +51,6 @@ using namespace MathConst;
#define DELTA_MEMSTR 1024
#define EPSILON 1.0e-6
-enum{LAYOUT_UNIFORM,LAYOUT_NONUNIFORM,LAYOUT_TILED}; // several files
-
/* ---------------------------------------------------------------------- */
Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
@@ -881,7 +879,7 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset,
sublo[2] = domain->sublo_lamda[2]; subhi[2] = domain->subhi_lamda[2];
}
- if (comm->layout != LAYOUT_TILED) {
+ if (comm->layout != Comm::LAYOUT_TILED) {
if (domain->xperiodic) {
if (comm->myloc[0] == 0) sublo[0] -= epsilon[0];
if (comm->myloc[0] == comm->procgrid[0]-1) subhi[0] += epsilon[0];
diff --git a/src/atom_map.cpp b/src/atom_map.cpp
index 4b1be77a061464728e8769f8fef48ef37d667c00..46593432cfe07cd6806a0fcfca4f1ab282f7cc03 100644
--- a/src/atom_map.cpp
+++ b/src/atom_map.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "atom.h"
#include "comm.h"
#include "memory.h"
diff --git a/src/atom_vec.cpp b/src/atom_vec.cpp
index 14091cbb77ff41bbb8864f717c96ef97c6958455..b04bfba34c91295b0858c6f0833d75172fed20c9 100644
--- a/src/atom_vec.cpp
+++ b/src/atom_vec.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
-#include <stdlib.h>
+#include <cstring>
+#include <cstdlib>
#include "atom_vec.h"
#include "atom.h"
#include "force.h"
diff --git a/src/atom_vec.h b/src/atom_vec.h
index 5be955a06c39b0c4c501f862ecf9b0e1d841bb39..87fb35d9c72042e478d8cb8dde75549fddd70b17 100644
--- a/src/atom_vec.h
+++ b/src/atom_vec.h
@@ -14,7 +14,7 @@
#ifndef LMP_ATOM_VEC_H
#define LMP_ATOM_VEC_H
-#include <stdio.h>
+#include <cstdio>
#include "pointers.h"
namespace LAMMPS_NS {
diff --git a/src/atom_vec_atomic.cpp b/src/atom_vec_atomic.cpp
index eda1a33152a0f5d513d115fb04e8f07d3642a0b3..e1c9a1e524c2ae99e3cdc2aff74217404f4240bb 100644
--- a/src/atom_vec_atomic.cpp
+++ b/src/atom_vec_atomic.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <stdlib.h>
+#include <cstdlib>
#include "atom_vec_atomic.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/atom_vec_body.cpp b/src/atom_vec_body.cpp
index b7422cf229785feaf714d3c914acd15c3a01767f..4d3b5643aea121a788d41345f2a1be43e2e0a667 100644
--- a/src/atom_vec_body.cpp
+++ b/src/atom_vec_body.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "atom_vec_body.h"
#include "style_body.h"
#include "body.h"
diff --git a/src/atom_vec_charge.cpp b/src/atom_vec_charge.cpp
index a93a29662b0d5fe2885c8af9b64e6380ef8c4e1e..440393385dad38b24735ce7120b67be1ec83df6c 100644
--- a/src/atom_vec_charge.cpp
+++ b/src/atom_vec_charge.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <stdlib.h>
+#include <cstdlib>
#include "atom_vec_charge.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/atom_vec_ellipsoid.cpp b/src/atom_vec_ellipsoid.cpp
index 858b89d62b47036a3025607c00f1844fc53172f3..c569f89a0933ef4b594f0fc581647140140a93d3 100644
--- a/src/atom_vec_ellipsoid.cpp
+++ b/src/atom_vec_ellipsoid.cpp
@@ -15,7 +15,7 @@
Contributing author: Mike Brown (SNL)
------------------------------------------------------------------------- */
-#include <stdlib.h>
+#include <cstdlib>
#include "atom_vec_ellipsoid.h"
#include "math_extra.h"
#include "atom.h"
diff --git a/src/atom_vec_hybrid.cpp b/src/atom_vec_hybrid.cpp
index 40c744afc5461bb83822053291f01e0701f341e3..7e1fb01e5ddc6318a578a1740f2a8acad7ded7bb 100644
--- a/src/atom_vec_hybrid.cpp
+++ b/src/atom_vec_hybrid.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <stdlib.h>
-#include <string.h>
+#include <cstdlib>
+#include <cstring>
#include "atom_vec_hybrid.h"
#include "atom.h"
#include "domain.h"
diff --git a/src/atom_vec_hybrid.h b/src/atom_vec_hybrid.h
index fd8a3e433cc9bf594171149c5aa7f9b2ab35bc8f..a027923a1717a0385943e2885122f25c677e1430 100644
--- a/src/atom_vec_hybrid.h
+++ b/src/atom_vec_hybrid.h
@@ -20,7 +20,7 @@ AtomStyle(hybrid,AtomVecHybrid)
#ifndef LMP_ATOM_VEC_HYBRID_H
#define LMP_ATOM_VEC_HYBRID_H
-#include <stdio.h>
+#include <cstdio>
#include "atom_vec.h"
namespace LAMMPS_NS {
diff --git a/src/atom_vec_line.cpp b/src/atom_vec_line.cpp
index ec278562f9ea702abeeeb0b595cfef36487f2ac4..9babfe3735ca1eb03ce0c67f3b4033517dc16998 100644
--- a/src/atom_vec_line.cpp
+++ b/src/atom_vec_line.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "atom_vec_line.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/atom_vec_sphere.cpp b/src/atom_vec_sphere.cpp
index a72704b4c62941af07ff48c99b05d0d1a2efd600..dec98e5200d2ec45fe9b3a3b32789802d88eee45 100644
--- a/src/atom_vec_sphere.cpp
+++ b/src/atom_vec_sphere.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "atom_vec_sphere.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/atom_vec_tri.cpp b/src/atom_vec_tri.cpp
index eb87e75b18dfa34e602dde516679d5e53d650134..2c31b95cfe3adf07520fdb39426c34597c1e16d1 100644
--- a/src/atom_vec_tri.cpp
+++ b/src/atom_vec_tri.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "atom_vec_tri.h"
#include "math_extra.h"
#include "atom.h"
diff --git a/src/balance.cpp b/src/balance.cpp
index 45f185a6fc0ba06d4b5cddb7409d73eccff26b82..86deb55b47ff716f6e05f1ce0d4adcc3f7d4d793 100644
--- a/src/balance.cpp
+++ b/src/balance.cpp
@@ -19,9 +19,9 @@
//#define BALANCE_DEBUG 1
#include <mpi.h>
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "balance.h"
#include "atom.h"
#include "comm.h"
@@ -48,8 +48,6 @@ using namespace LAMMPS_NS;
enum{XYZ,SHIFT,BISECTION};
enum{NONE,UNIFORM,USER};
enum{X,Y,Z};
-enum{LAYOUT_UNIFORM,LAYOUT_NONUNIFORM,LAYOUT_TILED}; // several files
-
/* ---------------------------------------------------------------------- */
Balance::Balance(LAMMPS *lmp) : Pointers(lmp)
@@ -281,7 +279,7 @@ void Balance::command(int narg, char **arg)
// no load-balance if imbalance doesn't exceed threshold
// unless switching from tiled to non tiled layout, then force rebalance
- if (comm->layout == LAYOUT_TILED && style != BISECTION) {
+ if (comm->layout == Comm::LAYOUT_TILED && style != BISECTION) {
} else if (imbinit < thresh) return;
// debug output of initial state
@@ -296,16 +294,16 @@ void Balance::command(int narg, char **arg)
// style XYZ = explicit setting of cutting planes of logical 3d grid
if (style == XYZ) {
- if (comm->layout == LAYOUT_UNIFORM) {
+ if (comm->layout == Comm::LAYOUT_UNIFORM) {
if (xflag == USER || yflag == USER || zflag == USER)
- comm->layout = LAYOUT_NONUNIFORM;
- } else if (comm->layout == LAYOUT_NONUNIFORM) {
+ comm->layout = Comm::LAYOUT_NONUNIFORM;
+ } else if (comm->layout == Comm::LAYOUT_NONUNIFORM) {
if (xflag == UNIFORM && yflag == UNIFORM && zflag == UNIFORM)
- comm->layout = LAYOUT_UNIFORM;
- } else if (comm->layout == LAYOUT_TILED) {
+ comm->layout = Comm::LAYOUT_UNIFORM;
+ } else if (comm->layout == Comm::LAYOUT_TILED) {
if (xflag == UNIFORM && yflag == UNIFORM && zflag == UNIFORM)
- comm->layout = LAYOUT_UNIFORM;
- else comm->layout = LAYOUT_NONUNIFORM;
+ comm->layout = Comm::LAYOUT_UNIFORM;
+ else comm->layout = Comm::LAYOUT_NONUNIFORM;
}
if (xflag == UNIFORM) {
@@ -333,7 +331,7 @@ void Balance::command(int narg, char **arg)
// style SHIFT = adjust cutting planes of logical 3d grid
if (style == SHIFT) {
- comm->layout = LAYOUT_NONUNIFORM;
+ comm->layout = Comm::LAYOUT_NONUNIFORM;
shift_setup_static(bstr);
niter = shift();
}
@@ -341,7 +339,7 @@ void Balance::command(int narg, char **arg)
// style BISECTION = recursive coordinate bisectioning
if (style == BISECTION) {
- comm->layout = LAYOUT_TILED;
+ comm->layout = Comm::LAYOUT_TILED;
bisection(1);
}
@@ -745,7 +743,7 @@ void Balance::shift_setup_static(char *str)
// if current layout is TILED, set initial uniform splits in Comm
// this gives starting point to subsequent shift balancing
- if (comm->layout == LAYOUT_TILED) {
+ if (comm->layout == Comm::LAYOUT_TILED) {
int *procgrid = comm->procgrid;
double *xsplit = comm->xsplit;
double *ysplit = comm->ysplit;
diff --git a/src/balance.h b/src/balance.h
index 3e5e0e0d70a07e145b5864bd44dd822652577589..420031502a8f826a636c8d63e1a3a421beb37de6 100644
--- a/src/balance.h
+++ b/src/balance.h
@@ -20,7 +20,7 @@ CommandStyle(balance,Balance)
#ifndef LMP_BALANCE_H
#define LMP_BALANCE_H
-#include <stdio.h>
+#include <cstdio>
#include "pointers.h"
namespace LAMMPS_NS {
diff --git a/src/body.cpp b/src/body.cpp
index 144ee13c92bd9d7a516bd708053e1955080090ee..42f4ccbdd3fcaf9491d7656a7e138c1f7efe4ebe 100644
--- a/src/body.cpp
+++ b/src/body.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "body.h"
#include "error.h"
diff --git a/src/bond.cpp b/src/bond.cpp
index 825ff1b199a48b854f5b7d716eac80c77228345e..edcd869425bd0d7444915d6e1f16dd1f71cb1a17 100644
--- a/src/bond.cpp
+++ b/src/bond.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "bond.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/bond.h b/src/bond.h
index b34628d7575fc726ba5ab7cb69ddae7da2c2d298..9c353a1a6dae5fed06e2f9992d116e24d1d284a4 100644
--- a/src/bond.h
+++ b/src/bond.h
@@ -14,7 +14,7 @@
#ifndef LMP_BOND_H
#define LMP_BOND_H
-#include <stdio.h>
+#include <cstdio>
#include "pointers.h"
namespace LAMMPS_NS {
diff --git a/src/bond_hybrid.cpp b/src/bond_hybrid.cpp
index 9a16d0e1fd2e54a02a3b9d5eb8cedd451b59768c..c3a71ee71c2c85a6a0cbeb914f823423541f4637 100644
--- a/src/bond_hybrid.cpp
+++ b/src/bond_hybrid.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <string.h>
-#include <ctype.h>
+#include <cmath>
+#include <cstring>
+#include <cctype>
#include "bond_hybrid.h"
#include "atom.h"
#include "neighbor.h"
diff --git a/src/bond_hybrid.h b/src/bond_hybrid.h
index e1d567c886813755bc4fe42017ce8fbdd6ed8607..a385a2e3f856788f90dd8b2a2f8df5e83a5ca2c9 100644
--- a/src/bond_hybrid.h
+++ b/src/bond_hybrid.h
@@ -20,7 +20,7 @@ BondStyle(hybrid,BondHybrid)
#ifndef LMP_BOND_HYBRID_H
#define LMP_BOND_HYBRID_H
-#include <stdio.h>
+#include <cstdio>
#include "bond.h"
namespace LAMMPS_NS {
diff --git a/src/bond_zero.cpp b/src/bond_zero.cpp
index f38b7754f826e297e1f820e8dcb22f6f6315bc16..9fd9d4a580c5d83cf4c69a431330975a116ee330 100644
--- a/src/bond_zero.cpp
+++ b/src/bond_zero.cpp
@@ -15,9 +15,9 @@
Contributing author: Carsten Svaneborg (SDU)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "bond_zero.h"
#include "atom.h"
#include "force.h"
diff --git a/src/bond_zero.h b/src/bond_zero.h
index b7b7e999600e4f52b90ceaca4d1ace2956feed79..9443ff0784c64bba76ca5079ae79d90f31b8b1f8 100644
--- a/src/bond_zero.h
+++ b/src/bond_zero.h
@@ -20,7 +20,7 @@ BondStyle(zero,BondZero)
#ifndef LMP_BOND_ZERO_H
#define LMP_BOND_ZERO_H
-#include <stdio.h>
+#include <cstdio>
#include "bond.h"
namespace LAMMPS_NS {
diff --git a/src/change_box.cpp b/src/change_box.cpp
index c6ec078a01f647d4059b692b03250bc5bd52012d..93dff387c47ddceb622f20168deaca3c93ca5f83 100644
--- a/src/change_box.cpp
+++ b/src/change_box.cpp
@@ -12,9 +12,9 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "change_box.h"
#include "atom.h"
#include "modify.h"
diff --git a/src/citeme.h b/src/citeme.h
index 18e9a712db81a1ce5fed2f5f2ca4d26867a15688..262b284337a12dfca5f5c81bffcec5cc0c248eeb 100644
--- a/src/citeme.h
+++ b/src/citeme.h
@@ -15,7 +15,7 @@
#define LMP_CITEME_H
#include "pointers.h"
-#include <stdio.h>
+#include <cstdio>
#include <set>
namespace LAMMPS_NS {
diff --git a/src/comm.cpp b/src/comm.cpp
index 14d2d70c5a2ed125cf467e98b4dbb149ac306f52..f355a562fc03e3089c35bce57c0ceae4c9de95a3 100644
--- a/src/comm.cpp
+++ b/src/comm.cpp
@@ -12,8 +12,8 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cstdlib>
+#include <cstring>
#include "comm.h"
#include "universe.h"
#include "atom.h"
@@ -40,11 +40,8 @@ using namespace LAMMPS_NS;
#define BUFMIN 1000 // also in comm styles
-enum{SINGLE,MULTI}; // same as in Comm sub-styles
-enum{MULTIPLE}; // same as in ProcMap
enum{ONELEVEL,TWOLEVEL,NUMA,CUSTOM};
enum{CART,CARTREORDER,XYZ};
-enum{LAYOUT_UNIFORM,LAYOUT_NONUNIFORM,LAYOUT_TILED}; // several files
/* ---------------------------------------------------------------------- */
@@ -244,14 +241,14 @@ void Comm::modify_params(int narg, char **arg)
if (iarg+2 > narg) error->all(FLERR,"Illegal comm_modify command");
if (strcmp(arg[iarg+1],"single") == 0) {
// need to reset cutghostuser when switching comm mode
- if (mode == MULTI) cutghostuser = 0.0;
+ if (mode == Comm::MULTI) cutghostuser = 0.0;
memory->destroy(cutusermulti);
cutusermulti = NULL;
- mode = SINGLE;
+ mode = Comm::SINGLE;
} else if (strcmp(arg[iarg+1],"multi") == 0) {
// need to reset cutghostuser when switching comm mode
- if (mode == SINGLE) cutghostuser = 0.0;
- mode = MULTI;
+ if (mode == Comm::SINGLE) cutghostuser = 0.0;
+ mode = Comm::MULTI;
} else error->all(FLERR,"Illegal comm_modify command");
iarg += 2;
} else if (strcmp(arg[iarg],"group") == 0) {
@@ -265,7 +262,7 @@ void Comm::modify_params(int narg, char **arg)
iarg += 2;
} else if (strcmp(arg[iarg],"cutoff") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal comm_modify command");
- if (mode == MULTI)
+ if (mode == Comm::MULTI)
error->all(FLERR,
"Use cutoff/multi keyword to set cutoff in multi mode");
cutghostuser = force->numeric(FLERR,arg[iarg+1]);
@@ -275,7 +272,7 @@ void Comm::modify_params(int narg, char **arg)
} else if (strcmp(arg[iarg],"cutoff/multi") == 0) {
int i,nlo,nhi;
double cut;
- if (mode == SINGLE)
+ if (mode == Comm::SINGLE)
error->all(FLERR,"Use cutoff keyword to set cutoff in single mode");
if (domain->box_exist == 0)
error->all(FLERR,
@@ -415,7 +412,7 @@ void Comm::set_processors(int narg, char **arg)
if (strcmp(arg[iarg+3],"multiple") == 0) {
if (universe->iworld == irecv-1) {
otherflag = 1;
- other_style = MULTIPLE;
+ other_style = Comm::MULTIPLE;
}
} else error->all(FLERR,"Illegal processors command");
iarg += 4;
@@ -607,7 +604,7 @@ int Comm::coord2proc(double *x, int &igx, int &igy, int &igz)
triclinic = domain->triclinic;
- if (layout == LAYOUT_UNIFORM) {
+ if (layout == Comm::LAYOUT_UNIFORM) {
if (triclinic == 0) {
igx = static_cast<int> (procgrid[0] * (x[0]-boxlo[0]) / prd[0]);
igy = static_cast<int> (procgrid[1] * (x[1]-boxlo[1]) / prd[1]);
@@ -618,7 +615,7 @@ int Comm::coord2proc(double *x, int &igx, int &igy, int &igz)
igz = static_cast<int> (procgrid[2] * x[2]);
}
- } else if (layout == LAYOUT_NONUNIFORM) {
+ } else if (layout == Comm::LAYOUT_NONUNIFORM) {
if (triclinic == 0) {
igx = binary((x[0]-boxlo[0])/prd[0],procgrid[0],xsplit);
igy = binary((x[1]-boxlo[1])/prd[1],procgrid[1],ysplit);
diff --git a/src/comm.h b/src/comm.h
index aefcb14391c71df20f2157e11bd71e76c4b467ef..298f435c3d94f2e04af2077cfadb21ef3372896c 100644
--- a/src/comm.h
+++ b/src/comm.h
@@ -24,7 +24,9 @@ class Comm : protected Pointers {
int layout; // LAYOUT_UNIFORM = equal-sized bricks
// LAYOUT_NONUNIFORM = logical bricks, but diff sizes via LB
// LAYOUT_TILED = general tiling, due to RCB LB
+ enum{LAYOUT_UNIFORM,LAYOUT_NONUNIFORM,LAYOUT_TILED};
int mode; // 0 = single cutoff, 1 = multi-type cutoff
+ enum{SINGLE,MULTI};
int me,nprocs; // proc info
int ghost_velocity; // 1 if ghost atoms have velocity, 0 if not
@@ -137,6 +139,8 @@ class Comm : protected Pointers {
int ncores; // # of cores per node
int coregrid[3]; // 3d grid of cores within a node
int user_coregrid[3]; // user request for cores in each dim
+ public:
+ enum{MULTIPLE};
};
}
diff --git a/src/comm_brick.cpp b/src/comm_brick.cpp
index 992d988f902d553f1093341bcf17f61a963a030d..3aa6d7748ce96b2c095857ed5e9f6c2acbc9314d 100644
--- a/src/comm_brick.cpp
+++ b/src/comm_brick.cpp
@@ -16,10 +16,10 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <math.h>
-#include <string.h>
-#include <stdio.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstring>
+#include <cstdio>
+#include <cstdlib>
#include "comm_brick.h"
#include "comm_tiled.h"
#include "universe.h"
@@ -46,9 +46,6 @@ using namespace LAMMPS_NS;
#define BUFEXTRA 1000
#define BIG 1.0e20
-enum{SINGLE,MULTI}; // same as in Comm
-enum{LAYOUT_UNIFORM,LAYOUT_NONUNIFORM,LAYOUT_TILED}; // several files
-
/* ---------------------------------------------------------------------- */
CommBrick::CommBrick(LAMMPS *lmp) :
@@ -61,7 +58,7 @@ CommBrick::CommBrick(LAMMPS *lmp) :
sendlist(NULL), maxsendlist(NULL), buf_send(NULL), buf_recv(NULL)
{
style = 0;
- layout = LAYOUT_UNIFORM;
+ layout = Comm::LAYOUT_UNIFORM;
pbc_flag = NULL;
init_buffers();
}
@@ -71,7 +68,7 @@ CommBrick::CommBrick(LAMMPS *lmp) :
CommBrick::~CommBrick()
{
free_swap();
- if (mode == MULTI) {
+ if (mode == Comm::MULTI) {
free_multi();
memory->destroy(cutghostmulti);
}
@@ -93,7 +90,7 @@ CommBrick::~CommBrick()
CommBrick::CommBrick(LAMMPS *lmp, Comm *oldcomm) : Comm(*oldcomm)
{
- if (oldcomm->layout == LAYOUT_TILED)
+ if (oldcomm->layout == Comm::LAYOUT_TILED)
error->all(FLERR,"Cannot change to comm_style brick from tiled layout");
style = 0;
@@ -144,11 +141,11 @@ void CommBrick::init()
// memory for multi-style communication
- if (mode == MULTI && multilo == NULL) {
+ if (mode == Comm::MULTI && multilo == NULL) {
allocate_multi(maxswap);
memory->create(cutghostmulti,atom->ntypes+1,3,"comm:cutghostmulti");
}
- if (mode == SINGLE && multilo) {
+ if (mode == Comm::SINGLE && multilo) {
free_multi();
memory->destroy(cutghostmulti);
}
@@ -184,7 +181,7 @@ void CommBrick::setup()
subhi = domain->subhi;
cutghost[0] = cutghost[1] = cutghost[2] = cut;
- if (mode == MULTI) {
+ if (mode == Comm::MULTI) {
double *cuttype = neighbor->cuttype;
for (i = 1; i <= ntypes; i++) {
cut = 0.0;
@@ -208,7 +205,7 @@ void CommBrick::setup()
length2 = h_inv[2];
cutghost[2] = cut * length2;
- if (mode == MULTI) {
+ if (mode == Comm::MULTI) {
double *cuttype = neighbor->cuttype;
for (i = 1; i <= ntypes; i++) {
cut = 0.0;
@@ -240,7 +237,7 @@ void CommBrick::setup()
int *periodicity = domain->periodicity;
int left,right;
- if (layout == LAYOUT_UNIFORM) {
+ if (layout == Comm::LAYOUT_UNIFORM) {
maxneed[0] = static_cast<int> (cutghost[0] * procgrid[0] / prd[0]) + 1;
maxneed[1] = static_cast<int> (cutghost[1] * procgrid[1] / prd[1]) + 1;
maxneed[2] = static_cast<int> (cutghost[2] * procgrid[2] / prd[2]) + 1;
@@ -357,7 +354,7 @@ void CommBrick::setup()
if (ineed % 2 == 0) {
sendproc[iswap] = procneigh[dim][0];
recvproc[iswap] = procneigh[dim][1];
- if (mode == SINGLE) {
+ if (mode == Comm::SINGLE) {
if (ineed < 2) slablo[iswap] = -BIG;
else slablo[iswap] = 0.5 * (sublo[dim] + subhi[dim]);
slabhi[iswap] = sublo[dim] + cutghost[dim];
@@ -380,7 +377,7 @@ void CommBrick::setup()
} else {
sendproc[iswap] = procneigh[dim][1];
recvproc[iswap] = procneigh[dim][0];
- if (mode == SINGLE) {
+ if (mode == Comm::SINGLE) {
slablo[iswap] = subhi[dim] - cutghost[dim];
if (ineed < 2) slabhi[iswap] = BIG;
else slabhi[iswap] = 0.5 * (sublo[dim] + subhi[dim]);
@@ -737,7 +734,7 @@ void CommBrick::borders()
// store sent atom indices in sendlist for use in future timesteps
x = atom->x;
- if (mode == SINGLE) {
+ if (mode == Comm::SINGLE) {
lo = slablo[iswap];
hi = slabhi[iswap];
} else {
@@ -766,7 +763,7 @@ void CommBrick::borders()
if (sendflag) {
if (!bordergroup || ineed >= 2) {
- if (mode == SINGLE) {
+ if (mode == Comm::SINGLE) {
for (i = nfirst; i < nlast; i++)
if (x[i][dim] >= lo && x[i][dim] <= hi) {
if (nsend == maxsendlist[iswap]) grow_list(iswap,nsend);
@@ -783,7 +780,7 @@ void CommBrick::borders()
}
} else {
- if (mode == SINGLE) {
+ if (mode == Comm::SINGLE) {
ngroup = atom->nfirst;
for (i = 0; i < ngroup; i++)
if (x[i][dim] >= lo && x[i][dim] <= hi) {
@@ -1396,7 +1393,7 @@ void CommBrick::grow_swap(int n)
{
free_swap();
allocate_swap(n);
- if (mode == MULTI) {
+ if (mode == Comm::MULTI) {
free_multi();
allocate_multi(n);
}
diff --git a/src/comm_tiled.cpp b/src/comm_tiled.cpp
index 23b098a705a26bb477ab7199688d2375e2034699..584be94bf3f32f8bc91451f545fef888e3f54bc6 100644
--- a/src/comm_tiled.cpp
+++ b/src/comm_tiled.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "comm_tiled.h"
#include "comm_brick.h"
#include "atom.h"
@@ -38,15 +38,12 @@ using namespace LAMMPS_NS;
#define DELTA_PROCS 16
-enum{SINGLE,MULTI}; // same as in Comm
-enum{LAYOUT_UNIFORM,LAYOUT_NONUNIFORM,LAYOUT_TILED}; // several files
-
/* ---------------------------------------------------------------------- */
CommTiled::CommTiled(LAMMPS *lmp) : Comm(lmp)
{
style = 1;
- layout = LAYOUT_UNIFORM;
+ layout = Comm::LAYOUT_UNIFORM;
pbc_flag = NULL;
init_buffers();
}
@@ -115,7 +112,7 @@ void CommTiled::init()
if (triclinic)
error->all(FLERR,"Cannot yet use comm_style tiled with triclinic box");
- if (mode == MULTI)
+ if (mode == Comm::MULTI)
error->all(FLERR,"Cannot yet use comm_style tiled with multi-mode comm");
}
@@ -141,7 +138,7 @@ void CommTiled::setup()
// set function pointers
- if (layout != LAYOUT_TILED) {
+ if (layout != Comm::LAYOUT_TILED) {
box_drop = &CommTiled::box_drop_brick;
box_other = &CommTiled::box_other_brick;
box_touch = &CommTiled::box_touch_brick;
@@ -155,7 +152,7 @@ void CommTiled::setup()
// if RCB decomp exists and just changed, gather needed global RCB info
- if (layout == LAYOUT_TILED) coord2proc_setup();
+ if (layout == Comm::LAYOUT_TILED) coord2proc_setup();
// set cutoff for comm forward and comm reverse
// check that cutoff < any periodic box length
@@ -1807,7 +1804,7 @@ void CommTiled::coord2proc_setup()
int CommTiled::coord2proc(double *x, int &igx, int &igy, int &igz)
{
- if (layout != LAYOUT_TILED) return Comm::coord2proc(x,igx,igy,igz);
+ if (layout != Comm::LAYOUT_TILED) return Comm::coord2proc(x,igx,igy,igz);
return point_drop_tiled_recurse(x,0,nprocs-1);
}
diff --git a/src/compute.cpp b/src/compute.cpp
index 467faf9fe1e0e258fd4fb22b3a0c1e7fe9b902d2..207f825ec850b2118ce7dff45668045a295c40fd 100644
--- a/src/compute.cpp
+++ b/src/compute.cpp
@@ -12,9 +12,9 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <stdlib.h>
-#include <string.h>
-#include <ctype.h>
+#include <cstdlib>
+#include <cstring>
+#include <cctype>
#include "compute.h"
#include "atom.h"
#include "domain.h"
diff --git a/src/compute_aggregate_atom.cpp b/src/compute_aggregate_atom.cpp
index d61fd06397c04f982880a1dd2c814e1093bcdcd4..56855fcc29720bf8db93b8a2a6a52f8c1818fd45 100644
--- a/src/compute_aggregate_atom.cpp
+++ b/src/compute_aggregate_atom.cpp
@@ -15,8 +15,8 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <string.h>
-#include <math.h>
+#include <cstring>
+#include <cmath>
#include "compute_aggregate_atom.h"
#include "atom.h"
#include "atom_vec.h"
diff --git a/src/compute_angle.cpp b/src/compute_angle.cpp
index 8546350ecd9afc69398cf9d91b73c03172060843..59945f5832c3f78a7b32d8f6526f40c16da573c3 100644
--- a/src/compute_angle.cpp
+++ b/src/compute_angle.cpp
@@ -12,7 +12,7 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <string.h>
+#include <cstring>
#include "compute_angle.h"
#include "update.h"
#include "force.h"
diff --git a/src/compute_angle_local.cpp b/src/compute_angle_local.cpp
index 1e249554dcd136cf64676d03031bfbec637018a6..7137077158eb33e1dfc2abbea7378426639e0f65 100644
--- a/src/compute_angle_local.cpp
+++ b/src/compute_angle_local.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <string.h>
+#include <cmath>
+#include <cstring>
#include "compute_angle_local.h"
#include "atom.h"
#include "atom_vec.h"
diff --git a/src/compute_angmom_chunk.cpp b/src/compute_angmom_chunk.cpp
index 98c6ea044110e211e28c00765bc45a0c3a4384a2..a70eaaf49f3d334b87067a20f9f27b6560ee7829 100644
--- a/src/compute_angmom_chunk.cpp
+++ b/src/compute_angmom_chunk.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "compute_angmom_chunk.h"
#include "atom.h"
#include "update.h"
diff --git a/src/compute_bond.cpp b/src/compute_bond.cpp
index 29d7ce0ecec42556db00830cd80573ceb171adbf..896aaec9bdfa97c1c84d4fc22244f40396e4ebc3 100644
--- a/src/compute_bond.cpp
+++ b/src/compute_bond.cpp
@@ -12,7 +12,7 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <string.h>
+#include <cstring>
#include "compute_bond.h"
#include "update.h"
#include "force.h"
diff --git a/src/compute_bond_local.cpp b/src/compute_bond_local.cpp
index b7e84d0a29f64e0844931f0a095f406eb2efb07c..985e3ef0756260c9b6e9f258a5d3ab1b080f4605 100644
--- a/src/compute_bond_local.cpp
+++ b/src/compute_bond_local.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <string.h>
+#include <cmath>
+#include <cstring>
#include "compute_bond_local.h"
#include "atom.h"
#include "atom_vec.h"
diff --git a/src/compute_centro_atom.cpp b/src/compute_centro_atom.cpp
index 089c57798008527c99b5046565fce975492c0e41..48af45363598ab0ed8fd8e1b3b9aff5d9c996be3 100644
--- a/src/compute_centro_atom.cpp
+++ b/src/compute_centro_atom.cpp
@@ -15,8 +15,8 @@
Contributing author: Michel Perez (U Lyon) for non-fcc lattices
------------------------------------------------------------------------- */
-#include <string.h>
-#include <stdlib.h>
+#include <cstring>
+#include <cstdlib>
#include "compute_centro_atom.h"
#include "atom.h"
#include "update.h"
diff --git a/src/compute_chunk_atom.cpp b/src/compute_chunk_atom.cpp
index 6a81b181cf50a6f13602ccc35fc89cf8475b3ecb..ddad7eb62fd6e323756795b376a5fa9daa080915 100644
--- a/src/compute_chunk_atom.cpp
+++ b/src/compute_chunk_atom.cpp
@@ -14,8 +14,8 @@
// NOTE: allow for bin center to be variables for sphere/cylinder
#include <mpi.h>
-#include <string.h>
-#include <stdlib.h>
+#include <cstring>
+#include <cstdlib>
#include "compute_chunk_atom.h"
#include "atom.h"
#include "update.h"
diff --git a/src/compute_cluster_atom.cpp b/src/compute_cluster_atom.cpp
index 9a7df03e49ba5bcf919b7714b82a7a70f37c0510..146f8fd1b3c7d64491e1213038b94c4ba9d0a32a 100644
--- a/src/compute_cluster_atom.cpp
+++ b/src/compute_cluster_atom.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <string.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstring>
+#include <cstdlib>
#include "compute_cluster_atom.h"
#include "atom.h"
#include "update.h"
diff --git a/src/compute_cna_atom.cpp b/src/compute_cna_atom.cpp
index bd24e06cae4e289893e48f19affed911f74cdb1e..a1b97d94043dc537102f98cb3a05cbb7555a26a1 100644
--- a/src/compute_cna_atom.cpp
+++ b/src/compute_cna_atom.cpp
@@ -15,8 +15,9 @@
Contributing author: Wan Liang (Chinese Academy of Sciences)
------------------------------------------------------------------------- */
-#include <string.h>
-#include <stdlib.h>
+#include <cstring>
+#include <cstdlib>
+#include <cmath>
#include "compute_cna_atom.h"
#include "atom.h"
#include "update.h"
@@ -29,7 +30,6 @@
#include "comm.h"
#include "memory.h"
#include "error.h"
-#include <math.h>
using namespace LAMMPS_NS;
diff --git a/src/compute_com_chunk.cpp b/src/compute_com_chunk.cpp
index 3eb686783b2511e4db32e7e048aa8b52f1e527a6..ec667672454d66436276b94c64dd9d5f47355279 100644
--- a/src/compute_com_chunk.cpp
+++ b/src/compute_com_chunk.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "compute_com_chunk.h"
#include "atom.h"
#include "update.h"
diff --git a/src/compute_contact_atom.cpp b/src/compute_contact_atom.cpp
index b2186bd17502f735dfc732554739a44f959973f3..f3c4513b0152a2edd090c31d07a46f832d925021 100644
--- a/src/compute_contact_atom.cpp
+++ b/src/compute_contact_atom.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <string.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstring>
+#include <cstdlib>
#include "compute_contact_atom.h"
#include "atom.h"
#include "update.h"
diff --git a/src/compute_coord_atom.cpp b/src/compute_coord_atom.cpp
index 8c69aa787437131f1f376a29a3db7a99d6290def..b86d818d0608d99468658adb982df1afaccf7472 100644
--- a/src/compute_coord_atom.cpp
+++ b/src/compute_coord_atom.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <string.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstring>
+#include <cstdlib>
#include "compute_coord_atom.h"
#include "compute_orientorder_atom.h"
#include "atom.h"
diff --git a/src/compute_dihedral.cpp b/src/compute_dihedral.cpp
index 2afcb5e321ae655cee5c3af02a46a6543ca715e0..3595b2eda32f24e02287753dc04a8f8d9f1714e8 100644
--- a/src/compute_dihedral.cpp
+++ b/src/compute_dihedral.cpp
@@ -12,7 +12,7 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <string.h>
+#include <cstring>
#include "compute_dihedral.h"
#include "update.h"
#include "force.h"
diff --git a/src/compute_dihedral_local.cpp b/src/compute_dihedral_local.cpp
index 7a21d0f9d708a02a73e7deef3230fec065a62143..42d1476ad25fb368b08b36bf99195f3a0750235b 100644
--- a/src/compute_dihedral_local.cpp
+++ b/src/compute_dihedral_local.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <string.h>
+#include <cmath>
+#include <cstring>
#include "compute_dihedral_local.h"
#include "atom.h"
#include "atom_vec.h"
diff --git a/src/compute_dipole_chunk.cpp b/src/compute_dipole_chunk.cpp
index b4beacb9849a792e97e1acd6d44fce5992ef7609..b0474b6359c7a654a8ec97ced8121ac0d3da2b1f 100644
--- a/src/compute_dipole_chunk.cpp
+++ b/src/compute_dipole_chunk.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "compute_dipole_chunk.h"
#include "atom.h"
#include "update.h"
diff --git a/src/compute_displace_atom.cpp b/src/compute_displace_atom.cpp
index a5c32c53cc9496ced1a2ecd6000d55469639ce7e..0b6b40b62a35688d2ed7dde70d9526305c68f075 100644
--- a/src/compute_displace_atom.cpp
+++ b/src/compute_displace_atom.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <string.h>
+#include <cmath>
+#include <cstring>
#include "compute_displace_atom.h"
#include "atom.h"
#include "update.h"
diff --git a/src/compute_erotate_sphere_atom.cpp b/src/compute_erotate_sphere_atom.cpp
index b29c18c1e3438085a630197146af2457e083c6d0..999bc062c57406292cf7b0d469c9f5f1133e0f66 100644
--- a/src/compute_erotate_sphere_atom.cpp
+++ b/src/compute_erotate_sphere_atom.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "compute_erotate_sphere_atom.h"
#include "atom.h"
#include "update.h"
diff --git a/src/compute_fragment_atom.cpp b/src/compute_fragment_atom.cpp
index 8606f54933bda9738267d844747605d49228e6b9..b9fb2331ecf35bca18a9f5803baad10c0273eaa2 100644
--- a/src/compute_fragment_atom.cpp
+++ b/src/compute_fragment_atom.cpp
@@ -15,7 +15,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "compute_fragment_atom.h"
#include "atom.h"
#include "atom_vec.h"
diff --git a/src/compute_global_atom.cpp b/src/compute_global_atom.cpp
index 6cd79f919c9ac27cef83b1edb69b20594ab29c37..dc9ab52f4978268a7fe51dcbd03b5afbeff51a54 100644
--- a/src/compute_global_atom.cpp
+++ b/src/compute_global_atom.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
-#include <stdlib.h>
+#include <cstring>
+#include <cstdlib>
#include "compute_global_atom.h"
#include "atom.h"
#include "update.h"
diff --git a/src/compute_group_group.cpp b/src/compute_group_group.cpp
index 51c978cb530017af17c9cffaf4ca6217551608c8..dc94db50f645ee35f9c1e5b928881aa5a584f155 100644
--- a/src/compute_group_group.cpp
+++ b/src/compute_group_group.cpp
@@ -17,7 +17,8 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <string.h>
+#include <cstring>
+#include <cmath>
#include "compute_group_group.h"
#include "atom.h"
#include "update.h"
@@ -29,7 +30,6 @@
#include "group.h"
#include "kspace.h"
#include "error.h"
-#include <math.h>
#include "comm.h"
#include "domain.h"
#include "math_const.h"
diff --git a/src/compute_gyration.cpp b/src/compute_gyration.cpp
index 0877efa4d9214201442da4463d0c7f0bde1375ac..f8d19853e0e9805ff8d2e1891dd56c486487156a 100644
--- a/src/compute_gyration.cpp
+++ b/src/compute_gyration.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "compute_gyration.h"
#include "update.h"
#include "atom.h"
diff --git a/src/compute_gyration_chunk.cpp b/src/compute_gyration_chunk.cpp
index efb26c9ad2721f006da6ee4896baa313b7755453..6a23398aca3151533a39c317aafc73f1a5dc650e 100644
--- a/src/compute_gyration_chunk.cpp
+++ b/src/compute_gyration_chunk.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <string.h>
+#include <cmath>
+#include <cstring>
#include "compute_gyration_chunk.h"
#include "atom.h"
#include "update.h"
diff --git a/src/compute_heat_flux.cpp b/src/compute_heat_flux.cpp
index 108691aec240b46907fa4189199d99af5dc428a5..e402da7842a70ccf35ed3980e0bd8e93af6abded 100644
--- a/src/compute_heat_flux.cpp
+++ b/src/compute_heat_flux.cpp
@@ -16,8 +16,8 @@
Mario Pinto (Computational Research Lab, Pune, India)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <string.h>
+#include <cmath>
+#include <cstring>
#include "compute_heat_flux.h"
#include "atom.h"
#include "update.h"
diff --git a/src/compute_hexorder_atom.cpp b/src/compute_hexorder_atom.cpp
index 44525e67a2e9f2d5e7f0443d4574db2b1386f40f..cb2946beba8e7833feb9115566f38505108360cb 100644
--- a/src/compute_hexorder_atom.cpp
+++ b/src/compute_hexorder_atom.cpp
@@ -16,8 +16,8 @@
------------------------------------------------------------------------- */
#include <complex>
-#include <string.h>
-#include <stdlib.h>
+#include <cstring>
+#include <cstdlib>
#include "compute_hexorder_atom.h"
#include "atom.h"
#include "update.h"
diff --git a/src/compute_improper.cpp b/src/compute_improper.cpp
index 60d22d0d70d938d8718f62eb6e5a21d875afb37b..ac2a23e727cc87bb65e23063b4e105c87fa61afe 100644
--- a/src/compute_improper.cpp
+++ b/src/compute_improper.cpp
@@ -12,7 +12,7 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <string.h>
+#include <cstring>
#include "compute_improper.h"
#include "update.h"
#include "force.h"
diff --git a/src/compute_improper_local.cpp b/src/compute_improper_local.cpp
index e183405956721349fdc43c15a779e7f3661700bf..f54cb67535e2e1eed7ce88253b1a0284bdffe0cf 100644
--- a/src/compute_improper_local.cpp
+++ b/src/compute_improper_local.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <string.h>
+#include <cmath>
+#include <cstring>
#include "compute_improper_local.h"
#include "atom.h"
#include "atom_vec.h"
diff --git a/src/compute_inertia_chunk.cpp b/src/compute_inertia_chunk.cpp
index 1e3c595ed1db93406d9a8e1c1528ac09413f9e1b..a33073c35a8194f61302f2e7831d424f40aae1e7 100644
--- a/src/compute_inertia_chunk.cpp
+++ b/src/compute_inertia_chunk.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "compute_inertia_chunk.h"
#include "atom.h"
#include "update.h"
diff --git a/src/compute_ke_atom.cpp b/src/compute_ke_atom.cpp
index da159669dea4f88f615639f4379fbc9b36776ac6..c5506996dab5843e97260d51f7342088f77ae727 100644
--- a/src/compute_ke_atom.cpp
+++ b/src/compute_ke_atom.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "compute_ke_atom.h"
#include "atom.h"
#include "update.h"
diff --git a/src/compute_msd.cpp b/src/compute_msd.cpp
index ac510bca8eb59e7bd6c2ff315738aab8bc673cad..fc47b2609a264c3ef8d3e4a925d627818fcb51f7 100644
--- a/src/compute_msd.cpp
+++ b/src/compute_msd.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "compute_msd.h"
#include "atom.h"
#include "update.h"
diff --git a/src/compute_msd_chunk.cpp b/src/compute_msd_chunk.cpp
index 69cd87f96b6b62d800eb0a7e54587525bc779cfd..1f974cc06cd0163c7dfc511370bb55e5afe96df2 100644
--- a/src/compute_msd_chunk.cpp
+++ b/src/compute_msd_chunk.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "compute_msd_chunk.h"
#include "atom.h"
#include "group.h"
diff --git a/src/compute_omega_chunk.cpp b/src/compute_omega_chunk.cpp
index d89c57889e2ce515fca42ec070ef898eda1786c6..23447da602d492a6ad97924891f6cb56a6e8ce15 100644
--- a/src/compute_omega_chunk.cpp
+++ b/src/compute_omega_chunk.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "compute_omega_chunk.h"
#include "atom.h"
#include "update.h"
diff --git a/src/compute_orientorder_atom.cpp b/src/compute_orientorder_atom.cpp
index 4fc9ab060b39eda652f027023d1864535c6b3355..f263fdfaed0caa3cdeea54cf149b080c716bf7be 100644
--- a/src/compute_orientorder_atom.cpp
+++ b/src/compute_orientorder_atom.cpp
@@ -16,9 +16,9 @@
Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <string.h>
-#include <stdlib.h>
-#include <math.h>
+#include <cstring>
+#include <cstdlib>
+#include <cmath>
#include "compute_orientorder_atom.h"
#include "atom.h"
#include "update.h"
diff --git a/src/compute_pair.cpp b/src/compute_pair.cpp
index b00944e1bcc6b42a9eae7d9170fd402421a38d37..444395bae5dc999fbf9181be76822762a2eeec58 100644
--- a/src/compute_pair.cpp
+++ b/src/compute_pair.cpp
@@ -12,7 +12,7 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <string.h>
+#include <cstring>
#include "compute_pair.h"
#include "update.h"
#include "force.h"
diff --git a/src/compute_pair_local.cpp b/src/compute_pair_local.cpp
index 1d28ae8b769ebcbc7ea427fa9b5008e986a03fc2..3f1147ed2778c3640c749ee76c7db66b28f9ca24 100644
--- a/src/compute_pair_local.cpp
+++ b/src/compute_pair_local.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <string.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstring>
+#include <cstdlib>
#include "compute_pair_local.h"
#include "atom.h"
#include "update.h"
diff --git a/src/compute_pe.cpp b/src/compute_pe.cpp
index 342c1c5cc550f6d57165c71d35e214da433b3fe0..5839ec209599834366af029d48f37d03c2d2a6eb 100644
--- a/src/compute_pe.cpp
+++ b/src/compute_pe.cpp
@@ -12,7 +12,7 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <string.h>
+#include <cstring>
#include "compute_pe.h"
#include "atom.h"
#include "update.h"
diff --git a/src/compute_pe_atom.cpp b/src/compute_pe_atom.cpp
index c324a8eff7d4740b723c96559f0a69bf9dc92ed4..2f1dc5650eb5b7f507efece1cd7ac065547812d0 100644
--- a/src/compute_pe_atom.cpp
+++ b/src/compute_pe_atom.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "compute_pe_atom.h"
#include "atom.h"
#include "update.h"
diff --git a/src/compute_pressure.cpp b/src/compute_pressure.cpp
index 99046e864cc0f418c765fab9c80f65253b9edfa1..dde02a5aed62dabd961a4812b110db115505c70f 100644
--- a/src/compute_pressure.cpp
+++ b/src/compute_pressure.cpp
@@ -12,8 +12,8 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <string.h>
-#include <stdlib.h>
+#include <cstring>
+#include <cstdlib>
#include "compute_pressure.h"
#include "atom.h"
#include "update.h"
diff --git a/src/compute_property_atom.cpp b/src/compute_property_atom.cpp
index 8175e09b1c8e1f2f92e5a5f24118f64980474f6d..862a66e3f947312e68a649ccbae0e196413be89b 100644
--- a/src/compute_property_atom.cpp
+++ b/src/compute_property_atom.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <string.h>
+#include <cmath>
+#include <cstring>
#include "compute_property_atom.h"
#include "math_extra.h"
#include "atom.h"
diff --git a/src/compute_property_chunk.cpp b/src/compute_property_chunk.cpp
index c169e20d739a6ff6b1d59351abc1a9d126e570fc..489890e1cc4608f4fd7c54a33bef3ec33db0e843 100644
--- a/src/compute_property_chunk.cpp
+++ b/src/compute_property_chunk.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "compute_property_chunk.h"
#include "atom.h"
#include "update.h"
diff --git a/src/compute_property_local.cpp b/src/compute_property_local.cpp
index e38817b4ea8085a22f3dda409d9be22d272a4a7a..ad68459650a500a513f9d9e7718377f7a2870247 100644
--- a/src/compute_property_local.cpp
+++ b/src/compute_property_local.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "compute_property_local.h"
#include "atom.h"
#include "atom_vec.h"
diff --git a/src/compute_rdf.cpp b/src/compute_rdf.cpp
index bcb620f3b36c59dd842669dd626baebcda760f31..263e7f799ba02eb254dcc422fdddd86f2bfa798f 100644
--- a/src/compute_rdf.cpp
+++ b/src/compute_rdf.cpp
@@ -16,9 +16,9 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "compute_rdf.h"
#include "atom.h"
#include "update.h"
diff --git a/src/compute_rdf.h b/src/compute_rdf.h
index af4f56e838500eda3f4674537e42230c32bcc75f..52a93a38dd78deac22423ef8930b4f3371dc5fa9 100644
--- a/src/compute_rdf.h
+++ b/src/compute_rdf.h
@@ -20,7 +20,7 @@ ComputeStyle(rdf,ComputeRDF)
#ifndef LMP_COMPUTE_RDF_H
#define LMP_COMPUTE_RDF_H
-#include <stdio.h>
+#include <cstdio>
#include "compute.h"
namespace LAMMPS_NS {
diff --git a/src/compute_reduce.cpp b/src/compute_reduce.cpp
index 91379e9ba6dca5169c052530c71b53b032a869c7..7c61d666b2d9db9c9625b69bb08dfdafff49fa29 100644
--- a/src/compute_reduce.cpp
+++ b/src/compute_reduce.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
-#include <stdlib.h>
+#include <cstring>
+#include <cstdlib>
#include "compute_reduce.h"
#include "atom.h"
#include "update.h"
diff --git a/src/compute_reduce_region.cpp b/src/compute_reduce_region.cpp
index c867a0190ccde7331cb0060304124570891fd7f7..77cd6371c691170776926da985522f7923f69316 100644
--- a/src/compute_reduce_region.cpp
+++ b/src/compute_reduce_region.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
-#include <stdlib.h>
+#include <cstring>
+#include <cstdlib>
#include "compute_reduce_region.h"
#include "atom.h"
#include "update.h"
diff --git a/src/compute_slice.cpp b/src/compute_slice.cpp
index 23bed054ace3815a9a9cb19770ec17369e55b954..ac70e7dd15803751674ffaf9ee3fc25e5f674c06 100644
--- a/src/compute_slice.cpp
+++ b/src/compute_slice.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <stdlib.h>
-#include <string.h>
+#include <cstdlib>
+#include <cstring>
#include "compute_slice.h"
#include "update.h"
#include "modify.h"
diff --git a/src/compute_stress_atom.cpp b/src/compute_stress_atom.cpp
index fd38f13dbab0dd9c840b8db14e6ec3d9d4167706..5211f015abd19054f39552fa49f20f2fec68ebcb 100644
--- a/src/compute_stress_atom.cpp
+++ b/src/compute_stress_atom.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <stdlib.h>
-#include <string.h>
+#include <cstdlib>
+#include <cstring>
#include "compute_stress_atom.h"
#include "atom.h"
#include "update.h"
diff --git a/src/compute_temp.cpp b/src/compute_temp.cpp
index 1fbab924b83ddc63930f70f4da031fd27b7151cd..f7d3a890ec6d9a044ab6b2cfbac9af8ca28b5611 100644
--- a/src/compute_temp.cpp
+++ b/src/compute_temp.cpp
@@ -12,7 +12,7 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <string.h>
+#include <cstring>
#include "compute_temp.h"
#include "atom.h"
#include "update.h"
diff --git a/src/compute_temp_chunk.cpp b/src/compute_temp_chunk.cpp
index 1cc98c4ee83c9d63d3027b96271f74233573117f..920515e05c54ca3e4e9cb5437e3392b83a4a351b 100644
--- a/src/compute_temp_chunk.cpp
+++ b/src/compute_temp_chunk.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "compute_temp_chunk.h"
#include "atom.h"
#include "update.h"
diff --git a/src/compute_temp_com.cpp b/src/compute_temp_com.cpp
index 6d64ff5aee5af36ba8fb34b72d9fd6a25f32598b..35f4512ab2b76e8c7b16d1de171588b6c2a547f6 100644
--- a/src/compute_temp_com.cpp
+++ b/src/compute_temp_com.cpp
@@ -12,8 +12,8 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cstdlib>
+#include <cstring>
#include "compute_temp_com.h"
#include "atom.h"
#include "update.h"
diff --git a/src/compute_temp_deform.cpp b/src/compute_temp_deform.cpp
index c8b8200770e237d7b3d33c6698526f797fc5e758..8729204e700d5bd105ed4ac35f4468068dfb8547 100644
--- a/src/compute_temp_deform.cpp
+++ b/src/compute_temp_deform.cpp
@@ -16,7 +16,7 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <string.h>
+#include <cstring>
#include "compute_temp_deform.h"
#include "domain.h"
#include "atom.h"
@@ -32,8 +32,6 @@
using namespace LAMMPS_NS;
-enum{NO_REMAP,X_REMAP,V_REMAP}; // same as fix_deform.cpp
-
/* ---------------------------------------------------------------------- */
ComputeTempDeform::ComputeTempDeform(LAMMPS *lmp, int narg, char **arg) :
@@ -71,7 +69,7 @@ void ComputeTempDeform::init()
for (i = 0; i < modify->nfix; i++)
if (strcmp(modify->fix[i]->style,"deform") == 0) {
- if (((FixDeform *) modify->fix[i])->remapflag == X_REMAP &&
+ if (((FixDeform *) modify->fix[i])->remapflag == Domain::X_REMAP &&
comm->me == 0)
error->warning(FLERR,"Using compute temp/deform with inconsistent "
"fix deform remap option");
diff --git a/src/compute_temp_partial.cpp b/src/compute_temp_partial.cpp
index 9df8e8b580f137f1fe73cc0b26ccf00bd82827cb..4b87a2249ed1f96593a901d264b1b9bd61f20621 100644
--- a/src/compute_temp_partial.cpp
+++ b/src/compute_temp_partial.cpp
@@ -12,7 +12,7 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <stdlib.h>
+#include <cstdlib>
#include "compute_temp_partial.h"
#include "atom.h"
#include "update.h"
diff --git a/src/compute_temp_profile.cpp b/src/compute_temp_profile.cpp
index 236f5bc0960ff90b88c149c7d0dc9700172564cd..c7f0b28a6cb096184ad2f3b2cdd269df7af2664f 100644
--- a/src/compute_temp_profile.cpp
+++ b/src/compute_temp_profile.cpp
@@ -12,8 +12,8 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cstdlib>
+#include <cstring>
#include "compute_temp_profile.h"
#include "atom.h"
#include "update.h"
diff --git a/src/compute_temp_ramp.cpp b/src/compute_temp_ramp.cpp
index af6a730c9d2869c311afd572f1262023d0681839..42d258d8b2fe626d68524fc21af9b427dd477baf 100644
--- a/src/compute_temp_ramp.cpp
+++ b/src/compute_temp_ramp.cpp
@@ -12,8 +12,8 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cstdlib>
+#include <cstring>
#include "compute_temp_ramp.h"
#include "atom.h"
#include "update.h"
diff --git a/src/compute_temp_region.cpp b/src/compute_temp_region.cpp
index ed710bc73096a2093cf963eed78c4d717ed2b345..bde70a20f0c44058961dab409ca605bfe4e7a81e 100644
--- a/src/compute_temp_region.cpp
+++ b/src/compute_temp_region.cpp
@@ -12,7 +12,7 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <string.h>
+#include <cstring>
#include "compute_temp_region.h"
#include "atom.h"
#include "update.h"
diff --git a/src/compute_temp_sphere.cpp b/src/compute_temp_sphere.cpp
index ad5cf565e9a8ecc4b3e1339ed6696693edcfd280..651da6dee521309e8e8951445359f0e20f1f34f0 100644
--- a/src/compute_temp_sphere.cpp
+++ b/src/compute_temp_sphere.cpp
@@ -12,7 +12,7 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <string.h>
+#include <cstring>
#include "compute_temp_sphere.h"
#include "atom.h"
#include "atom_vec.h"
diff --git a/src/compute_torque_chunk.cpp b/src/compute_torque_chunk.cpp
index 25386ad40d7873e836dd40738f2a022072de8107..d9de99bcb2589e4c8bfcb6fc63bf43163efe0761 100644
--- a/src/compute_torque_chunk.cpp
+++ b/src/compute_torque_chunk.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "compute_torque_chunk.h"
#include "atom.h"
#include "update.h"
diff --git a/src/compute_vacf.cpp b/src/compute_vacf.cpp
index b3f487a4d758cfdf2c9af81f77887f2833ee2a04..3ef3acf0bf662100946755fe3034a2c52f97b1d6 100644
--- a/src/compute_vacf.cpp
+++ b/src/compute_vacf.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "compute_vacf.h"
#include "atom.h"
#include "update.h"
diff --git a/src/compute_vcm_chunk.cpp b/src/compute_vcm_chunk.cpp
index 0661bf44574d1f0a2ace74caa8fba70bc5172adf..a6dd796c63c7e71db984e60550ef4918d777cb83 100644
--- a/src/compute_vcm_chunk.cpp
+++ b/src/compute_vcm_chunk.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "compute_vcm_chunk.h"
#include "atom.h"
#include "update.h"
diff --git a/src/create_atoms.cpp b/src/create_atoms.cpp
index 6caa4157ce89e5b7b241415e0a357d111358eaf0..dcc36aa5d433e889d1baa5b7c09302aa66416ce9 100644
--- a/src/create_atoms.cpp
+++ b/src/create_atoms.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "create_atoms.h"
#include "atom.h"
#include "atom_vec.h"
@@ -44,7 +44,6 @@ using namespace MathConst;
enum{BOX,REGION,SINGLE,RANDOM};
enum{ATOM,MOLECULE};
-enum{LAYOUT_UNIFORM,LAYOUT_NONUNIFORM,LAYOUT_TILED}; // several files
/* ---------------------------------------------------------------------- */
@@ -314,7 +313,7 @@ void CreateAtoms::command(int narg, char **arg)
}
if (style == BOX || style == REGION) {
- if (comm->layout != LAYOUT_TILED) {
+ if (comm->layout != Comm::LAYOUT_TILED) {
if (domain->xperiodic) {
if (comm->myloc[0] == 0) sublo[0] -= epsilon[0];
if (comm->myloc[0] == comm->procgrid[0]-1) subhi[0] -= 2.0*epsilon[0];
diff --git a/src/create_bonds.cpp b/src/create_bonds.cpp
index f19458772086dd9831f517e9d22011780d2b3088..751c4746ba5286aaa39a2b9089a4e4d1ec217a49 100644
--- a/src/create_bonds.cpp
+++ b/src/create_bonds.cpp
@@ -15,8 +15,8 @@
Contributing authors: Mike Salerno (NRL) added single methods
------------------------------------------------------------------------- */
-#include <stdlib.h>
-#include <string.h>
+#include <cstdlib>
+#include <cstring>
#include "create_bonds.h"
#include "atom.h"
#include "domain.h"
@@ -323,9 +323,13 @@ void CreateBonds::single_bond()
// check that 2 atoms exist
+ const int nlocal = atom->nlocal;
+ const int idx1 = atom->map(batom1);
+ const int idx2 = atom->map(batom2);
+
int count = 0;
- if (atom->map(batom1) >= 0) count++;
- if (atom->map(batom2) >= 0) count++;
+ if ((idx1 >= 0) && (idx1 < nlocal)) count++;
+ if ((idx2 >= 0) && (idx2 < nlocal)) count++;
int allcount;
MPI_Allreduce(&count,&allcount,1,MPI_INT,MPI_SUM,world);
@@ -338,7 +342,7 @@ void CreateBonds::single_bond()
int **bond_type = atom->bond_type;
tagint **bond_atom = atom->bond_atom;
- if ((m = atom->map(batom1)) >= 0) {
+ if ((m = idx1) >= 0) {
if (num_bond[m] == atom->bond_per_atom)
error->one(FLERR,"New bond exceeded bonds per atom in create_bonds");
bond_type[m][num_bond[m]] = btype;
@@ -349,7 +353,7 @@ void CreateBonds::single_bond()
if (force->newton_bond) return;
- if ((m = atom->map(batom2)) >= 0) {
+ if ((m = idx2) >= 0) {
if (num_bond[m] == atom->bond_per_atom)
error->one(FLERR,"New bond exceeded bonds per atom in create_bonds");
bond_type[m][num_bond[m]] = btype;
@@ -366,10 +370,15 @@ void CreateBonds::single_angle()
// check that 3 atoms exist
+ const int nlocal = atom->nlocal;
+ const int idx1 = atom->map(aatom1);
+ const int idx2 = atom->map(aatom2);
+ const int idx3 = atom->map(aatom3);
+
int count = 0;
- if (atom->map(aatom1) >= 0) count++;
- if (atom->map(aatom2) >= 0) count++;
- if (atom->map(aatom3) >= 0) count++;
+ if ((idx1 >= 0) && (idx1 < nlocal)) count++;
+ if ((idx2 >= 0) && (idx2 < nlocal)) count++;
+ if ((idx3 >= 0) && (idx3 < nlocal)) count++;
int allcount;
MPI_Allreduce(&count,&allcount,1,MPI_INT,MPI_SUM,world);
@@ -384,7 +393,7 @@ void CreateBonds::single_angle()
tagint **angle_atom2 = atom->angle_atom2;
tagint **angle_atom3 = atom->angle_atom3;
- if ((m = atom->map(aatom2)) >= 0) {
+ if ((m = idx2) >= 0) {
if (num_angle[m] == atom->angle_per_atom)
error->one(FLERR,"New angle exceeded angles per atom in create_bonds");
angle_type[m][num_angle[m]] = atype;
@@ -397,7 +406,7 @@ void CreateBonds::single_angle()
if (force->newton_bond) return;
- if ((m = atom->map(aatom1)) >= 0) {
+ if ((m = idx1) >= 0) {
if (num_angle[m] == atom->angle_per_atom)
error->one(FLERR,"New angle exceeded angles per atom in create_bonds");
angle_type[m][num_angle[m]] = atype;
@@ -407,7 +416,7 @@ void CreateBonds::single_angle()
num_angle[m]++;
}
- if ((m = atom->map(aatom3)) >= 0) {
+ if ((m = idx3) >= 0) {
if (num_angle[m] == atom->angle_per_atom)
error->one(FLERR,"New angle exceeded angles per atom in create_bonds");
angle_type[m][num_angle[m]] = atype;
@@ -426,11 +435,17 @@ void CreateBonds::single_dihedral()
// check that 4 atoms exist
+ const int nlocal = atom->nlocal;
+ const int idx1 = atom->map(datom1);
+ const int idx2 = atom->map(datom2);
+ const int idx3 = atom->map(datom3);
+ const int idx4 = atom->map(datom4);
+
int count = 0;
- if (atom->map(datom1) >= 0) count++;
- if (atom->map(datom2) >= 0) count++;
- if (atom->map(datom3) >= 0) count++;
- if (atom->map(datom4) >= 0) count++;
+ if ((idx1 >= 0) && (idx1 < nlocal)) count++;
+ if ((idx2 >= 0) && (idx2 < nlocal)) count++;
+ if ((idx3 >= 0) && (idx3 < nlocal)) count++;
+ if ((idx4 >= 0) && (idx4 < nlocal)) count++;
int allcount;
MPI_Allreduce(&count,&allcount,1,MPI_INT,MPI_SUM,world);
@@ -446,7 +461,7 @@ void CreateBonds::single_dihedral()
tagint **dihedral_atom3 = atom->dihedral_atom3;
tagint **dihedral_atom4 = atom->dihedral_atom4;
- if ((m = atom->map(datom2)) >= 0) {
+ if ((m = idx2) >= 0) {
if (num_dihedral[m] == atom->dihedral_per_atom)
error->one(FLERR,
"New dihedral exceeded dihedrals per atom in create_bonds");
@@ -461,7 +476,7 @@ void CreateBonds::single_dihedral()
if (force->newton_bond) return;
- if ((m = atom->map(datom1)) >= 0) {
+ if ((m = idx1) >= 0) {
if (num_dihedral[m] == atom->dihedral_per_atom)
error->one(FLERR,
"New dihedral exceeded dihedrals per atom in create_bonds");
@@ -473,7 +488,7 @@ void CreateBonds::single_dihedral()
num_dihedral[m]++;
}
- if ((m = atom->map(datom3)) >= 0) {
+ if ((m = idx3) >= 0) {
if (num_dihedral[m] == atom->dihedral_per_atom)
error->one(FLERR,
"New dihedral exceeded dihedrals per atom in create_bonds");
@@ -485,7 +500,7 @@ void CreateBonds::single_dihedral()
num_dihedral[m]++;
}
- if ((m = atom->map(datom4)) >= 0) {
+ if ((m = idx4) >= 0) {
if (num_dihedral[m] == atom->dihedral_per_atom)
error->one(FLERR,
"New dihedral exceeded dihedrals per atom in create_bonds");
diff --git a/src/create_box.cpp b/src/create_box.cpp
index 3a131099813e086d1dd961a28748824959cfe50e..b5e37b759ca0bd4b6ec0cd7c49aeacf859450bde 100644
--- a/src/create_box.cpp
+++ b/src/create_box.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <stdlib.h>
-#include <string.h>
+#include <cstdlib>
+#include <cstring>
#include "create_box.h"
#include "atom.h"
#include "atom_vec.h"
diff --git a/src/delete_atoms.cpp b/src/delete_atoms.cpp
index f5324f95585417c787e149ddc0d3566cc79c49f1..e26ecad5f37a7e9fc44dce761dbf1f22b5895b40 100644
--- a/src/delete_atoms.cpp
+++ b/src/delete_atoms.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <stdlib.h>
-#include <string.h>
+#include <cstdlib>
+#include <cstring>
#include "delete_atoms.h"
#include "atom.h"
#include "atom_vec.h"
diff --git a/src/delete_bonds.cpp b/src/delete_bonds.cpp
index 97eb1c09a857246f3236be089f73c1cb46008325..fe32bca87977d92ac7c8b3a8f64509117cb1e619 100644
--- a/src/delete_bonds.cpp
+++ b/src/delete_bonds.cpp
@@ -12,8 +12,8 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cstdlib>
+#include <cstring>
#include "delete_bonds.h"
#include "atom.h"
#include "atom_vec.h"
diff --git a/src/dihedral.cpp b/src/dihedral.cpp
index f5c1c6c44c143604cec5ec3aa9b1bbd8ea03688d..adccf2a490b32d90828b69110bbb97e512934b09 100644
--- a/src/dihedral.cpp
+++ b/src/dihedral.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "dihedral.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/dihedral.h b/src/dihedral.h
index d27810c4d6e79ede7d5875daced83861f2461346..627104871b9b51f8b13966af119e64a3b12c6f1a 100644
--- a/src/dihedral.h
+++ b/src/dihedral.h
@@ -14,7 +14,7 @@
#ifndef LMP_DIHEDRAL_H
#define LMP_DIHEDRAL_H
-#include <stdio.h>
+#include <cstdio>
#include "pointers.h"
namespace LAMMPS_NS {
diff --git a/src/dihedral_hybrid.cpp b/src/dihedral_hybrid.cpp
index 372a858d023e19730129c4bf8d85083b383e6514..b9107ac874cc674f01cda6c7fce741f21c58432a 100644
--- a/src/dihedral_hybrid.cpp
+++ b/src/dihedral_hybrid.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <string.h>
-#include <ctype.h>
+#include <cmath>
+#include <cstring>
+#include <cctype>
#include "dihedral_hybrid.h"
#include "atom.h"
#include "neighbor.h"
diff --git a/src/dihedral_hybrid.h b/src/dihedral_hybrid.h
index 6e30d3d693373ca6859a52ac2a9f9acdab07c93b..0839fdfc61a8f6cdb9c45589d5cfbe6495d79167 100644
--- a/src/dihedral_hybrid.h
+++ b/src/dihedral_hybrid.h
@@ -20,7 +20,7 @@ DihedralStyle(hybrid,DihedralHybrid)
#ifndef LMP_DIHEDRAL_HYBRID_H
#define LMP_DIHEDRAL_HYBRID_H
-#include <stdio.h>
+#include <cstdio>
#include "dihedral.h"
namespace LAMMPS_NS {
diff --git a/src/dihedral_zero.cpp b/src/dihedral_zero.cpp
index 9b0c569fcac8743bf3124bcfe1359aeb35f07e40..bdd2eaadd3d484e5f709531be0ac43635b826ed1 100644
--- a/src/dihedral_zero.cpp
+++ b/src/dihedral_zero.cpp
@@ -15,9 +15,9 @@
Contributing author: Carsten Svaneborg (SDU)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "dihedral_zero.h"
#include "atom.h"
#include "force.h"
diff --git a/src/dihedral_zero.h b/src/dihedral_zero.h
index d27ff6abbad9f5acc0e00558a0a1482f4f89c7d9..e7dbb0d3a53a9dae1f675db394b6755f68efa42d 100644
--- a/src/dihedral_zero.h
+++ b/src/dihedral_zero.h
@@ -24,7 +24,7 @@ DihedralStyle(zero,DihedralZero)
#ifndef LMP_DIHEDRAL_ZERO_H
#define LMP_DIHEDRAL_ZERO_H
-#include <stdio.h>
+#include <cstdio>
#include "dihedral.h"
namespace LAMMPS_NS {
diff --git a/src/displace_atoms.cpp b/src/displace_atoms.cpp
index 66988d467339c4d56a3b6d93ed136ab700473d23..04088bec8ce76233552a9f39da188d853eb0e7e1 100644
--- a/src/displace_atoms.cpp
+++ b/src/displace_atoms.cpp
@@ -12,8 +12,8 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cstdlib>
+#include <cstring>
#include "displace_atoms.h"
#include "atom.h"
#include "modify.h"
diff --git a/src/domain.cpp b/src/domain.cpp
index c4dcf20b6423dc48d98c28243dbec9f97738b3ec..4c1d12018b1b6076819e3938239e70129c61d989 100644
--- a/src/domain.cpp
+++ b/src/domain.cpp
@@ -16,10 +16,10 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <stdlib.h>
-#include <string.h>
-#include <stdio.h>
-#include <math.h>
+#include <cstdlib>
+#include <cstring>
+#include <cstdio>
+#include <cmath>
#include "domain.h"
#include "style_region.h"
#include "atom.h"
@@ -44,10 +44,6 @@
using namespace LAMMPS_NS;
using namespace MathConst;
-enum{NO_REMAP,X_REMAP,V_REMAP}; // same as fix_deform.cpp
-enum{IGNORE,WARN,ERROR}; // same as thermo.cpp
-enum{LAYOUT_UNIFORM,LAYOUT_NONUNIFORM,LAYOUT_TILED}; // several files
-
#define BIG 1.0e20
#define SMALL 1.0e-4
#define DELTAREGION 4
@@ -155,7 +151,7 @@ void Domain::init()
for (int i = 0; i < modify->nfix; i++)
if (strcmp(modify->fix[i]->style,"deform") == 0) {
deform_flag = 1;
- if (((FixDeform *) modify->fix[i])->remapflag == V_REMAP) {
+ if (((FixDeform *) modify->fix[i])->remapflag == Domain::V_REMAP) {
deform_vremap = 1;
deform_groupbit = modify->fix[i]->groupbit;
}
@@ -276,7 +272,7 @@ void Domain::set_global_box()
void Domain::set_lamda_box()
{
- if (comm->layout != LAYOUT_TILED) {
+ if (comm->layout != Comm::LAYOUT_TILED) {
int *myloc = comm->myloc;
double *xsplit = comm->xsplit;
double *ysplit = comm->ysplit;
@@ -313,7 +309,7 @@ void Domain::set_local_box()
{
if (triclinic) return;
- if (comm->layout != LAYOUT_TILED) {
+ if (comm->layout != Comm::LAYOUT_TILED) {
int *myloc = comm->myloc;
int *procgrid = comm->procgrid;
double *xsplit = comm->xsplit;
@@ -518,7 +514,7 @@ void Domain::pbc()
coord = &x[0][0]; // note: x is always initialized to at least one element.
int flag = 0;
for (i = 0; i < n3; i++)
- if (!ISFINITE(*coord++)) flag = 1;
+ if (!std::isfinite(*coord++)) flag = 1;
if (flag) error->one(FLERR,"Non-numeric atom coords - simulation unstable");
// setup for PBC checks
@@ -762,7 +758,7 @@ void Domain::image_check()
if (k == -1) {
nmissing++;
- if (lostbond == ERROR)
+ if (lostbond == Thermo::ERROR)
error->one(FLERR,"Bond atom missing in image check");
continue;
}
@@ -785,7 +781,7 @@ void Domain::image_check()
if (flagall && comm->me == 0)
error->warning(FLERR,"Inconsistent image flags");
- if (lostbond == WARN) {
+ if (lostbond == Thermo::WARN) {
int all;
MPI_Allreduce(&nmissing,&all,1,MPI_INT,MPI_SUM,world);
if (all && comm->me == 0)
@@ -861,7 +857,7 @@ void Domain::box_too_small_check()
if (k == -1) {
nmissing++;
- if (lostbond == ERROR)
+ if (lostbond == Thermo::ERROR)
error->one(FLERR,"Bond atom missing in box size check");
continue;
}
@@ -875,7 +871,7 @@ void Domain::box_too_small_check()
}
}
- if (lostbond == WARN) {
+ if (lostbond == Thermo::WARN) {
int all;
MPI_Allreduce(&nmissing,&all,1,MPI_INT,MPI_SUM,world);
if (all && comm->me == 0)
diff --git a/src/domain.h b/src/domain.h
index 649e722c50723ee4283a5cdba205d4c48c5311f9..5581f9a45fc85eb2a5d79f353e5bc53e41ba2e89 100644
--- a/src/domain.h
+++ b/src/domain.h
@@ -14,7 +14,7 @@
#ifndef LMP_DOMAIN_H
#define LMP_DOMAIN_H
-#include <math.h>
+#include <cmath>
#include "pointers.h"
#include <map>
#include <string>
@@ -93,6 +93,7 @@ class Domain : protected Pointers {
class Region **regions; // list of defined Regions
int copymode;
+ enum{NO_REMAP,X_REMAP,V_REMAP};
typedef Region *(*RegionCreator)(LAMMPS *,int,char**);
typedef std::map<std::string,RegionCreator> RegionCreatorMap;
diff --git a/src/dump.cpp b/src/dump.cpp
index be42693b8dacb7e2886b7fb1018f4a1271e01754..7c171015bb4e201f8a8602294ad53c2c9937fbf6 100644
--- a/src/dump.cpp
+++ b/src/dump.cpp
@@ -12,9 +12,9 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <stdlib.h>
-#include <string.h>
-#include <stdio.h>
+#include <cstdlib>
+#include <cstring>
+#include <cstdio>
#include "dump.h"
#include "atom.h"
#include "irregular.h"
@@ -91,6 +91,11 @@ Dump::Dump(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
pbcflag = 0;
delay_flag = 0;
+ maxfiles = -1;
+ numfiles = 0;
+ fileidx = 0;
+ nameslist = NULL;
+
maxbuf = maxids = maxsort = maxproc = 0;
buf = bufsort = NULL;
ids = idsort = NULL;
@@ -187,6 +192,14 @@ Dump::~Dump()
if (multiproc) MPI_Comm_free(&clustercomm);
+ // delete storage for caching file names
+
+ if (maxfiles > 0) {
+ for (int idx=0; idx < numfiles; ++idx)
+ delete[] nameslist[idx];
+ delete[] nameslist;
+ }
+
// XTC style sets fp to NULL since it closes file in its destructor
if (multifile == 0 && fp != NULL) {
@@ -549,6 +562,19 @@ void Dump::openfile()
sprintf(filecurrent,pad,filestar,update->ntimestep,ptr+1);
}
*ptr = '*';
+ if (maxfiles > 0) {
+ if (numfiles < maxfiles) {
+ nameslist[numfiles] = new char[strlen(filecurrent)+1];
+ strcpy(nameslist[numfiles],filecurrent);
+ ++numfiles;
+ } else {
+ remove(nameslist[fileidx]);
+ delete[] nameslist[fileidx];
+ nameslist[fileidx] = new char[strlen(filecurrent)+1];
+ strcpy(nameslist[fileidx],filecurrent);
+ fileidx = (fileidx + 1) % maxfiles;
+ }
+ }
}
// each proc with filewriter = 1 opens a file
@@ -1003,6 +1029,27 @@ void Dump::modify_params(int narg, char **arg)
iarg += n;
}
+ } else if (strcmp(arg[iarg],"maxfiles") == 0) {
+ if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command");
+ if (!multifile)
+ error->all(FLERR,"Cannot use dump_modify maxfiles "
+ "without * in dump file name");
+ // wipe out existing storage
+ if (maxfiles > 0) {
+ for (int idx=0; idx < numfiles; ++idx)
+ delete[] nameslist[idx];
+ delete[] nameslist;
+ }
+ maxfiles = force->inumeric(FLERR,arg[iarg+1]);
+ if (maxfiles == 0) error->all(FLERR,"Illegal dump_modify command");
+ if (maxfiles > 0) {
+ nameslist = new char*[maxfiles];
+ numfiles = 0;
+ for (int idx=0; idx < maxfiles; ++idx)
+ nameslist[idx] = NULL;
+ fileidx = 0;
+ }
+ iarg += 2;
} else if (strcmp(arg[iarg],"nfile") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command");
if (!multiproc)
diff --git a/src/dump.h b/src/dump.h
index 472f69bfb9e95212c5d6e90579b0b46446fcb8b0..1c6a131f76088e060cf5cb697e7ef744d660d95e 100644
--- a/src/dump.h
+++ b/src/dump.h
@@ -15,7 +15,7 @@
#define LMP_DUMP_H
#include <mpi.h>
-#include <stdio.h>
+#include <cstdio>
#include "pointers.h"
namespace LAMMPS_NS {
@@ -94,6 +94,7 @@ class Dump : protected Pointers {
char *format_int_user;
char *format_bigint_user;
char **format_column_user;
+ enum{INT,DOUBLE,STRING,BIGINT};
FILE *fp; // file to write dump to
int size_one; // # of quantities for one atom
@@ -105,6 +106,11 @@ class Dump : protected Pointers {
double boxzlo,boxzhi;
double boxxy,boxxz,boxyz;
+ int maxfiles; // max number of files created, -1 == infinite
+ int numfiles; // number of files in names list
+ int fileidx; // index of file in names list
+ char **nameslist; // list of history file names
+
bigint ntotal; // total # of per-atom lines in snapshot
int reorderflag; // 1 if OK to reorder instead of sort
int ntotal_reorder; // # of atoms that must be in snapshot
diff --git a/src/dump_atom.cpp b/src/dump_atom.cpp
index 6221463920f18e1efdf7e87347ac274dc4d83e4e..74583f40131cead43003e76838ddeeac204555fd 100644
--- a/src/dump_atom.cpp
+++ b/src/dump_atom.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "dump_atom.h"
#include "domain.h"
#include "atom.h"
diff --git a/src/dump_cfg.cpp b/src/dump_cfg.cpp
index 6ebdd0f99af74d2f0cee0db72caeda8df0c856ee..ddd662c8a65c3ae0365672ed3e82f27c7587be52 100644
--- a/src/dump_cfg.cpp
+++ b/src/dump_cfg.cpp
@@ -16,9 +16,9 @@
Memory efficiency improved by Ray Shan (Sandia)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "dump_cfg.h"
#include "atom.h"
#include "domain.h"
@@ -33,8 +33,6 @@
using namespace LAMMPS_NS;
-enum{INT,DOUBLE,STRING,BIGINT}; // same as in DumpCustom
-
#define UNWRAPEXPAND 10.0
#define ONEFIELD 32
#define DELTA 1048576
@@ -181,15 +179,15 @@ int DumpCFG::convert_string(int n, double *mybuf)
} else if (j == 1) {
offset += sprintf(&sbuf[offset],"%s \n",typenames[(int) mybuf[m]]);
} else if (j >= 2) {
- if (vtype[j] == INT)
+ if (vtype[j] == Dump::INT)
offset +=
sprintf(&sbuf[offset],vformat[j],static_cast<int> (mybuf[m]));
- else if (vtype[j] == DOUBLE)
+ else if (vtype[j] == Dump::DOUBLE)
offset += sprintf(&sbuf[offset],vformat[j],mybuf[m]);
- else if (vtype[j] == STRING)
+ else if (vtype[j] == Dump::STRING)
offset +=
sprintf(&sbuf[offset],vformat[j],typenames[(int) mybuf[m]]);
- else if (vtype[j] == BIGINT)
+ else if (vtype[j] == Dump::BIGINT)
offset +=
sprintf(&sbuf[offset],vformat[j],static_cast<bigint> (mybuf[m]));
}
@@ -216,15 +214,15 @@ int DumpCFG::convert_string(int n, double *mybuf)
unwrap_coord = (mybuf[m] - 0.5)/UNWRAPEXPAND + 0.5;
offset += sprintf(&sbuf[offset],vformat[j],unwrap_coord);
} else if (j >= 5 ) {
- if (vtype[j] == INT)
+ if (vtype[j] == Dump::INT)
offset +=
sprintf(&sbuf[offset],vformat[j],static_cast<int> (mybuf[m]));
- else if (vtype[j] == DOUBLE)
+ else if (vtype[j] == Dump::DOUBLE)
offset += sprintf(&sbuf[offset],vformat[j],mybuf[m]);
- else if (vtype[j] == STRING)
+ else if (vtype[j] == Dump::STRING)
offset +=
sprintf(&sbuf[offset],vformat[j],typenames[(int) mybuf[m]]);
- else if (vtype[j] == BIGINT)
+ else if (vtype[j] == Dump::BIGINT)
offset +=
sprintf(&sbuf[offset],vformat[j],static_cast<bigint> (mybuf[m]));
}
@@ -266,13 +264,13 @@ void DumpCFG::write_lines(int n, double *mybuf)
} else if (j == 1) {
fprintf(fp,"%s \n",typenames[(int) mybuf[m]]);
} else if (j >= 2) {
- if (vtype[j] == INT)
+ if (vtype[j] == Dump::INT)
fprintf(fp,vformat[j],static_cast<int> (mybuf[m]));
- else if (vtype[j] == DOUBLE)
+ else if (vtype[j] == Dump::DOUBLE)
fprintf(fp,vformat[j],mybuf[m]);
- else if (vtype[j] == STRING)
+ else if (vtype[j] == Dump::STRING)
fprintf(fp,vformat[j],typenames[(int) mybuf[m]]);
- else if (vtype[j] == BIGINT)
+ else if (vtype[j] == Dump::BIGINT)
fprintf(fp,vformat[j],static_cast<bigint> (mybuf[m]));
}
m++;
@@ -292,13 +290,13 @@ void DumpCFG::write_lines(int n, double *mybuf)
unwrap_coord = (mybuf[m] - 0.5)/UNWRAPEXPAND + 0.5;
fprintf(fp,vformat[j],unwrap_coord);
} else if (j >= 5 ) {
- if (vtype[j] == INT)
+ if (vtype[j] == Dump::INT)
fprintf(fp,vformat[j],static_cast<int> (mybuf[m]));
- else if (vtype[j] == DOUBLE)
+ else if (vtype[j] == Dump::DOUBLE)
fprintf(fp,vformat[j],mybuf[m]);
- else if (vtype[j] == STRING)
+ else if (vtype[j] == Dump::STRING)
fprintf(fp,vformat[j],typenames[(int) mybuf[m]]);
- else if (vtype[j] == BIGINT)
+ else if (vtype[j] == Dump::BIGINT)
fprintf(fp,vformat[j],static_cast<bigint> (mybuf[m]));
}
m++;
diff --git a/src/dump_custom.cpp b/src/dump_custom.cpp
index 9f389d8a56915c87381a3138a3ffb07e611d8bd7..25925d61842af73db818c48625055cd09443fdd3 100644
--- a/src/dump_custom.cpp
+++ b/src/dump_custom.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "dump_custom.h"
#include "atom.h"
#include "force.h"
@@ -46,7 +46,6 @@ enum{ID,MOL,PROC,PROCP1,TYPE,ELEMENT,MASS,
TQX,TQY,TQZ,
COMPUTE,FIX,VARIABLE,INAME,DNAME};
enum{LT,LE,GT,GE,EQ,NEQ,XOR};
-enum{INT,DOUBLE,STRING,BIGINT}; // same as in DumpCFG
#define INVOKED_PERATOM 8
#define ONEFIELD 32
@@ -61,7 +60,7 @@ DumpCustom::DumpCustom(LAMMPS *lmp, int narg, char **arg) :
earg(NULL), vtype(NULL), vformat(NULL), columns(NULL), choose(NULL),
dchoose(NULL), clist(NULL), field2index(NULL), argindex(NULL), id_compute(NULL),
compute(NULL), id_fix(NULL), fix(NULL), id_variable(NULL), variable(NULL),
- vbuf(NULL), id_custom(NULL), flag_custom(NULL), typenames(NULL),
+ vbuf(NULL), id_custom(NULL), flag_custom(NULL), typenames(NULL),
pack_choice(NULL)
{
if (narg == 5) error->all(FLERR,"No dump custom arguments specified");
@@ -166,10 +165,10 @@ DumpCustom::DumpCustom(LAMMPS *lmp, int narg, char **arg) :
format_default[0] = '\0';
for (int i = 0; i < size_one; i++) {
- if (vtype[i] == INT) strcat(format_default,"%d ");
- else if (vtype[i] == DOUBLE) strcat(format_default,"%g ");
- else if (vtype[i] == STRING) strcat(format_default,"%s ");
- else if (vtype[i] == BIGINT) strcat(format_default,BIGINT_FORMAT " ");
+ if (vtype[i] == Dump::INT) strcat(format_default,"%d ");
+ else if (vtype[i] == Dump::DOUBLE) strcat(format_default,"%g ");
+ else if (vtype[i] == Dump::STRING) strcat(format_default,"%s ");
+ else if (vtype[i] == Dump::BIGINT) strcat(format_default,BIGINT_FORMAT " ");
vformat[i] = NULL;
}
@@ -285,13 +284,13 @@ void DumpCustom::init_style()
if (format_column_user[i]) {
vformat[i] = new char[strlen(format_column_user[i]) + 2];
strcpy(vformat[i],format_column_user[i]);
- } else if (vtype[i] == INT && format_int_user) {
+ } else if (vtype[i] == Dump::INT && format_int_user) {
vformat[i] = new char[strlen(format_int_user) + 2];
strcpy(vformat[i],format_int_user);
- } else if (vtype[i] == DOUBLE && format_float_user) {
+ } else if (vtype[i] == Dump::DOUBLE && format_float_user) {
vformat[i] = new char[strlen(format_float_user) + 2];
strcpy(vformat[i],format_float_user);
- } else if (vtype[i] == BIGINT && format_bigint_user) {
+ } else if (vtype[i] == Dump::BIGINT && format_bigint_user) {
vformat[i] = new char[strlen(format_bigint_user) + 2];
strcpy(vformat[i],format_bigint_user);
} else {
@@ -1085,13 +1084,13 @@ int DumpCustom::convert_string(int n, double *mybuf)
}
for (j = 0; j < size_one; j++) {
- if (vtype[j] == INT)
+ if (vtype[j] == Dump::INT)
offset += sprintf(&sbuf[offset],vformat[j],static_cast<int> (mybuf[m]));
- else if (vtype[j] == DOUBLE)
+ else if (vtype[j] == Dump::DOUBLE)
offset += sprintf(&sbuf[offset],vformat[j],mybuf[m]);
- else if (vtype[j] == STRING)
+ else if (vtype[j] == Dump::STRING)
offset += sprintf(&sbuf[offset],vformat[j],typenames[(int) mybuf[m]]);
- else if (vtype[j] == BIGINT)
+ else if (vtype[j] == Dump::BIGINT)
offset += sprintf(&sbuf[offset],vformat[j],
static_cast<bigint> (mybuf[m]));
m++;
@@ -1134,11 +1133,11 @@ void DumpCustom::write_lines(int n, double *mybuf)
int m = 0;
for (i = 0; i < n; i++) {
for (j = 0; j < size_one; j++) {
- if (vtype[j] == INT) fprintf(fp,vformat[j],static_cast<int> (mybuf[m]));
- else if (vtype[j] == DOUBLE) fprintf(fp,vformat[j],mybuf[m]);
- else if (vtype[j] == STRING)
+ if (vtype[j] == Dump::INT) fprintf(fp,vformat[j],static_cast<int> (mybuf[m]));
+ else if (vtype[j] == Dump::DOUBLE) fprintf(fp,vformat[j],mybuf[m]);
+ else if (vtype[j] == Dump::STRING)
fprintf(fp,vformat[j],typenames[(int) mybuf[m]]);
- else if (vtype[j] == BIGINT)
+ else if (vtype[j] == Dump::BIGINT)
fprintf(fp,vformat[j],static_cast<bigint> (mybuf[m]));
m++;
}
@@ -1158,191 +1157,192 @@ int DumpCustom::parse_fields(int narg, char **arg)
if (strcmp(arg[iarg],"id") == 0) {
pack_choice[i] = &DumpCustom::pack_id;
- if (sizeof(tagint) == sizeof(smallint)) vtype[i] = INT;
- else vtype[i] = BIGINT;
+ if (sizeof(tagint) == sizeof(smallint)) vtype[i] = Dump::INT;
+ else vtype[i] = Dump::BIGINT;
} else if (strcmp(arg[iarg],"mol") == 0) {
if (!atom->molecule_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[i] = &DumpCustom::pack_molecule;
- if (sizeof(tagint) == sizeof(smallint)) vtype[i] = INT;
- else vtype[i] = BIGINT;
+ if (sizeof(tagint) == sizeof(smallint)) vtype[i] = Dump::INT;
+ else vtype[i] = Dump::BIGINT;
} else if (strcmp(arg[iarg],"proc") == 0) {
pack_choice[i] = &DumpCustom::pack_proc;
- vtype[i] = INT;
+ vtype[i] = Dump::INT;
} else if (strcmp(arg[iarg],"procp1") == 0) {
pack_choice[i] = &DumpCustom::pack_procp1;
- vtype[i] = INT;
+ vtype[i] = Dump::INT;
} else if (strcmp(arg[iarg],"type") == 0) {
pack_choice[i] = &DumpCustom::pack_type;
- vtype[i] = INT;
+ vtype[i] = Dump::INT;
} else if (strcmp(arg[iarg],"element") == 0) {
pack_choice[i] = &DumpCustom::pack_type;
- vtype[i] = STRING;
+ vtype[i] = Dump::STRING;
} else if (strcmp(arg[iarg],"mass") == 0) {
pack_choice[i] = &DumpCustom::pack_mass;
- vtype[i] = DOUBLE;
+ vtype[i] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"x") == 0) {
pack_choice[i] = &DumpCustom::pack_x;
- vtype[i] = DOUBLE;
+ vtype[i] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"y") == 0) {
pack_choice[i] = &DumpCustom::pack_y;
- vtype[i] = DOUBLE;
+ vtype[i] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"z") == 0) {
pack_choice[i] = &DumpCustom::pack_z;
- vtype[i] = DOUBLE;
+ vtype[i] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"xs") == 0) {
if (domain->triclinic) pack_choice[i] = &DumpCustom::pack_xs_triclinic;
else pack_choice[i] = &DumpCustom::pack_xs;
- vtype[i] = DOUBLE;
+ vtype[i] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"ys") == 0) {
if (domain->triclinic) pack_choice[i] = &DumpCustom::pack_ys_triclinic;
else pack_choice[i] = &DumpCustom::pack_ys;
- vtype[i] = DOUBLE;
+ vtype[i] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"zs") == 0) {
if (domain->triclinic) pack_choice[i] = &DumpCustom::pack_zs_triclinic;
else pack_choice[i] = &DumpCustom::pack_zs;
- vtype[i] = DOUBLE;
+ vtype[i] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"xu") == 0) {
if (domain->triclinic) pack_choice[i] = &DumpCustom::pack_xu_triclinic;
else pack_choice[i] = &DumpCustom::pack_xu;
- vtype[i] = DOUBLE;
+ vtype[i] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"yu") == 0) {
if (domain->triclinic) pack_choice[i] = &DumpCustom::pack_yu_triclinic;
else pack_choice[i] = &DumpCustom::pack_yu;
- vtype[i] = DOUBLE;
+ vtype[i] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"zu") == 0) {
if (domain->triclinic) pack_choice[i] = &DumpCustom::pack_zu_triclinic;
else pack_choice[i] = &DumpCustom::pack_zu;
- vtype[i] = DOUBLE;
+ vtype[i] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"xsu") == 0) {
if (domain->triclinic) pack_choice[i] = &DumpCustom::pack_xsu_triclinic;
else pack_choice[i] = &DumpCustom::pack_xsu;
- vtype[i] = DOUBLE;
+ vtype[i] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"ysu") == 0) {
if (domain->triclinic) pack_choice[i] = &DumpCustom::pack_ysu_triclinic;
else pack_choice[i] = &DumpCustom::pack_ysu;
- vtype[i] = DOUBLE;
+ vtype[i] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"zsu") == 0) {
if (domain->triclinic) pack_choice[i] = &DumpCustom::pack_zsu_triclinic;
else pack_choice[i] = &DumpCustom::pack_zsu;
- vtype[i] = DOUBLE;
+ vtype[i] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"ix") == 0) {
pack_choice[i] = &DumpCustom::pack_ix;
- vtype[i] = INT;
+ vtype[i] = Dump::INT;
} else if (strcmp(arg[iarg],"iy") == 0) {
pack_choice[i] = &DumpCustom::pack_iy;
- vtype[i] = INT;
+ vtype[i] = Dump::INT;
} else if (strcmp(arg[iarg],"iz") == 0) {
pack_choice[i] = &DumpCustom::pack_iz;
- vtype[i] = INT;
+ vtype[i] = Dump::INT;
} else if (strcmp(arg[iarg],"vx") == 0) {
pack_choice[i] = &DumpCustom::pack_vx;
- vtype[i] = DOUBLE;
+ vtype[i] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"vy") == 0) {
pack_choice[i] = &DumpCustom::pack_vy;
- vtype[i] = DOUBLE;
+ vtype[i] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"vz") == 0) {
pack_choice[i] = &DumpCustom::pack_vz;
- vtype[i] = DOUBLE;
+ vtype[i] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"fx") == 0) {
pack_choice[i] = &DumpCustom::pack_fx;
- vtype[i] = DOUBLE;
+ vtype[i] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"fy") == 0) {
pack_choice[i] = &DumpCustom::pack_fy;
- vtype[i] = DOUBLE;
+ vtype[i] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"fz") == 0) {
pack_choice[i] = &DumpCustom::pack_fz;
- vtype[i] = DOUBLE;
+ vtype[i] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"q") == 0) {
if (!atom->q_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[i] = &DumpCustom::pack_q;
- vtype[i] = DOUBLE;
+ vtype[i] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"mux") == 0) {
if (!atom->mu_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[i] = &DumpCustom::pack_mux;
- vtype[i] = DOUBLE;
+ vtype[i] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"muy") == 0) {
if (!atom->mu_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[i] = &DumpCustom::pack_muy;
- vtype[i] = DOUBLE;
+ vtype[i] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"muz") == 0) {
if (!atom->mu_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[i] = &DumpCustom::pack_muz;
- vtype[i] = DOUBLE;
+ vtype[i] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"mu") == 0) {
if (!atom->mu_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[i] = &DumpCustom::pack_mu;
- vtype[i] = DOUBLE;
+ vtype[i] = Dump::DOUBLE;
+
} else if (strcmp(arg[iarg],"radius") == 0) {
if (!atom->radius_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[i] = &DumpCustom::pack_radius;
- vtype[i] = DOUBLE;
+ vtype[i] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"diameter") == 0) {
if (!atom->radius_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[i] = &DumpCustom::pack_diameter;
- vtype[i] = DOUBLE;
+ vtype[i] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"omegax") == 0) {
if (!atom->omega_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[i] = &DumpCustom::pack_omegax;
- vtype[i] = DOUBLE;
+ vtype[i] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"omegay") == 0) {
if (!atom->omega_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[i] = &DumpCustom::pack_omegay;
- vtype[i] = DOUBLE;
+ vtype[i] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"omegaz") == 0) {
if (!atom->omega_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[i] = &DumpCustom::pack_omegaz;
- vtype[i] = DOUBLE;
+ vtype[i] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"angmomx") == 0) {
if (!atom->angmom_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[i] = &DumpCustom::pack_angmomx;
- vtype[i] = DOUBLE;
+ vtype[i] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"angmomy") == 0) {
if (!atom->angmom_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[i] = &DumpCustom::pack_angmomy;
- vtype[i] = DOUBLE;
+ vtype[i] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"angmomz") == 0) {
if (!atom->angmom_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[i] = &DumpCustom::pack_angmomz;
- vtype[i] = DOUBLE;
+ vtype[i] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"tqx") == 0) {
if (!atom->torque_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[i] = &DumpCustom::pack_tqx;
- vtype[i] = DOUBLE;
+ vtype[i] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"tqy") == 0) {
if (!atom->torque_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[i] = &DumpCustom::pack_tqy;
- vtype[i] = DOUBLE;
+ vtype[i] = Dump::DOUBLE;
} else if (strcmp(arg[iarg],"tqz") == 0) {
if (!atom->torque_flag)
error->all(FLERR,"Dumping an atom property that isn't allocated");
pack_choice[i] = &DumpCustom::pack_tqz;
- vtype[i] = DOUBLE;
+ vtype[i] = Dump::DOUBLE;
// compute value = c_ID
// if no trailing [], then arg is set to 0, else arg is int between []
} else if (strncmp(arg[iarg],"c_",2) == 0) {
pack_choice[i] = &DumpCustom::pack_compute;
- vtype[i] = DOUBLE;
+ vtype[i] = Dump::DOUBLE;
int n = strlen(arg[iarg]);
char *suffix = new char[n];
@@ -1378,7 +1378,7 @@ int DumpCustom::parse_fields(int narg, char **arg)
} else if (strncmp(arg[iarg],"f_",2) == 0) {
pack_choice[i] = &DumpCustom::pack_fix;
- vtype[i] = DOUBLE;
+ vtype[i] = Dump::DOUBLE;
int n = strlen(arg[iarg]);
char *suffix = new char[n];
@@ -1411,7 +1411,7 @@ int DumpCustom::parse_fields(int narg, char **arg)
} else if (strncmp(arg[iarg],"v_",2) == 0) {
pack_choice[i] = &DumpCustom::pack_variable;
- vtype[i] = DOUBLE;
+ vtype[i] = Dump::DOUBLE;
int n = strlen(arg[iarg]);
char *suffix = new char[n];
@@ -1431,7 +1431,7 @@ int DumpCustom::parse_fields(int narg, char **arg)
} else if (strncmp(arg[iarg],"d_",2) == 0) {
pack_choice[i] = &DumpCustom::pack_custom;
- vtype[i] = DOUBLE;
+ vtype[i] = Dump::DOUBLE;
int n = strlen(arg[iarg]);
char *suffix = new char[n];
@@ -1453,7 +1453,7 @@ int DumpCustom::parse_fields(int narg, char **arg)
} else if (strncmp(arg[iarg],"i_",2) == 0) {
pack_choice[i] = &DumpCustom::pack_custom;
- vtype[i] = INT;
+ vtype[i] = Dump::INT;
int n = strlen(arg[iarg]);
char *suffix = new char[n];
@@ -1672,7 +1672,7 @@ int DumpCustom::modify_param(int narg, char **arg)
if (strcmp(arg[0],"refresh") == 0) {
if (narg < 2) error->all(FLERR,"Illegal dump_modify command");
- if (strncmp(arg[1],"c_",2) != 0)
+ if (strncmp(arg[1],"c_",2) != 0)
error->all(FLERR,"Illegal dump_modify command");
if (refreshflag) error->all(FLERR,"Dump modify can only have one refresh");
diff --git a/src/dump_dcd.cpp b/src/dump_dcd.cpp
index ca7246ab241f4875eeb0886215efa2baaa64d58a..384e9089c0a1781bfaaaf2eb87137a823382367b 100644
--- a/src/dump_dcd.cpp
+++ b/src/dump_dcd.cpp
@@ -16,11 +16,11 @@
Axel Kohlmeyer (Temple U), support for groups
------------------------------------------------------------------------- */
-#include <math.h>
-#include <inttypes.h>
-#include <stdio.h>
-#include <time.h>
-#include <string.h>
+#include <cmath>
+#include <inttypes.h> // <cinttypes> requires C++-11
+#include <cstdio>
+#include <ctime>
+#include <cstring>
#include "dump_dcd.h"
#include "domain.h"
#include "atom.h"
diff --git a/src/dump_image.cpp b/src/dump_image.cpp
index 9ca6ad34e90fa88c99d317bd36c755325fd72949..60a1f545c9715d951d07590891e4f31888b3746c 100644
--- a/src/dump_image.cpp
+++ b/src/dump_image.cpp
@@ -11,10 +11,10 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <ctype.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cctype>
+#include <cstdlib>
+#include <cstring>
#include "dump_image.h"
#include "image.h"
#include "atom.h"
diff --git a/src/dump_local.cpp b/src/dump_local.cpp
index ca8b1822a2611dfffae2fc6c6579f8995c434617..0d5172b5c1bdaf0de61828a464bc0e7b09a61006 100644
--- a/src/dump_local.cpp
+++ b/src/dump_local.cpp
@@ -12,8 +12,8 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <string.h>
-#include <stdlib.h>
+#include <cstring>
+#include <cstdlib>
#include "dump_local.h"
#include "atom.h"
#include "modify.h"
diff --git a/src/dump_movie.cpp b/src/dump_movie.cpp
index cb8982cabe38c400198d5427eda89b9677bccda3..59dfdc3d6e9e579ee49d851577182bbde622700a 100644
--- a/src/dump_movie.cpp
+++ b/src/dump_movie.cpp
@@ -15,9 +15,9 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "dump_movie.h"
#include "comm.h"
#include "force.h"
diff --git a/src/dump_xyz.cpp b/src/dump_xyz.cpp
index 7059e855908a1b15551febca652b028e8a85c68a..fd52671d8140056f8fce6995d5f8e7e4680e6410 100644
--- a/src/dump_xyz.cpp
+++ b/src/dump_xyz.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "dump_xyz.h"
#include "atom.h"
#include "group.h"
diff --git a/src/error.cpp b/src/error.cpp
index 9193314fc8c8674c445341d9e993c4690499da55..2ab816c992ac910fd0a2dd789a1c08d3f9da2576 100644
--- a/src/error.cpp
+++ b/src/error.cpp
@@ -12,8 +12,8 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cstdlib>
+#include <cstring>
#include "error.h"
#include "universe.h"
#include "output.h"
@@ -21,6 +21,20 @@
using namespace LAMMPS_NS;
+// helper function to truncate a string to a segment starting with "src/";
+
+static const char *truncpath(const char *path)
+{
+ if (path) {
+ int len = strlen(path);
+ for (int i = len-4; i > 0; --i) {
+ if (strncmp("src/",path+i,4) == 0)
+ return path+i;
+ }
+ }
+ return path;
+}
+
/* ---------------------------------------------------------------------- */
Error::Error(LAMMPS *lmp) : Pointers(lmp) {
@@ -42,9 +56,9 @@ void Error::universe_all(const char *file, int line, const char *str)
if (universe->me == 0) {
if (universe->uscreen) fprintf(universe->uscreen,
- "ERROR: %s (%s:%d)\n",str,file,line);
+ "ERROR: %s (%s:%d)\n",str,truncpath(file),line);
if (universe->ulogfile) fprintf(universe->ulogfile,
- "ERROR: %s (%s:%d)\n",str,file,line);
+ "ERROR: %s (%s:%d)\n",str,truncpath(file),line);
}
if (output) delete output;
@@ -73,7 +87,7 @@ void Error::universe_one(const char *file, int line, const char *str)
{
if (universe->uscreen)
fprintf(universe->uscreen,"ERROR on proc %d: %s (%s:%d)\n",
- universe->me,str,file,line);
+ universe->me,str,truncpath(file),line);
#ifdef LAMMPS_EXCEPTIONS
char msg[100];
@@ -93,7 +107,7 @@ void Error::universe_warn(const char *file, int line, const char *str)
{
if (universe->uscreen)
fprintf(universe->uscreen,"WARNING on proc %d: %s (%s:%d)\n",
- universe->me,str,file,line);
+ universe->me,str,truncpath(file),line);
}
/* ----------------------------------------------------------------------
@@ -116,10 +130,10 @@ void Error::all(const char *file, int line, const char *str)
if (input && input->line) lastcmd = input->line;
if (screen) fprintf(screen,"ERROR: %s (%s:%d)\n"
"Last command: %s\n",
- str,file,line,lastcmd);
+ str,truncpath(file),line,lastcmd);
if (logfile) fprintf(logfile,"ERROR: %s (%s:%d)\n"
"Last command: %s\n",
- str,file,line,lastcmd);
+ str,truncpath(file),line,lastcmd);
}
#ifdef LAMMPS_EXCEPTIONS
@@ -158,15 +172,15 @@ void Error::one(const char *file, int line, const char *str)
if (input && input->line) lastcmd = input->line;
if (screen) fprintf(screen,"ERROR on proc %d: %s (%s:%d)\n"
"Last command: %s\n",
- me,str,file,line,lastcmd);
+ me,str,truncpath(file),line,lastcmd);
if (logfile) fprintf(logfile,"ERROR on proc %d: %s (%s:%d)\n"
"Last command: %s\n",
- me,str,file,line,lastcmd);
+ me,str,truncpath(file),line,lastcmd);
if (universe->nworlds > 1)
if (universe->uscreen)
fprintf(universe->uscreen,"ERROR on proc %d: %s (%s:%d)\n",
- universe->me,str,file,line);
+ universe->me,str,truncpath(file),line);
#ifdef LAMMPS_EXCEPTIONS
char msg[100];
@@ -184,9 +198,9 @@ void Error::one(const char *file, int line, const char *str)
void Error::warning(const char *file, int line, const char *str, int logflag)
{
- if (screen) fprintf(screen,"WARNING: %s (%s:%d)\n",str,file,line);
+ if (screen) fprintf(screen,"WARNING: %s (%s:%d)\n",str,truncpath(file),line);
if (logflag && logfile) fprintf(logfile,"WARNING: %s (%s:%d)\n",
- str,file,line);
+ str,truncpath(file),line);
}
/* ----------------------------------------------------------------------
@@ -196,8 +210,8 @@ void Error::warning(const char *file, int line, const char *str, int logflag)
void Error::message(const char *file, int line, const char *str, int logflag)
{
- if (screen) fprintf(screen,"%s (%s:%d)\n",str,file,line);
- if (logflag && logfile) fprintf(logfile,"%s (%s:%d)\n",str,file,line);
+ if (screen) fprintf(screen,"%s (%s:%d)\n",str,truncpath(file),line);
+ if (logflag && logfile) fprintf(logfile,"%s (%s:%d)\n",str,truncpath(file),line);
}
/* ----------------------------------------------------------------------
diff --git a/src/finish.cpp b/src/finish.cpp
index c22b26782e7c63e9ae4ee1b7a9fcbdcbe2978770..f35fb7e3a502a785747b2c98476ee0aa4e2c3dd1 100644
--- a/src/finish.cpp
+++ b/src/finish.cpp
@@ -12,10 +12,10 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
-#include <stdio.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
+#include <cstdio>
#include "finish.h"
#include "timer.h"
#include "universe.h"
diff --git a/src/fix.cpp b/src/fix.cpp
index 297d184967617100ae2ea25804ec5beb9d7e1217..a54e2957985207ee6c5a27f59ae70483763d251b 100644
--- a/src/fix.cpp
+++ b/src/fix.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
-#include <ctype.h>
+#include <cstring>
+#include <cctype>
#include "fix.h"
#include "atom.h"
#include "group.h"
diff --git a/src/fix_adapt.cpp b/src/fix_adapt.cpp
index 10b09f4a7f56d5d14c49489eba9a0eb343ceebc9..754c9ea4da41230b46836b28ca69a6e990c77b05 100644
--- a/src/fix_adapt.cpp
+++ b/src/fix_adapt.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <string.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstring>
+#include <cstdlib>
#include "fix_adapt.h"
#include "atom.h"
#include "bond.h"
diff --git a/src/fix_addforce.cpp b/src/fix_addforce.cpp
index 6b1e89227985acb0dc12336520962ff7599ffee3..c2eedccd6151e6306bcf11d6f7a380413434850a 100644
--- a/src/fix_addforce.cpp
+++ b/src/fix_addforce.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
-#include <stdlib.h>
+#include <cstring>
+#include <cstdlib>
#include "fix_addforce.h"
#include "atom.h"
#include "atom_masks.h"
diff --git a/src/fix_ave_atom.cpp b/src/fix_ave_atom.cpp
index c4222f6fcd056dde4816de1629394ec2e03f0b21..a8c3be07af55fe5eab76b1c35fbd3afe0b2340f4 100644
--- a/src/fix_ave_atom.cpp
+++ b/src/fix_ave_atom.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <stdlib.h>
-#include <string.h>
+#include <cstdlib>
+#include <cstring>
#include "fix_ave_atom.h"
#include "atom.h"
#include "domain.h"
diff --git a/src/fix_ave_atom.h b/src/fix_ave_atom.h
index c2f5067309559903ede2270a424531224a23329e..e4baf6bda14bfc8672e1ae1818117826a1028ddd 100644
--- a/src/fix_ave_atom.h
+++ b/src/fix_ave_atom.h
@@ -20,7 +20,7 @@ FixStyle(ave/atom,FixAveAtom)
#ifndef LMP_FIX_AVE_ATOM_H
#define LMP_FIX_AVE_ATOM_H
-#include <stdio.h>
+#include <cstdio>
#include "fix.h"
namespace LAMMPS_NS {
diff --git a/src/fix_ave_chunk.cpp b/src/fix_ave_chunk.cpp
index 8558e8695c10d3e04a5ef218aee8bc32e499b657..5f727fd3f747f6c9ec21cf7fcdf873cf57ecf5cb 100644
--- a/src/fix_ave_chunk.cpp
+++ b/src/fix_ave_chunk.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <stdlib.h>
-#include <string.h>
+#include <cstdlib>
+#include <cstring>
#include <unistd.h>
#include "fix_ave_chunk.h"
#include "atom.h"
diff --git a/src/fix_ave_chunk.h b/src/fix_ave_chunk.h
index a69b07f5d07986b060548e72fc4f96b59563fbd8..4dc1c1c24602e8947a027866222f7b6e843cab69 100644
--- a/src/fix_ave_chunk.h
+++ b/src/fix_ave_chunk.h
@@ -20,7 +20,7 @@ FixStyle(ave/chunk,FixAveChunk)
#ifndef LMP_FIX_AVE_CHUNK_H
#define LMP_FIX_AVE_CHUNK_H
-#include <stdio.h>
+#include <cstdio>
#include "fix.h"
namespace LAMMPS_NS {
diff --git a/src/fix_ave_correlate.cpp b/src/fix_ave_correlate.cpp
index fffcc09d7ae7d3787397f229a918753b48d5abec..418464a2484b4884e58a2966a410eb9e092b1d38 100644
--- a/src/fix_ave_correlate.cpp
+++ b/src/fix_ave_correlate.cpp
@@ -17,8 +17,8 @@
Reese Jones (Sandia)
------------------------------------------------------------------------- */
-#include <stdlib.h>
-#include <string.h>
+#include <cstdlib>
+#include <cstring>
#include <unistd.h>
#include "fix_ave_correlate.h"
#include "update.h"
diff --git a/src/fix_ave_correlate.h b/src/fix_ave_correlate.h
index 6d2567e73073040d7332e3e41a1d2c84efac1e53..ff20e8ba94c2e54ec8c98cb735b734d0fb8a943f 100644
--- a/src/fix_ave_correlate.h
+++ b/src/fix_ave_correlate.h
@@ -20,7 +20,7 @@ FixStyle(ave/correlate,FixAveCorrelate)
#ifndef LMP_FIX_AVE_CORRELATE_H
#define LMP_FIX_AVE_CORRELATE_H
-#include <stdio.h>
+#include <cstdio>
#include "fix.h"
namespace LAMMPS_NS {
diff --git a/src/fix_ave_histo.cpp b/src/fix_ave_histo.cpp
index e104512479f07ed93af3dcadc866de7cf557cb70..7aa599389979bac8cdfe48614a5302c7834a2bac 100644
--- a/src/fix_ave_histo.cpp
+++ b/src/fix_ave_histo.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <stdlib.h>
-#include <string.h>
+#include <cstdlib>
+#include <cstring>
#include <unistd.h>
#include "fix_ave_histo.h"
#include "atom.h"
diff --git a/src/fix_ave_histo.h b/src/fix_ave_histo.h
index 123122b05182f9ba72d1b5fc2d52c83011a46510..3616959c612a0e66760eaa21b588ddc4728a4bb7 100644
--- a/src/fix_ave_histo.h
+++ b/src/fix_ave_histo.h
@@ -20,7 +20,7 @@ FixStyle(ave/histo,FixAveHisto)
#ifndef LMP_FIX_AVE_HISTO_H
#define LMP_FIX_AVE_HISTO_H
-#include <stdio.h>
+#include <cstdio>
#include "fix.h"
namespace LAMMPS_NS {
diff --git a/src/fix_ave_histo_weight.cpp b/src/fix_ave_histo_weight.cpp
index 37dd8c9898c74f16f5bea3d52aff364a12ab8d15..c78f4fa1e38765c2e150c59f840d00bc535deee4 100644
--- a/src/fix_ave_histo_weight.cpp
+++ b/src/fix_ave_histo_weight.cpp
@@ -15,8 +15,8 @@
Contributing author: Shawn Coleman (ARL)
------------------------------------------------------------------------- */
-#include <stdlib.h>
-#include <string.h>
+#include <cstdlib>
+#include <cstring>
#include <unistd.h>
#include "fix_ave_histo_weight.h"
#include "atom.h"
diff --git a/src/fix_ave_histo_weight.h b/src/fix_ave_histo_weight.h
index 22812384de036920a44fa25a3d96c1dd065447a6..e5638e121569cd5e328ad7760a3ea6b957af8938 100644
--- a/src/fix_ave_histo_weight.h
+++ b/src/fix_ave_histo_weight.h
@@ -20,7 +20,7 @@ FixStyle(ave/histo/weight,FixAveHistoWeight)
#ifndef LMP_FIX_AVE_HISTO_WEIGHT_H
#define LMP_FIX_AVE_HISTO_WEIGHT_H
-#include <stdio.h>
+#include <cstdio>
#include "fix_ave_histo.h"
namespace LAMMPS_NS {
diff --git a/src/fix_ave_time.cpp b/src/fix_ave_time.cpp
index 5de32c7faea287cb391f2520dacd7b5aedbc0eec..c3ace296842b0cb3738c62b635ed7fb48854e48a 100644
--- a/src/fix_ave_time.cpp
+++ b/src/fix_ave_time.cpp
@@ -15,8 +15,8 @@
Contributing author: Pieter in 't Veld (SNL)
------------------------------------------------------------------------- */
-#include <stdlib.h>
-#include <string.h>
+#include <cstdlib>
+#include <cstring>
#include <unistd.h>
#include "fix_ave_time.h"
#include "update.h"
diff --git a/src/fix_ave_time.h b/src/fix_ave_time.h
index aa1d2333cfa74d05ac886b59ce96701c20d78eaa..62dfbad2963e90b29679929dbfaf3b488df6d06c 100644
--- a/src/fix_ave_time.h
+++ b/src/fix_ave_time.h
@@ -20,7 +20,7 @@ FixStyle(ave/time,FixAveTime)
#ifndef LMP_FIX_AVE_TIME_H
#define LMP_FIX_AVE_TIME_H
-#include <stdio.h>
+#include <cstdio>
#include "fix.h"
namespace LAMMPS_NS {
diff --git a/src/fix_aveforce.cpp b/src/fix_aveforce.cpp
index 793c2d5c2b230756c34de697474180279839eca2..4432a5dd36d8aeb369a34c0523bc1592a83050a7 100644
--- a/src/fix_aveforce.cpp
+++ b/src/fix_aveforce.cpp
@@ -12,8 +12,8 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <string.h>
-#include <stdlib.h>
+#include <cstring>
+#include <cstdlib>
#include "fix_aveforce.h"
#include "atom.h"
#include "update.h"
diff --git a/src/fix_balance.cpp b/src/fix_balance.cpp
index 9f29400d9a5291590c5f7ed83e9a6d90b26b33b1..b2f545c73fbbefa4af2f2a46d244ea78be352a60 100644
--- a/src/fix_balance.cpp
+++ b/src/fix_balance.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
-#include <stdlib.h>
+#include <cstring>
+#include <cstdlib>
#include "fix_balance.h"
#include "balance.h"
#include "update.h"
@@ -33,7 +33,6 @@ using namespace LAMMPS_NS;
using namespace FixConst;
enum{SHIFT,BISECTION};
-enum{LAYOUT_UNIFORM,LAYOUT_NONUNIFORM,LAYOUT_TILED}; // several files
/* ---------------------------------------------------------------------- */
@@ -264,10 +263,10 @@ void FixBalance::rebalance()
int *sendproc;
if (lbstyle == SHIFT) {
itercount = balance->shift();
- comm->layout = LAYOUT_NONUNIFORM;
+ comm->layout = Comm::LAYOUT_NONUNIFORM;
} else if (lbstyle == BISECTION) {
sendproc = balance->bisection();
- comm->layout = LAYOUT_TILED;
+ comm->layout = Comm::LAYOUT_TILED;
}
// output of new decomposition
diff --git a/src/fix_balance.h b/src/fix_balance.h
index 8b8759ec9783f5c3dfe201dabab823a672497657..64383b59508bce2ded60e67a7311a28cd164a9bc 100644
--- a/src/fix_balance.h
+++ b/src/fix_balance.h
@@ -20,7 +20,7 @@ FixStyle(balance,FixBalance)
#ifndef LMP_FIX_BALANCE_H
#define LMP_FIX_BALANCE_H
-#include <stdio.h>
+#include <cstdio>
#include "fix.h"
namespace LAMMPS_NS {
diff --git a/src/fix_box_relax.cpp b/src/fix_box_relax.cpp
index 21bc09b259420113ec9b3c8307c1ebc6dc918479..a315330d149eb40f0f5fb7f4446f6495d8738149 100644
--- a/src/fix_box_relax.cpp
+++ b/src/fix_box_relax.cpp
@@ -15,9 +15,9 @@
Contributing author: Aidan Thompson (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <string.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstring>
+#include <cstdlib>
#include "fix_box_relax.h"
#include "atom.h"
#include "domain.h"
diff --git a/src/fix_controller.cpp b/src/fix_controller.cpp
index e283b1c19257b36758c4c685369fb03ae4fc8b26..eb7a79496253bd787e7baa1a33b59301cfa83773 100644
--- a/src/fix_controller.cpp
+++ b/src/fix_controller.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <stdlib.h>
-#include <string.h>
+#include <cstdlib>
+#include <cstring>
#include "fix_controller.h"
#include "force.h"
#include "update.h"
diff --git a/src/fix_deform.cpp b/src/fix_deform.cpp
index 705f1970afa1d15658ed014dd3168f24d5b96b7a..c960c310f618fda3816cd658768505161611d2e5 100644
--- a/src/fix_deform.cpp
+++ b/src/fix_deform.cpp
@@ -15,9 +15,9 @@
Contributing author: Pieter in 't Veld (SNL)
------------------------------------------------------------------------- */
-#include <string.h>
-#include <stdlib.h>
-#include <math.h>
+#include <cstring>
+#include <cstdlib>
+#include <cmath>
#include "fix_deform.h"
#include "atom.h"
#include "update.h"
@@ -40,10 +40,6 @@ using namespace MathConst;
enum{NONE=0,FINAL,DELTA,SCALE,VEL,ERATE,TRATE,VOLUME,WIGGLE,VARIABLE};
enum{ONE_FROM_ONE,ONE_FROM_TWO,TWO_FROM_ONE};
-// same as domain.cpp, fix_nvt_sllod.cpp, compute_temp_deform.cpp
-
-enum{NO_REMAP,X_REMAP,V_REMAP};
-
/* ---------------------------------------------------------------------- */
FixDeform::FixDeform(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg),
@@ -208,7 +204,7 @@ rfix(NULL), irregular(NULL), set(NULL)
// no x remap effectively moves atoms within box, so set restart_pbc
options(narg-iarg,&arg[iarg]);
- if (remapflag != X_REMAP) restart_pbc = 1;
+ if (remapflag != Domain::X_REMAP) restart_pbc = 1;
// setup dimflags used by other classes to check for volume-change conflicts
@@ -890,7 +886,7 @@ void FixDeform::end_of_step()
// convert atoms and rigid bodies to lamda coords
- if (remapflag == X_REMAP) {
+ if (remapflag == Domain::X_REMAP) {
double **x = atom->x;
int *mask = atom->mask;
int nlocal = atom->nlocal;
@@ -930,7 +926,7 @@ void FixDeform::end_of_step()
// convert atoms and rigid bodies back to box coords
- if (remapflag == X_REMAP) {
+ if (remapflag == Domain::X_REMAP) {
double **x = atom->x;
int *mask = atom->mask;
int nlocal = atom->nlocal;
@@ -992,7 +988,7 @@ void FixDeform::options(int narg, char **arg)
{
if (narg < 0) error->all(FLERR,"Illegal fix deform command");
- remapflag = X_REMAP;
+ remapflag = Domain::X_REMAP;
scaleflag = 1;
flipflag = 1;
@@ -1000,9 +996,9 @@ void FixDeform::options(int narg, char **arg)
while (iarg < narg) {
if (strcmp(arg[iarg],"remap") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix deform command");
- if (strcmp(arg[iarg+1],"x") == 0) remapflag = X_REMAP;
- else if (strcmp(arg[iarg+1],"v") == 0) remapflag = V_REMAP;
- else if (strcmp(arg[iarg+1],"none") == 0) remapflag = NO_REMAP;
+ if (strcmp(arg[iarg+1],"x") == 0) remapflag = Domain::X_REMAP;
+ else if (strcmp(arg[iarg+1],"v") == 0) remapflag = Domain::V_REMAP;
+ else if (strcmp(arg[iarg+1],"none") == 0) remapflag = Domain::NO_REMAP;
else error->all(FLERR,"Illegal fix deform command");
iarg += 2;
} else if (strcmp(arg[iarg],"units") == 0) {
diff --git a/src/fix_deprecated.cpp b/src/fix_deprecated.cpp
index 9c0b6686d10e6c48b264c30f11b34537ae884e26..d0a63b00964471cd76666ae655f6e7205b0a7b8b 100644
--- a/src/fix_deprecated.cpp
+++ b/src/fix_deprecated.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "fix_deprecated.h"
#include "comm.h"
#include "error.h"
diff --git a/src/fix_drag.cpp b/src/fix_drag.cpp
index 3fda219126cbccc3bc8463bb07eea26ae96d3259..6a69dddbf5d744a8028c3aac143def239e3991cf 100644
--- a/src/fix_drag.cpp
+++ b/src/fix_drag.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "fix_drag.h"
#include "atom.h"
#include "update.h"
diff --git a/src/fix_dt_reset.cpp b/src/fix_dt_reset.cpp
index 48d09150a5337a3ba67e451b83d55fdeae01dc73..006bf27e77729c1f45078642f80bec2014631f65 100644
--- a/src/fix_dt_reset.cpp
+++ b/src/fix_dt_reset.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "fix_dt_reset.h"
#include "atom.h"
#include "update.h"
diff --git a/src/fix_enforce2d.cpp b/src/fix_enforce2d.cpp
index 336fd125563579490a66d9107138c12f0fa5ca47..4ffd2ca7ac233342910b495e839ac293f5583dd4 100644
--- a/src/fix_enforce2d.cpp
+++ b/src/fix_enforce2d.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "fix_enforce2d.h"
#include "atom.h"
#include "update.h"
diff --git a/src/fix_external.cpp b/src/fix_external.cpp
index a3b697bb2b6a006d78101a156c423fe5e2dda54d..4fcc842f899401eebc0f21e2fdf0abe86a7f3e41 100644
--- a/src/fix_external.cpp
+++ b/src/fix_external.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <stdio.h>
-#include <string.h>
-#include <stdlib.h>
+#include <cstdio>
+#include <cstring>
+#include <cstdlib>
#include "fix_external.h"
#include "atom.h"
#include "update.h"
diff --git a/src/fix_gravity.cpp b/src/fix_gravity.cpp
index 5582357c075eba7df09984ffb0c1a86b9b67fd23..9ace9d45ffcad6a3a6b86f3111e503ec3237b764 100644
--- a/src/fix_gravity.cpp
+++ b/src/fix_gravity.cpp
@@ -11,10 +11,10 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "fix_gravity.h"
#include "atom.h"
#include "update.h"
diff --git a/src/fix_group.cpp b/src/fix_group.cpp
index 8479565891a77dd0ba1471d9560362755d097968..2447002bc5202350b779d390dc31124a7f5dd5a1 100644
--- a/src/fix_group.cpp
+++ b/src/fix_group.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "fix_group.h"
#include "group.h"
#include "update.h"
@@ -251,3 +251,13 @@ void FixGroup::set_group()
if (varflag) memory->destroy(var);
}
+
+/* ---------------------------------------------------------------------- */
+
+void *FixGroup::extract(const char *str, int &unused)
+{
+ if (strcmp(str,"property") == 0 && propflag) return (void *) idprop;
+ if (strcmp(str,"variable") == 0 && varflag) return (void *) idvar;
+ if (strcmp(str,"region") == 0 && regionflag) return (void *) idregion;
+ return NULL;
+}
diff --git a/src/fix_group.h b/src/fix_group.h
index 070b4801bca3a9e8ab1a15379a52a2182c7bc38c..f3fecac31605a8a38b84a11b35ca2b27456dd9c8 100644
--- a/src/fix_group.h
+++ b/src/fix_group.h
@@ -33,6 +33,7 @@ class FixGroup : public Fix {
void setup(int);
void post_integrate();
void post_integrate_respa(int,int);
+ void *extract(const char *,int &);
private:
int gbit,gbitinverse;
@@ -69,7 +70,7 @@ Self-explanatory.
E: Per atom property for group dynamic does not exist
-UNDOCUMENTED
+Self-explanatory.
E: Group dynamic parent group cannot be dynamic
@@ -79,10 +80,6 @@ E: Variable for group dynamic is invalid style
The variable must be an atom-style variable.
-E: Per-atom property for group dynamic does not exist
-
-UNDOCUMENTED
-
W: One or more dynamic groups may not be updated at correct point in timestep
If there are other fixes that act immediately after the initial stage
diff --git a/src/fix_halt.cpp b/src/fix_halt.cpp
index 48d0f5da25ae55b9de9683980e41126cfb930ae4..7de09a0fa4b9add400543a97a62f2f8a73ad2f74 100644
--- a/src/fix_halt.cpp
+++ b/src/fix_halt.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "fix_halt.h"
#include "update.h"
#include "force.h"
diff --git a/src/fix_halt.h b/src/fix_halt.h
index 73c8d0115a100979da441c3629e9166901133126..d3b39cc1e2af13ee04d1813e738df6f5ad11c6e3 100644
--- a/src/fix_halt.h
+++ b/src/fix_halt.h
@@ -20,7 +20,7 @@ FixStyle(halt,FixHalt)
#ifndef LMP_FIX_HALT_H
#define LMP_FIX_HALT_H
-#include <stdio.h>
+#include <cstdio>
#include "fix.h"
namespace LAMMPS_NS {
diff --git a/src/fix_heat.cpp b/src/fix_heat.cpp
index 846531dbb987eaa3c1870c4c5c20e1ba1448f82c..f34845785c03b583e508ddd671d97023c4dd3e9a 100644
--- a/src/fix_heat.cpp
+++ b/src/fix_heat.cpp
@@ -15,9 +15,9 @@
Contributing author: Paul Crozier (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "fix_heat.h"
#include "atom.h"
#include "domain.h"
diff --git a/src/fix_indent.cpp b/src/fix_indent.cpp
index 331d84ff9aa61edded4b18edfb69382c41f52c3c..ade8cee5328d711ddbfd6ccb4088fe49120f7b88 100644
--- a/src/fix_indent.cpp
+++ b/src/fix_indent.cpp
@@ -15,9 +15,9 @@
Contributing author: Ravi Agrawal (Northwestern U)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <string.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstring>
+#include <cstdlib>
#include "fix_indent.h"
#include "atom.h"
#include "input.h"
diff --git a/src/fix_langevin.cpp b/src/fix_langevin.cpp
index 22993530010c9b0a016bb04e67006d6232e111e1..e4c36cc73917fe0f7d6b8b7ad094741d94cb1f8d 100644
--- a/src/fix_langevin.cpp
+++ b/src/fix_langevin.cpp
@@ -17,9 +17,9 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <math.h>
-#include <string.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstring>
+#include <cstdlib>
#include "fix_langevin.h"
#include "math_extra.h"
#include "atom.h"
diff --git a/src/fix_lineforce.cpp b/src/fix_lineforce.cpp
index 1e78bf3ec390130d229509bdec35d17d4a52e9c1..e90152c4e1092ef95b94df1371f6131f94e8d979 100644
--- a/src/fix_lineforce.cpp
+++ b/src/fix_lineforce.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <string.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstring>
+#include <cstdlib>
#include "fix_lineforce.h"
#include "atom.h"
#include "update.h"
diff --git a/src/fix_minimize.cpp b/src/fix_minimize.cpp
index cc00cc286ac98e625984b438ba228a45d99364f0..06a3ac900d7cd28209682056d923b6889ecc37d2 100644
--- a/src/fix_minimize.cpp
+++ b/src/fix_minimize.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <stdlib.h>
+#include <cstdlib>
#include "fix_minimize.h"
#include "atom.h"
#include "domain.h"
diff --git a/src/fix_momentum.cpp b/src/fix_momentum.cpp
index 63ec71f10d592f4d8f782f87f7fb8a37a0b302f1..680251e670a44330782eaab69619a55119a2c7de 100644
--- a/src/fix_momentum.cpp
+++ b/src/fix_momentum.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <stdlib.h>
-#include <string.h>
+#include <cstdlib>
+#include <cstring>
#include "fix_momentum.h"
#include "atom.h"
#include "domain.h"
diff --git a/src/fix_move.cpp b/src/fix_move.cpp
index a32c80c1e9e7d29fa5d098c086171a1cbb40ab3b..9eadfa5ab4c7c9b2a41102e9997f90178633d9bc 100644
--- a/src/fix_move.cpp
+++ b/src/fix_move.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
-#include <stdlib.h>
-#include <math.h>
+#include <cstring>
+#include <cstdlib>
+#include <cmath>
#include "fix_move.h"
#include "atom.h"
#include "group.h"
diff --git a/src/fix_move.h b/src/fix_move.h
index 13c9bc66b83cc4627eb6b5ee20f7becf7954bd88..5993d7d6e808f0e57b3427660c8d58e6bea6daeb 100644
--- a/src/fix_move.h
+++ b/src/fix_move.h
@@ -20,7 +20,7 @@ FixStyle(move,FixMove)
#ifndef LMP_FIX_MOVE_H
#define LMP_FIX_MOVE_H
-#include <stdio.h>
+#include <cstdio>
#include "fix.h"
namespace LAMMPS_NS {
diff --git a/src/fix_neigh_history.cpp b/src/fix_neigh_history.cpp
index e8bfe840d8059b6b9ac0d20ad1e7132e995b357f..3329b604efa4a0e2f6310e34cce95d7ca6902a14 100644
--- a/src/fix_neigh_history.cpp
+++ b/src/fix_neigh_history.cpp
@@ -12,8 +12,8 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <string.h>
-#include <stdio.h>
+#include <cstring>
+#include <cstdio>
#include "fix_neigh_history.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/fix_nh.cpp b/src/fix_nh.cpp
index e4500b19ca09c189f867b1e11819cd7af7e407bd..186376d95230bc8d2bbbf977c95fba8c5c16243f 100644
--- a/src/fix_nh.cpp
+++ b/src/fix_nh.cpp
@@ -15,9 +15,9 @@
Contributing authors: Mark Stevens (SNL), Aidan Thompson (SNL)
------------------------------------------------------------------------- */
-#include <string.h>
-#include <stdlib.h>
-#include <math.h>
+#include <cstring>
+#include <cstdlib>
+#include <cmath>
#include "fix_nh.h"
#include "math_extra.h"
#include "atom.h"
@@ -1034,7 +1034,7 @@ void FixNH::couple()
p_current[2] = tensor[2];
}
- if (!ISFINITE(p_current[0]) || !ISFINITE(p_current[1]) || !ISFINITE(p_current[2]))
+ if (!std::isfinite(p_current[0]) || !std::isfinite(p_current[1]) || !std::isfinite(p_current[2]))
error->all(FLERR,"Non-numeric pressure - simulation unstable");
// switch order from xy-xz-yz to Voigt
@@ -1044,7 +1044,7 @@ void FixNH::couple()
p_current[4] = tensor[4];
p_current[5] = tensor[3];
- if (!ISFINITE(p_current[3]) || !ISFINITE(p_current[4]) || !ISFINITE(p_current[5]))
+ if (!std::isfinite(p_current[3]) || !std::isfinite(p_current[4]) || !std::isfinite(p_current[5]))
error->all(FLERR,"Non-numeric pressure - simulation unstable");
}
}
diff --git a/src/fix_nh_sphere.cpp b/src/fix_nh_sphere.cpp
index cc59e4a1016eef159e0b4e04f21dc9f21bfa111c..f1764932429c84c80f9660a777153eff82470060 100644
--- a/src/fix_nh_sphere.cpp
+++ b/src/fix_nh_sphere.cpp
@@ -15,7 +15,7 @@
Contributing author: Mike Brown (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "fix_nh_sphere.h"
#include "atom.h"
#include "atom_vec.h"
diff --git a/src/fix_nph.cpp b/src/fix_nph.cpp
index a331a07d2404c30b0b61bfd27580dd2a76782f95..40265ef57c6e278a5260a5a007d3a1597d758c44 100644
--- a/src/fix_nph.cpp
+++ b/src/fix_nph.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "fix_nph.h"
#include "modify.h"
#include "error.h"
diff --git a/src/fix_nph_sphere.cpp b/src/fix_nph_sphere.cpp
index 852234074f0c212bf53691508e1275289fbbe878..3fcbe5e9c686e7801156570b42021c03ab60e9fa 100644
--- a/src/fix_nph_sphere.cpp
+++ b/src/fix_nph_sphere.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "fix_nph_sphere.h"
#include "modify.h"
#include "error.h"
diff --git a/src/fix_npt.cpp b/src/fix_npt.cpp
index e14200f6a2617af055f13ca0ddffe015bb897fbe..d17577d68d7c1e751f3d19a43eb4f5d1da9ac497 100644
--- a/src/fix_npt.cpp
+++ b/src/fix_npt.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "fix_npt.h"
#include "modify.h"
#include "error.h"
diff --git a/src/fix_npt_sphere.cpp b/src/fix_npt_sphere.cpp
index d3773e0d177296eeab5edc912bae43e1ce41fc93..50ac990dafc0ad3295ff6821472611e9b3011e76 100644
--- a/src/fix_npt_sphere.cpp
+++ b/src/fix_npt_sphere.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "fix_npt_sphere.h"
#include "modify.h"
#include "error.h"
diff --git a/src/fix_nve.cpp b/src/fix_nve.cpp
index 64ec3373f12c81137a7884c25f358bcc2e609174..58e33b9744b7c84eac6ca72b6d05ae7b502b571d 100644
--- a/src/fix_nve.cpp
+++ b/src/fix_nve.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <stdio.h>
-#include <string.h>
+#include <cstdio>
+#include <cstring>
#include "fix_nve.h"
#include "atom.h"
#include "force.h"
diff --git a/src/fix_nve_limit.cpp b/src/fix_nve_limit.cpp
index 6f85d107f113c178332c03450d55a77d0ee44747..f659597af7aeeb0d35081ed02aa43736d58fe8a1 100644
--- a/src/fix_nve_limit.cpp
+++ b/src/fix_nve_limit.cpp
@@ -11,10 +11,10 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "fix_nve_limit.h"
#include "atom.h"
#include "force.h"
diff --git a/src/fix_nve_noforce.cpp b/src/fix_nve_noforce.cpp
index aa24c26e03ff9bc7462da80aafb913dcc2258938..3403f4f5ec6b7f2eb7b71229159c18f3136b252e 100644
--- a/src/fix_nve_noforce.cpp
+++ b/src/fix_nve_noforce.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <stdio.h>
-#include <string.h>
+#include <cstdio>
+#include <cstring>
#include "fix_nve_noforce.h"
#include "atom.h"
#include "update.h"
diff --git a/src/fix_nve_sphere.cpp b/src/fix_nve_sphere.cpp
index daf89871ab60a459f339959d2bf5abb4dce22d99..fe37324cfbac2164ea0bd04940df8145f12f7e7f 100644
--- a/src/fix_nve_sphere.cpp
+++ b/src/fix_nve_sphere.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstring>
#include "fix_nve_sphere.h"
#include "atom.h"
#include "domain.h"
diff --git a/src/fix_nvt.cpp b/src/fix_nvt.cpp
index 35ee085da1bb86a49038ae8da123357e80fd7009..7247612dd470bc71ce513e2ae2c1aef042508572 100644
--- a/src/fix_nvt.cpp
+++ b/src/fix_nvt.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "fix_nvt.h"
#include "group.h"
#include "modify.h"
diff --git a/src/fix_nvt_sllod.cpp b/src/fix_nvt_sllod.cpp
index 87e86f235179e6e726719a4bed540990ed0f0365..012d67c3187c82b795ea6eaf60e4a8abed5e678a 100644
--- a/src/fix_nvt_sllod.cpp
+++ b/src/fix_nvt_sllod.cpp
@@ -15,8 +15,8 @@
Contributing author: Pieter in 't Veld (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <string.h>
+#include <cmath>
+#include <cstring>
#include "fix_nvt_sllod.h"
#include "math_extra.h"
#include "atom.h"
@@ -31,8 +31,6 @@
using namespace LAMMPS_NS;
using namespace FixConst;
-enum{NO_REMAP,X_REMAP,V_REMAP}; // same as fix_deform.cpp
-
/* ---------------------------------------------------------------------- */
FixNVTSllod::FixNVTSllod(LAMMPS *lmp, int narg, char **arg) :
@@ -83,7 +81,7 @@ void FixNVTSllod::init()
int i;
for (i = 0; i < modify->nfix; i++)
if (strcmp(modify->fix[i]->style,"deform") == 0) {
- if (((FixDeform *) modify->fix[i])->remapflag != V_REMAP)
+ if (((FixDeform *) modify->fix[i])->remapflag != Domain::V_REMAP)
error->all(FLERR,"Using fix nvt/sllod with inconsistent fix deform "
"remap option");
break;
diff --git a/src/fix_nvt_sphere.cpp b/src/fix_nvt_sphere.cpp
index b65b3adfae38b1509e347ee53201b00b7fffc4bb..44046699ba96e16da7a787695a35bd49a00e7c67 100644
--- a/src/fix_nvt_sphere.cpp
+++ b/src/fix_nvt_sphere.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "fix_nvt_sphere.h"
#include "group.h"
#include "modify.h"
diff --git a/src/fix_planeforce.cpp b/src/fix_planeforce.cpp
index 5e999c888cfdc9e2ab2b30a4e89bb8e9146f6da3..f90be6a233a330a9687ce56b7864d2bdda6128e6 100644
--- a/src/fix_planeforce.cpp
+++ b/src/fix_planeforce.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <string.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstring>
+#include <cstdlib>
#include "fix_planeforce.h"
#include "atom.h"
#include "update.h"
diff --git a/src/fix_press_berendsen.cpp b/src/fix_press_berendsen.cpp
index 04e2b3d39c535724b92f29fbc080d8b14c801b22..792154e93fe6dc222d1e9902019297731f48a486 100644
--- a/src/fix_press_berendsen.cpp
+++ b/src/fix_press_berendsen.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
-#include <stdlib.h>
-#include <math.h>
+#include <cstring>
+#include <cstdlib>
+#include <cmath>
#include "fix_press_berendsen.h"
#include "atom.h"
#include "force.h"
diff --git a/src/fix_print.cpp b/src/fix_print.cpp
index b553a94e3a19eebfe1777eba3b54c2c92f5b9f64..16218e0088e7ab0d04c560bbb975bdace7d41ebd 100644
--- a/src/fix_print.cpp
+++ b/src/fix_print.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <stdlib.h>
-#include <string.h>
+#include <cstdlib>
+#include <cstring>
#include "fix_print.h"
#include "update.h"
#include "input.h"
diff --git a/src/fix_print.h b/src/fix_print.h
index c3897b815f5fd8a7783a7aabc8f3cbda7f0d8181..1f6efdf10851f9c9780b09caf145555a9ac471da 100644
--- a/src/fix_print.h
+++ b/src/fix_print.h
@@ -20,7 +20,7 @@ FixStyle(print,FixPrint)
#ifndef LMP_FIX_PRINT_H
#define LMP_FIX_PRINT_H
-#include <stdio.h>
+#include <cstdio>
#include "fix.h"
namespace LAMMPS_NS {
diff --git a/src/fix_property_atom.cpp b/src/fix_property_atom.cpp
index 9ef939c58dc2a836ab0c143446b7736680bd4c0e..5ad4dfa4ba1bf2a3d4cee54695d80d28aa98bc71 100644
--- a/src/fix_property_atom.cpp
+++ b/src/fix_property_atom.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <stdlib.h>
-#include <string.h>
+#include <cstdlib>
+#include <cstring>
#include "fix_property_atom.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/fix_read_restart.cpp b/src/fix_read_restart.cpp
index f174e8160d709d394985d3d3ace43bc5f9b19e95..b384234b99973c51aa8c8a8ce765e99257bc5b0d 100644
--- a/src/fix_read_restart.cpp
+++ b/src/fix_read_restart.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <stdlib.h>
+#include <cstdlib>
#include "fix_read_restart.h"
#include "atom.h"
#include "memory.h"
diff --git a/src/fix_recenter.cpp b/src/fix_recenter.cpp
index 499e1a4158cd57540b52d72f4af25153df0d1074..49e370ac806ead4df1a1845dacdd1341503d9630 100644
--- a/src/fix_recenter.cpp
+++ b/src/fix_recenter.cpp
@@ -15,8 +15,8 @@
Contributing author: Naveen Michaud-Agrawal (Johns Hopkins U)
------------------------------------------------------------------------- */
-#include <stdlib.h>
-#include <string.h>
+#include <cstdlib>
+#include <cstring>
#include "fix_recenter.h"
#include "atom.h"
#include "group.h"
diff --git a/src/fix_respa.cpp b/src/fix_respa.cpp
index 0b6febd7b8329c0db139a35173b3d2dfaeee4bdb..3b9aad1286c4e62dbab97e505cdd3afcd7ab6cee 100644
--- a/src/fix_respa.cpp
+++ b/src/fix_respa.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <stdlib.h>
-#include <string.h>
+#include <cstdlib>
+#include <cstring>
#include "fix_respa.h"
#include "atom.h"
#include "force.h"
diff --git a/src/fix_restrain.cpp b/src/fix_restrain.cpp
index af11136d78d666851d4f446dac505ed526409632..6ad229fea7e70e16099b90cf9aee1e7b615e0ed3 100644
--- a/src/fix_restrain.cpp
+++ b/src/fix_restrain.cpp
@@ -16,9 +16,9 @@
support for bond and angle restraints by Andres Jaramillo-Botero (Caltech)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <string.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstring>
+#include <cstdlib>
#include "fix_restrain.h"
#include "atom.h"
#include "force.h"
@@ -45,7 +45,7 @@ enum{BOND,ANGLE,DIHEDRAL};
FixRestrain::FixRestrain(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg),
- rstyle(NULL), ids(NULL), kstart(NULL), kstop(NULL), target(NULL),
+ rstyle(NULL), mult(NULL), ids(NULL), kstart(NULL), kstop(NULL), target(NULL),
cos_target(NULL), sin_target(NULL)
{
if (narg < 4) error->all(FLERR,"Illegal fix restrain command");
@@ -53,6 +53,9 @@ FixRestrain::FixRestrain(LAMMPS *lmp, int narg, char **arg) :
scalar_flag = 1;
global_freq = 1;
extscalar = 1;
+ vector_flag = 1;
+ size_vector = 3;
+ extvector = 1;
respa_level_support = 1;
ilevel_respa = 0;
@@ -65,6 +68,7 @@ FixRestrain::FixRestrain(LAMMPS *lmp, int narg, char **arg) :
if (nrestrain == maxrestrain) {
maxrestrain += DELTA;
memory->grow(rstyle,maxrestrain,"restrain:rstyle");
+ memory->grow(mult,maxrestrain,"restrain:mult");
memory->grow(ids,maxrestrain,4,"restrain:ids");
memory->grow(kstart,maxrestrain,"restrain:kstart");
memory->grow(kstop,maxrestrain,"restrain:kstop");
@@ -96,6 +100,7 @@ FixRestrain::FixRestrain(LAMMPS *lmp, int narg, char **arg) :
} else if (strcmp(arg[iarg],"dihedral") == 0) {
if (iarg+8 > narg) error->all(FLERR,"Illegal fix restrain command");
rstyle[nrestrain] = DIHEDRAL;
+ mult[nrestrain] = 1;
ids[nrestrain][0] = force->inumeric(FLERR,arg[iarg+1]);
ids[nrestrain][1] = force->inumeric(FLERR,arg[iarg+2]);
ids[nrestrain][2] = force->inumeric(FLERR,arg[iarg+3]);
@@ -107,6 +112,13 @@ FixRestrain::FixRestrain(LAMMPS *lmp, int narg, char **arg) :
cos_target[nrestrain] = cos(target[nrestrain]);
sin_target[nrestrain] = sin(target[nrestrain]);
iarg += 8;
+ if ((iarg < narg) && (strcmp("mult",arg[iarg]) == 0)) {
+ if (iarg+1 > narg) error->all(FLERR,"Illegal fix restrain command");
+ mult[nrestrain] = force->inumeric(FLERR,arg[iarg+1]);
+ if (mult[nrestrain] < 0)
+ error->all(FLERR,"Illegal fix restrain command");
+ iarg += 2;
+ }
} else error->all(FLERR,"Illegal fix restrain command");
nrestrain++;
@@ -123,6 +135,7 @@ FixRestrain::FixRestrain(LAMMPS *lmp, int narg, char **arg) :
FixRestrain::~FixRestrain()
{
memory->destroy(rstyle);
+ memory->destroy(mult);
memory->destroy(ids);
memory->destroy(kstart);
memory->destroy(kstop);
@@ -178,6 +191,10 @@ void FixRestrain::min_setup(int vflag)
void FixRestrain::post_force(int vflag)
{
energy = 0.0;
+
+ ebond = 0.0;
+ eangle = 0.0;
+ edihed = 0.0;
for (int m = 0; m < nrestrain; m++)
if (rstyle[m] == BOND) restrain_bond(m);
@@ -261,7 +278,8 @@ void FixRestrain::restrain_bond(int m)
if (r > 0.0) fbond = -2.0*rk/r;
else fbond = 0.0;
- energy = rk*dr;
+ ebond += rk*dr;
+ energy += rk*dr;
// apply force to each of 2 atoms
@@ -368,7 +386,8 @@ void FixRestrain::restrain_angle(int m)
dtheta = acos(c) - target[m];
tk = k * dtheta;
- energy = tk*dtheta;
+ eangle += tk*dtheta;
+ energy += tk*dtheta;
a = -2.0 * tk * s;
a11 = a*c / rsq1;
@@ -410,7 +429,7 @@ void FixRestrain::restrain_angle(int m)
void FixRestrain::restrain_dihedral(int m)
{
- int i1,i2,i3,i4,i,mult;
+ int i1,i2,i3,i4,i;
double vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,vb2xm,vb2ym,vb2zm;
double f1[3],f2[3],f3[3],f4[3];
double ax,ay,az,bx,by,bz,rasq,rbsq,rgsq,rg,rginv,ra2inv,rb2inv,rabinv;
@@ -534,11 +553,10 @@ void FixRestrain::restrain_dihedral(int m)
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
- mult = 1; // multiplicity
p = 1.0;
df1 = 0.0;
- for (i = 0; i < mult; i++) {
+ for (i = 0; i < mult[m]; i++) {
ddf1 = p*c - df1*s;
df1 = p*s + df1*c;
p = ddf1;
@@ -546,10 +564,11 @@ void FixRestrain::restrain_dihedral(int m)
p = p*cos_target[m] + df1*sin_target[m];
df1 = df1*cos_target[m] - ddf1*sin_target[m];
- df1 *= -mult;
+ df1 *= -mult[m];
p += 1.0;
- energy = k * p;
+ edihed += k * p;
+ energy += k * p;
fg = vb1x*vb2xm + vb1y*vb2ym + vb1z*vb2zm;
hg = vb3x*vb2xm + vb3y*vb2ym + vb3z*vb2zm;
@@ -626,3 +645,23 @@ double FixRestrain::compute_scalar()
MPI_Allreduce(&energy,&energy_all,1,MPI_DOUBLE,MPI_SUM,world);
return energy_all;
}
+
+/* ----------------------------------------------------------------------
+ return individual energy contributions
+------------------------------------------------------------------------- */
+
+double FixRestrain::compute_vector(int n)
+{
+ if (n == 0) {
+ MPI_Allreduce(&ebond,&ebond_all,1,MPI_DOUBLE,MPI_SUM,world);
+ return ebond_all;
+ } else if (n == 1) {
+ MPI_Allreduce(&eangle,&eangle_all,1,MPI_DOUBLE,MPI_SUM,world);
+ return eangle_all;
+ } else if (n == 2) {
+ MPI_Allreduce(&edihed,&edihed_all,1,MPI_DOUBLE,MPI_SUM,world);
+ return edihed_all;
+ } else {
+ return 0.0;
+ }
+}
diff --git a/src/fix_restrain.h b/src/fix_restrain.h
index a6f23f86c6c311afeee63dac0b1da5b9456e20ce..4572905d46e1ae298d876fe91fb9c94f05e05d09 100644
--- a/src/fix_restrain.h
+++ b/src/fix_restrain.h
@@ -36,15 +36,20 @@ class FixRestrain : public Fix {
void post_force_respa(int, int, int);
void min_post_force(int);
double compute_scalar();
+ double compute_vector(int);
private:
int ilevel_respa;
int nrestrain,maxrestrain;
int *rstyle;
+ int *mult;
int **ids;
double *kstart,*kstop,*target;
double *cos_target,*sin_target;
double energy,energy_all;
+ double ebond,ebond_all;
+ double eangle,eangle_all;
+ double edihed,edihed_all;
void restrain_bond(int);
void restrain_angle(int);
diff --git a/src/fix_setforce.cpp b/src/fix_setforce.cpp
index 99176bb3799c76444f3555c7f028434868507391..89b340b0ae422558e666f81190bb3c4055abf69c 100644
--- a/src/fix_setforce.cpp
+++ b/src/fix_setforce.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
-#include <stdlib.h>
+#include <cstring>
+#include <cstdlib>
#include "fix_setforce.h"
#include "atom.h"
#include "update.h"
diff --git a/src/fix_spring.cpp b/src/fix_spring.cpp
index 9c6bd4084ffe53c568bd5edefe9ba0ecd4517bde..ecb84eeb0f0ead6b4aec161ae43b8a38d6e8fc89 100644
--- a/src/fix_spring.cpp
+++ b/src/fix_spring.cpp
@@ -15,9 +15,9 @@
Contributing author: Paul Crozier (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "fix_spring.h"
#include "atom.h"
#include "update.h"
diff --git a/src/fix_spring_chunk.cpp b/src/fix_spring_chunk.cpp
index 773e032388b225fc1590c37b7f715116ebb4106a..53e9285a9c7ddd4869bb760c8b5cc60be790b073 100644
--- a/src/fix_spring_chunk.cpp
+++ b/src/fix_spring_chunk.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "fix_spring_chunk.h"
#include "atom.h"
#include "update.h"
diff --git a/src/fix_spring_rg.cpp b/src/fix_spring_rg.cpp
index b7fd33ce7749c2dfb1b0c445edf41273a1a18a1c..c2e226a343dc657b5661f24b6991d390cac4f1ff 100644
--- a/src/fix_spring_rg.cpp
+++ b/src/fix_spring_rg.cpp
@@ -16,9 +16,9 @@
Paul Crozier (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "fix_spring_rg.h"
#include "atom.h"
#include "update.h"
diff --git a/src/fix_spring_self.cpp b/src/fix_spring_self.cpp
index b6d5e3c834d48a585658acf09999ae814c844199..1a5c89c6a15b43832f190d7f73dcfeaef3cf6383 100644
--- a/src/fix_spring_self.cpp
+++ b/src/fix_spring_self.cpp
@@ -15,8 +15,8 @@
Contributing author: Naveen Michaud-Agrawal (Johns Hopkins University)
------------------------------------------------------------------------- */
-#include <stdlib.h>
-#include <string.h>
+#include <cstdlib>
+#include <cstring>
#include "fix_spring_self.h"
#include "atom.h"
#include "update.h"
diff --git a/src/fix_store.cpp b/src/fix_store.cpp
index 3738629820e45e146b6ba569b7c2f459e815351c..3b1f3dca77dde1d15d645938e000a012c202ee9c 100644
--- a/src/fix_store.cpp
+++ b/src/fix_store.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <stdlib.h>
-#include <string.h>
+#include <cstdlib>
+#include <cstring>
#include "fix_store.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/fix_store.h b/src/fix_store.h
index 1aad56323244c937850134658b899a8b7def75ad..5524770a9700be426df90671e5be2336c499b6f9 100644
--- a/src/fix_store.h
+++ b/src/fix_store.h
@@ -20,7 +20,7 @@ FixStyle(STORE,FixStore)
#ifndef LMP_FIX_STORE_H
#define LMP_FIX_STORE_H
-#include <stdio.h>
+#include <cstdio>
#include "fix.h"
namespace LAMMPS_NS {
diff --git a/src/fix_store_force.cpp b/src/fix_store_force.cpp
index cfeace532627c68a28ddf00a5c8e9a09cffa8f6d..5e2150f68d004cdd6a82d0f416ddbd00311520d7 100644
--- a/src/fix_store_force.cpp
+++ b/src/fix_store_force.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "fix_store_force.h"
#include "atom.h"
#include "update.h"
diff --git a/src/fix_store_state.cpp b/src/fix_store_state.cpp
index 2f2ba3feff7ffbcf7deea48f91568e8cdc846874..3195e983e35019adb4c627f20a62bffa18dae2e3 100644
--- a/src/fix_store_state.cpp
+++ b/src/fix_store_state.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <stdlib.h>
-#include <string.h>
+#include <cstdlib>
+#include <cstring>
#include "fix_store_state.h"
#include "atom.h"
#include "domain.h"
diff --git a/src/fix_temp_berendsen.cpp b/src/fix_temp_berendsen.cpp
index 7b312cfb5f35dbc1777aeb9e63c3a530ed1e9d9c..55518015c4a1a5bfd743e369d7b92a500ee1e2ed 100644
--- a/src/fix_temp_berendsen.cpp
+++ b/src/fix_temp_berendsen.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
-#include <stdlib.h>
-#include <math.h>
+#include <cstring>
+#include <cstdlib>
+#include <cmath>
#include "fix_temp_berendsen.h"
#include "atom.h"
#include "force.h"
diff --git a/src/fix_temp_csld.cpp b/src/fix_temp_csld.cpp
index 63f27cdecb17968ecbc6f265ef78a45018a70535..7bdf7763555c56841348040e0f4f78bd246cd9b1 100644
--- a/src/fix_temp_csld.cpp
+++ b/src/fix_temp_csld.cpp
@@ -15,9 +15,9 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <string.h>
-#include <stdlib.h>
-#include <math.h>
+#include <cstring>
+#include <cstdlib>
+#include <cmath>
#include "fix_temp_csld.h"
#include "atom.h"
#include "force.h"
diff --git a/src/fix_temp_csvr.cpp b/src/fix_temp_csvr.cpp
index ae5868ff0ff7902859ac61b6b3cc40f072ac882c..495a1551135f48c37fb5c29d1a132434e5ed1f71 100644
--- a/src/fix_temp_csvr.cpp
+++ b/src/fix_temp_csvr.cpp
@@ -16,9 +16,9 @@
Based on code by Paolo Raiteri (Curtin U) and Giovanni Bussi (SISSA)
------------------------------------------------------------------------- */
-#include <string.h>
-#include <stdlib.h>
-#include <math.h>
+#include <cstring>
+#include <cstdlib>
+#include <cmath>
#include "fix_temp_csvr.h"
#include "atom.h"
#include "force.h"
diff --git a/src/fix_temp_rescale.cpp b/src/fix_temp_rescale.cpp
index 52e2da7b3de2b35e7afb35fae4746f404041c214..11dfa6a5fcdf05c4e75a459f3bc5d74503616e83 100644
--- a/src/fix_temp_rescale.cpp
+++ b/src/fix_temp_rescale.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
-#include <stdlib.h>
-#include <math.h>
+#include <cstring>
+#include <cstdlib>
+#include <cmath>
#include "fix_temp_rescale.h"
#include "atom.h"
#include "force.h"
diff --git a/src/fix_tmd.cpp b/src/fix_tmd.cpp
index f5ed970da7eb480a5b440ca94b5c6ef8e4253483..39d4173a63a058a40030512287d7441123266d63 100644
--- a/src/fix_tmd.cpp
+++ b/src/fix_tmd.cpp
@@ -17,9 +17,9 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "fix_tmd.h"
#include "atom.h"
#include "update.h"
diff --git a/src/fix_tmd.h b/src/fix_tmd.h
index 337b037c2dad317ec79c4b4986864b9a4f2094bf..b6db41dd5a158361be5d000fd416c0afc9b216c3 100644
--- a/src/fix_tmd.h
+++ b/src/fix_tmd.h
@@ -20,7 +20,7 @@ FixStyle(tmd,FixTMD)
#ifndef LMP_FIX_TMD_H
#define LMP_FIX_TMD_H
-#include <stdio.h>
+#include <cstdio>
#include "fix.h"
namespace LAMMPS_NS {
diff --git a/src/fix_vector.cpp b/src/fix_vector.cpp
index 4847926aaf60e6cb20060712a76a3e0e075b513c..9b7f01697084ce3e705dc1920de8b11f0b024a62 100644
--- a/src/fix_vector.cpp
+++ b/src/fix_vector.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "fix_vector.h"
#include "update.h"
#include "force.h"
diff --git a/src/fix_viscous.cpp b/src/fix_viscous.cpp
index 423bccc38323aecae8b07fc9cbbf34d7c7308e1c..1d2609c8b68ff782ba1e41c7798f4e944a6ed646 100644
--- a/src/fix_viscous.cpp
+++ b/src/fix_viscous.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "fix_viscous.h"
#include "atom.h"
#include "update.h"
diff --git a/src/fix_wall.cpp b/src/fix_wall.cpp
index 2c3aa4afa0bd01856af22e5dee54bfedc5f19414..096bbe618a5a9b3fa234292807912f32642d210c 100644
--- a/src/fix_wall.cpp
+++ b/src/fix_wall.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "fix_wall.h"
#include "atom.h"
#include "input.h"
diff --git a/src/fix_wall_harmonic.cpp b/src/fix_wall_harmonic.cpp
index 20d5dbebd4fef90efff97feb14114cde107efea4..4dc067178ad5d42da7f4f6c0eb580adff908df1e 100644
--- a/src/fix_wall_harmonic.cpp
+++ b/src/fix_wall_harmonic.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "fix_wall_harmonic.h"
#include "atom.h"
#include "error.h"
diff --git a/src/fix_wall_lj1043.cpp b/src/fix_wall_lj1043.cpp
index 35bfff1749e97c3392c6abf7ac5f79ad6af6ce5b..a93f4dd699c6424cfdc2d918aba8ab862df13cd9 100644
--- a/src/fix_wall_lj1043.cpp
+++ b/src/fix_wall_lj1043.cpp
@@ -15,7 +15,7 @@
Contributing author: Jonathan Lee (Sandia)
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "fix_wall_lj1043.h"
#include "atom.h"
#include "math_const.h"
diff --git a/src/fix_wall_lj126.cpp b/src/fix_wall_lj126.cpp
index f556952ab3de5ec9bd7dff1118b3848f09c0016a..369ef78c97875ee693c2e0151e8527270068cfeb 100644
--- a/src/fix_wall_lj126.cpp
+++ b/src/fix_wall_lj126.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "fix_wall_lj126.h"
#include "atom.h"
#include "error.h"
diff --git a/src/fix_wall_lj93.cpp b/src/fix_wall_lj93.cpp
index f5d6a7e147d19ae5c062fc6157fe57c43738cf0e..ce5a06c81b956fbafe3570c73903a7a52afdc802 100644
--- a/src/fix_wall_lj93.cpp
+++ b/src/fix_wall_lj93.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "fix_wall_lj93.h"
#include "atom.h"
#include "error.h"
diff --git a/src/fix_wall_reflect.cpp b/src/fix_wall_reflect.cpp
index 86607dbe8e611078ba7f59de9c5c8b0984b4dded..8acba720352dc38030263f29486b55c77be4e539 100644
--- a/src/fix_wall_reflect.cpp
+++ b/src/fix_wall_reflect.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <stdlib.h>
-#include <string.h>
+#include <cstdlib>
+#include <cstring>
#include "fix_wall_reflect.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/fix_wall_region.cpp b/src/fix_wall_region.cpp
index 67b0bcd713750403bcc007d741e90aeae26387ef..ea1b62bfa5e160688cd7913e9cad106e5db60535 100644
--- a/src/fix_wall_region.cpp
+++ b/src/fix_wall_region.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "fix_wall_region.h"
#include "atom.h"
#include "atom_vec.h"
diff --git a/src/force.cpp b/src/force.cpp
index df32930e0ab0aa750215dd7299d3611a13958e5e..8ee301982d168c6f5c8389bee86d3d2404bcf903 100644
--- a/src/force.cpp
+++ b/src/force.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <stdlib.h>
-#include <string.h>
-#include <ctype.h>
+#include <cstdlib>
+#include <cstring>
+#include <cctype>
#include "force.h"
#include "style_bond.h"
#include "style_angle.h"
diff --git a/src/force.h b/src/force.h
index 76cd69ed76e62146f6007a97b5bc7fede686daa2..ce593fa518a0b772f528be8a3cb5269c440f2c26 100644
--- a/src/force.h
+++ b/src/force.h
@@ -15,7 +15,7 @@
#define LMP_FORCE_H
#include "pointers.h"
-#include <stdio.h>
+#include <cstdio>
#include <map>
#include <string>
diff --git a/src/group.cpp b/src/group.cpp
index 72224dcf25b58c186b544f9135e93ca4082aa847..9d33da9acb4e623ea80a0e1f5e9e5fe1928ada07 100644
--- a/src/group.cpp
+++ b/src/group.cpp
@@ -12,10 +12,10 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <math.h>
-#include <stdio.h>
-#include <string.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdio>
+#include <cstring>
+#include <cstdlib>
#include "group.h"
#include "domain.h"
#include "atom.h"
diff --git a/src/group.h b/src/group.h
index 8f07fa19d00d23097e8267a9fce7ba448939a101..6b6cbb1def7e4d2e5340fa6ce3f0b14664f642f3 100644
--- a/src/group.h
+++ b/src/group.h
@@ -14,7 +14,7 @@
#ifndef LMP_GROUP_H
#define LMP_GROUP_H
-#include <stdio.h>
+#include <cstdio>
#include "pointers.h"
#include <map>
diff --git a/src/image.cpp b/src/image.cpp
index 033bcfb669d633dbb566b0ce5bc5cb42ad18157b..301a2af88f23588dfcdea129fe2c283ae6269cb0 100644
--- a/src/image.cpp
+++ b/src/image.cpp
@@ -16,10 +16,10 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <math.h>
-#include <ctype.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cctype>
+#include <cstdlib>
+#include <cstring>
#include "image.h"
#include "math_extra.h"
#include "random_mars.h"
@@ -35,7 +35,7 @@
#ifdef LAMMPS_PNG
#include <png.h>
#include <zlib.h>
-#include <setjmp.h>
+#include <csetjmp>
#include "version.h"
#endif
@@ -1065,7 +1065,7 @@ void Image::write_PNG(FILE *fp)
png_set_text(png_ptr,info_ptr,text_ptr,1);
png_write_info(png_ptr,info_ptr);
- png_bytep row_pointers[height];
+ png_bytep *row_pointers = new png_bytep[height];
for (int i=0; i < height; ++i)
row_pointers[i] = (png_bytep) &writeBuffer[(height-i-1)*3*width];
@@ -1073,6 +1073,7 @@ void Image::write_PNG(FILE *fp)
png_write_end(png_ptr, info_ptr);
png_destroy_write_struct(&png_ptr, &info_ptr);
+ delete[] row_pointers;
#endif
}
diff --git a/src/image.h b/src/image.h
index 58050ada3278f8b8f4d140b2a43883c450ef049c..5672bf85c571d801876d37ebe889fefb12c1707c 100644
--- a/src/image.h
+++ b/src/image.h
@@ -14,8 +14,8 @@
#ifndef LMP_IMAGE_H
#define LMP_IMAGE_H
-#include <math.h>
-#include <stdio.h>
+#include <cmath>
+#include <cstdio>
#include "pointers.h"
namespace LAMMPS_NS {
diff --git a/src/imbalance.h b/src/imbalance.h
index ce7b700b9d66ddfb46db8d8132b3b8515d477e67..d3c3b9a64262c4dbd0aca56f83798a85db6b14b5 100644
--- a/src/imbalance.h
+++ b/src/imbalance.h
@@ -14,7 +14,7 @@
#ifndef LMP_IMBALANCE_H
#define LMP_IMBALANCE_H
-#include <stdio.h>
+#include <cstdio>
#include "pointers.h"
namespace LAMMPS_NS {
diff --git a/src/imbalance_store.cpp b/src/imbalance_store.cpp
index 2903f8497ea29ed6940db945c0195f58ddf4f097..6b69caf785c964e831236c65a2b545ca4ec85ec6 100644
--- a/src/imbalance_store.cpp
+++ b/src/imbalance_store.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "imbalance_store.h"
#include "atom.h"
#include "input.h"
diff --git a/src/imbalance_var.cpp b/src/imbalance_var.cpp
index 394a9af3657f2788950041c338448594ad8254e7..acb3da8d1370ed6215549effa3a340abd492f82c 100644
--- a/src/imbalance_var.cpp
+++ b/src/imbalance_var.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "imbalance_var.h"
#include "atom.h"
#include "group.h"
diff --git a/src/improper.cpp b/src/improper.cpp
index 089fc43aad09205a0e72aecaa886ef3b78a87d50..17e2df4e590e65fe61000c948d129163173f0b97 100644
--- a/src/improper.cpp
+++ b/src/improper.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "improper.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/improper.h b/src/improper.h
index df3c966cdc4704b5d91c03332274fabd0e3ab9b5..adcf6d29c867251342105212f90c0a8cff947956 100644
--- a/src/improper.h
+++ b/src/improper.h
@@ -14,7 +14,7 @@
#ifndef LMP_IMPROPER_H
#define LMP_IMPROPER_H
-#include <stdio.h>
+#include <cstdio>
#include "pointers.h"
namespace LAMMPS_NS {
diff --git a/src/improper_hybrid.cpp b/src/improper_hybrid.cpp
index abaaae02dabeee2e79519f363dcdce22f045ea29..3c17e42eafe77e26b1af427561f010ea130cb667 100644
--- a/src/improper_hybrid.cpp
+++ b/src/improper_hybrid.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <string.h>
-#include <ctype.h>
+#include <cmath>
+#include <cstring>
+#include <cctype>
#include "improper_hybrid.h"
#include "atom.h"
#include "neighbor.h"
diff --git a/src/improper_hybrid.h b/src/improper_hybrid.h
index dbba347cf947e96238e3b587ef933f1380627ce8..89595ccfc44ff6f07ecfac4641b9440769a1f7fd 100644
--- a/src/improper_hybrid.h
+++ b/src/improper_hybrid.h
@@ -20,7 +20,7 @@ ImproperStyle(hybrid,ImproperHybrid)
#ifndef LMP_IMPROPER_HYBRID_H
#define LMP_IMPROPER_HYBRID_H
-#include <stdio.h>
+#include <cstdio>
#include "improper.h"
namespace LAMMPS_NS {
diff --git a/src/improper_zero.cpp b/src/improper_zero.cpp
index 556e427ff8b9203112c8cb53f475ceab4bb6379a..25ab3e7bbafa554104b440245c07dda93a18f924 100644
--- a/src/improper_zero.cpp
+++ b/src/improper_zero.cpp
@@ -15,9 +15,9 @@
Contributing author: Carsten Svaneborg (SDU)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "improper_zero.h"
#include "atom.h"
#include "force.h"
diff --git a/src/improper_zero.h b/src/improper_zero.h
index 0e16411fefac513a33415f66142cbd34e4f76729..0a2290b6f747a45013639005239284fe59c548fe 100644
--- a/src/improper_zero.h
+++ b/src/improper_zero.h
@@ -20,7 +20,7 @@ ImproperStyle(zero,ImproperZero)
#ifndef LMP_IMPROPER_ZERO_H
#define LMP_IMPROPER_ZERO_H
-#include <stdio.h>
+#include <cstdio>
#include "improper.h"
namespace LAMMPS_NS {
diff --git a/src/info.cpp b/src/info.cpp
index e1103c0530b8638d3505ec9a13b50023d280bad9..65c0cd9b53dcb4f480b54d4095752b9179546a6b 100644
--- a/src/info.cpp
+++ b/src/info.cpp
@@ -16,7 +16,7 @@
Richard Berger (Temple U)
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "info.h"
#include "accelerator_kokkos.h"
#include "atom.h"
@@ -43,7 +43,7 @@
#include "update.h"
#include "error.h"
-#include <time.h>
+#include <ctime>
#include <vector>
#include <string>
#include <algorithm>
@@ -51,7 +51,7 @@
#ifdef _WIN32
#define PSAPI_VERSION 1
#include <windows.h>
-#include <stdint.h>
+#include <stdint.h> // <cstdint> requires C++-11
#include <psapi.h>
#else
#include <sys/time.h>
diff --git a/src/input.cpp b/src/input.cpp
index a0691f78a49c119ad65ce1b16f777e472f8b9d7e..b83a3683e4a3eae3984e842f55f33e672471fd85 100644
--- a/src/input.cpp
+++ b/src/input.cpp
@@ -12,11 +12,11 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include <errno.h>
-#include <ctype.h>
+#include <cctype>
#include <unistd.h>
#include <sys/stat.h>
#include "input.h"
diff --git a/src/input.h b/src/input.h
index 55d93e630373be8934d928cf1868d685f5b9e4d0..80b3e8c7da3d1f7a1e2f0378c37eb7785d5da7a2 100644
--- a/src/input.h
+++ b/src/input.h
@@ -14,7 +14,7 @@
#ifndef LMP_INPUT_H
#define LMP_INPUT_H
-#include <stdio.h>
+#include <cstdio>
#include "pointers.h"
#include <map>
#include <string>
diff --git a/src/integrate.cpp b/src/integrate.cpp
index 4aeb6e18c93e721e489c046348938f70c3287d69..97d28d6d7c2b6bccbc70d6f973017f31d86cc6d4 100644
--- a/src/integrate.cpp
+++ b/src/integrate.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <stdlib.h>
+#include <cstdlib>
#include "integrate.h"
#include "update.h"
#include "force.h"
diff --git a/src/irregular.cpp b/src/irregular.cpp
index 6cd1b22c2fefc099d4ce1b976756a5fc53bc8941..9c15f135d0e4bfc13e40e799f69499a754af68bf 100644
--- a/src/irregular.cpp
+++ b/src/irregular.cpp
@@ -12,8 +12,8 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cstdlib>
+#include <cstring>
#include "irregular.h"
#include "atom.h"
#include "atom_vec.h"
@@ -34,8 +34,6 @@ static int compare_standalone(const void *, const void *);
static int compare_standalone(const int, const int, void *);
#endif
-enum{LAYOUT_UNIFORM,LAYOUT_NONUNIFORM,LAYOUT_TILED}; // several files
-
#define BUFFACTOR 1.5
#define BUFMIN 1000
#define BUFEXTRA 1000
@@ -222,7 +220,7 @@ int Irregular::migrate_check()
// migrate required if comm layout is tiled
// cannot use myloc[] logic below
- if (comm->layout == LAYOUT_TILED) return 1;
+ if (comm->layout == Comm::LAYOUT_TILED) return 1;
// subbox bounds for orthogonal or triclinic box
diff --git a/src/kspace.cpp b/src/kspace.cpp
index b2db585f121f7a537dc2d75d9b222e9545b106e7..fc8b12288ba0679f17d0cbca31287c24208f142b 100644
--- a/src/kspace.cpp
+++ b/src/kspace.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <stdlib.h>
-#include <string.h>
+#include <cstdlib>
+#include <cstring>
#include "kspace.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/lammps.cpp b/src/lammps.cpp
index dd91ea7c19780f3d34d99864efc892203df9131f..56af95767bc9901ae60df9e2d2df3d7765de3567 100644
--- a/src/lammps.cpp
+++ b/src/lammps.cpp
@@ -12,8 +12,8 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <string.h>
-#include <ctype.h>
+#include <cstring>
+#include <cctype>
#include "lammps.h"
#include "style_angle.h"
#include "style_atom.h"
diff --git a/src/lammps.h b/src/lammps.h
index 26714ab072bd76f3748bf845d87bd8d6a2f588b8..1323dcccc810a29634d7d6348844925daf34004a 100644
--- a/src/lammps.h
+++ b/src/lammps.h
@@ -14,7 +14,7 @@
#ifndef LMP_LAMMPS_H
#define LMP_LAMMPS_H
-#include <stdio.h>
+#include <cstdio>
namespace LAMMPS_NS {
diff --git a/src/lattice.cpp b/src/lattice.cpp
index 5f6d05db8932a9e7f8acf86571961413c9bec21e..ee2fea2a758dca955bb4a8841ff481d99974dac9 100644
--- a/src/lattice.cpp
+++ b/src/lattice.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <string.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstring>
+#include <cstdlib>
#include "lattice.h"
#include "update.h"
#include "domain.h"
diff --git a/src/library.cpp b/src/library.cpp
index 07c4cae9c16327b5efd618391d3096f1551ac4e3..0162c560cea7e21b66cc759a481aae6420c86d51 100644
--- a/src/library.cpp
+++ b/src/library.cpp
@@ -15,8 +15,8 @@
// customize by adding new LAMMPS-specific functions
#include <mpi.h>
-#include <string.h>
-#include <stdlib.h>
+#include <cstring>
+#include <cstdlib>
#include "library.h"
#include "lmptype.h"
#include "lammps.h"
@@ -480,10 +480,13 @@ void *lammps_extract_atom(void *ptr, char *name)
compute's internal data structure for the entity
caller should cast it to (double *) for a scalar or vector
caller should cast it to (double **) for an array
- for per-atom or local data, returns a pointer to the
+ for per-atom or local vector/array data, returns a pointer to the
compute's internal data structure for the entity
caller should cast it to (double *) for a vector
caller should cast it to (double **) for an array
+ for local data, accessing scalar data for the compute (type = 0),
+ returns a pointer that should be cast to (int *) which points to
+ an int with the number of local rows, i.e. the length of the local array.
returns a void pointer to the compute's internal data structure
for the entity which the caller can cast to the proper data type
returns a NULL if id is not recognized or style/type not supported
@@ -541,6 +544,11 @@ void *lammps_extract_compute(void *ptr, char *id, int style, int type)
if (style == 2) {
if (!compute->local_flag) return NULL;
+ if (type == 0) {
+ if (compute->invoked_local != lmp->update->ntimestep)
+ compute->compute_local();
+ return (void *) &compute->size_local_rows;
+ }
if (type == 1) {
if (compute->invoked_local != lmp->update->ntimestep)
compute->compute_local();
@@ -925,7 +933,7 @@ void lammps_gather_atoms_concat(void *ptr, char *name,
BEGIN_CAPTURE
{
- int i,j,offset;
+ int i,offset;
// error if tags are not defined
// NOTE: test that name = image or ids is not a 64-bit int in code?
@@ -967,7 +975,6 @@ void lammps_gather_atoms_concat(void *ptr, char *name,
lmp->memory->create(copy,count*natoms,"lib/gather:copy");
for (i = 0; i < count*natoms; i++) copy[i] = 0;
- tagint *tag = lmp->atom->tag;
int nlocal = lmp->atom->nlocal;
if (count == 1) {
@@ -1109,7 +1116,6 @@ void lammps_gather_atoms_subset(void *ptr, char *name,
lmp->memory->create(copy,count*ndata,"lib/gather:copy");
for (i = 0; i < count*ndata; i++) copy[i] = 0;
- tagint *tag = lmp->atom->tag;
int nlocal = lmp->atom->nlocal;
if (count == 1) {
@@ -1155,7 +1161,6 @@ void lammps_gather_atoms_subset(void *ptr, char *name,
lmp->memory->create(copy,count*ndata,"lib/gather:copy");
for (i = 0; i < count*ndata; i++) copy[i] = 0.0;
- tagint *tag = lmp->atom->tag;
int nlocal = lmp->atom->nlocal;
if (count == 1) {
diff --git a/src/lmptype.h b/src/lmptype.h
index 253f9a7470a400ef4330e7619c9d89a6e60e7a7f..2be1d2ac385ccdb0e1dad96a4c23f2143a4bf10a 100644
--- a/src/lmptype.h
+++ b/src/lmptype.h
@@ -36,9 +36,9 @@
#define __STDC_FORMAT_MACROS
#endif
-#include <limits.h>
-#include <stdint.h>
-#include <inttypes.h>
+#include <climits>
+#include <stdint.h> // <cstdint> requires C++-11
+#include <inttypes.h> // <cinttypes> requires C++-11
// grrr - IBM Power6 does not provide this def in their system header files
@@ -200,8 +200,6 @@ typedef int bigint;
#define _noalias
#endif
-#define ISFINITE(x) isfinite(x)
-
// settings to enable LAMMPS to build under Windows
#ifdef _WIN32
diff --git a/src/lmpwindows.h b/src/lmpwindows.h
index d20d0f87baa274d29a5be8610f4f34f15826d018..ae2a5457179ad9eec7c10e0645959dd05dc9c71e 100644
--- a/src/lmpwindows.h
+++ b/src/lmpwindows.h
@@ -1,9 +1,9 @@
-#include <iso646.h>
+#include <ciso646>
#if !defined(__MINGW32__)
#include "erf.h"
#endif
#include <direct.h>
-#include <math.h>
+#include <cmath>
// LAMMPS uses usleep with 100 ms arguments, no microsecond precision needed
#if !defined(__MINGW32__)
#include "sleep.h"
diff --git a/src/main.cpp b/src/main.cpp
index 95368385bd0b31b5e5ef878f1827c63f225e8a44..8eb5e4e5433da594017958784de1de0790b37b82 100644
--- a/src/main.cpp
+++ b/src/main.cpp
@@ -15,8 +15,8 @@
#include "lammps.h"
#include "input.h"
#include "error.h"
-#include <stdio.h>
-#include <stdlib.h>
+#include <cstdio>
+#include <cstdlib>
#if defined(LAMMPS_TRAP_FPE) && defined(_GNU_SOURCE)
#include <fenv.h>
diff --git a/src/math_extra.cpp b/src/math_extra.cpp
index d1700a3070cb6cc546e7e39ed0c1c10a5ad2a9f7..b70986ce914904edc8b3a2cbf41fb3b3e9ade210 100644
--- a/src/math_extra.cpp
+++ b/src/math_extra.cpp
@@ -15,8 +15,8 @@
Contributing author: Mike Brown (SNL)
------------------------------------------------------------------------- */
-#include <stdio.h>
-#include <string.h>
+#include <cstdio>
+#include <cstring>
#include "math_extra.h"
#define MAXJACOBI 50
diff --git a/src/math_extra.h b/src/math_extra.h
index eec9855b8066deb3f75ae3dc92e2b1f5881f679a..85f57224cfb97a3f6a7bde21dddbae18409dae93 100644
--- a/src/math_extra.h
+++ b/src/math_extra.h
@@ -18,9 +18,9 @@
#ifndef LMP_MATH_EXTRA_H
#define LMP_MATH_EXTRA_H
-#include <math.h>
-#include <stdio.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstring>
#include "error.h"
namespace MathExtra {
diff --git a/src/math_special.cpp b/src/math_special.cpp
index 4b9197f0fc150e7452351b3eee441872641a5457..31567bdc77fa90bab58d307356d3a9b67aa109ba 100644
--- a/src/math_special.cpp
+++ b/src/math_special.cpp
@@ -1,5 +1,5 @@
-#include <math.h>
-#include <stdint.h>
+#include <cmath>
+#include <stdint.h> // <cstdint> requires C++-11
#include "math_special.h"
using namespace LAMMPS_NS;
diff --git a/src/math_special.h b/src/math_special.h
index 8cd328f5fcdb25232932a68a3cfbd7cc148cad79..1e7b10d9fdc46201e8833127098777fe58bda88c 100644
--- a/src/math_special.h
+++ b/src/math_special.h
@@ -14,7 +14,7 @@
#ifndef LMP_MATH_SPECIAL_H
#define LMP_MATH_SPECIAL_H
-#include <math.h>
+#include <cmath>
namespace LAMMPS_NS {
diff --git a/src/math_vector.h b/src/math_vector.h
index 9304cf0804d1133fcf33f7d61ce1941ba2cb802b..c2227572729a96367f3ca35d1d11fd12c1391592 100644
--- a/src/math_vector.h
+++ b/src/math_vector.h
@@ -18,8 +18,8 @@
#ifndef LMP_MATH_VECTOR_H
#define LMP_MATH_VECTOR_H
-#include <math.h>
-#include <string.h>
+#include <cmath>
+#include <cstring>
#define VECTOR_NULL {0, 0, 0}
#define SHAPE_NULL {0, 0, 0, 0, 0, 0}
diff --git a/src/memory.cpp b/src/memory.cpp
index eb5309b8b7930292a812141ded0747e2c56e33b1..429cf75c00ab9975a7859201301c9e963b1bf1e8 100644
--- a/src/memory.cpp
+++ b/src/memory.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "memory.h"
#include "error.h"
diff --git a/src/mergesort.h b/src/mergesort.h
index 1df6cb4b819375e68fbdd2c745a4c7cee4a49009..50addd0a729a23766b21a764465ac254ce6f5909 100644
--- a/src/mergesort.h
+++ b/src/mergesort.h
@@ -14,7 +14,7 @@
#ifndef LMP_MERGESORT
#define LMP_MERGESORT
-#include <string.h>
+#include <cstring>
// custom hybrid upward merge sort implementation with support to pass
// an opaque pointer to the comparison function, e.g. for access to
diff --git a/src/min.cpp b/src/min.cpp
index 0caa9a9acf0584eac39ad0a55c8ddf634f56906e..cd9253f8d30f31fdab356efca3ff50a7bd2e710b 100644
--- a/src/min.cpp
+++ b/src/min.cpp
@@ -19,9 +19,9 @@
JR Shewchuk, http://www-2.cs.cmu.edu/~jrs/jrspapers.html#cg
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "min.h"
#include "atom.h"
#include "atom_vec.h"
diff --git a/src/min_cg.cpp b/src/min_cg.cpp
index eda59bd3d4fd19fe586ccb459b327d337ff4ebc8..20e8cc30dd35f05355eb44869f48a2dc914a7c90 100644
--- a/src/min_cg.cpp
+++ b/src/min_cg.cpp
@@ -12,8 +12,8 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <math.h>
-#include <string.h>
+#include <cmath>
+#include <cstring>
#include "min_cg.h"
#include "atom.h"
#include "update.h"
diff --git a/src/min_fire.cpp b/src/min_fire.cpp
index 698b00b7a6781a021ce133e41e88ebe5ef3d8eff..a50071d56204e197a9a4d321640ec50c7d897b99 100644
--- a/src/min_fire.cpp
+++ b/src/min_fire.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "min_fire.h"
#include "universe.h"
#include "atom.h"
diff --git a/src/min_hftn.cpp b/src/min_hftn.cpp
index 84793e33a4f9741767d1f75691028a8f3419f161..0c834fbeb442e71e5227989de328dbe252339ae8 100644
--- a/src/min_hftn.cpp
+++ b/src/min_hftn.cpp
@@ -17,8 +17,8 @@
"Parallel Unconstrained Min", Plantenga, SAND98-8201
------------------------------------------------------------------------- */
-#include <math.h>
-#include <string.h>
+#include <cmath>
+#include <cstring>
#include "atom.h"
#include "fix_minimize.h"
#include "min_hftn.h"
diff --git a/src/min_linesearch.cpp b/src/min_linesearch.cpp
index ddc0c64321ccd84372e8bb2a2420bd732667b955..f93a56b09d93895dddd0770a377629b50e0b8412 100644
--- a/src/min_linesearch.cpp
+++ b/src/min_linesearch.cpp
@@ -21,7 +21,7 @@
JR Shewchuk, http://www-2.cs.cmu.edu/~jrs/jrspapers.html#cg
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "min_linesearch.h"
#include "atom.h"
#include "update.h"
diff --git a/src/min_quickmin.cpp b/src/min_quickmin.cpp
index 491387406d10a6f1407cf0b970bacfdf5dc25865..8b48816355b0a5b64db0a77fd3c11a9fccff1886 100644
--- a/src/min_quickmin.cpp
+++ b/src/min_quickmin.cpp
@@ -12,7 +12,7 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <math.h>
+#include <cmath>
#include "min_quickmin.h"
#include "universe.h"
#include "atom.h"
diff --git a/src/min_sd.cpp b/src/min_sd.cpp
index 73a3867d8a29cce5667ace0a367a2689b9b6f3ec..5d44437ca07e6ca372068e5ae2516cc32d05a045 100644
--- a/src/min_sd.cpp
+++ b/src/min_sd.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include <mpi.h>
#include "min_sd.h"
#include "atom.h"
diff --git a/src/minimize.cpp b/src/minimize.cpp
index e4e89804bf6e07ef9d63533d910b40b654423def..e27fffd74bb15c1e005052a3669e09a8b20d13d7 100644
--- a/src/minimize.cpp
+++ b/src/minimize.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <stdlib.h>
+#include <cstdlib>
#include "minimize.h"
#include "domain.h"
#include "update.h"
diff --git a/src/modify.cpp b/src/modify.cpp
index 86cfdda8b684e26bce89d09a9a0dc6d9102b0dc7..61b9f1d71dcb535f4cb1b8ebaf4d2cfd0516e753 100644
--- a/src/modify.cpp
+++ b/src/modify.cpp
@@ -12,8 +12,8 @@ eoundary p f f
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <stdio.h>
-#include <string.h>
+#include <cstdio>
+#include <cstring>
#include "modify.h"
#include "style_compute.h"
#include "style_fix.h"
diff --git a/src/modify.h b/src/modify.h
index 1163d44b16f54e4b39f296d166c685118ed714ba..eca4e078599573cf280fde726399069b9091837c 100644
--- a/src/modify.h
+++ b/src/modify.h
@@ -14,7 +14,7 @@
#ifndef LMP_MODIFY_H
#define LMP_MODIFY_H
-#include <stdio.h>
+#include <cstdio>
#include "pointers.h"
#include <map>
#include <string>
diff --git a/src/molecule.cpp b/src/molecule.cpp
index 78dc4b82b3ed2374dbae7cafa4f3e5d296408c1e..56e56dab2cd16ef45c9c6068161c29a4815d51ca 100644
--- a/src/molecule.cpp
+++ b/src/molecule.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <stdlib.h>
-#include <string.h>
+#include <cstdlib>
+#include <cstring>
#include "molecule.h"
#include "atom.h"
#include "atom_vec.h"
@@ -1111,7 +1111,7 @@ void Molecule::special_generate()
{
int newton_bond = force->newton_bond;
tagint atom1,atom2;
- int count[natoms];
+ int *count = new int[natoms];
// temporary array for special atoms
@@ -1197,6 +1197,7 @@ void Molecule::special_generate()
}
}
}
+ delete[] count;
maxspecial = 0;
for (int i = 0; i < natoms; i++)
diff --git a/src/my_page.h b/src/my_page.h
index 5d95217968e75e34e0f781533662bd50564be442..5cd7098d8c9132654b0cf4c7ec4d01a179910fc5 100644
--- a/src/my_page.h
+++ b/src/my_page.h
@@ -52,7 +52,7 @@ methods:
#define LAMMPS_MEMALIGN 64
#endif
-#include <stdlib.h>
+#include <cstdlib>
namespace LAMMPS_NS {
template<class T>
diff --git a/src/my_pool_chunk.h b/src/my_pool_chunk.h
index c2f4f190f84bb87a3a3980336c179e19b50fa296..8bf88d35bbe425c67193daeba0d309aff73eb78c 100644
--- a/src/my_pool_chunk.h
+++ b/src/my_pool_chunk.h
@@ -43,7 +43,7 @@ public variables:
#ifndef LAMMPS_MY_POOL_CHUNK_H
#define LAMMPS_MY_POOL_CHUNK_H
-#include <stdlib.h>
+#include <cstdlib>
namespace LAMMPS_NS {
diff --git a/src/nbin.cpp b/src/nbin.cpp
index 6bd1ce322f6f93d93a80c50058d598f8abccfcc9..a30b76cca03770562ef0d7f9da2a0c0fd576a0cc 100644
--- a/src/nbin.cpp
+++ b/src/nbin.cpp
@@ -117,7 +117,7 @@ int NBin::coord2bin(double *x)
{
int ix,iy,iz;
- if (!ISFINITE(x[0]) || !ISFINITE(x[1]) || !ISFINITE(x[2]))
+ if (!std::isfinite(x[0]) || !std::isfinite(x[1]) || !std::isfinite(x[2]))
error->one(FLERR,"Non-numeric positions - simulation unstable");
if (x[0] >= bboxhi[0])
diff --git a/src/nbin_standard.cpp b/src/nbin_standard.cpp
index e6941014f9f60e441bc99831656465f2bb2d7a0e..9a28121384bcfd15bf5c3fe13b8b406e6bc1fa18 100644
--- a/src/nbin_standard.cpp
+++ b/src/nbin_standard.cpp
@@ -22,8 +22,6 @@
using namespace LAMMPS_NS;
-enum{NSQ,BIN,MULTI}; // also in Neighbor
-
#define SMALL 1.0e-6
#define CUT2BIN_RATIO 100
@@ -94,7 +92,7 @@ void NBinStandard::setup_bins(int style)
double binsize_optimal;
if (binsizeflag) binsize_optimal = binsize_user;
- else if (style == BIN) binsize_optimal = 0.5*cutneighmax;
+ else if (style == Neighbor::BIN) binsize_optimal = 0.5*cutneighmax;
else binsize_optimal = 0.5*cutneighmin;
if (binsize_optimal == 0.0) binsize_optimal = bbox[0];
double binsizeinv = 1.0/binsize_optimal;
diff --git a/src/neigh_list.cpp b/src/neigh_list.cpp
index 2851bae14fa4fec3d1dfe233465c6d03bb002acb..6bdb9beae62e6924b201af00b3c60bb5086dcc9a 100644
--- a/src/neigh_list.cpp
+++ b/src/neigh_list.cpp
@@ -26,8 +26,6 @@ using namespace LAMMPS_NS;
#define PGDELTA 1
-enum{NSQ,BIN,MULTI}; // also in Neighbor
-
/* ---------------------------------------------------------------------- */
NeighList::NeighList(LAMMPS *lmp) : Pointers(lmp)
diff --git a/src/neighbor.cpp b/src/neighbor.cpp
index 31dddd9f15eb39964967a9308feee577fe1162a5..912a636227b84b0fb81a549a7297698bbd98c1b0 100644
--- a/src/neighbor.cpp
+++ b/src/neighbor.cpp
@@ -16,9 +16,9 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
@@ -57,7 +57,6 @@ using namespace NeighConst;
#define BIG 1.0e20
-enum{NSQ,BIN,MULTI}; // also in NBin, NeighList, NStencil
enum{NONE,ALL,PARTIAL,TEMPLATE};
static const char cite_neigh_multi[] =
@@ -85,7 +84,7 @@ pairclass(NULL), pairnames(NULL), pairmasks(NULL)
firsttime = 1;
- style = BIN;
+ style = Neighbor::BIN;
every = 1;
delay = 10;
dist_check = 1;
@@ -651,7 +650,7 @@ int Neighbor::init_pair()
// at time of binning when neighbor lists are rebuilt,
// similar to what vanilla Nbin::coord2atom() does now in atom2bin
- if (style == BIN) {
+ if (style == Neighbor::BIN) {
for (i = 0; i < nrequest; i++)
if (requests[i]->occasional && requests[i]->ghost)
error->all(FLERR,"Cannot request an occasional binned neighbor list "
@@ -1420,7 +1419,7 @@ void Neighbor::print_pairwise_info()
bbox[1] = bboxhi[1]-bboxlo[1];
bbox[2] = bboxhi[2]-bboxlo[2];
if (binsizeflag) binsize = binsize_user;
- else if (style == BIN) binsize = 0.5*cutneighmax;
+ else if (style == Neighbor::BIN) binsize = 0.5*cutneighmax;
else binsize = 0.5*cutneighmin;
if (binsize == 0.0) binsize = bbox[0];
@@ -1445,7 +1444,7 @@ void Neighbor::print_pairwise_info()
oneatom, pgsize);
fprintf(out," master list distance cutoff = %g\n",cutneighmax);
fprintf(out," ghost atom cutoff = %g\n",cutghost);
- if (style != NSQ)
+ if (style != Neighbor::NSQ)
fprintf(out," binsize = %g, bins = %g %g %g\n",binsize,
ceil(bbox[0]/binsize), ceil(bbox[1]/binsize),
ceil(bbox[2]/binsize));
@@ -1595,7 +1594,7 @@ int Neighbor::choose_bin(NeighRequest *rq)
{
// no binning needed
- if (style == NSQ) return 0;
+ if (style == Neighbor::NSQ) return 0;
if (rq->skip || rq->copy || rq->halffull) return 0;
// use request settings to match exactly one NBin class mask
@@ -1635,7 +1634,7 @@ int Neighbor::choose_stencil(NeighRequest *rq)
{
// no stencil creation needed
- if (style == NSQ) return 0;
+ if (style == Neighbor::NSQ) return 0;
if (rq->skip || rq->copy || rq->halffull) return 0;
// convert newton request to newtflag = on or off
@@ -1686,9 +1685,9 @@ int Neighbor::choose_stencil(NeighRequest *rq)
// neighbor style is BIN or MULTI and must match
- if (style == BIN) {
+ if (style == Neighbor::BIN) {
if (!(mask & NS_BIN)) continue;
- } else if (style == MULTI) {
+ } else if (style == Neighbor::MULTI) {
if (!(mask & NS_MULTI)) continue;
}
@@ -1817,11 +1816,11 @@ int Neighbor::choose_pair(NeighRequest *rq)
// neighbor style is one of NSQ,BIN,MULTI and must match
- if (style == NSQ) {
+ if (style == Neighbor::NSQ) {
if (!(mask & NP_NSQ)) continue;
- } else if (style == BIN) {
+ } else if (style == Neighbor::BIN) {
if (!(mask & NP_BIN)) continue;
- } else if (style == MULTI) {
+ } else if (style == Neighbor::MULTI) {
if (!(mask & NP_MULTI)) continue;
}
@@ -2063,7 +2062,7 @@ void Neighbor::build(int topoflag)
// if bin then, atoms may have moved outside of proc domain & bin extent,
// leading to errors or even a crash
- if (style != NSQ) {
+ if (style != Neighbor::NSQ) {
for (int i = 0; i < nbin; i++) {
neigh_bin[i]->bin_atoms_setup(nall);
neigh_bin[i]->bin_atoms();
@@ -2180,12 +2179,12 @@ void Neighbor::set(int narg, char **arg)
skin = force->numeric(FLERR,arg[0]);
if (skin < 0.0) error->all(FLERR,"Illegal neighbor command");
- if (strcmp(arg[1],"nsq") == 0) style = NSQ;
- else if (strcmp(arg[1],"bin") == 0) style = BIN;
- else if (strcmp(arg[1],"multi") == 0) style = MULTI;
+ if (strcmp(arg[1],"nsq") == 0) style = Neighbor::NSQ;
+ else if (strcmp(arg[1],"bin") == 0) style = Neighbor::BIN;
+ else if (strcmp(arg[1],"multi") == 0) style = Neighbor::MULTI;
else error->all(FLERR,"Illegal neighbor command");
- if (style == MULTI && lmp->citeme) lmp->citeme->add(cite_neigh_multi);
+ if (style == Neighbor::MULTI && lmp->citeme) lmp->citeme->add(cite_neigh_multi);
}
/* ----------------------------------------------------------------------
diff --git a/src/neighbor.h b/src/neighbor.h
index 12f90556c2512013e99663a9d7f92cebd7f5f5da..751beeae4baa47d40cdcf0e7c852e0d056207cd7 100644
--- a/src/neighbor.h
+++ b/src/neighbor.h
@@ -21,6 +21,7 @@ namespace LAMMPS_NS {
class Neighbor : protected Pointers {
public:
+ enum{NSQ,BIN,MULTI};
int style; // 0,1,2 = nsq, bin, multi
int every; // build every this many steps
int delay; // delay build for this many steps
diff --git a/src/npair.cpp b/src/npair.cpp
index 4d06850e659197846c426199673ca44747aa1312..24cdc7750af504f1f510fdd0e29a5ba0b0b9355a 100644
--- a/src/npair.cpp
+++ b/src/npair.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "npair.h"
#include "neighbor.h"
#include "neigh_request.h"
@@ -208,7 +208,7 @@ int NPair::exclusion(int i, int j, int itype, int jtype,
int NPair::coord2bin(double *x, int &ix, int &iy, int &iz)
{
- if (!ISFINITE(x[0]) || !ISFINITE(x[1]) || !ISFINITE(x[2]))
+ if (!std::isfinite(x[0]) || !std::isfinite(x[1]) || !std::isfinite(x[2]))
error->one(FLERR,"Non-numeric positions - simulation unstable");
if (x[0] >= bboxhi[0])
diff --git a/src/npair_half_size_bin_newtoff.cpp b/src/npair_half_size_bin_newtoff.cpp
index 6cd97c71d13383cb34a1c7a7ba21d1cef2461293..021452028b3802f68c759707dbd9f00d4bb6c320 100644
--- a/src/npair_half_size_bin_newtoff.cpp
+++ b/src/npair_half_size_bin_newtoff.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "npair_half_size_bin_newtoff.h"
#include "neighbor.h"
#include "neigh_list.h"
diff --git a/src/npair_half_size_bin_newton.cpp b/src/npair_half_size_bin_newton.cpp
index c0ed03816625f3bc91de2b43c4fe472e8895b36a..760c09570a0dcad90ae2e66ec1d3e3a2480f93df 100644
--- a/src/npair_half_size_bin_newton.cpp
+++ b/src/npair_half_size_bin_newton.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "npair_half_size_bin_newton.h"
#include "neighbor.h"
#include "neigh_list.h"
diff --git a/src/npair_half_size_bin_newton_tri.cpp b/src/npair_half_size_bin_newton_tri.cpp
index 044847ba8ce9d38d534e5aecfc13e841e5d81a9b..d831982ed6033842b85cbdf677ca5e59b1a40a66 100644
--- a/src/npair_half_size_bin_newton_tri.cpp
+++ b/src/npair_half_size_bin_newton_tri.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "npair_half_size_bin_newton_tri.h"
#include "neighbor.h"
#include "neigh_list.h"
diff --git a/src/npair_half_size_nsq_newtoff.cpp b/src/npair_half_size_nsq_newtoff.cpp
index 50a32c87ba5d3ed2ab5883eb7e47167f626adbca..1c2fe5f3d57b4666a0807c7765bb380bce935204 100644
--- a/src/npair_half_size_nsq_newtoff.cpp
+++ b/src/npair_half_size_nsq_newtoff.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "npair_half_size_nsq_newtoff.h"
#include "neighbor.h"
#include "neigh_list.h"
diff --git a/src/npair_half_size_nsq_newton.cpp b/src/npair_half_size_nsq_newton.cpp
index 343172fb986c0a316d705c186a892aeee10a002d..ce9f8ec18631876d99d0b5bb1d2641aabee72da4 100644
--- a/src/npair_half_size_nsq_newton.cpp
+++ b/src/npair_half_size_nsq_newton.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "npair_half_size_nsq_newton.h"
#include "neighbor.h"
#include "neigh_list.h"
diff --git a/src/npair_skip_size.cpp b/src/npair_skip_size.cpp
index b75856dde409a3e060cf1831f6ecc8684c965977..67717ae57660ca11e71685c7c445bab8eff6602b 100644
--- a/src/npair_skip_size.cpp
+++ b/src/npair_skip_size.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "npair_skip_size.h"
#include "neighbor.h"
#include "neigh_list.h"
diff --git a/src/npair_skip_size_off2on.cpp b/src/npair_skip_size_off2on.cpp
index 8d728a3c0ad73074bb06b4786462f854fd0cc4a2..74a80e6d3d3e2da207aaa1c424069bac4148020a 100644
--- a/src/npair_skip_size_off2on.cpp
+++ b/src/npair_skip_size_off2on.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "npair_skip_size_off2on.h"
#include "neighbor.h"
#include "neigh_list.h"
diff --git a/src/npair_skip_size_off2on_oneside.cpp b/src/npair_skip_size_off2on_oneside.cpp
index a04fc7782c2bcfdecd88d6f8e2df6b438bfc08a8..a042acd1c6bb034d4a84e568487c48170c1dfbca 100644
--- a/src/npair_skip_size_off2on_oneside.cpp
+++ b/src/npair_skip_size_off2on_oneside.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "npair_skip_size_off2on_oneside.h"
#include "neighbor.h"
#include "neigh_list.h"
diff --git a/src/nstencil.cpp b/src/nstencil.cpp
index 18e815d0c998c37f814441ee4333dfbddc5a8b8d..431906e89856a9fe7f03767b0635dc11d5f5566c 100644
--- a/src/nstencil.cpp
+++ b/src/nstencil.cpp
@@ -22,8 +22,6 @@
using namespace LAMMPS_NS;
-enum{NSQ,BIN,MULTI}; // also in Neighbor
-
/* ----------------------------------------------------------------------
NStencil classes
each has method to create a stencil = list of bin offsets
@@ -161,7 +159,7 @@ void NStencil::create_setup()
// reallocate stencil structs if necessary
// for BIN and MULTI styles
- if (neighstyle == BIN) {
+ if (neighstyle == Neighbor::BIN) {
if (smax > maxstencil) {
maxstencil = smax;
memory->destroy(stencil);
@@ -227,10 +225,10 @@ double NStencil::bin_distance(int i, int j, int k)
bigint NStencil::memory_usage()
{
bigint bytes = 0;
- if (neighstyle == BIN) {
+ if (neighstyle == Neighbor::BIN) {
bytes += memory->usage(stencil,maxstencil);
bytes += memory->usage(stencilxyz,maxstencil,3);
- } else if (neighstyle == MULTI) {
+ } else if (neighstyle == Neighbor::MULTI) {
bytes += atom->ntypes*maxstencil_multi * sizeof(int);
bytes += atom->ntypes*maxstencil_multi * sizeof(double);
}
diff --git a/src/ntopo.cpp b/src/ntopo.cpp
index 124fa6687c498ceae9c688dfe437f25e70c736d2..8a87a5d6e5fa9003e78a7e5be6ce9d744ee1ca89 100644
--- a/src/ntopo.cpp
+++ b/src/ntopo.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "ntopo.h"
#include "atom.h"
#include "neighbor.h"
diff --git a/src/ntopo.h b/src/ntopo.h
index 9512606ba49a3ebd45ca87fbab91f2513f625f22..b115b329654c7468d7d41057d03c3a83fb89912b 100644
--- a/src/ntopo.h
+++ b/src/ntopo.h
@@ -31,8 +31,6 @@ class NTopo : protected Pointers {
bigint memory_usage();
protected:
- enum{IGNORE,WARN,ERROR}; // same as thermo.cpp
-
int me,nprocs;
int maxbond,maxangle,maxdihedral,maximproper;
int cluster_check; // copy from Neighbor
diff --git a/src/ntopo_angle_all.cpp b/src/ntopo_angle_all.cpp
index 3a079ab4677533c46902cf337702c7dec60d74b5..2a358c8ce574e4291ec8a492e7904402d7622a90 100644
--- a/src/ntopo_angle_all.cpp
+++ b/src/ntopo_angle_all.cpp
@@ -58,7 +58,7 @@ void NTopoAngleAll::build()
atom3 = atom->map(angle_atom3[i][m]);
if (atom1 == -1 || atom2 == -1 || atom3 == -1) {
nmissing++;
- if (lostbond == ERROR) {
+ if (lostbond == Thermo::ERROR) {
char str[128];
sprintf(str,"Angle atoms "
TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT
@@ -86,7 +86,7 @@ void NTopoAngleAll::build()
}
if (cluster_check) angle_check();
- if (lostbond == IGNORE) return;
+ if (lostbond == Thermo::IGNORE) return;
int all;
MPI_Allreduce(&nmissing,&all,1,MPI_INT,MPI_SUM,world);
diff --git a/src/ntopo_angle_partial.cpp b/src/ntopo_angle_partial.cpp
index f1d668a3ba2503e0c3992078b518a3239d3d24b6..c82110cda5309f01f3a223c1c4eabc6d3e615051 100644
--- a/src/ntopo_angle_partial.cpp
+++ b/src/ntopo_angle_partial.cpp
@@ -59,7 +59,7 @@ void NTopoAnglePartial::build()
atom3 = atom->map(angle_atom3[i][m]);
if (atom1 == -1 || atom2 == -1 || atom3 == -1) {
nmissing++;
- if (lostbond == ERROR) {
+ if (lostbond == Thermo::ERROR) {
char str[128];
sprintf(str,"Angle atoms "
TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT
@@ -87,7 +87,7 @@ void NTopoAnglePartial::build()
}
if (cluster_check) angle_check();
- if (lostbond == IGNORE) return;
+ if (lostbond == Thermo::IGNORE) return;
int all;
MPI_Allreduce(&nmissing,&all,1,MPI_INT,MPI_SUM,world);
diff --git a/src/ntopo_angle_template.cpp b/src/ntopo_angle_template.cpp
index 05d5de28a473389bb7c791ce56cf0095b70a2a63..15a8b658f328357e0a27368a22d888bc6b9f9387 100644
--- a/src/ntopo_angle_template.cpp
+++ b/src/ntopo_angle_template.cpp
@@ -76,7 +76,7 @@ void NTopoAngleTemplate::build()
atom3 = atom->map(angle_atom3[iatom][m]+tagprev);
if (atom1 == -1 || atom2 == -1 || atom3 == -1) {
nmissing++;
- if (lostbond == ERROR) {
+ if (lostbond == Thermo::ERROR) {
char str[128];
sprintf(str,"Angle atoms "
TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT
@@ -106,7 +106,7 @@ void NTopoAngleTemplate::build()
}
if (cluster_check) angle_check();
- if (lostbond == IGNORE) return;
+ if (lostbond == Thermo::IGNORE) return;
int all;
MPI_Allreduce(&nmissing,&all,1,MPI_INT,MPI_SUM,world);
diff --git a/src/ntopo_bond_all.cpp b/src/ntopo_bond_all.cpp
index 03cb2ad86bc83027190c34386adbc5a1d062b503..42e9e2303d7af91b2bf3086f14defc3465bf48b0 100644
--- a/src/ntopo_bond_all.cpp
+++ b/src/ntopo_bond_all.cpp
@@ -55,7 +55,7 @@ void NTopoBondAll::build()
atom1 = atom->map(bond_atom[i][m]);
if (atom1 == -1) {
nmissing++;
- if (lostbond == ERROR) {
+ if (lostbond == Thermo::ERROR) {
char str[128];
sprintf(str,"Bond atoms " TAGINT_FORMAT " " TAGINT_FORMAT
" missing on proc %d at step " BIGINT_FORMAT,
@@ -78,7 +78,7 @@ void NTopoBondAll::build()
}
if (cluster_check) bond_check();
- if (lostbond == IGNORE) return;
+ if (lostbond == Thermo::IGNORE) return;
int all;
MPI_Allreduce(&nmissing,&all,1,MPI_INT,MPI_SUM,world);
diff --git a/src/ntopo_bond_partial.cpp b/src/ntopo_bond_partial.cpp
index cda4bdcf09cbd0150dacd076392e8e5630839c37..5a1acd9191b7a1485d435382fcc1c909622d336d 100644
--- a/src/ntopo_bond_partial.cpp
+++ b/src/ntopo_bond_partial.cpp
@@ -56,7 +56,7 @@ void NTopoBondPartial::build()
atom1 = atom->map(bond_atom[i][m]);
if (atom1 == -1) {
nmissing++;
- if (lostbond == ERROR) {
+ if (lostbond == Thermo::ERROR) {
char str[128];
sprintf(str,"Bond atoms " TAGINT_FORMAT " " TAGINT_FORMAT
" missing on proc %d at step " BIGINT_FORMAT,
@@ -79,7 +79,7 @@ void NTopoBondPartial::build()
}
if (cluster_check) bond_check();
- if (lostbond == IGNORE) return;
+ if (lostbond == Thermo::IGNORE) return;
int all;
MPI_Allreduce(&nmissing,&all,1,MPI_INT,MPI_SUM,world);
diff --git a/src/ntopo_bond_template.cpp b/src/ntopo_bond_template.cpp
index de16d78585cf65175babe696dafb14aa4bd5a2d6..fa98658ad0d640023e80149bdd2b878906120930 100644
--- a/src/ntopo_bond_template.cpp
+++ b/src/ntopo_bond_template.cpp
@@ -72,7 +72,7 @@ void NTopoBondTemplate::build()
atom1 = atom->map(bond_atom[iatom][m]+tagprev);
if (atom1 == -1) {
nmissing++;
- if (lostbond == ERROR) {
+ if (lostbond == Thermo::ERROR) {
char str[128];
sprintf(str,"Bond atoms " TAGINT_FORMAT " " TAGINT_FORMAT
" missing on proc %d at step " BIGINT_FORMAT,
@@ -96,7 +96,7 @@ void NTopoBondTemplate::build()
}
if (cluster_check) bond_check();
- if (lostbond == IGNORE) return;
+ if (lostbond == Thermo::IGNORE) return;
int all;
MPI_Allreduce(&nmissing,&all,1,MPI_INT,MPI_SUM,world);
diff --git a/src/ntopo_dihedral_all.cpp b/src/ntopo_dihedral_all.cpp
index 7a5b350fa018096a7bd46cea5226003d5248ca83..9c94fb10f959e93a9f56db10474039f62feb39b1 100644
--- a/src/ntopo_dihedral_all.cpp
+++ b/src/ntopo_dihedral_all.cpp
@@ -60,7 +60,7 @@ void NTopoDihedralAll::build()
atom4 = atom->map(dihedral_atom4[i][m]);
if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1) {
nmissing++;
- if (lostbond == ERROR) {
+ if (lostbond == Thermo::ERROR) {
char str[128];
sprintf(str,"Dihedral atoms "
TAGINT_FORMAT " " TAGINT_FORMAT " "
@@ -93,7 +93,7 @@ void NTopoDihedralAll::build()
}
if (cluster_check) dihedral_check(ndihedrallist,dihedrallist);
- if (lostbond == IGNORE) return;
+ if (lostbond == Thermo::IGNORE) return;
int all;
MPI_Allreduce(&nmissing,&all,1,MPI_INT,MPI_SUM,world);
diff --git a/src/ntopo_dihedral_partial.cpp b/src/ntopo_dihedral_partial.cpp
index 603c81e68c674487f48fdd241c93516e9cc47439..14749e6511d74d26fc09ee55cedfab9b272c0443 100644
--- a/src/ntopo_dihedral_partial.cpp
+++ b/src/ntopo_dihedral_partial.cpp
@@ -62,7 +62,7 @@ void NTopoDihedralPartial::build()
atom4 = atom->map(dihedral_atom4[i][m]);
if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1) {
nmissing++;
- if (lostbond == ERROR) {
+ if (lostbond == Thermo::ERROR) {
char str[128];
sprintf(str,"Dihedral atoms "
TAGINT_FORMAT " " TAGINT_FORMAT " "
@@ -95,7 +95,7 @@ void NTopoDihedralPartial::build()
}
if (cluster_check) dihedral_check(ndihedrallist,dihedrallist);
- if (lostbond == IGNORE) return;
+ if (lostbond == Thermo::IGNORE) return;
int all;
MPI_Allreduce(&nmissing,&all,1,MPI_INT,MPI_SUM,world);
diff --git a/src/ntopo_dihedral_template.cpp b/src/ntopo_dihedral_template.cpp
index 38d319fb9643b6ed5c18cb185f2eea22fbffed5a..8ea860c2e21fdb9b5ee4bc548866b13c2d91a6c0 100644
--- a/src/ntopo_dihedral_template.cpp
+++ b/src/ntopo_dihedral_template.cpp
@@ -78,7 +78,7 @@ void NTopoDihedralTemplate::build()
atom4 = atom->map(dihedral_atom4[iatom][m]+tagprev);
if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1) {
nmissing++;
- if (lostbond == ERROR) {
+ if (lostbond == Thermo::ERROR) {
char str[128];
sprintf(str,"Dihedral atoms "
TAGINT_FORMAT " " TAGINT_FORMAT " "
@@ -114,7 +114,7 @@ void NTopoDihedralTemplate::build()
}
if (cluster_check) dihedral_check(ndihedrallist,dihedrallist);
- if (lostbond == IGNORE) return;
+ if (lostbond == Thermo::IGNORE) return;
int all;
MPI_Allreduce(&nmissing,&all,1,MPI_INT,MPI_SUM,world);
diff --git a/src/ntopo_improper_all.cpp b/src/ntopo_improper_all.cpp
index ada3927e79c7f70cd2188b46bd40886412e74035..6c478dec527c8e3d75e6c1bdfe0a3dfe5c7396a6 100644
--- a/src/ntopo_improper_all.cpp
+++ b/src/ntopo_improper_all.cpp
@@ -60,7 +60,7 @@ void NTopoImproperAll::build()
atom4 = atom->map(improper_atom4[i][m]);
if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1) {
nmissing++;
- if (lostbond == ERROR) {
+ if (lostbond == Thermo::ERROR) {
char str[128];
sprintf(str,"Improper atoms "
TAGINT_FORMAT " " TAGINT_FORMAT " "
@@ -93,7 +93,7 @@ void NTopoImproperAll::build()
}
if (cluster_check) dihedral_check(nimproperlist,improperlist);
- if (lostbond == IGNORE) return;
+ if (lostbond == Thermo::IGNORE) return;
int all;
MPI_Allreduce(&nmissing,&all,1,MPI_INT,MPI_SUM,world);
diff --git a/src/ntopo_improper_partial.cpp b/src/ntopo_improper_partial.cpp
index 072a2aa76790d0f762e070c8034dc78e0b73607c..2c37668ca850eb80bcb661ad7857c89bdc185162 100644
--- a/src/ntopo_improper_partial.cpp
+++ b/src/ntopo_improper_partial.cpp
@@ -62,7 +62,7 @@ void NTopoImproperPartial::build()
atom4 = atom->map(improper_atom4[i][m]);
if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1) {
nmissing++;
- if (lostbond == ERROR) {
+ if (lostbond == Thermo::ERROR) {
char str[128];
sprintf(str,"Improper atoms "
TAGINT_FORMAT " " TAGINT_FORMAT " "
@@ -95,7 +95,7 @@ void NTopoImproperPartial::build()
}
if (cluster_check) dihedral_check(nimproperlist,improperlist);
- if (lostbond == IGNORE) return;
+ if (lostbond == Thermo::IGNORE) return;
int all;
MPI_Allreduce(&nmissing,&all,1,MPI_INT,MPI_SUM,world);
diff --git a/src/ntopo_improper_template.cpp b/src/ntopo_improper_template.cpp
index cb15a077d5a30e928cbd35fc20fdac0ce1322a84..953e010d89a0bd5f1e2f862349216edfdaf97a91 100644
--- a/src/ntopo_improper_template.cpp
+++ b/src/ntopo_improper_template.cpp
@@ -78,7 +78,7 @@ void NTopoImproperTemplate::build()
atom4 = atom->map(improper_atom4[iatom][m]+tagprev);
if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1) {
nmissing++;
- if (lostbond == ERROR) {
+ if (lostbond == Thermo::ERROR) {
char str[128];
sprintf(str,"Improper atoms "
TAGINT_FORMAT " " TAGINT_FORMAT " "
@@ -114,7 +114,7 @@ void NTopoImproperTemplate::build()
}
if (cluster_check) dihedral_check(nimproperlist,improperlist);
- if (lostbond == IGNORE) return;
+ if (lostbond == Thermo::IGNORE) return;
int all;
MPI_Allreduce(&nmissing,&all,1,MPI_INT,MPI_SUM,world);
diff --git a/src/output.cpp b/src/output.cpp
index 11c6fa073e8c05c38056efbdc1765e5f6f8da999..884647f478bbb89d1d963048828eabbd51a36458 100644
--- a/src/output.cpp
+++ b/src/output.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "output.h"
#include "style_dump.h"
#include "atom.h"
diff --git a/src/pair.cpp b/src/pair.cpp
index 8b3178415c28156203b0ff57ca937794c8d85a9d..3b839dff497808a033a97f9c551381b80658e267 100644
--- a/src/pair.cpp
+++ b/src/pair.cpp
@@ -16,13 +16,13 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <ctype.h>
-#include <float.h>
-#include <limits.h>
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cctype>
+#include <cfloat>
+#include <climits>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair.h"
#include "atom.h"
#include "neighbor.h"
diff --git a/src/pair.h b/src/pair.h
index 3ce567876cf38cd97093abcd26cb0baea3abd758..26488103a05e2044d537f31dcf8a4b8b2fa0073b 100644
--- a/src/pair.h
+++ b/src/pair.h
@@ -96,6 +96,8 @@ class Pair : protected Pointers {
// public so external driver can check
int compute_flag; // 0 if skip compute()
+ enum{GEOMETRIC,ARITHMETIC,SIXTHPOWER}; // mixing options
+
// KOKKOS host/device flag and data masks
ExecutionSpace execution_space;
@@ -191,8 +193,6 @@ class Pair : protected Pointers {
protected:
int instance_me; // which Pair class instantiation I am
- enum{GEOMETRIC,ARITHMETIC,SIXTHPOWER}; // mixing options
-
int special_lj[4]; // copied from force->special_lj for Kokkos
int suffix_flag; // suffix compatibility flag
diff --git a/src/pair_beck.cpp b/src/pair_beck.cpp
index 36e44e5c2ebc5203f97a8fc20041fe3b07fbfd25..cc8e14bf2c6c93164a1795b79352a7568f24f515 100644
--- a/src/pair_beck.cpp
+++ b/src/pair_beck.cpp
@@ -15,9 +15,9 @@
Contributing author: Jonathan Zimmerman (Sandia)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
#include "pair_beck.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/pair_born.cpp b/src/pair_born.cpp
index 979499488e0e3dbf34f4d6a3a77a897429b3946e..ce7a255fd4935a41e1a20d00fe4ea8757894600f 100644
--- a/src/pair_born.cpp
+++ b/src/pair_born.cpp
@@ -15,10 +15,10 @@
Contributing Author: Sai Jayaraman (Sandia)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_born.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/pair_born_coul_dsf.cpp b/src/pair_born_coul_dsf.cpp
index 3700aa46d7f5b83df7bf20fd4c0c21714a4f85c4..be7f41ca2b69ddb9a86eae3a72e3a77b81e2e891 100644
--- a/src/pair_born_coul_dsf.cpp
+++ b/src/pair_born_coul_dsf.cpp
@@ -16,10 +16,10 @@
References: Fennell and Gezelter, JCP 124, 234104 (2006)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_born_coul_dsf.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/pair_born_coul_wolf.cpp b/src/pair_born_coul_wolf.cpp
index fbec4f3da74362d51c6d99e541574be8758f6658..22dcfa9f2dd6e623e0a738168970fa4205c7beb3 100644
--- a/src/pair_born_coul_wolf.cpp
+++ b/src/pair_born_coul_wolf.cpp
@@ -15,10 +15,10 @@
Contributing author: Yongfeng Zhang (INL), yongfeng.zhang@inl.gov
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_born_coul_wolf.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/pair_buck.cpp b/src/pair_buck.cpp
index 8cbf97a6badc13f8bd22c20d85e6175626f897e7..450ce291cb9814629e0ade5d1398cd595744d95c 100644
--- a/src/pair_buck.cpp
+++ b/src/pair_buck.cpp
@@ -11,10 +11,10 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_buck.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/pair_buck_coul_cut.cpp b/src/pair_buck_coul_cut.cpp
index 2764a8e4e4c05abb2e19394a4d73e2f98d3f453e..7eecb621214e89fc78428a896874cf36e0f126f4 100644
--- a/src/pair_buck_coul_cut.cpp
+++ b/src/pair_buck_coul_cut.cpp
@@ -15,9 +15,9 @@
Contributing author: Eduardo Bringa (LLNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
#include "pair_buck_coul_cut.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/pair_coul_cut.cpp b/src/pair_coul_cut.cpp
index b505dcb02ce5836c8edc0a2e568a622634e67474..edcf26bffe990d91219eaeaa60d53e20bf57181a 100644
--- a/src/pair_coul_cut.cpp
+++ b/src/pair_coul_cut.cpp
@@ -11,10 +11,10 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_coul_cut.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/pair_coul_debye.cpp b/src/pair_coul_debye.cpp
index df4555753f2c5782060892cf2ec13e794acefb9e..ee08ab3294909b1865bc16100b3a390468fa31d3 100644
--- a/src/pair_coul_debye.cpp
+++ b/src/pair_coul_debye.cpp
@@ -11,10 +11,10 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_coul_debye.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/pair_coul_dsf.cpp b/src/pair_coul_dsf.cpp
index 3595f9cbee8d8b64369b5eff1c3a77ee28df8c4f..f20eae43bdbdde3fe252d25f3f6194404e8e81bb 100644
--- a/src/pair_coul_dsf.cpp
+++ b/src/pair_coul_dsf.cpp
@@ -16,10 +16,10 @@
References: Fennell and Gezelter, JCP 124, 234104 (2006)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_coul_dsf.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/pair_coul_streitz.cpp b/src/pair_coul_streitz.cpp
index 82ecd1d8104723b2aced06c7e886150b8c187abd..1d725f4ca87c637ffb1e9855a126fe1e95f0cf41 100644
--- a/src/pair_coul_streitz.cpp
+++ b/src/pair_coul_streitz.cpp
@@ -15,10 +15,10 @@
Contributing author: Ray Shan (Sandia)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_coul_streitz.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/pair_coul_wolf.cpp b/src/pair_coul_wolf.cpp
index 1a7f4772608c98aeb8da19bb7f273e8fe64a18de..cd582f0693abaafffb3d04af52996cf7ea033c8a 100644
--- a/src/pair_coul_wolf.cpp
+++ b/src/pair_coul_wolf.cpp
@@ -15,10 +15,10 @@
Contributing author: Yongfeng Zhang (INL), yongfeng.zhang@inl.gov
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_coul_wolf.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/pair_dpd.cpp b/src/pair_dpd.cpp
index 61f700a33ecda8c04197d5055d9ef4df1bdfbc75..c209de87ed15e7aad81c1e1c01322509d4045720 100644
--- a/src/pair_dpd.cpp
+++ b/src/pair_dpd.cpp
@@ -15,9 +15,9 @@
Contributing author: Kurt Smith (U Pittsburgh)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
#include "pair_dpd.h"
#include "atom.h"
#include "atom_vec.h"
diff --git a/src/pair_dpd_tstat.cpp b/src/pair_dpd_tstat.cpp
index 0a5ebd33f85728d573097d354662dab87fa60ed7..f2c0b157eae27a8bc150bfdbe8e9a427c5099d6e 100644
--- a/src/pair_dpd_tstat.cpp
+++ b/src/pair_dpd_tstat.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
+#include <cmath>
#include "pair_dpd_tstat.h"
#include "atom.h"
#include "update.h"
diff --git a/src/pair_gauss.cpp b/src/pair_gauss.cpp
index c66cfc2c8058dd424ea204d415641b74870496fa..fe53bcc9e1b2af7b61b3074170521887b8166252 100644
--- a/src/pair_gauss.cpp
+++ b/src/pair_gauss.cpp
@@ -15,10 +15,10 @@
Contributing author: Sai Jayaraman (Sandia)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_gauss.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/pair_hybrid.cpp b/src/pair_hybrid.cpp
index 751560deffd56355b97cf7d4f5e63c7b044c880e..dc74dd040dde23f9b72fe87ab39417a54de263a6 100644
--- a/src/pair_hybrid.cpp
+++ b/src/pair_hybrid.cpp
@@ -11,10 +11,10 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
-#include <ctype.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
+#include <cctype>
#include "pair_hybrid.h"
#include "atom.h"
#include "force.h"
diff --git a/src/pair_hybrid.h b/src/pair_hybrid.h
index 202847b028b8583cc88b0afcdc5db97a197c2096..08f5a574df832cfa3f0e43ff8012e30fd1140683 100644
--- a/src/pair_hybrid.h
+++ b/src/pair_hybrid.h
@@ -20,7 +20,7 @@ PairStyle(hybrid,PairHybrid)
#ifndef LMP_PAIR_HYBRID_H
#define LMP_PAIR_HYBRID_H
-#include <stdio.h>
+#include <cstdio>
#include "pair.h"
namespace LAMMPS_NS {
diff --git a/src/pair_hybrid_overlay.cpp b/src/pair_hybrid_overlay.cpp
index 6776e90ff423c412b4a2652d0a92c468d4c842c7..717c0de1d1a19d7c9aa264e14d3134ccfceb42a9 100644
--- a/src/pair_hybrid_overlay.cpp
+++ b/src/pair_hybrid_overlay.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <stdlib.h>
-#include <string.h>
-#include <ctype.h>
+#include <cstdlib>
+#include <cstring>
+#include <cctype>
#include "pair_hybrid_overlay.h"
#include "atom.h"
#include "force.h"
diff --git a/src/pair_lj96_cut.cpp b/src/pair_lj96_cut.cpp
index 842b918fe154ad8db4865e2b14cd44d8141c7ff3..28677a393ef3745a969ae3ca03dcb47f09ed5e53 100644
--- a/src/pair_lj96_cut.cpp
+++ b/src/pair_lj96_cut.cpp
@@ -15,10 +15,10 @@
Contributing author: Chuanfu Luo (luochuanfu@gmail.com)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_lj96_cut.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/pair_lj_cubic.cpp b/src/pair_lj_cubic.cpp
index c96d4490cbddf7cbaabb5314f46d32627a1842e5..4b140e5f05d416fce943890c9412d8f1962a5a3e 100644
--- a/src/pair_lj_cubic.cpp
+++ b/src/pair_lj_cubic.cpp
@@ -16,10 +16,10 @@
Contributing author: Aidan Thompson (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_lj_cubic.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/pair_lj_cut.cpp b/src/pair_lj_cut.cpp
index 215fabecbbca976d2a01c46c163bf2f0aadff734..bb2db6aa2fc025cbec62d10111ee2d838caf1715 100644
--- a/src/pair_lj_cut.cpp
+++ b/src/pair_lj_cut.cpp
@@ -15,10 +15,10 @@
Contributing author: Paul Crozier (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_lj_cut.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/pair_lj_cut_coul_cut.cpp b/src/pair_lj_cut_coul_cut.cpp
index 85cf9dc97dea6a84d862d9f27265ffb68a024d24..15c06ab36a02f53453e644cd5974c36b72cbf47f 100644
--- a/src/pair_lj_cut_coul_cut.cpp
+++ b/src/pair_lj_cut_coul_cut.cpp
@@ -11,10 +11,10 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_lj_cut_coul_cut.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/pair_lj_cut_coul_debye.cpp b/src/pair_lj_cut_coul_debye.cpp
index 8f5e8e7a1721d74a39df8d98539230f52f08ae7b..dfd866ca7a01537d96737760ee8443155a6e5ab4 100644
--- a/src/pair_lj_cut_coul_debye.cpp
+++ b/src/pair_lj_cut_coul_debye.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdlib>
#include "pair_lj_cut_coul_debye.h"
#include "atom.h"
#include "neigh_list.h"
diff --git a/src/pair_lj_cut_coul_dsf.cpp b/src/pair_lj_cut_coul_dsf.cpp
index 429058650191af04433757140d58843b5306c244..a49af13fb2737fa8d8a6a09ba19ee92db98b23e7 100644
--- a/src/pair_lj_cut_coul_dsf.cpp
+++ b/src/pair_lj_cut_coul_dsf.cpp
@@ -16,10 +16,10 @@
References: Fennell and Gezelter, JCP 124, 234104 (2006)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_lj_cut_coul_dsf.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/pair_lj_cut_coul_wolf.cpp b/src/pair_lj_cut_coul_wolf.cpp
index 2043de4c7d46514845288d6f437f0b56502a85bd..fc8a858ce1aee20d2e72c50cf2b70fb3e71c7fd5 100644
--- a/src/pair_lj_cut_coul_wolf.cpp
+++ b/src/pair_lj_cut_coul_wolf.cpp
@@ -15,10 +15,10 @@
Contributing author: Vishal Boddu (FAU)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_lj_cut_coul_wolf.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/pair_lj_expand.cpp b/src/pair_lj_expand.cpp
index f2f49c872dcb5f0436ceb4062094eb934fed3441..ba72d7d45f39884c80c061d3b6a3b9bc6b5157dd 100644
--- a/src/pair_lj_expand.cpp
+++ b/src/pair_lj_expand.cpp
@@ -11,10 +11,10 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_lj_expand.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/pair_lj_gromacs.cpp b/src/pair_lj_gromacs.cpp
index 3375c6c4e203ea41a14c4587e1f2fe99da952e87..6b2219d2c5cef92f4da305e343e4111eb4fc751b 100644
--- a/src/pair_lj_gromacs.cpp
+++ b/src/pair_lj_gromacs.cpp
@@ -15,10 +15,10 @@
Contributing author: Mark Stevens (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_lj_gromacs.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/pair_lj_gromacs_coul_gromacs.cpp b/src/pair_lj_gromacs_coul_gromacs.cpp
index 26e433b38113a6ef282c7034f1ddcdb9f1b5539e..414bfea92a0f2bab8db52a1ba2f0a1f9ffcb7cd0 100644
--- a/src/pair_lj_gromacs_coul_gromacs.cpp
+++ b/src/pair_lj_gromacs_coul_gromacs.cpp
@@ -15,10 +15,10 @@
Contributing author: Mark Stevens (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_lj_gromacs_coul_gromacs.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/pair_lj_smooth.cpp b/src/pair_lj_smooth.cpp
index 1afaef9235a6c0ddbf837bbcb58db5bbeb798817..23256d486ed09fcf2a48e31ebefd65aead569372 100644
--- a/src/pair_lj_smooth.cpp
+++ b/src/pair_lj_smooth.cpp
@@ -15,9 +15,9 @@
Contributing author: Craig Maloney (UCSB)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
#include "pair_lj_smooth.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/pair_lj_smooth_linear.cpp b/src/pair_lj_smooth_linear.cpp
index 415ca7b6d3650a1b2f71f8060da75f47221eb3c1..592a7f6f41a1ad75eae1a537e3e02e5c88b29bfb 100644
--- a/src/pair_lj_smooth_linear.cpp
+++ b/src/pair_lj_smooth_linear.cpp
@@ -15,9 +15,9 @@
Contributing author: Jonathan Zimmerman (Sandia)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
#include "pair_lj_smooth_linear.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/pair_mie_cut.cpp b/src/pair_mie_cut.cpp
index 04f8de8d7d335b32aa4c00fe66cc764ea1e3abde..1f9267ca30898ed75de80279c23bb3b74d670e88 100644
--- a/src/pair_mie_cut.cpp
+++ b/src/pair_mie_cut.cpp
@@ -15,10 +15,10 @@
Contributing author: Cassiano Aimoli (aimoli@gmail.com)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_mie_cut.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/pair_morse.cpp b/src/pair_morse.cpp
index 0e40fc75512277a36b3ef83c3bc5c299134090d7..32ddd723b2c0dcf062a2f3f1261651786b092bbc 100644
--- a/src/pair_morse.cpp
+++ b/src/pair_morse.cpp
@@ -11,10 +11,10 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_morse.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/pair_soft.cpp b/src/pair_soft.cpp
index b05058b4dcdc20699f0d4892b31f7c8bdfd28554..f428893fd107a0726dcf9532a49d55ddb288b8b3 100644
--- a/src/pair_soft.cpp
+++ b/src/pair_soft.cpp
@@ -11,10 +11,10 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_soft.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/pair_table.cpp b/src/pair_table.cpp
index 0ee4effb0190b989d966689293d6fbd07d875e62..9e9e41a54c6eac3671c7260937d9ca401254b35b 100644
--- a/src/pair_table.cpp
+++ b/src/pair_table.cpp
@@ -16,9 +16,9 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "pair_table.h"
#include "atom.h"
#include "force.h"
diff --git a/src/pair_ufm.cpp b/src/pair_ufm.cpp
index e036e2cdd96cfbf0472c6b61a0c736bda90ede6f..965fe0204e739a526f5f7ebe13e981f2b5c22984 100644
--- a/src/pair_ufm.cpp
+++ b/src/pair_ufm.cpp
@@ -17,10 +17,10 @@
Maurice de Koning (Unicamp/Brazil) - dekoning@ifi.unicamp.br
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_ufm.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/pair_yukawa.cpp b/src/pair_yukawa.cpp
index 9be9237734343588dda84aceb4d650c067c8f525..040664abec071e8b776a9315f2e33521d6221f2a 100644
--- a/src/pair_yukawa.cpp
+++ b/src/pair_yukawa.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstdlib>
#include "pair_yukawa.h"
#include "atom.h"
#include "force.h"
diff --git a/src/pair_zbl.cpp b/src/pair_zbl.cpp
index d2dbaeae702adeb0b5505d4a0c0d411a182591e7..98048f61d0751393e4a23b672b84c6698e669db2 100644
--- a/src/pair_zbl.cpp
+++ b/src/pair_zbl.cpp
@@ -15,10 +15,10 @@
Contributing authors: Stephen Foiles, Aidan Thompson (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_zbl.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/pair_zero.cpp b/src/pair_zero.cpp
index ab6d713cc4aa433524eff1484a38b7dd4eba5d31..d423e196af0f47a8789cefb6430d3b5d7a0f36eb 100644
--- a/src/pair_zero.cpp
+++ b/src/pair_zero.cpp
@@ -15,10 +15,10 @@
Contributing author: Carsten Svaneborg (SDU)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "pair_zero.h"
#include "atom.h"
#include "comm.h"
diff --git a/src/procmap.cpp b/src/procmap.cpp
index f54ac1915c4b4c934d18d3ae0e848c57df856808..9d1ed83e7382a75dd418b311f6ad9bc10c0ca8a0 100644
--- a/src/procmap.cpp
+++ b/src/procmap.cpp
@@ -17,6 +17,7 @@
#include "procmap.h"
#include "universe.h"
+#include "comm.h"
#include "domain.h"
#include "math_extra.h"
#include "memory.h"
@@ -29,8 +30,6 @@ using namespace LAMMPS_NS;
#define MAXLINE 128
-enum{MULTIPLE}; // same as in Comm
-
/* ---------------------------------------------------------------------- */
ProcMap::ProcMap(LAMMPS *lmp) : Pointers(lmp) {}
@@ -811,7 +810,7 @@ int ProcMap::cull_other(int n, int **factors, int m,
{
int i = 0;
while (i < n) {
- if (other_style == MULTIPLE) {
+ if (other_style == Comm::MULTIPLE) {
int flag = 0;
if ((other_procgrid[0]/other_coregrid[0]) % factors[i][0]) flag = 1;
if ((other_procgrid[1]/other_coregrid[1]) % factors[i][1]) flag = 1;
diff --git a/src/random_mars.cpp b/src/random_mars.cpp
index 1300cbbb8d8bbefb755b1769c0636ea60a875c41..464e640eab5b73489d4216467de4e848da23e293 100644
--- a/src/random_mars.cpp
+++ b/src/random_mars.cpp
@@ -14,7 +14,7 @@
// Marsaglia random number generator
// see RANMAR in F James, Comp Phys Comm, 60, 329 (1990)
-#include <math.h>
+#include <cmath>
#include "random_mars.h"
#include "error.h"
diff --git a/src/random_park.cpp b/src/random_park.cpp
index 80460a39fd26168a8e24b034795e87f2e97d325f..fc00939bd471f4f07f863141a4f22da586f564cc 100644
--- a/src/random_park.cpp
+++ b/src/random_park.cpp
@@ -13,7 +13,7 @@
// Park/Miller RNG
-#include <math.h>
+#include <cmath>
#include "random_park.h"
#include "error.h"
diff --git a/src/rcb.cpp b/src/rcb.cpp
index 2ef3e0c136b2dac029ee0e769b0303f3014f484e..3027920310055351370fd6bff70f61038f01b726 100644
--- a/src/rcb.cpp
+++ b/src/rcb.cpp
@@ -12,7 +12,7 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <string.h>
+#include <cstring>
#include "rcb.h"
#include "irregular.h"
#include "memory.h"
diff --git a/src/read_data.cpp b/src/read_data.cpp
index 4b84016744c9d462fbe564f8c71d0f57e561fa8b..5faa8f9646517ff8952a5d035372099c256d2070 100644
--- a/src/read_data.cpp
+++ b/src/read_data.cpp
@@ -17,10 +17,10 @@
#include "lmptype.h"
#include <mpi.h>
-#include <math.h>
-#include <string.h>
-#include <stdlib.h>
-#include <ctype.h>
+#include <cmath>
+#include <cstring>
+#include <cstdlib>
+#include <cctype>
#include "read_data.h"
#include "atom.h"
#include "atom_vec.h"
diff --git a/src/read_data.h b/src/read_data.h
index 9b7ca66259d266bc0cdd39b39068f73ef9b55ce1..9dce8cfcf581c20a145b3684b1b42f14dde214ef 100644
--- a/src/read_data.h
+++ b/src/read_data.h
@@ -20,7 +20,7 @@ CommandStyle(read_data,ReadData)
#ifndef LMP_READ_DATA_H
#define LMP_READ_DATA_H
-#include <stdio.h>
+#include <cstdio>
#include "pointers.h"
namespace LAMMPS_NS {
diff --git a/src/read_dump.cpp b/src/read_dump.cpp
index 7f2488fbb2ecd451468a0e09c934fdaa79b1c7c8..30934f123b853ee5d2c035b564a6f8a2db73f42b 100644
--- a/src/read_dump.cpp
+++ b/src/read_dump.cpp
@@ -21,8 +21,8 @@
#include "lmptype.h"
#include <mpi.h>
-#include <string.h>
-#include <stdlib.h>
+#include <cstring>
+#include <cstdlib>
#include "read_dump.h"
#include "reader.h"
#include "style_reader.h"
diff --git a/src/read_dump.h b/src/read_dump.h
index 3fc554b5116475f407a686a6cd0af0cf8aa3a596..eb70b9980898b1665ca93fc2f755ba06f824fa86 100644
--- a/src/read_dump.h
+++ b/src/read_dump.h
@@ -22,7 +22,7 @@ CommandStyle(read_dump,ReadDump)
#ifndef LMP_READ_DUMP_H
#define LMP_READ_DUMP_H
-#include <stdio.h>
+#include <cstdio>
#include "pointers.h"
namespace LAMMPS_NS {
diff --git a/src/read_restart.cpp b/src/read_restart.cpp
index 60d4a7199eea14804c559f720eb03636de28d6ca..1164de6faa91acea7ebc08b985d317618c723e9f 100644
--- a/src/read_restart.cpp
+++ b/src/read_restart.cpp
@@ -12,8 +12,8 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <string.h>
-#include <stdlib.h>
+#include <cstring>
+#include <cstdlib>
#include <dirent.h>
#include "read_restart.h"
#include "atom.h"
diff --git a/src/read_restart.h b/src/read_restart.h
index 0c4661cb55abce8719427f87ac75d77f4d11cf41..8d2547fb1055673945e77b650b7004e6f0f01720 100644
--- a/src/read_restart.h
+++ b/src/read_restart.h
@@ -20,7 +20,7 @@ CommandStyle(read_restart,ReadRestart)
#ifndef LMP_READ_RESTART_H
#define LMP_READ_RESTART_H
-#include <stdio.h>
+#include <cstdio>
#include "pointers.h"
namespace LAMMPS_NS {
diff --git a/src/reader.cpp b/src/reader.cpp
index b8914d1b1003136dcc14a16d894c9a056d667967..f6e8bd39ebec8522ea68c9e0ca099f9ea07edd9f 100644
--- a/src/reader.cpp
+++ b/src/reader.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <stdio.h>
-#include <string.h>
+#include <cstdio>
+#include <cstring>
#include "reader.h"
#include "error.h"
diff --git a/src/reader_native.cpp b/src/reader_native.cpp
index 529325ed18927f6c0eeed92b06d7cbf5dbf3be08..2c60ffdfd48f6a0d81c942a091d83e71bf8c6183 100644
--- a/src/reader_native.cpp
+++ b/src/reader_native.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
-#include <stdlib.h>
+#include <cstring>
+#include <cstdlib>
#include "reader_native.h"
#include "atom.h"
#include "memory.h"
diff --git a/src/reader_xyz.cpp b/src/reader_xyz.cpp
index a56b503f5e329d2fcd5aecfef8122f5ba8aa30b6..5cb3476510f093abbe51f745043e0d063356fe29 100644
--- a/src/reader_xyz.cpp
+++ b/src/reader_xyz.cpp
@@ -15,8 +15,8 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <string.h>
-#include <stdlib.h>
+#include <cstring>
+#include <cstdlib>
#include "reader_xyz.h"
#include "atom.h"
#include "memory.h"
diff --git a/src/region.cpp b/src/region.cpp
index 047c43ce4b0aa1b6a3e5eb0abc8701e769bd6c52..88a414b13438fb2acc8008c7e635645fb1026c30 100644
--- a/src/region.cpp
+++ b/src/region.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "region.h"
#include "update.h"
#include "domain.h"
diff --git a/src/region_block.cpp b/src/region_block.cpp
index 8e1659aa13489b2890abb8c92a26565a5250ace4..eeca1323786390c43e434cb0cf89817c5b5ecb52 100644
--- a/src/region_block.cpp
+++ b/src/region_block.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <stdlib.h>
-#include <string.h>
+#include <cstdlib>
+#include <cstring>
#include "region_block.h"
#include "force.h"
#include "domain.h"
diff --git a/src/region_cone.cpp b/src/region_cone.cpp
index 2af39f93a933f210acd712bda94e93fccebb328f..72f56a268fe4ece8ce5771c6bda9ad5bd56a7523 100644
--- a/src/region_cone.cpp
+++ b/src/region_cone.cpp
@@ -15,9 +15,9 @@
Contributing author: Pim Schravendijk
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "region_cone.h"
#include "domain.h"
#include "error.h"
diff --git a/src/region_cylinder.cpp b/src/region_cylinder.cpp
index 959992f77b89f7cb1e7fa4f1c9538016c0db750f..0b15a3644df2b454f9794a11dab2f495898b1222 100644
--- a/src/region_cylinder.cpp
+++ b/src/region_cylinder.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "region_cylinder.h"
#include "update.h"
#include "domain.h"
diff --git a/src/region_intersect.cpp b/src/region_intersect.cpp
index 4fb84dda5999f047a115d1fcb26c1acbe6bc6619..96d3bed16c319657aa20c10e6d6eff2f21f44179 100644
--- a/src/region_intersect.cpp
+++ b/src/region_intersect.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <stdlib.h>
-#include <string.h>
+#include <cstdlib>
+#include <cstring>
#include "region_intersect.h"
#include "domain.h"
#include "error.h"
diff --git a/src/region_plane.cpp b/src/region_plane.cpp
index 3c945eb553401844159156b549577d4f975d5816..e67a2c85bd8d7e7bf6aa842171c20d05df893279 100644
--- a/src/region_plane.cpp
+++ b/src/region_plane.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "region_plane.h"
#include "error.h"
#include "force.h"
diff --git a/src/region_prism.cpp b/src/region_prism.cpp
index b8b7b30368ad2dfe565065c69e4b6c6b95376b6c..22fc504c37537b14e2370ef822ba4c17a4547d09 100644
--- a/src/region_prism.cpp
+++ b/src/region_prism.cpp
@@ -15,9 +15,9 @@
Contributing author: Pieter in 't Veld (SNL)
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "region_prism.h"
#include "domain.h"
#include "force.h"
diff --git a/src/region_sphere.cpp b/src/region_sphere.cpp
index 8aef087d38eab60b8d46b910951797d1405c36bc..5645b3369d7f64ea0fd2cccbb52027f39c6d153d 100644
--- a/src/region_sphere.cpp
+++ b/src/region_sphere.cpp
@@ -11,9 +11,9 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "region_sphere.h"
#include "update.h"
#include "input.h"
diff --git a/src/region_union.cpp b/src/region_union.cpp
index abb6f854e3675f821c7c9ee51f7c599e5447d5a3..33ac6fedd709acf0f6b06d99fb095e6facd799c6 100644
--- a/src/region_union.cpp
+++ b/src/region_union.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <stdlib.h>
-#include <string.h>
+#include <cstdlib>
+#include <cstring>
#include "region_union.h"
#include "domain.h"
#include "error.h"
diff --git a/src/replicate.cpp b/src/replicate.cpp
index 1251688211950d97bbc62dd497b40cb14e6f8162..cdadf1fd1f6e1636f02ef227d2a4a912153f81ba 100644
--- a/src/replicate.cpp
+++ b/src/replicate.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <stdlib.h>
-#include <string.h>
+#include <cstdlib>
+#include <cstring>
#include "replicate.h"
#include "atom.h"
#include "atom_vec.h"
@@ -30,8 +30,6 @@ using namespace LAMMPS_NS;
#define LB_FACTOR 1.1
#define EPSILON 1.0e-6
-enum{LAYOUT_UNIFORM,LAYOUT_NONUNIFORM,LAYOUT_TILED}; // several files
-
/* ---------------------------------------------------------------------- */
Replicate::Replicate(LAMMPS *lmp) : Pointers(lmp) {}
@@ -267,7 +265,7 @@ void Replicate::command(int narg, char **arg)
sublo[2] = domain->sublo_lamda[2]; subhi[2] = domain->subhi_lamda[2];
}
- if (comm->layout != LAYOUT_TILED) {
+ if (comm->layout != Comm::LAYOUT_TILED) {
if (domain->xperiodic) {
if (comm->myloc[0] == 0) sublo[0] -= epsilon[0];
if (comm->myloc[0] == comm->procgrid[0]-1) subhi[0] += epsilon[0];
diff --git a/src/rerun.cpp b/src/rerun.cpp
index 6081a6fc4721026ba3c89db20a3098cb7718735c..f8a37b59462a89a3f4c1e5c0e3e2fd6fe3105fff 100644
--- a/src/rerun.cpp
+++ b/src/rerun.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <stdlib.h>
-#include <string.h>
+#include <cstdlib>
+#include <cstring>
#include "rerun.h"
#include "read_dump.h"
#include "domain.h"
diff --git a/src/respa.cpp b/src/respa.cpp
index 7080a739484de0c772463b72963c501b8312dc52..73e280b03d806fa038d388e2943d067465cce3d2 100644
--- a/src/respa.cpp
+++ b/src/respa.cpp
@@ -15,8 +15,8 @@
Contributing authors: Mark Stevens (SNL), Paul Crozier (SNL)
------------------------------------------------------------------------- */
-#include <stdlib.h>
-#include <string.h>
+#include <cstdlib>
+#include <cstring>
#include "respa.h"
#include "neighbor.h"
#include "atom.h"
diff --git a/src/run.cpp b/src/run.cpp
index 37af977e3450f2b2b07ff38c3c35199447ddcc44..beb71be52c1faafeecfb8b3e4fd6c6cb2315e2fc 100644
--- a/src/run.cpp
+++ b/src/run.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <stdlib.h>
-#include <string.h>
+#include <cstdlib>
+#include <cstring>
#include "run.h"
#include "domain.h"
#include "update.h"
diff --git a/src/set.cpp b/src/set.cpp
index 704ab6921671ac0d8597e717dbcbb58f642161c5..d5221a57a0019a5215f78e8a206190e56286e507 100644
--- a/src/set.cpp
+++ b/src/set.cpp
@@ -12,9 +12,9 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "set.h"
#include "atom.h"
#include "atom_vec.h"
diff --git a/src/special.cpp b/src/special.cpp
index 56529e748b8d52e070696543627bfba255b87e0a..fccc930353ce3a71458f5997355b49110f9006dd 100644
--- a/src/special.cpp
+++ b/src/special.cpp
@@ -12,7 +12,7 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <stdio.h>
+#include <cstdio>
#include "special.h"
#include "atom.h"
#include "atom_vec.h"
diff --git a/src/thermo.cpp b/src/thermo.cpp
index 211ace5232b3b89f3a64ad4a0a102628e4990383..ade7a3c333ab893fdd14a17adaa94a966328b64a 100644
--- a/src/thermo.cpp
+++ b/src/thermo.cpp
@@ -17,9 +17,9 @@
#include "lmptype.h"
#include <mpi.h>
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "thermo.h"
#include "atom.h"
#include "update.h"
@@ -72,7 +72,6 @@ using namespace MathConst;
#define ONE "step temp epair emol etotal press"
#define MULTI "etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press"
-enum{IGNORE,WARN,ERROR}; // same as several files
enum{ONELINE,MULTILINE};
enum{INT,FLOAT,BIGINT};
enum{SCALAR,VECTOR,ARRAY};
@@ -98,7 +97,7 @@ Thermo::Thermo(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
modified = 0;
normuserflag = 0;
lineflag = ONELINE;
- lostflag = lostbond = ERROR;
+ lostflag = lostbond = Thermo::ERROR;
lostbefore = 0;
flushflag = 0;
@@ -427,14 +426,14 @@ bigint Thermo::lost_check()
if (ntotal == atom->natoms) return ntotal;
// if not checking or already warned, just return
- if (lostflag == IGNORE) return ntotal;
- if (lostflag == WARN && lostbefore == 1) {
+ if (lostflag == Thermo::IGNORE) return ntotal;
+ if (lostflag == Thermo::WARN && lostbefore == 1) {
return ntotal;
}
// error message
- if (lostflag == ERROR) {
+ if (lostflag == Thermo::ERROR) {
char str[64];
sprintf(str,
"Lost atoms: original " BIGINT_FORMAT " current " BIGINT_FORMAT,
@@ -536,17 +535,17 @@ void Thermo::modify_params(int narg, char **arg)
} else if (strcmp(arg[iarg],"lost") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal thermo_modify command");
- if (strcmp(arg[iarg+1],"ignore") == 0) lostflag = IGNORE;
- else if (strcmp(arg[iarg+1],"warn") == 0) lostflag = WARN;
- else if (strcmp(arg[iarg+1],"error") == 0) lostflag = ERROR;
+ if (strcmp(arg[iarg+1],"ignore") == 0) lostflag = Thermo::IGNORE;
+ else if (strcmp(arg[iarg+1],"warn") == 0) lostflag = Thermo::WARN;
+ else if (strcmp(arg[iarg+1],"error") == 0) lostflag = Thermo::ERROR;
else error->all(FLERR,"Illegal thermo_modify command");
iarg += 2;
} else if (strcmp(arg[iarg],"lost/bond") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal thermo_modify command");
- if (strcmp(arg[iarg+1],"ignore") == 0) lostbond = IGNORE;
- else if (strcmp(arg[iarg+1],"warn") == 0) lostbond = WARN;
- else if (strcmp(arg[iarg+1],"error") == 0) lostbond = ERROR;
+ if (strcmp(arg[iarg+1],"ignore") == 0) lostbond = Thermo::IGNORE;
+ else if (strcmp(arg[iarg+1],"warn") == 0) lostbond = Thermo::WARN;
+ else if (strcmp(arg[iarg+1],"error") == 0) lostbond = Thermo::ERROR;
else error->all(FLERR,"Illegal thermo_modify command");
iarg += 2;
diff --git a/src/thermo.h b/src/thermo.h
index 8023a8867cf337b17b73059775d7e3314b6559d6..8c32f24d3c2142f4953126e97dbd6bdd38921928 100644
--- a/src/thermo.h
+++ b/src/thermo.h
@@ -33,6 +33,8 @@ class Thermo : protected Pointers {
int lostflag; // IGNORE,WARN,ERROR
int lostbond; // ditto for atoms in bonds
+ enum {IGNORE,WARN,ERROR};
+
Thermo(class LAMMPS *, int, char **);
~Thermo();
void init();
diff --git a/src/timer.cpp b/src/timer.cpp
index 9c1aa8794398c03345fe3882f40399725e6bfcf5..65cb6ab5d8fef698784258a1c80220848f96d9bb 100644
--- a/src/timer.cpp
+++ b/src/timer.cpp
@@ -12,8 +12,8 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <string.h>
-#include <stdlib.h>
+#include <cstring>
+#include <cstdlib>
#include "timer.h"
#include "comm.h"
#include "error.h"
@@ -22,13 +22,13 @@
#ifdef _WIN32
#include <windows.h>
-#include <stdint.h>
+#include <stdint.h> // <cstdint> requires C++-11
#else
#include <sys/time.h>
#include <sys/resource.h>
#endif
-#include <time.h>
+#include <ctime>
using namespace LAMMPS_NS;
diff --git a/src/universe.cpp b/src/universe.cpp
index c2a6754fac7799ec7882572fac0365407dd41654..45b4318ec900862d85d8a7c3999ae181bd1b1f6d 100644
--- a/src/universe.cpp
+++ b/src/universe.cpp
@@ -12,10 +12,10 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <ctype.h>
-#include <stdlib.h>
-#include <string.h>
-#include <stdio.h>
+#include <cctype>
+#include <cstdlib>
+#include <cstring>
+#include <cstdio>
#include "universe.h"
#include "version.h"
#include "error.h"
diff --git a/src/universe.h b/src/universe.h
index 4ff4d7dd14971c691b9f29417c789a3627255a97..3073409b8677a41a1c0326e4c965591170aa3403 100644
--- a/src/universe.h
+++ b/src/universe.h
@@ -14,7 +14,7 @@
#ifndef LMP_UNIVERSE_H
#define LMP_UNIVERSE_H
-#include <stdio.h>
+#include <cstdio>
#include "pointers.h"
namespace LAMMPS_NS {
diff --git a/src/update.cpp b/src/update.cpp
index 6282c0a875aec481d0ed3df46e1fa3f7988ff637..aa152a850857e729f78da1db98e678e41140f1d7 100644
--- a/src/update.cpp
+++ b/src/update.cpp
@@ -11,8 +11,8 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
-#include <stdlib.h>
+#include <cstring>
+#include <cstdlib>
#include "update.h"
#include "integrate.h"
#include "min.h"
diff --git a/src/variable.cpp b/src/variable.cpp
index 34dc33da39a084d46fef21a6727b04ec5d341095..b5c19a48439cd2342273e7af4b7d21936ffe9bd2 100644
--- a/src/variable.cpp
+++ b/src/variable.cpp
@@ -11,10 +11,10 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
-#include <ctype.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
+#include <cctype>
#include <unistd.h>
#include "variable.h"
#include "universe.h"
diff --git a/src/variable.h b/src/variable.h
index 9dcbaebd4fa82e6860fd836b20929fbe3efc1fa7..a74cdba980f4cee3c75486a08706e3c3ba4f96ca 100644
--- a/src/variable.h
+++ b/src/variable.h
@@ -14,7 +14,7 @@
#ifndef LMP_VARIABLE_H
#define LMP_VARIABLE_H
-#include <stdlib.h>
+#include <cstdlib>
#include "pointers.h"
namespace LAMMPS_NS {
diff --git a/src/velocity.cpp b/src/velocity.cpp
index 260a11bb4ee90dc2116907688e9b5bda4503e4cb..f83f778f8b15dfecfbd7b755da0fc7dfb19f93d7 100644
--- a/src/velocity.cpp
+++ b/src/velocity.cpp
@@ -12,10 +12,10 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "velocity.h"
#include "atom.h"
#include "update.h"
diff --git a/src/verlet.cpp b/src/verlet.cpp
index f0314bd7d0428940e2c117fb63ebfe589eeb3f07..a00b470e60637fc86aabf161b7b181a08921063c 100644
--- a/src/verlet.cpp
+++ b/src/verlet.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "verlet.h"
#include "neighbor.h"
#include "domain.h"
diff --git a/src/version.h b/src/version.h
index eda788fad6773bb16161275945120f9ce15f5383..981ec8eeb8c8e47627ab4d756be509e7b7fe2872 100644
--- a/src/version.h
+++ b/src/version.h
@@ -1 +1 @@
-#define LAMMPS_VERSION "20 Apr 2018"
+#define LAMMPS_VERSION "11 May 2018"
diff --git a/src/write_coeff.cpp b/src/write_coeff.cpp
index 0556d647cf36d1046f4864002f2e6fa5e5d656f5..5f82a480fd9242a745998709bc6748ed80212fb0 100644
--- a/src/write_coeff.cpp
+++ b/src/write_coeff.cpp
@@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include <unistd.h>
#include "write_coeff.h"
#include "pair.h"
diff --git a/src/write_coeff.h b/src/write_coeff.h
index 9228e879bc365486a44e50711144b5dd217ec6c7..569a615e6e577f06386fd0accb394971a7ab1edc 100644
--- a/src/write_coeff.h
+++ b/src/write_coeff.h
@@ -20,7 +20,7 @@ CommandStyle(write_coeff,WriteCoeff)
#ifndef LMP_WRITE_COEFF_H
#define LMP_WRITE_COEFF_H
-#include <stdio.h>
+#include <cstdio>
#include "pointers.h"
namespace LAMMPS_NS {
diff --git a/src/write_data.cpp b/src/write_data.cpp
index d9694f7cd355e593dbee401b252dfc1d6efd042e..96bf081157eaf13096dd215477950a5ee0792201 100644
--- a/src/write_data.cpp
+++ b/src/write_data.cpp
@@ -12,7 +12,7 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <string.h>
+#include <cstring>
#include "write_data.h"
#include "atom.h"
#include "atom_vec.h"
@@ -36,7 +36,6 @@
using namespace LAMMPS_NS;
-enum{IGNORE,WARN,ERROR}; // same as thermo.cpp
enum{II,IJ};
/* ---------------------------------------------------------------------- */
@@ -153,7 +152,7 @@ void WriteData::write(char *file)
bigint nblocal = atom->nlocal;
bigint natoms;
MPI_Allreduce(&nblocal,&natoms,1,MPI_LMP_BIGINT,MPI_SUM,world);
- if (natoms != atom->natoms && output->thermo->lostflag == ERROR)
+ if (natoms != atom->natoms && output->thermo->lostflag == Thermo::ERROR)
error->all(FLERR,"Atom count is inconsistent, cannot write data file");
// sum up bond,angle,dihedral,improper counts
diff --git a/src/write_data.h b/src/write_data.h
index ced6a3be8b4ceee0e07c06463d561d996c357320..6f1bb2ec47f9a609c7a6bf1823a7869561480942 100644
--- a/src/write_data.h
+++ b/src/write_data.h
@@ -20,7 +20,7 @@ CommandStyle(write_data,WriteData)
#ifndef LMP_WRITE_DATA_H
#define LMP_WRITE_DATA_H
-#include <stdio.h>
+#include <cstdio>
#include "pointers.h"
namespace LAMMPS_NS {
diff --git a/src/write_dump.cpp b/src/write_dump.cpp
index dcf6c05a14db5629dd01a157756d40cce194f550..bb79c654b418569101a1f601f31fe93ce420bd97 100644
--- a/src/write_dump.cpp
+++ b/src/write_dump.cpp
@@ -15,7 +15,7 @@
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
-#include <string.h>
+#include <cstring>
#include "write_dump.h"
#include "style_dump.h"
#include "dump.h"
diff --git a/src/write_restart.cpp b/src/write_restart.cpp
index c92fd15334778cf8267033b8a638e17b4844b743..69b731870d0c28fe6f389da0183f1905664a0400 100644
--- a/src/write_restart.cpp
+++ b/src/write_restart.cpp
@@ -12,7 +12,7 @@
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <string.h>
+#include <cstring>
#include "write_restart.h"
#include "atom.h"
#include "atom_vec.h"
@@ -63,8 +63,6 @@ enum{VERSION,SMALLINT,TAGINT,BIGINT,
ATOM_ID,ATOM_MAP_STYLE,ATOM_MAP_USER,ATOM_SORTFREQ,ATOM_SORTBIN,
COMM_MODE,COMM_CUTOFF,COMM_VEL,NO_PAIR};
-enum{IGNORE,WARN,ERROR}; // same as thermo.cpp
-
/* ---------------------------------------------------------------------- */
WriteRestart::WriteRestart(LAMMPS *lmp) : Pointers(lmp)
@@ -252,7 +250,7 @@ void WriteRestart::write(char *file)
bigint nblocal = atom->nlocal;
MPI_Allreduce(&nblocal,&natoms,1,MPI_LMP_BIGINT,MPI_SUM,world);
- if (natoms != atom->natoms && output->thermo->lostflag == ERROR)
+ if (natoms != atom->natoms && output->thermo->lostflag == Thermo::ERROR)
error->all(FLERR,"Atom count is inconsistent, cannot write restart file");
// open single restart file or base file for multiproc case
diff --git a/src/write_restart.h b/src/write_restart.h
index 2253977bdad8868fce56246dc4de315fa088e8b2..c6202acbfd1bf08f47baacb33ebb3832f35b2f89 100644
--- a/src/write_restart.h
+++ b/src/write_restart.h
@@ -20,7 +20,7 @@ CommandStyle(write_restart,WriteRestart)
#ifndef LMP_WRITE_RESTART_H
#define LMP_WRITE_RESTART_H
-#include <stdio.h>
+#include <cstdio>
#include "pointers.h"
namespace LAMMPS_NS {