diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index c15011b2af..fd93814574 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -322,7 +322,7 @@ pkg_depends(USER-SCAFACOS MPI) find_package(OpenMP QUIET) option(BUILD_OMP "Build with OpenMP support" ${OpenMP_FOUND}) -if(BUILD_OMP OR PKG_KOKKOS OR PKG_USER-INTEL) +if(BUILD_OMP) find_package(OpenMP REQUIRED) set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}") set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}") @@ -560,6 +560,20 @@ if(PKG_USER-PLUMED) option(DOWNLOAD_PLUMED "Download Plumed package instead of using an already installed one" OFF) if(DOWNLOAD_PLUMED) + if(BUILD_MPI) + set(PLUMED_CONFIG_MPI "--enable-mpi") + set(PLUMED_CONFIG_CC ${CMAKE_MPI_C_COMPILER}) + set(PLUMED_CONFIG_CXX ${CMAKE_MPI_CXX_COMPILER}) + else() + set(PLUMED_CONFIG_MPI "--disable-mpi") + set(PLUMED_CONFIG_CC ${CMAKE_C_COMPILER}) + set(PLUMED_CONFIG_CXX ${CMAKE_CXX_COMPILER}) + endif() + if(BUILD_OMP) + set(PLUMED_CONFIG_OMP "--enable-openmp") + else() + set(PLUMED_CONFIG_OMP "--disable-openmp") + endif() message(STATUS "PLUMED download requested - we will build our own") include(ExternalProject) ExternalProject_Add(plumed_build @@ -568,9 +582,11 @@ if(PKG_USER-PLUMED) BUILD_IN_SOURCE 1 CONFIGURE_COMMAND /configure --prefix= ${CONFIGURE_REQUEST_PIC} - --enable-modules=all - CXX=${CMAKE_MPI_CXX_COMPILER} - CC=${CMAKE_MPI_C_COMPILER} + --enable-modules=all + ${PLUMED_CONFIG_MPI} + ${PLUMED_CONFIG_OMP} + CXX=${PLUMED_CONFIG_CXX} + CC=${PLUMED_CONFIG_CC} ) ExternalProject_get_property(plumed_build INSTALL_DIR) set(PLUMED_INSTALL_DIR ${INSTALL_DIR}) @@ -607,7 +623,10 @@ if(PKG_USER-MOLFILE) set(MOLFILE_INCLUDE_DIRS "${LAMMPS_LIB_SOURCE_DIR}/molfile" CACHE STRING "Path to VMD molfile plugin headers") add_library(molfile INTERFACE) target_include_directories(molfile INTERFACE ${MOLFILE_INCLUDE_DIRS}) - target_link_libraries(molfile INTERFACE ${CMAKE_DL_LIBS}) + # no need to link with -ldl on windows + if(NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows") + target_link_libraries(molfile INTERFACE ${CMAKE_DL_LIBS}) + endif() list(APPEND LAMMPS_LINK_LIBS molfile) endif() @@ -709,6 +728,7 @@ if(PKG_MESSAGE) set_target_properties(cslib PROPERTIES OUTPUT_NAME "csmpi") else() target_compile_definitions(cslib PRIVATE -DMPI_NO) + target_include_directories(cslib PRIVATE ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/src/STUBS_MPI) set_target_properties(cslib PROPERTIES OUTPUT_NAME "csnompi") endif() @@ -944,7 +964,7 @@ if(PKG_USER-OMP) # detects styles which have USER-OMP version RegisterStylesExt(${USER-OMP_SOURCES_DIR} omp OMP_SOURCES) - RegisterFixStyle("${USER-OMP_SOURCES_DIR}/fix_omp.h") + RegisterFixStyle(${USER-OMP_SOURCES_DIR}/fix_omp.h) get_property(USER-OMP_SOURCES GLOBAL PROPERTY OMP_SOURCES) @@ -1057,37 +1077,79 @@ if(PKG_OPT) endif() if(PKG_USER-INTEL) - find_package(TBB REQUIRED) - find_package(MKL REQUIRED) + if(LAMMPS_SIZES STREQUAL BIGBIG) + message(FATAL_ERROR "The USER-INTEL Package is not compatible with -DLAMMPS_BIGBIG") + endif() + add_definitions(-DLMP_USER_INTEL) - if(NOT CMAKE_CXX_COMPILER_ID STREQUAL "Intel") - message(FATAL_ERROR "USER-INTEL is only useful together with intel compiler") - endif() + set(INTEL_ARCH "cpu" CACHE STRING "Architectures used by USER-INTEL (cpu or knl)") + set(INTEL_ARCH_VALUES cpu knl) + set_property(CACHE INTEL_ARCH PROPERTY STRINGS ${INTEL_ARCH_VALUES}) + validate_option(INTEL_ARCH INTEL_ARCH_VALUES) + string(TOUPPER ${INTEL_ARCH} INTEL_ARCH) - if(CMAKE_CXX_COMPILER_VERSION VERSION_LESS 16) - message(FATAL_ERROR "USER-INTEL needs at least a 2016 intel compiler, found ${CMAKE_CXX_COMPILER_VERSION}") - endif() - - if(NOT BUILD_OMP) - message(FATAL_ERROR "USER-INTEL requires OpenMP") - endif() - - if(NOT ${LAMMPS_MEMALIGN} STREQUAL "64") - message(FATAL_ERROR "USER-INTEL is only useful with LAMMPS_MEMALIGN=64") - endif() - - set(INTEL_ARCH "cpu" CACHE STRING "Architectures used by USER-INTEL (cpu or knl)") - set(INTEL_ARCH_VALUES cpu knl) - set_property(CACHE INTEL_ARCH PROPERTY STRINGS ${INTEL_ARCH_VALUES}) - validate_option(INTEL_ARCH INTEL_ARCH_VALUES) - string(TOUPPER ${INTEL_ARCH} INTEL_ARCH) - - if(INTEL_ARCH STREQUAL "KNL") - set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -xHost -qopenmp -qoffload") - set(MIC_OPTIONS "-qoffload-option,mic,compiler,\"-fp-model fast=2 -mGLOB_default_function_attrs=\\\"gather_scatter_loop_unroll=4\\\"\"") - add_compile_options(-xMIC-AVX512 -qoffload -fno-alias -ansi-alias -restrict -qoverride-limits ${MIC_OPTIONS}) - add_definitions(-DLMP_INTEL_OFFLOAD) + find_package(Threads QUIET) + if(Threads_FOUND) + set(INTEL_LRT_MODE "threads" CACHE STRING "Long-range threads mode (none, threads, or c++11)") + else() + set(INTEL_LRT_MODE "none" CACHE STRING "Long-range threads mode (none, threads, or c++11)") + endif() + set(INTEL_LRT_VALUES none threads c++11) + set_property(CACHE INTEL_LRT_MODE PROPERTY STRINGS ${INTEL_LRT_VALUES}) + validate_option(INTEL_LRT_MODE INTEL_LRT_VALUES) + string(TOUPPER ${INTEL_LRT_MODE} INTEL_LRT_MODE) + if(INTEL_LRT_MODE STREQUAL "THREADS") + if(Threads_FOUND) + add_definitions(-DLMP_INTEL_USELRT) + list(APPEND LAMMPS_LINK_LIBS ${CMAKE_THREAD_LIBS_INIT}) else() + message(FATAL_ERROR "Must have working threads library for Long-range thread support") + endif() + endif() + if(INTEL_LRT_MODE STREQUAL "C++11") + add_definitions(-DLMP_INTEL_USERLRT -DLMP_INTEL_LRT11) + endif() + + if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel") + if(CMAKE_CXX_COMPILER_VERSION VERSION_LESS 16) + message(FATAL_ERROR "USER-INTEL needs at least a 2016 Intel compiler, found ${CMAKE_CXX_COMPILER_VERSION}") + endif() + else() + message(WARNING "USER-INTEL gives best performance with Intel compilers") + endif() + + find_package(TBB QUIET) + if(TBB_FOUND) + list(APPEND LAMMPS_LINK_LIBS ${TBB_MALLOC_LIBRARIES}) + else() + add_definitions(-DLMP_INTEL_NO_TBB) + if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel") + message(WARNING "USER-INTEL with Intel compilers should use TBB malloc libraries") + endif() + endif() + + find_package(MKL QUIET) + if(MKL_FOUND) + add_definitions(-DLMP_USE_MKL_RNG) + list(APPEND LAMMPS_LINK_LIBS ${MKL_LIBRARIES}) + else() + message(STATUS "Pair style dpd/intel will be faster with MKL libraries") + endif() + + if((NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows") AND (NOT ${LAMMPS_MEMALIGN} STREQUAL "64") AND (NOT ${LAMMPS_MEMALIGN} STREQUAL "128") AND (NOT ${LAMMPS_MEMALIGN} STREQUAL "256")) + message(FATAL_ERROR "USER-INTEL only supports memory alignment of 64, 128 or 256 on this platform") + endif() + + if(INTEL_ARCH STREQUAL "KNL") + if(NOT CMAKE_CXX_COMPILER_ID STREQUAL "Intel") + message(FATAL_ERROR "Must use Intel compiler with USER-INTEL for KNL architecture") + endif() + set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -xHost -qopenmp -qoffload") + set(MIC_OPTIONS "-qoffload-option,mic,compiler,\"-fp-model fast=2 -mGLOB_default_function_attrs=\\\"gather_scatter_loop_unroll=4\\\"\"") + add_compile_options(-xMIC-AVX512 -qoffload -fno-alias -ansi-alias -restrict -qoverride-limits ${MIC_OPTIONS}) + add_definitions(-DLMP_INTEL_OFFLOAD) + else() + if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel") if(CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.3 OR CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.4) set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -xCOMMON-AVX512") else() @@ -1100,33 +1162,33 @@ if(PKG_USER-INTEL) add_compile_options(${_FLAG}) endif() endforeach() + else() + add_compile_options(-O3 -ffast-math) endif() + endif() - add_definitions(-DLMP_INTEL_USELRT -DLMP_USE_MKL_RNG) + # collect sources + set(USER-INTEL_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/USER-INTEL) + set(USER-INTEL_SOURCES ${USER-INTEL_SOURCES_DIR}/fix_intel.cpp + ${USER-INTEL_SOURCES_DIR}/fix_nh_intel.cpp + ${USER-INTEL_SOURCES_DIR}/intel_buffers.cpp + ${USER-INTEL_SOURCES_DIR}/nbin_intel.cpp + ${USER-INTEL_SOURCES_DIR}/npair_intel.cpp + ${USER-INTEL_SOURCES_DIR}/verlet_lrt_intel.cpp) - list(APPEND LAMMPS_LINK_LIBS ${TBB_MALLOC_LIBRARIES} ${MKL_LIBRARIES}) + set_property(GLOBAL PROPERTY "USER-INTEL_SOURCES" "${USER-INTEL_SOURCES}") - set(USER-INTEL_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/USER-INTEL) - set(USER-INTEL_SOURCES ${USER-INTEL_SOURCES_DIR}/intel_preprocess.h - ${USER-INTEL_SOURCES_DIR}/intel_buffers.h - ${USER-INTEL_SOURCES_DIR}/intel_buffers.cpp - ${USER-INTEL_SOURCES_DIR}/math_extra_intel.h - ${USER-INTEL_SOURCES_DIR}/nbin_intel.h - ${USER-INTEL_SOURCES_DIR}/nbin_intel.cpp - ${USER-INTEL_SOURCES_DIR}/npair_intel.h - ${USER-INTEL_SOURCES_DIR}/npair_intel.cpp - ${USER-INTEL_SOURCES_DIR}/intel_simd.h - ${USER-INTEL_SOURCES_DIR}/intel_intrinsics.h) + # detect styles which have a USER-INTEL version + RegisterStylesExt(${USER-INTEL_SOURCES_DIR} intel USER-INTEL_SOURCES) + RegisterNBinStyle(${USER-INTEL_SOURCES_DIR}/nbin_intel.h) + RegisterNPairStyle(${USER-INTEL_SOURCES_DIR}/npair_intel.h) + RegisterFixStyle(${USER-INTEL_SOURCES_DIR}/fix_intel.h) + RegisterIntegrateStyle(${USER-INTEL_SOURCES_DIR}/verlet_lrt_intel.h) - set_property(GLOBAL PROPERTY "USER-INTEL_SOURCES" "${USER-INTEL_SOURCES}") + get_property(USER-INTEL_SOURCES GLOBAL PROPERTY USER-INTEL_SOURCES) - # detects styles which have USER-INTEL version - RegisterStylesExt(${USER-INTEL_SOURCES_DIR} opt USER-INTEL_SOURCES) - - get_property(USER-INTEL_SOURCES GLOBAL PROPERTY USER-INTEL_SOURCES) - - list(APPEND LIB_SOURCES ${USER-INTEL_SOURCES}) - include_directories(${USER-INTEL_SOURCES_DIR}) + list(APPEND LIB_SOURCES ${USER-INTEL_SOURCES}) + include_directories(${USER-INTEL_SOURCES_DIR}) endif() if(PKG_GPU) diff --git a/cmake/Modules/StyleHeaderUtils.cmake b/cmake/Modules/StyleHeaderUtils.cmake index a7b23b4cf1..ebaa5dae8e 100644 --- a/cmake/Modules/StyleHeaderUtils.cmake +++ b/cmake/Modules/StyleHeaderUtils.cmake @@ -91,6 +91,10 @@ function(RegisterFixStyle path) AddStyleHeader(${path} FIX) endfunction(RegisterFixStyle) +function(RegisterIntegrateStyle path) + AddStyleHeader(${path} INTEGRATE) +endfunction(RegisterIntegrateStyle) + function(RegisterStyles search_path) FindStyleHeaders(${search_path} ANGLE_CLASS angle_ ANGLE ) # angle ) # force FindStyleHeaders(${search_path} ATOM_CLASS atom_vec_ ATOM_VEC ) # atom ) # atom atom_vec_hybrid diff --git a/cmake/README.md b/cmake/README.md index 1c37ecc92e..a635f3e06d 100644 --- a/cmake/README.md +++ b/cmake/README.md @@ -155,11 +155,13 @@ make The CMake build exposes a lot of different options. In the old build system some of the package selections were possible by using special make target like -`make yes-std` or `make no-lib`. Achieving the same result with cmake requires +`make yes-std` or `make no-lib`. Achieving a similar result with cmake requires specifying all options manually. This can quickly become a very long command line that is hard to handle. While these could be stored in a simple script file, there is another way of defining "presets" to compile LAMMPS in a certain -way. +way. Since the cmake build process - contrary to the conventional build system - +includes the compilation of the bundled libraries into the standard build process, +the grouping of those presets is somewhat different. A preset is a regular CMake script file that can use constructs such as variables, lists and for-loops to manipulate configuration options and create @@ -171,10 +173,10 @@ Such a file can then be passed to cmake via the `-C` flag. Several examples of presets can be found in the `cmake/presets` folder. ```bash -# build LAMMPS with all "standard" packages which don't use libraries and enable GPU package +# build LAMMPS with all packages enabled which don't use external libraries and enable GPU package mkdir build cd build -cmake -C ../cmake/presets/std_nolib.cmake -D PKG_GPU=on ../cmake +cmake -C ../cmake/presets/all_on.cmake -C ../cmake/presets/nolib.cmake -D PKG_GPU=on ../cmake ``` # Reference @@ -1429,6 +1431,17 @@ TODO + + INTEL_LRT_MODE + How to support Long-range thread mode in Verlet integration + +
+
threads (default, if pthreads available)
+
none (default, if pthreads not available)
+
c++11
+
+ + diff --git a/cmake/presets/all_off.cmake b/cmake/presets/all_off.cmake index b434796d7c..9d03be99ec 100644 --- a/cmake/presets/all_off.cmake +++ b/cmake/presets/all_off.cmake @@ -1,21 +1,17 @@ -set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU - GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MEAM MISC - MOLECULE MPIIO MSCG OPT PERI POEMS - PYTHON QEQ REAX REPLICA RIGID SHOCK SNAP SRD VORONOI) +# preset that turns on all existing packages off. can be used to reset +# an existing package selection without losing any other settings -set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS - USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD - USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO - USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE - USER-NETCDF USER-OMP USER-PHONON USER-QMMM USER-QTB - USER-QUIP USER-REAXC USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY - USER-UEF USER-VTK) - -set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI - USER-ATC USER-AWPMD USER-COLVARS USER-H5MD USER-LB USER-MOLFILE - USER-NETCDF USER-PLUMED USER-QMMM USER-QUIP USER-SMD USER-VTK) - -set(ALL_PACKAGES ${STANDARD_PACKAGES} ${USER_PACKAGES}) +set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU + GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MISC MESSAGE MOLECULE + MPIIO MSCG OPT PERI POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN + SRD VORONOI + USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK + USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP + USER-H5MD USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO + USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP + USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP + USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH + USER-TALLY USER-UEF USER-VTK USER-YAFF) foreach(PKG ${ALL_PACKAGES}) set(PKG_${PKG} OFF CACHE BOOL "" FORCE) diff --git a/cmake/presets/all_on.cmake b/cmake/presets/all_on.cmake index 3a1100f337..2ff107975a 100644 --- a/cmake/presets/all_on.cmake +++ b/cmake/presets/all_on.cmake @@ -1,21 +1,19 @@ -set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU - GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MEAM MISC - MOLECULE MPIIO MSCG OPT PERI POEMS - PYTHON QEQ REAX REPLICA RIGID SHOCK SNAP SRD VORONOI) +# preset that turns on all existing packages. using the combination +# this preset followed by the nolib.cmake preset should configure a +# LAMMPS binary, with as many packages included, that can be compiled +# with just a working C++ compiler and an MPI library. -set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS - USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD - USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO - USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE - USER-NETCDF USER-OMP USER-PHONON USER-QMMM USER-QTB - USER-QUIP USER-REAXC USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY - USER-UEF USER-VTK) - -set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI - USER-ATC USER-AWPMD USER-COLVARS USER-H5MD USER-LB USER-MOLFILE - USER-NETCDF USER-PLUMED USER-QMMM USER-QUIP USER-SMD USER-VTK) - -set(ALL_PACKAGES ${STANDARD_PACKAGES} ${USER_PACKAGES}) +set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU + GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MISC MESSAGE MOLECULE + MPIIO MSCG OPT PERI POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN + SRD VORONOI + USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK + USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP + USER-H5MD USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO + USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP + USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP + USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH + USER-TALLY USER-UEF USER-VTK USER-YAFF) foreach(PKG ${ALL_PACKAGES}) set(PKG_${PKG} ON CACHE BOOL "" FORCE) diff --git a/cmake/presets/manual_selection.cmake b/cmake/presets/manual_selection.cmake deleted file mode 100644 index 6db41b708c..0000000000 --- a/cmake/presets/manual_selection.cmake +++ /dev/null @@ -1,71 +0,0 @@ -set(PKG_ASPHERE OFF CACHE BOOL "" FORCE) -set(PKG_BODY OFF CACHE BOOL "" FORCE) -set(PKG_CLASS2 OFF CACHE BOOL "" FORCE) -set(PKG_COLLOID OFF CACHE BOOL "" FORCE) -set(PKG_COMPRESS OFF CACHE BOOL "" FORCE) -set(PKG_CORESHELL OFF CACHE BOOL "" FORCE) -set(PKG_DIPOLE OFF CACHE BOOL "" FORCE) -set(PKG_GPU OFF CACHE BOOL "" FORCE) -set(PKG_GRANULAR OFF CACHE BOOL "" FORCE) -set(PKG_KIM OFF CACHE BOOL "" FORCE) -set(PKG_KOKKOS OFF CACHE BOOL "" FORCE) -set(PKG_KSPACE OFF CACHE BOOL "" FORCE) -set(PKG_LATTE OFF CACHE BOOL "" FORCE) -set(PKG_LIB OFF CACHE BOOL "" FORCE) -set(PKG_MANYBODY OFF CACHE BOOL "" FORCE) -set(PKG_MC OFF CACHE BOOL "" FORCE) -set(PKG_MEAM OFF CACHE BOOL "" FORCE) -set(PKG_MISC OFF CACHE BOOL "" FORCE) -set(PKG_MOLECULE OFF CACHE BOOL "" FORCE) -set(PKG_MPIIO OFF CACHE BOOL "" FORCE) -set(PKG_MSCG OFF CACHE BOOL "" FORCE) -set(PKG_OPT OFF CACHE BOOL "" FORCE) -set(PKG_PERI OFF CACHE BOOL "" FORCE) -set(PKG_POEMS OFF CACHE BOOL "" FORCE) -set(PKG_PYTHOFF OFF CACHE BOOL "" FORCE) -set(PKG_QEQ OFF CACHE BOOL "" FORCE) -set(PKG_REAX OFF CACHE BOOL "" FORCE) -set(PKG_REPLICA OFF CACHE BOOL "" FORCE) -set(PKG_RIGID OFF CACHE BOOL "" FORCE) -set(PKG_SHOCK OFF CACHE BOOL "" FORCE) -set(PKG_SNAP OFF CACHE BOOL "" FORCE) -set(PKG_SRD OFF CACHE BOOL "" FORCE) -set(PKG_VOROFFOI OFF CACHE BOOL "" FORCE) - -set(PKG_USER OFF CACHE BOOL "" FORCE) -set(PKG_USER-ATC OFF CACHE BOOL "" FORCE) -set(PKG_USER-AWPMD OFF CACHE BOOL "" FORCE) -set(PKG_USER-BOCS OFF CACHE BOOL "" FORCE) -set(PKG_USER-CGDNA OFF CACHE BOOL "" FORCE) -set(PKG_USER-CGSDK OFF CACHE BOOL "" FORCE) -set(PKG_USER-COLVARS OFF CACHE BOOL "" FORCE) -set(PKG_USER-DIFFRACTIOFF OFF CACHE BOOL "" FORCE) -set(PKG_USER-DPD OFF CACHE BOOL "" FORCE) -set(PKG_USER-DRUDE OFF CACHE BOOL "" FORCE) -set(PKG_USER-EFF OFF CACHE BOOL "" FORCE) -set(PKG_USER-FEP OFF CACHE BOOL "" FORCE) -set(PKG_USER-H5MD OFF CACHE BOOL "" FORCE) -set(PKG_USER-INTEL OFF CACHE BOOL "" FORCE) -set(PKG_USER-LB OFF CACHE BOOL "" FORCE) -set(PKG_USER-MANIFOLD OFF CACHE BOOL "" FORCE) -set(PKG_USER-MEAMC OFF CACHE BOOL "" FORCE) -set(PKG_USER-MESO OFF CACHE BOOL "" FORCE) -set(PKG_USER-MGPT OFF CACHE BOOL "" FORCE) -set(PKG_USER-MISC OFF CACHE BOOL "" FORCE) -set(PKG_USER-MOFFF OFF CACHE BOOL "" FORCE) -set(PKG_USER-MOLFILE OFF CACHE BOOL "" FORCE) -set(PKG_USER-NETCDF OFF CACHE BOOL "" FORCE) -set(PKG_USER-OMP OFF CACHE BOOL "" FORCE) -set(PKG_USER-PHONON OFF CACHE BOOL "" FORCE) -set(PKG_USER-PLUMED OFF CACHE BOOL "" FORCE) -set(PKG_USER-QMMM OFF CACHE BOOL "" FORCE) -set(PKG_USER-QTB OFF CACHE BOOL "" FORCE) -set(PKG_USER-QUIP OFF CACHE BOOL "" FORCE) -set(PKG_USER-REAXC OFF CACHE BOOL "" FORCE) -set(PKG_USER-SDPD OFF CACHE BOOL "" FORCE) -set(PKG_USER-SMD OFF CACHE BOOL "" FORCE) -set(PKG_USER-SMTBQ OFF CACHE BOOL "" FORCE) -set(PKG_USER-SPH OFF CACHE BOOL "" FORCE) -set(PKG_USER-TALLY OFF CACHE BOOL "" FORCE) -set(PKG_USER-UEF OFF CACHE BOOL "" FORCE) -set(PKG_USER-VTK OFF CACHE BOOL "" FORCE) diff --git a/cmake/presets/mingw-cross.cmake b/cmake/presets/mingw-cross.cmake new file mode 100644 index 0000000000..b53e5a7b93 --- /dev/null +++ b/cmake/presets/mingw-cross.cmake @@ -0,0 +1,17 @@ +set(WIN_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU + GRANULAR KSPACE MANYBODY MC MISC MOLECULE OPT PERI POEMS QEQ + REPLICA RIGID SHOCK SNAP SPIN SRD VORONOI USER-ATC USER-AWPMD + USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS USER-DIFFRACTION + USER-DPD USER-DRUDE USER-EFF USER-FEP USER-INTEL USER-MANIFOLD + USER-MEAMC USER-MESO USER-MISC USER-MOFFF USER-MOLFILE USER-OMP + USER-PHONON USER-PTM USER-QTB USER-REAXC USER-SDPD USER-SMD + USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-YAFF) + +foreach(PKG ${WIN_PACKAGES}) + set(PKG_${PKG} ON CACHE BOOL "" FORCE) +endforeach() + +set(DOWNLOAD_VORO ON CACHE BOOL "" FORCE) +set(DOWNLOAD_EIGEN3 ON CACHE BOOL "" FORCE) +set(LAMMPS_MEMALIGN "0" CACHE STRING "" FORCE) +set(INTEL_LRT_MODE "none" CACHE STRING "" FORCE) diff --git a/cmake/presets/minimal.cmake b/cmake/presets/minimal.cmake new file mode 100644 index 0000000000..e9ce6d6103 --- /dev/null +++ b/cmake/presets/minimal.cmake @@ -0,0 +1,8 @@ +# preset that turns on just a few, frequently used packages +# this will be compiled quickly and handle a lot of common inputs. + +set(ALL_PACKAGES KSPACE MANYBODY MOLECULE RIGID) + +foreach(PKG ${ALL_PACKAGES}) + set(PKG_${PKG} ON CACHE BOOL "" FORCE) +endforeach() diff --git a/cmake/presets/most.cmake b/cmake/presets/most.cmake new file mode 100644 index 0000000000..35ad7ba55c --- /dev/null +++ b/cmake/presets/most.cmake @@ -0,0 +1,15 @@ +# preset that turns on a wide range of packages, some of which require +# external libraries. Compared to all_on.cmake some more unusual packages +# are removed. The resulting binary should be able to run most inputs. + +set(ALL_PACKAGES ASPHERE CLASS2 COLLOID CORESHELL DIPOLE + GRANULAR KSPACE MANYBODY MC MISC MOLECULE OPT PERI + PYTHON QEQ REPLICA RIGID SHOCK SRD VORONOI + USER-CGDNA USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD + USER-DRUDE USER-FEP USER-MEAMC USER-MESO + USER-MISC USER-MOFFF USER-OMP USER-PLUMED USER-PHONON USER-REAXC + USER-SPH USER-SMD USER-UEF USER-YAFF) + +foreach(PKG ${ALL_PACKAGES}) + set(PKG_${PKG} ON CACHE BOOL "" FORCE) +endforeach() diff --git a/cmake/presets/nolib.cmake b/cmake/presets/nolib.cmake index 4c02fb6210..c0968a8d82 100644 --- a/cmake/presets/nolib.cmake +++ b/cmake/presets/nolib.cmake @@ -1,21 +1,10 @@ -set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU - GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MEAM MISC - MOLECULE MPIIO MSCG OPT PERI POEMS - PYTHON QEQ REAX REPLICA RIGID SHOCK SNAP SRD VORONOI) +# preset that turns off all packages that require some form of external +# library or special compiler (fortran or cuda) or equivalent. -set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS - USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD - USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO - USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE - USER-NETCDF USER-OMP USER-PHONON USER-QMMM USER-QTB - USER-QUIP USER-REAXC USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY - USER-UEF USER-VTK) - -set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI - USER-ATC USER-AWPMD USER-COLVARS USER-H5MD USER-LB USER-MOLFILE - USER-NETCDF USER-PLUMED USER-QMMM USER-QUIP USER-SMD USER-VTK) - -set(ALL_PACKAGES ${STANDARD_PACKAGES} ${USER_PACKAGES}) +set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MPIIO MSCG PYTHON + VORONOI USER-ADIOS USER-ATC USER-AWPMD USER-H5MD USER-LB + USER-MOLFILE USER-NETCDF USER-PLUMED USER-QMMM USER-QUIP + USER-SCAFACOS USER-SMD USER-VTK) foreach(PKG ${PACKAGES_WITH_LIB}) set(PKG_${PKG} OFF CACHE BOOL "" FORCE) diff --git a/cmake/presets/std.cmake b/cmake/presets/std.cmake deleted file mode 100644 index 4176aba44e..0000000000 --- a/cmake/presets/std.cmake +++ /dev/null @@ -1,22 +0,0 @@ -set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU - GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MEAM MISC - MOLECULE MPIIO MSCG OPT PERI POEMS - PYTHON QEQ REAX REPLICA RIGID SHOCK SNAP SRD VORONOI) - -set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS - USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD - USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO - USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE - USER-NETCDF USER-OMP USER-PHONON USER-QMMM USER-QTB - USER-QUIP USER-REAXC USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY - USER-UEF USER-VTK) - -set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI - USER-ATC USER-AWPMD USER-COLVARS USER-H5MD USER-LB USER-MOLFILE - USER-NETCDF USER-QMMM USER-QUIP USER-SMD USER-VTK) - -set(ALL_PACKAGES ${STANDARD_PACKAGES} ${USER_PACKAGES}) - -foreach(PKG ${STANDARD_PACKAGES}) - set(PKG_${PKG} ON CACHE BOOL "" FORCE) -endforeach() diff --git a/cmake/presets/std_nolib.cmake b/cmake/presets/std_nolib.cmake deleted file mode 100644 index aa067f2ba0..0000000000 --- a/cmake/presets/std_nolib.cmake +++ /dev/null @@ -1,26 +0,0 @@ -set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU - GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MEAM MISC - MOLECULE MPIIO MSCG OPT PERI POEMS - PYTHON QEQ REAX REPLICA RIGID SHOCK SNAP SRD VORONOI) - -set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS - USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD - USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO - USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE - USER-NETCDF USER-OMP USER-PHONON USER-QMMM USER-QTB - USER-QUIP USER-REAXC USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY - USER-UEF USER-VTK) - -set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI - USER-ATC USER-AWPMD USER-COLVARS USER-H5MD USER-LB USER-MOLFILE - USER-NETCDF USER-QMMM USER-QUIP USER-SMD USER-VTK) - -set(ALL_PACKAGES ${STANDARD_PACKAGES} ${USER_PACKAGES}) - -foreach(PKG ${STANDARD_PACKAGES}) - set(PKG_${PKG} ON CACHE BOOL "" FORCE) -endforeach() - -foreach(PKG ${PACKAGES_WITH_LIB}) - set(PKG_${PKG} OFF CACHE BOOL "" FORCE) -endforeach() diff --git a/cmake/presets/user.cmake b/cmake/presets/user.cmake deleted file mode 100644 index af606203e9..0000000000 --- a/cmake/presets/user.cmake +++ /dev/null @@ -1,22 +0,0 @@ -set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU - GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MEAM MISC - MOLECULE MPIIO MSCG OPT PERI POEMS - PYTHON QEQ REAX REPLICA RIGID SHOCK SNAP SRD VORONOI) - -set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS - USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD - USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO - USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE - USER-NETCDF USER-OMP USER-PHONON USER-QMMM USER-QTB - USER-QUIP USER-REAXC USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY - USER-UEF USER-VTK) - -set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI - USER-ATC USER-AWPMD USER-COLVARS USER-H5MD USER-LB USER-MOLFILE - USER-NETCDF USER-PLUMED USER-QMMM USER-QUIP USER-SMD USER-VTK) - -set(ALL_PACKAGES ${STANDARD_PACKAGES} ${USER_PACKAGES}) - -foreach(PKG ${USER_PACKAGES}) - set(PKG_${PKG} ON CACHE BOOL "" FORCE) -endforeach() diff --git a/doc/src/Build_cmake.txt b/doc/src/Build_cmake.txt index 5c29e11280..265c16e3d4 100644 --- a/doc/src/Build_cmake.txt +++ b/doc/src/Build_cmake.txt @@ -28,7 +28,7 @@ Makefile(s). Example: cd lammps # change to the LAMMPS distribution directory mkdir build; cd build # create a new directory (folder) for build -cmake ../cmake \[options ...\] # configuration with (command-line) cmake +cmake \[options ...\] ../cmake # configuration with (command-line) cmake make # compilation :pre The cmake command will detect available features, enable selected @@ -41,7 +41,8 @@ If your machine has multiple CPU cores (most do these days), using a command like "make -jN" (with N being the number of available local CPU cores) can be much faster. If you plan to do development on LAMMPS or need to re-compile LAMMPS repeatedly, installation of the -ccache (= Compiler Cache) software may speed up compilation even more. +ccache (= Compiler Cache) software may speed up repeated compilation +even more. After compilation, you can optionally copy the LAMMPS executable and library into your system folders (by default under $HOME/.local) with: @@ -108,7 +109,8 @@ command-line options. Several useful ones are: -D CMAKE_BUILD_TYPE=type # type = Release or Debug -G output # style of output CMake generates -DVARIABLE=value # setting for a LAMMPS feature to enable --D VARIABLE=value # ditto, but cannot come after CMakeLists.txt dir :pre +-D VARIABLE=value # ditto, but cannot come after CMakeLists.txt dir +-C path/to/preset/file # load some CMake settings before configuring :pre All the LAMMPS-specific -D variables that a LAMMPS build supports are described on the pages linked to from the "Build"_Build.html doc page. diff --git a/doc/src/Build_extras.txt b/doc/src/Build_extras.txt index 2aa304faff..17d18243f2 100644 --- a/doc/src/Build_extras.txt +++ b/doc/src/Build_extras.txt @@ -859,23 +859,34 @@ file. USER-INTEL package :h4,link(user-intel) To build with this package, you must choose which hardware you want to -build for, either Intel CPUs or Intel KNLs. You should also typically -"install the USER-OMP package"_#user-omp, as it can be used in tandem -with the USER-INTEL package to good effect, as explained on the "Speed -intel"_Speed_intel.html doc page. +build for, either x86 CPUs or Intel KNLs in offload mode. You should +also typically "install the USER-OMP package"_#user-omp, as it can be +used in tandem with the USER-INTEL package to good effect, as explained +on the "Speed intel"_Speed_intel.html doc page. [CMake build]: -D INTEL_ARCH=value # value = cpu (default) or knl --D BUILD_OMP=yes # also required to build with the USER-INTEl package :pre +-D INTEL_LRT_MODE=value # value = threads, none, or c++11 :pre -Requires an Intel compiler as well as the Intel TBB and MKL libraries. +In Long-range thread mode (LRT) a modified verlet style is used, that +operates the Kspace calculation in a separate thread concurrently to +other calculations. This has to be enabled in the "package intel"_package.html +command at runtime. With the setting "threads" it used the pthreads +library, while c++11 will use the built-in thread support of C++11 +compilers. The option "none" skips compilation of this feature. The +default is to use "threads" if pthreads is available and otherwise "none". + +Best performance is achieved with Intel hardware, Intel compilers, as well as +the Intel TBB and MKL libraries. However, the code also compiles, links, and +runs with other compilers and without TBB and MKL. [Traditional make]: Choose which hardware to compile for in Makefile.machine via the following settings. See src/MAKE/OPTIONS/Makefile.intel_cpu* and -Makefile.knl files for examples. +Makefile.knl files for examples. and src/USER-INTEL/README for +additional information. For CPUs: diff --git a/doc/src/Build_package.txt b/doc/src/Build_package.txt index c5eca96edb..e37936e052 100644 --- a/doc/src/Build_package.txt +++ b/doc/src/Build_package.txt @@ -149,26 +149,39 @@ system. Using these files you can enable/disable portions of the available packages in LAMMPS. If you need a custom preset you can take one of them as a starting point and customize it to your needs. -cmake -C ../cmake/presets/all_on.cmake \[OPTIONS\] ../cmake | enable all packages -cmake -C ../cmake/presets/all_off.cmake \[OPTIONS\] ../cmake | disable all packages -cmake -C ../cmake/presets/std.cmake \[OPTIONS\] ../cmake | enable standard packages -cmake -C ../cmake/presets/user.cmake \[OPTIONS\] ../cmake | enable user packages -cmake -C ../cmake/presets/std_nolib.cmake \[OPTIONS\] ../cmake | enable standard packages that do not require extra libraries -cmake -C ../cmake/presets/nolib.cmake \[OPTIONS\] ../cmake | disable all packages that do not require extra libraries -cmake -C ../cmake/presets/manual_selection.cmake \[OPTIONS\] ../cmake | example of how to create a manual selection of packages :tb(s=|,a=l) +cmake -C ../cmake/presets/all_on.cmake \[OPTIONS\] ../cmake | + enable all packages | +cmake -C ../cmake/presets/all_off.cmake \[OPTIONS\] ../cmake | + disable all packages | +cmake -C ../cmake/presets/minimal.cmake \[OPTIONS\] ../cmake | + enable just a few core packages | +cmake -C ../cmake/presets/most.cmake \[OPTIONS\] ../cmake | + enable most common packages | +cmake -C ../cmake/presets/nolib.cmake \[OPTIONS\] ../cmake | + disable packages that do require extra libraries or tools | +cmake -C ../cmake/presets/mingw.cmake \[OPTIONS\] ../cmake | + enable all packages compatible with MinGW compilers :tb(c=2,s=|,a=l) NOTE: Running cmake this way manipulates the variable cache in your -current build directory. You can combine presets and options with -multiple cmake runs. +current build directory. You can combine multiple presets and options +in a single cmake run, or change settings incrementally by running +cmake with new flags. [Example:] -# build LAMMPS with all "standard" packages which don't -# use libraries and enable GPU package +# build LAMMPS with most commonly used packages, but then remove +# those requiring additional library or tools, but still enable +# GPU package and configure it for using CUDA. You can run. mkdir build cd build -cmake -C ../cmake/presets/std_nolib.cmake -D PKG_GPU=on ../cmake :pre +cmake -C ../cmake/presets/most.cmake -C ../cmake/presets/nolib.cmake -D PKG_GPU=on -D GPU_API=cuda ../cmake :pre +# to add another package, say BODY to the previous configuration you can run: +cmake -D PKG_BODY=on . :pre + +# to reset the package selection from above to the default of no packages +# but leaving all other settings untouched. You can run: +cmake -C ../cmake/presets/no_all.cmake . :pre :line [Make shortcuts for installing many packages]: diff --git a/doc/src/Build_settings.txt b/doc/src/Build_settings.txt index f1db9f0130..287cd39ff6 100644 --- a/doc/src/Build_settings.txt +++ b/doc/src/Build_settings.txt @@ -57,10 +57,10 @@ FFT_INC = -DFFT_SINGLE # do not specify for double precision FFT_INC = -DFFT_PACK_ARRAY # or -DFFT_PACK_POINTER or -DFFT_PACK_MEMCPY :pre # default is FFT_PACK_ARRAY if not specified -FFT_INC = -I/usr/local/include +FFT_INC = -I/usr/local/include FFT_PATH = -L/usr/local/lib -FFT_LIB = -lfftw3 # FFTW3 double precision -FFT_LIB = -lfftw3 -lfftw3f # FFTW3 single precision +FFT_LIB = -lfftw3 # FFTW3 double precision +FFT_LIB = -lfftw3 -lfftw3f # FFTW3 single precision FFT_LIB = -lmkl_intel_lp64 -lmkl_sequential -lmkl_core # MKL with Intel compiler FFT_LIB = -lmkl_gf_lp64 -lmkl_sequential -lmkl_core # MKL with GNU compier :pre @@ -179,8 +179,11 @@ e.g. from 511 to -512, which can cause diagnostics like the mean-squared displacement, as calculated by the "compute msd"_compute_msd.html command, to be faulty. -Note that the USER-ATC package is not currently compatible with the -"bigbig" setting. +Note that the USER-ATC package and the USER-INTEL package are currently +not compatible with the "bigbig" setting. Also, there are limitations +when using the library interface. Some functions with known issues +have been replaced by dummy calls printing a corresponding error rather +than crashing randomly or corrupting data. Also note that the GPU package requires its lib/gpu library to be compiled with the same size setting, or the link will fail. A CMake diff --git a/doc/src/Build_windows.txt b/doc/src/Build_windows.txt index bf1ec265a1..b3dbf775c9 100644 --- a/doc/src/Build_windows.txt +++ b/doc/src/Build_windows.txt @@ -51,11 +51,10 @@ provides a unix/linux interface to low-level Windows functions, so LAMMPS can be compiled on Windows. The necessary (minor) modifications to LAMMPS are included, but may not always up-to-date for recently added functionality and the corresponding new code. A machine makefile for using cygwin for -the old build system is provided. The CMake build system is untested -for this; you will have to request that makefiles are generated and -manually set the compiler. +the old build system is provided. Using CMake for this mode of compilation +is untested and not likely to work. -When compiling for Windows [not] set the -DLAMMPS_MEMALIGN define +When compiling for Windows do [not] set the -DLAMMPS_MEMALIGN define in the LMP_INC makefile variable and add -lwsock32 -lpsapi to the linker flags in LIB makefile variable. Try adding -static-libgcc or -static or both to the linker flags when your resulting LAMMPS Windows executable @@ -79,7 +78,13 @@ probably the currently best tested and supported way to build LAMMPS executables for Windows. There are makefiles provided for the traditional build system, but CMake has also been successfully tested using the mingw32-cmake and mingw64-cmake wrappers that are bundled -with the cross-compiler environment on Fedora machines. +with the cross-compiler environment on Fedora machines. A CMake preset +selecting all packages compatible with this cross-compilation build +is provided. You likely need to disable the GPU package unless you +download and install the contents of the pre-compiled "OpenCL ICD loader +library"_https://download.lammps.org/thirdparty/opencl-win-devel.tar.gz +into your MinGW64 cross-compiler environment. The cross-compilation +currently will only produce non-MPI serial binaries. Please keep in mind, though, that this only applies to compiling LAMMPS. Whether the resulting binaries do work correctly is no tested by the diff --git a/doc/src/Commands_pair.txt b/doc/src/Commands_pair.txt index b18d852c09..e887f0178a 100644 --- a/doc/src/Commands_pair.txt +++ b/doc/src/Commands_pair.txt @@ -98,6 +98,7 @@ OPT. "gran/hertz/history (o)"_pair_gran.html, "gran/hooke (o)"_pair_gran.html, "gran/hooke/history (ko)"_pair_gran.html, +"granular"_pair_granular.html, "gw"_pair_gw.html, "gw/zbl"_pair_gw.html, "hbond/dreiding/lj (o)"_pair_hbond_dreiding.html, diff --git a/doc/src/Howto_library.txt b/doc/src/Howto_library.txt index 40a8bf0a70..ba009cfad9 100644 --- a/doc/src/Howto_library.txt +++ b/doc/src/Howto_library.txt @@ -166,9 +166,6 @@ void lammps_gather_atoms_subset(void *, char *, int, int, int, int *, void *) void lammps_scatter_atoms(void *, char *, int, int, void *) void lammps_scatter_atoms_subset(void *, char *, int, int, int, int *, void *) :pre -void lammps_create_atoms(void *, int, tagint *, int *, double *, double *, - imageint *, int) :pre - The gather functions collect peratom info of the requested type (atom coords, atom types, forces, etc) from all processors, and returns the same vector of values to each calling processor. The scatter @@ -176,6 +173,11 @@ functions do the inverse. They distribute a vector of peratom values, passed by all calling processors, to individual atoms, which may be owned by different processors. +IMPORTANT NOTE: These functions are not compatible with the +-DLAMMPS_BIGBIG setting when compiling LAMMPS. Dummy functions +that result in an error message and abort will be substituted +instead of resulting in random crashes and memory corruption. + The lammps_gather_atoms() function does this for all N atoms in the system, ordered by atom ID, from 1 to N. The lammps_gather_atoms_concat() function does it for all N atoms, but @@ -196,6 +198,9 @@ those values to each atom in the system. The lammps_scatter_atoms_subset() function takes a subset of IDs as an argument and only scatters those values to the owning atoms. +void lammps_create_atoms(void *, int, tagint *, int *, double *, double *, + imageint *, int) :pre + The lammps_create_atoms() function takes a list of N atoms as input with atom types and coords (required), an optionally atom IDs and velocities and image flags. It uses the coords of each atom to assign diff --git a/doc/src/Speed_intel.txt b/doc/src/Speed_intel.txt index dc38cb0956..2688b43e6f 100644 --- a/doc/src/Speed_intel.txt +++ b/doc/src/Speed_intel.txt @@ -24,7 +24,7 @@ LAMMPS to run on the CPU cores and co-processor cores simultaneously. Angle Styles: charmm, harmonic :ulb,l Bond Styles: fene, fourier, harmonic :l -Dihedral Styles: charmm, harmonic, opls :l +Dihedral Styles: charmm, fourier, harmonic, opls :l Fixes: nve, npt, nvt, nvt/sllod, nve/asphere :l Improper Styles: cvff, harmonic :l Pair Styles: airebo, airebo/morse, buck/coul/cut, buck/coul/long, diff --git a/doc/src/kim_query.txt b/doc/src/kim_query.txt index be46783d82..c581de0ebb 100644 --- a/doc/src/kim_query.txt +++ b/doc/src/kim_query.txt @@ -26,12 +26,13 @@ kim_query latconst get_test_result test=TE_156715955670 model=MO_800509458712 & The kim_query command allows to retrieve properties from the OpenKIM through a web query. The result is stored in a string style "variable"_variable.html, the name of which must be given as the first -argument of the kim_query command. The second required argument is the -name of the actual query function (e.g. {get_test_result}). All following +argument of the kim_query command. The second required argument is the +name of the actual query function (e.g. {get_test_result}). All following arguments are parameters handed over to the web query in the format -{keyword=value}. This list of supported keywords and the type of how -the value has to be encoded depends on the query function used. -For more details on this, please refer to the OpenKIM homepage. +{keyword=value}. The list of supported keywords and the type of how +the value has to be encoded depends on the query function used. This +mirrors the functionality available on the OpenKIM webpage at +"https://query.openkim.org"_https://query.openkim.org/ [Restrictions:] diff --git a/doc/src/pair_granular.txt b/doc/src/pair_granular.txt index e4b9bb3250..d287123246 100644 --- a/doc/src/pair_granular.txt +++ b/doc/src/pair_granular.txt @@ -19,7 +19,7 @@ pair_style granular command :h3 pair_style granular cutoff :pre -cutoff = global cutoff (optional). See discussion below. :l +cutoff = global cutoff (optional). See discussion below. :ul [Examples:] diff --git a/doc/src/velocity.txt b/doc/src/velocity.txt index 96d3fa6dc4..decdf2a923 100644 --- a/doc/src/velocity.txt +++ b/doc/src/velocity.txt @@ -134,7 +134,7 @@ The {mom} and {rot} keywords are used by {create}. If mom = yes, the linear momentum of the newly created ensemble of velocities is zeroed; if rot = yes, the angular momentum is zeroed. -*line +:line If specified, the {temp} keyword is used by {create} and {scale} to specify a "compute"_compute.html that calculates temperature in a diff --git a/examples/micelle/in.micelle b/examples/micelle/in.micelle index 2abdd18734..34bc9ad359 100644 --- a/examples/micelle/in.micelle +++ b/examples/micelle/in.micelle @@ -58,7 +58,7 @@ pair_coeff 1 4 1.0 1.0 1.12246 pair_coeff 2 3 1.0 0.88 1.12246 pair_coeff 2 4 1.0 0.75 1.12246 -thermo 1000 +thermo 50 #dump 1 all atom 2000 dump.micelle @@ -69,4 +69,4 @@ thermo 1000 #dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 reset_timestep 0 -run 60000 +run 1000 diff --git a/examples/micelle/in.micelle-rigid b/examples/micelle/in.micelle-rigid new file mode 100644 index 0000000000..93cb2655f8 --- /dev/null +++ b/examples/micelle/in.micelle-rigid @@ -0,0 +1,87 @@ +# 2d micelle simulation + +dimension 2 + +neighbor 0.3 bin +neigh_modify delay 5 + +atom_style bond + +# Soft potential push-off + +read_data data.micelle +special_bonds fene + +pair_style soft 1.12246 +pair_coeff * * 0.0 1.12246 + +bond_style harmonic +bond_coeff 1 50.0 0.75 + +velocity all create 0.45 2349852 + +variable prefactor equal ramp(1.0,20.0) + +fix 1 all nve +fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0 +fix 3 all adapt 1 pair soft a * * v_prefactor +fix 4 all enforce2d + +thermo 50 +run 500 + +unfix 3 + +# Main run + +pair_style lj/cut 2.5 + +# solvent/head - full-size and long-range + +pair_coeff 1 1 1.0 1.0 2.5 +pair_coeff 2 2 1.0 1.0 2.5 +pair_coeff 1 2 1.0 1.0 2.5 + +# tail/tail - size-averaged and long-range + +pair_coeff 3 3 1.0 0.75 2.5 +pair_coeff 4 4 1.0 0.50 2.5 +pair_coeff 3 4 1.0 0.67 2.5 + +# solvent/tail - full-size and repulsive + +pair_coeff 1 3 1.0 1.0 1.12246 +pair_coeff 1 4 1.0 1.0 1.12246 + +# head/tail - size-averaged and repulsive + +pair_coeff 2 3 1.0 0.88 1.12246 +pair_coeff 2 4 1.0 0.75 1.12246 + +thermo 50 + +#dump 1 all atom 2000 dump.micelle + +#dump 2 all image 2000 image.*.jpg type type zoom 1.6 +#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 + +#dump 3 all movie 2000 movie.mpg type type zoom 1.6 +#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 + +reset_timestep 0 +group solvent molecule 0 +group solute subtract all solvent +unfix 1 +unfix 2 +unfix 4 +fix 1 solvent nve +fix 2 solvent temp/rescale 100 0.45 0.45 0.02 1.0 +fix 5 solute rigid molecule langevin 0.45 0.45 0.5 112211 +fix 4 all enforce2d +run 500 +unfix 2 +unfix 4 +unfix 5 +fix 5 solute rigid/small molecule +fix 4 all enforce2d +run 500 diff --git a/examples/micelle/log.28Feb2019.micelle.g++.1 b/examples/micelle/log.28Feb2019.micelle.g++.1 deleted file mode 100644 index c2bbc7cde4..0000000000 --- a/examples/micelle/log.28Feb2019.micelle.g++.1 +++ /dev/null @@ -1,259 +0,0 @@ -LAMMPS (28 Feb 2019) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88) - using 1 OpenMP thread(s) per MPI task -# 2d micelle simulation - -dimension 2 - -neighbor 0.3 bin -neigh_modify delay 5 - -atom_style bond - -# Soft potential push-off - -read_data data.micelle - orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 1200 atoms - scanning bonds ... - 1 = max bonds/atom - reading bonds ... - 300 bonds - 2 = max # of 1-2 neighbors - 1 = max # of 1-3 neighbors - 1 = max # of 1-4 neighbors - 2 = max # of special neighbors - special bonds CPU = 0.000394821 secs - read_data CPU = 0.00212336 secs -special_bonds fene - 2 = max # of 1-2 neighbors - 2 = max # of special neighbors - special bonds CPU = 0.00018549 secs - -pair_style soft 1.12246 -pair_coeff * * 0.0 1.12246 - -bond_style harmonic -bond_coeff 1 50.0 0.75 - -velocity all create 0.45 2349852 - -variable prefactor equal ramp(1.0,20.0) - -fix 1 all nve -fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0 -fix 3 all adapt 1 pair soft a * * v_prefactor -fix 4 all enforce2d - -thermo 50 -run 1000 -Neighbor list info ... - update every 1 steps, delay 5 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 1.42246 - ghost atom cutoff = 1.42246 - binsize = 0.71123, bins = 51 51 1 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair soft, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/2d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.799 | 3.799 | 3.799 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518 - 50 0.47411013 0.67721272 0.057404514 1.2083323 1.3375852 - 100 0.45 0.73046745 0.054836584 1.234929 2.3196516 - 150 0.67521742 0.72402001 0.043490075 1.4421648 2.8744416 - 200 0.45 0.78481891 0.076931503 1.3113754 3.0412388 - 250 0.66479018 0.69790602 0.081075564 1.4432178 3.6917024 - 300 0.45 0.76820218 0.066727591 1.2845548 3.7861054 - 350 0.67619136 0.625715 0.072722727 1.3740656 4.2861621 - 400 0.45 0.68527759 0.090724527 1.2256271 4.4725214 - 450 0.56702844 0.64402767 0.080555563 1.2911391 4.7402211 - 500 0.45 0.64883009 0.078376672 1.1768318 4.7919294 - 550 0.564664 0.58260368 0.080779475 1.2275766 4.9855705 - 600 0.45 0.58193041 0.088386617 1.119942 5.131481 - 650 0.52110993 0.5415273 0.097683746 1.1598867 5.2500294 - 700 0.45 0.50856787 0.088471208 1.0466641 5.2550165 - 750 0.51510855 0.47441291 0.089429375 1.0785216 5.375763 - 800 0.45 0.49926696 0.085958476 1.0348504 5.4665914 - 850 0.50688494 0.46614429 0.088962292 1.0615691 5.556932 - 900 0.45 0.47785593 0.10150857 1.0289895 5.7765975 - 950 0.49590559 0.46050477 0.096404887 1.052402 5.8649245 - 1000 0.45 0.47691182 0.08808163 1.0146185 6.0177568 -Loop time of 0.113919 on 1 procs for 1000 steps with 1200 atoms - -Performance: 3792167.464 tau/day, 8778.165 timesteps/s -99.8% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.076825 | 0.076825 | 0.076825 | 0.0 | 67.44 -Bond | 0.0041864 | 0.0041864 | 0.0041864 | 0.0 | 3.67 -Neigh | 0.017061 | 0.017061 | 0.017061 | 0.0 | 14.98 -Comm | 0.0019042 | 0.0019042 | 0.0019042 | 0.0 | 1.67 -Output | 0.00017285 | 0.00017285 | 0.00017285 | 0.0 | 0.15 -Modify | 0.011218 | 0.011218 | 0.011218 | 0.0 | 9.85 -Other | | 0.002551 | | | 2.24 - -Nlocal: 1200 ave 1200 max 1200 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 195 ave 195 max 195 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 3136 ave 3136 max 3136 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 3136 -Ave neighs/atom = 2.61333 -Ave special neighs/atom = 0.5 -Neighbor list builds = 92 -Dangerous builds = 0 - -unfix 3 - -# Main run - -pair_style lj/cut 2.5 - -# solvent/head - full-size and long-range - -pair_coeff 1 1 1.0 1.0 2.5 -pair_coeff 2 2 1.0 1.0 2.5 -pair_coeff 1 2 1.0 1.0 2.5 - -# tail/tail - size-averaged and long-range - -pair_coeff 3 3 1.0 0.75 2.5 -pair_coeff 4 4 1.0 0.50 2.5 -pair_coeff 3 4 1.0 0.67 2.5 - -# solvent/tail - full-size and repulsive - -pair_coeff 1 3 1.0 1.0 1.12246 -pair_coeff 1 4 1.0 1.0 1.12246 - -# head/tail - size-averaged and repulsive - -pair_coeff 2 3 1.0 0.88 1.12246 -pair_coeff 2 4 1.0 0.75 1.12246 - -thermo 1000 - -#dump 1 all atom 2000 dump.micelle - -#dump 2 all image 2000 image.*.jpg type type zoom 1.6 -#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 - -#dump 3 all movie 2000 movie.mpg type type zoom 1.6 -#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 - -reset_timestep 0 -run 60000 -Neighbor list info ... - update every 1 steps, delay 5 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 26 26 1 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/2d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 4.024 | 4.024 | 4.024 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0.45 -1.7056163 0.08808163 -1.1679097 3.9431686 - 1000 0.45 -1.9727644 0.05860769 -1.4645317 1.9982326 - 2000 0.46143408 -1.9889684 0.058103225 -1.4698156 1.7806269 - 3000 0.44459291 -1.9997961 0.068724164 -1.4868496 1.4369618 - 4000 0.46939549 -2.0330437 0.073499424 -1.4905399 1.3780016 - 5000 0.44411088 -2.0339936 0.05862049 -1.5316323 1.2544164 - 6000 0.44034597 -2.0265475 0.066481992 -1.5200864 1.2362891 - 7000 0.45097378 -2.0331083 0.058467565 -1.5240428 1.2762333 - 8000 0.45797632 -2.0330255 0.060048036 -1.5153828 1.3862396 - 9000 0.45297811 -2.0383417 0.067056519 -1.5186845 1.2762554 - 10000 0.45 -2.0628269 0.065650067 -1.5475518 1.0566213 - 11000 0.44466757 -2.0593977 0.06190999 -1.5531907 1.1452469 - 12000 0.46743534 -2.0684295 0.061056278 -1.5403274 1.0824225 - 13000 0.45601091 -2.0689708 0.054868536 -1.5584713 0.96703283 - 14000 0.44111882 -2.0553174 0.058249816 -1.5563164 1.0986427 - 15000 0.43894405 -2.0866829 0.064117804 -1.5839869 0.90031836 - 16000 0.43856814 -2.0879319 0.056024166 -1.593705 0.96387323 - 17000 0.45977841 -2.103188 0.058097306 -1.5856955 0.83352919 - 18000 0.43423341 -2.0813151 0.066623991 -1.5808196 0.98157638 - 19000 0.44245939 -2.0851261 0.057637655 -1.5853978 0.84228341 - 20000 0.43144678 -2.0895403 0.06536727 -1.5930858 0.88177768 - 21000 0.45014968 -2.106686 0.059137572 -1.5977739 0.89408935 - 22000 0.4575126 -2.1024115 0.063013023 -1.5822672 0.84886734 - 23000 0.45 -2.10897 0.06724784 -1.5920971 0.66205013 - 24000 0.43055602 -2.0894725 0.061566464 -1.5977089 0.81764789 - 25000 0.4366384 -2.0926743 0.059609321 -1.5967905 0.85549875 - 26000 0.4521714 -2.0963996 0.062031863 -1.5825731 0.80137118 - 27000 0.45734834 -2.1060987 0.061712636 -1.5874188 0.82899415 - 28000 0.44803467 -2.0859226 0.061871856 -1.5763894 0.97007526 - 29000 0.45 -2.1106243 0.063825481 -1.5971738 0.63798376 - 30000 0.44932806 -2.1006036 0.053053934 -1.598596 0.63907113 - 31000 0.44713779 -2.1096164 0.066470416 -1.5963808 0.66832708 - 32000 0.4373357 -2.0941237 0.058871613 -1.5982808 0.78176106 - 33000 0.44030485 -2.105644 0.058804306 -1.6069017 0.66286458 - 34000 0.43781175 -2.1233209 0.064611206 -1.6212628 0.56342584 - 35000 0.45670132 -2.1059408 0.053049584 -1.5965705 0.73992396 - 36000 0.45555427 -2.1149877 0.057627709 -1.6021854 0.85854939 - 37000 0.44134236 -2.1106202 0.064444306 -1.6052013 0.74674603 - 38000 0.44812623 -2.1003681 0.057266258 -1.5953491 0.78239359 - 39000 0.44167062 -2.11141 0.055354 -1.6147534 0.7066385 - 40000 0.46103176 -2.1166687 0.062155412 -1.5938657 0.73620955 - 41000 0.44537102 -2.0993898 0.05631213 -1.5980778 0.87348756 - 42000 0.44752506 -2.1115212 0.057506521 -1.6068625 0.72999561 - 43000 0.4483886 -2.1184719 0.066943915 -1.6035131 0.78112063 - 44000 0.45944897 -2.0916657 0.055242781 -1.5773568 0.98660473 - 45000 0.46238513 -2.1163075 0.0530031 -1.6013046 0.74416054 - 46000 0.45979064 -2.1165545 0.060657581 -1.5964895 0.63516974 - 47000 0.45936546 -2.1140678 0.049931919 -1.6051532 0.76425182 - 48000 0.45424613 -2.1122681 0.061885599 -1.5965149 0.71981142 - 49000 0.44449524 -2.1147361 0.06626748 -1.6043438 0.78720467 - 50000 0.4641185 -2.1114668 0.055104874 -1.5926302 0.70195865 - 51000 0.44220655 -2.1075773 0.0589109 -1.6068283 0.73806859 - 52000 0.43097906 -2.1189493 0.061502241 -1.6268271 0.69622593 - 53000 0.45 -2.137688 0.053631829 -1.6344311 0.48269158 - 54000 0.43777118 -2.1089246 0.047098534 -1.6244197 0.70423814 - 55000 0.46061985 -2.1129502 0.062520353 -1.5901938 0.72492307 - 56000 0.4524841 -2.1195648 0.06580089 -1.6016569 0.52709892 - 57000 0.44914574 -2.1041993 0.061040876 -1.594387 0.7979988 - 58000 0.46446286 -2.1181238 0.055741995 -1.598306 0.51009146 - 59000 0.4632674 -2.1169321 0.050672678 -1.6033781 0.83110911 - 60000 0.46340478 -2.122846 0.058485209 -1.6013422 0.69966471 -Loop time of 8.01683 on 1 procs for 60000 steps with 1200 atoms - -Performance: 3233199.903 tau/day, 7484.259 timesteps/s -99.8% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 5.4027 | 5.4027 | 5.4027 | 0.0 | 67.39 -Bond | 0.23585 | 0.23585 | 0.23585 | 0.0 | 2.94 -Neigh | 1.5188 | 1.5188 | 1.5188 | 0.0 | 18.95 -Comm | 0.14452 | 0.14452 | 0.14452 | 0.0 | 1.80 -Output | 0.00060487 | 0.00060487 | 0.00060487 | 0.0 | 0.01 -Modify | 0.56352 | 0.56352 | 0.56352 | 0.0 | 7.03 -Other | | 0.1508 | | | 1.88 - -Nlocal: 1200 ave 1200 max 1200 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 395 ave 395 max 395 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 9652 ave 9652 max 9652 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 9652 -Ave neighs/atom = 8.04333 -Ave special neighs/atom = 0.5 -Neighbor list builds = 4886 -Dangerous builds = 0 -Total wall time: 0:00:08 diff --git a/examples/micelle/log.28Feb2019.micelle.g++.4 b/examples/micelle/log.28Feb2019.micelle.g++.4 deleted file mode 100644 index 6af9051ed2..0000000000 --- a/examples/micelle/log.28Feb2019.micelle.g++.4 +++ /dev/null @@ -1,259 +0,0 @@ -LAMMPS (28 Feb 2019) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88) - using 1 OpenMP thread(s) per MPI task -# 2d micelle simulation - -dimension 2 - -neighbor 0.3 bin -neigh_modify delay 5 - -atom_style bond - -# Soft potential push-off - -read_data data.micelle - orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1) - 2 by 2 by 1 MPI processor grid - reading atoms ... - 1200 atoms - scanning bonds ... - 1 = max bonds/atom - reading bonds ... - 300 bonds - 2 = max # of 1-2 neighbors - 1 = max # of 1-3 neighbors - 1 = max # of 1-4 neighbors - 2 = max # of special neighbors - special bonds CPU = 0.000130415 secs - read_data CPU = 0.00132132 secs -special_bonds fene - 2 = max # of 1-2 neighbors - 2 = max # of special neighbors - special bonds CPU = 4.76837e-05 secs - -pair_style soft 1.12246 -pair_coeff * * 0.0 1.12246 - -bond_style harmonic -bond_coeff 1 50.0 0.75 - -velocity all create 0.45 2349852 - -variable prefactor equal ramp(1.0,20.0) - -fix 1 all nve -fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0 -fix 3 all adapt 1 pair soft a * * v_prefactor -fix 4 all enforce2d - -thermo 50 -run 1000 -Neighbor list info ... - update every 1 steps, delay 5 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 1.42246 - ghost atom cutoff = 1.42246 - binsize = 0.71123, bins = 51 51 1 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair soft, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/2d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.758 | 3.85 | 4.126 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518 - 50 0.47411013 0.67721272 0.057404514 1.2083323 1.3375852 - 100 0.45 0.73046745 0.054836584 1.234929 2.3196516 - 150 0.67521742 0.72402001 0.043490075 1.4421648 2.8744416 - 200 0.45 0.78481891 0.076931503 1.3113754 3.0412388 - 250 0.66479018 0.69790602 0.081075564 1.4432178 3.6917024 - 300 0.45 0.76820218 0.066727591 1.2845548 3.7861054 - 350 0.67619136 0.625715 0.072722727 1.3740656 4.2861621 - 400 0.45 0.68527759 0.090724527 1.2256271 4.4725214 - 450 0.56702844 0.64402767 0.080555563 1.2911391 4.7402211 - 500 0.45 0.64883009 0.078376672 1.1768318 4.7919294 - 550 0.564664 0.58260368 0.080779475 1.2275766 4.9855705 - 600 0.45 0.58193041 0.088386617 1.119942 5.131481 - 650 0.52110993 0.5415273 0.097683746 1.1598867 5.2500294 - 700 0.45 0.50856787 0.088471208 1.0466641 5.2550165 - 750 0.51510855 0.47441291 0.089429375 1.0785216 5.375763 - 800 0.45 0.49926696 0.085958476 1.0348504 5.4665914 - 850 0.50688494 0.46614429 0.088962292 1.0615691 5.556932 - 900 0.45 0.47785593 0.10150857 1.0289895 5.7765975 - 950 0.49590559 0.46050477 0.096404887 1.052402 5.8649245 - 1000 0.45 0.47691182 0.08808163 1.0146185 6.0177568 -Loop time of 0.0377742 on 4 procs for 1000 steps with 1200 atoms - -Performance: 11436375.633 tau/day, 26473.092 timesteps/s -96.6% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.016871 | 0.017299 | 0.018185 | 0.4 | 45.80 -Bond | 0.0010128 | 0.0010633 | 0.001116 | 0.1 | 2.81 -Neigh | 0.004832 | 0.0048565 | 0.0048807 | 0.0 | 12.86 -Comm | 0.0066509 | 0.0077528 | 0.0084352 | 0.8 | 20.52 -Output | 0.00022054 | 0.00028259 | 0.00046587 | 0.0 | 0.75 -Modify | 0.0035386 | 0.0036086 | 0.0036943 | 0.1 | 9.55 -Other | | 0.002912 | | | 7.71 - -Nlocal: 300 ave 305 max 292 min -Histogram: 1 0 0 0 0 0 1 0 1 1 -Nghost: 100.25 ave 108 max 93 min -Histogram: 1 0 1 0 0 0 1 0 0 1 -Neighs: 784 ave 815 max 739 min -Histogram: 1 0 0 0 0 0 1 1 0 1 - -Total # of neighbors = 3136 -Ave neighs/atom = 2.61333 -Ave special neighs/atom = 0.5 -Neighbor list builds = 92 -Dangerous builds = 0 - -unfix 3 - -# Main run - -pair_style lj/cut 2.5 - -# solvent/head - full-size and long-range - -pair_coeff 1 1 1.0 1.0 2.5 -pair_coeff 2 2 1.0 1.0 2.5 -pair_coeff 1 2 1.0 1.0 2.5 - -# tail/tail - size-averaged and long-range - -pair_coeff 3 3 1.0 0.75 2.5 -pair_coeff 4 4 1.0 0.50 2.5 -pair_coeff 3 4 1.0 0.67 2.5 - -# solvent/tail - full-size and repulsive - -pair_coeff 1 3 1.0 1.0 1.12246 -pair_coeff 1 4 1.0 1.0 1.12246 - -# head/tail - size-averaged and repulsive - -pair_coeff 2 3 1.0 0.88 1.12246 -pair_coeff 2 4 1.0 0.75 1.12246 - -thermo 1000 - -#dump 1 all atom 2000 dump.micelle - -#dump 2 all image 2000 image.*.jpg type type zoom 1.6 -#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 - -#dump 3 all movie 2000 movie.mpg type type zoom 1.6 -#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 - -reset_timestep 0 -run 60000 -Neighbor list info ... - update every 1 steps, delay 5 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 26 26 1 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/2d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 4.001 | 4.032 | 4.124 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0.45 -1.7056163 0.08808163 -1.1679097 3.9431686 - 1000 0.45 -1.9727652 0.058608073 -1.4645321 1.9982444 - 2000 0.44428815 -1.9902282 0.064240544 -1.4820698 1.7051263 - 3000 0.46641766 -1.9856844 0.065017468 -1.4546379 1.6939772 - 4000 0.45734058 -2.0242583 0.070494626 -1.4968042 1.3474276 - 5000 0.44904747 -2.0086954 0.058801142 -1.501221 1.4632351 - 6000 0.44961405 -2.0334509 0.05721299 -1.5269985 1.3093586 - 7000 0.45474928 -2.0453645 0.064725006 -1.5262692 1.1581035 - 8000 0.44274767 -2.0375379 0.062216035 -1.5329431 1.312914 - 9000 0.46176571 -2.0473031 0.065581966 -1.5203402 1.2013868 - 10000 0.45046977 -2.0540466 0.065402724 -1.5385495 0.95819581 - 11000 0.45016671 -2.0610028 0.056993955 -1.5542172 1.0433435 - 12000 0.43823039 -2.073155 0.065171939 -1.5701178 1.1400059 - 13000 0.44482161 -2.0678338 0.063901045 -1.5594819 0.97993813 - 14000 0.45 -2.0892562 0.061753632 -1.5778776 0.89841778 - 15000 0.44328626 -2.0859346 0.059956258 -1.5830615 0.90664821 - 16000 0.45666508 -2.0859262 0.059582346 -1.5700593 0.9702235 - 17000 0.44832038 -2.0762124 0.059153394 -1.5691122 0.93020504 - 18000 0.4555831 -2.0844959 0.057986324 -1.5713062 0.87398232 - 19000 0.45257867 -2.0671736 0.062190389 -1.5527816 0.89208496 - 20000 0.44010419 -2.1020944 0.062053708 -1.6003033 0.84140973 - 21000 0.45239369 -2.0820308 0.060981799 -1.5690323 0.98502522 - 22000 0.44607468 -2.0820602 0.051731316 -1.5846259 0.86120529 - 23000 0.45088473 -2.0865286 0.05727778 -1.5787418 1.1479844 - 24000 0.45526919 -2.1086678 0.057378327 -1.5963997 0.86944138 - 25000 0.46536624 -2.1055425 0.05665328 -1.5839108 0.72895438 - 26000 0.46716668 -2.1035267 0.057498747 -1.5792505 0.85105386 - 27000 0.44374699 -2.0932213 0.060937242 -1.5889069 0.93200759 - 28000 0.45944001 -2.0968869 0.053052954 -1.5847768 0.78909249 - 29000 0.4543632 -2.10493 0.061511018 -1.5894345 0.85862527 - 30000 0.44987776 -2.0942536 0.062431086 -1.5823197 0.7349894 - 31000 0.43829016 -2.0951259 0.060245682 -1.5969553 0.86702973 - 32000 0.45416601 -2.0991679 0.055978905 -1.5894015 0.75777153 - 33000 0.4605079 -2.1118364 0.058205688 -1.5935066 0.86041104 - 34000 0.43638213 -2.0925345 0.067533519 -1.5889825 0.85100425 - 35000 0.46912252 -2.1082718 0.051646432 -1.5878938 0.73613751 - 36000 0.45 -2.0966442 0.052507159 -1.5945121 0.88722487 - 37000 0.44970507 -2.1029685 0.065454263 -1.588184 0.76033821 - 38000 0.44910233 -2.097751 0.05767009 -1.5913528 0.95830923 - 39000 0.4322161 -2.1060426 0.062453704 -1.611733 0.74681695 - 40000 0.46143858 -2.1328575 0.057333011 -1.6144704 0.58326322 - 41000 0.43180549 -2.1070656 0.064150563 -1.6114694 0.82842684 - 42000 0.46738909 -2.1067947 0.058017036 -1.5817781 0.73292362 - 43000 0.43699124 -2.1171964 0.062817262 -1.6177521 0.73354741 - 44000 0.45262916 -2.1281307 0.055228619 -1.6206502 0.64167946 - 45000 0.43905419 -2.088789 0.055597999 -1.5945027 0.8002542 - 46000 0.44485569 -2.1035061 0.067828181 -1.5911929 0.71861494 - 47000 0.44496824 -2.0968296 0.0632326 -1.5889996 0.75202899 - 48000 0.46567244 -2.1235948 0.061032118 -1.5972783 0.64094556 - 49000 0.43202506 -2.0986097 0.053464022 -1.6134806 0.83857984 - 50000 0.45454698 -2.1263344 0.058119708 -1.6140465 0.67030037 - 51000 0.43702766 -2.1292347 0.074047424 -1.6185238 0.52896462 - 52000 0.46367081 -2.1177288 0.06726625 -1.5871781 0.74343227 - 53000 0.45 -2.1341074 0.062769314 -1.6217131 0.51130365 - 54000 0.44862492 -2.1272108 0.057723381 -1.6212364 0.54735429 - 55000 0.44926027 -2.1350444 0.066186625 -1.6199719 0.66821299 - 56000 0.4544227 -2.1325537 0.065298628 -1.6132111 0.63597556 - 57000 0.45697003 -2.1323238 0.053312855 -1.6224218 0.55572633 - 58000 0.45698902 -2.1043208 0.055835989 -1.5918766 0.63502658 - 59000 0.4425306 -2.1120353 0.056617261 -1.6132563 0.65681272 - 60000 0.44319296 -2.1171981 0.058330294 -1.6160442 0.63602511 -Loop time of 2.63918 on 4 procs for 60000 steps with 1200 atoms - -Performance: 9821248.084 tau/day, 22734.371 timesteps/s -97.3% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 1.1742 | 1.278 | 1.3471 | 5.9 | 48.43 -Bond | 0.046621 | 0.06565 | 0.081322 | 5.1 | 2.49 -Neigh | 0.46642 | 0.46917 | 0.47105 | 0.3 | 17.78 -Comm | 0.47295 | 0.55928 | 0.67758 | 10.5 | 21.19 -Output | 0.00073624 | 0.00173 | 0.0047016 | 4.1 | 0.07 -Modify | 0.14511 | 0.15226 | 0.15887 | 1.5 | 5.77 -Other | | 0.1131 | | | 4.28 - -Nlocal: 300 ave 309 max 281 min -Histogram: 1 0 0 0 0 0 0 1 0 2 -Nghost: 232.75 ave 234 max 231 min -Histogram: 1 0 0 1 0 0 0 0 0 2 -Neighs: 2450.25 ave 2576 max 2179 min -Histogram: 1 0 0 0 0 0 0 0 1 2 - -Total # of neighbors = 9801 -Ave neighs/atom = 8.1675 -Ave special neighs/atom = 0.5 -Neighbor list builds = 4887 -Dangerous builds = 0 -Total wall time: 0:00:02 diff --git a/examples/micelle/log.28Feb2019.micelle.rigid.g++.1 b/examples/micelle/log.28Feb2019.micelle.rigid.g++.1 deleted file mode 100644 index ec0079818d..0000000000 --- a/examples/micelle/log.28Feb2019.micelle.rigid.g++.1 +++ /dev/null @@ -1,290 +0,0 @@ -LAMMPS (28 Feb 2019) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88) - using 1 OpenMP thread(s) per MPI task -# 2d micelle simulation - -dimension 2 - -neighbor 0.3 bin -neigh_modify delay 5 - -atom_style bond - -# Soft potential push-off - -read_data data.micelle - orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 1200 atoms - scanning bonds ... - 1 = max bonds/atom - reading bonds ... - 300 bonds - 2 = max # of 1-2 neighbors - 1 = max # of 1-3 neighbors - 1 = max # of 1-4 neighbors - 2 = max # of special neighbors - special bonds CPU = 0.000271559 secs - read_data CPU = 0.00115585 secs -special_bonds fene - 2 = max # of 1-2 neighbors - 2 = max # of special neighbors - special bonds CPU = 8.39233e-05 secs - -pair_style soft 1.12246 -pair_coeff * * 0.0 1.12246 - -bond_style harmonic -bond_coeff 1 50.0 0.75 - -velocity all create 0.45 2349852 - -variable prefactor equal ramp(1.0,20.0) - -fix 1 all nve -fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0 -fix 3 all adapt 1 pair soft a * * v_prefactor -fix 4 all enforce2d - -thermo 50 -run 1000 -Neighbor list info ... - update every 1 steps, delay 5 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 1.42246 - ghost atom cutoff = 1.42246 - binsize = 0.71123, bins = 51 51 1 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair soft, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/2d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.799 | 3.799 | 3.799 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518 - 50 0.47411013 0.67721272 0.057404514 1.2083323 1.3375852 - 100 0.45 0.73046745 0.054836584 1.234929 2.3196516 - 150 0.67521742 0.72402001 0.043490075 1.4421648 2.8744416 - 200 0.45 0.78481891 0.076931503 1.3113754 3.0412388 - 250 0.66479018 0.69790602 0.081075564 1.4432178 3.6917024 - 300 0.45 0.76820218 0.066727591 1.2845548 3.7861054 - 350 0.67619136 0.625715 0.072722727 1.3740656 4.2861621 - 400 0.45 0.68527759 0.090724527 1.2256271 4.4725214 - 450 0.56702844 0.64402767 0.080555563 1.2911391 4.7402211 - 500 0.45 0.64883009 0.078376672 1.1768318 4.7919294 - 550 0.564664 0.58260368 0.080779475 1.2275766 4.9855705 - 600 0.45 0.58193041 0.088386617 1.119942 5.131481 - 650 0.52110993 0.5415273 0.097683746 1.1598867 5.2500294 - 700 0.45 0.50856787 0.088471208 1.0466641 5.2550165 - 750 0.51510855 0.47441291 0.089429375 1.0785216 5.375763 - 800 0.45 0.49926696 0.085958476 1.0348504 5.4665914 - 850 0.50688494 0.46614429 0.088962292 1.0615691 5.556932 - 900 0.45 0.47785593 0.10150857 1.0289895 5.7765975 - 950 0.49590559 0.46050477 0.096404887 1.052402 5.8649245 - 1000 0.45 0.47691182 0.08808163 1.0146185 6.0177568 -Loop time of 0.107201 on 1 procs for 1000 steps with 1200 atoms - -Performance: 4029800.456 tau/day, 9328.242 timesteps/s -99.8% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.072035 | 0.072035 | 0.072035 | 0.0 | 67.20 -Bond | 0.0039918 | 0.0039918 | 0.0039918 | 0.0 | 3.72 -Neigh | 0.016078 | 0.016078 | 0.016078 | 0.0 | 15.00 -Comm | 0.0018375 | 0.0018375 | 0.0018375 | 0.0 | 1.71 -Output | 0.00016379 | 0.00016379 | 0.00016379 | 0.0 | 0.15 -Modify | 0.010665 | 0.010665 | 0.010665 | 0.0 | 9.95 -Other | | 0.002429 | | | 2.27 - -Nlocal: 1200 ave 1200 max 1200 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 195 ave 195 max 195 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 3136 ave 3136 max 3136 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 3136 -Ave neighs/atom = 2.61333 -Ave special neighs/atom = 0.5 -Neighbor list builds = 92 -Dangerous builds = 0 - -unfix 3 - -# Main run - -pair_style lj/cut 2.5 - -# solvent/head - full-size and long-range - -pair_coeff 1 1 1.0 1.0 2.5 -pair_coeff 2 2 1.0 1.0 2.5 -pair_coeff 1 2 1.0 1.0 2.5 - -# tail/tail - size-averaged and long-range - -pair_coeff 3 3 1.0 0.75 2.5 -pair_coeff 4 4 1.0 0.50 2.5 -pair_coeff 3 4 1.0 0.67 2.5 - -# solvent/tail - full-size and repulsive - -pair_coeff 1 3 1.0 1.0 1.12246 -pair_coeff 1 4 1.0 1.0 1.12246 - -# head/tail - size-averaged and repulsive - -pair_coeff 2 3 1.0 0.88 1.12246 -pair_coeff 2 4 1.0 0.75 1.12246 - -thermo 1000 - -#dump 1 all atom 2000 dump.micelle - -#dump 2 all image 2000 image.*.jpg type type zoom 1.6 -#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 - -#dump 3 all movie 2000 movie.mpg type type zoom 1.6 -#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 - -reset_timestep 0 -group solvent molecule 0 -750 atoms in group solvent -group solute subtract all solvent -450 atoms in group solute -unfix 1 -unfix 2 -unfix 4 -fix 1 solvent nve -fix 2 solvent temp/rescale 100 0.45 0.45 0.02 1.0 -fix 5 solute rigid molecule langevin 0.45 0.45 0.5 112211 -150 rigid bodies with 450 atoms -fix 4 all enforce2d -run 20000 -Neighbor list info ... - update every 1 steps, delay 5 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 26 26 1 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/2d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 5.274 | 5.274 | 5.274 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0.44603578 -1.7056163 0.08808163 -1.2555023 3.4039736 - 1000 0.46008168 -1.9040837 0.08808163 -1.4425691 0.93225457 - 2000 0.44520658 -1.9317253 0.08808163 -1.4822843 3.8192896 - 3000 0.43988556 -1.945898 0.08808163 -1.5007759 3.0371634 - 4000 0.4646519 -1.9753553 0.08808163 -1.5101312 -1.8041178 - 5000 0.4362993 -1.9763715 0.08808163 -1.5341603 1.5037284 - 6000 0.47007384 -1.9833154 0.08808163 -1.5136905 2.1227653 - 7000 0.44854623 -1.9914288 0.08808163 -1.5392772 3.9458099 - 8000 0.43841372 -1.9779603 0.08808163 -1.5340328 -4.5429769 - 9000 0.4518303 -1.9834387 0.08808163 -1.5286215 4.4230447 - 10000 0.43562904 -2.001471 0.08808163 -1.5598038 1.8919582 - 11000 0.44014575 -1.9820611 0.08808163 -1.5367278 -2.1189418 - 12000 0.44466956 -2.0134014 0.08808163 -1.5643963 -2.5218497 - 13000 0.45274369 -2.021443 0.08808163 -1.5658844 2.4795173 - 14000 0.44742645 -2.011108 0.08808163 -1.5598653 -0.74697767 - 15000 0.4674843 -2.024737 0.08808163 -1.5572139 -1.9539999 - 16000 0.45610154 -2.0401029 0.08808163 -1.5818189 -0.53082066 - 17000 0.44679292 -2.0365577 0.08808163 -1.5858291 -6.5040295 - 18000 0.44279107 -2.0500326 0.08808163 -1.6025522 -0.051597102 - 19000 0.45603993 -2.0306289 0.08808163 -1.5723948 1.0986608 - 20000 0.44519606 -2.0412229 0.08808163 -1.5917904 -1.0406746 -Loop time of 3.68102 on 1 procs for 20000 steps with 1200 atoms - -Performance: 2347175.802 tau/day, 5433.277 timesteps/s -99.8% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 1.7349 | 1.7349 | 1.7349 | 0.0 | 47.13 -Bond | 0.079483 | 0.079483 | 0.079483 | 0.0 | 2.16 -Neigh | 0.49063 | 0.49063 | 0.49063 | 0.0 | 13.33 -Comm | 0.049093 | 0.049093 | 0.049093 | 0.0 | 1.33 -Output | 0.00022578 | 0.00022578 | 0.00022578 | 0.0 | 0.01 -Modify | 1.273 | 1.273 | 1.273 | 0.0 | 34.58 -Other | | 0.05369 | | | 1.46 - -Nlocal: 1200 ave 1200 max 1200 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 395 ave 395 max 395 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 8915 ave 8915 max 8915 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 8915 -Ave neighs/atom = 7.42917 -Ave special neighs/atom = 0.5 -Neighbor list builds = 1580 -Dangerous builds = 0 -unfix 5 -unfix 4 -fix 5 solute rigid/small molecule langevin 0.45 0.45 0.5 112211 - create bodies CPU = 0.00012517 secs -150 rigid bodies with 450 atoms - 1.04536 = max distance from body owner to body atom -fix 4 all enforce2d -run 20000 -Per MPI rank memory allocation (min/avg/max) = 8.633 | 8.633 | 8.633 Mbytes -Step Temp E_pair E_mol TotEng Press - 20000 0.44519606 -2.0412229 0.08808163 -1.5917904 1.3058893 - 21000 0.4353376 -2.0483342 0.08808163 -1.6069035 0.53023317 - 22000 0.44034324 -2.0416876 0.08808163 -1.5961941 4.0327077 - 23000 0.4685403 -2.05295 0.08808163 -1.5845698 3.6792349 - 24000 0.44872075 -2.0320623 0.08808163 -1.579769 -2.0476923 - 25000 0.46829594 -2.0671408 0.08808163 -1.5989589 2.180811 - 26000 0.45257544 -2.0418792 0.08808163 -1.5864572 3.3924018 - 27000 0.44269664 -2.0409905 0.08808163 -1.5935868 -0.17012673 - 28000 0.46961216 -2.0552479 0.08808163 -1.5859978 -7.2870888 - 29000 0.46683129 -2.0438334 0.08808163 -1.5768404 3.0583141 - 30000 0.44262228 -2.036737 0.08808163 -1.5893937 0.087520915 - 31000 0.43517227 -2.0479672 0.08808163 -1.6066708 -0.3426009 - 32000 0.44543779 -2.0538031 0.08808163 -1.6041744 -0.2093148 - 33000 0.44629079 -2.0409901 0.08808163 -1.5906691 3.310113 - 34000 0.43058831 -2.0713827 0.08808163 -1.6338069 0.14128843 - 35000 0.44546512 -2.0427068 0.08808163 -1.593056 -3.1386697 - 36000 0.42971129 -2.0527435 0.08808163 -1.6158795 -2.7334963 - 37000 0.44707969 -2.0461803 0.08808163 -1.595219 -3.8777678 - 38000 0.43150818 -2.0435276 0.08808163 -1.6052052 0.2905487 - 39000 0.44463343 -2.0522113 0.08808163 -1.6032355 3.543123 - 40000 0.44582593 -2.052213 0.08808163 -1.6022693 1.1486536 -Loop time of 3.69012 on 1 procs for 20000 steps with 1200 atoms - -Performance: 2341388.948 tau/day, 5419.882 timesteps/s -99.8% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 1.756 | 1.756 | 1.756 | 0.0 | 47.59 -Bond | 0.079221 | 0.079221 | 0.079221 | 0.0 | 2.15 -Neigh | 0.49085 | 0.49085 | 0.49085 | 0.0 | 13.30 -Comm | 0.048317 | 0.048317 | 0.048317 | 0.0 | 1.31 -Output | 0.0002315 | 0.0002315 | 0.0002315 | 0.0 | 0.01 -Modify | 1.2616 | 1.2616 | 1.2616 | 0.0 | 34.19 -Other | | 0.05386 | | | 1.46 - -Nlocal: 1200 ave 1200 max 1200 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 393 ave 393 max 393 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 9091 ave 9091 max 9091 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 9091 -Ave neighs/atom = 7.57583 -Ave special neighs/atom = 0.5 -Neighbor list builds = 1582 -Dangerous builds = 0 -Total wall time: 0:00:07 diff --git a/examples/micelle/log.28Feb2019.micelle.rigid.g++.4 b/examples/micelle/log.28Feb2019.micelle.rigid.g++.4 deleted file mode 100644 index a6687a3c00..0000000000 --- a/examples/micelle/log.28Feb2019.micelle.rigid.g++.4 +++ /dev/null @@ -1,290 +0,0 @@ -LAMMPS (28 Feb 2019) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88) - using 1 OpenMP thread(s) per MPI task -# 2d micelle simulation - -dimension 2 - -neighbor 0.3 bin -neigh_modify delay 5 - -atom_style bond - -# Soft potential push-off - -read_data data.micelle - orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1) - 2 by 2 by 1 MPI processor grid - reading atoms ... - 1200 atoms - scanning bonds ... - 1 = max bonds/atom - reading bonds ... - 300 bonds - 2 = max # of 1-2 neighbors - 1 = max # of 1-3 neighbors - 1 = max # of 1-4 neighbors - 2 = max # of special neighbors - special bonds CPU = 0.000175714 secs - read_data CPU = 0.00145626 secs -special_bonds fene - 2 = max # of 1-2 neighbors - 2 = max # of special neighbors - special bonds CPU = 7.22408e-05 secs - -pair_style soft 1.12246 -pair_coeff * * 0.0 1.12246 - -bond_style harmonic -bond_coeff 1 50.0 0.75 - -velocity all create 0.45 2349852 - -variable prefactor equal ramp(1.0,20.0) - -fix 1 all nve -fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0 -fix 3 all adapt 1 pair soft a * * v_prefactor -fix 4 all enforce2d - -thermo 50 -run 1000 -Neighbor list info ... - update every 1 steps, delay 5 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 1.42246 - ghost atom cutoff = 1.42246 - binsize = 0.71123, bins = 51 51 1 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair soft, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/2d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.758 | 3.85 | 4.126 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518 - 50 0.47411013 0.67721272 0.057404514 1.2083323 1.3375852 - 100 0.45 0.73046745 0.054836584 1.234929 2.3196516 - 150 0.67521742 0.72402001 0.043490075 1.4421648 2.8744416 - 200 0.45 0.78481891 0.076931503 1.3113754 3.0412388 - 250 0.66479018 0.69790602 0.081075564 1.4432178 3.6917024 - 300 0.45 0.76820218 0.066727591 1.2845548 3.7861054 - 350 0.67619136 0.625715 0.072722727 1.3740656 4.2861621 - 400 0.45 0.68527759 0.090724527 1.2256271 4.4725214 - 450 0.56702844 0.64402767 0.080555563 1.2911391 4.7402211 - 500 0.45 0.64883009 0.078376672 1.1768318 4.7919294 - 550 0.564664 0.58260368 0.080779475 1.2275766 4.9855705 - 600 0.45 0.58193041 0.088386617 1.119942 5.131481 - 650 0.52110993 0.5415273 0.097683746 1.1598867 5.2500294 - 700 0.45 0.50856787 0.088471208 1.0466641 5.2550165 - 750 0.51510855 0.47441291 0.089429375 1.0785216 5.375763 - 800 0.45 0.49926696 0.085958476 1.0348504 5.4665914 - 850 0.50688494 0.46614429 0.088962292 1.0615691 5.556932 - 900 0.45 0.47785593 0.10150857 1.0289895 5.7765975 - 950 0.49590559 0.46050477 0.096404887 1.052402 5.8649245 - 1000 0.45 0.47691182 0.08808163 1.0146185 6.0177568 -Loop time of 0.0389124 on 4 procs for 1000 steps with 1200 atoms - -Performance: 11101855.138 tau/day, 25698.739 timesteps/s -95.7% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.016776 | 0.017405 | 0.018435 | 0.5 | 44.73 -Bond | 0.0010033 | 0.0011995 | 0.0015519 | 0.6 | 3.08 -Neigh | 0.0044944 | 0.0045093 | 0.0045218 | 0.0 | 11.59 -Comm | 0.0080328 | 0.0093863 | 0.010242 | 0.9 | 24.12 -Output | 0.00021577 | 0.00027579 | 0.00045323 | 0.0 | 0.71 -Modify | 0.0034575 | 0.0036355 | 0.0040002 | 0.4 | 9.34 -Other | | 0.002501 | | | 6.43 - -Nlocal: 300 ave 305 max 292 min -Histogram: 1 0 0 0 0 0 1 0 1 1 -Nghost: 100.25 ave 108 max 93 min -Histogram: 1 0 1 0 0 0 1 0 0 1 -Neighs: 784 ave 815 max 739 min -Histogram: 1 0 0 0 0 0 1 1 0 1 - -Total # of neighbors = 3136 -Ave neighs/atom = 2.61333 -Ave special neighs/atom = 0.5 -Neighbor list builds = 92 -Dangerous builds = 0 - -unfix 3 - -# Main run - -pair_style lj/cut 2.5 - -# solvent/head - full-size and long-range - -pair_coeff 1 1 1.0 1.0 2.5 -pair_coeff 2 2 1.0 1.0 2.5 -pair_coeff 1 2 1.0 1.0 2.5 - -# tail/tail - size-averaged and long-range - -pair_coeff 3 3 1.0 0.75 2.5 -pair_coeff 4 4 1.0 0.50 2.5 -pair_coeff 3 4 1.0 0.67 2.5 - -# solvent/tail - full-size and repulsive - -pair_coeff 1 3 1.0 1.0 1.12246 -pair_coeff 1 4 1.0 1.0 1.12246 - -# head/tail - size-averaged and repulsive - -pair_coeff 2 3 1.0 0.88 1.12246 -pair_coeff 2 4 1.0 0.75 1.12246 - -thermo 1000 - -#dump 1 all atom 2000 dump.micelle - -#dump 2 all image 2000 image.*.jpg type type zoom 1.6 -#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 - -#dump 3 all movie 2000 movie.mpg type type zoom 1.6 -#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 - -reset_timestep 0 -group solvent molecule 0 -750 atoms in group solvent -group solute subtract all solvent -450 atoms in group solute -unfix 1 -unfix 2 -unfix 4 -fix 1 solvent nve -fix 2 solvent temp/rescale 100 0.45 0.45 0.02 1.0 -fix 5 solute rigid molecule langevin 0.45 0.45 0.5 112211 -150 rigid bodies with 450 atoms -fix 4 all enforce2d -run 20000 -Neighbor list info ... - update every 1 steps, delay 5 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 26 26 1 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/2d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 5.251 | 5.282 | 5.374 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0.44603578 -1.7056163 0.08808163 -1.2555023 3.4039736 - 1000 0.46008163 -1.9040835 0.08808163 -1.4425689 0.93225869 - 2000 0.44943348 -1.9355135 0.08808163 -1.4826417 3.8399671 - 3000 0.4448437 -1.9480307 0.08808163 -1.4988842 2.5506553 - 4000 0.46013872 -1.9783821 0.08808163 -1.5168212 -1.8963215 - 5000 0.45520233 -1.9659462 0.08808163 -1.5083921 1.9238897 - 6000 0.44942049 -1.9663403 0.08808163 -1.513479 3.0633512 - 7000 0.45975758 -1.988462 0.08808163 -1.5272105 4.8267309 - 8000 0.45125238 -1.9913522 0.08808163 -1.5370041 -4.6644852 - 9000 0.45863606 -1.9792375 0.08808163 -1.5188962 4.3655071 - 10000 0.46264541 -1.9864611 0.08808163 -1.5228656 2.2176464 - 11000 0.45048361 -1.9907235 0.08808163 -1.5369994 -0.055360699 - 12000 0.44536719 -2.012875 0.08808163 -1.5633037 -0.2583823 - 13000 0.44212663 -2.0060111 0.08808163 -1.55907 3.3616171 - 14000 0.44984353 -2.0335408 0.08808163 -1.5803361 -0.21585645 - 15000 0.44896672 -2.0385265 0.08808163 -1.5860335 -4.6186206 - 16000 0.46694997 -2.032795 0.08808163 -1.5657056 0.53443281 - 17000 0.43208201 -2.0272255 0.08808163 -1.5884373 -6.5239975 - 18000 0.43281873 -2.0331268 0.08808163 -1.5937406 -0.048319943 - 19000 0.44704527 -2.0286742 0.08808163 -1.5777408 1.6356417 - 20000 0.44279735 -2.0443561 0.08808163 -1.5968706 -3.8337952 -Loop time of 1.71924 on 4 procs for 20000 steps with 1200 atoms - -Performance: 5025468.853 tau/day, 11633.030 timesteps/s -98.2% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.39864 | 0.40873 | 0.42192 | 1.6 | 23.77 -Bond | 0.02118 | 0.021816 | 0.022785 | 0.4 | 1.27 -Neigh | 0.13931 | 0.14031 | 0.14117 | 0.2 | 8.16 -Comm | 0.13974 | 0.15328 | 0.16884 | 3.3 | 8.92 -Output | 0.00026131 | 0.00044435 | 0.00099206 | 0.0 | 0.03 -Modify | 0.93275 | 0.94138 | 0.95072 | 0.7 | 54.76 -Other | | 0.05327 | | | 3.10 - -Nlocal: 300 ave 303 max 298 min -Histogram: 1 0 1 0 1 0 0 0 0 1 -Nghost: 218.5 ave 226 max 215 min -Histogram: 2 1 0 0 0 0 0 0 0 1 -Neighs: 2258.75 ave 2283 max 2216 min -Histogram: 1 0 0 0 0 0 1 0 1 1 - -Total # of neighbors = 9035 -Ave neighs/atom = 7.52917 -Ave special neighs/atom = 0.5 -Neighbor list builds = 1580 -Dangerous builds = 0 -unfix 5 -unfix 4 -fix 5 solute rigid/small molecule langevin 0.45 0.45 0.5 112211 - create bodies CPU = 5.43594e-05 secs -150 rigid bodies with 450 atoms - 0.916597 = max distance from body owner to body atom -fix 4 all enforce2d -run 20000 -Per MPI rank memory allocation (min/avg/max) = 8.568 | 8.6 | 8.691 Mbytes -Step Temp E_pair E_mol TotEng Press - 20000 0.44279735 -2.0443561 0.08808163 -1.5968706 -1.033643 - 21000 0.4529129 -2.049461 0.08808163 -1.5937651 0.93160285 - 22000 0.45039188 -2.0530092 0.08808163 -1.5993595 -0.10608965 - 23000 0.45261583 -2.0336042 0.08808163 -1.5781494 -2.5769871 - 24000 0.4608331 -2.0404645 0.08808163 -1.57834 3.1931675 - 25000 0.43479001 -2.0617104 0.08808163 -1.6207242 2.8190122 - 26000 0.47009651 -2.0754873 0.08808163 -1.605844 -0.9158501 - 27000 0.45002704 -2.0782104 0.08808163 -1.6248568 0.98629661 - 28000 0.45126136 -2.0592619 0.08808163 -1.6049065 0.03305448 - 29000 0.44355328 -2.0572858 0.08808163 -1.6091868 -6.0797989 - 30000 0.45053899 -2.0530953 0.08808163 -1.5993261 0.38382951 - 31000 0.46931923 -2.0718827 0.08808163 -1.6028703 2.2346891 - 32000 0.45348857 -2.0744024 0.08808163 -1.6182393 4.5028966 - 33000 0.44767742 -2.0597127 0.08808163 -1.6082662 -2.8021641 - 34000 0.45287544 -2.0857303 0.08808163 -1.6300648 -5.384091 - 35000 0.44743898 -2.0927246 0.08808163 -1.6414717 1.4800508 - 36000 0.45627028 -2.0720546 0.08808163 -1.6136336 -2.9961696 - 37000 0.4641334 -2.0701098 0.08808163 -1.6053065 8.4186854 - 38000 0.45922901 -2.0962331 0.08808163 -1.6354106 0.38361763 - 39000 0.4692834 -2.0573815 0.08808163 -1.5883982 -2.2177345 - 40000 0.46206931 -2.057851 0.08808163 -1.5947231 -1.0405727 -Loop time of 1.25476 on 4 procs for 20000 steps with 1200 atoms - -Performance: 6885775.862 tau/day, 15939.296 timesteps/s -98.1% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.40627 | 0.43037 | 0.45515 | 2.6 | 34.30 -Bond | 0.020504 | 0.021573 | 0.022739 | 0.5 | 1.72 -Neigh | 0.14337 | 0.14438 | 0.1453 | 0.2 | 11.51 -Comm | 0.13776 | 0.16647 | 0.19351 | 5.0 | 13.27 -Output | 0.00025082 | 0.00052994 | 0.0013635 | 0.0 | 0.04 -Modify | 0.45467 | 0.45822 | 0.46259 | 0.5 | 36.52 -Other | | 0.03321 | | | 2.65 - -Nlocal: 300 ave 304 max 293 min -Histogram: 1 0 0 0 0 1 0 0 0 2 -Nghost: 215.25 ave 217 max 213 min -Histogram: 1 0 0 0 0 1 0 1 0 1 -Neighs: 2340 ave 2378 max 2290 min -Histogram: 1 0 0 1 0 0 0 0 0 2 - -Total # of neighbors = 9360 -Ave neighs/atom = 7.8 -Ave special neighs/atom = 0.5 -Neighbor list builds = 1579 -Dangerous builds = 0 -Total wall time: 0:00:03 diff --git a/examples/micelle/log.29Mar2019.micelle-rigid.g++.1 b/examples/micelle/log.29Mar2019.micelle-rigid.g++.1 new file mode 100644 index 0000000000..f1001e6cea --- /dev/null +++ b/examples/micelle/log.29Mar2019.micelle-rigid.g++.1 @@ -0,0 +1,260 @@ +LAMMPS (29 Mar 2019) + using 1 OpenMP thread(s) per MPI task +# 2d micelle simulation + +dimension 2 + +neighbor 0.3 bin +neigh_modify delay 5 + +atom_style bond + +# Soft potential push-off + +read_data data.micelle + orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 1200 atoms + scanning bonds ... + 1 = max bonds/atom + reading bonds ... + 300 bonds + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.000473022 secs + read_data CPU = 0.0024147 secs +special_bonds fene + 2 = max # of 1-2 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.00022316 secs + +pair_style soft 1.12246 +pair_coeff * * 0.0 1.12246 + +bond_style harmonic +bond_coeff 1 50.0 0.75 + +velocity all create 0.45 2349852 + +variable prefactor equal ramp(1.0,20.0) + +fix 1 all nve +fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0 +fix 3 all adapt 1 pair soft a * * v_prefactor +fix 4 all enforce2d + +thermo 50 +run 500 +Neighbor list info ... + update every 1 steps, delay 5 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.42246 + ghost atom cutoff = 1.42246 + binsize = 0.71123, bins = 51 51 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair soft, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.799 | 3.799 | 3.799 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518 + 50 0.54981866 0.93548899 0.068440043 1.5532895 1.9232786 + 100 0.45 0.99659327 0.079228519 1.5254468 3.2135679 + 150 0.86965411 0.90456016 0.07493355 1.8484231 4.3821925 + 200 0.45 1.01454 0.10663502 1.5708 4.7598476 + 250 0.79636561 0.82567712 0.12105337 1.7424325 5.4983899 + 300 0.45 0.86475538 0.11819875 1.4325791 5.8554758 + 350 0.72135464 0.70693069 0.10912636 1.5368106 6.0388247 + 400 0.45 0.75067331 0.14165013 1.3419484 6.3840708 + 450 0.64839221 0.62402486 0.14173679 1.4136135 6.4791009 + 500 0.45 0.66669513 0.13695201 1.2532721 6.807146 +Loop time of 0.103162 on 1 procs for 500 steps with 1200 atoms + +Performance: 2093802.885 tau/day, 4846.766 timesteps/s +99.6% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.068308 | 0.068308 | 0.068308 | 0.0 | 66.21 +Bond | 0.004235 | 0.004235 | 0.004235 | 0.0 | 4.11 +Neigh | 0.014069 | 0.014069 | 0.014069 | 0.0 | 13.64 +Comm | 0.0019219 | 0.0019219 | 0.0019219 | 0.0 | 1.86 +Output | 0.00017262 | 0.00017262 | 0.00017262 | 0.0 | 0.17 +Modify | 0.011728 | 0.011728 | 0.011728 | 0.0 | 11.37 +Other | | 0.002726 | | | 2.64 + +Nlocal: 1200 ave 1200 max 1200 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 197 ave 197 max 197 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 3094 ave 3094 max 3094 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 3094 +Ave neighs/atom = 2.57833 +Ave special neighs/atom = 0.5 +Neighbor list builds = 52 +Dangerous builds = 0 + +unfix 3 + +# Main run + +pair_style lj/cut 2.5 + +# solvent/head - full-size and long-range + +pair_coeff 1 1 1.0 1.0 2.5 +pair_coeff 2 2 1.0 1.0 2.5 +pair_coeff 1 2 1.0 1.0 2.5 + +# tail/tail - size-averaged and long-range + +pair_coeff 3 3 1.0 0.75 2.5 +pair_coeff 4 4 1.0 0.50 2.5 +pair_coeff 3 4 1.0 0.67 2.5 + +# solvent/tail - full-size and repulsive + +pair_coeff 1 3 1.0 1.0 1.12246 +pair_coeff 1 4 1.0 1.0 1.12246 + +# head/tail - size-averaged and repulsive + +pair_coeff 2 3 1.0 0.88 1.12246 +pair_coeff 2 4 1.0 0.75 1.12246 + +thermo 50 + +#dump 1 all atom 2000 dump.micelle + +#dump 2 all image 2000 image.*.jpg type type zoom 1.6 +#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 + +#dump 3 all movie 2000 movie.mpg type type zoom 1.6 +#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 + +reset_timestep 0 +group solvent molecule 0 +750 atoms in group solvent +group solute subtract all solvent +450 atoms in group solute +unfix 1 +unfix 2 +unfix 4 +fix 1 solvent nve +fix 2 solvent temp/rescale 100 0.45 0.45 0.02 1.0 +fix 5 solute rigid molecule langevin 0.45 0.45 0.5 112211 +150 rigid bodies with 450 atoms +fix 4 all enforce2d +run 500 +Neighbor list info ... + update every 1 steps, delay 5 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 26 26 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.274 | 5.274 | 5.274 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0.45318168 -1.3753652 0.13695201 -0.8705807 1.975423 + 50 0.77871641 -1.6955252 0.13695201 -0.92651507 0.64222539 + 100 0.5336062 -1.7124572 0.13695201 -1.1423948 -0.11959696 + 150 0.58789067 -1.7926109 0.13695201 -1.1784877 1.2592743 + 200 0.47864796 -1.8040298 0.13695201 -1.2785752 3.6739793 + 250 0.51124651 -1.8614797 0.13695201 -1.309566 2.5817722 + 300 0.45695639 -1.8708384 0.13695201 -1.3629901 3.0833794 + 350 0.477504 -1.8924359 0.13695201 -1.3679098 -5.1605926 + 400 0.45328205 -1.87754 0.13695201 -1.372674 -4.0355858 + 450 0.47465031 -1.9071924 0.13695201 -1.3849826 3.1949617 + 500 0.45533691 -1.9072316 0.13695201 -1.4006978 0.48079061 +Loop time of 0.178806 on 1 procs for 500 steps with 1200 atoms + +Performance: 1208012.705 tau/day, 2796.326 timesteps/s +99.6% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.086131 | 0.086131 | 0.086131 | 0.0 | 48.17 +Bond | 0.0042472 | 0.0042472 | 0.0042472 | 0.0 | 2.38 +Neigh | 0.021317 | 0.021317 | 0.021317 | 0.0 | 11.92 +Comm | 0.0025985 | 0.0025985 | 0.0025985 | 0.0 | 1.45 +Output | 0.000175 | 0.000175 | 0.000175 | 0.0 | 0.10 +Modify | 0.061408 | 0.061408 | 0.061408 | 0.0 | 34.34 +Other | | 0.00293 | | | 1.64 + +Nlocal: 1200 ave 1200 max 1200 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 416 ave 416 max 416 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 8769 ave 8769 max 8769 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 8769 +Ave neighs/atom = 7.3075 +Ave special neighs/atom = 0.5 +Neighbor list builds = 47 +Dangerous builds = 2 +unfix 2 +unfix 4 +unfix 5 +fix 5 solute rigid/small molecule + create bodies CPU = 0.00015378 secs +150 rigid bodies with 450 atoms + 1.30435 = max distance from body owner to body atom +fix 4 all enforce2d +run 500 +Per MPI rank memory allocation (min/avg/max) = 8.64 | 8.64 | 8.64 Mbytes +Step Temp E_pair E_mol TotEng Press + 500 0.45533691 -1.9072316 0.13695201 -1.4006978 2.4545793 + 550 0.45627282 -1.912409 0.13695201 -1.4051155 2.1845065 + 600 0.44734553 -1.8890695 0.13695201 -1.389022 2.3458965 + 650 0.46444648 -1.9042462 0.13695201 -1.3903185 2.1609319 + 700 0.47113236 -1.8977576 0.13695201 -1.3784032 2.2420351 + 750 0.48554548 -1.9253545 0.13695201 -1.3943015 2.143907 + 800 0.46350091 -1.8865749 0.13695201 -1.3734146 2.294431 + 850 0.4766104 -1.9094039 0.13695201 -1.3856031 2.2077157 + 900 0.48988467 -1.9051538 0.13695201 -1.3705787 2.0107056 + 950 0.48351943 -1.9162485 0.13695201 -1.3868399 2.1891332 + 1000 0.49033701 -1.9115165 0.13695201 -1.3765742 2.1508141 +Loop time of 0.166502 on 1 procs for 500 steps with 1200 atoms + +Performance: 1297278.008 tau/day, 3002.958 timesteps/s +99.6% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.085767 | 0.085767 | 0.085767 | 0.0 | 51.51 +Bond | 0.0042562 | 0.0042562 | 0.0042562 | 0.0 | 2.56 +Neigh | 0.018039 | 0.018039 | 0.018039 | 0.0 | 10.83 +Comm | 0.0024002 | 0.0024002 | 0.0024002 | 0.0 | 1.44 +Output | 0.00018239 | 0.00018239 | 0.00018239 | 0.0 | 0.11 +Modify | 0.052717 | 0.052717 | 0.052717 | 0.0 | 31.66 +Other | | 0.003141 | | | 1.89 + +Nlocal: 1200 ave 1200 max 1200 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 415 ave 415 max 415 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 8743 ave 8743 max 8743 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 8743 +Ave neighs/atom = 7.28583 +Ave special neighs/atom = 0.5 +Neighbor list builds = 40 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/micelle/log.29Mar2019.micelle-rigid.g++.4 b/examples/micelle/log.29Mar2019.micelle-rigid.g++.4 new file mode 100644 index 0000000000..e65f67a527 --- /dev/null +++ b/examples/micelle/log.29Mar2019.micelle-rigid.g++.4 @@ -0,0 +1,260 @@ +LAMMPS (29 Mar 2019) + using 1 OpenMP thread(s) per MPI task +# 2d micelle simulation + +dimension 2 + +neighbor 0.3 bin +neigh_modify delay 5 + +atom_style bond + +# Soft potential push-off + +read_data data.micelle + orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1) + 2 by 2 by 1 MPI processor grid + reading atoms ... + 1200 atoms + scanning bonds ... + 1 = max bonds/atom + reading bonds ... + 300 bonds + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.000422001 secs + read_data CPU = 0.00473404 secs +special_bonds fene + 2 = max # of 1-2 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.000183344 secs + +pair_style soft 1.12246 +pair_coeff * * 0.0 1.12246 + +bond_style harmonic +bond_coeff 1 50.0 0.75 + +velocity all create 0.45 2349852 + +variable prefactor equal ramp(1.0,20.0) + +fix 1 all nve +fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0 +fix 3 all adapt 1 pair soft a * * v_prefactor +fix 4 all enforce2d + +thermo 50 +run 500 +Neighbor list info ... + update every 1 steps, delay 5 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.42246 + ghost atom cutoff = 1.42246 + binsize = 0.71123, bins = 51 51 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair soft, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.758 | 3.85 | 4.126 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518 + 50 0.54981866 0.93548899 0.068440043 1.5532895 1.9232786 + 100 0.45 0.99659327 0.079228519 1.5254468 3.2135679 + 150 0.86965411 0.90456016 0.07493355 1.8484231 4.3821925 + 200 0.45 1.01454 0.10663502 1.5708 4.7598476 + 250 0.79636561 0.82567712 0.12105337 1.7424325 5.4983899 + 300 0.45 0.86475538 0.11819875 1.4325791 5.8554758 + 350 0.72135464 0.70693069 0.10912636 1.5368106 6.0388247 + 400 0.45 0.75067331 0.14165013 1.3419484 6.3840708 + 450 0.64839221 0.62402486 0.14173679 1.4136135 6.4791009 + 500 0.45 0.66669513 0.13695201 1.2532721 6.807146 +Loop time of 0.0426326 on 4 procs for 500 steps with 1200 atoms + +Performance: 5066547.720 tau/day, 11728.120 timesteps/s +98.7% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.016784 | 0.019254 | 0.022154 | 1.5 | 45.16 +Bond | 0.0010612 | 0.0012558 | 0.0014153 | 0.4 | 2.95 +Neigh | 0.0046048 | 0.0046697 | 0.0047245 | 0.1 | 10.95 +Comm | 0.0064592 | 0.0097114 | 0.012527 | 2.4 | 22.78 +Output | 0.00022507 | 0.00026393 | 0.00033951 | 0.0 | 0.62 +Modify | 0.0041659 | 0.0048084 | 0.0053945 | 0.8 | 11.28 +Other | | 0.002669 | | | 6.26 + +Nlocal: 300 ave 304 max 292 min +Histogram: 1 0 0 0 0 0 0 0 2 1 +Nghost: 103.5 ave 108 max 98 min +Histogram: 1 0 0 1 0 0 0 0 0 2 +Neighs: 773.5 ave 792 max 735 min +Histogram: 1 0 0 0 0 0 0 0 2 1 + +Total # of neighbors = 3094 +Ave neighs/atom = 2.57833 +Ave special neighs/atom = 0.5 +Neighbor list builds = 52 +Dangerous builds = 0 + +unfix 3 + +# Main run + +pair_style lj/cut 2.5 + +# solvent/head - full-size and long-range + +pair_coeff 1 1 1.0 1.0 2.5 +pair_coeff 2 2 1.0 1.0 2.5 +pair_coeff 1 2 1.0 1.0 2.5 + +# tail/tail - size-averaged and long-range + +pair_coeff 3 3 1.0 0.75 2.5 +pair_coeff 4 4 1.0 0.50 2.5 +pair_coeff 3 4 1.0 0.67 2.5 + +# solvent/tail - full-size and repulsive + +pair_coeff 1 3 1.0 1.0 1.12246 +pair_coeff 1 4 1.0 1.0 1.12246 + +# head/tail - size-averaged and repulsive + +pair_coeff 2 3 1.0 0.88 1.12246 +pair_coeff 2 4 1.0 0.75 1.12246 + +thermo 50 + +#dump 1 all atom 2000 dump.micelle + +#dump 2 all image 2000 image.*.jpg type type zoom 1.6 +#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 + +#dump 3 all movie 2000 movie.mpg type type zoom 1.6 +#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 + +reset_timestep 0 +group solvent molecule 0 +750 atoms in group solvent +group solute subtract all solvent +450 atoms in group solute +unfix 1 +unfix 2 +unfix 4 +fix 1 solvent nve +fix 2 solvent temp/rescale 100 0.45 0.45 0.02 1.0 +fix 5 solute rigid molecule langevin 0.45 0.45 0.5 112211 +150 rigid bodies with 450 atoms +fix 4 all enforce2d +run 500 +Neighbor list info ... + update every 1 steps, delay 5 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 26 26 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.251 | 5.282 | 5.374 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0.45318168 -1.3753652 0.13695201 -0.8705807 1.975423 + 50 0.77871641 -1.6955252 0.13695201 -0.92651507 0.64222539 + 100 0.5336062 -1.7124572 0.13695201 -1.1423948 -0.11959696 + 150 0.58789067 -1.7926109 0.13695201 -1.1784877 1.2592743 + 200 0.47864796 -1.8040298 0.13695201 -1.2785752 3.6739793 + 250 0.51124651 -1.8614797 0.13695201 -1.309566 2.5817722 + 300 0.45695639 -1.8708384 0.13695201 -1.3629901 3.0833794 + 350 0.477504 -1.8924359 0.13695201 -1.3679098 -5.1605926 + 400 0.45328205 -1.87754 0.13695201 -1.372674 -4.0355858 + 450 0.47465031 -1.9071924 0.13695201 -1.3849826 3.1949617 + 500 0.45533691 -1.9072316 0.13695201 -1.4006978 0.48079061 +Loop time of 0.0887392 on 4 procs for 500 steps with 1200 atoms + +Performance: 2434100.210 tau/day, 5634.491 timesteps/s +98.9% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.022611 | 0.022839 | 0.023082 | 0.1 | 25.74 +Bond | 0.0010793 | 0.0011569 | 0.0012515 | 0.2 | 1.30 +Neigh | 0.0064609 | 0.0064996 | 0.0065265 | 0.0 | 7.32 +Comm | 0.0071712 | 0.0073687 | 0.0077734 | 0.3 | 8.30 +Output | 0.00023389 | 0.00025356 | 0.00030327 | 0.0 | 0.29 +Modify | 0.047258 | 0.047683 | 0.048503 | 0.2 | 53.73 +Other | | 0.002938 | | | 3.31 + +Nlocal: 300 ave 309 max 291 min +Histogram: 1 0 0 1 0 0 1 0 0 1 +Nghost: 218.75 ave 223 max 216 min +Histogram: 1 0 2 0 0 0 0 0 0 1 +Neighs: 2192.25 ave 2251 max 2113 min +Histogram: 1 0 0 1 0 0 0 0 0 2 + +Total # of neighbors = 8769 +Ave neighs/atom = 7.3075 +Ave special neighs/atom = 0.5 +Neighbor list builds = 47 +Dangerous builds = 2 +unfix 2 +unfix 4 +unfix 5 +fix 5 solute rigid/small molecule + create bodies CPU = 7.70092e-05 secs +150 rigid bodies with 450 atoms + 1.30435 = max distance from body owner to body atom +fix 4 all enforce2d +run 500 +Per MPI rank memory allocation (min/avg/max) = 8.565 | 8.597 | 8.69 Mbytes +Step Temp E_pair E_mol TotEng Press + 500 0.45533691 -1.9072316 0.13695201 -1.4006978 2.4545793 + 550 0.45627282 -1.912409 0.13695201 -1.4051155 2.1845065 + 600 0.44734553 -1.8890695 0.13695201 -1.389022 2.3458965 + 650 0.46444648 -1.9042462 0.13695201 -1.3903185 2.1609319 + 700 0.47113236 -1.8977576 0.13695201 -1.3784032 2.2420351 + 750 0.48554548 -1.9253545 0.13695201 -1.3943015 2.143907 + 800 0.46350091 -1.8865749 0.13695201 -1.3734146 2.294431 + 850 0.4766104 -1.9094039 0.13695201 -1.3856031 2.2077157 + 900 0.48988467 -1.9051538 0.13695201 -1.3705787 2.0107056 + 950 0.48351942 -1.9162485 0.13695201 -1.3868399 2.1891332 + 1000 0.490337 -1.9115164 0.13695201 -1.3765742 2.1508141 +Loop time of 0.0588261 on 4 procs for 500 steps with 1200 atoms + +Performance: 3671840.233 tau/day, 8499.630 timesteps/s +98.3% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.022407 | 0.022631 | 0.0229 | 0.1 | 38.47 +Bond | 0.0010669 | 0.0011355 | 0.0012124 | 0.2 | 1.93 +Neigh | 0.0052333 | 0.00528 | 0.0053182 | 0.0 | 8.98 +Comm | 0.0063677 | 0.0066406 | 0.0068488 | 0.2 | 11.29 +Output | 0.00023055 | 0.00024778 | 0.00028086 | 0.0 | 0.42 +Modify | 0.020577 | 0.020651 | 0.020834 | 0.1 | 35.11 +Other | | 0.00224 | | | 3.81 + +Nlocal: 300 ave 303 max 295 min +Histogram: 1 0 0 0 0 0 1 0 1 1 +Nghost: 219 ave 224 max 215 min +Histogram: 1 0 0 1 1 0 0 0 0 1 +Neighs: 2185.75 ave 2244 max 2143 min +Histogram: 1 1 0 0 0 1 0 0 0 1 + +Total # of neighbors = 8743 +Ave neighs/atom = 7.28583 +Ave special neighs/atom = 0.5 +Neighbor list builds = 40 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/micelle/log.29Mar2019.micelle.g++.1 b/examples/micelle/log.29Mar2019.micelle.g++.1 new file mode 100644 index 0000000000..d482d6c890 --- /dev/null +++ b/examples/micelle/log.29Mar2019.micelle.g++.1 @@ -0,0 +1,218 @@ +LAMMPS (29 Mar 2019) + using 1 OpenMP thread(s) per MPI task +# 2d micelle simulation + +dimension 2 + +neighbor 0.3 bin +neigh_modify delay 5 + +atom_style bond + +# Soft potential push-off + +read_data data.micelle + orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 1200 atoms + scanning bonds ... + 1 = max bonds/atom + reading bonds ... + 300 bonds + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.00037837 secs + read_data CPU = 0.00206876 secs +special_bonds fene + 2 = max # of 1-2 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.000177383 secs + +pair_style soft 1.12246 +pair_coeff * * 0.0 1.12246 + +bond_style harmonic +bond_coeff 1 50.0 0.75 + +velocity all create 0.45 2349852 + +variable prefactor equal ramp(1.0,20.0) + +fix 1 all nve +fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0 +fix 3 all adapt 1 pair soft a * * v_prefactor +fix 4 all enforce2d + +thermo 50 +run 1000 +Neighbor list info ... + update every 1 steps, delay 5 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.42246 + ghost atom cutoff = 1.42246 + binsize = 0.71123, bins = 51 51 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair soft, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.799 | 3.799 | 3.799 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518 + 50 0.47411013 0.67721272 0.057404514 1.2083323 1.3375852 + 100 0.45 0.73046745 0.054836584 1.234929 2.3196516 + 150 0.67521742 0.72402001 0.043490075 1.4421648 2.8744416 + 200 0.45 0.78481891 0.076931503 1.3113754 3.0412388 + 250 0.66479018 0.69790602 0.081075564 1.4432178 3.6917024 + 300 0.45 0.76820218 0.066727591 1.2845548 3.7861054 + 350 0.67619136 0.625715 0.072722727 1.3740656 4.2861621 + 400 0.45 0.68527759 0.090724527 1.2256271 4.4725214 + 450 0.56702844 0.64402767 0.080555563 1.2911391 4.7402211 + 500 0.45 0.64883009 0.078376672 1.1768318 4.7919294 + 550 0.564664 0.58260368 0.080779475 1.2275766 4.9855705 + 600 0.45 0.58193041 0.088386617 1.119942 5.131481 + 650 0.52110993 0.5415273 0.097683746 1.1598867 5.2500294 + 700 0.45 0.50856787 0.088471208 1.0466641 5.2550165 + 750 0.51510855 0.47441291 0.089429375 1.0785216 5.375763 + 800 0.45 0.49926696 0.085958476 1.0348504 5.4665914 + 850 0.50688494 0.46614429 0.088962292 1.0615691 5.556932 + 900 0.45 0.47785593 0.10150857 1.0289895 5.7765975 + 950 0.49590559 0.46050477 0.096404887 1.052402 5.8649245 + 1000 0.45 0.47691182 0.08808163 1.0146185 6.0177568 +Loop time of 0.208895 on 1 procs for 1000 steps with 1200 atoms + +Performance: 2068027.282 tau/day, 4787.100 timesteps/s +99.4% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.14142 | 0.14142 | 0.14142 | 0.0 | 67.70 +Bond | 0.008441 | 0.008441 | 0.008441 | 0.0 | 4.04 +Neigh | 0.025716 | 0.025716 | 0.025716 | 0.0 | 12.31 +Comm | 0.0036864 | 0.0036864 | 0.0036864 | 0.0 | 1.76 +Output | 0.0003562 | 0.0003562 | 0.0003562 | 0.0 | 0.17 +Modify | 0.023699 | 0.023699 | 0.023699 | 0.0 | 11.35 +Other | | 0.00558 | | | 2.67 + +Nlocal: 1200 ave 1200 max 1200 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 195 ave 195 max 195 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 3136 ave 3136 max 3136 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 3136 +Ave neighs/atom = 2.61333 +Ave special neighs/atom = 0.5 +Neighbor list builds = 92 +Dangerous builds = 0 + +unfix 3 + +# Main run + +pair_style lj/cut 2.5 + +# solvent/head - full-size and long-range + +pair_coeff 1 1 1.0 1.0 2.5 +pair_coeff 2 2 1.0 1.0 2.5 +pair_coeff 1 2 1.0 1.0 2.5 + +# tail/tail - size-averaged and long-range + +pair_coeff 3 3 1.0 0.75 2.5 +pair_coeff 4 4 1.0 0.50 2.5 +pair_coeff 3 4 1.0 0.67 2.5 + +# solvent/tail - full-size and repulsive + +pair_coeff 1 3 1.0 1.0 1.12246 +pair_coeff 1 4 1.0 1.0 1.12246 + +# head/tail - size-averaged and repulsive + +pair_coeff 2 3 1.0 0.88 1.12246 +pair_coeff 2 4 1.0 0.75 1.12246 + +thermo 50 + +#dump 1 all atom 2000 dump.micelle + +#dump 2 all image 2000 image.*.jpg type type zoom 1.6 +#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 + +#dump 3 all movie 2000 movie.mpg type type zoom 1.6 +#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 + +reset_timestep 0 +run 1000 +Neighbor list info ... + update every 1 steps, delay 5 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 26 26 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.024 | 4.024 | 4.024 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0.45 -1.7056163 0.08808163 -1.1679097 3.9431686 + 50 0.59734982 -1.8103783 0.076066922 -1.1374593 3.2770557 + 100 0.45 -1.8347112 0.093132329 -1.2919539 3.024661 + 150 0.51924311 -1.8943977 0.076004124 -1.2995832 2.5570373 + 200 0.45 -1.8918672 0.082422107 -1.3598201 2.5629655 + 250 0.50281134 -1.920406 0.074011331 -1.3440023 2.3518682 + 300 0.45 -1.9351047 0.075337265 -1.4101424 2.3249947 + 350 0.47650026 -1.9313687 0.072115117 -1.3831504 2.1987532 + 400 0.45 -1.9554318 0.081603939 -1.4242028 2.0787066 + 450 0.47220236 -1.9468502 0.065625624 -1.4094157 2.0984288 + 500 0.4684673 -1.9444333 0.076696283 -1.3996601 2.0528682 + 550 0.47683128 -1.958676 0.070589719 -1.4116523 2.0856022 + 600 0.46851243 -1.9338267 0.07060548 -1.3950992 2.26405 + 650 0.46874142 -1.9462493 0.069134685 -1.4087638 2.1070263 + 700 0.46437384 -1.9309953 0.071977522 -1.3950309 2.2256923 + 750 0.47326225 -1.9484255 0.075435845 -1.4001218 2.0880254 + 800 0.45 -1.9646005 0.064159585 -1.4508159 2.0612696 + 850 0.46748307 -1.970559 0.060384874 -1.4430806 1.9472879 + 900 0.46909484 -1.953723 0.062470295 -1.4225488 2.0222909 + 950 0.45631531 -1.9387753 0.067536568 -1.4153037 2.0638421 + 1000 0.45 -1.9727646 0.058607721 -1.4645318 1.9982315 +Loop time of 0.252254 on 1 procs for 1000 steps with 1200 atoms + +Performance: 1712557.882 tau/day, 3964.254 timesteps/s +99.0% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.17177 | 0.17177 | 0.17177 | 0.0 | 68.09 +Bond | 0.0084555 | 0.0084555 | 0.0084555 | 0.0 | 3.35 +Neigh | 0.03991 | 0.03991 | 0.03991 | 0.0 | 15.82 +Comm | 0.0049119 | 0.0049119 | 0.0049119 | 0.0 | 1.95 +Output | 0.00039077 | 0.00039077 | 0.00039077 | 0.0 | 0.15 +Modify | 0.021131 | 0.021131 | 0.021131 | 0.0 | 8.38 +Other | | 0.005685 | | | 2.25 + +Nlocal: 1200 ave 1200 max 1200 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 415 ave 415 max 415 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 8586 ave 8586 max 8586 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 8586 +Ave neighs/atom = 7.155 +Ave special neighs/atom = 0.5 +Neighbor list builds = 86 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/micelle/log.29Mar2019.micelle.g++.4 b/examples/micelle/log.29Mar2019.micelle.g++.4 new file mode 100644 index 0000000000..f3a54970cf --- /dev/null +++ b/examples/micelle/log.29Mar2019.micelle.g++.4 @@ -0,0 +1,218 @@ +LAMMPS (29 Mar 2019) + using 1 OpenMP thread(s) per MPI task +# 2d micelle simulation + +dimension 2 + +neighbor 0.3 bin +neigh_modify delay 5 + +atom_style bond + +# Soft potential push-off + +read_data data.micelle + orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1) + 2 by 2 by 1 MPI processor grid + reading atoms ... + 1200 atoms + scanning bonds ... + 1 = max bonds/atom + reading bonds ... + 300 bonds + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.000413656 secs + read_data CPU = 0.00487924 secs +special_bonds fene + 2 = max # of 1-2 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.000178576 secs + +pair_style soft 1.12246 +pair_coeff * * 0.0 1.12246 + +bond_style harmonic +bond_coeff 1 50.0 0.75 + +velocity all create 0.45 2349852 + +variable prefactor equal ramp(1.0,20.0) + +fix 1 all nve +fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0 +fix 3 all adapt 1 pair soft a * * v_prefactor +fix 4 all enforce2d + +thermo 50 +run 1000 +Neighbor list info ... + update every 1 steps, delay 5 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.42246 + ghost atom cutoff = 1.42246 + binsize = 0.71123, bins = 51 51 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair soft, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.758 | 3.85 | 4.126 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518 + 50 0.47411013 0.67721272 0.057404514 1.2083323 1.3375852 + 100 0.45 0.73046745 0.054836584 1.234929 2.3196516 + 150 0.67521742 0.72402001 0.043490075 1.4421648 2.8744416 + 200 0.45 0.78481891 0.076931503 1.3113754 3.0412388 + 250 0.66479018 0.69790602 0.081075564 1.4432178 3.6917024 + 300 0.45 0.76820218 0.066727591 1.2845548 3.7861054 + 350 0.67619136 0.625715 0.072722727 1.3740656 4.2861621 + 400 0.45 0.68527759 0.090724527 1.2256271 4.4725214 + 450 0.56702844 0.64402767 0.080555563 1.2911391 4.7402211 + 500 0.45 0.64883009 0.078376672 1.1768318 4.7919294 + 550 0.564664 0.58260368 0.080779475 1.2275766 4.9855705 + 600 0.45 0.58193041 0.088386617 1.119942 5.131481 + 650 0.52110993 0.5415273 0.097683746 1.1598867 5.2500294 + 700 0.45 0.50856787 0.088471208 1.0466641 5.2550165 + 750 0.51510855 0.47441291 0.089429375 1.0785216 5.375763 + 800 0.45 0.49926696 0.085958476 1.0348504 5.4665914 + 850 0.50688494 0.46614429 0.088962292 1.0615691 5.556932 + 900 0.45 0.47785593 0.10150857 1.0289895 5.7765975 + 950 0.49590559 0.46050477 0.096404887 1.052402 5.8649245 + 1000 0.45 0.47691182 0.08808163 1.0146185 6.0177568 +Loop time of 0.0906248 on 4 procs for 1000 steps with 1200 atoms + +Performance: 4766906.584 tau/day, 11034.506 timesteps/s +98.9% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.036572 | 0.039266 | 0.041216 | 1.0 | 43.33 +Bond | 0.0023205 | 0.0024512 | 0.0025697 | 0.2 | 2.70 +Neigh | 0.0088909 | 0.0089301 | 0.0089679 | 0.0 | 9.85 +Comm | 0.022308 | 0.024047 | 0.027175 | 1.3 | 26.53 +Output | 0.00057411 | 0.00061274 | 0.00071025 | 0.0 | 0.68 +Modify | 0.0083182 | 0.0092374 | 0.0098341 | 0.6 | 10.19 +Other | | 0.006081 | | | 6.71 + +Nlocal: 300 ave 305 max 292 min +Histogram: 1 0 0 0 0 0 1 0 1 1 +Nghost: 100.25 ave 108 max 93 min +Histogram: 1 0 1 0 0 0 1 0 0 1 +Neighs: 784 ave 815 max 739 min +Histogram: 1 0 0 0 0 0 1 1 0 1 + +Total # of neighbors = 3136 +Ave neighs/atom = 2.61333 +Ave special neighs/atom = 0.5 +Neighbor list builds = 92 +Dangerous builds = 0 + +unfix 3 + +# Main run + +pair_style lj/cut 2.5 + +# solvent/head - full-size and long-range + +pair_coeff 1 1 1.0 1.0 2.5 +pair_coeff 2 2 1.0 1.0 2.5 +pair_coeff 1 2 1.0 1.0 2.5 + +# tail/tail - size-averaged and long-range + +pair_coeff 3 3 1.0 0.75 2.5 +pair_coeff 4 4 1.0 0.50 2.5 +pair_coeff 3 4 1.0 0.67 2.5 + +# solvent/tail - full-size and repulsive + +pair_coeff 1 3 1.0 1.0 1.12246 +pair_coeff 1 4 1.0 1.0 1.12246 + +# head/tail - size-averaged and repulsive + +pair_coeff 2 3 1.0 0.88 1.12246 +pair_coeff 2 4 1.0 0.75 1.12246 + +thermo 50 + +#dump 1 all atom 2000 dump.micelle + +#dump 2 all image 2000 image.*.jpg type type zoom 1.6 +#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 + +#dump 3 all movie 2000 movie.mpg type type zoom 1.6 +#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 + +reset_timestep 0 +run 1000 +Neighbor list info ... + update every 1 steps, delay 5 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 26 26 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.001 | 4.032 | 4.124 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0.45 -1.7056163 0.08808163 -1.1679097 3.9431686 + 50 0.59734982 -1.8103783 0.076066922 -1.1374593 3.2770557 + 100 0.45 -1.8347112 0.093132329 -1.2919539 3.024661 + 150 0.51924311 -1.8943977 0.076004124 -1.2995832 2.5570373 + 200 0.45 -1.8918672 0.082422107 -1.3598201 2.5629655 + 250 0.50281134 -1.920406 0.074011331 -1.3440023 2.3518682 + 300 0.45 -1.9351047 0.075337265 -1.4101424 2.3249947 + 350 0.47650026 -1.9313687 0.072115117 -1.3831504 2.1987532 + 400 0.45 -1.9554318 0.081603939 -1.4242028 2.0787066 + 450 0.47220236 -1.9468502 0.065625625 -1.4094157 2.0984288 + 500 0.4684673 -1.9444333 0.076696285 -1.3996601 2.0528682 + 550 0.47683128 -1.958676 0.070589721 -1.4116523 2.0856023 + 600 0.46851245 -1.9338267 0.070605469 -1.3950992 2.26405 + 650 0.46874143 -1.9462493 0.069134686 -1.4087638 2.1070262 + 700 0.4643739 -1.9309953 0.071977511 -1.3950309 2.225692 + 750 0.47326259 -1.9484258 0.075435808 -1.4001218 2.0880235 + 800 0.45 -1.9646003 0.06415956 -1.4508158 2.0612703 + 850 0.46748278 -1.9705588 0.06038513 -1.4430804 1.9472884 + 900 0.46909438 -1.9537221 0.062470305 -1.4225483 2.0223008 + 950 0.45631508 -1.9387742 0.067536066 -1.4153033 2.063854 + 1000 0.45 -1.9727651 0.058608085 -1.464532 1.9982447 +Loop time of 0.0878521 on 4 procs for 1000 steps with 1200 atoms + +Performance: 4917357.613 tau/day, 11382.772 timesteps/s +99.0% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.043517 | 0.044455 | 0.046903 | 0.7 | 50.60 +Bond | 0.0020199 | 0.0022303 | 0.0024347 | 0.4 | 2.54 +Neigh | 0.012207 | 0.012335 | 0.012512 | 0.1 | 14.04 +Comm | 0.014938 | 0.018265 | 0.020068 | 1.5 | 20.79 +Output | 0.00061369 | 0.00064814 | 0.00073504 | 0.0 | 0.74 +Modify | 0.0052264 | 0.0053691 | 0.0055039 | 0.2 | 6.11 +Other | | 0.00455 | | | 5.18 + +Nlocal: 300 ave 305 max 296 min +Histogram: 1 1 0 0 0 0 1 0 0 1 +Nghost: 219.5 ave 228 max 214 min +Histogram: 1 0 1 1 0 0 0 0 0 1 +Neighs: 2146.5 ave 2201 max 2114 min +Histogram: 1 1 0 1 0 0 0 0 0 1 + +Total # of neighbors = 8586 +Ave neighs/atom = 7.155 +Ave special neighs/atom = 0.5 +Neighbor list builds = 86 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/lib/message/cslib/src/STUBS_MPI/mpi.h b/lib/message/cslib/src/STUBS_MPI/mpi_dummy.h similarity index 100% rename from lib/message/cslib/src/STUBS_MPI/mpi.h rename to lib/message/cslib/src/STUBS_MPI/mpi_dummy.h diff --git a/lib/message/cslib/src/cslib.cpp b/lib/message/cslib/src/cslib.cpp index 874333607e..336ba87588 100644 --- a/lib/message/cslib/src/cslib.cpp +++ b/lib/message/cslib/src/cslib.cpp @@ -12,7 +12,11 @@ See the README file in the top-level CSlib directory. ------------------------------------------------------------------------- */ +#ifdef MPI_YES #include +#else +#include +#endif #include #include #include diff --git a/lib/message/cslib/src/cslib_wrap.cpp b/lib/message/cslib/src/cslib_wrap.cpp index c2d69eaf0d..64b4d53b25 100644 --- a/lib/message/cslib/src/cslib_wrap.cpp +++ b/lib/message/cslib/src/cslib_wrap.cpp @@ -14,7 +14,11 @@ // C style library interface to CSlib class +#ifdef MPI_YES #include +#else +#include +#endif #include #include #include diff --git a/lib/message/cslib/src/msg.cpp b/lib/message/cslib/src/msg.cpp index da22c81850..ff654ecbcf 100644 --- a/lib/message/cslib/src/msg.cpp +++ b/lib/message/cslib/src/msg.cpp @@ -12,7 +12,11 @@ See the README file in the top-level CSlib directory. ------------------------------------------------------------------------- */ +#ifdef MPI_YES #include +#else +#include +#endif #include #include #include diff --git a/lib/message/cslib/src/msg.h b/lib/message/cslib/src/msg.h index f75942b027..81c2d21cb9 100644 --- a/lib/message/cslib/src/msg.h +++ b/lib/message/cslib/src/msg.h @@ -15,7 +15,11 @@ #ifndef MSG_H #define MSG_H +#ifdef MPI_YES #include +#else +#include +#endif namespace CSLIB_NS { @@ -37,7 +41,7 @@ class Msg { int nfield; int *fieldID,*fieldtype,*fieldlen; int lengths[2]; - + void init(int); void allocate(int, int &, int *&, int, int &, char *&); void *smalloc(int); diff --git a/lib/message/cslib/src/msg_file.cpp b/lib/message/cslib/src/msg_file.cpp index d97e249fad..31cdfef544 100644 --- a/lib/message/cslib/src/msg_file.cpp +++ b/lib/message/cslib/src/msg_file.cpp @@ -12,7 +12,11 @@ See the README file in the top-level CSlib directory. ------------------------------------------------------------------------- */ +#ifdef MPI_YES #include +#else +#include +#endif #include #include #include diff --git a/lib/message/cslib/src/msg_mpi_one.cpp b/lib/message/cslib/src/msg_mpi_one.cpp index db11735b27..c6fbd8732f 100644 --- a/lib/message/cslib/src/msg_mpi_one.cpp +++ b/lib/message/cslib/src/msg_mpi_one.cpp @@ -12,7 +12,11 @@ See the README file in the top-level CSlib directory. ------------------------------------------------------------------------- */ +#ifdef MPI_YES #include +#else +#include +#endif #include #include #include diff --git a/lib/message/cslib/src/msg_mpi_two.cpp b/lib/message/cslib/src/msg_mpi_two.cpp index e9a9e87eeb..2a4fa65ff7 100644 --- a/lib/message/cslib/src/msg_mpi_two.cpp +++ b/lib/message/cslib/src/msg_mpi_two.cpp @@ -12,7 +12,11 @@ See the README file in the top-level CSlib directory. ------------------------------------------------------------------------- */ +#ifdef MPI_YES #include +#else +#include +#endif #include #include #include diff --git a/lib/message/cslib/src/msg_zmq.cpp b/lib/message/cslib/src/msg_zmq.cpp index c2d408f3a5..8bee3aebde 100644 --- a/lib/message/cslib/src/msg_zmq.cpp +++ b/lib/message/cslib/src/msg_zmq.cpp @@ -12,7 +12,11 @@ See the README file in the top-level CSlib directory. ------------------------------------------------------------------------- */ +#ifdef MPI_YES #include +#else +#include +#endif #include #include #include diff --git a/src/GRANULAR/pair_granular.cpp b/src/GRANULAR/pair_granular.cpp index 973acbbaf4..ce6cae75e4 100644 --- a/src/GRANULAR/pair_granular.cpp +++ b/src/GRANULAR/pair_granular.cpp @@ -872,16 +872,16 @@ void PairGranular::coeff(int narg, char **arg) if (iarg + 4 >= narg) error->all(FLERR,"Illegal pair_coeff command, " "not enough parameters provided for twist model"); - twist_model_one = TWIST_SDS; - twist_history = 1; - // kt and gammat and friction coeff - twist_coeffs_one[0] = force->numeric(FLERR,arg[iarg+2]); - twist_coeffs_one[1] = force->numeric(FLERR,arg[iarg+3]); - twist_coeffs_one[2] = force->numeric(FLERR,arg[iarg+4]); - iarg += 5; + twist_model_one = TWIST_SDS; + twist_history = 1; + // kt and gammat and friction coeff + twist_coeffs_one[0] = force->numeric(FLERR,arg[iarg+2]); + twist_coeffs_one[1] = force->numeric(FLERR,arg[iarg+3]); + twist_coeffs_one[2] = force->numeric(FLERR,arg[iarg+4]); + iarg += 5; } else { - error->all(FLERR, "Illegal pair_coeff command, " - "twisting friction model not recognized"); + error->all(FLERR, "Illegal pair_coeff command, " + "twisting friction model not recognized"); } } else if (strcmp(arg[iarg], "cutoff") == 0) { if (iarg + 1 >= narg) diff --git a/src/KOKKOS/domain_kokkos.h b/src/KOKKOS/domain_kokkos.h index 7b8504dba8..eccc36a021 100644 --- a/src/KOKKOS/domain_kokkos.h +++ b/src/KOKKOS/domain_kokkos.h @@ -36,10 +36,12 @@ class DomainKokkos : public Domain { void image_flip(int, int, int); void x2lamda(int); void lamda2x(int); - // these lines bring in the x2lamda signatures from Domain - // that are not overloaded here - using Domain::x2lamda; - using Domain::lamda2x; + // forward remaining x2lamda() and lambda2x() variants to parent class + void x2lamda(double *a, double *b) { Domain::x2lamda(a,b); } + void lamda2x(double *a, double *b) { Domain::lamda2x(a,b); } + void x2lamda(double *a, double *b, double *c, double *d) { + Domain::x2lamda(a,b,c,d); + } int closest_image(const int, int) const; diff --git a/src/KOKKOS/pair_exp6_rx_kokkos.cpp b/src/KOKKOS/pair_exp6_rx_kokkos.cpp index fa10c6d30f..0a6372fdf8 100644 --- a/src/KOKKOS/pair_exp6_rx_kokkos.cpp +++ b/src/KOKKOS/pair_exp6_rx_kokkos.cpp @@ -36,6 +36,10 @@ #include "atom_kokkos.h" #include "kokkos.h" +#ifdef _OPENMP +#include +#endif + using namespace LAMMPS_NS; using namespace MathConst; using namespace MathSpecialKokkos; diff --git a/src/KOKKOS/pair_reaxc_kokkos.cpp b/src/KOKKOS/pair_reaxc_kokkos.cpp index c6ee50c6ac..dda75782b2 100644 --- a/src/KOKKOS/pair_reaxc_kokkos.cpp +++ b/src/KOKKOS/pair_reaxc_kokkos.cpp @@ -447,23 +447,23 @@ int PairReaxCKokkos::Init_Lookup_Tables() num_atom_types = atom->ntypes; dr = control->nonb_cut / control->tabulate; h = (double*) - smalloc( (control->tabulate+2) * sizeof(double), "lookup:h", world ); + smalloc( control->error_ptr, (control->tabulate+2) * sizeof(double), "lookup:h"); fh = (double*) - smalloc( (control->tabulate+2) * sizeof(double), "lookup:fh", world ); + smalloc( control->error_ptr, (control->tabulate+2) * sizeof(double), "lookup:fh"); fvdw = (double*) - smalloc( (control->tabulate+2) * sizeof(double), "lookup:fvdw", world ); + smalloc( control->error_ptr, (control->tabulate+2) * sizeof(double), "lookup:fvdw"); fCEvd = (double*) - smalloc( (control->tabulate+2) * sizeof(double), "lookup:fCEvd", world ); + smalloc( control->error_ptr, (control->tabulate+2) * sizeof(double), "lookup:fCEvd"); fele = (double*) - smalloc( (control->tabulate+2) * sizeof(double), "lookup:fele", world ); + smalloc( control->error_ptr, (control->tabulate+2) * sizeof(double), "lookup:fele"); fCEclmb = (double*) - smalloc( (control->tabulate+2) * sizeof(double), "lookup:fCEclmb", world ); + smalloc( control->error_ptr, (control->tabulate+2) * sizeof(double), "lookup:fCEclmb"); LR = (LR_lookup_table**) - scalloc( num_atom_types+1, sizeof(LR_lookup_table*), "lookup:LR", world ); + scalloc( control->error_ptr, num_atom_types+1, sizeof(LR_lookup_table*), "lookup:LR"); for( i = 0; i < num_atom_types+1; ++i ) LR[i] = (LR_lookup_table*) - scalloc( num_atom_types+1, sizeof(LR_lookup_table), "lookup:LR[i]", world ); + scalloc( control->error_ptr, num_atom_types+1, sizeof(LR_lookup_table), "lookup:LR[i]"); for( i = 1; i <= num_atom_types; ++i ) { for( j = i; j <= num_atom_types; ++j ) { @@ -473,22 +473,18 @@ int PairReaxCKokkos::Init_Lookup_Tables() LR[i][j].dx = dr; LR[i][j].inv_dx = control->tabulate / control->nonb_cut; LR[i][j].y = (LR_data*) - smalloc( LR[i][j].n * sizeof(LR_data), "lookup:LR[i,j].y", world ); + smalloc( control->error_ptr, LR[i][j].n * sizeof(LR_data), "lookup:LR[i,j].y"); LR[i][j].H = (cubic_spline_coef*) - smalloc( LR[i][j].n*sizeof(cubic_spline_coef),"lookup:LR[i,j].H" , - world ); + smalloc( control->error_ptr, LR[i][j].n*sizeof(cubic_spline_coef),"lookup:LR[i,j].H"); LR[i][j].vdW = (cubic_spline_coef*) - smalloc( LR[i][j].n*sizeof(cubic_spline_coef),"lookup:LR[i,j].vdW", - world); + smalloc( control->error_ptr, LR[i][j].n*sizeof(cubic_spline_coef),"lookup:LR[i,j].vdW"); LR[i][j].CEvd = (cubic_spline_coef*) - smalloc( LR[i][j].n*sizeof(cubic_spline_coef),"lookup:LR[i,j].CEvd", - world); + smalloc( control->error_ptr, LR[i][j].n*sizeof(cubic_spline_coef),"lookup:LR[i,j].CEvd"); LR[i][j].ele = (cubic_spline_coef*) - smalloc( LR[i][j].n*sizeof(cubic_spline_coef),"lookup:LR[i,j].ele", - world ); + smalloc( control->error_ptr, LR[i][j].n*sizeof(cubic_spline_coef),"lookup:LR[i,j].ele"); LR[i][j].CEclmb = (cubic_spline_coef*) - smalloc( LR[i][j].n*sizeof(cubic_spline_coef), - "lookup:LR[i,j].CEclmb", world ); + smalloc( control->error_ptr, LR[i][j].n*sizeof(cubic_spline_coef), + "lookup:LR[i,j].CEclmb"); for( r = 1; r <= control->tabulate; ++r ) { LR_vdW_Coulomb(i, j, r * dr, &(LR[i][j].y[r]) ); @@ -512,24 +508,20 @@ int PairReaxCKokkos::Init_Lookup_Tables() vlast_vdw = fCEvd[r-1]; vlast_ele = fele[r-1]; - Natural_Cubic_Spline( &h[1], &fh[1], - &(LR[i][j].H[1]), control->tabulate+1, world ); + Natural_Cubic_Spline( control->error_ptr, &h[1], &fh[1], + &(LR[i][j].H[1]), control->tabulate+1 ); - Complete_Cubic_Spline( &h[1], &fvdw[1], v0_vdw, vlast_vdw, - &(LR[i][j].vdW[1]), control->tabulate+1, - world ); + Complete_Cubic_Spline( control->error_ptr, &h[1], &fvdw[1], v0_vdw, vlast_vdw, + &(LR[i][j].vdW[1]), control->tabulate+1 ); - Natural_Cubic_Spline( &h[1], &fCEvd[1], - &(LR[i][j].CEvd[1]), control->tabulate+1, - world ); + Natural_Cubic_Spline( control->error_ptr, &h[1], &fCEvd[1], + &(LR[i][j].CEvd[1]), control->tabulate+1 ); - Complete_Cubic_Spline( &h[1], &fele[1], v0_ele, vlast_ele, - &(LR[i][j].ele[1]), control->tabulate+1, - world ); + Complete_Cubic_Spline( control->error_ptr, &h[1], &fele[1], v0_ele, vlast_ele, + &(LR[i][j].ele[1]), control->tabulate+1 ); - Natural_Cubic_Spline( &h[1], &fCEclmb[1], - &(LR[i][j].CEclmb[1]), control->tabulate+1, - world ); + Natural_Cubic_Spline( control->error_ptr, &h[1], &fCEclmb[1], + &(LR[i][j].CEclmb[1]), control->tabulate+1 ); } } free(h); @@ -555,16 +547,16 @@ void PairReaxCKokkos::Deallocate_Lookup_Tables() for( i = 0; i <= ntypes; ++i ) { for( j = i; j <= ntypes; ++j ) if (LR[i][j].n) { - sfree( LR[i][j].y, "LR[i,j].y" ); - sfree( LR[i][j].H, "LR[i,j].H" ); - sfree( LR[i][j].vdW, "LR[i,j].vdW" ); - sfree( LR[i][j].CEvd, "LR[i,j].CEvd" ); - sfree( LR[i][j].ele, "LR[i,j].ele" ); - sfree( LR[i][j].CEclmb, "LR[i,j].CEclmb" ); + sfree( control->error_ptr, LR[i][j].y, "LR[i,j].y" ); + sfree( control->error_ptr, LR[i][j].H, "LR[i,j].H" ); + sfree( control->error_ptr, LR[i][j].vdW, "LR[i,j].vdW" ); + sfree( control->error_ptr, LR[i][j].CEvd, "LR[i,j].CEvd" ); + sfree( control->error_ptr, LR[i][j].ele, "LR[i,j].ele" ); + sfree( control->error_ptr, LR[i][j].CEclmb, "LR[i,j].CEclmb" ); } - sfree( LR[i], "LR[i]" ); + sfree( control->error_ptr, LR[i], "LR[i]" ); } - sfree( LR, "LR" ); + sfree( control->error_ptr, LR, "LR" ); } /* ---------------------------------------------------------------------- */ diff --git a/src/KOKKOS/pair_snap_kokkos_impl.h b/src/KOKKOS/pair_snap_kokkos_impl.h index 569783f926..bb2a5e9171 100644 --- a/src/KOKKOS/pair_snap_kokkos_impl.h +++ b/src/KOKKOS/pair_snap_kokkos_impl.h @@ -32,7 +32,7 @@ #define MAXLINE 1024 #define MAXWORD 3 -using namespace LAMMPS_NS; +namespace LAMMPS_NS { // Outstanding issues with quadratic term // 1. there seems to a problem with compute_optimized energy calc @@ -674,3 +674,4 @@ double PairSNAPKokkos::memory_usage() bytes += snaKK.memory_usage(); return bytes; } +} diff --git a/src/KOKKOS/sna_kokkos_impl.h b/src/KOKKOS/sna_kokkos_impl.h index 6a19c57829..0f2a450a3d 100644 --- a/src/KOKKOS/sna_kokkos_impl.h +++ b/src/KOKKOS/sna_kokkos_impl.h @@ -20,7 +20,7 @@ #include #include -using namespace LAMMPS_NS; +namespace LAMMPS_NS { static const double MY_PI = 3.14159265358979323846; // pi @@ -1300,3 +1300,5 @@ double SNAKokkos::memory_usage() bytes += jdim * jdim * jdim * jdim * jdim * sizeof(std::complex); return bytes; } + +} // namespace LAMMPS_NS diff --git a/src/MESSAGE/fix_client_md.cpp b/src/MESSAGE/fix_client_md.cpp index 9c1bfcc796..727481dcc0 100644 --- a/src/MESSAGE/fix_client_md.cpp +++ b/src/MESSAGE/fix_client_md.cpp @@ -89,7 +89,7 @@ FixClientMD::~FixClientMD() int nfield; int *fieldID,*fieldtype,*fieldlen; - int msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen); + cs->recv(nfield,fieldID,fieldtype,fieldlen); // clean-up @@ -173,8 +173,6 @@ void FixClientMD::min_setup(int vflag) void FixClientMD::post_force(int vflag) { - int i,j,m; - // energy and virial setup if (vflag) v_setup(vflag); @@ -286,7 +284,7 @@ void FixClientMD::receive_fev(int vflag) int nfield; int *fieldID,*fieldtype,*fieldlen; - int msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen); + cs->recv(nfield,fieldID,fieldtype,fieldlen); double *forces = (double *) cs->unpack(FORCES); double **f = atom->f; diff --git a/src/MESSAGE/message.cpp b/src/MESSAGE/message.cpp index e9bff7d38a..61221ca26e 100644 --- a/src/MESSAGE/message.cpp +++ b/src/MESSAGE/message.cpp @@ -22,10 +22,6 @@ using namespace LAMMPS_NS; using namespace CSLIB_NS; -// customize by adding a new server protocol enum - -enum{MD,MC}; - /* ---------------------------------------------------------------------- */ void Message::command(int narg, char **arg) @@ -38,12 +34,10 @@ void Message::command(int narg, char **arg) else error->all(FLERR,"Illegal message command"); lmp->clientserver = clientserver; - // customize by adding a new server protocol + // validate supported protocols - int protocol; - if (strcmp(arg[1],"md") == 0) protocol = MD; - else if (strcmp(arg[1],"mc") == 0) protocol = MC; - else error->all(FLERR,"Unknown message protocol"); + if ((strcmp(arg[1],"md") != 0) && (strcmp(arg[1],"mc") != 0)) + error->all(FLERR,"Unknown message protocol"); // instantiate CSlib with chosen communication mode diff --git a/src/MESSAGE/server_mc.cpp b/src/MESSAGE/server_mc.cpp index 8e9a297912..8152b1f772 100644 --- a/src/MESSAGE/server_mc.cpp +++ b/src/MESSAGE/server_mc.cpp @@ -37,8 +37,8 @@ ServerMC::ServerMC(LAMMPS *lmp) : Pointers(lmp) {} void ServerMC::loop() { - int i,j,m; - double xold[3],xnew[3]; + int m; + double xold[3]; tagint atomid; CSlib *cs = (CSlib *) lmp->cslib; diff --git a/src/MESSAGE/server_md.cpp b/src/MESSAGE/server_md.cpp index 8debd3a987..bef327616e 100644 --- a/src/MESSAGE/server_md.cpp +++ b/src/MESSAGE/server_md.cpp @@ -78,7 +78,7 @@ ServerMD::~ServerMD() void ServerMD::loop() { - int i,j,m; + int j,m; // cs = instance of CSlib diff --git a/src/STUBS/mpi.c b/src/STUBS/mpi.c index 053108fee8..09bb48ecdc 100644 --- a/src/STUBS/mpi.c +++ b/src/STUBS/mpi.c @@ -200,7 +200,11 @@ int MPI_Request_free(MPI_Request *request) int MPI_Send(const void *buf, int count, MPI_Datatype datatype, int dest, int tag, MPI_Comm comm) { - printf("MPI Stub WARNING: Should not send message to self\n"); + static int callcount=0; + if (callcount == 0) { + printf("MPI Stub WARNING: Should not send message to self\n"); + ++callcount; + } return 0; } @@ -209,7 +213,11 @@ int MPI_Send(const void *buf, int count, MPI_Datatype datatype, int MPI_Isend(const void *buf, int count, MPI_Datatype datatype, int source, int tag, MPI_Comm comm, MPI_Request *request) { - printf("MPI Stub WARNING: Should not send message to self\n"); + static int callcount=0; + if (callcount == 0) { + printf("MPI Stub WARNING: Should not send message to self\n"); + ++callcount; + } return 0; } @@ -218,7 +226,11 @@ int MPI_Isend(const void *buf, int count, MPI_Datatype datatype, int MPI_Rsend(const void *buf, int count, MPI_Datatype datatype, int dest, int tag, MPI_Comm comm) { - printf("MPI Stub WARNING: Should not rsend message to self\n"); + static int callcount=0; + if (callcount == 0) { + printf("MPI Stub WARNING: Should not rsend message to self\n"); + ++callcount; + } return 0; } @@ -227,7 +239,11 @@ int MPI_Rsend(const void *buf, int count, MPI_Datatype datatype, int MPI_Recv(void *buf, int count, MPI_Datatype datatype, int source, int tag, MPI_Comm comm, MPI_Status *status) { - printf("MPI Stub WARNING: Should not recv message from self\n"); + static int callcount=0; + if (callcount == 0) { + printf("MPI Stub WARNING: Should not recv message from self\n"); + ++callcount; + } return 0; } @@ -236,7 +252,11 @@ int MPI_Recv(void *buf, int count, MPI_Datatype datatype, int MPI_Irecv(void *buf, int count, MPI_Datatype datatype, int source, int tag, MPI_Comm comm, MPI_Request *request) { - printf("MPI Stub WARNING: Should not recv message from self\n"); + static int callcount=0; + if (callcount == 0) { + printf("MPI Stub WARNING: Should not recv message from self\n"); + ++callcount; + } return 0; } @@ -244,7 +264,11 @@ int MPI_Irecv(void *buf, int count, MPI_Datatype datatype, int MPI_Wait(MPI_Request *request, MPI_Status *status) { - printf("MPI Stub WARNING: Should not wait on message from self\n"); + static int callcount=0; + if (callcount == 0) { + printf("MPI Stub WARNING: Should not wait on message from self\n"); + ++callcount; + } return 0; } @@ -252,7 +276,11 @@ int MPI_Wait(MPI_Request *request, MPI_Status *status) int MPI_Waitall(int n, MPI_Request *request, MPI_Status *status) { - printf("MPI Stub WARNING: Should not wait on message from self\n"); + static int callcount=0; + if (callcount == 0) { + printf("MPI Stub WARNING: Should not wait on message from self\n"); + ++callcount; + } return 0; } @@ -261,7 +289,11 @@ int MPI_Waitall(int n, MPI_Request *request, MPI_Status *status) int MPI_Waitany(int count, MPI_Request *request, int *index, MPI_Status *status) { - printf("MPI Stub WARNING: Should not wait on message from self\n"); + static int callcount=0; + if (callcount == 0) { + printf("MPI Stub WARNING: Should not wait on message from self\n"); + ++callcount; + } return 0; } @@ -272,7 +304,11 @@ int MPI_Sendrecv(const void *sbuf, int scount, MPI_Datatype sdatatype, MPI_Datatype rdatatype, int source, int rtag, MPI_Comm comm, MPI_Status *status) { - printf("MPI Stub WARNING: Should not send message to self\n"); + static int callcount=0; + if (callcount == 0) { + printf("MPI Stub WARNING: Should not send message to self\n"); + ++callcount; + } return 0; } @@ -280,7 +316,11 @@ int MPI_Sendrecv(const void *sbuf, int scount, MPI_Datatype sdatatype, int MPI_Get_count(MPI_Status *status, MPI_Datatype datatype, int *count) { - printf("MPI Stub WARNING: Should not get count of message to self\n"); + static int callcount=0; + if (callcount == 0) { + printf("MPI Stub WARNING: Should not get count of message to self\n"); + ++callcount; + } return 0; } diff --git a/src/USER-MISC/README b/src/USER-MISC/README index 13e406d42f..8e821c03a9 100644 --- a/src/USER-MISC/README +++ b/src/USER-MISC/README @@ -67,14 +67,17 @@ improper_style distance, Paolo Raiteri, p.raiteri at curtin.edu.au, 2 Dec 15 pair_style agni, Axel Kohlmeyer, akohlmey at gmail.com, 9 Nov 16 pair_style buck/mdf, Paolo Raiteri, p.raiteri at curtin.edu.au, 2 Dec 15 pair_style coul/diel, Axel Kohlmeyer, akohlmey at gmail.com, 1 Dec 11 +pair_style coul/shield, Wengen Ouyang (Tel Aviv University), w.g.ouyang at gmail dot com, 30 Mar 18 pair_style dipole/sf, Mario Orsi, orsimario at gmail.com, 8 Aug 11 pair_style edip, Luca Ferraro, luca.ferraro at caspur.it, 15 Sep 11 pair_style extep, Jaap Kroes (Radboud U), jaapkroes at gmail dot com, 28 Nov 17 pair_style gauss/cut, Axel Kohlmeyer, akohlmey at gmail.com, 1 Dec 11 +pair_style ilp/graphene/hbn, Wengen Ouyang (Tel Aviv University), w.g.ouyang at gmail dot com, 30 Mar 18 pair_style lebedeva/z, Zbigniew Koziol (National Center for Nuclear Research), softquake at gmail dot com, 4 Jan 19 pair_style lennard/mdf, Paolo Raiteri, p.raiteri at curtin.edu.au, 2 Dec 15 pair_style list, Axel Kohlmeyer (Temple U), akohlmey at gmail.com, 1 Jun 13 pair_style lj/mdf, Paolo Raiteri, p.raiteri at curtin.edu.au, 2 Dec 15 +pair_style kolmogorov/crespi/full, Wengen Ouyang (Tel Aviv University), w.g.ouyang at gmail dot com, 30 Mar 18 pair_style kolmogorov/crespi/z, Jaap Kroes (Radboud U), jaapkroes at gmail dot com, 28 Feb 17 pair_style meam/spline, Alexander Stukowski (LLNL), alex at stukowski.com, 1 Feb 12 pair_style meam/sw/spline, Robert Rudd (LLNL), robert.rudd at llnl.gov, 1 Oct 12 diff --git a/src/USER-MISC/fix_pimd.cpp b/src/USER-MISC/fix_pimd.cpp index eba8ed5d0c..3929d47d6b 100644 --- a/src/USER-MISC/fix_pimd.cpp +++ b/src/USER-MISC/fix_pimd.cpp @@ -637,14 +637,14 @@ void FixPIMD::comm_exec(double **ptr) if(nsend > max_nsend) { max_nsend = nsend+200; - tag_send = (int*) memory->srealloc(tag_send, sizeof(int)*max_nsend, "FixPIMD:tag_send"); + tag_send = (tagint*) memory->srealloc(tag_send, sizeof(tagint)*max_nsend, "FixPIMD:tag_send"); buf_send = (double*) memory->srealloc(buf_send, sizeof(double)*max_nsend*3, "FixPIMD:x_send"); } // send tags - MPI_Sendrecv( atom->tag, nlocal, MPI_INT, plan_send[iplan], 0, - tag_send, nsend, MPI_INT, plan_recv[iplan], 0, universe->uworld, MPI_STATUS_IGNORE); + MPI_Sendrecv( atom->tag, nlocal, MPI_LMP_TAGINT, plan_send[iplan], 0, + tag_send, nsend, MPI_LMP_TAGINT, plan_recv[iplan], 0, universe->uworld, MPI_STATUS_IGNORE); // wrap positions @@ -661,7 +661,7 @@ void FixPIMD::comm_exec(double **ptr) sprintf(error_line, "Atom " TAGINT_FORMAT " is missing at world [%d] " "rank [%d] required by rank [%d] (" TAGINT_FORMAT ", " - TAGINT_FORMAT ", " TAGINT_FORMAT ").\n",tag_send[i], + TAGINT_FORMAT ", " TAGINT_FORMAT ").\n", tag_send[i], universe->iworld, comm->me, plan_recv[iplan], atom->tag[0], atom->tag[1], atom->tag[2]); diff --git a/src/USER-MISC/fix_pimd.h b/src/USER-MISC/fix_pimd.h index 411fa42c81..c298af0b69 100644 --- a/src/USER-MISC/fix_pimd.h +++ b/src/USER-MISC/fix_pimd.h @@ -68,7 +68,7 @@ class FixPIMD : public Fix { /* inter-partition communication */ int max_nsend; - int* tag_send; + tagint* tag_send; double *buf_send; int max_nlocal; diff --git a/src/USER-OMP/pair_reaxc_omp.cpp b/src/USER-OMP/pair_reaxc_omp.cpp index 7f2db420bf..92ba31048d 100644 --- a/src/USER-OMP/pair_reaxc_omp.cpp +++ b/src/USER-OMP/pair_reaxc_omp.cpp @@ -113,7 +113,7 @@ PairReaxCOMP::~PairReaxCOMP() if (setup_flag) { reax_list * bonds = lists+BONDS; for (int i=0; inum_intrs; ++i) - sfree(bonds->select.bond_list[i].bo_data.CdboReduction, "CdboReduction"); + sfree(error, bonds->select.bond_list[i].bo_data.CdboReduction, "CdboReduction"); } memory->destroy(num_nbrs_offset); @@ -209,7 +209,7 @@ void PairReaxCOMP::compute(int eflag, int vflag) setup(); - Reset( system, control, data, workspace, &lists, world ); + Reset( system, control, data, workspace, &lists ); // Why not update workspace like in MPI-only code? // Using the MPI-only way messes up the hb energy @@ -410,12 +410,12 @@ void PairReaxCOMP::setup( ) // initialize my data structures - PreAllocate_Space( system, control, workspace, world ); + PreAllocate_Space( system, control, workspace ); write_reax_atoms(); int num_nbrs = estimate_reax_lists(); if(!Make_List(system->total_cap, num_nbrs, TYP_FAR_NEIGHBOR, - lists+FAR_NBRS, world)) + lists+FAR_NBRS)) error->all(FLERR,"Pair reax/c problem in far neighbor list"); write_reax_lists(); @@ -445,7 +445,7 @@ void PairReaxCOMP::setup( ) // check if I need to shrink/extend my data-structs - ReAllocate( system, control, data, workspace, &lists, mpi_data ); + ReAllocate( system, control, data, workspace, &lists ); } } diff --git a/src/USER-OMP/reaxc_forces_omp.cpp b/src/USER-OMP/reaxc_forces_omp.cpp index 80741a46a8..1e1cf44f50 100644 --- a/src/USER-OMP/reaxc_forces_omp.cpp +++ b/src/USER-OMP/reaxc_forces_omp.cpp @@ -289,9 +289,10 @@ void Validate_ListsOMP( reax_system *system, storage * /*workspace */, reax_list else comp = bonds->num_intrs; if (End_Index(i, bonds) > comp) { - fprintf( stderr, "step%d-bondchk failed: i=%d end(i)=%d str(i+1)=%d\n", - step, i, End_Index(i,bonds), comp ); - MPI_Abort( comm, INSUFFICIENT_MEMORY ); + char errmsg[256]; + snprintf(errmsg, 256, "step%d-bondchk failed: i=%d end(i)=%d str(i+1)=%d\n", + step, i, End_Index(i,bonds), comp ); + system->error_ptr->one(FLERR,errmsg); } } } @@ -315,9 +316,10 @@ void Validate_ListsOMP( reax_system *system, storage * /*workspace */, reax_list else comp = hbonds->num_intrs; if (End_Index(Hindex, hbonds) > comp) { - fprintf(stderr,"step%d-hbondchk failed: H=%d end(H)=%d str(H+1)=%d\n", + char errmsg[256]; + snprintf(errmsg, 256, "step%d-hbondchk failed: H=%d end(H)=%d str(H+1)=%d\n", step, Hindex, End_Index(Hindex,hbonds), comp ); - MPI_Abort( comm, INSUFFICIENT_MEMORY ); + system->error_ptr->one(FLERR, errmsg); } } } diff --git a/src/USER-OMP/reaxc_init_md_omp.cpp b/src/USER-OMP/reaxc_init_md_omp.cpp index bd15b3b9df..fe7682d035 100644 --- a/src/USER-OMP/reaxc_init_md_omp.cpp +++ b/src/USER-OMP/reaxc_init_md_omp.cpp @@ -43,7 +43,7 @@ extern int Init_MPI_Datatypes(reax_system*, storage*, mpi_datatypes*, MPI_Comm, char*); extern int Init_System(reax_system*, control_params*, char*); extern int Init_Simulation_Data(reax_system*, control_params*, simulation_data*, char*); -extern int Init_Workspace(reax_system*, control_params*, storage*, MPI_Comm, char*); +extern int Init_Workspace(reax_system*, control_params*, storage*, char*); /* ---------------------------------------------------------------------- */ @@ -63,7 +63,7 @@ int Init_ListsOMP( reax_system *system, control_params *control, bond_top = (int*) calloc( system->total_cap, sizeof(int) ); hb_top = (int*) calloc( system->local_cap, sizeof(int) ); Estimate_Storages( system, control, lists, - &Htop, hb_top, bond_top, &num_3body, comm ); + &Htop, hb_top, bond_top, &num_3body ); if (control->hbond_cut > 0) { /* init H indexes */ @@ -75,9 +75,8 @@ int Init_ListsOMP( reax_system *system, control_params *control, total_hbonds = (int)(MAX( total_hbonds*saferzone, mincap*MIN_HBONDS )); if( !Make_List( system->Hcap, total_hbonds, TYP_HBOND, - *lists+HBONDS, comm ) ) { - fprintf( stderr, "not enough space for hbonds list. terminating!\n" ); - MPI_Abort( comm, INSUFFICIENT_MEMORY ); + *lists+HBONDS ) ) { + system->error_ptr->one( FLERR, "Not enough space for hbonds list. Terminating!" ); } } @@ -89,9 +88,8 @@ int Init_ListsOMP( reax_system *system, control_params *control, bond_cap = (int)(MAX( total_bonds*safezone, mincap*MIN_BONDS )); if( !Make_List( system->total_cap, bond_cap, TYP_BOND, - *lists+BONDS, comm ) ) { - fprintf( stderr, "not enough space for bonds list. terminating!\n" ); - MPI_Abort( comm, INSUFFICIENT_MEMORY ); + *lists+BONDS ) ) { + system->error_ptr->one( FLERR, "Not enough space for bonds list. Terminating!\n" ); } int nthreads = control->nthreads; @@ -99,15 +97,14 @@ int Init_ListsOMP( reax_system *system, control_params *control, for (i = 0; i < bonds->num_intrs; ++i) bonds->select.bond_list[i].bo_data.CdboReduction = - (double*) smalloc(sizeof(double)*nthreads, "CdboReduction", comm); + (double*) smalloc(system->error_ptr, sizeof(double)*nthreads, "CdboReduction"); /* 3bodies list */ cap_3body = (int)(MAX( num_3body*safezone, MIN_3BODIES )); if( !Make_List( bond_cap, cap_3body, TYP_THREE_BODY, - *lists+THREE_BODIES, comm ) ){ + *lists+THREE_BODIES ) ){ - fprintf( stderr, "Problem in initializing angles list. Terminating!\n" ); - MPI_Abort( comm, INSUFFICIENT_MEMORY ); + system->error_ptr->one( FLERR, "Problem in initializing angles list. Terminating!" ); } free( hb_top ); @@ -125,60 +122,50 @@ void InitializeOMP( reax_system *system, control_params *control, mpi_datatypes *mpi_data, MPI_Comm comm ) { char msg[MAX_STR]; + char errmsg[512]; if (Init_MPI_Datatypes(system, workspace, mpi_data, comm, msg) == FAILURE) { - fprintf( stderr, "p%d: init_mpi_datatypes: could not create datatypes\n", - system->my_rank ); - fprintf( stderr, "p%d: mpi_data couldn't be initialized! terminating.\n", - system->my_rank ); - MPI_Abort( mpi_data->world, CANNOT_INITIALIZE ); + system->error_ptr->one( FLERR, "init_mpi_datatypes: could not create datatypes. " + "Mpi_data couldn't be initialized! Terminating."); } if (Init_System(system, control, msg) == FAILURE) { - fprintf( stderr, "p%d: %s\n", system->my_rank, msg ); - fprintf( stderr, "p%d: system could not be initialized! terminating.\n", - system->my_rank ); - MPI_Abort( mpi_data->world, CANNOT_INITIALIZE ); + snprintf( errmsg, 512, "Error on: %s. " + "System could not be initialized! Terminating.", msg ); + system->error_ptr->one(FLERR, errmsg); } if (Init_Simulation_Data( system, control, data, msg ) == FAILURE) { - fprintf( stderr, "p%d: %s\n", system->my_rank, msg ); - fprintf( stderr, "p%d: sim_data couldn't be initialized! terminating.\n", - system->my_rank ); - MPI_Abort( mpi_data->world, CANNOT_INITIALIZE ); + snprintf( errmsg, 512, "Error on: %s. " + "Sim_data couldn't be initialized! Terminating.", msg ); + system->error_ptr->one(FLERR, errmsg); } - if (Init_Workspace( system, control, workspace, mpi_data->world, msg ) == + if (Init_Workspace( system, control, workspace, msg ) == FAILURE) { - fprintf( stderr, "p%d:init_workspace: not enough memory\n", - system->my_rank ); - fprintf( stderr, "p%d:workspace couldn't be initialized! terminating.\n", - system->my_rank ); - MPI_Abort( mpi_data->world, CANNOT_INITIALIZE ); + system->error_ptr->one(FLERR, "init_workspace: not enough memory. " + "Workspace couldn't be initialized! Terminating."); } if (Init_ListsOMP( system, control, data, workspace, lists, mpi_data, msg ) == FAILURE) { - fprintf( stderr, "p%d: %s\n", system->my_rank, msg ); - fprintf( stderr, "p%d: system could not be initialized! terminating.\n", - system->my_rank ); - MPI_Abort( mpi_data->world, CANNOT_INITIALIZE ); + snprintf( errmsg, 512, "Error on: %s. " + "System could not be initialized! Terminating.", msg ); + system->error_ptr->one(FLERR, errmsg); } if (Init_Output_Files(system,control,out_control,mpi_data,msg)== FAILURE) { - fprintf( stderr, "p%d: %s\n", system->my_rank, msg ); - fprintf( stderr, "p%d: could not open output files! terminating...\n", - system->my_rank ); - MPI_Abort( mpi_data->world, CANNOT_INITIALIZE ); + snprintf( errmsg, 512, "Error on: %s" + "Could not open output files! Terminating.", msg ); + system->error_ptr->one(FLERR, errmsg); } if (control->tabulate) { if (Init_Lookup_Tables( system, control, workspace, mpi_data, msg ) == FAILURE) { - fprintf( stderr, "p%d: %s\n", system->my_rank, msg ); - fprintf( stderr, "p%d: couldn't create lookup table! terminating.\n", - system->my_rank ); - MPI_Abort( mpi_data->world, CANNOT_INITIALIZE ); + snprintf( errmsg, 512, "Error on: %s." + " Couldn't create lookup table! Terminating.", msg ); + system->error_ptr->one(FLERR, errmsg); } } diff --git a/src/USER-OMP/reaxc_valence_angles_omp.cpp b/src/USER-OMP/reaxc_valence_angles_omp.cpp index 4164d39cab..195f16a75d 100644 --- a/src/USER-OMP/reaxc_valence_angles_omp.cpp +++ b/src/USER-OMP/reaxc_valence_angles_omp.cpp @@ -237,12 +237,12 @@ void Valence_AnglesOMP( reax_system *system, control_params *control, // Confirm that thb_intrs->num_intrs / nthreads is enough to hold all angles from a single atom if(my_offset >= (tid+1)*per_thread) { - int me; - MPI_Comm_rank(MPI_COMM_WORLD,&me); - fprintf( stderr, "step%d-ran out of space on angle_list on proc %i for atom %i:", data->step, me, j); - fprintf( stderr, " nthreads= %d, tid=%d, my_offset=%d, per_thread=%d\n", nthreads, tid, my_offset, per_thread); - fprintf( stderr, " num_intrs= %i N= %i\n",thb_intrs->num_intrs , system->N); - MPI_Abort( MPI_COMM_WORLD, INSUFFICIENT_MEMORY ); + char errmsg[512]; + snprintf( errmsg, 512, "step%d-ran out of space on angle_list for atom %i:\n" + " nthreads= %d, tid=%d, my_offset=%d, per_thread=%d\n" + " num_intrs= %i N= %i\n" + , data->step, j, nthreads, tid, my_offset, per_thread,thb_intrs->num_intrs , system->N); + control->error_ptr->one(FLERR, errmsg); } // Number of angles owned by this atom @@ -601,9 +601,10 @@ void Valence_AnglesOMP( reax_system *system, control_params *control, if (num_thb_intrs >= thb_intrs->num_intrs * DANGER_ZONE) { workspace->realloc.num_3body = num_thb_intrs * TWICE; if (num_thb_intrs > thb_intrs->num_intrs) { - fprintf( stderr, "step%d-ran out of space on angle_list: top=%d, max=%d", - data->step, num_thb_intrs, thb_intrs->num_intrs ); - MPI_Abort( MPI_COMM_WORLD, INSUFFICIENT_MEMORY ); + char errmsg[128]; + snprintf(errmsg, 128, "step%d-ran out of space on angle_list: top=%d, max=%d", + data->step, num_thb_intrs, thb_intrs->num_intrs); + control->error_ptr->one(FLERR, errmsg); } } diff --git a/src/USER-PTM/ptm_polar.cpp b/src/USER-PTM/ptm_polar.cpp index 7a2695b504..5e234127a9 100644 --- a/src/USER-PTM/ptm_polar.cpp +++ b/src/USER-PTM/ptm_polar.cpp @@ -88,6 +88,7 @@ #include #include #include +#include "ptm_polar.h" #include "ptm_quat.h" diff --git a/src/USER-REAXC/pair_reaxc.cpp b/src/USER-REAXC/pair_reaxc.cpp index b9d488d8cf..6bb2b9a197 100644 --- a/src/USER-REAXC/pair_reaxc.cpp +++ b/src/USER-REAXC/pair_reaxc.cpp @@ -91,6 +91,7 @@ PairReaxC::PairReaxC(LAMMPS *lmp) : Pair(lmp) memory->smalloc(sizeof(mpi_datatypes),"reax:mpi"); MPI_Comm_rank(world,&system->my_rank); + control->me = system->my_rank; system->my_coords[0] = 0; system->my_coords[1] = 0; @@ -108,6 +109,8 @@ PairReaxC::PairReaxC(LAMMPS *lmp) : Pair(lmp) system->bndry_cuts.ghost_cutoff = 0; system->my_atoms = NULL; system->pair_ptr = this; + system->error_ptr = error; + control->error_ptr = error; system->omp_active = 0; @@ -139,10 +142,10 @@ PairReaxC::~PairReaxC() if (control->tabulate ) Deallocate_Lookup_Tables( system); - if (control->hbond_cut > 0 ) Delete_List( lists+HBONDS, world); - Delete_List( lists+BONDS, world ); - Delete_List( lists+THREE_BODIES, world ); - Delete_List( lists+FAR_NBRS, world ); + if (control->hbond_cut > 0 ) Delete_List( lists+HBONDS ); + Delete_List( lists+BONDS ); + Delete_List( lists+THREE_BODIES ); + Delete_List( lists+FAR_NBRS ); DeAllocate_Workspace( control, workspace ); DeAllocate_System( system ); @@ -394,7 +397,8 @@ void PairReaxC::init_style( ) "increased neighbor list skin."); for( int i = 0; i < LIST_N; ++i ) - lists[i].allocated = 0; + if (lists[i].allocated != 1) + lists[i].allocated = 0; if (fix_reax == NULL) { char **fixarg = new char*[3]; @@ -436,13 +440,14 @@ void PairReaxC::setup( ) // initialize my data structures - PreAllocate_Space( system, control, workspace, world ); + PreAllocate_Space( system, control, workspace ); write_reax_atoms(); int num_nbrs = estimate_reax_lists(); if(!Make_List(system->total_cap, num_nbrs, TYP_FAR_NEIGHBOR, - lists+FAR_NBRS, world)) - error->all(FLERR,"Pair reax/c problem in far neighbor list"); + lists+FAR_NBRS)) + error->one(FLERR,"Pair reax/c problem in far neighbor list"); + (lists+FAR_NBRS)->error_ptr=error; write_reax_lists(); Initialize( system, control, data, workspace, &lists, out_control, @@ -465,7 +470,7 @@ void PairReaxC::setup( ) // check if I need to shrink/extend my data-structs - ReAllocate( system, control, data, workspace, &lists, mpi_data ); + ReAllocate( system, control, data, workspace, &lists ); } bigint local_ngroup = list->inum; @@ -516,7 +521,7 @@ void PairReaxC::compute(int eflag, int vflag) setup(); - Reset( system, control, data, workspace, &lists, world ); + Reset( system, control, data, workspace, &lists ); workspace->realloc.num_far = write_reax_lists(); // timing for filling in the reax lists if (comm->me == 0) { diff --git a/src/USER-REAXC/reaxc_allocate.cpp b/src/USER-REAXC/reaxc_allocate.cpp index 700e68514c..460f8aeb6a 100644 --- a/src/USER-REAXC/reaxc_allocate.cpp +++ b/src/USER-REAXC/reaxc_allocate.cpp @@ -35,12 +35,14 @@ #include #endif +#include "error.h" + /* allocate space for my_atoms important: we cannot know the exact number of atoms that will fall into a process's box throughout the whole simulation. therefore we need to make upper bound estimates for various data structures */ int PreAllocate_Space( reax_system *system, control_params * /*control*/, - storage * workspace, MPI_Comm comm ) + storage * workspace ) { int mincap = system->mincap; double safezone = system->safezone; @@ -51,7 +53,7 @@ int PreAllocate_Space( reax_system *system, control_params * /*control*/, system->total_cap = MAX( (int)(system->N * safezone), mincap ); system->my_atoms = (reax_atom*) - scalloc( system->total_cap, sizeof(reax_atom), "my_atoms", comm ); + scalloc(system->error_ptr, system->total_cap, sizeof(reax_atom), "my_atoms"); // Nullify some arrays only used in omp styles // Should be safe to do here since called in pair->setup(); @@ -86,39 +88,39 @@ void DeAllocate_System( reax_system *system ) int ntypes; reax_interaction *ff_params; - // dealloocate the atom list - sfree( system->my_atoms, "system->my_atoms" ); + // deallocate the atom list + sfree(system->error_ptr, system->my_atoms, "system->my_atoms" ); // deallocate the ffield parameters storage ff_params = &(system->reax_param); ntypes = ff_params->num_atom_types; - sfree( ff_params->gp.l, "ff:globals" ); + sfree(system->error_ptr, ff_params->gp.l, "ff:globals" ); for( i = 0; i < ntypes; ++i ) { for( j = 0; j < ntypes; ++j ) { for( k = 0; k < ntypes; ++k ) { - sfree( ff_params->fbp[i][j][k], "ff:fbp[i,j,k]" ); + sfree(system->error_ptr, ff_params->fbp[i][j][k], "ff:fbp[i,j,k]" ); } - sfree( ff_params->fbp[i][j], "ff:fbp[i,j]" ); - sfree( ff_params->thbp[i][j], "ff:thbp[i,j]" ); - sfree( ff_params->hbp[i][j], "ff:hbp[i,j]" ); + sfree(system->error_ptr, ff_params->fbp[i][j], "ff:fbp[i,j]" ); + sfree(system->error_ptr, ff_params->thbp[i][j], "ff:thbp[i,j]" ); + sfree(system->error_ptr, ff_params->hbp[i][j], "ff:hbp[i,j]" ); } - sfree( ff_params->fbp[i], "ff:fbp[i]" ); - sfree( ff_params->thbp[i], "ff:thbp[i]" ); - sfree( ff_params->hbp[i], "ff:hbp[i]" ); - sfree( ff_params->tbp[i], "ff:tbp[i]" ); + sfree(system->error_ptr, ff_params->fbp[i], "ff:fbp[i]" ); + sfree(system->error_ptr, ff_params->thbp[i], "ff:thbp[i]" ); + sfree(system->error_ptr, ff_params->hbp[i], "ff:hbp[i]" ); + sfree(system->error_ptr, ff_params->tbp[i], "ff:tbp[i]" ); } - sfree( ff_params->fbp, "ff:fbp" ); - sfree( ff_params->thbp, "ff:thbp" ); - sfree( ff_params->hbp, "ff:hbp" ); - sfree( ff_params->tbp, "ff:tbp" ); - sfree( ff_params->sbp, "ff:sbp" ); + sfree(system->error_ptr, ff_params->fbp, "ff:fbp" ); + sfree(system->error_ptr, ff_params->thbp, "ff:thbp" ); + sfree(system->error_ptr, ff_params->hbp, "ff:hbp" ); + sfree(system->error_ptr, ff_params->tbp, "ff:tbp" ); + sfree(system->error_ptr, ff_params->sbp, "ff:sbp" ); } /************* workspace *************/ -void DeAllocate_Workspace( control_params * /*control*/, storage *workspace ) +void DeAllocate_Workspace( control_params * control, storage *workspace ) { int i; @@ -129,86 +131,86 @@ void DeAllocate_Workspace( control_params * /*control*/, storage *workspace ) /* communication storage */ for( i = 0; i < MAX_NBRS; ++i ) { - sfree( workspace->tmp_dbl[i], "tmp_dbl[i]" ); - sfree( workspace->tmp_rvec[i], "tmp_rvec[i]" ); - sfree( workspace->tmp_rvec2[i], "tmp_rvec2[i]" ); + sfree(control->error_ptr, workspace->tmp_dbl[i], "tmp_dbl[i]" ); + sfree(control->error_ptr, workspace->tmp_rvec[i], "tmp_rvec[i]" ); + sfree(control->error_ptr, workspace->tmp_rvec2[i], "tmp_rvec2[i]" ); } /* bond order storage */ - sfree( workspace->within_bond_box, "skin" ); - sfree( workspace->total_bond_order, "total_bo" ); - sfree( workspace->Deltap, "Deltap" ); - sfree( workspace->Deltap_boc, "Deltap_boc" ); - sfree( workspace->dDeltap_self, "dDeltap_self" ); - sfree( workspace->Delta, "Delta" ); - sfree( workspace->Delta_lp, "Delta_lp" ); - sfree( workspace->Delta_lp_temp, "Delta_lp_temp" ); - sfree( workspace->dDelta_lp, "dDelta_lp" ); - sfree( workspace->dDelta_lp_temp, "dDelta_lp_temp" ); - sfree( workspace->Delta_e, "Delta_e" ); - sfree( workspace->Delta_boc, "Delta_boc" ); - sfree( workspace->Delta_val, "Delta_val" ); - sfree( workspace->nlp, "nlp" ); - sfree( workspace->nlp_temp, "nlp_temp" ); - sfree( workspace->Clp, "Clp" ); - sfree( workspace->vlpex, "vlpex" ); - sfree( workspace->bond_mark, "bond_mark" ); - sfree( workspace->done_after, "done_after" ); + sfree(control->error_ptr, workspace->within_bond_box, "skin" ); + sfree(control->error_ptr, workspace->total_bond_order, "total_bo" ); + sfree(control->error_ptr, workspace->Deltap, "Deltap" ); + sfree(control->error_ptr, workspace->Deltap_boc, "Deltap_boc" ); + sfree(control->error_ptr, workspace->dDeltap_self, "dDeltap_self" ); + sfree(control->error_ptr, workspace->Delta, "Delta" ); + sfree(control->error_ptr, workspace->Delta_lp, "Delta_lp" ); + sfree(control->error_ptr, workspace->Delta_lp_temp, "Delta_lp_temp" ); + sfree(control->error_ptr, workspace->dDelta_lp, "dDelta_lp" ); + sfree(control->error_ptr, workspace->dDelta_lp_temp, "dDelta_lp_temp" ); + sfree(control->error_ptr, workspace->Delta_e, "Delta_e" ); + sfree(control->error_ptr, workspace->Delta_boc, "Delta_boc" ); + sfree(control->error_ptr, workspace->Delta_val, "Delta_val" ); + sfree(control->error_ptr, workspace->nlp, "nlp" ); + sfree(control->error_ptr, workspace->nlp_temp, "nlp_temp" ); + sfree(control->error_ptr, workspace->Clp, "Clp" ); + sfree(control->error_ptr, workspace->vlpex, "vlpex" ); + sfree(control->error_ptr, workspace->bond_mark, "bond_mark" ); + sfree(control->error_ptr, workspace->done_after, "done_after" ); /* QEq storage */ - sfree( workspace->Hdia_inv, "Hdia_inv" ); - sfree( workspace->b_s, "b_s" ); - sfree( workspace->b_t, "b_t" ); - sfree( workspace->b_prc, "b_prc" ); - sfree( workspace->b_prm, "b_prm" ); - sfree( workspace->s, "s" ); - sfree( workspace->t, "t" ); - sfree( workspace->droptol, "droptol" ); - sfree( workspace->b, "b" ); - sfree( workspace->x, "x" ); + sfree(control->error_ptr, workspace->Hdia_inv, "Hdia_inv" ); + sfree(control->error_ptr, workspace->b_s, "b_s" ); + sfree(control->error_ptr, workspace->b_t, "b_t" ); + sfree(control->error_ptr, workspace->b_prc, "b_prc" ); + sfree(control->error_ptr, workspace->b_prm, "b_prm" ); + sfree(control->error_ptr, workspace->s, "s" ); + sfree(control->error_ptr, workspace->t, "t" ); + sfree(control->error_ptr, workspace->droptol, "droptol" ); + sfree(control->error_ptr, workspace->b, "b" ); + sfree(control->error_ptr, workspace->x, "x" ); /* GMRES storage */ for( i = 0; i < RESTART+1; ++i ) { - sfree( workspace->h[i], "h[i]" ); - sfree( workspace->v[i], "v[i]" ); + sfree(control->error_ptr, workspace->h[i], "h[i]" ); + sfree(control->error_ptr, workspace->v[i], "v[i]" ); } - sfree( workspace->h, "h" ); - sfree( workspace->v, "v" ); - sfree( workspace->y, "y" ); - sfree( workspace->z, "z" ); - sfree( workspace->g, "g" ); - sfree( workspace->hs, "hs" ); - sfree( workspace->hc, "hc" ); + sfree(control->error_ptr, workspace->h, "h" ); + sfree(control->error_ptr, workspace->v, "v" ); + sfree(control->error_ptr, workspace->y, "y" ); + sfree(control->error_ptr, workspace->z, "z" ); + sfree(control->error_ptr, workspace->g, "g" ); + sfree(control->error_ptr, workspace->hs, "hs" ); + sfree(control->error_ptr, workspace->hc, "hc" ); /* CG storage */ - sfree( workspace->r, "r" ); - sfree( workspace->d, "d" ); - sfree( workspace->q, "q" ); - sfree( workspace->p, "p" ); - sfree( workspace->r2, "r2" ); - sfree( workspace->d2, "d2" ); - sfree( workspace->q2, "q2" ); - sfree( workspace->p2, "p2" ); + sfree(control->error_ptr, workspace->r, "r" ); + sfree(control->error_ptr, workspace->d, "d" ); + sfree(control->error_ptr, workspace->q, "q" ); + sfree(control->error_ptr, workspace->p, "p" ); + sfree(control->error_ptr, workspace->r2, "r2" ); + sfree(control->error_ptr, workspace->d2, "d2" ); + sfree(control->error_ptr, workspace->q2, "q2" ); + sfree(control->error_ptr, workspace->p2, "p2" ); /* integrator storage */ - sfree( workspace->v_const, "v_const" ); + sfree(control->error_ptr, workspace->v_const, "v_const" ); /* force related storage */ - sfree( workspace->f, "f" ); - sfree( workspace->CdDelta, "CdDelta" ); + sfree(control->error_ptr, workspace->f, "f" ); + sfree(control->error_ptr, workspace->CdDelta, "CdDelta" ); /* reductions */ #ifdef LMP_USER_OMP - if (workspace->CdDeltaReduction) sfree( workspace->CdDeltaReduction, "cddelta_reduce" ); - if (workspace->forceReduction) sfree( workspace->forceReduction, "f_reduce" ); - if (workspace->valence_angle_atom_myoffset) sfree( workspace->valence_angle_atom_myoffset, "valence_angle_atom_myoffset"); - if (workspace->my_ext_pressReduction) sfree( workspace->my_ext_pressReduction, "ext_press_reduce"); + if (workspace->CdDeltaReduction) sfree(control->error_ptr, workspace->CdDeltaReduction, "cddelta_reduce" ); + if (workspace->forceReduction) sfree(control->error_ptr, workspace->forceReduction, "f_reduce" ); + if (workspace->valence_angle_atom_myoffset) sfree(control->error_ptr, workspace->valence_angle_atom_myoffset, "valence_angle_atom_myoffset"); + if (workspace->my_ext_pressReduction) sfree(control->error_ptr, workspace->my_ext_pressReduction, "ext_press_reduce"); #endif } int Allocate_Workspace( reax_system * /*system*/, control_params * control, storage *workspace, int local_cap, int total_cap, - MPI_Comm comm, char * /*msg*/ ) + char * /*msg*/ ) { int i, total_real, total_rvec, local_rvec; @@ -220,94 +222,94 @@ int Allocate_Workspace( reax_system * /*system*/, control_params * control, /* communication storage */ for( i = 0; i < MAX_NBRS; ++i ) { workspace->tmp_dbl[i] = (double*) - scalloc( total_cap, sizeof(double), "tmp_dbl", comm ); + scalloc(control->error_ptr, total_cap, sizeof(double), "tmp_dbl"); workspace->tmp_rvec[i] = (rvec*) - scalloc( total_cap, sizeof(rvec), "tmp_rvec", comm ); + scalloc(control->error_ptr, total_cap, sizeof(rvec), "tmp_rvec"); workspace->tmp_rvec2[i] = (rvec2*) - scalloc( total_cap, sizeof(rvec2), "tmp_rvec2", comm ); + scalloc(control->error_ptr, total_cap, sizeof(rvec2), "tmp_rvec2"); } /* bond order related storage */ workspace->within_bond_box = (int*) - scalloc( total_cap, sizeof(int), "skin", comm ); - workspace->total_bond_order = (double*) smalloc( total_real, "total_bo", comm ); - workspace->Deltap = (double*) smalloc( total_real, "Deltap", comm ); - workspace->Deltap_boc = (double*) smalloc( total_real, "Deltap_boc", comm ); - workspace->dDeltap_self = (rvec*) smalloc( total_rvec, "dDeltap_self", comm ); - workspace->Delta = (double*) smalloc( total_real, "Delta", comm ); - workspace->Delta_lp = (double*) smalloc( total_real, "Delta_lp", comm ); + scalloc(control->error_ptr, total_cap, sizeof(int), "skin"); + workspace->total_bond_order = (double*) smalloc(control->error_ptr, total_real, "total_bo"); + workspace->Deltap = (double*) smalloc(control->error_ptr, total_real, "Deltap"); + workspace->Deltap_boc = (double*) smalloc(control->error_ptr, total_real, "Deltap_boc"); + workspace->dDeltap_self = (rvec*) smalloc(control->error_ptr, total_rvec, "dDeltap_self"); + workspace->Delta = (double*) smalloc(control->error_ptr, total_real, "Delta"); + workspace->Delta_lp = (double*) smalloc(control->error_ptr, total_real, "Delta_lp"); workspace->Delta_lp_temp = (double*) - smalloc( total_real, "Delta_lp_temp", comm ); - workspace->dDelta_lp = (double*) smalloc( total_real, "dDelta_lp", comm ); + smalloc(control->error_ptr, total_real, "Delta_lp_temp"); + workspace->dDelta_lp = (double*) smalloc(control->error_ptr, total_real, "dDelta_lp"); workspace->dDelta_lp_temp = (double*) - smalloc( total_real, "dDelta_lp_temp", comm ); - workspace->Delta_e = (double*) smalloc( total_real, "Delta_e", comm ); - workspace->Delta_boc = (double*) smalloc( total_real, "Delta_boc", comm ); - workspace->Delta_val = (double*) smalloc( total_real, "Delta_val", comm ); - workspace->nlp = (double*) smalloc( total_real, "nlp", comm ); - workspace->nlp_temp = (double*) smalloc( total_real, "nlp_temp", comm ); - workspace->Clp = (double*) smalloc( total_real, "Clp", comm ); - workspace->vlpex = (double*) smalloc( total_real, "vlpex", comm ); + smalloc(control->error_ptr, total_real, "dDelta_lp_temp"); + workspace->Delta_e = (double*) smalloc(control->error_ptr, total_real, "Delta_e"); + workspace->Delta_boc = (double*) smalloc(control->error_ptr, total_real, "Delta_boc"); + workspace->Delta_val = (double*) smalloc(control->error_ptr, total_real, "Delta_val"); + workspace->nlp = (double*) smalloc(control->error_ptr, total_real, "nlp"); + workspace->nlp_temp = (double*) smalloc(control->error_ptr, total_real, "nlp_temp"); + workspace->Clp = (double*) smalloc(control->error_ptr, total_real, "Clp"); + workspace->vlpex = (double*) smalloc(control->error_ptr, total_real, "vlpex"); workspace->bond_mark = (int*) - scalloc( total_cap, sizeof(int), "bond_mark", comm ); + scalloc(control->error_ptr, total_cap, sizeof(int), "bond_mark"); workspace->done_after = (int*) - scalloc( total_cap, sizeof(int), "done_after", comm ); + scalloc(control->error_ptr, total_cap, sizeof(int), "done_after"); /* QEq storage */ workspace->Hdia_inv = (double*) - scalloc( total_cap, sizeof(double), "Hdia_inv", comm ); - workspace->b_s = (double*) scalloc( total_cap, sizeof(double), "b_s", comm ); - workspace->b_t = (double*) scalloc( total_cap, sizeof(double), "b_t", comm ); - workspace->b_prc = (double*) scalloc( total_cap, sizeof(double), "b_prc", comm ); - workspace->b_prm = (double*) scalloc( total_cap, sizeof(double), "b_prm", comm ); - workspace->s = (double*) scalloc( total_cap, sizeof(double), "s", comm ); - workspace->t = (double*) scalloc( total_cap, sizeof(double), "t", comm ); + scalloc(control->error_ptr, total_cap, sizeof(double), "Hdia_inv"); + workspace->b_s = (double*) scalloc(control->error_ptr, total_cap, sizeof(double), "b_s"); + workspace->b_t = (double*) scalloc(control->error_ptr, total_cap, sizeof(double), "b_t"); + workspace->b_prc = (double*) scalloc(control->error_ptr, total_cap, sizeof(double), "b_prc"); + workspace->b_prm = (double*) scalloc(control->error_ptr, total_cap, sizeof(double), "b_prm"); + workspace->s = (double*) scalloc(control->error_ptr, total_cap, sizeof(double), "s"); + workspace->t = (double*) scalloc(control->error_ptr, total_cap, sizeof(double), "t"); workspace->droptol = (double*) - scalloc( total_cap, sizeof(double), "droptol", comm ); - workspace->b = (rvec2*) scalloc( total_cap, sizeof(rvec2), "b", comm ); - workspace->x = (rvec2*) scalloc( total_cap, sizeof(rvec2), "x", comm ); + scalloc(control->error_ptr, total_cap, sizeof(double), "droptol"); + workspace->b = (rvec2*) scalloc(control->error_ptr, total_cap, sizeof(rvec2), "b"); + workspace->x = (rvec2*) scalloc(control->error_ptr, total_cap, sizeof(rvec2), "x"); /* GMRES storage */ - workspace->y = (double*) scalloc( RESTART+1, sizeof(double), "y", comm ); - workspace->z = (double*) scalloc( RESTART+1, sizeof(double), "z", comm ); - workspace->g = (double*) scalloc( RESTART+1, sizeof(double), "g", comm ); - workspace->h = (double**) scalloc( RESTART+1, sizeof(double*), "h", comm ); - workspace->hs = (double*) scalloc( RESTART+1, sizeof(double), "hs", comm ); - workspace->hc = (double*) scalloc( RESTART+1, sizeof(double), "hc", comm ); - workspace->v = (double**) scalloc( RESTART+1, sizeof(double*), "v", comm ); + workspace->y = (double*) scalloc(control->error_ptr, RESTART+1, sizeof(double), "y"); + workspace->z = (double*) scalloc(control->error_ptr, RESTART+1, sizeof(double), "z"); + workspace->g = (double*) scalloc(control->error_ptr, RESTART+1, sizeof(double), "g"); + workspace->h = (double**) scalloc(control->error_ptr, RESTART+1, sizeof(double*), "h"); + workspace->hs = (double*) scalloc(control->error_ptr, RESTART+1, sizeof(double), "hs"); + workspace->hc = (double*) scalloc(control->error_ptr, RESTART+1, sizeof(double), "hc"); + workspace->v = (double**) scalloc(control->error_ptr, RESTART+1, sizeof(double*), "v"); for( i = 0; i < RESTART+1; ++i ) { - workspace->h[i] = (double*) scalloc( RESTART+1, sizeof(double), "h[i]", comm ); - workspace->v[i] = (double*) scalloc( total_cap, sizeof(double), "v[i]", comm ); + workspace->h[i] = (double*) scalloc(control->error_ptr, RESTART+1, sizeof(double), "h[i]"); + workspace->v[i] = (double*) scalloc(control->error_ptr, total_cap, sizeof(double), "v[i]"); } /* CG storage */ - workspace->r = (double*) scalloc( total_cap, sizeof(double), "r", comm ); - workspace->d = (double*) scalloc( total_cap, sizeof(double), "d", comm ); - workspace->q = (double*) scalloc( total_cap, sizeof(double), "q", comm ); - workspace->p = (double*) scalloc( total_cap, sizeof(double), "p", comm ); - workspace->r2 = (rvec2*) scalloc( total_cap, sizeof(rvec2), "r2", comm ); - workspace->d2 = (rvec2*) scalloc( total_cap, sizeof(rvec2), "d2", comm ); - workspace->q2 = (rvec2*) scalloc( total_cap, sizeof(rvec2), "q2", comm ); - workspace->p2 = (rvec2*) scalloc( total_cap, sizeof(rvec2), "p2", comm ); + workspace->r = (double*) scalloc(control->error_ptr, total_cap, sizeof(double), "r"); + workspace->d = (double*) scalloc(control->error_ptr, total_cap, sizeof(double), "d"); + workspace->q = (double*) scalloc(control->error_ptr, total_cap, sizeof(double), "q"); + workspace->p = (double*) scalloc(control->error_ptr, total_cap, sizeof(double), "p"); + workspace->r2 = (rvec2*) scalloc(control->error_ptr, total_cap, sizeof(rvec2), "r2"); + workspace->d2 = (rvec2*) scalloc(control->error_ptr, total_cap, sizeof(rvec2), "d2"); + workspace->q2 = (rvec2*) scalloc(control->error_ptr, total_cap, sizeof(rvec2), "q2"); + workspace->p2 = (rvec2*) scalloc(control->error_ptr, total_cap, sizeof(rvec2), "p2"); /* integrator storage */ - workspace->v_const = (rvec*) smalloc( local_rvec, "v_const", comm ); + workspace->v_const = (rvec*) smalloc(control->error_ptr, local_rvec, "v_const"); /* force related storage */ - workspace->f = (rvec*) scalloc( total_cap, sizeof(rvec), "f", comm ); + workspace->f = (rvec*) scalloc(control->error_ptr, total_cap, sizeof(rvec), "f"); workspace->CdDelta = (double*) - scalloc( total_cap, sizeof(double), "CdDelta", comm ); + scalloc(control->error_ptr, total_cap, sizeof(double), "CdDelta"); // storage for reductions with multiple threads #ifdef LMP_USER_OMP - workspace->CdDeltaReduction = (double *) scalloc(sizeof(double), total_cap*control->nthreads, - "cddelta_reduce", comm); + workspace->CdDeltaReduction = (double *) scalloc(control->error_ptr, sizeof(double), total_cap*control->nthreads, + "cddelta_reduce"); - workspace->forceReduction = (rvec *) scalloc(sizeof(rvec), total_cap*control->nthreads, - "forceReduction", comm); + workspace->forceReduction = (rvec *) scalloc(control->error_ptr, sizeof(rvec), total_cap*control->nthreads, + "forceReduction"); - workspace->valence_angle_atom_myoffset = (int *) scalloc(sizeof(int), total_cap, "valence_angle_atom_myoffset", comm); + workspace->valence_angle_atom_myoffset = (int *) scalloc(control->error_ptr, sizeof(int), total_cap, "valence_angle_atom_myoffset"); workspace->my_ext_pressReduction = (rvec *) calloc(sizeof(rvec), control->nthreads); #else LMP_UNUSED_PARAM(control); @@ -318,18 +320,16 @@ int Allocate_Workspace( reax_system * /*system*/, control_params * control, static void Reallocate_Neighbor_List( reax_list *far_nbrs, int n, - int num_intrs, MPI_Comm comm ) + int num_intrs ) { - Delete_List( far_nbrs, comm ); - if(!Make_List( n, num_intrs, TYP_FAR_NEIGHBOR, far_nbrs, comm )){ - fprintf(stderr, "Problem in initializing far nbrs list. Terminating!\n"); - MPI_Abort( comm, INSUFFICIENT_MEMORY ); + Delete_List( far_nbrs); + if(!Make_List( n, num_intrs, TYP_FAR_NEIGHBOR, far_nbrs )){ + far_nbrs->error_ptr->one(FLERR,"Problem in initializing far neighbors list"); } } -static int Reallocate_HBonds_List( reax_system *system, reax_list *hbonds, - MPI_Comm comm ) +static int Reallocate_HBonds_List( reax_system *system, reax_list *hbonds ) { int i, total_hbonds; @@ -343,10 +343,9 @@ static int Reallocate_HBonds_List( reax_system *system, reax_list *hbonds, } total_hbonds = (int)(MAX( total_hbonds*saferzone, mincap*MIN_HBONDS )); - Delete_List( hbonds, comm ); - if (!Make_List( system->Hcap, total_hbonds, TYP_HBOND, hbonds, comm )) { - fprintf( stderr, "not enough space for hbonds list. terminating!\n" ); - MPI_Abort( comm, INSUFFICIENT_MEMORY ); + Delete_List( hbonds); + if (!Make_List( system->Hcap, total_hbonds, TYP_HBOND, hbonds )) { + hbonds->error_ptr->one(FLERR, "Not enough space for hydrogen bonds list"); } return total_hbonds; @@ -354,8 +353,7 @@ static int Reallocate_HBonds_List( reax_system *system, reax_list *hbonds, static int Reallocate_Bonds_List( reax_system *system, reax_list *bonds, - int *total_bonds, int *est_3body, - MPI_Comm comm ) + int *total_bonds, int *est_3body ) { int i; @@ -373,13 +371,12 @@ static int Reallocate_Bonds_List( reax_system *system, reax_list *bonds, #ifdef LMP_USER_OMP if (system->omp_active) for (i = 0; i < bonds->num_intrs; ++i) - sfree(bonds->select.bond_list[i].bo_data.CdboReduction, "CdboReduction"); + sfree(system->error_ptr, bonds->select.bond_list[i].bo_data.CdboReduction, "CdboReduction"); #endif - Delete_List( bonds, comm ); - if(!Make_List(system->total_cap, *total_bonds, TYP_BOND, bonds, comm)) { - fprintf( stderr, "not enough space for bonds list. terminating!\n" ); - MPI_Abort( comm, INSUFFICIENT_MEMORY ); + Delete_List( bonds); + if(!Make_List(system->total_cap, *total_bonds, TYP_BOND, bonds)) { + bonds->error_ptr->one(FLERR, "Not enough space for bonds list"); } #ifdef LMP_USER_OMP @@ -392,7 +389,7 @@ static int Reallocate_Bonds_List( reax_system *system, reax_list *bonds, if (system->omp_active) for (i = 0; i < bonds->num_intrs; ++i) bonds->select.bond_list[i].bo_data.CdboReduction = - (double*) smalloc(sizeof(double)*nthreads, "CdboReduction", comm); + (double*) smalloc(system->error_ptr, sizeof(double)*nthreads, "CdboReduction"); #endif return SUCCESS; @@ -400,14 +397,12 @@ static int Reallocate_Bonds_List( reax_system *system, reax_list *bonds, void ReAllocate( reax_system *system, control_params *control, - simulation_data *data, storage *workspace, reax_list **lists, - mpi_datatypes *mpi_data ) + simulation_data *data, storage *workspace, reax_list **lists ) { int num_bonds, est_3body, Hflag, ret; int renbr, newsize; reallocate_data *realloc; reax_list *far_nbrs; - MPI_Comm comm; char msg[200]; int mincap = system->mincap; @@ -415,7 +410,6 @@ void ReAllocate( reax_system *system, control_params *control, double saferzone = system->saferzone; realloc = &(workspace->realloc); - comm = mpi_data->world; if( system->n >= DANGER_ZONE * system->local_cap || (0 && system->n <= LOOSE_ZONE * system->local_cap) ) { @@ -433,21 +427,19 @@ void ReAllocate( reax_system *system, control_params *control, /* system */ ret = Allocate_System( system, system->local_cap, system->total_cap, msg ); if (ret != SUCCESS) { - fprintf( stderr, "not enough space for atom_list: total_cap=%d", - system->total_cap ); - fprintf( stderr, "terminating...\n" ); - MPI_Abort( comm, INSUFFICIENT_MEMORY ); + char errmsg[256]; + snprintf(errmsg, 256, "Not enough space for atom_list: total_cap=%d", system->total_cap); + system->error_ptr->one(FLERR, errmsg); } /* workspace */ DeAllocate_Workspace( control, workspace ); ret = Allocate_Workspace( system, control, workspace, system->local_cap, - system->total_cap, comm, msg ); + system->total_cap, msg ); if (ret != SUCCESS) { - fprintf( stderr, "no space for workspace: local_cap=%d total_cap=%d", - system->local_cap, system->total_cap ); - fprintf( stderr, "terminating...\n" ); - MPI_Abort( comm, INSUFFICIENT_MEMORY ); + char errmsg[256]; + snprintf(errmsg, 256, "Not enough space for workspace: local_cap=%d total_cap=%d", system->local_cap, system->total_cap); + system->error_ptr->one(FLERR, errmsg); } } @@ -459,15 +451,15 @@ void ReAllocate( reax_system *system, control_params *control, if (Nflag || realloc->num_far >= far_nbrs->num_intrs * DANGER_ZONE) { if (realloc->num_far > far_nbrs->num_intrs) { - fprintf( stderr, "step%d-ran out of space on far_nbrs: top=%d, max=%d", - data->step, realloc->num_far, far_nbrs->num_intrs ); - MPI_Abort( comm, INSUFFICIENT_MEMORY ); + char errmsg[256]; + snprintf(errmsg, 256, "step%d-ran out of space on far_nbrs: top=%d, max=%d", data->step, realloc->num_far, far_nbrs->num_intrs); + system->error_ptr->one(FLERR, errmsg); } newsize = static_cast (MAX( realloc->num_far*safezone, mincap*MIN_NBRS )); - Reallocate_Neighbor_List( far_nbrs, system->total_cap, newsize, comm ); + Reallocate_Neighbor_List( far_nbrs, system->total_cap, newsize); realloc->num_far = 0; } } @@ -482,7 +474,7 @@ void ReAllocate( reax_system *system, control_params *control, } if (Hflag || realloc->hbonds) { - ret = Reallocate_HBonds_List( system, (*lists)+HBONDS, comm ); + ret = Reallocate_HBonds_List( system, (*lists)+HBONDS); realloc->hbonds = 0; } } @@ -491,14 +483,14 @@ void ReAllocate( reax_system *system, control_params *control, num_bonds = est_3body = -1; if (Nflag || realloc->bonds) { Reallocate_Bonds_List( system, (*lists)+BONDS, &num_bonds, - &est_3body, comm ); + &est_3body); realloc->bonds = 0; realloc->num_3body = MAX( realloc->num_3body, est_3body ) * 2; } /* 3-body list */ if (realloc->num_3body > 0) { - Delete_List( (*lists)+THREE_BODIES, comm ); + Delete_List( (*lists)+THREE_BODIES); if (num_bonds == -1) num_bonds = ((*lists)+BONDS)->num_intrs; @@ -506,9 +498,8 @@ void ReAllocate( reax_system *system, control_params *control, realloc->num_3body = (int)(MAX(realloc->num_3body*safezone, MIN_3BODIES)); if( !Make_List( num_bonds, realloc->num_3body, TYP_THREE_BODY, - (*lists)+THREE_BODIES, comm ) ) { - fprintf( stderr, "Problem in initializing angles list. Terminating!\n" ); - MPI_Abort( comm, CANNOT_INITIALIZE ); + (*lists)+THREE_BODIES ) ) { + system->error_ptr->one(FLERR, "Problem in initializing angles list"); } realloc->num_3body = -1; } diff --git a/src/USER-REAXC/reaxc_allocate.h b/src/USER-REAXC/reaxc_allocate.h index f8814859af..be203340f6 100644 --- a/src/USER-REAXC/reaxc_allocate.h +++ b/src/USER-REAXC/reaxc_allocate.h @@ -28,15 +28,15 @@ #define __ALLOCATE_H_ #include "reaxc_types.h" -int PreAllocate_Space( reax_system*, control_params*, storage*, MPI_Comm ); +int PreAllocate_Space( reax_system*, control_params*, storage* ); int Allocate_System( reax_system*, int, int, char* ); void DeAllocate_System( reax_system* ); int Allocate_Workspace( reax_system*, control_params*, storage*, - int, int, MPI_Comm, char* ); + int, int, char* ); void DeAllocate_Workspace( control_params*, storage* ); void ReAllocate( reax_system*, control_params*, simulation_data*, storage*, - reax_list**, mpi_datatypes* ); + reax_list** ); #endif diff --git a/src/USER-REAXC/reaxc_control.cpp b/src/USER-REAXC/reaxc_control.cpp index dd2b5a32ad..535226fff8 100644 --- a/src/USER-REAXC/reaxc_control.cpp +++ b/src/USER-REAXC/reaxc_control.cpp @@ -28,6 +28,8 @@ #include "reaxc_control.h" #include "reaxc_tool_box.h" +#include "error.h" + char Read_Control_File( char *control_file, control_params* control, output_controls *out_control ) { @@ -38,8 +40,7 @@ char Read_Control_File( char *control_file, control_params* control, /* open control file */ if ( (fp = fopen( control_file, "r" ) ) == NULL ) { - fprintf( stderr, "error opening the control file! terminating...\n" ); - MPI_Abort( MPI_COMM_WORLD, FILE_NOT_FOUND ); + control->error_ptr->all(FLERR, "The control file cannot be opened"); } /* assign default values */ @@ -364,8 +365,9 @@ char Read_Control_File( char *control_file, control_params* control, control->restrict_type = ival; } else { - fprintf( stderr, "WARNING: unknown parameter %s\n", tmp[0] ); - MPI_Abort( MPI_COMM_WORLD, 15 ); + char errmsg[128]; + snprintf(errmsg,128,"Unknown parameter %s in the control file", tmp[0]); + control->error_ptr->all(FLERR, errmsg); } } diff --git a/src/USER-REAXC/reaxc_ffield.cpp b/src/USER-REAXC/reaxc_ffield.cpp index dd8f12f9d2..13e928ad08 100644 --- a/src/USER-REAXC/reaxc_ffield.cpp +++ b/src/USER-REAXC/reaxc_ffield.cpp @@ -29,6 +29,7 @@ #include "reaxc_ffield.h" #include "reaxc_tool_box.h" + char Read_Force_Field( FILE *fp, reax_interaction *reax, control_params *control ) { @@ -41,7 +42,6 @@ char Read_Force_Field( FILE *fp, reax_interaction *reax, double val; MPI_Comm comm; int me; - comm = MPI_COMM_WORLD; MPI_Comm_rank(comm, &me); @@ -61,7 +61,7 @@ char Read_Force_Field( FILE *fp, reax_interaction *reax, n = atoi(tmp[0]); if (n < 1) { if (me == 0) - fprintf( stderr, "WARNING: number of globals in ffield file is 0!\n" ); + control->error_ptr->warning( FLERR, "Number of globals in ffield file is 0. The file will not be read." ); fclose(fp); free(s); free(tmp); @@ -96,61 +96,52 @@ char Read_Force_Field( FILE *fp, reax_interaction *reax, /* Allocating structures in reax_interaction */ reax->sbp = (single_body_parameters*) - scalloc( reax->num_atom_types, sizeof(single_body_parameters), "sbp", - comm ); + scalloc(control->error_ptr, reax->num_atom_types, sizeof(single_body_parameters), "sbp"); reax->tbp = (two_body_parameters**) - scalloc( reax->num_atom_types, sizeof(two_body_parameters*), "tbp", comm ); + scalloc(control->error_ptr, reax->num_atom_types, sizeof(two_body_parameters*), "tbp"); reax->thbp= (three_body_header***) - scalloc( reax->num_atom_types, sizeof(three_body_header**), "thbp", comm ); + scalloc(control->error_ptr, reax->num_atom_types, sizeof(three_body_header**), "thbp"); reax->hbp = (hbond_parameters***) - scalloc( reax->num_atom_types, sizeof(hbond_parameters**), "hbp", comm ); + scalloc(control->error_ptr, reax->num_atom_types, sizeof(hbond_parameters**), "hbp"); reax->fbp = (four_body_header****) - scalloc( reax->num_atom_types, sizeof(four_body_header***), "fbp", comm ); + scalloc(control->error_ptr, reax->num_atom_types, sizeof(four_body_header***), "fbp"); tor_flag = (char****) - scalloc( reax->num_atom_types, sizeof(char***), "tor_flag", comm ); + scalloc(control->error_ptr, reax->num_atom_types, sizeof(char***), "tor_flag"); for( i = 0; i < reax->num_atom_types; i++ ) { reax->tbp[i] = (two_body_parameters*) - scalloc( reax->num_atom_types, sizeof(two_body_parameters), "tbp[i]", - comm ); + scalloc(control->error_ptr, reax->num_atom_types, sizeof(two_body_parameters), "tbp[i]"); reax->thbp[i]= (three_body_header**) - scalloc( reax->num_atom_types, sizeof(three_body_header*), "thbp[i]", - comm ); + scalloc(control->error_ptr, reax->num_atom_types, sizeof(three_body_header*), "thbp[i]"); reax->hbp[i] = (hbond_parameters**) - scalloc( reax->num_atom_types, sizeof(hbond_parameters*), "hbp[i]", - comm ); + scalloc(control->error_ptr, reax->num_atom_types, sizeof(hbond_parameters*), "hbp[i]"); reax->fbp[i] = (four_body_header***) - scalloc( reax->num_atom_types, sizeof(four_body_header**), "fbp[i]", - comm ); + scalloc(control->error_ptr, reax->num_atom_types, sizeof(four_body_header**), "fbp[i]"); tor_flag[i] = (char***) - scalloc( reax->num_atom_types, sizeof(char**), "tor_flag[i]", comm ); + scalloc(control->error_ptr, reax->num_atom_types, sizeof(char**), "tor_flag[i]"); for( j = 0; j < reax->num_atom_types; j++ ) { reax->thbp[i][j]= (three_body_header*) - scalloc( reax->num_atom_types, sizeof(three_body_header), "thbp[i,j]", - comm ); + scalloc(control->error_ptr, reax->num_atom_types, sizeof(three_body_header), "thbp[i,j]"); reax->hbp[i][j] = (hbond_parameters*) - scalloc( reax->num_atom_types, sizeof(hbond_parameters), "hbp[i,j]", - comm ); + scalloc(control->error_ptr, reax->num_atom_types, sizeof(hbond_parameters), "hbp[i,j]"); reax->fbp[i][j] = (four_body_header**) - scalloc( reax->num_atom_types, sizeof(four_body_header*), "fbp[i,j]", - comm ); + scalloc(control->error_ptr, reax->num_atom_types, sizeof(four_body_header*), "fbp[i,j]"); tor_flag[i][j] = (char**) - scalloc( reax->num_atom_types, sizeof(char*), "tor_flag[i,j]", comm ); + scalloc(control->error_ptr, reax->num_atom_types, sizeof(char*), "tor_flag[i,j]"); for (k=0; k < reax->num_atom_types; k++) { reax->fbp[i][j][k] = (four_body_header*) - scalloc( reax->num_atom_types, sizeof(four_body_header), "fbp[i,j,k]", - comm ); + scalloc(control->error_ptr, reax->num_atom_types, sizeof(four_body_header), "fbp[i,j,k]"); tor_flag[i][j][k] = (char*) - scalloc( reax->num_atom_types, sizeof(char), "tor_flag[i,j,k]", - comm ); + scalloc(control->error_ptr, reax->num_atom_types, sizeof(char), "tor_flag[i,j,k]"); } } } reax->gp.vdw_type = 0; + char errmsg[1024]; for( i = 0; i < reax->num_atom_types; i++ ) { /* line one */ @@ -158,15 +149,12 @@ char Read_Force_Field( FILE *fp, reax_interaction *reax, c = Tokenize( s, &tmp ); /* Sanity checks */ - if (c == 2 && !lgflag) { - if (me == 0) - fprintf(stderr, "Force field file requires using 'lgvdw yes'\n"); - MPI_Abort( comm, FILE_NOT_FOUND ); - } + if (c == 2 && !lgflag) + control->error_ptr->all(FLERR, "Force field file requires using 'lgvdw yes'"); + if (c < 9) { - if (me == 0) - fprintf(stderr, "Inconsistent ffield file (reaxc_ffield.cpp) \n"); - MPI_Abort( comm, FILE_NOT_FOUND ); + snprintf (errmsg, 1024, "Missing parameter(s) in line %s", s); + control->error_ptr->all(FLERR, errmsg); } for( j = 0; j < (int)(strlen(tmp[0])); ++j ) @@ -188,9 +176,8 @@ char Read_Force_Field( FILE *fp, reax_interaction *reax, /* Sanity check */ if (c < 8) { - if (me == 0) - fprintf(stderr, "Inconsistent ffield file (reaxc_ffield.cpp) \n"); - MPI_Abort( comm, FILE_NOT_FOUND ); + snprintf (errmsg, 1024, "Missing parameter(s) in line %s", s); + control->error_ptr->all(FLERR, errmsg); } val = atof(tmp[0]); reax->sbp[i].alpha = val; @@ -208,9 +195,8 @@ char Read_Force_Field( FILE *fp, reax_interaction *reax, /* Sanity check */ if (c < 8) { - if (me == 0) - fprintf(stderr, "Inconsistent ffield file (reaxc_ffield.cpp) \n"); - MPI_Abort( comm, FILE_NOT_FOUND ); + snprintf (errmsg, 1024, "Missing parameter(s) in line %s", s); + control->error_ptr->all(FLERR, errmsg); } val = atof(tmp[0]); reax->sbp[i].r_pi_pi = val; @@ -228,9 +214,8 @@ char Read_Force_Field( FILE *fp, reax_interaction *reax, /* Sanity check */ if (c < 8) { - if (me == 0) - fprintf(stderr, "Inconsistent ffield file (reaxc_ffield.cpp) \n"); - MPI_Abort( comm, FILE_NOT_FOUND ); + snprintf (errmsg, 1024, "Missing parameter(s) in line %s", s); + control->error_ptr->all(FLERR, errmsg); } val = atof(tmp[0]); reax->sbp[i].p_ovun2 = val; @@ -249,9 +234,7 @@ char Read_Force_Field( FILE *fp, reax_interaction *reax, /* Sanity check */ if (c > 2) { - if (me == 0) - fprintf(stderr, "Force field file incompatible with 'lgvdw yes'\n"); - MPI_Abort( comm, FILE_NOT_FOUND ); + control->error_ptr->all(FLERR,"Force field file incompatible with 'lgvdw yes'"); } val = atof(tmp[0]); reax->sbp[i].lgcij = val; @@ -261,28 +244,32 @@ char Read_Force_Field( FILE *fp, reax_interaction *reax, if (reax->sbp[i].rcore2>0.01 && reax->sbp[i].acore2>0.01) { // Inner-wall if (reax->sbp[i].gamma_w>0.5) { // Shielding vdWaals if (reax->gp.vdw_type != 0 && reax->gp.vdw_type != 3) { - if (errorflag && (me == 0)) - fprintf( stderr, "Warning: inconsistent vdWaals-parameters\n" \ - "Force field parameters for element %s\n" \ - "indicate inner wall+shielding, but earlier\n" \ - "atoms indicate different vdWaals-method.\n" \ - "This may cause division-by-zero errors.\n" \ - "Keeping vdWaals-setting for earlier atoms.\n", - reax->sbp[i].name ); + if (errorflag && (me == 0)) { + char errmsg[512]; + snprintf(errmsg, 512, "VdWaals-parameters for element %s " + "indicate inner wall+shielding, but earlier " + "atoms indicate different vdWaals-method. " + "This may cause division-by-zero errors. " + "Keeping vdWaals-setting for earlier atoms.", + reax->sbp[i].name); + control->error_ptr->warning(FLERR,errmsg); + } errorflag = 0; } else { reax->gp.vdw_type = 3; } } else { // No shielding vdWaals parameters present if (reax->gp.vdw_type != 0 && reax->gp.vdw_type != 2) { - if (me == 0) - fprintf( stderr, "Warning: inconsistent vdWaals-parameters\n" \ - "Force field parameters for element %s\n" \ - "indicate inner wall without shielding, but earlier\n" \ - "atoms indicate different vdWaals-method.\n" \ - "This may cause division-by-zero errors.\n" \ - "Keeping vdWaals-setting for earlier atoms.\n", - reax->sbp[i].name ); + if (me == 0) { + char errmsg[512]; + snprintf(errmsg, 512, "VdWaals-parameters for element %s " + "indicate inner wall without shielding, but earlier " + "atoms indicate different vdWaals-method. " + "This may cause division-by-zero errors. " + "Keeping vdWaals-setting for earlier atoms.", + reax->sbp[i].name); + control->error_ptr->warning(FLERR,errmsg); + } } else { reax->gp.vdw_type = 2; } @@ -290,23 +277,25 @@ char Read_Force_Field( FILE *fp, reax_interaction *reax, } else { // No Inner wall parameters present if (reax->sbp[i].gamma_w>0.5) { // Shielding vdWaals if (reax->gp.vdw_type != 0 && reax->gp.vdw_type != 1) { - if (me == 0) - fprintf( stderr, "Warning: inconsistent vdWaals-parameters\n" \ - "Force field parameters for element %s\n" \ - "indicate shielding without inner wall, but earlier\n" \ - "atoms indicate different vdWaals-method.\n" \ - "This may cause division-by-zero errors.\n" \ - "Keeping vdWaals-setting for earlier atoms.\n", - reax->sbp[i].name ); + if (me == 0) { + char errmsg[512]; + snprintf(errmsg, 512, "VdWaals parameters for element %s " + "indicate shielding without inner wall, but earlier " + "elements indicate different vdWaals-method. " + "This may cause division-by-zero errors. " + "Keeping vdWaals-setting for earlier atoms.", + reax->sbp[i].name); + control->error_ptr->warning(FLERR,errmsg); + } } else { reax->gp.vdw_type = 1; } } else { - if (me == 0) - fprintf( stderr, "Error: inconsistent vdWaals-parameters\n" \ - "No shielding or inner-wall set for element %s\n", - reax->sbp[i].name ); - MPI_Abort( comm, INVALID_INPUT ); + char errmsg[256]; + snprintf(errmsg, 256, "Inconsistent vdWaals-parameters: " + "No shielding or inner-wall set for element %s", + reax->sbp[i].name); + control->error_ptr->all(FLERR, errmsg); } } } @@ -315,15 +304,23 @@ char Read_Force_Field( FILE *fp, reax_interaction *reax, for( i = 0; i < reax->num_atom_types; i++ ) if( reax->sbp[i].mass < 21 && reax->sbp[i].valency_val != reax->sbp[i].valency_boc ) { - if (me == 0) - fprintf(stderr,"Warning: changed valency_val to valency_boc for %s\n", - reax->sbp[i].name ); + if (me == 0) { + char errmsg[256]; + snprintf(errmsg, 256, "Changed valency_val to valency_boc for %s", + reax->sbp[i].name); + control->error_ptr->warning(FLERR,errmsg); + } reax->sbp[i].valency_val = reax->sbp[i].valency_boc; } /* next line is number of two body combination and some comments */ fgets(s,MAX_LINE,fp); c=Tokenize(s,&tmp); + + if (c == 2 && !lgflag) { + control->error_ptr->all(FLERR, "Force field file requires using 'lgvdw yes'"); + } + l = atoi(tmp[0]); /* a line of comments */ diff --git a/src/USER-REAXC/reaxc_forces.cpp b/src/USER-REAXC/reaxc_forces.cpp index 19b3cc4975..186cde681a 100644 --- a/src/USER-REAXC/reaxc_forces.cpp +++ b/src/USER-REAXC/reaxc_forces.cpp @@ -39,11 +39,14 @@ #include "reaxc_valence_angles.h" #include "reaxc_vector.h" +#include "error.h" + + interaction_function Interaction_Functions[NUM_INTRS]; void Dummy_Interaction( reax_system * /*system*/, control_params * /*control*/, simulation_data * /*data*/, storage * /*workspace*/, - reax_list **/*lists*/, output_controls * /*out_control*/ ) + reax_list ** /*lists*/, output_controls * /*out_control*/ ) { } @@ -115,7 +118,7 @@ void Compute_Total_Force( reax_system *system, control_params *control, } void Validate_Lists( reax_system *system, storage * /*workspace*/, reax_list **lists, - int step, int /*n*/, int N, int numH, MPI_Comm comm ) + int step, int /*n*/, int N, int numH ) { int i, comp, Hindex; reax_list *bonds, *hbonds; @@ -134,9 +137,10 @@ void Validate_Lists( reax_system *system, storage * /*workspace*/, reax_list **l else comp = bonds->num_intrs; if (End_Index(i, bonds) > comp) { - fprintf( stderr, "step%d-bondchk failed: i=%d end(i)=%d str(i+1)=%d\n", + char errmsg[256]; + snprintf(errmsg, 256, "step%d-bondchk failed: i=%d end(i)=%d str(i+1)=%d\n", step, i, End_Index(i,bonds), comp ); - MPI_Abort( comm, INSUFFICIENT_MEMORY ); + system->error_ptr->one(FLERR,errmsg); } } } @@ -161,9 +165,10 @@ void Validate_Lists( reax_system *system, storage * /*workspace*/, reax_list **l else comp = hbonds->num_intrs; if (End_Index(Hindex, hbonds) > comp) { - fprintf(stderr,"step%d-hbondchk failed: H=%d end(H)=%d str(H+1)=%d\n", + char errmsg[256]; + snprintf(errmsg, 256, "step%d-hbondchk failed: H=%d end(H)=%d str(H+1)=%d\n", step, Hindex, End_Index(Hindex,hbonds), comp ); - MPI_Abort( comm, INSUFFICIENT_MEMORY ); + system->error_ptr->one(FLERR, errmsg); } } } @@ -173,8 +178,7 @@ void Validate_Lists( reax_system *system, storage * /*workspace*/, reax_list **l void Init_Forces_noQEq( reax_system *system, control_params *control, simulation_data *data, storage *workspace, - reax_list **lists, output_controls * /*out_control*/, - MPI_Comm comm ) { + reax_list **lists, output_controls * /*out_control*/ ) { int i, j, pj; int start_i, end_i; int type_i, type_j; @@ -308,13 +312,13 @@ void Init_Forces_noQEq( reax_system *system, control_params *control, workspace->realloc.num_hbonds = num_hbonds; Validate_Lists( system, workspace, lists, data->step, - system->n, system->N, system->numH, comm ); + system->n, system->N, system->numH); } void Estimate_Storages( reax_system *system, control_params *control, reax_list **lists, int *Htop, int *hb_top, - int *bond_top, int *num_3body, MPI_Comm /*comm*/ ) + int *bond_top, int *num_3body ) { int i, j, pj; int start_i, end_i; @@ -436,10 +440,9 @@ void Compute_Forces( reax_system *system, control_params *control, reax_list **lists, output_controls *out_control, mpi_datatypes *mpi_data ) { - MPI_Comm comm = mpi_data->world; Init_Forces_noQEq( system, control, data, workspace, - lists, out_control, comm ); + lists, out_control); /********* bonded interactions ************/ Compute_Bonded_Forces( system, control, data, workspace, diff --git a/src/USER-REAXC/reaxc_forces.h b/src/USER-REAXC/reaxc_forces.h index 6c839a7023..bfad2e9b71 100644 --- a/src/USER-REAXC/reaxc_forces.h +++ b/src/USER-REAXC/reaxc_forces.h @@ -36,5 +36,5 @@ void Init_Force_Functions( control_params* ); void Compute_Forces( reax_system*, control_params*, simulation_data*, storage*, reax_list**, output_controls*, mpi_datatypes* ); void Estimate_Storages( reax_system*, control_params*, reax_list**, - int*, int*, int*, int*, MPI_Comm ); + int*, int*, int*, int* ); #endif diff --git a/src/USER-REAXC/reaxc_init_md.cpp b/src/USER-REAXC/reaxc_init_md.cpp index 5901b76326..c1239e0cbb 100644 --- a/src/USER-REAXC/reaxc_init_md.cpp +++ b/src/USER-REAXC/reaxc_init_md.cpp @@ -36,6 +36,8 @@ #include "reaxc_tool_box.h" #include "reaxc_vector.h" +#include "error.h" + int Init_System( reax_system *system, control_params *control, char * /*msg*/ ) { int i; @@ -80,7 +82,7 @@ int Init_Simulation_Data( reax_system *system, control_params *control, return SUCCESS; } -void Init_Taper( control_params *control, storage *workspace, MPI_Comm comm ) +void Init_Taper( control_params *control, storage *workspace ) { double d1, d7; double swa, swa2, swa3; @@ -89,15 +91,17 @@ void Init_Taper( control_params *control, storage *workspace, MPI_Comm comm ) swa = control->nonb_low; swb = control->nonb_cut; - if (fabs( swa ) > 0.01) - fprintf( stderr, "Warning: non-zero lower Taper-radius cutoff\n" ); + if (fabs( swa ) > 0.01 && control->me == 0) + control->error_ptr->warning( FLERR, "Non-zero lower Taper-radius cutoff" ); if (swb < 0) { - fprintf( stderr, "Negative upper Taper-radius cutoff\n" ); - MPI_Abort( comm, INVALID_INPUT ); + control->error_ptr->all(FLERR,"Negative upper Taper-radius cutoff"); + } + else if( swb < 5 && control->me == 0) { + char errmsg[256]; + snprintf(errmsg, 256, "Very low Taper-radius cutoff: %f", swb ); + control->error_ptr->warning( FLERR, errmsg ); } - else if( swb < 5 ) - fprintf( stderr, "Warning: very low Taper-radius cutoff: %f\n", swb ); d1 = swb - swa; d7 = pow( d1, 7.0 ); @@ -119,12 +123,12 @@ void Init_Taper( control_params *control, storage *workspace, MPI_Comm comm ) int Init_Workspace( reax_system *system, control_params *control, - storage *workspace, MPI_Comm comm, char *msg ) + storage *workspace, char *msg ) { int ret; ret = Allocate_Workspace( system, control, workspace, - system->local_cap, system->total_cap, comm, msg ); + system->local_cap, system->total_cap, msg ); if (ret != SUCCESS) return ret; @@ -132,7 +136,7 @@ int Init_Workspace( reax_system *system, control_params *control, Reset_Workspace( system, workspace ); /* Initialize the Taper function */ - Init_Taper( control, workspace, comm ); + Init_Taper( control, workspace); return SUCCESS; } @@ -156,17 +160,15 @@ int Init_Lists( reax_system *system, control_params *control, { int i, total_hbonds, total_bonds, bond_cap, num_3body, cap_3body, Htop; int *hb_top, *bond_top; - MPI_Comm comm; int mincap = system->mincap; double safezone = system->safezone; double saferzone = system->saferzone; - comm = mpi_data->world; bond_top = (int*) calloc( system->total_cap, sizeof(int) ); hb_top = (int*) calloc( system->local_cap, sizeof(int) ); Estimate_Storages( system, control, lists, - &Htop, hb_top, bond_top, &num_3body, comm ); + &Htop, hb_top, bond_top, &num_3body); if (control->hbond_cut > 0) { /* init H indexes */ @@ -178,10 +180,10 @@ int Init_Lists( reax_system *system, control_params *control, total_hbonds = (int)(MAX( total_hbonds*saferzone, mincap*MIN_HBONDS )); if( !Make_List( system->Hcap, total_hbonds, TYP_HBOND, - *lists+HBONDS, comm ) ) { - fprintf( stderr, "not enough space for hbonds list. terminating!\n" ); - MPI_Abort( comm, INSUFFICIENT_MEMORY ); + *lists+HBONDS ) ) { + control->error_ptr->one(FLERR, "Not enough space for hbonds list."); } + (*lists+HBONDS)->error_ptr = system->error_ptr; } total_bonds = 0; @@ -192,18 +194,18 @@ int Init_Lists( reax_system *system, control_params *control, bond_cap = (int)(MAX( total_bonds*safezone, mincap*MIN_BONDS )); if( !Make_List( system->total_cap, bond_cap, TYP_BOND, - *lists+BONDS, comm ) ) { - fprintf( stderr, "not enough space for bonds list. terminating!\n" ); - MPI_Abort( comm, INSUFFICIENT_MEMORY ); + *lists+BONDS ) ) { + control->error_ptr->one(FLERR, "Not enough space for bonds list."); } + (*lists+BONDS)->error_ptr = system->error_ptr; /* 3bodies list */ cap_3body = (int)(MAX( num_3body*safezone, MIN_3BODIES )); if( !Make_List( bond_cap, cap_3body, TYP_THREE_BODY, - *lists+THREE_BODIES, comm ) ){ - fprintf( stderr, "Problem in initializing angles list. Terminating!\n" ); - MPI_Abort( comm, INSUFFICIENT_MEMORY ); + *lists+THREE_BODIES ) ){ + control->error_ptr->one(FLERR,"Problem in initializing angles list."); } + (*lists+THREE_BODIES)->error_ptr = system->error_ptr; free( hb_top ); free( bond_top ); @@ -217,60 +219,38 @@ void Initialize( reax_system *system, control_params *control, mpi_datatypes *mpi_data, MPI_Comm comm ) { char msg[MAX_STR]; + char errmsg[128]; if (Init_MPI_Datatypes(system, workspace, mpi_data, comm, msg) == FAILURE) { - fprintf( stderr, "p%d: init_mpi_datatypes: could not create datatypes\n", - system->my_rank ); - fprintf( stderr, "p%d: mpi_data couldn't be initialized! terminating.\n", - system->my_rank ); - MPI_Abort( mpi_data->world, CANNOT_INITIALIZE ); + control->error_ptr->one(FLERR,"Could not create datatypes"); } if (Init_System(system, control, msg) == FAILURE) { - fprintf( stderr, "p%d: %s\n", system->my_rank, msg ); - fprintf( stderr, "p%d: system could not be initialized! terminating.\n", - system->my_rank ); - MPI_Abort( mpi_data->world, CANNOT_INITIALIZE ); + control->error_ptr->one(FLERR,"System could not be initialized"); } if (Init_Simulation_Data( system, control, data, msg ) == FAILURE) { - fprintf( stderr, "p%d: %s\n", system->my_rank, msg ); - fprintf( stderr, "p%d: sim_data couldn't be initialized! terminating.\n", - system->my_rank ); - MPI_Abort( mpi_data->world, CANNOT_INITIALIZE ); + control->error_ptr->one(FLERR,"Sim_data could not be initialized"); } - if (Init_Workspace( system, control, workspace, mpi_data->world, msg ) == + if (Init_Workspace( system, control, workspace, msg ) == FAILURE) { - fprintf( stderr, "p%d:init_workspace: not enough memory\n", - system->my_rank ); - fprintf( stderr, "p%d:workspace couldn't be initialized! terminating.\n", - system->my_rank ); - MPI_Abort( mpi_data->world, CANNOT_INITIALIZE ); + control->error_ptr->one(FLERR,"Workspace could not be initialized"); } if (Init_Lists( system, control, data, workspace, lists, mpi_data, msg ) == FAILURE) { - fprintf( stderr, "p%d: %s\n", system->my_rank, msg ); - fprintf( stderr, "p%d: system could not be initialized! terminating.\n", - system->my_rank ); - MPI_Abort( mpi_data->world, CANNOT_INITIALIZE ); + control->error_ptr->one(FLERR,"Lists could not be initialized"); } if (Init_Output_Files(system,control,out_control,mpi_data,msg)== FAILURE) { - fprintf( stderr, "p%d: %s\n", system->my_rank, msg ); - fprintf( stderr, "p%d: could not open output files! terminating...\n", - system->my_rank ); - MPI_Abort( mpi_data->world, CANNOT_INITIALIZE ); + control->error_ptr->one(FLERR,"Could not open output files"); } if (control->tabulate) { if (Init_Lookup_Tables( system, control, workspace, mpi_data, msg ) == FAILURE) { - fprintf( stderr, "p%d: %s\n", system->my_rank, msg ); - fprintf( stderr, "p%d: couldn't create lookup table! terminating.\n", - system->my_rank ); - MPI_Abort( mpi_data->world, CANNOT_INITIALIZE ); + control->error_ptr->one(FLERR,"Lookup table could not be created"); } } diff --git a/src/USER-REAXC/reaxc_init_md.h b/src/USER-REAXC/reaxc_init_md.h index 25333c744f..ab519a4c72 100644 --- a/src/USER-REAXC/reaxc_init_md.h +++ b/src/USER-REAXC/reaxc_init_md.h @@ -29,6 +29,7 @@ #include "reaxc_types.h" + void Initialize( reax_system*, control_params*, simulation_data*, storage*, reax_list**, output_controls*, mpi_datatypes*, MPI_Comm ); #endif diff --git a/src/USER-REAXC/reaxc_list.cpp b/src/USER-REAXC/reaxc_list.cpp index 8a3bb9d322..cd4f815286 100644 --- a/src/USER-REAXC/reaxc_list.cpp +++ b/src/USER-REAXC/reaxc_list.cpp @@ -28,117 +28,121 @@ #include "reaxc_list.h" #include "reaxc_tool_box.h" +#include "error.h" + /************* allocate list space ******************/ -int Make_List(int n, int num_intrs, int type, reax_list *l, MPI_Comm comm) +int Make_List(int n, int num_intrs, int type, reax_list *l ) { l->allocated = 1; l->n = n; l->num_intrs = num_intrs; - if (l->index) sfree(l->index, "list:index"); - if (l->end_index) sfree(l->end_index, "list:end_index"); - l->index = (int*) smalloc( n * sizeof(int), "list:index", comm ); - l->end_index = (int*) smalloc( n * sizeof(int), "list:end_index", comm ); + if (l->index) sfree(l->error_ptr, l->index, "list:index"); + if (l->end_index) sfree(l->error_ptr, l->end_index, "list:end_index"); + l->index = (int*) smalloc(l->error_ptr, n * sizeof(int), "list:index"); + l->end_index = (int*) smalloc(l->error_ptr, n * sizeof(int), "list:end_index"); l->type = type; switch(l->type) { case TYP_VOID: - if (l->select.v) sfree(l->select.v, "list:v"); - l->select.v = (void*) smalloc(l->num_intrs * sizeof(void*), "list:v", comm); + if (l->select.v) sfree(l->error_ptr, l->select.v, "list:v"); + l->select.v = (void*) smalloc(l->error_ptr, l->num_intrs * sizeof(void*), "list:v"); break; case TYP_THREE_BODY: - if (l->select.three_body_list) sfree(l->select.three_body_list,"list:three_bodies"); + if (l->select.three_body_list) sfree(l->error_ptr, l->select.three_body_list,"list:three_bodies"); l->select.three_body_list = (three_body_interaction_data*) - smalloc( l->num_intrs * sizeof(three_body_interaction_data), - "list:three_bodies", comm ); + smalloc(l->error_ptr, l->num_intrs * sizeof(three_body_interaction_data), + "list:three_bodies"); break; case TYP_BOND: - if (l->select.bond_list) sfree(l->select.bond_list,"list:bonds"); + if (l->select.bond_list) sfree(l->error_ptr, l->select.bond_list,"list:bonds"); l->select.bond_list = (bond_data*) - smalloc( l->num_intrs * sizeof(bond_data), "list:bonds", comm ); + smalloc(l->error_ptr, l->num_intrs * sizeof(bond_data), "list:bonds"); break; case TYP_DBO: - if (l->select.dbo_list) sfree(l->select.dbo_list,"list:dbonds"); + if (l->select.dbo_list) sfree(l->error_ptr, l->select.dbo_list,"list:dbonds"); l->select.dbo_list = (dbond_data*) - smalloc( l->num_intrs * sizeof(dbond_data), "list:dbonds", comm ); + smalloc(l->error_ptr, l->num_intrs * sizeof(dbond_data), "list:dbonds"); break; case TYP_DDELTA: - if (l->select.dDelta_list) sfree(l->select.dDelta_list,"list:dDeltas"); + if (l->select.dDelta_list) sfree(l->error_ptr, l->select.dDelta_list,"list:dDeltas"); l->select.dDelta_list = (dDelta_data*) - smalloc( l->num_intrs * sizeof(dDelta_data), "list:dDeltas", comm ); + smalloc(l->error_ptr, l->num_intrs * sizeof(dDelta_data), "list:dDeltas"); break; case TYP_FAR_NEIGHBOR: - if (l->select.far_nbr_list) sfree(l->select.far_nbr_list,"list:far_nbrs"); + if (l->select.far_nbr_list) sfree(l->error_ptr, l->select.far_nbr_list,"list:far_nbrs"); l->select.far_nbr_list = (far_neighbor_data*) - smalloc(l->num_intrs * sizeof(far_neighbor_data), "list:far_nbrs", comm); + smalloc(l->error_ptr, l->num_intrs * sizeof(far_neighbor_data), "list:far_nbrs"); break; case TYP_HBOND: - if (l->select.hbond_list) sfree(l->select.hbond_list,"list:hbonds"); + if (l->select.hbond_list) sfree(l->error_ptr, l->select.hbond_list,"list:hbonds"); l->select.hbond_list = (hbond_data*) - smalloc( l->num_intrs * sizeof(hbond_data), "list:hbonds", comm ); + smalloc(l->error_ptr, l->num_intrs * sizeof(hbond_data), "list:hbonds"); break; default: - fprintf( stderr, "ERROR: no %d list type defined!\n", l->type ); - MPI_Abort( comm, INVALID_INPUT ); + char errmsg[128]; + snprintf(errmsg, 128, "No %d list type defined", l->type); + l->error_ptr->one(FLERR,errmsg); } return SUCCESS; } -void Delete_List( reax_list *l, MPI_Comm comm ) +void Delete_List( reax_list *l ) { if (l->allocated == 0) return; l->allocated = 0; - sfree( l->index, "list:index" ); - sfree( l->end_index, "list:end_index" ); + sfree(l->error_ptr, l->index, "list:index" ); + sfree(l->error_ptr, l->end_index, "list:end_index" ); l->index = NULL; l->end_index = NULL; switch(l->type) { case TYP_VOID: - sfree( l->select.v, "list:v" ); + sfree(l->error_ptr, l->select.v, "list:v" ); l->select.v = NULL; break; case TYP_HBOND: - sfree( l->select.hbond_list, "list:hbonds" ); + sfree(l->error_ptr, l->select.hbond_list, "list:hbonds" ); l->select.hbond_list = NULL; break; case TYP_FAR_NEIGHBOR: - sfree( l->select.far_nbr_list, "list:far_nbrs" ); + sfree(l->error_ptr, l->select.far_nbr_list, "list:far_nbrs" ); l->select.far_nbr_list = NULL; break; case TYP_BOND: - sfree( l->select.bond_list, "list:bonds" ); + sfree(l->error_ptr, l->select.bond_list, "list:bonds" ); l->select.bond_list = NULL; break; case TYP_DBO: - sfree( l->select.dbo_list, "list:dbos" ); + sfree(l->error_ptr, l->select.dbo_list, "list:dbos" ); l->select.dbo_list = NULL; break; case TYP_DDELTA: - sfree( l->select.dDelta_list, "list:dDeltas" ); + sfree(l->error_ptr, l->select.dDelta_list, "list:dDeltas" ); l->select.dDelta_list = NULL; break; case TYP_THREE_BODY: - sfree( l->select.three_body_list, "list:three_bodies" ); + sfree(l->error_ptr, l->select.three_body_list, "list:three_bodies" ); l->select.three_body_list = NULL; break; default: - fprintf( stderr, "ERROR: no %d list type defined!\n", l->type ); - MPI_Abort( comm, INVALID_INPUT ); + char errmsg[128]; + snprintf(errmsg, 128, "No %d list type defined", l->type); + l->error_ptr->all(FLERR,errmsg); } } diff --git a/src/USER-REAXC/reaxc_list.h b/src/USER-REAXC/reaxc_list.h index ab7fbce19c..28567252da 100644 --- a/src/USER-REAXC/reaxc_list.h +++ b/src/USER-REAXC/reaxc_list.h @@ -29,8 +29,8 @@ #include "reaxc_types.h" -int Make_List( int, int, int, reax_list*, MPI_Comm ); -void Delete_List( reax_list*, MPI_Comm ); +int Make_List( int, int, int, reax_list* ); +void Delete_List( reax_list* ); inline int Num_Entries(int,reax_list*); inline int Start_Index( int, reax_list* ); diff --git a/src/USER-REAXC/reaxc_lookup.cpp b/src/USER-REAXC/reaxc_lookup.cpp index 92945ebdb5..74d8176522 100644 --- a/src/USER-REAXC/reaxc_lookup.cpp +++ b/src/USER-REAXC/reaxc_lookup.cpp @@ -50,19 +50,18 @@ void Tridiagonal_Solve( const double *a, const double *b, } -void Natural_Cubic_Spline( const double *h, const double *f, - cubic_spline_coef *coef, unsigned int n, - MPI_Comm comm ) +void Natural_Cubic_Spline( LAMMPS_NS::Error* error_ptr, const double *h, const double *f, + cubic_spline_coef *coef, unsigned int n ) { int i; double *a, *b, *c, *d, *v; /* allocate space for the linear system */ - a = (double*) smalloc( n * sizeof(double), "cubic_spline:a", comm ); - b = (double*) smalloc( n * sizeof(double), "cubic_spline:a", comm ); - c = (double*) smalloc( n * sizeof(double), "cubic_spline:a", comm ); - d = (double*) smalloc( n * sizeof(double), "cubic_spline:a", comm ); - v = (double*) smalloc( n * sizeof(double), "cubic_spline:a", comm ); + a = (double*) smalloc(error_ptr, n * sizeof(double), "cubic_spline:a"); + b = (double*) smalloc(error_ptr, n * sizeof(double), "cubic_spline:a"); + c = (double*) smalloc(error_ptr, n * sizeof(double), "cubic_spline:a"); + d = (double*) smalloc(error_ptr, n * sizeof(double), "cubic_spline:a"); + v = (double*) smalloc(error_ptr, n * sizeof(double), "cubic_spline:a"); /* build the linear system */ a[0] = a[1] = a[n-1] = 0; @@ -92,28 +91,27 @@ void Natural_Cubic_Spline( const double *h, const double *f, coef[i-1].a = f[i]; } - sfree( a, "cubic_spline:a" ); - sfree( b, "cubic_spline:b" ); - sfree( c, "cubic_spline:c" ); - sfree( d, "cubic_spline:d" ); - sfree( v, "cubic_spline:v" ); + sfree(error_ptr, a, "cubic_spline:a" ); + sfree(error_ptr, b, "cubic_spline:b" ); + sfree(error_ptr, c, "cubic_spline:c" ); + sfree(error_ptr, d, "cubic_spline:d" ); + sfree(error_ptr, v, "cubic_spline:v" ); } -void Complete_Cubic_Spline( const double *h, const double *f, double v0, double vlast, - cubic_spline_coef *coef, unsigned int n, - MPI_Comm comm ) +void Complete_Cubic_Spline( LAMMPS_NS::Error* error_ptr, const double *h, const double *f, double v0, double vlast, + cubic_spline_coef *coef, unsigned int n ) { int i; double *a, *b, *c, *d, *v; /* allocate space for the linear system */ - a = (double*) smalloc( n * sizeof(double), "cubic_spline:a", comm ); - b = (double*) smalloc( n * sizeof(double), "cubic_spline:a", comm ); - c = (double*) smalloc( n * sizeof(double), "cubic_spline:a", comm ); - d = (double*) smalloc( n * sizeof(double), "cubic_spline:a", comm ); - v = (double*) smalloc( n * sizeof(double), "cubic_spline:a", comm ); + a = (double*) smalloc(error_ptr, n * sizeof(double), "cubic_spline:a"); + b = (double*) smalloc(error_ptr, n * sizeof(double), "cubic_spline:a"); + c = (double*) smalloc(error_ptr, n * sizeof(double), "cubic_spline:a"); + d = (double*) smalloc(error_ptr, n * sizeof(double), "cubic_spline:a"); + v = (double*) smalloc(error_ptr, n * sizeof(double), "cubic_spline:a"); /* build the linear system */ a[0] = 0; @@ -142,11 +140,11 @@ void Complete_Cubic_Spline( const double *h, const double *f, double v0, double coef[i-1].a = f[i]; } - sfree( a, "cubic_spline:a" ); - sfree( b, "cubic_spline:b" ); - sfree( c, "cubic_spline:c" ); - sfree( d, "cubic_spline:d" ); - sfree( v, "cubic_spline:v" ); + sfree(error_ptr, a, "cubic_spline:a" ); + sfree(error_ptr, b, "cubic_spline:b" ); + sfree(error_ptr, c, "cubic_spline:c" ); + sfree(error_ptr, d, "cubic_spline:d" ); + sfree(error_ptr, v, "cubic_spline:v" ); } @@ -159,35 +157,33 @@ int Init_Lookup_Tables( reax_system *system, control_params *control, double dr; double *h, *fh, *fvdw, *fele, *fCEvd, *fCEclmb; double v0_vdw, v0_ele, vlast_vdw, vlast_ele; - MPI_Comm comm; /* initializations */ v0_vdw = 0; v0_ele = 0; vlast_vdw = 0; vlast_ele = 0; - comm = mpi_data->world; num_atom_types = system->reax_param.num_atom_types; dr = control->nonb_cut / control->tabulate; h = (double*) - smalloc( (control->tabulate+2) * sizeof(double), "lookup:h", comm ); + smalloc(system->error_ptr, (control->tabulate+2) * sizeof(double), "lookup:h"); fh = (double*) - smalloc( (control->tabulate+2) * sizeof(double), "lookup:fh", comm ); + smalloc(system->error_ptr, (control->tabulate+2) * sizeof(double), "lookup:fh"); fvdw = (double*) - smalloc( (control->tabulate+2) * sizeof(double), "lookup:fvdw", comm ); + smalloc(system->error_ptr, (control->tabulate+2) * sizeof(double), "lookup:fvdw"); fCEvd = (double*) - smalloc( (control->tabulate+2) * sizeof(double), "lookup:fCEvd", comm ); + smalloc(system->error_ptr, (control->tabulate+2) * sizeof(double), "lookup:fCEvd"); fele = (double*) - smalloc( (control->tabulate+2) * sizeof(double), "lookup:fele", comm ); + smalloc(system->error_ptr, (control->tabulate+2) * sizeof(double), "lookup:fele"); fCEclmb = (double*) - smalloc( (control->tabulate+2) * sizeof(double), "lookup:fCEclmb", comm ); + smalloc(system->error_ptr, (control->tabulate+2) * sizeof(double), "lookup:fCEclmb"); LR = (LR_lookup_table**) - scalloc( num_atom_types, sizeof(LR_lookup_table*), "lookup:LR", comm ); + scalloc(system->error_ptr, num_atom_types, sizeof(LR_lookup_table*), "lookup:LR"); for( i = 0; i < num_atom_types; ++i ) LR[i] = (LR_lookup_table*) - scalloc( num_atom_types, sizeof(LR_lookup_table), "lookup:LR[i]", comm ); + scalloc(system->error_ptr, num_atom_types, sizeof(LR_lookup_table), "lookup:LR[i]"); for( i = 0; i < MAX_ATOM_TYPES; ++i ) existing_types[i] = 0; @@ -207,22 +203,18 @@ int Init_Lookup_Tables( reax_system *system, control_params *control, LR[i][j].dx = dr; LR[i][j].inv_dx = control->tabulate / control->nonb_cut; LR[i][j].y = (LR_data*) - smalloc( LR[i][j].n * sizeof(LR_data), "lookup:LR[i,j].y", comm ); + smalloc(system->error_ptr, LR[i][j].n * sizeof(LR_data), "lookup:LR[i,j].y"); LR[i][j].H = (cubic_spline_coef*) - smalloc( LR[i][j].n*sizeof(cubic_spline_coef),"lookup:LR[i,j].H" , - comm ); + smalloc(system->error_ptr, LR[i][j].n*sizeof(cubic_spline_coef),"lookup:LR[i,j].H"); LR[i][j].vdW = (cubic_spline_coef*) - smalloc( LR[i][j].n*sizeof(cubic_spline_coef),"lookup:LR[i,j].vdW", - comm); + smalloc(system->error_ptr, LR[i][j].n*sizeof(cubic_spline_coef),"lookup:LR[i,j].vdW"); LR[i][j].CEvd = (cubic_spline_coef*) - smalloc( LR[i][j].n*sizeof(cubic_spline_coef),"lookup:LR[i,j].CEvd", - comm); + smalloc(system->error_ptr, LR[i][j].n*sizeof(cubic_spline_coef),"lookup:LR[i,j].CEvd"); LR[i][j].ele = (cubic_spline_coef*) - smalloc( LR[i][j].n*sizeof(cubic_spline_coef),"lookup:LR[i,j].ele", - comm ); + smalloc(system->error_ptr, LR[i][j].n*sizeof(cubic_spline_coef),"lookup:LR[i,j].ele"); LR[i][j].CEclmb = (cubic_spline_coef*) - smalloc( LR[i][j].n*sizeof(cubic_spline_coef), - "lookup:LR[i,j].CEclmb", comm ); + smalloc(system->error_ptr, LR[i][j].n*sizeof(cubic_spline_coef), + "lookup:LR[i,j].CEclmb"); for( r = 1; r <= control->tabulate; ++r ) { LR_vdW_Coulomb( system, workspace, control, i, j, r * dr, &(LR[i][j].y[r]) ); @@ -246,24 +238,20 @@ int Init_Lookup_Tables( reax_system *system, control_params *control, vlast_vdw = fCEvd[r-1]; vlast_ele = fele[r-1]; - Natural_Cubic_Spline( &h[1], &fh[1], - &(LR[i][j].H[1]), control->tabulate+1, comm ); + Natural_Cubic_Spline( control->error_ptr, &h[1], &fh[1], + &(LR[i][j].H[1]), control->tabulate+1); - Complete_Cubic_Spline( &h[1], &fvdw[1], v0_vdw, vlast_vdw, - &(LR[i][j].vdW[1]), control->tabulate+1, - comm ); + Complete_Cubic_Spline( control->error_ptr, &h[1], &fvdw[1], v0_vdw, vlast_vdw, + &(LR[i][j].vdW[1]), control->tabulate+1); - Natural_Cubic_Spline( &h[1], &fCEvd[1], - &(LR[i][j].CEvd[1]), control->tabulate+1, - comm ); + Natural_Cubic_Spline( control->error_ptr, &h[1], &fCEvd[1], + &(LR[i][j].CEvd[1]), control->tabulate+1); - Complete_Cubic_Spline( &h[1], &fele[1], v0_ele, vlast_ele, - &(LR[i][j].ele[1]), control->tabulate+1, - comm ); + Complete_Cubic_Spline( control->error_ptr, &h[1], &fele[1], v0_ele, vlast_ele, + &(LR[i][j].ele[1]), control->tabulate+1); - Natural_Cubic_Spline( &h[1], &fCEclmb[1], - &(LR[i][j].CEclmb[1]), control->tabulate+1, - comm ); + Natural_Cubic_Spline( control->error_ptr, &h[1], &fCEclmb[1], + &(LR[i][j].CEclmb[1]), control->tabulate+1); } else { LR[i][j].n = 0; } @@ -291,14 +279,14 @@ void Deallocate_Lookup_Tables( reax_system *system ) for( i = 0; i < ntypes; ++i ) { for( j = i; j < ntypes; ++j ) if (LR[i][j].n) { - sfree( LR[i][j].y, "LR[i,j].y" ); - sfree( LR[i][j].H, "LR[i,j].H" ); - sfree( LR[i][j].vdW, "LR[i,j].vdW" ); - sfree( LR[i][j].CEvd, "LR[i,j].CEvd" ); - sfree( LR[i][j].ele, "LR[i,j].ele" ); - sfree( LR[i][j].CEclmb, "LR[i,j].CEclmb" ); + sfree(system->error_ptr, LR[i][j].y, "LR[i,j].y" ); + sfree(system->error_ptr, LR[i][j].H, "LR[i,j].H" ); + sfree(system->error_ptr, LR[i][j].vdW, "LR[i,j].vdW" ); + sfree(system->error_ptr, LR[i][j].CEvd, "LR[i,j].CEvd" ); + sfree(system->error_ptr, LR[i][j].ele, "LR[i,j].ele" ); + sfree(system->error_ptr, LR[i][j].CEclmb, "LR[i,j].CEclmb" ); } - sfree( LR[i], "LR[i]" ); + sfree(system->error_ptr, LR[i], "LR[i]" ); } - sfree( LR, "LR" ); + sfree(system->error_ptr, LR, "LR" ); } diff --git a/src/USER-REAXC/reaxc_lookup.h b/src/USER-REAXC/reaxc_lookup.h index 66fa3c407c..3fd0c2581a 100644 --- a/src/USER-REAXC/reaxc_lookup.h +++ b/src/USER-REAXC/reaxc_lookup.h @@ -32,13 +32,11 @@ void Tridiagonal_Solve( const double *a, const double *b, double *c, double *d, double *x, unsigned int n); -void Natural_Cubic_Spline( const double *h, const double *f, - cubic_spline_coef *coef, unsigned int n, - MPI_Comm comm ); +void Natural_Cubic_Spline( LAMMPS_NS::Error*, const double *h, const double *f, + cubic_spline_coef *coef, unsigned int n ); -void Complete_Cubic_Spline( const double *h, const double *f, double v0, double vlast, - cubic_spline_coef *coef, unsigned int n, - MPI_Comm comm ); +void Complete_Cubic_Spline( LAMMPS_NS::Error*, const double *h, const double *f, double v0, double vlast, + cubic_spline_coef *coef, unsigned int n ); int Init_Lookup_Tables( reax_system*, control_params*, storage*, mpi_datatypes*, char* ); diff --git a/src/USER-REAXC/reaxc_reset_tools.cpp b/src/USER-REAXC/reaxc_reset_tools.cpp index 80faed1e9f..5439ee33a4 100644 --- a/src/USER-REAXC/reaxc_reset_tools.cpp +++ b/src/USER-REAXC/reaxc_reset_tools.cpp @@ -30,6 +30,9 @@ #include "reaxc_tool_box.h" #include "reaxc_vector.h" +#include "error.h" + + void Reset_Atoms( reax_system* system, control_params *control ) { int i; @@ -120,8 +123,7 @@ void Reset_Workspace( reax_system *system, storage *workspace ) void Reset_Neighbor_Lists( reax_system *system, control_params *control, - storage *workspace, reax_list **lists, - MPI_Comm comm ) + storage *workspace, reax_list **lists ) { int i, total_bonds, Hindex, total_hbonds; reax_list *bonds, *hbonds; @@ -142,10 +144,10 @@ void Reset_Neighbor_Lists( reax_system *system, control_params *control, if (total_bonds >= bonds->num_intrs * DANGER_ZONE) { workspace->realloc.bonds = 1; if (total_bonds >= bonds->num_intrs) { - fprintf(stderr, - "p%d: not enough space for bonds! total=%d allocated=%d\n", - system->my_rank, total_bonds, bonds->num_intrs ); - MPI_Abort( comm, INSUFFICIENT_MEMORY ); + char errmsg[256]; + snprintf(errmsg, 256, "Not enough space for bonds! total=%d allocated=%d\n", + total_bonds, bonds->num_intrs); + control->error_ptr->one(FLERR, errmsg); } } } @@ -168,10 +170,10 @@ void Reset_Neighbor_Lists( reax_system *system, control_params *control, if (total_hbonds >= hbonds->num_intrs * 0.90/*DANGER_ZONE*/) { workspace->realloc.hbonds = 1; if (total_hbonds >= hbonds->num_intrs) { - fprintf(stderr, - "p%d: not enough space for hbonds! total=%d allocated=%d\n", - system->my_rank, total_hbonds, hbonds->num_intrs ); - MPI_Abort( comm, INSUFFICIENT_MEMORY ); + char errmsg[256]; + snprintf(errmsg, 256, "Not enough space for hbonds! total=%d allocated=%d\n", + total_hbonds, hbonds->num_intrs); + control->error_ptr->one(FLERR, errmsg); } } } @@ -179,7 +181,7 @@ void Reset_Neighbor_Lists( reax_system *system, control_params *control, void Reset( reax_system *system, control_params *control, simulation_data *data, - storage *workspace, reax_list **lists, MPI_Comm comm ) + storage *workspace, reax_list **lists ) { Reset_Atoms( system, control ); @@ -187,6 +189,6 @@ void Reset( reax_system *system, control_params *control, simulation_data *data, Reset_Workspace( system, workspace ); - Reset_Neighbor_Lists( system, control, workspace, lists, comm ); + Reset_Neighbor_Lists( system, control, workspace, lists ); } diff --git a/src/USER-REAXC/reaxc_reset_tools.h b/src/USER-REAXC/reaxc_reset_tools.h index c2a90072d5..20d1ab6964 100644 --- a/src/USER-REAXC/reaxc_reset_tools.h +++ b/src/USER-REAXC/reaxc_reset_tools.h @@ -34,7 +34,7 @@ void Reset_Simulation_Data( simulation_data*, int ); void Reset_Timing( reax_timing* ); void Reset_Workspace( reax_system*, storage* ); void Reset_Neighbor_Lists( reax_system*, control_params*, storage*, - reax_list**, MPI_Comm ); + reax_list** ); void Reset( reax_system*, control_params*, simulation_data*, storage*, - reax_list**, MPI_Comm ); + reax_list** ); #endif diff --git a/src/USER-REAXC/reaxc_tool_box.cpp b/src/USER-REAXC/reaxc_tool_box.cpp index 9e662e7a45..b6058b2516 100644 --- a/src/USER-REAXC/reaxc_tool_box.cpp +++ b/src/USER-REAXC/reaxc_tool_box.cpp @@ -27,6 +27,8 @@ #include "pair_reaxc.h" #include "reaxc_tool_box.h" +#include "error.h" + struct timeval tim; double t_end; @@ -53,23 +55,25 @@ int Tokenize( char* s, char*** tok ) return count; } + + /* safe malloc */ -void *smalloc( rc_bigint n, const char *name, MPI_Comm comm ) +void *smalloc( LAMMPS_NS::Error *error_ptr, rc_bigint n, const char *name ) { void *ptr; + char errmsg[256]; if (n <= 0) { - fprintf( stderr, "WARNING: trying to allocate %ld bytes for array %s. ", - n, name ); - fprintf( stderr, "returning NULL.\n" ); + snprintf(errmsg, 256, "Trying to allocate %ld bytes for array %s. " + "returning NULL.", n, name); + error_ptr->one(FLERR,errmsg); return NULL; } ptr = malloc( n ); if (ptr == NULL) { - fprintf( stderr, "ERROR: failed to allocate %ld bytes for array %s", - n, name ); - MPI_Abort( comm, INSUFFICIENT_MEMORY ); + snprintf(errmsg, 256, "Failed to allocate %ld bytes for array %s", n, name); + error_ptr->one(FLERR,errmsg); } return ptr; @@ -77,29 +81,30 @@ void *smalloc( rc_bigint n, const char *name, MPI_Comm comm ) /* safe calloc */ -void *scalloc( rc_bigint n, rc_bigint size, const char *name, MPI_Comm comm ) +void *scalloc( LAMMPS_NS::Error *error_ptr, rc_bigint n, rc_bigint size, const char *name ) { void *ptr; + char errmsg[256]; if (n <= 0) { - fprintf( stderr, "WARNING: trying to allocate %ld elements for array %s. ", - n, name ); - fprintf( stderr, "returning NULL.\n" ); + snprintf(errmsg, 256, "Trying to allocate %ld elements for array %s. " + "returning NULL.\n", n, name ); + error_ptr->one(FLERR,errmsg); return NULL; } if (size <= 0) { - fprintf( stderr, "WARNING: elements size for array %s is %ld. ", - name, size ); - fprintf( stderr, "returning NULL.\n" ); + snprintf(errmsg, 256, "Elements size for array %s is %ld. " + "returning NULL", name, size ); + error_ptr->one(FLERR,errmsg); return NULL; } ptr = calloc( n, size ); if (ptr == NULL) { - fprintf( stderr, "ERROR: failed to allocate %ld bytes for array %s", - n*size, name ); - MPI_Abort( comm, INSUFFICIENT_MEMORY ); + char errmsg[256]; + snprintf(errmsg, 256, "Failed to allocate %ld bytes for array %s", n*size, name); + error_ptr->one(FLERR,errmsg); } return ptr; @@ -107,11 +112,12 @@ void *scalloc( rc_bigint n, rc_bigint size, const char *name, MPI_Comm comm ) /* safe free */ -void sfree( void *ptr, const char *name ) +void sfree( LAMMPS_NS::Error* error_ptr, void *ptr, const char *name ) { if (ptr == NULL) { - fprintf( stderr, "WARNING: trying to free the already NULL pointer %s!\n", - name ); + char errmsg[256]; + snprintf(errmsg, 256, "Trying to free the already NULL pointer %s", name ); + error_ptr->one(FLERR,errmsg); return; } diff --git a/src/USER-REAXC/reaxc_tool_box.h b/src/USER-REAXC/reaxc_tool_box.h index 7f8dd455ca..0465376dba 100644 --- a/src/USER-REAXC/reaxc_tool_box.h +++ b/src/USER-REAXC/reaxc_tool_box.h @@ -37,7 +37,7 @@ double Get_Time( ); int Tokenize( char*, char*** ); /* from lammps */ -void *smalloc( rc_bigint, const char*, MPI_Comm ); -void *scalloc( rc_bigint, rc_bigint, const char*, MPI_Comm ); -void sfree( void*, const char* ); +void *smalloc( LAMMPS_NS::Error*, rc_bigint, const char* ); +void *scalloc( LAMMPS_NS::Error*, rc_bigint, rc_bigint, const char* ); +void sfree( LAMMPS_NS::Error*, void*, const char* ); #endif diff --git a/src/USER-REAXC/reaxc_traj.cpp b/src/USER-REAXC/reaxc_traj.cpp index 54d8b3219c..5adc0cfbb9 100644 --- a/src/USER-REAXC/reaxc_traj.cpp +++ b/src/USER-REAXC/reaxc_traj.cpp @@ -29,8 +29,9 @@ #include "reaxc_list.h" #include "reaxc_tool_box.h" -int Reallocate_Output_Buffer( output_controls *out_control, int req_space, - MPI_Comm comm ) +#include "error.h" + +int Reallocate_Output_Buffer( LAMMPS_NS::Error *error_ptr, output_controls *out_control, int req_space ) { if (out_control->buffer_len > 0) free( out_control->buffer ); @@ -38,10 +39,9 @@ int Reallocate_Output_Buffer( output_controls *out_control, int req_space, out_control->buffer_len = (int)(req_space*SAFE_ZONE); out_control->buffer = (char*) malloc(out_control->buffer_len*sizeof(char)); if (out_control->buffer == NULL) { - fprintf( stderr, - "insufficient memory for required buffer size %d. terminating!\n", - (int) (req_space*SAFE_ZONE) ); - MPI_Abort( comm, INSUFFICIENT_MEMORY ); + char errmsg[256]; + snprintf(errmsg, 256, "Insufficient memory for required buffer size %d", (int) (req_space*SAFE_ZONE)); + error_ptr->one(FLERR,errmsg); } return SUCCESS; @@ -83,7 +83,7 @@ int Write_Header( reax_system *system, control_params *control, my_hdr_lines = num_hdr_lines * ( system->my_rank == MASTER_NODE ); buffer_req = my_hdr_lines * HEADER_LINE_LEN; if (buffer_req > out_control->buffer_len * DANGER_ZONE) - Reallocate_Output_Buffer( out_control, buffer_req, mpi_data->world ); + Reallocate_Output_Buffer( control->error_ptr, out_control, buffer_req ); /* only the master node writes into trajectory header */ if (system->my_rank == MASTER_NODE) { @@ -278,7 +278,7 @@ int Write_Init_Desc( reax_system *system, control_params * /*control*/, else buffer_req = system->n * INIT_DESC_LEN + 1; if (buffer_req > out_control->buffer_len * DANGER_ZONE) - Reallocate_Output_Buffer( out_control, buffer_req, mpi_data->world ); + Reallocate_Output_Buffer( system->error_ptr, out_control, buffer_req ); out_control->line[0] = 0; out_control->buffer[0] = 0; @@ -367,7 +367,7 @@ int Write_Frame_Header( reax_system *system, control_params *control, my_frm_hdr_lines = num_frm_hdr_lines * ( me == MASTER_NODE ); buffer_req = my_frm_hdr_lines * HEADER_LINE_LEN; if (buffer_req > out_control->buffer_len * DANGER_ZONE) - Reallocate_Output_Buffer( out_control, buffer_req, mpi_data->world ); + Reallocate_Output_Buffer( control->error_ptr, out_control, buffer_req ); /* only the master node writes into trajectory header */ if (me == MASTER_NODE) { @@ -500,7 +500,7 @@ int Write_Atoms( reax_system *system, control_params * /*control*/, else buffer_req = system->n * line_len + 1; if (buffer_req > out_control->buffer_len * DANGER_ZONE) - Reallocate_Output_Buffer( out_control, buffer_req, mpi_data->world ); + Reallocate_Output_Buffer( system->error_ptr, out_control, buffer_req ); /* fill in buffer */ out_control->line[0] = 0; @@ -531,9 +531,7 @@ int Write_Atoms( reax_system *system, control_params * /*control*/, p_atom->f[0], p_atom->f[1], p_atom->f[2], p_atom->q ); break; default: - fprintf( stderr, - "write_traj_atoms: unknown atom trajectroy format!\n"); - MPI_Abort( mpi_data->world, UNKNOWN_OPTION ); + system->error_ptr->one(FLERR,"Write_traj_atoms: unknown atom trajectory format"); } strncpy( out_control->buffer + i*line_len, out_control->line, line_len+1 ); @@ -592,7 +590,7 @@ int Write_Bonds(reax_system *system, control_params *control, reax_list *bonds, else buffer_req = my_bonds * line_len + 1; if (buffer_req > out_control->buffer_len * DANGER_ZONE) - Reallocate_Output_Buffer( out_control, buffer_req, mpi_data->world ); + Reallocate_Output_Buffer( system->error_ptr, out_control, buffer_req ); /* fill in the buffer */ out_control->line[0] = 0; @@ -619,8 +617,7 @@ int Write_Bonds(reax_system *system, control_params *control, reax_list *bonds, bo_ij->bo_data.BO_pi, bo_ij->bo_data.BO_pi2 ); break; default: - fprintf(stderr, "write_traj_bonds: FATAL! invalid bond_info option"); - MPI_Abort( mpi_data->world, UNKNOWN_OPTION ); + system->error_ptr->one(FLERR, "Write_traj_bonds: FATAL! invalid bond_info option"); } strncpy( out_control->buffer + my_bonds*line_len, out_control->line, line_len+1 ); @@ -693,7 +690,7 @@ int Write_Angles( reax_system *system, control_params *control, else buffer_req = my_angles * line_len + 1; if (buffer_req > out_control->buffer_len * DANGER_ZONE) - Reallocate_Output_Buffer( out_control, buffer_req, mpi_data->world ); + Reallocate_Output_Buffer( system->error_ptr, out_control, buffer_req ); /* fill in the buffer */ my_angles = 0; diff --git a/src/USER-REAXC/reaxc_types.h b/src/USER-REAXC/reaxc_types.h index 2666fcf85c..cdc2916a66 100644 --- a/src/USER-REAXC/reaxc_types.h +++ b/src/USER-REAXC/reaxc_types.h @@ -39,6 +39,9 @@ #include #include "accelerator_kokkos.h" + +namespace LAMMPS_NS { class Error;} + #if defined LMP_USER_OMP #define OMP_TIMING 0 @@ -392,8 +395,6 @@ typedef struct double ghost_cutoff; } boundary_cutoff; -using LAMMPS_NS::Pair; - struct _reax_system { reax_interaction reax_param; @@ -411,7 +412,8 @@ struct _reax_system boundary_cutoff bndry_cuts; reax_atom *my_atoms; - class Pair *pair_ptr; + class LAMMPS_NS::Error *error_ptr; + class LAMMPS_NS::Pair *pair_ptr; int my_bonds; int mincap; double safezone, saferzone; @@ -488,6 +490,8 @@ typedef struct int lgflag; int enobondsflag; + class LAMMPS_NS::Error *error_ptr; + int me; } control_params; @@ -774,6 +778,7 @@ struct _reax_list int type; list_type select; + class LAMMPS_NS::Error *error_ptr; }; typedef _reax_list reax_list; diff --git a/src/USER-REAXC/reaxc_valence_angles.cpp b/src/USER-REAXC/reaxc_valence_angles.cpp index af1f1f8003..4ba870b6d9 100644 --- a/src/USER-REAXC/reaxc_valence_angles.cpp +++ b/src/USER-REAXC/reaxc_valence_angles.cpp @@ -30,6 +30,8 @@ #include "reaxc_list.h" #include "reaxc_vector.h" +#include "error.h" + static double Dot( double* v1, double* v2, int k ) { double ret = 0.0; @@ -405,9 +407,10 @@ void Valence_Angles( reax_system *system, control_params *control, if (num_thb_intrs >= thb_intrs->num_intrs * DANGER_ZONE) { workspace->realloc.num_3body = num_thb_intrs; if (num_thb_intrs > thb_intrs->num_intrs) { - fprintf( stderr, "step%d-ran out of space on angle_list: top=%d, max=%d", - data->step, num_thb_intrs, thb_intrs->num_intrs ); - MPI_Abort( MPI_COMM_WORLD, INSUFFICIENT_MEMORY ); + char errmsg[128]; + snprintf(errmsg, 128, "step%d-ran out of space on angle_list: top=%d, max=%d", + data->step, num_thb_intrs, thb_intrs->num_intrs); + control->error_ptr->one(FLERR, errmsg); } } diff --git a/src/USER-SMD/smd_material_models.h b/src/USER-SMD/smd_material_models.h index acb498c04d..557612bdf5 100644 --- a/src/USER-SMD/smd_material_models.h +++ b/src/USER-SMD/smd_material_models.h @@ -22,10 +22,10 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#ifndef SMD_MATERIAL_MODELS_H_ -#define SMD_MATERIAL_MODELS_H_ +#ifndef SMD_MATERIAL_MODELS_H +#define SMD_MATERIAL_MODELS_H -using namespace Eigen; +#include /* * EOS models @@ -42,22 +42,22 @@ void PerfectGasEOS(const double gamma, const double vol, const double mass, cons /* * Material strength models */ -void LinearStrength(const double mu, const Matrix3d sigmaInitial_dev, const Matrix3d d_dev, const double dt, - Matrix3d &sigmaFinal_dev__, Matrix3d &sigma_dev_rate__); -void LinearPlasticStrength(const double G, const double yieldStress, const Matrix3d sigmaInitial_dev, const Matrix3d d_dev, - const double dt, Matrix3d &sigmaFinal_dev__, Matrix3d &sigma_dev_rate__, double &plastic_strain_increment); +void LinearStrength(const double mu, const Eigen::Matrix3d sigmaInitial_dev, const Eigen::Matrix3d d_dev, const double dt, + Eigen::Matrix3d &sigmaFinal_dev__, Eigen::Matrix3d &sigma_dev_rate__); +void LinearPlasticStrength(const double G, const double yieldStress, const Eigen::Matrix3d sigmaInitial_dev, const Eigen::Matrix3d d_dev, + const double dt, Eigen::Matrix3d &sigmaFinal_dev__, Eigen::Matrix3d &sigma_dev_rate__, double &plastic_strain_increment); void JohnsonCookStrength(const double G, const double cp, const double espec, const double A, const double B, const double a, const double C, const double epdot0, const double T0, const double Tmelt, const double M, const double dt, const double ep, - const double epdot, const Matrix3d sigmaInitial_dev, const Matrix3d d_dev, Matrix3d &sigmaFinal_dev__, - Matrix3d &sigma_dev_rate__, double &plastic_strain_increment); + const double epdot, const Eigen::Matrix3d sigmaInitial_dev, const Eigen::Matrix3d d_dev, Eigen::Matrix3d &sigmaFinal_dev__, + Eigen::Matrix3d &sigma_dev_rate__, double &plastic_strain_increment); /* * Damage models */ -bool IsotropicMaxStrainDamage(const Matrix3d E, const double maxStrain); -bool IsotropicMaxStressDamage(const Matrix3d E, const double maxStrain); -double JohnsonCookFailureStrain(const double p, const Matrix3d Sdev, const double d1, const double d2, const double d3, +bool IsotropicMaxStrainDamage(const Eigen::Matrix3d E, const double maxStrain); +bool IsotropicMaxStressDamage(const Eigen::Matrix3d E, const double maxStrain); +double JohnsonCookFailureStrain(const double p, const Eigen::Matrix3d Sdev, const double d1, const double d2, const double d3, const double d4, const double epdot0, const double epdot); diff --git a/src/USER-SMD/smd_math.h b/src/USER-SMD/smd_math.h index cea9e9dbc7..52e7c983d5 100644 --- a/src/USER-SMD/smd_math.h +++ b/src/USER-SMD/smd_math.h @@ -9,14 +9,11 @@ * * ----------------------------------------------------------------------- */ -//test -#ifndef SMD_MATH_H_ -#define SMD_MATH_H_ +#ifndef SMD_MATH_H +#define SMD_MATH_H #include #include -using namespace Eigen; -using namespace std; namespace SMD_Math { static inline void LimitDoubleMagnitude(double &x, const double limit) { @@ -31,8 +28,8 @@ static inline void LimitDoubleMagnitude(double &x, const double limit) { /* * deviator of a tensor */ -static inline Matrix3d Deviator(const Matrix3d M) { - Matrix3d eye; +static inline Eigen::Matrix3d Deviator(const Eigen::Matrix3d M) { + Eigen::Matrix3d eye; eye.setIdentity(); eye *= M.trace() / 3.0; return M - eye; @@ -53,14 +50,14 @@ static inline Matrix3d Deviator(const Matrix3d M) { * obtained again from an SVD. The rotation should proper now, i.e., det(R) = +1. */ -static inline bool PolDec(Matrix3d M, Matrix3d &R, Matrix3d &T, bool scaleF) { +static inline bool PolDec(Eigen::Matrix3d M, Eigen::Matrix3d &R, Eigen::Matrix3d &T, bool scaleF) { - JacobiSVD svd(M, ComputeFullU | ComputeFullV); // SVD(A) = U S V* - Vector3d S_eigenvalues = svd.singularValues(); - Matrix3d S = svd.singularValues().asDiagonal(); - Matrix3d U = svd.matrixU(); - Matrix3d V = svd.matrixV(); - Matrix3d eye; + Eigen::JacobiSVD svd(M, Eigen::ComputeFullU | Eigen::ComputeFullV); // SVD(A) = U S V* + Eigen::Vector3d S_eigenvalues = svd.singularValues(); + Eigen::Matrix3d S = svd.singularValues().asDiagonal(); + Eigen::Matrix3d U = svd.matrixU(); + Eigen::Matrix3d V = svd.matrixV(); + Eigen::Matrix3d eye; eye.setIdentity(); // now do polar decomposition into M = R * T, where R is rotation @@ -105,16 +102,12 @@ static inline bool PolDec(Matrix3d M, Matrix3d &R, Matrix3d &T, bool scaleF) { * Pseudo-inverse via SVD */ -static inline void pseudo_inverse_SVD(Matrix3d &M) { +static inline void pseudo_inverse_SVD(Eigen::Matrix3d &M) { - //JacobiSVD < Matrix3d > svd(M, ComputeFullU | ComputeFullV); - JacobiSVD svd(M, ComputeFullU); // one Eigevector base is sufficient because matrix is square and symmetric + Eigen::JacobiSVD svd(M, Eigen::ComputeFullU); // one Eigevector base is sufficient because matrix is square and symmetric - Vector3d singularValuesInv; - Vector3d singularValues = svd.singularValues(); - -//cout << "Here is the matrix V:" << endl << V * singularValues.asDiagonal() * U << endl; -//cout << "Its singular values are:" << endl << singularValues << endl; + Eigen::Vector3d singularValuesInv; + Eigen::Vector3d singularValues = svd.singularValues(); double pinvtoler = 1.0e-16; // 2d machining example goes unstable if this value is increased (1.0e-16). for (int row = 0; row < 3; row++) { @@ -126,39 +119,19 @@ static inline void pseudo_inverse_SVD(Matrix3d &M) { } M = svd.matrixU() * singularValuesInv.asDiagonal() * svd.matrixU().transpose(); - -// JacobiSVD < Matrix3d > svd(M, ComputeFullU | ComputeFullV); -// -// Vector3d singularValuesInv; -// Vector3d singularValues = svd.singularValues(); -// -// //cout << "Here is the matrix V:" << endl << V * singularValues.asDiagonal() * U << endl; -// //cout << "Its singular values are:" << endl << singularValues << endl; -// -// double pinvtoler = 1.0e-16; // 2d machining example goes unstable if this value is increased (1.0e-16). -// for (int row = 0; row < 3; row++) { -// if (singularValues(row) > pinvtoler) { -// singularValuesInv(row) = 1.0 / singularValues(row); -// } else { -// singularValuesInv(row) = 0.0; -// } -// } -// -// M = svd.matrixU() * singularValuesInv.asDiagonal() * svd.matrixV().transpose(); - } /* * test if two matrices are equal */ -static inline double TestMatricesEqual(Matrix3d A, Matrix3d B, double eps) { - Matrix3d diff; +static inline double TestMatricesEqual(Eigen::Matrix3d A, Eigen::Matrix3d B, double eps) { + Eigen::Matrix3d diff; diff = A - B; double norm = diff.norm(); if (norm > eps) { - printf("Matrices A and B are not equal! The L2-norm difference is: %g\n", norm); - cout << "Here is matrix A:" << endl << A << endl; - cout << "Here is matrix B:" << endl << B << endl; + std::cout << "Matrices A and B are not equal! The L2-norm difference is: " << norm << "\n" + << "Here is matrix A:\n" << A << "\n" + << "Here is matrix B:\n" << B << std::endl; } return norm; } @@ -167,12 +140,12 @@ static inline double TestMatricesEqual(Matrix3d A, Matrix3d B, double eps) { Limit eigenvalues of a matrix to upper and lower bounds. ------------------------------------------------------------------------- */ -static inline Matrix3d LimitEigenvalues(Matrix3d S, double limitEigenvalue) { +static inline Eigen::Matrix3d LimitEigenvalues(Eigen::Matrix3d S, double limitEigenvalue) { /* * compute Eigenvalues of matrix S */ - SelfAdjointEigenSolver < Matrix3d > es; + Eigen::SelfAdjointEigenSolver < Eigen::Matrix3d > es; es.compute(S); double max_eigenvalue = es.eigenvalues().maxCoeff(); @@ -183,17 +156,17 @@ static inline Matrix3d LimitEigenvalues(Matrix3d S, double limitEigenvalue) { if ((amax_eigenvalue > limitEigenvalue) || (amin_eigenvalue > limitEigenvalue)) { if (amax_eigenvalue > amin_eigenvalue) { // need to scale with max_eigenvalue double scale = amax_eigenvalue / limitEigenvalue; - Matrix3d V = es.eigenvectors(); - Matrix3d S_diag = V.inverse() * S * V; // diagonalized input matrix + Eigen::Matrix3d V = es.eigenvectors(); + Eigen::Matrix3d S_diag = V.inverse() * S * V; // diagonalized input matrix S_diag /= scale; - Matrix3d S_scaled = V * S_diag * V.inverse(); // undiagonalize matrix + Eigen::Matrix3d S_scaled = V * S_diag * V.inverse(); // undiagonalize matrix return S_scaled; } else { // need to scale using min_eigenvalue double scale = amin_eigenvalue / limitEigenvalue; - Matrix3d V = es.eigenvectors(); - Matrix3d S_diag = V.inverse() * S * V; // diagonalized input matrix + Eigen::Matrix3d V = es.eigenvectors(); + Eigen::Matrix3d S_diag = V.inverse() * S * V; // diagonalized input matrix S_diag /= scale; - Matrix3d S_scaled = V * S_diag * V.inverse(); // undiagonalize matrix + Eigen::Matrix3d S_scaled = V * S_diag * V.inverse(); // undiagonalize matrix return S_scaled; } } else { // limiting does not apply @@ -201,17 +174,17 @@ static inline Matrix3d LimitEigenvalues(Matrix3d S, double limitEigenvalue) { } } -static inline bool LimitMinMaxEigenvalues(Matrix3d &S, double min, double max) { +static inline bool LimitMinMaxEigenvalues(Eigen::Matrix3d &S, double min, double max) { /* * compute Eigenvalues of matrix S */ - SelfAdjointEigenSolver < Matrix3d > es; + Eigen::SelfAdjointEigenSolver < Eigen::Matrix3d > es; es.compute(S); if ((es.eigenvalues().maxCoeff() > max) || (es.eigenvalues().minCoeff() < min)) { - Matrix3d S_diag = es.eigenvalues().asDiagonal(); - Matrix3d V = es.eigenvectors(); + Eigen::Matrix3d S_diag = es.eigenvalues().asDiagonal(); + Eigen::Matrix3d V = es.eigenvectors(); for (int i = 0; i < 3; i++) { if (S_diag(i, i) < min) { //printf("limiting eigenvalue %f --> %f\n", S_diag(i, i), min); @@ -229,10 +202,10 @@ static inline bool LimitMinMaxEigenvalues(Matrix3d &S, double min, double max) { } } -static inline void reconstruct_rank_deficient_shape_matrix(Matrix3d &K) { +static inline void reconstruct_rank_deficient_shape_matrix(Eigen::Matrix3d &K) { - JacobiSVD svd(K, ComputeFullU | ComputeFullV); - Vector3d singularValues = svd.singularValues(); + Eigen::JacobiSVD svd(K, Eigen::ComputeFullU | Eigen::ComputeFullV); + Eigen::Vector3d singularValues = svd.singularValues(); for (int i = 0; i < 3; i++) { if (singularValues(i) < 1.0e-8) { diff --git a/src/hashlittle.cpp b/src/hashlittle.cpp index 0abcd2bcc5..38f192ad76 100644 --- a/src/hashlittle.cpp +++ b/src/hashlittle.cpp @@ -23,6 +23,16 @@ # endif #endif +// declaration to indicate intended fallthrough cases in switch statements +// and thus silence the warnings produced by g++ -Wextra + +#if defined(__GNUC__) +#define _fallthrough __attribute__ ((fallthrough)) +#else +#define _fallthrough +#endif + + #define rot(x,k) (((x)<<(k)) | ((x)>>(32-(k)))) /* @@ -291,17 +301,17 @@ uint32_t hashlittle( const void *key, size_t length, uint32_t initval) /*-------------------------------- last block: affect all 32 bits of (c) */ switch(length) /* all the case statements fall through */ { - case 12: c+=((uint32_t)k[11])<<24; - case 11: c+=((uint32_t)k[10])<<16; - case 10: c+=((uint32_t)k[9])<<8; - case 9 : c+=k[8]; - case 8 : b+=((uint32_t)k[7])<<24; - case 7 : b+=((uint32_t)k[6])<<16; - case 6 : b+=((uint32_t)k[5])<<8; - case 5 : b+=k[4]; - case 4 : a+=((uint32_t)k[3])<<24; - case 3 : a+=((uint32_t)k[2])<<16; - case 2 : a+=((uint32_t)k[1])<<8; + case 12: c+=((uint32_t)k[11])<<24; _fallthrough; + case 11: c+=((uint32_t)k[10])<<16; _fallthrough; + case 10: c+=((uint32_t)k[9])<<8; _fallthrough; + case 9 : c+=k[8]; _fallthrough; + case 8 : b+=((uint32_t)k[7])<<24; _fallthrough; + case 7 : b+=((uint32_t)k[6])<<16; _fallthrough; + case 6 : b+=((uint32_t)k[5])<<8; _fallthrough; + case 5 : b+=k[4]; _fallthrough; + case 4 : a+=((uint32_t)k[3])<<24; _fallthrough; + case 3 : a+=((uint32_t)k[2])<<16; _fallthrough; + case 2 : a+=((uint32_t)k[1])<<8; _fallthrough; case 1 : a+=k[0]; break; case 0 : return c; diff --git a/src/irregular.cpp b/src/irregular.cpp index 848d853f2a..1865f9cbf6 100644 --- a/src/irregular.cpp +++ b/src/irregular.cpp @@ -921,7 +921,7 @@ void Irregular::exchange_data(char *sendbuf, int nbytes, char *recvbuf) // post all receives, starting after self copies - bigint offset = num_self*nbytes; + bigint offset = num_self*(bigint)nbytes; for (int irecv = 0; irecv < nrecv_proc; irecv++) { MPI_Irecv(&recvbuf[offset],num_recv[irecv]*nbytes,MPI_CHAR, proc_recv[irecv],0,world,&request[irecv]); @@ -964,13 +964,6 @@ void Irregular::exchange_data(char *sendbuf, int nbytes, char *recvbuf) // wait on all incoming messages if (nrecv_proc) MPI_Waitall(nrecv_proc,request,status); - - // approximate memory tally - // DEBUG lines - - //bigint irregular_bytes = 2*nprocs*sizeof(int); - //irregular_bytes += maxindex*sizeof(int); - //irregular_bytes += maxbuf; } /* ---------------------------------------------------------------------- diff --git a/src/library.cpp b/src/library.cpp index d8c55159a2..a653b83adb 100644 --- a/src/library.cpp +++ b/src/library.cpp @@ -801,6 +801,17 @@ void lammps_reset_box(void *ptr, double *boxlo, double *boxhi, Allreduce to sum vector into data across all procs ------------------------------------------------------------------------- */ +#if defined(LAMMPS_BIGBIG) +void lammps_gather_atoms(void *ptr, char * /*name */, + int /*type*/, int /*count*/, void * /*data*/) +{ + LAMMPS *lmp = (LAMMPS *) ptr; + + BEGIN_CAPTURE + lmp->error->all(FLERR,"Library function lammps_gather_atoms() not compatible with -DLAMMPS_BIGBIG"); + END_CAPTURE +} +#else void lammps_gather_atoms(void *ptr, char *name, int type, int count, void *data) { @@ -905,6 +916,7 @@ void lammps_gather_atoms(void *ptr, char *name, } END_CAPTURE } +#endif /* ---------------------------------------------------------------------- gather the named atom-based entity for all atoms @@ -927,6 +939,17 @@ void lammps_gather_atoms(void *ptr, char *name, Allgather Nlocal atoms from each proc into data ------------------------------------------------------------------------- */ +#if defined(LAMMPS_BIGBIG) +void lammps_gather_atoms_concat(void *ptr, char * /*name */, + int /*type*/, int /*count*/, void * /*data*/) +{ + LAMMPS *lmp = (LAMMPS *) ptr; + + BEGIN_CAPTURE + lmp->error->all(FLERR,"Library function lammps_gather_atoms_concat() not compatible with -DLAMMPS_BIGBIG"); + END_CAPTURE +} +#else void lammps_gather_atoms_concat(void *ptr, char *name, int type, int count, void *data) { @@ -1047,6 +1070,7 @@ void lammps_gather_atoms_concat(void *ptr, char *name, } END_CAPTURE } +#endif /* ---------------------------------------------------------------------- gather the named atom-based entity for a subset of atoms @@ -1071,6 +1095,18 @@ void lammps_gather_atoms_concat(void *ptr, char *name, Allreduce to sum vector into data across all procs ------------------------------------------------------------------------- */ +#if defined(LAMMPS_BIGBIG) +void lammps_gather_atoms_subset(void *ptr, char * /*name */, + int /*type*/, int /*count*/, + int /*ndata*/, int * /*ids*/, void * /*data*/) +{ + LAMMPS *lmp = (LAMMPS *) ptr; + + BEGIN_CAPTURE + lmp->error->all(FLERR,"Library function lammps_gather_atoms_subset() not compatible with -DLAMMPS_BIGBIG"); + END_CAPTURE +} +#else void lammps_gather_atoms_subset(void *ptr, char *name, int type, int count, int ndata, int *ids, void *data) @@ -1188,6 +1224,7 @@ void lammps_gather_atoms_subset(void *ptr, char *name, } END_CAPTURE } +#endif /* ---------------------------------------------------------------------- scatter the named atom-based entity in data to all atoms @@ -1205,6 +1242,17 @@ void lammps_gather_atoms_subset(void *ptr, char *name, loop over Natoms, if I own atom ID, set its values from data ------------------------------------------------------------------------- */ +#if defined(LAMMPS_BIGBIG) +void lammps_scatter_atoms(void *ptr, char * /*name */, + int /*type*/, int /*count*/, void * /*data*/) +{ + LAMMPS *lmp = (LAMMPS *) ptr; + + BEGIN_CAPTURE + lmp->error->all(FLERR,"Library function lammps_scatter_atoms() not compatible with -DLAMMPS_BIGBIG"); + END_CAPTURE +} +#else void lammps_scatter_atoms(void *ptr, char *name, int type, int count, void *data) { @@ -1299,6 +1347,7 @@ void lammps_scatter_atoms(void *ptr, char *name, } END_CAPTURE } +#endif /* ---------------------------------------------------------------------- scatter the named atom-based entity in data to a subset of atoms @@ -1318,6 +1367,18 @@ void lammps_scatter_atoms(void *ptr, char *name, loop over Ndata, if I own atom ID, set its values from data ------------------------------------------------------------------------- */ +#if defined(LAMMPS_BIGBIG) +void lammps_scatter_atoms_subset(void *ptr, char * /*name */, + int /*type*/, int /*count*/, + int /*ndata*/, int * /*ids*/, void * /*data*/) +{ + LAMMPS *lmp = (LAMMPS *) ptr; + + BEGIN_CAPTURE + lmp->error->all(FLERR,"Library function lammps_scatter_atoms_subset() not compatible with -DLAMMPS_BIGBIG"); + END_CAPTURE +} +#else void lammps_scatter_atoms_subset(void *ptr, char *name, int type, int count, int ndata, int *ids, void *data) @@ -1420,6 +1481,7 @@ void lammps_scatter_atoms_subset(void *ptr, char *name, } END_CAPTURE } +#endif /* ---------------------------------------------------------------------- create N atoms and assign them to procs based on coords diff --git a/src/lmpwindows.h b/src/lmpwindows.h index 546fa62535..92a248a05e 100644 --- a/src/lmpwindows.h +++ b/src/lmpwindows.h @@ -24,14 +24,13 @@ inline double pow(int i, int j){ return pow((double)i,j); } -#endif -inline double sqrt(int i){ - return sqrt((double) i); -} - inline double fabs(int i){ return fabs((double) i); } +inline double sqrt(int i){ + return sqrt((double) i); +} +#endif inline double trunc(double x) { return x > 0 ? floor(x) : ceil(x); diff --git a/src/memory.cpp b/src/memory.cpp index 971de3dce6..b2f8a95b17 100644 --- a/src/memory.cpp +++ b/src/memory.cpp @@ -26,7 +26,7 @@ #endif #endif -#if defined(LMP_USER_INTEL) && !defined(LAMMPS_MEMALIGN) +#if defined(LMP_USER_INTEL) && !defined(LAMMPS_MEMALIGN) && !defined(_WIN32) #define LAMMPS_MEMALIGN 64 #endif diff --git a/src/my_page.h b/src/my_page.h index 5cd7098d8c..01542a9174 100644 --- a/src/my_page.h +++ b/src/my_page.h @@ -48,7 +48,7 @@ methods: #ifndef LAMMPS_MY_PAGE_H #define LAMMPS_MY_PAGE_H -#if defined(LMP_USER_INTEL) && !defined(LAMMPS_MEMALIGN) +#if defined(LMP_USER_INTEL) && !defined(LAMMPS_MEMALIGN) && !defined(_WIN32) #define LAMMPS_MEMALIGN 64 #endif diff --git a/src/special.cpp b/src/special.cpp index ab3764a156..903794c0f6 100644 --- a/src/special.cpp +++ b/src/special.cpp @@ -821,21 +821,26 @@ void Special::angle_trim() int nsend = 0; for (i = 0; i < nlocal; i++) { - for (j = 0; j < num_angle[i]; j++) { - if (tag[i] != angle_atom2[i][j]) continue; - m = atom->map(angle_atom1[i][j]); - if (m < 0 || m >= nlocal) nsend++; - m = atom->map(angle_atom3[i][j]); - if (m < 0 || m >= nlocal) nsend++; + if (num_angle) { + for (j = 0; j < num_angle[i]; j++) { + if (tag[i] != angle_atom2[i][j]) continue; + m = atom->map(angle_atom1[i][j]); + if (m < 0 || m >= nlocal) nsend++; + m = atom->map(angle_atom3[i][j]); + if (m < 0 || m >= nlocal) nsend++; + } } - for (j = 0; j < num_dihedral[i]; j++) { - if (tag[i] != dihedral_atom2[i][j]) continue; - m = atom->map(dihedral_atom1[i][j]); - if (m < 0 || m >= nlocal) nsend++; - m = atom->map(dihedral_atom3[i][j]); - if (m < 0 || m >= nlocal) nsend++; - m = atom->map(dihedral_atom4[i][j]); - if (m < 0 || m >= nlocal) nsend++; + + if (num_dihedral) { + for (j = 0; j < num_dihedral[i]; j++) { + if (tag[i] != dihedral_atom2[i][j]) continue; + m = atom->map(dihedral_atom1[i][j]); + if (m < 0 || m >= nlocal) nsend++; + m = atom->map(dihedral_atom3[i][j]); + if (m < 0 || m >= nlocal) nsend++; + m = atom->map(dihedral_atom4[i][j]); + if (m < 0 || m >= nlocal) nsend++; + } } } @@ -852,51 +857,55 @@ void Special::angle_trim() nsend = 0; for (i = 0; i < nlocal; i++) { - for (j = 0; j < num_angle[i]; j++) { - if (tag[i] != angle_atom2[i][j]) continue; + if (num_angle) { + for (j = 0; j < num_angle[i]; j++) { + if (tag[i] != angle_atom2[i][j]) continue; - m = atom->map(angle_atom1[i][j]); - if (m < 0 || m >= nlocal) { - proclist[nsend] = angle_atom1[i][j] % nprocs; - inbuf[nsend].atomID = angle_atom1[i][j]; - inbuf[nsend].partnerID = angle_atom3[i][j]; - nsend++; - } + m = atom->map(angle_atom1[i][j]); + if (m < 0 || m >= nlocal) { + proclist[nsend] = angle_atom1[i][j] % nprocs; + inbuf[nsend].atomID = angle_atom1[i][j]; + inbuf[nsend].partnerID = angle_atom3[i][j]; + nsend++; + } - m = atom->map(angle_atom3[i][j]); - if (m < 0 || m >= nlocal) { - proclist[nsend] = angle_atom3[i][j] % nprocs; - inbuf[nsend].atomID = angle_atom3[i][j]; - inbuf[nsend].partnerID = angle_atom1[i][j]; - nsend++; + m = atom->map(angle_atom3[i][j]); + if (m < 0 || m >= nlocal) { + proclist[nsend] = angle_atom3[i][j] % nprocs; + inbuf[nsend].atomID = angle_atom3[i][j]; + inbuf[nsend].partnerID = angle_atom1[i][j]; + nsend++; + } } } - for (j = 0; j < num_dihedral[i]; j++) { - if (tag[i] != dihedral_atom2[i][j]) continue; + if (num_dihedral) { + for (j = 0; j < num_dihedral[i]; j++) { + if (tag[i] != dihedral_atom2[i][j]) continue; - m = atom->map(dihedral_atom1[i][j]); - if (m < 0 || m >= nlocal) { - proclist[nsend] = dihedral_atom1[i][j] % nprocs; - inbuf[nsend].atomID = dihedral_atom1[i][j]; - inbuf[nsend].partnerID = dihedral_atom3[i][j]; - nsend++; - } + m = atom->map(dihedral_atom1[i][j]); + if (m < 0 || m >= nlocal) { + proclist[nsend] = dihedral_atom1[i][j] % nprocs; + inbuf[nsend].atomID = dihedral_atom1[i][j]; + inbuf[nsend].partnerID = dihedral_atom3[i][j]; + nsend++; + } - m = atom->map(dihedral_atom3[i][j]); - if (m < 0 || m >= nlocal) { - proclist[nsend] = dihedral_atom3[i][j] % nprocs; - inbuf[nsend].atomID = dihedral_atom3[i][j]; - inbuf[nsend].partnerID = dihedral_atom1[i][j]; - nsend++; - } + m = atom->map(dihedral_atom3[i][j]); + if (m < 0 || m >= nlocal) { + proclist[nsend] = dihedral_atom3[i][j] % nprocs; + inbuf[nsend].atomID = dihedral_atom3[i][j]; + inbuf[nsend].partnerID = dihedral_atom1[i][j]; + nsend++; + } - m = atom->map(dihedral_atom4[i][j]); - if (m < 0 || m >= nlocal) { - proclist[nsend] = dihedral_atom4[i][j] % nprocs; - inbuf[nsend].atomID = dihedral_atom4[i][j]; - inbuf[nsend].partnerID = dihedral_atom2[i][j]; - nsend++; + m = atom->map(dihedral_atom4[i][j]); + if (m < 0 || m >= nlocal) { + proclist[nsend] = dihedral_atom4[i][j] % nprocs; + inbuf[nsend].atomID = dihedral_atom4[i][j]; + inbuf[nsend].partnerID = dihedral_atom2[i][j]; + nsend++; + } } } } @@ -932,56 +941,60 @@ void Special::angle_trim() // output datums = pairs of atoms that are 1-3 neighbors for (i = 0; i < nlocal; i++) { - for (j = 0; j < num_angle[i]; j++) { - if (tag[i] != angle_atom2[i][j]) continue; + if (num_angle) { + for (j = 0; j < num_angle[i]; j++) { + if (tag[i] != angle_atom2[i][j]) continue; - m = atom->map(angle_atom1[i][j]); - if (m >= 0 && m < nlocal) { - for (k = 0; k < nspecial[m][1]; k++) - if (onethree[m][k] == angle_atom3[i][j]) { - flag[m][k] = 1; - break; - } - } + m = atom->map(angle_atom1[i][j]); + if (m >= 0 && m < nlocal) { + for (k = 0; k < nspecial[m][1]; k++) + if (onethree[m][k] == angle_atom3[i][j]) { + flag[m][k] = 1; + break; + } + } - m = atom->map(angle_atom3[i][j]); - if (m >= 0 && m < nlocal) { - for (k = 0; k < nspecial[m][1]; k++) - if (onethree[m][k] == angle_atom1[i][j]) { - flag[m][k] = 1; - break; - } + m = atom->map(angle_atom3[i][j]); + if (m >= 0 && m < nlocal) { + for (k = 0; k < nspecial[m][1]; k++) + if (onethree[m][k] == angle_atom1[i][j]) { + flag[m][k] = 1; + break; + } + } } } - for (j = 0; j < num_dihedral[i]; j++) { - if (tag[i] != dihedral_atom2[i][j]) continue; + if (num_dihedral) { + for (j = 0; j < num_dihedral[i]; j++) { + if (tag[i] != dihedral_atom2[i][j]) continue; - m = atom->map(dihedral_atom1[i][j]); - if (m >= 0 && m < nlocal) { - for (k = 0; k < nspecial[m][1]; k++) - if (onethree[m][k] == dihedral_atom3[i][j]) { - flag[m][k] = 1; - break; - } - } + m = atom->map(dihedral_atom1[i][j]); + if (m >= 0 && m < nlocal) { + for (k = 0; k < nspecial[m][1]; k++) + if (onethree[m][k] == dihedral_atom3[i][j]) { + flag[m][k] = 1; + break; + } + } - m = atom->map(dihedral_atom3[i][j]); - if (m >= 0 && m < nlocal) { - for (k = 0; k < nspecial[m][1]; k++) - if (onethree[m][k] == dihedral_atom1[i][j]) { - flag[m][k] = 1; - break; - } - } + m = atom->map(dihedral_atom3[i][j]); + if (m >= 0 && m < nlocal) { + for (k = 0; k < nspecial[m][1]; k++) + if (onethree[m][k] == dihedral_atom1[i][j]) { + flag[m][k] = 1; + break; + } + } - m = atom->map(dihedral_atom4[i][j]); - if (m >= 0 && m < nlocal) { - for (k = 0; k < nspecial[m][1]; k++) - if (onethree[m][k] == dihedral_atom2[i][j]) { - flag[m][k] = 1; - break; - } + m = atom->map(dihedral_atom4[i][j]); + if (m >= 0 && m < nlocal) { + for (k = 0; k < nspecial[m][1]; k++) + if (onethree[m][k] == dihedral_atom2[i][j]) { + flag[m][k] = 1; + break; + } + } } } } @@ -1012,7 +1025,7 @@ void Special::angle_trim() memory->destroy(flag); - // if no angles or dihedrals are defined, delete all 1-3 neighs + // if no angles or dihedrals are defined, delete all 1-3 neighs } else { for (i = 0; i < nlocal; i++) nspecial[i][1] = 0; @@ -1225,7 +1238,7 @@ void Special::dihedral_trim() ------------------------------------------------------------------------- */ int Special::rendezvous_ids(int n, char *inbuf, - int &flag, int *&proclist, char *&outbuf, + int &flag, int *& /*proclist*/, char *& /*outbuf*/, void *ptr) { Special *sptr = (Special *) ptr;