Merge pull request #2162 from akohlmey/collected-small-changes
Collected small changes
This commit is contained in:
Axel Kohlmeyer
@ -57,7 +57,6 @@ check_for_autogen_files(${LAMMPS_SOURCE_DIR})
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# compiler tests
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# these need ot be done early (before further tests).
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#####################################################################
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include(CheckCCompilerFlag)
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include(CheckIncludeFileCXX)
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# set required compiler flags and compiler/CPU arch specific optimizations
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@ -83,15 +82,6 @@ set(CMAKE_CXX_STANDARD 11)
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set(CMAKE_CXX_STANDARD_REQUIRED ON)
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set(CMAKE_CXX_EXTENSIONS OFF)
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# GNU compiler specific features for testing
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if (${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU")
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option(ENABLE_COVERAGE "Enable collecting code coverage data" OFF)
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mark_as_advanced(ENABLE_COVERAGE)
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if(ENABLE_COVERAGE)
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set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} --coverage")
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endif()
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endif()
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########################################################################
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# User input options #
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########################################################################
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@ -248,6 +238,48 @@ if(BUILD_OMP)
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target_link_libraries(lammps PRIVATE OpenMP::OpenMP_CXX)
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endif()
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# Compiler specific features for testing
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if(${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU")
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option(ENABLE_COVERAGE "Enable collecting code coverage data" OFF)
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mark_as_advanced(ENABLE_COVERAGE)
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if(ENABLE_COVERAGE)
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if(CMAKE_VERSION VERSION_LESS 3.13)
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if(CMAKE_CXX_FLAGS)
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set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} --coverage")
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else()
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set(CMAKE_CXX_FLAGS "${CMAKE_CXX_${CMAKE_BUILD_TYPE}_FLAGS} --coverage")
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endif()
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else()
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target_compile_options(lammps PUBLIC --coverage)
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target_link_options(lammps PUBLIC --coverage)
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endif()
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endif()
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endif()
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set(ENABLE_SANITIZER "none" CACHE STRING "Select a code sanitizer option (none (default), address, thread, undefined)")
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mark_as_advanced(ENABLE_SANITIZER)
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set(ENABLE_SANITIZER_VALUES none address thread undefined)
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set_property(CACHE ENABLE_SANITIZER PROPERTY STRINGS ${ENABLE_SANITIZER_VALUES})
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validate_option(ENABLE_SANITIZER ENABLE_SANITIZER_VALUES)
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string(TOLOWER ${ENABLE_SANITIZER} ENABLE_SANITIZER)
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if(NOT ENABLE_SANITIZER STREQUAL "none")
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if((${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU") OR (${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang"))
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if(CMAKE_VERSION VERSION_LESS 3.13)
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if(CMAKE_CXX_FLAGS)
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set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fsanitize=${ENABLE_SANITIZER}")
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else()
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set(CMAKE_CXX_FLAGS "${CMAKE_CXX_${CMAKE_BUILD_TYPE}_FLAGS} -fsanitize=${ENABLE_SANITIZER}")
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endif()
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else()
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target_compile_options(lammps PUBLIC -fsanitize=${ENABLE_SANITIZER})
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target_link_options(lammps PUBLIC -fsanitize=${ENABLE_SANITIZER})
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endif()
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else()
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message(WARNING "ENABLE_SANITIZER option not supported by ${CMAKE_CXX_COMPILER_ID} compilers. Ignoring.")
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set(ENABLE_SANITIZER "none")
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endif()
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endif()
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if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE)
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enable_language(C)
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find_package(LAPACK)
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@ -335,15 +367,8 @@ endforeach()
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set(CMAKE_TUNE_FLAGS "${CMAKE_TUNE_DEFAULT}" CACHE STRING "Compiler specific optimization or instrumentation")
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separate_arguments(CMAKE_TUNE_FLAGS)
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include(CheckCXXCompilerFlag)
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foreach(_FLAG ${CMAKE_TUNE_FLAGS})
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string(REGEX REPLACE "[=\"]" "" _FLAGX ${_FLAG})
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check_cxx_compiler_flag("${_FLAG}" COMPILER_SUPPORTS${_FLAGX})
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if(COMPILER_SUPPORTS${_FLAGX})
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target_compile_options(lammps PRIVATE ${_FLAG})
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else()
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message(WARNING "${_FLAG} found in CMAKE_TUNE_FLAGS, but not supported by the compiler, skipping")
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endif()
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target_compile_options(lammps PRIVATE ${_FLAG})
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endforeach()
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########################################################################
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# Basic system tests (standard libraries, headers, functions, types) #
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@ -14,40 +14,23 @@ endif()
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option(DOWNLOAD_SCAFACOS "Download ScaFaCoS library instead of using an already installed one" ${DOWNLOAD_SCAFACOS_DEFAULT})
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if(DOWNLOAD_SCAFACOS)
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message(STATUS "ScaFaCoS download requested - we will build our own")
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# create variables to pass our compiler flags along to the subsystem compile
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# need to apply -fallow-argument-mismatch, if the fortran compiler supports it
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include(CheckFortranCompilerFlag)
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check_fortran_compiler_flag("-fallow-argument-mismatch" GNUFortran_ARGUMENT_MISMATCH_FLAG)
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if(GNUFortran_ARGUMENT_MISMATCH_FLAG)
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set(APPEND_Fortran_FLAG "-fallow-argument-mismatch")
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endif()
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if(CMAKE_Fortran_FLAGS)
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set(SCAFACOS_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} ${APPEND_Fortran_FLAG}")
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else()
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set(SCAFACOS_Fortran_FLAGS "${CMAKE_Fortran_${CMAKE_BUILD_TYPE}_FLAGS} ${APPEND_Fortran_FLAG}")
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endif()
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if(CMAKE_CXX_FLAGS)
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set(SCAFACOS_CXX_FLAGS "${CMAKE_CXX_FLAGS}")
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else()
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set(SCAFACOS_CXX_FLAGS "${CMAKE_CXX_${CMAKE_BUILD_TYPE}_FLAGS}")
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endif()
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if(CMAKE_C_FLAGS)
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set(SCAFACOS_C_FLAGS "${CMAKE_C_FLAGS}")
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else()
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set(SCAFACOS_C_FLAGS "${CMAKE_C_${CMAKE_BUILD_TYPE}_FLAGS}")
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endif()
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# version 1.0.1 needs a patch to compile and linke cleanly with GCC 10 and later.
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file(DOWNLOAD https://download.lammps.org/thirdparty/scafacos-1.0.1-fix.diff ${CMAKE_CURRENT_BINARY_DIR}/scafacos-1.0.1.fix.diff
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EXPECTED_HASH MD5=4baa1333bb28fcce102d505e1992d032)
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include(ExternalProject)
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ExternalProject_Add(scafacos_build
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URL https://github.com/scafacos/scafacos/releases/download/v1.0.1/scafacos-1.0.1.tar.gz
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URL_MD5 bd46d74e3296bd8a444d731bb10c1738
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PATCH_COMMAND patch -p1 < ${CMAKE_CURRENT_BINARY_DIR}/scafacos-1.0.1.fix.diff
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CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR> --disable-doc
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--enable-fcs-solvers=fmm,p2nfft,direct,ewald,p3m
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--with-internal-fftw --with-internal-pfft
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--with-internal-pnfft ${CONFIGURE_REQUEST_PIC}
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FC=${CMAKE_MPI_Fortran_COMPILER} FCFLAGS=${SCAFACOS_Fortran_FLAGS}
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CXX=${CMAKE_MPI_CXX_COMPILER} CXXFLAGS=${SCAFACOS_CXX_FLAGS}
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CC=${CMAKE_MPI_C_COMPILER} CFLAGS=${SCAFACOS_C_FLAGS}
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FC=${CMAKE_MPI_Fortran_COMPILER}
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CXX=${CMAKE_MPI_CXX_COMPILER}
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CC=${CMAKE_MPI_C_COMPILER}
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F77=
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BUILD_BYPRODUCTS
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<INSTALL_DIR>/lib/libfcs.a
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@ -8,8 +8,8 @@ useful during development, testing or debugging.
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.. _compilation:
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Verify compilation flags
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------------------------
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Monitor compilation flags
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-------------------------
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Sometimes it is necessary to verify the complete sequence of compilation flags
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generated by the CMake build. To enable a more verbose output during
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@ -19,7 +19,8 @@ compilation you can use the following option.
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-D CMAKE_VERBOSE_MAKEFILE=value # value = no (default) or yes
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Another way of doing this without reconfiguration is calling make with variable VERBOSE set to 1:
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Another way of doing this without reconfiguration is calling make with
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variable VERBOSE set to 1:
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.. code-block:: bash
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@ -33,25 +34,26 @@ Address, Undefined Behavior, and Thread Sanitizer Support
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---------------------------------------------------------
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Compilers such as GCC and Clang support generating instrumented binaries
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which use different sanitizer libraries to detect problems in code
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which use different sanitizer libraries to detect problems in the code
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during run-time. They can detect issues like:
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- `memory leaks <https://clang.llvm.org/docs/AddressSanitizer.html>`_
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- `undefined behavior <https://clang.llvm.org/docs/UndefinedBehaviorSanitizer.html>`_
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- `data races <https://clang.llvm.org/docs/ThreadSanitizer.html>`_
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Please note that this kind of instrumentation usually comes with a small
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performance hit (much less than using tools like `Valgrind
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<https://valgrind.org>`_). The to enable these features additional
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compiler flags need to be added to the compilation and linking stages.
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This is most easily done through setting the ``CMAKE_TUNE_FLAGS``
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variable during configuration. Examples:
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Please note that this kind of instrumentation usually comes with a
|
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performance hit (but much less than using tools like `Valgrind
|
||||
<https://valgrind.org>`_ with a more low level approach). The to enable
|
||||
these features additional compiler flags need to be added to the
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compilation and linking stages. This is done through setting the
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``ENABLE_SANITIZER`` variable during configuration. Examples:
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.. code-block:: bash
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-D CMAKE_TUNE_FLAGS=-fsanitize=address # enable address sanitizer / memory leak checker
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-D CMAKE_TUNE_FLAGS=-fsanitize=undefined # enable undefined behavior sanitizer
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-D CMAKE_TUNE_FLAGS=-fsanitize=thread # enable thread sanitizer
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-D ENABLE_SANITIZER=none # no sanitizer active (default)
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-D ENABLE_SANITIZER=address # enable address sanitizer / memory leak checker
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-D ENABLE_SANITIZER=undefined # enable undefined behavior sanitizer
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-D ENABLE_SANITIZER=thread # enable thread sanitizer
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----------
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@ -86,19 +88,21 @@ The output of this command will be looking something like this::
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[...]$ ctest
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Test project /home/akohlmey/compile/lammps/build-testing
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Start 1: MolPairStyle:hybrid-overlay
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1/26 Test #1: MolPairStyle:hybrid-overlay ......... Passed 0.02 sec
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1/109 Test #1: MolPairStyle:hybrid-overlay ......... Passed 0.02 sec
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Start 2: MolPairStyle:hybrid
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2/26 Test #2: MolPairStyle:hybrid ................. Passed 0.01 sec
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2/109 Test #2: MolPairStyle:hybrid ................. Passed 0.01 sec
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Start 3: MolPairStyle:lj_class2
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[...]
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Start 25: AngleStyle:harmonic
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25/26 Test #25: AngleStyle:harmonic ................. Passed 0.01 sec
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Start 26: AngleStyle:zero
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26/26 Test #26: AngleStyle:zero ..................... Passed 0.01 sec
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Start 107: PotentialFileReader
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107/109 Test #107: PotentialFileReader ................ Passed 0.04 sec
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Start 108: EIMPotentialFileReader
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108/109 Test #108: EIMPotentialFileReader ............. Passed 0.03 sec
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Start 109: TestSimpleCommands
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109/109 Test #109: TestSimpleCommands ................. Passed 0.02 sec
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100% tests passed, 0 tests failed out of 26
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Total Test time (real) = 0.27 sec
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Total Test time (real) = 25.57 sec
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The ``ctest`` command has many options, the most important ones are:
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@ -193,8 +197,8 @@ In this particular case, 5 out of 6 sets of tests were conducted, the
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tests for the ``lj/cut/opt`` pair style was skipped, since the tests
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executable did not include it. To learn what individual tests are performed,
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you (currently) need to read the source code. You can use code coverage
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recording (see next section) to confirm how well the tests cover the individual
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source files.
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recording (see next section) to confirm how well the tests cover the code
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paths in the individual source files.
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The force style test programs have a common set of options:
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@ -211,6 +215,14 @@ The force style test programs have a common set of options:
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* - -v
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- verbose output: also print the executed LAMMPS commands
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The ``ctest`` tool has no mechanism to directly pass flags to the individual
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test programs, but a workaround has been implmented where these flags can be
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set in an environment variable ``TEST_ARGS``. Example:
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.. code-block:: bash
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env TEST_ARGS=-s ctest -V -R BondStyle
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To add a test for a style that is not yet covered, it is usually best
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to copy a YAML file for a similar style to a new file, edit the details
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of the style (how to call it, how to set its coefficients) and then
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@ -244,6 +256,16 @@ and working.
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of mis-compiled code (or an undesired large loss of precision due
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to significant reordering of operations and thus less error cancellation).
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Tests for other components and utility functions
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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Additional tests that validate utility functions or specific components
|
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of LAMMPS are implemented as standalone executable which may, or may not
|
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require creating a suitable LAMMPS instance. These tests are more specific
|
||||
and do not require YAML format input files. To add a test, either an
|
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existing source file needs to be extended or a new file added, which in turn
|
||||
requires additions to the ``CMakeLists.txt`` file in the source folder.
|
||||
|
||||
Collect and visualize code coverage metrics
|
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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@ -306,3 +328,23 @@ The images below illustrate how the data is presented.
|
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:target: JPG/coverage-file-branches.png
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||||
|
||||
Source page with branches
|
||||
|
||||
Coding style utilities
|
||||
----------------------
|
||||
|
||||
To aid with enforcing some of the coding style conventions in LAMMPS
|
||||
some additional build targets have been added. These require Python 3.5
|
||||
or later and will only work on Unix-like operating and file systems.
|
||||
The following options are available.
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
make check-whitespace # generate coverage report in HTML format
|
||||
make fix-whitespace # generate coverage report in XML format
|
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make check-permissions # delete folder with HTML format coverage report
|
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make fix-permissions # delete all collected coverage data and HTML output
|
||||
|
||||
For the code in the ``unittest`` tree we are using the `clang-format`
|
||||
tool (Clang version 8.0 or later is required). If available, the source
|
||||
code files in the ``unittest`` tree can be updated to conform to the
|
||||
formatting settings using ``make format-tests``.
|
||||
|
||||
@ -85,7 +85,8 @@ standard 12-6 Lennard-Jones written in the epsilon/sigma form:
|
||||
|
||||
.. math::
|
||||
|
||||
E(r) = 4\epsilon\biggl[\bigl(\frac{\sigma}{r}\bigr)^{12} - \bigl(\frac{\sigma}{r}\bigr)^6\biggr]
|
||||
E(r) = 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} -
|
||||
\left(\frac{\sigma}{r}\right)^6 \right]
|
||||
|
||||
Either the first two or all of the following coefficients must be
|
||||
defined for each pair of atoms types via the pair_coeff command as in
|
||||
@ -141,7 +142,7 @@ given or both left out:
|
||||
**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
|
||||
|
||||
For atom type pairs I,J and I != J, the :math:`\epsilon` and
|
||||
:math:`sigma` coefficients and cutoff distances for the lj/mdf pair
|
||||
:math:`\sigma` coefficients and cutoff distances for the lj/mdf pair
|
||||
style can be mixed. The default mix value is *geometric*\ . See the
|
||||
"pair_modify" command for details. The other two pair styles buck/mdf
|
||||
and lennard/mdf do not support mixing, so all I,J pairs of coefficients
|
||||
|
||||
@ -39,7 +39,7 @@ neigh_modify once no every 1 delay 0 check yes
|
||||
|
||||
# Run MD
|
||||
|
||||
velocity all create 300.0 4928459
|
||||
velocity all create 300.0 4928459 loop geom
|
||||
fix 1 all nve
|
||||
run ${nsteps}
|
||||
|
||||
|
||||
@ -39,7 +39,7 @@ neigh_modify once no every 1 delay 0 check yes
|
||||
|
||||
# Run MD
|
||||
|
||||
velocity all create 300.0 4928459
|
||||
velocity all create 300.0 4928459 loop geom
|
||||
fix 1 all nve
|
||||
run ${nsteps}
|
||||
|
||||
|
||||
@ -39,7 +39,7 @@ neigh_modify once no every 1 delay 0 check yes
|
||||
|
||||
# Run MD
|
||||
|
||||
velocity all create 300.0 4928459
|
||||
velocity all create 300.0 4928459 loop geom
|
||||
fix 1 all nve
|
||||
run ${nsteps}
|
||||
|
||||
|
||||
@ -42,7 +42,7 @@ neigh_modify once no every 1 delay 0 check yes
|
||||
|
||||
# Run MD
|
||||
|
||||
velocity all create 300.0 4928459
|
||||
velocity all create 300.0 4928459 loop geom
|
||||
fix 1 all nve
|
||||
run ${nsteps}
|
||||
|
||||
|
||||
@ -42,7 +42,7 @@ neigh_modify once no every 1 delay 0 check yes
|
||||
|
||||
# Run MD
|
||||
|
||||
velocity all create 300.0 4928459
|
||||
velocity all create 300.0 4928459 loop geom
|
||||
fix 1 all nve
|
||||
run ${nsteps}
|
||||
|
||||
|
||||
@ -1,13 +1,13 @@
|
||||
LAMMPS (27 Nov 2018)
|
||||
LAMMPS (15 Jun 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Demonstrate SNAP Ta potential
|
||||
# Demonstrate SNAP Mo potential
|
||||
|
||||
# Initialize simulation
|
||||
|
||||
variable nsteps index 100
|
||||
variable nrep equal 4
|
||||
variable a equal 3.160
|
||||
units metal
|
||||
units metal
|
||||
|
||||
# generate the box and atom positions using a BCC lattice
|
||||
|
||||
@ -18,21 +18,21 @@ variable ny equal 4
|
||||
variable nz equal ${nrep}
|
||||
variable nz equal 4
|
||||
|
||||
boundary p p p
|
||||
boundary p p p
|
||||
|
||||
lattice bcc $a
|
||||
lattice bcc 3.16
|
||||
Lattice spacing in x,y,z = 3.16 3.16 3.16
|
||||
region box block 0 ${nx} 0 ${ny} 0 ${nz}
|
||||
region box block 0 4 0 ${ny} 0 ${nz}
|
||||
region box block 0 4 0 4 0 ${nz}
|
||||
region box block 0 4 0 4 0 4
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (12.64 12.64 12.64)
|
||||
region box block 0 ${nx} 0 ${ny} 0 ${nz}
|
||||
region box block 0 4 0 ${ny} 0 ${nz}
|
||||
region box block 0 4 0 4 0 ${nz}
|
||||
region box block 0 4 0 4 0 4
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0.0 0.0 0.0) to (12.64 12.64 12.64)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
create_atoms 1 box
|
||||
Created 128 atoms
|
||||
Time spent = 0.00029707 secs
|
||||
create_atoms CPU = 0.000 seconds
|
||||
|
||||
mass 1 183.84
|
||||
|
||||
@ -40,11 +40,11 @@ mass 1 183.84
|
||||
|
||||
include Mo_Chen_PRM2017.snap
|
||||
|
||||
# DATE: 2017-09-18 CONTRIBUTOR: Chi Chen <chc273@eng.ucsd.edu> CITATION: C. Chen, Z. Deng, R. Tran, H. Tang, I.-H. Chu, S. P. Ong, "Accurate force field for molybdenum by machine learning large materials data" Physical Review Materials 1, 04 3603 (2017)
|
||||
# DATE: 2017-09-18 UNITS: metal CONTRIBUTOR: Chi Chen <chc273@eng.ucsd.edu> CITATION: C. Chen, Z. Deng, R. Tran, H. Tang, I.-H. Chu, S. P. Ong, "Accurate force field for molybdenum by machine learning large materials data" Physical Review Materials 1, 04 3603 (2017)
|
||||
# Generated by Materials Virtual Lab
|
||||
# Definition of SNAP potential.
|
||||
pair_style snap
|
||||
pair_coeff * * Mo_Chen_PRM2017.snapcoeff Mo Mo_Chen_PRM2017.snapparam Mo
|
||||
pair_coeff * * Mo_Chen_PRM2017.snapcoeff Mo_Chen_PRM2017.snapparam Mo
|
||||
Reading potential file Mo_Chen_PRM2017.snapcoeff with DATE: 2017-09-18
|
||||
SNAP Element = Mo, Radius 0.5, Weight 1
|
||||
Reading potential file Mo_Chen_PRM2017.snapparam with DATE: 2017-09-18
|
||||
@ -54,7 +54,7 @@ SNAP keyword twojmax 6
|
||||
|
||||
# Setup output
|
||||
|
||||
thermo 10
|
||||
thermo 10
|
||||
thermo_modify norm yes
|
||||
|
||||
# Set up NVE run
|
||||
@ -65,7 +65,7 @@ neigh_modify once no every 1 delay 0 check yes
|
||||
|
||||
# Run MD
|
||||
|
||||
velocity all create 300.0 4928459
|
||||
velocity all create 300.0 4928459 loop geom
|
||||
fix 1 all nve
|
||||
run ${nsteps}
|
||||
run 100
|
||||
@ -81,33 +81,33 @@ Neighbor list info ...
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.507 | 3.507 | 3.507 Mbytes
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.335 | 3.335 | 3.335 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 300 -22.405975 0 -22.3675 2575.7657
|
||||
10 294.77555 -22.405305 0 -22.3675 2756.6894
|
||||
20 279.53011 -22.40335 0 -22.3675 3285.8272
|
||||
30 255.52174 -22.40027 0 -22.3675 4122.8933
|
||||
40 224.7299 -22.396321 0 -22.367499 5204.3499
|
||||
50 189.67529 -22.391825 0 -22.367499 6449.1308
|
||||
60 153.18862 -22.387145 0 -22.367499 7765.911
|
||||
70 118.14998 -22.382652 0 -22.367499 9061.1616
|
||||
80 87.224916 -22.378685 0 -22.367499 10247.68
|
||||
90 62.623892 -22.37553 0 -22.367498 11250.067
|
||||
100 45.9103 -22.373386 0 -22.367498 12011.726
|
||||
Loop time of 7.00873 on 1 procs for 100 steps with 128 atoms
|
||||
10 294.8148 -22.40531 0 -22.3675 2762.0942
|
||||
20 279.68628 -22.40337 0 -22.3675 3306.7656
|
||||
30 255.84798 -22.400312 0 -22.3675 4168.2979
|
||||
40 225.22346 -22.396384 0 -22.367499 5281.9537
|
||||
50 190.25143 -22.391899 0 -22.367499 6565.6626
|
||||
60 153.66642 -22.387207 0 -22.367499 7927.3186
|
||||
70 118.25575 -22.382665 0 -22.367499 9271.9554
|
||||
80 86.616338 -22.378607 0 -22.367499 10510.959
|
||||
90 60.935787 -22.375314 0 -22.367498 11568.261
|
||||
100 42.815823 -22.37299 0 -22.367498 12385.433
|
||||
Loop time of 0.897752 on 1 procs for 100 steps with 128 atoms
|
||||
|
||||
Performance: 0.616 ns/day, 38.937 hours/ns, 14.268 timesteps/s
|
||||
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
Performance: 4.812 ns/day, 4.988 hours/ns, 111.389 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 7.0068 | 7.0068 | 7.0068 | 0.0 | 99.97
|
||||
Pair | 0.89711 | 0.89711 | 0.89711 | 0.0 | 99.93
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.00083661 | 0.00083661 | 0.00083661 | 0.0 | 0.01
|
||||
Output | 0.00025535 | 0.00025535 | 0.00025535 | 0.0 | 0.00
|
||||
Modify | 0.00034285 | 0.00034285 | 0.00034285 | 0.0 | 0.00
|
||||
Other | | 0.0005035 | | | 0.01
|
||||
Comm | 0.0002501 | 0.0002501 | 0.0002501 | 0.0 | 0.03
|
||||
Output | 0.00013161 | 0.00013161 | 0.00013161 | 0.0 | 0.01
|
||||
Modify | 0.00010276 | 0.00010276 | 0.00010276 | 0.0 | 0.01
|
||||
Other | | 0.0001559 | | | 0.02
|
||||
|
||||
Nlocal: 128 ave 128 max 128 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
@ -123,4 +123,4 @@ Ave neighs/atom = 58
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:07
|
||||
Total wall time: 0:00:00
|
||||
@ -1,13 +1,13 @@
|
||||
LAMMPS (27 Nov 2018)
|
||||
LAMMPS (15 Jun 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Demonstrate SNAP Ta potential
|
||||
# Demonstrate SNAP Mo potential
|
||||
|
||||
# Initialize simulation
|
||||
|
||||
variable nsteps index 100
|
||||
variable nrep equal 4
|
||||
variable a equal 3.160
|
||||
units metal
|
||||
units metal
|
||||
|
||||
# generate the box and atom positions using a BCC lattice
|
||||
|
||||
@ -18,21 +18,21 @@ variable ny equal 4
|
||||
variable nz equal ${nrep}
|
||||
variable nz equal 4
|
||||
|
||||
boundary p p p
|
||||
boundary p p p
|
||||
|
||||
lattice bcc $a
|
||||
lattice bcc 3.16
|
||||
Lattice spacing in x,y,z = 3.16 3.16 3.16
|
||||
region box block 0 ${nx} 0 ${ny} 0 ${nz}
|
||||
region box block 0 4 0 ${ny} 0 ${nz}
|
||||
region box block 0 4 0 4 0 ${nz}
|
||||
region box block 0 4 0 4 0 4
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (12.64 12.64 12.64)
|
||||
region box block 0 ${nx} 0 ${ny} 0 ${nz}
|
||||
region box block 0 4 0 ${ny} 0 ${nz}
|
||||
region box block 0 4 0 4 0 ${nz}
|
||||
region box block 0 4 0 4 0 4
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0.0 0.0 0.0) to (12.64 12.64 12.64)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
create_atoms 1 box
|
||||
Created 128 atoms
|
||||
Time spent = 0.000289917 secs
|
||||
create_atoms CPU = 0.000 seconds
|
||||
|
||||
mass 1 183.84
|
||||
|
||||
@ -40,11 +40,11 @@ mass 1 183.84
|
||||
|
||||
include Mo_Chen_PRM2017.snap
|
||||
|
||||
# DATE: 2017-09-18 CONTRIBUTOR: Chi Chen <chc273@eng.ucsd.edu> CITATION: C. Chen, Z. Deng, R. Tran, H. Tang, I.-H. Chu, S. P. Ong, "Accurate force field for molybdenum by machine learning large materials data" Physical Review Materials 1, 04 3603 (2017)
|
||||
# DATE: 2017-09-18 UNITS: metal CONTRIBUTOR: Chi Chen <chc273@eng.ucsd.edu> CITATION: C. Chen, Z. Deng, R. Tran, H. Tang, I.-H. Chu, S. P. Ong, "Accurate force field for molybdenum by machine learning large materials data" Physical Review Materials 1, 04 3603 (2017)
|
||||
# Generated by Materials Virtual Lab
|
||||
# Definition of SNAP potential.
|
||||
pair_style snap
|
||||
pair_coeff * * Mo_Chen_PRM2017.snapcoeff Mo Mo_Chen_PRM2017.snapparam Mo
|
||||
pair_coeff * * Mo_Chen_PRM2017.snapcoeff Mo_Chen_PRM2017.snapparam Mo
|
||||
Reading potential file Mo_Chen_PRM2017.snapcoeff with DATE: 2017-09-18
|
||||
SNAP Element = Mo, Radius 0.5, Weight 1
|
||||
Reading potential file Mo_Chen_PRM2017.snapparam with DATE: 2017-09-18
|
||||
@ -54,7 +54,7 @@ SNAP keyword twojmax 6
|
||||
|
||||
# Setup output
|
||||
|
||||
thermo 10
|
||||
thermo 10
|
||||
thermo_modify norm yes
|
||||
|
||||
# Set up NVE run
|
||||
@ -65,7 +65,7 @@ neigh_modify once no every 1 delay 0 check yes
|
||||
|
||||
# Run MD
|
||||
|
||||
velocity all create 300.0 4928459
|
||||
velocity all create 300.0 4928459 loop geom
|
||||
fix 1 all nve
|
||||
run ${nsteps}
|
||||
run 100
|
||||
@ -81,33 +81,33 @@ Neighbor list info ...
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.486 | 3.486 | 3.486 Mbytes
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.271 | 3.271 | 3.271 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 300 -22.405975 0 -22.3675 2575.7657
|
||||
10 294.63153 -22.405286 0 -22.3675 2753.4662
|
||||
20 278.98535 -22.40328 0 -22.3675 3272.416
|
||||
30 254.38916 -22.400125 0 -22.3675 4091.8933
|
||||
40 222.91191 -22.396088 0 -22.367499 5148.5505
|
||||
50 187.16984 -22.391504 0 -22.367499 6362.2454
|
||||
60 150.08253 -22.386747 0 -22.367499 7643.2732
|
||||
70 114.60307 -22.382197 0 -22.367499 8900.2448
|
||||
80 83.449257 -22.378201 0 -22.367499 10047.619
|
||||
90 58.862643 -22.375048 0 -22.367498 11012.233
|
||||
100 42.41931 -22.372939 0 -22.367498 11740.641
|
||||
Loop time of 2.15419 on 4 procs for 100 steps with 128 atoms
|
||||
10 294.8148 -22.40531 0 -22.3675 2762.0942
|
||||
20 279.68628 -22.40337 0 -22.3675 3306.7656
|
||||
30 255.84798 -22.400312 0 -22.3675 4168.2979
|
||||
40 225.22346 -22.396384 0 -22.367499 5281.9537
|
||||
50 190.25143 -22.391899 0 -22.367499 6565.6626
|
||||
60 153.66642 -22.387207 0 -22.367499 7927.3186
|
||||
70 118.25575 -22.382665 0 -22.367499 9271.9554
|
||||
80 86.616338 -22.378607 0 -22.367499 10510.959
|
||||
90 60.935787 -22.375314 0 -22.367498 11568.261
|
||||
100 42.815823 -22.37299 0 -22.367498 12385.433
|
||||
Loop time of 0.260783 on 4 procs for 100 steps with 128 atoms
|
||||
|
||||
Performance: 2.005 ns/day, 11.968 hours/ns, 46.421 timesteps/s
|
||||
92.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
Performance: 16.566 ns/day, 1.449 hours/ns, 383.461 timesteps/s
|
||||
97.1% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.7677 | 1.9028 | 1.9897 | 6.2 | 88.33
|
||||
Pair | 0.23045 | 0.23744 | 0.24455 | 1.2 | 91.05
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.15367 | 0.24295 | 0.38029 | 17.6 | 11.28
|
||||
Output | 0.00034404 | 0.0012512 | 0.0017219 | 1.6 | 0.06
|
||||
Modify | 0.00018859 | 0.00021273 | 0.00023699 | 0.0 | 0.01
|
||||
Other | | 0.007011 | | | 0.33
|
||||
Comm | 0.014524 | 0.021267 | 0.027713 | 3.7 | 8.15
|
||||
Output | 0.00014997 | 0.00040495 | 0.0011623 | 0.0 | 0.16
|
||||
Modify | 4.2439e-05 | 4.6909e-05 | 5.0068e-05 | 0.0 | 0.02
|
||||
Other | | 0.00162 | | | 0.62
|
||||
|
||||
Nlocal: 32 ave 32 max 32 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
@ -123,4 +123,4 @@ Ave neighs/atom = 58
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:02
|
||||
Total wall time: 0:00:00
|
||||
@ -1,4 +1,4 @@
|
||||
LAMMPS (27 Nov 2018)
|
||||
LAMMPS (15 Jun 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Demonstrate SNAP Ta potential
|
||||
|
||||
@ -7,7 +7,7 @@ LAMMPS (27 Nov 2018)
|
||||
variable nsteps index 100
|
||||
variable nrep equal 4
|
||||
variable a equal 3.316
|
||||
units metal
|
||||
units metal
|
||||
|
||||
# generate the box and atom positions using a BCC lattice
|
||||
|
||||
@ -18,28 +18,28 @@ variable ny equal 4
|
||||
variable nz equal ${nrep}
|
||||
variable nz equal 4
|
||||
|
||||
boundary p p p
|
||||
boundary p p p
|
||||
|
||||
lattice bcc $a
|
||||
lattice bcc 3.316
|
||||
Lattice spacing in x,y,z = 3.316 3.316 3.316
|
||||
region box block 0 ${nx} 0 ${ny} 0 ${nz}
|
||||
region box block 0 4 0 ${ny} 0 ${nz}
|
||||
region box block 0 4 0 4 0 ${nz}
|
||||
region box block 0 4 0 4 0 4
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (13.264 13.264 13.264)
|
||||
region box block 0 ${nx} 0 ${ny} 0 ${nz}
|
||||
region box block 0 4 0 ${ny} 0 ${nz}
|
||||
region box block 0 4 0 4 0 ${nz}
|
||||
region box block 0 4 0 4 0 4
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0.0 0.0 0.0) to (13.264 13.264 13.264)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
create_atoms 1 box
|
||||
Created 128 atoms
|
||||
Time spent = 0.000350714 secs
|
||||
create_atoms CPU = 0.000 seconds
|
||||
|
||||
mass 1 180.88
|
||||
|
||||
# choose potential
|
||||
|
||||
include Ta06A.snap
|
||||
# DATE: 2014-09-05 CONTRIBUTOR: Aidan Thompson athomps@sandia.gov CITATION: Thompson, Swiler, Trott, Foiles and Tucker, arxiv.org, 1409.3880 (2014)
|
||||
# DATE: 2014-09-05 UNITS: metal CONTRIBUTOR: Aidan Thompson athomps@sandia.gov CITATION: Thompson, Swiler, Trott, Foiles and Tucker, arxiv.org, 1409.3880 (2014)
|
||||
|
||||
# Definition of SNAP potential Ta_Cand06A
|
||||
# Assumes 1 LAMMPS atom type
|
||||
@ -56,7 +56,7 @@ pair_style hybrid/overlay zbl 4 4.8 snap
|
||||
pair_coeff 1 1 zbl ${zblz} ${zblz}
|
||||
pair_coeff 1 1 zbl 73 ${zblz}
|
||||
pair_coeff 1 1 zbl 73 73
|
||||
pair_coeff * * snap Ta06A.snapcoeff Ta Ta06A.snapparam Ta
|
||||
pair_coeff * * snap Ta06A.snapcoeff Ta06A.snapparam Ta
|
||||
Reading potential file Ta06A.snapcoeff with DATE: 2014-09-05
|
||||
SNAP Element = Ta, Radius 0.5, Weight 1
|
||||
Reading potential file Ta06A.snapparam with DATE: 2014-09-05
|
||||
@ -64,14 +64,13 @@ SNAP keyword rcutfac 4.67637
|
||||
SNAP keyword twojmax 6
|
||||
SNAP keyword rfac0 0.99363
|
||||
SNAP keyword rmin0 0
|
||||
SNAP keyword diagonalstyle 3
|
||||
SNAP keyword bzeroflag 0
|
||||
SNAP keyword quadraticflag 0
|
||||
|
||||
|
||||
# Setup output
|
||||
|
||||
thermo 10
|
||||
thermo 10
|
||||
thermo_modify norm yes
|
||||
|
||||
# Set up NVE run
|
||||
@ -82,7 +81,7 @@ neigh_modify once no every 1 delay 0 check yes
|
||||
|
||||
# Run MD
|
||||
|
||||
velocity all create 300.0 4928459
|
||||
velocity all create 300.0 4928459 loop geom
|
||||
fix 1 all nve
|
||||
run ${nsteps}
|
||||
run 100
|
||||
@ -103,33 +102,33 @@ Neighbor list info ...
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.138 | 4.138 | 4.138 Mbytes
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.967 | 3.967 | 3.967 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 300 -11.85157 0 -11.813095 2717.1661
|
||||
10 295.96579 -11.851053 0 -11.813095 2696.1559
|
||||
20 284.32535 -11.84956 0 -11.813095 2301.3713
|
||||
30 266.04602 -11.847215 0 -11.813095 1832.1745
|
||||
40 242.2862 -11.844168 0 -11.813095 1492.6765
|
||||
50 214.48968 -11.840603 0 -11.813094 1312.8908
|
||||
60 184.32523 -11.836734 0 -11.813094 1284.582
|
||||
70 153.58055 -11.832791 0 -11.813094 1374.4457
|
||||
80 124.04276 -11.829003 0 -11.813094 1537.703
|
||||
90 97.37622 -11.825582 0 -11.813094 1734.9662
|
||||
100 75.007873 -11.822714 0 -11.813094 1930.8005
|
||||
Loop time of 5.03244 on 1 procs for 100 steps with 128 atoms
|
||||
10 296.01467 -11.851059 0 -11.813095 2697.4796
|
||||
20 284.53666 -11.849587 0 -11.813095 2289.1527
|
||||
30 266.51577 -11.847275 0 -11.813095 1851.7131
|
||||
40 243.05007 -11.844266 0 -11.813095 1570.684
|
||||
50 215.51032 -11.840734 0 -11.813094 1468.1899
|
||||
60 185.48331 -11.836883 0 -11.813094 1524.8757
|
||||
70 154.6736 -11.832931 0 -11.813094 1698.3351
|
||||
80 124.79303 -11.829099 0 -11.813094 1947.0715
|
||||
90 97.448054 -11.825592 0 -11.813094 2231.9563
|
||||
100 74.035418 -11.822589 0 -11.813094 2515.8526
|
||||
Loop time of 0.702618 on 1 procs for 100 steps with 128 atoms
|
||||
|
||||
Performance: 0.858 ns/day, 27.958 hours/ns, 19.871 timesteps/s
|
||||
98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
Performance: 6.148 ns/day, 3.903 hours/ns, 142.325 timesteps/s
|
||||
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 5.0308 | 5.0308 | 5.0308 | 0.0 | 99.97
|
||||
Pair | 0.70188 | 0.70188 | 0.70188 | 0.0 | 99.90
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.00070858 | 0.00070858 | 0.00070858 | 0.0 | 0.01
|
||||
Output | 0.00024676 | 0.00024676 | 0.00024676 | 0.0 | 0.00
|
||||
Modify | 0.0002749 | 0.0002749 | 0.0002749 | 0.0 | 0.01
|
||||
Other | | 0.0004299 | | | 0.01
|
||||
Comm | 0.00025487 | 0.00025487 | 0.00025487 | 0.0 | 0.04
|
||||
Output | 0.00015402 | 0.00015402 | 0.00015402 | 0.0 | 0.02
|
||||
Modify | 0.00011039 | 0.00011039 | 0.00011039 | 0.0 | 0.02
|
||||
Other | | 0.000217 | | | 0.03
|
||||
|
||||
Nlocal: 128 ave 128 max 128 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
@ -145,4 +144,4 @@ Ave neighs/atom = 58
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:05
|
||||
Total wall time: 0:00:00
|
||||
@ -1,4 +1,4 @@
|
||||
LAMMPS (27 Nov 2018)
|
||||
LAMMPS (15 Jun 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Demonstrate SNAP Ta potential
|
||||
|
||||
@ -7,7 +7,7 @@ LAMMPS (27 Nov 2018)
|
||||
variable nsteps index 100
|
||||
variable nrep equal 4
|
||||
variable a equal 3.316
|
||||
units metal
|
||||
units metal
|
||||
|
||||
# generate the box and atom positions using a BCC lattice
|
||||
|
||||
@ -18,28 +18,28 @@ variable ny equal 4
|
||||
variable nz equal ${nrep}
|
||||
variable nz equal 4
|
||||
|
||||
boundary p p p
|
||||
boundary p p p
|
||||
|
||||
lattice bcc $a
|
||||
lattice bcc 3.316
|
||||
Lattice spacing in x,y,z = 3.316 3.316 3.316
|
||||
region box block 0 ${nx} 0 ${ny} 0 ${nz}
|
||||
region box block 0 4 0 ${ny} 0 ${nz}
|
||||
region box block 0 4 0 4 0 ${nz}
|
||||
region box block 0 4 0 4 0 4
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (13.264 13.264 13.264)
|
||||
region box block 0 ${nx} 0 ${ny} 0 ${nz}
|
||||
region box block 0 4 0 ${ny} 0 ${nz}
|
||||
region box block 0 4 0 4 0 ${nz}
|
||||
region box block 0 4 0 4 0 4
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0.0 0.0 0.0) to (13.264 13.264 13.264)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
create_atoms 1 box
|
||||
Created 128 atoms
|
||||
Time spent = 0.000299692 secs
|
||||
create_atoms CPU = 0.000 seconds
|
||||
|
||||
mass 1 180.88
|
||||
|
||||
# choose potential
|
||||
|
||||
include Ta06A.snap
|
||||
# DATE: 2014-09-05 CONTRIBUTOR: Aidan Thompson athomps@sandia.gov CITATION: Thompson, Swiler, Trott, Foiles and Tucker, arxiv.org, 1409.3880 (2014)
|
||||
# DATE: 2014-09-05 UNITS: metal CONTRIBUTOR: Aidan Thompson athomps@sandia.gov CITATION: Thompson, Swiler, Trott, Foiles and Tucker, arxiv.org, 1409.3880 (2014)
|
||||
|
||||
# Definition of SNAP potential Ta_Cand06A
|
||||
# Assumes 1 LAMMPS atom type
|
||||
@ -56,7 +56,7 @@ pair_style hybrid/overlay zbl 4 4.8 snap
|
||||
pair_coeff 1 1 zbl ${zblz} ${zblz}
|
||||
pair_coeff 1 1 zbl 73 ${zblz}
|
||||
pair_coeff 1 1 zbl 73 73
|
||||
pair_coeff * * snap Ta06A.snapcoeff Ta Ta06A.snapparam Ta
|
||||
pair_coeff * * snap Ta06A.snapcoeff Ta06A.snapparam Ta
|
||||
Reading potential file Ta06A.snapcoeff with DATE: 2014-09-05
|
||||
SNAP Element = Ta, Radius 0.5, Weight 1
|
||||
Reading potential file Ta06A.snapparam with DATE: 2014-09-05
|
||||
@ -64,14 +64,13 @@ SNAP keyword rcutfac 4.67637
|
||||
SNAP keyword twojmax 6
|
||||
SNAP keyword rfac0 0.99363
|
||||
SNAP keyword rmin0 0
|
||||
SNAP keyword diagonalstyle 3
|
||||
SNAP keyword bzeroflag 0
|
||||
SNAP keyword quadraticflag 0
|
||||
|
||||
|
||||
# Setup output
|
||||
|
||||
thermo 10
|
||||
thermo 10
|
||||
thermo_modify norm yes
|
||||
|
||||
# Set up NVE run
|
||||
@ -82,7 +81,7 @@ neigh_modify once no every 1 delay 0 check yes
|
||||
|
||||
# Run MD
|
||||
|
||||
velocity all create 300.0 4928459
|
||||
velocity all create 300.0 4928459 loop geom
|
||||
fix 1 all nve
|
||||
run ${nsteps}
|
||||
run 100
|
||||
@ -103,33 +102,33 @@ Neighbor list info ...
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.118 | 4.118 | 4.118 Mbytes
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.903 | 3.903 | 3.903 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 300 -11.85157 0 -11.813095 2717.1661
|
||||
10 295.8664 -11.85104 0 -11.813095 2702.935
|
||||
20 283.95868 -11.849513 0 -11.813095 2301.3242
|
||||
30 265.29535 -11.847119 0 -11.813095 1870.3173
|
||||
40 241.09337 -11.844015 0 -11.813095 1568.1549
|
||||
50 212.86732 -11.840395 0 -11.813094 1409.2092
|
||||
60 182.35256 -11.836481 0 -11.813094 1389.0527
|
||||
70 151.38968 -11.83251 0 -11.813094 1474.9232
|
||||
80 121.80051 -11.828715 0 -11.813094 1627.6911
|
||||
90 95.262635 -11.825311 0 -11.813094 1812.9327
|
||||
100 73.194645 -11.822481 0 -11.813094 1995.2199
|
||||
Loop time of 1.4959 on 4 procs for 100 steps with 128 atoms
|
||||
10 296.01467 -11.851059 0 -11.813095 2697.4796
|
||||
20 284.53666 -11.849587 0 -11.813095 2289.1527
|
||||
30 266.51577 -11.847275 0 -11.813095 1851.7131
|
||||
40 243.05007 -11.844266 0 -11.813095 1570.684
|
||||
50 215.51032 -11.840734 0 -11.813094 1468.1899
|
||||
60 185.48331 -11.836883 0 -11.813094 1524.8757
|
||||
70 154.6736 -11.832931 0 -11.813094 1698.3351
|
||||
80 124.79303 -11.829099 0 -11.813094 1947.0715
|
||||
90 97.448054 -11.825592 0 -11.813094 2231.9563
|
||||
100 74.035418 -11.822589 0 -11.813094 2515.8526
|
||||
Loop time of 0.230164 on 4 procs for 100 steps with 128 atoms
|
||||
|
||||
Performance: 2.888 ns/day, 8.311 hours/ns, 66.850 timesteps/s
|
||||
94.6% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
Performance: 18.769 ns/day, 1.279 hours/ns, 434.473 timesteps/s
|
||||
93.5% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.2973 | 1.3263 | 1.3444 | 1.6 | 88.66
|
||||
Pair | 0.1824 | 0.19154 | 0.21822 | 3.5 | 83.22
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.14155 | 0.16475 | 0.19518 | 5.0 | 11.01
|
||||
Output | 0.00055361 | 0.0006234 | 0.00078511 | 0.0 | 0.04
|
||||
Modify | 0.00016427 | 0.00020635 | 0.00032949 | 0.0 | 0.01
|
||||
Other | | 0.004009 | | | 0.27
|
||||
Comm | 0.010843 | 0.037176 | 0.046129 | 7.9 | 16.15
|
||||
Output | 0.00014973 | 0.00028926 | 0.00070024 | 0.0 | 0.13
|
||||
Modify | 5.3883e-05 | 5.6803e-05 | 6.1989e-05 | 0.0 | 0.02
|
||||
Other | | 0.001104 | | | 0.48
|
||||
|
||||
Nlocal: 32 ave 32 max 32 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
@ -145,4 +144,4 @@ Ave neighs/atom = 58
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:01
|
||||
Total wall time: 0:00:00
|
||||
@ -1,13 +1,13 @@
|
||||
LAMMPS (27 Nov 2018)
|
||||
LAMMPS (15 Jun 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Demonstrate SNAP Ta potential
|
||||
# Demonstrate SNAP W potential
|
||||
|
||||
# Initialize simulation
|
||||
|
||||
variable nsteps index 100
|
||||
variable nrep equal 4
|
||||
variable a equal 3.1803
|
||||
units metal
|
||||
units metal
|
||||
|
||||
# generate the box and atom positions using a BCC lattice
|
||||
|
||||
@ -18,28 +18,28 @@ variable ny equal 4
|
||||
variable nz equal ${nrep}
|
||||
variable nz equal 4
|
||||
|
||||
boundary p p p
|
||||
boundary p p p
|
||||
|
||||
lattice bcc $a
|
||||
lattice bcc 3.1803
|
||||
Lattice spacing in x,y,z = 3.1803 3.1803 3.1803
|
||||
region box block 0 ${nx} 0 ${ny} 0 ${nz}
|
||||
region box block 0 4 0 ${ny} 0 ${nz}
|
||||
region box block 0 4 0 4 0 ${nz}
|
||||
region box block 0 4 0 4 0 4
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (12.7212 12.7212 12.7212)
|
||||
region box block 0 ${nx} 0 ${ny} 0 ${nz}
|
||||
region box block 0 4 0 ${ny} 0 ${nz}
|
||||
region box block 0 4 0 4 0 ${nz}
|
||||
region box block 0 4 0 4 0 4
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0.0 0.0 0.0) to (12.7212 12.7212 12.7212)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
create_atoms 1 box
|
||||
Created 128 atoms
|
||||
Time spent = 0.000316143 secs
|
||||
create_atoms CPU = 0.000 seconds
|
||||
|
||||
mass 1 183.84
|
||||
|
||||
# choose potential
|
||||
|
||||
include W_2940_2017_2.snap
|
||||
# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph]
|
||||
# DATE: 2017-02-20 UNITS: metal CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph]
|
||||
#
|
||||
# Definition of SNAP+ZBL potential.
|
||||
variable zblcutinner equal 4
|
||||
@ -54,7 +54,7 @@ pair_style hybrid/overlay zbl 4 4.8 snap
|
||||
pair_coeff 1 1 zbl ${zblz} ${zblz}
|
||||
pair_coeff 1 1 zbl 74 ${zblz}
|
||||
pair_coeff 1 1 zbl 74 74
|
||||
pair_coeff * * snap W_2940_2017_2.snapcoeff W W_2940_2017_2.snapparam W
|
||||
pair_coeff * * snap W_2940_2017_2.snapcoeff W_2940_2017_2.snapparam W
|
||||
Reading potential file W_2940_2017_2.snapcoeff with DATE: 2017-02-20
|
||||
SNAP Element = W, Radius 0.5, Weight 1
|
||||
Reading potential file W_2940_2017_2.snapparam with DATE: 2017-02-20
|
||||
@ -62,7 +62,6 @@ SNAP keyword rcutfac 4.73442
|
||||
SNAP keyword twojmax 8
|
||||
SNAP keyword rfac0 0.99363
|
||||
SNAP keyword rmin0 0
|
||||
SNAP keyword diagonalstyle 3
|
||||
SNAP keyword bzeroflag 0
|
||||
SNAP keyword quadraticflag 0
|
||||
|
||||
@ -70,7 +69,7 @@ SNAP keyword quadraticflag 0
|
||||
|
||||
# Setup output
|
||||
|
||||
thermo 10
|
||||
thermo 10
|
||||
thermo_modify norm yes
|
||||
|
||||
# Set up NVE run
|
||||
@ -81,7 +80,7 @@ neigh_modify once no every 1 delay 0 check yes
|
||||
|
||||
# Run MD
|
||||
|
||||
velocity all create 300.0 4928459
|
||||
velocity all create 300.0 4928459 loop geom
|
||||
fix 1 all nve
|
||||
run ${nsteps}
|
||||
run 100
|
||||
@ -102,33 +101,33 @@ Neighbor list info ...
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.15 | 5.15 | 5.15 Mbytes
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.268 | 4.268 | 4.268 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 300 -11.028325 0 -10.98985 3010.497
|
||||
10 293.40666 -11.027479 0 -10.989849 3246.0559
|
||||
20 274.27375 -11.025025 0 -10.989849 3927.9497
|
||||
30 244.50457 -11.021207 0 -10.989849 4983.5484
|
||||
40 207.0784 -11.016407 0 -10.989849 6299.9473
|
||||
50 165.74442 -11.011105 0 -10.989848 7736.5123
|
||||
60 124.62181 -11.005831 0 -10.989848 9140.8587
|
||||
70 87.744792 -11.001101 0 -10.989848 10366.489
|
||||
80 58.605244 -10.997364 0 -10.989848 11289.914
|
||||
90 39.754503 -10.994946 0 -10.989848 11824.945
|
||||
100 32.524085 -10.994019 0 -10.989848 11932.118
|
||||
Loop time of 18.7678 on 1 procs for 100 steps with 128 atoms
|
||||
10 293.10848 -11.027441 0 -10.989849 3259.9445
|
||||
20 273.14727 -11.024881 0 -10.989849 3979.8968
|
||||
30 242.20285 -11.020912 0 -10.989849 5089.0797
|
||||
40 203.51992 -11.01595 0 -10.989849 6462.9419
|
||||
50 161.14556 -11.010515 0 -10.989848 7948.1798
|
||||
60 119.47232 -11.00517 0 -10.989848 9380.8543
|
||||
70 82.729175 -11.000458 0 -10.989848 10606.025
|
||||
80 54.483648 -10.996835 0 -10.989848 11496.424
|
||||
90 37.225263 -10.994622 0 -10.989847 11967.579
|
||||
100 32.094224 -10.993964 0 -10.989847 11987.181
|
||||
Loop time of 2.29953 on 1 procs for 100 steps with 128 atoms
|
||||
|
||||
Performance: 0.230 ns/day, 104.265 hours/ns, 5.328 timesteps/s
|
||||
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
Performance: 1.879 ns/day, 12.775 hours/ns, 43.487 timesteps/s
|
||||
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 18.766 | 18.766 | 18.766 | 0.0 | 99.99
|
||||
Pair | 2.2988 | 2.2988 | 2.2988 | 0.0 | 99.97
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.00081968 | 0.00081968 | 0.00081968 | 0.0 | 0.00
|
||||
Output | 0.00028563 | 0.00028563 | 0.00028563 | 0.0 | 0.00
|
||||
Modify | 0.0003283 | 0.0003283 | 0.0003283 | 0.0 | 0.00
|
||||
Other | | 0.0005233 | | | 0.00
|
||||
Comm | 0.00027108 | 0.00027108 | 0.00027108 | 0.0 | 0.01
|
||||
Output | 0.00014758 | 0.00014758 | 0.00014758 | 0.0 | 0.01
|
||||
Modify | 0.00010991 | 0.00010991 | 0.00010991 | 0.0 | 0.00
|
||||
Other | | 0.0001643 | | | 0.01
|
||||
|
||||
Nlocal: 128 ave 128 max 128 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
@ -144,4 +143,4 @@ Ave neighs/atom = 58
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:18
|
||||
Total wall time: 0:00:02
|
||||
@ -1,13 +1,13 @@
|
||||
LAMMPS (27 Nov 2018)
|
||||
LAMMPS (15 Jun 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Demonstrate SNAP Ta potential
|
||||
# Demonstrate SNAP W potential
|
||||
|
||||
# Initialize simulation
|
||||
|
||||
variable nsteps index 100
|
||||
variable nrep equal 4
|
||||
variable a equal 3.1803
|
||||
units metal
|
||||
units metal
|
||||
|
||||
# generate the box and atom positions using a BCC lattice
|
||||
|
||||
@ -18,28 +18,28 @@ variable ny equal 4
|
||||
variable nz equal ${nrep}
|
||||
variable nz equal 4
|
||||
|
||||
boundary p p p
|
||||
boundary p p p
|
||||
|
||||
lattice bcc $a
|
||||
lattice bcc 3.1803
|
||||
Lattice spacing in x,y,z = 3.1803 3.1803 3.1803
|
||||
region box block 0 ${nx} 0 ${ny} 0 ${nz}
|
||||
region box block 0 4 0 ${ny} 0 ${nz}
|
||||
region box block 0 4 0 4 0 ${nz}
|
||||
region box block 0 4 0 4 0 4
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (12.7212 12.7212 12.7212)
|
||||
region box block 0 ${nx} 0 ${ny} 0 ${nz}
|
||||
region box block 0 4 0 ${ny} 0 ${nz}
|
||||
region box block 0 4 0 4 0 ${nz}
|
||||
region box block 0 4 0 4 0 4
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0.0 0.0 0.0) to (12.7212 12.7212 12.7212)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
create_atoms 1 box
|
||||
Created 128 atoms
|
||||
Time spent = 0.000297546 secs
|
||||
create_atoms CPU = 0.000 seconds
|
||||
|
||||
mass 1 183.84
|
||||
|
||||
# choose potential
|
||||
|
||||
include W_2940_2017_2.snap
|
||||
# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph]
|
||||
# DATE: 2017-02-20 UNITS: metal CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph]
|
||||
#
|
||||
# Definition of SNAP+ZBL potential.
|
||||
variable zblcutinner equal 4
|
||||
@ -54,7 +54,7 @@ pair_style hybrid/overlay zbl 4 4.8 snap
|
||||
pair_coeff 1 1 zbl ${zblz} ${zblz}
|
||||
pair_coeff 1 1 zbl 74 ${zblz}
|
||||
pair_coeff 1 1 zbl 74 74
|
||||
pair_coeff * * snap W_2940_2017_2.snapcoeff W W_2940_2017_2.snapparam W
|
||||
pair_coeff * * snap W_2940_2017_2.snapcoeff W_2940_2017_2.snapparam W
|
||||
Reading potential file W_2940_2017_2.snapcoeff with DATE: 2017-02-20
|
||||
SNAP Element = W, Radius 0.5, Weight 1
|
||||
Reading potential file W_2940_2017_2.snapparam with DATE: 2017-02-20
|
||||
@ -62,7 +62,6 @@ SNAP keyword rcutfac 4.73442
|
||||
SNAP keyword twojmax 8
|
||||
SNAP keyword rfac0 0.99363
|
||||
SNAP keyword rmin0 0
|
||||
SNAP keyword diagonalstyle 3
|
||||
SNAP keyword bzeroflag 0
|
||||
SNAP keyword quadraticflag 0
|
||||
|
||||
@ -70,7 +69,7 @@ SNAP keyword quadraticflag 0
|
||||
|
||||
# Setup output
|
||||
|
||||
thermo 10
|
||||
thermo 10
|
||||
thermo_modify norm yes
|
||||
|
||||
# Set up NVE run
|
||||
@ -81,7 +80,7 @@ neigh_modify once no every 1 delay 0 check yes
|
||||
|
||||
# Run MD
|
||||
|
||||
velocity all create 300.0 4928459
|
||||
velocity all create 300.0 4928459 loop geom
|
||||
fix 1 all nve
|
||||
run ${nsteps}
|
||||
run 100
|
||||
@ -102,33 +101,33 @@ Neighbor list info ...
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.13 | 5.13 | 5.13 Mbytes
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.167 | 4.167 | 4.167 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 300 -11.028325 0 -10.98985 3010.497
|
||||
10 293.22504 -11.027456 0 -10.989849 3258.275
|
||||
20 273.60084 -11.024939 0 -10.989849 3973.9038
|
||||
30 243.15327 -11.021034 0 -10.989849 5077.9172
|
||||
40 205.01905 -11.016142 0 -10.989849 6448.4941
|
||||
50 163.10914 -11.010767 0 -10.989848 7935.6835
|
||||
60 121.67854 -11.005453 0 -10.989848 9378.9959
|
||||
70 84.846972 -11.000729 0 -10.989848 10626.301
|
||||
80 56.127265 -10.997046 0 -10.989848 11551.687
|
||||
90 38.025013 -10.994724 0 -10.989847 12069.936
|
||||
100 31.768127 -10.993922 0 -10.989847 12145.648
|
||||
Loop time of 5.38055 on 4 procs for 100 steps with 128 atoms
|
||||
10 293.10848 -11.027441 0 -10.989849 3259.9445
|
||||
20 273.14727 -11.024881 0 -10.989849 3979.8968
|
||||
30 242.20285 -11.020912 0 -10.989849 5089.0797
|
||||
40 203.51992 -11.01595 0 -10.989849 6462.9419
|
||||
50 161.14556 -11.010515 0 -10.989848 7948.1798
|
||||
60 119.47232 -11.00517 0 -10.989848 9380.8543
|
||||
70 82.729175 -11.000458 0 -10.989848 10606.025
|
||||
80 54.483648 -10.996835 0 -10.989848 11496.424
|
||||
90 37.225263 -10.994622 0 -10.989847 11967.579
|
||||
100 32.094224 -10.993964 0 -10.989847 11987.181
|
||||
Loop time of 0.700403 on 4 procs for 100 steps with 128 atoms
|
||||
|
||||
Performance: 0.803 ns/day, 29.892 hours/ns, 18.585 timesteps/s
|
||||
96.1% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
Performance: 6.168 ns/day, 3.891 hours/ns, 142.775 timesteps/s
|
||||
95.9% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 4.8254 | 5.0245 | 5.2817 | 7.7 | 93.38
|
||||
Pair | 0.59296 | 0.62019 | 0.6504 | 2.8 | 88.55
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.093845 | 0.34915 | 0.5466 | 29.1 | 6.49
|
||||
Output | 0.00032616 | 0.0011846 | 0.0037167 | 4.2 | 0.02
|
||||
Modify | 0.00022507 | 0.00025326 | 0.0002687 | 0.0 | 0.00
|
||||
Other | | 0.005432 | | | 0.10
|
||||
Comm | 0.048731 | 0.078938 | 0.10647 | 7.8 | 11.27
|
||||
Output | 0.00015879 | 0.00024194 | 0.00048518 | 0.0 | 0.03
|
||||
Modify | 6.4373e-05 | 6.9439e-05 | 7.7963e-05 | 0.0 | 0.01
|
||||
Other | | 0.0009654 | | | 0.14
|
||||
|
||||
Nlocal: 32 ave 32 max 32 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
@ -144,4 +143,4 @@ Ave neighs/atom = 58
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:05
|
||||
Total wall time: 0:00:00
|
||||
@ -1,4 +1,5 @@
|
||||
LAMMPS (7 Aug 2019)
|
||||
LAMMPS (15 Jun 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Demonstrate SNAP W-Be potential
|
||||
|
||||
# Initialize simulation
|
||||
@ -6,7 +7,7 @@ LAMMPS (7 Aug 2019)
|
||||
variable nsteps index 100
|
||||
variable nrep equal 4
|
||||
variable a equal 3.1803
|
||||
units metal
|
||||
units metal
|
||||
|
||||
# generate the box and atom positions using a BCC lattice
|
||||
|
||||
@ -17,33 +18,33 @@ variable ny equal 4
|
||||
variable nz equal ${nrep}
|
||||
variable nz equal 4
|
||||
|
||||
boundary p p p
|
||||
boundary p p p
|
||||
|
||||
lattice bcc $a
|
||||
lattice bcc 3.1803
|
||||
Lattice spacing in x,y,z = 3.1803 3.1803 3.1803
|
||||
region box block 0 ${nx} 0 ${ny} 0 ${nz}
|
||||
region box block 0 4 0 ${ny} 0 ${nz}
|
||||
region box block 0 4 0 4 0 ${nz}
|
||||
region box block 0 4 0 4 0 4
|
||||
create_box 2 box
|
||||
Created orthogonal box = (0 0 0) to (12.7212 12.7212 12.7212)
|
||||
region box block 0 ${nx} 0 ${ny} 0 ${nz}
|
||||
region box block 0 4 0 ${ny} 0 ${nz}
|
||||
region box block 0 4 0 4 0 ${nz}
|
||||
region box block 0 4 0 4 0 4
|
||||
create_box 2 box
|
||||
Created orthogonal box = (0.0 0.0 0.0) to (12.7212 12.7212 12.7212)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
create_atoms 1 box
|
||||
Created 128 atoms
|
||||
create_atoms CPU = 0.000234842 secs
|
||||
create_atoms CPU = 0.000 seconds
|
||||
mass 1 183.84
|
||||
mass 2 9.012182
|
||||
|
||||
set group all type/fraction 2 0.05 3590153 # Change 5% of W to He
|
||||
5 settings made for type/fraction
|
||||
group tungsten type 1
|
||||
set group all type/fraction 2 0.05 3590153 # Change 5% of W to He
|
||||
5 settings made for type/fractiongroup tungsten type 1
|
||||
123 atoms in group tungsten
|
||||
group beryllium type 2
|
||||
group beryllium type 2
|
||||
5 atoms in group beryllium
|
||||
# choose potential
|
||||
|
||||
include WBe_Wood_PRB2019.snap
|
||||
# DATE: 2019-09-18 UNITS: metal CONTRIBUTOR: Mary Alice Cusentino mcusent@sandia.gov CITATION: M.A. Wood, M.A. Cusentino, B.D. Wirth, and A.P. Thompson, "Data-driven material models for atomistic simulation", Physical Review B 99, 184305 (2019)
|
||||
# Definition of SNAP+ZBL potential.
|
||||
variable zblcutinner equal 4
|
||||
variable zblcutouter equal 4.8
|
||||
@ -77,7 +78,7 @@ SNAP keyword quadraticflag 0
|
||||
|
||||
# Setup output
|
||||
|
||||
thermo 10
|
||||
thermo 10
|
||||
thermo_modify norm yes
|
||||
|
||||
# Set up NVE run
|
||||
@ -88,7 +89,7 @@ neigh_modify once no every 1 delay 0 check yes
|
||||
|
||||
# Run MD
|
||||
|
||||
velocity all create 300.0 4928459
|
||||
velocity all create 300.0 4928459 loop geom
|
||||
fix 1 all nve
|
||||
run ${nsteps}
|
||||
run 100
|
||||
@ -112,43 +113,43 @@ Neighbor list info ...
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.268 | 4.268 | 4.268 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 300 -8.5980876 0 -8.5596125 -35284.855
|
||||
10 299.29029 -8.5979965 0 -8.5596125 -35299.259
|
||||
20 288.99334 -8.5966759 0 -8.5596124 -35004.093
|
||||
30 269.91027 -8.5942284 0 -8.5596123 -34447.077
|
||||
40 243.57361 -8.5908505 0 -8.5596121 -33687.105
|
||||
50 212.21385 -8.5868284 0 -8.5596119 -32821.864
|
||||
60 178.77144 -8.5825391 0 -8.5596116 -31971.17
|
||||
70 146.71854 -8.578428 0 -8.5596113 -31245.51
|
||||
80 119.50956 -8.5749383 0 -8.5596111 -30724.137
|
||||
90 99.872785 -8.5724197 0 -8.559611 -30440.244
|
||||
100 89.604584 -8.5711027 0 -8.5596109 -30392.805
|
||||
Loop time of 3.16831 on 1 procs for 100 steps with 128 atoms
|
||||
10 296.32664 -8.5976164 0 -8.5596124 -35188.339
|
||||
20 282.41417 -8.595832 0 -8.5596123 -34782.293
|
||||
30 259.69014 -8.5929175 0 -8.5596121 -34113.316
|
||||
40 230.50415 -8.5891741 0 -8.5596119 -33260.777
|
||||
50 197.88816 -8.5849908 0 -8.5596116 -32309.975
|
||||
60 165.27259 -8.5808076 0 -8.5596113 -31365.766
|
||||
70 136.15697 -8.5770733 0 -8.5596111 -30542.657
|
||||
80 113.58947 -8.5741788 0 -8.5596109 -29939.23
|
||||
90 99.477916 -8.572369 0 -8.5596109 -29619.939
|
||||
100 94.121939 -8.5716822 0 -8.559611 -29598.002
|
||||
Loop time of 2.26616 on 1 procs for 100 steps with 128 atoms
|
||||
|
||||
Performance: 1.364 ns/day, 17.602 hours/ns, 31.563 timesteps/s
|
||||
199.5% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
Performance: 1.906 ns/day, 12.590 hours/ns, 44.128 timesteps/s
|
||||
99.3% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 3.1672 | 3.1672 | 3.1672 | 0.0 | 99.97
|
||||
Neigh | 0.00030208 | 0.00030208 | 0.00030208 | 0.0 | 0.01
|
||||
Comm | 0.00029612 | 0.00029612 | 0.00029612 | 0.0 | 0.01
|
||||
Output | 0.00019813 | 0.00019813 | 0.00019813 | 0.0 | 0.01
|
||||
Modify | 0.00014448 | 0.00014448 | 0.00014448 | 0.0 | 0.00
|
||||
Other | | 0.0001433 | | | 0.00
|
||||
Pair | 2.2531 | 2.2531 | 2.2531 | 0.0 | 99.42
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.0002594 | 0.0002594 | 0.0002594 | 0.0 | 0.01
|
||||
Output | 0.012544 | 0.012544 | 0.012544 | 0.0 | 0.55
|
||||
Modify | 0.00010347 | 0.00010347 | 0.00010347 | 0.0 | 0.00
|
||||
Other | | 0.0001583 | | | 0.01
|
||||
|
||||
Nlocal: 128 ave 128 max 128 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 727 ave 727 max 727 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 3710 ave 3710 max 3710 min
|
||||
Neighs: 3712 ave 3712 max 3712 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 7420 ave 7420 max 7420 min
|
||||
FullNghs: 7424 ave 7424 max 7424 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 7420
|
||||
Ave neighs/atom = 57.9688
|
||||
Neighbor list builds = 1
|
||||
Total # of neighbors = 7424
|
||||
Ave neighs/atom = 58
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:03
|
||||
Total wall time: 0:00:02
|
||||
@ -1,4 +1,5 @@
|
||||
LAMMPS (7 Aug 2019)
|
||||
LAMMPS (15 Jun 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Demonstrate SNAP W-Be potential
|
||||
|
||||
# Initialize simulation
|
||||
@ -6,7 +7,7 @@ LAMMPS (7 Aug 2019)
|
||||
variable nsteps index 100
|
||||
variable nrep equal 4
|
||||
variable a equal 3.1803
|
||||
units metal
|
||||
units metal
|
||||
|
||||
# generate the box and atom positions using a BCC lattice
|
||||
|
||||
@ -17,33 +18,33 @@ variable ny equal 4
|
||||
variable nz equal ${nrep}
|
||||
variable nz equal 4
|
||||
|
||||
boundary p p p
|
||||
boundary p p p
|
||||
|
||||
lattice bcc $a
|
||||
lattice bcc 3.1803
|
||||
Lattice spacing in x,y,z = 3.1803 3.1803 3.1803
|
||||
region box block 0 ${nx} 0 ${ny} 0 ${nz}
|
||||
region box block 0 4 0 ${ny} 0 ${nz}
|
||||
region box block 0 4 0 4 0 ${nz}
|
||||
region box block 0 4 0 4 0 4
|
||||
create_box 2 box
|
||||
Created orthogonal box = (0 0 0) to (12.7212 12.7212 12.7212)
|
||||
region box block 0 ${nx} 0 ${ny} 0 ${nz}
|
||||
region box block 0 4 0 ${ny} 0 ${nz}
|
||||
region box block 0 4 0 4 0 ${nz}
|
||||
region box block 0 4 0 4 0 4
|
||||
create_box 2 box
|
||||
Created orthogonal box = (0.0 0.0 0.0) to (12.7212 12.7212 12.7212)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
create_atoms 1 box
|
||||
Created 128 atoms
|
||||
create_atoms CPU = 0.000317097 secs
|
||||
create_atoms CPU = 0.000 seconds
|
||||
mass 1 183.84
|
||||
mass 2 9.012182
|
||||
|
||||
set group all type/fraction 2 0.05 3590153 # Change 5% of W to He
|
||||
5 settings made for type/fraction
|
||||
group tungsten type 1
|
||||
set group all type/fraction 2 0.05 3590153 # Change 5% of W to He
|
||||
5 settings made for type/fractiongroup tungsten type 1
|
||||
123 atoms in group tungsten
|
||||
group beryllium type 2
|
||||
group beryllium type 2
|
||||
5 atoms in group beryllium
|
||||
# choose potential
|
||||
|
||||
include WBe_Wood_PRB2019.snap
|
||||
# DATE: 2019-09-18 UNITS: metal CONTRIBUTOR: Mary Alice Cusentino mcusent@sandia.gov CITATION: M.A. Wood, M.A. Cusentino, B.D. Wirth, and A.P. Thompson, "Data-driven material models for atomistic simulation", Physical Review B 99, 184305 (2019)
|
||||
# Definition of SNAP+ZBL potential.
|
||||
variable zblcutinner equal 4
|
||||
variable zblcutouter equal 4.8
|
||||
@ -77,7 +78,7 @@ SNAP keyword quadraticflag 0
|
||||
|
||||
# Setup output
|
||||
|
||||
thermo 10
|
||||
thermo 10
|
||||
thermo_modify norm yes
|
||||
|
||||
# Set up NVE run
|
||||
@ -88,7 +89,7 @@ neigh_modify once no every 1 delay 0 check yes
|
||||
|
||||
# Run MD
|
||||
|
||||
velocity all create 300.0 4928459
|
||||
velocity all create 300.0 4928459 loop geom
|
||||
fix 1 all nve
|
||||
run ${nsteps}
|
||||
run 100
|
||||
@ -112,43 +113,43 @@ Neighbor list info ...
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.167 | 4.167 | 4.167 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 300 -8.5980876 0 -8.5596125 -35284.855
|
||||
10 296.24946 -8.5976065 0 -8.5596124 -35140.29
|
||||
20 282.27904 -8.5958147 0 -8.5596123 -34710.3
|
||||
30 259.54978 -8.5928995 0 -8.5596121 -34060.43
|
||||
40 230.41412 -8.5891626 0 -8.5596119 -33258.275
|
||||
50 197.85135 -8.5849861 0 -8.5596116 -32389.527
|
||||
60 165.21732 -8.5808005 0 -8.5596113 -31550.426
|
||||
70 135.94024 -8.5770455 0 -8.5596111 -30839.006
|
||||
80 113.06617 -8.5741117 0 -8.5596109 -30339.177
|
||||
90 98.542347 -8.572249 0 -8.5596109 -30094.29
|
||||
100 92.524343 -8.5714774 0 -8.5596111 -30091.988
|
||||
Loop time of 0.813674 on 4 procs for 100 steps with 128 atoms
|
||||
10 296.32664 -8.5976164 0 -8.5596124 -35188.339
|
||||
20 282.41417 -8.595832 0 -8.5596123 -34782.293
|
||||
30 259.69014 -8.5929175 0 -8.5596121 -34113.316
|
||||
40 230.50415 -8.5891741 0 -8.5596119 -33260.777
|
||||
50 197.88816 -8.5849908 0 -8.5596116 -32309.975
|
||||
60 165.27259 -8.5808076 0 -8.5596113 -31365.766
|
||||
70 136.15697 -8.5770733 0 -8.5596111 -30542.657
|
||||
80 113.58947 -8.5741788 0 -8.5596109 -29939.23
|
||||
90 99.477916 -8.572369 0 -8.5596109 -29619.939
|
||||
100 94.121939 -8.5716822 0 -8.559611 -29598.002
|
||||
Loop time of 0.668977 on 4 procs for 100 steps with 128 atoms
|
||||
|
||||
Performance: 5.309 ns/day, 4.520 hours/ns, 122.899 timesteps/s
|
||||
99.7% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
Performance: 6.458 ns/day, 3.717 hours/ns, 149.482 timesteps/s
|
||||
97.2% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.79079 | 0.79788 | 0.80888 | 0.8 | 98.06
|
||||
Neigh | 7.1049e-05 | 8.0049e-05 | 9.2983e-05 | 0.0 | 0.01
|
||||
Comm | 0.0041246 | 0.01515 | 0.022235 | 5.5 | 1.86
|
||||
Output | 0.000144 | 0.00017095 | 0.00024796 | 0.0 | 0.02
|
||||
Modify | 4.4823e-05 | 5.8889e-05 | 7.2718e-05 | 0.0 | 0.01
|
||||
Other | | 0.000338 | | | 0.04
|
||||
Pair | 0.57811 | 0.60637 | 0.63609 | 2.6 | 90.64
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.031571 | 0.061612 | 0.090021 | 8.3 | 9.21
|
||||
Output | 0.00015521 | 0.00021636 | 0.00038552 | 0.0 | 0.03
|
||||
Modify | 5.4836e-05 | 6.1393e-05 | 7.2956e-05 | 0.0 | 0.01
|
||||
Other | | 0.0007139 | | | 0.11
|
||||
|
||||
Nlocal: 32 ave 37 max 28 min
|
||||
Histogram: 1 0 0 1 1 0 0 0 0 1
|
||||
Nghost: 431 ave 435 max 426 min
|
||||
Histogram: 1 0 0 0 0 1 1 0 0 1
|
||||
Neighs: 927 ave 1071 max 821 min
|
||||
Histogram: 1 0 1 0 1 0 0 0 0 1
|
||||
FullNghs: 1854 ave 2144 max 1624 min
|
||||
Histogram: 1 0 0 1 1 0 0 0 0 1
|
||||
Nlocal: 32 ave 32 max 32 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 431 ave 431 max 431 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 928 ave 928 max 928 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 1856 ave 1856 max 1856 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 7416
|
||||
Ave neighs/atom = 57.9375
|
||||
Neighbor list builds = 1
|
||||
Total # of neighbors = 7424
|
||||
Ave neighs/atom = 58
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:00
|
||||
@ -1,13 +1,13 @@
|
||||
LAMMPS (27 Nov 2018)
|
||||
LAMMPS (15 Jun 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Demonstrate SNAP Ta potential
|
||||
# Demonstrate SNAP W with tabulated He-He and W-He using hybrid pair style
|
||||
|
||||
# Initialize simulation
|
||||
|
||||
variable nsteps index 100
|
||||
variable nrep equal 4
|
||||
variable a equal 3.1803
|
||||
units metal
|
||||
units metal
|
||||
|
||||
# generate the box and atom positions using a BCC lattice
|
||||
|
||||
@ -18,34 +18,33 @@ variable ny equal 4
|
||||
variable nz equal ${nrep}
|
||||
variable nz equal 4
|
||||
|
||||
boundary p p p
|
||||
boundary p p p
|
||||
|
||||
lattice bcc $a
|
||||
lattice bcc 3.1803
|
||||
Lattice spacing in x,y,z = 3.1803 3.1803 3.1803
|
||||
region box block 0 ${nx} 0 ${ny} 0 ${nz}
|
||||
region box block 0 4 0 ${ny} 0 ${nz}
|
||||
region box block 0 4 0 4 0 ${nz}
|
||||
region box block 0 4 0 4 0 4
|
||||
create_box 2 box
|
||||
Created orthogonal box = (0 0 0) to (12.7212 12.7212 12.7212)
|
||||
region box block 0 ${nx} 0 ${ny} 0 ${nz}
|
||||
region box block 0 4 0 ${ny} 0 ${nz}
|
||||
region box block 0 4 0 4 0 ${nz}
|
||||
region box block 0 4 0 4 0 4
|
||||
create_box 2 box
|
||||
Created orthogonal box = (0.0 0.0 0.0) to (12.7212 12.7212 12.7212)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
create_atoms 1 box
|
||||
Created 128 atoms
|
||||
Time spent = 0.000426054 secs
|
||||
create_atoms CPU = 0.001 seconds
|
||||
mass 1 183.84
|
||||
mass 2 4.0026
|
||||
|
||||
set group all type/fraction 2 0.05 3590153 # Change 5% of W to He
|
||||
5 settings made for type/fraction
|
||||
group tungsten type 1
|
||||
set group all type/fraction 2 0.05 3590153 # Change 5% of W to He
|
||||
5 settings made for type/fractiongroup tungsten type 1
|
||||
123 atoms in group tungsten
|
||||
group helium type 2
|
||||
group helium type 2
|
||||
5 atoms in group helium
|
||||
# choose potential
|
||||
|
||||
include W_2940_2017_2_He_JW2013.snap
|
||||
# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph]
|
||||
# DATE: 2017-02-20 UNITS: metal CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph]
|
||||
#
|
||||
# Definition of SNAP+ZBL+Tabulated potential.
|
||||
variable zblcutinner equal 4
|
||||
@ -60,7 +59,7 @@ pair_style hybrid/overlay zbl 4 4.8 snap table spline 10000 table spline 10000
|
||||
pair_coeff 1 1 zbl ${zblz} ${zblz}
|
||||
pair_coeff 1 1 zbl 74 ${zblz}
|
||||
pair_coeff 1 1 zbl 74 74
|
||||
pair_coeff * * snap W_2940_2017_2.snapcoeff W W_2940_2017_2.snapparam W NULL
|
||||
pair_coeff * * snap W_2940_2017_2.snapcoeff W_2940_2017_2.snapparam W NULL
|
||||
Reading potential file W_2940_2017_2.snapcoeff with DATE: 2017-02-20
|
||||
SNAP Element = W, Radius 0.5, Weight 1
|
||||
Reading potential file W_2940_2017_2.snapparam with DATE: 2017-02-20
|
||||
@ -68,24 +67,23 @@ SNAP keyword rcutfac 4.73442
|
||||
SNAP keyword twojmax 8
|
||||
SNAP keyword rfac0 0.99363
|
||||
SNAP keyword rmin0 0
|
||||
SNAP keyword diagonalstyle 3
|
||||
SNAP keyword bzeroflag 0
|
||||
SNAP keyword quadraticflag 0
|
||||
pair_coeff 2 2 table 1 He_He_JW2013.table HeHe
|
||||
Reading potential file He_He_JW2013.table with DATE: 2017-02-20
|
||||
WARNING: 1 of 4999 force values in table are inconsistent with -dE/dr.
|
||||
Should only be flagged at inflection points (src/pair_table.cpp:481)
|
||||
Should only be flagged at inflection points (src/pair_table.cpp:467)
|
||||
pair_coeff 1 2 table 2 W_He_JW2013.table WHe
|
||||
Reading potential file W_He_JW2013.table with DATE: 2017-02-20
|
||||
WARNING: 3 of 325 force values in table are inconsistent with -dE/dr.
|
||||
Should only be flagged at inflection points (src/pair_table.cpp:481)
|
||||
Should only be flagged at inflection points (src/pair_table.cpp:467)
|
||||
#Hybrid/overlay will take all pair styles and add their contributions equally, order of pair_coeff doesnt matter here
|
||||
#This is not the case for pair_style hybrid ... where only one pair_coeff is read for each type combination, order matters here.
|
||||
|
||||
|
||||
# Setup output
|
||||
|
||||
thermo 10
|
||||
thermo 10
|
||||
thermo_modify norm yes
|
||||
|
||||
# Set up NVE run
|
||||
@ -96,7 +94,7 @@ neigh_modify once no every 1 delay 0 check yes
|
||||
|
||||
# Run MD
|
||||
|
||||
velocity all create 300.0 4928459
|
||||
velocity all create 300.0 4928459 loop geom
|
||||
fix 1 all nve
|
||||
run ${nsteps}
|
||||
run 100
|
||||
@ -137,33 +135,33 @@ Neighbor list info ...
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 7.676 | 7.676 | 7.676 Mbytes
|
||||
Per MPI rank memory allocation (min/avg/max) = 6.789 | 6.789 | 6.789 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 300 -10.438105 0 -10.39963 -5445.2808
|
||||
10 290.48923 -10.436885 0 -10.399629 -5646.4813
|
||||
20 271.18868 -10.434409 0 -10.399629 -5654.4646
|
||||
30 246.2601 -10.431212 0 -10.399629 -5281.8873
|
||||
40 218.69918 -10.427677 0 -10.399629 -4343.3636
|
||||
50 189.12519 -10.423885 0 -10.399629 -2903.1138
|
||||
60 155.55701 -10.419579 0 -10.399629 -1402.2278
|
||||
70 118.83581 -10.414869 0 -10.399629 -146.36141
|
||||
80 85.903126 -10.410645 0 -10.399628 857.74986
|
||||
90 65.223651 -10.407993 0 -10.399628 1494.2746
|
||||
100 59.833542 -10.407302 0 -10.399628 1938.9164
|
||||
Loop time of 17.6435 on 1 procs for 100 steps with 128 atoms
|
||||
10 292.90716 -10.437195 0 -10.39963 -5400.8323
|
||||
20 275.59696 -10.434975 0 -10.399629 -5055.199
|
||||
30 250.28699 -10.431729 0 -10.399629 -4317.4619
|
||||
40 218.58148 -10.427662 0 -10.399629 -3069.0256
|
||||
50 182.80754 -10.423074 0 -10.399629 -1514.9501
|
||||
60 144.77789 -10.418197 0 -10.399629 134.6083
|
||||
70 108.06164 -10.413487 0 -10.399628 1747.8913
|
||||
80 79.630821 -10.409841 0 -10.399628 2913.2733
|
||||
90 62.795831 -10.407682 0 -10.399628 3646.2528
|
||||
100 57.450965 -10.406996 0 -10.399628 4022.2665
|
||||
Loop time of 2.15336 on 1 procs for 100 steps with 128 atoms
|
||||
|
||||
Performance: 0.245 ns/day, 98.019 hours/ns, 5.668 timesteps/s
|
||||
98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
Performance: 2.006 ns/day, 11.963 hours/ns, 46.439 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 17.641 | 17.641 | 17.641 | 0.0 | 99.99
|
||||
Neigh | 0.00054359 | 0.00054359 | 0.00054359 | 0.0 | 0.00
|
||||
Comm | 0.00080729 | 0.00080729 | 0.00080729 | 0.0 | 0.00
|
||||
Output | 0.00026512 | 0.00026512 | 0.00026512 | 0.0 | 0.00
|
||||
Modify | 0.00033879 | 0.00033879 | 0.00033879 | 0.0 | 0.00
|
||||
Other | | 0.0005448 | | | 0.00
|
||||
Pair | 2.1524 | 2.1524 | 2.1524 | 0.0 | 99.96
|
||||
Neigh | 0.00030732 | 0.00030732 | 0.00030732 | 0.0 | 0.01
|
||||
Comm | 0.00026202 | 0.00026202 | 0.00026202 | 0.0 | 0.01
|
||||
Output | 0.00013041 | 0.00013041 | 0.00013041 | 0.0 | 0.01
|
||||
Modify | 0.00010085 | 0.00010085 | 0.00010085 | 0.0 | 0.00
|
||||
Other | | 0.0001643 | | | 0.01
|
||||
|
||||
Nlocal: 128 ave 128 max 128 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
@ -179,4 +177,4 @@ Ave neighs/atom = 53.5156
|
||||
Neighbor list builds = 1
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:17
|
||||
Total wall time: 0:00:02
|
||||
@ -1,13 +1,13 @@
|
||||
LAMMPS (27 Nov 2018)
|
||||
LAMMPS (15 Jun 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Demonstrate SNAP Ta potential
|
||||
# Demonstrate SNAP W with tabulated He-He and W-He using hybrid pair style
|
||||
|
||||
# Initialize simulation
|
||||
|
||||
variable nsteps index 100
|
||||
variable nrep equal 4
|
||||
variable a equal 3.1803
|
||||
units metal
|
||||
units metal
|
||||
|
||||
# generate the box and atom positions using a BCC lattice
|
||||
|
||||
@ -18,34 +18,33 @@ variable ny equal 4
|
||||
variable nz equal ${nrep}
|
||||
variable nz equal 4
|
||||
|
||||
boundary p p p
|
||||
boundary p p p
|
||||
|
||||
lattice bcc $a
|
||||
lattice bcc 3.1803
|
||||
Lattice spacing in x,y,z = 3.1803 3.1803 3.1803
|
||||
region box block 0 ${nx} 0 ${ny} 0 ${nz}
|
||||
region box block 0 4 0 ${ny} 0 ${nz}
|
||||
region box block 0 4 0 4 0 ${nz}
|
||||
region box block 0 4 0 4 0 4
|
||||
create_box 2 box
|
||||
Created orthogonal box = (0 0 0) to (12.7212 12.7212 12.7212)
|
||||
region box block 0 ${nx} 0 ${ny} 0 ${nz}
|
||||
region box block 0 4 0 ${ny} 0 ${nz}
|
||||
region box block 0 4 0 4 0 ${nz}
|
||||
region box block 0 4 0 4 0 4
|
||||
create_box 2 box
|
||||
Created orthogonal box = (0.0 0.0 0.0) to (12.7212 12.7212 12.7212)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
create_atoms 1 box
|
||||
Created 128 atoms
|
||||
Time spent = 0.000303984 secs
|
||||
create_atoms CPU = 0.000 seconds
|
||||
mass 1 183.84
|
||||
mass 2 4.0026
|
||||
|
||||
set group all type/fraction 2 0.05 3590153 # Change 5% of W to He
|
||||
5 settings made for type/fraction
|
||||
group tungsten type 1
|
||||
set group all type/fraction 2 0.05 3590153 # Change 5% of W to He
|
||||
5 settings made for type/fractiongroup tungsten type 1
|
||||
123 atoms in group tungsten
|
||||
group helium type 2
|
||||
group helium type 2
|
||||
5 atoms in group helium
|
||||
# choose potential
|
||||
|
||||
include W_2940_2017_2_He_JW2013.snap
|
||||
# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph]
|
||||
# DATE: 2017-02-20 UNITS: metal CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph]
|
||||
#
|
||||
# Definition of SNAP+ZBL+Tabulated potential.
|
||||
variable zblcutinner equal 4
|
||||
@ -60,7 +59,7 @@ pair_style hybrid/overlay zbl 4 4.8 snap table spline 10000 table spline 10000
|
||||
pair_coeff 1 1 zbl ${zblz} ${zblz}
|
||||
pair_coeff 1 1 zbl 74 ${zblz}
|
||||
pair_coeff 1 1 zbl 74 74
|
||||
pair_coeff * * snap W_2940_2017_2.snapcoeff W W_2940_2017_2.snapparam W NULL
|
||||
pair_coeff * * snap W_2940_2017_2.snapcoeff W_2940_2017_2.snapparam W NULL
|
||||
Reading potential file W_2940_2017_2.snapcoeff with DATE: 2017-02-20
|
||||
SNAP Element = W, Radius 0.5, Weight 1
|
||||
Reading potential file W_2940_2017_2.snapparam with DATE: 2017-02-20
|
||||
@ -68,24 +67,23 @@ SNAP keyword rcutfac 4.73442
|
||||
SNAP keyword twojmax 8
|
||||
SNAP keyword rfac0 0.99363
|
||||
SNAP keyword rmin0 0
|
||||
SNAP keyword diagonalstyle 3
|
||||
SNAP keyword bzeroflag 0
|
||||
SNAP keyword quadraticflag 0
|
||||
pair_coeff 2 2 table 1 He_He_JW2013.table HeHe
|
||||
Reading potential file He_He_JW2013.table with DATE: 2017-02-20
|
||||
WARNING: 1 of 4999 force values in table are inconsistent with -dE/dr.
|
||||
Should only be flagged at inflection points (src/pair_table.cpp:481)
|
||||
Should only be flagged at inflection points (src/pair_table.cpp:467)
|
||||
pair_coeff 1 2 table 2 W_He_JW2013.table WHe
|
||||
Reading potential file W_He_JW2013.table with DATE: 2017-02-20
|
||||
WARNING: 3 of 325 force values in table are inconsistent with -dE/dr.
|
||||
Should only be flagged at inflection points (src/pair_table.cpp:481)
|
||||
Should only be flagged at inflection points (src/pair_table.cpp:467)
|
||||
#Hybrid/overlay will take all pair styles and add their contributions equally, order of pair_coeff doesnt matter here
|
||||
#This is not the case for pair_style hybrid ... where only one pair_coeff is read for each type combination, order matters here.
|
||||
|
||||
|
||||
# Setup output
|
||||
|
||||
thermo 10
|
||||
thermo 10
|
||||
thermo_modify norm yes
|
||||
|
||||
# Set up NVE run
|
||||
@ -96,7 +94,7 @@ neigh_modify once no every 1 delay 0 check yes
|
||||
|
||||
# Run MD
|
||||
|
||||
velocity all create 300.0 4928459
|
||||
velocity all create 300.0 4928459 loop geom
|
||||
fix 1 all nve
|
||||
run ${nsteps}
|
||||
run 100
|
||||
@ -137,46 +135,46 @@ Neighbor list info ...
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 7.656 | 7.656 | 7.656 Mbytes
|
||||
Per MPI rank memory allocation (min/avg/max) = 6.687 | 6.69 | 6.692 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 300 -10.438105 0 -10.39963 -5445.2808
|
||||
10 292.13979 -10.437097 0 -10.39963 -5516.3963
|
||||
20 272.55728 -10.434585 0 -10.399629 -5460.4268
|
||||
30 245.06559 -10.431059 0 -10.399629 -5016.6351
|
||||
40 212.79459 -10.42692 0 -10.399629 -3924.2175
|
||||
50 178.03903 -10.422462 0 -10.399629 -2354.5485
|
||||
60 141.62155 -10.417791 0 -10.399628 -595.41345
|
||||
70 107.24843 -10.413383 0 -10.399628 1138.4107
|
||||
80 79.985938 -10.409886 0 -10.399628 2392.1106
|
||||
90 62.568933 -10.407652 0 -10.399628 3141.7027
|
||||
100 56.697933 -10.406899 0 -10.399628 3583.9538
|
||||
Loop time of 4.7853 on 4 procs for 100 steps with 128 atoms
|
||||
10 292.90716 -10.437195 0 -10.39963 -5400.8323
|
||||
20 275.59696 -10.434975 0 -10.399629 -5055.199
|
||||
30 250.28699 -10.431729 0 -10.399629 -4317.4619
|
||||
40 218.58148 -10.427662 0 -10.399629 -3069.0256
|
||||
50 182.80754 -10.423074 0 -10.399629 -1514.9501
|
||||
60 144.77789 -10.418197 0 -10.399629 134.6083
|
||||
70 108.06164 -10.413487 0 -10.399628 1747.8913
|
||||
80 79.630821 -10.409841 0 -10.399628 2913.2733
|
||||
90 62.795831 -10.407682 0 -10.399628 3646.2528
|
||||
100 57.450965 -10.406996 0 -10.399628 4022.2665
|
||||
Loop time of 0.652565 on 4 procs for 100 steps with 128 atoms
|
||||
|
||||
Performance: 0.903 ns/day, 26.585 hours/ns, 20.897 timesteps/s
|
||||
97.3% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
Performance: 6.620 ns/day, 3.625 hours/ns, 153.241 timesteps/s
|
||||
96.1% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 4.394 | 4.5813 | 4.7463 | 5.9 | 95.74
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.035261 | 0.19515 | 0.38629 | 28.5 | 4.08
|
||||
Output | 0.00031662 | 0.00060844 | 0.0014563 | 0.0 | 0.01
|
||||
Modify | 0.00018692 | 0.0001924 | 0.00020123 | 0.0 | 0.00
|
||||
Other | | 0.008012 | | | 0.17
|
||||
Pair | 0.5462 | 0.57357 | 0.59096 | 2.3 | 87.89
|
||||
Neigh | 8.2016e-05 | 8.3506e-05 | 8.4877e-05 | 0.0 | 0.01
|
||||
Comm | 0.060158 | 0.07569 | 0.10482 | 6.5 | 11.60
|
||||
Output | 0.00015974 | 0.00035232 | 0.00092149 | 0.0 | 0.05
|
||||
Modify | 5.6982e-05 | 6.777e-05 | 7.3671e-05 | 0.0 | 0.01
|
||||
Other | | 0.002799 | | | 0.43
|
||||
|
||||
Nlocal: 32 ave 32 max 32 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 431 ave 431 max 431 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 856.25 ave 885 max 818 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 1 1
|
||||
FullNghs: 1712.5 ave 1738 max 1658 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 2 1
|
||||
Nlocal: 32 ave 33 max 31 min
|
||||
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||
Nghost: 431 ave 432 max 430 min
|
||||
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||
Neighs: 856.25 ave 949 max 794 min
|
||||
Histogram: 1 1 0 0 0 1 0 0 0 1
|
||||
FullNghs: 1712.5 ave 1854 max 1604 min
|
||||
Histogram: 1 0 1 0 0 1 0 0 0 1
|
||||
|
||||
Total # of neighbors = 6850
|
||||
Ave neighs/atom = 53.5156
|
||||
Neighbor list builds = 0
|
||||
Neighbor list builds = 1
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:04
|
||||
Total wall time: 0:00:00
|
||||
@ -28,6 +28,8 @@
|
||||
#include "domain.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
#include "utils.h"
|
||||
#include "fmt/format.h"
|
||||
|
||||
#include "math_const.h"
|
||||
|
||||
@ -63,9 +65,6 @@ MSM::MSM(LAMMPS *lmp) : KSpace(lmp),
|
||||
factors[0] = 2;
|
||||
|
||||
MPI_Comm_rank(world,&me);
|
||||
procneigh_levels = NULL;
|
||||
world_levels = NULL;
|
||||
active_flag = NULL;
|
||||
|
||||
phi1d = dphi1d = NULL;
|
||||
|
||||
@ -81,15 +80,7 @@ MSM::MSM(LAMMPS *lmp) : KSpace(lmp),
|
||||
v0_direct_top = v1_direct_top = v2_direct_top = NULL;
|
||||
v3_direct_top = v4_direct_top = v5_direct_top = NULL;
|
||||
|
||||
cg_all = cg_peratom_all = NULL;
|
||||
cg = cg_peratom = NULL;
|
||||
|
||||
ngrid = NULL;
|
||||
cg = NULL;
|
||||
cg_peratom = NULL;
|
||||
procneigh_levels = NULL;
|
||||
world_levels = NULL;
|
||||
active_flag = NULL;
|
||||
|
||||
alpha = betax = betay = betaz = NULL;
|
||||
nx_msm = ny_msm = nz_msm = NULL;
|
||||
@ -150,10 +141,7 @@ MSM::~MSM()
|
||||
|
||||
void MSM::init()
|
||||
{
|
||||
if (me == 0) {
|
||||
if (screen) fprintf(screen,"MSM initialization ...\n");
|
||||
if (logfile) fprintf(logfile,"MSM initialization ...\n");
|
||||
}
|
||||
if (me == 0) utils::logmesg(lmp,"MSM initialization ...\n");
|
||||
|
||||
// error check
|
||||
|
||||
@ -169,13 +157,8 @@ void MSM::init()
|
||||
if ((slabflag == 1) && (me == 0))
|
||||
error->warning(FLERR,"Slab correction not needed for MSM");
|
||||
|
||||
if (order < 4 || order > 10) {
|
||||
char str[128];
|
||||
sprintf(str,"MSM order must be 4, 6, 8, or 10");
|
||||
error->all(FLERR,str);
|
||||
}
|
||||
|
||||
if (order%2 != 0) error->all(FLERR,"MSM order must be 4, 6, 8, or 10");
|
||||
if ((order < 4) || (order > 10) || (order%2 != 0))
|
||||
error->all(FLERR,"MSM order must be 4, 6, 8, or 10");
|
||||
|
||||
if (sizeof(FFT_SCALAR) != 8)
|
||||
error->all(FLERR,"Cannot (yet) use single precision with MSM "
|
||||
@ -221,33 +204,14 @@ void MSM::init()
|
||||
MPI_Allreduce(&ngrid[0],&ngrid_max,1,MPI_INT,MPI_MAX,world);
|
||||
|
||||
if (me == 0) {
|
||||
if (screen) {
|
||||
fprintf(screen," 3d grid size/proc = %d\n",
|
||||
ngrid_max);
|
||||
fprintf(screen," estimated absolute RMS force accuracy = %g\n",
|
||||
estimated_error);
|
||||
fprintf(screen," estimated relative force accuracy = %g\n",
|
||||
estimated_error/two_charge_force);
|
||||
}
|
||||
if (logfile) {
|
||||
fprintf(logfile," 3d grid size/proc = %d\n",
|
||||
ngrid_max);
|
||||
fprintf(logfile," estimated absolute RMS force accuracy = %g\n",
|
||||
estimated_error);
|
||||
fprintf(logfile," estimated relative force accuracy = %g\n",
|
||||
estimated_error/two_charge_force);
|
||||
}
|
||||
}
|
||||
|
||||
if (me == 0) {
|
||||
if (screen) {
|
||||
fprintf(screen," grid = %d %d %d\n",nx_msm[0],ny_msm[0],nz_msm[0]);
|
||||
fprintf(screen," order = %d\n",order);
|
||||
}
|
||||
if (logfile) {
|
||||
fprintf(logfile," grid = %d %d %d\n",nx_msm[0],ny_msm[0],nz_msm[0]);
|
||||
fprintf(logfile," order = %d\n",order);
|
||||
}
|
||||
std::string mesg = fmt::format(" 3d grid size/proc = {}\n", ngrid_max);
|
||||
mesg += fmt::format(" estimated absolute RMS force accuracy = {}\n",
|
||||
estimated_error);
|
||||
mesg += fmt::format(" estimated relative force accuracy = {}\n",
|
||||
estimated_error/two_charge_force);
|
||||
mesg += fmt::format(" grid = {} {} {}\n",nx_msm[0],ny_msm[0],nz_msm[0]);
|
||||
mesg += fmt::format(" order = {}\n",order);
|
||||
utils::logmesg(lmp,mesg);
|
||||
}
|
||||
}
|
||||
|
||||
@ -398,7 +362,6 @@ void MSM::setup()
|
||||
|
||||
nmax_direct = 8*(nxhi_direct+1)*(nyhi_direct+1)*(nzhi_direct+1);
|
||||
|
||||
deallocate();
|
||||
if (peratom_allocate_flag) deallocate_peratom();
|
||||
|
||||
// compute direct sum interaction weights
|
||||
@ -649,6 +612,8 @@ void MSM::compute(int eflag, int vflag)
|
||||
|
||||
void MSM::allocate()
|
||||
{
|
||||
deallocate();
|
||||
|
||||
// interpolation coeffs
|
||||
|
||||
order_allocated = order;
|
||||
@ -670,9 +635,9 @@ void MSM::allocate()
|
||||
// allocate memory for each grid level
|
||||
|
||||
for (int n=0; n<levels; n++) {
|
||||
|
||||
memory->create3d_offset(qgrid[n],nzlo_out[n],nzhi_out[n],
|
||||
nylo_out[n],nyhi_out[n],nxlo_out[n],nxhi_out[n],"msm:qgrid");
|
||||
|
||||
memory->create3d_offset(egrid[n],nzlo_out[n],nzhi_out[n],
|
||||
nylo_out[n],nyhi_out[n],nxlo_out[n],nxhi_out[n],"msm:egrid");
|
||||
|
||||
@ -685,7 +650,7 @@ void MSM::allocate()
|
||||
nxlo_out[n],nxhi_out[n],nylo_out[n],nyhi_out[n],nzlo_out[n],nzhi_out[n],
|
||||
procneigh[0][0],procneigh[0][1],procneigh[1][0],
|
||||
procneigh[1][1],procneigh[2][0],procneigh[2][1]);
|
||||
}
|
||||
} else cg[n] = nullptr;
|
||||
}
|
||||
}
|
||||
|
||||
@ -695,24 +660,23 @@ void MSM::allocate()
|
||||
|
||||
void MSM::deallocate()
|
||||
{
|
||||
delete cg_all;
|
||||
cg_all = nullptr;
|
||||
|
||||
memory->destroy2d_offset(phi1d,-order_allocated);
|
||||
memory->destroy2d_offset(dphi1d,-order_allocated);
|
||||
|
||||
if (cg_all) delete cg_all;
|
||||
|
||||
for (int n=0; n<levels; n++) {
|
||||
if (qgrid[n])
|
||||
memory->destroy3d_offset(qgrid[n],nzlo_out[n],nylo_out[n],nxlo_out[n]);
|
||||
memory->destroy3d_offset(qgrid[n],nzlo_out[n],nylo_out[n],nxlo_out[n]);
|
||||
memory->destroy3d_offset(egrid[n],nzlo_out[n],nylo_out[n],nxlo_out[n]);
|
||||
|
||||
if (egrid[n])
|
||||
memory->destroy3d_offset(egrid[n],nzlo_out[n],nylo_out[n],nxlo_out[n]);
|
||||
if (world_levels[n] != MPI_COMM_NULL)
|
||||
MPI_Comm_free(&world_levels[n]);
|
||||
world_levels[n] = MPI_COMM_NULL;
|
||||
active_flag[n] = 0;
|
||||
|
||||
if (world_levels)
|
||||
if (world_levels[n] != MPI_COMM_NULL)
|
||||
MPI_Comm_free(&world_levels[n]);
|
||||
|
||||
if (cg)
|
||||
if (cg[n]) delete cg[n];
|
||||
delete cg[n];
|
||||
cg[n] = nullptr;
|
||||
}
|
||||
}
|
||||
|
||||
@ -801,6 +765,7 @@ void MSM::deallocate_peratom()
|
||||
|
||||
void MSM::allocate_levels()
|
||||
{
|
||||
deallocate_levels();
|
||||
ngrid = new int[levels];
|
||||
|
||||
cg = new GridComm*[levels];
|
||||
@ -850,21 +815,21 @@ void MSM::allocate_levels()
|
||||
v5grid = new double***[levels];
|
||||
|
||||
for (int n=0; n<levels; n++) {
|
||||
cg[n] = NULL;
|
||||
cg[n] = nullptr;
|
||||
world_levels[n] = MPI_COMM_NULL;
|
||||
cg_peratom[n] = NULL;
|
||||
active_flag[n] = 0;
|
||||
cg_peratom[n] = nullptr;
|
||||
|
||||
qgrid[n] = NULL;
|
||||
egrid[n] = NULL;
|
||||
qgrid[n] = nullptr;
|
||||
egrid[n] = nullptr;
|
||||
|
||||
v0grid[n] = NULL;
|
||||
v1grid[n] = NULL;
|
||||
v2grid[n] = NULL;
|
||||
v3grid[n] = NULL;
|
||||
v4grid[n] = NULL;
|
||||
v5grid[n] = NULL;
|
||||
v0grid[n] = nullptr;
|
||||
v1grid[n] = nullptr;
|
||||
v2grid[n] = nullptr;
|
||||
v3grid[n] = nullptr;
|
||||
v4grid[n] = nullptr;
|
||||
v5grid[n] = nullptr;
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -873,7 +838,9 @@ void MSM::allocate_levels()
|
||||
|
||||
void MSM::deallocate_levels()
|
||||
{
|
||||
if (cg) deallocate();
|
||||
delete [] ngrid;
|
||||
ngrid = nullptr;
|
||||
|
||||
memory->destroy(procneigh_levels);
|
||||
delete [] world_levels;
|
||||
@ -919,6 +886,50 @@ void MSM::deallocate_levels()
|
||||
delete [] v3grid;
|
||||
delete [] v4grid;
|
||||
delete [] v5grid;
|
||||
|
||||
world_levels = nullptr;
|
||||
active_flag = nullptr;
|
||||
cg = nullptr;
|
||||
cg_peratom = nullptr;
|
||||
|
||||
alpha = nullptr;
|
||||
betax = nullptr;
|
||||
betay = nullptr;
|
||||
betaz = nullptr;
|
||||
|
||||
nx_msm = nullptr;
|
||||
ny_msm = nullptr;
|
||||
nz_msm = nullptr;
|
||||
|
||||
nxlo_in = nullptr;
|
||||
nylo_in = nullptr;
|
||||
nzlo_in = nullptr;
|
||||
|
||||
nxhi_in = nullptr;
|
||||
nyhi_in = nullptr;
|
||||
nzhi_in = nullptr;
|
||||
|
||||
nxlo_out = nullptr;
|
||||
nylo_out = nullptr;
|
||||
nzlo_out = nullptr;
|
||||
|
||||
nxhi_out = nullptr;
|
||||
nyhi_out = nullptr;
|
||||
nzhi_out = nullptr;
|
||||
|
||||
delxinv = nullptr;
|
||||
delyinv = nullptr;
|
||||
delzinv = nullptr;
|
||||
|
||||
qgrid = nullptr;
|
||||
egrid = nullptr;
|
||||
|
||||
v0grid = nullptr;
|
||||
v1grid = nullptr;
|
||||
v2grid = nullptr;
|
||||
v3grid = nullptr;
|
||||
v4grid = nullptr;
|
||||
v5grid = nullptr;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -1053,9 +1064,9 @@ void MSM::set_grid_global()
|
||||
double *p_cutoff = (double *) force->pair->extract("cut_coul",itmp);
|
||||
*p_cutoff = cutoff;
|
||||
|
||||
char str[128];
|
||||
sprintf(str,"Adjusting Coulombic cutoff for MSM, new cutoff = %g",cutoff);
|
||||
if (me == 0) error->warning(FLERR,str);
|
||||
if (me == 0)
|
||||
error->warning(FLERR,fmt::format("Adjusting Coulombic cutoff for "
|
||||
"MSM, new cutoff = {}", cutoff));
|
||||
}
|
||||
|
||||
if (triclinic == 0) {
|
||||
@ -1094,7 +1105,6 @@ void MSM::set_grid_global()
|
||||
|
||||
if (!domain->nonperiodic) levels -= 1;
|
||||
|
||||
deallocate_levels();
|
||||
allocate_levels();
|
||||
|
||||
// find number of grid levels in each direction
|
||||
@ -1318,8 +1328,8 @@ void MSM::set_grid_local()
|
||||
|
||||
void MSM::set_proc_grid(int n)
|
||||
{
|
||||
for (int i=0; i<3; i++)
|
||||
myloc[i] = comm->myloc[i];
|
||||
for (int i=0; i<3; i++)
|
||||
myloc[i] = comm->myloc[i];
|
||||
|
||||
// size of inner MSM grid owned by this proc
|
||||
|
||||
@ -1362,6 +1372,7 @@ void MSM::set_proc_grid(int n)
|
||||
|
||||
// define a new MPI communicator for this grid level that only includes active procs
|
||||
|
||||
if(world_levels[n] != MPI_COMM_NULL) MPI_Comm_free(&world_levels[n]);
|
||||
MPI_Comm_split(world,color,me,&world_levels[n]);
|
||||
|
||||
if (!active_flag[n]) return;
|
||||
@ -1479,16 +1490,13 @@ void MSM::particle_map()
|
||||
|
||||
void MSM::make_rho()
|
||||
{
|
||||
//fprintf(screen,"MSM aninterpolation\n\n");
|
||||
|
||||
int i,l,m,n,nx,ny,nz,mx,my,mz;
|
||||
double dx,dy,dz,x0,y0,z0;
|
||||
|
||||
// clear 3d density array
|
||||
|
||||
double ***qgridn = qgrid[0];
|
||||
|
||||
memset(&(qgridn[nzlo_out[0]][nylo_out[0]][nxlo_out[0]]),0,ngrid[0]*sizeof(double));
|
||||
double ***qgrid0 = qgrid[0];
|
||||
memset(&(qgrid0[nzlo_out[0]][nylo_out[0]][nxlo_out[0]]),0,ngrid[0]*sizeof(double));
|
||||
|
||||
// loop over my charges, add their contribution to nearby grid points
|
||||
// (nx,ny,nz) = global coords of grid pt to "lower left" of charge
|
||||
@ -1519,7 +1527,7 @@ void MSM::make_rho()
|
||||
x0 = y0*phi1d[1][m];
|
||||
for (l = nlower; l <= nupper; l++) {
|
||||
mx = l+nx;
|
||||
qgridn[mz][my][mx] += x0*phi1d[0][l];
|
||||
qgrid0[mz][my][mx] += x0*phi1d[0][l];
|
||||
}
|
||||
}
|
||||
}
|
||||
@ -1534,8 +1542,6 @@ void MSM::make_rho()
|
||||
|
||||
void MSM::direct(int n)
|
||||
{
|
||||
//fprintf(screen,"Direct contribution on level %i\n\n",n);
|
||||
|
||||
double ***qgridn = qgrid[n];
|
||||
double ***egridn = egrid[n];
|
||||
double ***v0gridn = v0grid[n];
|
||||
@ -1768,8 +1774,6 @@ void MSM::direct(int n)
|
||||
|
||||
void MSM::direct_peratom(int n)
|
||||
{
|
||||
//fprintf(screen,"Direct contribution on level %i\n\n",n);
|
||||
|
||||
double ***qgridn = qgrid[n];
|
||||
double ***v0gridn = v0grid[n];
|
||||
double ***v1gridn = v1grid[n];
|
||||
@ -1892,8 +1896,6 @@ void MSM::direct_peratom(int n)
|
||||
|
||||
void MSM::direct_top(int n)
|
||||
{
|
||||
//fprintf(screen,"Direct contribution on level %i\n\n",n);
|
||||
|
||||
double ***qgridn = qgrid[n];
|
||||
double ***egridn = egrid[n];
|
||||
double ***v0gridn = v0grid[n];
|
||||
@ -2257,8 +2259,6 @@ void MSM::direct_peratom_top(int n)
|
||||
|
||||
void MSM::restriction(int n)
|
||||
{
|
||||
//fprintf(screen,"Restricting from level %i to %i\n\n",n,n+1);
|
||||
|
||||
const int p = order-1;
|
||||
|
||||
double ***qgrid1 = qgrid[n];
|
||||
@ -2281,8 +2281,7 @@ void MSM::restriction(int n)
|
||||
|
||||
// zero out charge on coarser grid
|
||||
|
||||
memset(&(qgrid2[nzlo_out[n+1]][nylo_out[n+1]][nxlo_out[n+1]]),0,
|
||||
ngrid[n+1]*sizeof(double));
|
||||
memset(&(qgrid2[nzlo_out[n+1]][nylo_out[n+1]][nxlo_out[n+1]]),0,ngrid[n+1]*sizeof(double));
|
||||
|
||||
for (kp = nzlo_in[n+1]; kp <= nzhi_in[n+1]; kp++)
|
||||
for (jp = nylo_in[n+1]; jp <= nyhi_in[n+1]; jp++)
|
||||
@ -2331,8 +2330,6 @@ void MSM::restriction(int n)
|
||||
|
||||
void MSM::prolongation(int n)
|
||||
{
|
||||
//fprintf(screen,"Prolongating from level %i to %i\n\n",n+1,n);
|
||||
|
||||
const int p = order-1;
|
||||
|
||||
double ***egrid1 = egrid[n];
|
||||
@ -2721,8 +2718,6 @@ void MSM::unpack_reverse(int flag, double *buf, int nlist, int *list)
|
||||
|
||||
void MSM::fieldforce()
|
||||
{
|
||||
//fprintf(screen,"MSM interpolation\n\n");
|
||||
|
||||
double ***egridn = egrid[0];
|
||||
|
||||
int i,l,m,n,nx,ny,nz,mx,my,mz;
|
||||
|
||||
@ -257,12 +257,8 @@ PairBOP::~PairBOP()
|
||||
memory->destroy(gfunc6);
|
||||
memory->destroy(gpara);
|
||||
}
|
||||
if(allocate_sigma) {
|
||||
destroy_sigma();
|
||||
}
|
||||
if(allocate_pi) {
|
||||
destroy_pi();
|
||||
}
|
||||
memory->destroy(bt_sg);
|
||||
memory->destroy(bt_pi);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
@ -635,8 +631,6 @@ void PairBOP::coeff(int narg, char **arg)
|
||||
bop_step=0;
|
||||
nb_pi=0;
|
||||
nb_sg=0;
|
||||
allocate_sigma=0;
|
||||
allocate_pi=0;
|
||||
allocate_neigh=0;
|
||||
update_list=0;
|
||||
maxnall=0;
|
||||
@ -768,19 +762,18 @@ void PairBOP::gneigh()
|
||||
int *type = atom->type;
|
||||
|
||||
if(allocate_neigh==0) {
|
||||
memory->create (BOP_index,nall,"BOP_index");
|
||||
memory->create (BOP_index3,nall,"BOP_index3");
|
||||
memory->create (BOP_total,nall,"BOP_total");
|
||||
memory->create (BOP_total3,nall,"BOP_total");
|
||||
if (otfly==0) memory->create (cos_index,nall,"cos_index");
|
||||
memory->create(BOP_index,nall,"BOP_index");
|
||||
memory->create(BOP_index3,nall,"BOP_index3");
|
||||
memory->create(BOP_total,nall,"BOP_total");
|
||||
memory->create(BOP_total3,nall,"BOP_total");
|
||||
if (otfly==0) memory->create(cos_index,nall,"cos_index");
|
||||
allocate_neigh=1;
|
||||
}
|
||||
else {
|
||||
memory->grow (BOP_index,nall,"BOP_index");
|
||||
memory->grow (BOP_index3,nall,"BOP_index3");
|
||||
memory->grow (BOP_total,nall,"BOP_total");
|
||||
memory->grow (BOP_total3,nall,"BOP_total3");
|
||||
if (otfly==0) memory->grow (cos_index,nall,"cos_index");
|
||||
} else {
|
||||
memory->grow(BOP_index,nall,"BOP_index");
|
||||
memory->grow(BOP_index3,nall,"BOP_index3");
|
||||
memory->grow(BOP_total,nall,"BOP_total");
|
||||
memory->grow(BOP_total3,nall,"BOP_total3");
|
||||
if (otfly==0) memory->grow(cos_index,nall,"cos_index");
|
||||
allocate_neigh=1;
|
||||
}
|
||||
ilist = list->ilist;
|
||||
@ -1140,10 +1133,6 @@ double PairBOP::sigmaBo(int itmp, int jtmp)
|
||||
if(nb_sg==0) {
|
||||
nb_sg=(maxneigh)*(maxneigh/2);
|
||||
}
|
||||
if(allocate_sigma) {
|
||||
destroy_sigma();
|
||||
}
|
||||
|
||||
create_sigma(nb_sg);
|
||||
sigB=0;
|
||||
if(itmp<nlocal) {
|
||||
@ -3798,9 +3787,6 @@ double PairBOP::PiBo(int itmp, int jtmp)
|
||||
|
||||
// Loop over all local atoms for i
|
||||
|
||||
if(allocate_pi) {
|
||||
destroy_pi();
|
||||
}
|
||||
create_pi(nb_pi);
|
||||
piB=0;
|
||||
i = ilist[itmp];
|
||||
@ -4866,7 +4852,6 @@ double PairBOP::PiBo(int itmp, int jtmp)
|
||||
}
|
||||
}
|
||||
}
|
||||
destroy_pi();
|
||||
return(piB);
|
||||
}
|
||||
|
||||
@ -5670,26 +5655,14 @@ void PairBOP::memory_theta_destroy()
|
||||
|
||||
void PairBOP::create_pi(int n_tot)
|
||||
{
|
||||
memory->destroy(bt_pi);
|
||||
bt_pi = (B_PI *) memory->smalloc(n_tot*sizeof(B_PI),"BOP:bt_pi");
|
||||
allocate_pi=1;
|
||||
}
|
||||
|
||||
void PairBOP::create_sigma(int n_tot)
|
||||
{
|
||||
bt_sg = (B_SG *) memory->smalloc(n_tot*sizeof(B_SG),"BOP:bt_sg");
|
||||
allocate_sigma=1;
|
||||
}
|
||||
|
||||
void PairBOP::destroy_pi()
|
||||
{
|
||||
memory->destroy(bt_pi);
|
||||
allocate_pi=0;
|
||||
}
|
||||
|
||||
void PairBOP::destroy_sigma()
|
||||
{
|
||||
memory->destroy(bt_sg);
|
||||
allocate_sigma=0;
|
||||
bt_sg = (B_SG *) memory->smalloc(n_tot*sizeof(B_SG),"BOP:bt_sg");
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
@ -58,8 +58,6 @@ class PairBOP : public Pair {
|
||||
int ***elem2param;
|
||||
int nparams;
|
||||
int bop_step;
|
||||
int allocate_pi;
|
||||
int allocate_sigma;
|
||||
int allocate_neigh;
|
||||
int nb_pi,nb_sg;
|
||||
int ago1;
|
||||
|
||||
@ -1335,6 +1335,18 @@ void PairComb::sm_table()
|
||||
|
||||
// allocate arrays
|
||||
|
||||
memory->sfree(sht_first);
|
||||
memory->destroy(intype);
|
||||
memory->destroy(fafb);
|
||||
memory->destroy(dfafb);
|
||||
memory->destroy(ddfafb);
|
||||
memory->destroy(phin);
|
||||
memory->destroy(dphin);
|
||||
memory->destroy(erpaw);
|
||||
memory->destroy(NCo);
|
||||
memory->destroy(bbij);
|
||||
memory->destroy(sht_num);
|
||||
|
||||
memory->create(intype,n,n,"pair:intype");
|
||||
memory->create(fafb,ncoul,nntypes,"pair:fafb");
|
||||
memory->create(dfafb,ncoul,nntypes,"pair:dfafb");
|
||||
|
||||
@ -2258,6 +2258,26 @@ void PairComb3::tables()
|
||||
|
||||
int n = nelements;
|
||||
|
||||
memory->destroy(intype);
|
||||
memory->destroy(erpaw);
|
||||
memory->destroy(fafb);
|
||||
memory->destroy(dfafb);
|
||||
memory->destroy(ddfafb);
|
||||
memory->destroy(phin);
|
||||
memory->destroy(dphin);
|
||||
memory->destroy(afb);
|
||||
memory->destroy(dafb);
|
||||
memory->destroy(vvdw);
|
||||
memory->destroy(vdvdw);
|
||||
memory->destroy(dpl);
|
||||
memory->destroy(bbij);
|
||||
memory->destroy(xcctmp);
|
||||
memory->destroy(xchtmp);
|
||||
memory->destroy(xcotmp);
|
||||
memory->destroy(NCo);
|
||||
memory->destroy(sht_num);
|
||||
memory->sfree(sht_first);
|
||||
|
||||
dra = 0.001;
|
||||
drin = 0.100;
|
||||
drbuf = 0.100;
|
||||
|
||||
@ -62,7 +62,7 @@ PairEAMCD::~PairEAMCD()
|
||||
{
|
||||
memory->destroy(rhoB);
|
||||
memory->destroy(D_values);
|
||||
if (hcoeff) delete[] hcoeff;
|
||||
delete[] hcoeff;
|
||||
}
|
||||
|
||||
void PairEAMCD::compute(int eflag, int vflag)
|
||||
@ -521,6 +521,7 @@ void PairEAMCD::read_h_coeff(char *filename)
|
||||
if ((int)values.count() != nhcoeff + 1 || nhcoeff < 1)
|
||||
error->one(FLERR, "Failed to read h(x) function coefficients in EAM file.");
|
||||
|
||||
delete[] hcoeff;
|
||||
hcoeff = new double[nhcoeff];
|
||||
|
||||
int i = 0;
|
||||
@ -534,7 +535,10 @@ void PairEAMCD::read_h_coeff(char *filename)
|
||||
}
|
||||
|
||||
MPI_Bcast(&nhcoeff, 1, MPI_INT, 0, world);
|
||||
if (comm->me != 0) hcoeff = new double[nhcoeff];
|
||||
if (comm->me != 0) {
|
||||
delete[] hcoeff;
|
||||
hcoeff = new double[nhcoeff];
|
||||
}
|
||||
MPI_Bcast(hcoeff, nhcoeff, MPI_DOUBLE, 0, world);
|
||||
}
|
||||
|
||||
|
||||
@ -47,26 +47,26 @@ PairPolymorphic::PairPolymorphic(LAMMPS *lmp) : Pair(lmp)
|
||||
one_coeff = 1;
|
||||
|
||||
nelements = 0;
|
||||
elements = NULL;
|
||||
match = NULL;
|
||||
pairParameters = NULL;
|
||||
tripletParameters = NULL;
|
||||
elem2param = NULL;
|
||||
elem3param = NULL;
|
||||
map = NULL;
|
||||
elements = nullptr;
|
||||
match = nullptr;
|
||||
pairParameters = nullptr;
|
||||
tripletParameters = nullptr;
|
||||
elem2param = nullptr;
|
||||
elem3param = nullptr;
|
||||
map = nullptr;
|
||||
epsilon = 0.0;
|
||||
neighsize = 0;
|
||||
firstneighV = NULL;
|
||||
firstneighW = NULL;
|
||||
firstneighW1 = NULL;
|
||||
delxV = NULL;
|
||||
delyV = NULL;
|
||||
delzV = NULL;
|
||||
drV = NULL;
|
||||
delxW = NULL;
|
||||
delyW = NULL;
|
||||
delzW = NULL;
|
||||
drW = NULL;
|
||||
firstneighV = nullptr;
|
||||
firstneighW = nullptr;
|
||||
firstneighW1 = nullptr;
|
||||
delxV = nullptr;
|
||||
delyV = nullptr;
|
||||
delzV = nullptr;
|
||||
drV = nullptr;
|
||||
delxW = nullptr;
|
||||
delyW = nullptr;
|
||||
delzW = nullptr;
|
||||
drW = nullptr;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -79,8 +79,10 @@ PairPolymorphic::~PairPolymorphic()
|
||||
for (int i = 0; i < nelements; i++) delete [] elements[i];
|
||||
delete [] elements;
|
||||
delete [] match;
|
||||
memory->destroy(pairParameters);
|
||||
memory->destroy(tripletParameters);
|
||||
|
||||
delete [] pairParameters;
|
||||
delete [] tripletParameters;
|
||||
|
||||
memory->destroy(elem2param);
|
||||
memory->destroy(elem3param);
|
||||
if (allocated) {
|
||||
@ -487,7 +489,7 @@ void PairPolymorphic::coeff(int narg, char **arg)
|
||||
delete [] elements;
|
||||
}
|
||||
elements = new char*[atom->ntypes];
|
||||
for (i = 0; i < atom->ntypes; i++) elements[i] = NULL;
|
||||
for (i = 0; i < atom->ntypes; i++) elements[i] = nullptr;
|
||||
|
||||
nelements = 0;
|
||||
for (i = 3; i < narg; i++) {
|
||||
@ -581,6 +583,7 @@ void PairPolymorphic::read_file(char *file)
|
||||
eta = values.next_int();
|
||||
|
||||
// map the elements in the potential file to LAMMPS atom types
|
||||
delete [] match;
|
||||
match = new int[nelements];
|
||||
|
||||
for (int i = 0; i < nelements; i++) {
|
||||
@ -617,8 +620,10 @@ void PairPolymorphic::read_file(char *file)
|
||||
// cutoffs
|
||||
npair = nelements*(nelements+1)/2;
|
||||
ntriple = nelements*nelements*nelements;
|
||||
pairParameters = (PairParameters*) memory->srealloc(pairParameters,npair*sizeof(PairParameters), "pair:pairParameters");
|
||||
tripletParameters = (TripletParameters*) memory->srealloc(tripletParameters,ntriple*sizeof(TripletParameters), "pair:tripletParameters");
|
||||
delete [] pairParameters;
|
||||
delete [] tripletParameters;
|
||||
pairParameters = new PairParameters[npair];
|
||||
tripletParameters = new TripletParameters[ntriple];
|
||||
|
||||
for (int i = 0; i < npair; i++) {
|
||||
PairParameters & p = pairParameters[i];
|
||||
@ -641,9 +646,12 @@ void PairPolymorphic::read_file(char *file)
|
||||
MPI_Bcast(&ntriple, 1, MPI_INT, 0, world);
|
||||
|
||||
if(comm->me != 0) {
|
||||
delete [] match;
|
||||
match = new int[nelements];
|
||||
pairParameters = (PairParameters*) memory->srealloc(pairParameters,npair*sizeof(PairParameters), "pair:pairParameters");
|
||||
tripletParameters = (TripletParameters*) memory->srealloc(tripletParameters,ntriple*sizeof(TripletParameters), "pair:tripletParameters");
|
||||
delete [] pairParameters;
|
||||
delete [] tripletParameters;
|
||||
pairParameters = new PairParameters[npair];
|
||||
tripletParameters = new TripletParameters[ntriple];
|
||||
}
|
||||
|
||||
MPI_Bcast(match, nelements, MPI_INT, 0, world);
|
||||
|
||||
@ -50,14 +50,14 @@ class PairPolymorphic : public Pair {
|
||||
xmax = 0.0;
|
||||
xmaxsq = xmax*xmax;
|
||||
vmax = 0.0;
|
||||
xs = NULL;
|
||||
ys = NULL;
|
||||
ys1 = NULL;
|
||||
ys2 = NULL;
|
||||
ys3 = NULL;
|
||||
ys4 = NULL;
|
||||
ys5 = NULL;
|
||||
ys6 = NULL;
|
||||
xs = nullptr;
|
||||
ys = nullptr;
|
||||
ys1 = nullptr;
|
||||
ys2 = nullptr;
|
||||
ys3 = nullptr;
|
||||
ys4 = nullptr;
|
||||
ys5 = nullptr;
|
||||
ys6 = nullptr;
|
||||
}
|
||||
tabularFunction(int n) {
|
||||
size = n;
|
||||
@ -88,14 +88,14 @@ class PairPolymorphic : public Pair {
|
||||
ys6 = new double[n];
|
||||
}
|
||||
virtual ~tabularFunction() {
|
||||
if (xs) delete [] xs;
|
||||
if (ys) delete [] ys;
|
||||
if (ys1) delete [] ys1;
|
||||
if (ys2) delete [] ys2;
|
||||
if (ys3) delete [] ys3;
|
||||
if (ys4) delete [] ys4;
|
||||
if (ys5) delete [] ys5;
|
||||
if (ys6) delete [] ys6;
|
||||
delete [] xs;
|
||||
delete [] ys;
|
||||
delete [] ys1;
|
||||
delete [] ys2;
|
||||
delete [] ys3;
|
||||
delete [] ys4;
|
||||
delete [] ys5;
|
||||
delete [] ys6;
|
||||
}
|
||||
void set_xrange(double x1, double x2) {
|
||||
xmin = x1;
|
||||
@ -198,21 +198,21 @@ class PairPolymorphic : public Pair {
|
||||
void resize(int n) {
|
||||
if (n != size) {
|
||||
size = n;
|
||||
if (xs) delete [] xs;
|
||||
delete [] xs;
|
||||
xs = new double[n];
|
||||
if (ys) delete [] ys;
|
||||
delete [] ys;
|
||||
ys = new double[n];
|
||||
if (ys1) delete [] ys1;
|
||||
delete [] ys1;
|
||||
ys1 = new double[n];
|
||||
if (ys2) delete [] ys2;
|
||||
delete [] ys2;
|
||||
ys2 = new double[n];
|
||||
if (ys3) delete [] ys3;
|
||||
delete [] ys3;
|
||||
ys3 = new double[n];
|
||||
if (ys4) delete [] ys4;
|
||||
delete [] ys4;
|
||||
ys4 = new double[n];
|
||||
if (ys5) delete [] ys5;
|
||||
delete [] ys5;
|
||||
ys5 = new double[n];
|
||||
if (ys6) delete [] ys6;
|
||||
delete [] ys6;
|
||||
ys6 = new double[n];
|
||||
}
|
||||
}
|
||||
@ -248,35 +248,45 @@ class PairPolymorphic : public Pair {
|
||||
}
|
||||
int size;
|
||||
double xmin,xmax,xmaxsq,rdx,vmax;
|
||||
double * ys, * ys1, * ys2, * ys3, * ys4, * ys5, * ys6;
|
||||
double * xs;
|
||||
double *ys, *ys1, *ys2, *ys3, *ys4, *ys5, *ys6;
|
||||
double *xs;
|
||||
};
|
||||
|
||||
struct PairParameters {
|
||||
double cut;
|
||||
double cutsq;
|
||||
double xi;
|
||||
class tabularFunction * U;
|
||||
class tabularFunction * V;
|
||||
class tabularFunction * W;
|
||||
class tabularFunction * F;
|
||||
class tabularFunction *U;
|
||||
class tabularFunction *V;
|
||||
class tabularFunction *W;
|
||||
class tabularFunction *F;
|
||||
PairParameters() {
|
||||
cut = 0.0;
|
||||
cutsq = 0.0;
|
||||
xi = 1.0;
|
||||
U = NULL;
|
||||
V = NULL;
|
||||
W = NULL;
|
||||
F = NULL;
|
||||
U = nullptr;
|
||||
V = nullptr;
|
||||
W = nullptr;
|
||||
F = nullptr;
|
||||
};
|
||||
~PairParameters() {
|
||||
delete U;
|
||||
delete V;
|
||||
delete W;
|
||||
delete F;
|
||||
}
|
||||
};
|
||||
struct TripletParameters {
|
||||
class tabularFunction * P;
|
||||
class tabularFunction * G;
|
||||
class tabularFunction *P;
|
||||
class tabularFunction *G;
|
||||
TripletParameters() {
|
||||
P = NULL;
|
||||
G = NULL;
|
||||
P = nullptr;
|
||||
G = nullptr;
|
||||
};
|
||||
~TripletParameters() {
|
||||
delete P;
|
||||
delete G;
|
||||
}
|
||||
};
|
||||
|
||||
double epsilon;
|
||||
|
||||
@ -23,6 +23,7 @@
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
#include "utils.h"
|
||||
#include "fmt/format.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
@ -82,13 +83,11 @@ void BondFENE::compute(int eflag, int vflag)
|
||||
// if r -> r0, then rlogarg < 0.0 which is an error
|
||||
// issue a warning and reset rlogarg = epsilon
|
||||
// if r > 2*r0 something serious is wrong, abort
|
||||
printf("r = %g r0 = %g rlogarg = %g\n",sqrt(rsq),sqrt(r0sq),rlogarg);
|
||||
|
||||
if (rlogarg < 0.1) {
|
||||
char str[128];
|
||||
sprintf(str,"FENE bond too long: " BIGINT_FORMAT " "
|
||||
TAGINT_FORMAT " " TAGINT_FORMAT " %g",
|
||||
update->ntimestep,atom->tag[i1],atom->tag[i2],sqrt(rsq));
|
||||
error->warning(FLERR,str,0);
|
||||
error->warning(FLERR,fmt::format("FENE bond too long: {} {} {} {}",
|
||||
update->ntimestep,atom->tag[i1],atom->tag[i2],sqrt(rsq)));
|
||||
if (rlogarg <= -3.0) error->one(FLERR,"Bad FENE bond");
|
||||
rlogarg = 0.1;
|
||||
}
|
||||
|
||||
@ -61,14 +61,21 @@ PairTersoffTable::PairTersoffTable(LAMMPS *lmp) : Pair(lmp)
|
||||
manybody_flag = 1;
|
||||
|
||||
nelements = 0;
|
||||
elements = NULL;
|
||||
elements = nullptr;
|
||||
nparams = maxparam = 0;
|
||||
params = NULL;
|
||||
elem2param = NULL;
|
||||
params = nullptr;
|
||||
elem2param = nullptr;
|
||||
allocated = 0;
|
||||
|
||||
preGtetaFunction = preGtetaFunctionDerived = NULL;
|
||||
preCutoffFunction = preCutoffFunctionDerived = NULL;
|
||||
preGtetaFunction = preGtetaFunctionDerived = nullptr;
|
||||
preCutoffFunction = preCutoffFunctionDerived = nullptr;
|
||||
exponential = nullptr;
|
||||
gtetaFunction = nullptr;
|
||||
gtetaFunctionDerived = nullptr;
|
||||
cutoffFunction = nullptr;
|
||||
cutoffFunctionDerived = nullptr;
|
||||
betaZetaPower = nullptr;
|
||||
betaZetaPowerDerived = nullptr;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -88,9 +95,9 @@ PairTersoffTable::~PairTersoffTable()
|
||||
memory->destroy(cutsq);
|
||||
delete [] map;
|
||||
|
||||
deallocateGrids();
|
||||
deallocatePreLoops();
|
||||
}
|
||||
deallocateGrids();
|
||||
deallocatePreLoops();
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
@ -525,13 +532,15 @@ void PairTersoffTable::deallocatePreLoops(void)
|
||||
|
||||
void PairTersoffTable::allocatePreLoops(void)
|
||||
{
|
||||
memory->create(preGtetaFunction,leadingDimensionInteractionList,leadingDimensionInteractionList,"tersofftable:preGtetaFunction");
|
||||
|
||||
memory->create(preGtetaFunctionDerived,leadingDimensionInteractionList,leadingDimensionInteractionList,"tersofftable:preGtetaFunctionDerived");
|
||||
|
||||
memory->create(preCutoffFunction,leadingDimensionInteractionList,"tersofftable:preCutoffFunction");
|
||||
|
||||
memory->create(preCutoffFunctionDerived,leadingDimensionInteractionList,"tersofftable:preCutoffFunctionDerived");
|
||||
deallocatePreLoops();
|
||||
memory->create(preGtetaFunction,leadingDimensionInteractionList,
|
||||
leadingDimensionInteractionList,"tersofftable:preGtetaFunction");
|
||||
memory->create(preGtetaFunctionDerived,leadingDimensionInteractionList,
|
||||
leadingDimensionInteractionList,"tersofftable:preGtetaFunctionDerived");
|
||||
memory->create(preCutoffFunction,leadingDimensionInteractionList,
|
||||
"tersofftable:preCutoffFunction");
|
||||
memory->create(preCutoffFunctionDerived,leadingDimensionInteractionList,
|
||||
"tersofftable:preCutoffFunctionDerived");
|
||||
}
|
||||
|
||||
void PairTersoffTable::deallocateGrids()
|
||||
@ -557,6 +566,8 @@ void PairTersoffTable::allocateGrids(void)
|
||||
double r, minMu, maxLambda, maxCutoff;
|
||||
double const PI=acos(-1.0);
|
||||
|
||||
deallocateGrids();
|
||||
|
||||
// exponential
|
||||
|
||||
// find min and max argument
|
||||
@ -569,9 +580,7 @@ void PairTersoffTable::allocateGrids(void)
|
||||
maxCutoff=cutmax;
|
||||
|
||||
minArgumentExponential=minMu*GRIDSTART;
|
||||
|
||||
numGridPointsExponential=(int)((maxLambda*maxCutoff-minArgumentExponential)*GRIDDENSITY_EXP)+2;
|
||||
|
||||
memory->create(exponential,numGridPointsExponential,"tersofftable:exponential");
|
||||
|
||||
r = minArgumentExponential;
|
||||
|
||||
115
src/atom.cpp
115
src/atom.cpp
@ -249,115 +249,6 @@ Atom::~Atom()
|
||||
delete [] peratom[i].name;
|
||||
memory->sfree(peratom);
|
||||
|
||||
// --------------------------------------------------------------------
|
||||
// 2nd customization section: customize by adding new per-atom variables
|
||||
// delete atom arrays
|
||||
|
||||
memory->destroy(tag);
|
||||
memory->destroy(type);
|
||||
memory->destroy(mask);
|
||||
memory->destroy(image);
|
||||
memory->destroy(x);
|
||||
memory->destroy(v);
|
||||
memory->destroy(f);
|
||||
|
||||
memory->destroy(molecule);
|
||||
memory->destroy(molindex);
|
||||
memory->destroy(molatom);
|
||||
|
||||
memory->destroy(q);
|
||||
memory->destroy(mu);
|
||||
memory->destroy(omega);
|
||||
memory->destroy(angmom);
|
||||
memory->destroy(torque);
|
||||
memory->destroy(radius);
|
||||
memory->destroy(rmass);
|
||||
memory->destroy(ellipsoid);
|
||||
memory->destroy(line);
|
||||
memory->destroy(tri);
|
||||
memory->destroy(body);
|
||||
|
||||
memory->destroy(sp);
|
||||
memory->destroy(fm);
|
||||
memory->destroy(fm_long);
|
||||
|
||||
memory->destroy(vfrac);
|
||||
memory->destroy(s0);
|
||||
memory->destroy(x0);
|
||||
|
||||
memory->destroy(spin);
|
||||
memory->destroy(eradius);
|
||||
memory->destroy(ervel);
|
||||
memory->destroy(erforce);
|
||||
memory->destroy(ervelforce);
|
||||
memory->destroy(cs);
|
||||
memory->destroy(csforce);
|
||||
memory->destroy(vforce);
|
||||
memory->destroy(etag);
|
||||
|
||||
memory->destroy(rho);
|
||||
memory->destroy(drho);
|
||||
memory->destroy(esph);
|
||||
memory->destroy(desph);
|
||||
memory->destroy(cv);
|
||||
memory->destroy(vest);
|
||||
|
||||
// USER-MESONT package
|
||||
memory->destroy(length);
|
||||
memory->destroy(buckling);
|
||||
memory->destroy(bond_nt);
|
||||
|
||||
memory->destroy(contact_radius);
|
||||
memory->destroy(smd_data_9);
|
||||
memory->destroy(smd_stress);
|
||||
memory->destroy(eff_plastic_strain);
|
||||
memory->destroy(eff_plastic_strain_rate);
|
||||
memory->destroy(damage);
|
||||
|
||||
memory->destroy(dpdTheta);
|
||||
memory->destroy(uCond);
|
||||
memory->destroy(uMech);
|
||||
memory->destroy(uChem);
|
||||
memory->destroy(uCG);
|
||||
memory->destroy(uCGnew);
|
||||
memory->destroy(duChem);
|
||||
|
||||
memory->destroy(cc);
|
||||
memory->destroy(cc_flux);
|
||||
memory->destroy(edpd_temp);
|
||||
memory->destroy(edpd_flux);
|
||||
memory->destroy(edpd_cv);
|
||||
|
||||
memory->destroy(nspecial);
|
||||
memory->destroy(special);
|
||||
|
||||
memory->destroy(num_bond);
|
||||
memory->destroy(bond_type);
|
||||
memory->destroy(bond_atom);
|
||||
|
||||
memory->destroy(num_angle);
|
||||
memory->destroy(angle_type);
|
||||
memory->destroy(angle_atom1);
|
||||
memory->destroy(angle_atom2);
|
||||
memory->destroy(angle_atom3);
|
||||
|
||||
memory->destroy(num_dihedral);
|
||||
memory->destroy(dihedral_type);
|
||||
memory->destroy(dihedral_atom1);
|
||||
memory->destroy(dihedral_atom2);
|
||||
memory->destroy(dihedral_atom3);
|
||||
memory->destroy(dihedral_atom4);
|
||||
|
||||
memory->destroy(num_improper);
|
||||
memory->destroy(improper_type);
|
||||
memory->destroy(improper_atom1);
|
||||
memory->destroy(improper_atom2);
|
||||
memory->destroy(improper_atom3);
|
||||
memory->destroy(improper_atom4);
|
||||
|
||||
// end of customization section
|
||||
// --------------------------------------------------------------------
|
||||
|
||||
// delete custom atom arrays
|
||||
|
||||
for (int i = 0; i < nivector; i++) {
|
||||
@ -430,7 +321,7 @@ void Atom::peratom_create()
|
||||
nperatom = maxperatom = 0;
|
||||
|
||||
// --------------------------------------------------------------------
|
||||
// 3rd customization section: add peratom variables here, order does not matter
|
||||
// 2nd customization section: add peratom variables here, order does not matter
|
||||
// register tagint & imageint variables as INT or BIGINT
|
||||
|
||||
int tagintsize = INT;
|
||||
@ -671,7 +562,7 @@ void Atom::add_peratom_vary(const char *name, void *address,
|
||||
void Atom::set_atomflag_defaults()
|
||||
{
|
||||
// --------------------------------------------------------------------
|
||||
// 4th customization section: customize by adding new flag
|
||||
// 3rd customization section: customize by adding new flag
|
||||
// identical list as 2nd customization in atom.h
|
||||
|
||||
sphere_flag = ellipsoid_flag = line_flag = tri_flag = body_flag = 0;
|
||||
@ -2462,7 +2353,7 @@ void Atom::remove_custom(int flag, int index)
|
||||
void *Atom::extract(char *name)
|
||||
{
|
||||
// --------------------------------------------------------------------
|
||||
// 5th customization section: customize by adding new variable name
|
||||
// 4th customization section: customize by adding new variable name
|
||||
|
||||
if (strcmp(name,"mass") == 0) return (void *) mass;
|
||||
|
||||
|
||||
@ -90,9 +90,51 @@ AtomVec::AtomVec(LAMMPS *lmp) : Pointers(lmp)
|
||||
|
||||
AtomVec::~AtomVec()
|
||||
{
|
||||
int datatype,cols;
|
||||
void *pdata;
|
||||
|
||||
for (int i = 0; i < nargcopy; i++) delete [] argcopy[i];
|
||||
delete [] argcopy;
|
||||
|
||||
memory->destroy(atom->tag);
|
||||
memory->destroy(atom->type);
|
||||
memory->destroy(atom->mask);
|
||||
memory->destroy(atom->image);
|
||||
memory->destroy(atom->x);
|
||||
memory->destroy(atom->v);
|
||||
memory->destroy(atom->f);
|
||||
|
||||
for (int i = 0; i < ngrow; i++) {
|
||||
pdata = mgrow.pdata[i];
|
||||
datatype = mgrow.datatype[i];
|
||||
cols = mgrow.cols[i];
|
||||
if (datatype == Atom::DOUBLE) {
|
||||
if (cols == 0)
|
||||
memory->destroy(*((double **) pdata));
|
||||
else if (cols > 0)
|
||||
memory->destroy(*((double ***) pdata));
|
||||
else {
|
||||
memory->destroy(*((double ***) pdata));
|
||||
}
|
||||
} else if (datatype == Atom::INT) {
|
||||
if (cols == 0)
|
||||
memory->destroy(*((int **) pdata));
|
||||
else if (cols > 0)
|
||||
memory->destroy(*((int ***) pdata));
|
||||
else {
|
||||
memory->destroy(*((int ***) pdata));
|
||||
}
|
||||
} else if (datatype == Atom::BIGINT) {
|
||||
if (cols == 0)
|
||||
memory->destroy(*((bigint **) pdata));
|
||||
else if (cols > 0)
|
||||
memory->destroy(*((bigint ***) pdata));
|
||||
else {
|
||||
memory->destroy(*((bigint ***) pdata));
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
destroy_method(&mgrow);
|
||||
destroy_method(&mcopy);
|
||||
destroy_method(&mcomm);
|
||||
@ -2335,9 +2377,9 @@ void AtomVec::setup_fields()
|
||||
{
|
||||
int n,cols;
|
||||
|
||||
if (strstr(fields_data_atom,"id ") != fields_data_atom)
|
||||
if (!utils::strmatch(fields_data_atom,"^id "))
|
||||
error->all(FLERR,"Atom style fields_data_atom must have id as first field");
|
||||
if (strstr(fields_data_vel,"id v") != fields_data_vel)
|
||||
if (!utils::strmatch(fields_data_vel,"^id v"))
|
||||
error->all(FLERR,"Atom style fields_data_vel must have "
|
||||
"'id v' as first fields");
|
||||
|
||||
@ -2469,31 +2511,21 @@ int AtomVec::process_fields(char *str, const char *default_str, Method *method)
|
||||
|
||||
for (match = 0; match < nperatom; match++)
|
||||
if (strcmp(field, peratom[match].name) == 0) break;
|
||||
if (match == nperatom) {
|
||||
char str[128];
|
||||
sprintf(str,"Peratom field %s not recognized", field);
|
||||
error->all(FLERR,str);
|
||||
}
|
||||
if (match == nperatom)
|
||||
error->all(FLERR,fmt::format("Peratom field {} not recognized", field));
|
||||
index[i] = match;
|
||||
|
||||
// error if field appears multiple times
|
||||
|
||||
for (match = 0; match < i; match++)
|
||||
if (index[i] == index[match]) {
|
||||
char str[128];
|
||||
sprintf(str,"Peratom field %s is repeated", field);
|
||||
error->all(FLERR,str);
|
||||
}
|
||||
if (index[i] == index[match])
|
||||
error->all(FLERR,fmt::format("Peratom field {} is repeated", field));
|
||||
|
||||
// error if field is in default str
|
||||
|
||||
for (match = 0; match < ndef; match++)
|
||||
if (strcmp(field, def_words[match].c_str()) == 0) {
|
||||
char str[128];
|
||||
sprintf(str,"Peratom field %s is a default", field);
|
||||
error->all(FLERR,str);
|
||||
}
|
||||
|
||||
if (strcmp(field, def_words[match].c_str()) == 0)
|
||||
error->all(FLERR,fmt::format("Peratom field {} is a default", field));
|
||||
}
|
||||
|
||||
method->index = index;
|
||||
|
||||
23
src/comm.cpp
23
src/comm.cpp
@ -901,7 +901,9 @@ rendezvous_irregular(int n, char *inbuf, int insize, int inorder, int *procs,
|
||||
if (inorder) nrvous = irregular->create_data_grouped(n,procs);
|
||||
else nrvous = irregular->create_data(n,procs);
|
||||
|
||||
char *inbuf_rvous = (char *) memory->smalloc((bigint) nrvous*insize,
|
||||
// add 1 item to the allocated buffer size, so the returned pointer is not NULL
|
||||
|
||||
char *inbuf_rvous = (char *) memory->smalloc((bigint) nrvous*insize+1,
|
||||
"rendezvous:inbuf");
|
||||
irregular->exchange_data(inbuf,insize,inbuf_rvous);
|
||||
|
||||
@ -936,7 +938,9 @@ rendezvous_irregular(int n, char *inbuf, int insize, int inorder, int *procs,
|
||||
nout = irregular->create_data_grouped(nrvous_out,procs_rvous);
|
||||
else nout = irregular->create_data(nrvous_out,procs_rvous);
|
||||
|
||||
outbuf = (char *) memory->smalloc((bigint) nout*outsize,
|
||||
// add 1 item to the allocated buffer size, so the returned pointer is not NULL
|
||||
|
||||
outbuf = (char *) memory->smalloc((bigint) nout*outsize+1,
|
||||
"rendezvous:outbuf");
|
||||
irregular->exchange_data(outbuf_rvous,outsize,outbuf);
|
||||
|
||||
@ -975,7 +979,10 @@ rendezvous_all2all(int n, char *inbuf, int insize, int inorder, int *procs,
|
||||
|
||||
if (!inorder) {
|
||||
memory->create(procs_a2a,nprocs,"rendezvous:procs");
|
||||
inbuf_a2a = (char *) memory->smalloc((bigint) n*insize,
|
||||
|
||||
// add 1 item to the allocated buffer size, so the returned pointer is not NULL
|
||||
|
||||
inbuf_a2a = (char *) memory->smalloc((bigint) n*insize+1,
|
||||
"rendezvous:inbuf");
|
||||
memset(inbuf_a2a,0,(bigint)n*insize*sizeof(char));
|
||||
memory->create(offsets,nprocs,"rendezvous:offsets");
|
||||
@ -1038,8 +1045,9 @@ rendezvous_all2all(int n, char *inbuf, int insize, int inorder, int *procs,
|
||||
}
|
||||
|
||||
// all2all comm of inbuf from caller decomp to rendezvous decomp
|
||||
// add 1 item to the allocated buffer size, so the returned pointer is not NULL
|
||||
|
||||
char *inbuf_rvous = (char *) memory->smalloc((bigint) nrvous*insize,
|
||||
char *inbuf_rvous = (char *) memory->smalloc((bigint) nrvous*insize+1,
|
||||
"rendezvous:inbuf");
|
||||
memset(inbuf_rvous,0,(bigint) nrvous*insize*sizeof(char));
|
||||
|
||||
@ -1079,7 +1087,9 @@ rendezvous_all2all(int n, char *inbuf, int insize, int inorder, int *procs,
|
||||
if (!outorder) {
|
||||
memory->create(procs_a2a,nprocs,"rendezvous_a2a:procs");
|
||||
|
||||
outbuf_a2a = (char *) memory->smalloc((bigint) nrvous_out*outsize,
|
||||
// add 1 item to the allocated buffer size, so the returned pointer is not NULL
|
||||
|
||||
outbuf_a2a = (char *) memory->smalloc((bigint) nrvous_out*outsize+1,
|
||||
"rendezvous:outbuf");
|
||||
memory->create(offsets,nprocs,"rendezvous:offsets");
|
||||
|
||||
@ -1138,8 +1148,9 @@ rendezvous_all2all(int n, char *inbuf, int insize, int inorder, int *procs,
|
||||
|
||||
// all2all comm of outbuf from rendezvous decomp back to caller decomp
|
||||
// caller will free outbuf
|
||||
// add 1 item to the allocated buffer size, so the returned pointer is not NULL
|
||||
|
||||
outbuf = (char *) memory->smalloc((bigint) nout*outsize,"rendezvous:outbuf");
|
||||
outbuf = (char *) memory->smalloc((bigint) nout*outsize+1,"rendezvous:outbuf");
|
||||
|
||||
MPI_Alltoallv(outbuf_a2a,sendcount,sdispls,MPI_CHAR,
|
||||
outbuf,recvcount,rdispls,MPI_CHAR,world);
|
||||
|
||||
@ -193,7 +193,7 @@ void CreateAtoms::command(int narg, char **arg)
|
||||
if (iarg+5 > narg) error->all(FLERR,"Illegal create_atoms command");
|
||||
double thetaone;
|
||||
double axisone[3];
|
||||
thetaone = force->numeric(FLERR,arg[iarg+1]);
|
||||
thetaone = force->numeric(FLERR,arg[iarg+1]) / 180.0 * MY_PI;;
|
||||
axisone[0] = force->numeric(FLERR,arg[iarg+2]);
|
||||
axisone[1] = force->numeric(FLERR,arg[iarg+3]);
|
||||
axisone[2] = force->numeric(FLERR,arg[iarg+4]);
|
||||
|
||||
@ -107,6 +107,7 @@ void Error::universe_one(const std::string &file, int line, const std::string &s
|
||||
throw LAMMPSAbortException(mesg, universe->uworld);
|
||||
#else
|
||||
MPI_Abort(universe->uworld,1);
|
||||
exit(1); // to trick "smart" compilers into believing this does not return
|
||||
#endif
|
||||
}
|
||||
|
||||
@ -205,6 +206,7 @@ void Error::one(const std::string &file, int line, const std::string &str)
|
||||
if (screen) fflush(screen);
|
||||
if (logfile) fflush(logfile);
|
||||
MPI_Abort(world,1);
|
||||
exit(1); // to trick "smart" compilers into believing this does not return
|
||||
#endif
|
||||
}
|
||||
|
||||
|
||||
12
src/error.h
12
src/error.h
@ -27,20 +27,20 @@ class Error : protected Pointers {
|
||||
public:
|
||||
Error(class LAMMPS *);
|
||||
|
||||
void universe_all(const std::string &, int, const std::string &);
|
||||
void universe_one(const std::string &, int, const std::string &);
|
||||
[[ noreturn ]] void universe_all(const std::string &, int, const std::string &);
|
||||
[[ noreturn ]] void universe_one(const std::string &, int, const std::string &);
|
||||
void universe_warn(const std::string &, int, const std::string &);
|
||||
|
||||
void all(const std::string &, int, const std::string &);
|
||||
void one(const std::string &, int, const std::string &);
|
||||
[[ noreturn ]] void all(const std::string &, int, const std::string &);
|
||||
[[ noreturn ]] void one(const std::string &, int, const std::string &);
|
||||
void warning(const std::string &, int, const std::string &, int = 1);
|
||||
void message(const std::string &, int, const std::string &, int = 1);
|
||||
void done(int = 0); // 1 would be fully backwards compatible
|
||||
[[ noreturn ]] void done(int = 0); // 1 would be fully backwards compatible
|
||||
|
||||
#ifdef LAMMPS_EXCEPTIONS
|
||||
std::string get_last_error() const;
|
||||
ErrorType get_last_error_type() const;
|
||||
void set_last_error(const std::string &msg, ErrorType type = ERROR_NORMAL);
|
||||
void set_last_error(const std::string &msg, ErrorType type = ERROR_NORMAL);
|
||||
|
||||
private:
|
||||
std::string last_error_message;
|
||||
|
||||
@ -34,6 +34,7 @@
|
||||
#include "improper.h"
|
||||
#include "kspace.h"
|
||||
#include "error.h"
|
||||
#include "update.h"
|
||||
#include "utils.h"
|
||||
#include "fmt/format.h"
|
||||
|
||||
@ -1013,15 +1014,20 @@ tagint Force::tnumeric(const char *file, int line, char *str)
|
||||
FILE *Force::open_potential(const char *name)
|
||||
{
|
||||
std::string filepath = utils::get_potential_file_path(name);
|
||||
std::string date;
|
||||
|
||||
if(!filepath.empty()) {
|
||||
date = utils::get_potential_date(filepath, "potential");
|
||||
std::string unit_style = update->unit_style;
|
||||
std::string date = utils::get_potential_date(filepath, "potential");
|
||||
std::string units = utils::get_potential_units(filepath, "potential");
|
||||
|
||||
if(!date.empty()) {
|
||||
utils::logmesg(lmp, fmt::format("Reading potential file {} "
|
||||
"with DATE: {}\n", name, date));
|
||||
}
|
||||
if (!units.empty() && (units != unit_style)) {
|
||||
error->one(FLERR, fmt::format("Potential file {} requires {} units "
|
||||
"but {} units are in use", name, units, unit_style));
|
||||
}
|
||||
return fopen(filepath.c_str(), "r");
|
||||
}
|
||||
return nullptr;
|
||||
|
||||
@ -24,6 +24,7 @@ class Input : protected Pointers {
|
||||
friend class Info;
|
||||
friend class Error;
|
||||
friend class Deprecated;
|
||||
friend class SimpleCommandsTest_Echo_Test;
|
||||
|
||||
public:
|
||||
int narg; // # of command args
|
||||
|
||||
@ -1,10 +1,9 @@
|
||||
include(GTest)
|
||||
|
||||
add_subdirectory(force-styles)
|
||||
|
||||
add_subdirectory(utils)
|
||||
|
||||
add_subdirectory(formats)
|
||||
add_subdirectory(commands)
|
||||
|
||||
find_package(ClangFormat 8.0)
|
||||
|
||||
|
||||
4
unittest/commands/CMakeLists.txt
Normal file
4
unittest/commands/CMakeLists.txt
Normal file
@ -0,0 +1,4 @@
|
||||
|
||||
add_executable(test_simple_commands test_simple_commands.cpp)
|
||||
target_link_libraries(test_simple_commands PRIVATE lammps GTest::GMock GTest::GTest)
|
||||
add_test(NAME TestSimpleCommands COMMAND test_simple_commands WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
|
||||
135
unittest/commands/test_simple_commands.cpp
Normal file
135
unittest/commands/test_simple_commands.cpp
Normal file
@ -0,0 +1,135 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "input.h"
|
||||
#include "lammps.h"
|
||||
#include "utils.h"
|
||||
#include "gmock/gmock.h"
|
||||
#include "gtest/gtest.h"
|
||||
|
||||
#include <cstdio>
|
||||
#include <cstring>
|
||||
#include <fstream>
|
||||
#include <iostream>
|
||||
#include <mpi.h>
|
||||
|
||||
// whether to print verbose output (i.e. not capturing LAMMPS screen output).
|
||||
bool verbose = false;
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
using ::testing::Eq;
|
||||
|
||||
class SimpleCommandsTest : public ::testing::Test {
|
||||
protected:
|
||||
LAMMPS *lmp;
|
||||
|
||||
void SetUp() override
|
||||
{
|
||||
const char *args[] = {"SimpleCommandsTest", "-log", "none", "-echo", "screen", "-nocite"};
|
||||
char **argv = (char **)args;
|
||||
int argc = sizeof(args) / sizeof(char *);
|
||||
if (!verbose) ::testing::internal::CaptureStdout();
|
||||
lmp = new LAMMPS(argc, argv, MPI_COMM_WORLD);
|
||||
if (!verbose) ::testing::internal::GetCapturedStdout();
|
||||
}
|
||||
|
||||
void TearDown() override
|
||||
{
|
||||
if (!verbose) ::testing::internal::CaptureStdout();
|
||||
delete lmp;
|
||||
if (!verbose) ::testing::internal::GetCapturedStdout();
|
||||
}
|
||||
};
|
||||
|
||||
TEST_F(SimpleCommandsTest, Echo)
|
||||
{
|
||||
ASSERT_EQ(lmp->input->echo_screen, 1);
|
||||
ASSERT_EQ(lmp->input->echo_log, 0);
|
||||
|
||||
if (!verbose) ::testing::internal::CaptureStdout();
|
||||
lmp->input->one("echo none");
|
||||
if (!verbose) ::testing::internal::GetCapturedStdout();
|
||||
ASSERT_EQ(lmp->input->echo_screen, 0);
|
||||
ASSERT_EQ(lmp->input->echo_log, 0);
|
||||
|
||||
if (!verbose) ::testing::internal::CaptureStdout();
|
||||
lmp->input->one("echo both");
|
||||
if (!verbose) ::testing::internal::GetCapturedStdout();
|
||||
ASSERT_EQ(lmp->input->echo_screen, 1);
|
||||
ASSERT_EQ(lmp->input->echo_log, 1);
|
||||
|
||||
if (!verbose) ::testing::internal::CaptureStdout();
|
||||
lmp->input->one("echo screen");
|
||||
if (!verbose) ::testing::internal::GetCapturedStdout();
|
||||
ASSERT_EQ(lmp->input->echo_screen, 1);
|
||||
ASSERT_EQ(lmp->input->echo_log, 0);
|
||||
|
||||
if (!verbose) ::testing::internal::CaptureStdout();
|
||||
lmp->input->one("echo log");
|
||||
if (!verbose) ::testing::internal::GetCapturedStdout();
|
||||
ASSERT_EQ(lmp->input->echo_screen, 0);
|
||||
ASSERT_EQ(lmp->input->echo_log, 1);
|
||||
}
|
||||
|
||||
TEST_F(SimpleCommandsTest, Log)
|
||||
{
|
||||
ASSERT_EQ(lmp->logfile, nullptr);
|
||||
|
||||
if (!verbose) ::testing::internal::CaptureStdout();
|
||||
lmp->input->one("log simple_command_test.log");
|
||||
lmp->input->one("print 'test1'");
|
||||
if (!verbose) ::testing::internal::GetCapturedStdout();
|
||||
ASSERT_NE(lmp->logfile, nullptr);
|
||||
|
||||
if (!verbose) ::testing::internal::CaptureStdout();
|
||||
lmp->input->one("log none");
|
||||
if (!verbose) ::testing::internal::GetCapturedStdout();
|
||||
ASSERT_EQ(lmp->logfile, nullptr);
|
||||
|
||||
std::string text;
|
||||
std::ifstream in;
|
||||
in.open("simple_command_test.log");
|
||||
in >> text;
|
||||
in.close();
|
||||
ASSERT_THAT(text, Eq("test1"));
|
||||
|
||||
if (!verbose) ::testing::internal::CaptureStdout();
|
||||
lmp->input->one("log simple_command_test.log append");
|
||||
lmp->input->one("print 'test2'");
|
||||
if (!verbose) ::testing::internal::GetCapturedStdout();
|
||||
ASSERT_NE(lmp->logfile, nullptr);
|
||||
if (!verbose) ::testing::internal::CaptureStdout();
|
||||
lmp->input->one("log none");
|
||||
if (!verbose) ::testing::internal::GetCapturedStdout();
|
||||
ASSERT_EQ(lmp->logfile, nullptr);
|
||||
|
||||
in.open("simple_command_test.log");
|
||||
in >> text;
|
||||
ASSERT_THAT(text, Eq("test1"));
|
||||
in >> text;
|
||||
ASSERT_THAT(text, Eq("test2"));
|
||||
in.close();
|
||||
remove("simple_command_test.log");
|
||||
}
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
int main(int argc, char **argv)
|
||||
{
|
||||
MPI_Init(&argc, &argv);
|
||||
::testing::InitGoogleMock(&argc, argv);
|
||||
if ((argc > 1) && (strcmp(argv[1], "-v") == 0)) verbose = true;
|
||||
|
||||
int rv = RUN_ALL_TESTS();
|
||||
MPI_Finalize();
|
||||
return rv;
|
||||
}
|
||||
@ -15,6 +15,13 @@ if(BUILD_MPI)
|
||||
else()
|
||||
target_link_libraries(style_tests PUBLIC mpi_stubs)
|
||||
endif()
|
||||
# propagate sanitizer options to test tools
|
||||
if (NOT ENABLE_SANITIZER STREQUAL "none")
|
||||
if(CMAKE_VERSION VERSION_GREATER_EQUAL 3.13)
|
||||
target_compile_options(style_tests PUBLIC -fsanitize=${ENABLE_SANITIZER})
|
||||
target_link_options(style_tests PUBLIC -fsanitize=${ENABLE_SANITIZER})
|
||||
endif()
|
||||
endif()
|
||||
|
||||
# unit test for error stats class
|
||||
add_executable(test_error_stats test_error_stats.cpp)
|
||||
|
||||
@ -87,8 +87,8 @@ LAMMPS *init_lammps(int argc, char **argv, const TestConfig &cfg, const bool new
|
||||
|
||||
if (!info->has_style(prerequisite.first, style)) ++nfail;
|
||||
}
|
||||
delete info;
|
||||
if (nfail > 0) {
|
||||
delete info;
|
||||
cleanup_lammps(lmp, cfg);
|
||||
return nullptr;
|
||||
}
|
||||
|
||||
@ -87,8 +87,8 @@ LAMMPS *init_lammps(int argc, char **argv, const TestConfig &cfg, const bool new
|
||||
|
||||
if (!info->has_style(prerequisite.first, style)) ++nfail;
|
||||
}
|
||||
delete info;
|
||||
if (nfail > 0) {
|
||||
delete info;
|
||||
cleanup_lammps(lmp, cfg);
|
||||
return nullptr;
|
||||
}
|
||||
|
||||
@ -87,8 +87,8 @@ LAMMPS *init_lammps(int argc, char **argv, const TestConfig &cfg, const bool new
|
||||
|
||||
if (!info->has_style(prerequisite.first, style)) ++nfail;
|
||||
}
|
||||
delete info;
|
||||
if (nfail > 0) {
|
||||
delete info;
|
||||
cleanup_lammps(lmp, cfg);
|
||||
return nullptr;
|
||||
}
|
||||
|
||||
@ -14,6 +14,7 @@
|
||||
#include "test_main.h"
|
||||
#include "test_config.h"
|
||||
#include "test_config_reader.h"
|
||||
#include "gmock/gmock.h"
|
||||
#include "gtest/gtest.h"
|
||||
|
||||
#include <cstring>
|
||||
@ -63,7 +64,7 @@ std::string INPUT_FOLDER = STRINGIFY(TEST_INPUT_FOLDER);
|
||||
int main(int argc, char **argv)
|
||||
{
|
||||
MPI_Init(&argc, &argv);
|
||||
::testing::InitGoogleTest(&argc, argv);
|
||||
::testing::InitGoogleMock(&argc, argv);
|
||||
|
||||
if (argc < 2) {
|
||||
usage(std::cerr, argv[0]);
|
||||
@ -109,5 +110,8 @@ int main(int argc, char **argv)
|
||||
return 1;
|
||||
}
|
||||
}
|
||||
return RUN_ALL_TESTS();
|
||||
|
||||
int rv = RUN_ALL_TESTS();
|
||||
MPI_Finalize();
|
||||
return rv;
|
||||
}
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
---
|
||||
lammps_version: 5 May 2020
|
||||
date_generated: Tue May 26 21:02:07 202
|
||||
epsilon: 5.0e-12
|
||||
epsilon: 1.0e-11
|
||||
prerequisites: ! |
|
||||
pair eim
|
||||
pre_commands: ! ""
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
---
|
||||
lammps_version: 5 May 2020
|
||||
date_generated: Wed May 27 16:13:46 202
|
||||
epsilon: 2e-7
|
||||
epsilon: 5e-6
|
||||
prerequisites: ! |
|
||||
pair airebo
|
||||
pre_commands: ! |
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
---
|
||||
lammps_version: 5 May 2020
|
||||
date_generated: Thu May 28 20:29:01 202
|
||||
epsilon: 1e-12
|
||||
epsilon: 1e-11
|
||||
prerequisites: ! |
|
||||
pair polymorphic
|
||||
pre_commands: ! |
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
---
|
||||
lammps_version: 5 May 2020
|
||||
date_generated: Wed May 27 10:27:56 202
|
||||
epsilon: 1e-12
|
||||
epsilon: 5e-11
|
||||
prerequisites: ! |
|
||||
pair tersoff/mod
|
||||
pre_commands: ! |
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
---
|
||||
lammps_version: 5 May 2020
|
||||
date_generated: Wed May 27 10:28:17 202
|
||||
epsilon: 5e-13
|
||||
epsilon: 1e-12
|
||||
prerequisites: ! |
|
||||
pair tersoff/mod/c
|
||||
pre_commands: ! |
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
---
|
||||
lammps_version: 5 May 2020
|
||||
date_generated: Wed May 27 12:29:41 202
|
||||
epsilon: 5e-12
|
||||
epsilon: 5e-11
|
||||
prerequisites: ! |
|
||||
pair tersoff/table
|
||||
pre_commands: ! |
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
---
|
||||
lammps_version: 5 May 2020
|
||||
date_generated: Wed May 27 10:29:02 202
|
||||
epsilon: 5e-12
|
||||
epsilon: 5e-11
|
||||
prerequisites: ! |
|
||||
pair tersoff/zbl
|
||||
pre_commands: ! |
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
---
|
||||
lammps_version: 2 Jun 2020
|
||||
date_generated: Sun Jun 14 14:42:09 202
|
||||
epsilon: 2e-13
|
||||
epsilon: 1e-12
|
||||
prerequisites: ! |
|
||||
atom full
|
||||
pair coul/dsf
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
---
|
||||
lammps_version: 5 May 2020
|
||||
date_generated: Sat May 30 18:04:12 202
|
||||
epsilon: 5e-13
|
||||
epsilon: 5e-12
|
||||
prerequisites: ! |
|
||||
atom full
|
||||
pair lj/class2/coul/cut
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
---
|
||||
lammps_version: 5 May 2020
|
||||
date_generated: Fri May 15 19:08:06 202
|
||||
epsilon: 5.0e-13
|
||||
epsilon: 5.0e-12
|
||||
prerequisites: ! |
|
||||
atom full
|
||||
pair lj/class2/coul/long
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
---
|
||||
lammps_version: 5 May 2020
|
||||
date_generated: Fri May 15 19:08:06 202
|
||||
epsilon: 5.0e-13
|
||||
epsilon: 5.0e-12
|
||||
prerequisites: ! |
|
||||
atom full
|
||||
pair lj/class2/coul/long
|
||||
|
||||
@ -1,3 +1,8 @@
|
||||
|
||||
add_executable(test_atom_styles test_atom_styles.cpp)
|
||||
target_link_libraries(test_atom_styles PRIVATE lammps GTest::GMock GTest::GTest)
|
||||
add_test(NAME AtomStyles COMMAND test_atom_styles WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
|
||||
|
||||
add_executable(test_potential_file_reader test_potential_file_reader.cpp)
|
||||
target_link_libraries(test_potential_file_reader PRIVATE lammps GTest::GMock GTest::GTest)
|
||||
add_test(NAME PotentialFileReader COMMAND test_potential_file_reader WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
|
||||
|
||||
756
unittest/formats/test_atom_styles.cpp
Normal file
756
unittest/formats/test_atom_styles.cpp
Normal file
@ -0,0 +1,756 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "atom.h"
|
||||
#include "input.h"
|
||||
#include "lammps.h"
|
||||
#include "utils.h"
|
||||
#include "gmock/gmock.h"
|
||||
#include "gtest/gtest.h"
|
||||
|
||||
#include <cstdio>
|
||||
#include <cstring>
|
||||
#include <mpi.h>
|
||||
|
||||
#if !defined(_FORTIFY_SOURCE) || (_FORTIFY_SOURCE == 0)
|
||||
#if defined(__INTEL_COMPILER)
|
||||
#define _do_nothing
|
||||
#elif defined(__GNUC__)
|
||||
#if (__GNUC__ > 4) || ((__GNUC__ == 4) && (__GNUC_MINOR__ >= 9))
|
||||
#pragma GCC optimize("no-var-tracking-assignments", "O0")
|
||||
#else
|
||||
#pragma GCC optimize("no-var-tracking-assignments")
|
||||
#endif
|
||||
#else
|
||||
#define _do_nothing
|
||||
#endif
|
||||
#endif
|
||||
|
||||
// whether to print verbose output (i.e. not capturing LAMMPS screen output).
|
||||
bool verbose = false;
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
using ::testing::Eq;
|
||||
|
||||
class AtomStyleTest : public ::testing::Test {
|
||||
protected:
|
||||
LAMMPS *lmp;
|
||||
|
||||
void SetUp() override
|
||||
{
|
||||
const char *args[] = {"SimpleCommandsTest", "-log", "none", "-echo", "screen", "-nocite"};
|
||||
char **argv = (char **)args;
|
||||
int argc = sizeof(args) / sizeof(char *);
|
||||
if (!verbose) ::testing::internal::CaptureStdout();
|
||||
lmp = new LAMMPS(argc, argv, MPI_COMM_WORLD);
|
||||
if (!verbose) ::testing::internal::GetCapturedStdout();
|
||||
ASSERT_NE(lmp, nullptr);
|
||||
if (!verbose) ::testing::internal::CaptureStdout();
|
||||
lmp->input->one("units real");
|
||||
lmp->input->one("dimension 3");
|
||||
lmp->input->one("pair_style zero 4.0");
|
||||
lmp->input->one("region box block -4 4 -4 4 -4 4");
|
||||
if (!verbose) ::testing::internal::GetCapturedStdout();
|
||||
}
|
||||
|
||||
void TearDown() override
|
||||
{
|
||||
if (!verbose) ::testing::internal::CaptureStdout();
|
||||
delete lmp;
|
||||
if (!verbose) ::testing::internal::GetCapturedStdout();
|
||||
remove("test_atom_styles.data");
|
||||
remove("test_atom_styles.restart");
|
||||
}
|
||||
};
|
||||
|
||||
TEST_F(AtomStyleTest, atomic)
|
||||
{
|
||||
ASSERT_THAT(std::string(lmp->atom->atom_style), Eq("atomic"));
|
||||
ASSERT_NE(lmp->atom->avec, nullptr);
|
||||
ASSERT_EQ(lmp->atom->natoms, 0);
|
||||
ASSERT_EQ(lmp->atom->nlocal, 0);
|
||||
ASSERT_EQ(lmp->atom->nghost, 0);
|
||||
ASSERT_EQ(lmp->atom->nmax, 1);
|
||||
ASSERT_EQ(lmp->atom->tag_enable, 1);
|
||||
ASSERT_EQ(lmp->atom->molecular, 0);
|
||||
ASSERT_EQ(lmp->atom->nellipsoids, 0);
|
||||
ASSERT_EQ(lmp->atom->nlines, 0);
|
||||
ASSERT_EQ(lmp->atom->ntris, 0);
|
||||
ASSERT_EQ(lmp->atom->nbodies, 0);
|
||||
ASSERT_EQ(lmp->atom->nbonds, 0);
|
||||
ASSERT_EQ(lmp->atom->nangles, 0);
|
||||
ASSERT_EQ(lmp->atom->ndihedrals, 0);
|
||||
ASSERT_EQ(lmp->atom->nimpropers, 0);
|
||||
ASSERT_EQ(lmp->atom->ntypes, 0);
|
||||
ASSERT_EQ(lmp->atom->nbondtypes, 0);
|
||||
ASSERT_EQ(lmp->atom->nangletypes, 0);
|
||||
ASSERT_EQ(lmp->atom->ndihedraltypes, 0);
|
||||
ASSERT_EQ(lmp->atom->nimpropertypes, 0);
|
||||
ASSERT_EQ(lmp->atom->bond_per_atom, 0);
|
||||
ASSERT_EQ(lmp->atom->angle_per_atom, 0);
|
||||
ASSERT_EQ(lmp->atom->dihedral_per_atom, 0);
|
||||
ASSERT_EQ(lmp->atom->improper_per_atom, 0);
|
||||
ASSERT_EQ(lmp->atom->extra_bond_per_atom, 0);
|
||||
ASSERT_EQ(lmp->atom->extra_angle_per_atom, 0);
|
||||
ASSERT_EQ(lmp->atom->extra_dihedral_per_atom, 0);
|
||||
ASSERT_EQ(lmp->atom->extra_improper_per_atom, 0);
|
||||
|
||||
ASSERT_EQ(lmp->atom->sphere_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->ellipsoid_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->line_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->tri_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->body_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->peri_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->electron_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->wavepacket_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->sph_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->molecule_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->molindex_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->molatom_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->q_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->mu_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->rmass_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->radius_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->omega_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->torque_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->angmom_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->vfrac_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->spin_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->eradius_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->ervel_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->erforce_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->cs_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->csforce_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->vforce_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->ervelforce_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->etag_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->rho_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->esph_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->cv_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->vest_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->dpd_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->edpd_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->tdpd_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->mesont_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->sp_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->x0_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->smd_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->damage_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->contact_radius_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->smd_data_9_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->smd_stress_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->eff_plastic_strain_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->eff_plastic_strain_rate_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->pdscale, 1.0);
|
||||
|
||||
ASSERT_NE(lmp->atom->tag, nullptr);
|
||||
ASSERT_NE(lmp->atom->type, nullptr);
|
||||
ASSERT_NE(lmp->atom->mask, nullptr);
|
||||
ASSERT_NE(lmp->atom->image, nullptr);
|
||||
ASSERT_NE(lmp->atom->x, nullptr);
|
||||
ASSERT_NE(lmp->atom->v, nullptr);
|
||||
ASSERT_NE(lmp->atom->f, nullptr);
|
||||
ASSERT_EQ(lmp->atom->q, nullptr);
|
||||
ASSERT_EQ(lmp->atom->mu, nullptr);
|
||||
ASSERT_EQ(lmp->atom->omega, nullptr);
|
||||
ASSERT_EQ(lmp->atom->angmom, nullptr);
|
||||
ASSERT_EQ(lmp->atom->torque, nullptr);
|
||||
ASSERT_EQ(lmp->atom->radius, nullptr);
|
||||
ASSERT_EQ(lmp->atom->rmass, nullptr);
|
||||
ASSERT_EQ(lmp->atom->ellipsoid, nullptr);
|
||||
ASSERT_EQ(lmp->atom->line, nullptr);
|
||||
ASSERT_EQ(lmp->atom->tri, nullptr);
|
||||
ASSERT_EQ(lmp->atom->body, nullptr);
|
||||
ASSERT_EQ(lmp->atom->molecule, nullptr);
|
||||
ASSERT_EQ(lmp->atom->molindex, nullptr);
|
||||
ASSERT_EQ(lmp->atom->molatom, nullptr);
|
||||
ASSERT_EQ(lmp->atom->num_bond, nullptr);
|
||||
ASSERT_EQ(lmp->atom->bond_type, nullptr);
|
||||
ASSERT_EQ(lmp->atom->bond_atom, nullptr);
|
||||
ASSERT_EQ(lmp->atom->num_angle, nullptr);
|
||||
ASSERT_EQ(lmp->atom->angle_type, nullptr);
|
||||
ASSERT_EQ(lmp->atom->angle_atom1, nullptr);
|
||||
ASSERT_EQ(lmp->atom->angle_atom2, nullptr);
|
||||
ASSERT_EQ(lmp->atom->angle_atom3, nullptr);
|
||||
ASSERT_EQ(lmp->atom->num_dihedral, nullptr);
|
||||
ASSERT_EQ(lmp->atom->dihedral_type, nullptr);
|
||||
ASSERT_EQ(lmp->atom->dihedral_atom1, nullptr);
|
||||
ASSERT_EQ(lmp->atom->dihedral_atom2, nullptr);
|
||||
ASSERT_EQ(lmp->atom->dihedral_atom3, nullptr);
|
||||
ASSERT_EQ(lmp->atom->dihedral_atom4, nullptr);
|
||||
ASSERT_EQ(lmp->atom->num_improper, nullptr);
|
||||
ASSERT_EQ(lmp->atom->improper_type, nullptr);
|
||||
ASSERT_EQ(lmp->atom->improper_atom1, nullptr);
|
||||
ASSERT_EQ(lmp->atom->improper_atom2, nullptr);
|
||||
ASSERT_EQ(lmp->atom->improper_atom3, nullptr);
|
||||
ASSERT_EQ(lmp->atom->improper_atom4, nullptr);
|
||||
ASSERT_EQ(lmp->atom->maxspecial, 1);
|
||||
ASSERT_EQ(lmp->atom->nspecial, nullptr);
|
||||
ASSERT_EQ(lmp->atom->special, nullptr);
|
||||
ASSERT_EQ(lmp->atom->vfrac, nullptr);
|
||||
ASSERT_EQ(lmp->atom->s0, nullptr);
|
||||
ASSERT_EQ(lmp->atom->x0, nullptr);
|
||||
ASSERT_EQ(lmp->atom->sp, nullptr);
|
||||
ASSERT_EQ(lmp->atom->fm, nullptr);
|
||||
ASSERT_EQ(lmp->atom->fm_long, nullptr);
|
||||
ASSERT_EQ(lmp->atom->spin, nullptr);
|
||||
ASSERT_EQ(lmp->atom->eradius, nullptr);
|
||||
ASSERT_EQ(lmp->atom->ervel, nullptr);
|
||||
ASSERT_EQ(lmp->atom->erforce, nullptr);
|
||||
ASSERT_EQ(lmp->atom->ervelforce, nullptr);
|
||||
ASSERT_EQ(lmp->atom->cs, nullptr);
|
||||
ASSERT_EQ(lmp->atom->csforce, nullptr);
|
||||
ASSERT_EQ(lmp->atom->vforce, nullptr);
|
||||
ASSERT_EQ(lmp->atom->etag, nullptr);
|
||||
ASSERT_EQ(lmp->atom->uCond, nullptr);
|
||||
ASSERT_EQ(lmp->atom->uMech, nullptr);
|
||||
ASSERT_EQ(lmp->atom->uChem, nullptr);
|
||||
ASSERT_EQ(lmp->atom->uCG, nullptr);
|
||||
ASSERT_EQ(lmp->atom->uCGnew, nullptr);
|
||||
ASSERT_EQ(lmp->atom->duChem, nullptr);
|
||||
ASSERT_EQ(lmp->atom->dpdTheta, nullptr);
|
||||
ASSERT_EQ(lmp->atom->cc, nullptr);
|
||||
ASSERT_EQ(lmp->atom->cc_flux, nullptr);
|
||||
ASSERT_EQ(lmp->atom->edpd_temp, nullptr);
|
||||
ASSERT_EQ(lmp->atom->edpd_flux, nullptr);
|
||||
ASSERT_EQ(lmp->atom->edpd_cv, nullptr);
|
||||
ASSERT_EQ(lmp->atom->length, nullptr);
|
||||
ASSERT_EQ(lmp->atom->buckling, nullptr);
|
||||
ASSERT_EQ(lmp->atom->bond_nt, nullptr);
|
||||
ASSERT_EQ(lmp->atom->contact_radius, nullptr);
|
||||
ASSERT_EQ(lmp->atom->smd_data_9, nullptr);
|
||||
ASSERT_EQ(lmp->atom->smd_stress, nullptr);
|
||||
ASSERT_EQ(lmp->atom->eff_plastic_strain, nullptr);
|
||||
ASSERT_EQ(lmp->atom->eff_plastic_strain_rate, nullptr);
|
||||
ASSERT_EQ(lmp->atom->damage, nullptr);
|
||||
ASSERT_EQ(lmp->atom->rho, nullptr);
|
||||
ASSERT_EQ(lmp->atom->drho, nullptr);
|
||||
ASSERT_EQ(lmp->atom->esph, nullptr);
|
||||
ASSERT_EQ(lmp->atom->desph, nullptr);
|
||||
ASSERT_EQ(lmp->atom->cv, nullptr);
|
||||
ASSERT_EQ(lmp->atom->vest, nullptr);
|
||||
ASSERT_EQ(lmp->atom->nmolecule, 0);
|
||||
ASSERT_EQ(lmp->atom->molecules, nullptr);
|
||||
ASSERT_EQ(lmp->atom->nivector, 0);
|
||||
ASSERT_EQ(lmp->atom->ndvector, 0);
|
||||
ASSERT_EQ(lmp->atom->iname, nullptr);
|
||||
ASSERT_EQ(lmp->atom->dname, nullptr);
|
||||
ASSERT_EQ(lmp->atom->mass, nullptr);
|
||||
ASSERT_EQ(lmp->atom->mass_setflag, nullptr);
|
||||
ASSERT_EQ(lmp->atom->nextra_grow, 0);
|
||||
ASSERT_EQ(lmp->atom->nextra_restart, 0);
|
||||
ASSERT_EQ(lmp->atom->nextra_border, 0);
|
||||
ASSERT_EQ(lmp->atom->nextra_grow_max, 0);
|
||||
ASSERT_EQ(lmp->atom->nextra_restart_max, 0);
|
||||
ASSERT_EQ(lmp->atom->nextra_border_max, 0);
|
||||
ASSERT_EQ(lmp->atom->nextra_store, 0);
|
||||
ASSERT_EQ(lmp->atom->extra_grow, nullptr);
|
||||
ASSERT_EQ(lmp->atom->extra_restart, nullptr);
|
||||
ASSERT_EQ(lmp->atom->extra_border, nullptr);
|
||||
ASSERT_EQ(lmp->atom->extra, nullptr);
|
||||
ASSERT_EQ(lmp->atom->sametag, nullptr);
|
||||
ASSERT_EQ(lmp->atom->map_style, 0);
|
||||
ASSERT_EQ(lmp->atom->map_user, 0);
|
||||
ASSERT_EQ(lmp->atom->map_tag_max, -1);
|
||||
|
||||
if (!verbose) ::testing::internal::CaptureStdout();
|
||||
lmp->input->one("atom_style charge");
|
||||
lmp->input->one("atom_style atomic");
|
||||
if (!verbose) ::testing::internal::GetCapturedStdout();
|
||||
|
||||
ASSERT_THAT(std::string(lmp->atom->atom_style), Eq("atomic"));
|
||||
ASSERT_NE(lmp->atom->avec, nullptr);
|
||||
ASSERT_EQ(lmp->atom->natoms, 0);
|
||||
ASSERT_EQ(lmp->atom->nlocal, 0);
|
||||
ASSERT_EQ(lmp->atom->nghost, 0);
|
||||
ASSERT_EQ(lmp->atom->nmax, 1);
|
||||
ASSERT_EQ(lmp->atom->tag_enable, 1);
|
||||
ASSERT_EQ(lmp->atom->molecular, 0);
|
||||
ASSERT_EQ(lmp->atom->ntypes, 0);
|
||||
|
||||
ASSERT_EQ(lmp->atom->molecule_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->molindex_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->molatom_flag, 0);
|
||||
|
||||
ASSERT_EQ(lmp->atom->q_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->q, nullptr);
|
||||
|
||||
if (!verbose) ::testing::internal::CaptureStdout();
|
||||
lmp->input->one("atom_modify map hash");
|
||||
lmp->input->one("create_box 2 box");
|
||||
lmp->input->one("create_atoms 1 single -2.0 2.0 0.1");
|
||||
lmp->input->one("create_atoms 1 single -2.0 -2.0 -0.1");
|
||||
lmp->input->one("create_atoms 2 single 2.0 2.0 -0.1");
|
||||
lmp->input->one("create_atoms 2 single 2.0 -2.0 0.1");
|
||||
lmp->input->one("mass 1 4.0");
|
||||
lmp->input->one("mass 2 2.4");
|
||||
lmp->input->one("pair_coeff * *");
|
||||
if (!verbose) ::testing::internal::GetCapturedStdout();
|
||||
ASSERT_THAT(std::string(lmp->atom->atom_style), Eq("atomic"));
|
||||
ASSERT_NE(lmp->atom->avec, nullptr);
|
||||
ASSERT_EQ(lmp->atom->natoms, 4);
|
||||
ASSERT_EQ(lmp->atom->nlocal, 4);
|
||||
ASSERT_EQ(lmp->atom->nghost, 0);
|
||||
ASSERT_NE(lmp->atom->nmax, -1);
|
||||
ASSERT_EQ(lmp->atom->tag_enable, 1);
|
||||
ASSERT_EQ(lmp->atom->molecular, 0);
|
||||
ASSERT_EQ(lmp->atom->ntypes, 2);
|
||||
|
||||
ASSERT_NE(lmp->atom->mass, nullptr);
|
||||
ASSERT_NE(lmp->atom->mass_setflag, nullptr);
|
||||
ASSERT_NE(lmp->atom->sametag, nullptr);
|
||||
ASSERT_EQ(lmp->atom->map_style, 2);
|
||||
ASSERT_EQ(lmp->atom->map_user, 2);
|
||||
ASSERT_EQ(lmp->atom->map_tag_max, 4);
|
||||
if (!verbose) ::testing::internal::CaptureStdout();
|
||||
lmp->input->one("pair_coeff * *");
|
||||
lmp->input->one("write_data test_atom_styles.data nocoeff");
|
||||
lmp->input->one("clear");
|
||||
lmp->input->one("atom_style atomic");
|
||||
lmp->input->one("pair_style zero 4.0");
|
||||
lmp->input->one("atom_modify map array");
|
||||
lmp->input->one("units real");
|
||||
lmp->input->one("read_data test_atom_styles.data");
|
||||
if (!verbose) ::testing::internal::GetCapturedStdout();
|
||||
ASSERT_THAT(std::string(lmp->atom->atom_style), Eq("atomic"));
|
||||
ASSERT_NE(lmp->atom->avec, nullptr);
|
||||
ASSERT_EQ(lmp->atom->natoms, 4);
|
||||
ASSERT_EQ(lmp->atom->nlocal, 4);
|
||||
ASSERT_EQ(lmp->atom->nghost, 0);
|
||||
ASSERT_NE(lmp->atom->nmax, -1);
|
||||
ASSERT_EQ(lmp->atom->tag_enable, 1);
|
||||
ASSERT_EQ(lmp->atom->molecular, 0);
|
||||
ASSERT_EQ(lmp->atom->ntypes, 2);
|
||||
|
||||
double **x = lmp->atom->x;
|
||||
double **v = lmp->atom->v;
|
||||
ASSERT_DOUBLE_EQ(x[0][0], -2.0);
|
||||
ASSERT_DOUBLE_EQ(x[0][1], 2.0);
|
||||
ASSERT_DOUBLE_EQ(x[0][2], 0.1);
|
||||
ASSERT_DOUBLE_EQ(x[1][0], -2.0);
|
||||
ASSERT_DOUBLE_EQ(x[1][1], -2.0);
|
||||
ASSERT_DOUBLE_EQ(x[1][2], -0.1);
|
||||
ASSERT_DOUBLE_EQ(x[2][0], 2.0);
|
||||
ASSERT_DOUBLE_EQ(x[2][1], 2.0);
|
||||
ASSERT_DOUBLE_EQ(x[2][2], -0.1);
|
||||
ASSERT_DOUBLE_EQ(x[3][0], 2.0);
|
||||
ASSERT_DOUBLE_EQ(x[3][1], -2.0);
|
||||
ASSERT_DOUBLE_EQ(x[3][2], 0.1);
|
||||
ASSERT_DOUBLE_EQ(v[0][0], 0.0);
|
||||
ASSERT_DOUBLE_EQ(v[0][1], 0.0);
|
||||
ASSERT_DOUBLE_EQ(v[0][2], 0.0);
|
||||
ASSERT_DOUBLE_EQ(v[1][0], 0.0);
|
||||
ASSERT_DOUBLE_EQ(v[1][1], 0.0);
|
||||
ASSERT_DOUBLE_EQ(v[1][2], 0.0);
|
||||
ASSERT_DOUBLE_EQ(v[2][0], 0.0);
|
||||
ASSERT_DOUBLE_EQ(v[2][1], 0.0);
|
||||
ASSERT_DOUBLE_EQ(v[2][2], 0.0);
|
||||
ASSERT_DOUBLE_EQ(v[3][0], 0.0);
|
||||
ASSERT_DOUBLE_EQ(v[3][1], 0.0);
|
||||
ASSERT_DOUBLE_EQ(v[3][2], 0.0);
|
||||
|
||||
ASSERT_DOUBLE_EQ(lmp->atom->mass[1], 4.0);
|
||||
ASSERT_DOUBLE_EQ(lmp->atom->mass[2], 2.4);
|
||||
ASSERT_EQ(lmp->atom->mass_setflag[1], 1);
|
||||
ASSERT_EQ(lmp->atom->mass_setflag[2], 1);
|
||||
ASSERT_EQ(lmp->atom->map_style, 1);
|
||||
ASSERT_EQ(lmp->atom->map_user, 1);
|
||||
ASSERT_EQ(lmp->atom->map_tag_max, 4);
|
||||
ASSERT_EQ(lmp->atom->tag_consecutive(), 1);
|
||||
|
||||
if (!verbose) ::testing::internal::CaptureStdout();
|
||||
lmp->input->one("pair_coeff * *");
|
||||
lmp->input->one("group two id 2:4:2");
|
||||
lmp->input->one("delete_atoms group two compress no");
|
||||
lmp->input->one("write_restart test_atom_styles.restart");
|
||||
lmp->input->one("clear");
|
||||
lmp->input->one("read_restart test_atom_styles.restart");
|
||||
if (!verbose) ::testing::internal::GetCapturedStdout();
|
||||
ASSERT_THAT(std::string(lmp->atom->atom_style), Eq("atomic"));
|
||||
ASSERT_NE(lmp->atom->avec, nullptr);
|
||||
ASSERT_EQ(lmp->atom->natoms, 2);
|
||||
ASSERT_EQ(lmp->atom->nlocal, 2);
|
||||
ASSERT_EQ(lmp->atom->nghost, 0);
|
||||
ASSERT_NE(lmp->atom->nmax, -1);
|
||||
ASSERT_EQ(lmp->atom->tag_enable, 1);
|
||||
ASSERT_EQ(lmp->atom->molecular, 0);
|
||||
ASSERT_EQ(lmp->atom->ntypes, 2);
|
||||
ASSERT_EQ(lmp->atom->tag_consecutive(), 0);
|
||||
|
||||
x = lmp->atom->x;
|
||||
v = lmp->atom->v;
|
||||
ASSERT_DOUBLE_EQ(x[0][0], -2.0);
|
||||
ASSERT_DOUBLE_EQ(x[0][1], 2.0);
|
||||
ASSERT_DOUBLE_EQ(x[0][2], 0.1);
|
||||
ASSERT_DOUBLE_EQ(x[1][0], 2.0);
|
||||
ASSERT_DOUBLE_EQ(x[1][1], 2.0);
|
||||
ASSERT_DOUBLE_EQ(x[1][2], -0.1);
|
||||
ASSERT_DOUBLE_EQ(v[0][0], 0.0);
|
||||
ASSERT_DOUBLE_EQ(v[0][1], 0.0);
|
||||
ASSERT_DOUBLE_EQ(v[0][2], 0.0);
|
||||
ASSERT_DOUBLE_EQ(v[1][0], 0.0);
|
||||
ASSERT_DOUBLE_EQ(v[1][1], 0.0);
|
||||
ASSERT_DOUBLE_EQ(v[1][2], 0.0);
|
||||
|
||||
ASSERT_DOUBLE_EQ(lmp->atom->mass[1], 4.0);
|
||||
ASSERT_DOUBLE_EQ(lmp->atom->mass[2], 2.4);
|
||||
ASSERT_EQ(lmp->atom->mass_setflag[1], 1);
|
||||
ASSERT_EQ(lmp->atom->mass_setflag[2], 1);
|
||||
ASSERT_EQ(lmp->atom->map_style, 1);
|
||||
ASSERT_EQ(lmp->atom->map_user, 1);
|
||||
ASSERT_EQ(lmp->atom->map_tag_max, 3);
|
||||
if (!verbose) ::testing::internal::CaptureStdout();
|
||||
lmp->input->one("reset_ids");
|
||||
if (!verbose) ::testing::internal::GetCapturedStdout();
|
||||
ASSERT_EQ(lmp->atom->map_tag_max, 2);
|
||||
ASSERT_EQ(lmp->atom->tag_consecutive(), 1);
|
||||
}
|
||||
|
||||
TEST_F(AtomStyleTest, charge)
|
||||
{
|
||||
if (!verbose) ::testing::internal::CaptureStdout();
|
||||
lmp->input->one("atom_style charge");
|
||||
if (!verbose) ::testing::internal::GetCapturedStdout();
|
||||
ASSERT_THAT(std::string(lmp->atom->atom_style), Eq("charge"));
|
||||
ASSERT_NE(lmp->atom->avec, nullptr);
|
||||
ASSERT_EQ(lmp->atom->natoms, 0);
|
||||
ASSERT_EQ(lmp->atom->nlocal, 0);
|
||||
ASSERT_EQ(lmp->atom->nghost, 0);
|
||||
ASSERT_EQ(lmp->atom->nmax, 1);
|
||||
ASSERT_EQ(lmp->atom->tag_enable, 1);
|
||||
ASSERT_EQ(lmp->atom->molecular, 0);
|
||||
ASSERT_EQ(lmp->atom->nellipsoids, 0);
|
||||
ASSERT_EQ(lmp->atom->nlines, 0);
|
||||
ASSERT_EQ(lmp->atom->ntris, 0);
|
||||
ASSERT_EQ(lmp->atom->nbodies, 0);
|
||||
ASSERT_EQ(lmp->atom->nbonds, 0);
|
||||
ASSERT_EQ(lmp->atom->nangles, 0);
|
||||
ASSERT_EQ(lmp->atom->ndihedrals, 0);
|
||||
ASSERT_EQ(lmp->atom->nimpropers, 0);
|
||||
ASSERT_EQ(lmp->atom->ntypes, 0);
|
||||
ASSERT_EQ(lmp->atom->nbondtypes, 0);
|
||||
ASSERT_EQ(lmp->atom->nangletypes, 0);
|
||||
ASSERT_EQ(lmp->atom->ndihedraltypes, 0);
|
||||
ASSERT_EQ(lmp->atom->nimpropertypes, 0);
|
||||
ASSERT_EQ(lmp->atom->bond_per_atom, 0);
|
||||
ASSERT_EQ(lmp->atom->angle_per_atom, 0);
|
||||
ASSERT_EQ(lmp->atom->dihedral_per_atom, 0);
|
||||
ASSERT_EQ(lmp->atom->improper_per_atom, 0);
|
||||
ASSERT_EQ(lmp->atom->extra_bond_per_atom, 0);
|
||||
ASSERT_EQ(lmp->atom->extra_angle_per_atom, 0);
|
||||
ASSERT_EQ(lmp->atom->extra_dihedral_per_atom, 0);
|
||||
ASSERT_EQ(lmp->atom->extra_improper_per_atom, 0);
|
||||
|
||||
ASSERT_EQ(lmp->atom->sphere_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->ellipsoid_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->line_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->tri_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->body_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->peri_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->electron_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->wavepacket_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->sph_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->molecule_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->molindex_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->molatom_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->q_flag, 1);
|
||||
ASSERT_EQ(lmp->atom->mu_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->rmass_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->radius_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->omega_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->torque_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->angmom_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->vfrac_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->spin_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->eradius_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->ervel_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->erforce_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->cs_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->csforce_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->vforce_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->ervelforce_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->etag_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->rho_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->esph_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->cv_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->vest_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->dpd_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->edpd_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->tdpd_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->mesont_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->sp_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->x0_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->smd_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->damage_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->contact_radius_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->smd_data_9_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->smd_stress_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->eff_plastic_strain_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->eff_plastic_strain_rate_flag, 0);
|
||||
ASSERT_EQ(lmp->atom->pdscale, 1.0);
|
||||
|
||||
ASSERT_NE(lmp->atom->tag, nullptr);
|
||||
ASSERT_NE(lmp->atom->type, nullptr);
|
||||
ASSERT_NE(lmp->atom->mask, nullptr);
|
||||
ASSERT_NE(lmp->atom->image, nullptr);
|
||||
ASSERT_NE(lmp->atom->x, nullptr);
|
||||
ASSERT_NE(lmp->atom->v, nullptr);
|
||||
ASSERT_NE(lmp->atom->f, nullptr);
|
||||
ASSERT_NE(lmp->atom->q, nullptr);
|
||||
ASSERT_EQ(lmp->atom->mu, nullptr);
|
||||
ASSERT_EQ(lmp->atom->omega, nullptr);
|
||||
ASSERT_EQ(lmp->atom->angmom, nullptr);
|
||||
ASSERT_EQ(lmp->atom->torque, nullptr);
|
||||
ASSERT_EQ(lmp->atom->radius, nullptr);
|
||||
ASSERT_EQ(lmp->atom->rmass, nullptr);
|
||||
ASSERT_EQ(lmp->atom->ellipsoid, nullptr);
|
||||
ASSERT_EQ(lmp->atom->line, nullptr);
|
||||
ASSERT_EQ(lmp->atom->tri, nullptr);
|
||||
ASSERT_EQ(lmp->atom->body, nullptr);
|
||||
ASSERT_EQ(lmp->atom->molecule, nullptr);
|
||||
ASSERT_EQ(lmp->atom->molindex, nullptr);
|
||||
ASSERT_EQ(lmp->atom->molatom, nullptr);
|
||||
ASSERT_EQ(lmp->atom->num_bond, nullptr);
|
||||
ASSERT_EQ(lmp->atom->bond_type, nullptr);
|
||||
ASSERT_EQ(lmp->atom->bond_atom, nullptr);
|
||||
ASSERT_EQ(lmp->atom->num_angle, nullptr);
|
||||
ASSERT_EQ(lmp->atom->angle_type, nullptr);
|
||||
ASSERT_EQ(lmp->atom->angle_atom1, nullptr);
|
||||
ASSERT_EQ(lmp->atom->angle_atom2, nullptr);
|
||||
ASSERT_EQ(lmp->atom->angle_atom3, nullptr);
|
||||
ASSERT_EQ(lmp->atom->num_dihedral, nullptr);
|
||||
ASSERT_EQ(lmp->atom->dihedral_type, nullptr);
|
||||
ASSERT_EQ(lmp->atom->dihedral_atom1, nullptr);
|
||||
ASSERT_EQ(lmp->atom->dihedral_atom2, nullptr);
|
||||
ASSERT_EQ(lmp->atom->dihedral_atom3, nullptr);
|
||||
ASSERT_EQ(lmp->atom->dihedral_atom4, nullptr);
|
||||
ASSERT_EQ(lmp->atom->num_improper, nullptr);
|
||||
ASSERT_EQ(lmp->atom->improper_type, nullptr);
|
||||
ASSERT_EQ(lmp->atom->improper_atom1, nullptr);
|
||||
ASSERT_EQ(lmp->atom->improper_atom2, nullptr);
|
||||
ASSERT_EQ(lmp->atom->improper_atom3, nullptr);
|
||||
ASSERT_EQ(lmp->atom->improper_atom4, nullptr);
|
||||
ASSERT_EQ(lmp->atom->maxspecial, 1);
|
||||
ASSERT_EQ(lmp->atom->nspecial, nullptr);
|
||||
ASSERT_EQ(lmp->atom->special, nullptr);
|
||||
ASSERT_EQ(lmp->atom->vfrac, nullptr);
|
||||
ASSERT_EQ(lmp->atom->s0, nullptr);
|
||||
ASSERT_EQ(lmp->atom->x0, nullptr);
|
||||
ASSERT_EQ(lmp->atom->sp, nullptr);
|
||||
ASSERT_EQ(lmp->atom->fm, nullptr);
|
||||
ASSERT_EQ(lmp->atom->fm_long, nullptr);
|
||||
ASSERT_EQ(lmp->atom->spin, nullptr);
|
||||
ASSERT_EQ(lmp->atom->eradius, nullptr);
|
||||
ASSERT_EQ(lmp->atom->ervel, nullptr);
|
||||
ASSERT_EQ(lmp->atom->erforce, nullptr);
|
||||
ASSERT_EQ(lmp->atom->ervelforce, nullptr);
|
||||
ASSERT_EQ(lmp->atom->cs, nullptr);
|
||||
ASSERT_EQ(lmp->atom->csforce, nullptr);
|
||||
ASSERT_EQ(lmp->atom->vforce, nullptr);
|
||||
ASSERT_EQ(lmp->atom->etag, nullptr);
|
||||
ASSERT_EQ(lmp->atom->uCond, nullptr);
|
||||
ASSERT_EQ(lmp->atom->uMech, nullptr);
|
||||
ASSERT_EQ(lmp->atom->uChem, nullptr);
|
||||
ASSERT_EQ(lmp->atom->uCG, nullptr);
|
||||
ASSERT_EQ(lmp->atom->uCGnew, nullptr);
|
||||
ASSERT_EQ(lmp->atom->duChem, nullptr);
|
||||
ASSERT_EQ(lmp->atom->dpdTheta, nullptr);
|
||||
ASSERT_EQ(lmp->atom->cc, nullptr);
|
||||
ASSERT_EQ(lmp->atom->cc_flux, nullptr);
|
||||
ASSERT_EQ(lmp->atom->edpd_temp, nullptr);
|
||||
ASSERT_EQ(lmp->atom->edpd_flux, nullptr);
|
||||
ASSERT_EQ(lmp->atom->edpd_cv, nullptr);
|
||||
ASSERT_EQ(lmp->atom->length, nullptr);
|
||||
ASSERT_EQ(lmp->atom->buckling, nullptr);
|
||||
ASSERT_EQ(lmp->atom->bond_nt, nullptr);
|
||||
ASSERT_EQ(lmp->atom->contact_radius, nullptr);
|
||||
ASSERT_EQ(lmp->atom->smd_data_9, nullptr);
|
||||
ASSERT_EQ(lmp->atom->smd_stress, nullptr);
|
||||
ASSERT_EQ(lmp->atom->eff_plastic_strain, nullptr);
|
||||
ASSERT_EQ(lmp->atom->eff_plastic_strain_rate, nullptr);
|
||||
ASSERT_EQ(lmp->atom->damage, nullptr);
|
||||
ASSERT_EQ(lmp->atom->rho, nullptr);
|
||||
ASSERT_EQ(lmp->atom->drho, nullptr);
|
||||
ASSERT_EQ(lmp->atom->esph, nullptr);
|
||||
ASSERT_EQ(lmp->atom->desph, nullptr);
|
||||
ASSERT_EQ(lmp->atom->cv, nullptr);
|
||||
ASSERT_EQ(lmp->atom->vest, nullptr);
|
||||
ASSERT_EQ(lmp->atom->nmolecule, 0);
|
||||
ASSERT_EQ(lmp->atom->molecules, nullptr);
|
||||
ASSERT_EQ(lmp->atom->nivector, 0);
|
||||
ASSERT_EQ(lmp->atom->ndvector, 0);
|
||||
ASSERT_EQ(lmp->atom->iname, nullptr);
|
||||
ASSERT_EQ(lmp->atom->dname, nullptr);
|
||||
ASSERT_EQ(lmp->atom->mass, nullptr);
|
||||
ASSERT_EQ(lmp->atom->mass_setflag, nullptr);
|
||||
ASSERT_EQ(lmp->atom->nextra_grow, 0);
|
||||
ASSERT_EQ(lmp->atom->nextra_restart, 0);
|
||||
ASSERT_EQ(lmp->atom->nextra_border, 0);
|
||||
ASSERT_EQ(lmp->atom->nextra_grow_max, 0);
|
||||
ASSERT_EQ(lmp->atom->nextra_restart_max, 0);
|
||||
ASSERT_EQ(lmp->atom->nextra_border_max, 0);
|
||||
ASSERT_EQ(lmp->atom->nextra_store, 0);
|
||||
ASSERT_EQ(lmp->atom->extra_grow, nullptr);
|
||||
ASSERT_EQ(lmp->atom->extra_restart, nullptr);
|
||||
ASSERT_EQ(lmp->atom->extra_border, nullptr);
|
||||
ASSERT_EQ(lmp->atom->extra, nullptr);
|
||||
ASSERT_EQ(lmp->atom->sametag, nullptr);
|
||||
ASSERT_EQ(lmp->atom->map_style, 0);
|
||||
ASSERT_EQ(lmp->atom->map_user, 0);
|
||||
ASSERT_EQ(lmp->atom->map_tag_max, -1);
|
||||
|
||||
if (!verbose) ::testing::internal::CaptureStdout();
|
||||
lmp->input->one("create_box 2 box");
|
||||
lmp->input->one("create_atoms 1 single -2.0 2.0 0.1");
|
||||
lmp->input->one("create_atoms 1 single -2.0 -2.0 -0.1");
|
||||
lmp->input->one("create_atoms 2 single 2.0 2.0 -0.1");
|
||||
lmp->input->one("create_atoms 2 single 2.0 -2.0 0.1");
|
||||
lmp->input->one("mass 1 4.0");
|
||||
lmp->input->one("mass 2 2.4");
|
||||
lmp->input->one("set atom 1 charge -0.5");
|
||||
lmp->input->one("set atom 2 charge 0.5");
|
||||
lmp->input->one("set atom 3 charge -1.0");
|
||||
lmp->input->one("set atom 4 charge 1.0");
|
||||
lmp->input->one("pair_coeff * *");
|
||||
if (!verbose) ::testing::internal::GetCapturedStdout();
|
||||
ASSERT_THAT(std::string(lmp->atom->atom_style), Eq("charge"));
|
||||
ASSERT_NE(lmp->atom->avec, nullptr);
|
||||
ASSERT_EQ(lmp->atom->natoms, 4);
|
||||
ASSERT_EQ(lmp->atom->nlocal, 4);
|
||||
ASSERT_EQ(lmp->atom->nghost, 0);
|
||||
ASSERT_NE(lmp->atom->nmax, -1);
|
||||
ASSERT_EQ(lmp->atom->tag_enable, 1);
|
||||
ASSERT_EQ(lmp->atom->molecular, 0);
|
||||
ASSERT_EQ(lmp->atom->ntypes, 2);
|
||||
|
||||
ASSERT_NE(lmp->atom->mass, nullptr);
|
||||
ASSERT_NE(lmp->atom->mass_setflag, nullptr);
|
||||
if (!verbose) ::testing::internal::CaptureStdout();
|
||||
lmp->input->one("pair_coeff * *");
|
||||
lmp->input->one("write_data test_atom_styles.data nocoeff");
|
||||
lmp->input->one("clear");
|
||||
lmp->input->one("atom_style charge");
|
||||
lmp->input->one("pair_style zero 4.0");
|
||||
lmp->input->one("units real");
|
||||
lmp->input->one("atom_modify map array");
|
||||
lmp->input->one("read_data test_atom_styles.data");
|
||||
if (!verbose) ::testing::internal::GetCapturedStdout();
|
||||
ASSERT_THAT(std::string(lmp->atom->atom_style), Eq("charge"));
|
||||
ASSERT_NE(lmp->atom->avec, nullptr);
|
||||
ASSERT_EQ(lmp->atom->natoms, 4);
|
||||
ASSERT_EQ(lmp->atom->nlocal, 4);
|
||||
ASSERT_EQ(lmp->atom->nghost, 0);
|
||||
ASSERT_NE(lmp->atom->nmax, -1);
|
||||
ASSERT_EQ(lmp->atom->tag_enable, 1);
|
||||
ASSERT_EQ(lmp->atom->molecular, 0);
|
||||
ASSERT_EQ(lmp->atom->ntypes, 2);
|
||||
ASSERT_EQ(lmp->atom->q_flag, 1);
|
||||
ASSERT_NE(lmp->atom->sametag, nullptr);
|
||||
ASSERT_EQ(lmp->atom->tag_consecutive(), 1);
|
||||
ASSERT_EQ(lmp->atom->map_style, 1);
|
||||
ASSERT_EQ(lmp->atom->map_user, 1);
|
||||
ASSERT_EQ(lmp->atom->map_tag_max, 4);
|
||||
|
||||
double **x = lmp->atom->x;
|
||||
double **v = lmp->atom->v;
|
||||
double *q = lmp->atom->q;
|
||||
ASSERT_DOUBLE_EQ(x[0][0], -2.0);
|
||||
ASSERT_DOUBLE_EQ(x[0][1], 2.0);
|
||||
ASSERT_DOUBLE_EQ(x[0][2], 0.1);
|
||||
ASSERT_DOUBLE_EQ(x[1][0], -2.0);
|
||||
ASSERT_DOUBLE_EQ(x[1][1], -2.0);
|
||||
ASSERT_DOUBLE_EQ(x[1][2], -0.1);
|
||||
ASSERT_DOUBLE_EQ(x[2][0], 2.0);
|
||||
ASSERT_DOUBLE_EQ(x[2][1], 2.0);
|
||||
ASSERT_DOUBLE_EQ(x[2][2], -0.1);
|
||||
ASSERT_DOUBLE_EQ(x[3][0], 2.0);
|
||||
ASSERT_DOUBLE_EQ(x[3][1], -2.0);
|
||||
ASSERT_DOUBLE_EQ(x[3][2], 0.1);
|
||||
ASSERT_DOUBLE_EQ(v[0][0], 0.0);
|
||||
ASSERT_DOUBLE_EQ(v[0][1], 0.0);
|
||||
ASSERT_DOUBLE_EQ(v[0][2], 0.0);
|
||||
ASSERT_DOUBLE_EQ(v[1][0], 0.0);
|
||||
ASSERT_DOUBLE_EQ(v[1][1], 0.0);
|
||||
ASSERT_DOUBLE_EQ(v[1][2], 0.0);
|
||||
ASSERT_DOUBLE_EQ(v[2][0], 0.0);
|
||||
ASSERT_DOUBLE_EQ(v[2][1], 0.0);
|
||||
ASSERT_DOUBLE_EQ(v[2][2], 0.0);
|
||||
ASSERT_DOUBLE_EQ(v[3][0], 0.0);
|
||||
ASSERT_DOUBLE_EQ(v[3][1], 0.0);
|
||||
ASSERT_DOUBLE_EQ(v[3][2], 0.0);
|
||||
ASSERT_DOUBLE_EQ(q[0], -0.5);
|
||||
ASSERT_DOUBLE_EQ(q[1], 0.5);
|
||||
ASSERT_DOUBLE_EQ(q[2], -1.0);
|
||||
ASSERT_DOUBLE_EQ(q[3], 1.0);
|
||||
|
||||
ASSERT_DOUBLE_EQ(lmp->atom->mass[1], 4.0);
|
||||
ASSERT_DOUBLE_EQ(lmp->atom->mass[2], 2.4);
|
||||
ASSERT_EQ(lmp->atom->mass_setflag[1], 1);
|
||||
ASSERT_EQ(lmp->atom->mass_setflag[2], 1);
|
||||
|
||||
if (!verbose) ::testing::internal::CaptureStdout();
|
||||
lmp->input->one("pair_coeff * *");
|
||||
lmp->input->one("group two id 2:4:2");
|
||||
lmp->input->one("delete_atoms group two compress no");
|
||||
lmp->input->one("write_restart test_atom_styles.restart");
|
||||
lmp->input->one("clear");
|
||||
lmp->input->one("read_restart test_atom_styles.restart");
|
||||
if (!verbose) ::testing::internal::GetCapturedStdout();
|
||||
ASSERT_THAT(std::string(lmp->atom->atom_style), Eq("charge"));
|
||||
ASSERT_NE(lmp->atom->avec, nullptr);
|
||||
ASSERT_EQ(lmp->atom->natoms, 2);
|
||||
ASSERT_EQ(lmp->atom->nlocal, 2);
|
||||
ASSERT_EQ(lmp->atom->nghost, 0);
|
||||
ASSERT_NE(lmp->atom->nmax, -1);
|
||||
ASSERT_EQ(lmp->atom->tag_enable, 1);
|
||||
ASSERT_EQ(lmp->atom->molecular, 0);
|
||||
ASSERT_EQ(lmp->atom->ntypes, 2);
|
||||
ASSERT_EQ(lmp->atom->tag_consecutive(), 0);
|
||||
ASSERT_EQ(lmp->atom->map_tag_max, 3);
|
||||
|
||||
x = lmp->atom->x;
|
||||
v = lmp->atom->v;
|
||||
q = lmp->atom->q;
|
||||
ASSERT_DOUBLE_EQ(x[0][0], -2.0);
|
||||
ASSERT_DOUBLE_EQ(x[0][1], 2.0);
|
||||
ASSERT_DOUBLE_EQ(x[0][2], 0.1);
|
||||
ASSERT_DOUBLE_EQ(x[1][0], 2.0);
|
||||
ASSERT_DOUBLE_EQ(x[1][1], 2.0);
|
||||
ASSERT_DOUBLE_EQ(x[1][2], -0.1);
|
||||
ASSERT_DOUBLE_EQ(v[0][0], 0.0);
|
||||
ASSERT_DOUBLE_EQ(v[0][1], 0.0);
|
||||
ASSERT_DOUBLE_EQ(v[0][2], 0.0);
|
||||
ASSERT_DOUBLE_EQ(v[1][0], 0.0);
|
||||
ASSERT_DOUBLE_EQ(v[1][1], 0.0);
|
||||
ASSERT_DOUBLE_EQ(v[1][2], 0.0);
|
||||
ASSERT_DOUBLE_EQ(q[0], -0.5);
|
||||
ASSERT_DOUBLE_EQ(q[1], -1.0);
|
||||
|
||||
ASSERT_DOUBLE_EQ(lmp->atom->mass[1], 4.0);
|
||||
ASSERT_DOUBLE_EQ(lmp->atom->mass[2], 2.4);
|
||||
ASSERT_EQ(lmp->atom->mass_setflag[1], 1);
|
||||
ASSERT_EQ(lmp->atom->mass_setflag[2], 1);
|
||||
}
|
||||
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
int main(int argc, char **argv)
|
||||
{
|
||||
MPI_Init(&argc, &argv);
|
||||
::testing::InitGoogleMock(&argc, argv);
|
||||
if ((argc > 1) && (strcmp(argv[1], "-v") == 0)) verbose = true;
|
||||
|
||||
int rv = RUN_ALL_TESTS();
|
||||
MPI_Finalize();
|
||||
return rv;
|
||||
}
|
||||
@ -12,15 +12,21 @@
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "MANYBODY/pair_eim.h"
|
||||
#include "info.h"
|
||||
#include "input.h"
|
||||
#include "lammps.h"
|
||||
#include "utils.h"
|
||||
#include "gmock/gmock.h"
|
||||
#include "gtest/gtest.h"
|
||||
|
||||
#include <cstring>
|
||||
#include <mpi.h>
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
// whether to print verbose output (i.e. not capturing LAMMPS screen output).
|
||||
bool verbose = false;
|
||||
|
||||
class EIMPotentialFileReaderTest : public ::testing::Test {
|
||||
protected:
|
||||
LAMMPS *lmp;
|
||||
@ -33,9 +39,16 @@ protected:
|
||||
"PotentialFileReaderTest", "-log", "none", "-echo", "screen", "-nocite"};
|
||||
char **argv = (char **)args;
|
||||
int argc = sizeof(args) / sizeof(char *);
|
||||
::testing::internal::CaptureStdout();
|
||||
if (!verbose) ::testing::internal::CaptureStdout();
|
||||
lmp = new LAMMPS(argc, argv, MPI_COMM_WORLD);
|
||||
::testing::internal::GetCapturedStdout();
|
||||
lmp->input->one("units metal");
|
||||
if (!verbose) ::testing::internal::GetCapturedStdout();
|
||||
ASSERT_NE(lmp, nullptr);
|
||||
|
||||
// check if the prerequisite eim pair style is available
|
||||
Info *info = new Info(lmp);
|
||||
ASSERT_TRUE(info->has_style("pair", "eim"));
|
||||
delete info;
|
||||
|
||||
int npair = nelements * (nelements + 1) / 2;
|
||||
setfl.ielement = new int[nelements];
|
||||
@ -85,17 +98,17 @@ protected:
|
||||
delete[] setfl.rs;
|
||||
delete[] setfl.tp;
|
||||
|
||||
::testing::internal::CaptureStdout();
|
||||
if (!verbose) ::testing::internal::CaptureStdout();
|
||||
delete lmp;
|
||||
::testing::internal::GetCapturedStdout();
|
||||
if (!verbose) ::testing::internal::GetCapturedStdout();
|
||||
}
|
||||
};
|
||||
|
||||
TEST_F(EIMPotentialFileReaderTest, global_line)
|
||||
{
|
||||
::testing::internal::CaptureStdout();
|
||||
if (!verbose) ::testing::internal::CaptureStdout();
|
||||
EIMPotentialFileReader reader(lmp, "ffield.eim");
|
||||
::testing::internal::GetCapturedStdout();
|
||||
if (!verbose) ::testing::internal::GetCapturedStdout();
|
||||
|
||||
reader.get_global(&setfl);
|
||||
ASSERT_DOUBLE_EQ(setfl.division, 2.0);
|
||||
@ -105,9 +118,9 @@ TEST_F(EIMPotentialFileReaderTest, global_line)
|
||||
|
||||
TEST_F(EIMPotentialFileReaderTest, element_line_sequential)
|
||||
{
|
||||
::testing::internal::CaptureStdout();
|
||||
if (!verbose) ::testing::internal::CaptureStdout();
|
||||
EIMPotentialFileReader reader(lmp, "ffield.eim");
|
||||
::testing::internal::GetCapturedStdout();
|
||||
if (!verbose) ::testing::internal::GetCapturedStdout();
|
||||
|
||||
reader.get_element(&setfl, 0, "Li");
|
||||
ASSERT_EQ(setfl.ielement[0], 3);
|
||||
@ -130,9 +143,9 @@ TEST_F(EIMPotentialFileReaderTest, element_line_sequential)
|
||||
|
||||
TEST_F(EIMPotentialFileReaderTest, element_line_random)
|
||||
{
|
||||
::testing::internal::CaptureStdout();
|
||||
if (!verbose) ::testing::internal::CaptureStdout();
|
||||
EIMPotentialFileReader reader(lmp, "ffield.eim");
|
||||
::testing::internal::GetCapturedStdout();
|
||||
if (!verbose) ::testing::internal::GetCapturedStdout();
|
||||
|
||||
reader.get_element(&setfl, 0, "Id");
|
||||
ASSERT_EQ(setfl.ielement[0], 53);
|
||||
@ -146,9 +159,9 @@ TEST_F(EIMPotentialFileReaderTest, element_line_random)
|
||||
|
||||
TEST_F(EIMPotentialFileReaderTest, pair_line)
|
||||
{
|
||||
::testing::internal::CaptureStdout();
|
||||
if (!verbose) ::testing::internal::CaptureStdout();
|
||||
EIMPotentialFileReader reader(lmp, "ffield.eim");
|
||||
::testing::internal::GetCapturedStdout();
|
||||
if (!verbose) ::testing::internal::GetCapturedStdout();
|
||||
|
||||
reader.get_pair(&setfl, 0, "Li", "Li");
|
||||
ASSERT_DOUBLE_EQ(setfl.rcutphiA[0], 6.0490e+00);
|
||||
@ -169,9 +182,9 @@ TEST_F(EIMPotentialFileReaderTest, pair_line)
|
||||
|
||||
TEST_F(EIMPotentialFileReaderTest, pair_identical)
|
||||
{
|
||||
::testing::internal::CaptureStdout();
|
||||
if (!verbose) ::testing::internal::CaptureStdout();
|
||||
EIMPotentialFileReader reader(lmp, "ffield.eim");
|
||||
::testing::internal::GetCapturedStdout();
|
||||
if (!verbose) ::testing::internal::GetCapturedStdout();
|
||||
|
||||
reader.get_pair(&setfl, 0, "Li", "Na");
|
||||
reader.get_pair(&setfl, 1, "Na", "Li");
|
||||
@ -195,5 +208,9 @@ int main(int argc, char **argv)
|
||||
{
|
||||
MPI_Init(&argc, &argv);
|
||||
::testing::InitGoogleMock(&argc, argv);
|
||||
return RUN_ALL_TESTS();
|
||||
if ((argc > 1) && (strcmp(argv[1], "-v") == 0)) verbose = true;
|
||||
|
||||
int rv = RUN_ALL_TESTS();
|
||||
MPI_Finalize();
|
||||
return rv;
|
||||
}
|
||||
|
||||
@ -23,16 +23,21 @@
|
||||
#include "MANYBODY/pair_tersoff_mod_c.h"
|
||||
#include "MANYBODY/pair_tersoff_zbl.h"
|
||||
#include "MANYBODY/pair_vashishta.h"
|
||||
#include "input.h"
|
||||
#include "lammps.h"
|
||||
#include "potential_file_reader.h"
|
||||
#include "utils.h"
|
||||
#include "gmock/gmock.h"
|
||||
#include "gtest/gtest.h"
|
||||
|
||||
#include <cstring>
|
||||
#include <mpi.h>
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
// whether to print verbose output (i.e. not capturing LAMMPS screen output).
|
||||
bool verbose = false;
|
||||
|
||||
const int LAMMPS_NS::PairSW::NPARAMS_PER_LINE;
|
||||
const int LAMMPS_NS::PairComb::NPARAMS_PER_LINE;
|
||||
const int LAMMPS_NS::PairComb3::NPARAMS_PER_LINE;
|
||||
@ -55,24 +60,25 @@ protected:
|
||||
"PotentialFileReaderTest", "-log", "none", "-echo", "screen", "-nocite"};
|
||||
char **argv = (char **)args;
|
||||
int argc = sizeof(args) / sizeof(char *);
|
||||
::testing::internal::CaptureStdout();
|
||||
if (!verbose) ::testing::internal::CaptureStdout();
|
||||
lmp = new LAMMPS(argc, argv, MPI_COMM_WORLD);
|
||||
::testing::internal::GetCapturedStdout();
|
||||
if (!verbose) ::testing::internal::GetCapturedStdout();
|
||||
}
|
||||
|
||||
void TearDown() override
|
||||
{
|
||||
::testing::internal::CaptureStdout();
|
||||
if (!verbose) ::testing::internal::CaptureStdout();
|
||||
delete lmp;
|
||||
::testing::internal::GetCapturedStdout();
|
||||
if (!verbose) ::testing::internal::GetCapturedStdout();
|
||||
}
|
||||
};
|
||||
|
||||
TEST_F(PotentialFileReaderTest, Si)
|
||||
{
|
||||
::testing::internal::CaptureStdout();
|
||||
if (!verbose) ::testing::internal::CaptureStdout();
|
||||
lmp->input->one("units metal");
|
||||
PotentialFileReader reader(lmp, "Si.sw", "Stillinger-Weber");
|
||||
::testing::internal::GetCapturedStdout();
|
||||
if (!verbose) ::testing::internal::GetCapturedStdout();
|
||||
|
||||
auto line = reader.next_line(PairSW::NPARAMS_PER_LINE);
|
||||
ASSERT_EQ(utils::count_words(line), PairSW::NPARAMS_PER_LINE);
|
||||
@ -80,9 +86,10 @@ TEST_F(PotentialFileReaderTest, Si)
|
||||
|
||||
TEST_F(PotentialFileReaderTest, Comb)
|
||||
{
|
||||
::testing::internal::CaptureStdout();
|
||||
if (!verbose) ::testing::internal::CaptureStdout();
|
||||
lmp->input->one("units metal");
|
||||
PotentialFileReader reader(lmp, "ffield.comb", "COMB");
|
||||
::testing::internal::GetCapturedStdout();
|
||||
if (!verbose) ::testing::internal::GetCapturedStdout();
|
||||
|
||||
auto line = reader.next_line(PairComb::NPARAMS_PER_LINE);
|
||||
ASSERT_EQ(utils::count_words(line), PairComb::NPARAMS_PER_LINE);
|
||||
@ -90,9 +97,10 @@ TEST_F(PotentialFileReaderTest, Comb)
|
||||
|
||||
TEST_F(PotentialFileReaderTest, Comb3)
|
||||
{
|
||||
::testing::internal::CaptureStdout();
|
||||
if (!verbose) ::testing::internal::CaptureStdout();
|
||||
lmp->input->one("units metal");
|
||||
PotentialFileReader reader(lmp, "ffield.comb3", "COMB3");
|
||||
::testing::internal::GetCapturedStdout();
|
||||
if (!verbose) ::testing::internal::GetCapturedStdout();
|
||||
|
||||
auto line = reader.next_line(PairComb3::NPARAMS_PER_LINE);
|
||||
ASSERT_EQ(utils::count_words(line), PairComb3::NPARAMS_PER_LINE);
|
||||
@ -100,9 +108,10 @@ TEST_F(PotentialFileReaderTest, Comb3)
|
||||
|
||||
TEST_F(PotentialFileReaderTest, Tersoff)
|
||||
{
|
||||
::testing::internal::CaptureStdout();
|
||||
if (!verbose) ::testing::internal::CaptureStdout();
|
||||
lmp->input->one("units metal");
|
||||
PotentialFileReader reader(lmp, "Si.tersoff", "Tersoff");
|
||||
::testing::internal::GetCapturedStdout();
|
||||
if (!verbose) ::testing::internal::GetCapturedStdout();
|
||||
|
||||
auto line = reader.next_line(PairTersoff::NPARAMS_PER_LINE);
|
||||
ASSERT_EQ(utils::count_words(line), PairTersoff::NPARAMS_PER_LINE);
|
||||
@ -110,9 +119,10 @@ TEST_F(PotentialFileReaderTest, Tersoff)
|
||||
|
||||
TEST_F(PotentialFileReaderTest, TersoffMod)
|
||||
{
|
||||
::testing::internal::CaptureStdout();
|
||||
if (!verbose) ::testing::internal::CaptureStdout();
|
||||
lmp->input->one("units metal");
|
||||
PotentialFileReader reader(lmp, "Si.tersoff.mod", "Tersoff/Mod");
|
||||
::testing::internal::GetCapturedStdout();
|
||||
if (!verbose) ::testing::internal::GetCapturedStdout();
|
||||
|
||||
auto line = reader.next_line(PairTersoffMOD::NPARAMS_PER_LINE);
|
||||
ASSERT_EQ(utils::count_words(line), PairTersoffMOD::NPARAMS_PER_LINE);
|
||||
@ -120,9 +130,10 @@ TEST_F(PotentialFileReaderTest, TersoffMod)
|
||||
|
||||
TEST_F(PotentialFileReaderTest, TersoffModC)
|
||||
{
|
||||
::testing::internal::CaptureStdout();
|
||||
if (!verbose) ::testing::internal::CaptureStdout();
|
||||
lmp->input->one("units metal");
|
||||
PotentialFileReader reader(lmp, "Si.tersoff.modc", "Tersoff/ModC");
|
||||
::testing::internal::GetCapturedStdout();
|
||||
if (!verbose) ::testing::internal::GetCapturedStdout();
|
||||
|
||||
auto line = reader.next_line(PairTersoffMODC::NPARAMS_PER_LINE);
|
||||
ASSERT_EQ(utils::count_words(line), PairTersoffMODC::NPARAMS_PER_LINE);
|
||||
@ -130,9 +141,10 @@ TEST_F(PotentialFileReaderTest, TersoffModC)
|
||||
|
||||
TEST_F(PotentialFileReaderTest, TersoffZBL)
|
||||
{
|
||||
::testing::internal::CaptureStdout();
|
||||
if (!verbose) ::testing::internal::CaptureStdout();
|
||||
lmp->input->one("units metal");
|
||||
PotentialFileReader reader(lmp, "SiC.tersoff.zbl", "Tersoff/ZBL");
|
||||
::testing::internal::GetCapturedStdout();
|
||||
if (!verbose) ::testing::internal::GetCapturedStdout();
|
||||
|
||||
auto line = reader.next_line(PairTersoffZBL::NPARAMS_PER_LINE);
|
||||
ASSERT_EQ(utils::count_words(line), PairTersoffZBL::NPARAMS_PER_LINE);
|
||||
@ -140,9 +152,10 @@ TEST_F(PotentialFileReaderTest, TersoffZBL)
|
||||
|
||||
TEST_F(PotentialFileReaderTest, GW)
|
||||
{
|
||||
::testing::internal::CaptureStdout();
|
||||
if (!verbose) ::testing::internal::CaptureStdout();
|
||||
lmp->input->one("units metal");
|
||||
PotentialFileReader reader(lmp, "SiC.gw", "GW");
|
||||
::testing::internal::GetCapturedStdout();
|
||||
if (!verbose) ::testing::internal::GetCapturedStdout();
|
||||
|
||||
auto line = reader.next_line(PairGW::NPARAMS_PER_LINE);
|
||||
ASSERT_EQ(utils::count_words(line), PairGW::NPARAMS_PER_LINE);
|
||||
@ -150,9 +163,10 @@ TEST_F(PotentialFileReaderTest, GW)
|
||||
|
||||
TEST_F(PotentialFileReaderTest, GWZBL)
|
||||
{
|
||||
::testing::internal::CaptureStdout();
|
||||
if (!verbose) ::testing::internal::CaptureStdout();
|
||||
lmp->input->one("units metal");
|
||||
PotentialFileReader reader(lmp, "SiC.gw.zbl", "GW/ZBL");
|
||||
::testing::internal::GetCapturedStdout();
|
||||
if (!verbose) ::testing::internal::GetCapturedStdout();
|
||||
|
||||
auto line = reader.next_line(PairGWZBL::NPARAMS_PER_LINE);
|
||||
ASSERT_EQ(utils::count_words(line), PairGWZBL::NPARAMS_PER_LINE);
|
||||
@ -160,9 +174,10 @@ TEST_F(PotentialFileReaderTest, GWZBL)
|
||||
|
||||
TEST_F(PotentialFileReaderTest, Nb3bHarmonic)
|
||||
{
|
||||
::testing::internal::CaptureStdout();
|
||||
if (!verbose) ::testing::internal::CaptureStdout();
|
||||
lmp->input->one("units metal");
|
||||
PotentialFileReader reader(lmp, "MOH.nb3b.harmonic", "NB3B Harmonic");
|
||||
::testing::internal::GetCapturedStdout();
|
||||
if (!verbose) ::testing::internal::GetCapturedStdout();
|
||||
|
||||
auto line = reader.next_line(PairNb3bHarmonic::NPARAMS_PER_LINE);
|
||||
ASSERT_EQ(utils::count_words(line), PairNb3bHarmonic::NPARAMS_PER_LINE);
|
||||
@ -170,9 +185,10 @@ TEST_F(PotentialFileReaderTest, Nb3bHarmonic)
|
||||
|
||||
TEST_F(PotentialFileReaderTest, Vashishta)
|
||||
{
|
||||
::testing::internal::CaptureStdout();
|
||||
if (!verbose) ::testing::internal::CaptureStdout();
|
||||
lmp->input->one("units metal");
|
||||
PotentialFileReader reader(lmp, "SiC.vashishta", "Vashishta");
|
||||
::testing::internal::GetCapturedStdout();
|
||||
if (!verbose) ::testing::internal::GetCapturedStdout();
|
||||
|
||||
auto line = reader.next_line(PairVashishta::NPARAMS_PER_LINE);
|
||||
ASSERT_EQ(utils::count_words(line), PairVashishta::NPARAMS_PER_LINE);
|
||||
@ -182,5 +198,9 @@ int main(int argc, char **argv)
|
||||
{
|
||||
MPI_Init(&argc, &argv);
|
||||
::testing::InitGoogleMock(&argc, argv);
|
||||
return RUN_ALL_TESTS();
|
||||
if ((argc > 1) && (strcmp(argv[1], "-v") == 0)) verbose = true;
|
||||
|
||||
int rv = RUN_ALL_TESTS();
|
||||
MPI_Finalize();
|
||||
return rv;
|
||||
}
|
||||
|
||||
Reference in New Issue
Block a user