forked from lijiext/lammps
Merge pull request #2098 from lammps/unittest
Add first part of an integrated unit test framework
This commit is contained in:
Axel Kohlmeyer
GitHub
commit
8691579def
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@ -0,0 +1,30 @@
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# - Find libyaml
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# Find the native Yaml headers and libraries.
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#
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# YAML_INCLUDE_DIRS - where to find yaml.h
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# YAML_LIBRARIES - List of libraries when using libyaml
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# YAML_FOUND - True if libyaml is found.
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#
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find_path(YAML_INCLUDE_DIR yaml.h PATH_SUFFIXES yaml)
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find_library(YAML_LIBRARY NAMES yaml)
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# handle the QUIET and REQUIRED arguments and
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# set YAML_FOUND to TRUE if all variables are non-zero
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include(FindPackageHandleStandardArgs)
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find_package_handle_standard_args(YAML DEFAULT_MSG YAML_LIBRARY YAML_INCLUDE_DIR)
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# Copy the results to the output variables and target.
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if(YAML_FOUND)
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set(YAML_LIBRARIES ${YAML_LIBRARY})
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set(YAML_INCLUDE_DIRS ${YAML_INCLUDE_DIR})
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if(NOT TARGET Yaml::Yaml)
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add_library(Yaml::Yaml UNKNOWN IMPORTED)
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set_target_properties(Yaml::Yaml PROPERTIES
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IMPORTED_LOCATION "${YAML_LIBRARY}"
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INTERFACE_INCLUDE_DIRECTORIES "${YAML_INCLUDE_DIR}")
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endif()
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endif()
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mark_as_advanced(YAML_INCLUDE_DIR YAML_LIBRARY)
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@ -0,0 +1,77 @@
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message(STATUS "Downloading and building Google Test library")
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if(CMAKE_BUILD_TYPE STREQUAL Debug)
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set(GTEST_LIB_POSTFIX d)
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else()
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set(GTEST_LIB_POSTFIX)
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endif()
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include(ExternalProject)
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ExternalProject_Add(googletest
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GIT_REPOSITORY https://github.com/google/googletest.git
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GIT_TAG release-1.10.0
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SOURCE_DIR "${CMAKE_BINARY_DIR}/gtest-src"
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BINARY_DIR "${CMAKE_BINARY_DIR}/gtest-build"
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CMAKE_ARGS ${CMAKE_REQUEST_PIC} ${CMAKE_EXTRA_GTEST_OPTS}
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-DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}
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-DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>
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-DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
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-DCMAKE_MAKE_PROGRAM=${CMAKE_MAKE_PROGRAM}
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-DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}
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BUILD_BYPRODUCTS <BINARY_DIR>/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gtest${GTEST_LIB_POSTFIX}.a
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<BINARY_DIR>/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gmock${GTEST_LIB_POSTFIX}.a
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<BINARY_DIR>/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gtest_main${GTEST_LIB_POSTFIX}.a
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<BINARY_DIR>/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gmock_main${GTEST_LIB_POSTFIX}.a
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LOG_DOWNLOAD ON
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LOG_CONFIGURE ON
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LOG_BUILD ON
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INSTALL_COMMAND ""
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TEST_COMMAND "")
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ExternalProject_Get_Property(googletest SOURCE_DIR)
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set(GTEST_INCLUDE_DIR ${SOURCE_DIR}/googletest/include)
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set(GMOCK_INCLUDE_DIR ${SOURCE_DIR}/googlemock/include)
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# workaround for CMake 3.10 on ubuntu 18.04
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file(MAKE_DIRECTORY ${GTEST_INCLUDE_DIR})
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file(MAKE_DIRECTORY ${GMOCK_INCLUDE_DIR})
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ExternalProject_Get_Property(googletest BINARY_DIR)
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set(GTEST_LIBRARY_PATH ${BINARY_DIR}/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gtest${GTEST_LIB_POSTFIX}.a)
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set(GMOCK_LIBRARY_PATH ${BINARY_DIR}/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gmock${GTEST_LIB_POSTFIX}.a)
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set(GTEST_MAIN_LIBRARY_PATH ${BINARY_DIR}/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gtest_main${GTEST_LIB_POSTFIX}.a)
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set(GMOCK_MAIN_LIBRARY_PATH ${BINARY_DIR}/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gmock_main${GTEST_LIB_POSTFIX}.a)
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# Prevent GoogleTest from overriding our compiler/linker options
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# when building with Visual Studio
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set(gtest_force_shared_crt ON CACHE BOOL "" FORCE)
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find_package(Threads QUIET)
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add_library(GTest::GTest UNKNOWN IMPORTED)
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set_target_properties(GTest::GTest PROPERTIES
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IMPORTED_LOCATION ${GTEST_LIBRARY_PATH}
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INTERFACE_INCLUDE_DIRECTORIES ${GTEST_INCLUDE_DIR}
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IMPORTED_LINK_INTERFACE_LIBRARIES ${CMAKE_THREAD_LIBS_INIT})
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add_dependencies(GTest::GTest googletest)
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add_library(GTest::GMock UNKNOWN IMPORTED)
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set_target_properties(GTest::GMock PROPERTIES
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IMPORTED_LOCATION ${GMOCK_LIBRARY_PATH}
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INTERFACE_INCLUDE_DIRECTORIES ${GMOCK_INCLUDE_DIR}
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IMPORTED_LINK_INTERFACE_LIBRARIES ${CMAKE_THREAD_LIBS_INIT})
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add_dependencies(GTest::GMock googletest)
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add_library(GTest::GTestMain UNKNOWN IMPORTED)
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set_target_properties(GTest::GTestMain PROPERTIES
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IMPORTED_LOCATION ${GTEST_MAIN_LIBRARY_PATH}
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INTERFACE_INCLUDE_DIRECTORIES ${GTEST_INCLUDE_DIR}
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IMPORTED_LINK_INTERFACE_LIBRARIES ${CMAKE_THREAD_LIBS_INIT})
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add_dependencies(GTest::GTestMain googletest)
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add_library(GTest::GMockMain UNKNOWN IMPORTED)
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set_target_properties(GTest::GMockMain PROPERTIES
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IMPORTED_LOCATION ${GMOCK_MAIN_LIBRARY_PATH}
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INTERFACE_INCLUDE_DIRECTORIES ${GMOCK_INCLUDE_DIR}
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IMPORTED_LINK_INTERFACE_LIBRARIES ${CMAKE_THREAD_LIBS_INIT})
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add_dependencies(GTest::GMockMain googletest)
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@ -4,48 +4,7 @@
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option(ENABLE_TESTING "Enable testing" OFF)
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if(ENABLE_TESTING)
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enable_testing()
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option(LAMMPS_TESTING_SOURCE_DIR "Location of lammps-testing source directory" "")
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option(LAMMPS_TESTING_GIT_TAG "Git tag of lammps-testing" "master")
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mark_as_advanced(LAMMPS_TESTING_SOURCE_DIR LAMMPS_TESTING_GIT_TAG)
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if (CMAKE_VERSION VERSION_GREATER "3.10.3" AND NOT LAMMPS_TESTING_SOURCE_DIR)
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include(FetchContent)
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FetchContent_Declare(lammps-testing
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GIT_REPOSITORY https://github.com/lammps/lammps-testing.git
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GIT_TAG ${LAMMPS_TESTING_GIT_TAG}
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)
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FetchContent_GetProperties(lammps-testing)
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if(NOT lammps-testing_POPULATED)
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message(STATUS "Downloading tests...")
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FetchContent_Populate(lammps-testing)
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endif()
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set(LAMMPS_TESTING_SOURCE_DIR ${lammps-testing_SOURCE_DIR})
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elseif(NOT LAMMPS_TESTING_SOURCE_DIR)
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message(WARNING "Full test-suite requires CMake >= 3.11 or copy of\n"
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"https://github.com/lammps/lammps-testing in LAMMPS_TESTING_SOURCE_DIR")
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endif()
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add_test(NAME ShowHelp COMMAND $<TARGET_FILE:lmp> -help)
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if(EXISTS ${LAMMPS_TESTING_SOURCE_DIR})
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message(STATUS "Running test discovery...")
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file(GLOB_RECURSE TEST_SCRIPTS ${LAMMPS_TESTING_SOURCE_DIR}/tests/core/*/in.*)
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foreach(script_path ${TEST_SCRIPTS})
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get_filename_component(TEST_NAME ${script_path} EXT)
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get_filename_component(SCRIPT_NAME ${script_path} NAME)
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get_filename_component(PARENT_DIR ${script_path} DIRECTORY)
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string(SUBSTRING ${TEST_NAME} 1 -1 TEST_NAME)
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string(REPLACE "-" "_" TEST_NAME ${TEST_NAME})
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string(REPLACE "+" "_" TEST_NAME ${TEST_NAME})
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set(TEST_NAME "test_core_${TEST_NAME}_serial")
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add_test(NAME ${TEST_NAME} COMMAND $<TARGET_FILE:lmp> -in ${SCRIPT_NAME} WORKING_DIRECTORY ${PARENT_DIR})
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endforeach()
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list(LENGTH TEST_SCRIPTS NUM_TESTS)
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message(STATUS "Found ${NUM_TESTS} tests.")
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endif()
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get_filename_component(LAMMPS_UNITTEST_DIR ${LAMMPS_SOURCE_DIR}/../unittest ABSOLUTE)
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get_filename_component(LAMMPS_UNITTEST_BIN ${CMAKE_BINARY_DIR}/unittest ABSOLUTE)
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add_subdirectory(${LAMMPS_UNITTEST_DIR} ${LAMMPS_UNITTEST_BIN})
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endif()
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@ -57,33 +57,64 @@ variable during configuration. Examples:
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.. _testing:
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Code Coverage and Testing
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---------------------------------------
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Code Coverage and Unit Testing
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------------------------------
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We do extensive regression testing of the LAMMPS code base on a continuous
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basis. Some of the logic to do this has been added to the CMake build so
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developers can run the tests directly on their workstation.
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The LAMMPS code is subject to multiple levels of automated testing
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during development: integration testing (i.e. whether the code compiles
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on various platforms and with a variety of settings), unit testing
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(i.e. whether certain individual parts of the code produce the expected
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results for given inputs), run testing (whether selected complete input
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decks run without crashing for multiple configurations), and regression
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testing (i.e. whether selected input examples reproduce the same
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results over a given number of steps and operations within a given
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error margin). The status of this automated testing can be viewed on
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`https://ci.lammps.org <https://ci.lammps.org>`_.
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The unit testing facility is integrated into the CMake build process
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of the LAMMPS source code distribution itself. It can be enabled by
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setting ``-D ENABLE_TESTING=on`` during the CMake configuration step.
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It requires the `YAML <http://pyyaml.org/>`_ library and development
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headers to compile and will download and compile the
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`Googletest <https://github.com/google/googletest/>`_ C++ test framework
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for programming the tests.
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After compilation is complete, the unit testing is started in the build
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folder using the ``ctest`` command, which is part of the CMake software.
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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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Start 2: MolPairStyle:hybrid
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2/26 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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100% tests passed, 0 tests failed out of 26
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Total Test time (real) = 0.27 sec
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.. note::
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this is incomplete and only represents a small subset of tests that we run
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This unit test framework is new and still under development.
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The coverage is only minimal and will be expanded over time.
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Tests styles of the same kind of style (e.g. pair styles or
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bond styles) are performed with the same executable using
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different input files in YAML format. So to add a test for
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another pair style can be done by copying the YAML file and
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editing the style settings and then running the individual test
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program with a flag to update the computed reference data.
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Detailed documentation about how to add new test program and
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the contents of the YAML files for existing test programs
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will be provided in time as well.
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.. code-block:: bash
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-D ENABLE_TESTING=value # enable simple run tests of LAMMPS, value = no (default) or yes
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-D LAMMPS_TESTING_SOURCE_DIR=path # path to lammps-testing repository (option if in custom location)
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-D LAMMPS_TESTING_GIT_TAG=value # version of lammps-testing repository that should be used, value = master (default) or custom git commit or tag
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If you enable testing in the CMake build it will create an additional
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||||
target called "test". You can run them with:
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.. code-block:: bash
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cmake --build . test
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The test cases used come from the lammps-testing repository. They are
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derivatives of the examples folder with some modifications to make the
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run faster.
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------------
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You can also collect code coverage metrics while running the tests by
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enabling coverage support during building.
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@ -93,16 +124,15 @@ enabling coverage support during building.
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-D ENABLE_COVERAGE=value # enable coverage measurements, value = no (default) or yes
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This will also add the following targets to generate coverage reports
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||||
after running the LAMMPS executable:
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after running the LAMMPS executable or the unit tests:
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.. code-block:: bash
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make test # run tests first!
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make gen_coverage_html # generate coverage report in HTML format
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make gen_coverage_xml # generate coverage report in XML format
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||||
|
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These reports require GCOVR to be installed. The easiest way to do this
|
||||
to install it via pip:
|
||||
These reports require `GCOVR <https://gcovr.com/>`_ to be installed. The easiest way
|
||||
to do this to install it via pip:
|
||||
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.. code-block:: bash
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||||
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|
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@ -0,0 +1,3 @@
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include(GTest)
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add_subdirectory(force-styles)
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@ -0,0 +1,55 @@
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find_package(YAML)
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if(NOT YAML_FOUND)
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message(STATUS "Skipping tests because libyaml is not found")
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||||
return()
|
||||
endif()
|
||||
|
||||
set(TEST_INPUT_FOLDER ${CMAKE_CURRENT_SOURCE_DIR}/tests)
|
||||
add_library(style_tests STATIC yaml_writer.cpp error_stats.cpp test_config_reader.cpp test_main.cpp)
|
||||
target_compile_definitions(style_tests PRIVATE TEST_INPUT_FOLDER=${TEST_INPUT_FOLDER})
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||||
target_link_libraries(style_tests PRIVATE MPI::MPI_CXX Yaml::Yaml)
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||||
|
||||
# pair style tester
|
||||
add_executable(pair_style pair_style.cpp)
|
||||
target_link_libraries(pair_style PRIVATE lammps GTest::GTest GTest::GMock style_tests)
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||||
|
||||
# tests for a molecular systems and related pair styles
|
||||
file(GLOB MOL_PAIR_TESTS LIST_DIRECTORIES false ${TEST_INPUT_FOLDER}/mol-pair-*.yaml)
|
||||
foreach(TEST ${MOL_PAIR_TESTS})
|
||||
string(REGEX REPLACE "^.*mol-pair-(.*)\.yaml" "MolPairStyle:\\1" TNAME ${TEST})
|
||||
add_test(NAME ${TNAME} COMMAND pair_style ${TEST}
|
||||
WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
|
||||
endforeach()
|
||||
|
||||
# tests for atomic systems and related pair styles
|
||||
file(GLOB ATOMIC_PAIR_TESTS LIST_DIRECTORIES false ${TEST_INPUT_FOLDER}/atomic-pair-*.yaml)
|
||||
foreach(TEST ${ATOMIC_PAIR_TESTS})
|
||||
string(REGEX REPLACE "^.*atomic-pair-(.*)\.yaml" "AtomicPairStyle:\\1" TNAME ${TEST})
|
||||
add_test(NAME ${TNAME} COMMAND pair_style ${TEST}
|
||||
WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
|
||||
set_tests_properties(${TNAME} PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR}")
|
||||
endforeach()
|
||||
|
||||
# bond style tester
|
||||
add_executable(bond_style bond_style.cpp)
|
||||
target_link_libraries(bond_style PRIVATE lammps GTest::GTest GTest::GMock style_tests)
|
||||
|
||||
file(GLOB BOND_TESTS LIST_DIRECTORIES false ${TEST_INPUT_FOLDER}/bond-*.yaml)
|
||||
foreach(TEST ${BOND_TESTS})
|
||||
string(REGEX REPLACE "^.*bond-(.*)\.yaml" "BondStyle:\\1" TNAME ${TEST})
|
||||
add_test(NAME ${TNAME} COMMAND bond_style ${TEST}
|
||||
WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
|
||||
endforeach()
|
||||
|
||||
# angle style tester
|
||||
add_executable(angle_style angle_style.cpp)
|
||||
target_link_libraries(angle_style PRIVATE lammps GTest::GTest GTest::GMock style_tests)
|
||||
|
||||
file(GLOB ANGLE_TESTS LIST_DIRECTORIES false ${TEST_INPUT_FOLDER}/angle-*.yaml)
|
||||
foreach(TEST ${ANGLE_TESTS})
|
||||
string(REGEX REPLACE "^.*angle-(.*)\.yaml" "AngleStyle:\\1" TNAME ${TEST})
|
||||
add_test(NAME ${TNAME} COMMAND angle_style ${TEST}
|
||||
WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
|
||||
endforeach()
|
||||
|
||||
|
|
@ -0,0 +1,753 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
// unit tests for angle styles intended for molecular systems
|
||||
|
||||
#include "yaml_reader.h"
|
||||
#include "yaml_writer.h"
|
||||
#include "error_stats.h"
|
||||
#include "test_config.h"
|
||||
#include "test_config_reader.h"
|
||||
#include "test_main.h"
|
||||
|
||||
#include "gtest/gtest.h"
|
||||
#include "gmock/gmock.h"
|
||||
|
||||
#include "lammps.h"
|
||||
#include "atom.h"
|
||||
#include "modify.h"
|
||||
#include "compute.h"
|
||||
#include "force.h"
|
||||
#include "angle.h"
|
||||
#include "info.h"
|
||||
#include "input.h"
|
||||
#include "universe.h"
|
||||
|
||||
#include <mpi.h>
|
||||
#include <cstdio>
|
||||
#include <cstring>
|
||||
#include <cstdlib>
|
||||
#include <cctype>
|
||||
#include <ctime>
|
||||
|
||||
#include <iostream>
|
||||
#include <map>
|
||||
#include <string>
|
||||
#include <utility>
|
||||
#include <vector>
|
||||
|
||||
using ::testing::StartsWith;
|
||||
using ::testing::HasSubstr;
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
static void delete_file(const std::string & filename) {
|
||||
remove(filename.c_str());
|
||||
};
|
||||
|
||||
void cleanup_lammps(LAMMPS *lmp, const TestConfig &cfg)
|
||||
{
|
||||
delete_file(cfg.basename + ".restart");
|
||||
delete_file(cfg.basename + ".data");
|
||||
delete_file(cfg.basename + "-coeffs.in");
|
||||
delete lmp;
|
||||
}
|
||||
|
||||
LAMMPS *init_lammps(int argc, char **argv,
|
||||
const TestConfig &cfg,
|
||||
const bool newton=true)
|
||||
{
|
||||
LAMMPS *lmp;
|
||||
|
||||
lmp = new LAMMPS(argc, argv, MPI_COMM_WORLD);
|
||||
|
||||
// check if prerequisite styles are available
|
||||
Info *info = new Info(lmp);
|
||||
int nfail = 0;
|
||||
for (auto& prerequisite : cfg.prerequisites) {
|
||||
std::string style = prerequisite.second;
|
||||
|
||||
// this is a test for angle styles, so if the suffixed
|
||||
// version is not available, there is no reason to test.
|
||||
if (prerequisite.first == "angle") {
|
||||
if (lmp->suffix_enable) {
|
||||
style += "/";
|
||||
style += lmp->suffix;
|
||||
}
|
||||
}
|
||||
|
||||
if (!info->has_style(prerequisite.first,style)) ++nfail;
|
||||
}
|
||||
if (nfail > 0) {
|
||||
delete info;
|
||||
cleanup_lammps(lmp,cfg);
|
||||
return nullptr;
|
||||
}
|
||||
|
||||
// utility lambdas to improve readability
|
||||
auto command = [&](const std::string & line) {
|
||||
lmp->input->one(line.c_str());
|
||||
};
|
||||
auto parse_input_script = [&](const std::string & filename) {
|
||||
lmp->input->file(filename.c_str());
|
||||
};
|
||||
|
||||
if (newton) {
|
||||
command("variable newton_bond index on");
|
||||
} else {
|
||||
command("variable newton_bond index off");
|
||||
}
|
||||
|
||||
command("variable input_dir index " + INPUT_FOLDER);
|
||||
|
||||
for (auto& pre_command : cfg.pre_commands) {
|
||||
command(pre_command);
|
||||
}
|
||||
|
||||
std::string input_file = INPUT_FOLDER + PATH_SEP + cfg.input_file;
|
||||
parse_input_script(input_file);
|
||||
|
||||
command("angle_style " + cfg.angle_style);
|
||||
|
||||
for (auto& angle_coeff : cfg.angle_coeff) {
|
||||
command("angle_coeff " + angle_coeff);
|
||||
}
|
||||
|
||||
for (auto& post_command : cfg.post_commands) {
|
||||
command(post_command);
|
||||
}
|
||||
|
||||
command("run 0 post no");
|
||||
command("write_restart " + cfg.basename + ".restart");
|
||||
command("write_data " + cfg.basename + ".data");
|
||||
command("write_coeff " + cfg.basename + "-coeffs.in");
|
||||
|
||||
return lmp;
|
||||
}
|
||||
|
||||
void run_lammps(LAMMPS *lmp)
|
||||
{
|
||||
// utility lambda to improve readability
|
||||
auto command = [&](const std::string & line) {
|
||||
lmp->input->one(line.c_str());
|
||||
};
|
||||
|
||||
command("fix 1 all nve");
|
||||
command("compute pe all pe/atom");
|
||||
command("compute sum all reduce sum c_pe");
|
||||
command("thermo_style custom step temp pe press c_sum");
|
||||
command("thermo 2");
|
||||
command("run 4 post no");
|
||||
}
|
||||
|
||||
void restart_lammps(LAMMPS *lmp, const TestConfig &cfg)
|
||||
{
|
||||
// utility lambda to improve readability
|
||||
auto command = [&](const std::string & line) {
|
||||
lmp->input->one(line.c_str());
|
||||
};
|
||||
|
||||
command("clear");
|
||||
command("read_restart " + cfg.basename + ".restart");
|
||||
|
||||
if (!lmp->force->angle) {
|
||||
command("angle_style " + cfg.angle_style);
|
||||
}
|
||||
|
||||
if ((cfg.angle_style.substr(0,6) == "hybrid")
|
||||
|| !lmp->force->angle->writedata) {
|
||||
for (auto& angle_coeff : cfg.angle_coeff) {
|
||||
command("angle_coeff " + angle_coeff);
|
||||
}
|
||||
}
|
||||
|
||||
for (auto& post_command : cfg.post_commands) {
|
||||
command(post_command);
|
||||
}
|
||||
|
||||
command("run 0 post no");
|
||||
}
|
||||
|
||||
void data_lammps(LAMMPS *lmp, const TestConfig &cfg)
|
||||
{
|
||||
// utility lambdas to improve readability
|
||||
auto command = [&](const std::string & line) {
|
||||
lmp->input->one(line.c_str());
|
||||
};
|
||||
auto parse_input_script = [&](const std::string & filename) {
|
||||
lmp->input->file(filename.c_str());
|
||||
};
|
||||
|
||||
command("clear");
|
||||
command("variable angle_style delete");
|
||||
command("variable data_file delete");
|
||||
command("variable newton_bond delete");
|
||||
command("variable newton_bond index on");
|
||||
|
||||
for (auto& pre_command : cfg.pre_commands) {
|
||||
command(pre_command);
|
||||
}
|
||||
|
||||
command("variable angle_style index '" + cfg.angle_style + "'");
|
||||
command("variable data_file index " + cfg.basename + ".data");
|
||||
|
||||
std::string input_file = INPUT_FOLDER + PATH_SEP + cfg.input_file;
|
||||
parse_input_script(input_file);
|
||||
|
||||
for (auto& angle_coeff : cfg.angle_coeff) {
|
||||
command("angle_coeff " + angle_coeff);
|
||||
}
|
||||
|
||||
for (auto& post_command : cfg.post_commands) {
|
||||
command(post_command);
|
||||
}
|
||||
|
||||
command("run 0 post no");
|
||||
}
|
||||
|
||||
|
||||
// re-generate yaml file with current settings.
|
||||
|
||||
void generate_yaml_file(const char *outfile, const TestConfig &config)
|
||||
{
|
||||
// initialize system geometry
|
||||
const char *args[] = {"AngleStyle", "-log", "none", "-echo", "screen", "-nocite" };
|
||||
char **argv = (char **)args;
|
||||
int argc = sizeof(args)/sizeof(char *);
|
||||
LAMMPS *lmp = init_lammps(argc,argv,config);
|
||||
if (!lmp) {
|
||||
std::cerr << "One or more prerequisite styles are not available "
|
||||
"in this LAMMPS configuration:\n";
|
||||
for (auto& prerequisite : config.prerequisites) {
|
||||
std::cerr << prerequisite.first << "_style "
|
||||
<< prerequisite.second << "\n";
|
||||
}
|
||||
return;
|
||||
}
|
||||
|
||||
const int natoms = lmp->atom->natoms;
|
||||
const int bufsize = 256;
|
||||
char buf[bufsize];
|
||||
std::string block("");
|
||||
|
||||
YamlWriter writer(outfile);
|
||||
|
||||
// lammps_version
|
||||
writer.emit("lammps_version", lmp->universe->version);
|
||||
|
||||
// date_generated
|
||||
std::time_t now = time(NULL);
|
||||
block = ctime(&now);
|
||||
block = block.substr(0,block.find("\n")-1);
|
||||
writer.emit("date_generated", block);
|
||||
|
||||
// epsilon
|
||||
writer.emit("epsilon", config.epsilon);
|
||||
|
||||
// prerequisites
|
||||
block.clear();
|
||||
for (auto& prerequisite : config.prerequisites) {
|
||||
block += prerequisite.first + " " + prerequisite.second + "\n";
|
||||
}
|
||||
writer.emit_block("prerequisites", block);
|
||||
|
||||
// pre_commands
|
||||
block.clear();
|
||||
for (auto& command : config.pre_commands) {
|
||||
block += command + "\n";
|
||||
}
|
||||
writer.emit_block("pre_commands", block);
|
||||
|
||||
// post_commands
|
||||
block.clear();
|
||||
for (auto& command : config.post_commands) {
|
||||
block += command + "\n";
|
||||
}
|
||||
writer.emit_block("post_commands", block);
|
||||
|
||||
// input_file
|
||||
writer.emit("input_file", config.input_file);
|
||||
|
||||
// angle_style
|
||||
writer.emit("angle_style", config.angle_style);
|
||||
|
||||
// angle_coeff
|
||||
block.clear();
|
||||
for (auto& angle_coeff : config.angle_coeff) {
|
||||
block += angle_coeff + "\n";
|
||||
}
|
||||
writer.emit_block("angle_coeff", block);
|
||||
|
||||
// extract
|
||||
block.clear();
|
||||
std::stringstream outstr;
|
||||
for (auto& data : config.extract) {
|
||||
outstr << data.first << " " << data.second << std::endl;
|
||||
}
|
||||
writer.emit_block("extract", outstr.str());
|
||||
|
||||
// natoms
|
||||
writer.emit("natoms", natoms);
|
||||
|
||||
// init_energy
|
||||
writer.emit("init_energy", lmp->force->angle->energy);
|
||||
|
||||
// init_stress
|
||||
double *stress = lmp->force->angle->virial;
|
||||
snprintf(buf,bufsize,"% 23.16e % 23.16e % 23.16e % 23.16e % 23.16e % 23.16e",
|
||||
stress[0],stress[1],stress[2],stress[3],stress[4],stress[5]);
|
||||
writer.emit_block("init_stress", buf);
|
||||
|
||||
// init_forces
|
||||
block.clear();
|
||||
double **f = lmp->atom->f;
|
||||
tagint *tag = lmp->atom->tag;
|
||||
for (int i=0; i < natoms; ++i) {
|
||||
snprintf(buf,bufsize,"% 3d % 23.16e % 23.16e % 23.16e\n",
|
||||
(int)tag[i], f[i][0], f[i][1], f[i][2]);
|
||||
block += buf;
|
||||
}
|
||||
writer.emit_block("init_forces", block);
|
||||
|
||||
// do a few steps of MD
|
||||
run_lammps(lmp);
|
||||
|
||||
// run_energy
|
||||
writer.emit("run_energy", lmp->force->angle->energy);
|
||||
|
||||
// run_stress
|
||||
stress = lmp->force->angle->virial;
|
||||
snprintf(buf,bufsize,"% 23.16e % 23.16e % 23.16e % 23.16e % 23.16e % 23.16e",
|
||||
stress[0],stress[1],stress[2],stress[3],stress[4],stress[5]);
|
||||
writer.emit_block("run_stress", buf);
|
||||
|
||||
block.clear();
|
||||
f = lmp->atom->f;
|
||||
tag = lmp->atom->tag;
|
||||
for (int i=0; i < natoms; ++i) {
|
||||
snprintf(buf,bufsize,"% 3d % 23.16e % 23.16e % 23.16e\n",
|
||||
(int)tag[i], f[i][0], f[i][1], f[i][2]);
|
||||
block += buf;
|
||||
}
|
||||
writer.emit_block("run_forces", block);
|
||||
|
||||
cleanup_lammps(lmp,config);
|
||||
return;
|
||||
}
|
||||
|
||||
TEST(AngleStyle, plain) {
|
||||
const char *args[] = {"AngleStyle", "-log", "none", "-echo", "screen", "-nocite" };
|
||||
char **argv = (char **)args;
|
||||
int argc = sizeof(args)/sizeof(char *);
|
||||
|
||||
::testing::internal::CaptureStdout();
|
||||
LAMMPS *lmp = init_lammps(argc,argv,test_config,true);
|
||||
std::string output = ::testing::internal::GetCapturedStdout();
|
||||
|
||||
if (!lmp) {
|
||||
std::cerr << "One or more prerequisite styles are not available "
|
||||
"in this LAMMPS configuration:\n";
|
||||
for (auto& prerequisite : test_config.prerequisites) {
|
||||
std::cerr << prerequisite.first << "_style "
|
||||
<< prerequisite.second << "\n";
|
||||
}
|
||||
GTEST_SKIP();
|
||||
}
|
||||
|
||||
EXPECT_THAT(output, StartsWith("LAMMPS ("));
|
||||
EXPECT_THAT(output, HasSubstr("Loop time"));
|
||||
|
||||
// abort if running in parallel and not all atoms are local
|
||||
const int nlocal = lmp->atom->nlocal;
|
||||
ASSERT_EQ(lmp->atom->natoms,nlocal);
|
||||
|
||||
double epsilon = test_config.epsilon;
|
||||
double **f=lmp->atom->f;
|
||||
tagint *tag=lmp->atom->tag;
|
||||
ErrorStats stats;
|
||||
stats.reset();
|
||||
const std::vector<coord_t> &f_ref = test_config.init_forces;
|
||||
ASSERT_EQ(nlocal+1,f_ref.size());
|
||||
for (int i=0; i < nlocal; ++i) {
|
||||
EXPECT_FP_LE_WITH_EPS(f[i][0], f_ref[tag[i]].x, epsilon);
|
||||
EXPECT_FP_LE_WITH_EPS(f[i][1], f_ref[tag[i]].y, epsilon);
|
||||
EXPECT_FP_LE_WITH_EPS(f[i][2], f_ref[tag[i]].z, epsilon);
|
||||
}
|
||||
if (print_stats)
|
||||
std::cerr << "init_forces stats, newton on: " << stats << std::endl;
|
||||
|
||||
Angle *angle = lmp->force->angle;
|
||||
double *stress = angle->virial;
|
||||
stats.reset();
|
||||
EXPECT_FP_LE_WITH_EPS(stress[0], test_config.init_stress.xx, epsilon);
|
||||
EXPECT_FP_LE_WITH_EPS(stress[1], test_config.init_stress.yy, epsilon);
|
||||
EXPECT_FP_LE_WITH_EPS(stress[2], test_config.init_stress.zz, epsilon);
|
||||
EXPECT_FP_LE_WITH_EPS(stress[3], test_config.init_stress.xy, epsilon);
|
||||
EXPECT_FP_LE_WITH_EPS(stress[4], test_config.init_stress.xz, epsilon);
|
||||
EXPECT_FP_LE_WITH_EPS(stress[5], test_config.init_stress.yz, epsilon);
|
||||
if (print_stats)
|
||||
std::cerr << "init_stress stats, newton on: " << stats << std::endl;
|
||||
|
||||
stats.reset();
|
||||
EXPECT_FP_LE_WITH_EPS(angle->energy, test_config.init_energy, epsilon);
|
||||
if (print_stats)
|
||||
std::cerr << "init_energy stats, newton on: " << stats << std::endl;
|
||||
|
||||
if (!verbose) ::testing::internal::CaptureStdout();
|
||||
run_lammps(lmp);
|
||||
if (!verbose) ::testing::internal::GetCapturedStdout();
|
||||
|
||||
f = lmp->atom->f;
|
||||
stress = angle->virial;
|
||||
const std::vector<coord_t> &f_run = test_config.run_forces;
|
||||
ASSERT_EQ(nlocal+1,f_run.size());
|
||||
stats.reset();
|
||||
for (int i=0; i < nlocal; ++i) {
|
||||
EXPECT_FP_LE_WITH_EPS(f[i][0], f_run[tag[i]].x, 10*epsilon);
|
||||
EXPECT_FP_LE_WITH_EPS(f[i][1], f_run[tag[i]].y, 10*epsilon);
|
||||
EXPECT_FP_LE_WITH_EPS(f[i][2], f_run[tag[i]].z, 10*epsilon);
|
||||
}
|
||||
if (print_stats)
|
||||
std::cerr << "run_forces stats, newton on: " << stats << std::endl;
|
||||
|
||||
stress = angle->virial;
|
||||
stats.reset();
|
||||
EXPECT_FP_LE_WITH_EPS(stress[0], test_config.run_stress.xx, epsilon);
|
||||
EXPECT_FP_LE_WITH_EPS(stress[1], test_config.run_stress.yy, epsilon);
|
||||
EXPECT_FP_LE_WITH_EPS(stress[2], test_config.run_stress.zz, epsilon);
|
||||
EXPECT_FP_LE_WITH_EPS(stress[3], test_config.run_stress.xy, epsilon);
|
||||
EXPECT_FP_LE_WITH_EPS(stress[4], test_config.run_stress.xz, epsilon);
|
||||
EXPECT_FP_LE_WITH_EPS(stress[5], test_config.run_stress.yz, epsilon);
|
||||
if (print_stats)
|
||||
std::cerr << "run_stress stats, newton on: " << stats << std::endl;
|
||||
|
||||
stats.reset();
|
||||
int id = lmp->modify->find_compute("sum");
|
||||
double energy = lmp->modify->compute[id]->compute_scalar();
|
||||
EXPECT_FP_LE_WITH_EPS(angle->energy, test_config.run_energy, epsilon);
|
||||
EXPECT_FP_LE_WITH_EPS(angle->energy, energy, epsilon);
|
||||
if (print_stats)
|
||||
std::cerr << "run_energy stats, newton on: " << stats << std::endl;
|
||||
|
||||
if (!verbose) ::testing::internal::CaptureStdout();
|
||||
cleanup_lammps(lmp,test_config);
|
||||
lmp = init_lammps(argc,argv,test_config,false);
|
||||
if (!verbose) ::testing::internal::GetCapturedStdout();
|
||||
|
||||
f=lmp->atom->f;
|
||||
tag=lmp->atom->tag;
|
||||
stats.reset();
|
||||
for (int i=0; i < nlocal; ++i) {
|
||||
EXPECT_FP_LE_WITH_EPS(f[i][0], f_ref[tag[i]].x, epsilon);
|
||||
EXPECT_FP_LE_WITH_EPS(f[i][1], f_ref[tag[i]].y, epsilon);
|
||||
EXPECT_FP_LE_WITH_EPS(f[i][2], f_ref[tag[i]].z, epsilon);
|
||||
}
|
||||
if (print_stats)
|
||||
std::cerr << "init_forces stats, newton off:" << stats << std::endl;
|
||||
|
||||
angle = lmp->force->angle;
|
||||
stress = angle->virial;
|
||||
stats.reset();
|
||||
EXPECT_FP_LE_WITH_EPS(stress[0], test_config.init_stress.xx, 2*epsilon);
|
||||
EXPECT_FP_LE_WITH_EPS(stress[1], test_config.init_stress.yy, 2*epsilon);
|
||||
EXPECT_FP_LE_WITH_EPS(stress[2], test_config.init_stress.zz, 2*epsilon);
|
||||
EXPECT_FP_LE_WITH_EPS(stress[3], test_config.init_stress.xy, 2*epsilon);
|
||||
EXPECT_FP_LE_WITH_EPS(stress[4], test_config.init_stress.xz, 2*epsilon);
|
||||
EXPECT_FP_LE_WITH_EPS(stress[5], test_config.init_stress.yz, 2*epsilon);
|
||||
if (print_stats)
|
||||
std::cerr << "init_stress stats, newton off:" << stats << std::endl;
|
||||
|
||||
stats.reset();
|
||||
EXPECT_FP_LE_WITH_EPS(angle->energy, test_config.init_energy, epsilon);
|
||||
if (print_stats)
|
||||
std::cerr << "init_energy stats, newton off:" << stats << std::endl;
|
||||
|
||||
if (!verbose) ::testing::internal::CaptureStdout();
|
||||
run_lammps(lmp);
|
||||
if (!verbose) ::testing::internal::GetCapturedStdout();
|
||||
|
||||
f = lmp->atom->f;
|
||||
stress = angle->virial;
|
||||
stats.reset();
|
||||
for (int i=0; i < nlocal; ++i) {
|
||||
EXPECT_FP_LE_WITH_EPS(f[i][0], f_run[tag[i]].x, 10*epsilon);
|
||||
EXPECT_FP_LE_WITH_EPS(f[i][1], f_run[tag[i]].y, 10*epsilon);
|
||||
EXPECT_FP_LE_WITH_EPS(f[i][2], f_run[tag[i]].z, 10*epsilon);
|
||||
}
|
||||
if (print_stats)
|
||||
std::cerr << "run_forces stats, newton off:" << stats << std::endl;
|
||||
|
||||
stress = angle->virial;
|
||||
stats.reset();
|
||||
EXPECT_FP_LE_WITH_EPS(stress[0], test_config.run_stress.xx, epsilon);
|
||||
EXPECT_FP_LE_WITH_EPS(stress[1], test_config.run_stress.yy, epsilon);
|
||||
EXPECT_FP_LE_WITH_EPS(stress[2], test_config.run_stress.zz, epsilon);
|
||||
EXPECT_FP_LE_WITH_EPS(stress[3], test_config.run_stress.xy, epsilon);
|
||||
EXPECT_FP_LE_WITH_EPS(stress[4], test_config.run_stress.xz, epsilon);
|
||||
EXPECT_FP_LE_WITH_EPS(stress[5], test_config.run_stress.yz, epsilon);
|
||||
if (print_stats)
|
||||
std::cerr << "run_stress stats, newton off:" << stats << std::endl;
|
||||
|
||||
stats.reset();
|
||||
id = lmp->modify->find_compute("sum");
|
||||
energy = lmp->modify->compute[id]->compute_scalar();
|
||||
EXPECT_FP_LE_WITH_EPS(angle->energy, test_config.run_energy, epsilon);
|
||||
EXPECT_FP_LE_WITH_EPS(angle->energy, energy, epsilon);
|
||||
if (print_stats)
|
||||
std::cerr << "run_energy stats, newton off:" << stats << std::endl;
|
||||
|
||||
if (!verbose) ::testing::internal::CaptureStdout();
|
||||
restart_lammps(lmp, test_config);
|
||||
if (!verbose) ::testing::internal::GetCapturedStdout();
|
||||
|
||||
f=lmp->atom->f;
|
||||
tag=lmp->atom->tag;
|
||||
stats.reset();
|
||||
ASSERT_EQ(nlocal+1,f_ref.size());
|
||||
for (int i=0; i < nlocal; ++i) {
|
||||
EXPECT_FP_LE_WITH_EPS(f[i][0], f_ref[tag[i]].x, epsilon);
|
||||
EXPECT_FP_LE_WITH_EPS(f[i][1], f_ref[tag[i]].y, epsilon);
|
||||
EXPECT_FP_LE_WITH_EPS(f[i][2], f_ref[tag[i]].z, epsilon);
|
||||
}
|
||||
if (print_stats)
|
||||
std::cerr << "restart_forces stats:" << stats << std::endl;
|
||||
|
||||
angle = lmp->force->angle;
|
||||
stress = angle->virial;
|
||||
stats.reset();
|
||||
EXPECT_FP_LE_WITH_EPS(stress[0], test_config.init_stress.xx, epsilon);
|
||||
EXPECT_FP_LE_WITH_EPS(stress[1], test_config.init_stress.yy, epsilon);
|
||||
EXPECT_FP_LE_WITH_EPS(stress[2], test_config.init_stress.zz, epsilon);
|
||||
EXPECT_FP_LE_WITH_EPS(stress[3], test_config.init_stress.xy, epsilon);
|
||||
EXPECT_FP_LE_WITH_EPS(stress[4], test_config.init_stress.xz, epsilon);
|
||||
EXPECT_FP_LE_WITH_EPS(stress[5], test_config.init_stress.yz, epsilon);
|
||||
if (print_stats)
|
||||
std::cerr << "restart_stress stats:" << stats << std::endl;
|
||||
|
||||
stats.reset();
|
||||
EXPECT_FP_LE_WITH_EPS(angle->energy, test_config.init_energy, epsilon);
|
||||
if (print_stats)
|
||||
std::cerr << "restart_energy stats:" << stats << std::endl;
|
||||
|
||||
if (!verbose) ::testing::internal::CaptureStdout();
|
||||
data_lammps(lmp, test_config);
|
||||
if (!verbose) ::testing::internal::GetCapturedStdout();
|
||||
|
||||
f=lmp->atom->f;
|
||||
tag=lmp->atom->tag;
|
||||
stats.reset();
|
||||
ASSERT_EQ(nlocal+1,f_ref.size());
|
||||
for (int i=0; i < nlocal; ++i) {
|
||||
EXPECT_FP_LE_WITH_EPS(f[i][0], f_ref[tag[i]].x, epsilon);
|
||||
EXPECT_FP_LE_WITH_EPS(f[i][1], f_ref[tag[i]].y, epsilon);
|
||||
EXPECT_FP_LE_WITH_EPS(f[i][2], f_ref[tag[i]].z, epsilon);
|
||||
}
|
||||
if (print_stats)
|
||||
std::cerr << "data_forces stats:" << stats << std::endl;
|
||||
|
||||
angle = lmp->force->angle;
|
||||
stress = angle->virial;
|
||||
stats.reset();
|
||||
EXPECT_FP_LE_WITH_EPS(stress[0], test_config.init_stress.xx, epsilon);
|
||||
EXPECT_FP_LE_WITH_EPS(stress[1], test_config.init_stress.yy, epsilon);
|
||||
EXPECT_FP_LE_WITH_EPS(stress[2], test_config.init_stress.zz, epsilon);
|
||||
EXPECT_FP_LE_WITH_EPS(stress[3], test_config.init_stress.xy, epsilon);
|
||||
EXPECT_FP_LE_WITH_EPS(stress[4], test_config.init_stress.xz, epsilon);
|
||||
EXPECT_FP_LE_WITH_EPS(stress[5], test_config.init_stress.yz, epsilon);
|
||||
if (print_stats)
|
||||
std::cerr << "data_stress stats:" << stats << std::endl;
|
||||
|
||||
stats.reset();
|
||||
EXPECT_FP_LE_WITH_EPS(angle->energy, test_config.init_energy, epsilon);
|
||||
if (print_stats)
|
||||
std::cerr << "data_energy stats:" << stats << std::endl;
|
||||
|
||||
if (!verbose) ::testing::internal::CaptureStdout();
|
||||
cleanup_lammps(lmp,test_config);
|
||||
if (!verbose) ::testing::internal::GetCapturedStdout();
|
||||
};
|
||||
|
||||
TEST(AngleStyle, omp) {
|
||||
if (!LAMMPS::is_installed_pkg("USER-OMP")) GTEST_SKIP();
|
||||
const char *args[] = {"AngleStyle", "-log", "none", "-echo", "screen",
|
||||
"-nocite", "-pk", "omp", "4", "-sf", "omp"};
|
||||
char **argv = (char **)args;
|
||||
int argc = sizeof(args)/sizeof(char *);
|
||||
|
||||
::testing::internal::CaptureStdout();
|
||||
LAMMPS *lmp = init_lammps(argc,argv,test_config,true);
|
||||
std::string output = ::testing::internal::GetCapturedStdout();
|
||||
|
||||
if (!lmp) {
|
||||
std::cerr << "One or more prerequisite styles with /omp suffix\n"
|
||||
"are not available in this LAMMPS configuration:\n";
|
||||
for (auto& prerequisite : test_config.prerequisites) {
|
||||
std::cerr << prerequisite.first << "_style "
|
||||
<< prerequisite.second << "\n";
|
||||
}
|
||||
GTEST_SKIP();
|
||||
}
|
||||
|
||||
EXPECT_THAT(output, StartsWith("LAMMPS ("));
|
||||
EXPECT_THAT(output, HasSubstr("Loop time"));
|
||||
|
||||
// abort if running in parallel and not all atoms are local
|
||||
const int nlocal = lmp->atom->nlocal;
|
||||
ASSERT_EQ(lmp->atom->natoms,nlocal);
|
||||
|
||||
// relax error a bit for USER-OMP package
|
||||
double epsilon = 5.0*test_config.epsilon;
|
||||
double **f=lmp->atom->f;
|
||||
tagint *tag=lmp->atom->tag;
|
||||
const std::vector<coord_t> &f_ref = test_config.init_forces;
|
||||
ErrorStats stats;
|
||||
stats.reset();
|
||||
for (int i=0; i < nlocal; ++i) {
|
||||
EXPECT_FP_LE_WITH_EPS(f[i][0], f_ref[tag[i]].x, epsilon);
|
||||
EXPECT_FP_LE_WITH_EPS(f[i][1], f_ref[tag[i]].y, epsilon);
|
||||
EXPECT_FP_LE_WITH_EPS(f[i][2], f_ref[tag[i]].z, epsilon);
|
||||
}
|
||||
if (print_stats)
|
||||
std::cerr << "init_forces stats, newton on: " << stats << std::endl;
|
||||
|
||||
Angle *angle = lmp->force->angle;
|
||||
double *stress = angle->virial;
|
||||
|
||||
stats.reset();
|
||||
EXPECT_FP_LE_WITH_EPS(stress[0], test_config.init_stress.xx, 10*epsilon);
|
||||
EXPECT_FP_LE_WITH_EPS(stress[1], test_config.init_stress.yy, 10*epsilon);
|
||||
EXPECT_FP_LE_WITH_EPS(stress[2], test_config.init_stress.zz, 10*epsilon);
|
||||
EXPECT_FP_LE_WITH_EPS(stress[3], test_config.init_stress.xy, 10*epsilon);
|
||||
EXPECT_FP_LE_WITH_EPS(stress[4], test_config.init_stress.xz, 10*epsilon);
|
||||
EXPECT_FP_LE_WITH_EPS(stress[5], test_config.init_stress.yz, 10*epsilon);
|
||||
if (print_stats)
|
||||
std::cerr << "init_stress stats, newton on: " << stats << std::endl;
|
||||
|
||||
stats.reset();
|
||||
EXPECT_FP_LE_WITH_EPS(angle->energy, test_config.init_energy, epsilon);
|
||||
if (print_stats)
|
||||
std::cerr << "init_energy stats, newton on: " << stats << std::endl;
|
||||
|
||||
if (!verbose) ::testing::internal::CaptureStdout();
|
||||
run_lammps(lmp);
|
||||
if (!verbose) ::testing::internal::GetCapturedStdout();
|
||||
|
||||
f = lmp->atom->f;
|
||||
stress = angle->virial;
|
||||
const std::vector<coord_t> &f_run = test_config.run_forces;
|
||||
ASSERT_EQ(nlocal+1,f_run.size());
|
||||
stats.reset();
|
||||
for (int i=0; i < nlocal; ++i) {
|
||||
EXPECT_FP_LE_WITH_EPS(f[i][0], f_run[tag[i]].x, 10*epsilon);
|
||||
EXPECT_FP_LE_WITH_EPS(f[i][1], f_run[tag[i]].y, 10*epsilon);
|
||||
EXPECT_FP_LE_WITH_EPS(f[i][2], f_run[tag[i]].z, 10*epsilon);
|
||||
}
|
||||
if (print_stats)
|
||||
std::cerr << "run_forces stats, newton on: " << stats << std::endl;
|
||||
|
||||
stress = angle->virial;
|
||||
stats.reset();
|
||||
EXPECT_FP_LE_WITH_EPS(stress[0], test_config.run_stress.xx, 10*epsilon);
|
||||
EXPECT_FP_LE_WITH_EPS(stress[1], test_config.run_stress.yy, 10*epsilon);
|
||||
EXPECT_FP_LE_WITH_EPS(stress[2], test_config.run_stress.zz, 10*epsilon);
|
||||
EXPECT_FP_LE_WITH_EPS(stress[3], test_config.run_stress.xy, 10*epsilon);
|
||||
EXPECT_FP_LE_WITH_EPS(stress[4], test_config.run_stress.xz, 10*epsilon);
|
||||
EXPECT_FP_LE_WITH_EPS(stress[5], test_config.run_stress.yz, 10*epsilon);
|
||||
if (print_stats)
|
||||
std::cerr << "run_stress stats, newton on: " << stats << std::endl;
|
||||
|
||||
stats.reset();
|
||||
int id = lmp->modify->find_compute("sum");
|
||||
double energy = lmp->modify->compute[id]->compute_scalar();
|
||||
EXPECT_FP_LE_WITH_EPS(angle->energy, test_config.run_energy, epsilon);
|
||||
// TODO: this is currently broken for USER-OMP with angle style hybrid
|
||||
// needs to be fixed in the main code somewhere. Not sure where, though.
|
||||
if (test_config.angle_style.substr(0,6) != "hybrid")
|
||||
EXPECT_FP_LE_WITH_EPS(angle->energy, energy, epsilon);
|
||||
if (print_stats)
|
||||
std::cerr << "run_energy stats, newton on: " << stats << std::endl;
|
||||
|
||||
if (!verbose) ::testing::internal::CaptureStdout();
|
||||
cleanup_lammps(lmp,test_config);
|
||||
lmp = init_lammps(argc,argv,test_config,false);
|
||||
if (!verbose) ::testing::internal::GetCapturedStdout();
|
||||
|
||||
f=lmp->atom->f;
|
||||
tag=lmp->atom->tag;
|
||||
stats.reset();
|
||||
for (int i=0; i < nlocal; ++i) {
|
||||
EXPECT_FP_LE_WITH_EPS(f[i][0], f_ref[tag[i]].x, epsilon);
|
||||
EXPECT_FP_LE_WITH_EPS(f[i][1], f_ref[tag[i]].y, epsilon);
|
||||
EXPECT_FP_LE_WITH_EPS(f[i][2], f_ref[tag[i]].z, epsilon);
|
||||
}
|
||||
if (print_stats)
|
||||
std::cerr << "init_forces stats, newton off:" << stats << std::endl;
|
||||
|
||||
angle = lmp->force->angle;
|
||||
stress = angle->virial;
|
||||
stats.reset();
|
||||
EXPECT_FP_LE_WITH_EPS(stress[0], test_config.init_stress.xx, 10*epsilon);
|
||||
EXPECT_FP_LE_WITH_EPS(stress[1], test_config.init_stress.yy, 10*epsilon);
|
||||
EXPECT_FP_LE_WITH_EPS(stress[2], test_config.init_stress.zz, 10*epsilon);
|
||||
EXPECT_FP_LE_WITH_EPS(stress[3], test_config.init_stress.xy, 10*epsilon);
|
||||
EXPECT_FP_LE_WITH_EPS(stress[4], test_config.init_stress.xz, 10*epsilon);
|
||||
EXPECT_FP_LE_WITH_EPS(stress[5], test_config.init_stress.yz, 10*epsilon);
|
||||
if (print_stats)
|
||||
std::cerr << "init_stress stats, newton off:" << stats << std::endl;
|
||||
|
||||
stats.reset();
|
||||
EXPECT_FP_LE_WITH_EPS(angle->energy, test_config.init_energy, epsilon);
|
||||
if (print_stats)
|
||||
std::cerr << "init_energy stats, newton off:" << stats << std::endl;
|
||||
|
||||
if (!verbose) ::testing::internal::CaptureStdout();
|
||||
run_lammps(lmp);
|
||||
if (!verbose) ::testing::internal::GetCapturedStdout();
|
||||
|
||||
f = lmp->atom->f;
|
||||
stats.reset();
|
||||
for (int i=0; i < nlocal; ++i) {
|
||||
EXPECT_FP_LE_WITH_EPS(f[i][0], f_run[tag[i]].x, 10*epsilon);
|
||||
EXPECT_FP_LE_WITH_EPS(f[i][1], f_run[tag[i]].y, 10*epsilon);
|
||||
EXPECT_FP_LE_WITH_EPS(f[i][2], f_run[tag[i]].z, 10*epsilon);
|
||||
}
|
||||
if (print_stats)
|
||||
std::cerr << "run_forces stats, newton off:" << stats << std::endl;
|
||||
|
||||
stress = angle->virial;
|
||||
stats.reset();
|
||||
EXPECT_FP_LE_WITH_EPS(stress[0], test_config.run_stress.xx, 10*epsilon);
|
||||
EXPECT_FP_LE_WITH_EPS(stress[1], test_config.run_stress.yy, 10*epsilon);
|
||||
EXPECT_FP_LE_WITH_EPS(stress[2], test_config.run_stress.zz, 10*epsilon);
|
||||
EXPECT_FP_LE_WITH_EPS(stress[3], test_config.run_stress.xy, 10*epsilon);
|
||||
EXPECT_FP_LE_WITH_EPS(stress[4], test_config.run_stress.xz, 10*epsilon);
|
||||
EXPECT_FP_LE_WITH_EPS(stress[5], test_config.run_stress.yz, 10*epsilon);
|
||||
if (print_stats)
|
||||
std::cerr << "run_stress stats, newton off:" << stats << std::endl;
|
||||
|
||||
stats.reset();
|
||||
id = lmp->modify->find_compute("sum");
|
||||
energy = lmp->modify->compute[id]->compute_scalar();
|
||||
EXPECT_FP_LE_WITH_EPS(angle->energy, test_config.run_energy, epsilon);
|
||||
// TODO: this is currently broken for USER-OMP with angle style hybrid
|
||||
// needs to be fixed in the main code somewhere. Not sure where, though.
|
||||
if (test_config.angle_style.substr(0,6) != "hybrid")
|
||||
EXPECT_FP_LE_WITH_EPS(angle->energy, energy, epsilon);
|
||||
if (print_stats)
|
||||
std::cerr << "run_energy stats, newton off:" << stats << std::endl;
|
||||
|
||||
if (!verbose) ::testing::internal::CaptureStdout();
|
||||
cleanup_lammps(lmp,test_config);
|
||||
if (!verbose) ::testing::internal::GetCapturedStdout();
|
||||
};
|
||||
|
||||
File diff suppressed because it is too large
Load Diff
|
|
@ -0,0 +1,60 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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 "error_stats.h"
|
||||
#include <iostream>
|
||||
#include <string>
|
||||
#include <cmath>
|
||||
|
||||
void ErrorStats::reset() {
|
||||
num = 0;
|
||||
maxidx = -1;
|
||||
sum = sumsq = maxerr =0.0;
|
||||
}
|
||||
|
||||
void ErrorStats::add(const double &val) {
|
||||
++num;
|
||||
if (val > maxerr) {
|
||||
maxidx = num;
|
||||
maxerr = val;
|
||||
}
|
||||
sum += val;
|
||||
sumsq += val*val;
|
||||
}
|
||||
|
||||
double ErrorStats::avg() const {
|
||||
return (num > 0) ? sum/num : 0.0;
|
||||
}
|
||||
|
||||
double ErrorStats::dev() const {
|
||||
return (num > 0) ? sqrt(sumsq/num - sum/num*sum/num) : 0.0;
|
||||
}
|
||||
|
||||
std::ostream &operator<<(std::ostream &out, const ErrorStats &stats)
|
||||
{
|
||||
const std::ios_base::fmtflags flags = out.flags();
|
||||
const std::streamsize width = out.width(10);
|
||||
const std::streamsize prec = out.precision(3);
|
||||
|
||||
out << std::scientific
|
||||
<< "Average: " << stats.avg()
|
||||
<< " StdDev: " << stats.dev()
|
||||
<< " MaxErr: " << stats.max();
|
||||
|
||||
out.precision(prec);
|
||||
out.width(width);
|
||||
out.flags(flags);
|
||||
|
||||
return out << " @ item: " << stats.idx();
|
||||
}
|
||||
|
||||
|
|
@ -0,0 +1,42 @@
|
|||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifndef ERROR_STATS_H
|
||||
#define ERROR_STATS_H
|
||||
|
||||
#include <iostream>
|
||||
|
||||
class ErrorStats {
|
||||
public:
|
||||
friend std::ostream &operator<<(std::ostream &out, const ErrorStats &stats);
|
||||
|
||||
ErrorStats() {
|
||||
reset();
|
||||
}
|
||||
virtual ~ErrorStats() {}
|
||||
|
||||
void reset();
|
||||
void add(const double &val);
|
||||
double avg() const;
|
||||
double dev() const;
|
||||
double max() const { return maxerr; }
|
||||
double idx() const { return maxidx; }
|
||||
|
||||
private:
|
||||
double sum,sumsq,maxerr;
|
||||
int num,maxidx;
|
||||
};
|
||||
|
||||
extern std::ostream &operator<<(std::ostream &out, const ErrorStats &stats);
|
||||
|
||||
#endif
|
||||
File diff suppressed because it is too large
Load Diff
|
|
@ -0,0 +1,101 @@
|
|||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifndef TEST_CONFIG_H
|
||||
#define TEST_CONFIG_H
|
||||
|
||||
#include <string>
|
||||
#include <utility>
|
||||
#include <vector>
|
||||
|
||||
struct coord_t {
|
||||
double x,y,z;
|
||||
};
|
||||
|
||||
struct stress_t {
|
||||
double xx,yy,zz,xy,xz,yz;
|
||||
};
|
||||
|
||||
class TestConfig {
|
||||
public:
|
||||
std::string lammps_version;
|
||||
std::string date_generated;
|
||||
std::string basename;
|
||||
double epsilon;
|
||||
std::vector<std::pair<std::string,std::string>> prerequisites;
|
||||
std::vector<std::string> pre_commands;
|
||||
std::vector<std::string> post_commands;
|
||||
std::string input_file;
|
||||
std::string pair_style;
|
||||
std::string bond_style;
|
||||
std::string angle_style;
|
||||
std::string dihedral_style;
|
||||
std::string improper_style;
|
||||
std::string kspace_style;
|
||||
std::vector<std::string> pair_coeff;
|
||||
std::vector<std::string> bond_coeff;
|
||||
std::vector<std::string> angle_coeff;
|
||||
std::vector<std::string> dihedral_coeff;
|
||||
std::vector<std::string> improper_coeff;
|
||||
std::vector<std::pair<std::string,int>> extract;
|
||||
int natoms;
|
||||
double init_energy;
|
||||
double run_energy;
|
||||
double init_vdwl;
|
||||
double run_vdwl;
|
||||
double init_coul;
|
||||
double run_coul;
|
||||
stress_t init_stress;
|
||||
stress_t run_stress;
|
||||
std::vector<coord_t> init_forces;
|
||||
std::vector<coord_t> run_forces;
|
||||
|
||||
TestConfig() : lammps_version(""),
|
||||
date_generated(""),
|
||||
basename(""),
|
||||
epsilon(1.0e-14),
|
||||
input_file(""),
|
||||
pair_style("zero"),
|
||||
bond_style("zero"),
|
||||
angle_style("zero"),
|
||||
dihedral_style("zero"),
|
||||
improper_style("zero"),
|
||||
kspace_style("none"),
|
||||
natoms(0),
|
||||
init_energy(0),
|
||||
run_energy(0),
|
||||
init_vdwl(0),
|
||||
run_vdwl(0),
|
||||
init_coul(0),
|
||||
run_coul(0),
|
||||
init_stress({0,0,0,0,0,0}),
|
||||
run_stress({0,0,0,0,0,0}) {
|
||||
prerequisites.clear();
|
||||
pre_commands.clear();
|
||||
post_commands.clear();
|
||||
pair_coeff.clear();
|
||||
bond_coeff.clear();
|
||||
angle_coeff.clear();
|
||||
dihedral_coeff.clear();
|
||||
improper_coeff.clear();
|
||||
extract.clear();
|
||||
init_forces.clear();
|
||||
run_forces.clear();
|
||||
}
|
||||
virtual ~TestConfig() {};
|
||||
|
||||
private:
|
||||
TestConfig(const TestConfig &) {};
|
||||
};
|
||||
|
||||
#endif
|
||||
|
|
@ -0,0 +1,246 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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 "test_config.h"
|
||||
#include "test_config_reader.h"
|
||||
#include "yaml_reader.h"
|
||||
#include "yaml.h"
|
||||
|
||||
#include <cstring>
|
||||
#include <cstdlib>
|
||||
|
||||
#include <string>
|
||||
#include <iostream>
|
||||
#include <sstream>
|
||||
#include <utility>
|
||||
#include <vector>
|
||||
|
||||
TestConfigReader::TestConfigReader(TestConfig & config)
|
||||
: YamlReader(), config(config) {
|
||||
consumers["lammps_version"] = &TestConfigReader::lammps_version;
|
||||
consumers["date_generated"] = &TestConfigReader::date_generated;
|
||||
consumers["epsilon"] = &TestConfigReader::epsilon;
|
||||
consumers["prerequisites"] = &TestConfigReader::prerequisites;
|
||||
consumers["pre_commands"] = &TestConfigReader::pre_commands;
|
||||
consumers["post_commands"] = &TestConfigReader::post_commands;
|
||||
consumers["input_file"] = &TestConfigReader::input_file;
|
||||
consumers["extract"] = &TestConfigReader::extract;
|
||||
consumers["natoms"] = &TestConfigReader::natoms;
|
||||
consumers["init_stress"] = &TestConfigReader::init_stress;
|
||||
consumers["run_stress"] = &TestConfigReader::run_stress;
|
||||
consumers["init_forces"] = &TestConfigReader::init_forces;
|
||||
consumers["run_forces"] = &TestConfigReader::run_forces;
|
||||
|
||||
consumers["pair_style"] = &TestConfigReader::pair_style;
|
||||
consumers["pair_coeff"] = &TestConfigReader::pair_coeff;
|
||||
consumers["init_vdwl"] = &TestConfigReader::init_vdwl;
|
||||
consumers["init_coul"] = &TestConfigReader::init_coul;
|
||||
consumers["run_vdwl"] = &TestConfigReader::run_vdwl;
|
||||
consumers["run_coul"] = &TestConfigReader::run_coul;
|
||||
|
||||
consumers["bond_style"] = &TestConfigReader::bond_style;
|
||||
consumers["bond_coeff"] = &TestConfigReader::bond_coeff;
|
||||
consumers["init_energy"] = &TestConfigReader::init_energy;
|
||||
consumers["run_energy"] = &TestConfigReader::run_energy;
|
||||
|
||||
consumers["angle_style"] = &TestConfigReader::angle_style;
|
||||
consumers["angle_coeff"] = &TestConfigReader::angle_coeff;
|
||||
consumers["init_energy"] = &TestConfigReader::init_energy;
|
||||
consumers["run_energy"] = &TestConfigReader::run_energy;
|
||||
}
|
||||
|
||||
void TestConfigReader::prerequisites(const yaml_event_t & event) {
|
||||
config.prerequisites.clear();
|
||||
std::stringstream data((char *)event.data.scalar.value);
|
||||
std::string line;
|
||||
|
||||
while(std::getline(data, line, '\n')) {
|
||||
std::size_t found = line.find_first_of(" \t");
|
||||
std::string key = line.substr(0,found);
|
||||
found = line.find_first_not_of(" \t",found);
|
||||
// skip invalid data
|
||||
if (found == std::string::npos) {
|
||||
std::cerr << "Skipping invalid prerequisite line:\n"
|
||||
<< line << std::endl;
|
||||
continue;
|
||||
}
|
||||
std::string value = line.substr(found,line.find_first_of(" \t",found));
|
||||
config.prerequisites.push_back(std::make_pair(key,value));
|
||||
}
|
||||
}
|
||||
|
||||
void TestConfigReader::pre_commands(const yaml_event_t & event) {
|
||||
config.pre_commands.clear();
|
||||
std::stringstream data((char *)event.data.scalar.value);
|
||||
std::string line;
|
||||
|
||||
while(std::getline(data, line, '\n')) {
|
||||
config.pre_commands.push_back(line);
|
||||
}
|
||||
}
|
||||
|
||||
void TestConfigReader::post_commands(const yaml_event_t & event) {
|
||||
config.post_commands.clear();
|
||||
std::stringstream data((char *)event.data.scalar.value);
|
||||
std::string line;
|
||||
|
||||
while (std::getline(data, line, '\n')) {
|
||||
config.post_commands.push_back(line);
|
||||
}
|
||||
}
|
||||
|
||||
void TestConfigReader::lammps_version(const yaml_event_t & event) {
|
||||
config.lammps_version = (char *)event.data.scalar.value;
|
||||
}
|
||||
|
||||
void TestConfigReader::date_generated(const yaml_event_t & event) {
|
||||
config.date_generated = (char *)event.data.scalar.value;
|
||||
}
|
||||
|
||||
void TestConfigReader::epsilon(const yaml_event_t & event) {
|
||||
config.epsilon = atof((char *)event.data.scalar.value);
|
||||
}
|
||||
|
||||
void TestConfigReader::input_file(const yaml_event_t & event) {
|
||||
config.input_file = (char *)event.data.scalar.value;
|
||||
}
|
||||
|
||||
void TestConfigReader::extract(const yaml_event_t & event) {
|
||||
config.extract.clear();
|
||||
std::stringstream data((char *)event.data.scalar.value);
|
||||
std::string line;
|
||||
|
||||
while (std::getline(data, line, '\n')) {
|
||||
std::size_t found = line.find_first_of(" \t");
|
||||
std::string name = line.substr(0,found);
|
||||
int value = atoi(line.substr(found).c_str());
|
||||
config.extract.push_back(make_pair(name, value));
|
||||
}
|
||||
}
|
||||
|
||||
void TestConfigReader::natoms(const yaml_event_t & event) {
|
||||
config.natoms = atoi((char *)event.data.scalar.value);
|
||||
}
|
||||
|
||||
void TestConfigReader::init_stress(const yaml_event_t & event) {
|
||||
stress_t stress;
|
||||
sscanf((char *)event.data.scalar.value,
|
||||
"%lg %lg %lg %lg %lg %lg",
|
||||
&stress.xx, &stress.yy, &stress.zz,
|
||||
&stress.xy, &stress.xz, &stress.yz);
|
||||
config.init_stress = stress;
|
||||
}
|
||||
|
||||
void TestConfigReader::run_stress(const yaml_event_t & event) {
|
||||
stress_t stress;
|
||||
sscanf((char *)event.data.scalar.value,
|
||||
"%lg %lg %lg %lg %lg %lg",
|
||||
&stress.xx, &stress.yy, &stress.zz,
|
||||
&stress.xy, &stress.xz, &stress.yz);
|
||||
config.run_stress = stress;
|
||||
}
|
||||
|
||||
void TestConfigReader::init_forces(const yaml_event_t & event) {
|
||||
config.init_forces.clear();
|
||||
config.init_forces.resize(config.natoms+1);
|
||||
std::stringstream data((const char*)event.data.scalar.value);
|
||||
std::string line;
|
||||
|
||||
while(std::getline(data, line, '\n')) {
|
||||
int tag = 0;
|
||||
coord_t xyz;
|
||||
sscanf(line.c_str(), "%d %lg %lg %lg", &tag, &xyz.x, &xyz.y, &xyz.z);
|
||||
config.init_forces[tag] = xyz;
|
||||
}
|
||||
}
|
||||
|
||||
void TestConfigReader::run_forces(const yaml_event_t & event) {
|
||||
config.run_forces.clear();
|
||||
config.run_forces.resize(config.natoms+1);
|
||||
std::stringstream data((char *)event.data.scalar.value);
|
||||
std::string line;
|
||||
|
||||
while(std::getline(data, line, '\n')) {
|
||||
int tag;
|
||||
coord_t xyz;
|
||||
sscanf(line.c_str(), "%d %lg %lg %lg", &tag, &xyz.x, &xyz.y, &xyz.z);
|
||||
config.run_forces[tag] = xyz;
|
||||
}
|
||||
}
|
||||
|
||||
void TestConfigReader::pair_style(const yaml_event_t & event) {
|
||||
config.pair_style = (char *)event.data.scalar.value;
|
||||
}
|
||||
|
||||
void TestConfigReader::pair_coeff(const yaml_event_t & event) {
|
||||
config.pair_coeff.clear();
|
||||
std::stringstream data((char *)event.data.scalar.value);
|
||||
std::string line;
|
||||
|
||||
while (std::getline(data, line, '\n')) {
|
||||
config.pair_coeff.push_back(line);
|
||||
}
|
||||
}
|
||||
|
||||
void TestConfigReader::bond_style(const yaml_event_t & event) {
|
||||
config.bond_style = (char *)event.data.scalar.value;
|
||||
}
|
||||
|
||||
void TestConfigReader::bond_coeff(const yaml_event_t & event) {
|
||||
config.bond_coeff.clear();
|
||||
std::stringstream data((char *)event.data.scalar.value);
|
||||
std::string line;
|
||||
|
||||
while (std::getline(data, line, '\n')) {
|
||||
config.bond_coeff.push_back(line);
|
||||
}
|
||||
}
|
||||
|
||||
void TestConfigReader::angle_style(const yaml_event_t & event) {
|
||||
config.angle_style = (char *)event.data.scalar.value;
|
||||
}
|
||||
|
||||
void TestConfigReader::angle_coeff(const yaml_event_t & event) {
|
||||
config.angle_coeff.clear();
|
||||
std::stringstream data((char *)event.data.scalar.value);
|
||||
std::string line;
|
||||
|
||||
while (std::getline(data, line, '\n')) {
|
||||
config.angle_coeff.push_back(line);
|
||||
}
|
||||
}
|
||||
|
||||
void TestConfigReader::init_vdwl(const yaml_event_t & event) {
|
||||
config.init_vdwl = atof((char *)event.data.scalar.value);
|
||||
}
|
||||
|
||||
void TestConfigReader::init_coul(const yaml_event_t & event) {
|
||||
config.init_coul = atof((char *)event.data.scalar.value);
|
||||
}
|
||||
|
||||
void TestConfigReader::run_vdwl(const yaml_event_t & event) {
|
||||
config.run_vdwl = atof((char *)event.data.scalar.value);
|
||||
}
|
||||
|
||||
void TestConfigReader::run_coul(const yaml_event_t & event) {
|
||||
config.run_coul = atof((char *)event.data.scalar.value);
|
||||
}
|
||||
|
||||
void TestConfigReader::init_energy(const yaml_event_t & event) {
|
||||
config.init_energy = atof((char *)event.data.scalar.value);
|
||||
}
|
||||
|
||||
void TestConfigReader::run_energy(const yaml_event_t & event) {
|
||||
config.run_energy = atof((char *)event.data.scalar.value);
|
||||
}
|
||||
|
||||
|
|
@ -0,0 +1,52 @@
|
|||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifndef TEST_CONFIG_READER_H
|
||||
#define TEST_CONFIG_READER_H
|
||||
|
||||
#include "yaml_reader.h"
|
||||
|
||||
class TestConfigReader : public YamlReader<TestConfigReader> {
|
||||
TestConfig & config;
|
||||
|
||||
public:
|
||||
TestConfigReader(TestConfig & config);
|
||||
|
||||
void prerequisites(const yaml_event_t & event);
|
||||
void pre_commands(const yaml_event_t & event);
|
||||
void post_commands(const yaml_event_t & event);
|
||||
void lammps_version(const yaml_event_t & event);
|
||||
void date_generated(const yaml_event_t & event);
|
||||
void epsilon(const yaml_event_t & event);
|
||||
void input_file(const yaml_event_t & event);
|
||||
void extract(const yaml_event_t & event);
|
||||
void natoms(const yaml_event_t & event);
|
||||
void init_stress(const yaml_event_t & event);
|
||||
void run_stress(const yaml_event_t & event);
|
||||
void init_forces(const yaml_event_t & event);
|
||||
void run_forces(const yaml_event_t & event);
|
||||
void pair_style(const yaml_event_t & event);
|
||||
void pair_coeff(const yaml_event_t & event);
|
||||
void bond_style(const yaml_event_t & event);
|
||||
void bond_coeff(const yaml_event_t & event);
|
||||
void angle_style(const yaml_event_t & event);
|
||||
void angle_coeff(const yaml_event_t & event);
|
||||
void init_vdwl(const yaml_event_t & event);
|
||||
void init_coul(const yaml_event_t & event);
|
||||
void run_vdwl(const yaml_event_t & event);
|
||||
void run_coul(const yaml_event_t & event);
|
||||
void init_energy(const yaml_event_t & event);
|
||||
void run_energy(const yaml_event_t & event);
|
||||
};
|
||||
|
||||
#endif
|
||||
|
|
@ -0,0 +1,114 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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 "test_main.h"
|
||||
#include "test_config.h"
|
||||
#include "test_config_reader.h"
|
||||
#include "gtest/gtest.h"
|
||||
|
||||
#include <mpi.h>
|
||||
#include <cstring>
|
||||
#include <iostream>
|
||||
|
||||
// common read_yaml_file function
|
||||
bool read_yaml_file(const char *infile, TestConfig &config)
|
||||
{
|
||||
auto reader = TestConfigReader(config);
|
||||
if (reader.parse_file(infile))
|
||||
return false;
|
||||
|
||||
config.basename = reader.get_basename();
|
||||
return true;
|
||||
}
|
||||
|
||||
// need to be defined in unit test body
|
||||
extern void generate_yaml_file(const char *, const TestConfig &);
|
||||
|
||||
void usage(std::ostream &out, const char *name)
|
||||
{
|
||||
out << "usage: " << name << " <testfile.yaml> [OPTIONS]\n\n"
|
||||
<< "Available options:\n"
|
||||
<< " -g <newfile.yaml> regenerate yaml file under a new name\n"
|
||||
<< " -d <folder> set folder where to find input files\n"
|
||||
<< " -u update the original yaml file\n"
|
||||
<< " -v run tests with verbose output\n"
|
||||
<< " -s run tests with error statistics output\n"
|
||||
<< " -h print this message\n"
|
||||
<< std::endl;
|
||||
}
|
||||
|
||||
// test configuration settings read from yaml file
|
||||
TestConfig test_config;
|
||||
|
||||
// whether to print error statistics
|
||||
bool print_stats = false;
|
||||
|
||||
// whether to print verbose output (i.e. not capturing LAMMPS screen output).
|
||||
bool verbose = false;
|
||||
|
||||
// location for 'in.*' and 'data.*' files required by tests
|
||||
#define STRINGIFY(val) XSTR(val)
|
||||
#define XSTR(val) #val
|
||||
std::string INPUT_FOLDER = STRINGIFY(TEST_INPUT_FOLDER);
|
||||
|
||||
int main(int argc, char **argv)
|
||||
{
|
||||
MPI_Init(&argc, &argv);
|
||||
::testing::InitGoogleTest(&argc, argv);
|
||||
|
||||
if (argc < 2) {
|
||||
usage(std::cerr, argv[0]);
|
||||
return 1;
|
||||
}
|
||||
|
||||
if (!read_yaml_file(argv[1], test_config)) {
|
||||
std::cerr << "Error parsing yaml file: " << argv[1] << std::endl;
|
||||
return 2;
|
||||
}
|
||||
|
||||
int iarg=2;
|
||||
while (iarg < argc) {
|
||||
|
||||
if (strcmp(argv[iarg],"-g") == 0) {
|
||||
if (iarg+1 < argc) {
|
||||
generate_yaml_file(argv[iarg+1], test_config);
|
||||
return 0;
|
||||
} else {
|
||||
usage(std::cerr,argv[0]);
|
||||
return 1;
|
||||
}
|
||||
} else if (strcmp(argv[iarg],"-u") == 0) {
|
||||
generate_yaml_file(argv[1], test_config);
|
||||
return 0;
|
||||
} else if (strcmp(argv[iarg],"-d") == 0) {
|
||||
if (iarg+1 < argc) {
|
||||
INPUT_FOLDER = argv[iarg+1];
|
||||
iarg += 2;
|
||||
} else {
|
||||
usage(std::cerr,argv[0]);
|
||||
return 1;
|
||||
}
|
||||
} else if (strcmp(argv[iarg],"-s") == 0) {
|
||||
print_stats = true;
|
||||
++iarg;
|
||||
} else if (strcmp(argv[iarg],"-v") == 0) {
|
||||
verbose = true;
|
||||
++iarg;
|
||||
} else {
|
||||
std::cerr << "unknown option: " << argv[iarg] << "\n\n";
|
||||
usage(std::cerr, argv[0]);
|
||||
return 1;
|
||||
}
|
||||
}
|
||||
return RUN_ALL_TESTS();
|
||||
}
|
||||
|
|
@ -0,0 +1,40 @@
|
|||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifndef TEST_MAIN_H
|
||||
#define TEST_MAIN_H
|
||||
|
||||
#include "test_config.h"
|
||||
#include <string>
|
||||
|
||||
extern TestConfig test_config;
|
||||
extern bool print_stats;
|
||||
extern bool verbose;
|
||||
extern std::string INPUT_FOLDER;
|
||||
|
||||
#define EXPECT_FP_LE_WITH_EPS(val1,val2,eps) \
|
||||
do { \
|
||||
const double diff = fabs(val1-val2); \
|
||||
const double div = std::min(fabs(val1),fabs(val2)); \
|
||||
const double err = (div == 0.0) ? diff : diff/div; \
|
||||
stats.add(err); \
|
||||
EXPECT_PRED_FORMAT2(::testing::DoubleLE, err, eps); \
|
||||
} while (0);
|
||||
|
||||
#endif
|
||||
|
||||
#if defined _WIN32
|
||||
static const char PATH_SEP = '\\';
|
||||
#else
|
||||
static const char PATH_SEP = '/';
|
||||
#endif
|
||||
|
|
@ -0,0 +1,85 @@
|
|||
---
|
||||
lammps_version: 5 May 2020
|
||||
date_generated: Tue May 19 19:19:41 202
|
||||
epsilon: 1.0e-13
|
||||
prerequisites: ! |
|
||||
atom full
|
||||
angle charmm
|
||||
pre_commands: ! ""
|
||||
post_commands: ! ""
|
||||
input_file: in.fourmol
|
||||
angle_style: charmm
|
||||
angle_coeff: ! |
|
||||
1 33.5 110.1 22.5 2.179
|
||||
2 46.1 111.3 0.0 0.000
|
||||
3 40.0 120.0 35.0 2.410
|
||||
4 33.0 108.5 30.0 2.163
|
||||
extract: ! ""
|
||||
natoms: 29
|
||||
init_energy: 85.4248638845977
|
||||
init_stress: ! |2-
|
||||
1.8143089201050887e+02 -4.4008327668528100e+00 1.1809359848490450e+02 1.3470039754098281e+02 9.3127587748087279e+01 2.3868960580224421e+01
|
||||
init_forces: ! |2
|
||||
21 1.5269813353706816e+00 1.9115283296031365e+00 -5.7126680835892021e+00
|
||||
22 -2.4212822369319898e+01 -1.1732635537541306e+01 -7.1373318326447102e+00
|
||||
23 2.2685841033949217e+01 9.8211072079381694e+00 1.2849999916233912e+01
|
||||
19 -1.8729001948214922e+01 -1.6361947190261777e+01 -3.2134590021289293e+00
|
||||
18 7.0507994374434446e-02 7.3680637947826888e-01 -2.9901987340388825e+00
|
||||
20 1.8658493953840487e+01 1.5625140810783508e+01 6.2036577361678118e+00
|
||||
28 -2.1397316777571888e+01 -6.8536308873550515e+00 -1.0104593869135021e+01
|
||||
4 -1.9280446193919857e+01 -1.0907565986617040e+01 -2.0121340659982309e+01
|
||||
10 1.5262370040243479e+01 1.7209374979747956e+01 -5.0097168024346068e+01
|
||||
11 -2.1025039799233362e+01 -6.8138721666064477e+00 9.3257489337892920e+00
|
||||
12 -3.7942492100969893e+00 -1.8949256479033437e+01 7.2924357616797710e+00
|
||||
14 -9.1419604634794620e+00 -5.8258733174381518e+00 -3.5139934203515040e+01
|
||||
3 2.6714408920784543e+00 -2.3742017076932243e-02 2.1100086635874408e+01
|
||||
6 2.1238309901668043e+01 5.7121253219257824e+00 -1.6787970380345595e+01
|
||||
7 -2.5311264980599468e+01 1.9532283354226724e+01 -2.4286994823128929e+01
|
||||
15 -3.9745927947694284e+00 2.5196516981363281e+01 3.2110867442129567e+01
|
||||
8 1.0452003565543395e+01 -2.3201291666991558e+01 9.0068263361646899e+01
|
||||
9 -1.5916624143704812e+01 1.6483610301406415e+01 -4.1516194400253736e-01
|
||||
16 -2.9503839293712968e+00 2.5409363689785007e+01 -7.2255876751122914e+00
|
||||
17 9.3355659152692783e-02 5.7971422477959977e-01 -3.5350080967767701e+00
|
||||
5 -1.8343508172093760e+01 -4.1071023429215984e+01 1.6108594011594683e+01
|
||||
13 2.6829248438599908e+01 -1.8477615701199301e+01 7.6270643598239811e+00
|
||||
2 4.8047222128896552e+00 5.8908874219218736e+00 -3.6078250436995862e+00
|
||||
1 3.8386618977092809e+01 9.2563644890222108e+00 -2.2416069655629478e+01
|
||||
27 -1.2828590583680111e-01 1.0531267905268624e+00 -3.5872993954368049e-01
|
||||
29 2.1525602683408689e+01 5.8005040968281891e+00 1.0463323808678702e+01
|
||||
24 -5.8307622758841404e-01 2.2664518498581661e+00 -1.3493584963979171e+00
|
||||
25 -1.9566415223447844e+01 -1.2547949048865153e+01 -1.0241193948074248e+01
|
||||
26 2.0149491451036258e+01 1.0281497199006987e+01 1.1590552444472165e+01
|
||||
run_energy: 69.5038576349246
|
||||
run_stress: ! |2-
|
||||
1.5649327850389238e+02 -1.3576175184752444e+01 1.0301817481047499e+02 1.1751125350905258e+02 8.1820504826714767e+01 8.0309752683500211e+00
|
||||
run_forces: ! |2
|
||||
21 -1.4384266302963056e-01 -1.6712728564325374e-01 5.3093449084065192e-01
|
||||
22 -1.9343247281638671e+01 -8.6574192096222582e+00 -8.4047349351069993e+00
|
||||
23 1.9487089944668302e+01 8.8245464952655119e+00 7.8738004442663474e+00
|
||||
19 -1.4296841483844430e+01 -1.2025900714259519e+01 -5.1480379176678346e+00
|
||||
18 -1.1328653272278899e-01 -8.7030074096365340e-01 3.4079850166128001e+00
|
||||
20 1.4410128016567219e+01 1.2896201455223173e+01 1.7400529010550347e+00
|
||||
28 -1.9195019940436467e+01 -4.6371717881364969e+00 -9.5643824275161027e+00
|
||||
4 -1.6927467901050289e+01 -7.3859651827093025e+00 -1.4353585997401646e+01
|
||||
10 1.7068495816883917e+01 1.3277171419237666e+01 -3.6716828531348568e+01
|
||||
11 -2.0022241908167199e+01 -4.3872495528933699e+00 8.3275988802544596e+00
|
||||
12 -7.7453219525172825e+00 -1.8894522494274831e+01 9.0662328749664240e+00
|
||||
14 -5.1588905300387884e+00 -1.8946152907089644e+00 -2.9531709636198215e+01
|
||||
3 7.2187270355452906e+00 -5.9092128037891003e+00 1.4203606972280422e+01
|
||||
6 2.0589410812493110e+01 8.0236562189313609e+00 -1.2960642418999164e+01
|
||||
7 -2.3631931177375314e+01 1.8664083313377326e+01 -2.1460676242173019e+01
|
||||
15 -2.5742212978495180e+00 2.1122073440175640e+01 2.4271434448540585e+01
|
||||
8 4.4078064602776070e+00 -1.9506406597487576e+01 7.6157986021827725e+01
|
||||
9 -1.2872279366933459e+01 1.3367415437083203e+01 -6.7987510304161081e-01
|
||||
16 -3.5711419901429564e-01 2.2624935653043305e+01 -8.4643921759749290e+00
|
||||
17 -3.9807644812623544e-01 1.4410769617604862e+00 -4.8103745925409314e+00
|
||||
5 -1.8409024900834989e+01 -3.4535581103141681e+01 1.3272518754203558e+01
|
||||
13 2.2164198238442463e+01 -1.6052737131589645e+01 7.1273217580409165e+00
|
||||
2 3.9740242751610664e+00 2.9513087966460372e+00 -5.0029928500601795e+00
|
||||
1 3.2673907043103924e+01 7.0945689163394468e+00 -1.8445622162375827e+01
|
||||
27 2.7630957147703228e-01 -2.0949168656441595e+00 6.7238481135276018e-01
|
||||
29 1.8918710368959434e+01 6.7320886537806564e+00 8.8919976161633425e+00
|
||||
24 6.6099237575914671e-01 -2.5342427128367895e+00 1.4932164263150582e+00
|
||||
25 -1.7526054501171469e+01 -8.8950231017495049e+00 -1.0437094403998735e+01
|
||||
26 1.6865062125412322e+01 1.1429265814586294e+01 8.9438779776836768e+00
|
||||
...
|
||||
|
|
@ -0,0 +1,85 @@
|
|||
---
|
||||
lammps_version: 5 May 2020
|
||||
date_generated: Tue May 19 19:00:35 202
|
||||
epsilon: 1.0e-13
|
||||
prerequisites: ! |
|
||||
atom full
|
||||
angle harmonic
|
||||
pre_commands: ! ""
|
||||
post_commands: ! ""
|
||||
input_file: in.fourmol
|
||||
angle_style: harmonic
|
||||
angle_coeff: ! |
|
||||
1 75.0 110.1
|
||||
2 45.0 111.0
|
||||
3 50.0 120.0
|
||||
4 100.0 108.5
|
||||
extract: ! ""
|
||||
natoms: 29
|
||||
init_energy: 41.530817896491
|
||||
init_stress: ! |2-
|
||||
8.9723357320869255e+01 -8.7188643750026529e+01 -2.5347135708427588e+00 9.2043419883119697e+01 -2.8187238090404989e+01 -1.5291148024927028e+00
|
||||
init_forces: ! |2
|
||||
21 3.4186149299343622e+00 4.2795410364249307e+00 -1.2789555411020601e+01
|
||||
22 -6.0875600315279446e+00 -4.1504951869796436e+00 4.5212856070195588e+00
|
||||
23 2.6689451015935823e+00 -1.2904584944528708e-01 8.2682698040010418e+00
|
||||
19 -1.9328033033421517e+00 -2.4078805870919515e+00 2.8669575541313312e+00
|
||||
18 1.5785371874873189e-01 1.6495665212200037e+00 -6.6944747776989910e+00
|
||||
20 1.7749495845934198e+00 7.5831406587194772e-01 3.8275172235676602e+00
|
||||
28 -6.2799575211499037e-01 -1.4097313073755557e+00 3.2747938980615732e-02
|
||||
4 -1.6032230038990651e+01 -2.4560529343731371e+01 1.2891625920422349e+01
|
||||
10 9.9863759179364777e+00 4.1873540105704535e+01 -6.6085640966037388e+01
|
||||
11 -2.0441876158908627e+01 -6.5186824168985984e+00 9.0023620309811072e+00
|
||||
12 -1.0772126658369636e+01 -1.0807367300158273e+01 -9.6049647456797036e+00
|
||||
14 1.5267407478336423e+01 -9.4754911480231527e+00 -6.6307012925544306e+00
|
||||
3 -5.9057050592858884e+00 5.3263619873546183e+01 5.2353380124691370e+01
|
||||
6 4.7083124388174838e+01 -9.5212933434476135e+00 -3.2526392870546800e+01
|
||||
7 -1.6208182775476303e+01 1.4458587960739102e+01 -3.5314745459502710e+00
|
||||
15 1.2402914209534794e+01 -6.2644630791613860e+00 1.8484576795819905e+01
|
||||
8 -6.5664612141880827e+00 -2.5126850154274180e+01 8.2187944731423329e+01
|
||||
9 -1.5504395262358301e+01 1.6121044185227817e+01 -4.2007069622477866e-01
|
||||
16 3.8927757686513598e-01 1.0690061587911142e+01 6.1542759189377589e+00
|
||||
17 1.4664194297570587e+00 -1.9971277376602155e+00 1.0776844613215855e+00
|
||||
5 -4.4802331573497668e+01 -4.8300919461089343e+01 -2.3310767889219321e+01
|
||||
13 2.8847886813946415e+00 7.2973241014859491e+00 -1.0414233993845645e-01
|
||||
2 -1.1124882516177386e+00 -9.0075464203887741e+00 -7.2431691227364725e+00
|
||||
1 4.7865489310693519e+01 7.8760925902181782e+00 -3.2694525514709809e+01
|
||||
27 -2.8720725187343144e-01 2.3577465459556626e+00 -8.0312673032167137e-01
|
||||
29 9.1520300398842180e-01 -9.4801523858010661e-01 7.7037879134105569e-01
|
||||
24 -1.3053945393770472e+00 5.0741459325182818e+00 -3.0209518576072751e+00
|
||||
25 -1.0471133765834191e+00 -3.5082261409793545e+00 5.7374874908500728e-01
|
||||
26 2.3525079159604663e+00 -1.5659197915389276e+00 2.4472031085222676e+00
|
||||
run_energy: 29.2286477697792
|
||||
run_stress: ! |2-
|
||||
6.7161703985479804e+01 -7.4680138065367487e+01 7.5184340798876628e+00 5.7521437901240859e+01 -2.7304190748521741e+01 -1.4932945649428730e+01
|
||||
run_forces: ! |2
|
||||
21 6.0524643645662579e-01 7.0314728523699110e-01 -2.2349906198624576e+00
|
||||
22 -1.0299517357238845e+00 -6.7850914711871291e-01 8.1029011311054200e-01
|
||||
23 4.2470529926725875e-01 -2.4638138118278141e-02 1.4247005067519156e+00
|
||||
19 9.8256914435044085e-01 1.2515894863018922e+00 -1.5372413162209382e+00
|
||||
18 -1.1709942604030477e-01 -8.9468235295761567e-01 3.5008479949198765e+00
|
||||
20 -8.6546971831013608e-01 -3.5690713334427648e-01 -1.9636066786989381e+00
|
||||
28 -2.8257906393508312e-02 -6.6089589395261994e-02 5.7412954785297787e-04
|
||||
4 -1.1598618479874565e+01 -1.4069946914275834e+01 1.1631964860700649e+01
|
||||
10 1.1736432849972278e+01 3.5147252452549246e+01 -4.9691358934493337e+01
|
||||
11 -1.9930599656448706e+01 -3.2836744898198571e+00 7.6150969595859577e+00
|
||||
12 -5.8293065548538978e+00 -1.3423749355667645e+01 -5.2738511429383701e+00
|
||||
14 1.2984672111772401e+01 -7.2763363322049823e-01 -4.8588140465034959e+00
|
||||
3 -7.1131175159873123e+00 3.1523130842685575e+01 3.9133327910920059e+01
|
||||
6 4.3880849952881221e+01 -6.1732167988806808e+00 -2.6034788339533922e+01
|
||||
7 -1.4366916728367741e+01 1.3135040103127027e+01 -3.0387136809768127e+00
|
||||
15 7.4743142834562555e+00 -3.4640965582760748e+00 9.4855052919847029e+00
|
||||
8 -8.5333281419768383e+00 -2.4737111100998256e+01 6.5176870591189868e+01
|
||||
9 -1.2996571868203590e+01 1.3674206710496604e+01 -6.7871105914534047e-01
|
||||
16 3.6043562512330887e+00 8.0382102532623243e+00 4.0048096667552189e+00
|
||||
17 5.4695804680833793e-01 -7.5537048761027403e-01 4.0487452808954988e-01
|
||||
5 -3.5092143924598361e+01 -3.4761325046913356e+01 -2.1062123798094685e+01
|
||||
13 7.7658418286980746e-01 2.0512357329017221e+00 1.8932242747136039e+00
|
||||
2 -1.7637583558698005e+00 -1.3758538851839576e+01 -1.1469071109412811e+01
|
||||
1 3.6220193547187421e+01 1.1585587142479543e+01 -1.7238241972840832e+01
|
||||
27 -1.4554421797154906e-02 1.1056084388051551e-01 -3.5467198058544314e-02
|
||||
29 4.2812328190663218e-02 -4.4471254485253520e-02 3.4893068510691336e-02
|
||||
24 4.1516966455944304e-01 -1.5912776575035221e+00 9.3767616296745859e-01
|
||||
25 3.0070697634261156e-01 1.0957067953103508e+00 -1.8209981159009775e-01
|
||||
26 -7.1587664090205461e-01 4.9557086219317126e-01 -7.5557635137736079e-01
|
||||
...
|
||||
|
|
@ -0,0 +1,85 @@
|
|||
---
|
||||
lammps_version: 5 May 2020
|
||||
date_generated: Mon May 18 18:18:26 202
|
||||
epsilon: 1e-14
|
||||
prerequisites: ! |
|
||||
atom full
|
||||
angle zero
|
||||
pre_commands: ! ""
|
||||
post_commands: ! ""
|
||||
input_file: in.fourmol
|
||||
angle_style: zero
|
||||
angle_coeff: ! |
|
||||
1 110.1
|
||||
2 111
|
||||
3 120
|
||||
4 108.5
|
||||
extract: ! ""
|
||||
natoms: 29
|
||||
init_energy: 0
|
||||
init_stress: ! |2-
|
||||
0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
init_forces: ! |2
|
||||
21 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
22 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
23 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
19 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
18 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
20 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
28 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
4 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
10 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
11 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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|
||||
26 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
run_energy: 0
|
||||
run_stress: ! |2-
|
||||
0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
run_forces: ! |2
|
||||
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|
||||
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||||
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||||
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||||
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||||
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||||
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||||
4 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
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||||
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||||
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||||
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||||
3 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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|
||||
1 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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||||
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||||
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||||
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||||
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||||
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|
||||
...
|
||||
|
|
@ -0,0 +1,90 @@
|
|||
---
|
||||
lammps_version: 5 May 2020
|
||||
date_generated: Fri May 15 23:19:20 202
|
||||
epsilon: 5.0e-12
|
||||
prerequisites: ! |
|
||||
pair eam
|
||||
pre_commands: ! |
|
||||
variable units index metal
|
||||
post_commands: ! ""
|
||||
input_file: in.metal
|
||||
pair_style: eam
|
||||
pair_coeff: ! |
|
||||
1 1 Ni_u3.eam
|
||||
2 2 Cu_u3.eam
|
||||
natoms: 32
|
||||
init_vdwl: -119.530487743563
|
||||
init_coul: 0
|
||||
init_stress: ! |2-
|
||||
4.8826272345202817e+01 4.5850488601145123e+01 4.1343857791628459e+01 4.4988644962998467e+00 -4.9951074981736998e-01 -2.1768789288131187e+00
|
||||
init_forces: ! |2
|
||||
29 8.0800296830781970e-01 2.3879075266467829e+00 -8.3048670580586403e-02
|
||||
4 2.7343534029869865e-01 -2.9878342106756367e-01 -1.2265223367116376e+00
|
||||
8 -1.4720323385487724e+00 -1.4228179264986509e+00 9.6490960676696425e-01
|
||||
13 -6.5176153773352563e-01 8.5767931224231297e-01 -1.0911744305807993e+00
|
||||
15 -7.3903169091302345e-01 7.5680244318270884e-01 -7.2708235694598555e-01
|
||||
3 -8.8972662160783789e-01 3.8990091972163423e+00 -1.0661156728781842e+00
|
||||
10 -7.8846939852443865e-01 -3.8705457047816734e+00 -2.4629929283458956e+00
|
||||
11 -9.8435494678902746e-01 -7.0900821618683274e-01 8.7706624584090875e-01
|
||||
16 2.4583295121993398e+00 -2.1972676866087717e+00 8.3284121924556553e-01
|
||||
21 4.0030874815543029e+00 1.0711165397007254e+00 2.4473954375123813e-01
|
||||
26 -1.3811106600228646e+00 -3.5588639228797661e+00 2.8632910127148117e+00
|
||||
7 -1.6363024522676575e+00 2.1007504896592857e+00 -3.9914508545625160e-01
|
||||
9 5.7947847523538809e-01 -1.0536323905325453e+00 -6.4053794186990365e-01
|
||||
12 1.1287163019780053e+00 -2.0776211837684415e+00 -2.0233323652665197e-01
|
||||
2 -4.1490810252266974e-01 -1.6223974813453232e+00 9.8899266934997998e-01
|
||||
18 -2.9490223023424624e+00 -6.7264893552133265e-01 -1.3875167298795910e+00
|
||||
19 -3.1847050581559415e+00 -1.8169235559519932e+00 8.0598800871995424e-01
|
||||
24 2.6007360409657871e+00 1.8259122746264185e+00 1.8348671705526824e+00
|
||||
6 9.3578152728737196e-01 4.2423394202927650e-01 -1.1063087875863249e-01
|
||||
20 4.8971016839265114e-01 3.9218805807784085e-01 -7.3184770760670148e-01
|
||||
22 1.8086294180444197e-02 -2.0048898956069334e+00 -2.5326361122481866e-01
|
||||
25 1.5827181697200143e+00 3.6148366642417934e-01 -1.0499794196925945e+00
|
||||
5 1.7730142843252130e+00 3.4084808701534719e+00 7.4953511407886242e-01
|
||||
27 1.1415770912387406e+00 3.1938755741801723e-02 1.8323119673595856e-01
|
||||
28 1.1504782845312334e-01 1.3053527012833483e+00 1.6722391212961463e+00
|
||||
1 -6.4076239230307086e-03 1.4271865784071405e+00 5.0439174022242561e-01
|
||||
14 1.2901780857744278e+00 -2.0966095595276873e-01 1.5801785995295483e+00
|
||||
17 9.9925856969280202e-01 2.8118162051561075e+00 -1.7641749946493385e-01
|
||||
23 1.0999852359764739e+00 2.9307377042640232e+00 -1.8605350165432875e+00
|
||||
30 -9.9030220835307969e-01 -5.9609338894221275e-01 -1.8459334541555570e+00
|
||||
31 -3.9990682938968608e-01 -2.4015626569287210e+00 1.6801191688208930e+00
|
||||
32 -4.8091016044865871e+00 -1.4798789422382359e+00 -4.6731344040392714e-01
|
||||
run_vdwl: -119.870792403123
|
||||
run_coul: 0
|
||||
run_stress: ! |2-
|
||||
4.7751995066352151e+01 4.4830156042194794e+01 4.0389886435910626e+01 4.2184912902327492e+00 -5.6543256799494823e-01 -2.0752485517795161e+00
|
||||
run_forces: ! |2
|
||||
29 7.5690592801898815e-01 2.3151863977187501e+00 -5.6022314357905889e-02
|
||||
4 2.6331390998279414e-01 -2.7131757020660047e-01 -1.2171723766818878e+00
|
||||
8 -1.4819123498210278e+00 -1.3892127647468901e+00 9.4351114037722761e-01
|
||||
13 -6.7030752430639429e-01 8.1027363373017303e-01 -1.0419798308062822e+00
|
||||
15 -7.2914425790656268e-01 7.3381515730032987e-01 -7.0649536261355972e-01
|
||||
3 -8.2862609949331145e-01 3.6488186893647363e+00 -1.0624581553334507e+00
|
||||
10 -6.1483994156789068e-01 -3.7021751622708732e+00 -2.3234131680128005e+00
|
||||
11 -9.5907408526990645e-01 -7.3338326161574841e-01 8.4459514391866075e-01
|
||||
16 2.2537479937597746e+00 -2.1115143339299585e+00 7.8862148815663591e-01
|
||||
21 3.8499378367182593e+00 9.5004430642537196e-01 2.6813205101176563e-01
|
||||
26 -1.2549911173346853e+00 -3.3303513611819771e+00 2.7419485545991917e+00
|
||||
7 -1.5803819585422452e+00 2.0775725635516813e+00 -4.1643485965418925e-01
|
||||
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|
||||
12 1.1188274327648378e+00 -1.9856343707557884e+00 -1.8931698797528046e-01
|
||||
2 -4.1672554481721213e-01 -1.6030271664710254e+00 9.7652355703236493e-01
|
||||
18 -2.8528759296970057e+00 -6.4627753964043022e-01 -1.3476345322887988e+00
|
||||
19 -3.0612708341260451e+00 -1.7499039144402915e+00 7.5685549599560620e-01
|
||||
24 2.4838924866176000e+00 1.7760409543710471e+00 1.7927340588029941e+00
|
||||
6 9.3519811444520051e-01 4.3790210252755352e-01 -1.1115261874946925e-01
|
||||
20 4.7860017665455917e-01 4.0873358602741239e-01 -7.2787329983734494e-01
|
||||
22 4.5683760799552345e-02 -1.9499040012633670e+00 -2.4911444772283134e-01
|
||||
25 1.5498059277046197e+00 3.7493980878195188e-01 -1.0267705215988105e+00
|
||||
5 1.6772659871839077e+00 3.2412248124601644e+00 7.8861775101712162e-01
|
||||
27 1.1181252050394743e+00 2.1210906682851027e-02 1.5259049481566841e-01
|
||||
28 8.6158085875367885e-02 1.2958084369079632e+00 1.6341119769792032e+00
|
||||
1 -6.8020837225162042e-02 1.3929213106632692e+00 4.9572035003963544e-01
|
||||
14 1.2851416793310484e+00 -1.0078910089733506e-01 1.4693455274495928e+00
|
||||
17 9.8653851440129303e-01 2.7301368714775602e+00 -1.8133160965911002e-01
|
||||
23 1.0757192308685777e+00 2.8092242654474213e+00 -1.7775969588994822e+00
|
||||
30 -9.5705266545383005e-01 -5.7810207051480700e-01 -1.7663162149693394e+00
|
||||
31 -4.2417243253557779e-01 -2.3534705046561171e+00 1.6411799159456588e+00
|
||||
32 -4.6616358258676422e+00 -1.4287865175152361e+00 -4.3077310874491803e-01
|
||||
...
|
||||
|
|
@ -0,0 +1,88 @@
|
|||
---
|
||||
lammps_version: 5 May 2020
|
||||
date_generated: Fri May 15 23:19:20 202
|
||||
epsilon: 5.0e-12
|
||||
prerequisites: ! |
|
||||
pair eam/alloy
|
||||
pre_commands: ! ""
|
||||
post_commands: ! ""
|
||||
input_file: in.metal
|
||||
pair_style: eam/alloy
|
||||
pair_coeff: ! |
|
||||
* * CuNi.eam.alloy Cu Ni
|
||||
natoms: 32
|
||||
init_vdwl: -118.717513292074
|
||||
init_coul: 0
|
||||
init_stress: ! |2-
|
||||
5.1014257789320709e+01 4.8593729597995065e+01 4.7112736045420640e+01 3.5405588622315474e+00 -1.0857130886013302e+00 -2.7579846998321549e+00
|
||||
init_forces: ! |2
|
||||
1 2.2840935622040651e-01 1.2888997258631352e+00 4.8026543691659340e-01
|
||||
2 -4.6125412740449800e-01 -1.9112192024545358e+00 9.0071701837979834e-01
|
||||
3 -9.9587989295031587e-01 4.2307284737084512e+00 -1.0685927600163529e+00
|
||||
4 3.2374116835015160e-01 -2.3702091668724223e-02 -1.0823801117368865e+00
|
||||
5 1.3542977130953364e+00 2.8020948427929824e+00 9.5113497310445239e-01
|
||||
6 9.4673434357367636e-01 4.8322726729554150e-01 -1.4847850887324249e-01
|
||||
7 -1.2730446091936882e+00 1.8281517398925333e+00 -3.7113641496736360e-01
|
||||
8 -1.5642829379491208e+00 -1.0500736894163398e+00 1.2890147020190135e+00
|
||||
9 6.4991513363052589e-01 -1.1735121363417000e+00 -5.7673263565626653e-01
|
||||
10 -5.3832008070468551e-01 -3.3293012612768522e+00 -2.3738715651129856e+00
|
||||
11 -9.1356804651435108e-01 -7.2053591109037929e-01 8.0120636188563743e-01
|
||||
12 8.4391680460489538e-01 -1.6525662824393184e+00 -2.3269717740755078e-01
|
||||
13 -6.2800745215314890e-01 6.7512342634999734e-01 -1.0476296581648779e+00
|
||||
14 1.4234594949105868e+00 -5.0423016715613178e-01 1.5291358244002888e+00
|
||||
15 -8.1293652727442678e-01 3.5358330556700263e-01 -4.6158103148920493e-01
|
||||
16 2.1085784822228311e+00 -1.9129323469522064e+00 7.9370451258988250e-01
|
||||
17 9.8428897306299656e-01 2.8790449061230849e+00 -3.1212563335942284e-01
|
||||
18 -2.9479251060685838e+00 -6.4774458459509554e-01 -1.3881462038728558e+00
|
||||
19 -3.3824027264357435e+00 -1.4402872943375322e+00 8.8378899536784206e-01
|
||||
20 5.9838499726080285e-01 5.8468229021840512e-01 -9.3326620058957754e-01
|
||||
21 3.6996796371163581e+00 6.2060024094268074e-01 5.7319661955693310e-02
|
||||
22 1.3692703809714415e-01 -1.4750726462226118e+00 -3.5974475017467683e-01
|
||||
23 8.5620305812453434e-01 2.6779904330376385e+00 -1.6554790201878267e+00
|
||||
24 2.2895427766419574e+00 2.0465814869010348e+00 1.6405745217852530e+00
|
||||
25 1.1920881422374321e+00 6.6889704238268705e-02 -9.7584220518029730e-01
|
||||
26 -9.5358563622453452e-01 -3.2497772634682329e+00 2.6658130478230966e+00
|
||||
27 1.1108427479812608e+00 -8.8179605617569282e-02 1.2390093197462654e-01
|
||||
28 -2.0742068147816028e-01 1.1588438550557982e+00 1.5305032274834602e+00
|
||||
29 1.1700450283412862e+00 1.9373940000280625e+00 -3.9870138798900556e-02
|
||||
30 -7.7628811007199061e-01 -1.1864112261858684e+00 -1.7057845890523824e+00
|
||||
31 -5.5170344013648301e-02 -2.3455335239818620e+00 1.3686542848487442e+00
|
||||
32 -4.4069686170352860e+00 -9.2275646480965812e-01 -2.8237489589371051e-01
|
||||
run_vdwl: -119.01346314091
|
||||
run_coul: 0
|
||||
run_stress: ! |2-
|
||||
5.0163665030040001e+01 4.7680228852249961e+01 4.6077773225979605e+01 3.3830790498090906e+00 -1.1731598776842909e+00 -2.6694718068658267e+00
|
||||
run_forces: ! |2
|
||||
1 1.6656370951687224e-01 1.2668180632727586e+00 4.6512485297556683e-01
|
||||
2 -4.6355934712710534e-01 -1.8865492277456797e+00 8.8559398025617497e-01
|
||||
3 -9.4063094819583548e-01 3.9885554759284059e+00 -1.0651876560035394e+00
|
||||
4 3.1809989421285695e-01 -1.5735553215512343e-03 -1.0739457289106022e+00
|
||||
5 1.3107085701461587e+00 2.7000436252294420e+00 9.6663082860580274e-01
|
||||
6 9.4560513816795355e-01 4.8856711744784481e-01 -1.4777906111423750e-01
|
||||
7 -1.2462601122119747e+00 1.8233940025762738e+00 -3.9005272587655360e-01
|
||||
8 -1.5724236097150643e+00 -1.0326685877501389e+00 1.2613834765742475e+00
|
||||
9 6.6499600201055986e-01 -1.2048800840156759e+00 -6.0041236575467516e-01
|
||||
10 -4.2918690454462260e-01 -3.2102647210747581e+00 -2.2423530055534227e+00
|
||||
11 -8.9306521974511965e-01 -7.3609588764692946e-01 7.7858707603166932e-01
|
||||
12 8.6395200517054016e-01 -1.5981432915146632e+00 -2.1679477568839745e-01
|
||||
13 -6.4494400058042478e-01 6.2756955493634248e-01 -1.0012212508165597e+00
|
||||
14 1.4121457183669881e+00 -3.8145518370890946e-01 1.4374334735700072e+00
|
||||
15 -8.0012105256118471e-01 3.3826645187577792e-01 -4.4188948688375512e-01
|
||||
16 1.9512996642081428e+00 -1.8484269993310276e+00 7.6647387636667308e-01
|
||||
17 9.6847667918444036e-01 2.8004906783494139e+00 -3.0748007851388115e-01
|
||||
18 -2.8449746205170134e+00 -6.1824996554122424e-01 -1.3472806126411994e+00
|
||||
19 -3.2477430400820975e+00 -1.3687972228229346e+00 8.3236229178971677e-01
|
||||
20 5.9315059333536402e-01 6.0128565847431148e-01 -9.1217508958587568e-01
|
||||
21 3.5879727016607603e+00 5.5038586867508599e-01 9.8753442724867704e-02
|
||||
22 1.5511768770985568e-01 -1.4315503989159941e+00 -3.5655100825750630e-01
|
||||
23 8.5405829958739810e-01 2.5896581671113488e+00 -1.5824438465222816e+00
|
||||
24 2.1822151145920117e+00 1.9809861442953116e+00 1.5846435537420727e+00
|
||||
25 1.1642513964511370e+00 7.8654670449493508e-02 -9.5490964373690435e-01
|
||||
26 -8.8370436766026839e-01 -3.0720569678955640e+00 2.5586883908525340e+00
|
||||
27 1.0905263045646054e+00 -9.2089563796464990e-02 9.5183608542272730e-02
|
||||
28 -2.2483303095995844e-01 1.1477992712823375e+00 1.4903422943362210e+00
|
||||
29 1.0962449966023380e+00 1.8651010391452665e+00 -2.5090548124359832e-02
|
||||
30 -7.5204116181154745e-01 -1.1523526863157827e+00 -1.6322014962960107e+00
|
||||
31 -9.0957260597904349e-02 -2.2978996297940468e+00 1.3386614339051799e+00
|
||||
32 -4.2909397991778597e+00 -9.1452181585807046e-01 -2.6209419999324374e-01
|
||||
...
|
||||
|
|
@ -0,0 +1,88 @@
|
|||
---
|
||||
lammps_version: 5 May 2020
|
||||
date_generated: Fri May 15 23:19:20 202
|
||||
epsilon: 5.0e-12
|
||||
prerequisites: ! |
|
||||
pair eam/fs
|
||||
pre_commands: ! ""
|
||||
post_commands: ! ""
|
||||
input_file: in.metal
|
||||
pair_style: eam/fs
|
||||
pair_coeff: ! |
|
||||
* * AlFe_mm.eam.fs Al Fe
|
||||
natoms: 32
|
||||
init_vdwl: -108.262111462389
|
||||
init_coul: 0
|
||||
init_stress: ! |2-
|
||||
9.9880622051717296e+01 9.1747240726677930e+01 8.7601365289659455e+01 5.9087784401945047e+00 -2.1299937451008777e+00 3.4718249594388439e-01
|
||||
init_forces: ! |2
|
||||
1 1.4220647505801736e+00 2.8000955383927590e+00 -9.2319050073781661e-02
|
||||
2 -5.5633074095781621e-01 -2.3647769633074764e+00 7.8868176319954686e-01
|
||||
3 -1.0778847439160915e+00 4.5596775142190262e+00 -1.0102225927248045e+00
|
||||
4 2.3378709218158031e-01 -8.3292676570515534e-02 -1.3329006533890759e+00
|
||||
5 9.9201541154787920e-01 5.9945826015938444e+00 1.2035564391465061e+00
|
||||
6 1.4306245643438618e+00 2.0549977651144062e+00 1.8180638296222192e-02
|
||||
7 -2.3038192949001317e+00 3.4287442993009449e+00 1.4446091589243593e-01
|
||||
8 -1.4647012677240703e+00 -1.3826121958965307e+00 1.3528676613878061e+00
|
||||
9 -7.0002491860199412e-01 -2.4319097344790448e+00 -1.7238433059900313e+00
|
||||
10 -1.0166690073670877e+00 -3.7407881655830764e+00 -4.2229197850609195e+00
|
||||
11 -1.6411568124995635e+00 -3.8659448317210319e+00 2.5005354485570450e+00
|
||||
12 1.3093866047607808e-01 -3.5116610088291154e+00 5.7277815561514200e-01
|
||||
13 6.1031266294744174e-02 7.0574737113421093e-01 -1.4146493204442210e+00
|
||||
14 1.4790295447530641e+00 -4.3134276808479749e-01 1.5232769366233945e+00
|
||||
15 -1.0963909466469939e+00 6.2457965041111041e-01 -1.9891144652287238e-01
|
||||
16 4.9208682430764341e+00 -3.5622966458847753e+00 1.5978213703961011e+00
|
||||
17 1.7172967257780336e+00 4.4833230131032371e+00 8.6651296155197477e-01
|
||||
18 -3.0418768827395826e+00 -8.4198067569250157e-01 -1.3469481862412083e+00
|
||||
19 -3.4740628338390791e+00 -1.5699309739845357e+00 7.4038432955001199e-01
|
||||
20 8.2905809585865176e-01 7.8229445413633147e-01 -1.1131849350555523e+00
|
||||
21 4.6304317520425782e+00 3.6483022560377498e+00 1.0942333727402151e+00
|
||||
22 -2.6563287132443747e-01 -1.9903139906951022e+00 -3.3293658854661151e-01
|
||||
23 1.5546501935324075e+00 3.1537689232958046e+00 -3.6308172935454626e+00
|
||||
24 2.4735088089599575e+00 2.1916364979867784e+00 1.7162964579096276e+00
|
||||
25 1.4961542139978541e+00 4.6166094159532584e-01 -9.8132505610006560e-01
|
||||
26 -2.0846432430440074e+00 -4.6626559139327997e+00 4.8192651763373124e+00
|
||||
27 4.9538055859465935e-01 -1.0501728328691109e+00 -7.0766065364565689e-01
|
||||
28 -3.5151036557319193e-01 8.9287294377213611e-01 1.3721446098470014e+00
|
||||
29 1.1470786976346550e+00 2.2129072730908512e+00 -1.8064557067363227e-01
|
||||
30 -1.0374660230195671e+00 -1.1402475422746554e+00 -1.7211546087860548e+00
|
||||
31 -1.0712777798403222e-01 -2.4507774686205819e+00 1.0846841028356100e+00
|
||||
32 -4.7946208495149687e+00 -2.9144866547588686e+00 -1.3852412930860005e+00
|
||||
run_vdwl: -109.421760327124
|
||||
run_coul: 0
|
||||
run_stress: ! |2-
|
||||
9.7321790151683032e+01 8.9726181847598752e+01 8.5108697468923864e+01 5.4985923819753797e+00 -2.2363627964466568e+00 4.7695776857019978e-01
|
||||
run_forces: ! |2
|
||||
1 1.2679194886054646e+00 2.6787268858296414e+00 9.7023827299581675e-03
|
||||
2 -5.5815898277144038e-01 -2.3090914306107573e+00 7.7129085256173746e-01
|
||||
3 -9.0701490664425277e-01 3.9988150514788630e+00 -9.0008377838410702e-01
|
||||
4 2.1760036877107486e-01 -3.5592028900505723e-02 -1.3241879269726802e+00
|
||||
5 8.7191382908658766e-01 5.5025947096510439e+00 1.2269578107092691e+00
|
||||
6 1.4320309112831469e+00 2.0271259799586265e+00 -4.5496868330302566e-03
|
||||
7 -2.0055825566447965e+00 3.2691589608305760e+00 1.0134836971121294e-01
|
||||
8 -1.4686427349869116e+00 -1.2816756190774403e+00 1.2930511003067942e+00
|
||||
9 -6.4120552539828712e-01 -2.4385069051766362e+00 -1.6951251844611397e+00
|
||||
10 -6.2209257619918201e-01 -3.4962227672673376e+00 -3.7799754582118790e+00
|
||||
11 -1.5341640045915756e+00 -3.6794922955899305e+00 2.3169074025641407e+00
|
||||
12 1.0716306131848929e-01 -3.1612337564358306e+00 5.4689025366733734e-01
|
||||
13 -3.4865083527509999e-02 6.2163633221569436e-01 -1.2767015747690553e+00
|
||||
14 1.4759289180607154e+00 -1.9983903928235117e-01 1.3165181136760309e+00
|
||||
15 -1.0859468934837868e+00 5.7512146638833528e-01 -1.9208548742570955e-01
|
||||
16 4.2650302076169417e+00 -3.3898349033764879e+00 1.5150959333645790e+00
|
||||
17 1.7075552543987051e+00 4.2197797415562528e+00 6.8658143676544903e-01
|
||||
18 -2.9282428817784707e+00 -8.1722879256446568e-01 -1.2768017170708874e+00
|
||||
19 -3.3028429922142437e+00 -1.4969402957853979e+00 6.6796170315879078e-01
|
||||
20 8.2458362952654385e-01 8.3101411589898766e-01 -1.1162304568819137e+00
|
||||
21 4.1973022930400949e+00 3.2131020492334490e+00 9.9992489898285064e-01
|
||||
22 -2.1782086247662638e-01 -1.8782889044649795e+00 -3.3002646429455057e-01
|
||||
23 1.3378055708885839e+00 2.8417725691838442e+00 -3.3299911840808853e+00
|
||||
24 2.3314022784432149e+00 2.1821654533604953e+00 1.6556156861679943e+00
|
||||
25 1.4357165303696771e+00 4.2664400867737490e-01 -9.4597021021657834e-01
|
||||
26 -1.7463565218649646e+00 -4.0460118685059721e+00 4.3667870871022822e+00
|
||||
27 4.1107143320055650e-01 -1.1331997756369530e+00 -7.2860925822132971e-01
|
||||
28 -4.1072299435514803e-01 9.1485902771452987e-01 1.3319976358714796e+00
|
||||
29 1.1026069599653305e+00 2.0767178601615672e+00 -1.4719919616790900e-01
|
||||
30 -9.3823645826167124e-01 -1.0624295742838414e+00 -1.6161620718496021e+00
|
||||
31 -1.4173053658599111e-01 -2.3849422802844553e+00 1.0354387068087780e+00
|
||||
32 -4.4420042227902661e+00 -2.5687039748959393e+00 -1.1783697183074275e+00
|
||||
...
|
||||
|
|
@ -0,0 +1,90 @@
|
|||
---
|
||||
lammps_version: 5 May 2020
|
||||
date_generated: Mon May 18 14:22:49 202
|
||||
epsilon: 5e-12
|
||||
prerequisites: ! |
|
||||
pair eam/fs
|
||||
pre_commands: ! ""
|
||||
post_commands: ! ""
|
||||
input_file: in.metal
|
||||
pair_style: hybrid lj/cut 8.0 eam
|
||||
pair_coeff: ! |
|
||||
1 * lj/cut 0.01014 3.0
|
||||
2 2 eam Ni_u3.eam
|
||||
extract: ! ""
|
||||
natoms: 32
|
||||
init_vdwl: 0.713225916338978
|
||||
init_coul: 0
|
||||
init_stress: ! |2-
|
||||
2.6556151567263032e+02 2.6660724159085703e+02 2.4812081237895359e+02 6.0264893464561915e+00 -6.6027371615114303e+00 -1.4187579099120772e+01
|
||||
init_forces: ! |2
|
||||
1 -6.7586482125865543e-02 4.9706477501213024e+00 1.2670989470204179e+00
|
||||
2 -1.5700573701218445e+00 -7.5529562390351002e+00 1.1772842395708361e+00
|
||||
3 -4.2429833624386450e+00 1.9349527250657509e+01 -3.5557002229877837e+00
|
||||
4 1.8550849554634552e+00 1.1008664640808090e+00 -2.1953957883365982e-01
|
||||
5 5.9744908585715111e+00 1.1742823663949734e+01 1.7416462589063628e+00
|
||||
6 3.0257350803700804e+00 1.5847132904510355e+00 -8.2906203748202068e-01
|
||||
7 -5.3007946436773707e+00 6.9970677759011384e+00 -8.9489819054939967e-01
|
||||
8 -4.6448667388294567e+00 -1.2546033914725536e+00 6.9100744050829652e+00
|
||||
9 1.2959381936787344e+00 -3.5546957320584367e+00 -2.0599746114035731e+00
|
||||
10 -3.5499506443793543e+00 -1.2965813617805704e+01 -8.5756020254950300e+00
|
||||
11 -2.6100480197239939e+00 -3.2981172904215144e+00 3.0128875803829169e+00
|
||||
12 3.1244931710116184e+00 -6.9886680292069130e+00 -4.4530289150329527e-01
|
||||
13 -1.5468234681905584e+00 1.5362933608996416e+00 -3.3155163626495727e+00
|
||||
14 5.3255445540876165e+00 -4.1034966882533075e+00 3.7446743737136541e+00
|
||||
15 -2.3650720705111974e+00 -6.8830548930542657e-01 2.5315199882832524e+00
|
||||
16 8.0910820536854153e+00 -6.7951006563580103e+00 2.8259508039607151e+00
|
||||
17 3.4577277480360227e+00 9.8286899814235920e+00 -7.1006724865196635e-01
|
||||
18 -4.8256863020573730e+00 -4.5005025608923088e-01 -1.8608365148097044e+00
|
||||
19 -8.3592385395973281e+00 1.7191284583053164e+00 2.1484111443112788e+00
|
||||
20 3.3025429889617013e+00 2.8402645183638562e+00 -4.1222293577210616e+00
|
||||
21 1.2904534654690750e+01 4.5572617600368748e+00 2.9907771592730525e-01
|
||||
22 -2.7325925127560840e-03 5.3602804455393860e-01 -5.7482170861908999e-01
|
||||
23 4.7951259585477333e+00 1.0576382862196359e+01 -6.0546273552100045e+00
|
||||
24 1.5447144864533726e+00 4.2880557089268780e+00 9.4350854397872430e-01
|
||||
25 -5.2231560429504476e-01 -1.0522106548193342e+00 -7.8122739446199729e-01
|
||||
26 -4.8939830060013279e+00 -1.2802497836684044e+01 1.0569608840309295e+01
|
||||
27 3.8521673292935157e+00 -9.8854973943266755e-01 -2.2861593927743451e-01
|
||||
28 -4.5445835368598706e+00 1.8110761223183225e-02 2.3302385514692601e+00
|
||||
29 4.1707423709756810e+00 1.9610559978185012e-02 -2.8558880361150057e-01
|
||||
30 -8.7442364632334701e-01 -8.5922993943854902e+00 -3.1671240722317777e+00
|
||||
31 3.1880080741982892e+00 -5.0021160844369490e+00 -2.7083467494366831e-01
|
||||
32 -1.5986786450380142e+01 -5.5759911113046883e+00 -1.5504124024744577e+00
|
||||
run_vdwl: -2.66375379444636
|
||||
run_coul: 0
|
||||
run_stress: ! |2-
|
||||
2.5240789931255762e+02 2.5310341558939220e+02 2.3543185866992556e+02 3.5794743941279328e+00 -6.5594623433970316e+00 -1.2031941810791363e+01
|
||||
run_forces: ! |2
|
||||
1 -7.3526208784876937e-02 4.6276320068176959e+00 1.3126264406665118e+00
|
||||
2 -1.5191460382260331e+00 -7.2498061177696114e+00 1.1823934281570776e+00
|
||||
3 -3.2833567945495470e+00 1.5927553463956462e+01 -2.9194944379847763e+00
|
||||
4 1.7820481436204219e+00 1.1974444662187944e+00 -2.4893842934590110e-01
|
||||
5 4.7368209750868262e+00 9.9036364584686591e+00 2.1027355832605523e+00
|
||||
6 2.8161555194400765e+00 1.7961276852999983e+00 -5.7078753323633125e-01
|
||||
7 -4.5078427357513151e+00 6.2991186370729713e+00 -8.0377899842111500e-01
|
||||
8 -4.4353940063558506e+00 -9.7188642407974235e-01 6.3230048169341826e+00
|
||||
9 1.3321375236984641e+00 -3.7787257273939892e+00 -2.0434694926966208e+00
|
||||
10 -1.9181848101178929e+00 -1.0676184991243765e+01 -7.1179944803771953e+00
|
||||
11 -2.4308670067274405e+00 -3.3248447289326091e+00 2.8133415240037296e+00
|
||||
12 2.8237193303412664e+00 -5.9086614687477743e+00 -3.1342585243749416e-01
|
||||
13 -1.6609055329084119e+00 1.1502077740387375e+00 -2.9812284538437752e+00
|
||||
14 4.9864847833340420e+00 -3.1069456640509343e+00 2.6407894626498329e+00
|
||||
15 -2.3096659810862570e+00 -7.1889956555863266e-01 2.4005929790782683e+00
|
||||
16 6.3388015605019676e+00 -5.9323183163022204e+00 2.5107086541588584e+00
|
||||
17 3.0224684980801002e+00 8.7577289282650828e+00 -7.8693201428206749e-01
|
||||
18 -4.6063549496955716e+00 -4.8952117895160330e-01 -1.7876069960758847e+00
|
||||
19 -7.6082515836661804e+00 1.7464009236580180e+00 1.7708127739610868e+00
|
||||
20 3.2358845256701860e+00 2.8607356592741970e+00 -4.0297737600168642e+00
|
||||
21 1.1010164765387213e+01 3.2330607311408555e+00 4.0042019178611621e-01
|
||||
22 4.4781828869438857e-02 6.0719403319623344e-01 -5.5908241440452000e-01
|
||||
23 3.5594522651794591e+00 8.5069620665211403e+00 -5.6129085441684339e+00
|
||||
24 1.3556306526283137e+00 4.1895383567136788e+00 8.5123633213127070e-01
|
||||
25 -4.7747651793878743e-01 -1.0333245427318232e+00 -7.2474339551019717e-01
|
||||
26 -3.6774542022592964e+00 -9.7618611587187978e+00 8.5271212642003018e+00
|
||||
27 3.4544370855467634e+00 -1.0186800522859873e+00 -2.8836655978984127e-01
|
||||
28 -4.4586745068280216e+00 1.3021742871288211e-01 2.1159918887153317e+00
|
||||
29 4.0230480986379309e+00 -9.9978144037769612e-02 -2.3050698755072571e-01
|
||||
30 -6.1379468567831041e-01 -7.9222717952796513e+00 -2.6496750288296882e+00
|
||||
31 2.6518561367509244e+00 -4.5192458764555550e+00 -2.0974012823704041e-01
|
||||
32 -1.3592996132199600e+01 -4.4204028668149364e+00 -1.0733218324946607e+00
|
||||
...
|
||||
|
|
@ -0,0 +1,90 @@
|
|||
---
|
||||
lammps_version: 5 May 2020
|
||||
date_generated: Mon May 18 14:23:15 202
|
||||
epsilon: 5e-12
|
||||
prerequisites: ! |
|
||||
pair eam/fs
|
||||
pre_commands: ! ""
|
||||
post_commands: ! ""
|
||||
input_file: in.metal
|
||||
pair_style: hybrid lj/cut 8.0 eam/fs
|
||||
pair_coeff: ! |
|
||||
1 * lj/cut 0.01014 3.0
|
||||
* * eam/fs AlFe_mm.eam.fs NULL Al
|
||||
extract: ! ""
|
||||
natoms: 32
|
||||
init_vdwl: 15.6583494469006
|
||||
init_coul: 0
|
||||
init_stress: ! |2-
|
||||
3.1757662346015599e+02 3.1488042003987044e+02 2.9518192213010605e+02 8.0970202601485379e+00 -4.6038792816319125e+00 -1.1521259274290610e+01
|
||||
init_forces: ! |2
|
||||
1 -6.7586482125865543e-02 4.9706477501213024e+00 1.2670989470204179e+00
|
||||
2 -1.4449911436544765e+00 -5.9239923976216469e+00 2.3626572120265843e+00
|
||||
3 -3.6428903939842701e+00 1.6719012553324998e+01 -3.7629778690805842e+00
|
||||
4 1.2982956924349240e+00 1.7909023449535547e-01 -1.9210443504104735e+00
|
||||
5 5.9744908585715111e+00 1.1742823663949734e+01 1.7416462589063628e+00
|
||||
6 3.0257350803700804e+00 1.5847132904510355e+00 -8.2906203748202068e-01
|
||||
7 -5.3007946436773707e+00 6.9970677759011384e+00 -8.9489819054939967e-01
|
||||
8 -4.6605352318708730e+00 -3.0006322761849118e+00 4.9977847779403284e+00
|
||||
9 1.2959381936787344e+00 -3.5546957320584367e+00 -2.0599746114035731e+00
|
||||
10 -3.5499506443793543e+00 -1.2965813617805704e+01 -8.5756020254950300e+00
|
||||
11 -2.6100480197239939e+00 -3.2981172904215144e+00 3.0128875803829169e+00
|
||||
12 3.1244931710116184e+00 -6.9886680292069130e+00 -4.4530289150329527e-01
|
||||
13 -1.5468234681905584e+00 1.5362933608996416e+00 -3.3155163626495727e+00
|
||||
14 4.7231953507940965e+00 -2.3330444753363877e+00 4.7731104251729848e+00
|
||||
15 -2.0534455195530730e+00 7.8519776471530123e-01 -1.1962673768666337e-02
|
||||
16 8.0910820536854153e+00 -6.7951006563580103e+00 2.8259508039607151e+00
|
||||
17 3.4577277480360227e+00 9.8286899814235920e+00 -7.1006724865196635e-01
|
||||
18 -5.8763515423064252e+00 -3.7797993865228519e-01 -2.6352837760635270e+00
|
||||
19 -8.5925788901564157e+00 -1.2953716148181162e+00 2.4013853517912715e+00
|
||||
20 2.1676584547331541e+00 1.8449822199481989e+00 -3.0773083703770627e+00
|
||||
21 1.2904534654690750e+01 4.5572617600368748e+00 2.9907771592730525e-01
|
||||
22 7.1713668059147473e-02 -2.9176444807983977e+00 -5.4602076473768479e-01
|
||||
23 4.7951259585477333e+00 1.0576382862196359e+01 -6.0546273552100045e+00
|
||||
24 3.7998884249438638e+00 4.2456756942258567e+00 2.8231067817667697e+00
|
||||
25 2.2446373085412210e+00 4.7178057347893189e-02 -1.7971307155595491e+00
|
||||
26 -4.8939830060013279e+00 -1.2802497836684044e+01 1.0569608840309295e+01
|
||||
27 3.8521673292935157e+00 -9.8854973943266755e-01 -2.2861593927743451e-01
|
||||
28 -2.0735760680382374e+00 1.8771069576900596e+00 3.9080866893137225e+00
|
||||
29 2.3306521160866436e+00 3.1021445725227297e+00 -8.1526960815962446e-02
|
||||
30 -2.0584055270338175e+00 -5.2207163606526530e+00 -4.6304543222177532e+00
|
||||
31 1.2014109675977875e+00 -6.5554529419137078e+00 2.1453874832093329e+00
|
||||
32 -1.5986786450380142e+01 -5.5759911113046883e+00 -1.5504124024744577e+00
|
||||
run_vdwl: 11.4858562707976
|
||||
run_coul: 0
|
||||
run_stress: ! |2-
|
||||
3.0206281119895192e+02 2.9839150289953903e+02 2.7908748751032857e+02 5.2322850515137054e+00 -4.4239479114146283e+00 -8.4608706993722507e+00
|
||||
run_forces: ! |2
|
||||
1 -1.1849858890514021e-01 4.7242432545697088e+00 1.3265451237218602e+00
|
||||
2 -1.3250768345508559e+00 -5.3511603765145770e+00 2.1410052830224986e+00
|
||||
3 -2.2700257027423225e+00 1.1882640655984687e+01 -2.6893578040536417e+00
|
||||
4 9.2467426254256924e-01 4.7472136350787353e-01 -1.9054352365531899e+00
|
||||
5 4.7363491800017670e+00 9.8438006258188651e+00 1.9732492208585084e+00
|
||||
6 2.7680034258340784e+00 1.8171614620504244e+00 -3.6035747489478603e-01
|
||||
7 -4.4919044715564649e+00 6.3872035608307183e+00 -8.2274250075750177e-01
|
||||
8 -4.2041699436029045e+00 -2.4646139599222829e+00 4.0605229910239533e+00
|
||||
9 1.4629904265694940e+00 -3.8814409140350206e+00 -2.0274374837861129e+00
|
||||
10 -1.8917309349531379e+00 -1.0478812541228589e+01 -6.7381196596711090e+00
|
||||
11 -2.4118490286273033e+00 -3.3214814331743030e+00 2.7677127410903135e+00
|
||||
12 3.0519151897635446e+00 -5.7757394077502502e+00 -3.0038765160829517e-01
|
||||
13 -1.7057375614102981e+00 1.0854340974897752e+00 -2.8355940344663870e+00
|
||||
14 4.0183527421571297e+00 -1.2067382913714841e+00 3.2102889327660686e+00
|
||||
15 -1.9580383412386364e+00 4.8390607508432104e-01 -7.5740122183371242e-02
|
||||
16 6.0677348392979713e+00 -5.7378693262646001e+00 2.4974286052812276e+00
|
||||
17 2.8547982360336568e+00 8.5493890206088938e+00 -8.4565046086350093e-01
|
||||
18 -5.1749897015544475e+00 -4.7312180095976142e-01 -2.2371554847310056e+00
|
||||
19 -7.1675344296007797e+00 -1.0118502862174970e+00 1.7882195840126567e+00
|
||||
20 2.0161347706407526e+00 1.8417839323791756e+00 -2.8671273527748875e+00
|
||||
21 1.0578411106115118e+01 3.3304963159644583e+00 7.3282301526571236e-01
|
||||
22 1.7893814500606164e-01 -2.6448785628600362e+00 -6.3104856433780721e-01
|
||||
23 3.5387062116822832e+00 8.2619934075188315e+00 -5.5800038194270147e+00
|
||||
24 3.1160414704593657e+00 3.8864959234902394e+00 2.4094721723738313e+00
|
||||
25 2.0051152564142143e+00 1.7701772456340975e-01 -1.6642079255120197e+00
|
||||
26 -3.7855143773897071e+00 -9.1165837952426152e+00 7.9299986973321710e+00
|
||||
27 3.3936982993989577e+00 -1.1159969847487432e+00 -1.9289487597647970e-01
|
||||
28 -2.0849071615339776e+00 1.7673677200016646e+00 3.4512964427566213e+00
|
||||
29 2.0695057271768094e+00 2.6685623735706621e+00 5.1113802725358676e-03
|
||||
30 -1.6314063838809783e+00 -4.4318986602461869e+00 -3.6140235345662295e+00
|
||||
31 6.4100992367021226e-01 -5.6703633267329838e+00 2.0418124408970137e+00
|
||||
32 -1.3200995751217025e+01 -4.4996678461647708e+00 -9.4820264451162939e-01
|
||||
...
|
||||
|
|
@ -0,0 +1,87 @@
|
|||
---
|
||||
lammps_version: 5 May 2020
|
||||
date_generated: Mon May 18 18:18:26 202
|
||||
epsilon: 1e-13
|
||||
prerequisites: ! |
|
||||
atom full
|
||||
bond class2
|
||||
pre_commands: ! ""
|
||||
post_commands: ! ""
|
||||
input_file: in.fourmol
|
||||
bond_style: class2
|
||||
bond_coeff: ! |
|
||||
1 1.42 470.83 -627.61 1327.63
|
||||
2 1.1 372.82 -803.45 894.33
|
||||
3 1.3 299.67 -501.77 679.81
|
||||
4 1.2 345.00 -691.89 844.60
|
||||
5 0.97 532.50 -1282.90 2004.76
|
||||
extract: ! |
|
||||
r0 1
|
||||
natoms: 29
|
||||
init_energy: 26.4298596421327
|
||||
init_stress: ! |-
|
||||
-3.0141734112468595e+02 -3.1150388091129679e+02 -2.6058470202224748e+02 -1.9292943555936553e+01 -1.4107089561246062e+00 1.2759470887440076e+01
|
||||
init_forces: ! |2
|
||||
21 7.1042357682646404e+00 1.1134804697492651e+01 -3.8368402885663073e+01
|
||||
22 1.9200692242554261e+01 4.6531060525874279e+00 3.0123746382612186e+01
|
||||
23 -2.6304928010818902e+01 -1.5787910750080078e+01 8.2446565030508907e+00
|
||||
19 2.7924176309592106e+01 1.7864374209535594e+01 3.3829318447430467e+01
|
||||
18 -6.8243320112081278e+00 4.5837440084223076e+00 -4.8061490502468466e+01
|
||||
20 -2.1099844298383978e+01 -2.2448118217957902e+01 1.4232172055038001e+01
|
||||
28 2.1551008635816927e+01 -9.2616399704789991e+00 1.4581621559271095e+01
|
||||
4 5.9502197247616113e+00 -1.6680826308132446e+00 4.2218335642085876e+00
|
||||
10 8.1188263973809995e+01 -6.1075218904782398e+00 2.8418048943082294e+01
|
||||
11 -4.6385122980445714e-01 -1.1490005546317998e+00 -1.8852784469117345e+00
|
||||
12 -3.7815067902031942e+01 -3.7768774735713166e+01 2.5928451502802925e+01
|
||||
14 3.5661540054267613e+00 -7.2566505558946637e-01 9.2481860419315911e+00
|
||||
3 7.8193691709543742e+01 -3.6596608366065141e+01 -4.8323005748617874e+01
|
||||
6 -8.1174741545190599e+01 8.1076516681367011e+01 3.8793650376973197e+01
|
||||
7 -8.7231319177681635e-02 4.4743601081267120e-01 2.2322556715451980e+00
|
||||
15 3.0625241186147151e-01 -1.1767634638580507e+01 -4.1935682904441007e+00
|
||||
8 1.7727792025598848e+01 -4.9060964866335288e+00 3.0054710141579413e+01
|
||||
9 -5.4384717483109544e+00 -5.8575677401837627e+00 -2.4067122128118815e+01
|
||||
16 -4.2216718511275438e+01 5.9354313862666594e+01 -4.0503014976237310e+01
|
||||
17 6.1858469664013427e+00 -4.3137429831398029e+00 -1.6411243346787664e+01
|
||||
5 -1.6158453067593426e+00 -2.4831170760984631e+00 8.2507138342254258e+00
|
||||
13 -1.3250683645615497e+01 5.2418335903084801e+00 2.4904753378273239e-01
|
||||
2 -2.4793732733641569e+01 -2.0403328205609661e+01 2.9181516921770921e+01
|
||||
1 1.3738123124403696e+01 -1.2372959781617972e+01 -4.1195181594784785e+01
|
||||
27 2.2674229580362422e+00 3.6953663496240573e+01 -8.8003614900515856e+00
|
||||
29 -2.3818431593853170e+01 -2.7692023525761574e+01 -5.7812600692195097e+00
|
||||
24 -1.3172636156350135e+01 3.1394962897312048e+01 -2.2650917497159423e+01
|
||||
25 2.9082917709582546e+01 -4.6819283224527286e+00 2.4449463036092890e+01
|
||||
26 -1.5910281553232410e+01 -2.6713034574859321e+01 -1.7985455389334679e+00
|
||||
run_energy: 11.0473171333048
|
||||
run_stress: ! |-
|
||||
-1.4852712504356052e+02 -1.9983434269203804e+02 -1.6958399346360650e+02 2.4915064894614105e+01 2.6429352567045122e+01 1.1402862872836554e+01
|
||||
run_forces: ! |2
|
||||
21 -1.2939143040659487e+00 -1.6310318578056515e-01 -2.9670329043561345e+00
|
||||
22 1.8698597825995587e+00 4.9273673214457669e-01 2.8002381199733750e+00
|
||||
23 -5.7594547853361000e-01 -3.2963354636401154e-01 1.6679478438275974e-01
|
||||
19 3.7030996483351912e+00 2.4471642173460157e+00 4.3118693019952339e+00
|
||||
18 1.2970338177081336e+01 1.5269368987959455e+01 -1.4709441761879583e+01
|
||||
20 -1.6673437825416528e+01 -1.7716533205305470e+01 1.0397572459884350e+01
|
||||
28 4.0052153544933905e-01 -1.6613934988368023e-01 2.6451006164923158e-01
|
||||
4 1.0657056692901113e+01 -2.8987400139072070e+00 7.4380897526676470e+00
|
||||
10 5.1799901634548057e+01 -7.5345801673577899e+00 1.0355887001939042e+01
|
||||
11 2.8490552058403762e+00 6.4295335852166620e+00 1.0639003325745083e+01
|
||||
12 -2.6767357398146597e+01 -2.9041586107390195e+01 1.4798850320310191e+01
|
||||
14 4.4351200917545039e+00 -8.7592876807178788e-01 1.1844986091191039e+01
|
||||
3 4.5938955094915151e+01 -1.4876607602671008e+01 -2.0881097471003674e+01
|
||||
6 -4.2290686184681540e+01 4.2224824761005884e+01 1.8529188607548278e+01
|
||||
7 -8.7647510815200691e-01 3.4382971960812156e+00 1.5493615318132404e+01
|
||||
15 3.1074972597108347e-01 -8.3731012118651407e+00 -3.0761396502245972e+00
|
||||
8 3.0477512143977243e+00 -2.3136645583767042e+00 -5.5160504880049643e-01
|
||||
9 -9.1772746647337811e-01 -9.6069468430258709e-01 -4.0536371195689593e+00
|
||||
16 -3.1141292673296054e+01 4.4882099933939173e+01 -2.8367658133311600e+01
|
||||
17 5.2309713463802394e+00 -3.6149016132166203e+00 -1.4475056806593008e+01
|
||||
5 1.2479840534608451e+00 1.7133652758827786e+00 -5.8796845220898595e+00
|
||||
13 -1.2723199064464621e+01 4.6042668036810674e+00 2.8681948350869607e-01
|
||||
2 -7.2376429946058520e+00 -6.1508458361605616e+00 8.1367348066584384e+00
|
||||
1 -3.5631641703490464e+00 -2.6651736992487173e+01 -2.0238295956108619e+01
|
||||
27 2.3146874422269574e+00 3.3337796720029980e+00 4.6938982241463839e-01
|
||||
29 -2.7152089776762964e+00 -3.1676403221193179e+00 -7.3389988406386997e-01
|
||||
24 4.1876740324734651e+00 -5.2749970947748643e+00 5.3300662359604090e+00
|
||||
25 -6.8200185358534435e+00 8.9526747058374445e-01 -5.7340586378034830e+00
|
||||
26 2.6323445033799779e+00 4.3797296241911194e+00 4.0399240184307428e-01
|
||||
...
|
||||
|
|
@ -0,0 +1,88 @@
|
|||
---
|
||||
lammps_version: 5 May 2020
|
||||
date_generated: Mon May 18 18:18:26 202
|
||||
epsilon: 2.5e-13
|
||||
prerequisites: ! |
|
||||
atom full
|
||||
bond harmonic
|
||||
pre_commands: ! ""
|
||||
post_commands: ! ""
|
||||
input_file: in.fourmol
|
||||
bond_style: harmonic
|
||||
bond_coeff: ! |
|
||||
1 250.0 1.5
|
||||
2 300.0 1.1
|
||||
3 350.0 1.3
|
||||
4 650.0 1.2
|
||||
5 450.0 1.0
|
||||
extract: !
|
||||
kappa 1
|
||||
r0 1
|
||||
natoms: 29
|
||||
init_energy: 4.78937402460125
|
||||
init_stress: ! |-
|
||||
-7.8339576416581650e+01 -1.1712828041794818e+02 -9.5949529209186267e+01 -7.1916460767231181e+00 8.3588128261115031e+00 -4.3565947473672914e+01
|
||||
init_forces: ! |2
|
||||
21 -1.5332952658285048e+00 5.9630208068632040e-01 -7.4967230017303281e+00
|
||||
22 4.2380253233105529e+00 1.0270453290850614e+00 6.6489894421385651e+00
|
||||
23 -2.7047300574820481e+00 -1.6233474097713818e+00 8.4773355959176278e-01
|
||||
19 1.2597490501067170e+01 8.0591915019111742e+00 1.5261489294231819e+01
|
||||
18 -9.0963607969319646e+00 -4.3343406270234155e+00 -1.7623055551859267e+01
|
||||
20 -3.5011297041352050e+00 -3.7248508748877587e+00 2.3615662576274494e+00
|
||||
28 -8.8466157439236681e-01 3.8018717064230995e-01 -5.9857060538593476e-01
|
||||
4 4.9515988613836521e+00 -1.3881295880648545e+00 3.5132864392371754e+00
|
||||
10 6.1553322543113023e+00 -2.2433216433517429e+00 1.0077919615506113e+01
|
||||
11 -3.6965429185303017e-01 -9.1566640135935162e-01 -1.5024241059632979e+00
|
||||
12 5.3354247763252225e+00 3.4693872991926265e+00 -2.5769463436217106e+00
|
||||
14 3.0021293944569267e+00 -6.1089352579843248e-01 7.7854885458225027e+00
|
||||
3 3.2179063381273927e+01 2.7678516114804015e+01 -6.9925499819535162e+00
|
||||
6 -3.1162678242357686e+01 2.9093203520848988e+01 1.9628673689480447e+00
|
||||
7 -1.6600535560497887e-01 8.5149204191370942e-01 4.2480888750665819e+00
|
||||
15 2.6101748011558590e-01 -1.0029499267005084e+01 -3.5741583918022086e+00
|
||||
8 1.3018665172824681e+01 -1.2902789438539877e+01 3.2406676637830003e+00
|
||||
9 7.4343536239661590e-01 8.0072549738604493e-01 3.2899591078538779e+00
|
||||
16 -1.8652324245822157e+01 1.7955465494587671e+01 2.4259133427839036e+01
|
||||
17 1.2692419458756444e+01 -8.8511461205982513e+00 -3.3673381434835903e+01
|
||||
5 -1.2535323383072501e+00 -1.9263400658909466e+00 6.4006972462376623e+00
|
||||
13 -1.1391739280608117e+01 4.5064543996480326e+00 2.1410854331807169e-01
|
||||
2 -9.4281609567839944e+00 -7.7586487054273015e+00 1.1096676787527940e+01
|
||||
1 -5.9149914305071416e+00 -3.7728809612345245e+01 -2.7769433362963369e+01
|
||||
27 6.6999960289138851e+00 6.3808952243186141e+00 2.0100808779497248e+00
|
||||
29 -5.8153344545215182e+00 -6.7610823949609244e+00 -1.4115102725637900e+00
|
||||
24 -6.6588083188726532e+00 3.5110922792825918e+00 -6.5625174267043489e+00
|
||||
25 7.9844426562464141e+00 -1.2853795683286129e+00 6.7123710742192300e+00
|
||||
26 -1.3256343373737607e+00 -2.2257127109539789e+00 -1.4985364751488087e-01
|
||||
run_energy: 2.83684860023705
|
||||
run_stress: ! |-
|
||||
-3.8845087273848591e+01 -8.1129831334544605e+01 -7.2148686127846176e+01 6.0616019783955668e+00 1.8209147944256966e+01 -1.9550003899165365e+01
|
||||
run_forces: ! |2
|
||||
21 -2.4947171840915869e+00 -1.8301499314042944e+00 3.0384167705842424e+00
|
||||
22 -1.2708061166290454e+00 -3.3104329489702544e-01 -1.9230876962606467e+00
|
||||
23 3.7655233007206323e+00 2.1611932263013198e+00 -1.1153290743235955e+00
|
||||
19 -5.5501142419144456e-01 -3.6536974680872897e-01 -6.5214259764664040e-01
|
||||
18 1.2483325913879641e+01 1.3063074718773587e+01 -6.8971702953266796e+00
|
||||
20 -1.1928314489688196e+01 -1.2697704971964857e+01 7.5493128929733198e+00
|
||||
28 -3.6996573174115897e+00 1.5606345314733694e+00 -2.4509265379052949e+00
|
||||
4 6.5221791595560790e+00 -1.6768327218224681e+00 4.6889272682189098e+00
|
||||
10 7.8293718314586460e+00 -8.8088917119527501e+00 2.0632944299945866e+00
|
||||
11 1.4289449452688718e+00 3.5030228307558806e+00 5.7585599974007362e+00
|
||||
12 7.1036941681672672e-01 -1.9280521842084131e+00 -4.9989138600792495e+00
|
||||
14 3.4610701659618148e+00 -5.7128292882003495e-01 8.9192549102655683e+00
|
||||
3 2.2021680087825608e+01 1.6602219779536021e+01 -3.5830697224507624e+00
|
||||
6 -1.8635662486158147e+01 1.6654550461254956e+01 -4.0511489699458352e+00
|
||||
7 -6.6385724496932808e-01 3.0468914215284397e+00 1.4336157841115863e+01
|
||||
15 1.9839135771552102e-01 -4.0967296313583157e+00 -1.5505984773608759e+00
|
||||
8 2.7199518446703106e+00 -2.3615257673626768e+00 1.2945878341881591e+00
|
||||
9 -4.0546571195059888e-02 -4.2574614866484208e-02 -1.7930016735330342e-01
|
||||
16 -1.1166321863118815e+01 1.3119964300691947e+01 3.1795412792252655e+00
|
||||
17 4.9397320214751650e+00 -3.4941707018827093e+00 -1.3257562782906669e+01
|
||||
5 1.0214635110435490e-01 1.5611943221737712e-01 -5.0323627149029626e-01
|
||||
13 -8.1055792591227274e+00 3.0496276199864645e+00 1.2620656378364231e-01
|
||||
2 -4.4977044304336369e+00 -3.8337728675436282e+00 5.0461421358707099e+00
|
||||
1 -6.8241653268553852e+00 -2.9318562716153608e+01 -1.7288842008476450e+01
|
||||
27 2.5775039024618946e+00 -2.8811820695598049e+00 2.1511068222696847e+00
|
||||
29 1.1221534149496948e+00 1.3205475380864353e+00 2.9981971563561016e-01
|
||||
24 4.8856830027728240e+00 -9.4469527796070771e+00 7.4808498283266793e+00
|
||||
25 -9.7142716248063898e+00 1.3432566023937309e+00 -8.1922635057573245e+00
|
||||
26 4.8285886220335659e+00 8.1036961772133456e+00 7.1141367743064510e-01
|
||||
...
|
||||
|
|
@ -0,0 +1,87 @@
|
|||
---
|
||||
lammps_version: 5 May 2020
|
||||
date_generated: Mon May 18 18:18:26 202
|
||||
epsilon: 2.5e-13
|
||||
prerequisites: ! |
|
||||
atom full
|
||||
bond morse
|
||||
bond harmonic
|
||||
pre_commands: ! ""
|
||||
post_commands: ! ""
|
||||
input_file: in.fourmol
|
||||
bond_style: hybrid harmonic morse
|
||||
bond_coeff: ! |
|
||||
1 harmonic 250.0 1.5
|
||||
2 morse 6000.0 0.3 1.1
|
||||
3 morse 7000.0 0.2 1.3
|
||||
4 harmonic 650.0 1.2
|
||||
5 harmonic 450.0 1.0
|
||||
extract: ! ""
|
||||
natoms: 29
|
||||
init_energy: 4.63957309438403
|
||||
init_stress: ! |-
|
||||
-9.1714487491693831e+01 -1.1475291850911708e+02 -9.7902687629822026e+01 3.3666145598018780e+00 2.9841452462201108e+00 -4.0641761740546514e+01
|
||||
init_forces: ! |2
|
||||
21 -1.5332952658285048e+00 5.9630208068632040e-01 -7.4967230017303281e+00
|
||||
22 4.2380253233105529e+00 1.0270453290850614e+00 6.6489894421385651e+00
|
||||
23 -2.7047300574820481e+00 -1.6233474097713818e+00 8.4773355959176278e-01
|
||||
19 1.2597490501067170e+01 8.0591915019111742e+00 1.5261489294231819e+01
|
||||
18 -9.0963607969319646e+00 -4.3343406270234155e+00 -1.7623055551859267e+01
|
||||
20 -3.5011297041352050e+00 -3.7248508748877587e+00 2.3615662576274494e+00
|
||||
28 -8.8466157439236681e-01 3.8018717064230995e-01 -5.9857060538593476e-01
|
||||
4 8.8713463313619556e+00 -2.4869902981383678e+00 6.2944478412455851e+00
|
||||
10 7.0500441309881738e+00 -2.1698193341175673e+00 1.1079990798364344e+01
|
||||
11 -6.6627555421674023e-01 -1.6504235240582910e+00 -2.7080125293588715e+00
|
||||
12 1.1688299175371535e+01 8.3002370040851812e+00 -6.0772994904252551e+00
|
||||
14 5.3700342562960186e+00 -1.0927307685485257e+00 1.3926228586369799e+01
|
||||
3 2.5940715940638306e+01 2.0455023666793618e+01 -1.8574982949978697e+01
|
||||
6 -2.9062602766491054e+01 2.7377051044121011e+01 3.4298215329255726e+00
|
||||
7 -1.6600535560497887e-01 8.5149204191370942e-01 4.2480888750665819e+00
|
||||
15 4.6609400189370959e-01 -1.7909488085925670e+01 -6.3823073745841539e+00
|
||||
8 1.0320499082644886e+01 -1.0525382148347132e+01 1.9772307403428178e+00
|
||||
9 7.4343536239661590e-01 8.0072549738604493e-01 3.2899591078538779e+00
|
||||
16 -1.8652324245822157e+01 1.7955465494587671e+01 2.4259133427839036e+01
|
||||
17 1.2692419458756444e+01 -8.8511461205982513e+00 -3.3673381434835903e+01
|
||||
5 -2.2678975048300209e+00 -3.4851448944569343e+00 1.1580176171216390e+01
|
||||
13 -2.0317595063271646e+01 8.0374307564261560e+00 3.8187063235626600e-01
|
||||
2 -9.4281609567839944e+00 -7.7586487054273015e+00 1.1096676787527940e+01
|
||||
1 -2.5820262933270559e+00 -2.7847651625695352e+01 -2.4147640721925328e+01
|
||||
27 6.6999960289138851e+00 6.3808952243186141e+00 2.0100808779497248e+00
|
||||
29 -5.8153344545215182e+00 -6.7610823949609244e+00 -1.4115102725637900e+00
|
||||
24 -6.6588083188726532e+00 3.5110922792825918e+00 -6.5625174267043489e+00
|
||||
25 7.9844426562464141e+00 -1.2853795683286129e+00 6.7123710742192300e+00
|
||||
26 -1.3256343373737607e+00 -2.2257127109539789e+00 -1.4985364751488087e-01
|
||||
run_energy: 2.72020085611266
|
||||
run_stress: ! |-
|
||||
-3.7602582117112696e+01 -7.5177491246772860e+01 -8.0496376546390593e+01 5.8650301198124719e+00 1.8568949712590435e+01 -1.7092803849573546e+01
|
||||
run_forces: ! |2
|
||||
21 -2.4947171840915869e+00 -1.8301499314042944e+00 3.0384167705842424e+00
|
||||
22 -1.2708061166290454e+00 -3.3104329489702544e-01 -1.9230876962606467e+00
|
||||
23 3.7655233007206323e+00 2.1611932263013198e+00 -1.1153290743235955e+00
|
||||
19 -5.5501142419144456e-01 -3.6536974680872897e-01 -6.5214259764664040e-01
|
||||
18 1.2483325913879641e+01 1.3063074718773587e+01 -6.8971702953266796e+00
|
||||
20 -1.1928314489688196e+01 -1.2697704971964857e+01 7.5493128929733198e+00
|
||||
28 -3.6996573174115897e+00 1.5606345314733694e+00 -2.4509265379052949e+00
|
||||
4 6.5316067081501794e+00 -1.6964534314417670e+00 4.6863926017456139e+00
|
||||
10 7.3589409427634980e+00 -1.0251236193821910e+01 -1.9373930391790326e+00
|
||||
11 2.3367507948564419e+00 5.7238486963636017e+00 9.4103181737417483e+00
|
||||
12 -1.5057296559864404e+00 -4.2658894812025583e+00 -6.4218409320065728e+00
|
||||
14 3.8647266189743146e+00 -6.2670509497653226e-01 9.9150862546987142e+00
|
||||
3 1.9369911704623934e+01 1.1046188555404491e+01 -2.9524362244736047e-01
|
||||
6 -1.8547456674617141e+01 1.6430043701092902e+01 -4.5851832091104177e+00
|
||||
7 -6.6828311831073306e-01 3.0889832044221124e+00 1.4560663517158423e+01
|
||||
15 8.9917225641572396e-02 -1.8033052368122520e+00 -6.8525146606533316e-01
|
||||
8 3.0661838854451711e+00 -2.6232962080427971e+00 1.4955890131085310e+00
|
||||
9 -7.9088093294027273e-02 -8.2693869800314665e-02 -3.4901905084988727e-01
|
||||
16 -1.1164622865977545e+01 1.3117018504572005e+01 3.1764757438731355e+00
|
||||
17 4.9393632695159706e+00 -3.4939226203342146e+00 -1.3256504173129066e+01
|
||||
5 1.0375744224750958e+00 1.5888436683858376e+00 -5.1654406551651846e+00
|
||||
13 -6.7989870669322876e+00 2.5666290999906285e+00 9.8525201687339442e-02
|
||||
2 -4.0687851261583159e+00 -3.4575616702945675e+00 4.5760484473173797e+00
|
||||
1 -5.7620229711696869e+00 -2.5260491623504663e+01 -1.5223222805378031e+01
|
||||
27 2.5775039024618946e+00 -2.8811820695598049e+00 2.1511068222696847e+00
|
||||
29 1.1221534149496948e+00 1.3205475380864353e+00 2.9981971563561016e-01
|
||||
24 4.8856830027728240e+00 -9.4469527796070771e+00 7.4808498283266793e+00
|
||||
25 -9.7142716248063898e+00 1.3432566023937309e+00 -8.1922635057573245e+00
|
||||
26 4.8285886220335659e+00 8.1036961772133456e+00 7.1141367743064510e-01
|
||||
...
|
||||
|
|
@ -0,0 +1,87 @@
|
|||
---
|
||||
lammps_version: 5 May 2020
|
||||
date_generated: Mon May 18 18:18:26 202
|
||||
epsilon: 2.5e-13
|
||||
prerequisites: ! |
|
||||
atom full
|
||||
bond morse
|
||||
pre_commands: ! ""
|
||||
post_commands: ! ""
|
||||
input_file: in.fourmol
|
||||
bond_style: morse
|
||||
bond_coeff: ! |
|
||||
1 5000.0 0.25 1.5
|
||||
2 6000.0 0.3 1.1
|
||||
3 7000.0 0.2 1.3
|
||||
4 7500.0 0.4 1.2
|
||||
5 7000.0 0.3 1.0
|
||||
extract: ! |
|
||||
r0 1
|
||||
natoms: 29
|
||||
init_energy: 5.60715454070921
|
||||
init_stress: ! |-
|
||||
-1.1365471352755087e+02 -1.3117272554114714e+02 -1.4763909124402684e+02 4.5922194837084724e+00 1.3188910497152156e+01 -4.9709355153349769e+01
|
||||
init_forces: ! |2
|
||||
21 -2.1292522778401484e+00 8.3681902993574631e-01 -1.0456543554470633e+01
|
||||
22 5.9096952509299348e+00 1.4321587156167632e+00 9.2716532658646909e+00
|
||||
23 -3.7804429730897864e+00 -2.2689777455525095e+00 1.1848902886059425e+00
|
||||
19 1.7449104703805535e+01 1.1162991258691960e+01 2.1139077231969274e+01
|
||||
18 -1.2561303666996233e+01 -5.9628611559046174e+00 -2.4435974798743782e+01
|
||||
20 -4.8878010368093019e+00 -5.2001301027873428e+00 3.2968975667745082e+00
|
||||
28 -1.2392285181626443e+00 5.3256386141007839e-01 -8.3847404001650405e-01
|
||||
4 8.8713463313619556e+00 -2.4869902981383678e+00 6.2944478412455851e+00
|
||||
10 9.1471753211686533e+00 -3.6683071593134176e+00 1.2852548988418468e+01
|
||||
11 -6.6627555421674023e-01 -1.6504235240582910e+00 -2.7080125293588715e+00
|
||||
12 1.1001196263293442e+01 7.6447730080941589e+00 -5.6225811750320291e+00
|
||||
14 5.3700342562960186e+00 -1.0927307685485257e+00 1.3926228586369799e+01
|
||||
3 3.0456205073524366e+01 1.5809915985625832e+01 -2.1598944037856057e+01
|
||||
6 -3.3438238480111224e+01 3.1304807931964429e+01 2.8749236595464831e+00
|
||||
7 -3.0585877487086727e-01 1.5688428352380774e+00 7.8269478363230354e+00
|
||||
15 4.6609400189370959e-01 -1.7909488085925670e+01 -6.3823073745841539e+00
|
||||
8 1.0021319252154896e+01 -1.0847617181403265e+01 6.5325631298484199e-01
|
||||
9 1.0426151928866081e+00 1.1229605304421777e+00 4.6139335352118538e+00
|
||||
16 -3.0404842380534426e+01 2.7321823844657757e+01 4.9470802433074290e+01
|
||||
17 2.3034909315366320e+01 -1.6063552649481462e+01 -6.1112326945518511e+01
|
||||
5 -2.2678975048300209e+00 -3.4851448944569343e+00 1.1580176171216390e+01
|
||||
13 -2.0317595063271646e+01 8.0374307564261560e+00 3.8187063235626600e-01
|
||||
2 -1.3090999877896955e+01 -1.0772882402088289e+01 1.5407733823855041e+01
|
||||
1 1.0808126277859049e+00 -2.4833417929034365e+01 -2.8458697758252427e+01
|
||||
27 9.3440280239221600e+00 8.8903193246933316e+00 2.8056881098030990e+00
|
||||
29 -8.1047995057595159e+00 -9.4228831861034106e+00 -1.9672140697865950e+00
|
||||
24 -9.2661563457622229e+00 4.9020582513564221e+00 -9.1385479515926846e+00
|
||||
25 1.1119638105723428e+01 -1.7901006048460335e+00 9.3480710414084971e+00
|
||||
26 -1.8534817599612055e+00 -3.1119576465103886e+00 -2.0952308981581247e-01
|
||||
run_energy: 2.93512285189547
|
||||
run_stress: ! |-
|
||||
-3.1267924237437434e+01 -7.7178064407406936e+01 -7.4572643231772119e+01 1.3014493603880005e+01 2.0921266501526119e+01 -1.3402544258943628e+01
|
||||
run_forces: ! |2
|
||||
21 -2.4258823844294564e+00 -2.3049533124775818e+00 5.9876217328634826e+00
|
||||
22 -2.9133830811925550e+00 -7.5905907922828242e-01 -4.4082871396010610e+00
|
||||
23 5.3392654656220113e+00 3.0640123917058641e+00 -1.5793345932624214e+00
|
||||
19 -4.4086320218577528e+00 -2.9041876446945807e+00 -5.1723085521178698e+00
|
||||
18 1.7957969728657570e+01 1.7322107185310820e+01 -3.3780033338614492e+00
|
||||
20 -1.3549337706799816e+01 -1.4417919540616237e+01 8.5503118859793190e+00
|
||||
28 -4.0752072342618000e+00 1.7169408304671268e+00 -2.6991936440855149e+00
|
||||
4 7.0664804632073395e+00 -1.8424346114624681e+00 5.0573486784908388e+00
|
||||
10 9.4915657011755776e+00 -1.1508588857399364e+01 -3.2964294453993653e-01
|
||||
11 2.4068795295812935e+00 5.8756512305229496e+00 9.6725936037311033e+00
|
||||
12 -2.3892652603353697e+00 -5.1165179952683895e+00 -5.7890543146688884e+00
|
||||
14 3.8845330174617585e+00 -6.3211029927418838e-01 9.9722691728496251e+00
|
||||
3 2.1730756816916443e+01 8.7795470509783868e+00 -1.8197697574427512e+00
|
||||
6 -2.0392267920708051e+01 1.7186577883679512e+01 -1.0144536450282487e+01
|
||||
7 -1.0505961556650811e+00 4.7766846328594976e+00 2.2422433551783566e+01
|
||||
15 9.4902474816440249e-02 -1.9112306616715593e+00 -7.2587167172707878e-01
|
||||
8 2.9453615500167256e+00 -2.1119950390766897e+00 2.1326154124333536e+00
|
||||
9 -3.2924743415825569e-01 -3.4422903876528793e-01 -1.4529178750978800e+00
|
||||
16 -8.3030755036620096e+00 1.2330023321044887e+01 -1.0824196111117136e+01
|
||||
17 6.3535466156689069e-01 -4.4893744419945164e-01 -1.7080958581810448e+00
|
||||
5 1.1477030718746297e+00 1.7412871497471325e+00 -5.6863495147956025e+00
|
||||
13 -6.9084170863190266e+00 2.6061306737033436e+00 1.0100429670491046e-01
|
||||
2 -2.0523781926098521e+00 -1.7443657459368178e+00 2.3077543476068776e+00
|
||||
1 -7.9782897331594516e+00 -2.7635492249481491e+01 -1.3185584565747471e+01
|
||||
27 8.3432986828220290e-01 -5.5321449653710282e+00 1.8334651187311577e+00
|
||||
29 3.2408773659795971e+00 3.8152041349039014e+00 8.6572852535435707e-01
|
||||
24 8.1687687509411617e+00 -1.2535294430952119e+01 1.1259156626988446e+01
|
||||
25 -1.4447730301886924e+01 2.0000528212963182e+00 -1.2185178183672727e+01
|
||||
26 6.2789615509457635e+00 1.0535241609655801e+01 9.2602155668428099e-01
|
||||
...
|
||||
|
|
@ -0,0 +1,87 @@
|
|||
---
|
||||
lammps_version: 5 May 2020
|
||||
date_generated: Mon May 18 18:18:26 202
|
||||
epsilon: 1e-14
|
||||
prerequisites: ! |
|
||||
atom full
|
||||
bond zero
|
||||
pre_commands: ! ""
|
||||
post_commands: ! ""
|
||||
input_file: in.fourmol
|
||||
bond_style: zero
|
||||
bond_coeff: ! |
|
||||
1 1.5
|
||||
2 1.1
|
||||
3 1.3
|
||||
4 1.2
|
||||
5 1.0
|
||||
extract: ! |
|
||||
r0 1
|
||||
natoms: 29
|
||||
init_energy: 0
|
||||
init_stress: ! |2-
|
||||
0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
init_forces: ! |2
|
||||
21 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
22 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
23 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
19 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
18 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
20 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
28 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
4 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
10 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
11 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
12 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
14 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
3 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
6 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
7 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
15 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
8 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
9 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
16 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
17 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
5 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
13 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
2 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
1 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
27 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
29 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
24 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
25 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
26 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
run_energy: 0
|
||||
run_stress: ! |2-
|
||||
0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
run_forces: ! |2
|
||||
21 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
22 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
23 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
19 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
18 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
20 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
28 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
4 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
10 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
11 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
12 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
14 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
3 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
6 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
7 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
15 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
8 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
9 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
16 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
17 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
5 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
13 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
2 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
1 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
27 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
29 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
24 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
25 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
26 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
...
|
||||
|
|
@ -0,0 +1,210 @@
|
|||
LAMMPS data file via write_data, version 5 May 2020, timestep = 0
|
||||
|
||||
29 atoms
|
||||
5 atom types
|
||||
24 bonds
|
||||
5 bond types
|
||||
30 angles
|
||||
4 angle types
|
||||
31 dihedrals
|
||||
5 dihedral types
|
||||
2 impropers
|
||||
2 improper types
|
||||
|
||||
-6.024572 8.975428 xlo xhi
|
||||
-7.692866 7.307134 ylo yhi
|
||||
-8.086924 6.913076 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
1 12.0107
|
||||
2 4.00794
|
||||
3 14.0067
|
||||
4 15.9994
|
||||
5 15.9994
|
||||
|
||||
Pair Coeffs # zero
|
||||
|
||||
1
|
||||
2
|
||||
3
|
||||
4
|
||||
5
|
||||
|
||||
Bond Coeffs # zero
|
||||
|
||||
1 1.5
|
||||
2 1.1
|
||||
3 1.3
|
||||
4 1.2
|
||||
5 1
|
||||
|
||||
Angle Coeffs # zero
|
||||
|
||||
1 110.1
|
||||
2 111
|
||||
3 120
|
||||
4 108.5
|
||||
|
||||
Atoms # full
|
||||
|
||||
10 2 1 7.0000000000000007e-02 2.0185283555536988e+00 -1.4283966846517357e+00 -9.6733527271133024e-01 0 0 0
|
||||
11 2 2 8.9999999999999997e-02 1.7929780509347666e+00 -1.9871047540768743e+00 -1.8840626643185674e+00 0 0 0
|
||||
12 2 1 -2.7000000000000002e-01 3.0030247876861225e+00 -4.8923319967572748e-01 -1.6188658531537248e+00 0 0 0
|
||||
13 2 2 8.9999999999999997e-02 4.0447273787895934e+00 -9.0131998547446246e-01 -1.6384447268320836e+00 0 0 0
|
||||
14 2 2 8.9999999999999997e-02 2.6033152817257075e+00 -4.0789761505963579e-01 -2.6554413538823063e+00 0 0 0
|
||||
2 1 2 3.1000000000000000e-01 3.0197083955402204e-01 2.9515239068888608e+00 -8.5689735572907566e-01 0 0 0
|
||||
3 1 1 -2.0000000000000000e-02 -6.9435377880558602e-01 1.2440473127136711e+00 -6.2233801468892025e-01 0 0 0
|
||||
4 1 2 8.9999999999999997e-02 -1.5771614164685133e+00 1.4915333140468066e+00 -1.2487126845040522e+00 0 0 0
|
||||
6 1 1 5.1000000000000001e-01 2.9412607937706009e-01 2.2719282656652909e-01 -1.2843094067857870e+00 0 0 0
|
||||
7 1 4 -5.1000000000000001e-01 3.4019871062879609e-01 -9.1277350075786561e-03 -2.4633113224304561e+00 0 0 0
|
||||
19 3 2 4.2359999999999998e-01 1.5349125211132961e+00 2.6315969880333707e+00 -4.2472859440220647e+00 0 0 0
|
||||
15 2 2 8.9999999999999997e-02 2.9756315249791303e+00 5.6334269722969288e-01 -1.2437650754599008e+00 0 0 0
|
||||
18 3 4 -8.4719999999999995e-01 2.1384791188033843e+00 3.0177261773770208e+00 -3.5160827596876225e+00 0 0 0
|
||||
20 3 2 4.2359999999999998e-01 2.7641167828863153e+00 3.6833419064000221e+00 -3.9380850623312638e+00 0 0 0
|
||||
8 2 3 -4.6999999999999997e-01 1.1641187171852805e+00 -4.8375305955385234e-01 -6.7659823767368688e-01 0 0 0
|
||||
9 2 2 3.1000000000000000e-01 1.3777459838125838e+00 -2.5366338669522998e-01 2.6877644730326306e-01 0 0 0
|
||||
16 2 1 5.1000000000000001e-01 2.6517554244980306e+00 -2.3957110424978438e+00 3.2908335999178327e-02 0 0 0
|
||||
17 2 4 -5.1000000000000001e-01 2.2309964792710639e+00 -2.1022918943319384e+00 1.1491948328949437e+00 0 0 0
|
||||
1 1 3 -4.6999999999999997e-01 -2.7993683669226832e-01 2.4726588069312840e+00 -1.7200860244148433e-01 0 0 0
|
||||
5 1 2 8.9999999999999997e-02 -8.9501761359359255e-01 9.3568128743071344e-01 4.0227731871484346e-01 0 0 0
|
||||
21 4 5 -8.4719999999999995e-01 4.9064454390208301e+00 -4.0751205255383196e+00 -3.6215576073601046e+00 0 0 0
|
||||
22 4 2 4.2359999999999998e-01 4.3687453488627543e+00 -4.2054270536772504e+00 -4.4651491269372565e+00 0 0 0
|
||||
23 4 2 4.2359999999999998e-01 5.7374928154769504e+00 -3.5763355905184966e+00 -3.8820297194230728e+00 0 0 0
|
||||
24 5 5 -8.4719999999999995e-01 2.0684115301174013e+00 3.1518221747664397e+00 3.1554242678474576e+00 0 0 0
|
||||
25 5 2 4.2359999999999998e-01 1.2998381073113014e+00 3.2755513587518097e+00 2.5092990173114837e+00 0 0 0
|
||||
26 5 2 4.2359999999999998e-01 2.5807438597688113e+00 4.0120175892854135e+00 3.2133398379059099e+00 0 0 0
|
||||
27 6 5 -8.4719999999999995e-01 -1.9613581876744359e+00 -4.3556300596085160e+00 2.1101467673534788e+00 0 0 0
|
||||
28 6 2 4.2359999999999998e-01 -2.7406520384725965e+00 -4.0207251278130975e+00 1.5828689861678511e+00 0 0 0
|
||||
29 6 2 4.2359999999999998e-01 -1.3108232656499081e+00 -3.5992986322410760e+00 2.2680459788743503e+00 0 0 0
|
||||
|
||||
Velocities
|
||||
|
||||
1 7.7867804888392077e-04 5.8970331623292821e-04 -2.2179517633030531e-04
|
||||
2 2.7129529964126462e-03 4.6286427111164284e-03 3.5805549693846352e-03
|
||||
3 -1.2736791029204805e-03 1.6108674226414498e-03 -3.3618185901550799e-04
|
||||
4 -9.2828595122009308e-04 -1.2537885319521818e-03 -4.1204974953432108e-03
|
||||
5 -1.1800848061603740e-03 7.5424401975844038e-04 6.9023177964912290e-05
|
||||
6 -3.0914004879905335e-04 1.2755385764678133e-03 7.9574303350202582e-04
|
||||
7 -1.1037894966874103e-04 -7.6764845099077425e-04 -7.7217630460203659e-04
|
||||
8 3.9060281273221989e-04 -8.1444231918053418e-04 1.5134641148324972e-04
|
||||
9 1.2475530960659720e-03 -2.6608454451432528e-03 1.1117602907112732e-03
|
||||
10 4.5008983776042893e-04 4.9530197647538077e-04 -2.3336234361093645e-04
|
||||
11 -3.6977669078869707e-04 -1.5289071951960539e-03 -2.9176389881837113e-03
|
||||
12 1.0850834530183159e-03 -6.4965897903201833e-04 -1.2971152622619948e-03
|
||||
13 4.0754559196230639e-03 3.5043502394946119e-03 -7.8324487687854666e-04
|
||||
14 -1.3837220448746613e-04 -4.0656048637594394e-03 -3.9333461173944500e-03
|
||||
15 -4.3301707382721859e-03 -3.1802661664634938e-03 3.2037919043360571e-03
|
||||
16 -9.6715751018414326e-05 -5.0016572678960377e-04 1.4945658875149626e-03
|
||||
17 6.5692180538157174e-04 3.6635779995305095e-04 8.3495414466050911e-04
|
||||
18 -6.0936815808025862e-04 -9.3774557532468582e-04 -3.3558072507805731e-04
|
||||
19 -6.9919768291957119e-04 -3.6060777270430031e-03 4.2833405289822791e-03
|
||||
20 4.7777805013736515e-03 5.1003745845520452e-03 1.8002873923729241e-03
|
||||
21 -9.5568188553430398e-04 1.6594630943762931e-04 -1.8199788009966615e-04
|
||||
22 -3.3137518957653462e-03 -2.8683968287936054e-03 3.6384389958326871e-03
|
||||
23 2.4209481134686401e-04 -4.5457709985051130e-03 2.7663581642115042e-03
|
||||
24 2.5447450568861086e-04 4.8412447786110117e-04 -4.8021914527341357e-04
|
||||
25 4.3722771097312743e-03 -4.5184411669545515e-03 2.5200952006556795e-03
|
||||
26 -1.9250110555001179e-03 -3.0342169883610837e-03 3.5062814567984532e-03
|
||||
27 -2.6510179146429716e-04 3.6306203629019116e-04 -5.6235585400647747e-04
|
||||
28 -2.3068708109787484e-04 -8.5663070212203200e-04 2.1302563179109169e-03
|
||||
29 -2.5054744388303732e-03 -1.6773997805290820e-04 2.8436699761004796e-03
|
||||
|
||||
Bonds
|
||||
|
||||
1 5 1 2
|
||||
2 3 1 3
|
||||
3 2 3 4
|
||||
4 2 3 5
|
||||
5 1 3 6
|
||||
6 3 6 8
|
||||
7 4 6 7
|
||||
8 5 8 9
|
||||
9 3 8 10
|
||||
10 2 10 11
|
||||
11 1 10 12
|
||||
12 1 10 16
|
||||
13 2 12 13
|
||||
14 2 12 14
|
||||
15 2 12 15
|
||||
16 4 16 17
|
||||
17 5 18 19
|
||||
18 5 18 20
|
||||
19 5 21 22
|
||||
20 5 21 23
|
||||
21 5 24 25
|
||||
22 5 24 26
|
||||
23 5 27 28
|
||||
24 5 27 29
|
||||
|
||||
Angles
|
||||
|
||||
1 4 2 1 3
|
||||
2 4 1 3 5
|
||||
3 4 1 3 4
|
||||
4 4 1 3 6
|
||||
5 4 4 3 5
|
||||
6 2 5 3 6
|
||||
7 2 4 3 6
|
||||
8 3 3 6 7
|
||||
9 3 3 6 8
|
||||
10 3 7 6 8
|
||||
11 2 6 8 9
|
||||
12 2 9 8 10
|
||||
13 3 6 8 10
|
||||
14 2 8 10 11
|
||||
15 3 8 10 16
|
||||
16 2 11 10 12
|
||||
17 1 12 10 16
|
||||
18 1 8 10 12
|
||||
19 2 11 10 16
|
||||
20 2 10 12 15
|
||||
21 2 10 12 14
|
||||
22 2 10 12 13
|
||||
23 4 13 12 15
|
||||
24 4 13 12 14
|
||||
25 4 14 12 15
|
||||
26 4 10 16 17
|
||||
27 1 19 18 20
|
||||
28 1 22 21 23
|
||||
29 1 25 24 26
|
||||
30 1 28 27 29
|
||||
|
||||
Dihedrals
|
||||
|
||||
1 2 2 1 3 6
|
||||
2 2 2 1 3 4
|
||||
3 3 2 1 3 5
|
||||
4 1 1 3 6 8
|
||||
5 1 1 3 6 7
|
||||
6 5 4 3 6 8
|
||||
7 5 4 3 6 7
|
||||
8 5 5 3 6 8
|
||||
9 5 5 3 6 7
|
||||
10 4 3 6 8 9
|
||||
11 3 3 6 8 10
|
||||
12 3 7 6 8 9
|
||||
13 4 7 6 8 10
|
||||
14 2 6 8 10 12
|
||||
15 2 6 8 10 16
|
||||
16 2 6 8 10 11
|
||||
17 2 9 8 10 12
|
||||
18 4 9 8 10 16
|
||||
19 5 9 8 10 11
|
||||
20 5 8 10 12 13
|
||||
21 1 8 10 12 14
|
||||
22 5 8 10 12 15
|
||||
23 4 8 10 16 17
|
||||
24 5 11 10 12 13
|
||||
25 5 11 10 12 14
|
||||
26 5 11 10 12 15
|
||||
27 2 11 10 16 17
|
||||
28 2 12 10 16 17
|
||||
29 5 16 10 12 13
|
||||
30 5 16 10 12 14
|
||||
31 5 16 10 12 15
|
||||
|
||||
Impropers
|
||||
|
||||
1 1 6 3 8 7
|
||||
2 2 8 6 10 9
|
||||
|
|
@ -0,0 +1,83 @@
|
|||
LAMMPS data file via write_data, version 5 May 2020, timestep = 0
|
||||
|
||||
32 atoms
|
||||
2 atom types
|
||||
|
||||
0.0000000000000000e+00 7.0000000000000000e+00 xlo xhi
|
||||
0.0000000000000000e+00 7.0000000000000000e+00 ylo yhi
|
||||
0.0000000000000000e+00 7.0000000000000000e+00 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
1 58.71
|
||||
2 63.55
|
||||
|
||||
Atoms # atomic
|
||||
|
||||
1 1 6.9251806026209053e+00 6.8103882495595087e+00 6.8953103466636083e+00 -1 -1 -1
|
||||
2 2 1.7691645120126960e+00 1.9479533973838918e+00 6.9027498310677471e+00 0 0 -1
|
||||
3 2 1.6291954268837325e+00 6.9375396348943656e+00 1.7786436695971730e+00 0 -1 0
|
||||
4 2 6.9769767664498543e+00 1.6985137226984435e+00 1.9201373927388978e+00 -1 0 0
|
||||
5 1 3.3446304744084507e+00 6.8043833828318787e+00 6.8715152553848524e+00 0 -1 -1
|
||||
6 1 5.1519172516427556e+00 1.5732483597813400e+00 6.9351828449802388e+00 0 0 -1
|
||||
7 1 5.3194400198848166e+00 6.8784142041245540e+00 1.7575287213816908e+00 0 -1 0
|
||||
8 2 3.6919462979035202e+00 1.7914288644638978e+00 1.6449250447307364e+00 0 0 0
|
||||
9 1 6.9030865617343622e+00 3.6758430694350244e+00 9.4467994451740367e-02 -1 0 0
|
||||
10 1 1.6665300250363211e+00 5.4701307854476067e+00 1.3811101791826541e-01 0 0 0
|
||||
11 1 1.8557548873386136e+00 3.6223915000783240e+00 1.5839418163913961e+00 0 0 0
|
||||
12 1 6.8956498385619600e+00 5.3368367108687931e+00 1.8145995718029326e+00 -1 0 0
|
||||
13 1 3.6523843528248299e+00 3.4238179269124838e+00 7.8976181139687185e-03 0 0 0
|
||||
14 2 5.1004218632822962e+00 5.1902561855457057e+00 6.9857104666697376e+00 0 0 -1
|
||||
15 2 5.3440121668595886e+00 3.4624884090910144e+00 1.8926915926824750e+00 0 0 0
|
||||
16 1 3.3986357306822370e+00 5.4207255763563911e+00 1.6347618218673217e+00 0 0 0
|
||||
17 1 6.8912317324156094e+00 6.8317267091394065e+00 3.6308005059979855e+00 -1 -1 0
|
||||
18 2 1.9072040785603244e+00 1.8789483633725663e+00 3.5351432027226051e+00 0 0 0
|
||||
19 2 1.8960842031501626e+00 3.7202344782278907e-02 5.1098087557637166e+00 0 0 0
|
||||
20 2 6.9313221529504849e+00 1.6814246388065743e+00 5.4039044220950014e+00 -1 0 0
|
||||
21 1 3.2812039239477384e+00 6.9943497896400979e+00 3.3369144811234039e+00 0 -1 0
|
||||
22 2 5.2148282493068034e+00 1.8183860994495387e+00 3.6651734483964620e+00 0 0 0
|
||||
23 1 5.2002930083313466e+00 6.7745910249299328e+00 5.4013559973805005e+00 0 -1 0
|
||||
24 2 3.3941404012703056e+00 1.5677241500316765e+00 5.1397895823883779e+00 0 0 0
|
||||
25 2 6.9935384426468694e+00 3.4006055659384491e+00 3.5777467275167565e+00 -1 0 0
|
||||
26 1 1.8122783596684591e+00 5.3623909477900673e+00 3.2546595076586398e+00 0 0 0
|
||||
27 1 1.7707132053890793e+00 3.6268429742552537e+00 5.2998683080542222e+00 0 0 0
|
||||
28 2 1.2640995465983185e-01 5.1221079677911980e+00 5.0686146666615333e+00 0 0 0
|
||||
29 2 3.4428214167676963e+00 3.3995516146763931e+00 3.4639878661436900e+00 0 0 0
|
||||
30 2 5.2217783430692641e+00 5.3286119651182613e+00 3.5312977426132646e+00 0 0 0
|
||||
31 2 5.3115760999319956e+00 3.7095115570628603e+00 5.1107395554942734e+00 0 0 0
|
||||
32 1 3.6820379392393110e+00 5.2616447951000396e+00 5.1640712463595300e+00 0 0 0
|
||||
|
||||
Velocities
|
||||
|
||||
1 8.3142142875272096e-01 5.3018877054577906e-01 2.3672876575693383e-01
|
||||
2 1.9230002104827290e-01 1.2524792537825311e-01 4.4604808196838402e-01
|
||||
3 7.9168477296999518e-01 6.3268796867476074e-01 4.6576192945860018e-01
|
||||
4 -4.3473294319396177e-01 -3.3853350184134096e-01 -5.5542559307799122e-01
|
||||
5 1.0556233129043906e-01 4.5966475014577479e-01 2.0696137230275274e-01
|
||||
6 1.4848094794143299e-01 -1.6860956406325553e-01 1.9757082777940729e-01
|
||||
7 7.3021476335390134e-02 -7.1983424883753178e-01 4.6269188064987915e-01
|
||||
8 5.5076417271703060e-01 4.3333271179601146e-01 -3.6738784484495857e-01
|
||||
9 -2.5718570124869944e-01 6.3277740898069912e-01 5.4780116639027077e-01
|
||||
10 -1.4974325867034999e-01 9.3064919665076296e-02 -4.0381464877152434e-01
|
||||
11 4.7818229323689510e-02 6.2320473313120761e-01 2.5362846619826834e-01
|
||||
12 -1.1231656505090443e-02 1.5819512160232438e-01 -7.2179120440993033e-02
|
||||
13 -3.7446192652100023e-02 1.3752144116299114e-01 -7.6583393033556446e-01
|
||||
14 -3.2160733814053960e-01 -5.8066126595625478e-01 2.7417589688981298e-01
|
||||
15 -1.8272372717017926e-02 -2.1685149931129227e-01 -5.2976345003907166e-01
|
||||
16 7.9045293888684709e-01 -1.7417167713922208e-01 5.1327936838179022e-01
|
||||
17 -5.1453651726995175e-01 4.7881970179647018e-04 -3.0193318363687632e-01
|
||||
18 -1.5709914791072033e-01 1.0564114961285988e-01 6.2965230727924215e-01
|
||||
19 -1.8371579383916323e-01 4.3262829749976811e-01 5.8417694297080081e-01
|
||||
20 1.0882019091021228e-01 -2.1166403436380410e-01 -3.6263161099868824e-02
|
||||
21 -4.0111116088894477e-01 5.3271966337727594e-01 1.3792503546429732e-01
|
||||
22 -4.5910055611599498e-01 -5.8401620956067346e-01 -6.8618584853818843e-01
|
||||
23 -4.3161041639472653e-01 -4.4203303118078013e-01 -5.4281759123661022e-01
|
||||
24 2.5183551805769588e-01 2.2482074012152781e-01 -1.8838882874510199e-01
|
||||
25 -4.6721830371801637e-01 -5.8533759910128336e-01 -1.5583609796196654e-01
|
||||
26 -5.0930624705991323e-01 -2.0777682865238548e-01 -7.8460078152095367e-02
|
||||
27 -4.3388755497611564e-01 -3.4193357425427884e-01 5.6810074666354726e-01
|
||||
28 -5.8853999789660418e-02 -1.0394492105861351e-01 -1.8952269932421037e-01
|
||||
29 3.7239466286208767e-01 -1.4599510727485882e-01 -5.9856190302214463e-01
|
||||
30 -8.2566562682300657e-02 -7.0947366457228134e-01 -2.1259852525041717e-01
|
||||
31 5.2021621936729534e-01 6.1299338885942370e-02 7.7247547046206289e-02
|
||||
32 1.4445281331015636e-01 3.4736296688580842e-01 8.3222169277389901e-02
|
||||
|
|
@ -0,0 +1,32 @@
|
|||
variable newton_pair index on
|
||||
variable newton_bond index on
|
||||
variable bond_factor index 0.10
|
||||
variable angle_factor index 0.25
|
||||
variable dihedral_factor index 0.50
|
||||
variable units index real
|
||||
variable input_dir index .
|
||||
variable data_file index ${input_dir}/data.fourmol
|
||||
variable pair_style index 'zero 8.0'
|
||||
variable bond_style index zero
|
||||
variable angle_style index zero
|
||||
variable dihedral_style index zero
|
||||
variable improper_style index zero
|
||||
|
||||
atom_style full
|
||||
atom_modify map array
|
||||
neigh_modify delay 2 every 2 check no
|
||||
timestep 0.1
|
||||
units ${units}
|
||||
newton ${newton_pair} ${newton_bond}
|
||||
special_bonds lj/coul ${bond_factor} ${angle_factor} ${dihedral_factor}
|
||||
|
||||
pair_style ${pair_style}
|
||||
bond_style ${bond_style}
|
||||
angle_style ${angle_style}
|
||||
dihedral_style ${dihedral_style}
|
||||
improper_style ${improper_style}
|
||||
|
||||
read_data ${data_file}
|
||||
dihedral_coeff *
|
||||
improper_coeff *
|
||||
|
||||
|
|
@ -0,0 +1,16 @@
|
|||
variable newton_pair index on
|
||||
variable newton_bond index on
|
||||
variable units index metal
|
||||
variable input_dir index .
|
||||
variable data_file index ${input_dir}/data.metal
|
||||
variable pair_style index 'zero 8.0'
|
||||
|
||||
atom_style atomic
|
||||
atom_modify map array
|
||||
neigh_modify delay 2 every 2 check no
|
||||
timestep 0.0001
|
||||
units ${units}
|
||||
newton ${newton_pair} ${newton_bond}
|
||||
|
||||
pair_style ${pair_style}
|
||||
read_data ${data_file}
|
||||
|
|
@ -0,0 +1,100 @@
|
|||
---
|
||||
lammps_version: 5 May 2020
|
||||
date_generated: Fri May 15 19:08:06 202
|
||||
epsilon: 5.0e-14
|
||||
prerequisites: ! |
|
||||
atom full
|
||||
pair lj/cut
|
||||
pair coul/cut
|
||||
pre_commands: ! ""
|
||||
post_commands: ! |
|
||||
pair_modify mix arithmetic
|
||||
input_file: in.fourmol
|
||||
pair_style: hybrid/overlay lj/cut 8.0 coul/cut 8.0
|
||||
pair_coeff: ! |
|
||||
1 1 lj/cut 0.02 2.5 8
|
||||
1 2 lj/cut 0.01 1.75 8
|
||||
1 3 lj/cut 0.02 2.85 8
|
||||
1 4 lj/cut 0.0173205 2.8 8
|
||||
1 5 lj/cut 0.0173205 2.8 8
|
||||
2 2 lj/cut 0.005 1 8
|
||||
2 3 lj/cut 0.01 2.1 8
|
||||
2 4 lj/cut 0.005 0.5 8
|
||||
2 5 lj/cut 0.00866025 2.05 8
|
||||
3 3 lj/cut 0.02 3.2 8
|
||||
3 4 lj/cut 0.0173205 3.15 8
|
||||
3 5 lj/cut 0.0173205 3.15 8
|
||||
4 4 lj/cut 0.015 3.1 8
|
||||
4 5 lj/cut 0.015 3.1 8
|
||||
5 5 lj/cut 0.015 3.1 8
|
||||
* * coul/cut
|
||||
natoms: 29
|
||||
init_vdwl: 749.237031537357
|
||||
init_coul: -127.494586297384
|
||||
init_stress: ! |2-
|
||||
2.1525607963688685e+03 2.1557327421151899e+03 4.6078904881742919e+03 -7.6038602729615206e+02 1.6844266627640316e+01 6.6957549356541904e+02
|
||||
init_forces: ! |2
|
||||
21 -6.9075184494915916e+01 -8.0130885501011278e+01 2.1539206802020570e+02
|
||||
22 -1.0659100672969126e+02 -2.5122518903211912e+01 -1.6283765584018167e+02
|
||||
23 1.7515797811309091e+02 1.0400246780074602e+02 -5.2024018223038112e+01
|
||||
19 1.6184514948299680e+00 -1.6594104323923884e+00 5.6561121961572223e+00
|
||||
18 1.2559081069243214e+00 6.6417071126352401e+00 -9.8829024661057083e+00
|
||||
20 -3.4526823962510336e+00 -3.1794201827804485e+00 4.2593058942069533e+00
|
||||
28 -1.7556665080686602e+02 7.2243004627719102e+01 -1.1798867746650107e+02
|
||||
4 -7.8195539840070643e+00 2.1451967639963558e+00 -5.9041143405612999e+00
|
||||
10 5.3089511229361369e+02 -6.0998478582862322e+02 -1.8376190026890427e+02
|
||||
11 -3.3416993160125812e+00 -4.7792759715873308e+00 -1.0199030124309976e+01
|
||||
12 2.0837574127335213e+01 9.8678992274266921e+00 -6.6547856883058829e+00
|
||||
14 -4.6138299494911639e+00 1.1336312962250332e+00 -8.7660603717255832e+00
|
||||
3 -1.3530454720678361e+02 -3.8712939850050407e+02 -1.4565941679363837e+02
|
||||
6 -8.2989063447195736e+02 9.6019318342576571e+02 1.1479359629470548e+03
|
||||
7 5.7874538635311936e+01 -3.3533985555183068e+02 -1.7140659049826711e+03
|
||||
15 1.6301594996052212e-02 8.3212544078493291e+00 2.0473863128880430e+00
|
||||
8 1.4280513303191131e+02 -1.0509295075299345e+02 4.0233495763755388e+02
|
||||
9 8.0984846358566287e+01 7.9600519879262990e+01 3.5197302607961126e+02
|
||||
16 4.6221152690976908e+02 -3.3124444344467344e+02 -1.1865036959698600e+03
|
||||
17 -4.5568726200724092e+02 3.2159231068141992e+02 1.1980747895060381e+03
|
||||
5 -2.9163954623584245e+00 -3.3469203159528891e+00 1.2074681739853981e+01
|
||||
13 7.7163253261199216e+00 -3.2213746930547997e+00 -1.5767800864580894e-01
|
||||
2 1.5859534558925552e+02 1.2807631885753918e+02 -1.8817306436807144e+02
|
||||
1 -2.1092656751925425e+01 2.6988675971196511e+02 3.3315496490210148e+02
|
||||
27 4.8962849172262665e+01 -2.1594262411895852e+02 8.6423873663236122e+01
|
||||
29 1.2734696054095977e+02 1.4335517724642804e+02 3.2138218235426962e+01
|
||||
24 3.4171625917777114e+01 -2.0194713552213176e+02 1.0982444762500101e+02
|
||||
25 -1.4493448920889654e+02 2.0799041369281703e+01 -1.2091050237305346e+02
|
||||
26 1.0983611557367320e+02 1.8026252731144598e+02 1.2199612526237862e+01
|
||||
run_vdwl: 147.040065814649
|
||||
run_coul: -127.747672342407
|
||||
run_stress: ! |2-
|
||||
6.0353509820250508e+02 6.2447471116277541e+02 4.3791294157096706e+02 -3.1645318541172105e+02 -3.0029798575498035e+01 1.2366108597811234e+02
|
||||
run_forces: ! |2
|
||||
21 -9.0117457730121355e+00 -1.2245005015929308e+01 3.4149936200903596e+01
|
||||
22 -1.8574631445394388e+01 -3.4425623886537839e+00 -2.6438008043441616e+01
|
||||
23 2.6836518382487309e+01 1.4678672942582715e+01 -6.8586307159717981e+00
|
||||
19 2.0601991693593105e+00 -2.0654589608626632e+00 5.3342092678817314e+00
|
||||
18 1.7867907806054892e-01 7.0934614357985906e+00 -8.1844141958354655e+00
|
||||
20 -3.2420367329211275e+00 -3.2567434492056524e+00 3.4326643925936779e+00
|
||||
28 -2.3474877047306364e+01 8.9025648931823174e+00 -1.5678531186995576e+01
|
||||
4 -8.7489075884776160e+00 3.2824727936520817e+00 -6.5528798306918095e+00
|
||||
10 6.4066997022166078e+01 -7.5535419832111913e+01 -7.5482793144574828e+01
|
||||
11 -7.4023562406880670e+00 -6.6466433894459529e+00 -1.6954367240728217e+01
|
||||
12 1.7791559823640885e+01 1.1417548579903798e+01 -6.8410096513254501e+00
|
||||
14 -4.3979315220313415e+00 8.9942304798025985e-01 -7.0797565188053522e+00
|
||||
3 -2.4593633701115834e+02 1.0324846670571520e+02 8.5001166000982366e+01
|
||||
6 1.1566131521214062e+02 -9.9315663534270840e+01 -1.4165902676145916e+02
|
||||
7 4.0530505100252476e+00 -1.0452547067632675e+01 -4.1479272246007291e+01
|
||||
15 -3.6033014868002700e-01 7.7431258533822884e+00 2.0411497412228172e+00
|
||||
8 -2.0168008364678318e+01 2.2738988000067643e+01 5.6628323305217698e+01
|
||||
9 1.3835859409009439e+01 6.0277308745157825e+00 5.3337858214897246e+01
|
||||
16 5.2319712931355340e+01 -6.8429084217935340e+01 1.4574303577719457e+01
|
||||
17 -1.8290397829438874e+01 1.7655932720572732e+01 3.5962621645704566e+01
|
||||
5 -2.2204206343813988e+00 -1.8704582015328923e+00 1.0433415108183867e+01
|
||||
13 7.0142861686879012e+00 -2.7644703601833713e+00 -2.3054062295858999e-01
|
||||
2 1.9651626448525320e+01 1.2289294477288282e+01 -2.5586353371037866e+01
|
||||
1 1.4816258935374702e+01 7.9738868793090887e+01 6.1442737817877052e+01
|
||||
27 1.4388299191593470e+00 -3.2689051660410506e+01 9.3413587271242218e+00
|
||||
29 2.3348257665117334e+01 2.4017147271469948e+01 6.6807468981591338e+00
|
||||
24 1.0582727383347613e+01 -3.1420812038055800e+01 2.3645383857939045e+01
|
||||
25 -2.9311976591768808e+01 3.1879557244811685e+00 -2.4340490474783000e+01
|
||||
26 1.7484078871479785e+01 2.7212266002547196e+01 1.3601992482095069e+00
|
||||
...
|
||||
|
|
@ -0,0 +1,97 @@
|
|||
---
|
||||
lammps_version: 5 May 2020
|
||||
date_generated: Fri May 15 19:08:06 202
|
||||
epsilon: 5.0e-14
|
||||
prerequisites: ! |
|
||||
atom full
|
||||
pair lj/cut
|
||||
pre_commands: ! ""
|
||||
post_commands: ! ""
|
||||
input_file: in.fourmol
|
||||
pair_style: hybrid lj/cut 8.0 lj/cut 8.0
|
||||
pair_coeff: ! |
|
||||
1 1 lj/cut 1 0.02 2.5 8
|
||||
1 2 lj/cut 1 0.01 1.75 8
|
||||
1 3 lj/cut 1 0.02 2.85 8
|
||||
1 4 lj/cut 1 0.0173205 2.8 8
|
||||
1 5 lj/cut 1 0.0173205 2.8 8
|
||||
2 2 lj/cut 1 0.005 1 8
|
||||
2 3 lj/cut 1 0.01 2.1 8
|
||||
2 4 lj/cut 2 0.005 0.5 8
|
||||
2 5 lj/cut 2 0.00866025 2.05 8
|
||||
3 3 lj/cut 2 0.02 3.2 8
|
||||
3 4 lj/cut 2 0.0173205 3.15 8
|
||||
3 5 lj/cut 2 0.0173205 3.15 8
|
||||
4 4 lj/cut 2 0.015 3.1 8
|
||||
4 5 lj/cut 2 0.015 3.1 8
|
||||
5 5 lj/cut 2 0.015 3.1 8
|
||||
natoms: 29
|
||||
init_vdwl: 749.237031537357
|
||||
init_coul: 0
|
||||
init_stress: ! |2-
|
||||
2.1793853434038251e+03 2.1988955172192786e+03 4.6653977523326275e+03 -7.5956547636050641e+02 2.4751536734034119e+01 6.6652028436400667e+02
|
||||
init_forces: ! |2
|
||||
21 -7.1566125273265527e+01 -8.1615678329920812e+01 2.2589561408339878e+02
|
||||
22 -1.0808835729977487e+02 -2.6193787235943859e+01 -1.6957904943161384e+02
|
||||
23 1.7964455474779510e+02 1.0782097695276961e+02 -5.6305786479140700e+01
|
||||
19 3.1843079640570080e-04 -2.3918627818763423e-04 1.7427252638513441e-03
|
||||
18 -1.8862623280672657e-02 -3.3402010907951640e-02 3.1000479299095243e-02
|
||||
20 -9.9760831209706009e-04 -1.0209184826753088e-03 3.6910972636601454e-04
|
||||
28 -1.8041307121444072e+02 7.7534042932772934e+01 -1.2206956760706599e+02
|
||||
4 -7.8711096705893420e+00 2.1350518625373542e+00 -5.5954532185548151e+00
|
||||
10 5.3118875219105416e+02 -6.1040990859419469e+02 -1.8355872642619312e+02
|
||||
11 -2.3530157267965532e+00 -5.9077640073819744e+00 -9.6590723955414326e+00
|
||||
12 1.7527155146800411e+01 1.0633119523437488e+01 -7.9254398064483143e+00
|
||||
14 -3.3852721292265100e+00 6.8636181241903504e-01 -8.7507190862499726e+00
|
||||
3 -1.3528903738169089e+02 -3.8704313358320059e+02 -1.4568978437133126e+02
|
||||
6 -8.3190662465252262e+02 9.6394149462625705e+02 1.1509093566509250e+03
|
||||
7 5.8203388932513640e+01 -3.3608997951626816e+02 -1.7179617996573054e+03
|
||||
15 -2.0454999188605286e-01 8.4846165523049883e+00 3.0131615419406708e+00
|
||||
8 1.4451392284291583e+02 -1.0927475861089046e+02 3.9990593492420493e+02
|
||||
9 7.9156945283097571e+01 8.5273009783986680e+01 3.5032175698445252e+02
|
||||
16 4.6326310311812085e+02 -3.3087715736498177e+02 -1.1893024561782547e+03
|
||||
17 -4.5334300923766710e+02 3.1554283255882558e+02 1.2058417793481196e+03
|
||||
5 -2.5176757268228527e+00 -4.0521510681020221e+00 1.2152704057877008e+01
|
||||
13 8.0986409579532861e+00 -3.2098088264781510e+00 -1.4896399843793828e-01
|
||||
2 1.5828554630414868e+02 1.3025008843535846e+02 -1.8629682358935690e+02
|
||||
1 -2.3333390280895383e+01 2.6994567613322732e+02 3.3272827850356794e+02
|
||||
27 5.1810388677546058e+01 -2.2705458321213791e+02 9.0849111082069683e+01
|
||||
29 1.2861057254925004e+02 1.4952711274394565e+02 3.1216025556267869e+01
|
||||
24 3.6591406576585001e+01 -2.1181587621785556e+02 1.1218301872572404e+02
|
||||
25 -1.4851489147738829e+02 2.3907118122949107e+01 -1.2485634873166315e+02
|
||||
26 1.1191129453598201e+02 1.8789774664223359e+02 1.2650137204319886e+01
|
||||
run_vdwl: 146.141836987454
|
||||
run_coul: 0
|
||||
run_stress: ! |2-
|
||||
6.2607988552877578e+02 6.7186280241273096e+02 4.8484819691920609e+02 -3.1994902849391821e+02 -2.8454539240635299e+01 1.2292176520346769e+02
|
||||
run_forces: ! |2
|
||||
21 -9.9360372198460070e+00 -1.2017932968052305e+01 3.8871041034331796e+01
|
||||
22 -1.8317762813232619e+01 -4.4399941394322759e+00 -2.9440618398390594e+01
|
||||
23 2.8242493946263711e+01 1.6470734211867914e+01 -9.4179972623790267e+00
|
||||
19 2.5526682113820960e-04 -2.4264461640287623e-04 1.6746264185020616e-03
|
||||
18 -1.8062194307514216e-02 -3.1579322126553462e-02 2.9610641532920361e-02
|
||||
20 -8.8300470711392097e-04 -9.1308556306666610e-04 3.5978614842012722e-04
|
||||
28 -2.5472496456851680e+01 1.1754691498741272e+01 -1.7174782055443067e+01
|
||||
4 -8.6006925534652421e+00 3.1744203980427432e+00 -6.2092172202266447e+00
|
||||
10 6.4812484185184985e+01 -7.6374994239094534e+01 -7.5660079469021809e+01
|
||||
11 -6.2988689622844021e+00 -8.0952569922471049e+00 -1.6391410763300943e+01
|
||||
12 1.4369424941840268e+01 1.2193286907138495e+01 -8.2527851277097728e+00
|
||||
14 -2.7952431412531218e+00 4.3888485932889676e-01 -7.1101001485813109e+00
|
||||
3 -2.4823726947100783e+02 1.0508771501194346e+02 8.6172357110011120e+01
|
||||
6 1.1683391960947706e+02 -9.8726695183085397e+01 -1.4208735499091139e+02
|
||||
7 3.8041613300899502e+00 -1.0704960296538383e+01 -4.2399902752909654e+01
|
||||
15 -3.9779897784867790e-01 8.1106017381646627e+00 3.0711122407595379e+00
|
||||
8 -1.9935814763091376e+01 1.9886801199499324e+01 5.5348117494317826e+01
|
||||
9 1.1205804510458954e+01 1.3198927444631410e+01 4.9879829976468997e+01
|
||||
16 5.2787469038597280e+01 -6.7733534943232669e+01 1.5088280949220392e+01
|
||||
17 -1.4633179608614546e+01 1.0014131160474449e+01 4.0800233262287627e+01
|
||||
5 -1.7308376123887230e+00 -2.5575751550228349e+00 1.0273464025428190e+01
|
||||
13 7.3377072945505901e+00 -2.7955027633737624e+00 -1.0299065873202272e-01
|
||||
2 1.8550226578809266e+01 1.4016238769007140e+01 -2.2757523569074309e+01
|
||||
1 1.2964030026503499e+01 8.0892417983392860e+01 6.0323171805698586e+01
|
||||
27 3.4725392000145359e+00 -3.8995311241163883e+01 1.1703192201614458e+01
|
||||
29 2.2007778142526295e+01 2.7247233468088044e+01 5.4673570898110109e+00
|
||||
24 1.2413322573750337e+01 -3.6423454531495011e+01 2.3794740530518389e+01
|
||||
25 -3.0031409430564317e+01 5.3796477034973407e+00 -2.5778433763492661e+01
|
||||
26 1.7604739564575269e+01 3.1032215151226218e+01 1.9586534056054055e+00
|
||||
...
|
||||
|
|
@ -0,0 +1,92 @@
|
|||
---
|
||||
lammps_version: 5 May 2020
|
||||
date_generated: Fri May 15 19:08:06 202
|
||||
epsilon: 5.0e-14
|
||||
prerequisites: ! |
|
||||
atom full
|
||||
pair lj/class2
|
||||
pre_commands: ! ""
|
||||
post_commands: ! |
|
||||
pair_modify mix arithmetic
|
||||
input_file: in.fourmol
|
||||
pair_style: lj/class2 8.0
|
||||
pair_coeff: ! |
|
||||
1 1 0.02 2.5
|
||||
2 2 0.005 1.0
|
||||
2 4 0.005 0.5
|
||||
3 3 0.02 3.2
|
||||
4 4 0.015 3.1
|
||||
5 5 0.015 3.1
|
||||
extract: ! |
|
||||
epsilon 2
|
||||
sigma 2
|
||||
natoms: 29
|
||||
init_vdwl: 33.5760671323649
|
||||
init_coul: 0
|
||||
init_stress: ! |2-
|
||||
8.1987691502414791e+01 8.3009725941738679e+01 1.5303015406513060e+02 -2.2810640625844286e+01 4.9269726337367228e+00 1.9929429215282934e+01
|
||||
init_forces: ! |2
|
||||
21 -2.9023276623248226e+00 -3.3588038110702407e+00 9.4690458306705292e+00
|
||||
22 -4.5445364188546238e+00 -1.1011297810562644e+00 -7.1302914280003078e+00
|
||||
23 7.4411712140978166e+00 4.4662879532240121e+00 -2.3325868461522181e+00
|
||||
19 3.5856439527329567e-04 1.1471479094339663e-04 6.0296079948055602e-04
|
||||
18 -1.4189856841252090e-02 -2.4290749569986152e-02 2.0931813540153020e-02
|
||||
20 -5.4851401081508055e-04 -5.4399509323722472e-04 8.4918767970835243e-05
|
||||
28 -7.3682981937517198e+00 3.1669679119534848e+00 -4.9856163529580284e+00
|
||||
4 -7.8031253456108729e-01 1.9854105069521086e-01 -5.5607240653088763e-01
|
||||
10 1.7951917764181754e+01 -2.1109630406464284e+01 -6.0991340497915054e+00
|
||||
11 -2.1998915351044729e-01 -5.6884051186377560e-01 -9.1994196883010593e-01
|
||||
12 1.1666346243343124e+00 5.0845046363857860e-01 -4.2279211760813662e-01
|
||||
14 -3.3098334670291890e-01 6.8298213141584935e-02 -8.6414900853471355e-01
|
||||
3 -5.2128354087304896e+00 -1.5119425649552539e+01 -5.9194600664695827e+00
|
||||
6 -2.6763845886140444e+01 3.0000233276875015e+01 3.0840200618177771e+01
|
||||
7 1.3146595250629693e+00 -9.5140644165546107e+00 -5.0614914459078001e+01
|
||||
15 -9.6365852688070942e-03 8.4913621074359091e-01 2.9559121683046807e-01
|
||||
8 3.2549713175415609e+00 -2.7762068292887747e+00 1.3131159894943904e+01
|
||||
9 2.9164018147350808e+00 3.1476093995631271e+00 1.2918924512015295e+01
|
||||
16 1.4571735448520343e+01 -1.0694059017152986e+01 -3.5937885131281753e+01
|
||||
17 -1.3873452534754520e+01 9.6104985445574638e+00 3.7138460556155835e+01
|
||||
5 -2.5071207645748772e-01 -4.1735326061412181e-01 1.1386881203250789e+00
|
||||
13 8.0963099917205650e-01 -3.2085687003540908e-01 -1.4993590980669824e-02
|
||||
2 6.2196993352719643e+00 5.1180909365072047e+00 -7.3191291855323790e+00
|
||||
1 -7.4224716595136930e-01 1.1039966637903220e+01 1.3192803117119254e+01
|
||||
27 1.9470947395789979e+00 -9.4718634154663608e+00 3.6661077043913615e+00
|
||||
29 5.4261127187922513e+00 6.3089559593072444e+00 1.3167924699154427e+00
|
||||
24 1.6636712097318496e+00 -8.7861797065109304e+00 4.7580513771265291e+00
|
||||
25 -6.2956148793668847e+00 1.0134943324455639e+00 -5.2930751667879390e+00
|
||||
26 4.6254709418114475e+00 7.7666028149472792e+00 5.2259666775716429e-01
|
||||
run_vdwl: 30.7669719012008
|
||||
run_coul: 0
|
||||
run_stress: ! |2-
|
||||
7.9136207567186872e+01 7.9607828632355080e+01 1.3325422686754521e+02 -2.0777385917448161e+01 5.9532528005971104e+00 1.8364492129715465e+01
|
||||
run_forces: ! |2
|
||||
21 -2.9622283962573377e+00 -3.1221222453351363e+00 9.1341353960748304e+00
|
||||
22 -4.5299641026963622e+00 -1.1743778906978988e+00 -6.8836224637708687e+00
|
||||
23 7.4864560471413979e+00 4.3029192689006752e+00 -2.2442900804965058e+00
|
||||
19 3.0779951763449883e-04 7.2352271761717487e-05 5.9991789595708711e-04
|
||||
18 -1.4213632800113502e-02 -2.4307342400779700e-02 2.0957577983657830e-02
|
||||
20 -4.8462904187052895e-04 -4.8982048890138202e-04 8.9625077392507858e-05
|
||||
28 -7.2688609354523379e+00 3.0962987387988594e+00 -4.8237251142338300e+00
|
||||
4 -7.4084134872265817e-01 1.8442220456228106e-01 -5.4070380104616300e-01
|
||||
10 1.7299174137393255e+01 -2.0337215459882643e+01 -6.0819871239265693e+00
|
||||
11 -2.0303480091074094e-01 -5.0919542096542936e-01 -8.2780579347021477e-01
|
||||
12 1.1617019581474322e+00 4.8411818632811876e-01 -5.2487935491213744e-01
|
||||
14 -2.9866530388551099e-01 5.0616451980998303e-02 -7.7740274746494575e-01
|
||||
3 -5.1539740455000098e+00 -1.4169374038983115e+01 -5.5868989094487311e+00
|
||||
6 -2.3966860047827822e+01 2.6398105337726218e+01 2.2540423441721142e+01
|
||||
7 1.1991100726533528e+00 -7.8865425633173629e+00 -4.0080781415567408e+01
|
||||
15 -2.6051512700693891e-02 8.5891312860075553e-01 3.1584057101408997e-01
|
||||
8 1.5842617494081925e+00 -1.2906817188189366e+00 1.2069062683547472e+01
|
||||
9 2.6462037191310377e+00 2.7370054642440187e+00 1.1582644249513473e+01
|
||||
16 1.2711812406259678e+01 -9.5689969445870382e+00 -3.1116191951116210e+01
|
||||
17 -1.2010675400189923e+01 8.4765600996061856e+00 3.2319577182902201e+01
|
||||
5 -2.4055992934632561e-01 -4.0240824953711490e-01 1.1018577587985452e+00
|
||||
13 7.7361539799575219e-01 -2.9115330606278883e-01 -1.2533320559757886e-02
|
||||
2 5.5914775661602887e+00 4.6672725010623743e+00 -6.3782649181997000e+00
|
||||
1 -3.0497501573125252e-01 1.0618884929485422e+01 1.1985335137681993e+01
|
||||
27 2.0659693003689581e+00 -9.2344924913591395e+00 3.4348341169410710e+00
|
||||
29 5.2077980712295622e+00 6.1422517145534217e+00 1.3861866509355112e+00
|
||||
24 2.3322774672668420e+00 -9.3014753803047725e+00 5.3981635963693648e+00
|
||||
25 -7.2502178738417475e+00 1.0183468318460600e+00 -6.1201641268829992e+00
|
||||
26 4.9114412822313289e+00 8.2770456627739026e+00 7.0954321463934678e-01
|
||||
...
|
||||
|
|
@ -0,0 +1,97 @@
|
|||
---
|
||||
lammps_version: 5 May 2020
|
||||
date_generated: Fri May 15 19:08:06 202
|
||||
epsilon: 5.0e-13
|
||||
prerequisites: ! |
|
||||
atom full
|
||||
pair lj/class2/coul/long
|
||||
pre_commands: ! ""
|
||||
post_commands: ! |
|
||||
pair_modify mix arithmetic
|
||||
pair_modify table 0
|
||||
kspace_style ewald 1.0e-6
|
||||
kspace_modify gewald 0.3
|
||||
kspace_modify compute no
|
||||
input_file: in.fourmol
|
||||
pair_style: lj/class2/coul/long 8.0
|
||||
pair_coeff: ! |
|
||||
1 1 0.02 2.5
|
||||
2 2 0.005 1.0
|
||||
2 4 0.005 0.5
|
||||
3 3 0.02 3.2
|
||||
4 4 0.015 3.1
|
||||
5 5 0.015 3.1
|
||||
extract: ! |
|
||||
epsilon 2
|
||||
sigma 2
|
||||
cut_coul 0
|
||||
natoms: 29
|
||||
init_vdwl: 33.5760671323649
|
||||
init_coul: 225.821815126925
|
||||
init_stress: ! |2-
|
||||
5.9211583142611758e+01 4.0166219914825973e+01 1.1428416008630550e+02 -1.8313121047528654e+01 -1.5970284066690270e+00 2.9609281429548130e+01
|
||||
init_forces: ! |2
|
||||
21 -1.0013064183886018e+00 1.0112958057638552e+00 5.6449651694847924e-01
|
||||
22 -2.7314830975219859e+00 -1.6700824834639403e+00 -1.2132464309269517e+00
|
||||
23 3.3192437397782637e+00 1.0710461462515826e+00 1.1503887418533845e+00
|
||||
19 1.9902652623177426e+00 -7.2102366994869393e-01 5.5212242193523373e+00
|
||||
18 3.5889793759497657e-01 4.7755638419907438e+00 -7.8622334754561480e+00
|
||||
20 -2.9131584798125281e+00 -3.9872331848692100e+00 4.1251970455937537e+00
|
||||
28 -3.0389823738199273e+00 -1.0653678498230301e+00 -1.4404928569144864e+00
|
||||
4 -8.6150302517796951e-01 2.1648505566304177e-01 -7.9748953371626452e-01
|
||||
10 1.7709036356639874e+01 -2.0756354048425735e+01 -6.3344805782225864e+00
|
||||
11 -1.1210233411182371e+00 4.5868406700638076e-01 -1.4838453092947013e+00
|
||||
12 4.0274747794390446e+00 2.6063282624707675e-02 1.0062818529281141e+00
|
||||
14 -1.3854957607874523e+00 4.2491552489154716e-01 -9.6019818510337263e-01
|
||||
3 -5.1991416765704859e+00 -1.5203288926763475e+01 -5.9044114512381700e+00
|
||||
6 -2.5264578473892222e+01 2.6116860206579755e+01 2.8273833952331216e+01
|
||||
7 1.2314286256091465e+00 -8.6226294657787150e+00 -4.6794390864984834e+01
|
||||
15 3.4468609004636702e-01 6.4898021976928455e-01 -7.1535766832304770e-01
|
||||
8 1.6863359601815064e+00 1.7590683253671566e+00 1.5499620684301401e+01
|
||||
9 4.5421213329184518e+00 -2.6637110080605968e+00 1.4335405089362594e+01
|
||||
16 1.3836278183935208e+01 -1.1205639459218588e+01 -3.4017907512167000e+01
|
||||
17 -1.6294794969019062e+01 1.5780089151553890e+01 3.0498575906631810e+01
|
||||
5 -7.9126897488244419e-01 2.4641688872286854e-01 1.0690019163922497e+00
|
||||
13 7.3593440120182696e-01 -3.2875149250961716e-01 -1.9280659694921740e-01
|
||||
2 5.9773559336301236e+00 2.2287093015884536e+00 -8.6410588200838028e+00
|
||||
1 1.9726803446375933e+00 1.0652536075309900e+01 1.3504244307189191e+01
|
||||
27 -7.3960092505173103e-02 5.6121962052620200e-01 -1.2623171994937926e-02
|
||||
29 3.5044276800389929e+00 4.9934304480946157e-01 1.4320880409749164e+00
|
||||
24 9.6210116420070449e-02 3.7639304108316168e-01 -2.6029630790715941e-01
|
||||
25 -3.2435054521751874e+00 -1.9205376402908565e+00 -1.8821077852280255e+00
|
||||
26 2.5878253912820757e+00 1.2909496296504646e+00 1.5325882746512651e+00
|
||||
run_vdwl: 31.2381433071159
|
||||
run_coul: 225.412871184765
|
||||
run_stress: ! |2-
|
||||
5.6896514006631762e+01 3.7173465325544029e+01 9.7159008229697733e+01 -1.6133914451166369e+01 -7.0922237643763986e-01 2.7432388946646739e+01
|
||||
run_forces: ! |2
|
||||
21 -1.2055629257991081e+00 8.4549910672859385e-01 8.7127633964992357e-01
|
||||
22 -2.7625456607861936e+00 -1.6281285733989832e+00 -1.3611493410358015e+00
|
||||
23 3.5523099674618441e+00 1.1896098913840625e+00 9.9530574245822168e-01
|
||||
19 2.4111368864615441e+00 -3.9616736355716953e-01 5.7001920720700241e+00
|
||||
18 -1.4169170461658745e-01 4.3050988892641655e+00 -7.5496312433287525e+00
|
||||
20 -2.8437737383500137e+00 -3.8485060831143305e+00 3.6485590471016058e+00
|
||||
28 -3.3090586506998938e+00 -9.4859126037912489e-01 -1.6430264529876857e+00
|
||||
4 -8.2102817084144253e-01 2.0615382505613863e-01 -7.8499961561366249e-01
|
||||
10 1.6897840757640495e+01 -1.9825758472541157e+01 -6.2807985316950852e+00
|
||||
11 -1.1100055705857286e+00 5.2961534232305096e-01 -1.3863091956394025e+00
|
||||
12 4.0138545074514766e+00 1.2103538956258330e-02 9.2259023757384206e-01
|
||||
14 -1.3754928028906186e+00 4.1774693288584369e-01 -8.5891802067653411e-01
|
||||
3 -5.1336173303440660e+00 -1.4242689749191451e+01 -5.5751677380204576e+00
|
||||
6 -2.2730870504929236e+01 2.2808460489222242e+01 2.0636187161011485e+01
|
||||
7 1.1874699093697643e+00 -7.1383195947324927e+00 -3.7141842793024807e+01
|
||||
15 3.3410360278628798e-01 6.3248882976618159e-01 -7.2000218625576307e-01
|
||||
8 4.3220196238266717e-01 2.9468242278111538e+00 1.4430743651522047e+01
|
||||
9 4.3310853842238952e+00 -3.2580642382714080e+00 1.3255802548072870e+01
|
||||
16 1.2178717557993828e+01 -1.0262106940173862e+01 -2.9695114929831281e+01
|
||||
17 -1.4693440170455304e+01 1.4997008153066593e+01 2.6083838365348520e+01
|
||||
5 -7.7390536294205103e-01 2.6338645353977519e-01 1.0379094880359461e+00
|
||||
13 6.9654478100503092e-01 -3.0679535123882018e-01 -1.9611444921608789e-01
|
||||
2 5.3854024994557568e+00 1.8452830191268854e+00 -7.8277742280632774e+00
|
||||
1 2.3348605295201672e+00 1.0142046773937388e+01 1.2410304554033228e+01
|
||||
27 9.8000321445767480e-02 3.1717009594636858e-01 1.6000098084133127e-01
|
||||
29 3.5995344274473520e+00 6.2995290730052034e-01 1.4569224501884304e+00
|
||||
24 5.8789159698526861e-01 -5.8672006822472145e-01 4.7931789577687473e-01
|
||||
25 -4.2330541256871985e+00 -1.8106870297915438e+00 -2.7235083534683291e+00
|
||||
26 3.0930920272963029e+00 2.1640862482998395e+00 1.6554065451725886e+00
|
||||
...
|
||||
|
|
@ -0,0 +1,97 @@
|
|||
---
|
||||
lammps_version: 5 May 2020
|
||||
date_generated: Fri May 15 19:08:06 202
|
||||
epsilon: 5.0e-13
|
||||
prerequisites: ! |
|
||||
atom full
|
||||
pair lj/class2/coul/long
|
||||
pre_commands: ! ""
|
||||
post_commands: ! |
|
||||
pair_modify mix arithmetic
|
||||
pair_modify table 16
|
||||
kspace_style ewald 1.0e-6
|
||||
kspace_modify gewald 0.3
|
||||
kspace_modify compute no
|
||||
input_file: in.fourmol
|
||||
pair_style: lj/class2/coul/long 8.0
|
||||
pair_coeff: ! |
|
||||
1 1 0.02 2.5
|
||||
2 2 0.005 1.0
|
||||
2 4 0.005 0.5
|
||||
3 3 0.02 3.2
|
||||
4 4 0.015 3.1
|
||||
5 5 0.015 3.1
|
||||
extract: ! |
|
||||
epsilon 2
|
||||
sigma 2
|
||||
cut_coul 0
|
||||
natoms: 29
|
||||
init_vdwl: 33.5760671323649
|
||||
init_coul: 225.821851347828
|
||||
init_stress: ! |2-
|
||||
5.9211603405333648e+01 4.0166225670894562e+01 1.1428417351092986e+02 -1.8313117752935337e+01 -1.5970189115215223e+00 2.9609285520207152e+01
|
||||
init_forces: ! |2
|
||||
21 -1.0013067903099848e+00 1.0112963705900986e+00 5.6449708719791114e-01
|
||||
22 -2.7314857986849690e+00 -1.6700841396423489e+00 -1.2132480667919039e+00
|
||||
23 3.3192469323902469e+00 1.0710473212385865e+00 1.1503896265996594e+00
|
||||
19 1.9902632601712587e+00 -7.2102508842746027e-01 5.5212240875813068e+00
|
||||
18 3.5889848850238026e-01 4.7755637971175693e+00 -7.8622343417737861e+00
|
||||
20 -2.9131566582016259e+00 -3.9872319889513359e+00 4.1251981344187270e+00
|
||||
28 -3.0389850853623903e+00 -1.0653687847256605e+00 -1.4404940729751226e+00
|
||||
4 -8.6150302859409689e-01 2.1648551835245883e-01 -7.9748934348230849e-01
|
||||
10 1.7709036473478072e+01 -2.0756353611823592e+01 -6.3344811863875039e+00
|
||||
11 -1.1210234555117795e+00 4.5868476830247717e-01 -1.4838452052499236e+00
|
||||
12 4.0274749481960992e+00 2.6063340543437809e-02 1.0062809493318754e+00
|
||||
14 -1.3854959051982552e+00 4.2491540436132436e-01 -9.6019804306733969e-01
|
||||
3 -5.1991415679059401e+00 -1.5203289042087629e+01 -5.9044115757630102e+00
|
||||
6 -2.5264578929753505e+01 2.6116861149676456e+01 2.8273832156642243e+01
|
||||
7 1.2314278279956967e+00 -8.6226295120228080e+00 -4.6794392926611458e+01
|
||||
15 3.4468603912102214e-01 6.4897992793865145e-01 -7.1535707304713181e-01
|
||||
8 1.6863352306080546e+00 1.7590680606507785e+00 1.5499622725845988e+01
|
||||
9 4.5421231315027599e+00 -2.6637115989636873e+00 1.4335406988187017e+01
|
||||
16 1.3836279378850588e+01 -1.1205640656509287e+01 -3.4017907187670978e+01
|
||||
17 -1.6294795201745742e+01 1.5780089411819709e+01 3.0498575844195784e+01
|
||||
5 -7.9126880707378877e-01 2.4641783621046168e-01 1.0690021515207444e+00
|
||||
13 7.3593448104370440e-01 -3.2875162543583508e-01 -1.9280646663463022e-01
|
||||
2 5.9773554334964372e+00 2.2287085690115060e+00 -8.6410574819335615e+00
|
||||
1 1.9726788406673605e+00 1.0652535652948396e+01 1.3504242515573146e+01
|
||||
27 -7.3960207868523087e-02 5.6121978624344637e-01 -1.2623365917105417e-02
|
||||
29 3.5044303034130113e+00 4.9934355407807918e-01 1.4320895467999217e+00
|
||||
24 9.6210412804661694e-02 3.7639343310396045e-01 -2.6029675458685475e-01
|
||||
25 -3.2435074278288627e+00 -1.9205389375894191e+00 -1.8821086306204449e+00
|
||||
26 2.5878276817981161e+00 1.2909510839916682e+00 1.5325899086187420e+00
|
||||
run_vdwl: 31.2381431724517
|
||||
run_coul: 225.412906260833
|
||||
run_stress: ! |2-
|
||||
5.6896531807680304e+01 3.7173465326595945e+01 9.7159022446947844e+01 -1.6133908564612518e+01 -7.0921776866299557e-01 2.7432393219208787e+01
|
||||
run_forces: ! |2
|
||||
21 -1.2055633257768064e+00 8.4549978470435949e-01 8.7127670881309827e-01
|
||||
22 -2.7625482218442610e+00 -1.6281302971057046e+00 -1.3611507882368714e+00
|
||||
23 3.5523131127886032e+00 1.1896108813070840e+00 9.9530657328641114e-01
|
||||
19 2.4111350738390542e+00 -3.9616889824595419e-01 5.7001916852066596e+00
|
||||
18 -1.4169132015400324e-01 4.3050983921115087e+00 -7.5496321083737241e+00
|
||||
20 -2.8437717980191919e+00 -3.8485046392236315e+00 3.6485596548025629e+00
|
||||
28 -3.3090612285603669e+00 -9.4859229563116987e-01 -1.6430276092035754e+00
|
||||
4 -8.2102810961665740e-01 2.0615438841366032e-01 -7.8499943824664320e-01
|
||||
10 1.6897840862268119e+01 -1.9825758076749004e+01 -6.2807990864728884e+00
|
||||
11 -1.1100057039042242e+00 5.2961597974741659e-01 -1.3863091127744707e+00
|
||||
12 4.0138548701163481e+00 1.2104049779693826e-02 9.2258920742353612e-01
|
||||
14 -1.3754929746024402e+00 4.1774687626387502e-01 -8.5891783956736578e-01
|
||||
3 -5.1336172096722965e+00 -1.4242689896419133e+01 -5.5751678811009775e+00
|
||||
6 -2.2730870563177618e+01 2.2808460871078690e+01 2.0636185552114778e+01
|
||||
7 1.1874693891620132e+00 -7.1383192175945762e+00 -3.7141845193380348e+01
|
||||
15 3.3410364550238236e-01 6.3248848814539971e-01 -7.2000166400580579e-01
|
||||
8 4.3220148775033085e-01 2.9468231439745201e+00 1.4430746640267813e+01
|
||||
9 4.3310867073071542e+00 -3.2580646208569521e+00 1.3255804559456905e+01
|
||||
16 1.2178717933256884e+01 -1.0262107053831510e+01 -2.9695114738365589e+01
|
||||
17 -1.4693440434456498e+01 1.4997009063389351e+01 2.6083837609521826e+01
|
||||
5 -7.7390518152710719e-01 2.6338742377392760e-01 1.0379097332157670e+00
|
||||
13 6.9654488236339840e-01 -3.0679553519537062e-01 -1.9611430027392213e-01
|
||||
2 5.3854018883253918e+00 1.8452824764633970e+00 -7.8277729825216529e+00
|
||||
1 2.3348595354023018e+00 1.0142045860231777e+01 1.2410303990431604e+01
|
||||
27 9.7999995930949768e-02 3.1717026013231997e-01 1.6000078590931424e-01
|
||||
29 3.5995369527679815e+00 6.2995337748987346e-01 1.4569239812877377e+00
|
||||
24 5.8789146609400433e-01 -5.8671979342468006e-01 4.7931688214845181e-01
|
||||
25 -4.2330556542839410e+00 -1.8106883777470766e+00 -2.7235087940759017e+00
|
||||
26 3.0930939227205014e+00 2.1640873850179121e+00 1.6554079727132640e+00
|
||||
...
|
||||
|
|
@ -0,0 +1,92 @@
|
|||
---
|
||||
lammps_version: 5 May 2020
|
||||
date_generated: Fri May 15 19:08:06 202
|
||||
epsilon: 5.0e-14
|
||||
prerequisites: ! |
|
||||
atom full
|
||||
pair lj/cut
|
||||
pre_commands: ! ""
|
||||
post_commands: ! |
|
||||
pair_modify mix arithmetic
|
||||
input_file: in.fourmol
|
||||
pair_style: lj/cut 8.0
|
||||
pair_coeff: ! |
|
||||
1 1 0.02 2.5
|
||||
2 2 0.005 1.0
|
||||
2 4 0.005 0.5
|
||||
3 3 0.02 3.2
|
||||
4 4 0.015 3.1
|
||||
5 5 0.015 3.1
|
||||
extract: ! |
|
||||
epsilon 2
|
||||
sigma 2
|
||||
natoms: 29
|
||||
init_vdwl: 749.23722617441
|
||||
init_coul: 0
|
||||
init_stress: ! |2-
|
||||
2.1793857186503233e+03 2.1988957679770601e+03 4.6653994738862330e+03 -7.5956544622684294e+02 2.4751393539192360e+01 6.6652061873806701e+02
|
||||
init_forces: ! |2
|
||||
21 -7.1566158640374354e+01 -8.1615716383825756e+01 2.2589571940670788e+02
|
||||
22 -1.0808840769631149e+02 -2.6193799449067580e+01 -1.6957912849816358e+02
|
||||
23 1.7964463850759611e+02 1.0782102722442450e+02 -5.6305812731665995e+01
|
||||
19 3.1843079948447594e-04 -2.3918628211596124e-04 1.7427252652160224e-03
|
||||
18 -1.8862629870158503e-02 -3.3402022492930034e-02 3.1000492146377390e-02
|
||||
20 -9.9760831169755002e-04 -1.0209184785886856e-03 3.6910973051849135e-04
|
||||
28 -1.8041315533250560e+02 7.7534079082878250e+01 -1.2206962452216491e+02
|
||||
4 -7.8711096705734178e+00 2.1350518625352004e+00 -5.5954532185292409e+00
|
||||
10 5.3118875219106906e+02 -6.1040990846582008e+02 -1.8355872692632030e+02
|
||||
11 -2.3530157265571860e+00 -5.9077640075588898e+00 -9.6590723956614433e+00
|
||||
12 1.7527155197359406e+01 1.0633119514682475e+01 -7.9254397903886167e+00
|
||||
14 -3.3852721291218528e+00 6.8636181224987958e-01 -8.7507190862837820e+00
|
||||
3 -1.3528903744071795e+02 -3.8704313350789641e+02 -1.4568978426110141e+02
|
||||
6 -8.3190665562047559e+02 9.6394165349388834e+02 1.1509101492424436e+03
|
||||
7 5.8203416066164444e+01 -3.3609013622052356e+02 -1.7179626006587685e+03
|
||||
15 -2.0454999188607306e-01 8.4846165523012136e+00 3.0131615419840618e+00
|
||||
8 1.4451392646293456e+02 -1.0927476052490434e+02 3.9990594285329479e+02
|
||||
9 7.9156945283109010e+01 8.5273009784086454e+01 3.5032175698457490e+02
|
||||
16 4.6326331471561195e+02 -3.3087730492363471e+02 -1.1893030175606582e+03
|
||||
17 -4.5334322060634037e+02 3.1554297967975316e+02 1.2058423415744448e+03
|
||||
5 -2.5176757267276133e+00 -4.0521510680612858e+00 1.2152704057983797e+01
|
||||
13 8.0986409580712841e+00 -3.2098088269317295e+00 -1.4896399871387664e-01
|
||||
2 1.5828554630423912e+02 1.3025008843536872e+02 -1.8629682358915147e+02
|
||||
1 -2.3333390274530558e+01 2.6994567613591141e+02 3.3272827850621582e+02
|
||||
27 5.1810412832327984e+01 -2.2705468907750401e+02 9.0849153441059272e+01
|
||||
29 1.2861063251415729e+02 1.4952718246094855e+02 3.1216040111076961e+01
|
||||
24 3.6591423637378945e+01 -2.1181597497621908e+02 1.1218307103182990e+02
|
||||
25 -1.4851496072162055e+02 2.3907129270267117e+01 -1.2485640694398953e+02
|
||||
26 1.1191134671510581e+02 1.8789783424990623e+02 1.2650143102803204e+01
|
||||
run_vdwl: 146.141845881934
|
||||
run_coul: 0
|
||||
run_stress: ! |2-
|
||||
6.2607996919539414e+02 6.7186287711451007e+02 4.8484814811319825e+02 -3.1994912366099993e+02 -2.8454570233694202e+01 1.2292177984785774e+02
|
||||
run_forces: ! |2
|
||||
21 -9.9360349613693106e+00 -1.2017930751810615e+01 3.8871035002640411e+01
|
||||
22 -1.8317759630270601e+01 -4.4399932580014960e+00 -2.9440613848490948e+01
|
||||
23 2.8242488499993318e+01 1.6470731119742439e+01 -9.4179957751083716e+00
|
||||
19 2.5526683623032693e-04 -2.4264459877787570e-04 1.6746263982979498e-03
|
||||
18 -1.8062200355604661e-02 -3.1579332593788222e-02 2.9610653727964883e-02
|
||||
20 -8.8300470444450951e-04 -9.1308555583455059e-04 3.5978615104468762e-04
|
||||
28 -2.5472491016132231e+01 1.1754689301175528e+01 -1.7174778481945946e+01
|
||||
4 -8.6006926615992221e+00 3.1744204309217805e+00 -6.2092173142411182e+00
|
||||
10 6.4812481374149925e+01 -7.6374989222973383e+01 -7.5660087866976198e+01
|
||||
11 -6.2988690058862247e+00 -8.0952570407173248e+00 -1.6391410857465811e+01
|
||||
12 1.4369425068541616e+01 1.2193286964902716e+01 -8.2527851881139291e+00
|
||||
14 -2.7952431407275968e+00 4.3888485898644758e-01 -7.1101001480669570e+00
|
||||
3 -2.4823737467155107e+02 1.0508780361006465e+02 8.6172398279574821e+01
|
||||
6 1.1683402508628048e+02 -9.8726787907693534e+01 -1.4208741286778547e+02
|
||||
7 3.8041576193059332e+00 -1.0704953187717335e+01 -4.2399881156863238e+01
|
||||
15 -3.9779897755537197e-01 8.1106017384425098e+00 3.0711122406901890e+00
|
||||
8 -1.9935816824605183e+01 1.9886802905972718e+01 5.5348113977772961e+01
|
||||
9 1.1205804476066335e+01 1.3198927883119472e+01 4.9879830769414433e+01
|
||||
16 5.2787469706921414e+01 -6.7733540563012909e+01 1.5088305700997223e+01
|
||||
17 -1.4633172233841803e+01 1.0014125744838747e+01 4.0800214574133925e+01
|
||||
5 -1.7308376123424425e+00 -2.5575751812921999e+00 1.0273464092969368e+01
|
||||
13 7.3377072957109331e+00 -2.7955027646062254e+00 -1.0299065890019726e-01
|
||||
2 1.8550226580094343e+01 1.4016238769424406e+01 -2.2757523570742769e+01
|
||||
1 1.2964030360656510e+01 8.0892418867139781e+01 6.0323172149265375e+01
|
||||
27 3.4725372932416243e+00 -3.8995305110569163e+01 1.1703189641257278e+01
|
||||
29 2.2007774610068502e+01 2.7247229536758095e+01 5.4673560754821722e+00
|
||||
24 1.2413321115135656e+01 -3.6423447910437126e+01 2.3794736840993508e+01
|
||||
25 -3.0031404252373655e+01 5.3796471699550121e+00 -2.5778429463380107e+01
|
||||
26 1.7604735840312014e+01 3.1032209060135433e+01 1.9586527866121384e+00
|
||||
...
|
||||
|
|
@ -0,0 +1,93 @@
|
|||
---
|
||||
lammps_version: 5 May 2020
|
||||
date_generated: Fri May 15 19:08:06 202
|
||||
epsilon: 5.0e-14
|
||||
prerequisites: ! |
|
||||
atom full
|
||||
pair lj/cut/coul/cut
|
||||
pre_commands: ! ""
|
||||
post_commands: ! |
|
||||
pair_modify mix arithmetic
|
||||
input_file: in.fourmol
|
||||
pair_style: lj/cut/coul/cut 8.0
|
||||
pair_coeff: ! |
|
||||
1 1 0.02 2.5
|
||||
2 2 0.005 1.0
|
||||
2 4 0.005 0.5
|
||||
3 3 0.02 3.2
|
||||
4 4 0.015 3.1
|
||||
5 5 0.015 3.1
|
||||
extract: ! |
|
||||
epsilon 2
|
||||
sigma 2
|
||||
cut_coul 2
|
||||
natoms: 29
|
||||
init_vdwl: 749.23722617441
|
||||
init_coul: -127.494586297384
|
||||
init_stress: ! |2-
|
||||
2.1525611716153662e+03 2.1557329928729714e+03 4.6078922097278992e+03 -7.6038599716248871e+02 1.6844123432798593e+01 6.6957582793947995e+02
|
||||
init_forces: ! |2
|
||||
21 -6.9075217862024729e+01 -8.0130923554916222e+01 2.1539217334351468e+02
|
||||
22 -1.0659105712622791e+02 -2.5122531116335626e+01 -1.6283773490673144e+02
|
||||
23 1.7515806187289186e+02 1.0400251807240087e+02 -5.2024044475563407e+01
|
||||
19 1.6184514948330486e+00 -1.6594104323963157e+00 5.6561121961585874e+00
|
||||
18 1.2559081003348347e+00 6.6417071010502644e+00 -9.8829024532584242e+00
|
||||
20 -3.4526823962506339e+00 -3.1794201827763624e+00 4.2593058942111073e+00
|
||||
28 -1.7556673492493090e+02 7.2243040777824405e+01 -1.1798873438160003e+02
|
||||
4 -7.8195539839911401e+00 2.1451967639942007e+00 -5.9041143405357257e+00
|
||||
10 5.3089511229362836e+02 -6.0998478570024906e+02 -1.8376190076903140e+02
|
||||
11 -3.3416993157732144e+00 -4.7792759717642461e+00 -1.0199030124429990e+01
|
||||
12 2.0837574177894211e+01 9.8678992186716794e+00 -6.6547856722461791e+00
|
||||
14 -4.6138299493865063e+00 1.1336312960558785e+00 -8.7660603717593801e+00
|
||||
3 -1.3530454726581058e+02 -3.8712939842519984e+02 -1.4565941668340852e+02
|
||||
6 -8.2989066543991021e+02 9.6019334229339688e+02 1.1479367555385732e+03
|
||||
7 5.7874565768962732e+01 -3.3534001225608625e+02 -1.7140667059841346e+03
|
||||
15 1.6301594996032190e-02 8.3212544078455526e+00 2.0473863129314336e+00
|
||||
8 1.4280513665193016e+02 -1.0509295266700725e+02 4.0233496556664352e+02
|
||||
9 8.0984846358577755e+01 7.9600519879362793e+01 3.5197302607973376e+02
|
||||
16 4.6221173850726012e+02 -3.3124459100332649e+02 -1.1865042573522639e+03
|
||||
17 -4.5568747337591418e+02 3.2159245780234755e+02 1.1980753517323640e+03
|
||||
5 -2.9163954622631838e+00 -3.3469203159121546e+00 1.2074681739960770e+01
|
||||
13 7.7163253262379232e+00 -3.2213746935083791e+00 -1.5767800892174699e-01
|
||||
2 1.5859534558934598e+02 1.2807631885754938e+02 -1.8817306436786598e+02
|
||||
1 -2.1092656745560582e+01 2.6988675971464920e+02 3.3315496490474936e+02
|
||||
27 4.8962873327044548e+01 -2.1594272998432456e+02 8.6423916022225754e+01
|
||||
29 1.2734702050586698e+02 1.4335524696343094e+02 3.2138232790236046e+01
|
||||
24 3.4171642978571064e+01 -2.0194723428049528e+02 1.0982449993110693e+02
|
||||
25 -1.4493455845312886e+02 2.0799052516599719e+01 -1.2091056058537984e+02
|
||||
26 1.0983616775279704e+02 1.8026261491911859e+02 1.2199618424721184e+01
|
||||
run_vdwl: 147.040074247861
|
||||
run_coul: -127.747670332952
|
||||
run_stress: ! |2-
|
||||
6.0353517979442461e+02 6.2447478504848948e+02 4.3791289213232773e+02 -3.1645327985666916e+02 -3.0029829817918461e+01 1.2366110043709419e+02
|
||||
run_forces: ! |2
|
||||
21 -9.0117437110976208e+00 -1.2245002769510558e+01 3.4149930665027604e+01
|
||||
22 -1.8574628130247383e+01 -3.4425614243623759e+00 -2.6438003631560957e+01
|
||||
23 2.6836512900560486e+01 1.4678669844998341e+01 -6.8586294639912868e+00
|
||||
19 2.0601990795228655e+00 -2.0654591624016017e+00 5.3342092406989181e+00
|
||||
18 1.7867918017204881e-01 7.0934616451774222e+00 -8.1844140157389447e+00
|
||||
20 -3.2420367636703245e+00 -3.2567435108459528e+00 3.4326643507650694e+00
|
||||
28 -2.3474871411852092e+01 8.9025628034955400e+00 -1.5678527522469286e+01
|
||||
4 -8.7489077305197966e+00 3.2824728394222484e+00 -6.5528799573062919e+00
|
||||
10 6.4066994216039774e+01 -7.5535414830831073e+01 -7.5482801528224059e+01
|
||||
11 -7.4023563023183270e+00 -6.6466434385434114e+00 -1.6954367419722207e+01
|
||||
12 1.7791559893799452e+01 1.1417548631540143e+01 -6.8410096003357665e+00
|
||||
14 -4.3979315901951148e+00 8.9942305965266567e-01 -7.0797565928935784e+00
|
||||
3 -2.4593644124097807e+02 1.0324855454274562e+02 8.5001206846979514e+01
|
||||
6 1.1566141963558714e+02 -9.9315755376883999e+01 -1.4165908414891499e+02
|
||||
7 4.0530470234906968e+00 -1.0452540107716739e+01 -4.1479250736990721e+01
|
||||
15 -3.6033012007078330e-01 7.7431258565450438e+00 2.0411497046102869e+00
|
||||
8 -2.0168010454983431e+01 2.2738989716140548e+01 5.6628319680633581e+01
|
||||
9 1.3835859550747433e+01 6.0277311554736261e+00 5.3337859370227775e+01
|
||||
16 5.2319713741321443e+01 -6.8429089937297093e+01 1.4574327949254149e+01
|
||||
17 -1.8290390749253813e+01 1.7655927425392367e+01 3.5962602984966971e+01
|
||||
5 -2.2204206882210045e+00 -1.8704582174988531e+00 1.0433415249486350e+01
|
||||
13 7.0142861949738426e+00 -2.7644703358745439e+00 -2.3054066305694912e-01
|
||||
2 1.9651626467903323e+01 1.2289294619079556e+01 -2.5586353509806141e+01
|
||||
1 1.4816259361577874e+01 7.9738869562670203e+01 6.1442738232730541e+01
|
||||
27 1.4388278299715864e+00 -3.2689045840403274e+01 9.3413561221835106e+00
|
||||
29 2.3348254236732291e+01 2.4017143531533620e+01 6.6807458470145322e+00
|
||||
24 1.0582726005225370e+01 -3.1420805532367773e+01 2.3645380201169598e+01
|
||||
25 -2.9311971392394881e+01 3.1879553971926993e+00 -2.4340486203032285e+01
|
||||
26 1.7484074968176976e+01 2.7212259853477590e+01 1.3601985482950725e+00
|
||||
...
|
||||
|
|
@ -0,0 +1,97 @@
|
|||
---
|
||||
lammps_version: 5 May 2020
|
||||
date_generated: Fri May 15 19:08:06 202
|
||||
epsilon: 7.5e-14
|
||||
prerequisites: ! |
|
||||
atom full
|
||||
pair lj/cut/coul/long
|
||||
pre_commands: ! ""
|
||||
post_commands: ! |
|
||||
pair_modify mix arithmetic
|
||||
pair_modify table 0
|
||||
kspace_style ewald 1.0e-6
|
||||
kspace_modify gewald 0.3
|
||||
kspace_modify compute no
|
||||
input_file: in.fourmol
|
||||
pair_style: lj/cut/coul/long 8.0
|
||||
pair_coeff: ! |
|
||||
1 1 0.02 2.5
|
||||
2 2 0.005 1.0
|
||||
2 4 0.005 0.5
|
||||
3 3 0.02 3.2
|
||||
4 4 0.015 3.1
|
||||
5 5 0.015 3.1
|
||||
extract: ! |
|
||||
epsilon 2
|
||||
sigma 2
|
||||
cut_coul 0
|
||||
natoms: 29
|
||||
init_vdwl: 749.23722617441
|
||||
init_coul: 225.821815126925
|
||||
init_stress: ! |2-
|
||||
2.1566096102905212e+03 2.1560522619501480e+03 4.6266534799074097e+03 -7.5506792664852810e+02 1.8227392498787179e+01 6.7620047095233247e+02
|
||||
init_forces: ! |2
|
||||
21 -6.9665137396438112e+01 -7.7245616766991660e+01 2.1699117009298578e+02
|
||||
22 -1.0627535437497887e+02 -2.6762752151475254e+01 -1.6366208350109022e+02
|
||||
23 1.7552271103327649e+02 1.0442578541745208e+02 -5.2822837143660387e+01
|
||||
19 1.9902251287219543e+00 -7.2137757102175326e-01 5.5223639838180727e+00
|
||||
18 3.5422516456607112e-01 4.7664525690678010e+00 -7.8521647968499169e+00
|
||||
20 -2.9136075741134135e+00 -3.9877101082545643e+00 4.1254812365563023e+00
|
||||
28 -1.7608383951257380e+02 7.3301743321101739e+01 -1.1852450102612136e+02
|
||||
4 -7.9523001611903004e+00 2.1529958675030305e+00 -5.8368703457146163e+00
|
||||
10 5.3094587078352731e+02 -6.1005663210778175e+02 -1.8379407345475141e+02
|
||||
11 -3.2540499141649786e+00 -4.8802394286887329e+00 -1.0222975736126038e+01
|
||||
12 2.0387995352464142e+01 1.0150732333668605e+01 -6.4963658198523637e+00
|
||||
14 -4.4397845432063852e+00 1.0429791239998418e+00 -8.8467682628524411e+00
|
||||
3 -1.3527534370855790e+02 -3.8712699678510739e+02 -1.4567473564586999e+02
|
||||
6 -8.3040738820822730e+02 9.6005828042359281e+02 1.1483437825765977e+03
|
||||
7 5.8120185166710627e+01 -3.3519870126974780e+02 -1.7141420770646753e+03
|
||||
15 1.4977268342910116e-01 8.2844605613269025e+00 2.0022126568305456e+00
|
||||
8 1.4294529110557448e+02 -1.0473948537024830e+02 4.0227440364265198e+02
|
||||
9 8.0782664801292412e+01 7.9461689376462743e+01 3.5173823756192235e+02
|
||||
16 4.6252785745102693e+02 -3.3138888536570045e+02 -1.1873830399415435e+03
|
||||
17 -4.5576456304060491e+02 3.2171257028674950e+02 1.1992024569249213e+03
|
||||
5 -3.0582326251525678e+00 -3.3883809187242964e+00 1.2083017854050967e+01
|
||||
13 8.0249443601010526e+00 -3.2177034494059380e+00 -3.2677700468242432e-01
|
||||
2 1.5804320290259730e+02 1.2736070680044999e+02 -1.8761875322370290e+02
|
||||
1 -2.0618462763941597e+01 2.6955824557331817e+02 3.3303971969628577e+02
|
||||
27 4.9789358000243809e+01 -2.1702160604151146e+02 8.7170422564672961e+01
|
||||
29 1.2668894747540401e+02 1.4371756954645073e+02 3.1331335682136434e+01
|
||||
24 3.5023962544067167e+01 -2.0265340222862497e+02 1.0716472334679622e+02
|
||||
25 -1.4546285129442887e+02 2.0973097297530700e+01 -1.2144543956242963e+02
|
||||
26 1.0987370116457643e+02 1.8142218106460939e+02 1.3660134709697306e+01
|
||||
run_vdwl: 146.969932845685
|
||||
run_coul: 231.547223819221
|
||||
run_stress: ! |2-
|
||||
6.0915003500707246e+02 6.3099734489395064e+02 4.5850631347176483e+02 -3.1002781778199568e+02 -2.9989785213832519e+01 1.3053414139517639e+02
|
||||
run_forces: ! |2
|
||||
21 -9.8190589026954900e+00 -9.2646568261250746e+00 3.5602732479020787e+01
|
||||
22 -1.7981862279708128e+01 -5.1466131620539572e+00 -2.7099137281623833e+01
|
||||
23 2.7159817699916164e+01 1.5032332828113882e+01 -7.6944563510728319e+00
|
||||
19 2.4125111059935511e+00 -8.7925981492705563e-01 5.4232992638105104e+00
|
||||
18 -6.3726923555038051e-01 4.7973251807363830e+00 -6.5668081899777073e+00
|
||||
20 -2.7248803445351588e+00 -3.8904686920602902e+00 3.4619755015532667e+00
|
||||
28 -2.4164736062669249e+01 9.4962417865107938e+00 -1.5922775191014225e+01
|
||||
4 -8.8799790196154174e+00 3.3241582453182850e+00 -6.4497295145390607e+00
|
||||
10 6.4064118589590365e+01 -7.5531391512657578e+01 -7.5546937349480885e+01
|
||||
11 -7.3191394313773790e+00 -6.8855181594816397e+00 -1.7097024407609748e+01
|
||||
12 1.7332128235292799e+01 1.1587338382628545e+01 -6.6950974554233937e+00
|
||||
14 -4.2029786654038359e+00 8.3858585765595739e-01 -7.1469688262826514e+00
|
||||
3 -2.4626010838248081e+02 1.0353987453079894e+02 8.5144848064076527e+01
|
||||
6 1.1514350774120550e+02 -9.9343273705726290e+01 -1.4128643713842419e+02
|
||||
7 4.4121943913120507e+00 -1.0659283246845636e+01 -4.1672997953406181e+01
|
||||
15 -2.3374818519103110e-01 7.7706237191767702e+00 2.0011105405761827e+00
|
||||
8 -1.9867783268323649e+01 2.2748959518230702e+01 5.6456512822888548e+01
|
||||
9 1.3497118196591632e+01 6.1641778280888868e+00 5.3035388456119485e+01
|
||||
16 5.2778367300681317e+01 -6.8528214427924539e+01 1.3739542066296107e+01
|
||||
17 -1.8300842492788746e+01 1.7606322050821845e+01 3.7169239078137288e+01
|
||||
5 -2.3921298369027211e+00 -1.8640446027230397e+00 1.0409771237667691e+01
|
||||
13 7.3167736710828617e+00 -2.7360217555016577e+00 -4.0451132381702781e-01
|
||||
2 1.9396976103452584e+01 1.2345009578188996e+01 -2.5332936381019135e+01
|
||||
1 1.5318919850572806e+01 7.9282401393560946e+01 6.1573406079985290e+01
|
||||
27 2.2656453938690255e+00 -3.4112795985711898e+01 1.0080919795658271e+01
|
||||
29 2.2535473617034118e+01 2.4637995446318733e+01 5.7705996450135073e+00
|
||||
24 1.1638953097463977e+01 -3.2222663983679347e+01 2.1229971509788882e+01
|
||||
25 -2.9814603307050731e+01 3.4701648992084406e+00 -2.4986494993856635e+01
|
||||
26 1.7326614420233987e+01 2.8422694630059919e+01 2.8029958169551819e+00
|
||||
...
|
||||
|
|
@ -0,0 +1,98 @@
|
|||
---
|
||||
lammps_version: 5 May 2020
|
||||
date_generated: Fri May 15 19:08:06 202
|
||||
epsilon: 5.0e-14
|
||||
prerequisites: ! |
|
||||
atom full
|
||||
pair lj/cut/coul/msm
|
||||
pre_commands: ! ""
|
||||
post_commands: ! |
|
||||
pair_modify mix arithmetic
|
||||
pair_modify table 0
|
||||
kspace_style msm 1.0e-4
|
||||
kspace_modify compute no
|
||||
kspace_modify cutoff/adjust no
|
||||
kspace_modify pressure/scalar no # required for USER-OMP with msm
|
||||
input_file: in.fourmol
|
||||
pair_style: lj/cut/coul/msm 12.0
|
||||
pair_coeff: ! |
|
||||
1 1 0.02 2.5
|
||||
2 2 0.005 1.0
|
||||
2 4 0.005 0.5
|
||||
3 3 0.02 3.2
|
||||
4 4 0.015 3.1
|
||||
5 5 0.015 3.1
|
||||
extract: ! |
|
||||
epsilon 2
|
||||
sigma 2
|
||||
cut_coul 0
|
||||
natoms: 29
|
||||
init_vdwl: 749.234609413223
|
||||
init_coul: 114.131380823567
|
||||
init_stress: ! |2-
|
||||
2.1551147118149142e+03 2.1531310016450821e+03 4.6224274885907998e+03 -7.5399488884461846e+02 1.8659600825010816e+01 6.7753815235266666e+02
|
||||
init_forces: ! |2
|
||||
8 1.4278724025640088e+02 -1.0530389447014019e+02 4.0279744438123942e+02
|
||||
10 5.3091483101457425e+02 -6.0996228502800284e+02 -1.8384019943029980e+02
|
||||
11 -3.3126807128460176e+00 -4.7549653053698986e+00 -1.0302167741449942e+01
|
||||
12 2.0709153219724037e+01 9.7697671123327332e+00 -6.3353019591219484e+00
|
||||
13 7.9282218638906894e+00 -3.1210248845494526e+00 -3.4425992467768834e-01
|
||||
14 -4.5709573891916682e+00 1.1642595010194223e+00 -8.8700619959300848e+00
|
||||
21 -6.9535714029277429e+01 -7.6484217175455555e+01 2.1607515226454146e+02
|
||||
22 -1.0635913016151144e+02 -2.7019986794330784e+01 -1.6313649082317843e+02
|
||||
23 1.7538864882747620e+02 1.0405353807714272e+02 -5.2357141245958552e+01
|
||||
2 1.5822912207263175e+02 1.2711045740058714e+02 -1.8785632280853179e+02
|
||||
3 -1.3530169472483195e+02 -3.8713571709926504e+02 -1.4564908007858847e+02
|
||||
4 -7.8363271181753893e+00 2.1760460209726138e+00 -5.9378537791468391e+00
|
||||
6 -8.2993095356149126e+02 9.6044557378796685e+02 1.1474899757606170e+03
|
||||
7 5.7828224510872907e+01 -3.3555018600570963e+02 -1.7136025040428560e+03
|
||||
19 1.8462853118611895e+00 -1.3982672058117223e+00 6.2353852730166475e+00
|
||||
15 5.3785918282939153e-02 8.3655504537713874e+00 1.9471305012681563e+00
|
||||
18 7.8834015170699856e-01 6.0999277007337671e+00 -8.9956151871830698e+00
|
||||
20 -3.1298215708666732e+00 -4.5665463679663034e+00 4.7511024797788082e+00
|
||||
9 8.0982805461699229e+01 7.9758825278316181e+01 3.5169424205669787e+02
|
||||
27 4.9268806567247346e+01 -2.1540599266520917e+02 8.6345394436784431e+01
|
||||
28 -1.7572634923909956e+02 7.2424827393790522e+01 -1.1807149056284722e+02
|
||||
29 1.2694498092952055e+02 1.4289100071158703e+02 3.1729222911990778e+01
|
||||
16 4.6240562015276009e+02 -3.3111358811847782e+02 -1.1870498722103234e+03
|
||||
17 -4.5579535293132835e+02 3.2144023284905097e+02 1.1985160009651768e+03
|
||||
1 -2.1016398356966974e+01 2.6961779611484451e+02 3.3338430317495994e+02
|
||||
5 -2.9416331677900525e+00 -3.3161141742156843e+00 1.2025305438500135e+01
|
||||
25 -1.4529091397370476e+02 2.0347045151799009e+01 -1.2117180309713224e+02
|
||||
24 3.4874995395976718e+01 -2.0109952743653054e+02 1.0666645780790178e+02
|
||||
26 1.0979686528245566e+02 1.8056746517711989e+02 1.3863047434751961e+01
|
||||
run_vdwl: 147.043158293232
|
||||
run_coul: 120.800133568184
|
||||
run_stress: ! |2-
|
||||
6.0714736178199996e+02 6.2725764177379574e+02 4.5374246696160844e+02 -3.0771618211335505e+02 -2.8793232490221200e+01 1.3172685327790495e+02
|
||||
run_forces: ! |2
|
||||
8 -2.0278671065073532e+01 2.2416743324882720e+01 5.7007585309011439e+01
|
||||
10 6.4034498202885743e+01 -7.5459355451933178e+01 -7.5613086118755277e+01
|
||||
11 -7.3900440825588758e+00 -6.7494588207315127e+00 -1.7185399982016623e+01
|
||||
12 1.7678272698747335e+01 1.1269091206486449e+01 -6.5110680123955236e+00
|
||||
13 7.2168880103155031e+00 -2.6444826435940221e+00 -4.2612452408505841e-01
|
||||
14 -4.3479905182835603e+00 9.4719508865379132e-01 -7.1776577935096615e+00
|
||||
21 -9.6780947508028436e+00 -8.5051159538315542e+00 3.4792558615710917e+01
|
||||
22 -1.8186663092251703e+01 -5.4051681192769436e+00 -2.6632304952295339e+01
|
||||
23 2.7110231811687829e+01 1.4702212710562977e+01 -7.2378958778892555e+00
|
||||
2 1.9582047807065450e+01 1.2033716111587802e+01 -2.5527890849545621e+01
|
||||
3 -2.4595994776578007e+02 1.0320598804297596e+02 8.5016525898038509e+01
|
||||
4 -8.7666838955959570e+00 3.3307148955442347e+00 -6.5800974544778326e+00
|
||||
6 1.1566145203968264e+02 -9.8961460001337485e+01 -1.4206288177802986e+02
|
||||
7 4.0310214007184113e+00 -1.0796589046204041e+01 -4.1053720345307482e+01
|
||||
19 2.2961499554879796e+00 -1.7083543392295206e+00 5.9508355438033469e+00
|
||||
15 -3.2415867625154432e-01 7.8105556767018367e+00 1.9327787399546656e+00
|
||||
18 -2.7787652857121087e-01 6.3930913892933505e+00 -7.3568724155247649e+00
|
||||
20 -2.9296176078546390e+00 -4.5612278049900050e+00 3.9549252590661639e+00
|
||||
9 1.3831275838761206e+01 6.3233083481016310e+00 5.3125632501675732e+01
|
||||
27 1.6512844269882598e+00 -3.2507877868527643e+01 9.2893210890173936e+00
|
||||
28 -2.3920410543003026e+01 8.5646512291710888e+00 -1.5561036534939182e+01
|
||||
29 2.3043627097427251e+01 2.3800907389135812e+01 6.2424235355667932e+00
|
||||
16 5.2553213225186234e+01 -6.8222972483339788e+01 1.4027042239369928e+01
|
||||
17 -1.8352944471521234e+01 1.7361877908286655e+01 3.6403366175682187e+01
|
||||
1 1.4901675541185393e+01 7.9362893190165494e+01 6.1758304021013508e+01
|
||||
5 -2.2550234258401574e+00 -1.8189556044156958e+00 1.0381639896835960e+01
|
||||
25 -2.9706819413926937e+01 2.8110979952854009e+00 -2.4644098698605937e+01
|
||||
24 1.1387734102372550e+01 -3.0705433937299183e+01 2.0564412733372382e+01
|
||||
26 1.7395573678803508e+01 2.7712407567875360e+01 3.1227837792584263e+00
|
||||
...
|
||||
|
|
@ -0,0 +1,97 @@
|
|||
---
|
||||
lammps_version: 5 May 2020
|
||||
date_generated: Fri May 15 19:08:06 202
|
||||
epsilon: 5.0e-13
|
||||
prerequisites: ! |
|
||||
atom full
|
||||
pair lj/cut/coul/long
|
||||
pre_commands: ! ""
|
||||
post_commands: ! |
|
||||
pair_modify mix arithmetic
|
||||
pair_modify table 16
|
||||
kspace_style ewald 1.0e-6
|
||||
kspace_modify gewald 0.3
|
||||
kspace_modify compute no
|
||||
input_file: in.fourmol
|
||||
pair_style: lj/cut/coul/long 8.0
|
||||
pair_coeff: ! |
|
||||
1 1 0.02 2.5
|
||||
2 2 0.005 1.0
|
||||
2 4 0.005 0.5
|
||||
3 3 0.02 3.2
|
||||
4 4 0.015 3.1
|
||||
5 5 0.015 3.1
|
||||
extract: ! |
|
||||
epsilon 2
|
||||
sigma 2
|
||||
cut_coul 0
|
||||
natoms: 29
|
||||
init_vdwl: 749.23722617441
|
||||
init_coul: 225.821851347828
|
||||
init_stress: ! |2-
|
||||
2.1566096305532428e+03 2.1560522677062158e+03 4.6266534933320354e+03 -7.5506792335393379e+02 1.8227401993933608e+01 6.7620047504299214e+02
|
||||
init_forces: ! |2
|
||||
21 -6.9665137768359514e+01 -7.7245616202165436e+01 2.1699117066323527e+02
|
||||
22 -1.0627535707614186e+02 -2.6762753807653660e+01 -1.6366208513695517e+02
|
||||
23 1.7552271422588854e+02 1.0442578659243907e+02 -5.2822836258914116e+01
|
||||
19 1.9902231265754700e+00 -7.2137898950051871e-01 5.5223638520470431e+00
|
||||
18 3.5422571547347614e-01 4.7664525241946274e+00 -7.8521656631675647e+00
|
||||
20 -2.9136057525025101e+00 -3.9877089123366902e+00 4.1254823253812729e+00
|
||||
28 -1.7608384222411630e+02 7.3301742386199109e+01 -1.1852450224218201e+02
|
||||
4 -7.9523001646064291e+00 2.1529963301924471e+00 -5.8368701554806615e+00
|
||||
10 5.3094587090036543e+02 -6.1005663167117950e+02 -1.8379407406291628e+02
|
||||
11 -3.2540500285585203e+00 -4.8802387273926380e+00 -1.0222975632081258e+01
|
||||
12 2.0387995521221185e+01 1.0150732391587335e+01 -6.4963667234486069e+00
|
||||
14 -4.4397846876171876e+00 1.0429790034696189e+00 -8.8467681208164048e+00
|
||||
3 -1.3527534359989338e+02 -3.8712699690043149e+02 -1.4567473577039485e+02
|
||||
6 -8.3040738866408844e+02 9.6005828136668970e+02 1.1483437807809082e+03
|
||||
7 5.8120184369097160e+01 -3.3519870131599180e+02 -1.7141420791263022e+03
|
||||
15 1.4977263250375636e-01 8.2844602694962735e+00 2.0022132521064626e+00
|
||||
8 1.4294529037600086e+02 -1.0473948563496474e+02 4.0227440568419655e+02
|
||||
9 8.0782666599876720e+01 7.9461688785559645e+01 3.5173823946074668e+02
|
||||
16 4.6252785864594227e+02 -3.3138888656299093e+02 -1.1873830396170474e+03
|
||||
17 -4.5576456327333159e+02 3.2171257054701533e+02 1.1992024568624847e+03
|
||||
5 -3.0582324573439124e+00 -3.3883799712367040e+00 1.2083018089179465e+01
|
||||
13 8.0249444399429350e+00 -3.2177035823321547e+00 -3.2677687436783698e-01
|
||||
2 1.5804320240246361e+02 1.2736070606787304e+02 -1.8761875188555263e+02
|
||||
1 -2.0618464267911786e+01 2.6955824515095657e+02 3.3303971790466971e+02
|
||||
27 4.9789357884880488e+01 -2.1702160587579414e+02 8.7170422370750828e+01
|
||||
29 1.2668895009877801e+02 1.4371757005571936e+02 3.1331337187961438e+01
|
||||
24 3.5023962840451759e+01 -2.0265340183660416e+02 1.0716472290011653e+02
|
||||
25 -1.4546285327008255e+02 2.0973096000232136e+01 -1.2144544040782203e+02
|
||||
26 1.0987370345509248e+02 1.8142218251895059e+02 1.3660136343664782e+01
|
||||
run_vdwl: 146.969932394973
|
||||
run_coul: 231.547231027259
|
||||
run_stress: ! |2-
|
||||
6.0915004559646684e+02 6.3099733874173205e+02 4.5850630772502740e+02 -3.1002780853804836e+02 -2.9989782729351909e+01 1.3053414635397095e+02
|
||||
run_forces: ! |2
|
||||
21 -9.8190594543264798e+00 -9.2646555708689924e+00 3.5602732603740016e+01
|
||||
22 -1.7981863440577431e+01 -5.1466143340317450e+00 -2.7099137891686084e+01
|
||||
23 2.7159819315283109e+01 1.5032333117821219e+01 -7.6944558215758123e+00
|
||||
19 2.4125091433118486e+00 -8.7926146006510375e-01 5.4232990590521926e+00
|
||||
18 -6.3726835259723758e-01 4.7973251619048618e+00 -6.5668096068804322e+00
|
||||
20 -2.7248785129452946e+00 -3.8904675805353075e+00 3.4619764299980011e+00
|
||||
28 -2.4164737463031166e+01 9.4962408965485530e+00 -1.5922775772772074e+01
|
||||
4 -8.8799793333953971e+00 3.3241589367507962e+00 -6.4497293597128627e+00
|
||||
10 6.4064118449943933e+01 -7.5531390901048468e+01 -7.5546937006353559e+01
|
||||
11 -7.3191394758279866e+00 -6.8855176883411877e+00 -1.7097024484707848e+01
|
||||
12 1.7332128989954910e+01 1.1587337945376177e+01 -6.6950986294568242e+00
|
||||
14 -4.2029787248146784e+00 8.3858573354128096e-01 -7.1469687848927164e+00
|
||||
3 -2.4626010819298389e+02 1.0353987390000911e+02 8.5144847833756302e+01
|
||||
6 1.1514351252024848e+02 -9.9343277045289526e+01 -1.4128644060090235e+02
|
||||
7 4.4121937585568691e+00 -1.0659282122293529e+01 -4.1672994426592965e+01
|
||||
15 -2.3374852087826420e-01 7.7706234158029703e+00 2.0011111418920482e+00
|
||||
8 -1.9867787327847278e+01 2.2748961526464992e+01 5.6456512542354062e+01
|
||||
9 1.3497119328072609e+01 6.1641760514132971e+00 5.3035389141893411e+01
|
||||
16 5.2778366262337954e+01 -6.8528213317173908e+01 1.3739545725184309e+01
|
||||
17 -1.8300841112803944e+01 1.7606322828257291e+01 3.7169233988593675e+01
|
||||
5 -2.3921296273181305e+00 -1.8640436356405086e+00 1.0409771669906656e+01
|
||||
13 7.3167737972056504e+00 -2.7360218586026361e+00 -4.0451118789154500e-01
|
||||
2 1.9396975392512381e+01 1.2345008979618576e+01 -2.5332934850094649e+01
|
||||
1 1.5318918280577572e+01 7.9282401106958375e+01 6.1573405787971858e+01
|
||||
27 2.2656449067225992e+00 -3.4112795339715859e+01 1.0080919387176698e+01
|
||||
29 2.2535474805527961e+01 2.4637995225775605e+01 5.7706008105849014e+00
|
||||
24 1.1638953036548925e+01 -3.2222662903256705e+01 2.1229970497291735e+01
|
||||
25 -2.9814604103781551e+01 3.4701637896625570e+00 -2.4986495288736702e+01
|
||||
26 1.7326615656323938e+01 2.8422695140957792e+01 2.8029970928606471e+00
|
||||
...
|
||||
|
|
@ -0,0 +1,104 @@
|
|||
---
|
||||
lammps_version: 5 May 2020
|
||||
date_generated: Fri May 15 19:08:06 202
|
||||
epsilon: 1.0e-13
|
||||
prerequisites: ! |
|
||||
atom full
|
||||
pair lj/cut/tip4p/long
|
||||
pre_commands: ! |
|
||||
variable newton_pair delete
|
||||
variable newton_pair index on
|
||||
post_commands: ! |
|
||||
pair_modify mix arithmetic
|
||||
pair_modify table 0
|
||||
kspace_style pppm/tip4p 1.0e-6
|
||||
kspace_modify gewald 0.3
|
||||
kspace_modify compute no
|
||||
input_file: in.fourmol
|
||||
pair_style: lj/cut/tip4p/long 5 2 5 1 0.15 10.0
|
||||
pair_coeff: ! |
|
||||
1 1 0.02 2.5
|
||||
2 2 0.0 1.0
|
||||
2 4 0.005 0.5
|
||||
3 3 0.02 3.2
|
||||
4 4 0.015 3.1
|
||||
5 5 0.015 3.1
|
||||
extract: ! |
|
||||
epsilon 2
|
||||
sigma 2
|
||||
cut_coul 0
|
||||
qdist 0
|
||||
typeO 0
|
||||
typeH 0
|
||||
typeA 0
|
||||
typeB 0
|
||||
natoms: 29
|
||||
init_vdwl: 584.670383161597
|
||||
init_coul: 220.904555359383
|
||||
init_stress: ! |2-
|
||||
1.4179908002675882e+03 1.6981521472771326e+03 3.8247898365498659e+03 -1.0685165973996445e+03 -2.2301723469314501e+02 7.0678972133133993e+02
|
||||
init_forces: ! |2
|
||||
8 2.2222305975187413e+02 -1.9487727502660317e+01 7.5254098660516127e+02
|
||||
10 5.2854808750532732e+02 -6.1591056046926769e+02 -1.9340282225226667e+02
|
||||
11 -9.3766462457826905e-01 1.0563563299185068e+00 -5.5775022539970631e-01
|
||||
12 2.4920347090319872e+01 1.6044703403776552e+01 -1.2382381138510290e+01
|
||||
13 -7.5720425159299595e-02 3.8772041103398963e-02 -1.8346431648817585e-01
|
||||
14 -1.0557020156519512e+00 3.6717714938726143e-01 -1.0728817695848940e-01
|
||||
21 1.5193592132463731e+00 3.2144198763444232e+00 -6.7582252673322509e+00
|
||||
22 4.4657588078956723e+00 1.0585032152255676e+00 5.8268290139589860e+00
|
||||
23 -6.2938601634201303e+00 -3.9616631352879410e+00 1.3192732707154482e+00
|
||||
2 -1.9557407939667784e-01 -2.8434279090485344e+00 -1.2037666274486341e+00
|
||||
3 -1.4543663403399538e+02 -3.8854700044105402e+02 -1.3922266457674951e+02
|
||||
4 -7.9314978889013857e-02 1.6212643266693107e-02 -2.3663785465653561e-01
|
||||
6 -8.3044669697571737e+02 9.6003930443804506e+02 1.1483694854778576e+03
|
||||
7 5.8135895738828353e+01 -3.3519692236360061e+02 -1.7141558378818361e+03
|
||||
19 1.9911596893384120e+00 -7.2195675725850206e-01 5.5334689749229105e+00
|
||||
15 3.5162907632314466e-01 -1.9165325094615621e-01 -1.0148660141104417e+00
|
||||
18 3.5327038190601812e-01 4.7616027705645063e+00 -7.8715620952516669e+00
|
||||
20 -2.9127135301570397e+00 -4.0021946638596519e+00 4.1375019377447915e+00
|
||||
9 1.5618105874324246e+00 -5.8578891996706437e+00 1.3701350515471384e+00
|
||||
27 -1.5292288824966405e+00 7.3670370809055621e+00 -2.7248017347638225e+00
|
||||
28 6.4035032875423159e+00 -2.1779017025677483e+00 4.1727109672631357e+00
|
||||
29 -4.5201953782892055e+00 -5.1735155675050022e+00 -1.4886429234413563e+00
|
||||
16 4.6235900379292781e+02 -3.3129451959604160e+02 -1.1872104846434017e+03
|
||||
17 -4.5562419584375363e+02 3.2174933377566850e+02 1.1991777288967187e+03
|
||||
1 1.3731384428493121e+02 3.9920027854840788e+02 1.4671535403601735e+02
|
||||
5 -5.4637120859630939e-01 6.5600989679059629e-01 -6.8980117595427104e-02
|
||||
25 4.9746167445264264e+00 -5.2361422570157790e-01 3.9262159421100877e+00
|
||||
24 -1.0905447268336348e+00 6.8024490705444629e+00 -3.6841665762708757e+00
|
||||
26 -4.3769290854851999e+00 -6.4816134554785325e+00 -8.1534775153570904e-01
|
||||
run_vdwl: 102.179240398644
|
||||
run_coul: 221.720424546992
|
||||
run_stress: ! |2-
|
||||
3.9536843184623075e+02 4.7478735082143152e+02 2.6697778872541824e+02 -3.2473557133602441e+02 -9.3384532451696117e+01 1.1447113381864786e+02
|
||||
run_forces: ! |2
|
||||
8 -1.6165014052240547e+00 3.2404345058645795e+01 1.0398184289445268e+02
|
||||
10 3.9959095982478168e+01 -6.7059878898971292e+01 -8.8447803032655685e+01
|
||||
11 -1.0802301059782982e+00 1.1219888940584297e+00 -8.4425239997392743e-01
|
||||
12 2.0545804720403741e+01 1.6756506821178750e+01 -1.0147383979092723e+01
|
||||
13 -4.0343321874813348e-02 1.7788265176798995e-01 -2.9853594465807470e-01
|
||||
14 -1.3513516710629265e+00 4.4595934938156750e-01 -2.6265884551665236e-01
|
||||
21 1.4156882123083809e+00 3.1994560956847562e+00 -6.4435678999424217e+00
|
||||
22 4.7559025720967556e+00 1.1887804903972874e+00 5.7934257053883416e+00
|
||||
23 -6.5791547151845498e+00 -3.9974753494116477e+00 1.1725336611476698e+00
|
||||
2 -2.6293126959640789e-01 -1.8753551336903787e+00 -6.6074949251544546e-01
|
||||
3 -2.3593857243623478e+02 9.7836073928631833e+01 8.4490011242546615e+01
|
||||
4 -3.7637774235278060e-01 1.4515275288094828e-01 -2.8559910145119410e-01
|
||||
6 1.0933365729165321e+02 -9.6549045037005016e+01 -1.2841653298209613e+02
|
||||
7 4.9593737826049917e+00 -1.0982207225663631e+01 -4.0074345311087725e+01
|
||||
19 2.3514102714689615e+00 -7.5578860560606387e-01 5.6642936508687214e+00
|
||||
15 3.1593487998441483e-01 -2.5515183537208080e-01 -1.0797891014048080e+00
|
||||
18 -1.6194696510616974e-01 4.5570017780853052e+00 -7.3322970257924407e+00
|
||||
20 -2.8597552719569386e+00 -3.9142546520933768e+00 3.6472607860602464e+00
|
||||
9 1.3998347047175768e+00 -6.8051250780067472e+00 5.7998397476985875e-01
|
||||
27 -1.8378768075421317e+00 7.4880775093473533e+00 -2.6847264242122688e+00
|
||||
28 6.6966633089203391e+00 -2.2313684816363604e+00 4.2842114180410844e+00
|
||||
29 -4.4013620273780845e+00 -5.2116284583392112e+00 -1.6564246240672249e+00
|
||||
16 5.1256244569865018e+01 -6.6172009677024661e+01 1.2070939136664409e+01
|
||||
17 -1.7692907416727866e+01 1.6463320315378233e+01 3.6795640394681172e+01
|
||||
1 3.2379540774112940e+01 8.3517527414743427e+01 3.0446322576408370e+01
|
||||
5 -6.8204117190800306e-01 6.2446578533889874e-01 2.7378988248683184e-01
|
||||
25 5.3901883576076450e+00 -3.4508321180203627e-01 4.2395901334590524e+00
|
||||
24 -1.2476216693532436e+00 7.0412609028878901e+00 -3.7704984044487455e+00
|
||||
26 -4.6303654307411399e+00 -6.8134281037859301e+00 -1.0346808880595877e+00
|
||||
...
|
||||
|
|
@ -0,0 +1,104 @@
|
|||
---
|
||||
lammps_version: 5 May 2020
|
||||
date_generated: Fri May 15 19:08:06 202
|
||||
epsilon: 5.0e-13
|
||||
prerequisites: ! |
|
||||
atom full
|
||||
pair lj/cut/tip4p/long
|
||||
pre_commands: ! |
|
||||
variable newton_pair delete
|
||||
variable newton_pair index on
|
||||
post_commands: ! |
|
||||
pair_modify mix arithmetic
|
||||
pair_modify table 16
|
||||
kspace_style pppm/tip4p 1.0e-6
|
||||
kspace_modify gewald 0.3
|
||||
kspace_modify compute no
|
||||
input_file: in.fourmol
|
||||
pair_style: lj/cut/tip4p/long 5 2 5 1 0.15 10.0
|
||||
pair_coeff: ! |
|
||||
1 1 0.02 2.5
|
||||
2 2 0.0 1.0
|
||||
2 4 0.005 0.5
|
||||
3 3 0.02 3.2
|
||||
4 4 0.015 3.1
|
||||
5 5 0.015 3.1
|
||||
extract: ! |
|
||||
epsilon 2
|
||||
sigma 2
|
||||
cut_coul 0
|
||||
qdist 0
|
||||
typeO 0
|
||||
typeH 0
|
||||
typeA 0
|
||||
typeB 0
|
||||
natoms: 29
|
||||
init_vdwl: 584.670383161597
|
||||
init_coul: 220.904588455609
|
||||
init_stress: ! |2-
|
||||
1.4179908194794866e+03 1.6981521517100007e+03 3.8247898490384250e+03 -1.0685165954305710e+03 -2.2301722609703918e+02 7.0678972492750643e+02
|
||||
init_forces: ! |2
|
||||
8 2.2222305907114117e+02 -1.9487727724318262e+01 7.5254098859086264e+02
|
||||
10 5.2854808762099549e+02 -6.1591056007977613e+02 -1.9340282286619947e+02
|
||||
11 -9.3766468714515061e-01 1.0563570081719669e+00 -5.5775016157678947e-01
|
||||
12 2.4920347175940520e+01 1.6044703559688728e+01 -1.2382381962363933e+01
|
||||
13 -7.5720341868659613e-02 3.8771870463785031e-02 -1.8346420143728470e-01
|
||||
14 -1.0557021360462451e+00 3.6717699327037651e-01 -1.0728805745474071e-01
|
||||
21 1.5193589985453577e+00 3.2144199479391911e+00 -6.7582250028542115e+00
|
||||
22 4.4657560788388375e+00 1.0585017750862749e+00 5.8268274399136137e+00
|
||||
23 -6.2938570049582916e+00 -3.9616619683096346e+00 1.3192742125017083e+00
|
||||
2 -1.9557447317357343e-01 -2.8434285081522317e+00 -1.2037651950271924e+00
|
||||
3 -1.4543663391923076e+02 -3.8854700055097300e+02 -1.3922266469593490e+02
|
||||
4 -7.9314985076196248e-02 1.6213100389693782e-02 -2.3663766119408827e-01
|
||||
6 -8.3044669753026062e+02 9.6003930520948552e+02 1.1483694838125878e+03
|
||||
7 5.8135894976125222e+01 -3.3519692238213986e+02 -1.7141558400143274e+03
|
||||
19 1.9911576767872563e+00 -7.2195818815492241e-01 5.5334687249487846e+00
|
||||
15 3.5162903411425839e-01 -1.9165356159914390e-01 -1.0148654643051216e+00
|
||||
18 3.5327098235417681e-01 4.7616027558737439e+00 -7.8715630868265229e+00
|
||||
20 -2.9127117202365591e+00 -4.0021932942639236e+00 4.1375029574097324e+00
|
||||
9 1.5618123600658955e+00 -5.8578897456975190e+00 1.3701369934457412e+00
|
||||
27 -1.5292288657572302e+00 7.3670372933400197e+00 -2.7248019284366976e+00
|
||||
28 6.4035005649493479e+00 -2.1779026033513014e+00 4.1727097093108574e+00
|
||||
29 -4.5201927345996555e+00 -5.1735150000565087e+00 -1.4886414114327997e+00
|
||||
16 4.6235900473074264e+02 -3.3129452068302044e+02 -1.1872104839749913e+03
|
||||
17 -4.5562419604336907e+02 3.2174933415042017e+02 1.1991777287808720e+03
|
||||
1 1.3731384283548081e+02 3.9920027811413058e+02 1.4671535235573168e+02
|
||||
5 -5.4637104265427694e-01 6.5601084479287308e-01 -6.8979874489125209e-02
|
||||
25 4.9746148340477232e+00 -5.2361546171101681e-01 3.9262151074199716e+00
|
||||
24 -1.0905446993217227e+00 6.8024491702255219e+00 -3.6841668240304775e+00
|
||||
26 -4.3769267564308079e+00 -6.4816120417538805e+00 -8.1534630212244097e-01
|
||||
run_vdwl: 102.179240281819
|
||||
run_coul: 221.72043369007
|
||||
run_stress: ! |2-
|
||||
3.9536844685406197e+02 4.7478735366545340e+02 2.6697778712793865e+02 -3.2473556197508509e+02 -9.3384529246395616e+01 1.1447113568800172e+02
|
||||
run_forces: ! |2
|
||||
8 -1.6165053869904651e+00 3.2404346873061620e+01 1.0398184151912643e+02
|
||||
10 3.9959095810012961e+01 -6.7059878243072802e+01 -8.8447802744729799e+01
|
||||
11 -1.0802302719514865e+00 1.1219894748386876e+00 -8.4425247683472560e-01
|
||||
12 2.0545804874003100e+01 1.6756506862182029e+01 -1.0147384903004356e+01
|
||||
13 -4.0343127361420671e-02 1.7788248239998272e-01 -2.9853580182052586e-01
|
||||
14 -1.3513519617740402e+00 4.4595903368860967e-01 -2.6265873012314578e-01
|
||||
21 1.4156879408475120e+00 3.1994561323777044e+00 -6.4435674872296671e+00
|
||||
22 4.7559002343686556e+00 1.1887791928870963e+00 5.7934241510228901e+00
|
||||
23 -6.5791517502191210e+00 -3.9974743969812185e+00 1.1725342766620361e+00
|
||||
2 -2.6293176067774748e-01 -1.8753559256825343e+00 -6.6074805412350757e-01
|
||||
3 -2.3593857200361191e+02 9.7836073260611272e+01 8.4490010947326468e+01
|
||||
4 -3.7637798569411851e-01 1.4515335713562016e-01 -2.8559897785164967e-01
|
||||
6 1.0933366022646435e+02 -9.6549048092587924e+01 -1.2841653624074331e+02
|
||||
7 4.9593739734408855e+00 -1.0982206357338827e+01 -4.0074341840062111e+01
|
||||
19 2.3514081526937800e+00 -7.5579018716331670e-01 5.6642935667801204e+00
|
||||
15 3.1593459896798887e-01 -2.5515203222240529e-01 -1.0797884994466638e+00
|
||||
18 -1.6194608116032930e-01 4.5570024281493904e+00 -7.3322988040856369e+00
|
||||
20 -2.8597532637256351e+00 -3.9142531545167625e+00 3.6472614532374061e+00
|
||||
9 1.3998364906824199e+00 -6.8051265118796431e+00 5.7998551394435172e-01
|
||||
27 -1.8378773182657191e+00 7.4880773687654925e+00 -2.6847264500512029e+00
|
||||
28 6.6966605937639985e+00 -2.2313693477537879e+00 4.2842101037191496e+00
|
||||
29 -4.4013595210884091e+00 -5.2116279982831486e+00 -1.6564229411980371e+00
|
||||
16 5.1256243181143134e+01 -6.6172008507524183e+01 1.2070943382988711e+01
|
||||
17 -1.7692905581269478e+01 1.6463320079069746e+01 3.6795635735036896e+01
|
||||
1 3.2379539694040083e+01 8.3517527420396235e+01 3.0446322003427230e+01
|
||||
5 -6.8204117043071300e-01 6.2446673118754414e-01 2.7379021833098716e-01
|
||||
25 5.3901862848597801e+00 -3.4508437671681635e-01 4.2395892090132064e+00
|
||||
24 -1.2476217506160352e+00 7.0412610417789230e+00 -3.7704986625434631e+00
|
||||
26 -4.6303631204520315e+00 -6.8134266068066900e+00 -1.0346794667680241e+00
|
||||
...
|
||||
|
|
@ -0,0 +1,83 @@
|
|||
---
|
||||
lammps_version: 5 May 2020
|
||||
date_generated: Fri May 15 19:08:06 202
|
||||
epsilon: 1.0e-14
|
||||
prerequisites: ! |
|
||||
atom full
|
||||
pair zero
|
||||
pre_commands: ! ""
|
||||
post_commands: ! ""
|
||||
input_file: in.fourmol
|
||||
pair_style: zero 8.0
|
||||
pair_coeff: ! |
|
||||
* *
|
||||
natoms: 29
|
||||
init_vdwl: 0
|
||||
init_coul: 0
|
||||
init_stress: ! |2-
|
||||
0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
init_forces: ! |2
|
||||
21 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
22 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
23 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
19 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
18 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
20 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
28 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
4 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
10 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
11 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
12 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
14 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
3 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
6 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
7 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
15 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
8 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
9 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
16 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
17 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
5 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
13 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
2 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
1 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
27 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
29 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
24 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
25 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
26 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
run_vdwl: 0
|
||||
run_coul: 0
|
||||
run_stress: ! |2-
|
||||
0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
run_forces: ! |2
|
||||
21 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
22 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
23 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
19 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
18 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
20 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
28 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
4 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
10 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
11 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
12 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
14 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
3 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
6 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
7 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
15 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
8 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
9 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
16 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
17 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
5 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
13 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
2 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
1 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
27 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
29 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
24 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
25 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
26 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
|
||||
...
|
||||
|
|
@ -0,0 +1,177 @@
|
|||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifndef YAML_READER_H
|
||||
#define YAML_READER_H
|
||||
|
||||
#include "yaml.h"
|
||||
|
||||
#include <cstdio>
|
||||
#include <map>
|
||||
#include <string>
|
||||
#include <iostream>
|
||||
|
||||
template<typename ConsumerClass> class YamlReader {
|
||||
private:
|
||||
enum StateValue {
|
||||
START,
|
||||
ACCEPT_KEY,
|
||||
ACCEPT_VALUE,
|
||||
STOP,
|
||||
ERROR,
|
||||
};
|
||||
|
||||
StateValue state;
|
||||
bool accepted;
|
||||
std::string key;
|
||||
std::string basename;
|
||||
|
||||
protected:
|
||||
typedef void (ConsumerClass::*EventConsumer)(const yaml_event_t & event);
|
||||
std::map<std::string, EventConsumer> consumers;
|
||||
|
||||
public:
|
||||
YamlReader() {}
|
||||
virtual ~YamlReader() {}
|
||||
|
||||
std::string get_basename() const { return basename; }
|
||||
|
||||
int parse_file(const std::string & infile) {
|
||||
basename = infile;
|
||||
std::size_t found = basename.rfind(".yaml");
|
||||
if (found > 0) basename = basename.substr(0,found);
|
||||
found = basename.find_last_of("/\\");
|
||||
if (found != std::string::npos) basename = basename.substr(found+1);
|
||||
|
||||
FILE *fp = fopen(infile.c_str(),"r");
|
||||
yaml_parser_t parser;
|
||||
yaml_event_t event;
|
||||
|
||||
if (!fp) {
|
||||
std::cerr << "Cannot open yaml file '" << infile
|
||||
<< "': " << strerror(errno) << std::endl;
|
||||
return 1;
|
||||
}
|
||||
yaml_parser_initialize(&parser);
|
||||
yaml_parser_set_input_file(&parser, fp);
|
||||
state = START;
|
||||
do {
|
||||
if (!yaml_parser_parse(&parser, &event)) {
|
||||
state = STOP;
|
||||
}
|
||||
|
||||
if (!consume_event(event)) {
|
||||
state = STOP;
|
||||
}
|
||||
|
||||
if (accepted) {
|
||||
if(!consume_key_value(key, event)) {
|
||||
std::cerr << "Ignoring unknown key/value pair: " << key
|
||||
<< " = " << event.data.scalar.value << std::endl;
|
||||
}
|
||||
}
|
||||
yaml_event_delete(&event);
|
||||
} while (state != STOP);
|
||||
|
||||
yaml_parser_delete(&parser);
|
||||
fclose(fp);
|
||||
return 0;
|
||||
}
|
||||
|
||||
protected:
|
||||
bool consume_key_value(const std::string & key, const yaml_event_t & event) {
|
||||
auto it = consumers.find(key);
|
||||
ConsumerClass *consumer = dynamic_cast<ConsumerClass*>(this);
|
||||
|
||||
if(consumer) {
|
||||
if(it != consumers.end()) {
|
||||
//std::cerr << "Loading: " << key << std::endl;
|
||||
(consumer->*(it->second))(event);
|
||||
return true;
|
||||
}
|
||||
std::cerr << "UNKNOWN" << std::endl;
|
||||
} else {
|
||||
std::cerr << "ConsumerClass is not valid" << std::endl;
|
||||
}
|
||||
return false;
|
||||
}
|
||||
|
||||
bool consume_event(yaml_event_t & event) {
|
||||
accepted = false;
|
||||
switch (state) {
|
||||
case START:
|
||||
switch (event.type) {
|
||||
case YAML_MAPPING_START_EVENT:
|
||||
state = ACCEPT_KEY;
|
||||
break;
|
||||
case YAML_SCALAR_EVENT:
|
||||
case YAML_SEQUENCE_START_EVENT:
|
||||
state = ERROR;
|
||||
break;
|
||||
case YAML_STREAM_END_EVENT:
|
||||
state = STOP;
|
||||
break;
|
||||
case YAML_STREAM_START_EVENT:
|
||||
case YAML_DOCUMENT_START_EVENT:
|
||||
case YAML_DOCUMENT_END_EVENT:
|
||||
// ignore
|
||||
break;
|
||||
default:
|
||||
std::cerr << "UNHANDLED YAML EVENT: " << event.type << std::endl;
|
||||
state = ERROR;
|
||||
break;
|
||||
}
|
||||
break;
|
||||
|
||||
case ACCEPT_KEY:
|
||||
switch (event.type) {
|
||||
case YAML_SCALAR_EVENT:
|
||||
key = (char *) event.data.scalar.value;
|
||||
state = ACCEPT_VALUE;
|
||||
break;
|
||||
case YAML_MAPPING_END_EVENT:
|
||||
state = STOP;
|
||||
break;
|
||||
default:
|
||||
std::cerr << "UNHANDLED YAML EVENT (key): " << event.type
|
||||
<< "\nVALUE: " << event.data.scalar.value
|
||||
<< std::endl;
|
||||
state = ERROR;
|
||||
break;
|
||||
}
|
||||
break;
|
||||
|
||||
case ACCEPT_VALUE:
|
||||
switch (event.type) {
|
||||
case YAML_SCALAR_EVENT:
|
||||
accepted = true;
|
||||
state = ACCEPT_KEY;
|
||||
break;
|
||||
default:
|
||||
std::cerr << "UNHANDLED YAML EVENT (value): " << event.type
|
||||
<< "\nVALUE: " << event.data.scalar.value
|
||||
<< std::endl;
|
||||
state = ERROR;
|
||||
break;
|
||||
}
|
||||
break;
|
||||
|
||||
case ERROR:
|
||||
case STOP:
|
||||
break;
|
||||
}
|
||||
return (state != ERROR);
|
||||
}
|
||||
};
|
||||
|
||||
#endif
|
||||
|
|
@ -0,0 +1,131 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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 "yaml_writer.h"
|
||||
#include "yaml.h"
|
||||
|
||||
#include <string>
|
||||
#include <cstdio>
|
||||
|
||||
YamlWriter::YamlWriter(const char * outfile) {
|
||||
yaml_emitter_initialize(&emitter);
|
||||
fp = fopen(outfile, "w");
|
||||
if (!fp) {
|
||||
perror(__FILE__);
|
||||
return;
|
||||
}
|
||||
|
||||
yaml_emitter_set_output_file(&emitter, fp);
|
||||
|
||||
yaml_stream_start_event_initialize(&event, YAML_UTF8_ENCODING);
|
||||
yaml_emitter_emit(&emitter, &event);
|
||||
yaml_document_start_event_initialize(&event, NULL, NULL, NULL, 0);
|
||||
yaml_emitter_emit(&emitter, &event);
|
||||
yaml_mapping_start_event_initialize(&event, NULL,
|
||||
(yaml_char_t *)YAML_MAP_TAG,
|
||||
1, YAML_ANY_MAPPING_STYLE);
|
||||
yaml_emitter_emit(&emitter, &event);
|
||||
}
|
||||
|
||||
YamlWriter::~YamlWriter() {
|
||||
yaml_mapping_end_event_initialize(&event);
|
||||
yaml_emitter_emit(&emitter, &event);
|
||||
yaml_document_end_event_initialize(&event, 0);
|
||||
yaml_emitter_emit(&emitter, &event);
|
||||
yaml_stream_end_event_initialize(&event);
|
||||
yaml_emitter_emit(&emitter, &event);
|
||||
yaml_emitter_delete(&emitter);
|
||||
fclose(fp);
|
||||
}
|
||||
|
||||
void YamlWriter::emit(const std::string &key, const double value) {
|
||||
yaml_scalar_event_initialize(&event, NULL,
|
||||
(yaml_char_t *)YAML_STR_TAG,
|
||||
(yaml_char_t *) key.c_str(),
|
||||
key.size(), 1, 0,
|
||||
YAML_PLAIN_SCALAR_STYLE);
|
||||
yaml_emitter_emit(&emitter, &event);
|
||||
char buf[256];
|
||||
snprintf(buf,256,"%.15g",value);
|
||||
yaml_scalar_event_initialize(&event, NULL,
|
||||
(yaml_char_t *)YAML_STR_TAG,
|
||||
(yaml_char_t *)buf,
|
||||
strlen(buf), 1, 0,
|
||||
YAML_PLAIN_SCALAR_STYLE);
|
||||
yaml_emitter_emit(&emitter, &event);
|
||||
}
|
||||
|
||||
void YamlWriter::emit(const std::string &key, const long value) {
|
||||
yaml_scalar_event_initialize(&event, NULL,
|
||||
(yaml_char_t *)YAML_STR_TAG,
|
||||
(yaml_char_t *) key.c_str(),
|
||||
key.size(), 1, 0,
|
||||
YAML_PLAIN_SCALAR_STYLE);
|
||||
yaml_emitter_emit(&emitter, &event);
|
||||
char buf[256];
|
||||
snprintf(buf,256,"%ld",value);
|
||||
yaml_scalar_event_initialize(&event, NULL,
|
||||
(yaml_char_t *)YAML_STR_TAG,
|
||||
(yaml_char_t *)buf,
|
||||
strlen(buf), 1, 0,
|
||||
YAML_PLAIN_SCALAR_STYLE);
|
||||
yaml_emitter_emit(&emitter, &event);
|
||||
}
|
||||
|
||||
void YamlWriter::emit(const std::string &key, const int value) {
|
||||
yaml_scalar_event_initialize(&event, NULL,
|
||||
(yaml_char_t *)YAML_STR_TAG,
|
||||
(yaml_char_t *) key.c_str(),
|
||||
key.size(), 1, 0,
|
||||
YAML_PLAIN_SCALAR_STYLE);
|
||||
yaml_emitter_emit(&emitter, &event);
|
||||
char buf[256];
|
||||
snprintf(buf,256,"%d",value);
|
||||
yaml_scalar_event_initialize(&event, NULL,
|
||||
(yaml_char_t *)YAML_STR_TAG,
|
||||
(yaml_char_t *)buf,
|
||||
strlen(buf), 1, 0,
|
||||
YAML_PLAIN_SCALAR_STYLE);
|
||||
yaml_emitter_emit(&emitter, &event);
|
||||
}
|
||||
|
||||
void YamlWriter::emit(const std::string &key, const std::string &value)
|
||||
{
|
||||
yaml_scalar_event_initialize(&event, NULL,
|
||||
(yaml_char_t *)YAML_STR_TAG,
|
||||
(yaml_char_t *) key.c_str(),
|
||||
key.size(), 1, 0,
|
||||
YAML_PLAIN_SCALAR_STYLE);
|
||||
yaml_emitter_emit(&emitter, &event);
|
||||
yaml_scalar_event_initialize(&event, NULL,
|
||||
(yaml_char_t *)YAML_STR_TAG,
|
||||
(yaml_char_t *)value.c_str(),
|
||||
value.size(), 1, 0,
|
||||
YAML_PLAIN_SCALAR_STYLE);
|
||||
yaml_emitter_emit(&emitter, &event);
|
||||
}
|
||||
|
||||
void YamlWriter::emit_block(const std::string &key, const std::string &value) {
|
||||
yaml_scalar_event_initialize(&event, NULL,
|
||||
(yaml_char_t *)YAML_STR_TAG,
|
||||
(yaml_char_t *) key.c_str(),
|
||||
key.size(), 1, 0,
|
||||
YAML_PLAIN_SCALAR_STYLE);
|
||||
yaml_emitter_emit(&emitter, &event);
|
||||
yaml_scalar_event_initialize(&event, NULL,
|
||||
(yaml_char_t *)YAML_STR_TAG,
|
||||
(yaml_char_t *)value.c_str(),
|
||||
value.size(), 1, 0,
|
||||
YAML_LITERAL_SCALAR_STYLE);
|
||||
yaml_emitter_emit(&emitter, &event);
|
||||
}
|
||||
|
|
@ -0,0 +1,43 @@
|
|||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifndef YAML_WRITER_H
|
||||
#define YAML_WRITER_H
|
||||
|
||||
#include "yaml.h"
|
||||
#include <cstdio>
|
||||
#include <string>
|
||||
|
||||
class YamlWriter {
|
||||
public:
|
||||
YamlWriter(const char * outfile);
|
||||
virtual ~YamlWriter();
|
||||
|
||||
// emitters
|
||||
void emit(const std::string &key, const double value);
|
||||
void emit(const std::string &key, const long value);
|
||||
void emit(const std::string &key, const int value);
|
||||
void emit(const std::string &key, const std::string &value);
|
||||
void emit_block(const std::string &key, const std::string &value);
|
||||
|
||||
private:
|
||||
FILE *fp;
|
||||
yaml_emitter_t emitter;
|
||||
yaml_event_t event;
|
||||
|
||||
private:
|
||||
YamlWriter() {};
|
||||
YamlWriter(const YamlWriter &) {};
|
||||
};
|
||||
|
||||
#endif
|
||||
Loading…
Reference in New Issue