forked from lijiext/lammps
Steve Plimpton
commit
aca8ce1f53
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@ -0,0 +1,21 @@
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|||
---
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||||
name: Generic Issue
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||||
about: For issues that do not fit any of the other categories
|
||||
title: "_Replace With a Descriptive Title_"
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||||
labels:
|
||||
assignees: ''
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||||
|
||||
---
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||||
|
||||
**Summary**
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||||
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||||
_Please provide a clear and concise description of what this issue report is about._
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||||
|
||||
**LAMMPS Version and Platform**
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||||
|
||||
_Please specify precisely which LAMMPS version this issue was detected with (the first line of the output) and what platform (operating system and its version, hardware) you are running on. If possible, test with the most recent LAMMPS patch version_
|
||||
|
||||
**Details**
|
||||
|
||||
_Please explain the issue in detail here_
|
||||
|
||||
|
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@ -0,0 +1,15 @@
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|||
---
|
||||
name: Request for Help
|
||||
about: "Don't post help requests here, email the lammps-users mailing list"
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||||
title: ""
|
||||
labels: invalid
|
||||
assignees: ''
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||||
|
||||
---
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||||
|
||||
Please **do not** post requests for help (e.g. with installing or using LAMMPS) here.
|
||||
Instead send an e-mail to the lammps-users mailing list.
|
||||
|
||||
This issue tracker is for tracking LAMMPS development related issues only.
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||||
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||||
Thanks for your cooperation.
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||||
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@ -4,22 +4,19 @@ _Briefly describe the new feature(s), enhancement(s), or bugfix(es) included in
|
|||
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||||
**Related Issues**
|
||||
|
||||
__If this addresses an open GitHub Issue, mention the issue number here. Use the phrases `fixes #221` or `closes #135`, when you want those issues to be automatically closed when the pull request is merged_
|
||||
_If this addresses an open GitHub issue for this project, please mention the issue number here, and describe the relation. Use the phrases `fixes #221` or `closes #135`, when you want an issue to be automatically closed when the pull request is merged_
|
||||
|
||||
**Author(s)**
|
||||
|
||||
_Please state name and affiliation of the author or authors that should be credited with the changes in this pull request. If this pull request adds new files to the distribution, please also provide a suitable "long-lived" e-mail address (e.g. from gmail, yahoo, outlook, etc.) for the *corresponding* author, i.e. the person the LAMMPS developers can contact directly with questions and requests related to maintenance and support of this code. now and in the future_
|
||||
_Please state name and affiliation of the author or authors that should be credited with the changes in this pull request. If this pull request adds new files to the distribution, please also provide a suitable "long-lived" e-mail address (ideally something that can outlive your institution's e-mail, in case you change jobs) for the *corresponding* author, i.e. the person the LAMMPS developers can contact directly with questions and requests related to maintenance and support of this contributed code._
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**Licensing**
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||||
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||||
By submitting this pull request, I agree, that my contribution will be included in LAMMPS and redistributed under the GNU General Public License version 2.
|
||||
|
||||
_Please complete the following statement by adding "yes" or "no":_
|
||||
My contribution may be re-licensed as LGPL (for use of LAMMPS as a library linked to proprietary software):
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||||
By submitting this pull request, I agree, that my contribution will be included in LAMMPS and redistributed under either the GNU General Public License version 2 (GPL v2) or the GNU Lesser General Public License version 2.1 (LGPL v2.1).
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|
||||
**Backward Compatibility**
|
||||
|
||||
_Please state whether any changes in the pull request break backward compatibility for inputs, and - if yes - explain what has been changed and why_
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||||
_Please state whether any changes in the pull request will break backward compatibility for inputs, and - if yes - explain what has been changed and why_
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||||
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**Implementation Notes**
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||||
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@ -27,7 +24,7 @@ _Provide any relevant details about how the changes are implemented, how correct
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|||
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**Post Submission Checklist**
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||||
|
||||
_Please check the fields below as they are completed **after** the pull request has been submitted_
|
||||
_Please check the fields below as they are completed **after** the pull request has been submitted. Delete lines that don't apply_
|
||||
|
||||
- [ ] The feature or features in this pull request is complete
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||||
- [ ] Licensing information is complete
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@ -11,6 +11,8 @@ get_filename_component(LAMMPS_LIB_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../lib
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get_filename_component(LAMMPS_LIB_BINARY_DIR ${CMAKE_BINARY_DIR}/lib ABSOLUTE)
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get_filename_component(LAMMPS_DOC_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../doc ABSOLUTE)
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find_package(Git)
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# by default, install into $HOME/.local (not /usr/local), so that no root access (and sudo!!) is needed
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if (CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
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set(CMAKE_INSTALL_PREFIX "$ENV{HOME}/.local" CACHE PATH "default install path" FORCE )
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@ -85,7 +87,7 @@ string(TOUPPER "${CMAKE_BUILD_TYPE}" BTYPE)
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# this is fast, so check for it all the time
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message(STATUS "Running check for auto-generated files from make-based build system")
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file(GLOB SRC_AUTOGEN_FILES ${LAMMPS_SOURCE_DIR}/style_*.h)
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list(APPEND SRC_AUTOGEN_FILES ${LAMMPS_SOURCE_DIR}/lmpinstalledpkgs.h)
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list(APPEND SRC_AUTOGEN_FILES ${LAMMPS_SOURCE_DIR}/lmpinstalledpkgs.h ${LAMMPS_SOURCE_DIR}/lmpgitversion.h)
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foreach(_SRC ${SRC_AUTOGEN_FILES})
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get_filename_component(FILENAME "${_SRC}" NAME)
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if(EXISTS ${LAMMPS_SOURCE_DIR}/${FILENAME})
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@ -178,7 +180,7 @@ set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE GRANULAR
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USER-MEAMC USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF
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USER-PHONON USER-PLUMED USER-PTM USER-QTB USER-REAXC USER-SCAFACOS
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USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK
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USER-QUIP USER-QMMM USER-YAFF)
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USER-QUIP USER-QMMM USER-YAFF USER-ADIOS)
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set(ACCEL_PACKAGES USER-OMP KOKKOS OPT USER-INTEL GPU)
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set(OTHER_PACKAGES CORESHELL QEQ)
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foreach(PKG ${DEFAULT_PACKAGES})
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@ -201,6 +203,17 @@ endif()
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include_directories(${LAMMPS_SOURCE_DIR})
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if(PKG_USER-ADIOS)
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# The search for ADIOS2 must come before MPI because
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# it includes its own MPI search with the latest FindMPI.cmake
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# script that defines the MPI::MPI_C target
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enable_language(C)
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find_package(ADIOS2 REQUIRED)
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list(APPEND LAMMPS_LINK_LIBS adios2::adios2)
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endif()
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# do MPI detection after language activation, if MPI for these language is required
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find_package(MPI QUIET)
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option(BUILD_MPI "Build MPI version" ${MPI_FOUND})
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@ -613,6 +626,7 @@ if(PKG_USER-NETCDF)
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add_definitions(-DLMP_HAS_NETCDF -DNC_64BIT_DATA=0x0020)
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endif()
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if(PKG_USER-SMD)
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option(DOWNLOAD_EIGEN3 "Download Eigen3 instead of using an already installed one)" OFF)
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if(DOWNLOAD_EIGEN3)
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@ -656,28 +670,34 @@ if(PKG_USER-VTK)
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endif()
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if(PKG_KIM)
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option(DOWNLOAD_KIM "Download KIM-API v1 from OpenKIM instead of using an already installed one)" OFF)
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option(DOWNLOAD_KIM "Download KIM-API v2 from OpenKIM instead of using an already installed one" OFF)
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if(DOWNLOAD_KIM)
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message(STATUS "KIM-API v1 download requested - we will build our own")
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message(STATUS "KIM-API v2 download requested - we will build our own")
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enable_language(C)
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enable_language(Fortran)
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include(ExternalProject)
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ExternalProject_Add(kim_build
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URL https://github.com/openkim/kim-api/archive/v1.9.5.tar.gz
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URL_MD5 9f66efc128da33039e30659f36fc6d00
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BUILD_IN_SOURCE 1
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CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR>
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URL https://s3.openkim.org/kim-api/kim-api-v2-2.0.1.txz
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URL_MD5 289c57f0c3bc2a549662283cac1c4ef1
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BINARY_DIR build
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CMAKE_ARGS -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
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-DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}
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-DCMAKE_Fortran_COMPILER=${CMAKE_Fortran_COMPILER}
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-DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>
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-DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
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)
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ExternalProject_get_property(kim_build INSTALL_DIR)
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set(KIM_INCLUDE_DIRS ${INSTALL_DIR}/include/kim-api-v1)
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set(KIM_LIBRARIES ${INSTALL_DIR}/lib/libkim-api-v1.so)
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set(KIM-API-V2_INCLUDE_DIRS ${INSTALL_DIR}/include/kim-api-v2)
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set(KIM-API-V2_LDFLAGS ${INSTALL_DIR}/${CMAKE_INSTALL_LIBDIR}/libkim-api-v2${CMAKE_SHARED_LIBRARY_SUFFIX})
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list(APPEND LAMMPS_DEPS kim_build)
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else()
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find_package(KIM)
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if(NOT KIM_FOUND)
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message(FATAL_ERROR "KIM-API v1 not found, help CMake to find it by setting KIM_LIBRARY and KIM_INCLUDE_DIR, or set DOWNLOAD_KIM=ON to download it")
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find_package(KIM-API-V2)
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if(NOT KIM-API-V2_FOUND)
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message(FATAL_ERROR "KIM-API v2 not found, help CMake to find it by setting PKG_CONFIG_PATH, or set DOWNLOAD_KIM=ON to download it")
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endif()
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endif()
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list(APPEND LAMMPS_LINK_LIBS ${KIM_LIBRARIES})
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include_directories(${KIM_INCLUDE_DIRS})
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list(APPEND LAMMPS_LINK_LIBS "${KIM-API-V2_LDFLAGS}")
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include_directories(${KIM-API-V2_INCLUDE_DIRS})
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endif()
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if(PKG_MESSAGE)
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@ -1308,6 +1328,40 @@ message(STATUS "Generating lmpinstalledpkgs.h...")
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file(WRITE "${LAMMPS_STYLE_HEADERS_DIR}/lmpinstalledpkgs.h.tmp" "${temp}" )
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execute_process(COMMAND ${CMAKE_COMMAND} -E copy_if_different "${LAMMPS_STYLE_HEADERS_DIR}/lmpinstalledpkgs.h.tmp" "${LAMMPS_STYLE_HEADERS_DIR}/lmpinstalledpkgs.h")
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######################################
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# Generate lmpgitversion.h
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######################################
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set(temp "#ifndef LMP_GIT_VERSION_H\n#define LMP_GIT_VERSION_H\n")
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set(temp_git_commit "(unknown)")
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set(temp_git_branch "(unknown)")
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set(temp_git_describe "(unknown)")
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set(temp_git_info "false")
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if(GIT_FOUND AND EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/../.git)
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set(temp_git_info "true")
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execute_process(COMMAND ${GIT_EXECUTABLE} -C ${CMAKE_CURRENT_SOURCE_DIR}/../.git rev-parse HEAD
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OUTPUT_VARIABLE temp_git_commit
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ERROR_QUIET
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OUTPUT_STRIP_TRAILING_WHITESPACE)
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execute_process(COMMAND ${GIT_EXECUTABLE} -C ${CMAKE_CURRENT_SOURCE_DIR}/../.git rev-parse --abbrev-ref HEAD
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OUTPUT_VARIABLE temp_git_branch
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ERROR_QUIET
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OUTPUT_STRIP_TRAILING_WHITESPACE)
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execute_process(COMMAND ${GIT_EXECUTABLE} -C ${CMAKE_CURRENT_SOURCE_DIR}/../.git describe --dirty=-modified
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OUTPUT_VARIABLE temp_git_describe
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ERROR_QUIET
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OUTPUT_STRIP_TRAILING_WHITESPACE)
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endif()
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set(temp "${temp}const bool LAMMPS_NS::LAMMPS::has_git_info = ${temp_git_info};\n")
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set(temp "${temp}const char LAMMPS_NS::LAMMPS::git_commit[] = \"${temp_git_commit}\";\n")
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set(temp "${temp}const char LAMMPS_NS::LAMMPS::git_branch[] = \"${temp_git_branch}\";\n")
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set(temp "${temp}const char LAMMPS_NS::LAMMPS::git_descriptor[] = \"${temp_git_describe}\";\n")
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set(temp "${temp}#endif\n\n")
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message(STATUS "Generating lmpgitversion.h...")
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file(WRITE "${LAMMPS_STYLE_HEADERS_DIR}/lmpgitversion.h.tmp" "${temp}" )
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execute_process(COMMAND ${CMAKE_COMMAND} -E copy_if_different "${LAMMPS_STYLE_HEADERS_DIR}/lmpgitversion.h.tmp" "${LAMMPS_STYLE_HEADERS_DIR}/lmpgitversion.h")
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###########################################
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# Actually add executable and lib to build
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############################################
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@ -1354,6 +1408,7 @@ if(BUILD_EXE)
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endif()
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endif()
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###############################################################################
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# Build documentation
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###############################################################################
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|
|
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|||
|
|
@ -0,0 +1,50 @@
|
|||
#
|
||||
# CDDL HEADER START
|
||||
#
|
||||
# The contents of this file are subject to the terms of the Common Development
|
||||
# and Distribution License Version 1.0 (the "License").
|
||||
#
|
||||
# You can obtain a copy of the license at
|
||||
# http://www.opensource.org/licenses/CDDL-1.0. See the License for the
|
||||
# specific language governing permissions and limitations under the License.
|
||||
#
|
||||
# When distributing Covered Code, include this CDDL HEADER in each file and
|
||||
# include the License file in a prominent location with the name LICENSE.CDDL.
|
||||
# If applicable, add the following below this CDDL HEADER, with the fields
|
||||
# enclosed by brackets "[]" replaced with your own identifying information:
|
||||
#
|
||||
# Portions Copyright (c) [yyyy] [name of copyright owner]. All rights reserved.
|
||||
#
|
||||
# CDDL HEADER END
|
||||
#
|
||||
|
||||
#
|
||||
# Copyright (c) 2013--2018, Regents of the University of Minnesota.
|
||||
# All rights reserved.
|
||||
#
|
||||
# Contributors:
|
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# Richard Berger
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# Christoph Junghans
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# Ryan S. Elliott
|
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#
|
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|
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# - Find KIM-API-V2
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#
|
||||
# sets standard pkg_check_modules variables plus:
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#
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# KIM-API-V2-CMAKE_C_COMPILER
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# KIM-API-V2-CMAKE_CXX_COMPILER
|
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# KIM-API-V2-CMAKE_Fortran_COMPILER
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#
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find_package(PkgConfig REQUIRED)
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include(FindPackageHandleStandardArgs)
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||||
|
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pkg_check_modules(KIM-API-V2 REQUIRED libkim-api-v2>=2.0)
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|
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pkg_get_variable(KIM-API-V2-CMAKE_C_COMPILER libkim-api-v2 CMAKE_C_COMPILER)
|
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pkg_get_variable(KIM-API-V2-CMAKE_CXX_COMPILER libkim-api-v2 CMAKE_CXX_COMPILER)
|
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pkg_get_variable(KIM-API-V2_CMAKE_Fortran_COMPILER libkim-api-v2 CMAKE_Fortran_COMPILER)
|
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|
||||
# handle the QUIETLY and REQUIRED arguments and set KIM-API-V2_FOUND to TRUE
|
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# if all listed variables are TRUE
|
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find_package_handle_standard_args(KIM-API-V2 REQUIRED_VARS KIM-API-V2_LIBRARIES)
|
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|
|
@ -1,22 +0,0 @@
|
|||
# - Find kim
|
||||
# Find the native KIM headers and libraries.
|
||||
#
|
||||
# KIM_INCLUDE_DIRS - where to find kim.h, etc.
|
||||
# KIM_LIBRARIES - List of libraries when using kim.
|
||||
# KIM_FOUND - True if kim found.
|
||||
#
|
||||
|
||||
find_path(KIM_INCLUDE_DIR KIM_API.h PATH_SUFFIXES kim-api-v1)
|
||||
|
||||
find_library(KIM_LIBRARY NAMES kim-api-v1)
|
||||
|
||||
set(KIM_LIBRARIES ${KIM_LIBRARY})
|
||||
set(KIM_INCLUDE_DIRS ${KIM_INCLUDE_DIR})
|
||||
|
||||
include(FindPackageHandleStandardArgs)
|
||||
# handle the QUIETLY and REQUIRED arguments and set KIM_FOUND to TRUE
|
||||
# if all listed variables are TRUE
|
||||
|
||||
find_package_handle_standard_args(KIM DEFAULT_MSG KIM_LIBRARY KIM_INCLUDE_DIR)
|
||||
|
||||
mark_as_advanced(KIM_INCLUDE_DIR KIM_LIBRARY )
|
||||
|
|
@ -1,3 +1,4 @@
|
|||
/old
|
||||
/html
|
||||
/latex
|
||||
/spelling
|
||||
|
|
|
|||
57
doc/Makefile
57
doc/Makefile
|
|
@ -39,7 +39,7 @@ help:
|
|||
@echo "Please use \`make <target>' where <target> is one of"
|
||||
@echo " html create HTML doc pages in html dir"
|
||||
@echo " pdf create Developer.pdf and Manual.pdf in this dir"
|
||||
@echo " old create old-style HTML doc pages in old dir"
|
||||
@echo " old create old-style HTML doc pages and Manual.pdf in old dir"
|
||||
@echo " fetch fetch HTML and PDF files from LAMMPS web site"
|
||||
@echo " epub create ePUB format manual for e-book readers"
|
||||
@echo " mobi convert ePUB to MOBI format manual for e-book readers (e.g. Kindle)"
|
||||
|
|
@ -56,7 +56,7 @@ clean-all: clean
|
|||
rm -rf $(BUILDDIR)/* utils/txt2html/txt2html.exe
|
||||
|
||||
clean:
|
||||
rm -rf $(RSTDIR) html old epub
|
||||
rm -rf $(RSTDIR) html old epub latex
|
||||
rm -rf spelling
|
||||
|
||||
clean-spelling:
|
||||
|
|
@ -115,21 +115,44 @@ mobi: epub
|
|||
@ebook-convert LAMMPS.epub LAMMPS.mobi
|
||||
@echo "Conversion finished. The MOBI manual file is created."
|
||||
|
||||
pdf: utils/txt2html/txt2html.exe
|
||||
pdf: $(OBJECTS) $(ANCHORCHECK)
|
||||
@(\
|
||||
. $(VENV)/bin/activate ;\
|
||||
cp -r src/* $(RSTDIR)/ ;\
|
||||
sphinx-build $(SPHINXEXTRA) -b latex -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) latex ;\
|
||||
echo "############################################" ;\
|
||||
doc_anchor_check src/*.txt ;\
|
||||
echo "############################################" ;\
|
||||
deactivate ;\
|
||||
)
|
||||
@cd latex && \
|
||||
sed 's/latexmk -pdf -dvi- -ps-/pdflatex/g' Makefile > temp && \
|
||||
mv temp Makefile && \
|
||||
sed 's/\\begin{equation}//g' LAMMPS.tex > tmp.tex && \
|
||||
mv tmp.tex LAMMPS.tex && \
|
||||
sed 's/\\end{equation}//g' LAMMPS.tex > tmp.tex && \
|
||||
mv tmp.tex LAMMPS.tex && \
|
||||
make && \
|
||||
make && \
|
||||
mv LAMMPS.pdf ../Manual.pdf && \
|
||||
cd ../;
|
||||
@(\
|
||||
set -e; \
|
||||
cd src/Developer; \
|
||||
pdflatex developer; \
|
||||
pdflatex developer; \
|
||||
mv developer.pdf ../../Developer.pdf; \
|
||||
cd ..; \
|
||||
../utils/txt2html/txt2html.exe -b *.txt; \
|
||||
htmldoc --batch lammps.book; \
|
||||
for s in `echo *.txt | sed -e 's/ \(pairs\|bonds\|angles\|dihedrals\|impropers\|commands_list\|fixes\|computes\).txt/ /g' | sed -e 's,\.txt,\.html,g'` ; \
|
||||
do grep -q ^$$s lammps.book || \
|
||||
echo WARNING: doc file $$s missing in src/lammps.book; done; \
|
||||
rm *.html; \
|
||||
cd ../../; \
|
||||
)
|
||||
@rm -rf latex/_sources
|
||||
@rm -rf latex/PDF
|
||||
@rm -rf latex/USER
|
||||
@cp -r src/PDF latex/PDF
|
||||
@cp -r src/USER latex/USER
|
||||
@rm -rf latex/PDF/.[sg]*
|
||||
@rm -rf latex/USER/.[sg]*
|
||||
@rm -rf latex/USER/*/.[sg]*
|
||||
@rm -rf latex/USER/*/*.[sg]*
|
||||
@echo "Build finished. Manual.pdf and Developer.pdf are in this directory."
|
||||
|
||||
old: utils/txt2html/txt2html.exe
|
||||
@rm -rf old
|
||||
|
|
@ -139,6 +162,18 @@ old: utils/txt2html/txt2html.exe
|
|||
cp Eqs/*.jpg ../old/Eqs; \
|
||||
cp JPG/* ../old/JPG; \
|
||||
cp PDF/* ../old/PDF;
|
||||
@( set -e;\
|
||||
cd src/Developer; \
|
||||
pdflatex developer; \
|
||||
pdflatex developer; \
|
||||
mv developer.pdf ../../old/Developer.pdf; \
|
||||
cd ../../old; \
|
||||
for s in `echo ../src/*.txt | sed -e 's,\.\./src/,,g' -e 's/ \(pairs\|bonds\|angles\|dihedrals\|impropers\|commands_list\|fixes\|computes\).txt/ /g' | sed -e 's,\.txt,\.html,g'` ; \
|
||||
do grep -q ^$$s ../src/lammps.book || \
|
||||
echo WARNING: doc file $$s missing in src/lammps.book; done; \
|
||||
htmldoc --batch ../src/lammps.book; \
|
||||
)
|
||||
|
||||
|
||||
fetch:
|
||||
@rm -rf html_www Manual_www.pdf Developer_www.pdf
|
||||
|
|
|
|||
|
|
@ -37,6 +37,7 @@ This is the list of packages that may require additional steps.
|
|||
"POEMS"_#poems,
|
||||
"PYTHON"_#python,
|
||||
"VORONOI"_#voronoi,
|
||||
"USER-ADIOS"_#user-adios,
|
||||
"USER-ATC"_#user-atc,
|
||||
"USER-AWPMD"_#user-awpmd,
|
||||
"USER-COLVARS"_#user-colvars,
|
||||
|
|
@ -180,27 +181,19 @@ library with all its models, may take around 30 min to build. Of
|
|||
course you only need to do that once.
|
||||
|
||||
See the list of KIM model drivers here:
|
||||
https://openkim.org/kim-items/model-drivers/alphabetical
|
||||
https://openkim.org/browse/model-drivers/alphabetical
|
||||
|
||||
See the list of all KIM models here:
|
||||
https://openkim.org/kim-items/models/by-model-drivers
|
||||
|
||||
See the list of example KIM models included by default here:
|
||||
https://openkim.org/kim-api on the "What is in the KIM API source
|
||||
package?" page.
|
||||
https://openkim.org/browse/models/by-model-drivers
|
||||
|
||||
[CMake build]:
|
||||
|
||||
-D DOWNLOAD_KIM=value # download OpenKIM API v1 for build, value = no (default) or yes
|
||||
-D KIM_LIBRARY=path # KIM library file (only needed if a custom location)
|
||||
-D KIM_INCLUDE_DIR=path # KIM include directory (only needed if a custom location) :pre
|
||||
-D DOWNLOAD_KIM=value # download OpenKIM API v2 for build, value = no (default) or yes :pre
|
||||
|
||||
If DOWNLOAD_KIM is set, the KIM library will be downloaded and built
|
||||
inside the CMake build directory. If the KIM library is already on
|
||||
your system (in a location CMake cannot find it), KIM_LIBRARY is the
|
||||
filename (plus path) of the KIM library file, not the directory the
|
||||
library file is in. KIM_INCLUDE_DIR is the directory the KIM include
|
||||
file is in.
|
||||
your system (in a location CMake cannot find it), set the PKG_CONFIG_PATH
|
||||
environment variable so that libkim-api-v2 can be found.
|
||||
|
||||
[Traditional make]:
|
||||
|
||||
|
|
@ -214,8 +207,8 @@ make lib-kim args="-b " # (re-)install KIM API lib with only example models
|
|||
make lib-kim args="-b -a Glue_Ercolessi_Adams_Al__MO_324507536345_001" # ditto plus one model
|
||||
make lib-kim args="-b -a everything" # install KIM API lib with all models
|
||||
make lib-kim args="-n -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # add one model or model driver
|
||||
make lib-kim args="-p /usr/local/kim-api" # use an existing KIM API installation at the provided location
|
||||
make lib-kim args="-p /usr/local/kim-api -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # ditto but add one model or driver :pre
|
||||
make lib-kim args="-p /usr/local" # use an existing KIM API installation at the provided location
|
||||
make lib-kim args="-p /usr/local -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # ditto but add one model or driver :pre
|
||||
|
||||
:line
|
||||
|
||||
|
|
@ -576,6 +569,32 @@ the lib/voronoi/Makefile.lammps file.
|
|||
|
||||
:line
|
||||
|
||||
USER-ADIOS package :h4,link(user-adios)
|
||||
|
||||
The USER-ADIOS package requires the "ADIOS I/O library"_https://github.com/ornladios/ADIOS2,
|
||||
version 2.3.1 or newer. Make sure that you have ADIOS built either with or
|
||||
without MPI to match if you build LAMMPS with or without MPI.
|
||||
ADIOS compilation settings for LAMMPS are automatically detected, if the PATH
|
||||
and LD_LIBRARY_PATH environment variables have been updated for the local ADIOS
|
||||
installation and the instructions below are followed for the respective build systems.
|
||||
|
||||
[CMake build]:
|
||||
|
||||
-D ADIOS2_DIR=path # path is where ADIOS 2.x is installed
|
||||
-D PKG_USER-ADIOS=yes :pre
|
||||
|
||||
[Traditional make]:
|
||||
|
||||
Turn on the USER-ADIOS package before building LAMMPS. If the ADIOS 2.x software is installed in PATH, there is nothing else to do:
|
||||
|
||||
make yes-user-adios :pre
|
||||
|
||||
otherwise, set ADIOS2_DIR environment variable when turning on the package:
|
||||
|
||||
ADIOS2_DIR=path make yes-user-adios # path is where ADIOS 2.x is installed :pre
|
||||
|
||||
:line
|
||||
|
||||
USER-ATC package :h4,link(user-atc)
|
||||
|
||||
The USER-ATC package requires the MANYBODY package also be installed.
|
||||
|
|
|
|||
|
|
@ -48,6 +48,7 @@ packages:
|
|||
"POEMS"_Build_extras.html#poems,
|
||||
"PYTHON"_Build_extras.html#python,
|
||||
"VORONOI"_Build_extras.html#voronoi,
|
||||
"USER-ADIOS"_Build_extras.html#user-adios,
|
||||
"USER-ATC"_Build_extras.html#user-atc,
|
||||
"USER-AWPMD"_Build_extras.html#user-awpmd,
|
||||
"USER-COLVARS"_Build_extras.html#user-colvars,
|
||||
|
|
|
|||
|
|
@ -48,12 +48,14 @@ An alphabetic list of all general LAMMPS commands.
|
|||
"dimension"_dimension.html,
|
||||
"displace_atoms"_displace_atoms.html,
|
||||
"dump"_dump.html,
|
||||
"dump adios"_dump_adios.html,
|
||||
"dump image"_dump_image.html,
|
||||
"dump_modify"_dump_modify.html,
|
||||
"dump movie"_dump_image.html,
|
||||
"dump netcdf"_dump_netcdf.html,
|
||||
"dump netcdf/mpiio"_dump_netcdf.html,
|
||||
"dump vtk"_dump_vtk.html,
|
||||
"dynamical_matrix"_dynamical_matrix.html,
|
||||
"echo"_echo.html,
|
||||
"fix"_fix.html,
|
||||
"fix_modify"_fix_modify.html,
|
||||
|
|
|
|||
|
|
@ -6988,12 +6988,6 @@ The atom style defined does not have this attribute. :dd
|
|||
|
||||
The atom style defined does not have these attributes. :dd
|
||||
|
||||
{KIM neighbor iterator exceeded range} :dt
|
||||
|
||||
This should not happen. It likely indicates a bug
|
||||
in the KIM implementation of the interatomic potential
|
||||
where it is requesting neighbors incorrectly. :dd
|
||||
|
||||
{KOKKOS package does not yet support comm_style tiled} :dt
|
||||
|
||||
Self-explanatory. :dd
|
||||
|
|
@ -10185,10 +10179,6 @@ valid. :dd
|
|||
|
||||
Self-explanatory. :dd
|
||||
|
||||
{Unrecognized virial argument in pair_style command} :dt
|
||||
|
||||
Only two options are supported: LAMMPSvirial and KIMvirial :dd
|
||||
|
||||
{Unsupported mixing rule in kspace_style ewald/disp} :dt
|
||||
|
||||
Only geometric mixing is supported. :dd
|
||||
|
|
|
|||
|
|
@ -178,12 +178,6 @@ When using fixes like box/relax, the potential energy used by the minimizer
|
|||
is augmented by an additional energy provided by the fix. Thus the printed
|
||||
converged energy may be different from the total potential energy. :dd
|
||||
|
||||
{Energy tally does not account for 'zero yes'} :dt
|
||||
|
||||
The energy removed by using the 'zero yes' flag is not accounted
|
||||
for in the energy tally and thus energy conservation cannot be
|
||||
monitored in this case. :dd
|
||||
|
||||
{Estimated error in splitting of dispersion coeffs is %g} :dt
|
||||
|
||||
Error is greater than 0.0001 percent. :dd
|
||||
|
|
|
|||
Binary file not shown.
|
Before Width: | Height: | Size: 12 KiB After Width: | Height: | Size: 38 KiB |
Binary file not shown.
|
Before Width: | Height: | Size: 12 KiB After Width: | Height: | Size: 35 KiB |
Binary file not shown.
|
Before Width: | Height: | Size: 12 KiB After Width: | Height: | Size: 37 KiB |
|
|
@ -1,7 +1,7 @@
|
|||
<!-- HTML_ONLY -->
|
||||
<HEAD>
|
||||
<TITLE>LAMMPS Users Manual</TITLE>
|
||||
<META NAME="docnumber" CONTENT="8 Feb 2019 version">
|
||||
<META NAME="docnumber" CONTENT="28 Feb 2019 version">
|
||||
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
|
||||
<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
|
||||
</HEAD>
|
||||
|
|
@ -21,7 +21,7 @@
|
|||
:line
|
||||
|
||||
LAMMPS Documentation :c,h1
|
||||
8 Feb 2019 version :c,h2
|
||||
28 Feb 2019 version :c,h2
|
||||
|
||||
"What is a LAMMPS version?"_Manual_version.html
|
||||
|
||||
|
|
|
|||
|
|
@ -63,6 +63,7 @@ as contained in the file name.
|
|||
"SRD"_#PKG-SRD,
|
||||
"VORONOI"_#PKG-VORONOI :tb(c=6,ea=c)
|
||||
|
||||
"USER-ADIOS"_#PKG-USER-ADIOS,
|
||||
"USER-ATC"_#PKG-USER-ATC,
|
||||
"USER-AWPMD"_#PKG-USER-AWPMD,
|
||||
"USER-BOCS"_#PKG-USER-BOCS,
|
||||
|
|
@ -346,12 +347,11 @@ system.
|
|||
|
||||
Information about the KIM project can be found at its website:
|
||||
https://openkim.org. The KIM project is led by Ellad Tadmor and Ryan
|
||||
Elliott (U Minnesota) and James Sethna (Cornell U).
|
||||
Elliott (U Minnesota).
|
||||
|
||||
[Authors:] Ryan Elliott (U Minnesota) is the main developer for the KIM
|
||||
API which the "pair_style kim"_pair_kim.html command uses. He
|
||||
developed the pair style in collaboration with Valeriu Smirichinski (U
|
||||
Minnesota).
|
||||
developed the pair style.
|
||||
|
||||
[Install:]
|
||||
|
||||
|
|
@ -975,6 +975,31 @@ examples/voronoi :ul
|
|||
|
||||
:line
|
||||
|
||||
USER-ADIOS package :link(PKG-USER-ADIOS),h4
|
||||
|
||||
[Contents:]
|
||||
|
||||
ADIOS is a high-performance I/O library. This package implements the
|
||||
dump "atom/adios" and dump "custom/adios" commands to write data using
|
||||
the ADIOS library.
|
||||
|
||||
[Authors:] Norbert Podhorszki (ORNL) from the ADIOS developer team.
|
||||
|
||||
[Install:]
|
||||
|
||||
This package has "specific installation
|
||||
instructions"_Build_extras.html#user-adios on the "Build
|
||||
extras"_Build_extras.html doc page.
|
||||
|
||||
[Supporting info:]
|
||||
|
||||
src/USER-ADIOS: filenames -> commands
|
||||
src/USER-ADIOS/README
|
||||
examples/USER/adios
|
||||
https://github.com/ornladios/ADIOS2 :ul
|
||||
|
||||
:line
|
||||
|
||||
USER-ATC package :link(PKG-USER-ATC),h4
|
||||
|
||||
[Contents:]
|
||||
|
|
@ -1700,14 +1725,19 @@ USER-PHONON package :link(PKG-USER-PHONON),h4
|
|||
A "fix phonon"_fix_phonon.html command that calculates dynamical
|
||||
matrices, which can then be used to compute phonon dispersion
|
||||
relations, directly from molecular dynamics simulations.
|
||||
And a "dynamical_matrix" command to compute the dynamical matrix
|
||||
from finite differences.
|
||||
|
||||
[Authors:] Ling-Ti Kong (Shanghai Jiao Tong University) for "fix phonon"
|
||||
and Charlie Sievers (UC Davis) for "dynamical_matrix"
|
||||
|
||||
[Author:] Ling-Ti Kong (Shanghai Jiao Tong University).
|
||||
|
||||
[Supporting info:]
|
||||
|
||||
src/USER-PHONON: filenames -> commands
|
||||
src/USER-PHONON/README
|
||||
"fix phonon"_fix_phonon.html
|
||||
"dynamical_matrix"_dynamical_matrix.html
|
||||
examples/USER/phonon :ul
|
||||
|
||||
:line
|
||||
|
|
@ -2102,5 +2132,3 @@ src/USER-YAFF/README
|
|||
"pair_style mm3/switch3/coulgauss/long"_pair_mm3_switch3_coulgauss.html
|
||||
"pair_style lj/switch3/coulgauss/long"_pair_lj_switch3_coulgauss.html
|
||||
examples/USER/yaff :ul
|
||||
|
||||
|
||||
|
|
|
|||
|
|
@ -38,6 +38,7 @@ int = internal library: provided with LAMMPS, but you may need to build it
|
|||
ext = external library: you will need to download and install it on your machine :ul
|
||||
|
||||
Package, Description, Doc page, Example, Library
|
||||
"USER-ADIOS"_Packages_details.html#PKG-USER-ADIOS, dump output via ADIOS, "dump adios"_dump_adios.html, USER/adios, ext
|
||||
"USER-ATC"_Packages_details.html#PKG-USER-ATC, Atom-to-Continuum coupling, "fix atc"_fix_atc.html, USER/atc, int
|
||||
"USER-AWPMD"_Packages_details.html#PKG-USER-AWPMD, wave packet MD, "pair_style awpmd/cut"_pair_awpmd.html, USER/awpmd, int
|
||||
"USER-BOCS"_Packages_details.html#PKG-USER-BOCS, BOCS bottom up coarse graining, "fix bocs"_fix_bocs.html, USER/bocs, no
|
||||
|
|
|
|||
|
|
@ -32,6 +32,7 @@ Commands :h1
|
|||
dimension
|
||||
displace_atoms
|
||||
dump
|
||||
dump_adios
|
||||
dump_cfg_uef
|
||||
dump_h5md
|
||||
dump_image
|
||||
|
|
@ -39,6 +40,7 @@ Commands :h1
|
|||
dump_molfile
|
||||
dump_netcdf
|
||||
dump_vtk
|
||||
dynamical_matrix
|
||||
echo
|
||||
fix
|
||||
fix_modify
|
||||
|
|
|
|||
|
|
@ -137,11 +137,12 @@ Not all pair styles can be evaluated in a pairwise mode as required by
|
|||
this compute. For example, 3-body and other many-body potentials,
|
||||
such as "Tersoff"_pair_tersoff.html and
|
||||
"Stillinger-Weber"_pair_sw.html cannot be used. "EAM"_pair_eam.html
|
||||
potentials only include the pair potential portion of the EAM
|
||||
interaction when used by this compute, not the embedding term.
|
||||
potentials will re-use previously computed embedding term contributions,
|
||||
so the computed pairwise forces and energies are based on the whole
|
||||
system and not valid if particles have been moved since.
|
||||
|
||||
Not all Kspace styles support calculation of group/group interactions.
|
||||
The {ewald} and {pppm} styles do.
|
||||
Not all "Kspace styles"_kspace_style.html support the calculation of
|
||||
group/group interactions. The regular {ewald} and {pppm} styles do.
|
||||
|
||||
[Related commands:] none
|
||||
|
||||
|
|
|
|||
|
|
@ -13,6 +13,7 @@ dump command :h3
|
|||
"dump netcdf"_dump_netcdf.html command :h3
|
||||
"dump image"_dump_image.html command :h3
|
||||
"dump movie"_dump_image.html command :h3
|
||||
"dump adios"_dump_adios.html command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
|
|
@ -27,10 +28,12 @@ args = list of arguments for a particular style :l
|
|||
{atom} args = none
|
||||
{atom/gz} args = none
|
||||
{atom/mpiio} args = none
|
||||
{atom/adios} args = none, discussed on "dump adios"_dump_adios.html doc page
|
||||
{cfg} args = same as {custom} args, see below
|
||||
{cfg/gz} args = same as {custom} args, see below
|
||||
{cfg/mpiio} args = same as {custom} args, see below
|
||||
{custom}, {custom/gz}, {custom/mpiio} args = see below
|
||||
{custom/adios} args = same as {custom} args, discussed on "dump adios"_dump_adios.html doc page
|
||||
{dcd} args = none
|
||||
{h5md} args = discussed on "dump h5md"_dump_h5md.html doc page
|
||||
{image} args = discussed on "dump image"_dump_image.html doc page
|
||||
|
|
@ -653,7 +656,7 @@ package"_Build_package.html doc page for more info.
|
|||
|
||||
[Related commands:]
|
||||
|
||||
"dump h5md"_dump_h5md.html, "dump image"_dump_image.html,
|
||||
"dump adios"_dump_adios.html "dump h5md"_dump_h5md.html, "dump image"_dump_image.html,
|
||||
"dump molfile"_dump_molfile.html, "dump_modify"_dump_modify.html,
|
||||
"undump"_undump.html
|
||||
|
||||
|
|
|
|||
|
|
@ -0,0 +1,73 @@
|
|||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
dump atoms/adios command :h3
|
||||
dump custom/adios command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
dump ID group-ID atoms/adios N file.bp :pre
|
||||
dump ID group-ID custom/adios N file.bp args :pre
|
||||
|
||||
ID = user-assigned name for the dump :ulb,l
|
||||
group-ID = ID of the group of atoms to be imaged :l
|
||||
adios = style of dump command (other styles {atom} or {cfg} or {dcd} or {xtc} or {xyz} or {local} or {custom} are discussed on the "dump"_dump.html doc page) :l
|
||||
N = dump every this many timesteps :l
|
||||
file.bp = name of file/stream to write to :l
|
||||
args = same options as in "{dump custom}"_dump.html command :l
|
||||
:ule
|
||||
|
||||
|
||||
[Examples:]
|
||||
|
||||
dump adios1 all atom/adios 100 atoms.bp
|
||||
dump 4a all custom/adios 100 dump_adios.bp id v_p x y z
|
||||
dump 2 subgroup custom/adios 100 dump_adios.bp mass type xs ys zs vx vy vz :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Dump a snapshot of atom coordinates every N timesteps in the
|
||||
"ADIOS"_adios based "BP" file format, or using different I/O solutions in ADIOS,
|
||||
to a stream that can be read on-line by another program.
|
||||
ADIOS-BP files are binary, portable and self-describing.
|
||||
|
||||
:link(adios,https://github.com/ornladios/ADIOS2)
|
||||
|
||||
|
||||
[Use from write_dump:]
|
||||
|
||||
It is possible to use these dump styles with the
|
||||
"write_dump"_write_dump.html command. In this case, the sub-intervals
|
||||
must not be set at all. The write_dump command can be used to
|
||||
create a new file at each individual dump.
|
||||
|
||||
dump 4 all atom/adios 100 dump.bp
|
||||
write_dump all atom/adios singledump.bp :pre
|
||||
|
||||
:line
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
The number of atoms per snapshot CAN change with the adios style.
|
||||
When using the ADIOS tool 'bpls' to list the content of a .bp file,
|
||||
bpls will print {__} for the size of the output table indicating that
|
||||
its size is changing every step.
|
||||
|
||||
The {atom/adios} and {custom/adios} dump styles are part of the USER-ADIOS
|
||||
package. They are only enabled if LAMMPS was built with that package.
|
||||
See the "Build package"_Build_package.html doc page for more info.
|
||||
|
||||
|
||||
:line
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"dump"_dump.html, "dump_modify"_dump_modify.html, "undump"_undump.html
|
||||
|
||||
:line
|
||||
|
||||
|
|
@ -0,0 +1,52 @@
|
|||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
dynamical_matrix command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
dynamical_matrix group-ID style gamma args keyword value ... :pre
|
||||
|
||||
group-ID = ID of group of atoms to displace :ulb,l
|
||||
style = {regular} or {eskm} :l
|
||||
gamma = finite different displacement length (distance units) :l
|
||||
one or more keyword/arg pairs may be appended :l
|
||||
keyword = {file} or {binary}
|
||||
{file} name = name of output file for the dynamical matrix
|
||||
{binary} arg = {yes} or {no} or {gzip} :pre
|
||||
:ule
|
||||
|
||||
[Examples:]
|
||||
|
||||
dynamical_matrix 1 regular 0.000001
|
||||
dynamical_matrix 1 eskm 0.000001
|
||||
dynamical_matrix 3 regular 0.00004 file dynmat.dat
|
||||
dynamical_matrix 5 eskm 0.00000001 file dynamical.dat binary yes :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Calculate the dynamical matrix of the selected group.
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
The command collects the entire dynamical matrix a single MPI rank,
|
||||
so the memory requirements can be very significant for large systems.
|
||||
|
||||
This command assumes a periodic system.
|
||||
|
||||
This command is part of the USER-PHONON package. It is only enabled if
|
||||
LAMMPS was built with that package. See the "Build
|
||||
package"_Build_package.html doc page for more info.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"fix phonon"_fix_phonon.html
|
||||
|
||||
[Default:]
|
||||
|
||||
The default settings are file = "dynmat.dyn", binary = no
|
||||
|
|
@ -158,12 +158,6 @@ the pair_*.cpp file associated with the potential.
|
|||
|
||||
Some parameters are global settings for the pair style, e.g. the
|
||||
viscosity setting "mu" for "pair_style lubricate"_pair_lubricate.html.
|
||||
For "pair_kim"_pair_kim.html, all free parameters supported by the
|
||||
KIM Model are available (e.g., PARAM_FREE_sigmas provided by the
|
||||
LennardJones612_Universal__MO_826355984548_001 Model). If the free
|
||||
parameter corresponds to an array, then the particular array element
|
||||
to be adapted must be specified (e.g., "PARAM_FREE_sigmas:10", to
|
||||
adapt the tenth entry of the sigmas array).
|
||||
Other parameters apply to atom type pairs within the pair style,
|
||||
e.g. the prefactor "a" for "pair_style soft"_pair_soft.html.
|
||||
|
||||
|
|
|
|||
|
|
@ -217,10 +217,6 @@ the particles. As described below, this energy can then be printed
|
|||
out or added to the potential energy of the system to monitor energy
|
||||
conservation.
|
||||
|
||||
NOTE: this accumulated energy does NOT include kinetic energy removed
|
||||
by the {zero} flag. LAMMPS will print a warning when both options are
|
||||
active.
|
||||
|
||||
The keyword {zero} can be used to eliminate drift due to the
|
||||
thermostat. Because the random forces on different atoms are
|
||||
independent, they do not sum exactly to zero. As a result, this fix
|
||||
|
|
|
|||
|
|
@ -179,7 +179,8 @@ settings"_Build_settings.html doc page for details.
|
|||
|
||||
[Related commands:]
|
||||
|
||||
"compute msd"_compute_msd.html
|
||||
"compute msd"_compute_msd.html,
|
||||
"dynamical_matrix"_dynamical_matrix.html
|
||||
|
||||
[Default:]
|
||||
|
||||
|
|
|
|||
|
|
@ -1,5 +1,5 @@
|
|||
#HTMLDOC 1.8.28
|
||||
-t pdf14 -f "../Manual.pdf" --book --toclevels 4 --no-numbered --toctitle "Table of Contents" --title --textcolor #000000 --linkcolor #0000ff --linkstyle plain --bodycolor #ffffff --size Universal --left 1.00in --right 0.50in --top 0.50in --bottom 0.50in --header .t. --header1 ... --footer ..1 --nup 1 --tocheader .t. --tocfooter ..i --portrait --color --no-pscommands --no-xrxcomments --compression=9 --jpeg=0 --fontsize 11.0 --fontspacing 1.2 --headingfont Sans --bodyfont Serif --headfootsize 11.0 --headfootfont Sans-Bold --charset iso-8859-15 --links --embedfonts --pagemode document --pagelayout single --firstpage c1 --pageeffect none --pageduration 10 --effectduration 1.0 --no-encryption --permissions all --owner-password "" --user-password "" --browserwidth 680 --no-strict --no-overflow
|
||||
-t pdf14 -f "Manual.pdf" --book --toclevels 4 --no-numbered --toctitle "Table of Contents" --title --textcolor #000000 --linkcolor #0000ff --linkstyle plain --bodycolor #ffffff --size Universal --left 1.00in --right 0.50in --top 0.50in --bottom 0.50in --header .t. --header1 ... --footer ..1 --nup 1 --tocheader .t. --tocfooter ..i --portrait --color --no-pscommands --no-xrxcomments --compression=9 --jpeg=0 --fontsize 11.0 --fontspacing 1.2 --headingfont Sans --bodyfont Serif --headfootsize 11.0 --headfootfont Sans-Bold --charset iso-8859-15 --links --embedfonts --pagemode document --pagelayout single --firstpage c1 --pageeffect none --pageduration 10 --effectduration 1.0 --no-encryption --permissions all --owner-password "" --user-password "" --browserwidth 680 --no-strict --no-overflow
|
||||
Manual.html
|
||||
Intro.html
|
||||
Intro_overview.html
|
||||
|
|
@ -150,6 +150,7 @@ dielectric.html
|
|||
dimension.html
|
||||
displace_atoms.html
|
||||
dump.html
|
||||
dump_adios.html
|
||||
dump_h5md.html
|
||||
dump_image.html
|
||||
dump_modify.html
|
||||
|
|
@ -157,6 +158,7 @@ dump_molfile.html
|
|||
dump_netcdf.html
|
||||
dump_vtk.html
|
||||
dump_cfg_uef.html
|
||||
dynamical_matrix.html
|
||||
echo.html
|
||||
group.html
|
||||
group2ndx.html
|
||||
|
|
|
|||
|
|
@ -10,18 +10,13 @@ pair_style kim command :h3
|
|||
|
||||
[Syntax:]
|
||||
|
||||
pair_style kim virialmode model printflag :pre
|
||||
pair_style kim model :pre
|
||||
|
||||
virialmode = KIMvirial or LAMMPSvirial
|
||||
model = name of KIM model (potential)
|
||||
printflag = 1/0 do or do not print KIM descriptor file, optional :ul
|
||||
|
||||
[Examples:]
|
||||
|
||||
pair_style kim KIMvirial model_Ar_P_Morse
|
||||
pair_coeff * * Ar Ar :pre
|
||||
|
||||
pair_style kim KIMvirial model_Ar_P_Morse 1
|
||||
pair_style kim ex_model_Ar_P_LJ
|
||||
pair_coeff * * Ar Ar :pre
|
||||
|
||||
[Description:]
|
||||
|
|
@ -36,14 +31,10 @@ element or alloy and set of parameters, e.g. EAM for Cu with a
|
|||
specific EAM potential file.
|
||||
|
||||
See the current list of "KIM model
|
||||
drivers"_https://openkim.org/kim-items/model-drivers/alphabetical.
|
||||
drivers"_https://openkim.org/browse/model-drivers/alphabetical.
|
||||
|
||||
See the current list of all "KIM
|
||||
models"_https://openkim.org/kim-items/models/by-model-drivers
|
||||
|
||||
See the list of "example KIM models"_https://openkim.org/kim-api which
|
||||
are included in the KIM library by default, in the "What is in the KIM
|
||||
API source package?" section.
|
||||
models"_https://openkim.org/browse/models/by-model-drivers
|
||||
|
||||
To use this pair style, you must first download and install the KIM
|
||||
API library from the "OpenKIM website"_https://openkim.org. The KIM
|
||||
|
|
@ -51,25 +42,19 @@ section of the "Packages details"_Packages_details.html doc page has
|
|||
instructions on how to do this with a simple make command, when
|
||||
building LAMMPS.
|
||||
|
||||
See the examples/kim dir for an input script that uses a KIM model
|
||||
(potential) for Lennard-Jones.
|
||||
See the examples/kim dir for an input script that uses a KIM model (potential)
|
||||
for Lennard-Jones. Note, for this example input script, the example models
|
||||
shipped with with kim-api package must be installed. See the "Build
|
||||
package"_Build_package.html section and the ./lib/kim/README for details
|
||||
on how to build LAMMSPS with the kim-api and how to install the example models.
|
||||
|
||||
:line
|
||||
|
||||
The argument {virialmode} determines how the global virial is
|
||||
calculated. If {KIMvirial} is specified, the KIM model performs the
|
||||
global virial calculation (if it knows how). If {LAMMPSvirial} is
|
||||
specified, LAMMPS computes the global virial using its fdotr mechanism.
|
||||
|
||||
The argument {model} is the name of the KIM model for a specific
|
||||
potential as KIM defines it. In principle, LAMMPS can invoke any KIM
|
||||
model. You should get an error or warning message from either LAMMPS
|
||||
or KIM if there is an incompatibility.
|
||||
|
||||
The argument {printflag} is optional. If it is set to a non-zero
|
||||
value then a KIM descriptor file is printed when KIM is invoked. This
|
||||
can be useful for debugging. The default is to not print this file.
|
||||
|
||||
Only a single pair_coeff command is used with the {kim} style which
|
||||
specifies the mapping of LAMMPS atom types to KIM elements. This is
|
||||
done by specifying N additional arguments after the * * in the
|
||||
|
|
@ -86,18 +71,14 @@ pair_coeff * * Si Si Si C :pre
|
|||
The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
|
||||
The first three Si arguments map LAMMPS atom types 1,2,3 to Si as
|
||||
defined within KIM. The final C argument maps LAMMPS atom type 4 to C
|
||||
as defined within KIM. If a mapping value is specified as NULL, the
|
||||
mapping is not performed. This can only be used when a {kim}
|
||||
potential is used as part of the {hybrid} pair style. The NULL values
|
||||
are placeholders for atom types that will be used with other
|
||||
potentials.
|
||||
as defined within KIM.
|
||||
|
||||
:line
|
||||
|
||||
In addition to the usual LAMMPS error messages, the KIM library itself
|
||||
may generate errors, which should be printed to the screen. In this
|
||||
case it is also useful to check the kim.log file for additional error
|
||||
information. This file kim.log should be generated in the same
|
||||
information. The file kim.log should be generated in the same
|
||||
directory where LAMMPS is running.
|
||||
|
||||
To download, build, and install the KIM library on your system, see
|
||||
|
|
@ -130,7 +111,7 @@ LAMMPS was built with that package. See the "Build
|
|||
package"_Build_package.html doc page for more info.
|
||||
|
||||
This current version of pair_style kim is compatible with the
|
||||
kim-api package version 1.6.0 and higher.
|
||||
kim-api package version 2.0.0 and higher.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
|
|
|
|||
|
|
@ -211,7 +211,9 @@ latex_elements = {
|
|||
#'pointsize': '10pt',
|
||||
|
||||
# Additional stuff for the LaTeX preamble.
|
||||
#'preamble': '',
|
||||
'preamble': r'''
|
||||
\setcounter{tocdepth}{2}
|
||||
'''
|
||||
}
|
||||
|
||||
# Grouping the document tree into LaTeX files. List of tuples
|
||||
|
|
@ -229,7 +231,7 @@ latex_documents = [
|
|||
# For "manual" documents, if this is true, then toplevel headings are parts,
|
||||
# not chapters.
|
||||
#latex_use_parts = False
|
||||
|
||||
latex_toplevel_sectioning = 'part'
|
||||
# If true, show page references after internal links.
|
||||
#latex_show_pagerefs = False
|
||||
|
||||
|
|
|
|||
|
|
@ -251,6 +251,8 @@ Botero
|
|||
Botu
|
||||
Bouguet
|
||||
boxcolor
|
||||
bp
|
||||
bpls
|
||||
bpclermont
|
||||
br
|
||||
Branduardi
|
||||
|
|
@ -625,8 +627,10 @@ dVx
|
|||
dW
|
||||
dx
|
||||
dy
|
||||
dyn
|
||||
dyne
|
||||
dynes
|
||||
dynmat
|
||||
Dyre
|
||||
Dzyaloshinskii
|
||||
Eaa
|
||||
|
|
@ -1384,6 +1388,7 @@ libfftw
|
|||
libgcc
|
||||
libgpu
|
||||
libjpeg
|
||||
libkim
|
||||
liblammps
|
||||
Liblammps
|
||||
liblink
|
||||
|
|
@ -2083,6 +2088,7 @@ Pmolrotate
|
|||
Pmoltrans
|
||||
pN
|
||||
png
|
||||
Podhorszki
|
||||
Poiseuille
|
||||
Polak
|
||||
polarizabilities
|
||||
|
|
@ -2435,6 +2441,7 @@ shockvel
|
|||
si
|
||||
SiC
|
||||
Siepmann
|
||||
Sievers
|
||||
Sij
|
||||
Sikandar
|
||||
Silbert
|
||||
|
|
|
|||
|
|
@ -0,0 +1,41 @@
|
|||
<?xml version="1.0"?>
|
||||
<adios-config>
|
||||
|
||||
<!-- example engines
|
||||
|
||||
<engine type="BPFile">
|
||||
<parameter key="substreams" value="10"/>
|
||||
</engine>
|
||||
|
||||
<engine type="HDF5">
|
||||
|
||||
|
||||
The 'substreams' parameter in BPFile controls how many
|
||||
files on disk are created. This number should be proportional
|
||||
to the number of servers in the parallel file system,
|
||||
NOT to the number of processes.
|
||||
substreams=1 is generally a very inefficient setting for large parallel runs.
|
||||
-->
|
||||
|
||||
<!--====================================================
|
||||
Configuration for the dump atom/adios command
|
||||
====================================================-->
|
||||
|
||||
<io name="atom">
|
||||
<engine type="BPFile">
|
||||
<parameter key="substreams" value="1"/>
|
||||
</engine>
|
||||
</io>
|
||||
|
||||
<!--====================================================
|
||||
Configuration for the dump custom/adios command
|
||||
====================================================-->
|
||||
|
||||
<io name="custom">
|
||||
<engine type="BPFile">
|
||||
<parameter key="substreams" value="1"/>
|
||||
</engine>
|
||||
</io>
|
||||
|
||||
|
||||
</adios-config>
|
||||
|
|
@ -0,0 +1,57 @@
|
|||
# 2d circle of particles inside a box with LJ walls
|
||||
|
||||
variable b index 0
|
||||
|
||||
variable x index 50
|
||||
variable y index 20
|
||||
variable d index 20
|
||||
variable v index 5
|
||||
variable w index 2
|
||||
|
||||
units lj
|
||||
dimension 2
|
||||
atom_style atomic
|
||||
boundary f f p
|
||||
|
||||
lattice hex 0.85
|
||||
region box block 0 $x 0 $y -0.5 0.5
|
||||
create_box 1 box
|
||||
region circle sphere $(v_d/2+1) $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
|
||||
create_atoms 1 region circle
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 0.5 87287 loop geom
|
||||
velocity all set $v $w 0 sum yes
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 10.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi $x 1 1 2.5
|
||||
fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi $y 1 1 2.5
|
||||
|
||||
comm_style tiled
|
||||
fix 10 all balance 50 0.9 rcb
|
||||
|
||||
compute 1 all property/atom proc
|
||||
variable p atom c_1%10
|
||||
dump 2 all custom 50 balance.dump id v_p x y z
|
||||
dump 3 all custom/adios 50 balance_custom.bp id v_p x y z
|
||||
dump 4 all atom/adios 50 balance_atom.bp
|
||||
|
||||
#dump 3 all image 50 image.*.jpg v_p type &
|
||||
# adiam 1.0 view 0 0 zoom 1.8 subbox yes 0.02
|
||||
#variable colors string &
|
||||
# "red green blue yellow white &
|
||||
# purple pink orange lime gray"
|
||||
#dump_modify 3 pad 5 amap 0 10 sa 1 10 ${colors}
|
||||
|
||||
thermo_style custom step temp epair press f_10[3] f_10
|
||||
thermo 100
|
||||
|
||||
run 200
|
||||
write_dump all atom/adios balance_atom_final.bp
|
||||
|
|
@ -0,0 +1,114 @@
|
|||
LAMMPS (4 Jan 2019)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# 2d circle of particles inside a box with LJ walls
|
||||
|
||||
variable b index 0
|
||||
|
||||
variable x index 50
|
||||
variable y index 20
|
||||
variable d index 20
|
||||
variable v index 5
|
||||
variable w index 2
|
||||
|
||||
units lj
|
||||
dimension 2
|
||||
atom_style atomic
|
||||
boundary f f p
|
||||
|
||||
lattice hex 0.85
|
||||
Lattice spacing in x,y,z = 1.16553 2.01877 1.16553
|
||||
region box block 0 $x 0 $y -0.5 0.5
|
||||
region box block 0 50 0 $y -0.5 0.5
|
||||
region box block 0 50 0 20 -0.5 0.5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 -0.582767) to (58.2767 40.3753 0.582767)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
region circle sphere $(v_d/2+1) $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
|
||||
region circle sphere 11 $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
|
||||
region circle sphere 11 6.7735026918962581988 0.0 $(v_d/2)
|
||||
region circle sphere 11 6.7735026918962581988 0.0 10
|
||||
create_atoms 1 region circle
|
||||
Created 361 atoms
|
||||
Time spent = 0.00171804 secs
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 0.5 87287 loop geom
|
||||
velocity all set $v $w 0 sum yes
|
||||
velocity all set 5 $w 0 sum yes
|
||||
velocity all set 5 2 0 sum yes
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 10.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi $x 1 1 2.5
|
||||
fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi 50 1 1 2.5
|
||||
fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi $y 1 1 2.5
|
||||
fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi 20 1 1 2.5
|
||||
|
||||
comm_style tiled
|
||||
fix 10 all balance 50 0.9 rcb
|
||||
|
||||
compute 1 all property/atom proc
|
||||
variable p atom c_1%10
|
||||
dump 2 all custom 50 balance.dump id v_p x y z
|
||||
dump 3 all custom/adios 50 balance_custom.bp id v_p x y z
|
||||
dump 4 all atom/adios 50 balance_atom.bp
|
||||
|
||||
#dump 3 all image 50 image.*.jpg v_p type # adiam 1.0 view 0 0 zoom 1.8 subbox yes 0.02
|
||||
#variable colors string # "red green blue yellow white # purple pink orange lime gray"
|
||||
#dump_modify 3 pad 5 amap 0 10 sa 1 10 ${colors}
|
||||
|
||||
thermo_style custom step temp epair press f_10[3] f_10
|
||||
thermo 100
|
||||
|
||||
run 200
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 42 29 1
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/2d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.926 | 4.933 | 4.944 Mbytes
|
||||
Step Temp E_pair Press f_10[3] f_10
|
||||
0 25.701528 -29.143179 -1.2407285 3.2354571 1.0526316
|
||||
100 26.269576 -29.713313 7.9052334 1.2742382 1.0304709
|
||||
200 26.368336 -29.809962 1.6412462 1.2520776 1.0083102
|
||||
Loop time of 0.0992351 on 4 procs for 200 steps with 361 atoms
|
||||
|
||||
Performance: 870660.046 tau/day, 2015.417 timesteps/s
|
||||
32.2% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0078368 | 0.0081607 | 0.0085468 | 0.3 | 8.22
|
||||
Neigh | 0.002804 | 0.0045915 | 0.0092173 | 3.9 | 4.63
|
||||
Comm | 0.044407 | 0.05352 | 0.062051 | 3.0 | 53.93
|
||||
Output | 0.011406 | 0.012025 | 0.01342 | 0.7 | 12.12
|
||||
Modify | 0.006305 | 0.0064294 | 0.0066617 | 0.2 | 6.48
|
||||
Other | | 0.01451 | | | 14.62
|
||||
|
||||
Nlocal: 90.25 ave 91 max 90 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 58.25 ave 64 max 51 min
|
||||
Histogram: 1 0 0 0 0 0 2 0 0 1
|
||||
Neighs: 730.75 ave 801 max 671 min
|
||||
Histogram: 1 0 1 0 0 1 0 0 0 1
|
||||
|
||||
Total # of neighbors = 2923
|
||||
Ave neighs/atom = 8.09695
|
||||
Neighbor list builds = 60
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
|
|
@ -0,0 +1,21 @@
|
|||
# LAMMPS LATTICE DYNAMICS COMMANDS
|
||||
|
||||
## DYNAMICAL MATRIX CALCULATOR
|
||||
|
||||
This directory contains the ingredients to calculate a dynamical matrix.
|
||||
|
||||
Example:
|
||||
```
|
||||
NP=4 #number of processors
|
||||
mpirun -np $NP lmp_mpi -in in.silicon -out out.silicon
|
||||
```
|
||||
|
||||
To test out a different silicon example:
|
||||
```
|
||||
LMP_FILE=amorphous_silicon.lmp
|
||||
cp lmp_bank/$LMP_FILE ./silicon_input_file.lmp
|
||||
NP=4 #number of processors
|
||||
mpirun -np $NP lmp_mpi -in in.silicon -out out.silicon
|
||||
```
|
||||
|
||||
## Requires: MANYBODY and MOLECULE packages
|
||||
|
|
@ -0,0 +1,66 @@
|
|||
# Tersoff parameters for various elements and mixtures
|
||||
# multiple entries can be added to this file, LAMMPS reads the ones it needs
|
||||
# these entries are in LAMMPS "metal" units:
|
||||
# A,B = eV; lambda1,lambda2,lambda3 = 1/Angstroms; R,D = Angstroms
|
||||
# other quantities are unitless
|
||||
|
||||
# Aidan Thompson (athomps at sandia.gov) takes full blame for this
|
||||
# file. It specifies various potentials published by J. Tersoff for
|
||||
# silicon, carbon and germanium. Since Tersoff published several
|
||||
# different silicon potentials, I refer to them using atom types
|
||||
# Si(B), Si(C) and Si(D). The last two are almost almost identical but
|
||||
# refer to two different publications. These names should be used in
|
||||
# the LAMMPS command when the file is invoked. For example:
|
||||
# pair_coeff * * SiCGe.tersoff Si(B). The Si(D), C and Ge potentials
|
||||
# can be used pure silicon, pure carbon, pure germanium, binary SiC,
|
||||
# and binary SiGe, but not binary GeC or ternary SiGeC. LAMMPS will
|
||||
# generate an error if this file is used with any combination
|
||||
# involving C and Ge, since there are no entries for the GeC
|
||||
# interactions (Tersoff did not publish parameters for this
|
||||
# cross-interaction.)
|
||||
|
||||
# format of a single entry (one or more lines):
|
||||
# element 1, element 2, element 3,
|
||||
# m, gamma, lambda3, c, d, costheta0, n, beta, lambda2, B, R, D, lambda1, A
|
||||
|
||||
# The original Tersoff potential for Silicon, Si(B)
|
||||
# J. Tersoff, PRB, 37, 6991 (1988)
|
||||
|
||||
Si(B) Si(B) Si(B) 3.0 1.0 1.3258 4.8381 2.0417 0.0000 22.956
|
||||
0.33675 1.3258 95.373 3.0 0.2 3.2394 3264.7
|
||||
|
||||
# The later Tersoff potential for Silicon, Si(C)
|
||||
# J. Tersoff, PRB, 38, 9902 (1988)
|
||||
|
||||
Si(C) Si(C) Si(C) 3.0 1.0 1.7322 1.0039e5 16.218 -0.59826 0.78734
|
||||
1.0999e-6 1.7322 471.18 2.85 0.15 2.4799 1830.8
|
||||
|
||||
# The later Tersoff potential for Carbon, Silicon, and Germanium
|
||||
# J. Tersoff, PRB, 39, 5566 (1989) + errata (PRB 41, 3248)
|
||||
# The Si and C parameters are very close to those in SiC.tersoff
|
||||
|
||||
C C C 3.0 1.0 0.0 3.8049e4 4.3484 -0.57058 0.72751 1.5724e-7 2.2119 346.74 1.95 0.15 3.4879 1393.6
|
||||
Si(D) Si(D) Si(D) 3.0 1.0 0.0 1.0039e5 16.217 -0.59825 0.78734 1.1000e-6 1.7322 471.18 2.85 0.15 2.4799 1830.8
|
||||
Ge Ge Ge 3.0 1.0 0.0 1.0643e5 15.652 -0.43884 0.75627 9.0166e-7 1.7047 419.23 2.95 0.15 2.4451 1769.0
|
||||
|
||||
C Si(D) Si(D) 3.0 1.0 0.0 3.8049e4 4.3484 -0.57058 0.72751 1.5724e-7 1.97205 395.1451 2.3573 0.1527 2.9839 1597.3111
|
||||
C Si(D) C 3.0 1.0 0.0 3.8049e4 4.3484 -0.57058 0.72751 0.0 0.0 0.0 1.95 0.15 0.0 0.0
|
||||
C C Si(D) 3.0 1.0 0.0 3.8049e4 4.3484 -0.57058 0.72751 0.0 0.0 0.0 2.3573 0.1527 0.0 0.0
|
||||
|
||||
Si(D) C C 3.0 1.0 0.0 1.0039e5 16.217 -0.59825 0.78734 1.1000e-6 1.97205 395.1451 2.3573 0.1527 2.9839 1597.3111
|
||||
Si(D) Si(D) C 3.0 1.0 0.0 1.0039e5 16.217 -0.59825 0.78734 0.0 0.0 0.0 2.3573 0.1527 0.0 0.0
|
||||
Si(D) C Si(D) 3.0 1.0 0.0 1.0039e5 16.217 -0.59825 0.78734 0.0 0.0 0.0 2.85 0.15 0.0 0.0
|
||||
|
||||
Si(D) Ge Ge 3.0 1.0 0.0 1.0039e5 16.217 -0.59825 0.78734 1.1000e-6 1.71845 444.7177 2.8996 0.1500 2.4625 1799.6347
|
||||
Si(D) Si(D) Ge 3.0 1.0 0.0 1.0039e5 16.217 -0.59825 0.78734 0.0 0.0 0.0 2.8996 0.1500 0.0 0.0
|
||||
Si(D) Ge Si(D) 3.0 1.0 0.0 1.0039e5 16.217 -0.59825 0.78734 0.0 0.0 0.0 2.85 0.15 0.0 0.0
|
||||
|
||||
Ge Si(D) Si(D) 3.0 1.0 0.0 1.0643e5 15.652 -0.43884 0.75627 9.0166e-7 1.71845 444.7177 2.8996 0.1500 2.4625 1799.6347
|
||||
Ge Si(D) Ge 3.0 1.0 0.0 1.0643e5 15.652 -0.43884 0.75627 0.0 0.0 0.0 2.95 0.15 0.0 0.0
|
||||
Ge Ge Si(D) 3.0 1.0 0.0 1.0643e5 15.652 -0.43884 0.75627 0.0 0.0 0.0 2.8996 0.1500 0.0 0.0
|
||||
|
||||
# Optimized Tersoff for Carbon: Lindsay and Broido PRB 81, 205441 (2010)
|
||||
# element 1, element 2, element 3,
|
||||
# m, gamma, lambda3, c, d, costheta0, n, beta, lambda2, B, R, D, lambda1, A
|
||||
C(O) C(O) C(O) 3.0 1.0 0.0 3.8049e4 4.3484 -0.930 0.72751 1.5724e-7 2.2119 430.0 1.95 0.15 3.4879 1393.6
|
||||
|
||||
|
|
@ -0,0 +1,19 @@
|
|||
#############################
|
||||
#Atoms types - mass - charge#
|
||||
#############################
|
||||
#@ 1 atom types #!THIS LINE IS NECESSARY DON'T SPEND HOURS FINDING THAT OUT!#
|
||||
|
||||
variable Si equal 1
|
||||
|
||||
#############
|
||||
#Atom Masses#
|
||||
#############
|
||||
|
||||
mass ${Si} 28.08550
|
||||
|
||||
###########################
|
||||
#Pair Potentials - Tersoff#
|
||||
###########################
|
||||
|
||||
pair_style tersoff
|
||||
pair_coeff * * Si.opt.tersoff Si(D)
|
||||
|
|
@ -0,0 +1,89 @@
|
|||
###############################mm
|
||||
# Atom style - charge/vdw/bonded#
|
||||
#################################
|
||||
atom_style full
|
||||
|
||||
##############################################
|
||||
#Units Metal : eV - ps - angstrom - bar#
|
||||
# Real : kcal/mol - fs - angstrom - atm#
|
||||
##############################################
|
||||
units metal
|
||||
|
||||
############
|
||||
#Run number#
|
||||
############
|
||||
variable run_no equal 0 # is it a restart?
|
||||
variable res_no equal ${run_no}-1 # restart file number
|
||||
|
||||
#######################################
|
||||
#Random Seeds and Domain Decomposition#
|
||||
#######################################
|
||||
variable iseed0 equal 2357
|
||||
variable iseed1 equal 26488
|
||||
variable iseed2 equal 10669
|
||||
processors * * *
|
||||
|
||||
###########
|
||||
#Data File#
|
||||
###########
|
||||
variable inpfile string silicon_input_file.lmp
|
||||
variable resfile string final_restart.${res_no}
|
||||
variable ff_file string ff-silicon.lmp
|
||||
|
||||
##########
|
||||
#Run Type#
|
||||
##########
|
||||
variable minimise equal 0 #Energy Minimization
|
||||
|
||||
###############################
|
||||
#Molecular Dynamics Parameters#
|
||||
###############################
|
||||
neighbor 1 bin
|
||||
|
||||
################################
|
||||
#Energy Minimization Parameters#
|
||||
################################
|
||||
variable mtraj equal 1 # trajectory output frequency - all system
|
||||
variable etol equal 1e-5 # % change in energy
|
||||
variable ftol equal 1e-5 # max force threshold (force units)
|
||||
variable maxiter equal 10000 # max # of iterations
|
||||
|
||||
########################
|
||||
#3D Periodic Simulation#
|
||||
########################
|
||||
boundary p p p
|
||||
|
||||
#############################
|
||||
#Reading the input structure#
|
||||
#############################
|
||||
if "${run_no} == 0" then "read_data ${inpfile}" else "read_restart ${resfile}"
|
||||
|
||||
#############
|
||||
#Force Field#
|
||||
#############
|
||||
include ${ff_file}
|
||||
|
||||
######################
|
||||
#Thermodynamic Output#
|
||||
######################
|
||||
variable str_basic string 'step time pe temp press'
|
||||
|
||||
#####################
|
||||
#Energy Minimization#
|
||||
#####################
|
||||
if "${minimise} <= 0 || ${run_no} > 0" then "jump SELF end_minimise"
|
||||
print "Doing CG minimisation"
|
||||
dump mdcd all dcd ${mtraj} min.dcd
|
||||
dump_modify mdcd unwrap yes
|
||||
min_style cg
|
||||
min_modify line quadratic
|
||||
minimize ${etol} ${ftol} ${maxiter} ${maxiter}
|
||||
reset_timestep 0
|
||||
undump mdcd
|
||||
label end_minimise
|
||||
|
||||
##################
|
||||
#Dynamical Matrix#
|
||||
##################
|
||||
dynamical_matrix all eskm 0.000001 file dynmat.dat binary no
|
||||
|
||||
|
|
@ -0,0 +1,534 @@
|
|||
LAMMPS description
|
||||
|
||||
512 atoms
|
||||
0 bonds
|
||||
0 angles
|
||||
0 dihedrals
|
||||
0 impropers
|
||||
|
||||
1 atom types
|
||||
0 bond types
|
||||
0 angle types
|
||||
0 dihedral types
|
||||
0 improper types
|
||||
|
||||
|
||||
0.0000000 21.848000 xlo xhi
|
||||
0.0000000 21.848000 ylo yhi
|
||||
0.0000000 21.848000 zlo zhi
|
||||
|
||||
Atoms
|
||||
|
||||
1 1 1 0.0000000 6.2030000 5.5980000 12.9980000
|
||||
2 2 1 0.0000000 21.3100000 5.6310000 21.1380000
|
||||
3 3 1 0.0000000 19.5320000 6.1170000 3.6940000
|
||||
4 4 1 0.0000000 4.3700000 14.0260000 0.0900000
|
||||
5 5 1 0.0000000 10.1930000 7.4590000 2.3530000
|
||||
6 6 1 0.0000000 17.5070000 14.1860000 3.6790000
|
||||
7 7 1 0.0000000 11.2050000 15.9160000 15.0480000
|
||||
8 8 1 0.0000000 8.6050000 19.8970000 21.0040000
|
||||
9 9 1 0.0000000 15.0360000 17.5650000 1.3640000
|
||||
10 10 1 0.0000000 12.0450000 3.3600000 7.2720000
|
||||
11 11 1 0.0000000 7.1330000 17.4130000 18.0480000
|
||||
12 12 1 0.0000000 8.7340000 6.3830000 3.8480000
|
||||
13 13 1 0.0000000 13.0940000 3.2490000 3.5840000
|
||||
14 14 1 0.0000000 11.3200000 7.2770000 20.4120000
|
||||
15 15 1 0.0000000 19.7770000 8.9110000 0.3000000
|
||||
16 16 1 0.0000000 11.9710000 20.8500000 1.5140000
|
||||
17 17 1 0.0000000 10.4480000 10.3650000 15.4040000
|
||||
18 18 1 0.0000000 9.2060000 9.4670000 10.2240000
|
||||
19 19 1 0.0000000 8.4360000 13.6240000 17.6570000
|
||||
20 20 1 0.0000000 18.2020000 21.1230000 0.1380000
|
||||
21 21 1 0.0000000 3.2970000 19.5740000 14.7410000
|
||||
22 22 1 0.0000000 12.5330000 17.3580000 7.5960000
|
||||
23 23 1 0.0000000 1.4040000 18.1060000 3.1510000
|
||||
24 24 1 0.0000000 17.7440000 13.1530000 16.7940000
|
||||
25 25 1 0.0000000 12.1070000 12.6630000 18.0340000
|
||||
26 26 1 0.0000000 8.7270000 17.1140000 10.4200000
|
||||
27 27 1 0.0000000 13.2330000 16.0380000 13.9210000
|
||||
28 28 1 0.0000000 15.2360000 14.8650000 7.0150000
|
||||
29 29 1 0.0000000 5.5190000 20.8660000 19.9260000
|
||||
30 30 1 0.0000000 16.5810000 9.7460000 15.1710000
|
||||
31 31 1 0.0000000 2.0500000 13.8550000 21.8010000
|
||||
32 32 1 0.0000000 21.2670000 20.8970000 13.6740000
|
||||
33 33 1 0.0000000 9.6900000 6.7650000 0.1950000
|
||||
34 34 1 0.0000000 11.2570000 13.2440000 2.8190000
|
||||
35 35 1 0.0000000 10.7810000 12.7310000 12.1920000
|
||||
36 36 1 0.0000000 16.2630000 7.4100000 1.5360000
|
||||
37 37 1 0.0000000 19.6100000 18.1440000 19.6830000
|
||||
38 38 1 0.0000000 8.1790000 0.1200000 10.1620000
|
||||
39 39 1 0.0000000 17.0520000 20.4210000 15.0450000
|
||||
40 40 1 0.0000000 12.3690000 12.6710000 4.8320000
|
||||
41 41 1 0.0000000 7.8300000 16.6790000 14.2470000
|
||||
42 42 1 0.0000000 1.6790000 9.9500000 1.2660000
|
||||
43 43 1 0.0000000 16.6160000 14.6580000 13.2790000
|
||||
44 44 1 0.0000000 13.7430000 11.9730000 21.5360000
|
||||
45 45 1 0.0000000 5.2590000 15.1850000 9.5720000
|
||||
46 46 1 0.0000000 20.5980000 14.7930000 20.4140000
|
||||
47 47 1 0.0000000 1.5640000 16.8080000 13.0450000
|
||||
48 48 1 0.0000000 21.3670000 11.4610000 20.6420000
|
||||
49 49 1 0.0000000 14.5890000 5.9510000 7.1950000
|
||||
50 50 1 0.0000000 1.0870000 13.5410000 11.3300000
|
||||
51 51 1 0.0000000 6.2040000 4.8970000 16.9420000
|
||||
52 52 1 0.0000000 0.4800000 4.1450000 0.8710000
|
||||
53 53 1 0.0000000 2.0120000 5.7530000 1.8950000
|
||||
54 54 1 0.0000000 9.8460000 19.1320000 7.3060000
|
||||
55 55 1 0.0000000 18.3760000 21.3430000 4.0940000
|
||||
56 56 1 0.0000000 5.2900000 6.5400000 5.3620000
|
||||
57 57 1 0.0000000 1.4110000 6.5750000 4.0580000
|
||||
58 58 1 0.0000000 16.1600000 15.1390000 11.0380000
|
||||
59 59 1 0.0000000 21.0670000 18.3830000 8.6900000
|
||||
60 60 1 0.0000000 18.0250000 17.7750000 1.4340000
|
||||
61 61 1 0.0000000 19.0570000 16.2190000 6.6410000
|
||||
62 62 1 0.0000000 5.1170000 16.5510000 11.5540000
|
||||
63 63 1 0.0000000 14.4810000 7.8720000 12.6320000
|
||||
64 64 1 0.0000000 11.7990000 10.9690000 13.5430000
|
||||
65 65 1 0.0000000 11.2980000 18.5410000 1.5740000
|
||||
66 66 1 0.0000000 16.1280000 19.0390000 19.6440000
|
||||
67 67 1 0.0000000 6.0950000 7.0580000 9.6530000
|
||||
68 68 1 0.0000000 5.3890000 20.2540000 10.7060000
|
||||
69 69 1 0.0000000 17.9160000 18.9070000 21.1540000
|
||||
70 70 1 0.0000000 13.0780000 2.1790000 17.4030000
|
||||
71 71 1 0.0000000 8.0450000 14.3440000 14.0640000
|
||||
72 72 1 0.0000000 14.4380000 6.8780000 14.6950000
|
||||
73 73 1 0.0000000 0.4570000 21.6180000 8.3670000
|
||||
74 74 1 0.0000000 6.4350000 16.9720000 21.7330000
|
||||
75 75 1 0.0000000 8.0530000 4.0310000 20.1860000
|
||||
76 76 1 0.0000000 6.8130000 19.7870000 12.5790000
|
||||
77 77 1 0.0000000 19.0490000 10.8480000 6.0760000
|
||||
78 78 1 0.0000000 2.2540000 7.7370000 0.5320000
|
||||
79 79 1 0.0000000 16.3920000 9.0880000 3.1430000
|
||||
80 80 1 0.0000000 2.3620000 2.5500000 7.5690000
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||||
379 379 1 0.0000000 18.9350000 15.8660000 19.2180000
|
||||
380 380 1 0.0000000 19.6110000 0.3890000 20.4600000
|
||||
381 381 1 0.0000000 1.6460000 14.9430000 1.9780000
|
||||
382 382 1 0.0000000 16.9420000 8.7780000 9.0500000
|
||||
383 383 1 0.0000000 15.0770000 11.3050000 19.7190000
|
||||
384 384 1 0.0000000 6.2370000 17.3890000 15.8170000
|
||||
385 385 1 0.0000000 14.6890000 16.8390000 8.2540000
|
||||
386 386 1 0.0000000 5.9660000 6.4540000 15.1720000
|
||||
387 387 1 0.0000000 6.1100000 4.8320000 21.2820000
|
||||
388 388 1 0.0000000 5.9710000 14.6570000 4.7110000
|
||||
389 389 1 0.0000000 3.1780000 19.7080000 5.8410000
|
||||
390 390 1 0.0000000 5.7600000 19.5340000 14.8080000
|
||||
391 391 1 0.0000000 18.1190000 11.5110000 15.1550000
|
||||
392 392 1 0.0000000 17.0450000 3.0230000 19.5700000
|
||||
393 393 1 0.0000000 11.7520000 21.8180000 19.7610000
|
||||
394 394 1 0.0000000 15.5870000 18.5610000 6.9700000
|
||||
395 395 1 0.0000000 6.0680000 8.8370000 18.0920000
|
||||
396 396 1 0.0000000 14.2730000 18.8060000 21.1250000
|
||||
397 397 1 0.0000000 14.8640000 7.7480000 18.0510000
|
||||
398 398 1 0.0000000 7.1970000 14.3360000 8.4160000
|
||||
399 399 1 0.0000000 12.4080000 8.9750000 12.3640000
|
||||
400 400 1 0.0000000 15.7690000 0.5910000 7.2330000
|
||||
401 401 1 0.0000000 14.1880000 18.6730000 16.7170000
|
||||
402 402 1 0.0000000 0.1070000 17.0650000 14.8780000
|
||||
403 403 1 0.0000000 1.2690000 21.0730000 19.1580000
|
||||
404 404 1 0.0000000 8.3320000 15.5390000 0.1550000
|
||||
405 405 1 0.0000000 3.4890000 20.2250000 18.9410000
|
||||
406 406 1 0.0000000 16.7760000 7.8120000 16.6050000
|
||||
407 407 1 0.0000000 0.5070000 4.7570000 5.2510000
|
||||
408 408 1 0.0000000 19.1810000 3.0200000 9.7780000
|
||||
409 409 1 0.0000000 4.7160000 9.7900000 16.3110000
|
||||
410 410 1 0.0000000 2.4040000 18.9600000 12.6390000
|
||||
411 411 1 0.0000000 3.3380000 4.6500000 7.9680000
|
||||
412 412 1 0.0000000 17.7990000 4.9620000 9.4940000
|
||||
413 413 1 0.0000000 12.7390000 16.3390000 11.5840000
|
||||
414 414 1 0.0000000 17.5550000 6.7730000 20.3200000
|
||||
415 415 1 0.0000000 14.1770000 9.8840000 3.2060000
|
||||
416 416 1 0.0000000 14.4790000 10.5810000 15.6890000
|
||||
417 417 1 0.0000000 14.7570000 21.0200000 10.8010000
|
||||
418 418 1 0.0000000 19.6820000 0.5930000 12.8140000
|
||||
419 419 1 0.0000000 8.6600000 0.3420000 21.6710000
|
||||
420 420 1 0.0000000 9.6300000 4.0130000 11.4620000
|
||||
421 421 1 0.0000000 21.1990000 7.8220000 3.8780000
|
||||
422 422 1 0.0000000 1.0220000 15.3220000 20.3160000
|
||||
423 423 1 0.0000000 19.5230000 9.5210000 18.2400000
|
||||
424 424 1 0.0000000 6.0420000 4.8470000 1.8140000
|
||||
425 425 1 0.0000000 19.0970000 2.7310000 20.7130000
|
||||
426 426 1 0.0000000 20.7220000 12.9310000 18.9570000
|
||||
427 427 1 0.0000000 12.0420000 5.2830000 19.3670000
|
||||
428 428 1 0.0000000 12.3510000 14.1340000 10.8070000
|
||||
429 429 1 0.0000000 0.6760000 0.6980000 4.6080000
|
||||
430 430 1 0.0000000 17.9010000 21.6070000 7.6530000
|
||||
431 431 1 0.0000000 12.9910000 4.6940000 10.9090000
|
||||
432 432 1 0.0000000 4.1650000 0.3790000 10.2450000
|
||||
433 433 1 0.0000000 11.0350000 2.5880000 2.7230000
|
||||
434 434 1 0.0000000 0.8260000 16.8030000 9.2410000
|
||||
435 435 1 0.0000000 1.2930000 1.5320000 19.6910000
|
||||
436 436 1 0.0000000 3.6360000 0.6300000 7.9720000
|
||||
437 437 1 0.0000000 18.7690000 21.6650000 18.3160000
|
||||
438 438 1 0.0000000 15.9900000 1.2130000 10.5660000
|
||||
439 439 1 0.0000000 3.6880000 0.2170000 17.3680000
|
||||
440 440 1 0.0000000 15.4550000 13.7970000 16.7760000
|
||||
441 441 1 0.0000000 13.6260000 0.3920000 16.0690000
|
||||
442 442 1 0.0000000 2.2090000 7.7760000 18.5900000
|
||||
443 443 1 0.0000000 7.5390000 1.2670000 1.6990000
|
||||
444 444 1 0.0000000 5.8870000 7.1350000 20.9610000
|
||||
445 445 1 0.0000000 3.5460000 9.4970000 8.9750000
|
||||
446 446 1 0.0000000 1.7030000 10.1450000 12.4300000
|
||||
447 447 1 0.0000000 4.5220000 7.2320000 19.0140000
|
||||
448 448 1 0.0000000 12.0790000 18.5320000 17.7390000
|
||||
449 449 1 0.0000000 11.8150000 12.7440000 20.4040000
|
||||
450 450 1 0.0000000 14.1450000 16.3300000 20.6400000
|
||||
451 451 1 0.0000000 13.9790000 11.9100000 13.7820000
|
||||
452 452 1 0.0000000 5.7860000 9.0870000 8.2180000
|
||||
453 453 1 0.0000000 5.7610000 18.5920000 3.4730000
|
||||
454 454 1 0.0000000 17.1860000 12.2100000 20.2580000
|
||||
455 455 1 0.0000000 19.9590000 17.8190000 5.1360000
|
||||
456 456 1 0.0000000 17.0590000 15.4900000 5.5810000
|
||||
457 457 1 0.0000000 3.6710000 3.1920000 4.2290000
|
||||
458 458 1 0.0000000 9.3110000 4.4320000 0.2320000
|
||||
459 459 1 0.0000000 7.2900000 10.5480000 9.3640000
|
||||
460 460 1 0.0000000 3.1990000 11.3340000 19.5640000
|
||||
461 461 1 0.0000000 18.7960000 19.0310000 15.8960000
|
||||
462 462 1 0.0000000 16.4530000 21.1730000 18.6370000
|
||||
463 463 1 0.0000000 19.0360000 1.4790000 16.6070000
|
||||
464 464 1 0.0000000 15.1190000 6.7220000 5.0610000
|
||||
465 465 1 0.0000000 14.6980000 6.3460000 10.8900000
|
||||
466 466 1 0.0000000 9.5270000 15.6660000 5.6890000
|
||||
467 467 1 0.0000000 9.8670000 0.7250000 18.4290000
|
||||
468 468 1 0.0000000 3.5070000 11.8220000 15.5670000
|
||||
469 469 1 0.0000000 5.2170000 0.8530000 1.6550000
|
||||
470 470 1 0.0000000 14.2830000 11.9310000 17.5860000
|
||||
471 471 1 0.0000000 21.4650000 11.2840000 8.7140000
|
||||
472 472 1 0.0000000 0.2700000 13.5140000 17.1240000
|
||||
473 473 1 0.0000000 8.7330000 20.7300000 17.4130000
|
||||
474 474 1 0.0000000 7.4140000 12.9760000 3.8660000
|
||||
475 475 1 0.0000000 8.5520000 8.7210000 12.3480000
|
||||
476 476 1 0.0000000 7.4770000 9.7280000 1.7090000
|
||||
477 477 1 0.0000000 16.9200000 14.6800000 20.0740000
|
||||
478 478 1 0.0000000 6.5920000 20.9910000 6.6400000
|
||||
479 479 1 0.0000000 18.3870000 7.4290000 18.2380000
|
||||
480 480 1 0.0000000 21.2320000 15.1360000 2.5810000
|
||||
481 481 1 0.0000000 16.7390000 8.6780000 21.4380000
|
||||
482 482 1 0.0000000 18.2260000 6.2380000 5.6140000
|
||||
483 483 1 0.0000000 12.7550000 3.5820000 20.8720000
|
||||
484 484 1 0.0000000 14.8870000 9.0010000 20.0300000
|
||||
485 485 1 0.0000000 6.1970000 16.3000000 3.0880000
|
||||
486 486 1 0.0000000 6.9450000 13.1810000 15.8140000
|
||||
487 487 1 0.0000000 20.1770000 18.7700000 1.5020000
|
||||
488 488 1 0.0000000 19.8750000 14.4220000 0.7710000
|
||||
489 489 1 0.0000000 13.0770000 5.0280000 14.9330000
|
||||
490 490 1 0.0000000 10.9540000 0.5380000 0.0170000
|
||||
491 491 1 0.0000000 0.3310000 3.0520000 18.1720000
|
||||
492 492 1 0.0000000 8.8200000 14.8310000 10.0110000
|
||||
493 493 1 0.0000000 6.9570000 20.3870000 8.9230000
|
||||
494 494 1 0.0000000 21.4900000 6.8560000 12.0490000
|
||||
495 495 1 0.0000000 8.1550000 13.1990000 21.7210000
|
||||
496 496 1 0.0000000 2.1970000 4.5290000 11.8290000
|
||||
497 497 1 0.0000000 14.2880000 5.5560000 18.5960000
|
||||
498 498 1 0.0000000 15.0910000 15.4110000 18.5470000
|
||||
499 499 1 0.0000000 18.9760000 15.1930000 16.8970000
|
||||
500 500 1 0.0000000 19.4100000 5.3490000 17.7540000
|
||||
501 501 1 0.0000000 0.5430000 8.3990000 13.7700000
|
||||
502 502 1 0.0000000 18.0770000 19.1690000 4.8770000
|
||||
503 503 1 0.0000000 3.3760000 17.8650000 19.2940000
|
||||
504 504 1 0.0000000 16.3760000 0.5870000 3.6340000
|
||||
505 505 1 0.0000000 10.4990000 18.5190000 21.1770000
|
||||
506 506 1 0.0000000 15.7320000 12.7570000 3.0200000
|
||||
507 507 1 0.0000000 16.9190000 8.1780000 5.2430000
|
||||
508 508 1 0.0000000 6.9450000 7.4210000 6.8040000
|
||||
509 509 1 0.0000000 11.6120000 21.2610000 15.3620000
|
||||
510 510 1 0.0000000 18.0500000 0.6840000 14.5470000
|
||||
511 511 1 0.0000000 20.4340000 4.0240000 4.2040000
|
||||
512 512 1 0.0000000 18.0190000 10.7210000 0.2160000
|
||||
|
||||
|
|
@ -0,0 +1,238 @@
|
|||
LAMMPS description
|
||||
|
||||
216 atoms
|
||||
0 bonds
|
||||
0 angles
|
||||
0 dihedrals
|
||||
0 impropers
|
||||
|
||||
1 atom types
|
||||
0 bond types
|
||||
0 angle types
|
||||
0 dihedral types
|
||||
0 improper types
|
||||
|
||||
|
||||
0.0000000 16.293000 xlo xhi
|
||||
0.0000000 16.293000 ylo yhi
|
||||
0.0000000 16.293000 zlo zhi
|
||||
|
||||
Atoms
|
||||
|
||||
1 1 1 0.0000000 0.0000000 0.0000000 0.0000000
|
||||
2 2 1 0.0000000 0.0000000 2.7160000 2.7160000
|
||||
3 3 1 0.0000000 2.7160000 2.7160000 0.0000000
|
||||
4 4 1 0.0000000 2.7160000 0.0000000 2.7160000
|
||||
5 5 1 0.0000000 4.0730000 1.3580000 4.0730000
|
||||
6 6 1 0.0000000 1.3580000 1.3580000 1.3580000
|
||||
7 7 1 0.0000000 1.3580000 4.0730000 4.0730000
|
||||
8 8 1 0.0000000 4.0730000 4.0730000 1.3580000
|
||||
9 9 1 0.0000000 0.0000000 0.0000000 5.4310000
|
||||
10 10 1 0.0000000 0.0000000 2.7160000 8.1460000
|
||||
11 11 1 0.0000000 2.7160000 2.7160000 5.4310000
|
||||
12 12 1 0.0000000 2.7160000 0.0000000 8.1460000
|
||||
13 13 1 0.0000000 4.0730000 1.3580000 9.5040000
|
||||
14 14 1 0.0000000 1.3580000 1.3580000 6.7890000
|
||||
15 15 1 0.0000000 1.3580000 4.0730000 9.5040000
|
||||
16 16 1 0.0000000 4.0730000 4.0730000 6.7890000
|
||||
17 17 1 0.0000000 0.0000000 0.0000000 10.8620000
|
||||
18 18 1 0.0000000 0.0000000 2.7160000 13.5780000
|
||||
19 19 1 0.0000000 2.7160000 2.7160000 10.8620000
|
||||
20 20 1 0.0000000 2.7160000 0.0000000 13.5780000
|
||||
21 21 1 0.0000000 4.0730000 1.3580000 14.9350000
|
||||
22 22 1 0.0000000 1.3580000 1.3580000 12.2200000
|
||||
23 23 1 0.0000000 1.3580000 4.0730000 14.9350000
|
||||
24 24 1 0.0000000 4.0730000 4.0730000 12.2200000
|
||||
25 25 1 0.0000000 0.0000000 5.4310000 0.0000000
|
||||
26 26 1 0.0000000 0.0000000 8.1460000 2.7160000
|
||||
27 27 1 0.0000000 2.7160000 8.1460000 0.0000000
|
||||
28 28 1 0.0000000 2.7160000 5.4310000 2.7160000
|
||||
29 29 1 0.0000000 4.0730000 6.7890000 4.0730000
|
||||
30 30 1 0.0000000 1.3580000 6.7890000 1.3580000
|
||||
31 31 1 0.0000000 1.3580000 9.5040000 4.0730000
|
||||
32 32 1 0.0000000 4.0730000 9.5040000 1.3580000
|
||||
33 33 1 0.0000000 0.0000000 5.4310000 5.4310000
|
||||
34 34 1 0.0000000 0.0000000 8.1460000 8.1460000
|
||||
35 35 1 0.0000000 2.7160000 8.1460000 5.4310000
|
||||
36 36 1 0.0000000 2.7160000 5.4310000 8.1460000
|
||||
37 37 1 0.0000000 4.0730000 6.7890000 9.5040000
|
||||
38 38 1 0.0000000 1.3580000 6.7890000 6.7890000
|
||||
39 39 1 0.0000000 1.3580000 9.5040000 9.5040000
|
||||
40 40 1 0.0000000 4.0730000 9.5040000 6.7890000
|
||||
41 41 1 0.0000000 0.0000000 5.4310000 10.8620000
|
||||
42 42 1 0.0000000 0.0000000 8.1460000 13.5780000
|
||||
43 43 1 0.0000000 2.7160000 8.1460000 10.8620000
|
||||
44 44 1 0.0000000 2.7160000 5.4310000 13.5780000
|
||||
45 45 1 0.0000000 4.0730000 6.7890000 14.9350000
|
||||
46 46 1 0.0000000 1.3580000 6.7890000 12.2200000
|
||||
47 47 1 0.0000000 1.3580000 9.5040000 14.9350000
|
||||
48 48 1 0.0000000 4.0730000 9.5040000 12.2200000
|
||||
49 49 1 0.0000000 0.0000000 10.8620000 0.0000000
|
||||
50 50 1 0.0000000 0.0000000 13.5780000 2.7160000
|
||||
51 51 1 0.0000000 2.7160000 13.5780000 0.0000000
|
||||
52 52 1 0.0000000 2.7160000 10.8620000 2.7160000
|
||||
53 53 1 0.0000000 4.0730000 12.2200000 4.0730000
|
||||
54 54 1 0.0000000 1.3580000 12.2200000 1.3580000
|
||||
55 55 1 0.0000000 1.3580000 14.9350000 4.0730000
|
||||
56 56 1 0.0000000 4.0730000 14.9350000 1.3580000
|
||||
57 57 1 0.0000000 0.0000000 10.8620000 5.4310000
|
||||
58 58 1 0.0000000 0.0000000 13.5780000 8.1460000
|
||||
59 59 1 0.0000000 2.7160000 13.5780000 5.4310000
|
||||
60 60 1 0.0000000 2.7160000 10.8620000 8.1460000
|
||||
61 61 1 0.0000000 4.0730000 12.2200000 9.5040000
|
||||
62 62 1 0.0000000 1.3580000 12.2200000 6.7890000
|
||||
63 63 1 0.0000000 1.3580000 14.9350000 9.5040000
|
||||
64 64 1 0.0000000 4.0730000 14.9350000 6.7890000
|
||||
65 65 1 0.0000000 0.0000000 10.8620000 10.8620000
|
||||
66 66 1 0.0000000 0.0000000 13.5780000 13.5780000
|
||||
67 67 1 0.0000000 2.7160000 13.5780000 10.8620000
|
||||
68 68 1 0.0000000 2.7160000 10.8620000 13.5780000
|
||||
69 69 1 0.0000000 4.0730000 12.2200000 14.9350000
|
||||
70 70 1 0.0000000 1.3580000 12.2200000 12.2200000
|
||||
71 71 1 0.0000000 1.3580000 14.9350000 14.9350000
|
||||
72 72 1 0.0000000 4.0730000 14.9350000 12.2200000
|
||||
73 73 1 0.0000000 5.4310000 0.0000000 0.0000000
|
||||
74 74 1 0.0000000 5.4310000 2.7160000 2.7160000
|
||||
75 75 1 0.0000000 8.1460000 2.7160000 0.0000000
|
||||
76 76 1 0.0000000 8.1460000 0.0000000 2.7160000
|
||||
77 77 1 0.0000000 9.5040000 1.3580000 4.0730000
|
||||
78 78 1 0.0000000 6.7890000 1.3580000 1.3580000
|
||||
79 79 1 0.0000000 6.7890000 4.0730000 4.0730000
|
||||
80 80 1 0.0000000 9.5040000 4.0730000 1.3580000
|
||||
81 81 1 0.0000000 5.4310000 0.0000000 5.4310000
|
||||
82 82 1 0.0000000 5.4310000 2.7160000 8.1460000
|
||||
83 83 1 0.0000000 8.1460000 2.7160000 5.4310000
|
||||
84 84 1 0.0000000 8.1460000 0.0000000 8.1460000
|
||||
85 85 1 0.0000000 9.5040000 1.3580000 9.5040000
|
||||
86 86 1 0.0000000 6.7890000 1.3580000 6.7890000
|
||||
87 87 1 0.0000000 6.7890000 4.0730000 9.5040000
|
||||
88 88 1 0.0000000 9.5040000 4.0730000 6.7890000
|
||||
89 89 1 0.0000000 5.4310000 0.0000000 10.8620000
|
||||
90 90 1 0.0000000 5.4310000 2.7160000 13.5780000
|
||||
91 91 1 0.0000000 8.1460000 2.7160000 10.8620000
|
||||
92 92 1 0.0000000 8.1460000 0.0000000 13.5780000
|
||||
93 93 1 0.0000000 9.5040000 1.3580000 14.9350000
|
||||
94 94 1 0.0000000 6.7890000 1.3580000 12.2200000
|
||||
95 95 1 0.0000000 6.7890000 4.0730000 14.9350000
|
||||
96 96 1 0.0000000 9.5040000 4.0730000 12.2200000
|
||||
97 97 1 0.0000000 5.4310000 5.4310000 0.0000000
|
||||
98 98 1 0.0000000 5.4310000 8.1460000 2.7160000
|
||||
99 99 1 0.0000000 8.1460000 8.1460000 0.0000000
|
||||
100 100 1 0.0000000 8.1460000 5.4310000 2.7160000
|
||||
101 101 1 0.0000000 9.5040000 6.7890000 4.0730000
|
||||
102 102 1 0.0000000 6.7890000 6.7890000 1.3580000
|
||||
103 103 1 0.0000000 6.7890000 9.5040000 4.0730000
|
||||
104 104 1 0.0000000 9.5040000 9.5040000 1.3580000
|
||||
105 105 1 0.0000000 5.4310000 5.4310000 5.4310000
|
||||
106 106 1 0.0000000 5.4310000 8.1460000 8.1460000
|
||||
107 107 1 0.0000000 8.1460000 8.1460000 5.4310000
|
||||
108 108 1 0.0000000 8.1460000 5.4310000 8.1460000
|
||||
109 109 1 0.0000000 9.5040000 6.7890000 9.5040000
|
||||
110 110 1 0.0000000 6.7890000 6.7890000 6.7890000
|
||||
111 111 1 0.0000000 6.7890000 9.5040000 9.5040000
|
||||
112 112 1 0.0000000 9.5040000 9.5040000 6.7890000
|
||||
113 113 1 0.0000000 5.4310000 5.4310000 10.8620000
|
||||
114 114 1 0.0000000 5.4310000 8.1460000 13.5780000
|
||||
115 115 1 0.0000000 8.1460000 8.1460000 10.8620000
|
||||
116 116 1 0.0000000 8.1460000 5.4310000 13.5780000
|
||||
117 117 1 0.0000000 9.5040000 6.7890000 14.9350000
|
||||
118 118 1 0.0000000 6.7890000 6.7890000 12.2200000
|
||||
119 119 1 0.0000000 6.7890000 9.5040000 14.9350000
|
||||
120 120 1 0.0000000 9.5040000 9.5040000 12.2200000
|
||||
121 121 1 0.0000000 5.4310000 10.8620000 0.0000000
|
||||
122 122 1 0.0000000 5.4310000 13.5780000 2.7160000
|
||||
123 123 1 0.0000000 8.1460000 13.5780000 0.0000000
|
||||
124 124 1 0.0000000 8.1460000 10.8620000 2.7160000
|
||||
125 125 1 0.0000000 9.5040000 12.2200000 4.0730000
|
||||
126 126 1 0.0000000 6.7890000 12.2200000 1.3580000
|
||||
127 127 1 0.0000000 6.7890000 14.9350000 4.0730000
|
||||
128 128 1 0.0000000 9.5040000 14.9350000 1.3580000
|
||||
129 129 1 0.0000000 5.4310000 10.8620000 5.4310000
|
||||
130 130 1 0.0000000 5.4310000 13.5780000 8.1460000
|
||||
131 131 1 0.0000000 8.1460000 13.5780000 5.4310000
|
||||
132 132 1 0.0000000 8.1460000 10.8620000 8.1460000
|
||||
133 133 1 0.0000000 9.5040000 12.2200000 9.5040000
|
||||
134 134 1 0.0000000 6.7890000 12.2200000 6.7890000
|
||||
135 135 1 0.0000000 6.7890000 14.9350000 9.5040000
|
||||
136 136 1 0.0000000 9.5040000 14.9350000 6.7890000
|
||||
137 137 1 0.0000000 5.4310000 10.8620000 10.8620000
|
||||
138 138 1 0.0000000 5.4310000 13.5780000 13.5780000
|
||||
139 139 1 0.0000000 8.1460000 13.5780000 10.8620000
|
||||
140 140 1 0.0000000 8.1460000 10.8620000 13.5780000
|
||||
141 141 1 0.0000000 9.5040000 12.2200000 14.9350000
|
||||
142 142 1 0.0000000 6.7890000 12.2200000 12.2200000
|
||||
143 143 1 0.0000000 6.7890000 14.9350000 14.9350000
|
||||
144 144 1 0.0000000 9.5040000 14.9350000 12.2200000
|
||||
145 145 1 0.0000000 10.8620000 0.0000000 0.0000000
|
||||
146 146 1 0.0000000 10.8620000 2.7160000 2.7160000
|
||||
147 147 1 0.0000000 13.5780000 2.7160000 0.0000000
|
||||
148 148 1 0.0000000 13.5780000 0.0000000 2.7160000
|
||||
149 149 1 0.0000000 14.9350000 1.3580000 4.0730000
|
||||
150 150 1 0.0000000 12.2200000 1.3580000 1.3580000
|
||||
151 151 1 0.0000000 12.2200000 4.0730000 4.0730000
|
||||
152 152 1 0.0000000 14.9350000 4.0730000 1.3580000
|
||||
153 153 1 0.0000000 10.8620000 0.0000000 5.4310000
|
||||
154 154 1 0.0000000 10.8620000 2.7160000 8.1460000
|
||||
155 155 1 0.0000000 13.5780000 2.7160000 5.4310000
|
||||
156 156 1 0.0000000 13.5780000 0.0000000 8.1460000
|
||||
157 157 1 0.0000000 14.9350000 1.3580000 9.5040000
|
||||
158 158 1 0.0000000 12.2200000 1.3580000 6.7890000
|
||||
159 159 1 0.0000000 12.2200000 4.0730000 9.5040000
|
||||
160 160 1 0.0000000 14.9350000 4.0730000 6.7890000
|
||||
161 161 1 0.0000000 10.8620000 0.0000000 10.8620000
|
||||
162 162 1 0.0000000 10.8620000 2.7160000 13.5780000
|
||||
163 163 1 0.0000000 13.5780000 2.7160000 10.8620000
|
||||
164 164 1 0.0000000 13.5780000 0.0000000 13.5780000
|
||||
165 165 1 0.0000000 14.9350000 1.3580000 14.9350000
|
||||
166 166 1 0.0000000 12.2200000 1.3580000 12.2200000
|
||||
167 167 1 0.0000000 12.2200000 4.0730000 14.9350000
|
||||
168 168 1 0.0000000 14.9350000 4.0730000 12.2200000
|
||||
169 169 1 0.0000000 10.8620000 5.4310000 0.0000000
|
||||
170 170 1 0.0000000 10.8620000 8.1460000 2.7160000
|
||||
171 171 1 0.0000000 13.5780000 8.1460000 0.0000000
|
||||
172 172 1 0.0000000 13.5780000 5.4310000 2.7160000
|
||||
173 173 1 0.0000000 14.9350000 6.7890000 4.0730000
|
||||
174 174 1 0.0000000 12.2200000 6.7890000 1.3580000
|
||||
175 175 1 0.0000000 12.2200000 9.5040000 4.0730000
|
||||
176 176 1 0.0000000 14.9350000 9.5040000 1.3580000
|
||||
177 177 1 0.0000000 10.8620000 5.4310000 5.4310000
|
||||
178 178 1 0.0000000 10.8620000 8.1460000 8.1460000
|
||||
179 179 1 0.0000000 13.5780000 8.1460000 5.4310000
|
||||
180 180 1 0.0000000 13.5780000 5.4310000 8.1460000
|
||||
181 181 1 0.0000000 14.9350000 6.7890000 9.5040000
|
||||
182 182 1 0.0000000 12.2200000 6.7890000 6.7890000
|
||||
183 183 1 0.0000000 12.2200000 9.5040000 9.5040000
|
||||
184 184 1 0.0000000 14.9350000 9.5040000 6.7890000
|
||||
185 185 1 0.0000000 10.8620000 5.4310000 10.8620000
|
||||
186 186 1 0.0000000 10.8620000 8.1460000 13.5780000
|
||||
187 187 1 0.0000000 13.5780000 8.1460000 10.8620000
|
||||
188 188 1 0.0000000 13.5780000 5.4310000 13.5780000
|
||||
189 189 1 0.0000000 14.9350000 6.7890000 14.9350000
|
||||
190 190 1 0.0000000 12.2200000 6.7890000 12.2200000
|
||||
191 191 1 0.0000000 12.2200000 9.5040000 14.9350000
|
||||
192 192 1 0.0000000 14.9350000 9.5040000 12.2200000
|
||||
193 193 1 0.0000000 10.8620000 10.8620000 0.0000000
|
||||
194 194 1 0.0000000 10.8620000 13.5780000 2.7160000
|
||||
195 195 1 0.0000000 13.5780000 13.5780000 0.0000000
|
||||
196 196 1 0.0000000 13.5780000 10.8620000 2.7160000
|
||||
197 197 1 0.0000000 14.9350000 12.2200000 4.0730000
|
||||
198 198 1 0.0000000 12.2200000 12.2200000 1.3580000
|
||||
199 199 1 0.0000000 12.2200000 14.9350000 4.0730000
|
||||
200 200 1 0.0000000 14.9350000 14.9350000 1.3580000
|
||||
201 201 1 0.0000000 10.8620000 10.8620000 5.4310000
|
||||
202 202 1 0.0000000 10.8620000 13.5780000 8.1460000
|
||||
203 203 1 0.0000000 13.5780000 13.5780000 5.4310000
|
||||
204 204 1 0.0000000 13.5780000 10.8620000 8.1460000
|
||||
205 205 1 0.0000000 14.9350000 12.2200000 9.5040000
|
||||
206 206 1 0.0000000 12.2200000 12.2200000 6.7890000
|
||||
207 207 1 0.0000000 12.2200000 14.9350000 9.5040000
|
||||
208 208 1 0.0000000 14.9350000 14.9350000 6.7890000
|
||||
209 209 1 0.0000000 10.8620000 10.8620000 10.8620000
|
||||
210 210 1 0.0000000 10.8620000 13.5780000 13.5780000
|
||||
211 211 1 0.0000000 13.5780000 13.5780000 10.8620000
|
||||
212 212 1 0.0000000 13.5780000 10.8620000 13.5780000
|
||||
213 213 1 0.0000000 14.9350000 12.2200000 14.9350000
|
||||
214 214 1 0.0000000 12.2200000 12.2200000 12.2200000
|
||||
215 215 1 0.0000000 12.2200000 14.9350000 14.9350000
|
||||
216 216 1 0.0000000 14.9350000 14.9350000 12.2200000
|
||||
|
||||
|
|
@ -0,0 +1,534 @@
|
|||
LAMMPS description
|
||||
|
||||
512 atoms
|
||||
0 bonds
|
||||
0 angles
|
||||
0 dihedrals
|
||||
0 impropers
|
||||
|
||||
1 atom types
|
||||
0 bond types
|
||||
0 angle types
|
||||
0 dihedral types
|
||||
0 improper types
|
||||
|
||||
|
||||
0.0000000 21.724000 xlo xhi
|
||||
0.0000000 21.724000 ylo yhi
|
||||
0.0000000 21.724000 zlo zhi
|
||||
|
||||
Atoms
|
||||
|
||||
1 1 1 0.0000000 0.0000000 0.0000000 0.0000000
|
||||
2 2 1 0.0000000 0.0000000 2.7150000 2.7150000
|
||||
3 3 1 0.0000000 2.7150000 2.7150000 0.0000000
|
||||
4 4 1 0.0000000 2.7150000 0.0000000 2.7150000
|
||||
5 5 1 0.0000000 4.0730000 1.3580000 4.0730000
|
||||
6 6 1 0.0000000 1.3580000 1.3580000 1.3580000
|
||||
7 7 1 0.0000000 1.3580000 4.0730000 4.0730000
|
||||
8 8 1 0.0000000 4.0730000 4.0730000 1.3580000
|
||||
9 9 1 0.0000000 0.0000000 0.0000000 5.4310000
|
||||
10 10 1 0.0000000 0.0000000 2.7150000 8.1460000
|
||||
11 11 1 0.0000000 2.7150000 2.7150000 5.4310000
|
||||
12 12 1 0.0000000 2.7150000 0.0000000 8.1460000
|
||||
13 13 1 0.0000000 4.0730000 1.3580000 9.5040000
|
||||
14 14 1 0.0000000 1.3580000 1.3580000 6.7890000
|
||||
15 15 1 0.0000000 1.3580000 4.0730000 9.5040000
|
||||
16 16 1 0.0000000 4.0730000 4.0730000 6.7890000
|
||||
17 17 1 0.0000000 0.0000000 0.0000000 10.8620000
|
||||
18 18 1 0.0000000 0.0000000 2.7150000 13.5770000
|
||||
19 19 1 0.0000000 2.7150000 2.7150000 10.8620000
|
||||
20 20 1 0.0000000 2.7150000 0.0000000 13.5770000
|
||||
21 21 1 0.0000000 4.0730000 1.3580000 14.9350000
|
||||
22 22 1 0.0000000 1.3580000 1.3580000 12.2200000
|
||||
23 23 1 0.0000000 1.3580000 4.0730000 14.9350000
|
||||
24 24 1 0.0000000 4.0730000 4.0730000 12.2200000
|
||||
25 25 1 0.0000000 0.0000000 0.0000000 16.2930000
|
||||
26 26 1 0.0000000 0.0000000 2.7150000 19.0080000
|
||||
27 27 1 0.0000000 2.7150000 2.7150000 16.2930000
|
||||
28 28 1 0.0000000 2.7150000 0.0000000 19.0080000
|
||||
29 29 1 0.0000000 4.0730000 1.3580000 20.3660000
|
||||
30 30 1 0.0000000 1.3580000 1.3580000 17.6510000
|
||||
31 31 1 0.0000000 1.3580000 4.0730000 20.3660000
|
||||
32 32 1 0.0000000 4.0730000 4.0730000 17.6510000
|
||||
33 33 1 0.0000000 0.0000000 5.4310000 0.0000000
|
||||
34 34 1 0.0000000 0.0000000 8.1460000 2.7150000
|
||||
35 35 1 0.0000000 2.7150000 8.1460000 0.0000000
|
||||
36 36 1 0.0000000 2.7150000 5.4310000 2.7150000
|
||||
37 37 1 0.0000000 4.0730000 6.7890000 4.0730000
|
||||
38 38 1 0.0000000 1.3580000 6.7890000 1.3580000
|
||||
39 39 1 0.0000000 1.3580000 9.5040000 4.0730000
|
||||
40 40 1 0.0000000 4.0730000 9.5040000 1.3580000
|
||||
41 41 1 0.0000000 0.0000000 5.4310000 5.4310000
|
||||
42 42 1 0.0000000 0.0000000 8.1460000 8.1460000
|
||||
43 43 1 0.0000000 2.7150000 8.1460000 5.4310000
|
||||
44 44 1 0.0000000 2.7150000 5.4310000 8.1460000
|
||||
45 45 1 0.0000000 4.0730000 6.7890000 9.5040000
|
||||
46 46 1 0.0000000 1.3580000 6.7890000 6.7890000
|
||||
47 47 1 0.0000000 1.3580000 9.5040000 9.5040000
|
||||
48 48 1 0.0000000 4.0730000 9.5040000 6.7890000
|
||||
49 49 1 0.0000000 0.0000000 5.4310000 10.8620000
|
||||
50 50 1 0.0000000 0.0000000 8.1460000 13.5770000
|
||||
51 51 1 0.0000000 2.7150000 8.1460000 10.8620000
|
||||
52 52 1 0.0000000 2.7150000 5.4310000 13.5770000
|
||||
53 53 1 0.0000000 4.0730000 6.7890000 14.9350000
|
||||
54 54 1 0.0000000 1.3580000 6.7890000 12.2200000
|
||||
55 55 1 0.0000000 1.3580000 9.5040000 14.9350000
|
||||
56 56 1 0.0000000 4.0730000 9.5040000 12.2200000
|
||||
57 57 1 0.0000000 0.0000000 5.4310000 16.2930000
|
||||
58 58 1 0.0000000 0.0000000 8.1460000 19.0080000
|
||||
59 59 1 0.0000000 2.7150000 8.1460000 16.2930000
|
||||
60 60 1 0.0000000 2.7150000 5.4310000 19.0080000
|
||||
61 61 1 0.0000000 4.0730000 6.7890000 20.3660000
|
||||
62 62 1 0.0000000 1.3580000 6.7890000 17.6510000
|
||||
63 63 1 0.0000000 1.3580000 9.5040000 20.3660000
|
||||
64 64 1 0.0000000 4.0730000 9.5040000 17.6510000
|
||||
65 65 1 0.0000000 0.0000000 10.8620000 0.0000000
|
||||
66 66 1 0.0000000 0.0000000 13.5770000 2.7150000
|
||||
67 67 1 0.0000000 2.7150000 13.5770000 0.0000000
|
||||
68 68 1 0.0000000 2.7150000 10.8620000 2.7150000
|
||||
69 69 1 0.0000000 4.0730000 12.2200000 4.0730000
|
||||
70 70 1 0.0000000 1.3580000 12.2200000 1.3580000
|
||||
71 71 1 0.0000000 1.3580000 14.9350000 4.0730000
|
||||
72 72 1 0.0000000 4.0730000 14.9350000 1.3580000
|
||||
73 73 1 0.0000000 0.0000000 10.8620000 5.4310000
|
||||
74 74 1 0.0000000 0.0000000 13.5770000 8.1460000
|
||||
75 75 1 0.0000000 2.7150000 13.5770000 5.4310000
|
||||
76 76 1 0.0000000 2.7150000 10.8620000 8.1460000
|
||||
77 77 1 0.0000000 4.0730000 12.2200000 9.5040000
|
||||
78 78 1 0.0000000 1.3580000 12.2200000 6.7890000
|
||||
79 79 1 0.0000000 1.3580000 14.9350000 9.5040000
|
||||
80 80 1 0.0000000 4.0730000 14.9350000 6.7890000
|
||||
81 81 1 0.0000000 0.0000000 10.8620000 10.8620000
|
||||
82 82 1 0.0000000 0.0000000 13.5770000 13.5770000
|
||||
83 83 1 0.0000000 2.7150000 13.5770000 10.8620000
|
||||
84 84 1 0.0000000 2.7150000 10.8620000 13.5770000
|
||||
85 85 1 0.0000000 4.0730000 12.2200000 14.9350000
|
||||
86 86 1 0.0000000 1.3580000 12.2200000 12.2200000
|
||||
87 87 1 0.0000000 1.3580000 14.9350000 14.9350000
|
||||
88 88 1 0.0000000 4.0730000 14.9350000 12.2200000
|
||||
89 89 1 0.0000000 0.0000000 10.8620000 16.2930000
|
||||
90 90 1 0.0000000 0.0000000 13.5770000 19.0080000
|
||||
91 91 1 0.0000000 2.7150000 13.5770000 16.2930000
|
||||
92 92 1 0.0000000 2.7150000 10.8620000 19.0080000
|
||||
93 93 1 0.0000000 4.0730000 12.2200000 20.3660000
|
||||
94 94 1 0.0000000 1.3580000 12.2200000 17.6510000
|
||||
95 95 1 0.0000000 1.3580000 14.9350000 20.3660000
|
||||
96 96 1 0.0000000 4.0730000 14.9350000 17.6510000
|
||||
97 97 1 0.0000000 0.0000000 16.2930000 0.0000000
|
||||
98 98 1 0.0000000 0.0000000 19.0080000 2.7150000
|
||||
99 99 1 0.0000000 2.7150000 19.0080000 0.0000000
|
||||
100 100 1 0.0000000 2.7150000 16.2930000 2.7150000
|
||||
101 101 1 0.0000000 4.0730000 17.6510000 4.0730000
|
||||
102 102 1 0.0000000 1.3580000 17.6510000 1.3580000
|
||||
103 103 1 0.0000000 1.3580000 20.3660000 4.0730000
|
||||
104 104 1 0.0000000 4.0730000 20.3660000 1.3580000
|
||||
105 105 1 0.0000000 0.0000000 16.2930000 5.4310000
|
||||
106 106 1 0.0000000 0.0000000 19.0080000 8.1460000
|
||||
107 107 1 0.0000000 2.7150000 19.0080000 5.4310000
|
||||
108 108 1 0.0000000 2.7150000 16.2930000 8.1460000
|
||||
109 109 1 0.0000000 4.0730000 17.6510000 9.5040000
|
||||
110 110 1 0.0000000 1.3580000 17.6510000 6.7890000
|
||||
111 111 1 0.0000000 1.3580000 20.3660000 9.5040000
|
||||
112 112 1 0.0000000 4.0730000 20.3660000 6.7890000
|
||||
113 113 1 0.0000000 0.0000000 16.2930000 10.8620000
|
||||
114 114 1 0.0000000 0.0000000 19.0080000 13.5770000
|
||||
115 115 1 0.0000000 2.7150000 19.0080000 10.8620000
|
||||
116 116 1 0.0000000 2.7150000 16.2930000 13.5770000
|
||||
117 117 1 0.0000000 4.0730000 17.6510000 14.9350000
|
||||
118 118 1 0.0000000 1.3580000 17.6510000 12.2200000
|
||||
119 119 1 0.0000000 1.3580000 20.3660000 14.9350000
|
||||
120 120 1 0.0000000 4.0730000 20.3660000 12.2200000
|
||||
121 121 1 0.0000000 0.0000000 16.2930000 16.2930000
|
||||
122 122 1 0.0000000 0.0000000 19.0080000 19.0080000
|
||||
123 123 1 0.0000000 2.7150000 19.0080000 16.2930000
|
||||
124 124 1 0.0000000 2.7150000 16.2930000 19.0080000
|
||||
125 125 1 0.0000000 4.0730000 17.6510000 20.3660000
|
||||
126 126 1 0.0000000 1.3580000 17.6510000 17.6510000
|
||||
127 127 1 0.0000000 1.3580000 20.3660000 20.3660000
|
||||
128 128 1 0.0000000 4.0730000 20.3660000 17.6510000
|
||||
129 129 1 0.0000000 5.4310000 0.0000000 0.0000000
|
||||
130 130 1 0.0000000 5.4310000 2.7150000 2.7150000
|
||||
131 131 1 0.0000000 8.1460000 2.7150000 0.0000000
|
||||
132 132 1 0.0000000 8.1460000 0.0000000 2.7150000
|
||||
133 133 1 0.0000000 9.5040000 1.3580000 4.0730000
|
||||
134 134 1 0.0000000 6.7890000 1.3580000 1.3580000
|
||||
135 135 1 0.0000000 6.7890000 4.0730000 4.0730000
|
||||
136 136 1 0.0000000 9.5040000 4.0730000 1.3580000
|
||||
137 137 1 0.0000000 5.4310000 0.0000000 5.4310000
|
||||
138 138 1 0.0000000 5.4310000 2.7150000 8.1460000
|
||||
139 139 1 0.0000000 8.1460000 2.7150000 5.4310000
|
||||
140 140 1 0.0000000 8.1460000 0.0000000 8.1460000
|
||||
141 141 1 0.0000000 9.5040000 1.3580000 9.5040000
|
||||
142 142 1 0.0000000 6.7890000 1.3580000 6.7890000
|
||||
143 143 1 0.0000000 6.7890000 4.0730000 9.5040000
|
||||
144 144 1 0.0000000 9.5040000 4.0730000 6.7890000
|
||||
145 145 1 0.0000000 5.4310000 0.0000000 10.8620000
|
||||
146 146 1 0.0000000 5.4310000 2.7150000 13.5770000
|
||||
147 147 1 0.0000000 8.1460000 2.7150000 10.8620000
|
||||
148 148 1 0.0000000 8.1460000 0.0000000 13.5770000
|
||||
149 149 1 0.0000000 9.5040000 1.3580000 14.9350000
|
||||
150 150 1 0.0000000 6.7890000 1.3580000 12.2200000
|
||||
151 151 1 0.0000000 6.7890000 4.0730000 14.9350000
|
||||
152 152 1 0.0000000 9.5040000 4.0730000 12.2200000
|
||||
153 153 1 0.0000000 5.4310000 0.0000000 16.2930000
|
||||
154 154 1 0.0000000 5.4310000 2.7150000 19.0080000
|
||||
155 155 1 0.0000000 8.1460000 2.7150000 16.2930000
|
||||
156 156 1 0.0000000 8.1460000 0.0000000 19.0080000
|
||||
157 157 1 0.0000000 9.5040000 1.3580000 20.3660000
|
||||
158 158 1 0.0000000 6.7890000 1.3580000 17.6510000
|
||||
159 159 1 0.0000000 6.7890000 4.0730000 20.3660000
|
||||
160 160 1 0.0000000 9.5040000 4.0730000 17.6510000
|
||||
161 161 1 0.0000000 5.4310000 5.4310000 0.0000000
|
||||
162 162 1 0.0000000 5.4310000 8.1460000 2.7150000
|
||||
163 163 1 0.0000000 8.1460000 8.1460000 0.0000000
|
||||
164 164 1 0.0000000 8.1460000 5.4310000 2.7150000
|
||||
165 165 1 0.0000000 9.5040000 6.7890000 4.0730000
|
||||
166 166 1 0.0000000 6.7890000 6.7890000 1.3580000
|
||||
167 167 1 0.0000000 6.7890000 9.5040000 4.0730000
|
||||
168 168 1 0.0000000 9.5040000 9.5040000 1.3580000
|
||||
169 169 1 0.0000000 5.4310000 5.4310000 5.4310000
|
||||
170 170 1 0.0000000 5.4310000 8.1460000 8.1460000
|
||||
171 171 1 0.0000000 8.1460000 8.1460000 5.4310000
|
||||
172 172 1 0.0000000 8.1460000 5.4310000 8.1460000
|
||||
173 173 1 0.0000000 9.5040000 6.7890000 9.5040000
|
||||
174 174 1 0.0000000 6.7890000 6.7890000 6.7890000
|
||||
175 175 1 0.0000000 6.7890000 9.5040000 9.5040000
|
||||
176 176 1 0.0000000 9.5040000 9.5040000 6.7890000
|
||||
177 177 1 0.0000000 5.4310000 5.4310000 10.8620000
|
||||
178 178 1 0.0000000 5.4310000 8.1460000 13.5770000
|
||||
179 179 1 0.0000000 8.1460000 8.1460000 10.8620000
|
||||
180 180 1 0.0000000 8.1460000 5.4310000 13.5770000
|
||||
181 181 1 0.0000000 9.5040000 6.7890000 14.9350000
|
||||
182 182 1 0.0000000 6.7890000 6.7890000 12.2200000
|
||||
183 183 1 0.0000000 6.7890000 9.5040000 14.9350000
|
||||
184 184 1 0.0000000 9.5040000 9.5040000 12.2200000
|
||||
185 185 1 0.0000000 5.4310000 5.4310000 16.2930000
|
||||
186 186 1 0.0000000 5.4310000 8.1460000 19.0080000
|
||||
187 187 1 0.0000000 8.1460000 8.1460000 16.2930000
|
||||
188 188 1 0.0000000 8.1460000 5.4310000 19.0080000
|
||||
189 189 1 0.0000000 9.5040000 6.7890000 20.3660000
|
||||
190 190 1 0.0000000 6.7890000 6.7890000 17.6510000
|
||||
191 191 1 0.0000000 6.7890000 9.5040000 20.3660000
|
||||
192 192 1 0.0000000 9.5040000 9.5040000 17.6510000
|
||||
193 193 1 0.0000000 5.4310000 10.8620000 0.0000000
|
||||
194 194 1 0.0000000 5.4310000 13.5770000 2.7150000
|
||||
195 195 1 0.0000000 8.1460000 13.5770000 0.0000000
|
||||
196 196 1 0.0000000 8.1460000 10.8620000 2.7150000
|
||||
197 197 1 0.0000000 9.5040000 12.2200000 4.0730000
|
||||
198 198 1 0.0000000 6.7890000 12.2200000 1.3580000
|
||||
199 199 1 0.0000000 6.7890000 14.9350000 4.0730000
|
||||
200 200 1 0.0000000 9.5040000 14.9350000 1.3580000
|
||||
201 201 1 0.0000000 5.4310000 10.8620000 5.4310000
|
||||
202 202 1 0.0000000 5.4310000 13.5770000 8.1460000
|
||||
203 203 1 0.0000000 8.1460000 13.5770000 5.4310000
|
||||
204 204 1 0.0000000 8.1460000 10.8620000 8.1460000
|
||||
205 205 1 0.0000000 9.5040000 12.2200000 9.5040000
|
||||
206 206 1 0.0000000 6.7890000 12.2200000 6.7890000
|
||||
207 207 1 0.0000000 6.7890000 14.9350000 9.5040000
|
||||
208 208 1 0.0000000 9.5040000 14.9350000 6.7890000
|
||||
209 209 1 0.0000000 5.4310000 10.8620000 10.8620000
|
||||
210 210 1 0.0000000 5.4310000 13.5770000 13.5770000
|
||||
211 211 1 0.0000000 8.1460000 13.5770000 10.8620000
|
||||
212 212 1 0.0000000 8.1460000 10.8620000 13.5770000
|
||||
213 213 1 0.0000000 9.5040000 12.2200000 14.9350000
|
||||
214 214 1 0.0000000 6.7890000 12.2200000 12.2200000
|
||||
215 215 1 0.0000000 6.7890000 14.9350000 14.9350000
|
||||
216 216 1 0.0000000 9.5040000 14.9350000 12.2200000
|
||||
217 217 1 0.0000000 5.4310000 10.8620000 16.2930000
|
||||
218 218 1 0.0000000 5.4310000 13.5770000 19.0080000
|
||||
219 219 1 0.0000000 8.1460000 13.5770000 16.2930000
|
||||
220 220 1 0.0000000 8.1460000 10.8620000 19.0080000
|
||||
221 221 1 0.0000000 9.5040000 12.2200000 20.3660000
|
||||
222 222 1 0.0000000 6.7890000 12.2200000 17.6510000
|
||||
223 223 1 0.0000000 6.7890000 14.9350000 20.3660000
|
||||
224 224 1 0.0000000 9.5040000 14.9350000 17.6510000
|
||||
225 225 1 0.0000000 5.4310000 16.2930000 0.0000000
|
||||
226 226 1 0.0000000 5.4310000 19.0080000 2.7150000
|
||||
227 227 1 0.0000000 8.1460000 19.0080000 0.0000000
|
||||
228 228 1 0.0000000 8.1460000 16.2930000 2.7150000
|
||||
229 229 1 0.0000000 9.5040000 17.6510000 4.0730000
|
||||
230 230 1 0.0000000 6.7890000 17.6510000 1.3580000
|
||||
231 231 1 0.0000000 6.7890000 20.3660000 4.0730000
|
||||
232 232 1 0.0000000 9.5040000 20.3660000 1.3580000
|
||||
233 233 1 0.0000000 5.4310000 16.2930000 5.4310000
|
||||
234 234 1 0.0000000 5.4310000 19.0080000 8.1460000
|
||||
235 235 1 0.0000000 8.1460000 19.0080000 5.4310000
|
||||
236 236 1 0.0000000 8.1460000 16.2930000 8.1460000
|
||||
237 237 1 0.0000000 9.5040000 17.6510000 9.5040000
|
||||
238 238 1 0.0000000 6.7890000 17.6510000 6.7890000
|
||||
239 239 1 0.0000000 6.7890000 20.3660000 9.5040000
|
||||
240 240 1 0.0000000 9.5040000 20.3660000 6.7890000
|
||||
241 241 1 0.0000000 5.4310000 16.2930000 10.8620000
|
||||
242 242 1 0.0000000 5.4310000 19.0080000 13.5770000
|
||||
243 243 1 0.0000000 8.1460000 19.0080000 10.8620000
|
||||
244 244 1 0.0000000 8.1460000 16.2930000 13.5770000
|
||||
245 245 1 0.0000000 9.5040000 17.6510000 14.9350000
|
||||
246 246 1 0.0000000 6.7890000 17.6510000 12.2200000
|
||||
247 247 1 0.0000000 6.7890000 20.3660000 14.9350000
|
||||
248 248 1 0.0000000 9.5040000 20.3660000 12.2200000
|
||||
249 249 1 0.0000000 5.4310000 16.2930000 16.2930000
|
||||
250 250 1 0.0000000 5.4310000 19.0080000 19.0080000
|
||||
251 251 1 0.0000000 8.1460000 19.0080000 16.2930000
|
||||
252 252 1 0.0000000 8.1460000 16.2930000 19.0080000
|
||||
253 253 1 0.0000000 9.5040000 17.6510000 20.3660000
|
||||
254 254 1 0.0000000 6.7890000 17.6510000 17.6510000
|
||||
255 255 1 0.0000000 6.7890000 20.3660000 20.3660000
|
||||
256 256 1 0.0000000 9.5040000 20.3660000 17.6510000
|
||||
257 257 1 0.0000000 10.8620000 0.0000000 0.0000000
|
||||
258 258 1 0.0000000 10.8620000 2.7150000 2.7150000
|
||||
259 259 1 0.0000000 13.5770000 2.7150000 0.0000000
|
||||
260 260 1 0.0000000 13.5770000 0.0000000 2.7150000
|
||||
261 261 1 0.0000000 14.9350000 1.3580000 4.0730000
|
||||
262 262 1 0.0000000 12.2200000 1.3580000 1.3580000
|
||||
263 263 1 0.0000000 12.2200000 4.0730000 4.0730000
|
||||
264 264 1 0.0000000 14.9350000 4.0730000 1.3580000
|
||||
265 265 1 0.0000000 10.8620000 0.0000000 5.4310000
|
||||
266 266 1 0.0000000 10.8620000 2.7150000 8.1460000
|
||||
267 267 1 0.0000000 13.5770000 2.7150000 5.4310000
|
||||
268 268 1 0.0000000 13.5770000 0.0000000 8.1460000
|
||||
269 269 1 0.0000000 14.9350000 1.3580000 9.5040000
|
||||
270 270 1 0.0000000 12.2200000 1.3580000 6.7890000
|
||||
271 271 1 0.0000000 12.2200000 4.0730000 9.5040000
|
||||
272 272 1 0.0000000 14.9350000 4.0730000 6.7890000
|
||||
273 273 1 0.0000000 10.8620000 0.0000000 10.8620000
|
||||
274 274 1 0.0000000 10.8620000 2.7150000 13.5770000
|
||||
275 275 1 0.0000000 13.5770000 2.7150000 10.8620000
|
||||
276 276 1 0.0000000 13.5770000 0.0000000 13.5770000
|
||||
277 277 1 0.0000000 14.9350000 1.3580000 14.9350000
|
||||
278 278 1 0.0000000 12.2200000 1.3580000 12.2200000
|
||||
279 279 1 0.0000000 12.2200000 4.0730000 14.9350000
|
||||
280 280 1 0.0000000 14.9350000 4.0730000 12.2200000
|
||||
281 281 1 0.0000000 10.8620000 0.0000000 16.2930000
|
||||
282 282 1 0.0000000 10.8620000 2.7150000 19.0080000
|
||||
283 283 1 0.0000000 13.5770000 2.7150000 16.2930000
|
||||
284 284 1 0.0000000 13.5770000 0.0000000 19.0080000
|
||||
285 285 1 0.0000000 14.9350000 1.3580000 20.3660000
|
||||
286 286 1 0.0000000 12.2200000 1.3580000 17.6510000
|
||||
287 287 1 0.0000000 12.2200000 4.0730000 20.3660000
|
||||
288 288 1 0.0000000 14.9350000 4.0730000 17.6510000
|
||||
289 289 1 0.0000000 10.8620000 5.4310000 0.0000000
|
||||
290 290 1 0.0000000 10.8620000 8.1460000 2.7150000
|
||||
291 291 1 0.0000000 13.5770000 8.1460000 0.0000000
|
||||
292 292 1 0.0000000 13.5770000 5.4310000 2.7150000
|
||||
293 293 1 0.0000000 14.9350000 6.7890000 4.0730000
|
||||
294 294 1 0.0000000 12.2200000 6.7890000 1.3580000
|
||||
295 295 1 0.0000000 12.2200000 9.5040000 4.0730000
|
||||
296 296 1 0.0000000 14.9350000 9.5040000 1.3580000
|
||||
297 297 1 0.0000000 10.8620000 5.4310000 5.4310000
|
||||
298 298 1 0.0000000 10.8620000 8.1460000 8.1460000
|
||||
299 299 1 0.0000000 13.5770000 8.1460000 5.4310000
|
||||
300 300 1 0.0000000 13.5770000 5.4310000 8.1460000
|
||||
301 301 1 0.0000000 14.9350000 6.7890000 9.5040000
|
||||
302 302 1 0.0000000 12.2200000 6.7890000 6.7890000
|
||||
303 303 1 0.0000000 12.2200000 9.5040000 9.5040000
|
||||
304 304 1 0.0000000 14.9350000 9.5040000 6.7890000
|
||||
305 305 1 0.0000000 10.8620000 5.4310000 10.8620000
|
||||
306 306 1 0.0000000 10.8620000 8.1460000 13.5770000
|
||||
307 307 1 0.0000000 13.5770000 8.1460000 10.8620000
|
||||
308 308 1 0.0000000 13.5770000 5.4310000 13.5770000
|
||||
309 309 1 0.0000000 14.9350000 6.7890000 14.9350000
|
||||
310 310 1 0.0000000 12.2200000 6.7890000 12.2200000
|
||||
311 311 1 0.0000000 12.2200000 9.5040000 14.9350000
|
||||
312 312 1 0.0000000 14.9350000 9.5040000 12.2200000
|
||||
313 313 1 0.0000000 10.8620000 5.4310000 16.2930000
|
||||
314 314 1 0.0000000 10.8620000 8.1460000 19.0080000
|
||||
315 315 1 0.0000000 13.5770000 8.1460000 16.2930000
|
||||
316 316 1 0.0000000 13.5770000 5.4310000 19.0080000
|
||||
317 317 1 0.0000000 14.9350000 6.7890000 20.3660000
|
||||
318 318 1 0.0000000 12.2200000 6.7890000 17.6510000
|
||||
319 319 1 0.0000000 12.2200000 9.5040000 20.3660000
|
||||
320 320 1 0.0000000 14.9350000 9.5040000 17.6510000
|
||||
321 321 1 0.0000000 10.8620000 10.8620000 0.0000000
|
||||
322 322 1 0.0000000 10.8620000 13.5770000 2.7150000
|
||||
323 323 1 0.0000000 13.5770000 13.5770000 0.0000000
|
||||
324 324 1 0.0000000 13.5770000 10.8620000 2.7150000
|
||||
325 325 1 0.0000000 14.9350000 12.2200000 4.0730000
|
||||
326 326 1 0.0000000 12.2200000 12.2200000 1.3580000
|
||||
327 327 1 0.0000000 12.2200000 14.9350000 4.0730000
|
||||
328 328 1 0.0000000 14.9350000 14.9350000 1.3580000
|
||||
329 329 1 0.0000000 10.8620000 10.8620000 5.4310000
|
||||
330 330 1 0.0000000 10.8620000 13.5770000 8.1460000
|
||||
331 331 1 0.0000000 13.5770000 13.5770000 5.4310000
|
||||
332 332 1 0.0000000 13.5770000 10.8620000 8.1460000
|
||||
333 333 1 0.0000000 14.9350000 12.2200000 9.5040000
|
||||
334 334 1 0.0000000 12.2200000 12.2200000 6.7890000
|
||||
335 335 1 0.0000000 12.2200000 14.9350000 9.5040000
|
||||
336 336 1 0.0000000 14.9350000 14.9350000 6.7890000
|
||||
337 337 1 0.0000000 10.8620000 10.8620000 10.8620000
|
||||
338 338 1 0.0000000 10.8620000 13.5770000 13.5770000
|
||||
339 339 1 0.0000000 13.5770000 13.5770000 10.8620000
|
||||
340 340 1 0.0000000 13.5770000 10.8620000 13.5770000
|
||||
341 341 1 0.0000000 14.9350000 12.2200000 14.9350000
|
||||
342 342 1 0.0000000 12.2200000 12.2200000 12.2200000
|
||||
343 343 1 0.0000000 12.2200000 14.9350000 14.9350000
|
||||
344 344 1 0.0000000 14.9350000 14.9350000 12.2200000
|
||||
345 345 1 0.0000000 10.8620000 10.8620000 16.2930000
|
||||
346 346 1 0.0000000 10.8620000 13.5770000 19.0080000
|
||||
347 347 1 0.0000000 13.5770000 13.5770000 16.2930000
|
||||
348 348 1 0.0000000 13.5770000 10.8620000 19.0080000
|
||||
349 349 1 0.0000000 14.9350000 12.2200000 20.3660000
|
||||
350 350 1 0.0000000 12.2200000 12.2200000 17.6510000
|
||||
351 351 1 0.0000000 12.2200000 14.9350000 20.3660000
|
||||
352 352 1 0.0000000 14.9350000 14.9350000 17.6510000
|
||||
353 353 1 0.0000000 10.8620000 16.2930000 0.0000000
|
||||
354 354 1 0.0000000 10.8620000 19.0080000 2.7150000
|
||||
355 355 1 0.0000000 13.5770000 19.0080000 0.0000000
|
||||
356 356 1 0.0000000 13.5770000 16.2930000 2.7150000
|
||||
357 357 1 0.0000000 14.9350000 17.6510000 4.0730000
|
||||
358 358 1 0.0000000 12.2200000 17.6510000 1.3580000
|
||||
359 359 1 0.0000000 12.2200000 20.3660000 4.0730000
|
||||
360 360 1 0.0000000 14.9350000 20.3660000 1.3580000
|
||||
361 361 1 0.0000000 10.8620000 16.2930000 5.4310000
|
||||
362 362 1 0.0000000 10.8620000 19.0080000 8.1460000
|
||||
363 363 1 0.0000000 13.5770000 19.0080000 5.4310000
|
||||
364 364 1 0.0000000 13.5770000 16.2930000 8.1460000
|
||||
365 365 1 0.0000000 14.9350000 17.6510000 9.5040000
|
||||
366 366 1 0.0000000 12.2200000 17.6510000 6.7890000
|
||||
367 367 1 0.0000000 12.2200000 20.3660000 9.5040000
|
||||
368 368 1 0.0000000 14.9350000 20.3660000 6.7890000
|
||||
369 369 1 0.0000000 10.8620000 16.2930000 10.8620000
|
||||
370 370 1 0.0000000 10.8620000 19.0080000 13.5770000
|
||||
371 371 1 0.0000000 13.5770000 19.0080000 10.8620000
|
||||
372 372 1 0.0000000 13.5770000 16.2930000 13.5770000
|
||||
373 373 1 0.0000000 14.9350000 17.6510000 14.9350000
|
||||
374 374 1 0.0000000 12.2200000 17.6510000 12.2200000
|
||||
375 375 1 0.0000000 12.2200000 20.3660000 14.9350000
|
||||
376 376 1 0.0000000 14.9350000 20.3660000 12.2200000
|
||||
377 377 1 0.0000000 10.8620000 16.2930000 16.2930000
|
||||
378 378 1 0.0000000 10.8620000 19.0080000 19.0080000
|
||||
379 379 1 0.0000000 13.5770000 19.0080000 16.2930000
|
||||
380 380 1 0.0000000 13.5770000 16.2930000 19.0080000
|
||||
381 381 1 0.0000000 14.9350000 17.6510000 20.3660000
|
||||
382 382 1 0.0000000 12.2200000 17.6510000 17.6510000
|
||||
383 383 1 0.0000000 12.2200000 20.3660000 20.3660000
|
||||
384 384 1 0.0000000 14.9350000 20.3660000 17.6510000
|
||||
385 385 1 0.0000000 16.2930000 0.0000000 0.0000000
|
||||
386 386 1 0.0000000 16.2930000 2.7150000 2.7150000
|
||||
387 387 1 0.0000000 19.0080000 2.7150000 0.0000000
|
||||
388 388 1 0.0000000 19.0080000 0.0000000 2.7150000
|
||||
389 389 1 0.0000000 20.3660000 1.3580000 4.0730000
|
||||
390 390 1 0.0000000 17.6510000 1.3580000 1.3580000
|
||||
391 391 1 0.0000000 17.6510000 4.0730000 4.0730000
|
||||
392 392 1 0.0000000 20.3660000 4.0730000 1.3580000
|
||||
393 393 1 0.0000000 16.2930000 0.0000000 5.4310000
|
||||
394 394 1 0.0000000 16.2930000 2.7150000 8.1460000
|
||||
395 395 1 0.0000000 19.0080000 2.7150000 5.4310000
|
||||
396 396 1 0.0000000 19.0080000 0.0000000 8.1460000
|
||||
397 397 1 0.0000000 20.3660000 1.3580000 9.5040000
|
||||
398 398 1 0.0000000 17.6510000 1.3580000 6.7890000
|
||||
399 399 1 0.0000000 17.6510000 4.0730000 9.5040000
|
||||
400 400 1 0.0000000 20.3660000 4.0730000 6.7890000
|
||||
401 401 1 0.0000000 16.2930000 0.0000000 10.8620000
|
||||
402 402 1 0.0000000 16.2930000 2.7150000 13.5770000
|
||||
403 403 1 0.0000000 19.0080000 2.7150000 10.8620000
|
||||
404 404 1 0.0000000 19.0080000 0.0000000 13.5770000
|
||||
405 405 1 0.0000000 20.3660000 1.3580000 14.9350000
|
||||
406 406 1 0.0000000 17.6510000 1.3580000 12.2200000
|
||||
407 407 1 0.0000000 17.6510000 4.0730000 14.9350000
|
||||
408 408 1 0.0000000 20.3660000 4.0730000 12.2200000
|
||||
409 409 1 0.0000000 16.2930000 0.0000000 16.2930000
|
||||
410 410 1 0.0000000 16.2930000 2.7150000 19.0080000
|
||||
411 411 1 0.0000000 19.0080000 2.7150000 16.2930000
|
||||
412 412 1 0.0000000 19.0080000 0.0000000 19.0080000
|
||||
413 413 1 0.0000000 20.3660000 1.3580000 20.3660000
|
||||
414 414 1 0.0000000 17.6510000 1.3580000 17.6510000
|
||||
415 415 1 0.0000000 17.6510000 4.0730000 20.3660000
|
||||
416 416 1 0.0000000 20.3660000 4.0730000 17.6510000
|
||||
417 417 1 0.0000000 16.2930000 5.4310000 0.0000000
|
||||
418 418 1 0.0000000 16.2930000 8.1460000 2.7150000
|
||||
419 419 1 0.0000000 19.0080000 8.1460000 0.0000000
|
||||
420 420 1 0.0000000 19.0080000 5.4310000 2.7150000
|
||||
421 421 1 0.0000000 20.3660000 6.7890000 4.0730000
|
||||
422 422 1 0.0000000 17.6510000 6.7890000 1.3580000
|
||||
423 423 1 0.0000000 17.6510000 9.5040000 4.0730000
|
||||
424 424 1 0.0000000 20.3660000 9.5040000 1.3580000
|
||||
425 425 1 0.0000000 16.2930000 5.4310000 5.4310000
|
||||
426 426 1 0.0000000 16.2930000 8.1460000 8.1460000
|
||||
427 427 1 0.0000000 19.0080000 8.1460000 5.4310000
|
||||
428 428 1 0.0000000 19.0080000 5.4310000 8.1460000
|
||||
429 429 1 0.0000000 20.3660000 6.7890000 9.5040000
|
||||
430 430 1 0.0000000 17.6510000 6.7890000 6.7890000
|
||||
431 431 1 0.0000000 17.6510000 9.5040000 9.5040000
|
||||
432 432 1 0.0000000 20.3660000 9.5040000 6.7890000
|
||||
433 433 1 0.0000000 16.2930000 5.4310000 10.8620000
|
||||
434 434 1 0.0000000 16.2930000 8.1460000 13.5770000
|
||||
435 435 1 0.0000000 19.0080000 8.1460000 10.8620000
|
||||
436 436 1 0.0000000 19.0080000 5.4310000 13.5770000
|
||||
437 437 1 0.0000000 20.3660000 6.7890000 14.9350000
|
||||
438 438 1 0.0000000 17.6510000 6.7890000 12.2200000
|
||||
439 439 1 0.0000000 17.6510000 9.5040000 14.9350000
|
||||
440 440 1 0.0000000 20.3660000 9.5040000 12.2200000
|
||||
441 441 1 0.0000000 16.2930000 5.4310000 16.2930000
|
||||
442 442 1 0.0000000 16.2930000 8.1460000 19.0080000
|
||||
443 443 1 0.0000000 19.0080000 8.1460000 16.2930000
|
||||
444 444 1 0.0000000 19.0080000 5.4310000 19.0080000
|
||||
445 445 1 0.0000000 20.3660000 6.7890000 20.3660000
|
||||
446 446 1 0.0000000 17.6510000 6.7890000 17.6510000
|
||||
447 447 1 0.0000000 17.6510000 9.5040000 20.3660000
|
||||
448 448 1 0.0000000 20.3660000 9.5040000 17.6510000
|
||||
449 449 1 0.0000000 16.2930000 10.8620000 0.0000000
|
||||
450 450 1 0.0000000 16.2930000 13.5770000 2.7150000
|
||||
451 451 1 0.0000000 19.0080000 13.5770000 0.0000000
|
||||
452 452 1 0.0000000 19.0080000 10.8620000 2.7150000
|
||||
453 453 1 0.0000000 20.3660000 12.2200000 4.0730000
|
||||
454 454 1 0.0000000 17.6510000 12.2200000 1.3580000
|
||||
455 455 1 0.0000000 17.6510000 14.9350000 4.0730000
|
||||
456 456 1 0.0000000 20.3660000 14.9350000 1.3580000
|
||||
457 457 1 0.0000000 16.2930000 10.8620000 5.4310000
|
||||
458 458 1 0.0000000 16.2930000 13.5770000 8.1460000
|
||||
459 459 1 0.0000000 19.0080000 13.5770000 5.4310000
|
||||
460 460 1 0.0000000 19.0080000 10.8620000 8.1460000
|
||||
461 461 1 0.0000000 20.3660000 12.2200000 9.5040000
|
||||
462 462 1 0.0000000 17.6510000 12.2200000 6.7890000
|
||||
463 463 1 0.0000000 17.6510000 14.9350000 9.5040000
|
||||
464 464 1 0.0000000 20.3660000 14.9350000 6.7890000
|
||||
465 465 1 0.0000000 16.2930000 10.8620000 10.8620000
|
||||
466 466 1 0.0000000 16.2930000 13.5770000 13.5770000
|
||||
467 467 1 0.0000000 19.0080000 13.5770000 10.8620000
|
||||
468 468 1 0.0000000 19.0080000 10.8620000 13.5770000
|
||||
469 469 1 0.0000000 20.3660000 12.2200000 14.9350000
|
||||
470 470 1 0.0000000 17.6510000 12.2200000 12.2200000
|
||||
471 471 1 0.0000000 17.6510000 14.9350000 14.9350000
|
||||
472 472 1 0.0000000 20.3660000 14.9350000 12.2200000
|
||||
473 473 1 0.0000000 16.2930000 10.8620000 16.2930000
|
||||
474 474 1 0.0000000 16.2930000 13.5770000 19.0080000
|
||||
475 475 1 0.0000000 19.0080000 13.5770000 16.2930000
|
||||
476 476 1 0.0000000 19.0080000 10.8620000 19.0080000
|
||||
477 477 1 0.0000000 20.3660000 12.2200000 20.3660000
|
||||
478 478 1 0.0000000 17.6510000 12.2200000 17.6510000
|
||||
479 479 1 0.0000000 17.6510000 14.9350000 20.3660000
|
||||
480 480 1 0.0000000 20.3660000 14.9350000 17.6510000
|
||||
481 481 1 0.0000000 16.2930000 16.2930000 0.0000000
|
||||
482 482 1 0.0000000 16.2930000 19.0080000 2.7150000
|
||||
483 483 1 0.0000000 19.0080000 19.0080000 0.0000000
|
||||
484 484 1 0.0000000 19.0080000 16.2930000 2.7150000
|
||||
485 485 1 0.0000000 20.3660000 17.6510000 4.0730000
|
||||
486 486 1 0.0000000 17.6510000 17.6510000 1.3580000
|
||||
487 487 1 0.0000000 17.6510000 20.3660000 4.0730000
|
||||
488 488 1 0.0000000 20.3660000 20.3660000 1.3580000
|
||||
489 489 1 0.0000000 16.2930000 16.2930000 5.4310000
|
||||
490 490 1 0.0000000 16.2930000 19.0080000 8.1460000
|
||||
491 491 1 0.0000000 19.0080000 19.0080000 5.4310000
|
||||
492 492 1 0.0000000 19.0080000 16.2930000 8.1460000
|
||||
493 493 1 0.0000000 20.3660000 17.6510000 9.5040000
|
||||
494 494 1 0.0000000 17.6510000 17.6510000 6.7890000
|
||||
495 495 1 0.0000000 17.6510000 20.3660000 9.5040000
|
||||
496 496 1 0.0000000 20.3660000 20.3660000 6.7890000
|
||||
497 497 1 0.0000000 16.2930000 16.2930000 10.8620000
|
||||
498 498 1 0.0000000 16.2930000 19.0080000 13.5770000
|
||||
499 499 1 0.0000000 19.0080000 19.0080000 10.8620000
|
||||
500 500 1 0.0000000 19.0080000 16.2930000 13.5770000
|
||||
501 501 1 0.0000000 20.3660000 17.6510000 14.9350000
|
||||
502 502 1 0.0000000 17.6510000 17.6510000 12.2200000
|
||||
503 503 1 0.0000000 17.6510000 20.3660000 14.9350000
|
||||
504 504 1 0.0000000 20.3660000 20.3660000 12.2200000
|
||||
505 505 1 0.0000000 16.2930000 16.2930000 16.2930000
|
||||
506 506 1 0.0000000 16.2930000 19.0080000 19.0080000
|
||||
507 507 1 0.0000000 19.0080000 19.0080000 16.2930000
|
||||
508 508 1 0.0000000 19.0080000 16.2930000 19.0080000
|
||||
509 509 1 0.0000000 20.3660000 17.6510000 20.3660000
|
||||
510 510 1 0.0000000 17.6510000 17.6510000 17.6510000
|
||||
511 511 1 0.0000000 17.6510000 20.3660000 20.3660000
|
||||
512 512 1 0.0000000 20.3660000 20.3660000 17.6510000
|
||||
|
||||
|
|
@ -0,0 +1,29 @@
|
|||
LAMMPS description
|
||||
|
||||
8 atoms
|
||||
0 bonds
|
||||
0 angles
|
||||
0 dihedrals
|
||||
0 impropers
|
||||
|
||||
1 atom types
|
||||
0 bond types
|
||||
0 angle types
|
||||
0 dihedral types
|
||||
0 improper types
|
||||
|
||||
|
||||
0.0000000 5.4310000 xlo xhi
|
||||
0.0000000 5.4310000 ylo yhi
|
||||
0.0000000 5.4310000 zlo zhi
|
||||
|
||||
Atoms
|
||||
|
||||
1 1 1 0.0000000 0.0000000 0.0000000 0.0000000
|
||||
2 2 1 0.0000000 1.3577500 1.3577500 1.3572000
|
||||
3 3 1 0.0000000 2.7155000 2.7155000 0.0000000
|
||||
4 4 1 0.0000000 4.0732500 4.0732500 1.3572000
|
||||
5 5 1 0.0000000 2.7155000 0.0000000 2.7144000
|
||||
6 6 1 0.0000000 4.0732500 1.3577500 4.0732500
|
||||
7 7 1 0.0000000 0.0000000 2.7155000 2.7155000
|
||||
8 8 1 0.0000000 1.3577500 4.0732500 4.0732500
|
||||
|
|
@ -0,0 +1,192 @@
|
|||
5409.83472486 3.05075234 0.00000214
|
||||
-1277.48270695 -863.24917964 -862.95613831
|
||||
-193.14095266 0.11071645 0.00000015
|
||||
-1277.48270619 -863.24917934 862.95613793
|
||||
-193.17613831 0.34066975 -0.00000031
|
||||
-1276.01088244 861.54715125 -861.62537402
|
||||
83.46959051 -0.09801326 0.00000000
|
||||
-1276.01088167 861.54715064 861.62537387
|
||||
3.05073556 5409.83419867 0.00000137
|
||||
-863.13224993 -1277.34160622 -862.92133430
|
||||
0.12865796 -193.14095472 -0.00000023
|
||||
-863.13224825 -1277.34160485 862.92133392
|
||||
-0.23661028 83.46934214 -0.00000046
|
||||
861.66402909 -1276.15172701 861.66024333
|
||||
-0.00634065 -193.17585981 -0.00000015
|
||||
861.66402909 -1276.15172686 -861.66024394
|
||||
0.00000031 0.00000031 5410.11037330
|
||||
-862.89766079 -862.97973912 -1277.71823542
|
||||
0.00000000 -0.00000008 83.84059083
|
||||
862.89766018 862.97973851 -1277.71823557
|
||||
0.00000015 0.00000015 -193.17558390
|
||||
-861.60900269 861.52691291 -1276.08157137
|
||||
-0.00000015 -0.00000031 -193.17573821
|
||||
861.60900330 -861.52691284 -1276.08157236
|
||||
-1277.48271824 -863.13225435 -862.89768596
|
||||
5409.83567916 3.04882502 2.82007861
|
||||
-1277.34161080 -863.24919475 862.97975804
|
||||
-193.14089260 0.11950100 0.11994134
|
||||
-1277.52243157 863.24943259 -863.11331046
|
||||
-193.17597070 0.16713301 -0.02106496
|
||||
-1274.64156872 859.96385388 860.17328202
|
||||
83.46945758 -0.16730525 -0.06100253
|
||||
-863.24919444 -1277.34161103 -862.97975804
|
||||
3.04882666 5409.83567944 -2.82007731
|
||||
-863.13225496 -1277.48271916 862.89768688
|
||||
0.11950094 -193.14089255 -0.11994043
|
||||
863.24943320 -1277.52243118 863.11331076
|
||||
-0.16730522 83.46945778 0.06100314
|
||||
859.96385365 -1274.64156819 -860.17328225
|
||||
0.16713979 -193.17596607 0.02106008
|
||||
-862.95611199 -862.92132598 -1277.71824411
|
||||
2.82004085 -2.82004013 5410.11000835
|
||||
862.92132743 862.95611344 -1277.71824587
|
||||
-0.11994722 0.11994786 83.84083834
|
||||
-862.88110757 862.88110699 -1277.34764097
|
||||
0.02099713 0.06108924 -193.17561785
|
||||
860.25587487 -860.25587502 -1274.81548840
|
||||
-0.06108897 -0.02099687 -193.17561808
|
||||
-193.14095465 0.12865765 0.00000015
|
||||
-1277.34160508 -863.13224794 862.92133361
|
||||
5409.83419867 3.05073968 0.00000092
|
||||
-1277.34160584 -863.13224924 -862.92133483
|
||||
83.46934214 -0.23660998 -0.00000076
|
||||
-1276.15172724 861.66402917 861.66024325
|
||||
-193.17585988 -0.00634042 -0.00000031
|
||||
-1276.15172694 861.66402940 -861.66024325
|
||||
0.11071645 -193.14095243 0.00000046
|
||||
-863.24917949 -1277.48270718 862.95613831
|
||||
3.05075524 5409.83472478 -0.00000046
|
||||
-863.24918117 -1277.48270825 -862.95613923
|
||||
0.34066922 -193.17613823 0.00000046
|
||||
861.54715094 -1276.01088228 -861.62537295
|
||||
-0.09801303 83.46959035 0.00000015
|
||||
861.54713538 -1276.01088145 861.62537387
|
||||
-0.00000046 -0.00000023 83.84059068
|
||||
862.97973867 862.89766010 -1277.71823633
|
||||
-0.00000214 -0.00000053 5410.11037574
|
||||
-862.97973943 -862.89766079 -1277.71823633
|
||||
0.00000015 0.00000008 -193.17558374
|
||||
861.52691291 -861.60900269 -1276.08157198
|
||||
-0.00000015 -0.00000015 -193.17573814
|
||||
-861.52691368 861.60900261 -1276.08157243
|
||||
-1277.48271786 -863.13225450 862.89768520
|
||||
-193.14089232 0.11950085 -0.11994115
|
||||
-1277.34161255 -863.24919673 -862.97975957
|
||||
5409.83568051 3.04882517 -2.82007644
|
||||
-1277.52243110 863.24943259 863.11330990
|
||||
83.46945732 -0.16730494 0.06100319
|
||||
-1274.64156796 859.96385342 -860.17328103
|
||||
-193.17597041 0.16713331 0.02106477
|
||||
-863.24919482 -1277.34161057 862.97975774
|
||||
0.11950077 -193.14089270 0.11994160
|
||||
-863.13225473 -1277.48271839 -862.89768673
|
||||
3.04882502 5409.83568081 2.82007903
|
||||
863.24943084 -1277.52242966 -863.11330868
|
||||
0.16713324 -193.17597064 -0.02106522
|
||||
859.96385510 -1274.64156926 860.17328255
|
||||
-0.16730411 83.46945641 -0.06100350
|
||||
862.95611161 862.92132537 -1277.71824365
|
||||
0.11994725 -0.11994740 83.84083859
|
||||
-862.92132606 -862.95611207 -1277.71824548
|
||||
-2.82003936 2.82004013 5410.11000806
|
||||
862.88110509 -862.88110547 -1277.34764015
|
||||
0.06108893 0.02099703 -193.17561792
|
||||
-860.25587388 860.25587441 -1274.81548916
|
||||
-0.02099726 -0.06108878 -193.17561777
|
||||
-193.17613465 -0.23660693 0.00000015
|
||||
-1277.52241409 863.24943328 -862.88111478
|
||||
83.46934549 0.34066334 -0.00000015
|
||||
-1277.52241425 863.24943335 862.88111508
|
||||
5404.58897235 -9.71806749 0.00000015
|
||||
-1273.31333522 -858.38273960 -858.96245956
|
||||
-193.21062369 -0.11938368 0.00000000
|
||||
-1273.31333598 -858.38273967 858.96245926
|
||||
0.34066342 83.46934572 0.00000015
|
||||
863.24943335 -1277.52241402 862.88111478
|
||||
-0.23660723 -193.17613480 -0.00000046
|
||||
863.24943320 -1277.52241425 -862.88111432
|
||||
-9.71806582 5404.58897135 -0.00000183
|
||||
-858.38273891 -1273.31333552 -858.96245926
|
||||
-0.11938338 -193.21062369 0.00000000
|
||||
-858.38273937 -1273.31333598 858.96245987
|
||||
-0.00000031 -0.00000008 -193.17559595
|
||||
-863.11328229 863.11328297 -1277.34763999
|
||||
0.00000000 -0.00000015 -193.17559595
|
||||
863.11328305 -863.11328282 -1277.34763984
|
||||
0.00000122 -0.00000259 5404.30470550
|
||||
-858.80486827 -858.80486866 -1273.17865241
|
||||
-0.00000031 0.00000000 83.09905870
|
||||
858.80486827 858.80486812 -1273.17865272
|
||||
-1276.01089136 861.66402482 -861.60900483
|
||||
-193.17596134 -0.16730494 0.02099535
|
||||
-1276.15175745 861.54714988 861.52691337
|
||||
83.46947097 0.16714109 0.06108436
|
||||
-1273.31334651 -858.38273311 -858.80488185
|
||||
5404.58493608 -3.04507687 -2.81778617
|
||||
-1276.19187193 -861.66399965 861.74280750
|
||||
-193.21058304 -0.11920641 -0.12012575
|
||||
861.54714972 -1276.15175730 861.52691337
|
||||
0.16714140 83.46947120 0.06108451
|
||||
861.66402345 -1276.01089022 -861.60900330
|
||||
-0.16730487 -193.17596164 0.02099489
|
||||
-858.38273281 -1273.31334681 -858.80488063
|
||||
-3.04507603 5404.58493554 -2.81778617
|
||||
-861.66400079 -1276.19187270 861.74280887
|
||||
-0.11920511 -193.21058281 -0.12012498
|
||||
-861.62536929 861.66025668 -1276.08157121
|
||||
-0.02106026 0.06099877 -193.17561197
|
||||
861.66025752 -861.62537051 -1276.08157274
|
||||
0.06099923 -0.02106049 -193.17561227
|
||||
-858.96244980 -858.96244965 -1273.17866523
|
||||
-2.81780608 -2.81780615 5404.30474272
|
||||
861.58531232 861.58531248 -1275.71087663
|
||||
0.12013467 0.12013460 83.09915619
|
||||
83.46958166 -0.00634218 -0.00000023
|
||||
-1274.64157002 859.96383191 860.25587098
|
||||
-193.17585332 -0.09802844 0.00000023
|
||||
-1274.64157155 859.96383290 -860.25587243
|
||||
-193.21062064 -0.11939070 -0.00000008
|
||||
-1276.19189573 -861.66398638 861.58531118
|
||||
5404.58377546 3.62403097 0.00000015
|
||||
-1276.19189558 -861.66398615 -861.58531103
|
||||
-0.09802859 -193.17585355 -0.00000015
|
||||
859.96383206 -1274.64156979 -860.25587113
|
||||
-0.00634187 83.46958204 -0.00000008
|
||||
859.96383282 -1274.64157132 860.25587212
|
||||
-0.11939055 -193.21062041 0.00000000
|
||||
-861.66398576 -1276.19189528 861.58531087
|
||||
3.62402982 5404.58377698 -0.00000076
|
||||
-861.66398927 -1276.19189772 -861.58531331
|
||||
0.00000000 0.00000000 -193.17573654
|
||||
860.17327676 -860.17327637 -1274.81551212
|
||||
0.00000031 0.00000023 -193.17573676
|
||||
-860.17327615 860.17327645 -1274.81551258
|
||||
0.00000000 0.00000015 83.09907327
|
||||
861.74281299 861.74281299 -1275.71086763
|
||||
-0.00000046 -0.00000015 5404.30514861
|
||||
-861.74281406 -861.74281421 -1275.71086938
|
||||
-1276.01088968 861.66402284 861.60900330
|
||||
83.46947136 0.16714109 -0.06108436
|
||||
-1276.15175722 861.54714957 -861.52691391
|
||||
-193.17596141 -0.16730510 -0.02099527
|
||||
-1273.31334666 -858.38273281 858.80488124
|
||||
-193.21058304 -0.11920641 0.12012636
|
||||
-1276.19187285 -861.66400087 -861.74280773
|
||||
5404.58493638 -3.04507565 2.81778602
|
||||
861.54715133 -1276.15175913 -861.52691490
|
||||
-0.16730502 -193.17596118 -0.02099497
|
||||
861.66402314 -1276.01088976 861.60900383
|
||||
0.16714125 83.46947151 -0.06108497
|
||||
-858.38273296 -1273.31334681 858.80488139
|
||||
-0.11920686 -193.21058311 0.12012605
|
||||
-861.66400079 -1276.19187255 -861.74280811
|
||||
-3.04506703 5404.58493432 2.81779319
|
||||
861.62536952 -861.66025637 -1276.08157175
|
||||
-0.06099938 0.02106080 -193.17561235
|
||||
-861.66025645 861.62536929 -1276.08157213
|
||||
0.02106049 -0.06099862 -193.17561189
|
||||
858.96245049 858.96245041 -1273.17866553
|
||||
-0.12013444 -0.12013475 83.09915550
|
||||
-861.58531232 -861.58531217 -1275.71087655
|
||||
2.81780737 2.81780753 5404.30474547
|
||||
|
|
@ -0,0 +1,58 @@
|
|||
LAMMPS (16 Jul 2018)
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (5.431 5.431 5.431)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
8 atoms
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
0 = max # of 1-2 neighbors
|
||||
0 = max # of 1-3 neighbors
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 4
|
||||
ghost atom cutoff = 4
|
||||
binsize = 2, bins = 3 3 3
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair tersoff, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Calculating Dynamical Matrix...
|
||||
Dynamical Matrix calculation took 0.001183 seconds
|
||||
Finished Calculating Dynamical Matrix
|
||||
Loop time of 1.22396e+06 on 4 procs for 0 steps with 8 atoms
|
||||
|
||||
0.0% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.00016781 | 0.00041345 | 0.00051464 | 0.0 | 0.00
|
||||
Bond | 1.9255e-06 | 2.1775e-06 | 2.4787e-06 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.00056143 | 0.00066602 | 0.00090865 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 1.224e+06 | | |100.00
|
||||
|
||||
Nlocal: 2 ave 3 max 1 min
|
||||
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||
Nghost: 56 ave 57 max 55 min
|
||||
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 32 ave 48 max 16 min
|
||||
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||
|
||||
Total # of neighbors = 128
|
||||
Ave neighs/atom = 16
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
|
|
@ -0,0 +1,29 @@
|
|||
LAMMPS description
|
||||
|
||||
8 atoms
|
||||
0 bonds
|
||||
0 angles
|
||||
0 dihedrals
|
||||
0 impropers
|
||||
|
||||
1 atom types
|
||||
0 bond types
|
||||
0 angle types
|
||||
0 dihedral types
|
||||
0 improper types
|
||||
|
||||
|
||||
0.0000000 5.4310000 xlo xhi
|
||||
0.0000000 5.4310000 ylo yhi
|
||||
0.0000000 5.4310000 zlo zhi
|
||||
|
||||
Atoms
|
||||
|
||||
1 1 1 0.0000000 0.0000000 0.0000000 0.0000000
|
||||
2 2 1 0.0000000 1.3577500 1.3577500 1.3572000
|
||||
3 3 1 0.0000000 2.7155000 2.7155000 0.0000000
|
||||
4 4 1 0.0000000 4.0732500 4.0732500 1.3572000
|
||||
5 5 1 0.0000000 2.7155000 0.0000000 2.7144000
|
||||
6 6 1 0.0000000 4.0732500 1.3577500 4.0732500
|
||||
7 7 1 0.0000000 0.0000000 2.7155000 2.7155000
|
||||
8 8 1 0.0000000 1.3577500 4.0732500 4.0732500
|
||||
|
|
@ -38,8 +38,9 @@ mass 2 1.007970
|
|||
|
||||
## This part defines the reax pair potential in methane, force field coefficients are specified in "ffield.reax"
|
||||
#Pair Potentials
|
||||
pair_style reax 10.0 1 1 1.0e-6
|
||||
pair_coeff * * ffield.reax 1 2
|
||||
pair_style reax/c NULL
|
||||
pair_coeff * * ffield.reax C H
|
||||
fix 0 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
|
||||
|
||||
#Neighbor Style
|
||||
neighbor 2.5 bin
|
||||
|
|
|
|||
|
|
@ -44,8 +44,9 @@ mass 2 1.007970
|
|||
|
||||
## This part defines the reax pair potential in methane, force field coefficients are specified in "ffield.reax"
|
||||
#Pair Potentials
|
||||
pair_style reax 10.0 1 1 1.0e-6
|
||||
pair_coeff * * ffield.reax 1 2
|
||||
pair_style reax/c NULL
|
||||
pair_coeff * * ffield.reax C H
|
||||
fix 0 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
|
||||
|
||||
#Neighbor Style
|
||||
neighbor 2.5 bin
|
||||
|
|
|
|||
|
|
@ -10,6 +10,7 @@ variable zz equal 20*$z
|
|||
|
||||
units metal
|
||||
atom_style atomic
|
||||
newton off
|
||||
|
||||
lattice fcc 4.4300
|
||||
region box block 0 ${xx} 0 ${yy} 0 ${zz}
|
||||
|
|
@ -17,13 +18,12 @@ create_box 1 box
|
|||
create_atoms 1 box
|
||||
|
||||
pair_style lj/cut 8.1500
|
||||
pair_coeff 1 1 0.0031 2.7400
|
||||
pair_modify shift yes
|
||||
pair_coeff 1 1 0.0104 3.4000
|
||||
|
||||
#pair_style kim KIMvirial ex_model_Ne_P_fastLJ
|
||||
#pair_coeff * * Ne
|
||||
#pair_style kim LennardJones_Ar
|
||||
#pair_coeff * * Ar
|
||||
|
||||
mass 1 20.18
|
||||
mass 1 39.95
|
||||
velocity all create 200.0 232345 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
|
|
@ -10,20 +10,20 @@ variable zz equal 20*$z
|
|||
|
||||
units metal
|
||||
atom_style atomic
|
||||
newton on
|
||||
|
||||
lattice fcc 4.4300
|
||||
region box block 0 ${xx} 0 ${yy} 0 ${zz}
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
|
||||
#pair_style lj/cut 8.1500
|
||||
#pair_coeff 1 1 0.0031 2.7400
|
||||
#pair_modify shift yes
|
||||
pair_style lj/cut 8.1500
|
||||
pair_coeff 1 1 0.0104 3.4000
|
||||
|
||||
pair_style kim KIMvirial ex_model_Ne_P_fastLJ
|
||||
pair_coeff * * Ne
|
||||
#pair_style kim LennardJones_Ar
|
||||
#pair_coeff * * Ar
|
||||
|
||||
mass 1 20.18
|
||||
mass 1 39.95
|
||||
velocity all create 200.0 232345 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
|
|
@ -0,0 +1,41 @@
|
|||
# 3d Lennard-Jones melt
|
||||
#
|
||||
# This example requires that the example models provided with
|
||||
# the kim-api package are installed. see the ./lib/kim/README or
|
||||
# ./lib/kim/Install.py files for details on how to install these
|
||||
# example models.
|
||||
#
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
variable xx equal 20*$x
|
||||
variable yy equal 20*$y
|
||||
variable zz equal 20*$z
|
||||
|
||||
units metal
|
||||
atom_style atomic
|
||||
newton off
|
||||
|
||||
lattice fcc 4.4300
|
||||
region box block 0 ${xx} 0 ${yy} 0 ${zz}
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
|
||||
#pair_style lj/cut 8.1500
|
||||
#pair_coeff 1 1 0.0104 3.4000
|
||||
|
||||
pair_style kim LennardJones_Ar
|
||||
pair_coeff * * Ar
|
||||
|
||||
mass 1 39.95
|
||||
velocity all create 200.0 232345 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
|
||||
|
||||
run 100
|
||||
|
|
@ -0,0 +1,41 @@
|
|||
# 3d Lennard-Jones melt
|
||||
#
|
||||
# This example requires that the example models provided with
|
||||
# the kim-api package are installed. see the ./lib/kim/README or
|
||||
# ./lib/kim/Install.py files for details on how to install these
|
||||
# example models.
|
||||
#
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
variable xx equal 20*$x
|
||||
variable yy equal 20*$y
|
||||
variable zz equal 20*$z
|
||||
|
||||
units metal
|
||||
atom_style atomic
|
||||
newton on
|
||||
|
||||
lattice fcc 4.4300
|
||||
region box block 0 ${xx} 0 ${yy} 0 ${zz}
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
|
||||
#pair_style lj/cut 8.1500
|
||||
#pair_coeff 1 1 0.0104 3.4000
|
||||
|
||||
pair_style kim LennardJones_Ar
|
||||
pair_coeff * * Ar
|
||||
|
||||
mass 1 39.95
|
||||
velocity all create 200.0 232345 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
|
||||
|
||||
run 100
|
||||
|
|
@ -0,0 +1,55 @@
|
|||
LAMMPS (1 Feb 2019)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
Lattice spacing in x,y,z = 4.43 4.43 4.43
|
||||
Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
Created 32000 atoms
|
||||
Time spent = 0.004499 secs
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 8.45
|
||||
ghost atom cutoff = 8.45
|
||||
binsize = 4.225, bins = 21 21 21
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton off
|
||||
pair build: half/bin/newtoff
|
||||
stencil: half/bin/3d/newtoff
|
||||
bin: standard
|
||||
Setting up Verlet run ...
|
||||
Unit style : metal
|
||||
Current step : 0
|
||||
Time step : 0.001
|
||||
Per MPI rank memory allocation (min/avg/max) = 20.37 | 20.37 | 20.37 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 200 6290.8194 0 7118.0584 129712.25
|
||||
100 95.179725 6718.814 0 7112.496 133346.59
|
||||
Loop time of 2.92885 on 1 procs for 100 steps with 32000 atoms
|
||||
|
||||
Performance: 2.950 ns/day, 8.136 hours/ns, 34.143 timesteps/s
|
||||
99.1% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 2.5638 | 2.5638 | 2.5638 | 0.0 | 87.54
|
||||
Neigh | 0.31935 | 0.31935 | 0.31935 | 0.0 | 10.90
|
||||
Comm | 0.006833 | 0.006833 | 0.006833 | 0.0 | 0.23
|
||||
Output | 0.000107 | 0.000107 | 0.000107 | 0.0 | 0.00
|
||||
Modify | 0.027806 | 0.027806 | 0.027806 | 0.0 | 0.95
|
||||
Other | | 0.01091 | | | 0.37
|
||||
|
||||
Nlocal: 32000 ave 32000 max 32000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 19911 ave 19911 max 19911 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 2.3705e+06 ave 2.3705e+06 max 2.3705e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 2370499
|
||||
Ave neighs/atom = 74.0781
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:03
|
||||
|
|
@ -0,0 +1,55 @@
|
|||
LAMMPS (1 Feb 2019)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
Lattice spacing in x,y,z = 4.43 4.43 4.43
|
||||
Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
Created 32000 atoms
|
||||
Time spent = 0.001039 secs
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 8.45
|
||||
ghost atom cutoff = 8.45
|
||||
binsize = 4.225, bins = 21 21 21
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton off
|
||||
pair build: half/bin/newtoff
|
||||
stencil: half/bin/3d/newtoff
|
||||
bin: standard
|
||||
Setting up Verlet run ...
|
||||
Unit style : metal
|
||||
Current step : 0
|
||||
Time step : 0.001
|
||||
Per MPI rank memory allocation (min/avg/max) = 8.013 | 8.013 | 8.013 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 200 6290.8194 0 7118.0584 129712.25
|
||||
100 95.179725 6718.814 0 7112.496 133346.59
|
||||
Loop time of 0.778581 on 4 procs for 100 steps with 32000 atoms
|
||||
|
||||
Performance: 11.097 ns/day, 2.163 hours/ns, 128.439 timesteps/s
|
||||
99.8% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.65171 | 0.65891 | 0.67656 | 1.3 | 84.63
|
||||
Neigh | 0.07924 | 0.079548 | 0.07997 | 0.1 | 10.22
|
||||
Comm | 0.006755 | 0.0069015 | 0.007072 | 0.2 | 0.89
|
||||
Output | 4.6e-05 | 9.725e-05 | 0.000203 | 0.0 | 0.01
|
||||
Modify | 0.006841 | 0.006941 | 0.007015 | 0.1 | 0.89
|
||||
Other | | 0.02618 | | | 3.36
|
||||
|
||||
Nlocal: 8000 ave 8018 max 7967 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 0 2
|
||||
Nghost: 9131 ave 9164 max 9113 min
|
||||
Histogram: 2 0 0 1 0 0 0 0 0 1
|
||||
Neighs: 630904 ave 632094 max 628209 min
|
||||
Histogram: 1 0 0 0 0 0 0 1 0 2
|
||||
|
||||
Total # of neighbors = 2523614
|
||||
Ave neighs/atom = 78.8629
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
|
|
@ -0,0 +1,55 @@
|
|||
LAMMPS (1 Feb 2019)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
Lattice spacing in x,y,z = 4.43 4.43 4.43
|
||||
Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
Created 32000 atoms
|
||||
Time spent = 0.003479 secs
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 8.45
|
||||
ghost atom cutoff = 8.45
|
||||
binsize = 4.225, bins = 21 21 21
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Setting up Verlet run ...
|
||||
Unit style : metal
|
||||
Current step : 0
|
||||
Time step : 0.001
|
||||
Per MPI rank memory allocation (min/avg/max) = 19.23 | 19.23 | 19.23 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 200 6290.8194 0 7118.0584 129712.25
|
||||
100 95.179725 6718.814 0 7112.496 133346.59
|
||||
Loop time of 2.17978 on 1 procs for 100 steps with 32000 atoms
|
||||
|
||||
Performance: 3.964 ns/day, 6.055 hours/ns, 45.876 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.9892 | 1.9892 | 1.9892 | 0.0 | 91.26
|
||||
Neigh | 0.14506 | 0.14506 | 0.14506 | 0.0 | 6.65
|
||||
Comm | 0.011049 | 0.011049 | 0.011049 | 0.0 | 0.51
|
||||
Output | 9.1e-05 | 9.1e-05 | 9.1e-05 | 0.0 | 0.00
|
||||
Modify | 0.02347 | 0.02347 | 0.02347 | 0.0 | 1.08
|
||||
Other | | 0.01094 | | | 0.50
|
||||
|
||||
Nlocal: 32000 ave 32000 max 32000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 19911 ave 19911 max 19911 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 2.12688e+06 ave 2.12688e+06 max 2.12688e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 2126875
|
||||
Ave neighs/atom = 66.4648
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:02
|
||||
|
|
@ -0,0 +1,55 @@
|
|||
LAMMPS (1 Feb 2019)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
Lattice spacing in x,y,z = 4.43 4.43 4.43
|
||||
Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
Created 32000 atoms
|
||||
Time spent = 0.000919 secs
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 8.45
|
||||
ghost atom cutoff = 8.45
|
||||
binsize = 4.225, bins = 21 21 21
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Setting up Verlet run ...
|
||||
Unit style : metal
|
||||
Current step : 0
|
||||
Time step : 0.001
|
||||
Per MPI rank memory allocation (min/avg/max) = 7.632 | 7.632 | 7.632 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 200 6290.8194 0 7118.0584 129712.25
|
||||
100 95.179725 6718.814 0 7112.496 133346.59
|
||||
Loop time of 0.63515 on 4 procs for 100 steps with 32000 atoms
|
||||
|
||||
Performance: 13.603 ns/day, 1.764 hours/ns, 157.443 timesteps/s
|
||||
99.8% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.55365 | 0.5566 | 0.55868 | 0.2 | 87.63
|
||||
Neigh | 0.041495 | 0.0418 | 0.04211 | 0.1 | 6.58
|
||||
Comm | 0.019086 | 0.021075 | 0.023898 | 1.2 | 3.32
|
||||
Output | 4.4e-05 | 5.025e-05 | 6e-05 | 0.0 | 0.01
|
||||
Modify | 0.009315 | 0.0093595 | 0.009422 | 0.0 | 1.47
|
||||
Other | | 0.006263 | | | 0.99
|
||||
|
||||
Nlocal: 8000 ave 8018 max 7967 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 0 2
|
||||
Nghost: 9131 ave 9164 max 9113 min
|
||||
Histogram: 2 0 0 1 0 0 0 0 0 1
|
||||
Neighs: 531719 ave 533273 max 529395 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 2126875
|
||||
Ave neighs/atom = 66.4648
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
|
|
@ -0,0 +1,59 @@
|
|||
LAMMPS (1 Feb 2019)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
Lattice spacing in x,y,z = 4.43 4.43 4.43
|
||||
Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
Created 32000 atoms
|
||||
Time spent = 0.003446 secs
|
||||
WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097)
|
||||
WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 8.45
|
||||
ghost atom cutoff = 8.45
|
||||
binsize = 4.225, bins = 21 21 21
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair kim, perpetual
|
||||
attributes: full, newton off, cut 8.45
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Setting up Verlet run ...
|
||||
Unit style : metal
|
||||
Current step : 0
|
||||
Time step : 0.001
|
||||
Per MPI rank memory allocation (min/avg/max) = 28.51 | 28.51 | 28.51 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 200 6290.8194 0 7118.0584 129712.25
|
||||
100 95.179725 6718.814 0 7112.496 133346.59
|
||||
Loop time of 3.01669 on 1 procs for 100 steps with 32000 atoms
|
||||
|
||||
Performance: 2.864 ns/day, 8.380 hours/ns, 33.149 timesteps/s
|
||||
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 2.6562 | 2.6562 | 2.6562 | 0.0 | 88.05
|
||||
Neigh | 0.31903 | 0.31903 | 0.31903 | 0.0 | 10.58
|
||||
Comm | 0.00634 | 0.00634 | 0.00634 | 0.0 | 0.21
|
||||
Output | 9.1e-05 | 9.1e-05 | 9.1e-05 | 0.0 | 0.00
|
||||
Modify | 0.024723 | 0.024723 | 0.024723 | 0.0 | 0.82
|
||||
Other | | 0.01032 | | | 0.34
|
||||
|
||||
Nlocal: 32000 ave 32000 max 32000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 19911 ave 19911 max 19911 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 4.25375e+06 ave 4.25375e+06 max 4.25375e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 4253750
|
||||
Ave neighs/atom = 132.93
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:03
|
||||
|
|
@ -0,0 +1,65 @@
|
|||
LAMMPS (1 Feb 2019)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
Lattice spacing in x,y,z = 4.43 4.43 4.43
|
||||
Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
Created 32000 atoms
|
||||
Time spent = 0.000921 secs
|
||||
WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097)
|
||||
WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102)
|
||||
WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097)
|
||||
WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102)
|
||||
WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097)
|
||||
WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102)
|
||||
WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097)
|
||||
WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 8.45
|
||||
ghost atom cutoff = 8.45
|
||||
binsize = 4.225, bins = 21 21 21
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair kim, perpetual
|
||||
attributes: full, newton off, cut 8.45
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Setting up Verlet run ...
|
||||
Unit style : metal
|
||||
Current step : 0
|
||||
Time step : 0.001
|
||||
Per MPI rank memory allocation (min/avg/max) = 10.05 | 10.05 | 10.05 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 200 6290.8194 0 7118.0584 129712.25
|
||||
100 95.179725 6718.814 0 7112.496 133346.59
|
||||
Loop time of 0.890192 on 4 procs for 100 steps with 32000 atoms
|
||||
|
||||
Performance: 9.706 ns/day, 2.473 hours/ns, 112.335 timesteps/s
|
||||
99.7% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.77867 | 0.77906 | 0.7794 | 0.0 | 87.52
|
||||
Neigh | 0.087831 | 0.088176 | 0.088805 | 0.1 | 9.91
|
||||
Comm | 0.006358 | 0.0065898 | 0.006815 | 0.3 | 0.74
|
||||
Output | 4.9e-05 | 5.975e-05 | 6.8e-05 | 0.0 | 0.01
|
||||
Modify | 0.010265 | 0.010429 | 0.010678 | 0.2 | 1.17
|
||||
Other | | 0.005874 | | | 0.66
|
||||
|
||||
Nlocal: 8000 ave 8018 max 7967 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 0 2
|
||||
Nghost: 9131 ave 9164 max 9113 min
|
||||
Histogram: 2 0 0 1 0 0 0 0 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 1.06344e+06 ave 1.06594e+06 max 1.05881e+06 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 0 2
|
||||
|
||||
Total # of neighbors = 4253750
|
||||
Ave neighs/atom = 132.93
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
|
|
@ -0,0 +1,59 @@
|
|||
LAMMPS (1 Feb 2019)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
Lattice spacing in x,y,z = 4.43 4.43 4.43
|
||||
Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
Created 32000 atoms
|
||||
Time spent = 0.003089 secs
|
||||
WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097)
|
||||
WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 8.45
|
||||
ghost atom cutoff = 8.45
|
||||
binsize = 4.225, bins = 21 21 21
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair kim, perpetual
|
||||
attributes: full, newton off, cut 8.45
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Setting up Verlet run ...
|
||||
Unit style : metal
|
||||
Current step : 0
|
||||
Time step : 0.001
|
||||
Per MPI rank memory allocation (min/avg/max) = 28.12 | 28.12 | 28.12 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 200 6290.8194 0 7118.0584 129712.25
|
||||
100 95.179725 6718.814 0 7112.496 133346.59
|
||||
Loop time of 3.05849 on 1 procs for 100 steps with 32000 atoms
|
||||
|
||||
Performance: 2.825 ns/day, 8.496 hours/ns, 32.696 timesteps/s
|
||||
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 2.6786 | 2.6786 | 2.6786 | 0.0 | 87.58
|
||||
Neigh | 0.33105 | 0.33105 | 0.33105 | 0.0 | 10.82
|
||||
Comm | 0.012602 | 0.012602 | 0.012602 | 0.0 | 0.41
|
||||
Output | 9.5e-05 | 9.5e-05 | 9.5e-05 | 0.0 | 0.00
|
||||
Modify | 0.024858 | 0.024858 | 0.024858 | 0.0 | 0.81
|
||||
Other | | 0.01132 | | | 0.37
|
||||
|
||||
Nlocal: 32000 ave 32000 max 32000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 19911 ave 19911 max 19911 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 4.25375e+06 ave 4.25375e+06 max 4.25375e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 4253750
|
||||
Ave neighs/atom = 132.93
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:03
|
||||
|
|
@ -0,0 +1,65 @@
|
|||
LAMMPS (1 Feb 2019)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
Lattice spacing in x,y,z = 4.43 4.43 4.43
|
||||
Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
Created 32000 atoms
|
||||
Time spent = 0.000893 secs
|
||||
WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097)
|
||||
WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102)
|
||||
WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097)
|
||||
WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102)
|
||||
WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097)
|
||||
WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102)
|
||||
WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097)
|
||||
WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 8.45
|
||||
ghost atom cutoff = 8.45
|
||||
binsize = 4.225, bins = 21 21 21
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair kim, perpetual
|
||||
attributes: full, newton off, cut 8.45
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Setting up Verlet run ...
|
||||
Unit style : metal
|
||||
Current step : 0
|
||||
Time step : 0.001
|
||||
Per MPI rank memory allocation (min/avg/max) = 9.789 | 9.789 | 9.789 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 200 6290.8194 0 7118.0584 129712.25
|
||||
100 95.179725 6718.814 0 7112.496 133346.59
|
||||
Loop time of 0.903182 on 4 procs for 100 steps with 32000 atoms
|
||||
|
||||
Performance: 9.566 ns/day, 2.509 hours/ns, 110.720 timesteps/s
|
||||
99.6% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.76173 | 0.76349 | 0.76597 | 0.2 | 84.53
|
||||
Neigh | 0.088773 | 0.088938 | 0.089074 | 0.0 | 9.85
|
||||
Comm | 0.032018 | 0.03452 | 0.03638 | 0.9 | 3.82
|
||||
Output | 4e-05 | 4.425e-05 | 5.2e-05 | 0.0 | 0.00
|
||||
Modify | 0.009278 | 0.0093917 | 0.009528 | 0.1 | 1.04
|
||||
Other | | 0.006797 | | | 0.75
|
||||
|
||||
Nlocal: 8000 ave 8018 max 7967 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 0 2
|
||||
Nghost: 9131 ave 9164 max 9113 min
|
||||
Histogram: 2 0 0 1 0 0 0 0 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 1.06344e+06 ave 1.06594e+06 max 1.05881e+06 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 0 2
|
||||
|
||||
Total # of neighbors = 4253750
|
||||
Ave neighs/atom = 132.93
|
||||
Neighbor list builds = 3
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
|
|
@ -1,33 +0,0 @@
|
|||
LAMMPS (15 May 2015)
|
||||
Lattice spacing in x,y,z = 4.43 4.43 4.43
|
||||
Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
Created 32000 atoms
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
master list distance cutoff = 8.45
|
||||
Setting up run ...
|
||||
Memory usage per processor = 9.18789 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 200 -741.55469 0 85.684388 -34.939092
|
||||
100 108.37517 -362.56658 0 85.694308 3963.7892
|
||||
Loop time of 2.95205 on 1 procs for 100 steps with 32000 atoms
|
||||
|
||||
Pair time (%) = 2.52074 (85.3894)
|
||||
Neigh time (%) = 0.347949 (11.7867)
|
||||
Comm time (%) = 0.0228171 (0.772925)
|
||||
Outpt time (%) = 0.000188828 (0.00639649)
|
||||
Other time (%) = 0.0603588 (2.04464)
|
||||
|
||||
Nlocal: 32000 ave 32000 max 32000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 20131 ave 20131 max 20131 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 1.88909e+06 ave 1.88909e+06 max 1.88909e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 1889091
|
||||
Ave neighs/atom = 59.0341
|
||||
Neighbor list builds = 5
|
||||
Dangerous builds = 0
|
||||
|
|
@ -1,33 +0,0 @@
|
|||
LAMMPS (15 May 2015)
|
||||
Lattice spacing in x,y,z = 4.43 4.43 4.43
|
||||
Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
Created 32000 atoms
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
master list distance cutoff = 8.45
|
||||
Setting up run ...
|
||||
Memory usage per processor = 4.58461 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 200 -741.55469 0 85.684388 -34.939092
|
||||
100 108.37517 -362.56658 0 85.694308 3963.7892
|
||||
Loop time of 6.15911 on 4 procs for 100 steps with 32000 atoms
|
||||
|
||||
Pair time (%) = 1.76201 (28.6083)
|
||||
Neigh time (%) = 0.265002 (4.30261)
|
||||
Comm time (%) = 3.64452 (59.1729)
|
||||
Outpt time (%) = 0.0169877 (0.275815)
|
||||
Other time (%) = 0.470582 (7.64042)
|
||||
|
||||
Nlocal: 8000 ave 8010 max 7989 min
|
||||
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||
Nghost: 9240.25 ave 9249 max 9228 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 0 2
|
||||
Neighs: 472273 ave 473390 max 471652 min
|
||||
Histogram: 2 0 0 1 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 1889091
|
||||
Ave neighs/atom = 59.0341
|
||||
Neighbor list builds = 5
|
||||
Dangerous builds = 0
|
||||
|
|
@ -1,33 +0,0 @@
|
|||
LAMMPS (15 May 2015)
|
||||
Lattice spacing in x,y,z = 4.43 4.43 4.43
|
||||
Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
Created 32000 atoms
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
master list distance cutoff = 8.45
|
||||
Setting up run ...
|
||||
Memory usage per processor = 9.43789 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 200 -741.55469 0 85.684388 -34.939092
|
||||
100 108.37517 -362.56658 0 85.694308 3963.7892
|
||||
Loop time of 3.79746 on 1 procs for 100 steps with 32000 atoms
|
||||
|
||||
Pair time (%) = 3.18686 (83.9207)
|
||||
Neigh time (%) = 0.524724 (13.8178)
|
||||
Comm time (%) = 0.0244031 (0.642616)
|
||||
Outpt time (%) = 0.000174046 (0.00458321)
|
||||
Other time (%) = 0.061305 (1.61437)
|
||||
|
||||
Nlocal: 32000 ave 32000 max 32000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 20131 ave 20131 max 20131 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 2.09236e+06 ave 2.09236e+06 max 2.09236e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 2092355
|
||||
Ave neighs/atom = 65.3861
|
||||
Neighbor list builds = 5
|
||||
Dangerous builds = 0
|
||||
|
|
@ -1,33 +0,0 @@
|
|||
LAMMPS (15 May 2015)
|
||||
Lattice spacing in x,y,z = 4.43 4.43 4.43
|
||||
Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
Created 32000 atoms
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
master list distance cutoff = 8.45
|
||||
Setting up run ...
|
||||
Memory usage per processor = 4.70961 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 200 -741.55469 0 85.684388 -34.939092
|
||||
100 108.37517 -362.56658 0 85.694308 3963.7892
|
||||
Loop time of 7.25305 on 4 procs for 100 steps with 32000 atoms
|
||||
|
||||
Pair time (%) = 2.52571 (34.8227)
|
||||
Neigh time (%) = 0.500287 (6.8976)
|
||||
Comm time (%) = 3.70236 (51.0456)
|
||||
Outpt time (%) = 0.00146681 (0.0202234)
|
||||
Other time (%) = 0.523229 (7.21391)
|
||||
|
||||
Nlocal: 8000 ave 8010 max 7989 min
|
||||
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||
Nghost: 9240.25 ave 9249 max 9228 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 0 2
|
||||
Neighs: 555266 ave 555920 max 554805 min
|
||||
Histogram: 2 0 0 0 0 1 0 0 0 1
|
||||
|
||||
Total # of neighbors = 2221065
|
||||
Ave neighs/atom = 69.4083
|
||||
Neighbor list builds = 5
|
||||
Dangerous builds = 0
|
||||
|
|
@ -1,3 +1,2 @@
|
|||
/Makefile.KIM_DIR
|
||||
/Makefile.KIM_Config
|
||||
/kim-prefix.txt
|
||||
/installed-kim-api-*
|
||||
|
|
|
|||
|
|
@ -18,7 +18,7 @@ parser = ArgumentParser(prog='Install.py',
|
|||
# settings
|
||||
|
||||
thisdir = fullpath('.')
|
||||
version = "kim-api-v1.9.5"
|
||||
version = "kim-api-v2-2.0.1"
|
||||
|
||||
# help message
|
||||
|
||||
|
|
@ -35,19 +35,15 @@ Syntax from lib dir: python Install.py -b -v version -a kim-name
|
|||
Examples:
|
||||
|
||||
make lib-kim args="-b" # install KIM API lib with only example models
|
||||
make lib-kim args="-b -a Glue_Ercolessi_Adams_Al__MO_324507536345_001" # Ditto plus one model
|
||||
make lib-kim args="-b -a EAM_ErcolessiAdams_1994_Al__MO_324507536345_002" # Ditto plus one model
|
||||
make lib-kim args="-b -a everything" # install KIM API lib with all models
|
||||
make lib-kim args="-n -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # only add one model or model driver
|
||||
make lib-kim args="-n -a EAM_Dynamo_Ackland_2003_W__MO_141627196590_005" # only add one model or model driver
|
||||
|
||||
See the list of KIM model drivers here:
|
||||
https://openkim.org/kim-items/model-drivers/alphabetical
|
||||
https://openkim.org/browse/model-drivers/alphabetical
|
||||
|
||||
See the list of all KIM models here:
|
||||
https://openkim.org/kim-items/models/by-model-drivers
|
||||
|
||||
See the list of example KIM models included by default here:
|
||||
https://openkim.org/kim-api
|
||||
in the "What is in the KIM API source package?" section
|
||||
https://openkim.org/browse/models/by-model-drivers
|
||||
"""
|
||||
|
||||
pgroup = parser.add_mutually_exclusive_group()
|
||||
|
|
@ -94,13 +90,10 @@ url = "https://s3.openkim.org/kim-api/%s.txz" % version
|
|||
|
||||
if pathflag:
|
||||
# configure LAMMPS to use existing kim-api installation
|
||||
with open("%s/Makefile.KIM_DIR" % thisdir, 'w') as mkfile:
|
||||
mkfile.write("KIM_INSTALL_DIR=%s\n\n" % kimdir)
|
||||
mkfile.write(".DUMMY: print_dir\n\n")
|
||||
mkfile.write("print_dir:\n")
|
||||
mkfile.write(" @printf $(KIM_INSTALL_DIR)\n")
|
||||
with open("%s/kim-prefix.txt" % thisdir, 'w') as pffile:
|
||||
pffile.write("%s" % kimdir)
|
||||
|
||||
print("Created %s/Makefile.KIM_DIR\n using %s" % (thisdir, kimdir))
|
||||
print("Created %s/kim-prefix.txt\n using %s" % (thisdir,kimdir))
|
||||
else:
|
||||
kimdir = os.path.join(os.path.abspath(thisdir), "installed-" + version)
|
||||
if args.nobuild and not os.path.isdir(kimdir):
|
||||
|
|
@ -117,13 +110,10 @@ if buildflag:
|
|||
|
||||
# configure LAMMPS to use kim-api to be installed
|
||||
|
||||
with open("%s/Makefile.KIM_DIR" % thisdir, 'w') as mkfile:
|
||||
mkfile.write("KIM_INSTALL_DIR=%s\n\n" % kimdir)
|
||||
mkfile.write(".DUMMY: print_dir\n\n")
|
||||
mkfile.write("print_dir:\n")
|
||||
mkfile.write(" @printf $(KIM_INSTALL_DIR)\n")
|
||||
with open("%s/kim-prefix.txt" % thisdir, 'w') as pffile:
|
||||
pffile.write("%s" % kimdir)
|
||||
|
||||
print("Created %s/Makefile.KIM_DIR\n using %s" % (thisdir, kimdir))
|
||||
print("Created %s/kim-prefix.txt\n using %s" % (thisdir,kimdir))
|
||||
|
||||
# download entire kim-api tarball
|
||||
|
||||
|
|
@ -136,12 +126,13 @@ if buildflag:
|
|||
# configure kim-api
|
||||
|
||||
print("Configuring kim-api ...")
|
||||
cmd = 'cd "%s/%s"; ./configure --prefix="%s"' % (thisdir, version, kimdir)
|
||||
subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True)
|
||||
cmd = 'cd "%s/%s" && mkdir build && cd build && cmake .. -DCMAKE_INSTALL_PREFIX="%s" -DCMAKE_BUILD_TYPE=Release' % (thisdir,version,kimdir)
|
||||
txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
|
||||
if verboseflag: print(txt.decode("UTF-8"))
|
||||
|
||||
# build kim-api
|
||||
print("Building kim-api ...")
|
||||
cmd = 'cd "%s/%s"; make' % (thisdir, version)
|
||||
cmd = 'cd "%s/%s/build" && make' % (thisdir, version)
|
||||
txt = subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True)
|
||||
if verboseflag:
|
||||
print(txt.decode("UTF-8"))
|
||||
|
|
@ -149,23 +140,13 @@ if buildflag:
|
|||
# install kim-api
|
||||
|
||||
print("Installing kim-api ...")
|
||||
cmd = 'cd "%s/%s"; make install' % (thisdir, version)
|
||||
cmd = 'cd "%s/%s/build" && make install' % (thisdir, version)
|
||||
txt = subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True)
|
||||
if verboseflag:
|
||||
print(txt.decode("UTF-8"))
|
||||
|
||||
# remove source files
|
||||
|
||||
print("Building and installing example Models")
|
||||
cmd = 'cd "%s/%s/examples"; make model-drivers-all-system' % (thisdir, version)
|
||||
txt = subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True)
|
||||
if verboseflag:
|
||||
print(txt.decode("UTF-8"))
|
||||
cmd = 'cd "%s/%s/examples"; make models-all-system' % (thisdir, version)
|
||||
txt = subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True)
|
||||
if verboseflag:
|
||||
print(txt.decode("UTF-8"))
|
||||
|
||||
print("Removing kim-api source and build files ...")
|
||||
cmd = 'cd "%s"; rm -rf %s; rm -rf %s.txz' % (thisdir, version, version)
|
||||
subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True)
|
||||
|
|
@ -173,7 +154,7 @@ if buildflag:
|
|||
# add all OpenKIM models, if desired
|
||||
if everythingflag:
|
||||
print("Adding all OpenKIM models, this will take a while ...")
|
||||
cmd = '%s/bin/kim-api-v1-collections-management install system OpenKIM' % (kimdir)
|
||||
cmd = '%s/bin/kim-api-v2-collections-management install system OpenKIM' % (kimdir)
|
||||
txt = subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True)
|
||||
if verboseflag:
|
||||
print(txt.decode("UTF-8"))
|
||||
|
|
@ -181,16 +162,16 @@ if buildflag:
|
|||
# add single OpenKIM model
|
||||
if addflag:
|
||||
|
||||
makefile_path = os.path.join(thisdir, "Makefile.KIM_DIR")
|
||||
if os.path.isfile(makefile_path):
|
||||
cmd = 'make --no-print-directory -f %s print_dir' % makefile_path
|
||||
kimdir = subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True)
|
||||
pf_path = os.path.join(thisdir, "kim-prefix.txt")
|
||||
if os.path.isfile(pf_path):
|
||||
cmd = 'cat %s' % pf_path
|
||||
kimdir = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
|
||||
|
||||
if not os.path.isdir(kimdir):
|
||||
sys.exit("\nkim-api is not installed")
|
||||
|
||||
# download single model
|
||||
cmd = '%s/bin/kim-api-v1-collections-management install system %s' % (kimdir.decode("UTF-8"), addmodelname)
|
||||
cmd = '%s/bin/kim-api-v2-collections-management install system %s' % (kimdir.decode("UTF-8"), addmodelname)
|
||||
txt = subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True)
|
||||
if verboseflag:
|
||||
print(txt.decode("UTF-8"))
|
||||
|
|
|
|||
|
|
@ -5,8 +5,6 @@
|
|||
# The KIM API package can be downloaded from https://openkim.org/kim-api
|
||||
# Follow the instructions in the INSTALL file to build and install the
|
||||
# KIM API. Add the openkim.org Models you are interested in using.
|
||||
# Make sure the directory where the "kim-api-build-conifg" utility is
|
||||
# located is on the PATH.
|
||||
#
|
||||
# As long as you have followed the KIM API build and install instructions,
|
||||
# there should not be any reason to change this file.
|
||||
|
|
@ -16,17 +14,17 @@
|
|||
# Settings that the LAMMPS build will import when this package is installed
|
||||
|
||||
|
||||
include ../../lib/kim/Makefile.KIM_DIR
|
||||
|
||||
ifeq ($(wildcard $(KIM_INSTALL_DIR)/bin/kim-api-v1-build-config),)
|
||||
KIM_CONFIG_HELPER = kim-api-v1-build-config
|
||||
else
|
||||
KIM_CONFIG_HELPER = $(KIM_INSTALL_DIR)/bin/kim-api-v1-build-config
|
||||
endif
|
||||
ifeq ($(shell $(KIM_CONFIG_HELPER) --version 2> /dev/null),)
|
||||
$(error $(KIM_CONFIG_HELPER) utility is not available. Something is wrong with your KIM API package setup)
|
||||
ifeq ($(strip $(shell pkg-config --version)),)
|
||||
$(error 'pkg-config' not found, but is required to configure the KIM API)
|
||||
endif
|
||||
|
||||
kim_SYSINC = $(shell $(KIM_CONFIG_HELPER) --includes)
|
||||
kim_SYSLIB = $(shell $(KIM_CONFIG_HELPER) --ldlibs)
|
||||
kim_SYSPATH = $(shell $(KIM_CONFIG_HELPER) --ldflags)
|
||||
kim_PREFIX := $(shell cat ../../lib/kim/kim-prefix.txt 2> /dev/null)
|
||||
kim_PREFIX := $(if $(kim_PREFIX),$(kim_PREFIX)/lib/pkgconfig,)
|
||||
kim_PREFIX := $(if $(shell printf -- "$${PKG_CONFIG_PATH}"),$(kim_PREFIX):$(shell printf -- "$${PKG_CONFIG_PATH}"),$(kim_PREFIX))
|
||||
|
||||
kim_SYSINC := $(shell export PKG_CONFIG_PATH="$(kim_PREFIX)"; pkg-config --cflags libkim-api-v2 2> /dev/null)
|
||||
kim_SYSLIB := $(shell export PKG_CONFIG_PATH="$(kim_PREFIX)"; pkg-config --libs libkim-api-v2 2> /dev/null)
|
||||
|
||||
ifeq ($(strip $(kim_SYSINC)),)
|
||||
$(error 'pkg-config' could not find an installed KIM API library.)
|
||||
endif
|
||||
|
|
|
|||
|
|
@ -3,10 +3,9 @@ is required to use the KIM package and its pair_style kim command in a
|
|||
LAMMPS input script.
|
||||
|
||||
Information about the KIM project can be found at https://openkim.org.
|
||||
The KIM project is lead by Ellad Tadmor and Ryan Elliott (U Minn) and
|
||||
James Sethna (Cornell U). Ryan Elliott is the main developer for the
|
||||
KIM API and he also maintains the code that implements the pair_style
|
||||
kim command.
|
||||
The KIM project is lead by Ellad Tadmor and Ryan Elliott (U Minn).
|
||||
Ryan Elliott is the main developer for the KIM API and he also
|
||||
maintains the code that implements the pair_style kim command.
|
||||
|
||||
You can type "make lib-kim" from the src directory to see help on
|
||||
how to download and build this library via make commands, or you can
|
||||
|
|
@ -21,33 +20,34 @@ Instructions:
|
|||
1. Configure lammps for use with the kim-api library installed in this directory
|
||||
|
||||
# replace X.Y.Z as appropriate here and below
|
||||
$ printf "KIM_INSTALL_DIR=${PWD}/installed-kim-api-vX.Y.Z\n" > ./Makefile.KIM_DIR
|
||||
$ printf "${PWD}/installed-kim-api-vX-X.Y.Z" > ./kim-prefix.txt
|
||||
|
||||
2. Download and unpack the kim-api
|
||||
|
||||
$ wget http://s3.openkim.org/kim-api/kim-api-vX.Y.Z.txz
|
||||
$ tar zxvf kim-api-vX.Y.Z.txz
|
||||
$ wget http://s3.openkim.org/kim-api/kim-api-vX-X.Y.Z.txz
|
||||
$ tar zxvf kim-api-vX-X.Y.Z.txz
|
||||
|
||||
# configure the kim-api
|
||||
$ cd kim-api-vX.Y.Z
|
||||
$ ./configure --prefix=${PWD}/../installed-kim-api-vX.Y.Z
|
||||
$ cd kim-api-vX-X.Y.Z
|
||||
$ mkdir build && cd build
|
||||
$ cmake .. -DCMAKE_INSTALL_PREFIX=${PWD}/../../installed-kim-api-vX-X.Y.Z
|
||||
|
||||
3. Build and install the kim-api and model
|
||||
|
||||
$ make
|
||||
$ make install
|
||||
$ cd ..
|
||||
|
||||
4. Remove source and build files
|
||||
|
||||
$ rm -rf kim-api-vX.Y.Z
|
||||
$ rm -rf kim-api-vX.Y.Z.txz
|
||||
$ cd ../../
|
||||
$ rm -rf kim-api-vX-X.Y.Z
|
||||
$ rm -rf kim-api-vX-X.Y.Z.txz
|
||||
|
||||
5. To add items do the following (replace the kim item name with your
|
||||
desired value)
|
||||
|
||||
$ source ${PWD}/kim-api-vX.Y.Z/bin/kim-api-v1-activate
|
||||
$ kim-api-v1-collections-management install system Pair_Johnson_Fe__MO_857282754307_002
|
||||
$ source ${PWD}/kim-api-vX-X.Y.Z/bin/kim-api-vX-activate
|
||||
$ kim-api-vX-collections-management install system Pair_Johnson_Fe__MO_857282754307_002
|
||||
|
||||
|
||||
-----------------
|
||||
|
|
@ -59,6 +59,6 @@ $ cd lammpos/src
|
|||
$ make yes-kim
|
||||
$ make g++ (or whatever target you wish)
|
||||
|
||||
Note that the Makefile.lammps and Makefile.KIM_DIR files in this directory
|
||||
are required to allow the LAMMPS build to find the necessary KIM files.
|
||||
You should not normally need to edit these files.
|
||||
Note that the Makefile.lammps file in this directory is required to
|
||||
allow the LAMMPS build to find the necessary KIM files. You should
|
||||
not normally need to edit these files.
|
||||
|
|
|
|||
|
|
@ -85,14 +85,19 @@ class lammps(object):
|
|||
# fall back to loading with a relative path,
|
||||
# typically requires LD_LIBRARY_PATH to be set appropriately
|
||||
|
||||
if any([f.startswith('liblammps') and f.endswith('.dylib') for f in os.listdir(modpath)]):
|
||||
lib_ext = ".dylib"
|
||||
else:
|
||||
lib_ext = ".so"
|
||||
|
||||
if not self.lib:
|
||||
try:
|
||||
if not name: self.lib = CDLL(join(modpath,"liblammps.so"),RTLD_GLOBAL)
|
||||
else: self.lib = CDLL(join(modpath,"liblammps_%s.so" % name),
|
||||
if not name: self.lib = CDLL(join(modpath,"liblammps" + lib_ext),RTLD_GLOBAL)
|
||||
else: self.lib = CDLL(join(modpath,"liblammps_%s" % name + lib_ext),
|
||||
RTLD_GLOBAL)
|
||||
except:
|
||||
if not name: self.lib = CDLL("liblammps.so",RTLD_GLOBAL)
|
||||
else: self.lib = CDLL("liblammps_%s.so" % name,RTLD_GLOBAL)
|
||||
if not name: self.lib = CDLL("liblammps" + lib_ext,RTLD_GLOBAL)
|
||||
else: self.lib = CDLL("liblammps_%s" % name + lib_ext,RTLD_GLOBAL)
|
||||
|
||||
# define ctypes API for each library method
|
||||
# NOTE: should add one of these for each lib function
|
||||
|
|
|
|||
|
|
@ -6,6 +6,7 @@
|
|||
|
||||
/style_*.h
|
||||
/lmpinstalledpkgs.h
|
||||
/lmpgitversion.h
|
||||
|
||||
/*_gpu.h
|
||||
/*_gpu.cpp
|
||||
|
|
|
|||
|
|
@ -26,5 +26,4 @@ library you can test it using an input file from the examples dir:
|
|||
|
||||
./lmp_serial < lammps/examples/kim/in.kim.lj
|
||||
|
||||
This pair_style was written by Valeriu Smirichinski and Ryan
|
||||
S. Elliott (U Minn).
|
||||
This pair_style was written by Ryan S. Elliott (U Minn).
|
||||
|
|
|
|||
1526
src/KIM/pair_kim.cpp
1526
src/KIM/pair_kim.cpp
File diff suppressed because it is too large
Load Diff
|
|
@ -12,14 +12,45 @@
|
|||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing authors: Ryan S. Elliott,
|
||||
Valeriu Smirichinski,
|
||||
Ellad Tadmor (U Minn)
|
||||
Contributing authors: Ryan S. Elliott (UMinn)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Designed for use with the openkim-api-v1.5.0 package and for use with
|
||||
the kim-api-v1.6.0 (and newer) package
|
||||
This program is free software; you can redistribute it and/or modify it
|
||||
under the terms of the GNU General Public License as published by the Free
|
||||
Software Foundation; either version 2 of the License, or (at your option)
|
||||
any later version.
|
||||
|
||||
This program is distributed in the hope that it will be useful, but WITHOUT
|
||||
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
|
||||
FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for
|
||||
more details.
|
||||
|
||||
You should have received a copy of the GNU General Public License along with
|
||||
this program; if not, see <https://www.gnu.org/licenses>.
|
||||
|
||||
Linking LAMMPS statically or dynamically with other modules is making a
|
||||
combined work based on LAMMPS. Thus, the terms and conditions of the GNU
|
||||
General Public License cover the whole combination.
|
||||
|
||||
In addition, as a special exception, the copyright holders of LAMMPS give
|
||||
you permission to combine LAMMPS with free software programs or libraries
|
||||
that are released under the GNU LGPL and with code included in the standard
|
||||
release of the "kim-api" under the CDDL (or modified versions of such code,
|
||||
with unchanged license). You may copy and distribute such a system following
|
||||
the terms of the GNU GPL for LAMMPS and the licenses of the other code
|
||||
concerned, provided that you include the source code of that other code
|
||||
when and as the GNU GPL requires distribution of source code.
|
||||
|
||||
Note that people who make modified versions of LAMMPS are not obligated to
|
||||
grant this special exception for their modified versions; it is their choice
|
||||
whether to do so. The GNU General Public License gives permission to release
|
||||
a modified version without this exception; this exception also makes it
|
||||
possible to release a modified version which carries forward this exception.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Designed for use with the kim-api-v2-2.0.0 (and newer) package
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef PAIR_CLASS
|
||||
|
|
@ -34,6 +65,10 @@ PairStyle(kim,PairKIM)
|
|||
// includes from KIM & LAMMPS
|
||||
class KIM_API_model;
|
||||
#include "pair.h"
|
||||
extern "C" {
|
||||
#include "KIM_SimulatorHeaders.h"
|
||||
}
|
||||
#include <sstream>
|
||||
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
|
@ -48,14 +83,13 @@ namespace LAMMPS_NS {
|
|||
virtual void settings(int, char**);
|
||||
virtual void coeff(int, char**);
|
||||
virtual void init_style();
|
||||
virtual void init_list(int id, NeighList *ptr);
|
||||
virtual double init_one(int, int);
|
||||
virtual void reinit();
|
||||
virtual int pack_reverse_comm(int, int, double*);
|
||||
virtual void unpack_reverse_comm(int, int*, double*);
|
||||
virtual double memory_usage();
|
||||
void *extract(const char *, int &);
|
||||
|
||||
private:
|
||||
protected:
|
||||
// (nearly) all bool flags are not initialized in constructor, but set
|
||||
// explicitly in the indicated function. All other data members are
|
||||
// initialized in constructor
|
||||
|
|
@ -64,12 +98,11 @@ namespace LAMMPS_NS {
|
|||
|
||||
// values set in settings()
|
||||
char* kim_modelname;
|
||||
bool print_kim_file;
|
||||
|
||||
// values set in coeff()
|
||||
|
||||
// values set in allocate(), called by coeff()
|
||||
void allocate();
|
||||
virtual void allocate();
|
||||
int* lmps_map_species_to_unique;
|
||||
|
||||
// values set in coeff(), after calling allocate()
|
||||
|
|
@ -80,74 +113,59 @@ namespace LAMMPS_NS {
|
|||
// values set in set_lmps_flags(), called from init_style()
|
||||
bool lmps_using_newton;
|
||||
bool lmps_using_molecular;
|
||||
bool lmps_hybrid; // true if running with pair hybrid
|
||||
bool lmps_support_cluster; // true if running in mode compat.
|
||||
// with CLUSTER
|
||||
enum unit_sys {REAL, METAL, SI, CGS, ELECTRON};
|
||||
unit_sys lmps_units;
|
||||
KIM_LengthUnit lengthUnit;
|
||||
KIM_EnergyUnit energyUnit;
|
||||
KIM_ChargeUnit chargeUnit;
|
||||
KIM_TemperatureUnit temperatureUnit;
|
||||
KIM_TimeUnit timeUnit;
|
||||
|
||||
KIM_Model * pkim;
|
||||
KIM_ComputeArguments * pargs;
|
||||
|
||||
// values set in set_kim_model_has_flags(), called by kim_init()
|
||||
KIM_API_model* pkim;
|
||||
bool kim_model_has_energy;
|
||||
bool kim_model_has_forces;
|
||||
bool kim_model_has_particleEnergy;
|
||||
bool kim_model_has_particleVirial;
|
||||
KIM_SupportStatus kim_model_support_for_energy;
|
||||
KIM_SupportStatus kim_model_support_for_forces;
|
||||
KIM_SupportStatus kim_model_support_for_particleEnergy;
|
||||
KIM_SupportStatus kim_model_support_for_particleVirial;
|
||||
|
||||
// values set in kim_init(), after call to string_init(_)
|
||||
// values set in kim_init()
|
||||
bool kim_init_ok;
|
||||
bool kim_model_using_half;
|
||||
bool kim_model_using_cluster;
|
||||
bool kim_model_using_Rij;
|
||||
int kim_ind_coordinates;
|
||||
int kim_ind_numberOfParticles;
|
||||
int kim_ind_numberContributingParticles;
|
||||
int kim_ind_numberOfSpecies;
|
||||
int kim_ind_particleSpecies;
|
||||
int kim_ind_get_neigh;
|
||||
int kim_ind_neighObject;
|
||||
int kim_ind_cutoff;
|
||||
int kim_ind_energy;
|
||||
int kim_ind_particleEnergy;
|
||||
int kim_ind_forces;
|
||||
int kim_ind_virial;
|
||||
int kim_ind_particleVirial;
|
||||
int lmps_local_tot_num_atoms;
|
||||
double kim_global_influence_distance; // KIM Model cutoff value
|
||||
int kim_number_of_neighbor_lists;
|
||||
double const * kim_cutoff_values;
|
||||
int const * modelWillNotRequestNeighborsOfNoncontributingParticles;
|
||||
class NeighList ** neighborLists;
|
||||
|
||||
// values set in init_style(), after calling pkim->model_init()
|
||||
bool kim_model_init_ok;
|
||||
// values set in init_style()
|
||||
bool kim_particle_codes_ok;
|
||||
int *kim_particle_codes;
|
||||
|
||||
// values set in set_statics(), called at end of kim_init(),
|
||||
// then again in set_volatiles(), called in compute()
|
||||
int lmps_local_tot_num_atoms;
|
||||
double kim_global_cutoff; // KIM Model cutoff value
|
||||
|
||||
// values set in compute()
|
||||
int lmps_maxalloc; // max allocated memory value
|
||||
int* kim_particleSpecies; // array of KIM particle species
|
||||
double** lmps_force_tmp; // temp storage for f, when running in
|
||||
// hybrid mode needed to avoid resetting
|
||||
// f to zero in each object
|
||||
int* kim_particleContributing; // array of KIM particle contributing
|
||||
int* lmps_stripped_neigh_list; // neighbors of one atom, used when LAMMPS
|
||||
// is in molecular mode
|
||||
|
||||
// values used in get_neigh()
|
||||
int kim_iterator_position; //get_neigh iterator current position
|
||||
double *Rij;
|
||||
int** lmps_stripped_neigh_ptr; // pointer into lists
|
||||
|
||||
// KIM specific helper functions
|
||||
void kim_error(int, const char *, int);
|
||||
void kim_init();
|
||||
void kim_free();
|
||||
void set_statics();
|
||||
void set_volatiles();
|
||||
void set_lmps_flags();
|
||||
void set_kim_model_has_flags();
|
||||
void write_descriptor(char** test_descriptor_string);
|
||||
virtual void set_contributing();
|
||||
virtual void kim_init();
|
||||
virtual void kim_free();
|
||||
virtual void set_argument_pointers();
|
||||
virtual void set_lmps_flags();
|
||||
virtual void set_kim_model_has_flags();
|
||||
virtual int check_for_routine_compatibility();
|
||||
// static methods used as callbacks from KIM
|
||||
static int get_neigh(void** kimmdl, int* mode, int* request,
|
||||
int* atom, int* numnei, int** nei1atom,
|
||||
double** pRij);
|
||||
static int get_neigh(
|
||||
void const * const dataObject,
|
||||
int const numberOfCutoffs, double const * const cutoffs,
|
||||
int const neighborListIndex, int const particleNumber,
|
||||
int * const numberOfNeighbors,
|
||||
int const ** const neighborsOfParticle);
|
||||
};
|
||||
}
|
||||
|
||||
|
|
@ -156,81 +174,92 @@ namespace LAMMPS_NS {
|
|||
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
E: Illegal ... command
|
||||
E: Unable to set KIM particle species codes and/or contributing
|
||||
|
||||
Self-explanatory. Check the input script syntax and compare to the
|
||||
documentation for the command. You can use -echo screen as a
|
||||
command-line option when running LAMMPS to see the offending line.
|
||||
A low-level kim-api error has occurred.
|
||||
|
||||
E: Unrecognized virial argument in pair_style command
|
||||
E: KIM Compute returned error
|
||||
|
||||
Only two options are supported: LAMMPSvirial and KIMvirial
|
||||
The KIM model was unable, for some reason, to complete the computation.
|
||||
|
||||
E: 'KIMvirial' or 'LAMMPSvirial' not supported with kim-api-v2.
|
||||
|
||||
"KIMvirial or "LAMMPSvirial" found on the pair_style line. These keys are not supported kim-api-v2. (The virial computation is always performed by LAMMPS.) Please remove these keys, make sure the KIM model you are using supports kim-api-v2, and rerun.
|
||||
|
||||
E: Illegal pair_style command
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
E: Incorrect args for pair coefficients
|
||||
|
||||
Self-explanatory. Check the input script or data file.
|
||||
Self-explanatory.
|
||||
|
||||
E: Invalid args for non-hybrid pair coefficients
|
||||
E: create_kim_particle_codes: symbol not found: XX
|
||||
|
||||
"NULL" is only supported in pair_coeff calls when using pair hybrid
|
||||
The KIM model specified does not support the atomic species symbol
|
||||
|
||||
E: PairKIM only works with 3D problems
|
||||
|
||||
This is a current limitation.
|
||||
Self-explanatory.
|
||||
|
||||
E: All pair coeffs are not set
|
||||
|
||||
All pair coefficients must be set in the data file or by the
|
||||
pair_coeff command before running a simulation.
|
||||
Self-explanatory.
|
||||
|
||||
E: KIM neighbor iterator exceeded range
|
||||
E: Unable to destroy Compute Arguments Object
|
||||
|
||||
This should not happen. It likely indicates a bug
|
||||
in the KIM implementation of the interatomic potential
|
||||
where it is requesting neighbors incorrectly.
|
||||
A low-level kim-api error has occurred.
|
||||
|
||||
E: LAMMPS unit_style lj not supported by KIM models
|
||||
E: KIM ModelCreate failed
|
||||
|
||||
Self-explanatory. Check the input script or data file.
|
||||
The kim-api was not able to create a model object for the specified model.
|
||||
|
||||
E: Unknown unit_style
|
||||
E: KIM Model did not accept the requested unit system
|
||||
|
||||
Self-explanatory. Check the input script or data file.
|
||||
The KIM Model does not support the specified LAMMPS unit system
|
||||
|
||||
W: KIM Model does not provide `energy'; Potential energy will be zero
|
||||
E: KIM ComputeArgumentsCreate failed
|
||||
|
||||
UNDOCUMENTED
|
||||
A low-level kim-api error has occurred.
|
||||
|
||||
W: KIM Model does not provide `forces'; Forces will be zero
|
||||
E: Unable to register KIM pointers
|
||||
|
||||
UNDOCUMENTED
|
||||
A low-level kim-api error has occurred.
|
||||
|
||||
W: KIM Model does not provide `particleEnergy'; energy per atom will be zero
|
||||
E: Unable to set KIM argument pointers
|
||||
|
||||
UNDOCUMENTED
|
||||
A low-level kim-api error has occurred.
|
||||
|
||||
W: KIM Model does not provide `particleVirial'; virial per atom will be zero
|
||||
|
||||
UNDOCUMENTED
|
||||
|
||||
E: Test_descriptor_string already allocated
|
||||
|
||||
This is an internal error. Contact the developers.
|
||||
|
||||
U: KIM Model does not provide 'energy'; Potential energy will be zero
|
||||
E: pair_kim does not support hybrid
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
U: KIM Model does not provide 'forces'; Forces will be zero
|
||||
E: LAMMPS unit_style lj not suppored by KIM models
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
U: KIM Model does not provide 'particleEnergy'; energy per atom will be zero
|
||||
E: KIM Model requires unsupported compute argument: XXX
|
||||
|
||||
A low-level kim-api error has occurred.
|
||||
|
||||
W: KIM Model does not provide `partialEnergy'; Potential energy will be zero
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
U: KIM Model does not provide 'particleVirial'; virial per atom will be zero
|
||||
W: KIM Model does not provide `partialForce'; Forces will be zero
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
W: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
W: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
E: KIM Model requires unsupported compute callback
|
||||
|
||||
A low-level kim-api error has occurred.
|
||||
|
||||
*/
|
||||
|
|
|
|||
|
|
@ -447,7 +447,7 @@ void AngleCharmmKokkos<DeviceType>::ev_tally(EV_FLOAT &ev, const int i, const in
|
|||
|
||||
namespace LAMMPS_NS {
|
||||
template class AngleCharmmKokkos<LMPDeviceType>;
|
||||
#ifdef KOKKOS_HAVE_CUDA
|
||||
#ifdef KOKKOS_ENABLE_CUDA
|
||||
template class AngleCharmmKokkos<LMPHostType>;
|
||||
#endif
|
||||
}
|
||||
|
|
|
|||
|
|
@ -598,7 +598,7 @@ void AngleClass2Kokkos<DeviceType>::ev_tally(EV_FLOAT &ev, const int i, const in
|
|||
|
||||
namespace LAMMPS_NS {
|
||||
template class AngleClass2Kokkos<LMPDeviceType>;
|
||||
#ifdef KOKKOS_HAVE_CUDA
|
||||
#ifdef KOKKOS_ENABLE_CUDA
|
||||
template class AngleClass2Kokkos<LMPHostType>;
|
||||
#endif
|
||||
}
|
||||
|
|
|
|||
|
|
@ -387,7 +387,7 @@ void AngleCosineKokkos<DeviceType>::ev_tally(EV_FLOAT &ev, const int i, const in
|
|||
|
||||
namespace LAMMPS_NS {
|
||||
template class AngleCosineKokkos<LMPDeviceType>;
|
||||
#ifdef KOKKOS_HAVE_CUDA
|
||||
#ifdef KOKKOS_ENABLE_CUDA
|
||||
template class AngleCosineKokkos<LMPHostType>;
|
||||
#endif
|
||||
}
|
||||
|
|
|
|||
|
|
@ -405,7 +405,7 @@ void AngleHarmonicKokkos<DeviceType>::ev_tally(EV_FLOAT &ev, const int i, const
|
|||
|
||||
namespace LAMMPS_NS {
|
||||
template class AngleHarmonicKokkos<LMPDeviceType>;
|
||||
#ifdef KOKKOS_HAVE_CUDA
|
||||
#ifdef KOKKOS_ENABLE_CUDA
|
||||
template class AngleHarmonicKokkos<LMPHostType>;
|
||||
#endif
|
||||
}
|
||||
|
|
|
|||
|
|
@ -125,7 +125,7 @@ class AtomVecKokkos : public AtomVec {
|
|||
size_t buffer_size;
|
||||
void* buffer;
|
||||
|
||||
#ifdef KOKKOS_HAVE_CUDA
|
||||
#ifdef KOKKOS_ENABLE_CUDA
|
||||
template<class ViewType>
|
||||
Kokkos::View<typename ViewType::data_type,
|
||||
typename ViewType::array_layout,
|
||||
|
|
@ -139,11 +139,11 @@ class AtomVecKokkos : public AtomVec {
|
|||
Kokkos::CudaHostPinnedSpace,typename ViewType::memory_space>::type,
|
||||
Kokkos::MemoryTraits<Kokkos::Unmanaged> > mirror_type;
|
||||
if (buffer_size == 0) {
|
||||
buffer = Kokkos::kokkos_malloc<Kokkos::CudaHostPinnedSpace>(src.capacity());
|
||||
buffer_size = src.capacity();
|
||||
} else if (buffer_size < src.capacity()) {
|
||||
buffer = Kokkos::kokkos_realloc<Kokkos::CudaHostPinnedSpace>(buffer,src.capacity());
|
||||
buffer_size = src.capacity();
|
||||
buffer = Kokkos::kokkos_malloc<Kokkos::CudaHostPinnedSpace>(src.span());
|
||||
buffer_size = src.span();
|
||||
} else if (buffer_size < src.span()) {
|
||||
buffer = Kokkos::kokkos_realloc<Kokkos::CudaHostPinnedSpace>(buffer,src.span());
|
||||
buffer_size = src.span();
|
||||
}
|
||||
return mirror_type( buffer ,
|
||||
src.extent(0) ,
|
||||
|
|
@ -157,7 +157,7 @@ class AtomVecKokkos : public AtomVec {
|
|||
}
|
||||
|
||||
template<class ViewType>
|
||||
void perform_async_copy(const ViewType& src, unsigned int space) {
|
||||
void perform_async_copy(ViewType& src, unsigned int space) {
|
||||
typedef Kokkos::View<typename ViewType::data_type,
|
||||
typename ViewType::array_layout,
|
||||
typename std::conditional<
|
||||
|
|
@ -165,11 +165,11 @@ class AtomVecKokkos : public AtomVec {
|
|||
Kokkos::CudaHostPinnedSpace,typename ViewType::memory_space>::type,
|
||||
Kokkos::MemoryTraits<Kokkos::Unmanaged> > mirror_type;
|
||||
if (buffer_size == 0) {
|
||||
buffer = Kokkos::kokkos_malloc<Kokkos::CudaHostPinnedSpace>(src.capacity()*sizeof(typename ViewType::value_type));
|
||||
buffer_size = src.capacity();
|
||||
} else if (buffer_size < src.capacity()) {
|
||||
buffer = Kokkos::kokkos_realloc<Kokkos::CudaHostPinnedSpace>(buffer,src.capacity()*sizeof(typename ViewType::value_type));
|
||||
buffer_size = src.capacity();
|
||||
buffer = Kokkos::kokkos_malloc<Kokkos::CudaHostPinnedSpace>(src.span()*sizeof(typename ViewType::value_type));
|
||||
buffer_size = src.span();
|
||||
} else if (buffer_size < src.span()) {
|
||||
buffer = Kokkos::kokkos_realloc<Kokkos::CudaHostPinnedSpace>(buffer,src.span()*sizeof(typename ViewType::value_type));
|
||||
buffer_size = src.span();
|
||||
}
|
||||
mirror_type tmp_view( (typename ViewType::value_type*)buffer ,
|
||||
src.extent(0) ,
|
||||
|
|
@ -183,11 +183,11 @@ class AtomVecKokkos : public AtomVec {
|
|||
if(space == Device) {
|
||||
Kokkos::deep_copy(LMPHostType(),tmp_view,src.h_view),
|
||||
Kokkos::deep_copy(LMPHostType(),src.d_view,tmp_view);
|
||||
src.modified_device() = src.modified_host();
|
||||
src.clear_sync_state();
|
||||
} else {
|
||||
Kokkos::deep_copy(LMPHostType(),tmp_view,src.d_view),
|
||||
Kokkos::deep_copy(LMPHostType(),src.h_view,tmp_view);
|
||||
src.modified_device() = src.modified_host();
|
||||
src.clear_sync_state();
|
||||
}
|
||||
}
|
||||
#else
|
||||
|
|
|
|||
|
|
@ -366,7 +366,7 @@ void BondClass2Kokkos<DeviceType>::ev_tally(EV_FLOAT &ev, const int &i, const in
|
|||
|
||||
namespace LAMMPS_NS {
|
||||
template class BondClass2Kokkos<LMPDeviceType>;
|
||||
#ifdef KOKKOS_HAVE_CUDA
|
||||
#ifdef KOKKOS_ENABLE_CUDA
|
||||
template class BondClass2Kokkos<LMPHostType>;
|
||||
#endif
|
||||
}
|
||||
|
|
|
|||
|
|
@ -401,7 +401,7 @@ void BondFENEKokkos<DeviceType>::ev_tally(EV_FLOAT &ev, const int &i, const int
|
|||
|
||||
namespace LAMMPS_NS {
|
||||
template class BondFENEKokkos<LMPDeviceType>;
|
||||
#ifdef KOKKOS_HAVE_CUDA
|
||||
#ifdef KOKKOS_ENABLE_CUDA
|
||||
template class BondFENEKokkos<LMPHostType>;
|
||||
#endif
|
||||
}
|
||||
|
|
|
|||
|
|
@ -340,7 +340,7 @@ void BondHarmonicKokkos<DeviceType>::ev_tally(EV_FLOAT &ev, const int &i, const
|
|||
|
||||
namespace LAMMPS_NS {
|
||||
template class BondHarmonicKokkos<LMPDeviceType>;
|
||||
#ifdef KOKKOS_HAVE_CUDA
|
||||
#ifdef KOKKOS_ENABLE_CUDA
|
||||
template class BondHarmonicKokkos<LMPHostType>;
|
||||
#endif
|
||||
}
|
||||
|
|
|
|||
|
|
@ -153,7 +153,7 @@ void ComputeTempKokkos<DeviceType>::operator()(TagComputeTempVector<RMASS>, cons
|
|||
|
||||
namespace LAMMPS_NS {
|
||||
template class ComputeTempKokkos<LMPDeviceType>;
|
||||
#ifdef KOKKOS_HAVE_CUDA
|
||||
#ifdef KOKKOS_ENABLE_CUDA
|
||||
template class ComputeTempKokkos<LMPHostType>;
|
||||
#endif
|
||||
}
|
||||
|
|
|
|||
|
|
@ -786,7 +786,7 @@ void DihedralCharmmKokkos<DeviceType>::ev_tally(EVM_FLOAT &evm, const int i, con
|
|||
|
||||
namespace LAMMPS_NS {
|
||||
template class DihedralCharmmKokkos<LMPDeviceType>;
|
||||
#ifdef KOKKOS_HAVE_CUDA
|
||||
#ifdef KOKKOS_ENABLE_CUDA
|
||||
template class DihedralCharmmKokkos<LMPHostType>;
|
||||
#endif
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1127,7 +1127,7 @@ void DihedralClass2Kokkos<DeviceType>::ev_tally(EV_FLOAT &ev, const int i1, cons
|
|||
|
||||
namespace LAMMPS_NS {
|
||||
template class DihedralClass2Kokkos<LMPDeviceType>;
|
||||
#ifdef KOKKOS_HAVE_CUDA
|
||||
#ifdef KOKKOS_ENABLE_CUDA
|
||||
template class DihedralClass2Kokkos<LMPHostType>;
|
||||
#endif
|
||||
}
|
||||
|
|
|
|||
|
|
@ -536,7 +536,7 @@ void DihedralOPLSKokkos<DeviceType>::ev_tally(EV_FLOAT &ev, const int i1, const
|
|||
|
||||
namespace LAMMPS_NS {
|
||||
template class DihedralOPLSKokkos<LMPDeviceType>;
|
||||
#ifdef KOKKOS_HAVE_CUDA
|
||||
#ifdef KOKKOS_ENABLE_CUDA
|
||||
template class DihedralOPLSKokkos<LMPHostType>;
|
||||
#endif
|
||||
}
|
||||
|
|
|
|||
|
|
@ -90,7 +90,7 @@ void FixDPDenergyKokkos<DeviceType>::final_integrate()
|
|||
|
||||
namespace LAMMPS_NS {
|
||||
template class FixDPDenergyKokkos<LMPDeviceType>;
|
||||
#ifdef KOKKOS_HAVE_CUDA
|
||||
#ifdef KOKKOS_ENABLE_CUDA
|
||||
template class FixDPDenergyKokkos<LMPHostType>;
|
||||
#endif
|
||||
}
|
||||
|
|
|
|||
|
|
@ -162,7 +162,7 @@ void FixEnforce2DKokkos<DeviceType>::post_force_item( int i ) const
|
|||
|
||||
namespace LAMMPS_NS {
|
||||
template class FixEnforce2DKokkos<LMPDeviceType>;
|
||||
#ifdef KOKKOS_HAVE_CUDA
|
||||
#ifdef KOKKOS_ENABLE_CUDA
|
||||
template class FixEnforce2DKokkos<LMPHostType>;
|
||||
#endif
|
||||
}
|
||||
|
|
|
|||
|
|
@ -563,7 +563,7 @@ void FixEOStableRXKokkos<DeviceType>::create_kokkos_tables()
|
|||
|
||||
namespace LAMMPS_NS {
|
||||
template class FixEOStableRXKokkos<LMPDeviceType>;
|
||||
#ifdef KOKKOS_HAVE_CUDA
|
||||
#ifdef KOKKOS_ENABLE_CUDA
|
||||
template class FixEOStableRXKokkos<LMPHostType>;
|
||||
#endif
|
||||
}
|
||||
|
|
|
|||
|
|
@ -118,7 +118,7 @@ void FixFreezeKokkos<DeviceType>::operator()(const int i, OriginalForce &origina
|
|||
|
||||
namespace LAMMPS_NS {
|
||||
template class FixFreezeKokkos<LMPDeviceType>;
|
||||
#ifdef KOKKOS_HAVE_CUDA
|
||||
#ifdef KOKKOS_ENABLE_CUDA
|
||||
template class FixFreezeKokkos<LMPHostType>;
|
||||
#endif
|
||||
}
|
||||
|
|
|
|||
|
|
@ -115,7 +115,7 @@ void FixGravityKokkos<DeviceType>::operator()(TagFixGravityMass, const int i, do
|
|||
|
||||
namespace LAMMPS_NS {
|
||||
template class FixGravityKokkos<LMPDeviceType>;
|
||||
#ifdef KOKKOS_HAVE_CUDA
|
||||
#ifdef KOKKOS_ENABLE_CUDA
|
||||
template class FixGravityKokkos<LMPHostType>;
|
||||
#endif
|
||||
}
|
||||
|
|
|
|||
|
|
@ -774,7 +774,7 @@ void FixLangevinKokkos<DeviceType>::cleanup_copy()
|
|||
|
||||
namespace LAMMPS_NS {
|
||||
template class FixLangevinKokkos<LMPDeviceType>;
|
||||
#ifdef KOKKOS_HAVE_CUDA
|
||||
#ifdef KOKKOS_ENABLE_CUDA
|
||||
template class FixLangevinKokkos<LMPHostType>;
|
||||
#endif
|
||||
}
|
||||
|
|
|
|||
|
|
@ -199,7 +199,7 @@ void FixMomentumKokkos<DeviceType>::end_of_step()
|
|||
|
||||
namespace LAMMPS_NS {
|
||||
template class FixMomentumKokkos<LMPDeviceType>;
|
||||
#ifdef KOKKOS_HAVE_CUDA
|
||||
#ifdef KOKKOS_ENABLE_CUDA
|
||||
template class FixMomentumKokkos<LMPHostType>;
|
||||
#endif
|
||||
}
|
||||
|
|
|
|||
|
|
@ -329,7 +329,7 @@ int FixNeighHistoryKokkos<DeviceType>::unpack_exchange(int nlocal, double *buf)
|
|||
|
||||
namespace LAMMPS_NS {
|
||||
template class FixNeighHistoryKokkos<LMPDeviceType>;
|
||||
#ifdef KOKKOS_HAVE_CUDA
|
||||
#ifdef KOKKOS_ENABLE_CUDA
|
||||
template class FixNeighHistoryKokkos<LMPHostType>;
|
||||
#endif
|
||||
}
|
||||
|
|
|
|||
|
|
@ -733,7 +733,7 @@ void FixNHKokkos<DeviceType>::pre_exchange()
|
|||
|
||||
namespace LAMMPS_NS {
|
||||
template class FixNHKokkos<LMPDeviceType>;
|
||||
#ifdef KOKKOS_HAVE_CUDA
|
||||
#ifdef KOKKOS_ENABLE_CUDA
|
||||
template class FixNHKokkos<LMPHostType>;
|
||||
#endif
|
||||
}
|
||||
|
|
|
|||
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Reference in New Issue