Merge pull request #1518 from akohlmey/collected-small-changes
Collected small changes and fixes for the next patch release
This commit is contained in:
Axel Kohlmeyer
@ -106,6 +106,8 @@ if(BUILD_LIB)
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endif()
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endif()
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option(BUILD_TOOLS "Build and install LAMMPS tools (msi2lmp, binary2txt, chain)" OFF)
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if(NOT BUILD_EXE AND NOT BUILD_LIB)
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message(FATAL_ERROR "You need to at least enable one of two following options: BUILD_LIB or BUILD_EXE")
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endif()
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@ -222,6 +224,9 @@ if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-PLUMED OR PKG_USER-QUI
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find_package(LAPACK)
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find_package(BLAS)
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if(NOT LAPACK_FOUND OR NOT BLAS_FOUND)
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if(CMAKE_GENERATOR STREQUAL "Ninja")
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status(FATAL_ERROR "Cannot build internal linear algebra library with Ninja build tool due to lack for Fortran support")
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endif()
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enable_language(Fortran)
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file(GLOB LAPACK_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/linalg/[^.]*.[fF])
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add_library(linalg STATIC ${LAPACK_SOURCES})
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@ -517,6 +522,19 @@ if(BUILD_EXE)
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set_target_properties(lmp PROPERTIES OUTPUT_NAME ${LAMMPS_BINARY})
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install(TARGETS lmp DESTINATION ${CMAKE_INSTALL_BINDIR})
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install(FILES ${LAMMPS_DOC_DIR}/lammps.1 DESTINATION ${CMAKE_INSTALL_MANDIR}/man1 RENAME ${LAMMPS_BINARY}.1)
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endif()
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if(BUILD_TOOLS)
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add_executable(binary2txt ${LAMMPS_TOOLS_DIR}/binary2txt.cpp)
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install(TARGETS binary2txt DESTINATION ${CMAKE_INSTALL_BINDIR})
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# ninja-build currently does not support fortran. thus we skip building this tool
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if(NOT CMAKE_GENERATOR STREQUAL "Ninja")
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message(STATUS "Skipping building 'chain.x' with Ninja build tool due to lack of Fortran support")
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enable_language(Fortran)
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add_executable(chain.x ${LAMMPS_TOOLS_DIR}/chain.f)
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target_link_libraries(chain.x ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
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endif()
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enable_language(C)
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get_filename_component(MSI2LMP_SOURCE_DIR ${LAMMPS_TOOLS_DIR}/msi2lmp/src ABSOLUTE)
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@ -525,7 +543,6 @@ if(BUILD_EXE)
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target_link_libraries(msi2lmp m)
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install(TARGETS msi2lmp DESTINATION ${CMAKE_INSTALL_BINDIR})
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install(FILES ${LAMMPS_DOC_DIR}/msi2lmp.1 DESTINATION ${CMAKE_INSTALL_MANDIR}/man1)
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endif()
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include(Documentation)
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@ -13,6 +13,9 @@ if(PKG_KIM)
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endif()
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option(DOWNLOAD_KIM "Download KIM-API from OpenKIM instead of using an already installed one" ${DOWNLOAD_KIM_DEFAULT})
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if(DOWNLOAD_KIM)
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if(CMAKE_GENERATOR STREQUAL "Ninja")
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message(FATAL_ERROR "Cannot build downloaded KIM-API library with Ninja build tool")
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endif()
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message(STATUS "KIM-API 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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@ -11,6 +11,9 @@ if(PKG_LATTE)
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if (CMAKE_VERSION VERSION_LESS "3.7") # due to SOURCE_SUBDIR
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message(FATAL_ERROR "For downlading LATTE you need at least cmake-3.7")
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endif()
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if(CMAKE_GENERATOR STREQUAL "Ninja")
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message(FATAL_ERROR "Cannot build downloaded LATTE library with Ninja build tool")
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endif()
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message(STATUS "LATTE download requested - we will build our own")
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include(ExternalProject)
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ExternalProject_Add(latte_build
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@ -11,6 +11,9 @@ if(PKG_MSCG)
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if (CMAKE_VERSION VERSION_LESS "3.7") # due to SOURCE_SUBDIR
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message(FATAL_ERROR "For downlading MSCG you need at least cmake-3.7")
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endif()
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if(CMAKE_GENERATOR STREQUAL "Ninja")
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message(FATAL_ERROR "Cannot build downloaded MSCG library with Ninja build tool")
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endif()
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include(ExternalProject)
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if(NOT LAPACK_FOUND)
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set(EXTRA_MSCG_OPTS "-DLAPACK_LIBRARIES=${CMAKE_CURRENT_BINARY_DIR}/liblinalg.a")
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@ -17,6 +17,9 @@ if(PKG_USER-PLUMED)
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option(DOWNLOAD_PLUMED "Download Plumed package instead of using an already installed one" ${DOWNLOAD_PLUMED_DEFAULT})
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if(DOWNLOAD_PLUMED)
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if(CMAKE_GENERATOR STREQUAL "Ninja")
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message(FATAL_ERROR "Cannot build downloaded Plumed library with Ninja build tool")
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endif()
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if(BUILD_MPI)
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set(PLUMED_CONFIG_MPI "--enable-mpi")
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set(PLUMED_CONFIG_CC ${CMAKE_MPI_C_COMPILER})
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@ -13,6 +13,9 @@ if(PKG_USER-SCAFACOS)
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endif()
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option(DOWNLOAD_SCAFACOS "Download ScaFaCoS library instead of using an already installed one" ${DOWNLOAD_SCAFACOS_DEFAULT})
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if(DOWNLOAD_SCAFACOS)
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if(CMAKE_GENERATOR STREQUAL "Ninja")
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message(FATAL_ERROR "Cannot build downloaded ScaFaCoS library with Ninja build tool")
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endif()
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message(STATUS "ScaFaCoS download requested - we will build our own")
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include(ExternalProject)
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ExternalProject_Add(scafacos_build
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@ -7,6 +7,9 @@ if(PKG_VORONOI)
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endif()
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option(DOWNLOAD_VORO "Download and compile the Voro++ library instead of using an already installed one" ${DOWNLOAD_VORO_DEFAULT})
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if(DOWNLOAD_VORO)
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if(CMAKE_GENERATOR STREQUAL "Ninja")
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message(FATAL_ERROR "Cannot build downloaded Voro++ library with Ninja build tool")
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endif()
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message(STATUS "Voro++ download requested - we will build our own")
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include(ExternalProject)
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@ -32,10 +32,18 @@ cmake \[options ...\] ../cmake # configuration with (command-line) cmake
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make # compilation :pre
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The cmake command will detect available features, enable selected
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packages and options, and will generate the build environment. The make
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command will then compile and link LAMMPS, producing (by default) an
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executable called "lmp" and a library called "liblammps.a" in the
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"build" folder.
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packages and options, and will generate the build environment. By default
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this build environment will be created for "Unix Makefiles" on most
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platforms and particularly on Linux. However, alternate build tools
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(e.g. Ninja) and support files for Integrated Development Environments
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(IDE) like Eclipse, CodeBlocks, or Kate can be generated, too. This is
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selected via the "-G" command line flag. For the rest of the documentation
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we will assume that the build environment is generated for makefiles
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and thus the make command will be used to compile and link LAMMPS as
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indicated above, producing (by default) an executable called "lmp" and
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a library called "liblammps.a" in the "build" folder. When generating
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a build environment for the "Ninja" build tool, the build command would
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be "ninja" instead of "make".
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If your machine has multiple CPU cores (most do these days), using a
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command like "make -jN" (with N being the number of available local
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@ -88,6 +88,8 @@ potentials only include the pair potential portion of the EAM
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interaction when used by this compute, not the embedding term. Also
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bonded or Kspace interactions do not contribute to this compute.
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The computes in this package are not compatible with dynamic groups.
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[Related commands:]
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{compute group/group}_compute_group_group.html, {compute
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1
examples/USER/misc/kolmogorov_crespi_full/CH.rebo
Symbolic link
1
examples/USER/misc/kolmogorov_crespi_full/CH.rebo
Symbolic link
@ -0,0 +1 @@
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../../../../potentials/CH.rebo
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@ -18,7 +18,7 @@ group adsorbate type 2
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######################## Potential defition ########################
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pair_style hybrid/overlay rebo kolmogorov/crespi/full 16.0
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####################################################################
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pair_coeff * * rebo CH.airebo NULL C # chemical
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pair_coeff * * rebo CH.rebo NULL C # chemical
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pair_coeff * * kolmogorov/crespi/full CC.KC-full C C # long range
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####################################################################
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# Neighbor update settings
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@ -1,4 +1,5 @@
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LAMMPS (8 Mar 2018)
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LAMMPS (5 Jun 2019)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
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using 1 OpenMP thread(s) per MPI task
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# Initialization
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units metal
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@ -21,6 +22,8 @@ read_data Bi_gr_AB_stack_2L_noH_300K.data
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0 = max # of 1-3 neighbors
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0 = max # of 1-4 neighbors
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1 = max # of special neighbors
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special bonds CPU = 0.000353813 secs
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read_data CPU = 0.0043292 secs
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mass 1 12.0107 # carbon mass (g/mole) | membrane
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mass 2 12.0107 # carbon mass (g/mole) | adsorbate
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# Separate atom groups
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@ -32,8 +35,8 @@ group adsorbate type 2
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######################## Potential defition ########################
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pair_style hybrid/overlay rebo kolmogorov/crespi/full 16.0
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####################################################################
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pair_coeff * * rebo CH.airebo NULL C # chemical
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Reading potential file CH.airebo with DATE: 2011-10-25
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pair_coeff * * rebo CH.rebo NULL C # chemical
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Reading potential file CH.rebo with DATE: 2018-7-3
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pair_coeff * * kolmogorov/crespi/full CC.KC-full C C # long range
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####################################################################
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# Neighbor update settings
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@ -92,32 +95,32 @@ Neighbor list info ...
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 16.96 | 16.96 | 16.96 Mbytes
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Step TotEng PotEng KinEng v_REBO v_KC Temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
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0 -5025.3867722725 -5040.0767391239 14.6899668514 -5011.2636297759 -28.8131093480 83.6251135127 22.0155657205 20.2812150219 3.4623630945 0.0282287195 0.0535565745 0.2193320108
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100 -5025.3962433293 -5041.3829775585 15.9867342292 -5012.5109377234 -28.8720398351 91.0071804888 22.0181858078 20.2867731676 3.4456714402 0.0241525932 0.0573807336 -0.5235069014
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200 -5025.3942568861 -5041.9638220670 16.5695651809 -5012.7804299195 -29.1833921475 94.3250439654 22.0203529515 20.2926376511 3.3740502908 0.0186420748 0.0595018114 -0.7867265577
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300 -5025.3919463074 -5040.9705419367 15.5785956293 -5012.0510295102 -28.9195124265 88.6837826830 22.0218424095 20.2984380400 3.3199036613 0.0106250874 0.0544668352 -0.1513745908
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400 -5025.3965376948 -5041.6929964127 16.2964587179 -5012.6418090677 -29.0511873450 92.7703393702 22.0224243957 20.3034636122 3.3515794172 0.0006844935 0.0458598502 0.6967704496
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500 -5025.4050172900 -5042.1712310053 16.7662137153 -5013.1850218645 -28.9862091408 95.4444989087 22.0220673443 20.3074634962 3.4286173278 -0.0078273439 0.0340764532 0.6845095066
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||||
600 -5025.3985715734 -5041.2158947893 15.8173232159 -5012.4875319345 -28.7283628548 90.0427797270 22.0209262700 20.3103065099 3.4653840648 -0.0141442608 0.0229602847 0.0009001093
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||||
700 -5025.3997561572 -5041.6276721306 16.2279159734 -5012.7093581188 -28.9183140118 92.3801482386 22.0191651506 20.3120184840 3.4291788224 -0.0208485646 0.0104216414 -0.6668311564
|
||||
800 -5025.3967603736 -5042.3401685987 16.9434082251 -5013.3044877099 -29.0356808888 96.4532085367 22.0167259920 20.3122737443 3.3535033285 -0.0279747378 -0.0060833621 -0.7003492925
|
||||
900 -5025.3984542801 -5042.2820667481 16.8836124680 -5013.4066841442 -28.8753826039 96.1128111061 22.0136711877 20.3107854823 3.3206430872 -0.0331979094 -0.0237440547 0.1335648638
|
||||
1000 -5025.3988185618 -5041.9160822433 16.5172636815 -5012.8147737982 -29.1013084450 94.0273088606 22.0102627032 20.3075977018 3.3736867454 -0.0340065996 -0.0390649991 0.7872380119
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Loop time of 156.142 on 1 procs for 1000 steps with 1360 atoms
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0 -5025.3867727863 -5040.0767396377 14.6899668514 -5011.2636302897 -28.8131093480 83.6251135127 22.0155657205 20.2812150219 3.4623630945 0.0282287195 0.0535565745 0.2193320108
|
||||
100 -5025.3962438431 -5041.3829780735 15.9867342304 -5012.5109382383 -28.8720398352 91.0071804956 22.0181858078 20.2867731676 3.4456714402 0.0241525932 0.0573807336 -0.5235069015
|
||||
200 -5025.3942574000 -5041.9638225847 16.5695651847 -5012.7804304371 -29.1833921476 94.3250439874 22.0203529515 20.2926376511 3.3740502908 0.0186420748 0.0595018114 -0.7867265578
|
||||
300 -5025.3919468212 -5040.9705424499 15.5785956286 -5012.0510300232 -28.9195124266 88.6837826792 22.0218424095 20.2984380400 3.3199036613 0.0106250874 0.0544668352 -0.1513745907
|
||||
400 -5025.3965382086 -5041.6929969192 16.2964587107 -5012.6418095739 -29.0511873454 92.7703393292 22.0224243957 20.3034636122 3.3515794172 0.0006844935 0.0458598502 0.6967704497
|
||||
500 -5025.4050178038 -5042.1712315208 16.7662137170 -5013.1850223792 -28.9862091417 95.4444989189 22.0220673443 20.3074634962 3.4286173278 -0.0078273439 0.0340764532 0.6845095066
|
||||
600 -5025.3985720873 -5041.2158953052 15.8173232179 -5012.4875324499 -28.7283628553 90.0427797386 22.0209262700 20.3103065099 3.4653840648 -0.0141442608 0.0229602847 0.0009001092
|
||||
700 -5025.3997566711 -5041.6276726420 16.2279159709 -5012.7093586298 -28.9183140122 92.3801482242 22.0191651506 20.3120184840 3.4291788224 -0.0208485646 0.0104216414 -0.6668311565
|
||||
800 -5025.3967608874 -5042.3401691104 16.9434082230 -5013.3044882226 -29.0356808878 96.4532085250 22.0167259920 20.3122737443 3.3535033285 -0.0279747378 -0.0060833621 -0.7003492926
|
||||
900 -5025.3984547937 -5042.2820672614 16.8836124676 -5013.4066846579 -28.8753826035 96.1128111040 22.0136711877 20.3107854823 3.3206430872 -0.0331979094 -0.0237440547 0.1335648640
|
||||
1000 -5025.3988190757 -5041.9160827657 16.5172636900 -5012.8147743212 -29.1013084444 94.0273089090 22.0102627032 20.3075977018 3.3736867454 -0.0340065996 -0.0390649991 0.7872380119
|
||||
Loop time of 103.724 on 1 procs for 1000 steps with 1360 atoms
|
||||
|
||||
Performance: 0.553 ns/day, 43.373 hours/ns, 6.404 timesteps/s
|
||||
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
Performance: 0.833 ns/day, 28.812 hours/ns, 9.641 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 | 155.99 | 155.99 | 155.99 | 0.0 | 99.90
|
||||
Bond | 0.00075769 | 0.00075769 | 0.00075769 | 0.0 | 0.00
|
||||
Pair | 103.59 | 103.59 | 103.59 | 0.0 | 99.87
|
||||
Bond | 0.00022388 | 0.00022388 | 0.00022388 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.084217 | 0.084217 | 0.084217 | 0.0 | 0.05
|
||||
Output | 0.0016122 | 0.0016122 | 0.0016122 | 0.0 | 0.00
|
||||
Modify | 0.034797 | 0.034797 | 0.034797 | 0.0 | 0.02
|
||||
Other | | 0.02838 | | | 0.02
|
||||
Comm | 0.082476 | 0.082476 | 0.082476 | 0.0 | 0.08
|
||||
Output | 0.0010884 | 0.0010884 | 0.0010884 | 0.0 | 0.00
|
||||
Modify | 0.032938 | 0.032938 | 0.032938 | 0.0 | 0.03
|
||||
Other | | 0.01749 | | | 0.02
|
||||
|
||||
Nlocal: 1360 ave 1360 max 1360 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
@ -133,4 +136,4 @@ Ave neighs/atom = 195.004
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:02:36
|
||||
Total wall time: 0:01:43
|
||||
@ -1,4 +1,5 @@
|
||||
LAMMPS (8 Mar 2018)
|
||||
LAMMPS (5 Jun 2019)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Initialization
|
||||
units metal
|
||||
@ -21,6 +22,8 @@ read_data Bi_gr_AB_stack_2L_noH_300K.data
|
||||
0 = max # of 1-3 neighbors
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
special bonds CPU = 0.000187874 secs
|
||||
read_data CPU = 0.00234103 secs
|
||||
mass 1 12.0107 # carbon mass (g/mole) | membrane
|
||||
mass 2 12.0107 # carbon mass (g/mole) | adsorbate
|
||||
# Separate atom groups
|
||||
@ -32,8 +35,8 @@ group adsorbate type 2
|
||||
######################## Potential defition ########################
|
||||
pair_style hybrid/overlay rebo kolmogorov/crespi/full 16.0
|
||||
####################################################################
|
||||
pair_coeff * * rebo CH.airebo NULL C # chemical
|
||||
Reading potential file CH.airebo with DATE: 2011-10-25
|
||||
pair_coeff * * rebo CH.rebo NULL C # chemical
|
||||
Reading potential file CH.rebo with DATE: 2018-7-3
|
||||
pair_coeff * * kolmogorov/crespi/full CC.KC-full C C # long range
|
||||
####################################################################
|
||||
# Neighbor update settings
|
||||
@ -92,32 +95,32 @@ Neighbor list info ...
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 11.13 | 11.13 | 11.13 Mbytes
|
||||
Step TotEng PotEng KinEng v_REBO v_KC Temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
|
||||
0 -5025.3867722725 -5040.0767391239 14.6899668514 -5011.2636297759 -28.8131093480 83.6251135127 22.0155657205 20.2812150219 3.4623630945 0.0282287195 0.0535565745 0.2193320108
|
||||
100 -5025.3962433293 -5041.3829775585 15.9867342292 -5012.5109377234 -28.8720398351 91.0071804888 22.0181858078 20.2867731676 3.4456714402 0.0241525932 0.0573807336 -0.5235069014
|
||||
200 -5025.3942568861 -5041.9638220670 16.5695651809 -5012.7804299195 -29.1833921475 94.3250439654 22.0203529515 20.2926376511 3.3740502908 0.0186420748 0.0595018114 -0.7867265577
|
||||
300 -5025.3919463074 -5040.9705419367 15.5785956293 -5012.0510295103 -28.9195124265 88.6837826830 22.0218424095 20.2984380400 3.3199036613 0.0106250874 0.0544668352 -0.1513745908
|
||||
400 -5025.3965376948 -5041.6929964127 16.2964587179 -5012.6418090677 -29.0511873450 92.7703393702 22.0224243957 20.3034636122 3.3515794172 0.0006844935 0.0458598502 0.6967704496
|
||||
500 -5025.4050172900 -5042.1712310053 16.7662137153 -5013.1850218645 -28.9862091408 95.4444989088 22.0220673443 20.3074634962 3.4286173278 -0.0078273439 0.0340764532 0.6845095066
|
||||
600 -5025.3985715734 -5041.2158947893 15.8173232159 -5012.4875319345 -28.7283628548 90.0427797270 22.0209262700 20.3103065099 3.4653840648 -0.0141442608 0.0229602847 0.0009001093
|
||||
700 -5025.3997561572 -5041.6276721306 16.2279159734 -5012.7093581188 -28.9183140118 92.3801482386 22.0191651506 20.3120184840 3.4291788224 -0.0208485646 0.0104216414 -0.6668311564
|
||||
800 -5025.3967603736 -5042.3401685987 16.9434082251 -5013.3044877099 -29.0356808888 96.4532085367 22.0167259920 20.3122737443 3.3535033285 -0.0279747378 -0.0060833621 -0.7003492925
|
||||
900 -5025.3984542801 -5042.2820667481 16.8836124680 -5013.4066841442 -28.8753826039 96.1128111061 22.0136711877 20.3107854823 3.3206430872 -0.0331979094 -0.0237440547 0.1335648638
|
||||
1000 -5025.3988185618 -5041.9160822433 16.5172636815 -5012.8147737983 -29.1013084450 94.0273088606 22.0102627032 20.3075977018 3.3736867454 -0.0340065996 -0.0390649991 0.7872380119
|
||||
Loop time of 42.5422 on 4 procs for 1000 steps with 1360 atoms
|
||||
0 -5025.3867727863 -5040.0767396377 14.6899668514 -5011.2636302897 -28.8131093480 83.6251135127 22.0155657205 20.2812150219 3.4623630945 0.0282287195 0.0535565745 0.2193320108
|
||||
100 -5025.3962438431 -5041.3829780735 15.9867342304 -5012.5109382383 -28.8720398352 91.0071804956 22.0181858078 20.2867731676 3.4456714402 0.0241525932 0.0573807336 -0.5235069015
|
||||
200 -5025.3942574000 -5041.9638225847 16.5695651847 -5012.7804304371 -29.1833921476 94.3250439874 22.0203529515 20.2926376511 3.3740502908 0.0186420748 0.0595018114 -0.7867265578
|
||||
300 -5025.3919468212 -5040.9705424499 15.5785956286 -5012.0510300232 -28.9195124266 88.6837826792 22.0218424095 20.2984380400 3.3199036613 0.0106250874 0.0544668352 -0.1513745907
|
||||
400 -5025.3965382086 -5041.6929969192 16.2964587107 -5012.6418095739 -29.0511873454 92.7703393291 22.0224243957 20.3034636122 3.3515794172 0.0006844935 0.0458598502 0.6967704497
|
||||
500 -5025.4050178038 -5042.1712315208 16.7662137170 -5013.1850223792 -28.9862091417 95.4444989189 22.0220673443 20.3074634962 3.4286173278 -0.0078273439 0.0340764532 0.6845095066
|
||||
600 -5025.3985720873 -5041.2158953052 15.8173232179 -5012.4875324499 -28.7283628553 90.0427797386 22.0209262700 20.3103065099 3.4653840648 -0.0141442608 0.0229602847 0.0009001092
|
||||
700 -5025.3997566711 -5041.6276726420 16.2279159709 -5012.7093586298 -28.9183140122 92.3801482242 22.0191651506 20.3120184840 3.4291788224 -0.0208485646 0.0104216414 -0.6668311565
|
||||
800 -5025.3967608874 -5042.3401691104 16.9434082230 -5013.3044882226 -29.0356808878 96.4532085250 22.0167259920 20.3122737443 3.3535033285 -0.0279747378 -0.0060833621 -0.7003492926
|
||||
900 -5025.3984547938 -5042.2820672614 16.8836124676 -5013.4066846579 -28.8753826035 96.1128111040 22.0136711877 20.3107854823 3.3206430872 -0.0331979094 -0.0237440547 0.1335648640
|
||||
1000 -5025.3988190757 -5041.9160827657 16.5172636900 -5012.8147743212 -29.1013084444 94.0273089090 22.0102627032 20.3075977018 3.3736867454 -0.0340065996 -0.0390649991 0.7872380119
|
||||
Loop time of 33.7338 on 4 procs for 1000 steps with 1360 atoms
|
||||
|
||||
Performance: 2.031 ns/day, 11.817 hours/ns, 23.506 timesteps/s
|
||||
98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
Performance: 2.561 ns/day, 9.370 hours/ns, 29.644 timesteps/s
|
||||
94.1% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 39.928 | 40.992 | 42.377 | 15.8 | 96.36
|
||||
Bond | 0.0003643 | 0.00043392 | 0.00048113 | 0.0 | 0.00
|
||||
Pair | 30.833 | 31.356 | 32.18 | 9.1 | 92.95
|
||||
Bond | 0.00026059 | 0.00029182 | 0.00031185 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.12253 | 1.5076 | 2.5698 | 82.1 | 3.54
|
||||
Output | 0.0012577 | 0.0013637 | 0.0016453 | 0.4 | 0.00
|
||||
Modify | 0.010833 | 0.012247 | 0.013317 | 0.9 | 0.03
|
||||
Other | | 0.02864 | | | 0.07
|
||||
Comm | 1.443 | 2.2722 | 2.8091 | 34.3 | 6.74
|
||||
Output | 0.00068855 | 0.00095087 | 0.0017185 | 0.0 | 0.00
|
||||
Modify | 0.010187 | 0.011709 | 0.015284 | 1.9 | 0.03
|
||||
Other | | 0.09241 | | | 0.27
|
||||
|
||||
Nlocal: 340 ave 344 max 334 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 1 1
|
||||
@ -133,4 +136,4 @@ Ave neighs/atom = 195.004
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:42
|
||||
Total wall time: 0:00:33
|
||||
@ -547,6 +547,18 @@ FixLbFluid::~FixLbFluid()
|
||||
} else {
|
||||
delete [] NodeArea;
|
||||
}
|
||||
MPI_Type_free(&passxf);
|
||||
MPI_Type_free(&passyf);
|
||||
MPI_Type_free(&passzf);
|
||||
MPI_Type_free(&passxu);
|
||||
MPI_Type_free(&passyu);
|
||||
MPI_Type_free(&passzu);
|
||||
MPI_Type_free(&passxrho);
|
||||
MPI_Type_free(&passyrho);
|
||||
MPI_Type_free(&passzrho);
|
||||
MPI_Type_free(&passxtemp);
|
||||
MPI_Type_free(&passytemp);
|
||||
MPI_Type_free(&passztemp);
|
||||
}
|
||||
|
||||
int FixLbFluid::setmask()
|
||||
|
||||
@ -41,6 +41,7 @@ ComputeForceTally::ComputeForceTally(LAMMPS *lmp, int narg, char **arg) :
|
||||
vector_flag = 0;
|
||||
peratom_flag = 1;
|
||||
timeflag = 1;
|
||||
dynamic_group_allow = 0;
|
||||
|
||||
comm_reverse = size_peratom_cols = 3;
|
||||
extscalar = 1;
|
||||
|
||||
@ -38,6 +38,7 @@ ComputeHeatFluxTally::ComputeHeatFluxTally(LAMMPS *lmp, int narg, char **arg) :
|
||||
|
||||
vector_flag = 1;
|
||||
timeflag = 1;
|
||||
dynamic_group_allow = 0;
|
||||
|
||||
comm_reverse = 7;
|
||||
extvector = 1;
|
||||
|
||||
@ -39,6 +39,7 @@ ComputePEMolTally::ComputePEMolTally(LAMMPS *lmp, int narg, char **arg) :
|
||||
vector_flag = 1;
|
||||
size_vector = 4;
|
||||
timeflag = 1;
|
||||
dynamic_group_allow = 0;
|
||||
|
||||
extvector = 1;
|
||||
peflag = 1; // we need Pair::ev_tally() to be run
|
||||
|
||||
@ -40,6 +40,7 @@ ComputePETally::ComputePETally(LAMMPS *lmp, int narg, char **arg) :
|
||||
vector_flag = 0;
|
||||
peratom_flag = 1;
|
||||
timeflag = 1;
|
||||
dynamic_group_allow = 0;
|
||||
|
||||
comm_reverse = size_peratom_cols = 2;
|
||||
extscalar = 1;
|
||||
|
||||
@ -41,6 +41,7 @@ ComputeStressTally::ComputeStressTally(LAMMPS *lmp, int narg, char **arg) :
|
||||
vector_flag = 0;
|
||||
peratom_flag = 1;
|
||||
timeflag = 1;
|
||||
dynamic_group_allow = 0;
|
||||
|
||||
comm_reverse = size_peratom_cols = 6;
|
||||
extscalar = 0;
|
||||
|
||||
@ -211,7 +211,7 @@ typedef int bigint;
|
||||
#elif defined(__INTEL_COMPILER)
|
||||
# define _noopt
|
||||
#elif defined(__GNUC__)
|
||||
# if (__GNUC__ > 4) || ((__GNUC__ == 4) && (__GNUC_MINOR__ >= 4))
|
||||
# if (__GNUC__ > 4) || ((__GNUC__ == 4) && (__GNUC_MINOR__ >= 9))
|
||||
# define _noopt __attribute__((optimize("O0","no-var-tracking-assignments")))
|
||||
# else
|
||||
# define _noopt __attribute__((optimize("O0")))
|
||||
|
||||
@ -113,9 +113,11 @@ Thermo::Thermo(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
|
||||
|
||||
if (strcmp(style,"one") == 0) {
|
||||
line = new char[256+6*64];
|
||||
memset(line,0,256+6*64);
|
||||
strcpy(line,ONE);
|
||||
} else if (strcmp(style,"multi") == 0) {
|
||||
line = new char[256+12*64];
|
||||
memset(line,0,256+12*64);
|
||||
strcpy(line,MULTI);
|
||||
lineflag = MULTILINE;
|
||||
|
||||
|
||||
Reference in New Issue
Block a user