Merge pull request #3207 from lammps/remove-message-package
remove MESSAGE package
This commit is contained in:
Axel Kohlmeyer
1
.github/workflows/compile-msvc.yml
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1
.github/workflows/compile-msvc.yml
vendored
@ -26,6 +26,7 @@ jobs:
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shell: bash
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run: |
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python3 -m pip install numpy
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python3 -m pip install pyyaml
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cmake -C cmake/presets/windows.cmake \
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-D PKG_PYTHON=on \
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-S cmake -B build \
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1
.github/workflows/unittest-macos.yml
vendored
1
.github/workflows/unittest-macos.yml
vendored
@ -37,6 +37,7 @@ jobs:
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working-directory: build
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run: |
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ccache -z
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python3 -m pip install pyyaml
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cmake -C ../cmake/presets/clang.cmake \
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-C ../cmake/presets/most.cmake \
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-D CMAKE_CXX_COMPILER_LAUNCHER=ccache \
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@ -208,7 +208,6 @@ set(STANDARD_PACKAGES
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MDI
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MEAM
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MESONT
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MESSAGE
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MGPT
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MISC
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ML-HDNNP
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@ -451,7 +450,7 @@ else()
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endif()
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foreach(PKG_WITH_INCL KSPACE PYTHON ML-IAP VORONOI COLVARS ML-HDNNP MDI MOLFILE NETCDF
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PLUMED QMMM ML-QUIP SCAFACOS MACHDYN VTK KIM LATTE MESSAGE MSCG COMPRESS ML-PACE)
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PLUMED QMMM ML-QUIP SCAFACOS MACHDYN VTK KIM LATTE MSCG COMPRESS ML-PACE)
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if(PKG_${PKG_WITH_INCL})
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include(Packages/${PKG_WITH_INCL})
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endif()
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@ -1,31 +0,0 @@
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if(LAMMPS_SIZES STREQUAL "BIGBIG")
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message(FATAL_ERROR "The MESSAGE Package is not compatible with -DLAMMPS_BIGBIG")
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endif()
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option(MESSAGE_ZMQ "Use ZeroMQ in MESSAGE package" OFF)
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file(GLOB_RECURSE cslib_SOURCES
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${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.cpp)
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add_library(cslib STATIC ${cslib_SOURCES})
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target_compile_definitions(cslib PRIVATE -DLAMMPS_${LAMMPS_SIZES})
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set_target_properties(cslib PROPERTIES OUTPUT_NAME lammps_cslib${LAMMPS_MACHINE})
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if(BUILD_MPI)
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target_compile_definitions(cslib PRIVATE -DMPI_YES)
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set_target_properties(cslib PROPERTIES OUTPUT_NAME "csmpi")
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target_link_libraries(cslib PRIVATE MPI::MPI_CXX)
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else()
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target_compile_definitions(cslib PRIVATE -DMPI_NO)
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target_include_directories(cslib PRIVATE ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/src/STUBS_MPI)
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set_target_properties(cslib PROPERTIES OUTPUT_NAME "csnompi")
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endif()
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if(MESSAGE_ZMQ)
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target_compile_definitions(cslib PRIVATE -DZMQ_YES)
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find_package(ZMQ REQUIRED)
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target_link_libraries(cslib PUBLIC ZMQ::ZMQ)
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else()
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target_compile_definitions(cslib PRIVATE -DZMQ_NO)
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target_include_directories(cslib PRIVATE ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/src/STUBS_ZMQ)
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endif()
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target_link_libraries(lammps PRIVATE cslib)
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target_include_directories(lammps PRIVATE ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/src)
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@ -48,7 +48,6 @@ set(ALL_PACKAGES
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MDI
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MEAM
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MESONT
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MESSAGE
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MGPT
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MISC
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ML-HDNNP
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@ -50,7 +50,6 @@ set(ALL_PACKAGES
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MDI
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MEAM
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MESONT
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MESSAGE
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MGPT
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MISC
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ML-HDNNP
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@ -15,7 +15,6 @@ set(PACKAGES_WITH_LIB
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MACHDYN
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MDI
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MESONT
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MESSAGE
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ML-HDNNP
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ML-PACE
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ML-QUIP
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@ -45,7 +45,6 @@ This is the list of packages that may require additional steps.
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* :ref:`MACHDYN <machdyn>`
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* :ref:`MDI <mdi>`
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* :ref:`MESONT <mesont>`
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* :ref:`MESSAGE <message>`
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* :ref:`ML-HDNNP <ml-hdnnp>`
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* :ref:`ML-IAP <mliap>`
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* :ref:`ML-PACE <ml-pace>`
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@ -797,47 +796,6 @@ library.
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----------
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.. _message:
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MESSAGE package
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-----------------------------
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This package can optionally include support for messaging via sockets,
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using the open-source `ZeroMQ library <http://zeromq.org>`_, which must
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be installed on your system.
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.. tabs::
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.. tab:: CMake build
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.. code-block:: bash
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-D MESSAGE_ZMQ=value # build with ZeroMQ support, value = no (default) or yes
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-D ZMQ_LIBRARY=path # ZMQ library file (only needed if a custom location)
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-D ZMQ_INCLUDE_DIR=path # ZMQ include directory (only needed if a custom location)
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.. tab:: Traditional make
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Before building LAMMPS, you must build the CSlib library in
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``lib/message``\ . You can build the CSlib library manually if
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you prefer; follow the instructions in ``lib/message/README``\ .
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You can also do it in one step from the ``lammps/src`` dir, using
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a command like these, which simply invoke the
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``lib/message/Install.py`` script with the specified args:
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.. code-block:: bash
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$ make lib-message # print help message
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$ make lib-message args="-m -z" # build with MPI and socket (ZMQ) support
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$ make lib-message args="-s" # build as serial lib with no ZMQ support
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The build should produce two files: ``lib/message/cslib/src/libmessage.a``
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and ``lib/message/Makefile.lammps``. The latter is copied from an
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existing ``Makefile.lammps.*`` and has settings to link with the ZeroMQ
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library if requested in the build.
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----------
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.. _mliap:
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ML-IAP package
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@ -45,7 +45,6 @@ packages:
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* :ref:`KOKKOS <kokkos>`
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* :ref:`LATTE <latte>`
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* :ref:`MACHDYN <machdyn>`
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* :ref:`MESSAGE <message>`
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* :ref:`ML-HDNNP <ml-hdnnp>`
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* :ref:`ML-PACE <ml-pace>`
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* :ref:`ML-QUIP <ml-quip>`
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@ -68,7 +68,6 @@ An alphabetic list of all general LAMMPS commands.
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* :doc:`log <log>`
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* :doc:`mass <mass>`
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* :doc:`mdi <mdi>`
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* :doc:`message <message>`
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* :doc:`minimize <minimize>`
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* :doc:`min_modify <min_modify>`
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* :doc:`min_style <min_style>`
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@ -105,7 +104,6 @@ An alphabetic list of all general LAMMPS commands.
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* :doc:`restart <restart>`
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* :doc:`run <run>`
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* :doc:`run_style <run_style>`
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* :doc:`server <server>`
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* :doc:`set <set>`
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* :doc:`shell <shell>`
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* :doc:`special_bonds <special_bonds>`
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@ -51,7 +51,6 @@ OPT.
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* :doc:`bond/swap <fix_bond_swap>`
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* :doc:`box/relax <fix_box_relax>`
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* :doc:`charge/regulation <fix_charge_regulation>`
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* :doc:`client/md <fix_client_md>`
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* :doc:`cmap <fix_cmap>`
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* :doc:`colvars <fix_colvars>`
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* :doc:`controller <fix_controller>`
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@ -100,8 +100,6 @@ Lowercase directories
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+-------------+------------------------------------------------------------------+
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| melt | rapid melt of 3d LJ system |
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+-------------+------------------------------------------------------------------+
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| message | demos for LAMMPS client/server coupling with the MESSAGE package |
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+-------------+------------------------------------------------------------------+
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| micelle | self-assembly of small lipid-like molecules into 2d bilayers |
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+-------------+------------------------------------------------------------------+
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| min | energy minimization of 2d LJ melt |
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@ -22,7 +22,6 @@ General howto
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Howto_replica
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Howto_library
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Howto_couple
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Howto_client_server
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Howto_mdi
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Settings howto
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@ -1,163 +0,0 @@
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Using LAMMPS in client/server mode
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==================================
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Client/server coupling of two codes is where one code is the "client"
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and sends request messages to a "server" code. The server responds to
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each request with a reply message. This enables the two codes to work
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in tandem to perform a simulation. LAMMPS can act as either a client
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or server code.
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Some advantages of client/server coupling are that the two codes run
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as stand-alone executables; they are not linked together. Thus
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neither code needs to have a library interface. This often makes it
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easier to run the two codes on different numbers of processors. If a
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message protocol (format and content) is defined for a particular kind
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of simulation, then in principle any code that implements the
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client-side protocol can be used in tandem with any code that
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implements the server-side protocol, without the two codes needing to
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know anything more specific about each other.
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A simple example of client/server coupling is where LAMMPS is the
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client code performing MD timestepping. Each timestep it sends a
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message to a server quantum code containing current coords of all the
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atoms. The quantum code computes energy and forces based on the
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coords. It returns them as a message to LAMMPS, which completes the
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timestep.
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A more complex example is where LAMMPS is the client code and
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processes a series of data files, sending each configuration to a
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quantum code to compute energy and forces. Or LAMMPS runs dynamics
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with an atomistic force field, but pauses every N steps to ask the
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quantum code to compute energy and forces.
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Alternate methods for code coupling with LAMMPS are described on
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the :doc:`Howto couple <Howto_couple>` doc page.
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The protocol for using LAMMPS as a client is to use these 3 commands
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in this order (other commands may come in between):
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* :doc:`message client <message>` # initiate client/server interaction
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* :doc:`fix client/md <fix_client_md>` # any client fix which makes specific requests to the server
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* :doc:`message quit <message>` # terminate client/server interaction
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In between the two message commands, a client fix command and
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:doc:`unfix <unfix>` command can be used multiple times. Similarly,
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this sequence of 3 commands can be repeated multiple times, assuming
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the server program operates in a similar fashion, to initiate and
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terminate client/server communication.
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The protocol for using LAMMPS as a server is to use these 2 commands
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in this order (other commands may come in between):
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* :doc:`message server <message>` # initiate client/server interaction
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* :doc:`server md <server_md>` # any server command which responds to specific requests from the client
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This sequence of 2 commands can be repeated multiple times, assuming
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the client program operates in a similar fashion, to initiate and
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terminate client/server communication.
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LAMMPS support for client/server coupling is in its :ref:`MESSAGE package <PKG-MESSAGE>` which implements several
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commands that enable LAMMPS to act as a client or server, as discussed
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below. The MESSAGE package also wraps a client/server library called
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CSlib which enables two codes to exchange messages in different ways,
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either via files, sockets, or MPI. The CSlib is provided with LAMMPS
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in the lib/message dir. The CSlib has its own
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`website <https://cslib.sandia.gov>`_ with documentation and test
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programs.
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.. note::
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For client/server coupling to work between LAMMPS and another
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code, the other code also has to use the CSlib. This can sometimes be
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done without any modifications to the other code by simply wrapping it
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with a Python script that exchanges CSlib messages with LAMMPS and
|
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prepares input for or processes output from the other code. The other
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code also has to implement a matching protocol for the format and
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content of messages that LAMMPS exchanges with it.
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|
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These are the commands currently in the MESSAGE package for two
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protocols, MD and MC (Monte Carlo). New protocols can easily be
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defined and added to this directory, where LAMMPS acts as either the
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client or server.
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* :doc:`message <message>`
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* :doc:`fix client md <fix_client_md>` = LAMMPS is a client for running MD
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* :doc:`server md <server_md>` = LAMMPS is a server for computing MD forces
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* :doc:`server mc <server_mc>` = LAMMPS is a server for computing a Monte Carlo energy
|
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The server doc files give details of the message protocols
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for data that is exchanged between the client and server.
|
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|
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These example directories illustrate how to use LAMMPS as either a
|
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client or server code:
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* examples/message
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* examples/COUPLE/README
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* examples/COUPLE/lammps_mc
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* examples/COUPLE/lammps_nwchem
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* examples/COUPLE/lammps_vasp
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|
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The examples/message directory couples a client instance of LAMMPS to a
|
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server instance of LAMMPS.
|
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|
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The files in the *lammps_mc* folder show how to couple LAMMPS as
|
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a server to a simple Monte Carlo client code as the driver.
|
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|
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The files in the *lammps_nwchem* folder show how to couple LAMMPS
|
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as a client code running MD timestepping to NWChem acting as a
|
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server providing quantum DFT forces, through a Python wrapper script
|
||||
on NWChem.
|
||||
|
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The files in the *lammps_vasp* folder show how to couple LAMMPS as
|
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a client code running MD timestepping to VASP acting as a server
|
||||
providing quantum DFT forces, through a Python wrapper script on VASP.
|
||||
|
||||
Here is how to launch a client and server code together for any of the
|
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4 modes of message exchange that the :doc:`message <message>` command
|
||||
and the CSlib support. Here LAMMPS is used as both the client and
|
||||
server code. Another code could be substituted for either.
|
||||
|
||||
The examples below show launching both codes from the same window (or
|
||||
batch script), using the "&" character to launch the first code in the
|
||||
background. For all modes except *mpi/one*, you could also launch the
|
||||
codes in separate windows on your desktop machine. It does not
|
||||
matter whether you launch the client or server first.
|
||||
|
||||
In these examples either code can be run on one or more processors.
|
||||
If running in a non-MPI mode (file or zmq) you can launch a code on a
|
||||
single processor without using mpirun.
|
||||
|
||||
IMPORTANT: If you run in mpi/two mode, you must launch both codes via
|
||||
mpirun, even if one or both of them runs on a single processor. This
|
||||
is so that MPI can figure out how to connect both MPI processes
|
||||
together to exchange MPI messages between them.
|
||||
|
||||
For message exchange in *file*, *zmq*, or *mpi/two* modes:
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
% mpirun -np 1 lmp_mpi -log log.client < in.client &
|
||||
% mpirun -np 2 lmp_mpi -log log.server < in.server
|
||||
|
||||
% mpirun -np 4 lmp_mpi -log log.client < in.client &
|
||||
% mpirun -np 1 lmp_mpi -log log.server < in.server
|
||||
|
||||
% mpirun -np 2 lmp_mpi -log log.client < in.client &
|
||||
% mpirun -np 4 lmp_mpi -log log.server < in.server
|
||||
|
||||
For message exchange in *mpi/one* mode:
|
||||
|
||||
Launch both codes in a single mpirun command:
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
mpirun -np 2 lmp_mpi -mpicolor 0 -in in.message.client -log log.client : -np 4 lmp_mpi -mpicolor 1 -in in.message.server -log log.server
|
||||
|
||||
The two -np values determine how many procs the client and the server
|
||||
run on.
|
||||
|
||||
A LAMMPS executable run in this manner must use the -mpicolor color
|
||||
command-line option as their its option, where color is an integer
|
||||
label that will be used to distinguish one executable from another in
|
||||
the multiple executables that the mpirun command launches. In this
|
||||
example the client was colored with a 0, and the server with a 1.
|
||||
@ -5,7 +5,7 @@ LAMMPS can be downloaded, built, and configured for OS X on a Mac with
|
||||
`Homebrew <homebrew_>`_. (Alternatively, see the install instructions for
|
||||
:doc:`Download an executable via Conda <Install_conda>`.) The following LAMMPS
|
||||
packages are unavailable at this time because of additional needs not yet met:
|
||||
GPU, KOKKOS, LATTE, MSCG, MESSAGE, MPIIO POEMS VORONOI.
|
||||
GPU, KOKKOS, LATTE, MSCG, MPIIO, POEMS, VORONOI.
|
||||
|
||||
After installing Homebrew, you can install LAMMPS on your system with
|
||||
the following commands:
|
||||
|
||||
@ -72,7 +72,6 @@ page gives those details.
|
||||
* :ref:`MDI <PKG-MDI>`
|
||||
* :ref:`MEAM <PKG-MEAM>`
|
||||
* :ref:`MESONT <PKG-MESONT>`
|
||||
* :ref:`MESSAGE <PKG-MESSAGE>`
|
||||
* :ref:`MGPT <PKG-MGPT>`
|
||||
* :ref:`MISC <PKG-MISC>`
|
||||
* :ref:`ML-HDNNP <PKG-ML-HDNNP>`
|
||||
@ -1405,7 +1404,8 @@ workflows via the `MolSSI Driver Interface
|
||||
|
||||
**Install:**
|
||||
|
||||
This package has :ref:`specific installation instructions <message>` on the :doc:`Build extras <Build_extras>` page.
|
||||
This package has :ref:`specific installation instructions <mdi>` on
|
||||
the :doc:`Build extras <Build_extras>` page.
|
||||
|
||||
**Supporting info:**
|
||||
|
||||
@ -1490,32 +1490,6 @@ Philipp Kloza (U Cambridge)
|
||||
|
||||
----------
|
||||
|
||||
.. _PKG-MESSAGE:
|
||||
|
||||
MESSAGE package
|
||||
---------------
|
||||
|
||||
**Contents:**
|
||||
|
||||
Commands to use LAMMPS as either a client or server and couple it to
|
||||
another application.
|
||||
|
||||
**Install:**
|
||||
|
||||
This package has :ref:`specific installation instructions <message>` on the :doc:`Build extras <Build_extras>` page.
|
||||
|
||||
**Supporting info:**
|
||||
|
||||
* src/MESSAGE: filenames -> commands
|
||||
* lib/message/README
|
||||
* :doc:`message <message>`
|
||||
* :doc:`fix client/md <fix_client_md>`
|
||||
* :doc:`server md <server_md>`
|
||||
* :doc:`server mc <server_mc>`
|
||||
* examples/message
|
||||
|
||||
----------
|
||||
|
||||
.. _PKG-MGPT:
|
||||
|
||||
MGPT package
|
||||
|
||||
@ -258,11 +258,6 @@ whether an extra library is needed to build and use the package:
|
||||
- pair styles :doc:`mesont/tpm <pair_mesont_tpm>`, :doc:`mesocnt <pair_mesocnt>`
|
||||
- PACKAGES/mesont
|
||||
- int
|
||||
* - :ref:`MESSAGE <PKG-MESSAGE>`
|
||||
- client/server messaging
|
||||
- :doc:`message <message>`
|
||||
- message
|
||||
- int
|
||||
* - :ref:`MGPT <PKG-MGPT>`
|
||||
- fast MGPT multi-ion potentials
|
||||
- :doc:`pair_style mgpt <pair_mgpt>`
|
||||
|
||||
@ -226,15 +226,6 @@ other executable(s) perform an MPI_Comm_split() with their own colors
|
||||
to shrink the MPI_COMM_WORLD communication to be the subset of
|
||||
processors they are actually running on.
|
||||
|
||||
Currently, this is only used in LAMMPS to perform client/server
|
||||
messaging with another application. LAMMPS can act as either a client
|
||||
or server (or both). More details are given on the :doc:`Howto client/server <Howto_client_server>` doc page.
|
||||
|
||||
Specifically, this refers to the "mpi/one" mode of messaging provided
|
||||
by the :doc:`message <message>` command and the CSlib library LAMMPS
|
||||
links with from the lib/message directory. See the
|
||||
:doc:`message <message>` command for more details.
|
||||
|
||||
----------
|
||||
|
||||
.. _cite:
|
||||
|
||||
@ -60,7 +60,6 @@ Commands
|
||||
log
|
||||
mass
|
||||
mdi
|
||||
message
|
||||
min_modify
|
||||
min_spin
|
||||
min_style
|
||||
@ -96,9 +95,6 @@ Commands
|
||||
restart
|
||||
run
|
||||
run_style
|
||||
server
|
||||
server_mc
|
||||
server_md
|
||||
set
|
||||
shell
|
||||
special_bonds
|
||||
|
||||
@ -194,7 +194,6 @@ accelerated styles exist.
|
||||
* :doc:`bond/swap <fix_bond_swap>` - Monte Carlo bond swapping
|
||||
* :doc:`box/relax <fix_box_relax>` - relax box size during energy minimization
|
||||
* :doc:`charge/regulation <fix_charge_regulation>` - Monte Carlo sampling of charge regulation
|
||||
* :doc:`client/md <fix_client_md>` - MD client for client/server simulations
|
||||
* :doc:`cmap <fix_cmap>` - enables CMAP cross-terms of the CHARMM force field
|
||||
* :doc:`colvars <fix_colvars>` - interface to the collective variables "Colvars" library
|
||||
* :doc:`controller <fix_controller>` - apply control loop feedback mechanism
|
||||
|
||||
@ -1,118 +0,0 @@
|
||||
.. index:: fix client/md
|
||||
|
||||
fix client/md command
|
||||
=====================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
fix ID group-ID client/md
|
||||
|
||||
* ID, group-ID are documented in :doc:`fix <fix>` command
|
||||
* client/md = style name of this fix command
|
||||
|
||||
Examples
|
||||
""""""""
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
fix 1 all client/md
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
This fix style enables LAMMPS to run as a "client" code and
|
||||
communicate each timestep with a separate "server" code to perform an
|
||||
MD simulation together.
|
||||
|
||||
The :doc:`Howto client/server <Howto_client_server>` page gives an
|
||||
overview of client/server coupling of LAMMPS with another code where
|
||||
one code is the "client" and sends request messages to a "server"
|
||||
code. The server responds to each request with a reply message. This
|
||||
enables the two codes to work in tandem to perform a simulation.
|
||||
|
||||
When using this fix, LAMMPS (as the client code) passes the current
|
||||
coordinates of all particles to the server code each timestep, which
|
||||
computes their interaction, and returns the energy, forces, and virial
|
||||
for the interacting particles to LAMMPS, so it can complete the
|
||||
timestep.
|
||||
|
||||
Note that the server code can be a quantum code, or another classical
|
||||
MD code which encodes a force field (pair_style in LAMMPS lingo) which
|
||||
LAMMPS does not have. In the quantum case, this fix is a mechanism
|
||||
for running *ab initio* MD with quantum forces.
|
||||
|
||||
The group associated with this fix is ignored.
|
||||
|
||||
The protocol and :doc:`units <units>` for message format and content
|
||||
that LAMMPS exchanges with the server code is defined on the
|
||||
:doc:`server md <server_md>` doc page.
|
||||
|
||||
Note that when using LAMMPS as an MD client, your LAMMPS input script
|
||||
should not normally contain force field commands, like a
|
||||
:doc:`pair_style <pair_style>`, :doc:`bond_style <bond_style>`, or
|
||||
:doc:`kspace_style <kspace_style>` command. However it is possible
|
||||
for a server code to only compute a portion of the full force-field,
|
||||
while LAMMPS computes the remaining part. Your LAMMPS script can also
|
||||
specify boundary conditions or force constraints in the usual way,
|
||||
which will be added to the per-atom forces returned by the server
|
||||
code.
|
||||
|
||||
See the examples/message directory for example scripts where LAMMPS is both
|
||||
the "client" and/or "server" code for this kind of client/server MD
|
||||
simulation. The examples/message/README file explains how to launch
|
||||
LAMMPS and another code in tandem to perform a coupled simulation.
|
||||
|
||||
----------
|
||||
|
||||
Restart, fix_modify, output, run start/stop, minimize info
|
||||
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
|
||||
|
||||
No information about this fix is written to :doc:`binary restart files
|
||||
<restart>`.
|
||||
|
||||
The :doc:`fix_modify <fix_modify>` *energy* option is supported by
|
||||
this fix to add the potential energy set by the server application to
|
||||
the global potential energy of the system as part of
|
||||
:doc:`thermodynamic output <thermo_style>`. The default setting for
|
||||
this fix is :doc:`fix_modify energy yes <fix_modify>`.
|
||||
|
||||
The :doc:`fix_modify <fix_modify>` *virial* option is supported by
|
||||
this fix to add the contribution computed by the server application to
|
||||
the global pressure of the system via the :doc:`compute pressure
|
||||
<compute_pressure>` command. This can be accessed by
|
||||
:doc:`thermodynamic output <thermo_style>`. The default setting for
|
||||
this fix is :doc:`fix_modify virial yes <fix_modify>`.
|
||||
|
||||
This fix computes a global scalar which can be accessed by various
|
||||
:doc:`output commands <Howto_output>`. The scalar is the potential
|
||||
energy discussed above. The scalar value calculated by this fix is
|
||||
"extensive".
|
||||
|
||||
No parameter of this fix can be used with the *start/stop* keywords of
|
||||
the :doc:`run <run>` command.
|
||||
|
||||
This fix is not invoked during :doc:`energy minimization <minimize>`.
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
|
||||
This fix is part of the MESSAGE package. It is only enabled if LAMMPS
|
||||
was built with that package. See the :doc:`Build package
|
||||
<Build_package>` page for more info.
|
||||
|
||||
A script that uses this command must also use the
|
||||
:doc:`message <message>` command to setup and shut down the messaging
|
||||
protocol with the server code.
|
||||
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`message <message>`, :doc:`server <server>`
|
||||
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
@ -1,204 +0,0 @@
|
||||
.. index:: message
|
||||
|
||||
message command
|
||||
===============
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
message which protocol mode arg
|
||||
|
||||
* which = *client* or *server* or *quit*
|
||||
* protocol = *md* or *mc*
|
||||
* mode = *file* or *zmq* or *mpi/one* or *mpi/two*
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
*file* arg = filename
|
||||
filename = file used for message exchanges
|
||||
*zmq* arg = socket-ID
|
||||
socket-ID for client = localhost:5555, see description below
|
||||
socket-ID for server = \*:5555, see description below
|
||||
*mpi/one* arg = none
|
||||
*mpi/two* arg = filename
|
||||
filename = file used to establish communication between 2 MPI jobs
|
||||
|
||||
Examples
|
||||
""""""""
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
message client md file tmp.couple
|
||||
message server md file tmp.couple
|
||||
|
||||
message client md zmq localhost:5555
|
||||
message server md zmq *:5555
|
||||
|
||||
message client md mpi/one
|
||||
message server md mpi/one
|
||||
|
||||
message client md mpi/two tmp.couple
|
||||
message server md mpi/two tmp.couple
|
||||
|
||||
message quit
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
Establish a messaging protocol between LAMMPS and another code for the
|
||||
purpose of client/server coupling.
|
||||
|
||||
The :doc:`Howto client/server <Howto_client_server>` page gives an
|
||||
overview of client/server coupling of LAMMPS with another code where
|
||||
one code is the "client" and sends request messages to a "server"
|
||||
code. The server responds to each request with a reply message. This
|
||||
enables the two codes to work in tandem to perform a simulation.
|
||||
|
||||
----------
|
||||
|
||||
The *which* argument defines LAMMPS to be the client or the server.
|
||||
|
||||
As explained below the *quit* option should be used when LAMMPS is
|
||||
finished as a client. It sends a message to the server to tell it to
|
||||
shut down.
|
||||
|
||||
----------
|
||||
|
||||
The *protocol* argument defines the format and content of messages
|
||||
that will be exchanged between the two codes. The current options
|
||||
are:
|
||||
|
||||
* md = run dynamics with another code
|
||||
* mc = perform Monte Carlo moves with another code
|
||||
|
||||
For protocol *md*, LAMMPS can be either a client or server. See the
|
||||
:doc:`server md <server_md>` page for details on the protocol.
|
||||
|
||||
For protocol *mc*, LAMMPS can be the server. See the :doc:`server mc <server_mc>` page for details on the protocol.
|
||||
|
||||
----------
|
||||
|
||||
The *mode* argument specifies how messages are exchanged between the
|
||||
client and server codes. Both codes must use the same mode and use
|
||||
consistent parameters.
|
||||
|
||||
For mode *file*, the 2 codes communicate via binary files. They must
|
||||
use the same filename, which is actually a file prefix. Several files
|
||||
with that prefix will be created and deleted as a simulation runs.
|
||||
The filename can include a path. Both codes must be able to access
|
||||
the path/file in a common filesystem.
|
||||
|
||||
For mode *zmq*, the 2 codes communicate via a socket on the server
|
||||
code's machine. Support for socket messaging is provided by the
|
||||
open-source `ZeroMQ library <http://zeromq.org>`_, which must be
|
||||
installed on your system. The client specifies an IP address (IPv4
|
||||
format) or the DNS name of the machine the server code is running on,
|
||||
followed by a 4 or 5 digit port ID for the socket, separated by a colon.
|
||||
E.g.
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
localhost:5555 # client and server running on same machine
|
||||
192.168.1.1:5555 # server is 192.168.1.1
|
||||
deptbox.uni.edu:5555 # server is deptbox.uni.edu
|
||||
|
||||
The server specifies "\*:5555" where "\*" represents all available
|
||||
interfaces on the server's machine, and the port ID must match
|
||||
what the client specifies.
|
||||
|
||||
.. note::
|
||||
|
||||
On Linux or Unix machines port IDs below 1024 are reserved to the
|
||||
superuser and thus not available. Other ports may already be in
|
||||
use and cannot be opened by a second process. On a Linux machine
|
||||
the commands "netstat -t4an" or "ss -t4an" will list all locally
|
||||
used port IDs for IPv4 addresses.
|
||||
|
||||
.. note::
|
||||
|
||||
On many machines (and sometimes on local networks) also ports IDs
|
||||
may be blocked by default through firewalls. In that case either
|
||||
access to the required port (or a desired range of ports) has to
|
||||
be selectively enabled to the firewall disabled (the latter is
|
||||
usually not a good idea unless you are on a (small) local network
|
||||
that is already protected from outside access.
|
||||
|
||||
.. note::
|
||||
|
||||
Additional explanation is needed here about how to use the *zmq*
|
||||
mode on a parallel machine, e.g. a cluster with many nodes.
|
||||
|
||||
For mode *mpi/one*, the 2 codes communicate via MPI and are launched
|
||||
by the same mpirun command, e.g. with this syntax for OpenMPI:
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
mpirun -np 2 lmp_mpi -mpicolor 0 -in in.client -log log.client : -np 4 othercode args # LAMMPS is client
|
||||
mpirun -np 2 othercode args : -np 4 lmp_mpi -mpicolor 1 -in in.server # LAMMPS is server
|
||||
|
||||
Note the use of the "-mpicolor color" command-line argument with
|
||||
LAMMPS. See the :doc:`command-line args <Run_options>` page for
|
||||
further explanation.
|
||||
|
||||
For mode *mpi/two*, the 2 codes communicate via MPI, but are launched
|
||||
be 2 separate mpirun commands. The specified *filename* argument is a
|
||||
file the 2 MPI processes will use to exchange info so that an MPI
|
||||
inter-communicator can be established to enable the 2 codes to send
|
||||
MPI messages to each other. Both codes must be able to access the
|
||||
path/file in a common filesystem.
|
||||
|
||||
----------
|
||||
|
||||
Normally, the message client or message server command should be used
|
||||
at the top of a LAMMPS input script. It performs an initial handshake
|
||||
with the other code to setup messaging and to verify that both codes
|
||||
are using the same message protocol and mode. Assuming both codes are
|
||||
launched at (nearly) the same time, the other code should perform the
|
||||
same kind of initialization.
|
||||
|
||||
If LAMMPS is the client code, it will begin sending messages when a
|
||||
LAMMPS client command begins its operation. E.g. for the :doc:`fix client/md <fix_client_md>` command, it is when a :doc:`run <run>`
|
||||
command is executed.
|
||||
|
||||
If LAMMPS is the server code, it will begin receiving messages when
|
||||
the :doc:`server <server>` command is invoked.
|
||||
|
||||
If LAMMPS is being used as a client, the message quit command will
|
||||
terminate its messaging with the server. If you do not use this
|
||||
command and just allow LAMMPS to exit, then the server will continue
|
||||
to wait for further messages. This may not be a problem, but if both
|
||||
the client and server programs were launched in the same batch script,
|
||||
then if the server runs indefinitely, it may consume the full allocation
|
||||
of computer time, even if the calculation finishes sooner.
|
||||
|
||||
Note that if LAMMPS is the client or server, it will continue
|
||||
processing the rest of its input script after client/server
|
||||
communication terminates.
|
||||
|
||||
If both codes cooperate in this manner, a new round of client/server
|
||||
messaging can be initiated after termination by re-using a second message
|
||||
command in your LAMMPS input script, followed by a new fix client or
|
||||
server command, followed by another message quit command (if LAMMPS is
|
||||
the client). As an example, this can be performed in a loop to use a
|
||||
quantum code as a server to compute quantum forces for multiple LAMMPS
|
||||
data files or periodic snapshots while running dynamics.
|
||||
|
||||
----------
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
|
||||
This command is part of the MESSAGE package. It is only enabled if
|
||||
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` page for more info.
|
||||
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`server <server>`, :doc:`fix client/md <fix_client_md>`
|
||||
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
@ -485,7 +485,7 @@ CPUs a value of *on* is the default since it can often be faster, just
|
||||
as it is for non-accelerated pair styles
|
||||
|
||||
The *binsize* keyword sets the size of bins used to bin atoms during
|
||||
neighbor list builds. The same value can be set by the
|
||||
neighbor list builds. The same value can be set by the
|
||||
:doc:`neigh_modify binsize <neigh_modify>` command. Making it an option
|
||||
in the package kokkos command allows it to be set from the command line.
|
||||
The default value for CPUs is 0.0, which means the LAMMPS default will be
|
||||
|
||||
@ -1,74 +0,0 @@
|
||||
.. index:: server
|
||||
|
||||
server command
|
||||
==============
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
server protocol
|
||||
|
||||
* protocol = *md* or *mc*
|
||||
|
||||
Examples
|
||||
""""""""
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
server md
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
This command starts LAMMPS running in "server" mode, where it receives
|
||||
messages from a separate "client" code and responds by sending a reply
|
||||
message back to the client. The specified *protocol* determines the
|
||||
format and content of messages LAMMPS expects to receive and how it
|
||||
responds.
|
||||
|
||||
The :doc:`Howto client/server <Howto_client_server>` page gives an
|
||||
overview of client/server coupling of LAMMPS with another code where
|
||||
one code is the "client" and sends request messages to a "server"
|
||||
code. The server responds to each request with a reply message. This
|
||||
enables the two codes to work in tandem to perform a simulation.
|
||||
|
||||
When this command is invoked, LAMMPS will run in server mode in an
|
||||
endless loop, waiting for messages from the client code. The client
|
||||
signals when it is done sending messages to LAMMPS, at which point the
|
||||
loop will exit, and the remainder of the LAMMPS input script will be
|
||||
processed.
|
||||
|
||||
The *protocol* argument defines the format and content of messages
|
||||
that will be exchanged between the two codes. The current options
|
||||
are:
|
||||
|
||||
* :doc:`md <server_md>` = run dynamics with another code
|
||||
* :doc:`mc <server_mc>` = perform Monte Carlo moves with another code
|
||||
|
||||
For protocol *md*, LAMMPS can be either a client (via the :doc:`fix client/md <fix_client_md>` command) or server. See the :doc:`server md <server_md>` page for details on the protocol.
|
||||
|
||||
For protocol *mc*, LAMMPS can be the server. See the :doc:`server mc <server_mc>` page for details on the protocol.
|
||||
|
||||
----------
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
|
||||
This command is part of the MESSAGE package. It is only enabled if
|
||||
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` page for more info.
|
||||
|
||||
A script that uses this command must also use the
|
||||
:doc:`message <message>` command to setup the messaging protocol with
|
||||
the other client code.
|
||||
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`message <message>`, :doc:`fix client/md <fix_client_md>`
|
||||
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
@ -1,126 +0,0 @@
|
||||
.. index:: server mc
|
||||
|
||||
server mc command
|
||||
=================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
server mc
|
||||
|
||||
mc = the protocol argument to the :doc:`server <server>` command
|
||||
|
||||
Examples
|
||||
""""""""
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
server mc
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
This command starts LAMMPS running in "server" mode, where it will
|
||||
expect messages from a separate "client" code that match the *mc*
|
||||
protocol for format and content explained below. For each message
|
||||
LAMMPS receives it will send a message back to the client.
|
||||
|
||||
The :doc:`Howto client/server <Howto_client_server>` page gives an
|
||||
overview of client/server coupling of LAMMPS with another code where
|
||||
one code is the "client" and sends request messages to a "server"
|
||||
code. The server responds to each request with a reply message. This
|
||||
enables the two codes to work in tandem to perform a simulation.
|
||||
|
||||
When this command is invoked, LAMMPS will run in server mode in an
|
||||
endless loop, waiting for messages from the client code. The client
|
||||
signals when it is done sending messages to LAMMPS, at which point the
|
||||
loop will exit, and the remainder of the LAMMPS script will be
|
||||
processed.
|
||||
|
||||
The :doc:`server <server>` page gives other options for using LAMMPS
|
||||
See an example of how this command is used in
|
||||
examples/COUPLE/lammps_mc/in.server.
|
||||
|
||||
----------
|
||||
|
||||
When using this command, LAMMPS (as the server code) receives
|
||||
instructions from a Monte Carlo (MC) driver to displace random atoms,
|
||||
compute the energy before and after displacement, and run dynamics to
|
||||
equilibrate the system.
|
||||
|
||||
The MC driver performs the random displacements on random atoms,
|
||||
accepts or rejects the move in an MC sense, and orchestrates the MD
|
||||
runs.
|
||||
|
||||
The format and content of the exchanged messages are explained here in
|
||||
a conceptual sense. Python-style pseudo code for the library calls to
|
||||
the CSlib is shown, which performs the actual message exchange between
|
||||
the two codes. See the `CSlib website <https://cslib.sandia.gov>`_ doc
|
||||
pages for more details on the actual library syntax. The "cs" object
|
||||
in this pseudo code is a pointer to an instance of the CSlib.
|
||||
|
||||
See the src/MESSAGE/server_mc.cpp file for details on how LAMMPS uses
|
||||
these messages. See the examples/COUPLE/lammps_mc/mc.cpp file for an
|
||||
example of how an MC driver code can use these messages.
|
||||
|
||||
Define NATOMS=1, EINIT=2, DISPLACE=3, ACCEPT=4, RUN=5.
|
||||
|
||||
**Client sends one of these kinds of message**\ :
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
cs->send(NATOMS,0) # msgID = 1 with no fields
|
||||
|
||||
cs->send(EINIT,0) # msgID = 2 with no fields
|
||||
|
||||
cs->send(DISPLACE,2) # msgID = 3 with 2 fields
|
||||
cs->pack_int(1,ID) # 1st field = ID of atom to displace
|
||||
cs->pack(2,3,xnew) # 2nd field = new xyz coords of displaced atom
|
||||
|
||||
cs->send(ACCEPT,1) # msgID = 4 with 1 field
|
||||
cs->pack_int(1,flag) # 1st field = accept/reject flag
|
||||
|
||||
cs->send(RUN,1) # msgID = 5 with 1 field
|
||||
cs->pack_int(1,nsteps) # 1st field = # of timesteps to run MD
|
||||
|
||||
**Server replies**\ :
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
cs->send(NATOMS,1) # msgID = 1 with 1 field
|
||||
cs->pack_int(1,natoms) # 1st field = number of atoms
|
||||
|
||||
cs->send(EINIT,2) # msgID = 2 with 2 fields
|
||||
cs->pack_double(1,poteng) # 1st field = potential energy of system
|
||||
cs->pack(2,3\*natoms,x) # 2nd field = 3N coords of Natoms
|
||||
|
||||
cs->send(DISPLACE,1) # msgID = 3 with 1 field
|
||||
cs->pack_double(1,poteng) # 1st field = new potential energy of system
|
||||
|
||||
cs->send(ACCEPT,0) # msgID = 4 with no fields
|
||||
|
||||
cs->send(RUN,0) # msgID = 5 with no fields
|
||||
|
||||
----------
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
|
||||
This command is part of the MESSAGE package. It is only enabled if
|
||||
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` page for more info.
|
||||
|
||||
A script that uses this command must also use the
|
||||
:doc:`message <message>` command to setup the messaging protocol with
|
||||
the other client code.
|
||||
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`message <message>`
|
||||
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
@ -1,161 +0,0 @@
|
||||
.. index:: server md
|
||||
|
||||
server md command
|
||||
=================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
server md
|
||||
|
||||
md = the protocol argument to the :doc:`server <server>` command
|
||||
|
||||
Examples
|
||||
""""""""
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
server md
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
This command starts LAMMPS running in "server" mode, where it will
|
||||
expect messages from a separate "client" code that match the *md*
|
||||
protocol for format and content explained below. For each message
|
||||
LAMMPS receives it will send a message back to the client.
|
||||
|
||||
The :doc:`Howto client/server <Howto_client_server>` page gives an
|
||||
overview of client/server coupling of LAMMPS with another code where
|
||||
one code is the "client" and sends request messages to a "server"
|
||||
code. The server responds to each request with a reply message. This
|
||||
enables the two codes to work in tandem to perform a simulation.
|
||||
|
||||
When this command is invoked, LAMMPS will run in server mode in an
|
||||
endless loop, waiting for messages from the client code. The client
|
||||
signals when it is done sending messages to LAMMPS, at which point the
|
||||
loop will exit, and the remainder of the LAMMPS script will be
|
||||
processed.
|
||||
|
||||
The :doc:`server <server>` page gives other options for using LAMMPS
|
||||
in server mode. See an example of how this command is used in
|
||||
examples/message/in.message.server.
|
||||
|
||||
----------
|
||||
|
||||
When using this command, LAMMPS (as the server code) receives the
|
||||
current coordinates of all particles from the client code each
|
||||
timestep, computes their interaction, and returns the energy, forces,
|
||||
and pressure for the interacting particles to the client code, so it
|
||||
can complete the timestep. This command could also be used with a
|
||||
client code that performs energy minimization, using the server to
|
||||
compute forces and energy each iteration of its minimizer.
|
||||
|
||||
When using the :doc:`fix client/md <fix_client_md>` command, LAMMPS (as
|
||||
the client code) does the timestepping and receives needed energy,
|
||||
forces, and pressure values from the server code.
|
||||
|
||||
The format and content of the exchanged messages are explained here in
|
||||
a conceptual sense. Python-style pseudo code for the library calls to
|
||||
the CSlib is shown, which performs the actual message exchange between
|
||||
the two codes. See the `CSlib website <https://cslib.sandia.gov>`_ doc
|
||||
pages for more details on the actual library syntax. The "cs" object
|
||||
in this pseudo code is a pointer to an instance of the CSlib.
|
||||
|
||||
See the src/MESSAGE/server_md.cpp and src/MESSAGE/fix_client_md.cpp
|
||||
files for details on how LAMMPS uses these messages. See the
|
||||
examples/COUPLE/lammps_vasp/vasp_wrap.py or
|
||||
examples/COUPLE/lammps_nwchem/nwchem_wrap.py files for examples of how
|
||||
a quantum code (VASP or NWChem) can use these messages.
|
||||
|
||||
The following pseudo-code uses these values, defined as enums.
|
||||
|
||||
Define:
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
SETUP=1, STEP=2
|
||||
DIM=1, PERIODICITY=2, ORIGIN=3, BOX=4, NATOMS=5, NTYPES=6, TYPES=7, COORDS=8, UNITS-9, CHARGE=10
|
||||
FORCES=1, ENERGY=2, PRESSURE=3, ERROR=4
|
||||
|
||||
**Client sends 2 kinds of messages**\ :
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
# required fields: DIM, PERIODICTY, ORIGIN, BOX, NATOMS, NTYPES, TYPES, COORDS
|
||||
# optional fields: UNITS, CHARGE
|
||||
|
||||
cs->send(SETUP,nfields) # msgID with nfields
|
||||
|
||||
cs->pack_int(DIM,dim) # dimension (2,3) of simulation
|
||||
cs->pack(PERIODICITY,3,xyz) # periodicity flags in 3 dims
|
||||
cs->pack(ORIGIN,3,origin) # lower-left corner of simulation box
|
||||
cs->pack(BOX,9,box) # 3 edge vectors of simulation box
|
||||
cs->pack_int(NATOMS,natoms) # total number of atoms
|
||||
cs->pack_int(NTYPES,ntypes) # number of atom types
|
||||
cs->pack(TYPES,natoms,type) # vector of per-atom types
|
||||
cs->pack(COORDS,3\*natoms,x) # vector of 3N atom coords
|
||||
cs->pack_string(UNITS,units) # units = "lj", "real", "metal", etc
|
||||
cs->pack(CHARGE,natoms,q) # vector of per-atom charge
|
||||
|
||||
# required fields: COORDS
|
||||
# optional fields: ORIGIN, BOX
|
||||
|
||||
cs->send(STEP,nfields) # msgID with nfields
|
||||
|
||||
cs->pack(COORDS,3\*natoms,x) # vector of 3N atom coords
|
||||
cs->pack(ORIGIN,3,origin) # lower-left corner of simulation box
|
||||
cs->pack(BOX,9,box) # 3 edge vectors of simulation box
|
||||
|
||||
**Server replies to either kind of message**\ :
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
# required fields: FORCES, ENERGY, PRESSURE
|
||||
# optional fields: ERROR
|
||||
|
||||
cs->send(msgID,nfields) # msgID with nfields
|
||||
cs->pack(FORCES,3\*Natoms,f) # vector of 3N forces on atoms
|
||||
cs->pack(ENERGY,1,poteng) # total potential energy of system
|
||||
cs->pack(PRESSURE,6,press) # global pressure tensor (6-vector)
|
||||
cs->pack_int(ERROR,flag) # server had an error (e.g. DFT non-convergence)
|
||||
|
||||
----------
|
||||
|
||||
The units for various quantities that are sent and received iva
|
||||
messages are defined for atomic-scale simulations in the table below.
|
||||
The client and server codes (including LAMMPS) can use internal units
|
||||
different than these (e.g. :doc:`real units <units>` in LAMMPS), so long
|
||||
as they convert to these units for messaging.
|
||||
|
||||
* COORDS, ORIGIN, BOX = Angstroms
|
||||
* CHARGE = multiple of electron charge (1.0 is a proton)
|
||||
* ENERGY = eV
|
||||
* FORCES = eV/Angstrom
|
||||
* PRESSURE = bars
|
||||
|
||||
Note that these are :doc:`metal units <units>` in LAMMPS.
|
||||
|
||||
If you wish to run LAMMPS in another its non-atomic units, e.g. :doc:`lj units <units>`, then the client and server should exchange a UNITS
|
||||
message as indicated above, and both the client and server should
|
||||
agree on the units for the data they exchange.
|
||||
|
||||
----------
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
|
||||
This command is part of the MESSAGE package. It is only enabled if
|
||||
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` page for more info.
|
||||
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`message <message>`, :doc:`fix client/md <fix_client_md>`
|
||||
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
@ -5,3 +5,4 @@ sphinx_tabs
|
||||
breathe
|
||||
Pygments
|
||||
six
|
||||
pyyaml
|
||||
|
||||
@ -9,6 +9,11 @@ model a realistic problem.
|
||||
In many of the examples included here, LAMMPS must first be built as a
|
||||
library.
|
||||
|
||||
Also see the Howto_mdi doc page in the LAMMPS manual for a description
|
||||
of how LAMMPS can be coupled to other codes in a client/server fashion
|
||||
using the MDI Library created by the MolSSI consortium. The MDI
|
||||
package in LAMMPS has support for this style of code coupling.
|
||||
|
||||
See these sections of the LAMMPS manual for details:
|
||||
|
||||
Build LAMMPS as a library (doc/html/Build_basics.html)
|
||||
@ -28,15 +33,9 @@ These are the sub-directories included in this directory:
|
||||
simple simple example of driver code calling LAMMPS as a lib
|
||||
multiple example of driver code calling multiple instances of LAMMPS
|
||||
plugin example for loading LAMMPS at runtime from a shared library
|
||||
lammps_mc client/server coupling of Monte Carlo client
|
||||
with LAMMPS server for energy evaluation
|
||||
lammps_nwchem client/server coupling of LAMMPS client with
|
||||
NWChem quantum DFT as server for quantum forces
|
||||
lammps_quest MD with quantum forces, coupling to Quest DFT code
|
||||
lammps_spparks grain-growth Monte Carlo with strain via MD,
|
||||
coupling to SPPARKS kinetic MC code
|
||||
lammps_vasp client/server coupling of LAMMPS client with
|
||||
VASP quantum DFT as server for quantum forces
|
||||
library collection of useful inter-code communication routines
|
||||
fortran a simple wrapper on the LAMMPS library API that
|
||||
can be called from Fortran
|
||||
|
||||
@ -1,33 +0,0 @@
|
||||
# Makefile for MC
|
||||
|
||||
SHELL = /bin/sh
|
||||
|
||||
SRC = mc.cpp random_park.cpp
|
||||
OBJ = $(SRC:.cpp=.o)
|
||||
|
||||
# change this line for your machine to path for CSlib src dir
|
||||
|
||||
CSLIB = /home/sjplimp/lammps/lib/message/cslib/src
|
||||
|
||||
# compiler/linker settings
|
||||
|
||||
CC = g++
|
||||
CCFLAGS = -g -O3 -I$(CSLIB)
|
||||
LINK = g++
|
||||
LINKFLAGS = -g -O -L$(CSLIB)
|
||||
|
||||
# targets
|
||||
|
||||
mc: $(OBJ)
|
||||
# first line if built the CSlib within lib/message with ZMQ support
|
||||
# second line if built the CSlib without ZMQ support
|
||||
$(LINK) $(LINKFLAGS) $(OBJ) -lcsnompi -lzmq -o mc
|
||||
# $(LINK) $(LINKFLAGS) $(OBJ) -lcsnompi -o mc
|
||||
|
||||
clean:
|
||||
@rm -f *.o mc
|
||||
|
||||
# rules
|
||||
|
||||
%.o:%.cpp
|
||||
$(CC) $(CCFLAGS) -c $<
|
||||
@ -1,128 +0,0 @@
|
||||
Sample Monte Carlo (MC) wrapper on LAMMPS via client/server coupling
|
||||
|
||||
See the MESSAGE package documentation Build_extras.html#message
|
||||
and Build_extras.html#message for more details on how client/server
|
||||
coupling works in LAMMPS.
|
||||
|
||||
In this dir, the mc.cpp/h files are a standalone "client" MC code. It
|
||||
should be run on a single processor, though it could become a parallel
|
||||
program at some point. LAMMPS is also run as a standalone executable
|
||||
as a "server" on as many processors as desired using its "server mc"
|
||||
command; see it's doc page for details.
|
||||
|
||||
Messages are exchanged between MC and LAMMPS via a client/server
|
||||
library (CSlib), which is included in the LAMMPS distribution in
|
||||
lib/message. As explained below you can choose to exchange data
|
||||
between the two programs either via files or sockets (ZMQ). If the MC
|
||||
program became parallel, data could also be exchanged via MPI.
|
||||
|
||||
The MC code makes simple MC moves, by displacing a single random atom
|
||||
by a small random amount. It uses LAMMPS to calculate the energy
|
||||
change, and to run dynamics between MC moves.
|
||||
|
||||
----------------
|
||||
|
||||
Build LAMMPS with its MESSAGE package installed:
|
||||
|
||||
See the Build extras doc page and its MESSAGE package
|
||||
section for details.
|
||||
|
||||
CMake:
|
||||
|
||||
-D PKG_MESSAGE=yes # include the MESSAGE package
|
||||
-D MESSAGE_ZMQ=value # build with ZeroMQ support, value = no (default) or yes
|
||||
|
||||
Traditional make:
|
||||
|
||||
% cd lammps/lib/message
|
||||
% python Install.py -m -z # build CSlib with MPI and ZMQ support
|
||||
% cd lammps/src
|
||||
% make yes-message
|
||||
% make mpi
|
||||
|
||||
You can leave off the -z if you do not have ZMQ on your system.
|
||||
|
||||
----------------
|
||||
|
||||
Build the MC client code
|
||||
|
||||
The source files for the MC code are in this dir. It links with the
|
||||
CSlib library in lib/message/cslib.
|
||||
|
||||
You must first build the CSlib in serial mode, e.g.
|
||||
|
||||
% cd lammps/lib/message/cslib/src
|
||||
% make lib # build serial and parallel lib with ZMQ support
|
||||
% make lib zmq=no # build serial and parallel lib without ZMQ support
|
||||
|
||||
Then edit the Makefile in this dir. The CSLIB variable should be the
|
||||
path to where the LAMMPS lib/message/cslib/src dir is on your system.
|
||||
If you built the CSlib without ZMQ support you will also need to
|
||||
comment/uncomment one line. Then you can just type
|
||||
|
||||
% make
|
||||
|
||||
and you should get an "mc" executable.
|
||||
|
||||
----------------
|
||||
|
||||
To run in client/server mode:
|
||||
|
||||
Both the client (MC) and server (LAMMPS) must use the same messaging
|
||||
mode, namely file or zmq. This is an argument to the MC code; it can
|
||||
be selected by setting the "mode" variable when you run LAMMPS. The
|
||||
default mode = file.
|
||||
|
||||
Here we assume LAMMPS was built to run in parallel, and the MESSAGE
|
||||
package was installed with socket (ZMQ) support. This means either of
|
||||
the messaging modes can be used and LAMMPS can be run in serial or
|
||||
parallel. The MC code is always run in serial.
|
||||
|
||||
When you run, the server should print out thermodynamic info
|
||||
for every MD run it performs (between MC moves). The client
|
||||
will print nothing until the simulation ends, then it will
|
||||
print stats about the accepted MC moves.
|
||||
|
||||
The examples below are commands you should use in two different
|
||||
terminal windows. The order of the two commands (client or server
|
||||
launch) does not matter. You can run them both in the same window if
|
||||
you append a "&" character to the first one to run it in the
|
||||
background.
|
||||
|
||||
--------------
|
||||
|
||||
File mode of messaging:
|
||||
|
||||
% mpirun -np 1 mc in.mc file tmp.couple
|
||||
% mpirun -np 1 lmp_mpi -v mode file -in in.mc.server
|
||||
|
||||
% mpirun -np 1 mc in.mc file tmp.couple
|
||||
% mpirun -np 4 lmp_mpi -v mode file -in in.mc.server
|
||||
|
||||
ZMQ mode of messaging:
|
||||
|
||||
% mpirun -np 1 mc in.mc zmq localhost:5555
|
||||
% mpirun -np 1 lmp_mpi -v mode zmq -in in.mc.server
|
||||
|
||||
% mpirun -np 1 mc in.mc zmq localhost:5555
|
||||
% mpirun -np 4 lmp_mpi -v mode zmq -in in.mc.server
|
||||
|
||||
--------------
|
||||
|
||||
The input script for the MC program is in.mc. You can edit it to run
|
||||
longer simulations.
|
||||
|
||||
500 nsteps = total # of steps of MD
|
||||
100 ndynamics = # of MD steps between MC moves
|
||||
0.1 delta = displacement size of MC move
|
||||
1.0 temperature = used in MC Boltzman factor
|
||||
12345 seed = random number seed
|
||||
|
||||
--------------
|
||||
|
||||
The problem size that LAMMPS is computing the MC energy for and
|
||||
running dynamics on is set by the x,y,z variables in the LAMMPS
|
||||
in.mc.server script. The default size is 500 particles. You can
|
||||
adjust the size as follows:
|
||||
|
||||
lmp_mpi -v x 10 -v y 10 -v z 20 # 8000 particles
|
||||
@ -1,7 +0,0 @@
|
||||
# MC params
|
||||
|
||||
500 nsteps
|
||||
100 ndynamics
|
||||
0.1 delta
|
||||
1.0 temperature
|
||||
12345 seed
|
||||
@ -1,36 +0,0 @@
|
||||
# 3d Lennard-Jones Monte Carlo server script
|
||||
|
||||
variable mode index file
|
||||
|
||||
if "${mode} == file" then &
|
||||
"message server mc file tmp.couple" &
|
||||
elif "${mode} == zmq" &
|
||||
"message server mc zmq *:5555" &
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
atom_modify map yes
|
||||
|
||||
lattice fcc 0.8442
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
mass 1 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 20 check no
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 50
|
||||
|
||||
server mc
|
||||
@ -1,254 +0,0 @@
|
||||
LAMMPS (22 Aug 2018)
|
||||
# 3d Lennard-Jones Monte Carlo server script
|
||||
|
||||
variable mode index file
|
||||
|
||||
if "${mode} == file" then "message server mc file tmp.couple" elif "${mode} == zmq" "message server mc zmq *:5555"
|
||||
message server mc file tmp.couple
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
atom_modify map yes
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
Time spent = 0.000649929 secs
|
||||
mass 1 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 20 check no
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 50
|
||||
|
||||
server mc
|
||||
run 0
|
||||
Neighbor list info ...
|
||||
update every 20 steps, delay 0 steps, check no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 6 6 6
|
||||
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
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 -6.7733681 0 -4.6176881 -5.0221006
|
||||
Loop time of 2.14577e-06 on 1 procs for 0 steps with 500 atoms
|
||||
|
||||
93.2% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 2.146e-06 | | |100.00
|
||||
|
||||
Nlocal: 500 ave 500 max 500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1956 ave 1956 max 1956 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 19500 ave 19500 max 19500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 19500
|
||||
Ave neighs/atom = 39
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds not checked
|
||||
run 0
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 -6.7723127 0 -4.6166327 -5.015531
|
||||
Loop time of 2.14577e-06 on 1 procs for 0 steps with 500 atoms
|
||||
|
||||
93.2% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 2.146e-06 | | |100.00
|
||||
|
||||
Nlocal: 500 ave 500 max 500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1956 ave 1956 max 1956 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 19501 ave 19501 max 19501 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 19501
|
||||
Ave neighs/atom = 39.002
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds not checked
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 -6.7723127 0 -4.6166327 -5.015531
|
||||
50 0.70239211 -5.6763152 0 -4.6248342 0.59544428
|
||||
100 0.7565013 -5.757431 0 -4.6249485 0.21982657
|
||||
run 0
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
100 0.7565013 -5.7565768 0 -4.6240944 0.22436405
|
||||
Loop time of 1.90735e-06 on 1 procs for 0 steps with 500 atoms
|
||||
|
||||
157.3% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 1.907e-06 | | |100.00
|
||||
|
||||
Nlocal: 500 ave 500 max 500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1939 ave 1939 max 1939 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 18757 ave 18757 max 18757 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 18757
|
||||
Ave neighs/atom = 37.514
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds not checked
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
100 0.7565013 -5.757431 0 -4.6249485 0.21982657
|
||||
150 0.76110797 -5.7664315 0 -4.6270529 0.16005254
|
||||
200 0.73505651 -5.7266069 0 -4.6262273 0.34189744
|
||||
run 0
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
200 0.73505651 -5.7181381 0 -4.6177585 0.37629943
|
||||
Loop time of 2.14577e-06 on 1 procs for 0 steps with 500 atoms
|
||||
|
||||
139.8% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 2.146e-06 | | |100.00
|
||||
|
||||
Nlocal: 500 ave 500 max 500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1899 ave 1899 max 1899 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 18699 ave 18699 max 18699 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 18699
|
||||
Ave neighs/atom = 37.398
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds not checked
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
200 0.73505651 -5.7266069 0 -4.6262273 0.34189744
|
||||
250 0.73052476 -5.7206316 0 -4.627036 0.39287516
|
||||
300 0.76300831 -5.7675007 0 -4.6252773 0.16312925
|
||||
run 0
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
300 0.76300831 -5.768304 0 -4.6260806 0.15954325
|
||||
Loop time of 2.14577e-06 on 1 procs for 0 steps with 500 atoms
|
||||
|
||||
139.8% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 2.146e-06 | | |100.00
|
||||
|
||||
Nlocal: 500 ave 500 max 500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1903 ave 1903 max 1903 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 18715 ave 18715 max 18715 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 18715
|
||||
Ave neighs/atom = 37.43
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds not checked
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
300 0.76300831 -5.768304 0 -4.6260806 0.15954325
|
||||
350 0.72993309 -5.7193261 0 -4.6266162 0.3358374
|
||||
400 0.72469448 -5.713463 0 -4.6285954 0.44859547
|
||||
run 0
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
400 0.72469448 -5.7077332 0 -4.6228655 0.47669832
|
||||
Loop time of 1.90735e-06 on 1 procs for 0 steps with 500 atoms
|
||||
|
||||
157.3% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 1.907e-06 | | |100.00
|
||||
|
||||
Nlocal: 500 ave 500 max 500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1899 ave 1899 max 1899 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 18683 ave 18683 max 18683 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 18683
|
||||
Ave neighs/atom = 37.366
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds not checked
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
400 0.72469448 -5.713463 0 -4.6285954 0.44859547
|
||||
450 0.75305735 -5.7518283 0 -4.6245015 0.34658587
|
||||
500 0.73092571 -5.7206337 0 -4.6264379 0.43715809
|
||||
Total wall time: 0:00:02
|
||||
@ -1,254 +0,0 @@
|
||||
LAMMPS (22 Aug 2018)
|
||||
# 3d Lennard-Jones Monte Carlo server script
|
||||
|
||||
variable mode index file
|
||||
|
||||
if "${mode} == file" then "message server mc file tmp.couple" elif "${mode} == zmq" "message server mc zmq *:5555"
|
||||
message server mc file tmp.couple
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
atom_modify map yes
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
Time spent = 0.000592947 secs
|
||||
mass 1 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 20 check no
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 50
|
||||
|
||||
server mc
|
||||
run 0
|
||||
Neighbor list info ...
|
||||
update every 20 steps, delay 0 steps, check no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 6 6 6
|
||||
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
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 -6.7733681 0 -4.6176881 -5.0221006
|
||||
Loop time of 3.8147e-06 on 4 procs for 0 steps with 500 atoms
|
||||
|
||||
59.0% 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 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 3.815e-06 | | |100.00
|
||||
|
||||
Nlocal: 125 ave 125 max 125 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1099 ave 1099 max 1099 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 4875 ave 4875 max 4875 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 19500
|
||||
Ave neighs/atom = 39
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds not checked
|
||||
run 0
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 -6.7723127 0 -4.6166327 -5.015531
|
||||
Loop time of 3.03984e-06 on 4 procs for 0 steps with 500 atoms
|
||||
|
||||
106.9% 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 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 3.04e-06 | | |100.00
|
||||
|
||||
Nlocal: 125 ave 125 max 125 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1099 ave 1099 max 1099 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 4875.25 ave 4885 max 4866 min
|
||||
Histogram: 1 0 0 0 2 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 19501
|
||||
Ave neighs/atom = 39.002
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds not checked
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 -6.7723127 0 -4.6166327 -5.015531
|
||||
50 0.70210225 -5.6759068 0 -4.6248598 0.59609192
|
||||
100 0.75891559 -5.7611234 0 -4.6250267 0.20841608
|
||||
run 0
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
100 0.75891559 -5.7609392 0 -4.6248426 0.20981291
|
||||
Loop time of 3.75509e-06 on 4 procs for 0 steps with 500 atoms
|
||||
|
||||
113.2% 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 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 3.755e-06 | | |100.00
|
||||
|
||||
Nlocal: 125 ave 126 max 124 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Nghost: 1085.25 ave 1089 max 1079 min
|
||||
Histogram: 1 0 0 0 0 1 0 0 0 2
|
||||
Neighs: 4690.25 ave 4996 max 4401 min
|
||||
Histogram: 1 0 0 1 0 1 0 0 0 1
|
||||
|
||||
Total # of neighbors = 18761
|
||||
Ave neighs/atom = 37.522
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds not checked
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
100 0.75891559 -5.7609392 0 -4.6248426 0.20981291
|
||||
150 0.75437991 -5.7558622 0 -4.6265555 0.20681722
|
||||
200 0.73111257 -5.7193748 0 -4.6248993 0.35230715
|
||||
run 0
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
200 0.73111257 -5.7143906 0 -4.6199151 0.37126023
|
||||
Loop time of 2.563e-06 on 4 procs for 0 steps with 500 atoms
|
||||
|
||||
117.1% 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 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 2.563e-06 | | |100.00
|
||||
|
||||
Nlocal: 125 ave 126 max 123 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 0 2
|
||||
Nghost: 1068.5 ave 1076 max 1063 min
|
||||
Histogram: 2 0 0 0 0 0 1 0 0 1
|
||||
Neighs: 4674.75 ave 4938 max 4419 min
|
||||
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||
|
||||
Total # of neighbors = 18699
|
||||
Ave neighs/atom = 37.398
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds not checked
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
200 0.73111257 -5.7193748 0 -4.6248993 0.35230715
|
||||
250 0.73873144 -5.7312505 0 -4.6253696 0.33061033
|
||||
300 0.76392796 -5.7719207 0 -4.6283206 0.18197874
|
||||
run 0
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
300 0.76392796 -5.7725589 0 -4.6289588 0.17994628
|
||||
Loop time of 3.99351e-06 on 4 procs for 0 steps with 500 atoms
|
||||
|
||||
93.9% 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 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 3.994e-06 | | |100.00
|
||||
|
||||
Nlocal: 125 ave 128 max 121 min
|
||||
Histogram: 1 0 0 0 0 1 0 1 0 1
|
||||
Nghost: 1069 ave 1080 max 1055 min
|
||||
Histogram: 1 0 0 0 0 0 2 0 0 1
|
||||
Neighs: 4672 ave 4803 max 4600 min
|
||||
Histogram: 2 0 0 1 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 18688
|
||||
Ave neighs/atom = 37.376
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds not checked
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
300 0.76392796 -5.7725589 0 -4.6289588 0.17994628
|
||||
350 0.71953041 -5.7041632 0 -4.6270261 0.44866153
|
||||
400 0.7319047 -5.7216051 0 -4.6259438 0.46321355
|
||||
run 0
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
400 0.7319047 -5.7158168 0 -4.6201554 0.49192039
|
||||
Loop time of 3.57628e-06 on 4 procs for 0 steps with 500 atoms
|
||||
|
||||
111.8% 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 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 3.576e-06 | | |100.00
|
||||
|
||||
Nlocal: 125 ave 132 max 118 min
|
||||
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||
Nghost: 1057.5 ave 1068 max 1049 min
|
||||
Histogram: 1 0 0 1 1 0 0 0 0 1
|
||||
Neighs: 4685.75 ave 5045 max 4229 min
|
||||
Histogram: 1 0 0 1 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 18743
|
||||
Ave neighs/atom = 37.486
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds not checked
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
400 0.7319047 -5.7216051 0 -4.6259438 0.46321355
|
||||
450 0.74503154 -5.7405318 0 -4.6252196 0.33211879
|
||||
500 0.70570501 -5.6824439 0 -4.6260035 0.62020788
|
||||
Total wall time: 0:00:02
|
||||
@ -1,254 +0,0 @@
|
||||
LAMMPS (22 Aug 2018)
|
||||
# 3d Lennard-Jones Monte Carlo server script
|
||||
|
||||
variable mode index file
|
||||
|
||||
if "${mode} == file" then "message server mc file tmp.couple" elif "${mode} == zmq" "message server mc zmq *:5555"
|
||||
message server mc zmq *:5555
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
atom_modify map yes
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
Time spent = 0.000741005 secs
|
||||
mass 1 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 20 check no
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 50
|
||||
|
||||
server mc
|
||||
run 0
|
||||
Neighbor list info ...
|
||||
update every 20 steps, delay 0 steps, check no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 6 6 6
|
||||
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
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 -6.7733681 0 -4.6176881 -5.0221006
|
||||
Loop time of 1.90735e-06 on 1 procs for 0 steps with 500 atoms
|
||||
|
||||
52.4% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 1.907e-06 | | |100.00
|
||||
|
||||
Nlocal: 500 ave 500 max 500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1956 ave 1956 max 1956 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 19500 ave 19500 max 19500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 19500
|
||||
Ave neighs/atom = 39
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds not checked
|
||||
run 0
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 -6.7723127 0 -4.6166327 -5.015531
|
||||
Loop time of 1.90735e-06 on 1 procs for 0 steps with 500 atoms
|
||||
|
||||
52.4% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 1.907e-06 | | |100.00
|
||||
|
||||
Nlocal: 500 ave 500 max 500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1956 ave 1956 max 1956 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 19501 ave 19501 max 19501 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 19501
|
||||
Ave neighs/atom = 39.002
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds not checked
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 -6.7723127 0 -4.6166327 -5.015531
|
||||
50 0.70239211 -5.6763152 0 -4.6248342 0.59544428
|
||||
100 0.7565013 -5.757431 0 -4.6249485 0.21982657
|
||||
run 0
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
100 0.7565013 -5.7565768 0 -4.6240944 0.22436405
|
||||
Loop time of 1.19209e-06 on 1 procs for 0 steps with 500 atoms
|
||||
|
||||
83.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 1.192e-06 | | |100.00
|
||||
|
||||
Nlocal: 500 ave 500 max 500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1939 ave 1939 max 1939 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 18757 ave 18757 max 18757 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 18757
|
||||
Ave neighs/atom = 37.514
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds not checked
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
100 0.7565013 -5.757431 0 -4.6249485 0.21982657
|
||||
150 0.76110797 -5.7664315 0 -4.6270529 0.16005254
|
||||
200 0.73505651 -5.7266069 0 -4.6262273 0.34189744
|
||||
run 0
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
200 0.73505651 -5.7181381 0 -4.6177585 0.37629943
|
||||
Loop time of 9.53674e-07 on 1 procs for 0 steps with 500 atoms
|
||||
|
||||
209.7% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 9.537e-07 | | |100.00
|
||||
|
||||
Nlocal: 500 ave 500 max 500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1899 ave 1899 max 1899 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 18699 ave 18699 max 18699 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 18699
|
||||
Ave neighs/atom = 37.398
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds not checked
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
200 0.73505651 -5.7266069 0 -4.6262273 0.34189744
|
||||
250 0.73052476 -5.7206316 0 -4.627036 0.39287516
|
||||
300 0.76300831 -5.7675007 0 -4.6252773 0.16312925
|
||||
run 0
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
300 0.76300831 -5.768304 0 -4.6260806 0.15954325
|
||||
Loop time of 9.53674e-07 on 1 procs for 0 steps with 500 atoms
|
||||
|
||||
104.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 9.537e-07 | | |100.00
|
||||
|
||||
Nlocal: 500 ave 500 max 500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1903 ave 1903 max 1903 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 18715 ave 18715 max 18715 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 18715
|
||||
Ave neighs/atom = 37.43
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds not checked
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
300 0.76300831 -5.768304 0 -4.6260806 0.15954325
|
||||
350 0.72993309 -5.7193261 0 -4.6266162 0.3358374
|
||||
400 0.72469448 -5.713463 0 -4.6285954 0.44859547
|
||||
run 0
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
400 0.72469448 -5.7077332 0 -4.6228655 0.47669832
|
||||
Loop time of 9.53674e-07 on 1 procs for 0 steps with 500 atoms
|
||||
|
||||
209.7% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 9.537e-07 | | |100.00
|
||||
|
||||
Nlocal: 500 ave 500 max 500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1899 ave 1899 max 1899 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 18683 ave 18683 max 18683 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 18683
|
||||
Ave neighs/atom = 37.366
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds not checked
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.658 | 2.658 | 2.658 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
400 0.72469448 -5.713463 0 -4.6285954 0.44859547
|
||||
450 0.75305735 -5.7518283 0 -4.6245015 0.34658587
|
||||
500 0.73092571 -5.7206337 0 -4.6264379 0.43715809
|
||||
Total wall time: 0:00:00
|
||||
@ -1,254 +0,0 @@
|
||||
LAMMPS (22 Aug 2018)
|
||||
# 3d Lennard-Jones Monte Carlo server script
|
||||
|
||||
variable mode index file
|
||||
|
||||
if "${mode} == file" then "message server mc file tmp.couple" elif "${mode} == zmq" "message server mc zmq *:5555"
|
||||
message server mc zmq *:5555
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
atom_modify map yes
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
Time spent = 0.000576019 secs
|
||||
mass 1 1.0
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 20 check no
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 50
|
||||
|
||||
server mc
|
||||
run 0
|
||||
Neighbor list info ...
|
||||
update every 20 steps, delay 0 steps, check no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 6 6 6
|
||||
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
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 -6.7733681 0 -4.6176881 -5.0221006
|
||||
Loop time of 4.76837e-06 on 4 procs for 0 steps with 500 atoms
|
||||
|
||||
89.1% 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 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 4.768e-06 | | |100.00
|
||||
|
||||
Nlocal: 125 ave 125 max 125 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1099 ave 1099 max 1099 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 4875 ave 4875 max 4875 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 19500
|
||||
Ave neighs/atom = 39
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds not checked
|
||||
run 0
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 -6.7723127 0 -4.6166327 -5.015531
|
||||
Loop time of 3.45707e-06 on 4 procs for 0 steps with 500 atoms
|
||||
|
||||
94.0% 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 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 3.457e-06 | | |100.00
|
||||
|
||||
Nlocal: 125 ave 125 max 125 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1099 ave 1099 max 1099 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 4875.25 ave 4885 max 4866 min
|
||||
Histogram: 1 0 0 0 2 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 19501
|
||||
Ave neighs/atom = 39.002
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds not checked
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 -6.7723127 0 -4.6166327 -5.015531
|
||||
50 0.70210225 -5.6759068 0 -4.6248598 0.59609192
|
||||
100 0.75891559 -5.7611234 0 -4.6250267 0.20841608
|
||||
run 0
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
100 0.75891559 -5.7609392 0 -4.6248426 0.20981291
|
||||
Loop time of 3.03984e-06 on 4 procs for 0 steps with 500 atoms
|
||||
|
||||
115.1% 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 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 3.04e-06 | | |100.00
|
||||
|
||||
Nlocal: 125 ave 126 max 124 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Nghost: 1085.25 ave 1089 max 1079 min
|
||||
Histogram: 1 0 0 0 0 1 0 0 0 2
|
||||
Neighs: 4690.25 ave 4996 max 4401 min
|
||||
Histogram: 1 0 0 1 0 1 0 0 0 1
|
||||
|
||||
Total # of neighbors = 18761
|
||||
Ave neighs/atom = 37.522
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds not checked
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
100 0.75891559 -5.7609392 0 -4.6248426 0.20981291
|
||||
150 0.75437991 -5.7558622 0 -4.6265555 0.20681722
|
||||
200 0.73111257 -5.7193748 0 -4.6248993 0.35230715
|
||||
run 0
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
200 0.73111257 -5.7143906 0 -4.6199151 0.37126023
|
||||
Loop time of 2.38419e-06 on 4 procs for 0 steps with 500 atoms
|
||||
|
||||
125.8% 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 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 2.384e-06 | | |100.00
|
||||
|
||||
Nlocal: 125 ave 126 max 123 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 0 2
|
||||
Nghost: 1068.5 ave 1076 max 1063 min
|
||||
Histogram: 2 0 0 0 0 0 1 0 0 1
|
||||
Neighs: 4674.75 ave 4938 max 4419 min
|
||||
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||
|
||||
Total # of neighbors = 18699
|
||||
Ave neighs/atom = 37.398
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds not checked
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
200 0.73111257 -5.7193748 0 -4.6248993 0.35230715
|
||||
250 0.73873144 -5.7312505 0 -4.6253696 0.33061033
|
||||
300 0.76392796 -5.7719207 0 -4.6283206 0.18197874
|
||||
run 0
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
300 0.76392796 -5.7725589 0 -4.6289588 0.17994628
|
||||
Loop time of 2.44379e-06 on 4 procs for 0 steps with 500 atoms
|
||||
|
||||
112.5% 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 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 2.444e-06 | | |100.00
|
||||
|
||||
Nlocal: 125 ave 128 max 121 min
|
||||
Histogram: 1 0 0 0 0 1 0 1 0 1
|
||||
Nghost: 1069 ave 1080 max 1055 min
|
||||
Histogram: 1 0 0 0 0 0 2 0 0 1
|
||||
Neighs: 4672 ave 4803 max 4600 min
|
||||
Histogram: 2 0 0 1 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 18688
|
||||
Ave neighs/atom = 37.376
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds not checked
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
300 0.76392796 -5.7725589 0 -4.6289588 0.17994628
|
||||
350 0.71953041 -5.7041632 0 -4.6270261 0.44866153
|
||||
400 0.7319047 -5.7216051 0 -4.6259438 0.46321355
|
||||
run 0
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
400 0.7319047 -5.7158168 0 -4.6201554 0.49192039
|
||||
Loop time of 2.14577e-06 on 4 procs for 0 steps with 500 atoms
|
||||
|
||||
139.8% 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 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 2.146e-06 | | |100.00
|
||||
|
||||
Nlocal: 125 ave 132 max 118 min
|
||||
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||
Nghost: 1057.5 ave 1068 max 1049 min
|
||||
Histogram: 1 0 0 1 1 0 0 0 0 1
|
||||
Neighs: 4685.75 ave 5045 max 4229 min
|
||||
Histogram: 1 0 0 1 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 18743
|
||||
Ave neighs/atom = 37.486
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds not checked
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.619 | 2.619 | 2.619 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
400 0.7319047 -5.7216051 0 -4.6259438 0.46321355
|
||||
450 0.74503154 -5.7405318 0 -4.6252196 0.33211879
|
||||
500 0.70570501 -5.6824439 0 -4.6260035 0.62020788
|
||||
Total wall time: 0:00:00
|
||||
@ -1,263 +0,0 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
// MC code used with LAMMPS in client/server mode
|
||||
// MC is the client, LAMMPS is the server
|
||||
|
||||
// Syntax: mc infile mode modearg
|
||||
// mode = file, zmq
|
||||
// modearg = filename for file, localhost:5555 for zmq
|
||||
|
||||
#include <cmath>
|
||||
#include <cstdio>
|
||||
#include <cstdlib>
|
||||
#include <cstring>
|
||||
#include "mc.h"
|
||||
#include "random_park.h"
|
||||
|
||||
#include "cslib.h"
|
||||
using namespace CSLIB_NS;
|
||||
|
||||
void error(const char *);
|
||||
CSlib *cs_create(char *, char *);
|
||||
|
||||
#define MAXLINE 256
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
// main program
|
||||
|
||||
int main(int narg, char **arg)
|
||||
{
|
||||
if (narg != 4) {
|
||||
error("Syntax: mc infile mode modearg");
|
||||
exit(1);
|
||||
}
|
||||
|
||||
// initialize CSlib
|
||||
|
||||
CSlib *cs = cs_create(arg[2],arg[3]);
|
||||
|
||||
// create MC class and perform run
|
||||
|
||||
MC *mc = new MC(arg[1],cs);
|
||||
mc->run();
|
||||
|
||||
// final MC stats
|
||||
|
||||
int naccept = mc->naccept;
|
||||
int nattempt = mc->nattempt;
|
||||
|
||||
printf("------ MC stats ------\n");
|
||||
printf("MC attempts = %d\n",nattempt);
|
||||
printf("MC accepts = %d\n",naccept);
|
||||
printf("Acceptance ratio = %g\n",1.0*naccept/nattempt);
|
||||
|
||||
// clean up
|
||||
|
||||
delete cs;
|
||||
delete mc;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void error(const char *str)
|
||||
{
|
||||
printf("ERROR: %s\n",str);
|
||||
exit(1);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
CSlib *cs_create(char *mode, char *arg)
|
||||
{
|
||||
CSlib *cs = new CSlib(0,mode,arg,NULL);
|
||||
|
||||
// initial handshake to agree on protocol
|
||||
|
||||
cs->send(0,1);
|
||||
cs->pack_string(1,(char *) "mc");
|
||||
|
||||
int msgID,nfield;
|
||||
int *fieldID,*fieldtype,*fieldlen;
|
||||
msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen);
|
||||
|
||||
return cs;
|
||||
}
|
||||
|
||||
// ----------------------------------------------------------------------
|
||||
// MC class
|
||||
// ----------------------------------------------------------------------
|
||||
|
||||
MC::MC(char *mcfile, void *cs_caller)
|
||||
//MC::MC(char *mcfile, CSlib *cs_caller)
|
||||
{
|
||||
cs_void = cs_caller;
|
||||
|
||||
// setup MC params
|
||||
|
||||
options(mcfile);
|
||||
|
||||
// random # generator
|
||||
|
||||
random = new RanPark(seed);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
MC::~MC()
|
||||
{
|
||||
free(x);
|
||||
delete random;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void MC::run()
|
||||
{
|
||||
int iatom,accept,msgID,nfield;
|
||||
double pe_initial,pe_final,edelta;
|
||||
double dx,dy,dz;
|
||||
double xold[3],xnew[3];
|
||||
int *fieldID,*fieldtype,*fieldlen;
|
||||
|
||||
enum{NATOMS=1,EINIT,DISPLACE,ACCEPT,RUN};
|
||||
|
||||
CSlib *cs = (CSlib *) cs_void;
|
||||
|
||||
// one-time request for atom count from MD
|
||||
// allocate 1d coord buffer
|
||||
|
||||
cs->send(NATOMS,0);
|
||||
|
||||
msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen);
|
||||
natoms = cs->unpack_int(1);
|
||||
|
||||
x = (double *) malloc(3*natoms*sizeof(double));
|
||||
|
||||
// loop over MC moves
|
||||
|
||||
naccept = nattempt = 0;
|
||||
|
||||
for (int iloop = 0; iloop < nloop; iloop++) {
|
||||
|
||||
// request current energy from MD
|
||||
// recv energy, coords from MD
|
||||
|
||||
cs->send(EINIT,0);
|
||||
|
||||
msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen);
|
||||
pe_initial = cs->unpack_double(1);
|
||||
double *x = (double *) cs->unpack(2);
|
||||
|
||||
// perform simple MC event
|
||||
// displace a single atom by random amount
|
||||
|
||||
iatom = (int) natoms*random->uniform();
|
||||
xold[0] = x[3*iatom+0];
|
||||
xold[1] = x[3*iatom+1];
|
||||
xold[2] = x[3*iatom+2];
|
||||
|
||||
dx = 2.0*delta*random->uniform() - delta;
|
||||
dy = 2.0*delta*random->uniform() - delta;
|
||||
dz = 2.0*delta*random->uniform() - delta;
|
||||
|
||||
xnew[0] = xold[0] + dx;
|
||||
xnew[1] = xold[1] + dx;
|
||||
xnew[2] = xold[2] + dx;
|
||||
|
||||
// send atom ID and its new coords to MD
|
||||
// recv new energy
|
||||
|
||||
cs->send(DISPLACE,2);
|
||||
cs->pack_int(1,iatom+1);
|
||||
cs->pack(2,4,3,xnew);
|
||||
|
||||
msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen);
|
||||
pe_final = cs->unpack_double(1);
|
||||
|
||||
// decide whether to accept/reject MC event
|
||||
|
||||
if (pe_final <= pe_initial) accept = 1;
|
||||
else if (temperature == 0.0) accept = 0;
|
||||
else if (random->uniform() >
|
||||
exp(natoms*(pe_initial-pe_final)/temperature)) accept = 0;
|
||||
else accept = 1;
|
||||
|
||||
nattempt++;
|
||||
if (accept) naccept++;
|
||||
|
||||
// send accept (1) or reject (0) flag to MD
|
||||
|
||||
cs->send(ACCEPT,1);
|
||||
cs->pack_int(1,accept);
|
||||
|
||||
msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen);
|
||||
|
||||
// send dynamics timesteps
|
||||
|
||||
cs->send(RUN,1);
|
||||
cs->pack_int(1,ndynamics);
|
||||
|
||||
msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen);
|
||||
}
|
||||
|
||||
// send exit message to MD
|
||||
|
||||
cs->send(-1,0);
|
||||
msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void MC::options(char *filename)
|
||||
{
|
||||
// default params
|
||||
|
||||
nsteps = 0;
|
||||
ndynamics = 100;
|
||||
delta = 0.1;
|
||||
temperature = 1.0;
|
||||
seed = 12345;
|
||||
|
||||
// read and parse file
|
||||
|
||||
FILE *fp = fopen(filename,"r");
|
||||
if (fp == NULL) error("Could not open MC file");
|
||||
|
||||
char line[MAXLINE];
|
||||
char *keyword,*value;
|
||||
char *eof = fgets(line,MAXLINE,fp);
|
||||
|
||||
while (eof) {
|
||||
if (line[0] == '#') { // comment line
|
||||
eof = fgets(line,MAXLINE,fp);
|
||||
continue;
|
||||
}
|
||||
|
||||
value = strtok(line," \t\n\r\f");
|
||||
if (value == NULL) { // blank line
|
||||
eof = fgets(line,MAXLINE,fp);
|
||||
continue;
|
||||
}
|
||||
|
||||
keyword = strtok(NULL," \t\n\r\f");
|
||||
if (keyword == NULL) error("Missing keyword in MC file");
|
||||
|
||||
if (strcmp(keyword,"nsteps") == 0) nsteps = atoi(value);
|
||||
else if (strcmp(keyword,"ndynamics") == 0) ndynamics = atoi(value);
|
||||
else if (strcmp(keyword,"delta") == 0) delta = atof(value);
|
||||
else if (strcmp(keyword,"temperature") == 0) temperature = atof(value);
|
||||
else if (strcmp(keyword,"seed") == 0) seed = atoi(value);
|
||||
else error("Unknown param in MC file");
|
||||
|
||||
eof = fgets(line,MAXLINE,fp);
|
||||
}
|
||||
|
||||
// derived params
|
||||
|
||||
nloop = nsteps/ndynamics;
|
||||
}
|
||||
@ -1,40 +0,0 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/ Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifndef MC_H
|
||||
#define MC_H
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
class MC {
|
||||
public:
|
||||
int naccept; // # of accepted MC events
|
||||
int nattempt; // # of attempted MC events
|
||||
|
||||
MC(char *, void *);
|
||||
~MC();
|
||||
void run();
|
||||
|
||||
private:
|
||||
int nsteps; // total # of MD steps
|
||||
int ndynamics; // steps in one short dynamics run
|
||||
int nloop; // nsteps/ndynamics
|
||||
int natoms; // # of MD atoms
|
||||
|
||||
double delta; // MC displacement distance
|
||||
double temperature; // MC temperature for Boltzmann criterion
|
||||
double *x; // atom coords as 3N 1d vector
|
||||
double energy; // global potential energy
|
||||
|
||||
int seed; // RNG seed
|
||||
class RanPark *random;
|
||||
|
||||
void *cs_void; // messaging library
|
||||
|
||||
void options(char *);
|
||||
};
|
||||
|
||||
#endif
|
||||
@ -1,72 +0,0 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
// Park/Miller RNG
|
||||
|
||||
#include <math.h>
|
||||
#include "random_park.h"
|
||||
//#include "error.h"
|
||||
|
||||
#define IA 16807
|
||||
#define IM 2147483647
|
||||
#define AM (1.0/IM)
|
||||
#define IQ 127773
|
||||
#define IR 2836
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
RanPark::RanPark(int seed_init)
|
||||
{
|
||||
//if (seed_init <= 0)
|
||||
// error->one(FLERR,"Invalid seed for Park random # generator");
|
||||
seed = seed_init;
|
||||
save = 0;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
uniform RN
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double RanPark::uniform()
|
||||
{
|
||||
int k = seed/IQ;
|
||||
seed = IA*(seed-k*IQ) - IR*k;
|
||||
if (seed < 0) seed += IM;
|
||||
double ans = AM*seed;
|
||||
return ans;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
gaussian RN
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double RanPark::gaussian()
|
||||
{
|
||||
double first,v1,v2,rsq,fac;
|
||||
|
||||
if (!save) {
|
||||
do {
|
||||
v1 = 2.0*uniform()-1.0;
|
||||
v2 = 2.0*uniform()-1.0;
|
||||
rsq = v1*v1 + v2*v2;
|
||||
} while ((rsq >= 1.0) || (rsq == 0.0));
|
||||
fac = sqrt(-2.0*log(rsq)/rsq);
|
||||
second = v1*fac;
|
||||
first = v2*fac;
|
||||
save = 1;
|
||||
} else {
|
||||
first = second;
|
||||
save = 0;
|
||||
}
|
||||
return first;
|
||||
}
|
||||
@ -1,28 +0,0 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/ Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifndef RANPARK_H
|
||||
#define RANPARK_H
|
||||
|
||||
class RanPark {
|
||||
public:
|
||||
RanPark(int);
|
||||
double uniform();
|
||||
double gaussian();
|
||||
|
||||
private:
|
||||
int seed,save;
|
||||
double second;
|
||||
};
|
||||
|
||||
#endif
|
||||
@ -1,197 +0,0 @@
|
||||
Sample LAMMPS MD wrapper on NWChem via client/server coupling
|
||||
|
||||
See the MESSAGE package documentation Build_extras.html#message
|
||||
and Build_extras.html#message for more details on how client/server
|
||||
coupling works in LAMMPS.
|
||||
|
||||
In this dir, the nwchem_wrap.py is a wrapper on the NWChem electronic
|
||||
structure code so it can work as a "server" code which LAMMPS drives
|
||||
as a "client" code to perform ab initio MD. LAMMPS performs the MD
|
||||
timestepping, sends NWChem a current set of coordinates each timestep,
|
||||
NWChem computes forces and energy (and virial) and returns that info
|
||||
to LAMMPS.
|
||||
|
||||
Messages are exchanged between NWChem and LAMMPS via a client/server
|
||||
library (CSlib), which is included in the LAMMPS distribution in
|
||||
lib/message. As explained below you can choose to exchange data
|
||||
between the two programs either via files or sockets (ZMQ). If the
|
||||
nwchem_wrap.py program became parallel, or the CSlib library calls were
|
||||
integrated into NWChem directly, then data could also be exchanged via
|
||||
MPI.
|
||||
|
||||
There are 2 examples provided in the planeware and ao_basis
|
||||
sub-directories. See details below.
|
||||
|
||||
----------------
|
||||
|
||||
Build LAMMPS with its MESSAGE package installed:
|
||||
|
||||
See the Build extras doc page and its MESSAGE package
|
||||
section for details.
|
||||
|
||||
CMake:
|
||||
|
||||
-D PKG_MESSAGE=yes # include the MESSAGE package
|
||||
-D MESSAGE_ZMQ=value # build with ZeroMQ support, value = no (default) or yes
|
||||
|
||||
Traditional make:
|
||||
|
||||
cd lammps/lib/message
|
||||
python Install.py -m -z # build CSlib with MPI and ZMQ support
|
||||
cd lammps/src
|
||||
make yes-message
|
||||
make mpi
|
||||
|
||||
You can leave off the -z if you do not have ZMQ on your system.
|
||||
|
||||
----------------
|
||||
|
||||
Build the CSlib in a form usable by the nwchem_wrapper.py script:
|
||||
|
||||
% cd lammps/lib/message/cslib/src
|
||||
% make shlib # build serial and parallel shared lib with ZMQ support
|
||||
% make shlib zmq=no # build serial and parallel shared lib w/out ZMQ support
|
||||
|
||||
This will make a shared library versions of the CSlib, which Python
|
||||
requires. Python must be able to find both the cslib.py script and
|
||||
the libcsnompi.so library in your lammps/lib/message/cslib/src
|
||||
directory. If it is not able to do this, you will get an error when
|
||||
you run nwchem_wrapper.py.
|
||||
|
||||
You can do this by augmenting two environment variables, either from
|
||||
the command line, or in your shell start-up script. Here is the
|
||||
sample syntax for the csh or tcsh shells:
|
||||
|
||||
setenv PYTHONPATH ${PYTHONPATH}:/home/sjplimp/lammps/lib/message/cslib/src
|
||||
setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/home/sjplimp/lammps/lib/message/cslib/src
|
||||
|
||||
----------------
|
||||
|
||||
Prepare to use NWChem and the nwchem_wrap.py script
|
||||
|
||||
You can run the nwchem_wrap.py script as-is to test that the coupling
|
||||
between it and LAMMPS is functional. This will use the included
|
||||
nwchem_lammps.out files output by a previous NWChem run.
|
||||
|
||||
But note that the as-is version of nwchem_wrap.py will not attempt to
|
||||
run NWChem.
|
||||
|
||||
To do this, you must edit the 1st nwchemcmd line at the top of
|
||||
nwchem_wrapper.py to be the launch command needed to run NWChem on
|
||||
your system. It can be a command to run NWChem in serial or in
|
||||
parallel, e.g. an mpirun command. Then comment out the 2nd nwchemcmd
|
||||
line immediately following it.
|
||||
|
||||
Ensure you have the necessary NWChem input file in this directory,
|
||||
suitable for the NWChem calculation you want to perform.
|
||||
|
||||
Example input files are provided for both atom-centered AO basis sets
|
||||
and plane-wave basis sets. Note that the NWChem template file should
|
||||
be matched to the LAMMPS input script (# of atoms and atom types, box
|
||||
size, etc).
|
||||
|
||||
Once you run NWChem yourself, the nwchem_lammps.out file will be
|
||||
overwritten.
|
||||
|
||||
The syntax of the wrapper is:
|
||||
nwchem_wrap.py file/zmq ao/pw input_template
|
||||
* file/zmg = messaging mode, must match LAMMPS messaging mode
|
||||
* ao/pw = basis set mode, selects between atom-centered and plane-wave
|
||||
the input_template file must correspond to the appropriate basis set mode:
|
||||
the "ao" mode supports the scf and dft modules in NWChem,
|
||||
the "pw" mode supports the nwpw module.
|
||||
* input_template = NWChem input file used as template, must include a
|
||||
"geometry" block with the atoms in the simulation, dummy
|
||||
xyz coordinates should be included (but are not used).
|
||||
Atom ordering must match LAMMPS input.
|
||||
|
||||
During a simulation, the molecular orbitals from the previous timestep
|
||||
will be used as the initial guess for the next NWChem calculation. If
|
||||
a file named "nwchem_lammps.movecs" is in the directory the wrapper is
|
||||
called from, these orbitals will be used as the initial guess orbitals
|
||||
in the first step of the simulation.
|
||||
|
||||
----------------
|
||||
|
||||
Example directories
|
||||
|
||||
(1) planewave
|
||||
|
||||
Demonstrates coupling of the nwpw module in NWChem with LAMMPS. Only fully
|
||||
periodic boundary conditions and orthogonal simulation boxes are currently
|
||||
supported by the wrapper. The included files provide an example run using a
|
||||
2 atom unit cell of tungsten.
|
||||
|
||||
Files:
|
||||
* data.W LAMMPS input with geometry information
|
||||
* in.client.W LAMMPS simulation input
|
||||
* log.client.output LAMMPS simulation output
|
||||
* w.nw NWChem template input file
|
||||
* nwchem_lammps.out NWChem output
|
||||
|
||||
(2) ao_basis
|
||||
|
||||
Demonstrates coupling of the scf (or dft) modules in NWChem with
|
||||
LAMMPS. Only fully aperiodic boundary conditions are currently
|
||||
supported by the wrapper. The included files provide an example run
|
||||
using a single water molecule.
|
||||
|
||||
Files:
|
||||
* data.h2o LAMMPS input with geometry information
|
||||
* in.client.h2o LAMMPS simulation input
|
||||
* log.client.output LAMMPS simulation output
|
||||
* h2o.nw NWChem template input file
|
||||
* nwchem_lammps.out NWChem output
|
||||
|
||||
As noted above, you can run the nwchem_wrap.py script as-is to test that
|
||||
the coupling between it and LAMMPS is functional. This will use the included
|
||||
nwchem_lammps.out files.
|
||||
|
||||
----------------
|
||||
|
||||
To run in client/server mode:
|
||||
|
||||
NOTE: The nwchem_wrap.py script must be run with Python version 2, not
|
||||
3. This is because it used the CSlib python wrapper, which only
|
||||
supports version 2. We plan to upgrade CSlib to support Python 3.
|
||||
|
||||
Both the client (LAMMPS) and server (nwchem_wrap.py) must use the same
|
||||
messaging mode, namely file or zmq. This is an argument to the
|
||||
nwchem_wrap.py code; it can be selected by setting the "mode" variable
|
||||
when you run LAMMPS. The default mode = file.
|
||||
|
||||
Here we assume LAMMPS was built to run in parallel, and the MESSAGE
|
||||
package was installed with socket (ZMQ) support. This means either of
|
||||
the messaging modes can be used and LAMMPS can be run in serial or
|
||||
parallel. The nwchem_wrap.py code is always run in serial, but it
|
||||
launches NWChem from Python via an mpirun command which can run NWChem
|
||||
itself in parallel.
|
||||
|
||||
When you run, the server should print out thermodynamic info every
|
||||
timestep which corresponds to the forces and virial computed by NWChem.
|
||||
NWChem will also generate output files each timestep. Output files from
|
||||
previous timesteps are archived in a "nwchem_logs" directory.
|
||||
|
||||
The examples below are commands you should use in two different
|
||||
terminal windows. The order of the two commands (client or server
|
||||
launch) does not matter. You can run them both in the same window if
|
||||
you append a "&" character to the first one to run it in the
|
||||
background.
|
||||
|
||||
--------------
|
||||
|
||||
File mode of messaging:
|
||||
|
||||
% mpirun -np 1 lmp_mpi -v mode file -in in.client.W
|
||||
% python nwchem_wrap.py file pw w.nw
|
||||
|
||||
% mpirun -np 2 lmp_mpi -v mode file -in in.client.h2o
|
||||
% python nwchem_wrap.py file ao h2o.nw
|
||||
|
||||
ZMQ mode of messaging:
|
||||
|
||||
% mpirun -np 1 lmp_mpi -v mode zmq -in in.client.W
|
||||
% python nwchem_wrap.py zmq pw w.nw
|
||||
|
||||
% mpirun -np 2 lmp_mpi -v mode zmq -in in.client.h2o
|
||||
% python nwchem_wrap.py zmq ao h2o.nw
|
||||
@ -1,20 +0,0 @@
|
||||
LAMMPS H2O data file
|
||||
|
||||
3 atoms
|
||||
|
||||
2 atom types
|
||||
|
||||
-10.0 10.0 xlo xhi
|
||||
-10.0 10.0 ylo yhi
|
||||
-10.0 10.0 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
1 15.994915008544922
|
||||
2 1.0078250169754028
|
||||
|
||||
Atoms
|
||||
|
||||
1 1 0.0 0.0 0.0
|
||||
2 2 0.0 0.756723 -0.585799
|
||||
3 2 0.0 -0.756723 -0.585799
|
||||
@ -1,25 +0,0 @@
|
||||
echo
|
||||
|
||||
memory global 40 mb stack 23 mb heap 5 mb
|
||||
|
||||
geometry units angstrom noautosym
|
||||
O 0.0 0.0 0.0
|
||||
H 1.0 0.5 0.0
|
||||
H -1.0 0.5 0.0
|
||||
end
|
||||
|
||||
basis
|
||||
O library 6-31g*
|
||||
H library 6-31g*
|
||||
end
|
||||
|
||||
scf
|
||||
maxiter 100
|
||||
end
|
||||
|
||||
#dft
|
||||
# xc b3lyp
|
||||
#end
|
||||
|
||||
task scf gradient
|
||||
#task dft gradient
|
||||
@ -1,27 +0,0 @@
|
||||
# H2O with NWChem
|
||||
|
||||
variable mode index file
|
||||
|
||||
if "${mode} == file" then &
|
||||
"message client md file tmp.couple" &
|
||||
elif "${mode} == zmq" &
|
||||
"message client md zmq localhost:5555" &
|
||||
|
||||
units metal
|
||||
atom_style atomic
|
||||
atom_modify sort 0 0.0 map yes
|
||||
|
||||
boundary m m m
|
||||
read_data data.h2o
|
||||
|
||||
velocity all create 300.0 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 10 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all client/md
|
||||
fix_modify 2 energy yes
|
||||
|
||||
thermo 1
|
||||
run 3
|
||||
@ -1,30 +0,0 @@
|
||||
# H2O with NWChem
|
||||
|
||||
variable mode index file
|
||||
|
||||
if "${mode} == file" then &
|
||||
"message client md file tmp.couple" &
|
||||
elif "${mode} == zmq" &
|
||||
"message client md zmq localhost:5555" &
|
||||
|
||||
units metal
|
||||
atom_style atomic
|
||||
atom_modify sort 0 0.0 map yes
|
||||
|
||||
boundary m m m
|
||||
read_data data.h2o
|
||||
|
||||
group one id 2
|
||||
displace_atoms one move 0.1 0.2 0.3
|
||||
|
||||
velocity all create 300.0 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 10 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all client/md
|
||||
fix_modify 2 energy yes
|
||||
|
||||
thermo 1
|
||||
minimize 1.0e-6 1.0e-6 10 50
|
||||
@ -1,66 +0,0 @@
|
||||
LAMMPS (19 Sep 2019)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# H2O with NWChem
|
||||
|
||||
variable mode index file
|
||||
|
||||
if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555"
|
||||
message client md file tmp.couple
|
||||
units metal
|
||||
atom_style atomic
|
||||
atom_modify sort 0 0.0 map yes
|
||||
|
||||
boundary m m m
|
||||
read_data data.h2o
|
||||
orthogonal box = (-10 -10 -10) to (10 10 10)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
3 atoms
|
||||
read_data CPU = 0.000627125 secs
|
||||
|
||||
velocity all create 300.0 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 10 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all client/md
|
||||
fix_modify 2 energy yes
|
||||
|
||||
thermo 1
|
||||
run 3
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:166)
|
||||
Per MPI rank memory allocation (min/avg/max) = 0.0276 | 0.0276 | 0.0276 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 300 0 0 0.077556087 10.354878 8000
|
||||
1 300 0 0 0.077556087 10.354878 8000
|
||||
2 300 0 0 0.077556087 10.354878 8000
|
||||
3 300 0 0 0.077556087 10.354878 8000
|
||||
Loop time of 0.30198 on 1 procs for 3 steps with 3 atoms
|
||||
|
||||
Performance: 0.858 ns/day, 27.961 hours/ns, 9.934 timesteps/s
|
||||
0.0% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 2.5979e-06 | 2.5979e-06 | 2.5979e-06 | 0.0 | 0.00
|
||||
Output | 0.00012053 | 0.00012053 | 0.00012053 | 0.0 | 0.04
|
||||
Modify | 0.30185 | 0.30185 | 0.30185 | 0.0 | 99.96
|
||||
Other | | 8.211e-06 | | | 0.00
|
||||
|
||||
Nlocal: 3 ave 3 max 3 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 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
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds not checked
|
||||
Total wall time: 0:00:07
|
||||
@ -1,66 +0,0 @@
|
||||
LAMMPS (19 Sep 2019)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# H2O with NWChem
|
||||
|
||||
variable mode index file
|
||||
|
||||
if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555"
|
||||
message client md file tmp.couple
|
||||
units metal
|
||||
atom_style atomic
|
||||
atom_modify sort 0 0.0 map yes
|
||||
|
||||
boundary m m m
|
||||
read_data data.h2o
|
||||
orthogonal box = (-10 -10 -10) to (10 10 10)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
3 atoms
|
||||
read_data CPU = 0.000608759 secs
|
||||
|
||||
velocity all create 300.0 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 10 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all client/md
|
||||
fix_modify 2 energy yes
|
||||
|
||||
thermo 1
|
||||
run 3
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:166)
|
||||
Per MPI rank memory allocation (min/avg/max) = 0.0276 | 0.0276 | 0.0276 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 300 0 0 -2068.2746 10.354878 8000
|
||||
1 200.33191 0 0 -2068.2704 6.9147085 8000
|
||||
2 152.36218 0 0 -2068.269 5.2589726 8000
|
||||
3 227.40679 0 0 -2068.2722 7.8492321 8000
|
||||
Loop time of 1.90319 on 1 procs for 3 steps with 3 atoms
|
||||
|
||||
Performance: 0.136 ns/day, 176.221 hours/ns, 1.576 timesteps/s
|
||||
0.0% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 3.9274e-06 | 3.9274e-06 | 3.9274e-06 | 0.0 | 0.00
|
||||
Output | 0.00011798 | 0.00011798 | 0.00011798 | 0.0 | 0.01
|
||||
Modify | 1.9031 | 1.9031 | 1.9031 | 0.0 | 99.99
|
||||
Other | | 1.054e-05 | | | 0.00
|
||||
|
||||
Nlocal: 3 ave 3 max 3 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 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
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds not checked
|
||||
Total wall time: 0:00:07
|
||||
@ -1,82 +0,0 @@
|
||||
LAMMPS (19 Sep 2019)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# H2O with NWChem
|
||||
|
||||
variable mode index file
|
||||
|
||||
if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555"
|
||||
message client md file tmp.couple
|
||||
units metal
|
||||
atom_style atomic
|
||||
atom_modify sort 0 0.0 map yes
|
||||
|
||||
boundary m m m
|
||||
read_data data.h2o
|
||||
orthogonal box = (-10 -10 -10) to (10 10 10)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
3 atoms
|
||||
read_data CPU = 0.000615383 secs
|
||||
|
||||
group one id 2
|
||||
1 atoms in group one
|
||||
displace_atoms one move 0.1 0.2 0.3
|
||||
|
||||
velocity all create 300.0 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 10 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all client/md
|
||||
fix_modify 2 energy yes
|
||||
|
||||
thermo 1
|
||||
minimize 1.0e-6 1.0e-6 10 50
|
||||
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:174)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:166)
|
||||
Per MPI rank memory allocation (min/avg/max) = 0.0279 | 0.0279 | 0.0279 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 300 0 0 -2067.8909 10.354878 8000
|
||||
1 300 0 0 -2068.0707 10.354878 8000
|
||||
2 300 0 0 -2068.252 10.354878 8000
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:166)
|
||||
3 300 0 0 -2068.2797 10.354878 8000
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:166)
|
||||
4 300 0 0 -2068.2799 10.354878 8000
|
||||
Loop time of 5.71024 on 1 procs for 4 steps with 3 atoms
|
||||
|
||||
0.1% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = energy tolerance
|
||||
Energy initial, next-to-last, final =
|
||||
-2067.96847053 -2068.35730416 -2068.35745184
|
||||
Force two-norm initial, final = 4.54685 0.124714
|
||||
Force max component initial, final = 3.48924 0.0859263
|
||||
Final line search alpha, max atom move = 1 0.0859263
|
||||
Iterations, force evaluations = 4 8
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 6.2305e-07 | 6.2305e-07 | 6.2305e-07 | 0.0 | 0.00
|
||||
Comm | 1.1522e-05 | 1.1522e-05 | 1.1522e-05 | 0.0 | 0.00
|
||||
Output | 8.4217e-05 | 8.4217e-05 | 8.4217e-05 | 0.0 | 0.00
|
||||
Modify | 5.7099 | 5.7099 | 5.7099 | 0.0 | 99.99
|
||||
Other | | 0.0002355 | | | 0.00
|
||||
|
||||
Nlocal: 3 ave 3 max 3 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 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
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 2
|
||||
Dangerous builds not checked
|
||||
Total wall time: 0:00:10
|
||||
@ -1,626 +0,0 @@
|
||||
argument 1 = nwchem_lammps.nw
|
||||
|
||||
|
||||
|
||||
============================== echo of input deck ==============================
|
||||
echo
|
||||
|
||||
memory global 40 mb stack 23 mb heap 5 mb
|
||||
|
||||
geometry units angstrom noautosym nocenter
|
||||
O 0.00197082 0.0012463 -0.00298048
|
||||
H -0.0432066 0.769363 -0.596119
|
||||
H 0.0119282 -0.789143 -0.528177
|
||||
end
|
||||
|
||||
scf
|
||||
vectors input nwchem_lammps.movecs
|
||||
end
|
||||
|
||||
dft
|
||||
vectors input nwchem_lammps.movecs
|
||||
end
|
||||
|
||||
basis
|
||||
O library 6-31g*
|
||||
H library 6-31g*
|
||||
end
|
||||
|
||||
scf
|
||||
maxiter 100
|
||||
end
|
||||
|
||||
#dft
|
||||
# xc b3lyp
|
||||
#end
|
||||
|
||||
task scf gradient
|
||||
#task dft gradient
|
||||
================================================================================
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
Northwest Computational Chemistry Package (NWChem) 6.8
|
||||
------------------------------------------------------
|
||||
|
||||
|
||||
Environmental Molecular Sciences Laboratory
|
||||
Pacific Northwest National Laboratory
|
||||
Richland, WA 99352
|
||||
|
||||
Copyright (c) 1994-2018
|
||||
Pacific Northwest National Laboratory
|
||||
Battelle Memorial Institute
|
||||
|
||||
NWChem is an open-source computational chemistry package
|
||||
distributed under the terms of the
|
||||
Educational Community License (ECL) 2.0
|
||||
A copy of the license is included with this distribution
|
||||
in the LICENSE.TXT file
|
||||
|
||||
ACKNOWLEDGMENT
|
||||
--------------
|
||||
|
||||
This software and its documentation were developed at the
|
||||
EMSL at Pacific Northwest National Laboratory, a multiprogram
|
||||
national laboratory, operated for the U.S. Department of Energy
|
||||
by Battelle under Contract Number DE-AC05-76RL01830. Support
|
||||
for this work was provided by the Department of Energy Office
|
||||
of Biological and Environmental Research, Office of Basic
|
||||
Energy Sciences, and the Office of Advanced Scientific Computing.
|
||||
|
||||
|
||||
Job information
|
||||
---------------
|
||||
|
||||
hostname = almondjoy
|
||||
program = /home/jboschen/nwchem-6.8.1-release/bin/LINUX64/nwchem
|
||||
date = Fri Jan 31 00:31:00 2020
|
||||
|
||||
compiled = Tue_Oct_01_13:20:43_2019
|
||||
source = /home/jboschen/nwchem-6.8.1-release
|
||||
nwchem branch = Development
|
||||
nwchem revision = N/A
|
||||
ga revision = 5.6.5
|
||||
use scalapack = F
|
||||
input = nwchem_lammps.nw
|
||||
prefix = nwchem_lammps.
|
||||
data base = ./nwchem_lammps.db
|
||||
status = restart
|
||||
nproc = 1
|
||||
time left = -1s
|
||||
|
||||
|
||||
|
||||
Memory information
|
||||
------------------
|
||||
|
||||
heap = 655358 doubles = 5.0 Mbytes
|
||||
stack = 3014651 doubles = 23.0 Mbytes
|
||||
global = 5242880 doubles = 40.0 Mbytes (distinct from heap & stack)
|
||||
total = 8912889 doubles = 68.0 Mbytes
|
||||
verify = yes
|
||||
hardfail = no
|
||||
|
||||
|
||||
Directory information
|
||||
---------------------
|
||||
|
||||
0 permanent = .
|
||||
0 scratch = .
|
||||
|
||||
|
||||
Previous task information
|
||||
-------------------------
|
||||
|
||||
Theory = scf
|
||||
Operation = gradient
|
||||
Status = ok
|
||||
Qmmm = F
|
||||
Ignore = F
|
||||
|
||||
|
||||
Geometries in the database
|
||||
--------------------------
|
||||
|
||||
Name Natoms Last Modified
|
||||
-------------------------------- ------ ------------------------
|
||||
1 geometry 3 Fri Jan 31 00:30:59 2020
|
||||
|
||||
The geometry named "geometry" is the default for restart
|
||||
|
||||
|
||||
|
||||
Basis sets in the database
|
||||
--------------------------
|
||||
|
||||
Name Natoms Last Modified
|
||||
-------------------------------- ------ ------------------------
|
||||
1 ao basis 2 Fri Jan 31 00:30:59 2020
|
||||
|
||||
The basis set named "ao basis" is the default AO basis for restart
|
||||
|
||||
|
||||
|
||||
|
||||
NWChem Input Module
|
||||
-------------------
|
||||
|
||||
|
||||
|
||||
Scaling coordinates for geometry "geometry" by 1.889725989
|
||||
(inverse scale = 0.529177249)
|
||||
|
||||
|
||||
------
|
||||
auto-z
|
||||
------
|
||||
no constraints, skipping 0.0000000000000000
|
||||
no constraints, skipping 0.0000000000000000
|
||||
|
||||
|
||||
Geometry "geometry" -> ""
|
||||
-------------------------
|
||||
|
||||
Output coordinates in angstroms (scale by 1.889725989 to convert to a.u.)
|
||||
|
||||
No. Tag Charge X Y Z
|
||||
---- ---------------- ---------- -------------- -------------- --------------
|
||||
1 O 8.0000 0.00197082 0.00124630 -0.00298048
|
||||
2 H 1.0000 -0.04320660 0.76936300 -0.59611900
|
||||
3 H 1.0000 0.01192820 -0.78914300 -0.52817700
|
||||
|
||||
Atomic Mass
|
||||
-----------
|
||||
|
||||
O 15.994910
|
||||
H 1.007825
|
||||
|
||||
|
||||
Effective nuclear repulsion energy (a.u.) 9.1573270473
|
||||
|
||||
Nuclear Dipole moment (a.u.)
|
||||
----------------------------
|
||||
X Y Z
|
||||
---------------- ---------------- ----------------
|
||||
-0.0293131272 -0.0185374561 -2.1696696942
|
||||
|
||||
|
||||
|
||||
Z-matrix (autoz)
|
||||
--------
|
||||
|
||||
Units are Angstrom for bonds and degrees for angles
|
||||
|
||||
Type Name I J K L M Value
|
||||
----------- -------- ----- ----- ----- ----- ----- ----------
|
||||
1 Stretch 1 2 0.97152
|
||||
2 Stretch 1 3 0.94902
|
||||
3 Bend 2 1 3 108.72901
|
||||
|
||||
|
||||
XYZ format geometry
|
||||
-------------------
|
||||
3
|
||||
geometry
|
||||
O 0.00197082 0.00124630 -0.00298048
|
||||
H -0.04320660 0.76936300 -0.59611900
|
||||
H 0.01192820 -0.78914300 -0.52817700
|
||||
|
||||
==============================================================================
|
||||
internuclear distances
|
||||
------------------------------------------------------------------------------
|
||||
center one | center two | atomic units | angstroms
|
||||
------------------------------------------------------------------------------
|
||||
2 H | 1 O | 1.83591 | 0.97152
|
||||
3 H | 1 O | 1.79339 | 0.94902
|
||||
------------------------------------------------------------------------------
|
||||
number of included internuclear distances: 2
|
||||
==============================================================================
|
||||
|
||||
|
||||
|
||||
==============================================================================
|
||||
internuclear angles
|
||||
------------------------------------------------------------------------------
|
||||
center 1 | center 2 | center 3 | degrees
|
||||
------------------------------------------------------------------------------
|
||||
2 H | 1 O | 3 H | 108.73
|
||||
------------------------------------------------------------------------------
|
||||
number of included internuclear angles: 1
|
||||
==============================================================================
|
||||
|
||||
|
||||
|
||||
Basis "ao basis" -> "" (cartesian)
|
||||
-----
|
||||
O (Oxygen)
|
||||
----------
|
||||
Exponent Coefficients
|
||||
-------------- ---------------------------------------------------------
|
||||
1 S 5.48467170E+03 0.001831
|
||||
1 S 8.25234950E+02 0.013950
|
||||
1 S 1.88046960E+02 0.068445
|
||||
1 S 5.29645000E+01 0.232714
|
||||
1 S 1.68975700E+01 0.470193
|
||||
1 S 5.79963530E+00 0.358521
|
||||
|
||||
2 S 1.55396160E+01 -0.110778
|
||||
2 S 3.59993360E+00 -0.148026
|
||||
2 S 1.01376180E+00 1.130767
|
||||
|
||||
3 P 1.55396160E+01 0.070874
|
||||
3 P 3.59993360E+00 0.339753
|
||||
3 P 1.01376180E+00 0.727159
|
||||
|
||||
4 S 2.70005800E-01 1.000000
|
||||
|
||||
5 P 2.70005800E-01 1.000000
|
||||
|
||||
6 D 8.00000000E-01 1.000000
|
||||
|
||||
H (Hydrogen)
|
||||
------------
|
||||
Exponent Coefficients
|
||||
-------------- ---------------------------------------------------------
|
||||
1 S 1.87311370E+01 0.033495
|
||||
1 S 2.82539370E+00 0.234727
|
||||
1 S 6.40121700E-01 0.813757
|
||||
|
||||
2 S 1.61277800E-01 1.000000
|
||||
|
||||
|
||||
|
||||
Summary of "ao basis" -> "" (cartesian)
|
||||
------------------------------------------------------------------------------
|
||||
Tag Description Shells Functions and Types
|
||||
---------------- ------------------------------ ------ ---------------------
|
||||
O 6-31g* 6 15 3s2p1d
|
||||
H 6-31g* 2 2 2s
|
||||
|
||||
|
||||
NWChem SCF Module
|
||||
-----------------
|
||||
|
||||
|
||||
|
||||
ao basis = "ao basis"
|
||||
functions = 19
|
||||
atoms = 3
|
||||
closed shells = 5
|
||||
open shells = 0
|
||||
charge = 0.00
|
||||
wavefunction = RHF
|
||||
input vectors = ./nwchem_lammps.movecs
|
||||
output vectors = ./nwchem_lammps.movecs
|
||||
use symmetry = F
|
||||
symmetry adapt = F
|
||||
|
||||
|
||||
Summary of "ao basis" -> "ao basis" (cartesian)
|
||||
------------------------------------------------------------------------------
|
||||
Tag Description Shells Functions and Types
|
||||
---------------- ------------------------------ ------ ---------------------
|
||||
O 6-31g* 6 15 3s2p1d
|
||||
H 6-31g* 2 2 2s
|
||||
|
||||
|
||||
|
||||
Forming initial guess at 0.0s
|
||||
|
||||
|
||||
Loading old vectors from job with title :
|
||||
|
||||
|
||||
|
||||
|
||||
Starting SCF solution at 0.0s
|
||||
|
||||
|
||||
|
||||
----------------------------------------------
|
||||
Quadratically convergent ROHF
|
||||
|
||||
Convergence threshold : 1.000E-04
|
||||
Maximum no. of iterations : 100
|
||||
Final Fock-matrix accuracy: 1.000E-07
|
||||
----------------------------------------------
|
||||
|
||||
|
||||
#quartets = 1.540D+03 #integrals = 1.424D+04 #direct = 0.0% #cached =100.0%
|
||||
|
||||
|
||||
Integral file = ./nwchem_lammps.aoints.0
|
||||
Record size in doubles = 65536 No. of integs per rec = 43688
|
||||
Max. records in memory = 2 Max. records in file = 1392051
|
||||
No. of bits per label = 8 No. of bits per value = 64
|
||||
|
||||
|
||||
iter energy gnorm gmax time
|
||||
----- ------------------- --------- --------- --------
|
||||
1 -76.0095751323 4.63D-02 1.64D-02 0.1
|
||||
2 -76.0097628164 8.13D-04 2.83D-04 0.1
|
||||
3 -76.0097629130 3.92D-06 1.55D-06 0.1
|
||||
|
||||
|
||||
Final RHF results
|
||||
------------------
|
||||
|
||||
Total SCF energy = -76.009762913030
|
||||
One-electron energy = -123.002897732381
|
||||
Two-electron energy = 37.835807772101
|
||||
Nuclear repulsion energy = 9.157327047250
|
||||
|
||||
Time for solution = 0.0s
|
||||
|
||||
|
||||
Final eigenvalues
|
||||
-----------------
|
||||
|
||||
1
|
||||
1 -20.5584
|
||||
2 -1.3367
|
||||
3 -0.7128
|
||||
4 -0.5617
|
||||
5 -0.4959
|
||||
6 0.2104
|
||||
7 0.3038
|
||||
8 1.0409
|
||||
9 1.1202
|
||||
10 1.1606
|
||||
11 1.1691
|
||||
12 1.3840
|
||||
13 1.4192
|
||||
14 2.0312
|
||||
15 2.0334
|
||||
|
||||
ROHF Final Molecular Orbital Analysis
|
||||
-------------------------------------
|
||||
|
||||
Vector 2 Occ=2.000000D+00 E=-1.336749D+00
|
||||
MO Center= -2.8D-03, -1.3D-02, -1.7D-01, r^2= 5.1D-01
|
||||
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
|
||||
----- ------------ --------------- ----- ------------ ---------------
|
||||
2 0.476636 1 O s 6 0.442369 1 O s
|
||||
1 -0.210214 1 O s
|
||||
|
||||
Vector 3 Occ=2.000000D+00 E=-7.127948D-01
|
||||
MO Center= -4.9D-03, 3.9D-03, -2.1D-01, r^2= 7.8D-01
|
||||
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
|
||||
----- ------------ --------------- ----- ------------ ---------------
|
||||
4 0.504894 1 O py 8 0.303932 1 O py
|
||||
18 -0.234724 3 H s 16 0.229765 2 H s
|
||||
|
||||
Vector 4 Occ=2.000000D+00 E=-5.617306D-01
|
||||
MO Center= 3.6D-03, 9.0D-03, 5.6D-02, r^2= 6.9D-01
|
||||
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
|
||||
----- ------------ --------------- ----- ------------ ---------------
|
||||
5 0.559565 1 O pz 9 0.410981 1 O pz
|
||||
6 0.315892 1 O s 2 0.157960 1 O s
|
||||
|
||||
Vector 5 Occ=2.000000D+00 E=-4.959173D-01
|
||||
MO Center= 1.4D-03, 6.9D-05, -2.2D-02, r^2= 6.0D-01
|
||||
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
|
||||
----- ------------ --------------- ----- ------------ ---------------
|
||||
3 0.638390 1 O px 7 0.511530 1 O px
|
||||
|
||||
Vector 6 Occ=0.000000D+00 E= 2.103822D-01
|
||||
MO Center= -2.3D-02, 3.5D-02, -7.3D-01, r^2= 2.6D+00
|
||||
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
|
||||
----- ------------ --------------- ----- ------------ ---------------
|
||||
6 1.416869 1 O s 17 -1.068330 2 H s
|
||||
19 -1.014775 3 H s 9 -0.490951 1 O pz
|
||||
5 -0.212990 1 O pz
|
||||
|
||||
Vector 7 Occ=0.000000D+00 E= 3.037943D-01
|
||||
MO Center= -1.8D-02, -8.9D-02, -7.1D-01, r^2= 2.8D+00
|
||||
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
|
||||
----- ------------ --------------- ----- ------------ ---------------
|
||||
19 -1.426837 3 H s 17 1.332767 2 H s
|
||||
8 -0.842141 1 O py 4 -0.327553 1 O py
|
||||
|
||||
Vector 8 Occ=0.000000D+00 E= 1.040852D+00
|
||||
MO Center= -7.4D-03, 1.3D-01, -1.6D-01, r^2= 1.4D+00
|
||||
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
|
||||
----- ------------ --------------- ----- ------------ ---------------
|
||||
16 0.931594 2 H s 18 -0.747590 3 H s
|
||||
8 -0.655817 1 O py 17 -0.523035 2 H s
|
||||
19 0.366407 3 H s 14 -0.357109 1 O dyz
|
||||
|
||||
Vector 9 Occ=0.000000D+00 E= 1.120172D+00
|
||||
MO Center= -6.8D-03, -2.9D-02, -3.1D-01, r^2= 1.5D+00
|
||||
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
|
||||
----- ------------ --------------- ----- ------------ ---------------
|
||||
6 1.145090 1 O s 18 0.841596 3 H s
|
||||
2 -0.727471 1 O s 16 0.684927 2 H s
|
||||
9 0.559191 1 O pz 19 -0.546678 3 H s
|
||||
17 -0.538778 2 H s 10 -0.344609 1 O dxx
|
||||
15 -0.250035 1 O dzz
|
||||
|
||||
Vector 10 Occ=0.000000D+00 E= 1.160603D+00
|
||||
MO Center= 1.2D-02, -4.3D-02, 2.5D-01, r^2= 1.0D+00
|
||||
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
|
||||
----- ------------ --------------- ----- ------------ ---------------
|
||||
6 1.137949 1 O s 5 -0.844233 1 O pz
|
||||
9 0.595088 1 O pz 2 -0.475986 1 O s
|
||||
18 -0.455932 3 H s 16 -0.357325 2 H s
|
||||
13 -0.317117 1 O dyy 15 -0.196968 1 O dzz
|
||||
|
||||
Vector 11 Occ=0.000000D+00 E= 1.169054D+00
|
||||
MO Center= 1.9D-03, 1.2D-03, -6.4D-03, r^2= 1.1D+00
|
||||
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
|
||||
----- ------------ --------------- ----- ------------ ---------------
|
||||
7 -1.034653 1 O px 3 0.962043 1 O px
|
||||
|
||||
Vector 12 Occ=0.000000D+00 E= 1.384034D+00
|
||||
MO Center= 6.0D-04, -2.6D-03, -5.0D-02, r^2= 1.4D+00
|
||||
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
|
||||
----- ------------ --------------- ----- ------------ ---------------
|
||||
8 1.557767 1 O py 4 -1.035829 1 O py
|
||||
17 -0.900920 2 H s 19 0.901756 3 H s
|
||||
|
||||
Vector 13 Occ=0.000000D+00 E= 1.419205D+00
|
||||
MO Center= -1.3D-02, -4.9D-02, -5.2D-01, r^2= 1.4D+00
|
||||
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
|
||||
----- ------------ --------------- ----- ------------ ---------------
|
||||
6 3.605136 1 O s 2 -1.454853 1 O s
|
||||
9 -1.107532 1 O pz 19 -0.874208 3 H s
|
||||
17 -0.757016 2 H s 13 -0.634436 1 O dyy
|
||||
5 0.516593 1 O pz 15 -0.401100 1 O dzz
|
||||
10 -0.319873 1 O dxx 16 -0.260650 2 H s
|
||||
|
||||
Vector 14 Occ=0.000000D+00 E= 2.031234D+00
|
||||
MO Center= 1.9D-03, 2.3D-03, -3.0D-03, r^2= 6.1D-01
|
||||
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
|
||||
----- ------------ --------------- ----- ------------ ---------------
|
||||
11 1.727083 1 O dxy
|
||||
|
||||
Vector 15 Occ=0.000000D+00 E= 2.033369D+00
|
||||
MO Center= 3.4D-03, 3.4D-03, 4.3D-02, r^2= 6.2D-01
|
||||
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
|
||||
----- ------------ --------------- ----- ------------ ---------------
|
||||
15 1.012642 1 O dzz 13 -0.512441 1 O dyy
|
||||
10 -0.438481 1 O dxx 6 -0.226567 1 O s
|
||||
|
||||
|
||||
center of mass
|
||||
--------------
|
||||
x = -0.00000001 y = -0.00000003 z = -0.12388979
|
||||
|
||||
moments of inertia (a.u.)
|
||||
------------------
|
||||
6.378705068992 0.153373998471 -0.069687034145
|
||||
0.153373998471 2.014476065716 0.150739744400
|
||||
-0.069687034145 0.150739744400 4.379134195179
|
||||
|
||||
Mulliken analysis of the total density
|
||||
--------------------------------------
|
||||
|
||||
Atom Charge Shell Charges
|
||||
----------- ------ -------------------------------------------------------
|
||||
1 O 8 8.87 2.00 0.90 2.90 0.92 2.08 0.08
|
||||
2 H 1 0.56 0.46 0.11
|
||||
3 H 1 0.56 0.47 0.10
|
||||
|
||||
Multipole analysis of the density wrt the origin
|
||||
------------------------------------------------
|
||||
|
||||
L x y z total open nuclear
|
||||
- - - - ----- ---- -------
|
||||
0 0 0 0 -0.000000 0.000000 10.000000
|
||||
|
||||
1 1 0 0 -0.026417 0.000000 -0.029313
|
||||
1 0 1 0 -0.023604 0.000000 -0.018537
|
||||
1 0 0 1 -0.846090 0.000000 -2.169670
|
||||
|
||||
2 2 0 0 -5.373227 0.000000 0.007286
|
||||
2 1 1 0 -0.085617 0.000000 -0.152252
|
||||
2 1 0 1 0.038215 0.000000 0.069311
|
||||
2 0 2 0 -2.927589 0.000000 4.337695
|
||||
2 0 1 1 -0.071410 0.000000 -0.149465
|
||||
2 0 0 2 -4.159949 0.000000 2.265483
|
||||
|
||||
|
||||
Parallel integral file used 1 records with 0 large values
|
||||
|
||||
NWChem Gradients Module
|
||||
-----------------------
|
||||
|
||||
|
||||
|
||||
wavefunction = RHF
|
||||
|
||||
|
||||
|
||||
RHF ENERGY GRADIENTS
|
||||
|
||||
atom coordinates gradient
|
||||
x y z x y z
|
||||
1 O 0.003724 0.002355 -0.005632 0.000909 -0.019294 0.007866
|
||||
2 H -0.081649 1.453885 -1.126502 -0.001242 0.025549 -0.011605
|
||||
3 H 0.022541 -1.491264 -0.998110 0.000333 -0.006255 0.003739
|
||||
|
||||
----------------------------------------
|
||||
| Time | 1-e(secs) | 2-e(secs) |
|
||||
----------------------------------------
|
||||
| CPU | 0.00 | 0.03 |
|
||||
----------------------------------------
|
||||
| WALL | 0.00 | 0.03 |
|
||||
----------------------------------------
|
||||
|
||||
Task times cpu: 0.1s wall: 0.1s
|
||||
|
||||
|
||||
NWChem Input Module
|
||||
-------------------
|
||||
|
||||
|
||||
Summary of allocated global arrays
|
||||
-----------------------------------
|
||||
No active global arrays
|
||||
|
||||
|
||||
|
||||
GA Statistics for process 0
|
||||
------------------------------
|
||||
|
||||
create destroy get put acc scatter gather read&inc
|
||||
calls: 182 182 2869 728 468 0 0 68
|
||||
number of processes/call 1.00e+00 1.00e+00 1.00e+00 0.00e+00 0.00e+00
|
||||
bytes total: 6.18e+05 3.56e+05 1.04e+05 0.00e+00 0.00e+00 5.44e+02
|
||||
bytes remote: 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00
|
||||
Max memory consumed for GA by this process: 39432 bytes
|
||||
|
||||
MA_summarize_allocated_blocks: starting scan ...
|
||||
MA_summarize_allocated_blocks: scan completed: 0 heap blocks, 0 stack blocks
|
||||
MA usage statistics:
|
||||
|
||||
allocation statistics:
|
||||
heap stack
|
||||
---- -----
|
||||
current number of blocks 0 0
|
||||
maximum number of blocks 18 28
|
||||
current total bytes 0 0
|
||||
maximum total bytes 1060104 16000888
|
||||
maximum total K-bytes 1061 16001
|
||||
maximum total M-bytes 2 17
|
||||
|
||||
|
||||
CITATION
|
||||
--------
|
||||
Please cite the following reference when publishing
|
||||
results obtained with NWChem:
|
||||
|
||||
M. Valiev, E.J. Bylaska, N. Govind, K. Kowalski,
|
||||
T.P. Straatsma, H.J.J. van Dam, D. Wang, J. Nieplocha,
|
||||
E. Apra, T.L. Windus, W.A. de Jong
|
||||
"NWChem: a comprehensive and scalable open-source
|
||||
solution for large scale molecular simulations"
|
||||
Comput. Phys. Commun. 181, 1477 (2010)
|
||||
doi:10.1016/j.cpc.2010.04.018
|
||||
|
||||
AUTHORS
|
||||
-------
|
||||
E. Apra, E. J. Bylaska, W. A. de Jong, N. Govind, K. Kowalski,
|
||||
T. P. Straatsma, M. Valiev, H. J. J. van Dam, D. Wang, T. L. Windus,
|
||||
J. Hammond, J. Autschbach, K. Bhaskaran-Nair, J. Brabec, K. Lopata,
|
||||
S. A. Fischer, S. Krishnamoorthy, M. Jacquelin, W. Ma, M. Klemm, O. Villa,
|
||||
Y. Chen, V. Anisimov, F. Aquino, S. Hirata, M. T. Hackler, V. Konjkov,
|
||||
D. Mejia-Rodriguez, T. Risthaus, M. Malagoli, A. Marenich,
|
||||
A. Otero-de-la-Roza, J. Mullin, P. Nichols, R. Peverati, J. Pittner, Y. Zhao,
|
||||
P.-D. Fan, A. Fonari, M. J. Williamson, R. J. Harrison, J. R. Rehr,
|
||||
M. Dupuis, D. Silverstein, D. M. A. Smith, J. Nieplocha, V. Tipparaju,
|
||||
M. Krishnan, B. E. Van Kuiken, A. Vazquez-Mayagoitia, L. Jensen, M. Swart,
|
||||
Q. Wu, T. Van Voorhis, A. A. Auer, M. Nooijen, L. D. Crosby, E. Brown,
|
||||
G. Cisneros, G. I. Fann, H. Fruchtl, J. Garza, K. Hirao, R. A. Kendall,
|
||||
J. A. Nichols, K. Tsemekhman, K. Wolinski, J. Anchell, D. E. Bernholdt,
|
||||
P. Borowski, T. Clark, D. Clerc, H. Dachsel, M. J. O. Deegan, K. Dyall,
|
||||
D. Elwood, E. Glendening, M. Gutowski, A. C. Hess, J. Jaffe, B. G. Johnson,
|
||||
J. Ju, R. Kobayashi, R. Kutteh, Z. Lin, R. Littlefield, X. Long, B. Meng,
|
||||
T. Nakajima, S. Niu, L. Pollack, M. Rosing, K. Glaesemann, G. Sandrone,
|
||||
M. Stave, H. Taylor, G. Thomas, J. H. van Lenthe, A. T. Wong, Z. Zhang.
|
||||
|
||||
Total times cpu: 0.1s wall: 0.2s
|
||||
@ -1,626 +0,0 @@
|
||||
argument 1 = nwchem_lammps.nw
|
||||
|
||||
|
||||
|
||||
============================== echo of input deck ==============================
|
||||
echo
|
||||
|
||||
memory global 40 mb stack 23 mb heap 5 mb
|
||||
|
||||
geometry units angstrom noautosym nocenter
|
||||
O -0.00836667 0.0010006 0.0866404
|
||||
H 0.0968795 0.837453 -0.346117
|
||||
H 0.0114839 -0.638453 -0.612122
|
||||
end
|
||||
|
||||
scf
|
||||
vectors input nwchem_lammps.movecs
|
||||
end
|
||||
|
||||
dft
|
||||
vectors input nwchem_lammps.movecs
|
||||
end
|
||||
|
||||
basis
|
||||
O library 6-31g*
|
||||
H library 6-31g*
|
||||
end
|
||||
|
||||
scf
|
||||
maxiter 100
|
||||
end
|
||||
|
||||
#dft
|
||||
# xc b3lyp
|
||||
#end
|
||||
|
||||
task scf gradient
|
||||
#task dft gradient
|
||||
================================================================================
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
Northwest Computational Chemistry Package (NWChem) 6.8
|
||||
------------------------------------------------------
|
||||
|
||||
|
||||
Environmental Molecular Sciences Laboratory
|
||||
Pacific Northwest National Laboratory
|
||||
Richland, WA 99352
|
||||
|
||||
Copyright (c) 1994-2018
|
||||
Pacific Northwest National Laboratory
|
||||
Battelle Memorial Institute
|
||||
|
||||
NWChem is an open-source computational chemistry package
|
||||
distributed under the terms of the
|
||||
Educational Community License (ECL) 2.0
|
||||
A copy of the license is included with this distribution
|
||||
in the LICENSE.TXT file
|
||||
|
||||
ACKNOWLEDGMENT
|
||||
--------------
|
||||
|
||||
This software and its documentation were developed at the
|
||||
EMSL at Pacific Northwest National Laboratory, a multiprogram
|
||||
national laboratory, operated for the U.S. Department of Energy
|
||||
by Battelle under Contract Number DE-AC05-76RL01830. Support
|
||||
for this work was provided by the Department of Energy Office
|
||||
of Biological and Environmental Research, Office of Basic
|
||||
Energy Sciences, and the Office of Advanced Scientific Computing.
|
||||
|
||||
|
||||
Job information
|
||||
---------------
|
||||
|
||||
hostname = almondjoy
|
||||
program = /home/jboschen/nwchem-6.8.1-release/bin/LINUX64/nwchem
|
||||
date = Fri Jan 31 00:33:40 2020
|
||||
|
||||
compiled = Tue_Oct_01_13:20:43_2019
|
||||
source = /home/jboschen/nwchem-6.8.1-release
|
||||
nwchem branch = Development
|
||||
nwchem revision = N/A
|
||||
ga revision = 5.6.5
|
||||
use scalapack = F
|
||||
input = nwchem_lammps.nw
|
||||
prefix = nwchem_lammps.
|
||||
data base = ./nwchem_lammps.db
|
||||
status = restart
|
||||
nproc = 1
|
||||
time left = -1s
|
||||
|
||||
|
||||
|
||||
Memory information
|
||||
------------------
|
||||
|
||||
heap = 655358 doubles = 5.0 Mbytes
|
||||
stack = 3014651 doubles = 23.0 Mbytes
|
||||
global = 5242880 doubles = 40.0 Mbytes (distinct from heap & stack)
|
||||
total = 8912889 doubles = 68.0 Mbytes
|
||||
verify = yes
|
||||
hardfail = no
|
||||
|
||||
|
||||
Directory information
|
||||
---------------------
|
||||
|
||||
0 permanent = .
|
||||
0 scratch = .
|
||||
|
||||
|
||||
Previous task information
|
||||
-------------------------
|
||||
|
||||
Theory = scf
|
||||
Operation = gradient
|
||||
Status = ok
|
||||
Qmmm = F
|
||||
Ignore = F
|
||||
|
||||
|
||||
Geometries in the database
|
||||
--------------------------
|
||||
|
||||
Name Natoms Last Modified
|
||||
-------------------------------- ------ ------------------------
|
||||
1 geometry 3 Fri Jan 31 00:33:40 2020
|
||||
|
||||
The geometry named "geometry" is the default for restart
|
||||
|
||||
|
||||
|
||||
Basis sets in the database
|
||||
--------------------------
|
||||
|
||||
Name Natoms Last Modified
|
||||
-------------------------------- ------ ------------------------
|
||||
1 ao basis 2 Fri Jan 31 00:33:40 2020
|
||||
|
||||
The basis set named "ao basis" is the default AO basis for restart
|
||||
|
||||
|
||||
|
||||
|
||||
NWChem Input Module
|
||||
-------------------
|
||||
|
||||
|
||||
|
||||
Scaling coordinates for geometry "geometry" by 1.889725989
|
||||
(inverse scale = 0.529177249)
|
||||
|
||||
|
||||
------
|
||||
auto-z
|
||||
------
|
||||
no constraints, skipping 0.0000000000000000
|
||||
no constraints, skipping 0.0000000000000000
|
||||
|
||||
|
||||
Geometry "geometry" -> ""
|
||||
-------------------------
|
||||
|
||||
Output coordinates in angstroms (scale by 1.889725989 to convert to a.u.)
|
||||
|
||||
No. Tag Charge X Y Z
|
||||
---- ---------------- ---------- -------------- -------------- --------------
|
||||
1 O 8.0000 -0.00836667 0.00100060 0.08664040
|
||||
2 H 1.0000 0.09687950 0.83745300 -0.34611700
|
||||
3 H 1.0000 0.01148390 -0.63845300 -0.61212200
|
||||
|
||||
Atomic Mass
|
||||
-----------
|
||||
|
||||
O 15.994910
|
||||
H 1.007825
|
||||
|
||||
|
||||
Effective nuclear repulsion energy (a.u.) 9.2881144400
|
||||
|
||||
Nuclear Dipole moment (a.u.)
|
||||
----------------------------
|
||||
X Y Z
|
||||
---------------- ---------------- ----------------
|
||||
0.0782914233 0.3911823503 -0.5009962172
|
||||
|
||||
|
||||
|
||||
Z-matrix (autoz)
|
||||
--------
|
||||
|
||||
Units are Angstrom for bonds and degrees for angles
|
||||
|
||||
Type Name I J K L M Value
|
||||
----------- -------- ----- ----- ----- ----- ----- ----------
|
||||
1 Stretch 1 2 0.94763
|
||||
2 Stretch 1 3 0.94740
|
||||
3 Bend 2 1 3 104.86952
|
||||
|
||||
|
||||
XYZ format geometry
|
||||
-------------------
|
||||
3
|
||||
geometry
|
||||
O -0.00836667 0.00100060 0.08664040
|
||||
H 0.09687950 0.83745300 -0.34611700
|
||||
H 0.01148390 -0.63845300 -0.61212200
|
||||
|
||||
==============================================================================
|
||||
internuclear distances
|
||||
------------------------------------------------------------------------------
|
||||
center one | center two | atomic units | angstroms
|
||||
------------------------------------------------------------------------------
|
||||
2 H | 1 O | 1.79077 | 0.94763
|
||||
3 H | 1 O | 1.79032 | 0.94740
|
||||
------------------------------------------------------------------------------
|
||||
number of included internuclear distances: 2
|
||||
==============================================================================
|
||||
|
||||
|
||||
|
||||
==============================================================================
|
||||
internuclear angles
|
||||
------------------------------------------------------------------------------
|
||||
center 1 | center 2 | center 3 | degrees
|
||||
------------------------------------------------------------------------------
|
||||
2 H | 1 O | 3 H | 104.87
|
||||
------------------------------------------------------------------------------
|
||||
number of included internuclear angles: 1
|
||||
==============================================================================
|
||||
|
||||
|
||||
|
||||
Basis "ao basis" -> "" (cartesian)
|
||||
-----
|
||||
O (Oxygen)
|
||||
----------
|
||||
Exponent Coefficients
|
||||
-------------- ---------------------------------------------------------
|
||||
1 S 5.48467170E+03 0.001831
|
||||
1 S 8.25234950E+02 0.013950
|
||||
1 S 1.88046960E+02 0.068445
|
||||
1 S 5.29645000E+01 0.232714
|
||||
1 S 1.68975700E+01 0.470193
|
||||
1 S 5.79963530E+00 0.358521
|
||||
|
||||
2 S 1.55396160E+01 -0.110778
|
||||
2 S 3.59993360E+00 -0.148026
|
||||
2 S 1.01376180E+00 1.130767
|
||||
|
||||
3 P 1.55396160E+01 0.070874
|
||||
3 P 3.59993360E+00 0.339753
|
||||
3 P 1.01376180E+00 0.727159
|
||||
|
||||
4 S 2.70005800E-01 1.000000
|
||||
|
||||
5 P 2.70005800E-01 1.000000
|
||||
|
||||
6 D 8.00000000E-01 1.000000
|
||||
|
||||
H (Hydrogen)
|
||||
------------
|
||||
Exponent Coefficients
|
||||
-------------- ---------------------------------------------------------
|
||||
1 S 1.87311370E+01 0.033495
|
||||
1 S 2.82539370E+00 0.234727
|
||||
1 S 6.40121700E-01 0.813757
|
||||
|
||||
2 S 1.61277800E-01 1.000000
|
||||
|
||||
|
||||
|
||||
Summary of "ao basis" -> "" (cartesian)
|
||||
------------------------------------------------------------------------------
|
||||
Tag Description Shells Functions and Types
|
||||
---------------- ------------------------------ ------ ---------------------
|
||||
O 6-31g* 6 15 3s2p1d
|
||||
H 6-31g* 2 2 2s
|
||||
|
||||
|
||||
NWChem SCF Module
|
||||
-----------------
|
||||
|
||||
|
||||
|
||||
ao basis = "ao basis"
|
||||
functions = 19
|
||||
atoms = 3
|
||||
closed shells = 5
|
||||
open shells = 0
|
||||
charge = 0.00
|
||||
wavefunction = RHF
|
||||
input vectors = ./nwchem_lammps.movecs
|
||||
output vectors = ./nwchem_lammps.movecs
|
||||
use symmetry = F
|
||||
symmetry adapt = F
|
||||
|
||||
|
||||
Summary of "ao basis" -> "ao basis" (cartesian)
|
||||
------------------------------------------------------------------------------
|
||||
Tag Description Shells Functions and Types
|
||||
---------------- ------------------------------ ------ ---------------------
|
||||
O 6-31g* 6 15 3s2p1d
|
||||
H 6-31g* 2 2 2s
|
||||
|
||||
|
||||
|
||||
Forming initial guess at 0.0s
|
||||
|
||||
|
||||
Loading old vectors from job with title :
|
||||
|
||||
|
||||
|
||||
|
||||
Starting SCF solution at 0.0s
|
||||
|
||||
|
||||
|
||||
----------------------------------------------
|
||||
Quadratically convergent ROHF
|
||||
|
||||
Convergence threshold : 1.000E-04
|
||||
Maximum no. of iterations : 100
|
||||
Final Fock-matrix accuracy: 1.000E-07
|
||||
----------------------------------------------
|
||||
|
||||
|
||||
#quartets = 1.540D+03 #integrals = 1.424D+04 #direct = 0.0% #cached =100.0%
|
||||
|
||||
|
||||
Integral file = ./nwchem_lammps.aoints.0
|
||||
Record size in doubles = 65536 No. of integs per rec = 43688
|
||||
Max. records in memory = 2 Max. records in file = 1392051
|
||||
No. of bits per label = 8 No. of bits per value = 64
|
||||
|
||||
|
||||
iter energy gnorm gmax time
|
||||
----- ------------------- --------- --------- --------
|
||||
1 -76.0107350035 4.75D-05 2.49D-05 0.1
|
||||
|
||||
|
||||
Final RHF results
|
||||
------------------
|
||||
|
||||
Total SCF energy = -76.010735003510
|
||||
One-electron energy = -123.220958992568
|
||||
Two-electron energy = 37.922109549024
|
||||
Nuclear repulsion energy = 9.288114440035
|
||||
|
||||
Time for solution = 0.0s
|
||||
|
||||
|
||||
Final eigenvalues
|
||||
-----------------
|
||||
|
||||
1
|
||||
1 -20.5583
|
||||
2 -1.3466
|
||||
3 -0.7130
|
||||
4 -0.5721
|
||||
5 -0.4985
|
||||
6 0.2129
|
||||
7 0.3068
|
||||
8 1.0286
|
||||
9 1.1338
|
||||
10 1.1678
|
||||
11 1.1807
|
||||
12 1.3845
|
||||
13 1.4334
|
||||
14 2.0187
|
||||
15 2.0311
|
||||
|
||||
ROHF Final Molecular Orbital Analysis
|
||||
-------------------------------------
|
||||
|
||||
Vector 2 Occ=2.000000D+00 E=-1.346587D+00
|
||||
MO Center= 1.1D-02, 3.1D-02, -8.5D-02, r^2= 5.0D-01
|
||||
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
|
||||
----- ------------ --------------- ----- ------------ ---------------
|
||||
2 0.475648 1 O s 6 0.435095 1 O s
|
||||
1 -0.209463 1 O s
|
||||
|
||||
Vector 3 Occ=2.000000D+00 E=-7.129747D-01
|
||||
MO Center= 1.5D-02, 3.8D-02, -1.3D-01, r^2= 7.6D-01
|
||||
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
|
||||
----- ------------ --------------- ----- ------------ ---------------
|
||||
4 0.500246 1 O py 8 0.299047 1 O py
|
||||
16 0.232138 2 H s 18 -0.232195 3 H s
|
||||
|
||||
Vector 4 Occ=2.000000D+00 E=-5.720760D-01
|
||||
MO Center= -1.5D-02, -9.7D-03, 1.5D-01, r^2= 6.8D-01
|
||||
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
|
||||
----- ------------ --------------- ----- ------------ ---------------
|
||||
5 0.545527 1 O pz 9 0.395332 1 O pz
|
||||
6 0.326735 1 O s 2 0.164593 1 O s
|
||||
|
||||
Vector 5 Occ=2.000000D+00 E=-4.984552D-01
|
||||
MO Center= -6.2D-03, 4.4D-03, 6.7D-02, r^2= 6.0D-01
|
||||
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
|
||||
----- ------------ --------------- ----- ------------ ---------------
|
||||
3 0.634559 1 O px 7 0.507891 1 O px
|
||||
|
||||
Vector 6 Occ=0.000000D+00 E= 2.128732D-01
|
||||
MO Center= 7.5D-02, 1.3D-01, -6.6D-01, r^2= 2.6D+00
|
||||
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
|
||||
----- ------------ --------------- ----- ------------ ---------------
|
||||
6 1.437795 1 O s 17 -1.050892 2 H s
|
||||
19 -1.050374 3 H s 9 -0.494696 1 O pz
|
||||
5 -0.208359 1 O pz
|
||||
|
||||
Vector 7 Occ=0.000000D+00 E= 3.067764D-01
|
||||
MO Center= 7.1D-02, 1.3D-01, -6.3D-01, r^2= 2.7D+00
|
||||
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
|
||||
----- ------------ --------------- ----- ------------ ---------------
|
||||
17 1.413885 2 H s 19 -1.414835 3 H s
|
||||
8 -0.824411 1 O py 4 -0.320355 1 O py
|
||||
|
||||
Vector 8 Occ=0.000000D+00 E= 1.028607D+00
|
||||
MO Center= 7.1D-03, 2.6D-02, -5.2D-02, r^2= 1.4D+00
|
||||
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
|
||||
----- ------------ --------------- ----- ------------ ---------------
|
||||
16 0.839269 2 H s 18 -0.838060 3 H s
|
||||
8 -0.692349 1 O py 17 -0.426291 2 H s
|
||||
19 0.425092 3 H s 14 -0.319117 1 O dyz
|
||||
|
||||
Vector 9 Occ=0.000000D+00 E= 1.133833D+00
|
||||
MO Center= -2.7D-02, -2.9D-02, 2.6D-01, r^2= 1.5D+00
|
||||
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
|
||||
----- ------------ --------------- ----- ------------ ---------------
|
||||
6 1.621086 1 O s 2 -0.910150 1 O s
|
||||
9 0.744864 1 O pz 16 0.490586 2 H s
|
||||
18 0.491102 3 H s 5 -0.484186 1 O pz
|
||||
17 -0.426087 2 H s 19 -0.425823 3 H s
|
||||
10 -0.375325 1 O dxx 15 -0.317874 1 O dzz
|
||||
|
||||
Vector 10 Occ=0.000000D+00 E= 1.167849D+00
|
||||
MO Center= -8.0D-03, 1.6D-03, 8.3D-02, r^2= 1.1D+00
|
||||
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
|
||||
----- ------------ --------------- ----- ------------ ---------------
|
||||
7 -1.028149 1 O px 3 0.955686 1 O px
|
||||
|
||||
Vector 11 Occ=0.000000D+00 E= 1.180721D+00
|
||||
MO Center= 1.8D-02, 4.2D-02, -1.5D-01, r^2= 1.1D+00
|
||||
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
|
||||
----- ------------ --------------- ----- ------------ ---------------
|
||||
16 0.710073 2 H s 18 0.711177 3 H s
|
||||
5 0.704677 1 O pz 17 -0.389719 2 H s
|
||||
19 -0.389376 3 H s 6 -0.326170 1 O s
|
||||
9 -0.288739 1 O pz 13 0.229749 1 O dyy
|
||||
|
||||
Vector 12 Occ=0.000000D+00 E= 1.384514D+00
|
||||
MO Center= -7.4D-04, 1.3D-02, 1.8D-02, r^2= 1.4D+00
|
||||
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
|
||||
----- ------------ --------------- ----- ------------ ---------------
|
||||
8 1.510506 1 O py 4 -1.021750 1 O py
|
||||
17 -0.934844 2 H s 19 0.935260 3 H s
|
||||
9 0.272171 1 O pz 5 -0.184286 1 O pz
|
||||
|
||||
Vector 13 Occ=0.000000D+00 E= 1.433397D+00
|
||||
MO Center= 4.7D-02, 8.7D-02, -4.1D-01, r^2= 1.4D+00
|
||||
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
|
||||
----- ------------ --------------- ----- ------------ ---------------
|
||||
6 3.628985 1 O s 2 -1.436467 1 O s
|
||||
9 -1.143870 1 O pz 17 -0.805578 2 H s
|
||||
19 -0.806493 3 H s 13 -0.635948 1 O dyy
|
||||
5 0.489050 1 O pz 15 -0.410417 1 O dzz
|
||||
16 -0.312860 2 H s 18 -0.312722 3 H s
|
||||
|
||||
Vector 14 Occ=0.000000D+00 E= 2.018721D+00
|
||||
MO Center= -1.4D-02, -7.1D-03, 1.3D-01, r^2= 6.2D-01
|
||||
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
|
||||
----- ------------ --------------- ----- ------------ ---------------
|
||||
15 0.947149 1 O dzz 14 -0.531399 1 O dyz
|
||||
13 -0.526961 1 O dyy 10 -0.358371 1 O dxx
|
||||
12 -0.297495 1 O dxz 6 -0.233087 1 O s
|
||||
|
||||
Vector 15 Occ=0.000000D+00 E= 2.031133D+00
|
||||
MO Center= -8.4D-03, 1.0D-03, 8.7D-02, r^2= 6.1D-01
|
||||
Bfn. Coefficient Atom+Function Bfn. Coefficient Atom+Function
|
||||
----- ------------ --------------- ----- ------------ ---------------
|
||||
11 1.681563 1 O dxy 12 0.314688 1 O dxz
|
||||
|
||||
|
||||
center of mass
|
||||
--------------
|
||||
x = -0.00258245 y = 0.02272235 z = 0.04407491
|
||||
|
||||
moments of inertia (a.u.)
|
||||
------------------
|
||||
6.155330507195 -0.266185800841 0.185335033231
|
||||
-0.266185800841 2.211585220634 -0.350250164177
|
||||
0.185335033231 -0.350250164177 4.020009073007
|
||||
|
||||
Mulliken analysis of the total density
|
||||
--------------------------------------
|
||||
|
||||
Atom Charge Shell Charges
|
||||
----------- ------ -------------------------------------------------------
|
||||
1 O 8 8.87 2.00 0.90 2.91 0.91 2.06 0.08
|
||||
2 H 1 0.57 0.47 0.10
|
||||
3 H 1 0.57 0.47 0.10
|
||||
|
||||
Multipole analysis of the density wrt the origin
|
||||
------------------------------------------------
|
||||
|
||||
L x y z total open nuclear
|
||||
- - - - ----- ---- -------
|
||||
0 0 0 0 -0.000000 0.000000 10.000000
|
||||
|
||||
1 1 0 0 0.094145 0.000000 0.078291
|
||||
1 0 1 0 0.148179 0.000000 0.391182
|
||||
1 0 0 1 -0.851621 0.000000 -0.500996
|
||||
|
||||
2 2 0 0 -5.338111 0.000000 0.035987
|
||||
2 1 1 0 0.149191 0.000000 0.263306
|
||||
2 1 0 1 -0.084723 0.000000 -0.165556
|
||||
2 0 2 0 -3.114464 0.000000 3.960160
|
||||
2 0 1 1 0.205130 0.000000 0.362991
|
||||
2 0 0 2 -4.329185 0.000000 1.980308
|
||||
|
||||
|
||||
Parallel integral file used 1 records with 0 large values
|
||||
|
||||
NWChem Gradients Module
|
||||
-----------------------
|
||||
|
||||
|
||||
|
||||
wavefunction = RHF
|
||||
|
||||
|
||||
|
||||
RHF ENERGY GRADIENTS
|
||||
|
||||
atom coordinates gradient
|
||||
x y z x y z
|
||||
1 O -0.015811 0.001891 0.163727 -0.000201 -0.000505 0.001671
|
||||
2 H 0.183076 1.582557 -0.654066 0.000065 -0.000505 -0.001056
|
||||
3 H 0.021701 -1.206501 -1.156743 0.000136 0.001011 -0.000616
|
||||
|
||||
----------------------------------------
|
||||
| Time | 1-e(secs) | 2-e(secs) |
|
||||
----------------------------------------
|
||||
| CPU | 0.00 | 0.03 |
|
||||
----------------------------------------
|
||||
| WALL | 0.00 | 0.03 |
|
||||
----------------------------------------
|
||||
|
||||
Task times cpu: 0.1s wall: 0.1s
|
||||
|
||||
|
||||
NWChem Input Module
|
||||
-------------------
|
||||
|
||||
|
||||
Summary of allocated global arrays
|
||||
-----------------------------------
|
||||
No active global arrays
|
||||
|
||||
|
||||
|
||||
GA Statistics for process 0
|
||||
------------------------------
|
||||
|
||||
create destroy get put acc scatter gather read&inc
|
||||
calls: 46 46 2296 477 27 0 0 68
|
||||
number of processes/call 1.00e+00 1.00e+00 1.00e+00 0.00e+00 0.00e+00
|
||||
bytes total: 2.70e+05 1.39e+05 2.27e+04 0.00e+00 0.00e+00 5.44e+02
|
||||
bytes remote: 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00
|
||||
Max memory consumed for GA by this process: 37544 bytes
|
||||
|
||||
MA_summarize_allocated_blocks: starting scan ...
|
||||
MA_summarize_allocated_blocks: scan completed: 0 heap blocks, 0 stack blocks
|
||||
MA usage statistics:
|
||||
|
||||
allocation statistics:
|
||||
heap stack
|
||||
---- -----
|
||||
current number of blocks 0 0
|
||||
maximum number of blocks 18 28
|
||||
current total bytes 0 0
|
||||
maximum total bytes 1060104 16000888
|
||||
maximum total K-bytes 1061 16001
|
||||
maximum total M-bytes 2 17
|
||||
|
||||
|
||||
CITATION
|
||||
--------
|
||||
Please cite the following reference when publishing
|
||||
results obtained with NWChem:
|
||||
|
||||
M. Valiev, E.J. Bylaska, N. Govind, K. Kowalski,
|
||||
T.P. Straatsma, H.J.J. van Dam, D. Wang, J. Nieplocha,
|
||||
E. Apra, T.L. Windus, W.A. de Jong
|
||||
"NWChem: a comprehensive and scalable open-source
|
||||
solution for large scale molecular simulations"
|
||||
Comput. Phys. Commun. 181, 1477 (2010)
|
||||
doi:10.1016/j.cpc.2010.04.018
|
||||
|
||||
AUTHORS
|
||||
-------
|
||||
E. Apra, E. J. Bylaska, W. A. de Jong, N. Govind, K. Kowalski,
|
||||
T. P. Straatsma, M. Valiev, H. J. J. van Dam, D. Wang, T. L. Windus,
|
||||
J. Hammond, J. Autschbach, K. Bhaskaran-Nair, J. Brabec, K. Lopata,
|
||||
S. A. Fischer, S. Krishnamoorthy, M. Jacquelin, W. Ma, M. Klemm, O. Villa,
|
||||
Y. Chen, V. Anisimov, F. Aquino, S. Hirata, M. T. Hackler, V. Konjkov,
|
||||
D. Mejia-Rodriguez, T. Risthaus, M. Malagoli, A. Marenich,
|
||||
A. Otero-de-la-Roza, J. Mullin, P. Nichols, R. Peverati, J. Pittner, Y. Zhao,
|
||||
P.-D. Fan, A. Fonari, M. J. Williamson, R. J. Harrison, J. R. Rehr,
|
||||
M. Dupuis, D. Silverstein, D. M. A. Smith, J. Nieplocha, V. Tipparaju,
|
||||
M. Krishnan, B. E. Van Kuiken, A. Vazquez-Mayagoitia, L. Jensen, M. Swart,
|
||||
Q. Wu, T. Van Voorhis, A. A. Auer, M. Nooijen, L. D. Crosby, E. Brown,
|
||||
G. Cisneros, G. I. Fann, H. Fruchtl, J. Garza, K. Hirao, R. A. Kendall,
|
||||
J. A. Nichols, K. Tsemekhman, K. Wolinski, J. Anchell, D. E. Bernholdt,
|
||||
P. Borowski, T. Clark, D. Clerc, H. Dachsel, M. J. O. Deegan, K. Dyall,
|
||||
D. Elwood, E. Glendening, M. Gutowski, A. C. Hess, J. Jaffe, B. G. Johnson,
|
||||
J. Ju, R. Kobayashi, R. Kutteh, Z. Lin, R. Littlefield, X. Long, B. Meng,
|
||||
T. Nakajima, S. Niu, L. Pollack, M. Rosing, K. Glaesemann, G. Sandrone,
|
||||
M. Stave, H. Taylor, G. Thomas, J. H. van Lenthe, A. T. Wong, Z. Zhang.
|
||||
|
||||
Total times cpu: 0.1s wall: 0.1s
|
||||
@ -1,447 +0,0 @@
|
||||
#!/usr/bin/env python
|
||||
|
||||
# ----------------------------------------------------------------------
|
||||
# LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
# https://www.lammps.org/ Sandia National Laboratories
|
||||
# Steve Plimpton, sjplimp@sandia.gov
|
||||
# ----------------------------------------------------------------------
|
||||
|
||||
# Syntax: nwchem_wrap.py file/zmq ao/pw input_template
|
||||
# file/zmg = messaging mode, must match LAMMPS messaging mode
|
||||
# ao/pw = basis set mode, selects between atom-centered and plane-wave
|
||||
# the input_template file must correspond to the appropriate basis set mode:
|
||||
# the "ao" mode supports the scf and dft modules in NWChem,
|
||||
# the "pw" mode supports the nwpw module.
|
||||
# input_template = NWChem input file used as template, must include a
|
||||
# "geometry" block with the atoms in the simulation, dummy
|
||||
# xyz coordinates should be included (but are not used).
|
||||
# Atom ordering must match LAMMPS input.
|
||||
|
||||
# wrapper on NWChem
|
||||
# receives message with list of coords
|
||||
# creates NWChem inputs
|
||||
# invokes NWChem to calculate self-consistent energy of that config
|
||||
# reads NWChem outputs
|
||||
# sends message with energy, forces, pressure to client
|
||||
|
||||
from __future__ import print_function
|
||||
import sys
|
||||
|
||||
version = sys.version_info[0]
|
||||
if version == 3:
|
||||
sys.exit("The CSlib python wrapper does not yet support python 3")
|
||||
|
||||
import subprocess
|
||||
import re
|
||||
import os
|
||||
import shutil
|
||||
from cslib import CSlib
|
||||
|
||||
# comment out 2nd line once 1st line is correct for your system
|
||||
|
||||
nwchemcmd = "mpirun -np 1 /usr/bin/nwchem"
|
||||
nwchemcmd = "touch tmp"
|
||||
|
||||
# enums matching FixClientMD class in LAMMPS
|
||||
|
||||
SETUP,STEP = range(1,2+1)
|
||||
DIM,PERIODICITY,ORIGIN,BOX,NATOMS,NTYPES,TYPES,COORDS,UNITS,CHARGE = range(1,10+1)
|
||||
FORCES,ENERGY,VIRIAL,ERROR = range(1,4+1)
|
||||
|
||||
# -------------------------------------
|
||||
# functions
|
||||
|
||||
# error message and exit
|
||||
|
||||
def error(txt):
|
||||
print("ERROR:",txt)
|
||||
sys.exit(1)
|
||||
|
||||
# -------------------------------------
|
||||
# read initial input file to setup problem
|
||||
# return natoms
|
||||
|
||||
def nwchem_setup_ao(input):
|
||||
|
||||
template = open(input,'r')
|
||||
|
||||
geometry_block = False
|
||||
natoms = 0
|
||||
|
||||
while True:
|
||||
line = template.readline()
|
||||
if not line: break
|
||||
|
||||
if geometry_block and re.search("end",line):
|
||||
geometry_block = False
|
||||
if geometry_block and not re.match("#",line) :
|
||||
natoms += 1
|
||||
if re.search("geometry",line):
|
||||
geometry_block = True
|
||||
|
||||
return natoms
|
||||
|
||||
# -------------------------------------
|
||||
# write a new input file for NWChem
|
||||
# assumes the NWChem input geometry is to be specified in angstroms
|
||||
|
||||
def nwchem_input_write_ao(input,coords):
|
||||
|
||||
template = open(input,'r')
|
||||
new_input = open("nwchem_lammps.nw",'w')
|
||||
|
||||
geometry_block = False
|
||||
i = 0
|
||||
|
||||
while True:
|
||||
line = template.readline()
|
||||
if not line: break
|
||||
|
||||
if geometry_block and not re.match("#",line) and re.search("end",line):
|
||||
geometry_block = False
|
||||
if os.path.exists("nwchem_lammps.movecs"):
|
||||
# The below is hacky, but one of these lines will be ignored
|
||||
# by NWChem depending on if the input file is for scf/dft.
|
||||
append = "\nscf\n vectors input nwchem_lammps.movecs\nend\n"
|
||||
append2 = "\ndft\n vectors input nwchem_lammps.movecs\nend\n"
|
||||
line = line + append + append2
|
||||
|
||||
if geometry_block and not re.match("#",line):
|
||||
x = coords[3*i+0]
|
||||
y = coords[3*i+1]
|
||||
z = coords[3*i+2]
|
||||
coord_string = " %g %g %g \n" % (x,y,z)
|
||||
atom_string = line.split()[0]
|
||||
line = atom_string + coord_string
|
||||
i += 1
|
||||
|
||||
if (not re.match("#",line)) and re.search("geometry",line):
|
||||
geometry_block = True
|
||||
line = "geometry units angstrom noautosym nocenter\n"
|
||||
|
||||
print(line,file=new_input,end='')
|
||||
|
||||
new_input.close()
|
||||
|
||||
# -------------------------------------
|
||||
# read a NWChem output nwchem_lammps.out file
|
||||
|
||||
def nwchem_read_ao(natoms, log):
|
||||
|
||||
nwchem_output = open(log, 'r')
|
||||
energy_pattern = r"Total \w+ energy"
|
||||
gradient_pattern = "x y z x y z"
|
||||
|
||||
eout = 0.0
|
||||
fout = []
|
||||
|
||||
while True:
|
||||
line = nwchem_output.readline()
|
||||
if not line: break
|
||||
|
||||
# pattern match for energy
|
||||
if re.search(energy_pattern,line):
|
||||
eout = float(line.split()[4])
|
||||
|
||||
# pattern match for forces
|
||||
if re.search(gradient_pattern, line):
|
||||
for i in range(natoms):
|
||||
line = nwchem_output.readline()
|
||||
forces = line.split()
|
||||
fout += [float(forces[5]), float(forces[6]), float(forces[7])]
|
||||
|
||||
# convert units
|
||||
hartree2eV = 27.21138602
|
||||
bohr2angstrom = 0.52917721092
|
||||
eout = eout * hartree2eV
|
||||
fout = [i * -hartree2eV/bohr2angstrom for i in fout]
|
||||
|
||||
return eout,fout
|
||||
|
||||
# -------------------------------------
|
||||
# read initial planewave input file to setup problem
|
||||
# return natoms,box
|
||||
def nwchem_setup_pw(input):
|
||||
|
||||
template = open(input,'r')
|
||||
|
||||
geometry_block = False
|
||||
system_block = False
|
||||
coord_pattern = r"^\s*\w{1,2}(?:\s+-?(?:\d+.?\d*|\d*.?\d+)){3}"
|
||||
natoms = 0
|
||||
box = []
|
||||
|
||||
while True:
|
||||
line = template.readline()
|
||||
if not line: break
|
||||
|
||||
if geometry_block and re.search("system crystal",line):
|
||||
system_block = True
|
||||
for i in range(3):
|
||||
line = template.readline()
|
||||
line = re.sub(r'd|D', 'e', line)
|
||||
box += [float(line.split()[1])]
|
||||
|
||||
if geometry_block and not system_block and re.match("#",line) and re.search("end",line):
|
||||
geometry_block = False
|
||||
|
||||
if system_block and re.search("end",line):
|
||||
system_block = False
|
||||
|
||||
if geometry_block and not re.match("#",line) and re.search(coord_pattern,line):
|
||||
natoms += 1
|
||||
|
||||
if re.search("geometry",line) and not re.match("#",line):
|
||||
geometry_block = True
|
||||
|
||||
return natoms,box
|
||||
|
||||
# -------------------------------------
|
||||
# write a new planewave input file for NWChem
|
||||
# assumes the NWChem input geometry is to be specified fractional coordinates
|
||||
|
||||
def nwchem_input_write_pw(input,coords,box):
|
||||
|
||||
template = open(input,'r')
|
||||
new_input = open("nwchem_lammps.nw",'w')
|
||||
|
||||
writing_atoms = False
|
||||
geometry_block = False
|
||||
system_block = False
|
||||
coord_pattern = r"^\s*\w{1,2}(?:\s+-?(?:\d+.?\d*|\d*.?\d+)){3}"
|
||||
i = 0
|
||||
|
||||
while True:
|
||||
line = template.readline()
|
||||
if not line: break
|
||||
|
||||
if geometry_block and re.search("system crystal",line):
|
||||
system_block = True
|
||||
|
||||
if geometry_block and not system_block and not re.match("#",line) and re.search("end",line):
|
||||
geometry_block = False
|
||||
if os.path.exists("nwchem_lammps.movecs"):
|
||||
append = "\nnwpw\n vectors input nwchem_lammps.movecs\nend\n"
|
||||
line = line + append
|
||||
|
||||
if system_block and re.search("end",line):
|
||||
system_block = False
|
||||
|
||||
if geometry_block and not re.match("#",line) and re.search(coord_pattern,line):
|
||||
x = coords[3*i+0] / box[0]
|
||||
y = coords[3*i+1] / box[1]
|
||||
z = coords[3*i+2] / box[2]
|
||||
coord_string = " %g %g %g \n" % (x,y,z)
|
||||
atom_string = line.split()[0]
|
||||
line = atom_string + coord_string
|
||||
i += 1
|
||||
|
||||
if re.search("geometry",line) and not re.match("#",line):
|
||||
geometry_block = True
|
||||
|
||||
print(line,file=new_input,end='')
|
||||
|
||||
new_input.close()
|
||||
|
||||
# -------------------------------------
|
||||
# read a NWChem output nwchem_lammps.out file for planewave calculation
|
||||
|
||||
def nwchem_read_pw(log):
|
||||
nw_output = open(log, 'r')
|
||||
|
||||
eout = 0.0
|
||||
sout = []
|
||||
fout = []
|
||||
reading_forces = False
|
||||
|
||||
while True:
|
||||
line = nw_output.readline()
|
||||
if not line: break
|
||||
|
||||
# pattern match for energy
|
||||
if re.search("PSPW energy",line):
|
||||
eout = float(line.split()[4])
|
||||
|
||||
# pattern match for forces
|
||||
if re.search("C\.O\.M", line):
|
||||
reading_forces = False
|
||||
if reading_forces:
|
||||
forces = line.split()
|
||||
fout += [float(forces[3]), float(forces[4]), float(forces[5])]
|
||||
if re.search("Ion Forces",line):
|
||||
reading_forces = True
|
||||
|
||||
# pattern match for stress
|
||||
if re.search("=== total gradient ===",line):
|
||||
stensor = []
|
||||
for i in range(3):
|
||||
line = nw_output.readline()
|
||||
line = line.replace("S ="," ")
|
||||
stress = line.split()
|
||||
stensor += [float(stress[1]), float(stress[2]), float(stress[3])]
|
||||
sxx = stensor[0]
|
||||
syy = stensor[4]
|
||||
szz = stensor[8]
|
||||
sxy = 0.5 * (float(stensor[1]) + float(stensor[3]))
|
||||
sxz = 0.5 * (stensor[2] + stensor[6])
|
||||
syz = 0.5 * (stensor[5] + stensor[7])
|
||||
sout = [sxx,syy,szz,sxy,sxz,syz]
|
||||
|
||||
# convert units
|
||||
hartree2eV = 27.21138602
|
||||
bohr2angstrom = 0.52917721092
|
||||
austress2bar = 294210156.97
|
||||
eout = eout * hartree2eV
|
||||
fout = [i * hartree2eV/bohr2angstrom for i in fout]
|
||||
sout = [i * austress2bar for i in sout]
|
||||
|
||||
return eout,fout,sout
|
||||
|
||||
# -------------------------------------
|
||||
# main program
|
||||
|
||||
# command-line args
|
||||
#
|
||||
if len(sys.argv) != 4:
|
||||
print("Syntax: python nwchem_wrap.py file/zmq ao/pw input_template")
|
||||
sys.exit(1)
|
||||
|
||||
comm_mode = sys.argv[1]
|
||||
basis_type = sys.argv[2]
|
||||
input_template = sys.argv[3]
|
||||
|
||||
if comm_mode == "file": cs = CSlib(1,comm_mode,"tmp.couple",None)
|
||||
elif comm_mode == "zmq": cs = CSlib(1,comm_mode,"*:5555",None)
|
||||
else:
|
||||
print("Syntax: python nwchem_wrap.py file/zmq")
|
||||
sys.exit(1)
|
||||
|
||||
|
||||
natoms = 0
|
||||
box = []
|
||||
if basis_type == "ao":
|
||||
natoms = nwchem_setup_ao(input_template)
|
||||
elif basis_type == "pw":
|
||||
natoms,box = nwchem_setup_pw(input_template)
|
||||
|
||||
# initial message for AIMD protocol
|
||||
|
||||
msgID,nfield,fieldID,fieldtype,fieldlen = cs.recv()
|
||||
if msgID != 0: error("Bad initial client/server handshake")
|
||||
protocol = cs.unpack_string(1)
|
||||
if protocol != "md": error("Mismatch in client/server protocol")
|
||||
cs.send(0,0)
|
||||
|
||||
# endless server loop
|
||||
|
||||
i = 0
|
||||
if not os.path.exists("nwchem_logs"):
|
||||
os.mkdir("nwchem_logs")
|
||||
|
||||
while 1:
|
||||
|
||||
# recv message from client
|
||||
# msgID = 0 = all-done message
|
||||
|
||||
msgID,nfield,fieldID,fieldtype,fieldlen = cs.recv()
|
||||
if msgID < 0: break
|
||||
|
||||
# SETUP receive at beginning of each run
|
||||
# required fields: DIM, PERIODICITY, ORIGIN, BOX,
|
||||
# NATOMS, COORDS
|
||||
# optional fields: others in enum above, but NWChem ignores them
|
||||
|
||||
if msgID == SETUP:
|
||||
|
||||
origin = []
|
||||
box_lmp = []
|
||||
natoms_recv = ntypes_recv = 0
|
||||
types = []
|
||||
coords = []
|
||||
|
||||
for field in fieldID:
|
||||
if field == DIM:
|
||||
dim = cs.unpack_int(DIM)
|
||||
if dim != 3: error("NWChem only performs 3d simulations")
|
||||
elif field == PERIODICITY:
|
||||
periodicity = cs.unpack(PERIODICITY,1)
|
||||
if basis_type == "ao":
|
||||
if periodicity[0] or periodicity[1] or periodicity[2]:
|
||||
error("NWChem AO basis wrapper only currently supports fully aperiodic systems")
|
||||
elif basis_type == "pw":
|
||||
if not periodicity[0] or not periodicity[1] or not periodicity[2]:
|
||||
error("NWChem PW basis wrapper only currently supports fully periodic systems")
|
||||
elif field == ORIGIN:
|
||||
origin = cs.unpack(ORIGIN,1)
|
||||
elif field == BOX:
|
||||
box_lmp = cs.unpack(BOX,1)
|
||||
if (basis_type == "pw"):
|
||||
if (box[0] != box_lmp[0] or box[1] != box_lmp[4] or box[2] != box_lmp[8]):
|
||||
error("NWChem wrapper mismatch in box dimensions")
|
||||
elif field == NATOMS:
|
||||
natoms_recv = cs.unpack_int(NATOMS)
|
||||
if natoms != natoms_recv:
|
||||
error("NWChem wrapper mismatch in number of atoms")
|
||||
elif field == COORDS:
|
||||
coords = cs.unpack(COORDS,1)
|
||||
|
||||
if not origin or not box_lmp or not natoms or not coords:
|
||||
error("Required NWChem wrapper setup field not received");
|
||||
|
||||
# STEP receive at each timestep of run or minimization
|
||||
# required fields: COORDS
|
||||
# optional fields: ORIGIN, BOX
|
||||
|
||||
elif msgID == STEP:
|
||||
|
||||
coords = []
|
||||
|
||||
for field in fieldID:
|
||||
if field == COORDS:
|
||||
coords = cs.unpack(COORDS,1)
|
||||
|
||||
if not coords: error("Required NWChem wrapper step field not received");
|
||||
|
||||
else: error("NWChem wrapper received unrecognized message")
|
||||
|
||||
# unpack coords from client
|
||||
# create NWChem input
|
||||
|
||||
if basis_type == "ao":
|
||||
nwchem_input_write_ao(input_template,coords)
|
||||
elif basis_type == "pw":
|
||||
nwchem_input_write_pw(input_template,coords,box)
|
||||
|
||||
# invoke NWChem
|
||||
|
||||
i += 1
|
||||
log = "nwchem_lammps.out"
|
||||
archive = "nwchem_logs/nwchem_lammps" + str(i) + ".out"
|
||||
cmd = nwchemcmd + " nwchem_lammps.nw > " + log
|
||||
print("\nLaunching NWChem ...")
|
||||
print(cmd)
|
||||
subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
|
||||
|
||||
shutil.copyfile(log,archive)
|
||||
|
||||
# process NWChem output
|
||||
|
||||
if basis_type == "ao":
|
||||
energy,forces = nwchem_read_ao(natoms,log)
|
||||
virial = [0,0,0,0,0,0]
|
||||
elif basis_type == "pw":
|
||||
energy,forces,virial = nwchem_read_pw(log)
|
||||
|
||||
# return forces, energy to client
|
||||
cs.send(msgID,3)
|
||||
cs.pack(FORCES,4,3*natoms,forces)
|
||||
cs.pack_double(ENERGY,energy)
|
||||
cs.pack(VIRIAL,4,6,virial)
|
||||
|
||||
# final reply to client
|
||||
|
||||
cs.send(0,0)
|
||||
|
||||
# clean-up
|
||||
|
||||
del cs
|
||||
@ -1,15 +0,0 @@
|
||||
LAMMPS W data file
|
||||
|
||||
2 atoms
|
||||
|
||||
1 atom types
|
||||
|
||||
0.0 3.16 xlo xhi
|
||||
0.0 3.16 ylo yhi
|
||||
0.0 3.16 zlo zhi
|
||||
|
||||
Atoms
|
||||
|
||||
1 1 0.000 0.000 0.000
|
||||
2 1 1.58 1.58 1.58
|
||||
|
||||
@ -1,34 +0,0 @@
|
||||
# small W unit cell for use with NWChem
|
||||
|
||||
variable mode index file
|
||||
|
||||
if "${mode} == file" then &
|
||||
"message client md file tmp.couple" &
|
||||
elif "${mode} == zmq" &
|
||||
"message client md zmq localhost:5555" &
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
units metal
|
||||
atom_style atomic
|
||||
atom_modify sort 0 0.0 map yes
|
||||
|
||||
read_data data.W
|
||||
mass 1 183.85
|
||||
|
||||
replicate $x $y $z
|
||||
|
||||
velocity all create 300.0 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 10 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all client/md
|
||||
fix_modify 2 energy yes
|
||||
|
||||
thermo 1
|
||||
run 3
|
||||
|
||||
@ -1,38 +0,0 @@
|
||||
# small W unit cell for use with NWChem
|
||||
|
||||
variable mode index file
|
||||
|
||||
if "${mode} == file" then &
|
||||
"message client md file tmp.couple" &
|
||||
elif "${mode} == zmq" &
|
||||
"message client md zmq localhost:5555" &
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
units metal
|
||||
atom_style atomic
|
||||
atom_modify sort 0 0.0 map yes
|
||||
|
||||
read_data data.W
|
||||
mass 1 183.85
|
||||
|
||||
group one id 2
|
||||
displace_atoms one move 0.1 0.2 0.3
|
||||
|
||||
replicate $x $y $z
|
||||
|
||||
velocity all create 300.0 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 10 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all client/md
|
||||
fix_modify 2 energy yes
|
||||
|
||||
dump 1 all custom 1 dump.W.min id type x y z
|
||||
|
||||
thermo 1
|
||||
minimize 1.0e-6 1.0e-6 10 50
|
||||
@ -1,76 +0,0 @@
|
||||
LAMMPS (18 Sep 2018)
|
||||
# small W unit cell for use with NWChem
|
||||
|
||||
variable mode index file
|
||||
|
||||
if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555"
|
||||
message client md file tmp.couple
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
units metal
|
||||
atom_style atomic
|
||||
atom_modify sort 0 0.0 map yes
|
||||
|
||||
read_data data.W
|
||||
orthogonal box = (0 0 0) to (3.16 3.16 3.16)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
2 atoms
|
||||
mass 1 183.85
|
||||
|
||||
replicate $x $y $z
|
||||
replicate 1 $y $z
|
||||
replicate 1 1 $z
|
||||
replicate 1 1 1
|
||||
orthogonal box = (0 0 0) to (3.16 3.16 3.16)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
2 atoms
|
||||
Time spent = 0.000187325 secs
|
||||
|
||||
velocity all create 300.0 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 10 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all client/md
|
||||
fix_modify 2 energy yes
|
||||
|
||||
thermo 1
|
||||
run 3
|
||||
Per MPI rank memory allocation (min/avg/max) = 1.8 | 1.8 | 1.8 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 300 0 0 -549.75686 36815830
|
||||
1 300 0 0 -549.75686 36815830
|
||||
2 300 0 0 -549.75686 36815830
|
||||
3 300 0 0 -549.75686 36815830
|
||||
Loop time of 0.400933 on 1 procs for 3 steps with 2 atoms
|
||||
|
||||
Performance: 0.646 ns/day, 37.123 hours/ns, 7.483 timesteps/s
|
||||
0.1% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 4.755e-06 | 4.755e-06 | 4.755e-06 | 0.0 | 0.00
|
||||
Output | 0.00010114 | 0.00010114 | 0.00010114 | 0.0 | 0.03
|
||||
Modify | 0.40082 | 0.40082 | 0.40082 | 0.0 | 99.97
|
||||
Other | | 1.232e-05 | | | 0.00
|
||||
|
||||
Nlocal: 2 ave 2 max 2 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 7 ave 7 max 7 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds not checked
|
||||
|
||||
Total wall time: 0:00:09
|
||||
@ -1,78 +0,0 @@
|
||||
LAMMPS (19 Sep 2019)
|
||||
# small W unit cell for use with NWChem
|
||||
|
||||
variable mode index file
|
||||
|
||||
if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555"
|
||||
message client md file tmp.couple
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
units metal
|
||||
atom_style atomic
|
||||
atom_modify sort 0 0.0 map yes
|
||||
|
||||
read_data data.W
|
||||
orthogonal box = (0 0 0) to (3.16 3.16 3.16)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
2 atoms
|
||||
read_data CPU = 0.0014801 secs
|
||||
mass 1 183.85
|
||||
|
||||
replicate $x $y $z
|
||||
replicate 1 $y $z
|
||||
replicate 1 1 $z
|
||||
replicate 1 1 1
|
||||
orthogonal box = (0 0 0) to (3.16 3.16 3.16)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
2 atoms
|
||||
replicate CPU = 0.000123978 secs
|
||||
|
||||
velocity all create 300.0 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 10 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all client/md
|
||||
fix_modify 2 energy yes
|
||||
|
||||
thermo 1
|
||||
run 3
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:166)
|
||||
Per MPI rank memory allocation (min/avg/max) = 1.801 | 1.801 | 1.801 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 300 0 0 -549.75686 36815830
|
||||
1 298.93216 0 0 -549.75686 36815825
|
||||
2 295.76254 0 0 -549.75687 36814830
|
||||
3 290.55935 0 0 -549.75687 36811865
|
||||
Loop time of 2.60414 on 1 procs for 3 steps with 2 atoms
|
||||
|
||||
Performance: 0.100 ns/day, 241.124 hours/ns, 1.152 timesteps/s
|
||||
0.0% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 7.1526e-06 | 7.1526e-06 | 7.1526e-06 | 0.0 | 0.00
|
||||
Output | 0.00012779 | 0.00012779 | 0.00012779 | 0.0 | 0.00
|
||||
Modify | 2.604 | 2.604 | 2.604 | 0.0 | 99.99
|
||||
Other | | 9.06e-06 | | | 0.00
|
||||
|
||||
Nlocal: 2 ave 2 max 2 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 7 ave 7 max 7 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
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds not checked
|
||||
|
||||
Total wall time: 0:00:05
|
||||
@ -1,92 +0,0 @@
|
||||
LAMMPS (19 Sep 2019)
|
||||
# small W unit cell for use with NWChem
|
||||
|
||||
variable mode index file
|
||||
|
||||
if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555"
|
||||
message client md file tmp.couple
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
units metal
|
||||
atom_style atomic
|
||||
atom_modify sort 0 0.0 map yes
|
||||
|
||||
read_data data.W
|
||||
orthogonal box = (0 0 0) to (3.16 3.16 3.16)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
2 atoms
|
||||
read_data CPU = 0.00183487 secs
|
||||
mass 1 183.85
|
||||
|
||||
group one id 2
|
||||
1 atoms in group one
|
||||
displace_atoms one move 0.1 0.2 0.3
|
||||
|
||||
replicate $x $y $z
|
||||
replicate 1 $y $z
|
||||
replicate 1 1 $z
|
||||
replicate 1 1 1
|
||||
orthogonal box = (0 0 0) to (3.16 3.16 3.16)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
2 atoms
|
||||
replicate CPU = 0.000159979 secs
|
||||
|
||||
velocity all create 300.0 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 10 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all client/md
|
||||
fix_modify 2 energy yes
|
||||
|
||||
dump 1 all custom 1 tmp.dump id type x y z
|
||||
|
||||
thermo 1
|
||||
minimize 1.0e-6 1.0e-6 10 50
|
||||
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:174)
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:166)
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.676 | 4.676 | 4.676 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 300 0 0 -547.52142 28510277
|
||||
1 300 0 0 -549.43104 35614471
|
||||
2 300 0 0 -549.75661 36815830
|
||||
3 300 0 0 -549.75662 36815830
|
||||
Loop time of 7.71121 on 1 procs for 3 steps with 2 atoms
|
||||
|
||||
0.0% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = energy tolerance
|
||||
Energy initial, next-to-last, final =
|
||||
-547.560202518 -549.795386038 -549.795398827
|
||||
Force two-norm initial, final = 16.0041 0.00108353
|
||||
Force max component initial, final = 9.57978 0.000719909
|
||||
Final line search alpha, max atom move = 1 0.000719909
|
||||
Iterations, force evaluations = 3 5
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 9.5367e-07 | 9.5367e-07 | 9.5367e-07 | 0.0 | 0.00
|
||||
Comm | 1.3113e-05 | 1.3113e-05 | 1.3113e-05 | 0.0 | 0.00
|
||||
Output | 0.00017023 | 0.00017023 | 0.00017023 | 0.0 | 0.00
|
||||
Modify | 7.7109 | 7.7109 | 7.7109 | 0.0 |100.00
|
||||
Other | | 0.0001729 | | | 0.00
|
||||
|
||||
Nlocal: 2 ave 2 max 2 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 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
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 1
|
||||
Dangerous builds not checked
|
||||
Total wall time: 0:00:19
|
||||
File diff suppressed because it is too large
Load Diff
@ -1,817 +0,0 @@
|
||||
argument 1 = nwchem_lammps.nw
|
||||
|
||||
|
||||
|
||||
============================== echo of input deck ==============================
|
||||
echo
|
||||
|
||||
#**** Enter the geometry using fractional coordinates ****
|
||||
geometry units angstrom noautosym
|
||||
system crystal
|
||||
lat_a 3.16d0
|
||||
lat_b 3.16d0
|
||||
lat_c 3.16d0
|
||||
end
|
||||
W 0.999335 0.99967 0.998875
|
||||
W 0.500665 0.50033 0.501125
|
||||
end
|
||||
|
||||
nwpw
|
||||
vectors input nwchem_lammps.movecs
|
||||
end
|
||||
|
||||
#***** setup the nwpw gamma point code ****
|
||||
nwpw
|
||||
simulation_cell
|
||||
ngrid 16 16 16
|
||||
end
|
||||
ewald_ncut 8
|
||||
mulliken
|
||||
lcao #old default
|
||||
end
|
||||
|
||||
nwpw
|
||||
tolerances 1.0d-9 1.0d-9
|
||||
end
|
||||
|
||||
task pspw stress
|
||||
================================================================================
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
Northwest Computational Chemistry Package (NWChem) 6.8
|
||||
------------------------------------------------------
|
||||
|
||||
|
||||
Environmental Molecular Sciences Laboratory
|
||||
Pacific Northwest National Laboratory
|
||||
Richland, WA 99352
|
||||
|
||||
Copyright (c) 1994-2018
|
||||
Pacific Northwest National Laboratory
|
||||
Battelle Memorial Institute
|
||||
|
||||
NWChem is an open-source computational chemistry package
|
||||
distributed under the terms of the
|
||||
Educational Community License (ECL) 2.0
|
||||
A copy of the license is included with this distribution
|
||||
in the LICENSE.TXT file
|
||||
|
||||
ACKNOWLEDGMENT
|
||||
--------------
|
||||
|
||||
This software and its documentation were developed at the
|
||||
EMSL at Pacific Northwest National Laboratory, a multiprogram
|
||||
national laboratory, operated for the U.S. Department of Energy
|
||||
by Battelle under Contract Number DE-AC05-76RL01830. Support
|
||||
for this work was provided by the Department of Energy Office
|
||||
of Biological and Environmental Research, Office of Basic
|
||||
Energy Sciences, and the Office of Advanced Scientific Computing.
|
||||
|
||||
|
||||
Job information
|
||||
---------------
|
||||
|
||||
hostname = singsing
|
||||
program = /home/sjplimp/tools/nwchem-6.8.1-release/bin/LINUX64/nwchem
|
||||
date = Thu Oct 3 16:57:17 2019
|
||||
|
||||
compiled = Wed_Oct_02_09:25:27_2019
|
||||
source = /home/sjplimp/tools/nwchem-6.8.1-release
|
||||
nwchem branch = Development
|
||||
nwchem revision = N/A
|
||||
ga revision = 5.6.5
|
||||
use scalapack = F
|
||||
input = nwchem_lammps.nw
|
||||
prefix = nwchem_lammps.
|
||||
data base = ./nwchem_lammps.db
|
||||
status = restart
|
||||
nproc = 1
|
||||
time left = -1s
|
||||
|
||||
|
||||
|
||||
Memory information
|
||||
------------------
|
||||
|
||||
heap = 13107200 doubles = 100.0 Mbytes
|
||||
stack = 13107197 doubles = 100.0 Mbytes
|
||||
global = 26214400 doubles = 200.0 Mbytes (distinct from heap & stack)
|
||||
total = 52428797 doubles = 400.0 Mbytes
|
||||
verify = yes
|
||||
hardfail = no
|
||||
|
||||
|
||||
Directory information
|
||||
---------------------
|
||||
|
||||
0 permanent = .
|
||||
0 scratch = .
|
||||
|
||||
|
||||
Previous task information
|
||||
-------------------------
|
||||
|
||||
Theory = pspw
|
||||
Operation = stress
|
||||
Status = unknown
|
||||
Qmmm = F
|
||||
Ignore = F
|
||||
|
||||
|
||||
Geometries in the database
|
||||
--------------------------
|
||||
|
||||
Name Natoms Last Modified
|
||||
-------------------------------- ------ ------------------------
|
||||
1 geometry 2 Thu Oct 3 16:57:16 2019
|
||||
|
||||
The geometry named "geometry" is the default for restart
|
||||
|
||||
|
||||
|
||||
Basis sets in the database
|
||||
--------------------------
|
||||
|
||||
There are no basis sets in the database
|
||||
|
||||
|
||||
|
||||
NWChem Input Module
|
||||
-------------------
|
||||
|
||||
|
||||
|
||||
!!!!!!!!! geom_3d NEEDS TESTING !!!!!!!!!!
|
||||
|
||||
|
||||
Geometry "geometry" -> ""
|
||||
-------------------------
|
||||
|
||||
Output coordinates in angstroms (scale by 1.889725989 to convert to a.u.)
|
||||
|
||||
No. Tag Charge X Y Z
|
||||
---- ---------------- ---------- -------------- -------------- --------------
|
||||
1 W 74.0000 3.15789860 3.15895720 3.15644500
|
||||
2 W 74.0000 1.58210140 1.58104280 1.58355500
|
||||
|
||||
Lattice Parameters
|
||||
------------------
|
||||
|
||||
lattice vectors in angstroms (scale by 1.889725989 to convert to a.u.)
|
||||
|
||||
a1=< 3.160 0.000 0.000 >
|
||||
a2=< 0.000 3.160 0.000 >
|
||||
a3=< 0.000 0.000 3.160 >
|
||||
a= 3.160 b= 3.160 c= 3.160
|
||||
alpha= 90.000 beta= 90.000 gamma= 90.000
|
||||
omega= 31.6
|
||||
|
||||
reciprocal lattice vectors in a.u.
|
||||
|
||||
b1=< 1.052 0.000 -0.000 >
|
||||
b2=< -0.000 1.052 -0.000 >
|
||||
b3=< 0.000 0.000 1.052 >
|
||||
|
||||
Atomic Mass
|
||||
-----------
|
||||
|
||||
W 183.951000
|
||||
|
||||
|
||||
|
||||
XYZ format geometry
|
||||
-------------------
|
||||
2
|
||||
geometry
|
||||
W 3.15789860 3.15895720 3.15644500
|
||||
W 1.58210140 1.58104280 1.58355500
|
||||
|
||||
==============================================================================
|
||||
internuclear distances
|
||||
------------------------------------------------------------------------------
|
||||
center one | center two | atomic units | angstroms
|
||||
------------------------------------------------------------------------------
|
||||
2 W | 1 W | 5.15689 | 2.72891
|
||||
------------------------------------------------------------------------------
|
||||
number of included internuclear distances: 1
|
||||
==============================================================================
|
||||
|
||||
|
||||
|
||||
>>>> PSPW Parallel Module - stress <<<<
|
||||
****************************************************
|
||||
* *
|
||||
* NWPW PSPW Calculation *
|
||||
* *
|
||||
* [ (Grassmann/Stiefel manifold implementation) ] *
|
||||
* *
|
||||
* [ NorthWest Chemistry implementation ] *
|
||||
* *
|
||||
* version #5.10 06/12/02 *
|
||||
* *
|
||||
* This code was developed by Eric J. Bylaska, *
|
||||
* and was based upon algorithms and code *
|
||||
* developed by the group of Prof. John H. Weare *
|
||||
* *
|
||||
****************************************************
|
||||
>>> JOB STARTED AT Thu Oct 3 16:57:17 2019 <<<
|
||||
================ input data ========================
|
||||
|
||||
input psi filename:./nwchem_lammps.movecs
|
||||
|
||||
initializing pspw_APC data structure
|
||||
------------------------------------
|
||||
nga, ngs: 3 6
|
||||
Gc : 2.5000000000000000
|
||||
APC gamma: 1 0.59999999999999998
|
||||
APC gamma: 2 0.90000000000000002
|
||||
APC gamma: 3 1.3500000000000001
|
||||
|
||||
number of processors used: 1
|
||||
processor grid : 1 x 1
|
||||
parallel mapping :2d hilbert
|
||||
parallel mapping : balanced
|
||||
number of threads : 1
|
||||
parallel io : off
|
||||
|
||||
options:
|
||||
boundary conditions = periodic (version3)
|
||||
electron spin = restricted
|
||||
exchange-correlation = LDA (Vosko et al) parameterization
|
||||
|
||||
elements involved in the cluster:
|
||||
1: W valence charge: 6.0000 lmax= 2
|
||||
comment : Troullier-Martins pseudopotential
|
||||
pseudpotential type : 0
|
||||
highest angular component : 2
|
||||
local potential used : 0
|
||||
number of non-local projections: 8
|
||||
semicore corrections included : 1.800 (radius) 4.538 (charge)
|
||||
cutoff = 2.389 3.185 2.244
|
||||
|
||||
|
||||
total charge: 0.000
|
||||
|
||||
atomic composition:
|
||||
W : 2
|
||||
|
||||
number of electrons: spin up= 6 ( 6 per task) down= 6 ( 6 per task) (Fourier space)
|
||||
number of orbitals : spin up= 6 ( 6 per task) down= 6 ( 6 per task) (Fourier space)
|
||||
|
||||
supercell:
|
||||
cell_name: cell_default
|
||||
lattice: a1=< 5.972 0.000 0.000 >
|
||||
a2=< 0.000 5.972 0.000 >
|
||||
a3=< 0.000 0.000 5.972 >
|
||||
reciprocal: b1=< 1.052 0.000 -0.000 >
|
||||
b2=< -0.000 1.052 -0.000 >
|
||||
b3=< 0.000 0.000 1.052 >
|
||||
lattice: a= 5.972 b= 5.972 c= 5.972
|
||||
alpha= 90.000 beta= 90.000 gamma= 90.000
|
||||
omega= 212.9
|
||||
|
||||
density cutoff= 35.427 fft= 16x 16x 16( 1052 waves 1052 per task)
|
||||
wavefnc cutoff= 35.427 fft= 16x 16x 16( 1052 waves 1052 per task)
|
||||
Ewald summation: cut radius= 1.90 and 8
|
||||
Madelung Wigner-Seitz= 1.76011888 (alpha= 2.83729748 rs= 3.70444413)
|
||||
|
||||
technical parameters:
|
||||
time step= 5.80 fictitious mass= 400000.0
|
||||
tolerance=0.100E-08 (energy) 0.100E-08 (density)
|
||||
maximum iterations = 1000 ( 10 inner 100 outer )
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
== Energy Calculation ==
|
||||
|
||||
|
||||
====== Grassmann conjugate gradient iteration ======
|
||||
>>> ITERATION STARTED AT Thu Oct 3 16:57:17 2019 <<<
|
||||
iter. Energy DeltaE DeltaRho
|
||||
------------------------------------------------------
|
||||
10 -0.2020457267E+02 -0.12753E-06 0.54770E-09
|
||||
20 -0.2020457281E+02 -0.96520E-09 0.65680E-11
|
||||
*** tolerance ok. iteration terminated
|
||||
>>> ITERATION ENDED AT Thu Oct 3 16:57:18 2019 <<<
|
||||
|
||||
|
||||
== Summary Of Results ==
|
||||
|
||||
number of electrons: spin up= 6.00000 down= 6.00000 (real space)
|
||||
|
||||
total energy : -0.2020457281E+02 ( -0.10102E+02/ion)
|
||||
total orbital energy: 0.5093546150E+01 ( 0.84892E+00/electron)
|
||||
hartree energy : 0.2903382088E+00 ( 0.48390E-01/electron)
|
||||
exc-corr energy : -0.9445078100E+01 ( -0.15742E+01/electron)
|
||||
ion-ion energy : -0.2193939674E+02 ( -0.10970E+02/ion)
|
||||
|
||||
kinetic (planewave) : 0.1441586264E+02 ( 0.24026E+01/electron)
|
||||
V_local (planewave) : 0.1156111351E+02 ( 0.19269E+01/electron)
|
||||
V_nl (planewave) : -0.1508741234E+02 ( -0.25146E+01/electron)
|
||||
V_Coul (planewave) : 0.5806764176E+00 ( 0.96779E-01/electron)
|
||||
V_xc. (planewave) : -0.6376694082E+01 ( -0.10628E+01/electron)
|
||||
Virial Coefficient : -0.6466707350E+00
|
||||
|
||||
orbital energies:
|
||||
0.5414291E+00 ( 14.733eV)
|
||||
0.5414285E+00 ( 14.733eV)
|
||||
0.5414070E+00 ( 14.733eV)
|
||||
0.3596871E+00 ( 9.788eV)
|
||||
0.3596781E+00 ( 9.787eV)
|
||||
0.2031433E+00 ( 5.528eV)
|
||||
|
||||
Total PSPW energy : -0.2020457281E+02
|
||||
|
||||
|
||||
=== Spin Contamination ===
|
||||
|
||||
<Sexact^2> = 0.0000000000000000
|
||||
<S^2> = 0.0000000000000000
|
||||
|
||||
|
||||
|
||||
== Center of Charge ==
|
||||
|
||||
spin up ( -0.0030, -0.0015, -0.0050 )
|
||||
spin down ( -0.0030, -0.0015, -0.0050 )
|
||||
total ( -0.0030, -0.0015, -0.0050 )
|
||||
ionic ( -1.4929, -1.4929, -1.4929 )
|
||||
|
||||
|
||||
== Molecular Dipole wrt Center of Mass ==
|
||||
|
||||
mu = ( -17.8792, -17.8970, -17.8547 ) au
|
||||
|mu| = 30.9638 au, 78.6976 Debye
|
||||
|
||||
|
||||
Translation force removed: ( -0.00000 -0.00000 -0.00000)
|
||||
|
||||
|
||||
============= Ion Gradients =================
|
||||
Ion Forces:
|
||||
1 W ( 0.002737 0.001358 0.004631 )
|
||||
2 W ( -0.002737 -0.001358 -0.004631 )
|
||||
C.O.M. ( 0.000000 0.000000 0.000000 )
|
||||
===============================================
|
||||
|F| = 0.784689E-02
|
||||
|F|/nion = 0.392344E-02
|
||||
max|Fatom|= 0.554859E-02 ( 0.285eV/Angstrom)
|
||||
|
||||
|
||||
|
||||
|
||||
======================
|
||||
= Stress calculation =
|
||||
======================
|
||||
|
||||
|
||||
============= total gradient ==============
|
||||
S = ( 0.12512 0.00000 0.00000 )
|
||||
( 0.00000 0.12512 0.00001 )
|
||||
( 0.00000 0.00001 0.12511 )
|
||||
===================================================
|
||||
|S| = 0.21671E+00
|
||||
pressure = 0.125E+00 au
|
||||
= 0.368E+02 Mbar
|
||||
= 0.368E+04 GPa
|
||||
= 0.363E+08 atm
|
||||
|
||||
|
||||
dE/da = 0.12512
|
||||
dE/db = 0.12512
|
||||
dE/dc = 0.12511
|
||||
dE/dalpha = -0.00003
|
||||
dE/dbeta = -0.00002
|
||||
dE/dgamma = -0.00001
|
||||
|
||||
|
||||
|
||||
|
||||
*************************************************************
|
||||
** **
|
||||
** PSPW Mulliken analysis **
|
||||
** **
|
||||
** Population analysis algorithm devloped by Ryoichi Kawai **
|
||||
** **
|
||||
** Thu Oct 3 16:57 **
|
||||
** **
|
||||
*************************************************************
|
||||
|
||||
|
||||
== XYZ OUTPUT ==
|
||||
|
||||
|
||||
2
|
||||
|
||||
W -0.002101 -0.001043 -0.003555
|
||||
W -1.577898 -1.578956 -1.576444
|
||||
|
||||
|
||||
== Atomic Orbital Expansion ==
|
||||
|
||||
W nodamping
|
||||
|
||||
|
||||
=====================================================
|
||||
| POPULATION ANALYSIS OF FILLED MOLECULAR ORBITALS |
|
||||
=====================================================
|
||||
|
||||
|
||||
== Using pseudoatomic orbital expansion ==
|
||||
|
||||
|
||||
------------------------------------------------------------------------------
|
||||
|
||||
|
||||
*** ORBITAL= 1*** SPIN=BOTH SUM= 0.12471E+01 E= 0.54143E+00 ( 14.733eV)
|
||||
|
||||
NO ATOM L POPULATION
|
||||
s
|
||||
1 W 0 0.00000 0.00000
|
||||
px pz py
|
||||
1 W 1 0.00000 -0.00018 -0.00011 0.00005
|
||||
dx2-y2 dzx d3z2-1 dyz dxy
|
||||
1 W 2 0.49999 0.00003 -0.68532 0.00001 0.10591 0.13824
|
||||
fx(x2-3y2) fz(5z2-1) fx(5z2-1) fz(5z2-3) fy(5z2-1) fxyz fy(3x2-y2)
|
||||
1 W 3 0.00001 -0.00003 -0.00187 -0.00238 -0.00028 0.00001 0.00000 -0.00017
|
||||
s
|
||||
2 W 0 0.00000 0.00000
|
||||
px pz py
|
||||
2 W 1 0.00000 0.00018 0.00011 -0.00005
|
||||
dx2-y2 dzx d3z2-1 dyz dxy
|
||||
2 W 2 0.49999 0.00003 -0.68532 0.00001 0.10591 0.13824
|
||||
fx(x2-3y2) fz(5z2-1) fx(5z2-1) fz(5z2-3) fy(5z2-1) fxyz fy(3x2-y2)
|
||||
2 W 3 0.00001 -0.00003 0.00187 0.00238 0.00028 -0.00001 -0.00000 0.00017
|
||||
|
||||
|
||||
=== DISTRIBUTION ===
|
||||
|
||||
1(W ) 0.5000 2(W ) 0.5000
|
||||
|
||||
|
||||
== ANGULAR MOMENTUM POPULATIONS ===
|
||||
|
||||
s p d f
|
||||
0.0000 0.0000 1.0000 0.0000
|
||||
|
||||
|
||||
------------------------------------------------------------------------------
|
||||
|
||||
|
||||
*** ORBITAL= 2*** SPIN=BOTH SUM= 0.12472E+01 E= 0.54143E+00 ( 14.733eV)
|
||||
|
||||
NO ATOM L POPULATION
|
||||
s
|
||||
1 W 0 0.00000 0.00000
|
||||
px pz py
|
||||
1 W 1 0.00000 0.00002 -0.00005 -0.00011
|
||||
dx2-y2 dzx d3z2-1 dyz dxy
|
||||
1 W 2 0.49998 -0.00001 -0.02322 0.00001 -0.61187 0.35363
|
||||
fx(x2-3y2) fz(5z2-1) fx(5z2-1) fz(5z2-3) fy(5z2-1) fxyz fy(3x2-y2)
|
||||
1 W 3 0.00002 -0.00001 0.00071 -0.00049 -0.00015 -0.00283 0.00006 0.00266
|
||||
s
|
||||
2 W 0 0.00000 0.00000
|
||||
px pz py
|
||||
2 W 1 0.00000 -0.00002 0.00005 0.00011
|
||||
dx2-y2 dzx d3z2-1 dyz dxy
|
||||
2 W 2 0.49998 -0.00001 -0.02322 0.00001 -0.61187 0.35363
|
||||
fx(x2-3y2) fz(5z2-1) fx(5z2-1) fz(5z2-3) fy(5z2-1) fxyz fy(3x2-y2)
|
||||
2 W 3 0.00002 -0.00001 -0.00071 0.00049 0.00015 0.00283 -0.00006 -0.00266
|
||||
|
||||
|
||||
=== DISTRIBUTION ===
|
||||
|
||||
1(W ) 0.5000 2(W ) 0.5000
|
||||
|
||||
|
||||
== ANGULAR MOMENTUM POPULATIONS ===
|
||||
|
||||
s p d f
|
||||
0.0000 0.0000 1.0000 0.0000
|
||||
|
||||
|
||||
------------------------------------------------------------------------------
|
||||
|
||||
|
||||
*** ORBITAL= 3*** SPIN=BOTH SUM= 0.12472E+01 E= 0.54141E+00 ( 14.733eV)
|
||||
|
||||
NO ATOM L POPULATION
|
||||
s
|
||||
1 W 0 0.00000 -0.00000
|
||||
px pz py
|
||||
1 W 1 0.00000 0.00010 0.00006 0.00020
|
||||
dx2-y2 dzx d3z2-1 dyz dxy
|
||||
1 W 2 0.49999 0.00000 0.17259 0.00000 0.33820 0.59651
|
||||
fx(x2-3y2) fz(5z2-1) fx(5z2-1) fz(5z2-3) fy(5z2-1) fxyz fy(3x2-y2)
|
||||
1 W 3 0.00001 0.00000 0.00001 -0.00015 0.00015 -0.00033 -0.00325 -0.00033
|
||||
s
|
||||
2 W 0 0.00000 -0.00000
|
||||
px pz py
|
||||
2 W 1 0.00000 -0.00010 -0.00006 -0.00020
|
||||
dx2-y2 dzx d3z2-1 dyz dxy
|
||||
2 W 2 0.49999 0.00000 0.17259 0.00000 0.33820 0.59651
|
||||
fx(x2-3y2) fz(5z2-1) fx(5z2-1) fz(5z2-3) fy(5z2-1) fxyz fy(3x2-y2)
|
||||
2 W 3 0.00001 0.00000 -0.00001 0.00015 -0.00015 0.00033 0.00325 0.00033
|
||||
|
||||
|
||||
=== DISTRIBUTION ===
|
||||
|
||||
1(W ) 0.5000 2(W ) 0.5000
|
||||
|
||||
|
||||
== ANGULAR MOMENTUM POPULATIONS ===
|
||||
|
||||
s p d f
|
||||
0.0000 0.0000 1.0000 0.0000
|
||||
|
||||
|
||||
------------------------------------------------------------------------------
|
||||
|
||||
|
||||
*** ORBITAL= 4*** SPIN=BOTH SUM= 0.14577E+01 E= 0.35969E+00 ( 9.788eV)
|
||||
|
||||
NO ATOM L POPULATION
|
||||
s
|
||||
1 W 0 0.00000 -0.00000
|
||||
px pz py
|
||||
1 W 1 0.00002 0.00162 -0.00440 0.00049
|
||||
dx2-y2 dzx d3z2-1 dyz dxy
|
||||
1 W 2 0.48998 -0.09896 0.00001 0.69296 0.00001 -0.00001
|
||||
fx(x2-3y2) fz(5z2-1) fx(5z2-1) fz(5z2-3) fy(5z2-1) fxyz fy(3x2-y2)
|
||||
1 W 3 0.00999 -0.09993 0.00031 -0.00131 -0.00234 -0.00064 0.00000 0.00022
|
||||
s
|
||||
2 W 0 0.00000 0.00000
|
||||
px pz py
|
||||
2 W 1 0.00002 0.00162 -0.00440 0.00049
|
||||
dx2-y2 dzx d3z2-1 dyz dxy
|
||||
2 W 2 0.48998 0.09896 -0.00001 -0.69296 -0.00001 0.00001
|
||||
fx(x2-3y2) fz(5z2-1) fx(5z2-1) fz(5z2-3) fy(5z2-1) fxyz fy(3x2-y2)
|
||||
2 W 3 0.00999 0.09993 0.00031 -0.00131 -0.00234 -0.00064 0.00000 0.00022
|
||||
|
||||
|
||||
=== DISTRIBUTION ===
|
||||
|
||||
1(W ) 0.5000 2(W ) 0.5000
|
||||
|
||||
|
||||
== ANGULAR MOMENTUM POPULATIONS ===
|
||||
|
||||
s p d f
|
||||
0.0000 0.0000 0.9800 0.0200
|
||||
|
||||
|
||||
------------------------------------------------------------------------------
|
||||
|
||||
|
||||
*** ORBITAL= 5*** SPIN=BOTH SUM= 0.14616E+01 E= 0.35968E+00 ( 9.787eV)
|
||||
|
||||
NO ATOM L POPULATION
|
||||
s
|
||||
1 W 0 0.00000 0.00000
|
||||
px pz py
|
||||
1 W 1 0.00001 0.00206 0.00063 -0.00121
|
||||
dx2-y2 dzx d3z2-1 dyz dxy
|
||||
1 W 2 0.48871 -0.69206 -0.00002 -0.09883 0.00001 0.00000
|
||||
fx(x2-3y2) fz(5z2-1) fx(5z2-1) fz(5z2-3) fy(5z2-1) fxyz fy(3x2-y2)
|
||||
1 W 3 0.01129 -0.10621 0.00214 0.00009 0.00033 0.00014 0.00000 0.00063
|
||||
s
|
||||
2 W 0 0.00000 -0.00000
|
||||
px pz py
|
||||
2 W 1 0.00001 0.00206 0.00063 -0.00121
|
||||
dx2-y2 dzx d3z2-1 dyz dxy
|
||||
2 W 2 0.48871 0.69206 0.00002 0.09883 -0.00001 -0.00000
|
||||
fx(x2-3y2) fz(5z2-1) fx(5z2-1) fz(5z2-3) fy(5z2-1) fxyz fy(3x2-y2)
|
||||
2 W 3 0.01129 0.10621 0.00214 0.00009 0.00033 0.00014 0.00000 0.00063
|
||||
|
||||
|
||||
=== DISTRIBUTION ===
|
||||
|
||||
1(W ) 0.5000 2(W ) 0.5000
|
||||
|
||||
|
||||
== ANGULAR MOMENTUM POPULATIONS ===
|
||||
|
||||
s p d f
|
||||
0.0000 0.0000 0.9774 0.0226
|
||||
|
||||
|
||||
------------------------------------------------------------------------------
|
||||
|
||||
|
||||
*** ORBITAL= 6*** SPIN=BOTH SUM= 0.19540E+01 E= 0.20314E+00 ( 5.528eV)
|
||||
|
||||
NO ATOM L POPULATION
|
||||
s
|
||||
1 W 0 0.49974 -0.70692
|
||||
px pz py
|
||||
1 W 1 0.00000 0.00028 0.00047 0.00014
|
||||
dx2-y2 dzx d3z2-1 dyz dxy
|
||||
1 W 2 0.00000 -0.00000 -0.00000 -0.00000 -0.00000 -0.00000
|
||||
fx(x2-3y2) fz(5z2-1) fx(5z2-1) fz(5z2-3) fy(5z2-1) fxyz fy(3x2-y2)
|
||||
1 W 3 0.00026 0.01609 -0.00000 -0.00007 0.00021 -0.00003 0.00000 -0.00004
|
||||
s
|
||||
2 W 0 0.49974 -0.70692
|
||||
px pz py
|
||||
2 W 1 0.00000 -0.00028 -0.00047 -0.00014
|
||||
dx2-y2 dzx d3z2-1 dyz dxy
|
||||
2 W 2 0.00000 -0.00000 -0.00000 -0.00000 -0.00000 -0.00000
|
||||
fx(x2-3y2) fz(5z2-1) fx(5z2-1) fz(5z2-3) fy(5z2-1) fxyz fy(3x2-y2)
|
||||
2 W 3 0.00026 0.01609 0.00000 0.00007 -0.00021 0.00003 -0.00000 0.00004
|
||||
|
||||
|
||||
=== DISTRIBUTION ===
|
||||
|
||||
1(W ) 0.5000 2(W ) 0.5000
|
||||
|
||||
|
||||
== ANGULAR MOMENTUM POPULATIONS ===
|
||||
|
||||
s p d f
|
||||
0.9995 0.0000 0.0000 0.0005
|
||||
|
||||
|
||||
========================================
|
||||
| POPULATION ANALYSIS ON EACH ATOM |
|
||||
========================================
|
||||
|
||||
|
||||
NO ATOM SPIN TOTAL s p d f
|
||||
1 W UP 3.00000 0.49974 0.00003 2.47866 0.02157
|
||||
1 W DOWN 3.00000 0.49974 0.00003 2.47866 0.02157
|
||||
2 W UP 3.00000 0.49974 0.00003 2.47866 0.02157
|
||||
2 W DOWN 3.00000 0.49974 0.00003 2.47866 0.02157
|
||||
|
||||
|
||||
|
||||
=== TOTAL ANGULAR MOMENTUM POPULATION ===
|
||||
|
||||
SPIN s p d f
|
||||
UP 16.66% 0.00% 82.62% 0.72%
|
||||
UP 16.66% 0.00% 82.62% 0.72%
|
||||
TOTAL 16.66% 0.00% 82.62% 0.72%
|
||||
|
||||
*************************************************************
|
||||
** **
|
||||
** PSPW Atomic Point Charge (APC) Analysis **
|
||||
** **
|
||||
** Point charge analysis based on paper by P.E. Blochl **
|
||||
** (J. Chem. Phys. vol 103, page 7422, 1995) **
|
||||
** **
|
||||
*************************************************************
|
||||
|
||||
pspw_APC data structure
|
||||
-----------------------
|
||||
nga, ngs: 3 6
|
||||
Gc : 2.5000000000000000
|
||||
APC gamma: 1 0.59999999999999998
|
||||
APC gamma: 2 0.90000000000000002
|
||||
APC gamma: 3 1.3500000000000001
|
||||
|
||||
charge analysis on each atom
|
||||
----------------------------
|
||||
|
||||
no atom Qelc Qion Qtotal
|
||||
-- ---- ------- ------- -------
|
||||
1 W -6.000 6.000 -0.000
|
||||
2 W -6.000 6.000 -0.000
|
||||
Total Q -12.000 12.000 -0.000
|
||||
|
||||
|
||||
gaussian coefficients of model density
|
||||
--------------------------------------
|
||||
|
||||
no atom g=0.000 g=0.600 g=0.900 g=1.350
|
||||
-- ---- ------- ------- ------- -------
|
||||
1 W 6.000 -7.235 17.653 -16.419
|
||||
2 W 6.000 -7.235 17.653 -16.419
|
||||
|
||||
|
||||
=== Electric Field at Atoms ===
|
||||
|
||||
1 W Atomic Electric Field =( -0.00022 -0.00011 -0.00038 )
|
||||
(ion) =( 0.00094 0.00047 0.00159 )
|
||||
(electronic) =( -0.00116 -0.00058 -0.00197 )
|
||||
2 W Atomic Electric Field =( 0.00022 0.00011 0.00038 )
|
||||
(ion) =( -0.00094 -0.00047 -0.00159 )
|
||||
(electronic) =( 0.00116 0.00058 0.00197 )
|
||||
|
||||
output psi filename:./nwchem_lammps.movecs
|
||||
|
||||
|
||||
== Timing ==
|
||||
|
||||
cputime in seconds
|
||||
prologue : 0.114428E+00
|
||||
main loop : 0.475396E+00
|
||||
epilogue : 0.316691E-01
|
||||
total : 0.621493E+00
|
||||
cputime/step: 0.559289E-02 ( 85 evalulations, 20 linesearches)
|
||||
|
||||
|
||||
Time spent doing total step percent
|
||||
total time : 0.623259E+00 0.733246E-02 100.0 %
|
||||
i/o time : 0.103071E-01 0.121260E-03 1.7 %
|
||||
FFTs : 0.348712E-01 0.410250E-03 5.6 %
|
||||
dot products : 0.981057E-02 0.115418E-03 1.6 %
|
||||
geodesic : 0.696999E-01 0.819999E-03 11.2 %
|
||||
ffm_dgemm : 0.104145E-02 0.122523E-04 0.2 %
|
||||
fmf_dgemm : 0.565297E-01 0.665055E-03 9.1 %
|
||||
mmm_dgemm : 0.129490E-03 0.152342E-05 0.0 %
|
||||
m_diagonalize : 0.701885E-03 0.825747E-05 0.1 %
|
||||
exchange correlation : 0.764353E-01 0.899239E-03 12.3 %
|
||||
local pseudopotentials : 0.439882E-03 0.517509E-05 0.1 %
|
||||
non-local pseudopotentials : 0.271890E-01 0.319871E-03 4.4 %
|
||||
hartree potentials : 0.202482E-02 0.238214E-04 0.3 %
|
||||
ion-ion interaction : 0.104062E+00 0.122426E-02 16.7 %
|
||||
structure factors : 0.152984E-01 0.179981E-03 2.5 %
|
||||
phase factors : 0.107278E-04 0.126210E-06 0.0 %
|
||||
masking and packing : 0.304392E-01 0.358108E-03 4.9 %
|
||||
queue fft : 0.111536E+00 0.131219E-02 17.9 %
|
||||
queue fft (serial) : 0.708244E-01 0.833228E-03 11.4 %
|
||||
queue fft (message passing): 0.360800E-01 0.424470E-03 5.8 %
|
||||
non-local psp FFM : 0.860008E-02 0.101177E-03 1.4 %
|
||||
non-local psp FMF : 0.111482E-01 0.131155E-03 1.8 %
|
||||
non-local psp FFM A : 0.214632E-02 0.252509E-04 0.3 %
|
||||
non-local psp FFM B : 0.560879E-02 0.659858E-04 0.9 %
|
||||
|
||||
>>> JOB COMPLETED AT Thu Oct 3 16:57:18 2019 <<<
|
||||
|
||||
Task times cpu: 0.6s wall: 0.6s
|
||||
Summary of allocated global arrays
|
||||
-----------------------------------
|
||||
No active global arrays
|
||||
|
||||
|
||||
|
||||
GA Statistics for process 0
|
||||
------------------------------
|
||||
|
||||
create destroy get put acc scatter gather read&inc
|
||||
calls: 0 0 0 0 0 0 0 0
|
||||
number of processes/call 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00
|
||||
bytes total: 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00
|
||||
bytes remote: 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00
|
||||
Max memory consumed for GA by this process: 0 bytes
|
||||
MA_summarize_allocated_blocks: starting scan ...
|
||||
MA_summarize_allocated_blocks: scan completed: 0 heap blocks, 0 stack blocks
|
||||
MA usage statistics:
|
||||
|
||||
allocation statistics:
|
||||
heap stack
|
||||
---- -----
|
||||
current number of blocks 0 0
|
||||
maximum number of blocks 294 17
|
||||
current total bytes 0 0
|
||||
maximum total bytes 4879496 351944
|
||||
maximum total K-bytes 4880 352
|
||||
maximum total M-bytes 5 1
|
||||
|
||||
|
||||
NWChem Input Module
|
||||
-------------------
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
CITATION
|
||||
--------
|
||||
Please cite the following reference when publishing
|
||||
results obtained with NWChem:
|
||||
|
||||
M. Valiev, E.J. Bylaska, N. Govind, K. Kowalski,
|
||||
T.P. Straatsma, H.J.J. van Dam, D. Wang, J. Nieplocha,
|
||||
E. Apra, T.L. Windus, W.A. de Jong
|
||||
"NWChem: a comprehensive and scalable open-source
|
||||
solution for large scale molecular simulations"
|
||||
Comput. Phys. Commun. 181, 1477 (2010)
|
||||
doi:10.1016/j.cpc.2010.04.018
|
||||
|
||||
AUTHORS
|
||||
-------
|
||||
E. Apra, E. J. Bylaska, W. A. de Jong, N. Govind, K. Kowalski,
|
||||
T. P. Straatsma, M. Valiev, H. J. J. van Dam, D. Wang, T. L. Windus,
|
||||
J. Hammond, J. Autschbach, K. Bhaskaran-Nair, J. Brabec, K. Lopata,
|
||||
S. A. Fischer, S. Krishnamoorthy, M. Jacquelin, W. Ma, M. Klemm, O. Villa,
|
||||
Y. Chen, V. Anisimov, F. Aquino, S. Hirata, M. T. Hackler, V. Konjkov,
|
||||
D. Mejia-Rodriguez, T. Risthaus, M. Malagoli, A. Marenich,
|
||||
A. Otero-de-la-Roza, J. Mullin, P. Nichols, R. Peverati, J. Pittner, Y. Zhao,
|
||||
P.-D. Fan, A. Fonari, M. J. Williamson, R. J. Harrison, J. R. Rehr,
|
||||
M. Dupuis, D. Silverstein, D. M. A. Smith, J. Nieplocha, V. Tipparaju,
|
||||
M. Krishnan, B. E. Van Kuiken, A. Vazquez-Mayagoitia, L. Jensen, M. Swart,
|
||||
Q. Wu, T. Van Voorhis, A. A. Auer, M. Nooijen, L. D. Crosby, E. Brown,
|
||||
G. Cisneros, G. I. Fann, H. Fruchtl, J. Garza, K. Hirao, R. A. Kendall,
|
||||
J. A. Nichols, K. Tsemekhman, K. Wolinski, J. Anchell, D. E. Bernholdt,
|
||||
P. Borowski, T. Clark, D. Clerc, H. Dachsel, M. J. O. Deegan, K. Dyall,
|
||||
D. Elwood, E. Glendening, M. Gutowski, A. C. Hess, J. Jaffe, B. G. Johnson,
|
||||
J. Ju, R. Kobayashi, R. Kutteh, Z. Lin, R. Littlefield, X. Long, B. Meng,
|
||||
T. Nakajima, S. Niu, L. Pollack, M. Rosing, K. Glaesemann, G. Sandrone,
|
||||
M. Stave, H. Taylor, G. Thomas, J. H. van Lenthe, A. T. Wong, Z. Zhang.
|
||||
|
||||
Total times cpu: 0.6s wall: 0.7s
|
||||
@ -1,816 +0,0 @@
|
||||
argument 1 = nwchem_lammps.nw
|
||||
|
||||
|
||||
|
||||
============================== echo of input deck ==============================
|
||||
echo
|
||||
|
||||
#**** Enter the geometry using fractional coordinates ****
|
||||
geometry units angstrom noautosym
|
||||
system crystal
|
||||
lat_a 3.16d0
|
||||
lat_b 3.16d0
|
||||
lat_c 3.16d0
|
||||
end
|
||||
W 0.0158218 0.0316436 0.0474661
|
||||
W 0.515824 0.531647 0.547471
|
||||
end
|
||||
|
||||
nwpw
|
||||
vectors input nwchem_lammps.movecs
|
||||
end
|
||||
|
||||
#***** setup the nwpw gamma point code ****
|
||||
nwpw
|
||||
simulation_cell
|
||||
ngrid 16 16 16
|
||||
end
|
||||
ewald_ncut 8
|
||||
mulliken
|
||||
lcao #old default
|
||||
end
|
||||
|
||||
nwpw
|
||||
tolerances 1.0d-9 1.0d-9
|
||||
end
|
||||
|
||||
task pspw stress
|
||||
================================================================================
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
Northwest Computational Chemistry Package (NWChem) 6.8
|
||||
------------------------------------------------------
|
||||
|
||||
|
||||
Environmental Molecular Sciences Laboratory
|
||||
Pacific Northwest National Laboratory
|
||||
Richland, WA 99352
|
||||
|
||||
Copyright (c) 1994-2018
|
||||
Pacific Northwest National Laboratory
|
||||
Battelle Memorial Institute
|
||||
|
||||
NWChem is an open-source computational chemistry package
|
||||
distributed under the terms of the
|
||||
Educational Community License (ECL) 2.0
|
||||
A copy of the license is included with this distribution
|
||||
in the LICENSE.TXT file
|
||||
|
||||
ACKNOWLEDGMENT
|
||||
--------------
|
||||
|
||||
This software and its documentation were developed at the
|
||||
EMSL at Pacific Northwest National Laboratory, a multiprogram
|
||||
national laboratory, operated for the U.S. Department of Energy
|
||||
by Battelle under Contract Number DE-AC05-76RL01830. Support
|
||||
for this work was provided by the Department of Energy Office
|
||||
of Biological and Environmental Research, Office of Basic
|
||||
Energy Sciences, and the Office of Advanced Scientific Computing.
|
||||
|
||||
|
||||
Job information
|
||||
---------------
|
||||
|
||||
hostname = singsing
|
||||
program = /home/sjplimp/tools/nwchem-6.8.1-release/bin/LINUX64/nwchem
|
||||
date = Thu Oct 3 16:58:54 2019
|
||||
|
||||
compiled = Wed_Oct_02_09:25:27_2019
|
||||
source = /home/sjplimp/tools/nwchem-6.8.1-release
|
||||
nwchem branch = Development
|
||||
nwchem revision = N/A
|
||||
ga revision = 5.6.5
|
||||
use scalapack = F
|
||||
input = nwchem_lammps.nw
|
||||
prefix = nwchem_lammps.
|
||||
data base = ./nwchem_lammps.db
|
||||
status = restart
|
||||
nproc = 1
|
||||
time left = -1s
|
||||
|
||||
|
||||
|
||||
Memory information
|
||||
------------------
|
||||
|
||||
heap = 13107200 doubles = 100.0 Mbytes
|
||||
stack = 13107197 doubles = 100.0 Mbytes
|
||||
global = 26214400 doubles = 200.0 Mbytes (distinct from heap & stack)
|
||||
total = 52428797 doubles = 400.0 Mbytes
|
||||
verify = yes
|
||||
hardfail = no
|
||||
|
||||
|
||||
Directory information
|
||||
---------------------
|
||||
|
||||
0 permanent = .
|
||||
0 scratch = .
|
||||
|
||||
|
||||
Previous task information
|
||||
-------------------------
|
||||
|
||||
Theory = pspw
|
||||
Operation = stress
|
||||
Status = unknown
|
||||
Qmmm = F
|
||||
Ignore = F
|
||||
|
||||
|
||||
Geometries in the database
|
||||
--------------------------
|
||||
|
||||
Name Natoms Last Modified
|
||||
-------------------------------- ------ ------------------------
|
||||
1 geometry 2 Thu Oct 3 16:58:53 2019
|
||||
|
||||
The geometry named "geometry" is the default for restart
|
||||
|
||||
|
||||
|
||||
Basis sets in the database
|
||||
--------------------------
|
||||
|
||||
There are no basis sets in the database
|
||||
|
||||
|
||||
|
||||
NWChem Input Module
|
||||
-------------------
|
||||
|
||||
|
||||
|
||||
!!!!!!!!! geom_3d NEEDS TESTING !!!!!!!!!!
|
||||
|
||||
|
||||
Geometry "geometry" -> ""
|
||||
-------------------------
|
||||
|
||||
Output coordinates in angstroms (scale by 1.889725989 to convert to a.u.)
|
||||
|
||||
No. Tag Charge X Y Z
|
||||
---- ---------------- ---------- -------------- -------------- --------------
|
||||
1 W 74.0000 0.04999689 0.09999378 0.14999288
|
||||
2 W 74.0000 1.63000384 1.68000452 1.73000836
|
||||
|
||||
Lattice Parameters
|
||||
------------------
|
||||
|
||||
lattice vectors in angstroms (scale by 1.889725989 to convert to a.u.)
|
||||
|
||||
a1=< 3.160 0.000 0.000 >
|
||||
a2=< 0.000 3.160 0.000 >
|
||||
a3=< 0.000 0.000 3.160 >
|
||||
a= 3.160 b= 3.160 c= 3.160
|
||||
alpha= 90.000 beta= 90.000 gamma= 90.000
|
||||
omega= 31.6
|
||||
|
||||
reciprocal lattice vectors in a.u.
|
||||
|
||||
b1=< 1.052 0.000 -0.000 >
|
||||
b2=< -0.000 1.052 -0.000 >
|
||||
b3=< 0.000 0.000 1.052 >
|
||||
|
||||
Atomic Mass
|
||||
-----------
|
||||
|
||||
W 183.951000
|
||||
|
||||
|
||||
|
||||
XYZ format geometry
|
||||
-------------------
|
||||
2
|
||||
geometry
|
||||
W 0.04999689 0.09999378 0.14999288
|
||||
W 1.63000384 1.68000452 1.73000836
|
||||
|
||||
==============================================================================
|
||||
internuclear distances
|
||||
------------------------------------------------------------------------------
|
||||
center one | center two | atomic units | angstroms
|
||||
------------------------------------------------------------------------------
|
||||
2 W | 1 W | 5.17154 | 2.73666
|
||||
------------------------------------------------------------------------------
|
||||
number of included internuclear distances: 1
|
||||
==============================================================================
|
||||
|
||||
|
||||
|
||||
>>>> PSPW Parallel Module - stress <<<<
|
||||
****************************************************
|
||||
* *
|
||||
* NWPW PSPW Calculation *
|
||||
* *
|
||||
* [ (Grassmann/Stiefel manifold implementation) ] *
|
||||
* *
|
||||
* [ NorthWest Chemistry implementation ] *
|
||||
* *
|
||||
* version #5.10 06/12/02 *
|
||||
* *
|
||||
* This code was developed by Eric J. Bylaska, *
|
||||
* and was based upon algorithms and code *
|
||||
* developed by the group of Prof. John H. Weare *
|
||||
* *
|
||||
****************************************************
|
||||
>>> JOB STARTED AT Thu Oct 3 16:58:54 2019 <<<
|
||||
================ input data ========================
|
||||
|
||||
input psi filename:./nwchem_lammps.movecs
|
||||
|
||||
initializing pspw_APC data structure
|
||||
------------------------------------
|
||||
nga, ngs: 3 6
|
||||
Gc : 2.5000000000000000
|
||||
APC gamma: 1 0.59999999999999998
|
||||
APC gamma: 2 0.90000000000000002
|
||||
APC gamma: 3 1.3500000000000001
|
||||
|
||||
number of processors used: 1
|
||||
processor grid : 1 x 1
|
||||
parallel mapping :2d hilbert
|
||||
parallel mapping : balanced
|
||||
number of threads : 1
|
||||
parallel io : off
|
||||
|
||||
options:
|
||||
boundary conditions = periodic (version3)
|
||||
electron spin = restricted
|
||||
exchange-correlation = LDA (Vosko et al) parameterization
|
||||
|
||||
elements involved in the cluster:
|
||||
1: W valence charge: 6.0000 lmax= 2
|
||||
comment : Troullier-Martins pseudopotential
|
||||
pseudpotential type : 0
|
||||
highest angular component : 2
|
||||
local potential used : 0
|
||||
number of non-local projections: 8
|
||||
semicore corrections included : 1.800 (radius) 4.538 (charge)
|
||||
cutoff = 2.389 3.185 2.244
|
||||
|
||||
|
||||
total charge: 0.000
|
||||
|
||||
atomic composition:
|
||||
W : 2
|
||||
|
||||
number of electrons: spin up= 6 ( 6 per task) down= 6 ( 6 per task) (Fourier space)
|
||||
number of orbitals : spin up= 6 ( 6 per task) down= 6 ( 6 per task) (Fourier space)
|
||||
|
||||
supercell:
|
||||
cell_name: cell_default
|
||||
lattice: a1=< 5.972 0.000 0.000 >
|
||||
a2=< 0.000 5.972 0.000 >
|
||||
a3=< 0.000 0.000 5.972 >
|
||||
reciprocal: b1=< 1.052 0.000 -0.000 >
|
||||
b2=< -0.000 1.052 -0.000 >
|
||||
b3=< 0.000 0.000 1.052 >
|
||||
lattice: a= 5.972 b= 5.972 c= 5.972
|
||||
alpha= 90.000 beta= 90.000 gamma= 90.000
|
||||
omega= 212.9
|
||||
|
||||
density cutoff= 35.427 fft= 16x 16x 16( 1052 waves 1052 per task)
|
||||
wavefnc cutoff= 35.427 fft= 16x 16x 16( 1052 waves 1052 per task)
|
||||
Ewald summation: cut radius= 1.90 and 8
|
||||
Madelung Wigner-Seitz= 1.76011888 (alpha= 2.83729748 rs= 3.70444413)
|
||||
|
||||
technical parameters:
|
||||
time step= 5.80 fictitious mass= 400000.0
|
||||
tolerance=0.100E-08 (energy) 0.100E-08 (density)
|
||||
maximum iterations = 1000 ( 10 inner 100 outer )
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
== Energy Calculation ==
|
||||
|
||||
|
||||
====== Grassmann conjugate gradient iteration ======
|
||||
>>> ITERATION STARTED AT Thu Oct 3 16:58:54 2019 <<<
|
||||
iter. Energy DeltaE DeltaRho
|
||||
------------------------------------------------------
|
||||
10 -0.2020460841E+02 -0.37164E-09 0.13892E-11
|
||||
*** tolerance ok. iteration terminated
|
||||
>>> ITERATION ENDED AT Thu Oct 3 16:58:54 2019 <<<
|
||||
|
||||
|
||||
== Summary Of Results ==
|
||||
|
||||
number of electrons: spin up= 6.00000 down= 6.00000 (real space)
|
||||
|
||||
total energy : -0.2020460841E+02 ( -0.10102E+02/ion)
|
||||
total orbital energy: 0.5093526999E+01 ( 0.84892E+00/electron)
|
||||
hartree energy : 0.2902689593E+00 ( 0.48378E-01/electron)
|
||||
exc-corr energy : -0.9445045626E+01 ( -0.15742E+01/electron)
|
||||
ion-ion energy : -0.2193948849E+02 ( -0.10970E+02/ion)
|
||||
|
||||
kinetic (planewave) : 0.1441573280E+02 ( 0.24026E+01/electron)
|
||||
V_local (planewave) : 0.1156119613E+02 ( 0.19269E+01/electron)
|
||||
V_nl (planewave) : -0.1508727219E+02 ( -0.25145E+01/electron)
|
||||
V_Coul (planewave) : 0.5805379185E+00 ( 0.96756E-01/electron)
|
||||
V_xc. (planewave) : -0.6376667662E+01 ( -0.10628E+01/electron)
|
||||
Virial Coefficient : -0.6466688811E+00
|
||||
|
||||
orbital energies:
|
||||
0.5414223E+00 ( 14.733eV)
|
||||
0.5414201E+00 ( 14.733eV)
|
||||
0.5414174E+00 ( 14.733eV)
|
||||
0.3596809E+00 ( 9.787eV)
|
||||
0.3596804E+00 ( 9.787eV)
|
||||
0.2031424E+00 ( 5.528eV)
|
||||
|
||||
Total PSPW energy : -0.2020460841E+02
|
||||
|
||||
|
||||
=== Spin Contamination ===
|
||||
|
||||
<Sexact^2> = 0.0000000000000000
|
||||
<S^2> = 0.0000000000000000
|
||||
|
||||
|
||||
|
||||
== Center of Charge ==
|
||||
|
||||
spin up ( 0.0106, 0.0203, 0.0283 )
|
||||
spin down ( 0.0106, 0.0203, 0.0283 )
|
||||
total ( 0.0106, 0.0203, 0.0283 )
|
||||
ionic ( -1.3984, -1.3039, -1.2094 )
|
||||
|
||||
|
||||
== Molecular Dipole wrt Center of Mass ==
|
||||
|
||||
mu = ( -16.9083, -15.8910, -14.8528 ) au
|
||||
|mu| = 27.5503 au, 70.0218 Debye
|
||||
|
||||
|
||||
Translation force removed: ( -0.00002 0.00000 0.00002)
|
||||
|
||||
|
||||
============= Ion Gradients =================
|
||||
Ion Forces:
|
||||
1 W ( -0.000001 0.000005 0.000014 )
|
||||
2 W ( 0.000001 -0.000005 -0.000014 )
|
||||
C.O.M. ( -0.000000 0.000000 0.000000 )
|
||||
===============================================
|
||||
|F| = 0.216488E-04
|
||||
|F|/nion = 0.108244E-04
|
||||
max|Fatom|= 0.153080E-04 ( 0.001eV/Angstrom)
|
||||
|
||||
|
||||
|
||||
|
||||
======================
|
||||
= Stress calculation =
|
||||
======================
|
||||
|
||||
|
||||
============= total gradient ==============
|
||||
S = ( 0.12513 0.00001 -0.00003 )
|
||||
( 0.00001 0.12513 -0.00001 )
|
||||
( -0.00003 -0.00001 0.12513 )
|
||||
===================================================
|
||||
|S| = 0.21673E+00
|
||||
pressure = 0.125E+00 au
|
||||
= 0.368E+02 Mbar
|
||||
= 0.368E+04 GPa
|
||||
= 0.363E+08 atm
|
||||
|
||||
|
||||
dE/da = 0.12513
|
||||
dE/db = 0.12513
|
||||
dE/dc = 0.12513
|
||||
dE/dalpha = 0.00006
|
||||
dE/dbeta = 0.00020
|
||||
dE/dgamma = -0.00008
|
||||
|
||||
|
||||
|
||||
|
||||
*************************************************************
|
||||
** **
|
||||
** PSPW Mulliken analysis **
|
||||
** **
|
||||
** Population analysis algorithm devloped by Ryoichi Kawai **
|
||||
** **
|
||||
** Thu Oct 3 16:58 **
|
||||
** **
|
||||
*************************************************************
|
||||
|
||||
|
||||
== XYZ OUTPUT ==
|
||||
|
||||
|
||||
2
|
||||
|
||||
W 0.049997 0.099994 0.149993
|
||||
W -1.529995 -1.479995 -1.429991
|
||||
|
||||
|
||||
== Atomic Orbital Expansion ==
|
||||
|
||||
W nodamping
|
||||
|
||||
|
||||
=====================================================
|
||||
| POPULATION ANALYSIS OF FILLED MOLECULAR ORBITALS |
|
||||
=====================================================
|
||||
|
||||
|
||||
== Using pseudoatomic orbital expansion ==
|
||||
|
||||
|
||||
------------------------------------------------------------------------------
|
||||
|
||||
|
||||
*** ORBITAL= 1*** SPIN=BOTH SUM= 0.12471E+01 E= 0.54142E+00 ( 14.733eV)
|
||||
|
||||
NO ATOM L POPULATION
|
||||
s
|
||||
1 W 0 0.00000 0.00000
|
||||
px pz py
|
||||
1 W 1 0.00000 0.00000 0.00000 0.00000
|
||||
dx2-y2 dzx d3z2-1 dyz dxy
|
||||
1 W 2 0.50000 -0.00001 -0.03953 0.00002 0.50309 0.49532
|
||||
fx(x2-3y2) fz(5z2-1) fx(5z2-1) fz(5z2-3) fy(5z2-1) fxyz fy(3x2-y2)
|
||||
1 W 3 0.00000 -0.00001 -0.00000 -0.00000 0.00000 0.00000 -0.00001 -0.00000
|
||||
s
|
||||
2 W 0 0.00000 0.00000
|
||||
px pz py
|
||||
2 W 1 0.00000 -0.00000 -0.00000 -0.00000
|
||||
dx2-y2 dzx d3z2-1 dyz dxy
|
||||
2 W 2 0.50000 -0.00001 -0.03953 0.00002 0.50309 0.49532
|
||||
fx(x2-3y2) fz(5z2-1) fx(5z2-1) fz(5z2-3) fy(5z2-1) fxyz fy(3x2-y2)
|
||||
2 W 3 0.00000 -0.00001 0.00000 0.00000 -0.00000 -0.00000 0.00001 0.00000
|
||||
|
||||
|
||||
=== DISTRIBUTION ===
|
||||
|
||||
1(W ) 0.5000 2(W ) 0.5000
|
||||
|
||||
|
||||
== ANGULAR MOMENTUM POPULATIONS ===
|
||||
|
||||
s p d f
|
||||
0.0000 0.0000 1.0000 0.0000
|
||||
|
||||
|
||||
------------------------------------------------------------------------------
|
||||
|
||||
|
||||
*** ORBITAL= 2*** SPIN=BOTH SUM= 0.12471E+01 E= 0.54142E+00 ( 14.733eV)
|
||||
|
||||
NO ATOM L POPULATION
|
||||
s
|
||||
1 W 0 0.00000 -0.00000
|
||||
px pz py
|
||||
1 W 1 0.00000 0.00000 0.00000 0.00000
|
||||
dx2-y2 dzx d3z2-1 dyz dxy
|
||||
1 W 2 0.50000 0.00004 0.62658 0.00003 -0.20360 0.25680
|
||||
fx(x2-3y2) fz(5z2-1) fx(5z2-1) fz(5z2-3) fy(5z2-1) fxyz fy(3x2-y2)
|
||||
1 W 3 0.00000 -0.00004 0.00000 0.00000 -0.00000 -0.00000 -0.00001 0.00000
|
||||
s
|
||||
2 W 0 0.00000 -0.00000
|
||||
px pz py
|
||||
2 W 1 0.00000 -0.00000 -0.00000 -0.00000
|
||||
dx2-y2 dzx d3z2-1 dyz dxy
|
||||
2 W 2 0.50000 0.00004 0.62658 0.00003 -0.20360 0.25680
|
||||
fx(x2-3y2) fz(5z2-1) fx(5z2-1) fz(5z2-3) fy(5z2-1) fxyz fy(3x2-y2)
|
||||
2 W 3 0.00000 -0.00004 -0.00000 -0.00000 -0.00000 0.00000 0.00001 -0.00000
|
||||
|
||||
|
||||
=== DISTRIBUTION ===
|
||||
|
||||
1(W ) 0.5000 2(W ) 0.5000
|
||||
|
||||
|
||||
== ANGULAR MOMENTUM POPULATIONS ===
|
||||
|
||||
s p d f
|
||||
0.0000 0.0000 1.0000 0.0000
|
||||
|
||||
|
||||
------------------------------------------------------------------------------
|
||||
|
||||
|
||||
*** ORBITAL= 3*** SPIN=BOTH SUM= 0.12471E+01 E= 0.54142E+00 ( 14.733eV)
|
||||
|
||||
NO ATOM L POPULATION
|
||||
s
|
||||
1 W 0 0.00000 0.00001
|
||||
px pz py
|
||||
1 W 1 0.00000 0.00000 -0.00000 -0.00000
|
||||
dx2-y2 dzx d3z2-1 dyz dxy
|
||||
1 W 2 0.50000 -0.00001 -0.32532 -0.00000 -0.45327 0.43441
|
||||
fx(x2-3y2) fz(5z2-1) fx(5z2-1) fz(5z2-3) fy(5z2-1) fxyz fy(3x2-y2)
|
||||
1 W 3 0.00000 0.00001 0.00000 -0.00000 -0.00000 -0.00000 -0.00000 0.00000
|
||||
s
|
||||
2 W 0 0.00000 0.00001
|
||||
px pz py
|
||||
2 W 1 0.00000 -0.00000 0.00000 0.00000
|
||||
dx2-y2 dzx d3z2-1 dyz dxy
|
||||
2 W 2 0.50000 -0.00001 -0.32532 -0.00000 -0.45327 0.43441
|
||||
fx(x2-3y2) fz(5z2-1) fx(5z2-1) fz(5z2-3) fy(5z2-1) fxyz fy(3x2-y2)
|
||||
2 W 3 0.00000 0.00001 -0.00000 0.00001 0.00000 0.00000 0.00000 -0.00000
|
||||
|
||||
|
||||
=== DISTRIBUTION ===
|
||||
|
||||
1(W ) 0.5000 2(W ) 0.5000
|
||||
|
||||
|
||||
== ANGULAR MOMENTUM POPULATIONS ===
|
||||
|
||||
s p d f
|
||||
0.0000 0.0000 1.0000 0.0000
|
||||
|
||||
|
||||
------------------------------------------------------------------------------
|
||||
|
||||
|
||||
*** ORBITAL= 4*** SPIN=BOTH SUM= 0.14785E+01 E= 0.35968E+00 ( 9.787eV)
|
||||
|
||||
NO ATOM L POPULATION
|
||||
s
|
||||
1 W 0 0.00000 -0.00000
|
||||
px pz py
|
||||
1 W 1 0.00000 -0.00000 0.00001 -0.00000
|
||||
dx2-y2 dzx d3z2-1 dyz dxy
|
||||
1 W 2 0.48310 0.33381 0.00000 -0.60965 0.00000 0.00000
|
||||
fx(x2-3y2) fz(5z2-1) fx(5z2-1) fz(5z2-3) fy(5z2-1) fxyz fy(3x2-y2)
|
||||
1 W 3 0.01690 0.13001 -0.00000 0.00000 0.00000 0.00000 0.00000 -0.00000
|
||||
s
|
||||
2 W 0 0.00000 0.00000
|
||||
px pz py
|
||||
2 W 1 0.00000 -0.00000 0.00001 -0.00000
|
||||
dx2-y2 dzx d3z2-1 dyz dxy
|
||||
2 W 2 0.48310 -0.33381 -0.00000 0.60965 -0.00000 -0.00000
|
||||
fx(x2-3y2) fz(5z2-1) fx(5z2-1) fz(5z2-3) fy(5z2-1) fxyz fy(3x2-y2)
|
||||
2 W 3 0.01690 -0.13001 -0.00000 0.00000 0.00000 0.00000 0.00000 -0.00000
|
||||
|
||||
|
||||
=== DISTRIBUTION ===
|
||||
|
||||
1(W ) 0.5000 2(W ) 0.5000
|
||||
|
||||
|
||||
== ANGULAR MOMENTUM POPULATIONS ===
|
||||
|
||||
s p d f
|
||||
0.0000 0.0000 0.9662 0.0338
|
||||
|
||||
|
||||
------------------------------------------------------------------------------
|
||||
|
||||
|
||||
*** ORBITAL= 5*** SPIN=BOTH SUM= 0.14407E+01 E= 0.35968E+00 ( 9.787eV)
|
||||
|
||||
NO ATOM L POPULATION
|
||||
s
|
||||
1 W 0 0.00000 -0.00000
|
||||
px pz py
|
||||
1 W 1 0.00000 -0.00000 -0.00000 0.00001
|
||||
dx2-y2 dzx d3z2-1 dyz dxy
|
||||
1 W 2 0.49580 0.61761 -0.00000 0.33817 0.00000 -0.00000
|
||||
fx(x2-3y2) fz(5z2-1) fx(5z2-1) fz(5z2-3) fy(5z2-1) fxyz fy(3x2-y2)
|
||||
1 W 3 0.00420 0.06484 -0.00001 0.00000 -0.00000 -0.00000 -0.00000 -0.00000
|
||||
s
|
||||
2 W 0 0.00000 0.00000
|
||||
px pz py
|
||||
2 W 1 0.00000 -0.00000 -0.00000 0.00001
|
||||
dx2-y2 dzx d3z2-1 dyz dxy
|
||||
2 W 2 0.49580 -0.61761 0.00000 -0.33817 -0.00000 0.00000
|
||||
fx(x2-3y2) fz(5z2-1) fx(5z2-1) fz(5z2-3) fy(5z2-1) fxyz fy(3x2-y2)
|
||||
2 W 3 0.00420 -0.06484 -0.00001 0.00000 -0.00000 -0.00000 -0.00000 -0.00000
|
||||
|
||||
|
||||
=== DISTRIBUTION ===
|
||||
|
||||
1(W ) 0.5000 2(W ) 0.5000
|
||||
|
||||
|
||||
== ANGULAR MOMENTUM POPULATIONS ===
|
||||
|
||||
s p d f
|
||||
0.0000 0.0000 0.9916 0.0084
|
||||
|
||||
|
||||
------------------------------------------------------------------------------
|
||||
|
||||
|
||||
*** ORBITAL= 6*** SPIN=BOTH SUM= 0.19540E+01 E= 0.20314E+00 ( 5.528eV)
|
||||
|
||||
NO ATOM L POPULATION
|
||||
s
|
||||
1 W 0 0.49974 -0.70692
|
||||
px pz py
|
||||
1 W 1 0.00000 0.00000 -0.00000 0.00000
|
||||
dx2-y2 dzx d3z2-1 dyz dxy
|
||||
1 W 2 0.00000 0.00000 -0.00000 -0.00000 -0.00000 0.00000
|
||||
fx(x2-3y2) fz(5z2-1) fx(5z2-1) fz(5z2-3) fy(5z2-1) fxyz fy(3x2-y2)
|
||||
1 W 3 0.00026 0.01609 -0.00000 -0.00000 -0.00000 -0.00000 -0.00000 -0.00000
|
||||
s
|
||||
2 W 0 0.49974 -0.70692
|
||||
px pz py
|
||||
2 W 1 0.00000 -0.00000 0.00000 -0.00000
|
||||
dx2-y2 dzx d3z2-1 dyz dxy
|
||||
2 W 2 0.00000 0.00000 -0.00000 -0.00000 -0.00000 0.00000
|
||||
fx(x2-3y2) fz(5z2-1) fx(5z2-1) fz(5z2-3) fy(5z2-1) fxyz fy(3x2-y2)
|
||||
2 W 3 0.00026 0.01609 0.00000 0.00000 -0.00000 0.00000 0.00000 0.00000
|
||||
|
||||
|
||||
=== DISTRIBUTION ===
|
||||
|
||||
1(W ) 0.5000 2(W ) 0.5000
|
||||
|
||||
|
||||
== ANGULAR MOMENTUM POPULATIONS ===
|
||||
|
||||
s p d f
|
||||
0.9995 0.0000 0.0000 0.0005
|
||||
|
||||
|
||||
========================================
|
||||
| POPULATION ANALYSIS ON EACH ATOM |
|
||||
========================================
|
||||
|
||||
|
||||
NO ATOM SPIN TOTAL s p d f
|
||||
1 W UP 3.00000 0.49974 0.00000 2.47889 0.02137
|
||||
1 W DOWN 3.00000 0.49974 0.00000 2.47889 0.02137
|
||||
2 W UP 3.00000 0.49974 0.00000 2.47889 0.02137
|
||||
2 W DOWN 3.00000 0.49974 0.00000 2.47889 0.02137
|
||||
|
||||
|
||||
|
||||
=== TOTAL ANGULAR MOMENTUM POPULATION ===
|
||||
|
||||
SPIN s p d f
|
||||
UP 16.66% 0.00% 82.63% 0.71%
|
||||
UP 16.66% 0.00% 82.63% 0.71%
|
||||
TOTAL 16.66% 0.00% 82.63% 0.71%
|
||||
|
||||
*************************************************************
|
||||
** **
|
||||
** PSPW Atomic Point Charge (APC) Analysis **
|
||||
** **
|
||||
** Point charge analysis based on paper by P.E. Blochl **
|
||||
** (J. Chem. Phys. vol 103, page 7422, 1995) **
|
||||
** **
|
||||
*************************************************************
|
||||
|
||||
pspw_APC data structure
|
||||
-----------------------
|
||||
nga, ngs: 3 6
|
||||
Gc : 2.5000000000000000
|
||||
APC gamma: 1 0.59999999999999998
|
||||
APC gamma: 2 0.90000000000000002
|
||||
APC gamma: 3 1.3500000000000001
|
||||
|
||||
charge analysis on each atom
|
||||
----------------------------
|
||||
|
||||
no atom Qelc Qion Qtotal
|
||||
-- ---- ------- ------- -------
|
||||
1 W -6.000 6.000 -0.000
|
||||
2 W -6.000 6.000 0.000
|
||||
Total Q -12.000 12.000 -0.000
|
||||
|
||||
|
||||
gaussian coefficients of model density
|
||||
--------------------------------------
|
||||
|
||||
no atom g=0.000 g=0.600 g=0.900 g=1.350
|
||||
-- ---- ------- ------- ------- -------
|
||||
1 W 6.000 -7.235 17.654 -16.419
|
||||
2 W 6.000 -7.234 17.651 -16.418
|
||||
|
||||
|
||||
=== Electric Field at Atoms ===
|
||||
|
||||
1 W Atomic Electric Field =( -0.00002 0.00000 0.00001 )
|
||||
(ion) =( 0.00000 0.00000 0.00000 )
|
||||
(electronic) =( -0.00002 -0.00000 0.00001 )
|
||||
2 W Atomic Electric Field =( -0.00002 0.00000 0.00002 )
|
||||
(ion) =( -0.00000 -0.00000 -0.00000 )
|
||||
(electronic) =( -0.00002 0.00000 0.00002 )
|
||||
|
||||
output psi filename:./nwchem_lammps.movecs
|
||||
|
||||
|
||||
== Timing ==
|
||||
|
||||
cputime in seconds
|
||||
prologue : 0.991130E-01
|
||||
main loop : 0.101190E+00
|
||||
epilogue : 0.203540E-01
|
||||
total : 0.220657E+00
|
||||
cputime/step: 0.252975E-01 ( 4 evalulations, 1 linesearches)
|
||||
|
||||
|
||||
Time spent doing total step percent
|
||||
total time : 0.222262E+00 0.555655E-01 100.0 %
|
||||
i/o time : 0.847340E-02 0.211835E-02 3.8 %
|
||||
FFTs : 0.576015E-02 0.144004E-02 2.6 %
|
||||
dot products : 0.157053E-02 0.392634E-03 0.7 %
|
||||
geodesic : 0.203228E-02 0.508070E-03 0.9 %
|
||||
ffm_dgemm : 0.641376E-04 0.160344E-04 0.0 %
|
||||
fmf_dgemm : 0.202988E-02 0.507471E-03 0.9 %
|
||||
mmm_dgemm : 0.286302E-05 0.715756E-06 0.0 %
|
||||
m_diagonalize : 0.101088E-03 0.252721E-04 0.0 %
|
||||
exchange correlation : 0.287819E-02 0.719547E-03 1.3 %
|
||||
local pseudopotentials : 0.346661E-03 0.866652E-04 0.2 %
|
||||
non-local pseudopotentials : 0.268912E-02 0.672280E-03 1.2 %
|
||||
hartree potentials : 0.163791E-03 0.409476E-04 0.1 %
|
||||
ion-ion interaction : 0.699389E-01 0.174847E-01 31.5 %
|
||||
structure factors : 0.889608E-02 0.222402E-02 4.0 %
|
||||
phase factors : 0.102510E-04 0.256275E-05 0.0 %
|
||||
masking and packing : 0.839656E-02 0.209914E-02 3.8 %
|
||||
queue fft : 0.418949E-02 0.104737E-02 1.9 %
|
||||
queue fft (serial) : 0.264608E-02 0.661519E-03 1.2 %
|
||||
queue fft (message passing): 0.136477E-02 0.341193E-03 0.6 %
|
||||
non-local psp FFM : 0.391964E-03 0.979910E-04 0.2 %
|
||||
non-local psp FMF : 0.407219E-03 0.101805E-03 0.2 %
|
||||
non-local psp FFM A : 0.144235E-03 0.360588E-04 0.1 %
|
||||
non-local psp FFM B : 0.216961E-03 0.542402E-04 0.1 %
|
||||
|
||||
>>> JOB COMPLETED AT Thu Oct 3 16:58:54 2019 <<<
|
||||
|
||||
Task times cpu: 0.2s wall: 0.2s
|
||||
Summary of allocated global arrays
|
||||
-----------------------------------
|
||||
No active global arrays
|
||||
|
||||
|
||||
|
||||
GA Statistics for process 0
|
||||
------------------------------
|
||||
|
||||
create destroy get put acc scatter gather read&inc
|
||||
calls: 0 0 0 0 0 0 0 0
|
||||
number of processes/call 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00
|
||||
bytes total: 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00
|
||||
bytes remote: 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00 0.00e+00
|
||||
Max memory consumed for GA by this process: 0 bytes
|
||||
MA_summarize_allocated_blocks: starting scan ...
|
||||
MA_summarize_allocated_blocks: scan completed: 0 heap blocks, 0 stack blocks
|
||||
MA usage statistics:
|
||||
|
||||
allocation statistics:
|
||||
heap stack
|
||||
---- -----
|
||||
current number of blocks 0 0
|
||||
maximum number of blocks 294 17
|
||||
current total bytes 0 0
|
||||
maximum total bytes 4879496 351944
|
||||
maximum total K-bytes 4880 352
|
||||
maximum total M-bytes 5 1
|
||||
|
||||
|
||||
NWChem Input Module
|
||||
-------------------
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
CITATION
|
||||
--------
|
||||
Please cite the following reference when publishing
|
||||
results obtained with NWChem:
|
||||
|
||||
M. Valiev, E.J. Bylaska, N. Govind, K. Kowalski,
|
||||
T.P. Straatsma, H.J.J. van Dam, D. Wang, J. Nieplocha,
|
||||
E. Apra, T.L. Windus, W.A. de Jong
|
||||
"NWChem: a comprehensive and scalable open-source
|
||||
solution for large scale molecular simulations"
|
||||
Comput. Phys. Commun. 181, 1477 (2010)
|
||||
doi:10.1016/j.cpc.2010.04.018
|
||||
|
||||
AUTHORS
|
||||
-------
|
||||
E. Apra, E. J. Bylaska, W. A. de Jong, N. Govind, K. Kowalski,
|
||||
T. P. Straatsma, M. Valiev, H. J. J. van Dam, D. Wang, T. L. Windus,
|
||||
J. Hammond, J. Autschbach, K. Bhaskaran-Nair, J. Brabec, K. Lopata,
|
||||
S. A. Fischer, S. Krishnamoorthy, M. Jacquelin, W. Ma, M. Klemm, O. Villa,
|
||||
Y. Chen, V. Anisimov, F. Aquino, S. Hirata, M. T. Hackler, V. Konjkov,
|
||||
D. Mejia-Rodriguez, T. Risthaus, M. Malagoli, A. Marenich,
|
||||
A. Otero-de-la-Roza, J. Mullin, P. Nichols, R. Peverati, J. Pittner, Y. Zhao,
|
||||
P.-D. Fan, A. Fonari, M. J. Williamson, R. J. Harrison, J. R. Rehr,
|
||||
M. Dupuis, D. Silverstein, D. M. A. Smith, J. Nieplocha, V. Tipparaju,
|
||||
M. Krishnan, B. E. Van Kuiken, A. Vazquez-Mayagoitia, L. Jensen, M. Swart,
|
||||
Q. Wu, T. Van Voorhis, A. A. Auer, M. Nooijen, L. D. Crosby, E. Brown,
|
||||
G. Cisneros, G. I. Fann, H. Fruchtl, J. Garza, K. Hirao, R. A. Kendall,
|
||||
J. A. Nichols, K. Tsemekhman, K. Wolinski, J. Anchell, D. E. Bernholdt,
|
||||
P. Borowski, T. Clark, D. Clerc, H. Dachsel, M. J. O. Deegan, K. Dyall,
|
||||
D. Elwood, E. Glendening, M. Gutowski, A. C. Hess, J. Jaffe, B. G. Johnson,
|
||||
J. Ju, R. Kobayashi, R. Kutteh, Z. Lin, R. Littlefield, X. Long, B. Meng,
|
||||
T. Nakajima, S. Niu, L. Pollack, M. Rosing, K. Glaesemann, G. Sandrone,
|
||||
M. Stave, H. Taylor, G. Thomas, J. H. van Lenthe, A. T. Wong, Z. Zhang.
|
||||
|
||||
Total times cpu: 0.2s wall: 0.3s
|
||||
@ -1,28 +0,0 @@
|
||||
echo
|
||||
|
||||
#**** Enter the geometry using fractional coordinates ****
|
||||
geometry units angstrom noautosym
|
||||
system crystal
|
||||
lat_a 3.16d0
|
||||
lat_b 3.16d0
|
||||
lat_c 3.16d0
|
||||
end
|
||||
W 0.0 0.0 0.0
|
||||
W 0.5 0.5 0.5
|
||||
end
|
||||
|
||||
#***** setup the nwpw gamma point code ****
|
||||
nwpw
|
||||
simulation_cell
|
||||
ngrid 16 16 16
|
||||
end
|
||||
ewald_ncut 8
|
||||
mulliken
|
||||
lcao #old default
|
||||
end
|
||||
|
||||
nwpw
|
||||
tolerances 1.0d-9 1.0d-9
|
||||
end
|
||||
|
||||
task pspw stress
|
||||
@ -1,53 +0,0 @@
|
||||
# Startparameter for this run:
|
||||
NWRITE = 2 write-flag & timer
|
||||
PREC = normal normal or accurate (medium, high low for compatibility)
|
||||
ISTART = 0 job : 0-new 1-cont 2-samecut
|
||||
ICHARG = 2 charge: 1-file 2-atom 10-const
|
||||
ISPIN = 1 spin polarized calculation?
|
||||
LSORBIT = F spin-orbit coupling
|
||||
INIWAV = 1 electr: 0-lowe 1-rand 2-diag
|
||||
|
||||
# Electronic Relaxation 1
|
||||
ENCUT = 600.0 eV #Plane wave energy cutoff
|
||||
ENINI = 600.0 initial cutoff
|
||||
NELM = 100; NELMIN= 2; NELMDL= -5 # of ELM steps
|
||||
EDIFF = 0.1E-05 stopping-criterion for ELM
|
||||
# Ionic relaxation
|
||||
EDIFFG = 0.1E-02 stopping-criterion for IOM
|
||||
NSW = 0 number of steps for IOM
|
||||
NBLOCK = 1; KBLOCK = 1 inner block; outer block
|
||||
IBRION = -1 ionic relax: 0-MD 1-quasi-New 2-CG #No ion relaxation with -1
|
||||
NFREE = 0 steps in history (QN), initial steepest desc. (CG)
|
||||
ISIF = 2 stress and relaxation # 2: F-yes Sts-yes RlxIon-yes cellshape-no cellvol-no
|
||||
IWAVPR = 10 prediction: 0-non 1-charg 2-wave 3-comb # 10: TMPCAR stored in memory rather than file
|
||||
|
||||
POTIM = 0.5000 time-step for ionic-motion
|
||||
TEBEG = 3500.0; TEEND = 3500.0 temperature during run # Finite Temperature variables if AI-MD is on
|
||||
SMASS = -3.00 Nose mass-parameter (am)
|
||||
estimated Nose-frequenzy (Omega) = 0.10E-29 period in steps =****** mass= -0.366E-27a.u.
|
||||
PSTRESS= 0.0 pullay stress
|
||||
|
||||
# DOS related values:
|
||||
EMIN = 10.00; EMAX =-10.00 energy-range for DOS
|
||||
EFERMI = 0.00
|
||||
ISMEAR = 0; SIGMA = 0.10 broadening in eV -4-tet -1-fermi 0-gaus
|
||||
|
||||
# Electronic relaxation 2 (details)
|
||||
IALGO = 48 algorithm
|
||||
|
||||
# Write flags
|
||||
LWAVE = T write WAVECAR
|
||||
LCHARG = T write CHGCAR
|
||||
LVTOT = F write LOCPOT, total local potential
|
||||
LVHAR = F write LOCPOT, Hartree potential only
|
||||
LELF = F write electronic localiz. function (ELF)
|
||||
|
||||
# Dipole corrections
|
||||
LMONO = F monopole corrections only (constant potential shift)
|
||||
LDIPOL = F correct potential (dipole corrections)
|
||||
IDIPOL = 0 1-x, 2-y, 3-z, 4-all directions
|
||||
EPSILON= 1.0000000 bulk dielectric constant
|
||||
|
||||
# Exchange correlation treatment:
|
||||
GGA = -- GGA type
|
||||
|
||||
@ -1,6 +0,0 @@
|
||||
K-Points
|
||||
0
|
||||
Monkhorst Pack
|
||||
15 15 15
|
||||
0 0 0
|
||||
|
||||
@ -1,11 +0,0 @@
|
||||
W unit cell
|
||||
1.0
|
||||
3.16 0.00000000 0.00000000
|
||||
0.00000000 3.16 0.00000000
|
||||
0.00000000 0.00000000 3.16
|
||||
W
|
||||
2
|
||||
Direct
|
||||
0.00000000 0.00000000 0.00000000
|
||||
0.50000000 0.50000000 0.50000000
|
||||
|
||||
@ -1,149 +0,0 @@
|
||||
Sample LAMMPS MD wrapper on VASP quantum DFT via client/server
|
||||
coupling
|
||||
|
||||
See the MESSAGE package documentation Build_extras.html#message
|
||||
and Build_extras.html#message for more details on how client/server
|
||||
coupling works in LAMMPS.
|
||||
|
||||
In this dir, the vasp_wrap.py is a wrapper on the VASP quantum DFT
|
||||
code so it can work as a "server" code which LAMMPS drives as a
|
||||
"client" code to perform ab initio MD. LAMMPS performs the MD
|
||||
timestepping, sends VASP a current set of coordinates each timestep,
|
||||
VASP computes forces and energy and virial and returns that info to
|
||||
LAMMPS.
|
||||
|
||||
Messages are exchanged between MC and LAMMPS via a client/server
|
||||
library (CSlib), which is included in the LAMMPS distribution in
|
||||
lib/message. As explained below you can choose to exchange data
|
||||
between the two programs either via files or sockets (ZMQ). If the
|
||||
vasp_wrap.py program became parallel, or the CSlib library calls were
|
||||
integrated into VASP directly, then data could also be exchanged via
|
||||
MPI.
|
||||
|
||||
----------------
|
||||
|
||||
Build LAMMPS with its MESSAGE package installed:
|
||||
|
||||
See the Build extras doc page and its MESSAGE package
|
||||
section for details.
|
||||
|
||||
CMake:
|
||||
|
||||
-D PKG_MESSAGE=yes # include the MESSAGE package
|
||||
-D MESSAGE_ZMQ=value # build with ZeroMQ support, value = no (default) or yes
|
||||
|
||||
Traditional make:
|
||||
|
||||
cd lammps/lib/message
|
||||
python Install.py -m -z # build CSlib with MPI and ZMQ support
|
||||
cd lammps/src
|
||||
make yes-message
|
||||
make mpi
|
||||
|
||||
You can leave off the -z if you do not have ZMQ on your system.
|
||||
|
||||
----------------
|
||||
|
||||
Build the CSlib in a form usable by the vasp_wrapper.py script:
|
||||
|
||||
% cd lammps/lib/message/cslib/src
|
||||
% make shlib # build serial and parallel shared lib with ZMQ support
|
||||
% make shlib zmq=no # build serial and parallel shared lib w/out ZMQ support
|
||||
|
||||
This will make a shared library versions of the CSlib, which Python
|
||||
requires. Python must be able to find both the cslib.py script and
|
||||
the libcsnompi.so library in your lammps/lib/message/cslib/src
|
||||
directory. If it is not able to do this, you will get an error when
|
||||
you run vasp_wrapper.py.
|
||||
|
||||
You can do this by augmenting two environment variables, either
|
||||
from the command line, or in your shell start-up script.
|
||||
Here is the sample syntax for the csh or tcsh shells:
|
||||
|
||||
setenv PYTHONPATH ${PYTHONPATH}:/home/sjplimp/lammps/lib/message/cslib/src
|
||||
setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/home/sjplimp/lammps/lib/message/cslib/src
|
||||
|
||||
----------------
|
||||
|
||||
Prepare to use VASP and the vasp_wrapper.py script
|
||||
|
||||
You can run the vasp_wrap.py script as-is to test that the coupling
|
||||
between it and LAMMPS is functional. This will use the included
|
||||
vasprun.xml file output by a previous VASP run.
|
||||
|
||||
But note that the as-is version of vasp_wrap.py will not attempt to
|
||||
run VASP.
|
||||
|
||||
To do this, you must edit the 1st vaspcmd line at the top of
|
||||
vasp_wrapper.py to be the launch command needed to run VASP on your
|
||||
system. It can be a command to run VASP in serial or in parallel,
|
||||
e.g. an mpirun command. Then comment out the 2nd vaspcmd line
|
||||
immediately following it.
|
||||
|
||||
Insure you have the necessary VASP input files in this
|
||||
directory, suitable for the VASP calculation you want to perform:
|
||||
|
||||
INCAR
|
||||
KPOINTS
|
||||
POSCAR_template
|
||||
POTCAR
|
||||
|
||||
Examples of all but the POTCAR file are provided. As explained below,
|
||||
POSCAR_W is an input file for a 2-atom unit cell of tungsten and can
|
||||
be used to test the LAMMPS/VASP coupling. The POTCAR file is a
|
||||
proprietary VASP file, so use one from your VASP installation.
|
||||
|
||||
Note that the POSCAR_template file should be matched to the LAMMPS
|
||||
input script (# of atoms and atom types, box size, etc). The provided
|
||||
POSCAR_W matches in.client.W.
|
||||
|
||||
Once you run VASP yourself, the vasprun.xml file will be overwritten.
|
||||
|
||||
----------------
|
||||
|
||||
To run in client/server mode:
|
||||
|
||||
NOTE: The vasp_wrap.py script must be run with Python version 2, not
|
||||
3. This is because it used the CSlib python wrapper, which only
|
||||
supports version 2. We plan to upgrade CSlib to support Python 3.
|
||||
|
||||
Both the client (LAMMPS) and server (vasp_wrap.py) must use the same
|
||||
messaging mode, namely file or zmq. This is an argument to the
|
||||
vasp_wrap.py code; it can be selected by setting the "mode" variable
|
||||
when you run LAMMPS. The default mode = file.
|
||||
|
||||
Here we assume LAMMPS was built to run in parallel, and the MESSAGE
|
||||
package was installed with socket (ZMQ) support. This means either of
|
||||
the messaging modes can be used and LAMMPS can be run in serial or
|
||||
parallel. The vasp_wrap.py code is always run in serial, but it
|
||||
launches VASP from Python via an mpirun command which can run VASP
|
||||
itself in parallel.
|
||||
|
||||
When you run, the server should print out thermodynamic info every
|
||||
timestep which corresponds to the forces and virial computed by VASP.
|
||||
VASP will also generate output files each timestep. The vasp_wrapper.py
|
||||
script could be generalized to archive these.
|
||||
|
||||
The examples below are commands you should use in two different
|
||||
terminal windows. The order of the two commands (client or server
|
||||
launch) does not matter. You can run them both in the same window if
|
||||
you append a "&" character to the first one to run it in the
|
||||
background.
|
||||
|
||||
--------------
|
||||
|
||||
File mode of messaging:
|
||||
|
||||
% mpirun -np 1 lmp_mpi -v mode file -in in.client.W
|
||||
% python vasp_wrap.py file POSCAR_W
|
||||
|
||||
% mpirun -np 2 lmp_mpi -v mode file -in in.client.W
|
||||
% python vasp_wrap.py file POSCAR_W
|
||||
|
||||
ZMQ mode of messaging:
|
||||
|
||||
% mpirun -np 1 lmp_mpi -v mode zmq -in in.client.W
|
||||
% python vasp_wrap.py zmq POSCAR_W
|
||||
|
||||
% mpirun -np 2 lmp_mpi -v mode zmq -in in.client.W
|
||||
% python vasp_wrap.py zmq POSCAR_W
|
||||
@ -1,15 +0,0 @@
|
||||
LAMMPS W data file
|
||||
|
||||
2 atoms
|
||||
|
||||
1 atom types
|
||||
|
||||
0.0 3.16 xlo xhi
|
||||
0.0 3.16 ylo yhi
|
||||
0.0 3.16 zlo zhi
|
||||
|
||||
Atoms
|
||||
|
||||
1 1 0.000 0.000 0.000
|
||||
2 1 1.58 1.58 1.58
|
||||
|
||||
@ -1,35 +0,0 @@
|
||||
# small W unit cell for use with VASP
|
||||
|
||||
variable mode index file
|
||||
|
||||
if "${mode} == file" then &
|
||||
"message client md file tmp.couple" &
|
||||
elif "${mode} == zmq" &
|
||||
"message client md zmq localhost:5555" &
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
units metal
|
||||
atom_style atomic
|
||||
atom_modify sort 0 0.0 map yes
|
||||
|
||||
read_data data.W
|
||||
mass 1 183.85
|
||||
|
||||
replicate $x $y $z
|
||||
|
||||
velocity all create 300.0 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 10 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all client/md
|
||||
fix_modify 2 energy yes
|
||||
|
||||
thermo 1
|
||||
run 3
|
||||
|
||||
message quit
|
||||
@ -1,76 +0,0 @@
|
||||
LAMMPS (22 Aug 2018)
|
||||
# small W unit cell for use with VASP
|
||||
|
||||
variable mode index file
|
||||
|
||||
if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555"
|
||||
message client md zmq localhost:5555
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
units metal
|
||||
atom_style atomic
|
||||
atom_modify sort 0 0.0 map yes
|
||||
|
||||
read_data data.W
|
||||
orthogonal box = (0 0 0) to (3.16 3.16 3.16)
|
||||
1 by 1 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
2 atoms
|
||||
mass 1 183.85
|
||||
|
||||
replicate $x $y $z
|
||||
replicate 1 $y $z
|
||||
replicate 1 1 $z
|
||||
replicate 1 1 1
|
||||
orthogonal box = (0 0 0) to (3.16 3.16 3.16)
|
||||
1 by 1 by 2 MPI processor grid
|
||||
2 atoms
|
||||
Time spent = 0.000148058 secs
|
||||
|
||||
velocity all create 300.0 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 10 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all client/md
|
||||
fix_modify 2 energy yes
|
||||
|
||||
thermo 1
|
||||
run 3
|
||||
Per MPI rank memory allocation (min/avg/max) = 1.8 | 1.8 | 1.8 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 300 0 0 -48.030793 -78159.503
|
||||
1 298.24318 0 0 -48.03102 -78167.19
|
||||
2 296.85584 0 0 -48.031199 -78173.26
|
||||
3 295.83795 0 0 -48.031331 -78177.714
|
||||
Loop time of 0.457491 on 2 procs for 3 steps with 2 atoms
|
||||
|
||||
Performance: 0.567 ns/day, 42.360 hours/ns, 6.558 timesteps/s
|
||||
50.1% CPU use with 2 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 1.3828e-05 | 2.9922e-05 | 4.6015e-05 | 0.0 | 0.01
|
||||
Output | 7.5817e-05 | 9.3937e-05 | 0.00011206 | 0.0 | 0.02
|
||||
Modify | 0.45735 | 0.45736 | 0.45736 | 0.0 | 99.97
|
||||
Other | | 1.204e-05 | | | 0.00
|
||||
|
||||
Nlocal: 1 ave 1 max 1 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 4 ave 4 max 4 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds not checked
|
||||
|
||||
Total wall time: 0:01:21
|
||||
@ -1,300 +0,0 @@
|
||||
#!/usr/bin/env python
|
||||
|
||||
# ----------------------------------------------------------------------
|
||||
# LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
# https://www.lammps.org/ Sandia National Laboratories
|
||||
# Steve Plimpton, sjplimp@sandia.gov
|
||||
# ----------------------------------------------------------------------
|
||||
|
||||
# Syntax: vasp_wrap.py file/zmq POSCARfile
|
||||
|
||||
# wrapper on VASP to act as server program using CSlib
|
||||
# receives message with list of coords from client
|
||||
# creates VASP inputs
|
||||
# invokes VASP to calculate self-consistent energy of that config
|
||||
# reads VASP outputs
|
||||
# sends message with energy, forces, pressure to client
|
||||
|
||||
# NOTES:
|
||||
# check to insure basic VASP input files are in place?
|
||||
# could archive VASP input/output in special filenames or dirs?
|
||||
# need to check that POTCAR file is consistent with atom ordering?
|
||||
# could make syntax for launching VASP more flexible
|
||||
# e.g. command-line arg for # of procs
|
||||
# detect if VASP had an error and return ERROR field, e.g. non-convergence ??
|
||||
|
||||
from __future__ import print_function
|
||||
import sys
|
||||
|
||||
version = sys.version_info[0]
|
||||
if version == 3:
|
||||
sys.exit("The CSlib python wrapper does not yet support python 3")
|
||||
|
||||
import subprocess
|
||||
import xml.etree.ElementTree as ET
|
||||
from cslib import CSlib
|
||||
|
||||
# comment out 2nd line once 1st line is correct for your system
|
||||
|
||||
vaspcmd = "srun -N 1 --ntasks-per-node=4 " + \
|
||||
"-n 4 /projects/vasp/2017-build/cts1/vasp5.4.4/vasp_tfermi/bin/vasp_std"
|
||||
vaspcmd = "touch tmp"
|
||||
|
||||
# enums matching FixClientMD class in LAMMPS
|
||||
|
||||
SETUP,STEP = range(1,2+1)
|
||||
DIM,PERIODICITY,ORIGIN,BOX,NATOMS,NTYPES,TYPES,COORDS,UNITS,CHARGE = range(1,10+1)
|
||||
FORCES,ENERGY,VIRIAL,ERROR = range(1,4+1)
|
||||
|
||||
# -------------------------------------
|
||||
# functions
|
||||
|
||||
# error message and exit
|
||||
|
||||
def error(txt):
|
||||
print("ERROR:",txt)
|
||||
sys.exit(1)
|
||||
|
||||
# -------------------------------------
|
||||
# read initial VASP POSCAR file to setup problem
|
||||
# return natoms,ntypes,box
|
||||
|
||||
def vasp_setup(poscar):
|
||||
|
||||
ps = open(poscar,'r').readlines()
|
||||
|
||||
# box size
|
||||
|
||||
words = ps[2].split()
|
||||
xbox = float(words[0])
|
||||
words = ps[3].split()
|
||||
ybox = float(words[1])
|
||||
words = ps[4].split()
|
||||
zbox = float(words[2])
|
||||
box = [xbox,ybox,zbox]
|
||||
|
||||
ntypes = 0
|
||||
natoms = 0
|
||||
words = ps[6].split()
|
||||
for word in words:
|
||||
if word == '#': break
|
||||
ntypes += 1
|
||||
natoms += int(word)
|
||||
|
||||
return natoms,ntypes,box
|
||||
|
||||
# -------------------------------------
|
||||
# write a new POSCAR file for VASP
|
||||
|
||||
def poscar_write(poscar,natoms,ntypes,types,coords,box):
|
||||
|
||||
psold = open(poscar,'r').readlines()
|
||||
psnew = open("POSCAR",'w')
|
||||
|
||||
# header, including box size
|
||||
|
||||
psnew.write(psold[0])
|
||||
psnew.write(psold[1])
|
||||
psnew.write("%g %g %g\n" % (box[0],box[1],box[2]))
|
||||
psnew.write("%g %g %g\n" % (box[3],box[4],box[5]))
|
||||
psnew.write("%g %g %g\n" % (box[6],box[7],box[8]))
|
||||
psnew.write(psold[5])
|
||||
psnew.write(psold[6])
|
||||
|
||||
# per-atom coords
|
||||
# grouped by types
|
||||
|
||||
psnew.write("Cartesian\n")
|
||||
|
||||
for itype in range(1,ntypes+1):
|
||||
for i in range(natoms):
|
||||
if types[i] != itype: continue
|
||||
x = coords[3*i+0]
|
||||
y = coords[3*i+1]
|
||||
z = coords[3*i+2]
|
||||
aline = " %g %g %g\n" % (x,y,z)
|
||||
psnew.write(aline)
|
||||
|
||||
psnew.close()
|
||||
|
||||
# -------------------------------------
|
||||
# read a VASP output vasprun.xml file
|
||||
# uses ElementTree module
|
||||
# see https://docs.python.org/2/library/xml.etree.elementtree.html
|
||||
|
||||
def vasprun_read():
|
||||
tree = ET.parse('vasprun.xml')
|
||||
root = tree.getroot()
|
||||
|
||||
#fp = open("vasprun.xml","r")
|
||||
#root = ET.parse(fp)
|
||||
|
||||
scsteps = root.findall('calculation/scstep')
|
||||
energy = scsteps[-1].find('energy')
|
||||
for child in energy:
|
||||
if child.attrib["name"] == "e_0_energy":
|
||||
eout = float(child.text)
|
||||
|
||||
fout = []
|
||||
sout = []
|
||||
|
||||
varrays = root.findall('calculation/varray')
|
||||
for varray in varrays:
|
||||
if varray.attrib["name"] == "forces":
|
||||
forces = varray.findall("v")
|
||||
for line in forces:
|
||||
fxyz = line.text.split()
|
||||
fxyz = [float(value) for value in fxyz]
|
||||
fout += fxyz
|
||||
if varray.attrib["name"] == "stress":
|
||||
tensor = varray.findall("v")
|
||||
stensor = []
|
||||
for line in tensor:
|
||||
sxyz = line.text.split()
|
||||
sxyz = [float(value) for value in sxyz]
|
||||
stensor.append(sxyz)
|
||||
sxx = stensor[0][0]
|
||||
syy = stensor[1][1]
|
||||
szz = stensor[2][2]
|
||||
# symmetrize off-diagonal components
|
||||
sxy = 0.5 * (stensor[0][1] + stensor[1][0])
|
||||
sxz = 0.5 * (stensor[0][2] + stensor[2][0])
|
||||
syz = 0.5 * (stensor[1][2] + stensor[2][1])
|
||||
sout = [sxx,syy,szz,sxy,sxz,syz]
|
||||
|
||||
#fp.close()
|
||||
|
||||
return eout,fout,sout
|
||||
|
||||
# -------------------------------------
|
||||
# main program
|
||||
|
||||
# command-line args
|
||||
|
||||
if len(sys.argv) != 3:
|
||||
print("Syntax: python vasp_wrap.py file/zmq POSCARfile")
|
||||
sys.exit(1)
|
||||
|
||||
mode = sys.argv[1]
|
||||
poscar_template = sys.argv[2]
|
||||
|
||||
if mode == "file": cs = CSlib(1,mode,"tmp.couple",None)
|
||||
elif mode == "zmq": cs = CSlib(1,mode,"*:5555",None)
|
||||
else:
|
||||
print("Syntax: python vasp_wrap.py file/zmq POSCARfile")
|
||||
sys.exit(1)
|
||||
|
||||
natoms,ntypes,box = vasp_setup(poscar_template)
|
||||
|
||||
# initial message for MD protocol
|
||||
|
||||
msgID,nfield,fieldID,fieldtype,fieldlen = cs.recv()
|
||||
if msgID != 0: error("Bad initial client/server handshake")
|
||||
protocol = cs.unpack_string(1)
|
||||
if protocol != "md": error("Mismatch in client/server protocol")
|
||||
cs.send(0,0)
|
||||
|
||||
# endless server loop
|
||||
|
||||
while 1:
|
||||
|
||||
# recv message from client
|
||||
# msgID = 0 = all-done message
|
||||
|
||||
msgID,nfield,fieldID,fieldtype,fieldlen = cs.recv()
|
||||
if msgID < 0: break
|
||||
|
||||
# SETUP receive at beginning of each run
|
||||
# required fields: DIM, PERIODICTY, ORIGIN, BOX,
|
||||
# NATOMS, NTYPES, TYPES, COORDS
|
||||
# optional fields: others in enum above, but VASP ignores them
|
||||
|
||||
if msgID == SETUP:
|
||||
|
||||
origin = []
|
||||
box = []
|
||||
natoms_recv = ntypes_recv = 0
|
||||
types = []
|
||||
coords = []
|
||||
|
||||
for field in fieldID:
|
||||
if field == DIM:
|
||||
dim = cs.unpack_int(DIM)
|
||||
if dim != 3: error("VASP only performs 3d simulations")
|
||||
elif field == PERIODICITY:
|
||||
periodicity = cs.unpack(PERIODICITY,1)
|
||||
if not periodicity[0] or not periodicity[1] or not periodicity[2]:
|
||||
error("VASP wrapper only currently supports fully periodic systems")
|
||||
elif field == ORIGIN:
|
||||
origin = cs.unpack(ORIGIN,1)
|
||||
elif field == BOX:
|
||||
box = cs.unpack(BOX,1)
|
||||
elif field == NATOMS:
|
||||
natoms_recv = cs.unpack_int(NATOMS)
|
||||
if natoms != natoms_recv:
|
||||
error("VASP wrapper mis-match in number of atoms")
|
||||
elif field == NTYPES:
|
||||
ntypes_recv = cs.unpack_int(NTYPES)
|
||||
if ntypes != ntypes_recv:
|
||||
error("VASP wrapper mis-match in number of atom types")
|
||||
elif field == TYPES:
|
||||
types = cs.unpack(TYPES,1)
|
||||
elif field == COORDS:
|
||||
coords = cs.unpack(COORDS,1)
|
||||
|
||||
if not origin or not box or not natoms or not ntypes or \
|
||||
not types or not coords:
|
||||
error("Required VASP wrapper setup field not received");
|
||||
|
||||
# STEP receive at each timestep of run or minimization
|
||||
# required fields: COORDS
|
||||
# optional fields: ORIGIN, BOX
|
||||
|
||||
elif msgID == STEP:
|
||||
|
||||
coords = []
|
||||
|
||||
for field in fieldID:
|
||||
if field == COORDS:
|
||||
coords = cs.unpack(COORDS,1)
|
||||
elif field == ORIGIN:
|
||||
origin = cs.unpack(ORIGIN,1)
|
||||
elif field == BOX:
|
||||
box = cs.unpack(BOX,1)
|
||||
|
||||
if not coords: error("Required VASP wrapper step field not received");
|
||||
|
||||
else: error("VASP wrapper received unrecognized message")
|
||||
|
||||
# create POSCAR file
|
||||
|
||||
poscar_write(poscar_template,natoms,ntypes,types,coords,box)
|
||||
|
||||
# invoke VASP
|
||||
|
||||
print("\nLaunching VASP ...")
|
||||
print(vaspcmd)
|
||||
subprocess.check_output(vaspcmd,stderr=subprocess.STDOUT,shell=True)
|
||||
|
||||
# process VASP output
|
||||
|
||||
energy,forces,virial = vasprun_read()
|
||||
|
||||
# convert VASP kilobars to bars
|
||||
|
||||
for i,value in enumerate(virial): virial[i] *= 1000.0
|
||||
|
||||
# return forces, energy, pressure to client
|
||||
|
||||
cs.send(msgID,3);
|
||||
cs.pack(FORCES,4,3*natoms,forces)
|
||||
cs.pack_double(ENERGY,energy)
|
||||
cs.pack(VIRIAL,4,6,virial)
|
||||
|
||||
# final reply to client
|
||||
|
||||
cs.send(0,0)
|
||||
|
||||
# clean-up
|
||||
|
||||
del cs
|
||||
File diff suppressed because it is too large
Load Diff
@ -86,7 +86,6 @@ mc: MC package models: GCMC, Widom, fix mol/swap
|
||||
mdi: use of the MDI package and MolSSI MDI code coupling library
|
||||
meam: MEAM test for SiC and shear (same as shear examples)
|
||||
melt: rapid melt of 3d LJ system
|
||||
message: client/server coupling of 2 codes
|
||||
micelle: self-assembly of small lipid-like molecules into 2d bilayers
|
||||
min: energy minimization of 2d LJ melt
|
||||
mliap: examples for using several bundled MLIAP potentials
|
||||
|
||||
@ -1,116 +0,0 @@
|
||||
This dir contains scripts that demonstrate how to use LAMMPS as both a
|
||||
client and server code to run a simple MD simulation. LAMMPS as a
|
||||
client performs the MD timestepping. LAMMPS as a server provides the
|
||||
energy and forces between interacting particles. Every timestep the
|
||||
LAMMPS client sends a message to the LAMMPS server and receives a
|
||||
response message in return.
|
||||
|
||||
Another code could replace LAMMPS as the client, e.g. another MD code
|
||||
which wants to use a LAMMPS potential. Another code could replace
|
||||
LAMMPS as the server, e.g. a quantum code computing quantum forces, so
|
||||
that ab initio MD could be performed. See an example of the latter in
|
||||
examples/COUPLE/lammps_vasp.
|
||||
|
||||
See the MESSAGE package documentation Build_extras.html#message
|
||||
and Build_extras.html#message for more details on how client/server
|
||||
coupling works in LAMMPS.
|
||||
|
||||
--------------
|
||||
|
||||
Note that you can adjust the problem size run by these scripts by
|
||||
setting "x,y,z" variables when you run LAMMPS. The default problem size
|
||||
is x = y = z = 5, which is 500 particles.
|
||||
|
||||
lmp_mpi -v x 10 -v y 10 -v z 20 # 8000 particles
|
||||
|
||||
This applies to either in.message or in.message.client
|
||||
|
||||
You can also run the in.message scripts with an NPT integrator
|
||||
instead of NVE, if you comment/uncomment the correct lines.
|
||||
|
||||
The client and server script define a "mode" variable
|
||||
which can be set to file, zmq, mpi/one, or mpi/two,
|
||||
as illustrated below.
|
||||
|
||||
--------------
|
||||
|
||||
To run this problem in the traditional way (no client/server coupling)
|
||||
do one of these:
|
||||
|
||||
% lmp_serial -in in.message
|
||||
% mpirun -np 4 lmp_mpi -in in.message
|
||||
|
||||
Or run with in.message.tilt.
|
||||
|
||||
--------------
|
||||
|
||||
To run in client/server mode:
|
||||
|
||||
Both the client and server script must use the same messaging mode.
|
||||
This can be selected by setting the "mode" variable when you run
|
||||
LAMMPS. The default mode = file. The other options for the mode
|
||||
variable are zmq, mpione, mpitwo.
|
||||
|
||||
Here we assume LAMMPS was built to run in parallel, and the MESSAGE
|
||||
package was installed with socket (ZMQ) support. This means any of
|
||||
the 4 messaging modes can be used.
|
||||
|
||||
The next sections illustrate how to launch LAMMPS twice, once as a
|
||||
client, once as a server, for each of the messaging modes.
|
||||
|
||||
In all cases, the client should print out thermodynamic info for 50
|
||||
steps. The server should print out setup info, print nothing until
|
||||
the client exits, at which point the server should also exit.
|
||||
|
||||
The examples below show launching LAMMPS twice from the same window
|
||||
(or batch script), using the "&" character to launch the first time in
|
||||
the background. For all modes except {mpi/one}, you could also launch
|
||||
twice in separate windows on your desktop machine. It does not matter
|
||||
whether you launch the client or server first.
|
||||
|
||||
In these examples either the client or server can be run on one or
|
||||
more processors. If running in a non-MPI mode (file or zmq) you can
|
||||
launch LAMMPS on a single processor without using mpirun.
|
||||
|
||||
IMPORTANT: If you run in mpi/two mode, you must launch LAMMPS both
|
||||
times via mpirun, even if one or both of them runs on a single
|
||||
processor. This is so that MPI can figure out how to connect both MPI
|
||||
processes together to exchange MPI messages between them.
|
||||
|
||||
--------------
|
||||
|
||||
NOTE: the Script.sh file has comands to perform all the
|
||||
runs listed below.
|
||||
|
||||
--------------
|
||||
|
||||
File or ZMQ or mpi/two modes of messaging:
|
||||
|
||||
% mpirun -np 1 lmp_mpi -v mode file -log log.client -in in.message.client &
|
||||
% mpirun -np 2 lmp_mpi -v mode file -log log.server -in in.message.server
|
||||
|
||||
% mpirun -np 4 lmp_mpi -v mode zmq -log log.client -in in.message.client &
|
||||
% mpirun -np 1 lmp_mpi -v mode zmq -log log.server -in in.message.server
|
||||
|
||||
% mpirun -np 2 lmp_mpi -v mode mpitwo -log log.client -in in.message.client &
|
||||
% mpirun -np 4 lmp_mpi -v mode mpitwo -log log.server -in in.message.server
|
||||
|
||||
Or run with in.message.tilt.client/server.
|
||||
Don't run the tilt files with the "file" mode; they run too slow.
|
||||
|
||||
--------------
|
||||
|
||||
Mpi/one mode of messaging:
|
||||
|
||||
Launch LAMMPS twice in a single mpirun command:
|
||||
|
||||
% mpirun -np 2 lmp_mpi -mpicolor 0 -in in.message.client -v mode mpione -log log.client : -np 4 lmp_mpi -mpicolor 1 -in in.message.server -v mode mpione -log log.server
|
||||
|
||||
Or run with in.message.tilt.client/server.
|
||||
|
||||
The two -np values determine how many procs the client and the server
|
||||
run on.
|
||||
|
||||
A LAMMPS executable run in this manner must use the -mpicolor color
|
||||
command-line option as its first option, where color is set to one
|
||||
integer value for the 1st app, and another value for the 2nd app.
|
||||
@ -1,55 +0,0 @@
|
||||
# sample launch script
|
||||
|
||||
# message on 1 proc each
|
||||
|
||||
mpirun -np 1 lmp_mpi -log log.message.g++.1 < in.message
|
||||
|
||||
mpirun -np 1 lmp_mpi -v mode file -log log.message.client.file.g++.1 < in.message.client &
|
||||
mpirun -np 1 lmp_mpi -v mode file -log log.message.server.file.g++.1 < in.message.server
|
||||
|
||||
mpirun -np 1 lmp_mpi -v mode zmq -log log.message.client.zmq.g++.1 < in.message.client &
|
||||
mpirun -np 1 lmp_mpi -v mode zmq -log log.message.server.zmq.g++.1 < in.message.server
|
||||
|
||||
mpirun -np 1 lmp_mpi -v mode mpitwo -log log.message.client.mpitwo.g++.1 < in.message.client &
|
||||
mpirun -np 1 lmp_mpi -v mode mpitwo -log log.message.server.mpitwo.g++.1 < in.message.server
|
||||
|
||||
mpirun -np 1 lmp_mpi -m 0 -in in.message.client -v mode mpione -log log.message.client.mpione.g++.1 : -np 1 lmp_mpi -m 1 -in in.message.server -v mode mpione -log log.message.server.mpione.g++.1
|
||||
|
||||
# message on 2/4 procs each
|
||||
|
||||
mpirun -np 4 lmp_mpi -log log.message.g++.4 < in.message
|
||||
|
||||
mpirun -np 2 lmp_mpi -v mode file -log log.message.client.file.g++.2 < in.message.client &
|
||||
mpirun -np 4 lmp_mpi -v mode file -log log.message.server.file.g++.4 < in.message.server
|
||||
|
||||
mpirun -np 2 lmp_mpi -v mode zmq -log log.message.client.zmq.g++.2 < in.message.client &
|
||||
mpirun -np 4 lmp_mpi -v mode zmq -log log.message.server.zmq.g++.4 < in.message.server
|
||||
|
||||
mpirun -np 2 lmp_mpi -v mode mpitwo -log log.message.client.mpitwo.g++.2 < in.message.client &
|
||||
mpirun -np 4 lmp_mpi -v mode mpitwo -log log.message.server.mpitwo.g++.4 < in.message.server
|
||||
|
||||
mpirun -np 2 lmp_mpi -m 0 -in in.message.client -v mode mpione -log log.message.client.mpione.g++.2 : -np 4 lmp_mpi -m 1 -in in.message.server -v mode mpione -log log.message.server.mpione.g++.4
|
||||
|
||||
# message.tilt on 1 proc each
|
||||
|
||||
mpirun -np 1 lmp_mpi -log log.message.tilt.g++.1 < in.message.tilt
|
||||
|
||||
mpirun -np 1 lmp_mpi -v mode zmq -log log.message.tilt.client.zmq.g++.1 < in.message.tilt.client &
|
||||
mpirun -np 1 lmp_mpi -v mode zmq -log log.message.tilt.server.zmq.g++.1 < in.message.tilt.server
|
||||
|
||||
mpirun -np 1 lmp_mpi -v mode mpitwo -log log.message.tilt.client.mpitwo.g++.1 < in.message.tilt.client &
|
||||
mpirun -np 1 lmp_mpi -v mode mpitwo -log log.message.tilt.server.mpitwo.g++.1 < in.message.tilt.server
|
||||
|
||||
mpirun -np 1 lmp_mpi -m 0 -in in.message.tilt.client -v mode mpione -log log.message.tilt.client.mpione.g++.1 : -np 1 lmp_mpi -m 1 -in in.message.tilt.server -v mode mpione -log log.message.tilt.server.mpione.g++.1
|
||||
|
||||
# message.tilt on 2/4 procs each
|
||||
|
||||
mpirun -np 1 lmp_mpi -log log.message.tilt.g++.4 < in.message.tilt
|
||||
|
||||
mpirun -np 2 lmp_mpi -v mode zmq -log log.message.tilt.client.zmq.g++.2 < in.message.tilt.client &
|
||||
mpirun -np 4 lmp_mpi -v mode zmq -log log.message.tilt.server.zmq.g++.4 < in.message.tilt.server
|
||||
|
||||
mpirun -np 2 lmp_mpi -v mode mpitwo -log log.message.tilt.client.mpitwo.g++.2 < in.message.tilt.client &
|
||||
mpirun -np 4 lmp_mpi -v mode mpitwo -log log.message.tilt.server.mpitwo.g++.4 < in.message.tilt.server
|
||||
|
||||
mpirun -np 2 lmp_mpi -m 0 -in in.message.tilt.client -v mode mpione -log log.message.tilt.client.mpione.g++.2 : -np 4 lmp_mpi -m 1 -in in.message.tilt.server -v mode mpione -log log.message.tilt.server.mpione.g++.4
|
||||
@ -1,29 +0,0 @@
|
||||
# 3d Lennard-Jones melt - no client/server mode
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
# same with NPT
|
||||
#fix 1 all npt temp 1.0 1.0 0.1 iso 1 1 1.0
|
||||
|
||||
thermo 10
|
||||
run 50
|
||||
@ -1,43 +0,0 @@
|
||||
# 3d Lennard-Jones melt - client script
|
||||
|
||||
variable mode index file
|
||||
|
||||
if "${mode} == file" then &
|
||||
"message client md file tmp.couple" &
|
||||
elif "${mode} == zmq" &
|
||||
"message client md zmq localhost:5555" &
|
||||
elif "${mode} == mpione" &
|
||||
"message client md mpi/one" &
|
||||
elif "${mode} == mpitwo" &
|
||||
"message client md mpi/two tmp.couple"
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
atom_modify sort 0 0.0 map yes
|
||||
|
||||
lattice fcc 0.8442
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
# same with NPT
|
||||
#fix 1 all npt temp 1.0 1.0 0.1 iso 1 1 1.0
|
||||
|
||||
fix 2 all client/md
|
||||
fix_modify 2 energy yes
|
||||
|
||||
thermo 10
|
||||
run 50
|
||||
|
||||
message quit
|
||||
@ -1,29 +0,0 @@
|
||||
# 3d Lennard-Jones melt - server script
|
||||
|
||||
variable mode index file
|
||||
|
||||
if "${mode} == file" then &
|
||||
"message server md file tmp.couple" &
|
||||
elif "${mode} == zmq" &
|
||||
"message server md zmq *:5555" &
|
||||
elif "${mode} == mpione" &
|
||||
"message server md mpi/one" &
|
||||
elif "${mode} == mpitwo" &
|
||||
"message server md mpi/two tmp.couple"
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
atom_modify map yes
|
||||
|
||||
lattice fcc 0.8442
|
||||
region box block 0 1 0 1 0 1
|
||||
create_box 1 box
|
||||
mass * 1.0 # masses not used by server
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
server md
|
||||
@ -1,30 +0,0 @@
|
||||
# 2d NEMD simulation - no client/server mode
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
dimension 2
|
||||
|
||||
lattice sq2 0.8442
|
||||
region box prism 0 10 0 8 -0.5 0.5 0 0 0
|
||||
create_box 2 box
|
||||
create_atoms 1 box
|
||||
mass * 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
region slice block 4 6 INF INF INF INF
|
||||
set region slice type 2
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff * * 1.0 1.0 1.0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1
|
||||
fix 2 all deform 1 xy erate 0.01 remap v
|
||||
|
||||
thermo_style custom step temp epair etotal press xy
|
||||
|
||||
thermo 1000
|
||||
run 50000
|
||||
@ -1,44 +0,0 @@
|
||||
# 2d NEMD simulation - client script
|
||||
|
||||
variable mode index file
|
||||
|
||||
if "${mode} == file" then &
|
||||
"message client md file tmp.couple" &
|
||||
elif "${mode} == zmq" &
|
||||
"message client md zmq localhost:5555" &
|
||||
elif "${mode} == mpione" &
|
||||
"message client md mpi/one" &
|
||||
elif "${mode} == mpitwo" &
|
||||
"message client md mpi/two tmp.couple"
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
dimension 2
|
||||
atom_modify sort 0 0.0 map yes
|
||||
|
||||
lattice sq2 0.8442
|
||||
region box prism 0 10 0 8 -0.5 0.5 0 0 0
|
||||
create_box 2 box
|
||||
create_atoms 1 box
|
||||
mass * 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
region slice block 4 6 INF INF INF INF
|
||||
set region slice type 2
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1
|
||||
fix 2 all deform 1 xy erate 0.01 remap v
|
||||
|
||||
fix 3 all client/md
|
||||
fix_modify 3 energy yes
|
||||
|
||||
thermo_style custom step temp epair etotal press xy
|
||||
|
||||
thermo 1000
|
||||
run 50000
|
||||
|
||||
message quit
|
||||
@ -1,31 +0,0 @@
|
||||
# 3d Lennard-Jones melt - server script
|
||||
|
||||
variable mode index file
|
||||
|
||||
if "${mode} == file" then &
|
||||
"message server md file tmp.couple" &
|
||||
elif "${mode} == zmq" &
|
||||
"message server md zmq *:5555" &
|
||||
elif "${mode} == mpione" &
|
||||
"message server md mpi/one" &
|
||||
elif "${mode} == mpitwo" &
|
||||
"message server md mpi/two tmp.couple"
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
dimension 2
|
||||
atom_modify map yes
|
||||
|
||||
lattice sq2 0.8442
|
||||
region box prism 0 10 0 8 -0.5 0.5 0 0 0
|
||||
create_box 2 box
|
||||
create_atoms 1 box
|
||||
mass * 1.0 # masses not used by server
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff * * 1.0 1.0 1.0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
server md
|
||||
@ -1,79 +0,0 @@
|
||||
LAMMPS (22 Aug 2018)
|
||||
# 3d Lennard-Jones melt - client script
|
||||
|
||||
variable mode index file
|
||||
|
||||
if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple"
|
||||
message client md file tmp.couple
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
atom_modify sort 0 0.0 map yes
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
Time spent = 0.000752926 secs
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
# same with NPT
|
||||
#fix 1 all npt temp 1.0 1.0 0.1 iso 1 1 1.0
|
||||
|
||||
fix 2 all client/md
|
||||
fix_modify 2 energy yes
|
||||
|
||||
thermo 10
|
||||
run 50
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.303 | 2.303 | 2.303 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 0 0 -4.6176881 -5.0221006
|
||||
10 1.1347688 0 0 -4.6166043 -2.6072847
|
||||
20 0.628166 0 0 -4.62213 1.0186262
|
||||
30 0.73767593 0 0 -4.6254647 0.49629637
|
||||
40 0.69517962 0 0 -4.6253506 0.69303877
|
||||
50 0.70150496 0 0 -4.6259832 0.59551518
|
||||
Loop time of 5.0251 on 1 procs for 50 steps with 500 atoms
|
||||
|
||||
Performance: 4298.421 tau/day, 9.950 timesteps/s
|
||||
0.1% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 9.7752e-06 | 9.7752e-06 | 9.7752e-06 | 0.0 | 0.00
|
||||
Comm | 0.00014925 | 0.00014925 | 0.00014925 | 0.0 | 0.00
|
||||
Output | 0.00023127 | 0.00023127 | 0.00023127 | 0.0 | 0.00
|
||||
Modify | 5.0242 | 5.0242 | 5.0242 | 0.0 | 99.98
|
||||
Other | | 0.0004668 | | | 0.01
|
||||
|
||||
Nlocal: 500 ave 500 max 500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 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
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 4
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:05
|
||||
@ -1,79 +0,0 @@
|
||||
LAMMPS (22 Aug 2018)
|
||||
# 3d Lennard-Jones melt - client script
|
||||
|
||||
variable mode index file
|
||||
|
||||
if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple"
|
||||
message client md file tmp.couple
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
atom_modify sort 0 0.0 map yes
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
|
||||
1 by 1 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
Time spent = 0.000613928 secs
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
# same with NPT
|
||||
#fix 1 all npt temp 1.0 1.0 0.1 iso 1 1 1.0
|
||||
|
||||
fix 2 all client/md
|
||||
fix_modify 2 energy yes
|
||||
|
||||
thermo 10
|
||||
run 50
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.302 | 2.302 | 2.302 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 0 0 -4.6176881 -5.0221006
|
||||
10 1.1347688 0 0 -4.6166043 -2.6072847
|
||||
20 0.628166 0 0 -4.62213 1.0186262
|
||||
30 0.73767593 0 0 -4.6254647 0.49629637
|
||||
40 0.69517962 0 0 -4.6253506 0.69303877
|
||||
50 0.70150496 0 0 -4.6259832 0.59551518
|
||||
Loop time of 5.02384 on 2 procs for 50 steps with 500 atoms
|
||||
|
||||
Performance: 4299.499 tau/day, 9.953 timesteps/s
|
||||
50.1% CPU use with 2 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 1.9073e-06 | 3.3379e-06 | 4.7684e-06 | 0.0 | 0.00
|
||||
Comm | 0.00020742 | 0.00021136 | 0.00021529 | 0.0 | 0.00
|
||||
Output | 0.00026989 | 0.00048053 | 0.00069118 | 0.0 | 0.01
|
||||
Modify | 5.0171 | 5.0199 | 5.0228 | 0.1 | 99.92
|
||||
Other | | 0.003203 | | | 0.06
|
||||
|
||||
Nlocal: 250 ave 255 max 245 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 4
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:05
|
||||
@ -1,79 +0,0 @@
|
||||
LAMMPS (22 Aug 2018)
|
||||
# 3d Lennard-Jones melt - client script
|
||||
|
||||
variable mode index file
|
||||
|
||||
if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple"
|
||||
message client md mpi/one
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
atom_modify sort 0 0.0 map yes
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
Time spent = 0.000540018 secs
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
# same with NPT
|
||||
#fix 1 all npt temp 1.0 1.0 0.1 iso 1 1 1.0
|
||||
|
||||
fix 2 all client/md
|
||||
fix_modify 2 energy yes
|
||||
|
||||
thermo 10
|
||||
run 50
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.303 | 2.303 | 2.303 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 0 0 -4.6176881 -5.0221006
|
||||
10 1.1347688 0 0 -4.6166043 -2.6072847
|
||||
20 0.628166 0 0 -4.62213 1.0186262
|
||||
30 0.73767593 0 0 -4.6254647 0.49629637
|
||||
40 0.69517962 0 0 -4.6253506 0.69303877
|
||||
50 0.70150496 0 0 -4.6259832 0.59551518
|
||||
Loop time of 0.0403891 on 1 procs for 50 steps with 500 atoms
|
||||
|
||||
Performance: 534798.272 tau/day, 1237.959 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 4.7684e-06 | 4.7684e-06 | 4.7684e-06 | 0.0 | 0.01
|
||||
Comm | 6.3181e-05 | 6.3181e-05 | 6.3181e-05 | 0.0 | 0.16
|
||||
Output | 9.5367e-05 | 9.5367e-05 | 9.5367e-05 | 0.0 | 0.24
|
||||
Modify | 0.040053 | 0.040053 | 0.040053 | 0.0 | 99.17
|
||||
Other | | 0.0001726 | | | 0.43
|
||||
|
||||
Nlocal: 500 ave 500 max 500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 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
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 4
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
@ -1,79 +0,0 @@
|
||||
LAMMPS (22 Aug 2018)
|
||||
# 3d Lennard-Jones melt - client script
|
||||
|
||||
variable mode index file
|
||||
|
||||
if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple"
|
||||
message client md mpi/one
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
atom_modify sort 0 0.0 map yes
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
|
||||
1 by 1 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
Time spent = 0.000475883 secs
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
# same with NPT
|
||||
#fix 1 all npt temp 1.0 1.0 0.1 iso 1 1 1.0
|
||||
|
||||
fix 2 all client/md
|
||||
fix_modify 2 energy yes
|
||||
|
||||
thermo 10
|
||||
run 50
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.302 | 2.302 | 2.302 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 0 0 -4.6176881 -5.0221006
|
||||
10 1.1347688 0 0 -4.6166043 -2.6072847
|
||||
20 0.628166 0 0 -4.62213 1.0186262
|
||||
30 0.73767593 0 0 -4.6254647 0.49629637
|
||||
40 0.69517962 0 0 -4.6253506 0.69303877
|
||||
50 0.70150496 0 0 -4.6259832 0.59551518
|
||||
Loop time of 0.0208495 on 2 procs for 50 steps with 500 atoms
|
||||
|
||||
Performance: 1035997.740 tau/day, 2398.143 timesteps/s
|
||||
99.1% CPU use with 2 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 3.0994e-06 | 4.53e-06 | 5.9605e-06 | 0.0 | 0.02
|
||||
Comm | 0.00012422 | 0.00012457 | 0.00012493 | 0.0 | 0.60
|
||||
Output | 5.7697e-05 | 7.987e-05 | 0.00010204 | 0.0 | 0.38
|
||||
Modify | 0.020463 | 0.020464 | 0.020466 | 0.0 | 98.15
|
||||
Other | | 0.0001761 | | | 0.84
|
||||
|
||||
Nlocal: 250 ave 255 max 245 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 4
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
@ -1,79 +0,0 @@
|
||||
LAMMPS (22 Aug 2018)
|
||||
# 3d Lennard-Jones melt - client script
|
||||
|
||||
variable mode index file
|
||||
|
||||
if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple"
|
||||
message client md mpi/two tmp.couple
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
atom_modify sort 0 0.0 map yes
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
Time spent = 0.000603914 secs
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
# same with NPT
|
||||
#fix 1 all npt temp 1.0 1.0 0.1 iso 1 1 1.0
|
||||
|
||||
fix 2 all client/md
|
||||
fix_modify 2 energy yes
|
||||
|
||||
thermo 10
|
||||
run 50
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.303 | 2.303 | 2.303 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 0 0 -4.6176881 -5.0221006
|
||||
10 1.1347688 0 0 -4.6166043 -2.6072847
|
||||
20 0.628166 0 0 -4.62213 1.0186262
|
||||
30 0.73767593 0 0 -4.6254647 0.49629637
|
||||
40 0.69517962 0 0 -4.6253506 0.69303877
|
||||
50 0.70150496 0 0 -4.6259832 0.59551518
|
||||
Loop time of 0.069119 on 1 procs for 50 steps with 500 atoms
|
||||
|
||||
Performance: 312504.627 tau/day, 723.390 timesteps/s
|
||||
42.0% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 7.1526e-06 | 7.1526e-06 | 7.1526e-06 | 0.0 | 0.01
|
||||
Comm | 0.0001049 | 0.0001049 | 0.0001049 | 0.0 | 0.15
|
||||
Output | 0.00014019 | 0.00014019 | 0.00014019 | 0.0 | 0.20
|
||||
Modify | 0.068602 | 0.068602 | 0.068602 | 0.0 | 99.25
|
||||
Other | | 0.0002651 | | | 0.38
|
||||
|
||||
Nlocal: 500 ave 500 max 500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 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
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 4
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
@ -1,79 +0,0 @@
|
||||
LAMMPS (22 Aug 2018)
|
||||
# 3d Lennard-Jones melt - client script
|
||||
|
||||
variable mode index file
|
||||
|
||||
if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple"
|
||||
message client md mpi/two tmp.couple
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
atom_modify sort 0 0.0 map yes
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
|
||||
1 by 1 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
Time spent = 0.000667095 secs
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
# same with NPT
|
||||
#fix 1 all npt temp 1.0 1.0 0.1 iso 1 1 1.0
|
||||
|
||||
fix 2 all client/md
|
||||
fix_modify 2 energy yes
|
||||
|
||||
thermo 10
|
||||
run 50
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.302 | 2.302 | 2.302 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 0 0 -4.6176881 -5.0221006
|
||||
10 1.1347688 0 0 -4.6166043 -2.6072847
|
||||
20 0.628166 0 0 -4.62213 1.0186262
|
||||
30 0.73767593 0 0 -4.6254647 0.49629637
|
||||
40 0.69517962 0 0 -4.6253506 0.69303877
|
||||
50 0.70150496 0 0 -4.6259832 0.59551518
|
||||
Loop time of 0.0190214 on 2 procs for 50 steps with 500 atoms
|
||||
|
||||
Performance: 1135563.588 tau/day, 2628.619 timesteps/s
|
||||
58.5% CPU use with 2 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 1.9073e-06 | 2.861e-06 | 3.8147e-06 | 0.0 | 0.02
|
||||
Comm | 0.00017238 | 0.00017989 | 0.0001874 | 0.0 | 0.95
|
||||
Output | 0.00012803 | 0.00015497 | 0.00018191 | 0.0 | 0.81
|
||||
Modify | 0.018065 | 0.018181 | 0.018297 | 0.1 | 95.58
|
||||
Other | | 0.0005029 | | | 2.64
|
||||
|
||||
Nlocal: 250 ave 255 max 245 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 4
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:01
|
||||
@ -1,79 +0,0 @@
|
||||
LAMMPS (22 Aug 2018)
|
||||
# 3d Lennard-Jones melt - client script
|
||||
|
||||
variable mode index file
|
||||
|
||||
if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple"
|
||||
message client md zmq localhost:5555
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
atom_modify sort 0 0.0 map yes
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
Time spent = 0.000734091 secs
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
# same with NPT
|
||||
#fix 1 all npt temp 1.0 1.0 0.1 iso 1 1 1.0
|
||||
|
||||
fix 2 all client/md
|
||||
fix_modify 2 energy yes
|
||||
|
||||
thermo 10
|
||||
run 50
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.303 | 2.303 | 2.303 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 0 0 -4.6176881 -5.0221006
|
||||
10 1.1347688 0 0 -4.6166043 -2.6072847
|
||||
20 0.628166 0 0 -4.62213 1.0186262
|
||||
30 0.73767593 0 0 -4.6254647 0.49629637
|
||||
40 0.69517962 0 0 -4.6253506 0.69303877
|
||||
50 0.70150496 0 0 -4.6259832 0.59551518
|
||||
Loop time of 0.0778341 on 1 procs for 50 steps with 500 atoms
|
||||
|
||||
Performance: 277513.222 tau/day, 642.392 timesteps/s
|
||||
11.4% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 7.8678e-06 | 7.8678e-06 | 7.8678e-06 | 0.0 | 0.01
|
||||
Comm | 8.3685e-05 | 8.3685e-05 | 8.3685e-05 | 0.0 | 0.11
|
||||
Output | 0.00011373 | 0.00011373 | 0.00011373 | 0.0 | 0.15
|
||||
Modify | 0.07734 | 0.07734 | 0.07734 | 0.0 | 99.37
|
||||
Other | | 0.0002885 | | | 0.37
|
||||
|
||||
Nlocal: 500 ave 500 max 500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 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
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 4
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
@ -1,79 +0,0 @@
|
||||
LAMMPS (22 Aug 2018)
|
||||
# 3d Lennard-Jones melt - client script
|
||||
|
||||
variable mode index file
|
||||
|
||||
if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple"
|
||||
message client md zmq localhost:5555
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
atom_modify sort 0 0.0 map yes
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
|
||||
1 by 1 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
Time spent = 0.000570059 secs
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
# same with NPT
|
||||
#fix 1 all npt temp 1.0 1.0 0.1 iso 1 1 1.0
|
||||
|
||||
fix 2 all client/md
|
||||
fix_modify 2 energy yes
|
||||
|
||||
thermo 10
|
||||
run 50
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.302 | 2.302 | 2.302 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 0 0 -4.6176881 -5.0221006
|
||||
10 1.1347688 0 0 -4.6166043 -2.6072847
|
||||
20 0.628166 0 0 -4.62213 1.0186262
|
||||
30 0.73767593 0 0 -4.6254647 0.49629637
|
||||
40 0.69517962 0 0 -4.6253506 0.69303877
|
||||
50 0.70150496 0 0 -4.6259832 0.59551518
|
||||
Loop time of 0.0416595 on 2 procs for 50 steps with 500 atoms
|
||||
|
||||
Performance: 518489.499 tau/day, 1200.207 timesteps/s
|
||||
56.5% CPU use with 2 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 2.861e-06 | 3.3379e-06 | 3.8147e-06 | 0.0 | 0.01
|
||||
Comm | 0.00013399 | 0.00013685 | 0.00013971 | 0.0 | 0.33
|
||||
Output | 8.6784e-05 | 0.00011206 | 0.00013733 | 0.0 | 0.27
|
||||
Modify | 0.040948 | 0.04103 | 0.041112 | 0.0 | 98.49
|
||||
Other | | 0.0003769 | | | 0.90
|
||||
|
||||
Nlocal: 250 ave 255 max 245 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 4
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
@ -1,85 +0,0 @@
|
||||
LAMMPS (22 Aug 2018)
|
||||
# 3d Lennard-Jones melt - no client/server mode
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
Time spent = 0.000682831 secs
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
# same with NPT
|
||||
#fix 1 all npt temp 1.0 1.0 0.1 iso 1 1 1.0
|
||||
|
||||
thermo 10
|
||||
run 50
|
||||
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 = 6 6 6
|
||||
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
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.143 | 3.143 | 3.143 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 -6.7733681 0 -4.6176881 -5.0221006
|
||||
10 1.1347688 -6.3153532 0 -4.6166043 -2.6072847
|
||||
20 0.628166 -5.5624945 0 -4.62213 1.0186262
|
||||
30 0.73767593 -5.7297655 0 -4.6254647 0.49629637
|
||||
40 0.69517962 -5.6660345 0 -4.6253506 0.69303877
|
||||
50 0.70150496 -5.6761362 0 -4.6259832 0.59551518
|
||||
Loop time of 0.039681 on 1 procs for 50 steps with 500 atoms
|
||||
|
||||
Performance: 544341.699 tau/day, 1260.050 timesteps/s
|
||||
99.2% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.029993 | 0.029993 | 0.029993 | 0.0 | 75.59
|
||||
Neigh | 0.0073051 | 0.0073051 | 0.0073051 | 0.0 | 18.41
|
||||
Comm | 0.0012736 | 0.0012736 | 0.0012736 | 0.0 | 3.21
|
||||
Output | 0.00012803 | 0.00012803 | 0.00012803 | 0.0 | 0.32
|
||||
Modify | 0.00053287 | 0.00053287 | 0.00053287 | 0.0 | 1.34
|
||||
Other | | 0.000448 | | | 1.13
|
||||
|
||||
Nlocal: 500 ave 500 max 500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1946 ave 1946 max 1946 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 18820 ave 18820 max 18820 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 18820
|
||||
Ave neighs/atom = 37.64
|
||||
Neighbor list builds = 4
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
@ -1,85 +0,0 @@
|
||||
LAMMPS (22 Aug 2018)
|
||||
# 3d Lennard-Jones melt - no client/server mode
|
||||
|
||||
variable x index 5
|
||||
variable y index 5
|
||||
variable z index 5
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 5 0 $y 0 $z
|
||||
region box block 0 5 0 5 0 $z
|
||||
region box block 0 5 0 5 0 5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 500 atoms
|
||||
Time spent = 0.000656843 secs
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
# same with NPT
|
||||
#fix 1 all npt temp 1.0 1.0 0.1 iso 1 1 1.0
|
||||
|
||||
thermo 10
|
||||
run 50
|
||||
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 = 6 6 6
|
||||
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
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.109 | 3.109 | 3.109 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 -6.7733681 0 -4.6176881 -5.0221006
|
||||
10 1.1347688 -6.3153532 0 -4.6166043 -2.6072847
|
||||
20 0.628166 -5.5624945 0 -4.62213 1.0186262
|
||||
30 0.73767593 -5.7297655 0 -4.6254647 0.49629637
|
||||
40 0.69517962 -5.6660345 0 -4.6253506 0.69303877
|
||||
50 0.70150496 -5.6761362 0 -4.6259832 0.59551518
|
||||
Loop time of 0.0131519 on 4 procs for 50 steps with 500 atoms
|
||||
|
||||
Performance: 1642350.242 tau/day, 3801.737 timesteps/s
|
||||
97.9% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.006074 | 0.0065379 | 0.0072589 | 0.6 | 49.71
|
||||
Neigh | 0.0014219 | 0.0015552 | 0.0017018 | 0.3 | 11.82
|
||||
Comm | 0.003546 | 0.0043943 | 0.0049584 | 0.8 | 33.41
|
||||
Output | 0.000108 | 0.00012845 | 0.00016999 | 0.0 | 0.98
|
||||
Modify | 0.00014353 | 0.00014949 | 0.00015569 | 0.0 | 1.14
|
||||
Other | | 0.0003865 | | | 2.94
|
||||
|
||||
Nlocal: 125 ave 128 max 121 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 1 1
|
||||
Nghost: 1091 ave 1094 max 1089 min
|
||||
Histogram: 1 0 1 0 1 0 0 0 0 1
|
||||
Neighs: 4705 ave 4849 max 4648 min
|
||||
Histogram: 2 1 0 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 18820
|
||||
Ave neighs/atom = 37.64
|
||||
Neighbor list builds = 4
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
@ -1,44 +0,0 @@
|
||||
LAMMPS (22 Aug 2018)
|
||||
# 3d Lennard-Jones melt - server script
|
||||
|
||||
variable mode index file
|
||||
|
||||
if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple"
|
||||
message server md file tmp.couple
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
atom_modify map yes
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
region box block 0 1 0 1 0 1
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (1.6796 1.6796 1.6796)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
mass * 1.0 # masses not used by server
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
server md
|
||||
1 by 1 by 1 MPI processor grid
|
||||
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 6 6 6
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Server MD calls = 51
|
||||
Server MD reneighborings 5
|
||||
Total wall time: 0:00:05
|
||||
@ -1,44 +0,0 @@
|
||||
LAMMPS (22 Aug 2018)
|
||||
# 3d Lennard-Jones melt - server script
|
||||
|
||||
variable mode index file
|
||||
|
||||
if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple"
|
||||
message server md file tmp.couple
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
atom_modify map yes
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
region box block 0 1 0 1 0 1
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (1.6796 1.6796 1.6796)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
mass * 1.0 # masses not used by server
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
server md
|
||||
1 by 2 by 2 MPI processor grid
|
||||
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 6 6 6
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Server MD calls = 51
|
||||
Server MD reneighborings 5
|
||||
Total wall time: 0:00:05
|
||||
@ -1,44 +0,0 @@
|
||||
LAMMPS (22 Aug 2018)
|
||||
# 3d Lennard-Jones melt - server script
|
||||
|
||||
variable mode index file
|
||||
|
||||
if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple"
|
||||
message server md mpi/one
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
atom_modify map yes
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
region box block 0 1 0 1 0 1
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (1.6796 1.6796 1.6796)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
mass * 1.0 # masses not used by server
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
server md
|
||||
1 by 1 by 1 MPI processor grid
|
||||
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 6 6 6
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Server MD calls = 51
|
||||
Server MD reneighborings 5
|
||||
Total wall time: 0:00:00
|
||||
@ -1,44 +0,0 @@
|
||||
LAMMPS (22 Aug 2018)
|
||||
# 3d Lennard-Jones melt - server script
|
||||
|
||||
variable mode index file
|
||||
|
||||
if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple"
|
||||
message server md mpi/one
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
atom_modify map yes
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
region box block 0 1 0 1 0 1
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (1.6796 1.6796 1.6796)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
mass * 1.0 # masses not used by server
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
server md
|
||||
1 by 2 by 2 MPI processor grid
|
||||
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 6 6 6
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Server MD calls = 51
|
||||
Server MD reneighborings 5
|
||||
Total wall time: 0:00:00
|
||||
@ -1,44 +0,0 @@
|
||||
LAMMPS (22 Aug 2018)
|
||||
# 3d Lennard-Jones melt - server script
|
||||
|
||||
variable mode index file
|
||||
|
||||
if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple"
|
||||
message server md mpi/two tmp.couple
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
atom_modify map yes
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
region box block 0 1 0 1 0 1
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (1.6796 1.6796 1.6796)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
mass * 1.0 # masses not used by server
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
server md
|
||||
1 by 1 by 1 MPI processor grid
|
||||
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 6 6 6
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Server MD calls = 51
|
||||
Server MD reneighborings 5
|
||||
Total wall time: 0:00:00
|
||||
@ -1,44 +0,0 @@
|
||||
LAMMPS (22 Aug 2018)
|
||||
# 3d Lennard-Jones melt - server script
|
||||
|
||||
variable mode index file
|
||||
|
||||
if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple"
|
||||
message server md mpi/two tmp.couple
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
atom_modify map yes
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
region box block 0 1 0 1 0 1
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (1.6796 1.6796 1.6796)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
mass * 1.0 # masses not used by server
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
server md
|
||||
1 by 2 by 2 MPI processor grid
|
||||
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 6 6 6
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Server MD calls = 51
|
||||
Server MD reneighborings 5
|
||||
Total wall time: 0:00:00
|
||||
@ -1,44 +0,0 @@
|
||||
LAMMPS (22 Aug 2018)
|
||||
# 3d Lennard-Jones melt - server script
|
||||
|
||||
variable mode index file
|
||||
|
||||
if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple"
|
||||
message server md zmq *:5555
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
atom_modify map yes
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
region box block 0 1 0 1 0 1
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (1.6796 1.6796 1.6796)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
mass * 1.0 # masses not used by server
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
server md
|
||||
1 by 1 by 1 MPI processor grid
|
||||
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 6 6 6
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Server MD calls = 51
|
||||
Server MD reneighborings 5
|
||||
Total wall time: 0:00:00
|
||||
@ -1,44 +0,0 @@
|
||||
LAMMPS (22 Aug 2018)
|
||||
# 3d Lennard-Jones melt - server script
|
||||
|
||||
variable mode index file
|
||||
|
||||
if "${mode} == file" then "message server md file tmp.couple" elif "${mode} == zmq" "message server md zmq *:5555" elif "${mode} == mpione" "message server md mpi/one" elif "${mode} == mpitwo" "message server md mpi/two tmp.couple"
|
||||
message server md zmq *:5555
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
atom_modify map yes
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
region box block 0 1 0 1 0 1
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (1.6796 1.6796 1.6796)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
mass * 1.0 # masses not used by server
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
server md
|
||||
1 by 2 by 2 MPI processor grid
|
||||
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 6 6 6
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Server MD calls = 51
|
||||
Server MD reneighborings 5
|
||||
Total wall time: 0:00:00
|
||||
@ -1,130 +0,0 @@
|
||||
LAMMPS (22 Aug 2018)
|
||||
# 2d NEMD simulation - client script
|
||||
|
||||
variable mode index file
|
||||
|
||||
if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple"
|
||||
message client md mpi/one
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
dimension 2
|
||||
atom_modify sort 0 0.0 map yes
|
||||
|
||||
lattice sq2 0.8442
|
||||
Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
|
||||
region box prism 0 10 0 8 -0.5 0.5 0 0 0
|
||||
create_box 2 box
|
||||
Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 160 atoms
|
||||
Time spent = 0.000485897 secs
|
||||
mass * 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
region slice block 4 6 INF INF INF INF
|
||||
set region slice type 2
|
||||
40 settings made for type
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1
|
||||
fix 2 all deform 1 xy erate 0.01 remap v
|
||||
|
||||
fix 3 all client/md
|
||||
fix_modify 3 energy yes
|
||||
|
||||
thermo_style custom step temp epair etotal press xy
|
||||
|
||||
thermo 1000
|
||||
run 50000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 0
|
||||
ghost atom cutoff = 0
|
||||
binsize = 15.3919, bins = 1 1 1
|
||||
0 neighbor lists, perpetual/occasional/extra = 0 0 0
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.308 | 2.308 | 2.308 Mbytes
|
||||
Step Temp E_pair TotEng Press Xy
|
||||
0 1.44 0 1.431 1.2080502 0
|
||||
1000 1.0086399 0 1.3760711 6.8772078 0.61567613
|
||||
2000 1.0707188 0 1.3744107 6.628097 1.2313523
|
||||
3000 1.0627515 0 1.310096 6.1647179 1.8470284
|
||||
4000 0.94091054 0 1.268976 6.4723215 2.4627045
|
||||
5000 1.0218949 0 1.2430242 5.6945977 3.0783806
|
||||
6000 0.98649481 0 1.1997565 5.2870413 3.6940568
|
||||
7000 0.9047957 0 1.1461262 5.9291636 4.3097329
|
||||
8000 0.85697614 0 1.0437412 5.0652097 4.925409
|
||||
9000 0.84208329 0 1.109218 6.1749808 5.5410852
|
||||
10000 0.86418108 0 1.1594773 6.2581867 6.1567613
|
||||
11000 0.95136356 0 1.1650901 5.8389085 6.7724374
|
||||
12000 0.94571583 0 1.2210342 6.2498816 7.3881135
|
||||
13000 0.95994288 0 1.2172042 5.9608165 -7.3881135
|
||||
14000 0.99053999 0 1.2925597 6.9994446 -6.7724374
|
||||
15000 1.0316726 0 1.3346023 6.6902672 -6.1567613
|
||||
16000 0.99537481 0 1.3227696 7.0301123 -5.5410852
|
||||
17000 1.0306843 0 1.3101457 6.4750102 -4.925409
|
||||
18000 1.071154 0 1.2947547 5.695888 -4.3097329
|
||||
19000 0.97120752 0 1.3035465 7.3945362 -3.6940568
|
||||
20000 0.97198994 0 1.2244663 6.0047605 -3.0783806
|
||||
21000 0.97943545 0 1.2393394 6.3871012 -2.4627045
|
||||
22000 0.98550707 0 1.1768148 5.019967 -1.8470284
|
||||
23000 0.96920052 0 1.1730698 5.7944947 -1.2313523
|
||||
24000 0.94069959 0 1.184119 5.8434876 -0.61567613
|
||||
25000 0.91569312 0 1.1642118 5.668997 0
|
||||
26000 0.98882932 0 1.1999248 5.0115507 0.61567613
|
||||
27000 0.8972608 0 1.2556546 7.0837158 1.2313523
|
||||
28000 0.93554756 0 1.2221911 5.9302841 1.8470284
|
||||
29000 0.97894608 0 1.2168736 5.5766766 2.4627045
|
||||
30000 0.97877055 0 1.2575839 6.4308887 3.0783806
|
||||
31000 1.0002387 0 1.2338069 5.3873124 3.6940568
|
||||
32000 0.89608618 0 1.2382021 6.7892204 4.3097329
|
||||
33000 0.87439302 0 1.2252635 7.078134 4.925409
|
||||
34000 1.076102 0 1.2991393 5.5556892 5.5410852
|
||||
35000 1.0018689 0 1.272105 6.1320483 6.1567613
|
||||
36000 0.93327214 0 1.2428039 7.0030867 6.7724374
|
||||
37000 1.0770236 0 1.3002931 5.4996076 7.3881135
|
||||
38000 0.98715132 0 1.215562 5.5958335 -7.3881135
|
||||
39000 0.95028417 0 1.2566706 6.4133713 -6.7724374
|
||||
40000 1.0445585 0 1.241151 5.3589806 -6.1567613
|
||||
41000 0.93799713 0 1.2109086 6.4957845 -5.5410852
|
||||
42000 0.99231038 0 1.2228781 5.9363471 -4.925409
|
||||
43000 0.97913815 0 1.1854842 5.8837987 -4.3097329
|
||||
44000 0.86748838 0 1.1616201 6.8991278 -3.6940568
|
||||
45000 0.96284421 0 1.1549383 5.1226785 -3.0783806
|
||||
46000 0.98701623 0 1.170581 4.9719567 -2.4627045
|
||||
47000 0.92618683 0 1.2146576 6.7100075 -1.8470284
|
||||
48000 1.0092593 0 1.2523988 5.7067864 -1.2313523
|
||||
49000 1.0187472 0 1.271608 5.3355092 -0.61567613
|
||||
50000 1.0194881 0 1.2831094 6.2449759 0
|
||||
Loop time of 1.74559 on 1 procs for 50000 steps with 160 atoms
|
||||
|
||||
Performance: 12374053.445 tau/day, 28643.642 timesteps/s
|
||||
100.0% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0.0020533 | 0.0020533 | 0.0020533 | 0.0 | 0.12
|
||||
Comm | 0.015517 | 0.015517 | 0.015517 | 0.0 | 0.89
|
||||
Output | 0.00052404 | 0.00052404 | 0.00052404 | 0.0 | 0.03
|
||||
Modify | 1.6784 | 1.6784 | 1.6784 | 0.0 | 96.15
|
||||
Other | | 0.04905 | | | 2.81
|
||||
|
||||
Nlocal: 160 ave 160 max 160 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 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
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 5270
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:01
|
||||
@ -1,130 +0,0 @@
|
||||
LAMMPS (22 Aug 2018)
|
||||
# 2d NEMD simulation - client script
|
||||
|
||||
variable mode index file
|
||||
|
||||
if "${mode} == file" then "message client md file tmp.couple" elif "${mode} == zmq" "message client md zmq localhost:5555" elif "${mode} == mpione" "message client md mpi/one" elif "${mode} == mpitwo" "message client md mpi/two tmp.couple"
|
||||
message client md mpi/one
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
dimension 2
|
||||
atom_modify sort 0 0.0 map yes
|
||||
|
||||
lattice sq2 0.8442
|
||||
Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
|
||||
region box prism 0 10 0 8 -0.5 0.5 0 0 0
|
||||
create_box 2 box
|
||||
Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0)
|
||||
2 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 160 atoms
|
||||
Time spent = 0.000453949 secs
|
||||
mass * 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
region slice block 4 6 INF INF INF INF
|
||||
set region slice type 2
|
||||
40 settings made for type
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1
|
||||
fix 2 all deform 1 xy erate 0.01 remap v
|
||||
|
||||
fix 3 all client/md
|
||||
fix_modify 3 energy yes
|
||||
|
||||
thermo_style custom step temp epair etotal press xy
|
||||
|
||||
thermo 1000
|
||||
run 50000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 0
|
||||
ghost atom cutoff = 0
|
||||
binsize = 15.3919, bins = 1 1 1
|
||||
0 neighbor lists, perpetual/occasional/extra = 0 0 0
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.308 | 2.308 | 2.308 Mbytes
|
||||
Step Temp E_pair TotEng Press Xy
|
||||
0 1.44 0 1.431 1.2080502 0
|
||||
1000 1.0876599 0 1.3637783 6.063363 0.61567613
|
||||
2000 1.0722996 0 1.4108622 7.0518942 1.2313523
|
||||
3000 1.0580774 0 1.3845895 6.0395275 1.8470284
|
||||
4000 1.0068006 0 1.3804387 7.0944598 2.4627045
|
||||
5000 0.95391814 0 1.2578438 6.1878831 3.0783806
|
||||
6000 0.93492945 0 1.2711287 7.0440517 3.6940568
|
||||
7000 0.94107853 0 1.2384371 6.1438077 4.3097329
|
||||
8000 0.89711744 0 1.145748 6.3558305 4.925409
|
||||
9000 0.90190304 0 1.0860684 4.957098 5.5410852
|
||||
10000 0.84255749 0 1.0376892 5.2351795 6.1567613
|
||||
11000 0.90250882 0 1.0497695 4.3844838 6.7724374
|
||||
12000 0.83461274 0 1.0281949 5.1534361 7.3881135
|
||||
13000 0.80315331 0 1.0226333 5.757222 -7.3881135
|
||||
14000 0.81820939 0 0.99276466 4.6943725 -6.7724374
|
||||
15000 0.8239631 0 1.0408289 5.1669006 -6.1567613
|
||||
16000 0.88908894 0 1.1554855 6.3510278 -5.5410852
|
||||
17000 0.98268136 0 1.2086981 5.6302847 -4.925409
|
||||
18000 1.0098162 0 1.3687676 7.5243587 -4.3097329
|
||||
19000 1.0795086 0 1.4562691 7.639418 -3.6940568
|
||||
20000 1.1932155 0 1.5278988 7.0668432 -3.0783806
|
||||
21000 1.2424296 0 1.6048792 7.959585 -2.4627045
|
||||
22000 1.297169 0 1.7421262 8.9432388 -1.8470284
|
||||
23000 1.2863494 0 1.7236774 8.3584973 -1.2313523
|
||||
24000 1.4084347 0 1.7370339 7.2729078 -0.61567613
|
||||
25000 1.3339728 0 1.6883255 7.529098 0
|
||||
26000 1.1483243 0 1.5155578 7.3869994 0.61567613
|
||||
27000 1.1372606 0 1.4368323 7.0580136 1.2313523
|
||||
28000 1.0518579 0 1.355311 6.478857 1.8470284
|
||||
29000 1.0581145 0 1.2535509 5.3697479 2.4627045
|
||||
30000 0.93612564 0 1.185532 5.5520142 3.0783806
|
||||
31000 0.94387516 0 1.1716454 5.8655485 3.6940568
|
||||
32000 0.83953515 0 1.0737746 5.5551953 4.3097329
|
||||
33000 0.84862926 0 1.0564042 5.7795428 4.925409
|
||||
34000 0.83621877 0 1.079387 5.7514243 5.5410852
|
||||
35000 0.86938506 0 1.031783 4.5897825 6.1567613
|
||||
36000 0.88990609 0 1.0807597 5.3751744 6.7724374
|
||||
37000 0.89534631 0 1.1238882 5.2400355 7.3881135
|
||||
38000 0.98545003 0 1.2121125 5.7783854 -7.3881135
|
||||
39000 0.96737778 0 1.2472934 6.1139 -6.7724374
|
||||
40000 1.0664194 0 1.2956811 5.7353661 -6.1567613
|
||||
41000 1.0681494 0 1.3269435 6.3102722 -5.5410852
|
||||
42000 1.0875422 0 1.3963739 7.1208066 -4.925409
|
||||
43000 1.0968173 0 1.3388062 6.1704339 -4.3097329
|
||||
44000 1.1182109 0 1.3773214 7.0872686 -3.6940568
|
||||
45000 1.1243261 0 1.432186 6.884782 -3.0783806
|
||||
46000 1.039713 0 1.4389721 7.5585257 -2.4627045
|
||||
47000 1.0816108 0 1.4100361 6.4611126 -1.8470284
|
||||
48000 0.97637127 0 1.3605389 7.3992744 -1.2313523
|
||||
49000 1.0361978 0 1.2721873 5.8166109 -0.61567613
|
||||
50000 0.92367087 0 1.1875669 6.4685214 0
|
||||
Loop time of 2.82785 on 2 procs for 50000 steps with 160 atoms
|
||||
|
||||
Performance: 7638300.565 tau/day, 17681.251 timesteps/s
|
||||
100.0% CPU use with 2 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0.0011888 | 0.0012611 | 0.0013335 | 0.2 | 0.04
|
||||
Comm | 0.024838 | 0.025075 | 0.025312 | 0.1 | 0.89
|
||||
Output | 0.0003581 | 0.00052559 | 0.00069308 | 0.0 | 0.02
|
||||
Modify | 2.7209 | 2.7263 | 2.7318 | 0.3 | 96.41
|
||||
Other | | 0.07465 | | | 2.64
|
||||
|
||||
Nlocal: 80 ave 80 max 80 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 5257
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:02
|
||||
Some files were not shown because too many files have changed in this diff Show More
Reference in New Issue
Block a user