Merge pull request #2611 from MolSSI-MDI/mdi
Add MolSSI Driver Interface Support
This commit is contained in:
Axel Kohlmeyer
@ -121,7 +121,7 @@ set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE
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PLUGIN QEQ REPLICA RIGID SHOCK SPIN SNAP SRD KIM PYTHON MSCG MPIIO VORONOI
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USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-MESODPD USER-CGSDK
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USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD
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USER-LB USER-MANIFOLD USER-MEAMC USER-MESONT USER-MGPT USER-MISC USER-MOFFF
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USER-LB USER-MANIFOLD USER-MDI USER-MEAMC USER-MESONT USER-MGPT USER-MISC USER-MOFFF
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USER-MOLFILE USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB
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USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH
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USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM USER-YAFF USER-PACE USER-BROWNIAN)
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@ -324,8 +324,8 @@ else()
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set(CUDA_REQUEST_PIC)
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endif()
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foreach(PKG_WITH_INCL KSPACE PYTHON MLIAP VORONOI USER-COLVARS USER-MOLFILE USER-NETCDF USER-PLUMED USER-QMMM
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USER-QUIP USER-SCAFACOS USER-SMD USER-VTK KIM LATTE MESSAGE MSCG COMPRESS USER-PACE)
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foreach(PKG_WITH_INCL KSPACE PYTHON MLIAP VORONOI USER-COLVARS USER-MDI USER-MOLFILE USER-NETCDF USER-PLUMED
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USER-QMMM USER-QUIP USER-SCAFACOS USER-SMD USER-VTK KIM LATTE MESSAGE MSCG COMPRESS USER-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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66
cmake/Modules/Packages/USER-MDI.cmake
Normal file
66
cmake/Modules/Packages/USER-MDI.cmake
Normal file
@ -0,0 +1,66 @@
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find_package(mdi QUIET)
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if(${mdi_FOUND})
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set(DOWNLOAD_MDI_DEFAULT OFF)
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else()
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set(DOWNLOAD_MDI_DEFAULT ON)
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endif()
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option(DOWNLOAD_MDI "Download and compile the MDI library instead of using an already installed one" ${DOWNLOAD_MDI_DEFAULT})
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if(DOWNLOAD_MDI)
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message(STATUS "MDI download requested - we will build our own")
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set(MDI_URL "https://github.com/MolSSI-MDI/MDI_Library/archive/v1.2.9.tar.gz" CACHE STRING "URL for MDI tarball")
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set(MDI_MD5 "ddfa46d6ee15b4e59cfd527ec7212184" CACHE STRING "MD5 checksum for MDI tarball")
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mark_as_advanced(MDI_URL)
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mark_as_advanced(MDI_MD5)
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set(LAMMPS_LIB_MDI_BIN_DIR ${LAMMPS_LIB_BINARY_DIR}/mdi)
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include(ExternalProject)
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message(STATUS "Building mdi.")
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ExternalProject_Add(mdi_external
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URL ${MDI_URL}
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URL_MD5 ${MDI_MD5}
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UPDATE_COMMAND ""
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CMAKE_ARGS ${CMAKE_REQUEST_PIC}
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-DCMAKE_INSTALL_PREFIX=${LAMMPS_LIB_MDI_BIN_DIR}
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-DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
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-DCMAKE_INSTALL_LIBDIR=${CMAKE_INSTALL_LIBDIR}
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-DCMAKE_INSTALL_INCLUDEDIR=${CMAKE_INSTALL_INCLUDEDIR}
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-DBUILD_SHARED_LIBS=${BUILD_SHARED_LIBS}
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-Dlanguage=C
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CMAKE_CACHE_ARGS -DCMAKE_C_FLAGS:STRING=${CMAKE_C_FLAGS}
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-DCMAKE_CXX_FLAGS:STRING=${CMAKE_CXX_FLAGS}
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-DTargetOpenMP_FIND_COMPONENTS:STRING=C;CXX)
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# Link the lammps library against MDI
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target_include_directories(lammps PRIVATE ${LAMMPS_LIB_MDI_BIN_DIR}/${CMAKE_INSTALL_INCLUDEDIR}/mdi)
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target_link_directories(lammps PRIVATE ${LAMMPS_LIB_MDI_BIN_DIR}/${CMAKE_INSTALL_LIBDIR}/mdi)
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target_link_libraries(lammps PRIVATE mdi)
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add_dependencies(lammps mdi_external)
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# Link the lammps executable against MDI
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target_include_directories(lmp PRIVATE ${LAMMPS_LIB_MDI_BIN_DIR}/${CMAKE_INSTALL_INCLUDEDIR}/mdi)
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target_link_directories(lmp PRIVATE ${LAMMPS_LIB_MDI_BIN_DIR}/${CMAKE_INSTALL_LIBDIR}/mdi)
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target_link_libraries(lmp PRIVATE mdi)
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add_dependencies(lmp mdi_external)
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else()
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find_package(mdi)
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if(NOT mdi_FOUND)
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message(FATAL_ERROR "MDI library not found. Help CMake to find it "
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"by setting mdi_LIBRARY and mdi_INCLUDE_DIR, or set DOWNLOAD_MDI=ON "
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"to download and compile it")
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endif()
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# Link the lammps library against MDI
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target_include_directories(lammps PRIVATE ${mdi_INCLUDE_DIR})
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target_link_libraries(lammps PRIVATE ${mdi_LIBRARY})
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# Link the lammps executable against MDI
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target_include_directories(lmp PRIVATE ${mdi_INCLUDE_DIR})
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target_link_libraries(lmp PRIVATE ${mdi_LIBRARY})
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endif()
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target_compile_definitions(lammps PRIVATE -DLMP_USER_MDI)
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target_compile_definitions(lmp PRIVATE -DLMP_USER_MDI)
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@ -49,6 +49,7 @@ This is the list of packages that may require additional steps.
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* :ref:`USER-COLVARS <user-colvars>`
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* :ref:`USER-H5MD <user-h5md>`
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* :ref:`USER-INTEL <user-intel>`
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* :ref:`USER-MDI <user-mdi>`
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* :ref:`USER-MESONT <user-mesont>`
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* :ref:`USER-MOLFILE <user-molfile>`
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* :ref:`USER-NETCDF <user-netcdf>`
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@ -1539,6 +1540,35 @@ TBB and MKL.
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----------
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.. _user-mdi:
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USER-MDI package
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-----------------------------
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.. tabs::
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.. tab:: CMake build
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.. code-block:: bash
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-D DOWNLOAD_MDI=value # download MDI Library for build, value = no (default) or yes
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.. tab:: Traditional make
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Before building LAMMPS, you must build the MDI Library in
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``lib/mdi``\ . You can do this by executing a command like one
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of the following from the ``lib/mdi`` directory:
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.. code-block:: bash
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$ python Install.py -m gcc # build using gcc compiler
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$ python Install.py -m icc # build using icc compiler
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The build should produce two files: ``lib/mdi/includelink/mdi.h``
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and ``lib/mdi/liblink/libmdi.so``\ .
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----------
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.. _user-mesont:
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USER-MESONT package
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@ -67,6 +67,7 @@ An alphabetic list of all general LAMMPS commands.
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* :doc:`lattice <lattice>`
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* :doc:`log <log>`
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* :doc:`mass <mass>`
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* :doc:`mdi/engine <mdi_engine>`
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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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@ -101,6 +101,7 @@ OPT.
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* :doc:`lb/viscous <fix_lb_viscous>`
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* :doc:`lineforce <fix_lineforce>`
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* :doc:`manifoldforce <fix_manifoldforce>`
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* :doc:`mdi/engine <fix_mdi_engine>`
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* :doc:`meso/move <fix_meso_move>`
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* :doc:`momentum (k) <fix_momentum>`
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* :doc:`momentum/chunk <fix_momentum>`
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@ -23,6 +23,7 @@ General howto
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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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==============
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132
doc/src/Howto_mdi.rst
Normal file
132
doc/src/Howto_mdi.rst
Normal file
@ -0,0 +1,132 @@
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Using LAMMPS with the MDI library for code coupling
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===================================================
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..note::
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This Howto doc page will eventually replace the
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:doc:`Howto client/server <Howto_client_server>` doc page.
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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 (data) to a "server" code. The server
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responds to each request with a reply message. This enables the two
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codes to work in tandem to perform a simulation. LAMMPS can act as
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either a client or server code; it does this by using the `MolSSI
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Driver Interface (MDI) library
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<https://molssi-mdi.github.io/MDI_Library/html/index.html>`_,
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developed by the `Molecular Sciences Software Institute (MolSSI)
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<https://molssi.org>`_.
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Alternate methods for code coupling with LAMMPS are described on the
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:doc:`Howto couple <Howto_couple>` doc page.
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Some advantages of client/server coupling are that the two codes can run
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as stand-alone executables; they need not be linked together. Thus
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neither code needs to have a library interface. This also makes it easy
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to run the two codes on different numbers of processors. If a message
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protocol (format and content) is defined for a particular kind of
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simulation, then in principle any code which implements the client-side
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protocol can be used in tandem with any code which implements the
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server-side protocol. Neither code needs to know what specific other
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code it is working with.
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In MDI nomenclature, a client code is the "driver", and a server code is
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an "engine". One driver code can communicate with one or more instances
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of one or more engine codes. Driver and engine codes can be written in
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any language: C, C++, Fortran, Python, etc.
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In addition to allowing driver and engine(s) running to run as
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stand-alone executables, MDI also enables a server code to be a
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"plugin" to the client code. In this scenario, server code(s) are
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compiled as shared libraries, and one (or more) instances of the
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server are instantiated by the driver code. If the driver code runs
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in parallel, it can split its MPI communicator into multiple
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sub-communicators, and launch each plugin engine instance on a
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sub-communicator. Driver processors in that sub-communicator exchange
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messages with that engine instance, and can also send MPI messages to
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other processors in the driver. The driver code can also destroy
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engine instances and re-instantiate them.
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The way that a driver communicates with an engine is by making
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MDI_Send() and MDI_Recv() calls, which are conceptually similar to
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MPI_Send() and MPI_Recv() calls. Each send or receive has a string
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which identifies the command name, and optionally some data, which can
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be a single value or vector of values of any data type. Inside the
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MDI library, data is exchanged between the driver and engine via MPI
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calls or sockets. This a run-time choice by the user.
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-------------
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As an example, LAMMPS and the ``pw.x`` command from Quantum Espresso (a
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suite of quantum DFT codes), can work together via the MDI library to
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perform an ab initio MD (AIMD) simulation, where LAMMPS runs an MD
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simulation and sends a message each timestep to ``pw.x`` asking it to
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compute quantum forces on the current configuration of atoms. Here is
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how the 2 codes are launched to communicate by MPI:
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.. code-block:: bash
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% mpirun -np 2 lmp_mpi -mdi "-role DRIVER -name d -method MPI" \
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-in in.aimd : -np 16 pw.x -in qe.in -mdi "-role ENGINE -name e -method MPI"
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In this case LAMMPS runs on 2 processors (MPI tasks), ``pw.x`` runs on 16
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processors.
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Here is how the 2 codes are launched to communicate by sockets:
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.. code-block:: bash
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% mpirun -np 2 lmp_mpi -mdi "-role DRIVER -name d -method TCP -port 8021" -in in.aimd
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% mpirun -np 16 pw.x -in qe.in -mdi "-role ENGINE -name e -method TCP -port 8021 -hostname localhost"
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These commands could be issued in different windows on a desktop
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machine. Or in the same window, if the first command is ended with
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"&" so as to run in the background. If "localhost" is replaced by an
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IP address, ``pw.x`` could be run on another machine on the same network, or
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even on another machine across the country.
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After both codes initialize themselves to model the same system, this is
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what occurs each timestep:
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* LAMMPS send a ">COORDS" message to ``pw.x`` with a 3*N vector of current atom coords
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* ``pw.x`` receives the message/coords and computes quantum forces on all the atoms
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* LAMMPS send a "<FORCES" message to ``pw.x`` and waits for the result
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* ``pw.x`` receives the message (after its computation finishes) and sends a 3*N vector of forces
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* LAMMPS receives the forces and time integrates to complete a single timestep
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-------------
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Examples scripts for using LAMMPS as an MDI engine are in the
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examples/mdi directory. See the README file in that directory for
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instructions on how to run the examples.
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..note::
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Work is underway to add commands that allow LAMMPS to be used as an
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MDI driver, e.g. for the AIMD example discussed above. Example
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scripts for this usage mode will be added the same directory when
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available.
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If LAMMPS is used as a stand-alone engine it should set up the system
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it will be modeling in its input script, then invoke the
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:doc:`mdi/engine <mdi_engine>` command. This will put LAMMPS into
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engine mode where it waits for messages and data from the driver.
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When the driver sends an "EXIT" command, LAMMPS will exit engine mode
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and the input script will continue.
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If LAMMPS is used as a plugin engine it operates the same way, except
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that the driver will pass LAMMPS an input script to initialize itself.
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Upon receiving the "EXIT" command, LAMMPS will exit engine mode and the
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input script will continue. After finishing execution of the input
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script, the instance of LAMMPS will be destroyed.
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LAMMPS supports the full set of MD-appropriate engine commands defined
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by the MDI library. See the :doc:`mdi/engine <mdi_engine>` doc page for
|
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a list of these.
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If those commands are not sufficient for a user-developed driver to use
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LAMMPS as an engine, then new commands can be easily added. See these
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two files which implement the definition of MDI commands and the logic
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for responding to them:
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* src/MDI/mdi_engine.cpp
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* src/MDI/fix_mdi_engine.cpp
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@ -82,6 +82,7 @@ page gives those details.
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* :ref:`USER-INTEL <PKG-USER-INTEL>`
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* :ref:`USER-LB <PKG-USER-LB>`
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* :ref:`USER-MANIFOLD <PKG-USER-MANIFOLD>`
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* :ref:`USER-MDI <PKG-USER-MDI>`
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* :ref:`USER-MEAMC <PKG-USER-MEAMC>`
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* :ref:`USER-MESODPD <PKG-USER-MESODPD>`
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* :ref:`USER-MESONT <PKG-USER-MESONT>`
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@ -1791,6 +1792,28 @@ Waltham, MA, USA)
|
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|
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----------
|
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.. _PKG-USER-MDI:
|
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|
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USER-MDI package
|
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----------------
|
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|
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**Contents:**
|
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|
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A LAMMPS command and fix to allow client-server coupling of LAMMPS to
|
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other atomic or molecular simulation codes via the `MolSSI Driver Interface
|
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(MDI) library <https://molssi-mdi.github.io/MDI_Library/html/index.html>`_.
|
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**Author:** Taylor Barnes - MolSSI, taylor.a.barnes at gmail.com
|
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**Supporting info:**
|
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|
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* src/USER-MDI/README
|
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* :doc:`mdi/engine <mdi_engine>`
|
||||
* :doc:`fix mdi/engine <fix_mdi_engine>`
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* examples/USER/mdi
|
||||
|
||||
----------
|
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.. _PKG-USER-MEAMC:
|
||||
|
||||
USER-MEAMC package
|
||||
|
||||
@ -65,6 +65,8 @@ package:
|
||||
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
|
||||
| :ref:`USER-MANIFOLD <PKG-USER-MANIFOLD>` | motion on 2d surfaces | :doc:`fix manifoldforce <fix_manifoldforce>` | USER/manifold | no |
|
||||
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
|
||||
| :ref:`USER-MDI <PKG-USER-MDI>` | client-server coupling | :doc:`MDI Howto <Howto_mdi>` | USER/mdi | ext |
|
||||
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
|
||||
| :ref:`USER-MEAMC <PKG-USER-MEAMC>` | modified EAM potential (C++) | :doc:`pair_style meam/c <pair_meamc>` | meamc | no |
|
||||
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
|
||||
| :ref:`USER-MESODPD <PKG-USER-MESODPD>` | mesoscale DPD models | :doc:`pair_style edpd <pair_mesodpd>` | USER/mesodpd | no |
|
||||
|
||||
@ -34,7 +34,7 @@ Examples
|
||||
|
||||
comm_modify mode multi reduce/multi
|
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comm_modify mode multi group solvent
|
||||
comm_modift mode multi cutoff/multi 1 10.0 cutoff/multi 2*4 15.0
|
||||
comm_modify mode multi cutoff/multi 1 10.0 cutoff/multi 2*4 15.0
|
||||
comm_modify vel yes
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||||
comm_modify mode single cutoff 5.0 vel yes
|
||||
comm_modify cutoff/multi * 0.0
|
||||
@ -75,8 +75,8 @@ communicated. in *multi/old*, a similar technique is used but atoms
|
||||
are grouped by atom type. See the :doc:`neighbor multi <neighbor>` and
|
||||
:doc:`neighbor multi/old <neighbor>` commands for
|
||||
neighbor list construction options that may also be beneficial for
|
||||
simulations of this kind. The *multi* communiction mode is only compatable
|
||||
with the *multi* neighbor style. The *multi/old* communication mode is compatble
|
||||
simulations of this kind. The *multi* communication mode is only compatible
|
||||
with the *multi* neighbor style. The *multi/old* communication mode is comparable
|
||||
with both the *multi* and *multi/old* neighbor styles.
|
||||
|
||||
The *cutoff* keyword allows you to extend the ghost cutoff distance
|
||||
@ -97,18 +97,18 @@ warning is printed, if this bond based estimate is larger than the
|
||||
communication cutoff used.
|
||||
|
||||
The *cutoff/multi* option is equivalent to *cutoff*\ , but applies to
|
||||
communication mode *multi* instead. Since the communication
|
||||
cutoffs are determined per atom collections, a collection specifier is needed and
|
||||
cutoff for one or multiple collections can be extended. Also ranges of collections
|
||||
using the usual asterisk notation can be given.
|
||||
Collections are indexed from 1 to N where N is the total number of collections.
|
||||
communication mode *multi* instead. Since the communication cutoffs are
|
||||
determined per atom collections, a collection specifier is needed and
|
||||
cutoff for one or multiple collections can be extended. Also ranges of
|
||||
collections using the usual asterisk notation can be given. Collections
|
||||
are indexed from 1 to N where N is the total number of collections.
|
||||
Note that the arguments for *cutoff/multi* are parsed right before each
|
||||
simulation to account for potential changes in the number of collections.
|
||||
Custom cutoffs are preserved between runs but if collections are redefined,
|
||||
one may want to respecify communication cutoffs.
|
||||
For granular pair styles,the default cutoff is set to the sum of the
|
||||
current maximum atomic radii for each collection.
|
||||
The *cutoff/multi/old* option is similar to *cutoff/multi* except it
|
||||
simulation to account for potential changes in the number of
|
||||
collections. Custom cutoffs are preserved between runs but if
|
||||
collections are redefined, one may want to re-specify the communication
|
||||
cutoffs. For granular pair styles,the default cutoff is set to the sum
|
||||
of the current maximum atomic radii for each collection. The
|
||||
*cutoff/multi/old* option is similar to *cutoff/multi* except it
|
||||
operates on atom types as opposed to collections.
|
||||
|
||||
The *reduce/multi* option applies to *multi* and sets the communication
|
||||
@ -147,7 +147,7 @@ ghost cutoff should be set.
|
||||
In the last scenario, a :doc:`fix <fix>` or :doc:`compute <compute>` or
|
||||
:doc:`pairwise potential <pair_style>` needs to calculate with ghost
|
||||
atoms beyond the normal pairwise cutoff for some computation it
|
||||
performs (e.g. locate neighbors of ghost atoms in a multibody pair
|
||||
performs (e.g. locate neighbors of ghost atoms in a manybody pair
|
||||
potential). Setting the ghost cutoff appropriately can insure it will
|
||||
find the needed atoms.
|
||||
|
||||
|
||||
@ -59,6 +59,7 @@ Commands
|
||||
lattice
|
||||
log
|
||||
mass
|
||||
mdi_engine
|
||||
message
|
||||
min_modify
|
||||
min_spin
|
||||
|
||||
59
doc/src/fix_mdi_engine.rst
Normal file
59
doc/src/fix_mdi_engine.rst
Normal file
@ -0,0 +1,59 @@
|
||||
.. index:: fix move
|
||||
|
||||
fix mdi/engine command
|
||||
======================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
fix ID group-ID mdi/engine
|
||||
|
||||
* ID, group-ID are documented in :doc:`fix <fix>` command
|
||||
* mdi/engine = style name of this fix command
|
||||
|
||||
Examples
|
||||
""""""""
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
fix 1 all mdi/engine
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
This fix is used along with the :doc:`mdi/engine <mdi_engine>` command
|
||||
to enable LAMMPS to use the `MDI Library
|
||||
<https://molssi-mdi.github.io/MDI_Library/html/index.html>`_ to run as
|
||||
an MDI engine. The fix provides hooks that enable MDI driver codes to
|
||||
communicate with LAMMPS at various points within a LAMMPS timestep.
|
||||
|
||||
It is not generally necessary to add this fix to a LAMMPS input file,
|
||||
even when using the :doc:`mdi/engine <mdi_engine>` command. If the
|
||||
:doc:`mdi/engine <mdi_engine>` command is executed and this fix is not
|
||||
present, it will automatically be added and applied as a new fix for
|
||||
all atoms for the duration of the command. Thus it is only necessary
|
||||
to add this fix to an input file when you want to modify the group-ID
|
||||
or the ordering of this fix relative to other fixes in the input script.
|
||||
|
||||
For more information about running LAMMPS as an MDI engine, see the
|
||||
:doc:`mdi/engine <mdi_engine>` command and the :doc:`Howto mdi
|
||||
<Howto_mdi>` doc page.
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
|
||||
This command is part of the USER-MDI package. It is only enabled if
|
||||
LAMMPS was built with that package. See the :doc:`Build package
|
||||
<Build_package>` doc page for more info.
|
||||
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`mdi/engine <mdi_engine>`
|
||||
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
88
doc/src/mdi_engine.rst
Normal file
88
doc/src/mdi_engine.rst
Normal file
@ -0,0 +1,88 @@
|
||||
.. index:: mdi_engine
|
||||
|
||||
mdi_engine command
|
||||
==================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
mdi_engine
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
This command is used to have LAMMPS act as a server with another
|
||||
client code to effectively couple the two codes together in
|
||||
client/server mode.
|
||||
|
||||
More specifically, this command causes LAMMPS to begin using the `MDI
|
||||
Library <https://molssi-mdi.github.io/MDI_Library/html/index.html>`_
|
||||
to run as an MDI engine (server), responding to commands made by an
|
||||
external MDI driver code (client). See the :doc:`Howto mdi
|
||||
<Howto_mdi>` doc page for more information about how LAMMPS can work
|
||||
as both an MDI driver or engine.
|
||||
|
||||
General information about launching codes that communicate using the
|
||||
MDI Library can be found in the `corresponding page
|
||||
<https://molssi-mdi.github.io/MDI_Library/html/library_page.html#library_launching_sec>`_
|
||||
of the MDI Library's documentation.
|
||||
|
||||
----------
|
||||
|
||||
This command should typically be used in an input script after LAMMPS
|
||||
has setup the system it is going to model in collaboration with the
|
||||
driver code. Depending on how the driver code tells the LAMMPS engine
|
||||
to exit, other commands can be executed after this command, but
|
||||
typically it should be used at the end of the LAMMPS input script.
|
||||
|
||||
To act as a MD-based MDI engine, this is the list of MDI commands from
|
||||
a driver code which LAMMPS currently recognizes. See more details
|
||||
about these commands in the `MDI library documentation
|
||||
<https://molssi-mdi.github.io/MDI_Library/html/mdi_standard.html>`_
|
||||
.. NOTE: Taylor - is this the best link for this info? Can we flesh this
|
||||
.. out with the full list of supported commands? Maybe the distinction
|
||||
.. of what "node" the commands refer to is not needed in this table?
|
||||
|
||||
.. list-table::
|
||||
:widths: 20 80
|
||||
:header-rows: 1
|
||||
|
||||
* - Command name
|
||||
- Action
|
||||
* - >NATOMS
|
||||
- Driver sends the number of atoms in the system
|
||||
* - <NATOMS
|
||||
- Driver requests the number of atoms in the system
|
||||
* - <COORDS
|
||||
- Driver requests 3*N double-precision atom coordinates
|
||||
* - >FORCES
|
||||
- Driver sends 3*N double-precision atom forces
|
||||
* - <COORDS
|
||||
- Driver requests 3*N double-precision atom forces
|
||||
* - EXIT
|
||||
- Driver tells the engine (LAMMPS) to exit engine mode
|
||||
|
||||
If these commands are not sufficient to support what a driver which
|
||||
you write needs, additional commands can be defined by simply using a
|
||||
new command name not in this list. Code to support the new command
|
||||
needs to be added to the USER-MDI package within LAMMPS; see its
|
||||
src/USER-MDI/mdi_engine.cpp and fix_mdi_engine.cpp files.
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
|
||||
This command is part of the USER-MDI package. It is only enabled if
|
||||
LAMMPS was built with that package. See the :doc:`Build package
|
||||
<Build_package>` doc page for more info.
|
||||
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`fix mdi/engine <fix_mdi_engine>`
|
||||
|
||||
Default
|
||||
"""""""
|
||||
|
||||
None
|
||||
@ -221,14 +221,15 @@ from 1 to n (inclusive). A trailing asterisk means all types from n to M
|
||||
(inclusive). A middle asterisk means all types from m to n (inclusive).
|
||||
Note that all atom types must be included in exactly one of the N collections.
|
||||
|
||||
The *collection/interval* option provides a similar capability.
|
||||
This command allows a user to define collections by specifying a
|
||||
series of cutoff intervals. LAMMPS will automatically sort atoms into these intervals
|
||||
based on their type-dependent cutoffs or their finite size.
|
||||
You must first specify the number of collections N to be
|
||||
defined followed by N values representing the upper cutoff of each interval.
|
||||
This command is particularly useful for granular pairstyles where the interaction distance
|
||||
of particles depends on their radius and may not depend on their atom type.
|
||||
The *collection/interval* option provides a similar capability. This
|
||||
command allows a user to define collections by specifying a series of
|
||||
cutoff intervals. LAMMPS will automatically sort atoms into these
|
||||
intervals based on their type-dependent cutoffs or their finite size.
|
||||
You must first specify the number of collections N to be defined
|
||||
followed by N values representing the upper cutoff of each interval.
|
||||
This command is particularly useful for granular pair styles where the
|
||||
interaction distance of particles depends on their radius and may not
|
||||
depend on their atom type.
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
|
||||
@ -47,6 +47,7 @@ Agnolin
|
||||
Ai
|
||||
Aidan
|
||||
aij
|
||||
aimd
|
||||
airebo
|
||||
Aj
|
||||
ajs
|
||||
@ -196,6 +197,7 @@ Ballenegger
|
||||
Bammann
|
||||
Banna
|
||||
Barashev
|
||||
barnes
|
||||
barostat
|
||||
Barostats
|
||||
barostatted
|
||||
@ -1207,6 +1209,7 @@ Halver
|
||||
Hamaker
|
||||
Hamel
|
||||
Hammerschmidt
|
||||
Hanley
|
||||
haptic
|
||||
Hara
|
||||
Harpertown
|
||||
@ -1269,6 +1272,7 @@ holonomic
|
||||
Homebrew
|
||||
hooke
|
||||
Hookean
|
||||
hostname
|
||||
hotpink
|
||||
Houlle
|
||||
howto
|
||||
@ -1728,6 +1732,7 @@ Lmpsdata
|
||||
lmptype
|
||||
LMT
|
||||
ln
|
||||
localhost
|
||||
localTemp
|
||||
localvectors
|
||||
Loewen
|
||||
@ -1858,6 +1863,8 @@ mc
|
||||
McLachlan
|
||||
md
|
||||
mdf
|
||||
MDI
|
||||
mdi
|
||||
mdpd
|
||||
mDPD
|
||||
meam
|
||||
@ -3143,6 +3150,7 @@ Tanmoy
|
||||
Tartakovsky
|
||||
taskset
|
||||
taubi
|
||||
taylor
|
||||
tb
|
||||
tchain
|
||||
Tchain
|
||||
|
||||
24
examples/USER/mdi/README
Normal file
24
examples/USER/mdi/README
Normal file
@ -0,0 +1,24 @@
|
||||
This dir contains scripts that demonstrate how to use LAMMPS as an
|
||||
MDI engine. LAMMPS as an engine performs the MD timestepping.
|
||||
The driver is a simple Python script. Every timestep the driver
|
||||
sends one or more commands to LAMMPS.
|
||||
|
||||
--------------
|
||||
|
||||
The Script.sh file has comands to perform some very simple example
|
||||
runs.
|
||||
|
||||
--------------
|
||||
|
||||
More complex calculations using LAMMPS as an MDI engine will
|
||||
typically require the use of an MDI driver. Several MDI drivers
|
||||
support calculations with LAMMPS, and include:
|
||||
|
||||
Ab Initio Molecular Dynamics (AIMD) Driver:
|
||||
https://github.com/MolSSI-MDI/MDI_AIMD_Driver
|
||||
|
||||
Nudged Elastic Band (NEB) Driver:
|
||||
https://github.com/MolSSI-MDI/MDI_NEB_Driver
|
||||
|
||||
Metadynamics Driver:
|
||||
https://github.com/MolSSI-MDI/MDI_Metadynamics
|
||||
16
examples/USER/mdi/Script.sh
Normal file
16
examples/USER/mdi/Script.sh
Normal file
@ -0,0 +1,16 @@
|
||||
#!/bin/bash
|
||||
# sample launch scripts
|
||||
|
||||
|
||||
# TCP, running LAMMPS on one proc
|
||||
|
||||
python driver.py -mdi "-name driver -role DRIVER -method TCP -port 8021" &
|
||||
../../../src/lmp_mdi -mdi "-name LAMMPS -role ENGINE -method TCP -port 8021 -hostname localhost" -in lammps.in > lammps.out &
|
||||
wait
|
||||
|
||||
|
||||
# TCP, running LAMMPS on two procs
|
||||
|
||||
python driver.py -mdi "-name driver -role DRIVER -method TCP -port 8021" &
|
||||
mpiexec -n 2 ../../../src/lmp_mdi -mdi "-name LAMMPS -role ENGINE -method TCP -port 8021 -hostname localhost" -in lammps.in > lammps.out &
|
||||
wait
|
||||
24
examples/USER/mdi/driver.py
Normal file
24
examples/USER/mdi/driver.py
Normal file
@ -0,0 +1,24 @@
|
||||
import sys
|
||||
import mdi
|
||||
|
||||
use_mpi4py = False
|
||||
try:
|
||||
from mpi4py import MPI
|
||||
use_mpi4py = True
|
||||
except:
|
||||
pass
|
||||
|
||||
# Initialize the MDI Library
|
||||
mdi.MDI_Init(sys.argv[2])
|
||||
|
||||
# Connect to the engine
|
||||
comm = mdi.MDI_Accept_communicator()
|
||||
|
||||
# Determine the name of the engine
|
||||
mdi.MDI_Send_Command("<NAME", comm)
|
||||
name = mdi.MDI_Recv(mdi.MDI_NAME_LENGTH, mdi.MDI_CHAR, comm)
|
||||
|
||||
print("Engine name: " + str(name))
|
||||
|
||||
# Send the "EXIT" command to the engine
|
||||
mdi.MDI_Send_Command("EXIT", comm)
|
||||
92
examples/USER/mdi/lammps.data
Normal file
92
examples/USER/mdi/lammps.data
Normal file
@ -0,0 +1,92 @@
|
||||
LAMMPS data file for water
|
||||
|
||||
24 atoms
|
||||
16 bonds
|
||||
8 angles
|
||||
0 dihedrals
|
||||
0 impropers
|
||||
|
||||
2 atom types
|
||||
1 bond types
|
||||
1 angle types
|
||||
0 dihedral types
|
||||
0 improper types
|
||||
|
||||
0.0 4.9325 xlo xhi
|
||||
0.0 4.9325 ylo yhi
|
||||
0.0 4.9325 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
1 15.9994
|
||||
2 1.008
|
||||
|
||||
Pair Coeffs
|
||||
|
||||
1 0.102 3.188
|
||||
2 0.000 0.000
|
||||
|
||||
Bond Coeffs
|
||||
|
||||
1 450 0.9572
|
||||
|
||||
Angle Coeffs
|
||||
|
||||
1 55.0 104.52
|
||||
|
||||
Atoms
|
||||
|
||||
1 0 1 -0.83400 2.17919 0.196156 4.15513
|
||||
2 0 2 0.41700 2.29785 4.8353 0.126003
|
||||
3 0 2 0.41700 1.82037 1.07996 4.23498
|
||||
4 0 1 -0.83400 4.65839 0.120414 0.305758
|
||||
5 0 2 0.41700 4.67446 -0.0220991 4.29186
|
||||
6 0 2 0.41700 4.28188 0.994196 0.410515
|
||||
7 0 1 -0.83400 3.65045 2.40907 0.344349
|
||||
8 0 2 0.41700 3.52052 2.1838 4.35565
|
||||
9 0 2 0.41700 4.26579 3.14208 0.327669
|
||||
10 0 1 -0.83400 1.21327 2.62177 4.15519
|
||||
11 0 2 0.41700 1.47452 3.53837 4.0667
|
||||
12 0 2 0.41700 1.20743 2.46396 0.16677
|
||||
13 0 1 -0.83400 4.45777 4.47325 2.74192
|
||||
14 0 2 0.41700 4.53396 4.49652 1.78804
|
||||
15 0 2 0.41700 4.21354 3.56943 2.94119
|
||||
16 0 1 -0.83400 2.04119 4.41585 1.64725
|
||||
17 0 2 0.41700 2.26934 4.77582 2.50434
|
||||
18 0 2 0.41700 1.69079 3.54574 1.83793
|
||||
19 0 1 -0.83400 3.73384 1.97964 2.81949
|
||||
20 0 2 0.41700 3.41083 2.22014 1.95113
|
||||
21 0 2 0.41700 3.91914 1.04272 2.75561
|
||||
22 0 1 -0.83400 1.20859 2.09853 1.68186
|
||||
23 0 2 0.41700 1.01865 2.25693 2.60655
|
||||
24 0 2 0.41700 1.16884 1.14674 1.58832
|
||||
|
||||
Bonds
|
||||
|
||||
1 1 1 2
|
||||
2 1 1 3
|
||||
3 1 4 5
|
||||
4 1 4 6
|
||||
5 1 7 8
|
||||
6 1 7 9
|
||||
7 1 10 11
|
||||
8 1 10 12
|
||||
9 1 13 14
|
||||
10 1 13 15
|
||||
11 1 16 17
|
||||
12 1 16 18
|
||||
13 1 19 20
|
||||
14 1 19 21
|
||||
15 1 22 23
|
||||
16 1 22 24
|
||||
|
||||
Angles
|
||||
|
||||
1 1 2 1 3
|
||||
2 1 5 4 6
|
||||
3 1 8 7 9
|
||||
4 1 11 10 12
|
||||
5 1 14 13 15
|
||||
6 1 17 16 18
|
||||
7 1 20 19 21
|
||||
8 1 23 22 24
|
||||
28
examples/USER/mdi/lammps.in
Normal file
28
examples/USER/mdi/lammps.in
Normal file
@ -0,0 +1,28 @@
|
||||
units real
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
pair_style lj/cut/coul/long 10.0
|
||||
pair_modify mix arithmetic
|
||||
kspace_style pppm 1e-4
|
||||
special_bonds amber
|
||||
|
||||
atom_modify sort 0 0
|
||||
|
||||
read_data lammps.data
|
||||
|
||||
timestep 1.0
|
||||
|
||||
dump 1 all custom 1 dump.lammpstrj id element xu yu zu
|
||||
dump 2 all custom 1 dump.force id element fx fy fz
|
||||
dump 3 all xyz 1 dump.xyz
|
||||
dump_modify 1 element O H
|
||||
dump_modify 2 element O H
|
||||
|
||||
thermo_style multi
|
||||
thermo 1
|
||||
|
||||
fix 1 all nvt temp 300.0 300.0 70.0
|
||||
|
||||
mdi/engine
|
||||
69
lib/mdi/.gitignore
vendored
Normal file
69
lib/mdi/.gitignore
vendored
Normal file
@ -0,0 +1,69 @@
|
||||
# Prerequisites
|
||||
*.d
|
||||
|
||||
# Object files
|
||||
*.o
|
||||
*.ko
|
||||
*.obj
|
||||
*.elf
|
||||
|
||||
# Linker output
|
||||
*.ilk
|
||||
*.map
|
||||
*.exp
|
||||
|
||||
# Precompiled Headers
|
||||
*.gch
|
||||
*.pch
|
||||
|
||||
# Libraries
|
||||
*.lib
|
||||
*.a
|
||||
*.la
|
||||
*.lo
|
||||
|
||||
# Shared objects (inc. Windows DLLs)
|
||||
*.dll
|
||||
*.so
|
||||
*.so.*
|
||||
*.dylib
|
||||
|
||||
# Executables
|
||||
*.exe
|
||||
*.out
|
||||
*.app
|
||||
*.i*86
|
||||
*.x86_64
|
||||
*.hex
|
||||
|
||||
# Debug files
|
||||
*.dSYM/
|
||||
*.su
|
||||
*.idb
|
||||
*.pdb
|
||||
|
||||
# Kernel Module Compile Results
|
||||
*.mod*
|
||||
*.cmd
|
||||
.tmp_versions/
|
||||
modules.order
|
||||
Module.symvers
|
||||
Mkfile.old
|
||||
dkms.conf
|
||||
|
||||
# Emacs temporary files
|
||||
*~
|
||||
|
||||
# MacOS
|
||||
.DS_Store
|
||||
|
||||
# pip
|
||||
*.egg-info
|
||||
|
||||
# MDI files
|
||||
MDI_Library/
|
||||
build/
|
||||
libmdi.a
|
||||
mdi.h
|
||||
includelink
|
||||
liblink
|
||||
211
lib/mdi/Install.py
Normal file
211
lib/mdi/Install.py
Normal file
@ -0,0 +1,211 @@
|
||||
#!/usr/bin/env python
|
||||
|
||||
# install.py tool to do a generic build of a library
|
||||
# soft linked to by many of the lib/Install.py files
|
||||
# used to automate the steps described in the corresponding lib/README
|
||||
|
||||
from __future__ import print_function
|
||||
import sys,os,subprocess
|
||||
import glob
|
||||
|
||||
sys.path.append('..')
|
||||
from install_helpers import checkmd5sum
|
||||
|
||||
# help message
|
||||
|
||||
help = """
|
||||
Syntax from src dir: make lib-libname args="-m machine -e suffix"
|
||||
Syntax from lib dir: python Install.py -m machine -e suffix
|
||||
|
||||
libname = name of lib dir (e.g. atc, h5md, meam, poems, etc)
|
||||
specify -m and optionally -e, order does not matter
|
||||
|
||||
-m = peform a clean followed by "make -f Makefile.machine"
|
||||
machine = suffix of a lib/Makefile.* file
|
||||
-e = set EXTRAMAKE variable in Makefile.machine to Makefile.lammps.suffix
|
||||
does not alter existing Makefile.machine
|
||||
|
||||
Examples:
|
||||
|
||||
make lib-poems args="-m serial" # build POEMS lib with same settings as in the serial Makefile in src
|
||||
make lib-colvars args="-m mpi" # build USER-COLVARS lib with same settings as in the mpi Makefile in src
|
||||
make lib-meam args="-m ifort" # build MEAM lib with custom Makefile.ifort (using Intel Fortran)
|
||||
"""
|
||||
|
||||
# settings
|
||||
|
||||
version = "1.2.9"
|
||||
url = "https://github.com/MolSSI-MDI/MDI_Library/archive/v%s.tar.gz" % version
|
||||
|
||||
# known checksums for different MDI versions. used to validate the download.
|
||||
checksums = { \
|
||||
'1.2.7' : '2f3177b30ccdbd6ae28ea3bdd5fed0db', \
|
||||
'1.2.9' : 'ddfa46d6ee15b4e59cfd527ec7212184', \
|
||||
}
|
||||
|
||||
# print error message or help
|
||||
|
||||
def error(str=None):
|
||||
if not str: print(help)
|
||||
else: print("ERROR",str)
|
||||
sys.exit()
|
||||
|
||||
# expand to full path name
|
||||
# process leading '~' or relative path
|
||||
|
||||
def fullpath(path):
|
||||
return os.path.abspath(os.path.expanduser(path))
|
||||
|
||||
def which(program):
|
||||
def is_exe(fpath):
|
||||
return os.path.isfile(fpath) and os.access(fpath, os.X_OK)
|
||||
|
||||
fpath, fname = os.path.split(program)
|
||||
if fpath:
|
||||
if is_exe(program):
|
||||
return program
|
||||
else:
|
||||
for path in os.environ["PATH"].split(os.pathsep):
|
||||
path = path.strip('"')
|
||||
exe_file = os.path.join(path, program)
|
||||
if is_exe(exe_file):
|
||||
return exe_file
|
||||
|
||||
return None
|
||||
|
||||
def geturl(url,fname):
|
||||
success = False
|
||||
|
||||
if which('curl') != None:
|
||||
cmd = 'curl -L -o "%s" %s' % (fname,url)
|
||||
try:
|
||||
subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
|
||||
success = True
|
||||
except subprocess.CalledProcessError as e:
|
||||
print("Calling curl failed with: %s" % e.output.decode('UTF-8'))
|
||||
|
||||
if not success and which('wget') != None:
|
||||
cmd = 'wget -O "%s" %s' % (fname,url)
|
||||
try:
|
||||
subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
|
||||
success = True
|
||||
except subprocess.CalledProcessError as e:
|
||||
print("Calling wget failed with: %s" % e.output.decode('UTF-8'))
|
||||
|
||||
if not success:
|
||||
error("Failed to download source code with 'curl' or 'wget'")
|
||||
return
|
||||
|
||||
# parse args
|
||||
|
||||
args = sys.argv[1:]
|
||||
nargs = len(args)
|
||||
if nargs == 0: error()
|
||||
|
||||
machine = None
|
||||
extraflag = 0
|
||||
|
||||
iarg = 0
|
||||
while iarg < nargs:
|
||||
if args[iarg] == "-m":
|
||||
if iarg+2 > nargs: error()
|
||||
machine = args[iarg+1]
|
||||
iarg += 2
|
||||
elif args[iarg] == "-e":
|
||||
if iarg+2 > nargs: error()
|
||||
extraflag = 1
|
||||
suffix = args[iarg+1]
|
||||
iarg += 2
|
||||
else: error()
|
||||
|
||||
# set lib from working dir
|
||||
|
||||
cwd = os.getcwd()
|
||||
lib = os.path.basename(cwd)
|
||||
|
||||
# download and unpack MDI_Library tarball
|
||||
|
||||
homepath = "."
|
||||
homedir = "%s/MDI_Library" % homepath
|
||||
|
||||
print("Downloading MDI_Library ...")
|
||||
mditar = "%s/v%s.tar.gz" % (homepath,version)
|
||||
geturl(url, mditar)
|
||||
|
||||
# verify downloaded archive integrity via md5 checksum, if known.
|
||||
if version in checksums:
|
||||
if not checkmd5sum(checksums[version], mditar):
|
||||
sys.exit("Checksum for MDI library does not match")
|
||||
|
||||
print("Unpacking MDI_Library tarball ...")
|
||||
if os.path.exists("%s/v%s" % (homepath,version)):
|
||||
cmd = 'rm -rf "%s/v%s"' % (homepath,version)
|
||||
subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
|
||||
cmd = 'cd "%s"; tar -xzvf v%s.tar.gz' % (homepath,version)
|
||||
subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
|
||||
os.remove("%s/v%s.tar.gz" % (homepath,version))
|
||||
if os.path.basename(homedir) != version:
|
||||
if os.path.exists(homedir):
|
||||
cmd = 'rm -rf "%s"' % homedir
|
||||
subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
|
||||
os.rename("%s/MDI_Library-%s" % (homepath,version),homedir)
|
||||
|
||||
# create Makefile.auto as copy of Makefile.machine
|
||||
# reset EXTRAMAKE if requested
|
||||
|
||||
if not os.path.exists("Makefile.%s" % machine):
|
||||
error("lib/%s/Makefile.%s does not exist" % (lib,machine))
|
||||
|
||||
lines = open("Makefile.%s" % machine,'r').readlines()
|
||||
fp = open("Makefile.auto",'w')
|
||||
|
||||
has_extramake = False
|
||||
for line in lines:
|
||||
words = line.split()
|
||||
if len(words) == 3 and words[0] == "EXTRAMAKE" and words[1] == '=':
|
||||
has_extramake = True
|
||||
if extraflag:
|
||||
line = line.replace(words[2],"Makefile.lammps.%s" % suffix)
|
||||
fp.write(line)
|
||||
|
||||
fp.close()
|
||||
|
||||
# make the library via Makefile.auto optionally with parallel make
|
||||
|
||||
try:
|
||||
import multiprocessing
|
||||
n_cpus = multiprocessing.cpu_count()
|
||||
except:
|
||||
n_cpus = 1
|
||||
|
||||
print("Building lib%s.so ..." % lib)
|
||||
cmd = "make -f Makefile.auto clean; make -f Makefile.auto -j%d" % n_cpus
|
||||
txt = subprocess.check_output(cmd,shell=True,stderr=subprocess.STDOUT)
|
||||
print(txt.decode('UTF-8'))
|
||||
|
||||
# create 2 links in lib/mdi to MDI Library src dir
|
||||
|
||||
print("Creating links to MDI Library include and lib files")
|
||||
if os.path.isfile("includelink") or os.path.islink("includelink"):
|
||||
os.remove("includelink")
|
||||
if os.path.isfile("liblink") or os.path.islink("liblink"):
|
||||
os.remove("liblink")
|
||||
os.symlink(os.path.join(homedir, 'MDI_Library'), 'includelink')
|
||||
os.symlink(os.path.join(homepath, 'build', 'MDI_Library'), 'liblink')
|
||||
|
||||
# Append the -rpath option to Makefile.lammps
|
||||
|
||||
dir_path = os.path.dirname(os.path.realpath(__file__))
|
||||
rpath_option = "-Wl,-rpath=" + str(dir_path) + "/liblink"
|
||||
makefile_lammps = open(str(dir_path) + "/Makefile.lammps", "a")
|
||||
makefile_lammps.write(str(rpath_option) + "\n")
|
||||
makefile_lammps.close()
|
||||
|
||||
|
||||
shared_files = glob.glob( os.path.join( homepath, "liblink", "lib%s.so*" % lib) )
|
||||
if len(shared_files) > 0:
|
||||
print("Build was successful")
|
||||
else:
|
||||
error("Build of lib/%s/lib%s.so was NOT successful" % (lib,lib))
|
||||
if has_extramake and not os.path.exists("Makefile.lammps"):
|
||||
print("lib/%s/Makefile.lammps was NOT created" % lib)
|
||||
18
lib/mdi/Makefile.g++
Normal file
18
lib/mdi/Makefile.g++
Normal file
@ -0,0 +1,18 @@
|
||||
SHELL = /bin/sh
|
||||
|
||||
# which file will be copied to Makefile.lammps
|
||||
|
||||
EXTRAMAKE = Makefile.lammps.empty
|
||||
|
||||
# ------ MAKE PROCEDURE ------
|
||||
|
||||
lib: $(OBJ)
|
||||
mkdir -p build
|
||||
cd build; cmake -Dlibtype=SHARED -Dlanguage=CXX -D CMAKE_C_COMPILER=gcc -D CMAKE_CXX_COMPILER=g++ ../MDI_Library; make
|
||||
@cp $(EXTRAMAKE) Makefile.lammps
|
||||
|
||||
# ------ CLEAN ------
|
||||
|
||||
clean:
|
||||
-rm *.o *.h $(LIB)
|
||||
-rm -r build
|
||||
18
lib/mdi/Makefile.gcc
Normal file
18
lib/mdi/Makefile.gcc
Normal file
@ -0,0 +1,18 @@
|
||||
SHELL = /bin/sh
|
||||
|
||||
# which file will be copied to Makefile.lammps
|
||||
|
||||
EXTRAMAKE = Makefile.lammps.empty
|
||||
|
||||
# ------ MAKE PROCEDURE ------
|
||||
|
||||
lib: $(OBJ)
|
||||
mkdir -p build
|
||||
cd build; cmake -Dlibtype=SHARED -Dlanguage=C -D CMAKE_C_COMPILER=gcc ../MDI_Library; make
|
||||
@cp $(EXTRAMAKE) Makefile.lammps
|
||||
|
||||
# ------ CLEAN ------
|
||||
|
||||
clean:
|
||||
-rm *.o *.h $(LIB)
|
||||
-rm -r build
|
||||
18
lib/mdi/Makefile.icc
Normal file
18
lib/mdi/Makefile.icc
Normal file
@ -0,0 +1,18 @@
|
||||
SHELL = /bin/sh
|
||||
|
||||
# which file will be copied to Makefile.lammps
|
||||
|
||||
EXTRAMAKE = Makefile.lammps.empty
|
||||
|
||||
# ------ MAKE PROCEDURE ------
|
||||
|
||||
lib: $(OBJ)
|
||||
mkdir -p build
|
||||
cd build; cmake -Dlibtype=SHARED -Dlanguage=C -D CMAKE_C_COMPILER=icc -D CMAKE_CXX_COMPILER=icc ../MDI_Library; make
|
||||
@cp $(EXTRAMAKE) Makefile.lammps
|
||||
|
||||
# ------ CLEAN ------
|
||||
|
||||
clean:
|
||||
-rm *.o *.h $(LIB)
|
||||
-rm -r build
|
||||
5
lib/mdi/Makefile.lammps.empty
Normal file
5
lib/mdi/Makefile.lammps.empty
Normal file
@ -0,0 +1,5 @@
|
||||
# Settings that the LAMMPS build will import when this package library is used
|
||||
|
||||
mdi_SYSINC =
|
||||
mdi_SYSLIB =
|
||||
mdi_SYSPATH =
|
||||
18
lib/mdi/Makefile.mpi
Normal file
18
lib/mdi/Makefile.mpi
Normal file
@ -0,0 +1,18 @@
|
||||
SHELL = /bin/sh
|
||||
|
||||
# which file will be copied to Makefile.lammps
|
||||
|
||||
EXTRAMAKE = Makefile.lammps.empty
|
||||
|
||||
# ------ MAKE PROCEDURE ------
|
||||
|
||||
lib: $(OBJ)
|
||||
mkdir -p build
|
||||
cd build; cmake -Dlibtype=SHARED -Dlanguage=CXX -D CMAKE_C_COMPILER=mpicc -D CMAKE_CXX_COMPILER=mpicxx ../MDI_Library; make
|
||||
@cp $(EXTRAMAKE) Makefile.lammps
|
||||
|
||||
# ------ CLEAN ------
|
||||
|
||||
clean:
|
||||
-rm *.o *.h $(LIB)
|
||||
-rm -r build
|
||||
7
src/.gitignore
vendored
7
src/.gitignore
vendored
@ -27,6 +27,13 @@
|
||||
/*_ssa.h
|
||||
/*_ssa.cpp
|
||||
|
||||
/fix_mdi_engine.cpp
|
||||
/fix_mdi_engine.h
|
||||
/library_mdi.cpp
|
||||
/library_mdi.h
|
||||
/mdi_engine.cpp
|
||||
/mdi_engine.h
|
||||
|
||||
/fix_brownian*.cpp
|
||||
/fix_brownian*.h
|
||||
/fix_propel_self.cpp
|
||||
|
||||
@ -54,20 +54,21 @@ PACKAGE = asphere body class2 colloid compress coreshell dipole gpu \
|
||||
PACKUSER = user-adios user-atc user-awpmd user-brownian user-bocs user-cgdna \
|
||||
user-cgsdk user-colvars user-diffraction user-dpd user-drude \
|
||||
user-eff user-fep user-h5md user-intel user-lb user-manifold \
|
||||
user-meamc user-mesodpd user-mesont user-mgpt user-misc \
|
||||
user-mdi user-meamc user-mesodpd user-mesont user-mgpt user-misc \
|
||||
user-mofff \user-molfile user-netcdf user-omp user-phonon \
|
||||
user-pace user-plumed user-ptm user-qmmm user-qtb user-quip \
|
||||
user-reaction user-reaxc user-scafacos user-smd user-smtbq \
|
||||
user-sdpd user-sph user-tally user-uef user-vtk user-yaff
|
||||
|
||||
PACKLIB = compress gpu kim kokkos latte message mpiio mscg poems python voronoi \
|
||||
user-adios user-atc user-awpmd user-colvars user-h5md user-lb user-mesont \
|
||||
user-molfile user-netcdf user-pace user-plumed user-qmmm user-quip \
|
||||
user-adios user-atc user-awpmd user-colvars user-h5md user-lb user-mdi \
|
||||
user-mesont user-molfile user-netcdf user-pace user-plumed user-qmmm user-quip \
|
||||
user-scafacos user-smd user-vtk
|
||||
|
||||
PACKSYS = compress mpiio python user-lb
|
||||
|
||||
PACKINT = gpu kokkos message poems user-atc user-awpmd user-colvars user-mesont
|
||||
PACKINT = gpu kokkos message poems user-atc user-awpmd user-colvars user-mesont \
|
||||
user-mdi
|
||||
|
||||
PACKEXT = kim latte mscg voronoi \
|
||||
user-adios user-h5md user-molfile user-netcdf user-pace user-plumed \
|
||||
|
||||
71
src/USER-MDI/Install.sh
Executable file
71
src/USER-MDI/Install.sh
Executable file
@ -0,0 +1,71 @@
|
||||
# Install/unInstall package files in LAMMPS
|
||||
# mode = 0/1/2 for uninstall/install/update
|
||||
|
||||
mode=$1
|
||||
|
||||
# enforce using portable C locale
|
||||
LC_ALL=C
|
||||
export LC_ALL
|
||||
|
||||
# arg1 = file, arg2 = file it depends on
|
||||
|
||||
action () {
|
||||
if (test $mode = 0) then
|
||||
rm -f ../$1
|
||||
elif (! cmp -s $1 ../$1) then
|
||||
if (test -z "$2" || test -e ../$2) then
|
||||
cp $1 ..
|
||||
if (test $mode = 2) then
|
||||
echo " updating src/$1"
|
||||
fi
|
||||
fi
|
||||
elif (test -n "$2") then
|
||||
if (test ! -e ../$2) then
|
||||
rm -f ../$1
|
||||
fi
|
||||
fi
|
||||
}
|
||||
|
||||
# all package files with no dependencies
|
||||
|
||||
for file in *.cpp *.h; do
|
||||
test -f ${file} && action $file
|
||||
done
|
||||
|
||||
# edit 2 Makefile.package files to include/exclude package info
|
||||
|
||||
if (test $1 = 1) then
|
||||
|
||||
if (test -e ../Makefile.package) then
|
||||
sed -i -e 's/[^ \t]*mdi[^ \t]* //g' ../Makefile.package
|
||||
sed -i -e 's|^PKG_INC =[ \t]*|&-I../../lib/mdi/includelink |' ../Makefile.package
|
||||
sed -i -e 's/[^ \t]*MDI[^ \t]* //' ../Makefile.package
|
||||
sed -i -e 's|^PKG_INC =[ \t]*|&-DLMP_USER_MDI |' ../Makefile.package
|
||||
sed -i -e 's|^PKG_PATH =[ \t]*|&-L../../lib/mdi/liblink |' ../Makefile.package
|
||||
sed -i -e 's|^PKG_LIB =[ \t]*|&-lmdi |' ../Makefile.package
|
||||
sed -i -e 's|^PKG_SYSINC =[ \t]*|&$(mdi_SYSINC) |' ../Makefile.package
|
||||
sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(mdi_SYSLIB) |' ../Makefile.package
|
||||
sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(mdi_SYSPATH) |' ../Makefile.package
|
||||
fi
|
||||
|
||||
if (test -e ../Makefile.package.settings) then
|
||||
sed -i -e '/^include.*mdi.*$/d' ../Makefile.package.settings
|
||||
# multiline form needed for BSD sed on Macs
|
||||
sed -i -e '4 i \
|
||||
include ..\/..\/lib\/mdi\/Makefile.lammps
|
||||
' ../Makefile.package.settings
|
||||
|
||||
fi
|
||||
|
||||
elif (test $1 = 0) then
|
||||
|
||||
if (test -e ../Makefile.package) then
|
||||
sed -i -e 's/[^ \t]*mdi[^ \t]* //g' ../Makefile.package
|
||||
sed -i -e 's/[^ \t]*MDI[^ \t]* //' ../Makefile.package
|
||||
fi
|
||||
|
||||
if (test -e ../Makefile.package.settings) then
|
||||
sed -i -e '/^include.*mdi.*$/d' ../Makefile.package.settings
|
||||
fi
|
||||
|
||||
fi
|
||||
24
src/USER-MDI/README
Normal file
24
src/USER-MDI/README
Normal file
@ -0,0 +1,24 @@
|
||||
The USER-MDI package adds an mdi/engine command which enables LAMMPS
|
||||
to operate as a MolSSI Driver Interface (MDI) engine, responding to
|
||||
commands from an external MDI driver.
|
||||
|
||||
It uses the MDI Library, which is available at
|
||||
https://github.com/MolSSI-MDI/MDI_Library. The MDI Library is
|
||||
developed and maintained by Taylor Barnes (tbarnes1@vt.edu) at the
|
||||
Molecular Sciences Software Institute (MolSSI).
|
||||
|
||||
For more information about using MDI with LAMMPS, see the LAMMPS
|
||||
documentation for the mdi/engine command and the mdi/engine fix.
|
||||
For general purpose information about MDI, see the MDI Library
|
||||
documentation:
|
||||
https://molssi-mdi.github.io/MDI_Library/html/index.html
|
||||
|
||||
The MDI Library is required in order to use this package, and can be
|
||||
built using the Install.py file in lib/mdi. For example:
|
||||
|
||||
python Install.py -m gcc
|
||||
python Install.py -m icc
|
||||
|
||||
When using CMake to build LAMMPS the CMake configuration can use
|
||||
either a preinstalled MDI library or download and compile a
|
||||
private copy.
|
||||
953
src/USER-MDI/fix_mdi_engine.cpp
Normal file
953
src/USER-MDI/fix_mdi_engine.cpp
Normal file
@ -0,0 +1,953 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing author: Taylor Barnes (MolSSI)
|
||||
MolSSI Driver Interface (MDI) support for LAMMPS
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "fix_mdi_engine.h"
|
||||
#include "library_mdi.h"
|
||||
|
||||
#include "atom.h"
|
||||
#include "comm.h"
|
||||
#include "compute.h"
|
||||
#include "domain.h"
|
||||
#include "error.h"
|
||||
#include "force.h"
|
||||
#include "irregular.h"
|
||||
#include "library.h"
|
||||
#include "memory.h"
|
||||
#include "modify.h"
|
||||
#include "update.h"
|
||||
#include "verlet.h"
|
||||
|
||||
#include <limits>
|
||||
#include <string.h>
|
||||
|
||||
enum { NONE, REAL, METAL }; // LAMMPS units which MDI supports
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace FixConst;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
FixMDIEngine::FixMDIEngine(LAMMPS *lmp, int narg, char **arg) :
|
||||
Fix(lmp, narg, arg), id_pe(nullptr), pe(nullptr), id_ke(nullptr), ke(nullptr)
|
||||
{
|
||||
if (narg != 3) error->all(FLERR, "Illegal fix mdi command");
|
||||
|
||||
// The 2 atomic-scale units LAMMPS has are:
|
||||
// real: coords = Ang, eng = Kcal/mole, force = Kcal/mole/Ang
|
||||
// metal: coords = Ang, eng = eV, force = eV/Ang
|
||||
|
||||
lmpunits = NONE;
|
||||
if (strcmp(update->unit_style, "real") == 0) lmpunits = REAL;
|
||||
if (strcmp(update->unit_style, "metal") == 0) lmpunits = METAL;
|
||||
if (lmpunits == NONE) error->all(FLERR, "MDI requires real or metal units");
|
||||
|
||||
// MDI setup
|
||||
|
||||
most_recent_init = 0;
|
||||
exit_flag = false;
|
||||
local_exit_flag = false;
|
||||
target_command = new char[MDI_COMMAND_LENGTH + 1];
|
||||
command = new char[MDI_COMMAND_LENGTH + 1];
|
||||
current_node = new char[MDI_COMMAND_LENGTH];
|
||||
target_node = new char[MDI_COMMAND_LENGTH];
|
||||
strncpy(target_node, "\0", MDI_COMMAND_LENGTH);
|
||||
strncpy(current_node, "@DEFAULT", MDI_COMMAND_LENGTH);
|
||||
|
||||
// register the execute_command function with MDI
|
||||
|
||||
MDI_Set_execute_command_func(lammps_execute_mdi_command, this);
|
||||
|
||||
// accept a communicator to the driver
|
||||
// master = 1 for proc 0, otherwise 0
|
||||
|
||||
master = (comm->me == 0) ? 1 : 0;
|
||||
|
||||
MDI_Accept_communicator(&driver_socket);
|
||||
if (driver_socket <= 0) error->all(FLERR, "Unable to connect to driver");
|
||||
|
||||
// create computes for KE and PE
|
||||
|
||||
id_pe = utils::strdup(std::string(id) + "_pe");
|
||||
modify->add_compute(fmt::format("{} all pe", id_pe));
|
||||
|
||||
id_ke = utils::strdup(std::string(id) + "_ke");
|
||||
modify->add_compute(fmt::format("{} all ke", id_ke));
|
||||
|
||||
// irregular class and data structs used by MDI
|
||||
|
||||
irregular = new Irregular(lmp);
|
||||
add_force = nullptr;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
FixMDIEngine::~FixMDIEngine()
|
||||
{
|
||||
delete[] target_command;
|
||||
delete[] command;
|
||||
delete[] current_node;
|
||||
delete[] target_node;
|
||||
|
||||
modify->delete_compute(id_pe);
|
||||
modify->delete_compute(id_ke);
|
||||
delete irregular;
|
||||
memory->destroy(add_force);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
int FixMDIEngine::setmask()
|
||||
{
|
||||
int mask = 0;
|
||||
|
||||
mask |= POST_INTEGRATE;
|
||||
mask |= POST_FORCE;
|
||||
mask |= MIN_PRE_FORCE;
|
||||
mask |= MIN_POST_FORCE;
|
||||
|
||||
return mask;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixMDIEngine::exchange_forces()
|
||||
{
|
||||
double **f = atom->f;
|
||||
const int *const mask = atom->mask;
|
||||
const int nlocal = atom->nlocal;
|
||||
|
||||
// add forces from the driver
|
||||
|
||||
for (int i = 0; i < nlocal; ++i) {
|
||||
if (mask[i] & groupbit) {
|
||||
f[i][0] += add_force[3 * (atom->tag[i] - 1) + 0];
|
||||
f[i][1] += add_force[3 * (atom->tag[i] - 1) + 1];
|
||||
f[i][2] += add_force[3 * (atom->tag[i] - 1) + 2];
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixMDIEngine::init()
|
||||
{
|
||||
// confirm that two required computes are still available
|
||||
|
||||
int icompute_pe = modify->find_compute(id_pe);
|
||||
if (icompute_pe < 0) error->all(FLERR, "Potential energy ID for fix mdi/engine does not exist");
|
||||
int icompute_ke = modify->find_compute(id_ke);
|
||||
if (icompute_pe < 0) error->all(FLERR, "Kinetic energy ID for fix mdi/engine does not exist");
|
||||
|
||||
pe = modify->compute[icompute_pe];
|
||||
ke = modify->compute[icompute_ke];
|
||||
|
||||
// one-time allocation of add_force array
|
||||
|
||||
if (!add_force) {
|
||||
int64_t ncoords = 3 * atom->natoms;
|
||||
memory->create(add_force, ncoords, "mdi/engine:add_force");
|
||||
for (int64_t i = 0; i < ncoords; i++) add_force[i] = 0.0;
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixMDIEngine::min_setup(int vflag)
|
||||
{
|
||||
engine_mode("@FORCES");
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixMDIEngine::post_integrate()
|
||||
{
|
||||
engine_mode("@COORDS");
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixMDIEngine::min_pre_force(int vflag)
|
||||
{
|
||||
engine_mode("@COORDS");
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixMDIEngine::min_post_force(int vflag)
|
||||
{
|
||||
engine_mode("@FORCES");
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixMDIEngine::post_force(int vflag)
|
||||
{
|
||||
if (most_recent_init == 1)
|
||||
engine_mode("@FORCES");
|
||||
else if (most_recent_init == 2)
|
||||
engine_mode("@FORCES");
|
||||
}
|
||||
|
||||
// ----------------------------------------------------------------------
|
||||
// ----------------------------------------------------------------------
|
||||
// rest of file processes and responds to MDI driver commands
|
||||
// ----------------------------------------------------------------------
|
||||
// ----------------------------------------------------------------------
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
process a single command from driver
|
||||
---------------------------------------------------------------------- */
|
||||
|
||||
int FixMDIEngine::execute_command(const char *command, MDI_Comm mdicomm)
|
||||
{
|
||||
// confirm this command is supported at this node
|
||||
|
||||
int command_exists = 1;
|
||||
if (master) {
|
||||
ierr = MDI_Check_command_exists(current_node, command, MDI_COMM_NULL, &command_exists);
|
||||
}
|
||||
if (ierr != 0) error->all(FLERR, "MDI: Unable to check whether current command is supported");
|
||||
if (command_exists != 1)
|
||||
error->all(FLERR, "MDI: Received a command that is unsupported at current node");
|
||||
|
||||
// respond to any driver command
|
||||
|
||||
if (strcmp(command, ">NATOMS") == 0) {
|
||||
ierr = MDI_Recv((char *) &atom->natoms, 1, MDI_INT, mdicomm);
|
||||
if (ierr != 0) error->all(FLERR, "MDI: Unable to receive number of atoms from driver");
|
||||
MPI_Bcast(&atom->natoms, 1, MPI_INT, 0, world);
|
||||
|
||||
} else if (strcmp(command, "<NATOMS") == 0) {
|
||||
int64_t mdi_natoms = atom->natoms;
|
||||
ierr = MDI_Send((char *) &mdi_natoms, 1, MDI_INT64_T, mdicomm);
|
||||
if (ierr != 0) error->all(FLERR, "MDI: Unable to send number of atoms to driver");
|
||||
|
||||
} else if (strcmp(command, "<NTYPES") == 0) {
|
||||
ierr = MDI_Send((char *) &atom->ntypes, 1, MDI_INT, mdicomm);
|
||||
if (ierr != 0) error->all(FLERR, "MDI: Unable to send number of atom types to driver");
|
||||
|
||||
} else if (strcmp(command, "<TYPES") == 0) {
|
||||
send_types(error);
|
||||
|
||||
} else if (strcmp(command, "<LABELS") == 0) {
|
||||
send_labels(error);
|
||||
|
||||
} else if (strcmp(command, "<MASSES") == 0) {
|
||||
send_masses(error);
|
||||
|
||||
} else if (strcmp(command, "<CELL") == 0) {
|
||||
send_cell(error);
|
||||
|
||||
} else if (strcmp(command, ">CELL") == 0) {
|
||||
receive_cell(error);
|
||||
|
||||
} else if (strcmp(command, "<CELL_DISPL") == 0) {
|
||||
send_celldispl(error);
|
||||
|
||||
} else if (strcmp(command, ">CELL_DISPL") == 0) {
|
||||
receive_celldispl(error);
|
||||
|
||||
} else if (strcmp(command, ">COORDS") == 0) {
|
||||
receive_coordinates(error);
|
||||
|
||||
} else if (strcmp(command, "<COORDS") == 0) {
|
||||
send_coordinates(error);
|
||||
|
||||
} else if (strcmp(command, "<CHARGES") == 0) {
|
||||
send_charges(error);
|
||||
|
||||
} else if (strcmp(command, "<ENERGY") == 0) {
|
||||
send_energy(error);
|
||||
|
||||
} else if (strcmp(command, "<FORCES") == 0) {
|
||||
send_forces(error);
|
||||
|
||||
// replace current forces with forces received from the driver
|
||||
|
||||
} else if (strcmp(command, ">FORCES") == 0) {
|
||||
receive_forces(error, 0);
|
||||
|
||||
// add forces received from the driver to current forces
|
||||
|
||||
} else if (strcmp(command, ">+FORCES") == 0) {
|
||||
receive_forces(error, 1);
|
||||
|
||||
// initialize new MD simulation or minimization
|
||||
// return control to return to mdi/engine
|
||||
|
||||
} else if (strcmp(command, "@INIT_MD") == 0) {
|
||||
if (most_recent_init != 0) error->all(FLERR, "MDI: MDI is already performing a simulation");
|
||||
most_recent_init = 1;
|
||||
local_exit_flag = true;
|
||||
|
||||
// initialize new energy minimization
|
||||
// return control to return to mdi/engine
|
||||
|
||||
} else if (strcmp(command, "@INIT_OPTG") == 0) {
|
||||
if (most_recent_init != 0) error->all(FLERR, "MDI: MDI is already performing a simulation");
|
||||
most_recent_init = 2;
|
||||
local_exit_flag = true;
|
||||
|
||||
} else if (strcmp(command, "@") == 0) {
|
||||
strncpy(target_node, "\0", MDI_COMMAND_LENGTH);
|
||||
local_exit_flag = true;
|
||||
|
||||
} else if (strcmp(command, "<@") == 0) {
|
||||
ierr = MDI_Send(current_node, MDI_NAME_LENGTH, MDI_CHAR, mdicomm);
|
||||
if (ierr != 0) error->all(FLERR, "MDI: Unable to send node to driver");
|
||||
|
||||
} else if (strcmp(command, "<KE") == 0) {
|
||||
send_ke(error);
|
||||
|
||||
} else if (strcmp(command, "<PE") == 0) {
|
||||
send_pe(error);
|
||||
|
||||
} else if (strcmp(command, "@DEFAULT") == 0) {
|
||||
most_recent_init = 0;
|
||||
|
||||
strncpy(target_node, "@DEFAULT", MDI_COMMAND_LENGTH);
|
||||
local_exit_flag = true;
|
||||
|
||||
// are we in the middle of a geometry optimization?
|
||||
if (most_recent_init == 2) {
|
||||
// ensure that the energy and force tolerances are met
|
||||
update->etol = std::numeric_limits<double>::max();
|
||||
update->ftol = std::numeric_limits<double>::max();
|
||||
|
||||
// set the maximum number of force evaluations to 0
|
||||
update->max_eval = 0;
|
||||
}
|
||||
|
||||
} else if (strcmp(command, "@COORDS") == 0) {
|
||||
strncpy(target_node, "@COORDS", MDI_COMMAND_LENGTH);
|
||||
local_exit_flag = true;
|
||||
|
||||
} else if (strcmp(command, "@FORCES") == 0) {
|
||||
strncpy(target_node, "@FORCES", MDI_COMMAND_LENGTH);
|
||||
local_exit_flag = true;
|
||||
|
||||
} else if (strcmp(command, "EXIT") == 0) {
|
||||
// exit the driver code
|
||||
exit_flag = true;
|
||||
|
||||
// are we in the middle of a geometry optimization?
|
||||
if (most_recent_init == 2) {
|
||||
// ensure that the energy and force tolerances are met
|
||||
update->etol = std::numeric_limits<double>::max();
|
||||
update->ftol = std::numeric_limits<double>::max();
|
||||
|
||||
// set the maximum number of force evaluations to 0
|
||||
update->max_eval = 0;
|
||||
}
|
||||
|
||||
} else {
|
||||
error->all(FLERR, "MDI: Unknown command from driver");
|
||||
}
|
||||
|
||||
return 0;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
char *FixMDIEngine::engine_mode(const char *node)
|
||||
{
|
||||
/*
|
||||
if (screen)
|
||||
fprintf(screen,"MDI ENGINE MODE: %i\n",node);
|
||||
if (logfile)
|
||||
fprintf(logfile,"MDI ENGINE MODE: %i\n",node);
|
||||
*/
|
||||
|
||||
// do not process commands if engine and driver are not at same node
|
||||
// target_node = node that driver has set via a @ command
|
||||
// current_node = node that engine (LAMMPS) has set
|
||||
|
||||
strncpy(current_node, node, MDI_COMMAND_LENGTH);
|
||||
if (strcmp(target_node, "\0") != 0 && strcmp(target_node, current_node) != 0)
|
||||
local_exit_flag = true;
|
||||
|
||||
// respond to commands from the driver
|
||||
|
||||
while (not exit_flag and not local_exit_flag) {
|
||||
|
||||
// read the next command from the driver
|
||||
// all procs call this, but only proc 0 receives the command
|
||||
|
||||
ierr = MDI_Recv_command(command, driver_socket);
|
||||
if (ierr != 0) error->all(FLERR, "MDI: Unable to receive command from driver");
|
||||
|
||||
// broadcast command to the other MPI tasks
|
||||
|
||||
MPI_Bcast(command, MDI_COMMAND_LENGTH, MPI_CHAR, 0, world);
|
||||
|
||||
// execute the command
|
||||
|
||||
this->execute_command(command, driver_socket);
|
||||
|
||||
// check if the target node is something other than the current node
|
||||
|
||||
if (strcmp(target_node, "\0") != 0 && strcmp(target_node, current_node) != 0)
|
||||
local_exit_flag = true;
|
||||
}
|
||||
|
||||
// local exit occured so turn off local exit flag
|
||||
|
||||
local_exit_flag = false;
|
||||
|
||||
return command;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixMDIEngine::receive_coordinates(Error *error)
|
||||
{
|
||||
// get conversion factor to atomic units
|
||||
double posconv;
|
||||
|
||||
// real: coords = Ang, eng = Kcal/mole, force = Kcal/mole/Ang
|
||||
// metal: coords = Ang, eng = eV, force = eV/Ang
|
||||
|
||||
if (lmpunits == REAL) {
|
||||
double angstrom_to_bohr;
|
||||
MDI_Conversion_factor("angstrom", "bohr", &angstrom_to_bohr);
|
||||
posconv = force->angstrom / angstrom_to_bohr;
|
||||
} else if (lmpunits == METAL) {
|
||||
double angstrom_to_bohr;
|
||||
MDI_Conversion_factor("angstrom", "bohr", &angstrom_to_bohr);
|
||||
posconv = force->angstrom / angstrom_to_bohr;
|
||||
}
|
||||
|
||||
// create buffer to hold all coords
|
||||
|
||||
double *buffer;
|
||||
buffer = new double[3 * atom->natoms];
|
||||
|
||||
ierr = MDI_Recv((char *) buffer, 3 * atom->natoms, MDI_DOUBLE, driver_socket);
|
||||
if (ierr != 0) error->all(FLERR, "MDI: Unable to receive coordinates from driver");
|
||||
MPI_Bcast(buffer, 3 * atom->natoms, MPI_DOUBLE, 0, world);
|
||||
|
||||
// pick local atoms from the buffer
|
||||
|
||||
double **x = atom->x;
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
x[i][0] = buffer[3 * (atom->tag[i] - 1) + 0] * posconv;
|
||||
x[i][1] = buffer[3 * (atom->tag[i] - 1) + 1] * posconv;
|
||||
x[i][2] = buffer[3 * (atom->tag[i] - 1) + 2] * posconv;
|
||||
}
|
||||
|
||||
// ensure atoms are in current box & update box via shrink-wrap
|
||||
// has to be be done before invoking Irregular::migrate_atoms()
|
||||
// since it requires atoms be inside simulation box
|
||||
|
||||
if (domain->triclinic) domain->x2lamda(atom->nlocal);
|
||||
domain->pbc();
|
||||
domain->reset_box();
|
||||
if (domain->triclinic) domain->lamda2x(atom->nlocal);
|
||||
|
||||
// move atoms to new processors via irregular() only needed if
|
||||
// migrate_check() says an atom moves too far
|
||||
|
||||
if (domain->triclinic) domain->x2lamda(atom->nlocal);
|
||||
if (irregular->migrate_check()) irregular->migrate_atoms();
|
||||
if (domain->triclinic) domain->lamda2x(atom->nlocal);
|
||||
|
||||
delete[] buffer;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixMDIEngine::send_coordinates(Error *error)
|
||||
{
|
||||
// get conversion factor to atomic units
|
||||
double posconv;
|
||||
if (lmpunits == REAL) {
|
||||
double angstrom_to_bohr;
|
||||
MDI_Conversion_factor("angstrom", "bohr", &angstrom_to_bohr);
|
||||
posconv = force->angstrom / angstrom_to_bohr;
|
||||
} else if (lmpunits == METAL) {
|
||||
double angstrom_to_bohr;
|
||||
MDI_Conversion_factor("angstrom", "bohr", &angstrom_to_bohr);
|
||||
posconv = force->angstrom / angstrom_to_bohr;
|
||||
}
|
||||
|
||||
int64_t ncoords = 3 * atom->natoms;
|
||||
double *coords;
|
||||
double *coords_reduced;
|
||||
memory->create(coords, ncoords, "mdi/engine:coords");
|
||||
memory->create(coords_reduced, ncoords, "mdi/engine:coords_reduced");
|
||||
|
||||
// zero coords
|
||||
|
||||
for (int64_t icoord = 0; icoord < ncoords; icoord++) coords[icoord] = 0.0;
|
||||
|
||||
// copy local atoms into buffer at correct locations
|
||||
|
||||
double **x = atom->x;
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
coords[3 * (atom->tag[i] - 1) + 0] = x[i][0] / posconv;
|
||||
coords[3 * (atom->tag[i] - 1) + 1] = x[i][1] / posconv;
|
||||
coords[3 * (atom->tag[i] - 1) + 2] = x[i][2] / posconv;
|
||||
}
|
||||
|
||||
MPI_Reduce(coords, coords_reduced, 3 * atom->natoms, MPI_DOUBLE, MPI_SUM, 0, world);
|
||||
|
||||
ierr = MDI_Send((char *) coords_reduced, 3 * atom->natoms, MDI_DOUBLE, driver_socket);
|
||||
if (ierr != 0) error->all(FLERR, "MDI: Unable to send coordinates to driver");
|
||||
|
||||
memory->destroy(coords);
|
||||
memory->destroy(coords_reduced);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixMDIEngine::send_charges(Error *error)
|
||||
{
|
||||
double *charges;
|
||||
double *charges_reduced;
|
||||
|
||||
memory->create(charges, atom->natoms, "mdi/engine:charges");
|
||||
memory->create(charges_reduced, atom->natoms, "mdi/engine:charges_reduced");
|
||||
|
||||
// zero the charges array
|
||||
|
||||
for (int icharge = 0; icharge < atom->natoms; icharge++) charges[icharge] = 0.0;
|
||||
|
||||
// pick local atoms from the buffer
|
||||
|
||||
double *charge = atom->q;
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
for (int i = 0; i < nlocal; i++) { charges[atom->tag[i] - 1] = charge[i]; }
|
||||
|
||||
MPI_Reduce(charges, charges_reduced, atom->natoms, MPI_DOUBLE, MPI_SUM, 0, world);
|
||||
|
||||
ierr = MDI_Send((char *) charges_reduced, atom->natoms, MDI_DOUBLE, driver_socket);
|
||||
if (ierr != 0) error->all(FLERR, "MDI: Unable to send charges to driver");
|
||||
|
||||
memory->destroy(charges);
|
||||
memory->destroy(charges_reduced);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixMDIEngine::send_energy(Error *error)
|
||||
{
|
||||
// get conversion factor to atomic units
|
||||
double energy_conv;
|
||||
if (lmpunits == REAL) {
|
||||
double kelvin_to_hartree;
|
||||
MDI_Conversion_factor("kelvin_energy", "hartree", &kelvin_to_hartree);
|
||||
energy_conv = kelvin_to_hartree / force->boltz;
|
||||
} else if (lmpunits == METAL) {
|
||||
double ev_to_hartree;
|
||||
MDI_Conversion_factor("electron_volt", "hartree", &ev_to_hartree);
|
||||
energy_conv = ev_to_hartree;
|
||||
}
|
||||
|
||||
double kelvin_to_hartree;
|
||||
MDI_Conversion_factor("kelvin_energy", "hartree", &kelvin_to_hartree);
|
||||
|
||||
double potential_energy = pe->compute_scalar();
|
||||
double kinetic_energy = ke->compute_scalar();
|
||||
double total_energy;
|
||||
double *send_energy = &total_energy;
|
||||
|
||||
// convert the energy to atomic units
|
||||
potential_energy *= energy_conv;
|
||||
kinetic_energy *= energy_conv;
|
||||
total_energy = potential_energy + kinetic_energy;
|
||||
|
||||
ierr = MDI_Send((char *) send_energy, 1, MDI_DOUBLE, driver_socket);
|
||||
if (ierr != 0) error->all(FLERR, "MDI: Unable to send potential energy to driver");
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixMDIEngine::send_pe(Error *error)
|
||||
{
|
||||
// get conversion factor to atomic units
|
||||
double energy_conv;
|
||||
if (lmpunits == REAL) {
|
||||
double kelvin_to_hartree;
|
||||
MDI_Conversion_factor("kelvin_energy", "hartree", &kelvin_to_hartree);
|
||||
energy_conv = kelvin_to_hartree / force->boltz;
|
||||
} else if (lmpunits == METAL) {
|
||||
double ev_to_hartree;
|
||||
MDI_Conversion_factor("electron_volt", "hartree", &ev_to_hartree);
|
||||
energy_conv = ev_to_hartree;
|
||||
}
|
||||
|
||||
double potential_energy = pe->compute_scalar();
|
||||
double *send_energy = &potential_energy;
|
||||
|
||||
// convert the energy to atomic units
|
||||
potential_energy *= energy_conv;
|
||||
|
||||
ierr = MDI_Send((char *) send_energy, 1, MDI_DOUBLE, driver_socket);
|
||||
if (ierr != 0) error->all(FLERR, "MDI: Unable to send potential energy to driver");
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixMDIEngine::send_ke(Error *error)
|
||||
{
|
||||
// get conversion factor to atomic units
|
||||
double energy_conv;
|
||||
if (lmpunits == REAL) {
|
||||
double kelvin_to_hartree;
|
||||
MDI_Conversion_factor("kelvin_energy", "hartree", &kelvin_to_hartree);
|
||||
energy_conv = kelvin_to_hartree / force->boltz;
|
||||
} else if (lmpunits == METAL) {
|
||||
double ev_to_hartree;
|
||||
MDI_Conversion_factor("electron_volt", "hartree", &ev_to_hartree);
|
||||
energy_conv = ev_to_hartree;
|
||||
}
|
||||
|
||||
double kinetic_energy = ke->compute_scalar();
|
||||
double *send_energy = &kinetic_energy;
|
||||
|
||||
// convert the energy to atomic units
|
||||
kinetic_energy *= energy_conv;
|
||||
|
||||
ierr = MDI_Send((char *) send_energy, 1, MDI_DOUBLE, driver_socket);
|
||||
if (ierr != 0) error->all(FLERR, "MDI: Unable to send potential energy to driver");
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixMDIEngine::send_types(Error *error)
|
||||
{
|
||||
int *const type = atom->type;
|
||||
|
||||
ierr = MDI_Send((char *) type, atom->natoms, MDI_INT, driver_socket);
|
||||
if (ierr != 0) error->all(FLERR, "MDI: Unable to send atom types to driver");
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixMDIEngine::send_labels(Error *error)
|
||||
{
|
||||
char *labels = new char[atom->natoms * MDI_LABEL_LENGTH];
|
||||
memset(labels, ' ', atom->natoms * MDI_LABEL_LENGTH);
|
||||
|
||||
for (int iatom = 0; iatom < atom->natoms; iatom++) {
|
||||
std::string label = std::to_string(atom->type[iatom]);
|
||||
int label_len = std::min(int(label.length()), MDI_LABEL_LENGTH);
|
||||
strncpy(&labels[iatom * MDI_LABEL_LENGTH], label.c_str(), label_len);
|
||||
}
|
||||
|
||||
ierr = MDI_Send(labels, atom->natoms * MDI_LABEL_LENGTH, MDI_CHAR, driver_socket);
|
||||
if (ierr != 0) error->all(FLERR, "MDI: Unable to send atom types to driver");
|
||||
|
||||
delete[] labels;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixMDIEngine::send_masses(Error *error)
|
||||
{
|
||||
double *const rmass = atom->rmass;
|
||||
double *const mass = atom->mass;
|
||||
int *const type = atom->type;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
double *mass_by_atom;
|
||||
double *mass_by_atom_reduced;
|
||||
memory->create(mass_by_atom, atom->natoms, "mdi/engine:mass_by_atom");
|
||||
memory->create(mass_by_atom_reduced, atom->natoms, "mdi/engine:mass_by_atom_reduced");
|
||||
for (int iatom = 0; iatom < atom->natoms; iatom++) { mass_by_atom[iatom] = 0.0; }
|
||||
|
||||
// determine the atomic masses
|
||||
|
||||
if (rmass) {
|
||||
for (int iatom = 0; iatom < nlocal; iatom++) {
|
||||
mass_by_atom[atom->tag[iatom] - 1] = rmass[iatom];
|
||||
}
|
||||
} else {
|
||||
for (int iatom = 0; iatom < nlocal; iatom++) {
|
||||
mass_by_atom[atom->tag[iatom] - 1] = mass[type[iatom]];
|
||||
}
|
||||
}
|
||||
|
||||
MPI_Reduce(mass_by_atom, mass_by_atom_reduced, atom->natoms, MPI_DOUBLE, MPI_SUM, 0, world);
|
||||
|
||||
// send the atomic masses to the driver
|
||||
|
||||
ierr = MDI_Send((char *) mass_by_atom_reduced, atom->natoms, MDI_DOUBLE, driver_socket);
|
||||
if (ierr != 0) error->all(FLERR, "MDI: Unable to send atom masses to driver");
|
||||
|
||||
memory->destroy(mass_by_atom);
|
||||
memory->destroy(mass_by_atom_reduced);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixMDIEngine::send_forces(Error *error)
|
||||
{
|
||||
// get conversion factor to atomic units
|
||||
double force_conv;
|
||||
if (lmpunits == REAL) {
|
||||
double kelvin_to_hartree;
|
||||
double angstrom_to_bohr;
|
||||
MDI_Conversion_factor("kelvin_energy", "hartree", &kelvin_to_hartree);
|
||||
MDI_Conversion_factor("angstrom", "bohr", &angstrom_to_bohr);
|
||||
force_conv = (kelvin_to_hartree / force->boltz) * (force->angstrom / angstrom_to_bohr);
|
||||
} else if (lmpunits == METAL) {
|
||||
double ev_to_hartree;
|
||||
double angstrom_to_bohr;
|
||||
MDI_Conversion_factor("electron_volt", "hartree", &ev_to_hartree);
|
||||
MDI_Conversion_factor("angstrom", "bohr", &angstrom_to_bohr);
|
||||
force_conv = ev_to_hartree / angstrom_to_bohr;
|
||||
}
|
||||
|
||||
double *forces;
|
||||
double *forces_reduced;
|
||||
double *x_buf;
|
||||
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
int64_t ncoords = 3 * atom->natoms;
|
||||
|
||||
memory->create(forces, ncoords, "mdi/engine:forces");
|
||||
memory->create(forces_reduced, ncoords, "mdi/engine:forces_reduced");
|
||||
x_buf = new double[3 * nlocal];
|
||||
|
||||
// zero the forces array
|
||||
|
||||
for (int iforce = 0; iforce < 3 * atom->natoms; iforce++) forces[iforce] = 0.0;
|
||||
|
||||
// if not at a node, calculate the forces
|
||||
|
||||
if (strcmp(current_node, "@DEFAULT") == 0) {
|
||||
// certain fixes, such as shake, move the coordinates
|
||||
// to ensure that the coordinates do not change, store a copy
|
||||
double **x = atom->x;
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
x_buf[3 * i + 0] = x[i][0];
|
||||
x_buf[3 * i + 1] = x[i][1];
|
||||
x_buf[3 * i + 2] = x[i][2];
|
||||
}
|
||||
|
||||
// calculate the forces
|
||||
update->whichflag = 1; // 1 for dynamics
|
||||
update->nsteps = 1;
|
||||
lmp->init();
|
||||
update->integrate->setup_minimal(1);
|
||||
|
||||
if (strcmp(current_node, "@DEFAULT") == 0) {
|
||||
// restore the original set of coordinates
|
||||
double **x_new = atom->x;
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
x_new[i][0] = x_buf[3 * i + 0];
|
||||
x_new[i][1] = x_buf[3 * i + 1];
|
||||
x_new[i][2] = x_buf[3 * i + 2];
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
// pick local atoms from the buffer
|
||||
double **f = atom->f;
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
forces[3 * (atom->tag[i] - 1) + 0] = f[i][0] * force_conv;
|
||||
forces[3 * (atom->tag[i] - 1) + 1] = f[i][1] * force_conv;
|
||||
forces[3 * (atom->tag[i] - 1) + 2] = f[i][2] * force_conv;
|
||||
}
|
||||
|
||||
// reduce the forces onto rank 0
|
||||
MPI_Reduce(forces, forces_reduced, 3 * atom->natoms, MPI_DOUBLE, MPI_SUM, 0, world);
|
||||
|
||||
// send the forces through MDI
|
||||
ierr = MDI_Send((char *) forces_reduced, 3 * atom->natoms, MDI_DOUBLE, driver_socket);
|
||||
if (ierr != 0) error->all(FLERR, "MDI: Unable to send atom forces to driver");
|
||||
|
||||
memory->destroy(forces);
|
||||
memory->destroy(forces_reduced);
|
||||
delete[] x_buf;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
// Receive forces from the driver
|
||||
// mode = 0: replace current forces with forces from driver
|
||||
// mode = 1: add forces from driver to current forces
|
||||
|
||||
void FixMDIEngine::receive_forces(Error *error, int mode)
|
||||
{
|
||||
// get conversion factor to atomic units
|
||||
double force_conv;
|
||||
if (lmpunits == REAL) {
|
||||
double kelvin_to_hartree;
|
||||
double angstrom_to_bohr;
|
||||
MDI_Conversion_factor("kelvin_energy", "hartree", &kelvin_to_hartree);
|
||||
MDI_Conversion_factor("angstrom", "bohr", &angstrom_to_bohr);
|
||||
force_conv = (kelvin_to_hartree / force->boltz) * (force->angstrom / angstrom_to_bohr);
|
||||
} else if (lmpunits == METAL) {
|
||||
double ev_to_hartree;
|
||||
double angstrom_to_bohr;
|
||||
MDI_Conversion_factor("electron_volt", "hartree", &ev_to_hartree);
|
||||
MDI_Conversion_factor("angstrom", "bohr", &angstrom_to_bohr);
|
||||
force_conv = ev_to_hartree / angstrom_to_bohr;
|
||||
}
|
||||
|
||||
int64_t ncoords = 3 * atom->natoms;
|
||||
double *forces;
|
||||
memory->create(forces, ncoords, "mdi/engine:forces");
|
||||
|
||||
ierr = MDI_Recv((char *) forces, 3 * atom->natoms, MDI_DOUBLE, driver_socket);
|
||||
if (ierr != 0) error->all(FLERR, "MDI: Unable to receive atom forces to driver");
|
||||
MPI_Bcast(forces, 3 * atom->natoms, MPI_DOUBLE, 0, world);
|
||||
|
||||
// pick local atoms from the buffer
|
||||
double **f = atom->f;
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
if (mode == 0) { // Replace
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
f[i][0] = forces[3 * (atom->tag[i] - 1) + 0] / force_conv;
|
||||
f[i][1] = forces[3 * (atom->tag[i] - 1) + 1] / force_conv;
|
||||
f[i][2] = forces[3 * (atom->tag[i] - 1) + 2] / force_conv;
|
||||
}
|
||||
} else {
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
f[i][0] += forces[3 * (atom->tag[i] - 1) + 0] / force_conv;
|
||||
f[i][1] += forces[3 * (atom->tag[i] - 1) + 1] / force_conv;
|
||||
f[i][2] += forces[3 * (atom->tag[i] - 1) + 2] / force_conv;
|
||||
}
|
||||
}
|
||||
|
||||
memory->destroy(forces);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixMDIEngine::send_cell(Error *error)
|
||||
{
|
||||
double angstrom_to_bohr;
|
||||
MDI_Conversion_factor("angstrom", "bohr", &angstrom_to_bohr);
|
||||
|
||||
double celldata[9];
|
||||
|
||||
celldata[0] = domain->boxhi[0] - domain->boxlo[0];
|
||||
celldata[1] = 0.0;
|
||||
celldata[2] = 0.0;
|
||||
celldata[3] = domain->xy;
|
||||
celldata[4] = domain->boxhi[1] - domain->boxlo[1];
|
||||
celldata[5] = 0.0;
|
||||
celldata[6] = domain->xz;
|
||||
celldata[7] = domain->yz;
|
||||
celldata[8] = domain->boxhi[2] - domain->boxlo[2];
|
||||
|
||||
// convert the units to bohr
|
||||
|
||||
double unit_conv = force->angstrom * angstrom_to_bohr;
|
||||
for (int icell = 0; icell < 9; icell++) { celldata[icell] *= unit_conv; }
|
||||
|
||||
ierr = MDI_Send((char *) celldata, 9, MDI_DOUBLE, driver_socket);
|
||||
if (ierr != 0) error->all(FLERR, "MDI: Unable to send cell dimensions to driver");
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixMDIEngine::receive_cell(Error *error)
|
||||
{
|
||||
double celldata[9];
|
||||
|
||||
// receive the new cell vector from the driver
|
||||
ierr = MDI_Recv((char *) celldata, 9, MDI_DOUBLE, driver_socket);
|
||||
if (ierr != 0) error->all(FLERR, "MDI: Unable to send cell dimensions to driver");
|
||||
MPI_Bcast(&celldata[0], 9, MPI_DOUBLE, 0, world);
|
||||
|
||||
double angstrom_to_bohr;
|
||||
MDI_Conversion_factor("angstrom", "bohr", &angstrom_to_bohr);
|
||||
double unit_conv = force->angstrom * angstrom_to_bohr;
|
||||
for (int icell = 0; icell < 9; icell++) { celldata[icell] /= unit_conv; }
|
||||
|
||||
// ensure that the new cell vector is orthogonal
|
||||
double small = std::numeric_limits<double>::min();
|
||||
if (abs(celldata[1]) > small or abs(celldata[2]) > small or abs(celldata[3]) > small or
|
||||
abs(celldata[5]) > small or abs(celldata[6]) > small or abs(celldata[7]) > small) {
|
||||
error->all(FLERR,
|
||||
"MDI: LAMMPS currently only supports the >CELL command for orthogonal cell vectors");
|
||||
}
|
||||
|
||||
// set the new LAMMPS cell dimensions
|
||||
// This only works for orthogonal cell vectors.
|
||||
// Supporting the more general case would be possible,
|
||||
// but considerably more complex.
|
||||
domain->boxhi[0] = celldata[0] + domain->boxlo[0];
|
||||
domain->boxhi[1] = celldata[4] + domain->boxlo[1];
|
||||
domain->boxhi[2] = celldata[8] + domain->boxlo[2];
|
||||
domain->xy = 0.0;
|
||||
domain->xz = 0.0;
|
||||
domain->yz = 0.0;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixMDIEngine::send_celldispl(Error *error)
|
||||
{
|
||||
double angstrom_to_bohr;
|
||||
MDI_Conversion_factor("angstrom", "bohr", &angstrom_to_bohr);
|
||||
|
||||
double celldata[3];
|
||||
|
||||
celldata[0] = domain->boxlo[0];
|
||||
celldata[1] = domain->boxlo[1];
|
||||
celldata[2] = domain->boxlo[2];
|
||||
|
||||
// convert the units to bohr
|
||||
|
||||
double unit_conv = force->angstrom * angstrom_to_bohr;
|
||||
for (int icell = 0; icell < 3; icell++) { celldata[icell] *= unit_conv; }
|
||||
|
||||
ierr = MDI_Send((char *) celldata, 3, MDI_DOUBLE, driver_socket);
|
||||
if (ierr != 0) error->all(FLERR, "MDI: Unable to send cell displacement to driver");
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixMDIEngine::receive_celldispl(Error *error)
|
||||
{
|
||||
// receive the cell displacement from the driver
|
||||
double celldata[3];
|
||||
ierr = MDI_Recv((char *) celldata, 3, MDI_DOUBLE, driver_socket);
|
||||
if (ierr != 0) error->all(FLERR, "MDI: Unable to receive cell displacement from driver");
|
||||
MPI_Bcast(&celldata[0], 3, MPI_DOUBLE, 0, world);
|
||||
|
||||
double angstrom_to_bohr;
|
||||
MDI_Conversion_factor("angstrom", "bohr", &angstrom_to_bohr);
|
||||
double unit_conv = force->angstrom * angstrom_to_bohr;
|
||||
|
||||
double old_boxlo[3];
|
||||
old_boxlo[0] = domain->boxlo[0];
|
||||
old_boxlo[1] = domain->boxlo[1];
|
||||
old_boxlo[2] = domain->boxlo[2];
|
||||
|
||||
// adjust the values of boxlo and boxhi for the new cell displacement vector
|
||||
domain->boxlo[0] = celldata[0] / unit_conv;
|
||||
domain->boxlo[1] = celldata[1] / unit_conv;
|
||||
domain->boxlo[2] = celldata[2] / unit_conv;
|
||||
domain->boxhi[0] += domain->boxlo[0] - old_boxlo[0];
|
||||
domain->boxhi[1] += domain->boxlo[1] - old_boxlo[1];
|
||||
domain->boxhi[2] += domain->boxlo[2] - old_boxlo[2];
|
||||
}
|
||||
143
src/USER-MDI/fix_mdi_engine.h
Normal file
143
src/USER-MDI/fix_mdi_engine.h
Normal file
@ -0,0 +1,143 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef FIX_CLASS
|
||||
// clang-format off
|
||||
FixStyle(mdi/engine, FixMDIEngine);
|
||||
// clang-format on
|
||||
#else
|
||||
|
||||
#ifndef LMP_FIX_MDI_ENGINE_H
|
||||
#define LMP_FIX_MDI_ENGINE_H
|
||||
|
||||
#include "fix.h"
|
||||
#include "mdi.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class FixMDIEngine : public Fix {
|
||||
public:
|
||||
FixMDIEngine(class LAMMPS *, int, char **);
|
||||
~FixMDIEngine();
|
||||
int setmask();
|
||||
void init();
|
||||
|
||||
int execute_command(const char *command, MDI_Comm driver_socket);
|
||||
char *engine_mode(const char *node);
|
||||
|
||||
// receive and update forces
|
||||
|
||||
//void setup(int);
|
||||
void min_setup(int);
|
||||
void post_integrate();
|
||||
void post_force(int);
|
||||
void min_pre_force(int); //@COORDS
|
||||
void min_post_force(int); //@FORCES
|
||||
|
||||
double *add_force; // stores forces added using +FORCE command
|
||||
double potential_energy; // stores potential energy
|
||||
double kinetic_energy; // stores kinetic energy
|
||||
|
||||
// current command
|
||||
|
||||
char *command;
|
||||
|
||||
protected:
|
||||
void exchange_forces();
|
||||
|
||||
private:
|
||||
int lmpunits; // REAL or METAL
|
||||
int master, ierr;
|
||||
int driver_socket;
|
||||
int most_recent_init; // which MDI init command was most recently received?
|
||||
// 0 - none
|
||||
// 1 - MD
|
||||
// 2 - OPTG
|
||||
bool exit_flag;
|
||||
bool local_exit_flag;
|
||||
char *current_node;
|
||||
char *target_node; // is the code supposed to advance to a particular node?
|
||||
// 0 - none
|
||||
// 1 - @COORDS (before pre-force calculation)
|
||||
// 2 - @PRE-FORCES (before final force calculation)
|
||||
// 3 - @FORCES (before time integration)
|
||||
// -1 - after MD_INIT command
|
||||
// -2 - after MD_INIT command followed by @PRE-FORCES (actually @INIT_OPTG?)
|
||||
|
||||
// command to be executed at the target node
|
||||
|
||||
char *target_command;
|
||||
|
||||
char *id_pe;
|
||||
char *id_ke;
|
||||
class Irregular *irregular;
|
||||
class Minimize *minimizer;
|
||||
class Compute *pe;
|
||||
class Compute *ke;
|
||||
|
||||
void send_types(Error *);
|
||||
void send_labels(Error *);
|
||||
void send_masses(Error *);
|
||||
void receive_coordinates(Error *);
|
||||
void send_coordinates(Error *);
|
||||
void send_charges(Error *);
|
||||
void send_energy(Error *);
|
||||
void send_forces(Error *);
|
||||
void send_pe(Error *);
|
||||
void send_ke(Error *);
|
||||
void receive_forces(Error *, int);
|
||||
void send_cell(Error *);
|
||||
void receive_cell(Error *);
|
||||
void send_celldispl(Error *);
|
||||
void receive_celldispl(Error *);
|
||||
};
|
||||
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
E: Illegal ... command
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
E: Potential energy ID for fix mdi does not exist
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
E: Cannot use MDI command without atom IDs
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
E: MDI command requires consecutive atom IDs
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
E: Unable to connect to driver
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
E: Unable to ... driver
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
E: Unknown command from driver
|
||||
|
||||
The driver sent a command that is not supported by the LAMMPS
|
||||
interface. In some cases this might be because a nonsensical
|
||||
command was sent (i.e. "SCF"). In other cases, the LAMMPS
|
||||
interface might benefit from being expanded.
|
||||
|
||||
*/
|
||||
113
src/USER-MDI/library_mdi.cpp
Normal file
113
src/USER-MDI/library_mdi.cpp
Normal file
@ -0,0 +1,113 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://lammps.sandia.gov/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
// ----------------------------------------------------------------------
|
||||
// MolSSI Driver Interface functions
|
||||
// ----------------------------------------------------------------------
|
||||
|
||||
#include "library_mdi.h"
|
||||
|
||||
// needed to enable MPI support
|
||||
#define LAMMPS_LIB_MPI 1
|
||||
#include "library.h"
|
||||
|
||||
#include "fix_mdi_engine.h"
|
||||
|
||||
#include <cstring>
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
/** Initialize an instance of LAMMPS as an MDI plugin
|
||||
*
|
||||
\verbatim embed:rst
|
||||
|
||||
This function is called by the MolSSI Driver Interface library (MDI)
|
||||
when LAMMPS is run as a plugin, and should not otherwise be used.
|
||||
|
||||
The function initializes MDI, then creates and initializes an instance
|
||||
of LAMMPS. The command-line arguments ``argc`` and ``argv`` used to
|
||||
initialize LAMMPS are recieved from MDI. The LAMMPS instance runs an
|
||||
input file, which must include the ``mdi/engine`` command; when LAMMPS
|
||||
executes this command, it will begin listening for commands from the
|
||||
driver. The name of the input file is obtained from the ``-in``
|
||||
command-line argument, which must be provided by the MDI driver.
|
||||
|
||||
\endverbatim
|
||||
* \param command string buffer corresponding to the command to be executed
|
||||
* \param comm MDI communicator that can be used to communicated with the driver.
|
||||
* \param class_obj pointer to an instance of an mdi/engine fix cast to ``void *``.
|
||||
* \return 0 on no error. */
|
||||
|
||||
int MDI_Plugin_init_lammps()
|
||||
{
|
||||
// initialize MDI
|
||||
int mdi_argc;
|
||||
char **mdi_argv;
|
||||
if (MDI_Plugin_get_argc(&mdi_argc)) MPI_Abort(MPI_COMM_WORLD, 1);
|
||||
if (MDI_Plugin_get_argv(&mdi_argv)) MPI_Abort(MPI_COMM_WORLD, 1);
|
||||
if (MDI_Init(&mdi_argc, &mdi_argv)) MPI_Abort(MPI_COMM_WORLD, 1);
|
||||
|
||||
// get the MPI intra-communicator for this code
|
||||
MPI_Comm mpi_world_comm = MPI_COMM_WORLD;
|
||||
if (MDI_MPI_get_world_comm(&mpi_world_comm)) MPI_Abort(MPI_COMM_WORLD, 1);
|
||||
|
||||
// find the -in argument
|
||||
int iarg = 0;
|
||||
char *filename;
|
||||
bool found_filename = false;
|
||||
while (iarg < mdi_argc && !found_filename) {
|
||||
|
||||
if ((strcmp(mdi_argv[iarg], "-in") == 0) || (strcmp(mdi_argv[iarg], "-i") == 0)) {
|
||||
|
||||
if (iarg + 2 > mdi_argc) MPI_Abort(MPI_COMM_WORLD, 1);
|
||||
filename = mdi_argv[iarg + 1];
|
||||
found_filename = true;
|
||||
|
||||
// remove -in argument from the command list
|
||||
mdi_argc -= 2;
|
||||
for (int jarg = iarg; jarg < mdi_argc; jarg++) mdi_argv[jarg] = mdi_argv[jarg + 2];
|
||||
}
|
||||
iarg++;
|
||||
}
|
||||
if (!found_filename) MPI_Abort(MPI_COMM_WORLD, 1);
|
||||
|
||||
// create and run a LAMMPS instance
|
||||
void *lmp = nullptr;
|
||||
if (lammps_config_has_mpi_support() > 0)
|
||||
lmp = lammps_open(mdi_argc, mdi_argv, mpi_world_comm, nullptr);
|
||||
else
|
||||
lmp = lammps_open_no_mpi(mdi_argc, mdi_argv, nullptr);
|
||||
lammps_file(lmp, filename);
|
||||
lammps_close(lmp);
|
||||
|
||||
return 0;
|
||||
}
|
||||
|
||||
/** Execute an MDI command
|
||||
*
|
||||
\verbatim embed:rst
|
||||
|
||||
This function is called by the MolSSI Driver Interface Library (MDI)
|
||||
when LAMMPS is run as a plugin, and should not otherwise be used.
|
||||
The function executes a single command from an external MDI driver.
|
||||
|
||||
\endverbatim
|
||||
* \param command string buffer corresponding to the command to be executed
|
||||
* \param comm MDI communicator that can be used to communicated with the driver.
|
||||
* \param class_obj pointer to an instance of an mdi/engine fix cast to ``void *``.
|
||||
* \return 0 on no error, 1 on error. */
|
||||
int lammps_execute_mdi_command(const char *command, MDI_Comm comm, void *class_obj)
|
||||
{
|
||||
FixMDIEngine *mdi_fix = (FixMDIEngine *) class_obj;
|
||||
return mdi_fix->execute_command(command, comm);
|
||||
}
|
||||
26
src/USER-MDI/library_mdi.h
Normal file
26
src/USER-MDI/library_mdi.h
Normal file
@ -0,0 +1,26 @@
|
||||
/* -*- c -*- ------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://lammps.sandia.gov/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifndef LAMMPS_LIBRARY_MDI_H
|
||||
#define LAMMPS_LIBRARY_MDI_H
|
||||
|
||||
/* C style library calls to LAMMPS when a LAMMPS shared library is
|
||||
* used as a plugin through MolSSI Driver Interface (MDI). */
|
||||
|
||||
#include <mdi.h>
|
||||
|
||||
extern "C" {
|
||||
int MDI_Plugin_init_lammps();
|
||||
int lammps_execute_mdi_command(const char *, MDI_Comm, void *);
|
||||
}
|
||||
#endif
|
||||
354
src/USER-MDI/mdi_engine.cpp
Normal file
354
src/USER-MDI/mdi_engine.cpp
Normal file
@ -0,0 +1,354 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing author: Taylor Barnes (MolSSI)
|
||||
MolSSI Driver Interface (MDI) support for LAMMPS
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "mdi_engine.h"
|
||||
|
||||
#include "atom.h"
|
||||
#include "error.h"
|
||||
#include "fix_mdi_engine.h"
|
||||
#include "force.h"
|
||||
#include "mdi.h"
|
||||
#include "min.h"
|
||||
#include "minimize.h"
|
||||
#include "modify.h"
|
||||
#include "output.h"
|
||||
#include "timer.h"
|
||||
#include "update.h"
|
||||
#include "verlet.h"
|
||||
|
||||
#include <limits>
|
||||
#include <string.h>
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
trigger LAMMPS to start acting as an MDI engine
|
||||
endlessly loop over receiving commands from driver and responding
|
||||
much of the logic for this is in FixMDIEngine
|
||||
when EXIT command is received, mdi/engine command exits
|
||||
---------------------------------------------------------------------- */
|
||||
|
||||
void MDIEngine::command(int narg, char **arg)
|
||||
{
|
||||
// list of nodes and commands that a MDI-compliant MD code should support
|
||||
|
||||
// default node and its commands
|
||||
|
||||
MDI_Register_node("@DEFAULT");
|
||||
MDI_Register_command("@DEFAULT", "<@");
|
||||
MDI_Register_command("@DEFAULT", "<CELL");
|
||||
MDI_Register_command("@DEFAULT", "<CELL_DISPL");
|
||||
MDI_Register_command("@DEFAULT", "<CHARGES");
|
||||
MDI_Register_command("@DEFAULT", "<COORDS");
|
||||
MDI_Register_command("@DEFAULT", "<LABELS");
|
||||
MDI_Register_command("@DEFAULT", "<MASSES");
|
||||
MDI_Register_command("@DEFAULT", "<NATOMS");
|
||||
MDI_Register_command("@DEFAULT", "<TYPES");
|
||||
MDI_Register_command("@DEFAULT", ">CELL");
|
||||
MDI_Register_command("@DEFAULT", ">CELL_DISPL");
|
||||
MDI_Register_command("@DEFAULT", ">COORDS");
|
||||
MDI_Register_command("@DEFAULT", "@INIT_MD");
|
||||
MDI_Register_command("@DEFAULT", "@INIT_OPTG");
|
||||
MDI_Register_command("@DEFAULT", "EXIT");
|
||||
|
||||
// node for setting up and running a dynamics simulation
|
||||
|
||||
MDI_Register_node("@INIT_MD");
|
||||
MDI_Register_command("@INIT_MD", "<@");
|
||||
MDI_Register_command("@INIT_MD", "<CELL");
|
||||
MDI_Register_command("@INIT_MD", "<CELL_DISPL");
|
||||
MDI_Register_command("@INIT_MD", "<CHARGES");
|
||||
MDI_Register_command("@INIT_MD", "<COORDS");
|
||||
MDI_Register_command("@INIT_MD", "<ENERGY");
|
||||
MDI_Register_command("@INIT_MD", "<FORCES");
|
||||
MDI_Register_command("@INIT_MD", "<KE");
|
||||
MDI_Register_command("@INIT_MD", "<LABELS");
|
||||
MDI_Register_command("@INIT_MD", "<MASSES");
|
||||
MDI_Register_command("@INIT_MD", "<NATOMS");
|
||||
MDI_Register_command("@INIT_MD", "<PE");
|
||||
MDI_Register_command("@INIT_MD", "<TYPES");
|
||||
MDI_Register_command("@INIT_MD", ">CELL");
|
||||
MDI_Register_command("@INIT_MD", ">CELL_DISPL");
|
||||
MDI_Register_command("@INIT_MD", ">COORDS");
|
||||
MDI_Register_command("@INIT_MD", ">FORCES");
|
||||
MDI_Register_command("@INIT_MD", ">+FORCES");
|
||||
MDI_Register_command("@INIT_MD", "@");
|
||||
MDI_Register_command("@INIT_MD", "@COORDS");
|
||||
MDI_Register_command("@INIT_MD", "@DEFAULT");
|
||||
MDI_Register_command("@INIT_MD", "@FORCES");
|
||||
MDI_Register_command("@INIT_MD", "EXIT");
|
||||
|
||||
// node for setting up and running a minimization
|
||||
|
||||
MDI_Register_node("@INIT_OPTG");
|
||||
MDI_Register_command("@INIT_OPTG", "<@");
|
||||
MDI_Register_command("@INIT_OPTG", "<CELL");
|
||||
MDI_Register_command("@INIT_OPTG", "<CELL_DISPL");
|
||||
MDI_Register_command("@INIT_OPTG", "<CHARGES");
|
||||
MDI_Register_command("@INIT_OPTG", "<COORDS");
|
||||
MDI_Register_command("@INIT_OPTG", "<ENERGY");
|
||||
MDI_Register_command("@INIT_OPTG", "<FORCES");
|
||||
MDI_Register_command("@INIT_OPTG", "<KE");
|
||||
MDI_Register_command("@INIT_OPTG", "<LABELS");
|
||||
MDI_Register_command("@INIT_OPTG", "<MASSES");
|
||||
MDI_Register_command("@INIT_OPTG", "<NATOMS");
|
||||
MDI_Register_command("@INIT_OPTG", "<PE");
|
||||
MDI_Register_command("@INIT_OPTG", "<TYPES");
|
||||
MDI_Register_command("@INIT_OPTG", ">CELL");
|
||||
MDI_Register_command("@INIT_OPTG", ">CELL_DISPL");
|
||||
MDI_Register_command("@INIT_OPTG", ">COORDS");
|
||||
MDI_Register_command("@INIT_OPTG", ">FORCES");
|
||||
MDI_Register_command("@INIT_OPTG", ">+FORCES");
|
||||
MDI_Register_command("@INIT_OPTG", "@");
|
||||
MDI_Register_command("@INIT_OPTG", "@COORDS");
|
||||
MDI_Register_command("@INIT_OPTG", "@DEFAULT");
|
||||
MDI_Register_command("@INIT_OPTG", "@FORCES");
|
||||
MDI_Register_command("@INIT_OPTG", "EXIT");
|
||||
|
||||
// node at POST_FORCE location in timestep
|
||||
|
||||
MDI_Register_node("@FORCES");
|
||||
MDI_Register_callback("@FORCES", ">FORCES");
|
||||
MDI_Register_callback("@FORCES", ">+FORCES");
|
||||
MDI_Register_command("@FORCES", "<@");
|
||||
MDI_Register_command("@FORCES", "<CELL");
|
||||
MDI_Register_command("@FORCES", "<CELL_DISPL");
|
||||
MDI_Register_command("@FORCES", "<CHARGES");
|
||||
MDI_Register_command("@FORCES", "<COORDS");
|
||||
MDI_Register_command("@FORCES", "<ENERGY");
|
||||
MDI_Register_command("@FORCES", "<FORCES");
|
||||
MDI_Register_command("@FORCES", "<KE");
|
||||
MDI_Register_command("@FORCES", "<LABELS");
|
||||
MDI_Register_command("@FORCES", "<MASSES");
|
||||
MDI_Register_command("@FORCES", "<NATOMS");
|
||||
MDI_Register_command("@FORCES", "<PE");
|
||||
MDI_Register_command("@FORCES", "<TYPES");
|
||||
MDI_Register_command("@FORCES", ">CELL");
|
||||
MDI_Register_command("@FORCES", ">CELL_DISPL");
|
||||
MDI_Register_command("@FORCES", ">COORDS");
|
||||
MDI_Register_command("@FORCES", ">FORCES");
|
||||
MDI_Register_command("@FORCES", ">+FORCES");
|
||||
MDI_Register_command("@FORCES", "@");
|
||||
MDI_Register_command("@FORCES", "@COORDS");
|
||||
MDI_Register_command("@FORCES", "@DEFAULT");
|
||||
MDI_Register_command("@FORCES", "@FORCES");
|
||||
MDI_Register_command("@FORCES", "EXIT");
|
||||
|
||||
// node at POST_INTEGRATE location in timestep
|
||||
|
||||
MDI_Register_node("@COORDS");
|
||||
MDI_Register_command("@COORDS", "<@");
|
||||
MDI_Register_command("@COORDS", "<CELL");
|
||||
MDI_Register_command("@COORDS", "<CELL_DISPL");
|
||||
MDI_Register_command("@COORDS", "<CHARGES");
|
||||
MDI_Register_command("@COORDS", "<COORDS");
|
||||
MDI_Register_command("@COORDS", "<ENERGY");
|
||||
MDI_Register_command("@COORDS", "<FORCES");
|
||||
MDI_Register_command("@COORDS", "<KE");
|
||||
MDI_Register_command("@COORDS", "<LABELS");
|
||||
MDI_Register_command("@COORDS", "<MASSES");
|
||||
MDI_Register_command("@COORDS", "<NATOMS");
|
||||
MDI_Register_command("@COORDS", "<PE");
|
||||
MDI_Register_command("@COORDS", "<TYPES");
|
||||
MDI_Register_command("@COORDS", ">CELL");
|
||||
MDI_Register_command("@COORDS", ">CELL_DISPL");
|
||||
MDI_Register_command("@COORDS", ">COORDS");
|
||||
MDI_Register_command("@COORDS", ">FORCES");
|
||||
MDI_Register_command("@COORDS", ">+FORCES");
|
||||
MDI_Register_command("@COORDS", "@");
|
||||
MDI_Register_command("@COORDS", "@COORDS");
|
||||
MDI_Register_command("@COORDS", "@DEFAULT");
|
||||
MDI_Register_command("@COORDS", "@FORCES");
|
||||
MDI_Register_command("@COORDS", "EXIT");
|
||||
|
||||
// if the mdi/engine fix is not already present, add it now
|
||||
|
||||
int ifix = modify->find_fix_by_style("mdi/engine");
|
||||
bool added_mdi_engine_fix = false;
|
||||
if (ifix < 0) {
|
||||
modify->add_fix("MDI_ENGINE_INTERNAL all mdi/engine");
|
||||
added_mdi_engine_fix = true;
|
||||
}
|
||||
|
||||
// identify the mdi_engine fix
|
||||
|
||||
ifix = modify->find_fix_by_style("mdi/engine");
|
||||
mdi_fix = static_cast<FixMDIEngine *>(modify->fix[ifix]);
|
||||
|
||||
// check that LAMMPS is setup as a compatible MDI engine
|
||||
|
||||
if (narg > 0) error->all(FLERR, "Illegal mdi/engine command");
|
||||
|
||||
if (atom->tag_enable == 0) error->all(FLERR, "Cannot use mdi/engine without atom IDs");
|
||||
|
||||
if (atom->tag_consecutive() == 0) error->all(FLERR, "mdi/engine requires consecutive atom IDs");
|
||||
|
||||
// endless engine loop, responding to driver commands
|
||||
|
||||
char *command;
|
||||
|
||||
while (1) {
|
||||
|
||||
// mdi/engine command only recognizes three nodes
|
||||
// DEFAULT, INIT_MD, INIT_OPTG
|
||||
|
||||
command = mdi_fix->engine_mode("@DEFAULT");
|
||||
|
||||
// MDI commands for dynamics or minimization
|
||||
|
||||
if (strcmp(command, "@INIT_MD") == 0) {
|
||||
command = mdi_md();
|
||||
if (strcmp(command, "EXIT")) break;
|
||||
|
||||
} else if (strcmp(command, "@INIT_OPTG") == 0) {
|
||||
command = mdi_optg();
|
||||
if (strcmp(command, "EXIT")) break;
|
||||
|
||||
} else if (strcmp(command, "EXIT") == 0) {
|
||||
break;
|
||||
|
||||
} else
|
||||
error->all(FLERR,
|
||||
fmt::format("MDI node exited with "
|
||||
"invalid command: {}",
|
||||
command));
|
||||
}
|
||||
|
||||
// remove mdi/engine fix that mdi/engine instantiated
|
||||
|
||||
if (added_mdi_engine_fix) modify->delete_fix("MDI_ENGINE_INTERNAL");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
run an MD simulation under control of driver
|
||||
---------------------------------------------------------------------- */
|
||||
|
||||
char *MDIEngine::mdi_md()
|
||||
{
|
||||
// initialize an MD simulation
|
||||
|
||||
update->whichflag = 1;
|
||||
timer->init_timeout();
|
||||
update->nsteps = 1;
|
||||
update->ntimestep = 0;
|
||||
update->firststep = update->ntimestep;
|
||||
update->laststep = update->ntimestep + update->nsteps;
|
||||
update->beginstep = update->firststep;
|
||||
update->endstep = update->laststep;
|
||||
|
||||
lmp->init();
|
||||
|
||||
// engine is now at @INIT_MD node
|
||||
|
||||
char *command = nullptr;
|
||||
command = mdi_fix->engine_mode("@INIT_MD");
|
||||
|
||||
if (strcmp(command, "@DEFAULT") == 0 || strcmp(command, "EXIT") == 0) return command;
|
||||
|
||||
// setup the MD simulation
|
||||
|
||||
update->integrate->setup(1);
|
||||
|
||||
command = mdi_fix->engine_mode("@FORCES");
|
||||
|
||||
if (strcmp(command, "@DEFAULT") == 0 || strcmp(command, "EXIT") == 0) return command;
|
||||
|
||||
// run MD one step at a time
|
||||
|
||||
while (1) {
|
||||
update->whichflag = 1;
|
||||
timer->init_timeout();
|
||||
update->nsteps += 1;
|
||||
update->laststep += 1;
|
||||
update->endstep = update->laststep;
|
||||
output->next = update->ntimestep + 1;
|
||||
|
||||
// single MD timestep
|
||||
|
||||
update->integrate->run(1);
|
||||
|
||||
// done with MD if driver sends @DEFAULT or EXIT
|
||||
|
||||
command = mdi_fix->command;
|
||||
|
||||
if (strcmp(command, "@DEFAULT") == 0 || strcmp(command, "EXIT") == 0) return command;
|
||||
}
|
||||
|
||||
return nullptr;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
perform minimization under control of driver
|
||||
---------------------------------------------------------------------- */
|
||||
|
||||
char *MDIEngine::mdi_optg()
|
||||
{
|
||||
// initialize an energy minization
|
||||
|
||||
Minimize *minimizer = new Minimize(lmp);
|
||||
|
||||
// setup the minimizer in a way that ensures optimization
|
||||
// will continue until MDI driver exits
|
||||
|
||||
update->etol = std::numeric_limits<double>::min();
|
||||
update->ftol = std::numeric_limits<double>::min();
|
||||
update->nsteps = std::numeric_limits<int>::max();
|
||||
update->max_eval = std::numeric_limits<int>::max();
|
||||
|
||||
update->whichflag = 2;
|
||||
update->beginstep = update->firststep = update->ntimestep;
|
||||
update->endstep = update->laststep = update->firststep + update->nsteps;
|
||||
|
||||
lmp->init();
|
||||
|
||||
// engine is now at @INIT_OPTG node
|
||||
|
||||
char *command = nullptr;
|
||||
command = mdi_fix->engine_mode("@INIT_OPTG");
|
||||
|
||||
if (strcmp(command, "@DEFAULT") == 0 || strcmp(command, "EXIT") == 0) return command;
|
||||
|
||||
// setup the minimization
|
||||
|
||||
update->minimize->setup();
|
||||
|
||||
// get new command
|
||||
|
||||
command = mdi_fix->command;
|
||||
|
||||
if (strcmp(command, "@DEFAULT") == 0 || strcmp(command, "EXIT") == 0) return command;
|
||||
|
||||
// Start a minimization, which is configured to run (essentially)
|
||||
// infinite steps. When the driver sends the EXIT command,
|
||||
// the minimizer's energy and force tolerances are set to
|
||||
// extremely large values, causing the minimization to end.
|
||||
|
||||
update->minimize->iterate(update->nsteps);
|
||||
|
||||
// return if driver sends @DEFAULT or EXIT
|
||||
|
||||
command = mdi_fix->command;
|
||||
|
||||
if (strcmp(command, "@DEFAULT") == 0 || strcmp(command, "EXIT") == 0) return command;
|
||||
|
||||
error->all(FLERR,
|
||||
fmt::format("MDI reached end of OPTG simulation "
|
||||
"with invalid command: {}",
|
||||
command));
|
||||
return nullptr;
|
||||
}
|
||||
53
src/USER-MDI/mdi_engine.h
Normal file
53
src/USER-MDI/mdi_engine.h
Normal file
@ -0,0 +1,53 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef COMMAND_CLASS
|
||||
// clang-format off
|
||||
CommandStyle(mdi/engine, MDIEngine);
|
||||
// clang-format on
|
||||
#else
|
||||
|
||||
#ifndef LMP_MDI_ENGINE_H
|
||||
#define LMP_MDI_ENGINE_H
|
||||
|
||||
#include "command.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class MDIEngine : public Command {
|
||||
public:
|
||||
MDIEngine(LAMMPS *lmp) : Command(lmp) {}
|
||||
virtual ~MDIEngine() {}
|
||||
void command(int, char **);
|
||||
|
||||
private:
|
||||
class FixMDIEngine *mdi_fix;
|
||||
|
||||
char *mdi_md();
|
||||
char *mdi_optg();
|
||||
};
|
||||
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
E: Illegal ... command
|
||||
|
||||
Self-explanatory. Check the input script syntax and compare to the
|
||||
documentation for the command. You can use -echo screen as a
|
||||
command-line option when running LAMMPS to see the offending line.
|
||||
|
||||
*/
|
||||
@ -673,7 +673,8 @@ void lammps_extract_box(void *handle, double *boxlo, double *boxhi,
|
||||
|
||||
This function sets the simulation box dimensions (upper and lower bounds
|
||||
and tilt factors) from the provided data and then re-initializes the box
|
||||
information and all derived settings.
|
||||
information and all derived settings. It may only be called before atoms
|
||||
are created.
|
||||
|
||||
\endverbatim
|
||||
*
|
||||
@ -692,12 +693,16 @@ void lammps_reset_box(void *handle, double *boxlo, double *boxhi,
|
||||
|
||||
BEGIN_CAPTURE
|
||||
{
|
||||
// error if box does not exist
|
||||
if ((lmp->domain->box_exist == 0)
|
||||
&& (lmp->comm->me == 0)) {
|
||||
lmp->error->warning(FLERR,"Calling lammps_reset_box without a box");
|
||||
if (lmp->atom->natoms > 0)
|
||||
lmp->error->all(FLERR,"Calling lammps_reset_box not supported when atoms exist");
|
||||
|
||||
// warn and do nothing if no box exists
|
||||
if (lmp->domain->box_exist == 0) {
|
||||
if (lmp->comm->me == 0)
|
||||
lmp->error->warning(FLERR,"Ignoring call to lammps_reset_box without a box");
|
||||
return;
|
||||
}
|
||||
|
||||
domain->boxlo[0] = boxlo[0];
|
||||
domain->boxlo[1] = boxlo[1];
|
||||
domain->boxlo[2] = boxlo[2];
|
||||
|
||||
79
src/main.cpp
79
src/main.cpp
@ -12,10 +12,11 @@
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "lammps.h"
|
||||
|
||||
#include "input.h"
|
||||
|
||||
#include <mpi.h>
|
||||
#include <cstdlib>
|
||||
#include <mpi.h>
|
||||
|
||||
#if defined(LAMMPS_TRAP_FPE) && defined(_GNU_SOURCE)
|
||||
#include <fenv.h>
|
||||
@ -25,6 +26,41 @@
|
||||
#include "exceptions.h"
|
||||
#endif
|
||||
|
||||
// import real or dummy calls to MolSSI Driver Interface library
|
||||
#if defined(LMP_USER_MDI)
|
||||
|
||||
// true interface to MDI
|
||||
#include <mdi.h>
|
||||
|
||||
#else
|
||||
|
||||
// dummy interface to MDI
|
||||
// needed for compiling when MDI is not installed
|
||||
|
||||
typedef int MDI_Comm;
|
||||
static int MDI_Init(int *argc, char ***argv)
|
||||
{
|
||||
return 0;
|
||||
}
|
||||
static int MDI_Initialized(int *flag)
|
||||
{
|
||||
return 0;
|
||||
}
|
||||
static int MDI_MPI_get_world_comm(void *world_comm)
|
||||
{
|
||||
return 0;
|
||||
}
|
||||
static int MDI_Plugin_get_argc(int *argc)
|
||||
{
|
||||
return 0;
|
||||
}
|
||||
static int MDI_Plugin_get_argv(char ***argv)
|
||||
{
|
||||
return 0;
|
||||
}
|
||||
|
||||
#endif
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -33,11 +69,24 @@ using namespace LAMMPS_NS;
|
||||
|
||||
int main(int argc, char **argv)
|
||||
{
|
||||
MPI_Init(&argc,&argv);
|
||||
MPI_Init(&argc, &argv);
|
||||
|
||||
// enable trapping selected floating point exceptions.
|
||||
// this uses GNU extensions and is only tested on Linux
|
||||
// therefore we make it depend on -D_GNU_SOURCE, too.
|
||||
// initialize MDI or MDI dummy interface
|
||||
|
||||
int mdi_flag;
|
||||
if (MDI_Init(&argc, &argv)) MPI_Abort(MPI_COMM_WORLD, 1);
|
||||
if (MDI_Initialized(&mdi_flag)) MPI_Abort(MPI_COMM_WORLD, 1);
|
||||
|
||||
// get the MPI communicator that spans all ranks running LAMMPS
|
||||
// when using MDI, this may be a subset of MPI_COMM_WORLD
|
||||
|
||||
MPI_Comm lammps_comm = MPI_COMM_WORLD;
|
||||
if (mdi_flag)
|
||||
if (MDI_MPI_get_world_comm(&lammps_comm)) MPI_Abort(MPI_COMM_WORLD, 1);
|
||||
|
||||
// enable trapping selected floating point exceptions.
|
||||
// this uses GNU extensions and is only tested on Linux
|
||||
// therefore we make it depend on -D_GNU_SOURCE, too.
|
||||
|
||||
#if defined(LAMMPS_TRAP_FPE) && defined(_GNU_SOURCE)
|
||||
fesetenv(FE_NOMASK_ENV);
|
||||
@ -49,31 +98,31 @@ int main(int argc, char **argv)
|
||||
|
||||
#ifdef LAMMPS_EXCEPTIONS
|
||||
try {
|
||||
LAMMPS *lammps = new LAMMPS(argc,argv,MPI_COMM_WORLD);
|
||||
LAMMPS *lammps = new LAMMPS(argc, argv, lammps_comm);
|
||||
lammps->input->file();
|
||||
delete lammps;
|
||||
} catch(LAMMPSAbortException &ae) {
|
||||
} catch (LAMMPSAbortException &ae) {
|
||||
MPI_Abort(ae.universe, 1);
|
||||
} catch(LAMMPSException &e) {
|
||||
MPI_Barrier(MPI_COMM_WORLD);
|
||||
} catch (LAMMPSException &e) {
|
||||
MPI_Barrier(lammps_comm);
|
||||
MPI_Finalize();
|
||||
exit(1);
|
||||
} catch(fmt::format_error &fe) {
|
||||
fprintf(stderr,"fmt::format_error: %s\n", fe.what());
|
||||
} catch (fmt::format_error &fe) {
|
||||
fprintf(stderr, "fmt::format_error: %s\n", fe.what());
|
||||
MPI_Abort(MPI_COMM_WORLD, 1);
|
||||
exit(1);
|
||||
}
|
||||
#else
|
||||
try {
|
||||
LAMMPS *lammps = new LAMMPS(argc,argv,MPI_COMM_WORLD);
|
||||
LAMMPS *lammps = new LAMMPS(argc, argv, lammps_comm);
|
||||
lammps->input->file();
|
||||
delete lammps;
|
||||
} catch(fmt::format_error &fe) {
|
||||
fprintf(stderr,"fmt::format_error: %s\n", fe.what());
|
||||
} catch (fmt::format_error &fe) {
|
||||
fprintf(stderr, "fmt::format_error: %s\n", fe.what());
|
||||
MPI_Abort(MPI_COMM_WORLD, 1);
|
||||
exit(1);
|
||||
}
|
||||
#endif
|
||||
MPI_Barrier(MPI_COMM_WORLD);
|
||||
MPI_Barrier(lammps_comm);
|
||||
MPI_Finalize();
|
||||
}
|
||||
|
||||
@ -54,6 +54,7 @@ PLUMED_URL="https://github.com/plumed/plumed2/releases/download/v2.7.0/plumed-sr
|
||||
PACELIB_URL="https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2021.4.9.tar.gz"
|
||||
LATTE_URL="https://github.com/lanl/LATTE/archive/v1.2.2.tar.gz"
|
||||
SCAFACOS_URL="https://github.com/scafacos/scafacos/releases/download/v1.0.1/scafacos-1.0.1.tar.gz"
|
||||
MDI_URL="https://github.com/MolSSI-MDI/MDI_Library/archive/v1.2.9.tar.gz"
|
||||
|
||||
GTEST_FILENAME="gtest-1.10.0.tar.gz"
|
||||
MATHJAX_FILENAME="mathjax-3.1.2.tar.gz"
|
||||
@ -81,6 +82,7 @@ TARBALLS=(
|
||||
PACELIB_URL
|
||||
LATTE_URL
|
||||
SCAFACOS_URL
|
||||
MDI_URL
|
||||
)
|
||||
|
||||
###############################################################################
|
||||
|
||||
@ -161,6 +161,8 @@ TEST_F(LibraryProperties, box)
|
||||
boxhi[1] = 7.3;
|
||||
xy = 0.1;
|
||||
if (!verbose) ::testing::internal::CaptureStdout();
|
||||
// lammps_reset_box() may only be called without atoms
|
||||
lammps_command(lmp, "delete_atoms group all bond yes");
|
||||
lammps_reset_box(lmp, boxlo, boxhi, xy, yz, xz);
|
||||
if (!verbose) ::testing::internal::GetCapturedStdout();
|
||||
lammps_extract_box(lmp, boxlo, boxhi, &xy, &yz, &xz, pflags, &boxflag);
|
||||
|
||||
Reference in New Issue
Block a user