Merge pull request #3307 from lammps/fix-mdi-aimd-enhance
MDI package enhancements
This commit is contained in:
Axel Kohlmeyer
@ -8,8 +8,8 @@ option(DOWNLOAD_MDI "Download and compile the MDI library instead of using an al
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if(DOWNLOAD_MDI)
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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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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/v1.3.2.tar.gz" CACHE STRING "URL for MDI tarball")
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set(MDI_URL "https://github.com/MolSSI-MDI/MDI_Library/archive/v1.4.1.tar.gz" CACHE STRING "URL for MDI tarball")
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set(MDI_MD5 "836f5da400d8cff0f0e4435640f9454f" CACHE STRING "MD5 checksum for MDI tarball")
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set(MDI_MD5 "f9505fccd4c79301a619f6452dad4ad9" CACHE STRING "MD5 checksum for MDI tarball")
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mark_as_advanced(MDI_URL)
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mark_as_advanced(MDI_URL)
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mark_as_advanced(MDI_MD5)
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mark_as_advanced(MDI_MD5)
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enable_language(C)
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enable_language(C)
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@ -44,7 +44,7 @@ if(DOWNLOAD_MDI)
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ExternalProject_Add(mdi_build
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ExternalProject_Add(mdi_build
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URL ${MDI_URL}
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URL ${MDI_URL}
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URL_MD5 ${MDI_MD5}
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URL_MD5 ${MDI_MD5}
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CMAKE_ARGS ${CMAKE_REQUEST_PIC}
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CMAKE_ARGS
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-DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>
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-DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>
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-DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
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-DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
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-DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
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-DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
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@ -54,6 +54,7 @@ if(DOWNLOAD_MDI)
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-Dlanguage=C
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-Dlanguage=C
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-Dlibtype=STATIC
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-Dlibtype=STATIC
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-Dmpi=${MDI_USE_MPI}
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-Dmpi=${MDI_USE_MPI}
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-Dplugins=ON
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-Dpython_plugins=${MDI_USE_PYTHON_PLUGINS}
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-Dpython_plugins=${MDI_USE_PYTHON_PLUGINS}
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UPDATE_COMMAND ""
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UPDATE_COMMAND ""
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INSTALL_COMMAND ""
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INSTALL_COMMAND ""
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@ -103,7 +103,7 @@ OPT.
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* :doc:`lb/viscous <fix_lb_viscous>`
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* :doc:`lb/viscous <fix_lb_viscous>`
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* :doc:`lineforce <fix_lineforce>`
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* :doc:`lineforce <fix_lineforce>`
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* :doc:`manifoldforce <fix_manifoldforce>`
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* :doc:`manifoldforce <fix_manifoldforce>`
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* :doc:`mdi/aimd <fix_mdi_aimd>`
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* :doc:`mdi/qm <fix_mdi_qm>`
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* :doc:`meso/move <fix_meso_move>`
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* :doc:`meso/move <fix_meso_move>`
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* :doc:`mol/swap <fix_mol_swap>`
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* :doc:`mol/swap <fix_mol_swap>`
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* :doc:`momentum (k) <fix_momentum>`
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* :doc:`momentum (k) <fix_momentum>`
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@ -5,9 +5,9 @@ Client/server coupling of two (or more) codes is where one code is the
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"client" and sends request messages (data) to one (or more) "server"
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"client" and sends request messages (data) to one (or more) "server"
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code(s). A server responds to each request with a reply message
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code(s). A server responds to each request with a reply message
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(data). This enables two (or more) codes to work in tandem to perform
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(data). This enables two (or more) codes to work in tandem to perform
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a simulation. LAMMPS can act as either a client or server code; it
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a simulation. In this context, LAMMPS can act as either a client or
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does this by using the `MolSSI Driver Interface (MDI) library
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server code. It does this by using the `MolSSI Driver Interface (MDI)
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<https://molssi-mdi.github.io/MDI_Library/html/index.html>`_,
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library <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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developed by the `Molecular Sciences Software Institute (MolSSI)
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<https://molssi.org>`_, which is supported by the :ref:`MDI <PKG-MDI>`
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<https://molssi.org>`_, which is supported by the :ref:`MDI <PKG-MDI>`
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package.
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package.
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@ -63,22 +63,39 @@ The package also provides a :doc:`mdi plugin <mdi>` command which
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enables LAMMPS to operate as an MDI driver and load an MDI engine as a
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enables LAMMPS to operate as an MDI driver and load an MDI engine as a
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plugin library.
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plugin library.
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The package also has a `fix mdi/aimd <fix_mdi_aimd>` command in which
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The package also has a `fix mdi/qm <fix_mdi_qm>` command in which
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LAMMPS operates as an MDI driver to perform *ab initio* MD simulations
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LAMMPS operates as an MDI driver in conjunction with a quantum
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in conjunction with a quantum mechanics code. Its post_force() method
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mechanics code as an MDI engine. The post_force() method of the
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illustrates how a driver issues MDI commands to another code. This
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fix_mdi_qm.cpp file shows how a driver issues MDI commands to another
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command can be used to couple to an MDI engine which is either a
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code. This command can be used to couple to an MDI engine which is
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stand-alone code or a plugin library.
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either a stand-alone code or a plugin library.
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As explained on the `fix mdi/qm <fix_mdi_qm>` command doc page, it can
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be used to perform *ab initio* MD simulations or energy minimizations,
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or to evaluate the quantum energy and forces for a series of
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independent systems. The examples/mdi directory has example input
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scripts for all of these use cases.
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----------
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----------
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The examples/mdi directory contains Python scripts and LAMMPS input
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The examples/mdi directory contains Python scripts and LAMMPS input
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script which use LAMMPS as either an MDI driver or engine or both.
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script which use LAMMPS as either an MDI driver or engine or both.
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Three example use cases are provided:
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Currently, 5 example use cases are provided:
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* Run ab initio MD (AIMD) using 2 instances of LAMMPS, one as driver
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* Run ab initio MD (AIMD) using 2 instances of LAMMPS. As a driver
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and one as an engine. As an engine, LAMMPS is a surrogate for a
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LAMMPS performs the timestepping in either NVE or NPT mode. As an
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quantum code.
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engine, LAMMPS computes forces and is a surrogate for a quantum
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code.
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* As a driver, LAMMPS runs an MD simulation. Every N steps it passes
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the current snapshot to an MDI engine to evaluate the energy,
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virial, and peratom forces. As the engine LAMMPS is a surrogate for
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a quantum code.
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* As a driver, LAMMPS loops over a series of data files and passes the
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configuration to an MDI engine to evaluate the energy, virial, and
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peratom forces. As the engine LAMMPS is a surrogate for a quantum
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code.
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* A Python script driver invokes a sequence of unrelated LAMMPS
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* A Python script driver invokes a sequence of unrelated LAMMPS
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calculations. Calculations can be single-point energy/force
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calculations. Calculations can be single-point energy/force
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@ -91,20 +108,22 @@ Three example use cases are provided:
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Note that in any of these example where LAMMPS is used as an engine,
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Note that in any of these example where LAMMPS is used as an engine,
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an actual QM code (which supports MDI) could be used in its place,
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an actual QM code (which supports MDI) could be used in its place,
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without modifying other code or scripts, except to specify the name of
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without modifying the input scripts or launch commands, except to
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the QM code.
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specify the name of the QM code.
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The examples/mdi/README file explains how to launch both driver and
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The examples/mdi/Run.sh file illustrates how to launch both driver and
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engine codes so that they communicate using the MDI library via either
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engine codes so that they communicate using the MDI library via either
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MPI or sockets.
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MPI or sockets. Or using the engine as a stand-alone code or plugin
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library.
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-------------
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-------------
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Currently there are two quantum DFT codes which have direct MDI
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Currently there are at least two quantum DFT codes which have direct
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support, `Quantum ESPRESSO (QE) <https://www.quantum-espresso.org/>`_
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MDI support, `Quantum ESPRESSO (QE)
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and `INQ <https://qsg.llnl.gov/node/101.html>`_. There are also
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<https://www.quantum-espresso.org/>`_ and `INQ
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several QM codes which have indirect support through QCEngine or i-PI.
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<https://qsg.llnl.gov/node/101.html>`_. There are also several QM
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The former means they require a wrapper program (QCEngine) with MDI
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codes which have indirect support through QCEngine or i-PI. The
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former means they require a wrapper program (QCEngine) with MDI
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support which writes/read files to pass data to the quantum code
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support which writes/read files to pass data to the quantum code
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itself. The list of QCEngine-supported and i-PI-supported quantum
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itself. The list of QCEngine-supported and i-PI-supported quantum
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codes is on the `MDI webpage
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codes is on the `MDI webpage
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@ -1479,7 +1479,7 @@ the :doc:`Build extras <Build_extras>` page.
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* lib/mdi/README
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* lib/mdi/README
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* :doc:`Howto MDI <Howto_mdi>`
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* :doc:`Howto MDI <Howto_mdi>`
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* :doc:`mdi <mdi>`
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* :doc:`mdi <mdi>`
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* :doc:`fix mdi/aimd <fix_mdi_aimd>`
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* :doc:`fix mdi/qm <fix_mdi_qm>`
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* examples/PACKAGES/mdi
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* examples/PACKAGES/mdi
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----------
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----------
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@ -246,7 +246,7 @@ accelerated styles exist.
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* :doc:`lb/viscous <fix_lb_viscous>` -
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* :doc:`lb/viscous <fix_lb_viscous>` -
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* :doc:`lineforce <fix_lineforce>` - constrain atoms to move in a line
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* :doc:`lineforce <fix_lineforce>` - constrain atoms to move in a line
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* :doc:`manifoldforce <fix_manifoldforce>` - restrain atoms to a manifold during minimization
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* :doc:`manifoldforce <fix_manifoldforce>` - restrain atoms to a manifold during minimization
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* :doc:`mdi/aimd <fix_mdi_aimd>` - LAMMPS operates as driver for ab initio MD (AIMD) via the MolSSI Driver Interface (MDI)
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* :doc:`mdi/qm <fix_mdi_qm>` - LAMMPS operates as driver for a quantum code via the MolSSI Driver Interface (MDI)
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* :doc:`meso/move <fix_meso_move>` - move mesoscopic SPH/SDPD particles in a prescribed fashion
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* :doc:`meso/move <fix_meso_move>` - move mesoscopic SPH/SDPD particles in a prescribed fashion
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* :doc:`mol/swap <fix_mol_swap>` - Monte Carlo atom type swapping with a molecule
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* :doc:`mol/swap <fix_mol_swap>` - Monte Carlo atom type swapping with a molecule
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* :doc:`momentum <fix_momentum>` - zero the linear and/or angular momentum of a group of atoms
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* :doc:`momentum <fix_momentum>` - zero the linear and/or angular momentum of a group of atoms
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@ -116,13 +116,6 @@ potential energy of the system as part of :doc:`thermodynamic output
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<thermo_style>`. The default setting for this fix is :doc:`fix_modify
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<thermo_style>`. The default setting for this fix is :doc:`fix_modify
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energy yes <fix_modify>`.
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energy yes <fix_modify>`.
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The :doc:`fix_modify <fix_modify>` *virial* option is supported by
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this fix to add the contribution compute by LATTE to the global
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pressure of the system via the :doc:`compute pressure
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<compute_pressure>` command. This can be accessed by
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:doc:`thermodynamic output <thermo_style>`. The default setting for
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this fix is :doc:`fix_modify virial yes <fix_modify>`.
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The :doc:`fix_modify <fix_modify>` *virial* option is supported by
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The :doc:`fix_modify <fix_modify>` *virial* option is supported by
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this fix to add the contribution computed by LATTE to the global
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this fix to add the contribution computed by LATTE to the global
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pressure of the system as part of :doc:`thermodynamic output
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pressure of the system as part of :doc:`thermodynamic output
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@ -137,7 +130,7 @@ energy discussed above. The scalar value calculated by this fix is
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No parameter of this fix can be used with the *start/stop* keywords of
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No parameter of this fix can be used with the *start/stop* keywords of
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the :doc:`run <run>` command.
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the :doc:`run <run>` command.
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The DFTB forces computed by LATTE via this fix are imposed during an
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The DFTB forces computed by LATTE via this fix are used during an
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energy minimization, invoked by the :doc:`minimize <minimize>`
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energy minimization, invoked by the :doc:`minimize <minimize>`
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command.
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command.
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@ -1,93 +0,0 @@
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.. index:: fix mdi/aimd
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fix mdi/aimd command
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======================
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Syntax
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""""""
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.. parsed-literal::
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fix ID group-ID mdi/aimd keyword
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* ID, group-ID are documented in :doc:`fix <fix>` command
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* mdi/aimd = style name of this fix command
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Examples
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""""""""
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.. code-block:: LAMMPS
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fix 1 all mdi/aimd
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Description
|
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"""""""""""
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This command enables LAMMPS to act as a client with another server
|
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code to couple the two codes together to perform ab initio MD (AIMD)
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simulations.
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More specifically, this command causes LAMMPS to begin using the `MDI
|
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Library <https://molssi-mdi.github.io/MDI_Library/html/index.html>`_
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to run as an MDI driver (client), which sends MDI commands to an
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external MDI engine code (server) which in the case of AIMD is a
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quantum mechanics (QM) code, or could be LAMMPS itself, acting as a
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surrogate for a QM code. See the :doc:`Howto mdi <Howto_mdi>` page
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for more information about how LAMMPS can operate as either an MDI
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driver or engine.
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The examples/mdi directory contains input scripts performing AIMD in
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this manner with LAMMPS acting as both a driver and an engine
|
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(surrogate for a QM code). The examples/mdi/README file explains how
|
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to launch both driver and engine codes so that they communicate using
|
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the MDI library via either MPI or sockets. Any QM code that supports
|
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MDI could be used in place of LAMMPS acting as a QM surrogate. See
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the :doc:`Howto mdi <Howto_mdi>` page for a current list (March 2022)
|
|
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of such QM codes.
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The engine code can run either as a stand-alone code, launched at the
|
|
||||||
same time as LAMMPS, or as a plugin library. See the :doc:`mdi plugin
|
|
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<mdi>` command for how to trigger LAMMPS to load the plugin library.
|
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Again, the examples/mdi/README file explains how to launch both driver
|
|
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and engine codes so that engine is used in plugin mode.
|
|
||||||
|
|
||||||
----------
|
|
||||||
|
|
||||||
This fix performs the timestepping portion of an AIMD simulation.
|
|
||||||
Both LAMMPS and the engine code (QM or LAMMPS) should define the same
|
|
||||||
system (simulation box, atoms and their types) in their respective
|
|
||||||
input scripts. LAMMPS then begins its timestepping.
|
|
||||||
|
|
||||||
At the point in each timestep when LAMMPS needs the force on each
|
|
||||||
atom, it communicates with the engine code. It sends the current
|
|
||||||
simulation box size and shape (if they change dynamically, e.g. during
|
|
||||||
an NPT simulation), and the current atom coordinates. The engine code
|
|
||||||
computes quantum forces on each atom and returns them to LAMMPS. If
|
|
||||||
LAMMPS also needs the system energy and/or virial, it requests those
|
|
||||||
values from the engine code as well.
|
|
||||||
|
|
||||||
Restrictions
|
|
||||||
""""""""""""
|
|
||||||
|
|
||||||
This command is part of the MDI package. It is only enabled if
|
|
||||||
LAMMPS was built with that package. See the :doc:`Build package
|
|
||||||
<Build_package>` page for more info.
|
|
||||||
|
|
||||||
To use LAMMPS as an MDI driver in conjunction with other MDI-enabled
|
|
||||||
atomistic codes, the :doc:`units <units>` command should be used to
|
|
||||||
specify *real* or *metal* units. This will ensure the correct unit
|
|
||||||
conversions between LAMMPS and MDI units, which the other codes will
|
|
||||||
also perform in their preferred units.
|
|
||||||
|
|
||||||
LAMMPS can also be used as an MDI driver in other unit choices it
|
|
||||||
supports, e.g. *lj*, but then no unit conversion is performed.
|
|
||||||
|
|
||||||
Related commands
|
|
||||||
""""""""""""""""
|
|
||||||
|
|
||||||
:doc:`mdi engine <mdi>`
|
|
||||||
|
|
||||||
Default
|
|
||||||
"""""""
|
|
||||||
|
|
||||||
none
|
|
||||||
276
doc/src/fix_mdi_qm.rst
Normal file
276
doc/src/fix_mdi_qm.rst
Normal file
@ -0,0 +1,276 @@
|
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|
.. index:: fix mdi/qm
|
||||||
|
|
||||||
|
fix mdi/qm command
|
||||||
|
======================
|
||||||
|
|
||||||
|
Syntax
|
||||||
|
""""""
|
||||||
|
|
||||||
|
.. parsed-literal::
|
||||||
|
|
||||||
|
fix ID group-ID mdi/qm keyword
|
||||||
|
|
||||||
|
* ID, group-ID are documented in :doc:`fix <fix>` command
|
||||||
|
* mdi/qm = style name of this fix command
|
||||||
|
* zero or more keyword/value pairs may be appended
|
||||||
|
* keyword = *virial* or *add* or *every* or *connect* or *elements*
|
||||||
|
|
||||||
|
.. parsed-literal::
|
||||||
|
|
||||||
|
*virial* args = *yes* or *no*
|
||||||
|
yes = request virial tensor from server code
|
||||||
|
no = do not request virial tensor from server code
|
||||||
|
*add* args = *yes* or *no*
|
||||||
|
yes = add returned value from server code to LAMMPS quantities
|
||||||
|
no = do not add returned values to LAMMPS quantities
|
||||||
|
*every* args = Nevery
|
||||||
|
Nevery = request values from server code once every Nevery steps
|
||||||
|
*connect* args = *yes* or *no*
|
||||||
|
yes = perform a one-time connection to the MDI engine code
|
||||||
|
no = do not perform the connection operation
|
||||||
|
*elements* args = N_1 N_2 ... N_ntypes
|
||||||
|
N_1,N_2,...N_ntypes = atomic number for each of ntypes LAMMPS atom types
|
||||||
|
|
||||||
|
Examples
|
||||||
|
""""""""
|
||||||
|
|
||||||
|
.. code-block:: LAMMPS
|
||||||
|
|
||||||
|
fix 1 all mdi/qm
|
||||||
|
fix 1 all mdi/qm virial yes
|
||||||
|
fix 1 all mdi/qm add no every 100 elements 13 29
|
||||||
|
|
||||||
|
Description
|
||||||
|
"""""""""""
|
||||||
|
|
||||||
|
This command enables LAMMPS to act as a client with another server
|
||||||
|
code that will compute the total energy, per-atom forces, and total
|
||||||
|
virial for atom conformations and simulation box size/shapes that
|
||||||
|
LAMMPS sends it.
|
||||||
|
|
||||||
|
Typically the server code will be a quantum mechanics (QM) code, hence
|
||||||
|
the name of the fix. However this is not required, the server code
|
||||||
|
could be another classical molecular dynamics code or LAMMPS itself.
|
||||||
|
The server code must support use of the `MDI Library
|
||||||
|
<https://molssi-mdi.github.io/MDI_Library/html/index.html>`_ as
|
||||||
|
explained below.
|
||||||
|
|
||||||
|
These are example use cases for this fix, discussed further below:
|
||||||
|
|
||||||
|
* perform an ab initio MD (AIMD) simulation with quantum forces
|
||||||
|
* perform an energy minimization with quantum forces
|
||||||
|
* perform a nudged elastic band (NEB) calculation with quantum forces
|
||||||
|
* perform a QM calculation for a series of independent systems which LAMMPS reads or generates
|
||||||
|
|
||||||
|
The code coupling performed by this command is done via the `MDI
|
||||||
|
Library <https://molssi-mdi.github.io/MDI_Library/html/index.html>`_.
|
||||||
|
LAMMPS runs as an MDI driver (client), and sends MDI commands to an
|
||||||
|
external MDI engine code (server), e.g. a QM code which has support
|
||||||
|
for MDI. See the :doc:`Howto mdi <Howto_mdi>` page for more
|
||||||
|
information about how LAMMPS can operate as either an MDI driver or
|
||||||
|
engine.
|
||||||
|
|
||||||
|
The examples/mdi directory contains input scripts using this fix in
|
||||||
|
the various use cases discussed below. In each case, two instances of
|
||||||
|
LAMMPS are used, once as an MDI driver, once as an MDI engine
|
||||||
|
(surrogate for a QM code). The examples/mdi/README file explains how
|
||||||
|
to launch two codes so that they communicate via the MDI library using
|
||||||
|
either MPI or sockets. Any QM code that supports MDI could be used in
|
||||||
|
place of LAMMPS acting as a QM surrogate. See the :doc:`Howto mdi
|
||||||
|
<Howto_mdi>` page for a current list (March 2022) of such QM codes.
|
||||||
|
|
||||||
|
Note that an engine code can support MDI in either or both of two
|
||||||
|
modes. It can be used as a stand-alone code, launched at the same
|
||||||
|
time as LAMMPS. Or it can be used as a plugin library, which LAMMPS
|
||||||
|
loads. See the :doc:`mdi plugin <mdi>` command for how to trigger
|
||||||
|
LAMMPS to load a plugin library. The examples/mdi/README file
|
||||||
|
explains how to launch the two codes in either mode.
|
||||||
|
|
||||||
|
----------
|
||||||
|
|
||||||
|
The *virial* keyword setting of yes or no determines whether
|
||||||
|
LAMMPS will request the QM code to also compute and return
|
||||||
|
a 6-element symmetric virial tensor for the system.
|
||||||
|
|
||||||
|
The *add* keyword setting of *yes* or *no* determines whether the
|
||||||
|
energy and forces and virial returned by the QM code will be added to
|
||||||
|
the LAMMPS internal energy and forces and virial or not. If the
|
||||||
|
setting is *no* then the default :doc:`fix_modify energy <fix_modify>`
|
||||||
|
and :doc:`fix_modify virial <fix_modify>` settings are also set to
|
||||||
|
*no* and your input scripts should not set them to yes. See more
|
||||||
|
details on these fix_modify settings below.
|
||||||
|
|
||||||
|
Whatever the setting for the *add* keyword, the QM energy, forces, and
|
||||||
|
virial will be stored by the fix, so they can be accessed by other
|
||||||
|
commands. See details below.
|
||||||
|
|
||||||
|
The *every* keyword determines how often the QM code will be invoked
|
||||||
|
during a dynamics run with the current LAMMPS simulation box and
|
||||||
|
configuration of atoms. The QM code will be called once every
|
||||||
|
*Nevery* timesteps.
|
||||||
|
|
||||||
|
The *connect* keyword determines whether this fix performs a one-time
|
||||||
|
connection to the QM code. The default is *yes*. The only time a
|
||||||
|
*no* is needed is if this command is used multiple times in an input
|
||||||
|
script. E.g. if it used inside a loop which also uses the :doc:`clear
|
||||||
|
<clear>` command to destroy the system (including any defined fixes).
|
||||||
|
See the examples/mdi/in.series.driver script as an example of this,
|
||||||
|
where LAMMPS is using the QM code to compute energy and forces for a
|
||||||
|
series of system configurations. In this use case *connect no*
|
||||||
|
is used along with the :doc:`mdi connect and exit <mdi>` command
|
||||||
|
to one-time initiate/terminate the connection outside the loop.
|
||||||
|
|
||||||
|
The *elements* keyword allows specification of what element each
|
||||||
|
LAMMPS atom type corresponds to. This is specified by the atomic
|
||||||
|
number of the element, e.g. 13 for Al. An atomic number must be
|
||||||
|
specified for each of the ntypes LAMMPS atom types. Ntypes is
|
||||||
|
typically specified via the create_box command or in the data file
|
||||||
|
read by the read_data command. If this keyword is not specified, then
|
||||||
|
this fix will send the LAMMPS atom type for each atom to the MDI
|
||||||
|
engine. If both the LAMMPS driver and the MDI engine are initialized
|
||||||
|
so that atom type values are consistent in both codes, then the
|
||||||
|
*elements* keyword is not needed. Otherwise the keyword can be used
|
||||||
|
to insure the two codes are consistent in their definition of atomic
|
||||||
|
species.
|
||||||
|
|
||||||
|
----------
|
||||||
|
|
||||||
|
The following 3 example use cases are illustrated in the examples/mdi
|
||||||
|
directory. See its README file for more details.
|
||||||
|
|
||||||
|
(1) To run an ab initio MD (AIMD) dynamics simulation, or an energy
|
||||||
|
minimization with QM forces, or a multi-replica NEB calculation, use
|
||||||
|
*add yes* and *every 1* (the defaults). This is so that every time
|
||||||
|
LAMMPS needs energy and forces, the QM code will be invoked.
|
||||||
|
|
||||||
|
Both LAMMPS and the QM code should define the same system (simulation
|
||||||
|
box, atoms and their types) in their respective input scripts. Note
|
||||||
|
that on this scenario, it may not be necessary for LAMMPS to define a
|
||||||
|
pair style or use a neighbor list.
|
||||||
|
|
||||||
|
LAMMPS will then perform the timestepping or minimization iterations
|
||||||
|
for the simulation. At the point in each timestep or iteration when
|
||||||
|
LAMMPS needs the force on each atom, it communicates with the engine
|
||||||
|
code. It sends the current simulation box size and shape (if they
|
||||||
|
change dynamically, e.g. during an NPT simulation), and the current
|
||||||
|
atom coordinates. The engine code computes quantum forces on each
|
||||||
|
atom and the total energy of the system and returns them to LAMMPS.
|
||||||
|
|
||||||
|
Note that if the AIMD simulation is an NPT or NPH model, or the energy
|
||||||
|
minimization includes :doc:`fix box relax <fix_box_relax>` to
|
||||||
|
equilibrate the box size/shape, then LAMMPS computes a pressure. This
|
||||||
|
means the *virial* keyword should be set to *yes* so that the QM
|
||||||
|
contribution to the pressure can be included.
|
||||||
|
|
||||||
|
(2) To run dynamics with a LAMMPS interatomic potential, and evaluate
|
||||||
|
the QM energy and forces once every 1000 steps, use *add no* and
|
||||||
|
*every 1000*. This could be useful for using an MD run to generate
|
||||||
|
randomized configurations which are then passed to the QM code to
|
||||||
|
produce training data for a machine learning potential. A :doc:`dump
|
||||||
|
custom <dump>` command could be invoked every 1000 steps to dump the
|
||||||
|
atom coordinates and QM forces to a file. Likewise the QM energy and
|
||||||
|
virial could be output with the :doc:`thermo_style custom
|
||||||
|
<thermo_style>` command.
|
||||||
|
|
||||||
|
(3) To do a QM evaluation of energy and forces for a series of *N*
|
||||||
|
independent systems (simulation box and atoms), use *add no* and
|
||||||
|
*every 1*. Write a LAMMPS input script which loops over the *N*
|
||||||
|
systems. See the :doc:`Howto multiple <Howto_multiple>` doc page for
|
||||||
|
details on looping and removing old systems. The series of systems
|
||||||
|
could be initialized by reading them from data files with
|
||||||
|
:doc:`read_data <read_data>` commands. Or, for example, by using the
|
||||||
|
:doc:`lattice <lattice>` , :doc:`create_atoms <create_atoms>`,
|
||||||
|
:doc:`delete_atoms <delete_atoms>`, and/or :doc:`displace_atoms
|
||||||
|
random <displace_atoms>` commands to generate a series of different
|
||||||
|
systems. At the end of the loop perform :doc:`run 0 <run>` and
|
||||||
|
:doc:`write_dump <write_dump>` commands to invoke the QM code and
|
||||||
|
output the QM energy and forces. As in (2) this be useful to produce
|
||||||
|
QM data for training a machine learning potential.
|
||||||
|
|
||||||
|
----------
|
||||||
|
|
||||||
|
Restart, fix_modify, output, run start/stop, minimize info
|
||||||
|
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
|
||||||
|
|
||||||
|
No information about this fix is written to :doc:`binary restart files
|
||||||
|
<restart>`.
|
||||||
|
|
||||||
|
The :doc:`fix_modify <fix_modify>` *energy* option is supported by
|
||||||
|
this fix to add the potential energy computed by the QM code to the
|
||||||
|
global potential energy of the system as part of :doc:`thermodynamic
|
||||||
|
output <thermo_style>`. The default setting for this fix is
|
||||||
|
:doc:`fix_modify energy yes <fix_modify>`, unless the *add* keyword is
|
||||||
|
set to *no*, in which case the default setting is *no*.
|
||||||
|
|
||||||
|
The :doc:`fix_modify <fix_modify>` *virial* option is supported by
|
||||||
|
this fix to add the contribution computed by the QM code to the global
|
||||||
|
pressure of the system as part of :doc:`thermodynamic output
|
||||||
|
<thermo_style>`. The default setting for this fix is :doc:`fix_modify
|
||||||
|
virial yes <fix_modify>`, unless the *add* keyword is set to *no*, in
|
||||||
|
which case the default setting is *no*.
|
||||||
|
|
||||||
|
This fix computes a global scalar which can be accessed by various
|
||||||
|
:doc:`output commands <Howto_output>`. The scalar is the energy
|
||||||
|
returned by the QM code. The scalar value calculated by this fix is
|
||||||
|
"extensive".
|
||||||
|
|
||||||
|
This fix also computes a global vector with of length 6 which contains
|
||||||
|
the symmetric virial tensor values returned by the QM code. It can
|
||||||
|
likewise be accessed by various :doc:`output commands <Howto_output>`.
|
||||||
|
|
||||||
|
The ordering of values in the symmetric virial tensor is as follows:
|
||||||
|
vxx, vyy, vzz, vxy, vxz, vyz. The values will be in pressure
|
||||||
|
:doc:`units <units>`.
|
||||||
|
|
||||||
|
This fix also computes a peratom array with 3 columns which contains
|
||||||
|
the peratom forces returned by the QM code. It can likewise be
|
||||||
|
accessed by various :doc:`output commands <Howto_output>`.
|
||||||
|
|
||||||
|
No parameter of this fix can be used with the *start/stop* keywords of
|
||||||
|
the :doc:`run <run>` command.
|
||||||
|
|
||||||
|
Assuming the *add* keyword is set to *yes* (the default), the forces
|
||||||
|
computed by the QM code are used during an energy minimization,
|
||||||
|
invoked by the :doc:`minimize <minimize>` command.
|
||||||
|
|
||||||
|
.. note::
|
||||||
|
|
||||||
|
If you want the potential energy associated with the QM forces to
|
||||||
|
be included in the total potential energy of the system (the
|
||||||
|
quantity being minimized), you MUST not disable the
|
||||||
|
:doc:`fix_modify <fix_modify>` *energy* option for this fix, which
|
||||||
|
means the *add* keyword should also be set to *yes* (the default).
|
||||||
|
|
||||||
|
|
||||||
|
Restrictions
|
||||||
|
""""""""""""
|
||||||
|
|
||||||
|
This command is part of the MDI package. It is only enabled if
|
||||||
|
LAMMPS was built with that package. See the :doc:`Build package
|
||||||
|
<Build_package>` page for more info.
|
||||||
|
|
||||||
|
The QM code does not currently compute and return per-atom energy or
|
||||||
|
per-atom virial contributions. So they will not show up as part of
|
||||||
|
the calculations performed by the :doc:`compute pe/atom
|
||||||
|
<compute_pe_atom>` or :doc:`compute stress/atom <compute_stress_atom>`
|
||||||
|
commands.
|
||||||
|
|
||||||
|
To use LAMMPS as an MDI driver in conjunction with other MDI-enabled
|
||||||
|
codes (MD or QM codes), the :doc:`units <units>` command should be
|
||||||
|
used to specify *real* or *metal* units. This will ensure the correct
|
||||||
|
unit conversions between LAMMPS and MDI units. The other code will
|
||||||
|
also perform similar unit conversions into its preferred units.
|
||||||
|
|
||||||
|
LAMMPS can also be used as an MDI driver in other unit choices it
|
||||||
|
supports, e.g. *lj*, but then no unit conversion is performed.
|
||||||
|
|
||||||
|
Related commands
|
||||||
|
""""""""""""""""
|
||||||
|
|
||||||
|
:doc:`mdi plugin <mdi>`, :doc:`mdi engine <mdi>`
|
||||||
|
|
||||||
|
Default
|
||||||
|
"""""""
|
||||||
|
|
||||||
|
The default for the optional keywords are virial = no, add = yes,
|
||||||
|
every = 1, connect = yes.
|
||||||
113
doc/src/mdi.rst
113
doc/src/mdi.rst
@ -8,21 +8,26 @@ Syntax
|
|||||||
|
|
||||||
.. parsed-literal::
|
.. parsed-literal::
|
||||||
|
|
||||||
mdi mode args
|
mdi option args
|
||||||
|
|
||||||
* mode = *engine* or *plugin*
|
* option = *engine* or *plugin* or *connect* or *exit*
|
||||||
|
|
||||||
.. parsed-literal::
|
.. parsed-literal::
|
||||||
|
|
||||||
*engine* args = none
|
*engine* args = zero or more keyword arg pairs
|
||||||
*plugin* args = name keyword value keyword value
|
keywords = *elements*
|
||||||
|
*elements* args = N_1 N_2 ... N_ntypes
|
||||||
|
N_1,N_2,...N_ntypes = atomic number for each of ntypes LAMMPS atom types
|
||||||
|
*plugin* args = name keyword value keyword value ...
|
||||||
name = name of plugin library, e.g. lammps means a liblammps.so library will be loaded
|
name = name of plugin library, e.g. lammps means a liblammps.so library will be loaded
|
||||||
|
keyword/value pairs in any order, some are required, some are optional
|
||||||
keywords = *mdi* or *infile* or *extra* or *command*
|
keywords = *mdi* or *infile* or *extra* or *command*
|
||||||
*mdi* value = args passed to MDI for driver to operate with plugins
|
*mdi* value = args passed to MDI for driver to operate with plugins (required)
|
||||||
*infile* value = filename the engine will read at start-up
|
*infile* value = filename the engine will read at start-up (optional)
|
||||||
*extra* value = aditional command-line args to pass to engine library when loaded
|
*extra* value = aditional command-line args to pass to engine library when loaded
|
||||||
*command* value = a LAMMPS input script command to execute
|
*command* value = a LAMMPS input script command to execute (required)
|
||||||
|
*connect* args = none
|
||||||
|
*exit* args = none
|
||||||
|
|
||||||
Examples
|
Examples
|
||||||
""""""""
|
""""""""
|
||||||
@ -30,26 +35,19 @@ Examples
|
|||||||
.. code-block:: LAMMPS
|
.. code-block:: LAMMPS
|
||||||
|
|
||||||
mdi engine
|
mdi engine
|
||||||
|
mdi engine elements 13 29
|
||||||
mdi plugin lammps mdi "-role ENGINE -name lammps -method LINK" &
|
mdi plugin lammps mdi "-role ENGINE -name lammps -method LINK" &
|
||||||
infile in.aimd.engine extra "-log log.aimd.engine.plugin" &
|
infile in.aimd.engine extra "-log log.aimd.engine.plugin" &
|
||||||
command "run 5"
|
command "run 5"
|
||||||
|
mdi connect
|
||||||
|
mdi exit
|
||||||
|
|
||||||
Description
|
Description
|
||||||
"""""""""""
|
"""""""""""
|
||||||
|
|
||||||
This command implements two high-level operations within LAMMPS to use
|
This command implements operations within LAMMPS to use the `MDI
|
||||||
the `MDI Library
|
Library <https://molssi-mdi.github.io/MDI_Library/html/index.html>`
|
||||||
<https://molssi-mdi.github.io/MDI_Library/html/index.html>` for
|
for coupling to other codes in a client/server protocol.
|
||||||
coupling to other codes in a client/server protocol.
|
|
||||||
|
|
||||||
The *engine* mode enables LAMMPS to act as an MDI engine (server),
|
|
||||||
responding to requests from an MDI driver (client) code.
|
|
||||||
|
|
||||||
The *plugin* mode enables LAMMPS to act as an MDI driver (client), and
|
|
||||||
load the MDI engine (server) code as a library plugin. In this case
|
|
||||||
the MDI engine is a library plugin. It can also be a stand-alone
|
|
||||||
code, launched separately from LAMMPS, in which case the mdi plugin
|
|
||||||
command is not used.
|
|
||||||
|
|
||||||
See the Howto MDI doc page for a discussion of all the different ways
|
See the Howto MDI doc page for a discussion of all the different ways
|
||||||
2 or more codes can interact via MDI.
|
2 or more codes can interact via MDI.
|
||||||
@ -61,6 +59,22 @@ stand-alone code or as a plugin. The README file in that directory
|
|||||||
shows how to launch and couple codes for all the 4 usage modes, and so
|
shows how to launch and couple codes for all the 4 usage modes, and so
|
||||||
they communicate via the MDI library using either MPI or sockets.
|
they communicate via the MDI library using either MPI or sockets.
|
||||||
|
|
||||||
|
The scripts in that directory illustrate the use of all the options
|
||||||
|
for this command.
|
||||||
|
|
||||||
|
The *engine* option enables LAMMPS to act as an MDI engine (server),
|
||||||
|
responding to requests from an MDI driver (client) code.
|
||||||
|
|
||||||
|
The *plugin* option enables LAMMPS to act as an MDI driver (client),
|
||||||
|
and load the MDI engine (server) code as a library plugin. In this
|
||||||
|
case the MDI engine is a library plugin. An MDI engine can also be a
|
||||||
|
stand-alone code, launched separately from LAMMPS, in which case the
|
||||||
|
mdi plugin command is not used.
|
||||||
|
|
||||||
|
The *connect* and *exit* options are only used when LAMMPS is acting
|
||||||
|
as an MDI driver. As explained below, these options are normally not
|
||||||
|
needed, except for a specific kind of use case.
|
||||||
|
|
||||||
----------
|
----------
|
||||||
|
|
||||||
The *mdi engine* command is used to make LAMMPS operate as an MDI
|
The *mdi engine* command is used to make LAMMPS operate as an MDI
|
||||||
@ -100,6 +114,8 @@ commands, which are described further below.
|
|||||||
- Send/request charge on each atom (N values)
|
- Send/request charge on each atom (N values)
|
||||||
* - >COORDS or <COORDS
|
* - >COORDS or <COORDS
|
||||||
- Send/request coordinates of each atom (3N values)
|
- Send/request coordinates of each atom (3N values)
|
||||||
|
* - >ELEMENTS
|
||||||
|
- Send elements (atomic numbers) for each atom (N values)
|
||||||
* - <ENERGY
|
* - <ENERGY
|
||||||
- Request total energy (potential + kinetic) of the system (1 value)
|
- Request total energy (potential + kinetic) of the system (1 value)
|
||||||
* - >FORCES or <FORCES
|
* - >FORCES or <FORCES
|
||||||
@ -121,11 +137,11 @@ commands, which are described further below.
|
|||||||
* - <PE
|
* - <PE
|
||||||
- Request potential energy of the system (1 value)
|
- Request potential energy of the system (1 value)
|
||||||
* - <STRESS
|
* - <STRESS
|
||||||
- Request stress tensor (virial) of the system (6 values)
|
- Request symmetric stress tensor (virial) of the system (9 values)
|
||||||
* - >TOLERANCE
|
* - >TOLERANCE
|
||||||
- Send 4 tolerance parameters for next MD minimization via OPTG command
|
- Send 4 tolerance parameters for next MD minimization via OPTG command
|
||||||
* - >TYPES or <TYPES
|
* - >TYPES or <TYPES
|
||||||
- Send/request the numeric type of each atom (N values)
|
- Send/request the LAMMPS atom type for each atom (N values)
|
||||||
* - >VELOCITIES or <VELOCITIES
|
* - >VELOCITIES or <VELOCITIES
|
||||||
- Send/request the velocity of each atom (3N values)
|
- Send/request the velocity of each atom (3N values)
|
||||||
* - @INIT_MD or @INIT_OPTG
|
* - @INIT_MD or @INIT_OPTG
|
||||||
@ -145,9 +161,25 @@ commands, which are described further below.
|
|||||||
builds. If the change in atom positions is large (since the
|
builds. If the change in atom positions is large (since the
|
||||||
previous >COORDS command), then LAMMPS will do a more expensive
|
previous >COORDS command), then LAMMPS will do a more expensive
|
||||||
operation to migrate atoms to new processors as needed and
|
operation to migrate atoms to new processors as needed and
|
||||||
re-neighbor. If the >NATOMS or >TYPES commands have been sent
|
re-neighbor. If the >NATOMS or >TYPES or >ELEMENTS commands have
|
||||||
(since the previous >COORDS command), then LAMMPS assumes the
|
been sent (since the previous >COORDS command), then LAMMPS assumes
|
||||||
system is new and re-initializes an entirely new simulation.
|
the system is new and re-initializes an entirely new simulation.
|
||||||
|
|
||||||
|
.. note::
|
||||||
|
|
||||||
|
The >TYPES or >ELEMENTS commands are how the MDI driver tells the
|
||||||
|
LAMMPS engine which LAMMPS atom type to assign to each atom. If
|
||||||
|
both the MDI driver and the LAMMPS engine are initialized so that
|
||||||
|
atom type values are consistent in both codes, then the >TYPES
|
||||||
|
command can be used. If not, the optional *elements* keyword can
|
||||||
|
be used to specify what element each LAMMPS atom type corresponds
|
||||||
|
to. This is specified by the atomic number of the element, e.g. 13
|
||||||
|
for Al. An atomic number must be specified for each of the ntypes
|
||||||
|
LAMMPS atom types. Ntypes is typically specified via the
|
||||||
|
create_box command or in the data file read by the read_data
|
||||||
|
command. In this has been done, the MDI driver can send an
|
||||||
|
>ELEMENTS command to the LAMMPS driver with the atomic number of
|
||||||
|
each atom.
|
||||||
|
|
||||||
The MD and OPTG commands perform an entire MD simulation or energy
|
The MD and OPTG commands perform an entire MD simulation or energy
|
||||||
minimization (to convergence) with no communication from the driver
|
minimization (to convergence) with no communication from the driver
|
||||||
@ -270,7 +302,7 @@ The *command* keyword is required. It specifies a LAMMPS input script
|
|||||||
command (as a single argument in quotes if it is multiple words).
|
command (as a single argument in quotes if it is multiple words).
|
||||||
Once the plugin library is launched, LAMMPS will execute this command.
|
Once the plugin library is launched, LAMMPS will execute this command.
|
||||||
Other previously-defined commands in the input script, such as the
|
Other previously-defined commands in the input script, such as the
|
||||||
:doc:`fix mdi/aimd <fix_mdi_aimd>` command, should perform MDI
|
:doc:`fix mdi/qm <fix_mdi_qm>` command, should perform MDI
|
||||||
communication with the engine, while the specified *command* executes.
|
communication with the engine, while the specified *command* executes.
|
||||||
Note that if *command* is an :doc:`include <include>` command, then it
|
Note that if *command* is an :doc:`include <include>` command, then it
|
||||||
could specify a filename with multiple LAMMPS commands.
|
could specify a filename with multiple LAMMPS commands.
|
||||||
@ -284,6 +316,31 @@ could specify a filename with multiple LAMMPS commands.
|
|||||||
"mdi plugin" command could then load the same library plugin or
|
"mdi plugin" command could then load the same library plugin or
|
||||||
a different one if desired.
|
a different one if desired.
|
||||||
|
|
||||||
|
----------
|
||||||
|
|
||||||
|
The *mdi connect* and *mdi exit* commands are only used when LAMMPS is
|
||||||
|
operating as an MDI driver. And when other LAMMPS command(s) which
|
||||||
|
send MDI commands and associated data to/from the MDI engine are not
|
||||||
|
able to initiate and terminate the connection to the engine code.
|
||||||
|
|
||||||
|
The only current MDI driver command in LAMMPS is the :doc:`fix mdi/qm
|
||||||
|
<fix_mdi_qm>` command. If it is only used once in an input script
|
||||||
|
then it can initiate and terminate the connection. But if it is being
|
||||||
|
issued multiple times, e.g. in a loop that issues a :doc:`clear
|
||||||
|
<clear>` command, then it cannot initiate or terminate the connection
|
||||||
|
multiple times. Instead, the *mdi connect* and *mdi exit* commands
|
||||||
|
should be used outside the loop to initiate or terminate the connection.
|
||||||
|
|
||||||
|
See the examples/mdi/in.series.driver script for an example of how
|
||||||
|
this is done. The LOOP in that script is reading a series of data
|
||||||
|
file configurations and passing them to an MDI engine (e.g. quantum
|
||||||
|
code) for energy and force evaluation. A *clear* command inside the
|
||||||
|
loop wipes out the current system so a new one can be defined. This
|
||||||
|
operation also destroys all fixes. So the :doc:`fix mdi/qm
|
||||||
|
<fix_mdi_qm>` command is issued once per loop iteration. Note that it
|
||||||
|
includes a "connect no" option which disables the initiate/terminate
|
||||||
|
logic within that fix.
|
||||||
|
|
||||||
|
|
||||||
Restrictions
|
Restrictions
|
||||||
""""""""""""
|
""""""""""""
|
||||||
@ -304,7 +361,7 @@ supports, e.g. *lj*, but then no unit conversion is performed.
|
|||||||
Related commands
|
Related commands
|
||||||
""""""""""""""""
|
""""""""""""""""
|
||||||
|
|
||||||
:doc:`fix mdi/aimd <fix_mdi_aimd>`
|
:doc:`fix mdi/qm <fix_mdi_qm>`
|
||||||
|
|
||||||
Default
|
Default
|
||||||
"""""""
|
"""""""
|
||||||
|
|||||||
@ -3679,13 +3679,19 @@ vx
|
|||||||
Vx
|
Vx
|
||||||
vxcm
|
vxcm
|
||||||
vxmu
|
vxmu
|
||||||
|
vxx
|
||||||
|
vxy
|
||||||
|
vxz
|
||||||
vy
|
vy
|
||||||
Vy
|
Vy
|
||||||
vycm
|
vycm
|
||||||
|
vyy
|
||||||
|
vyz
|
||||||
vz
|
vz
|
||||||
Vz
|
Vz
|
||||||
vzcm
|
vzcm
|
||||||
vzi
|
vzi
|
||||||
|
vzz
|
||||||
Waals
|
Waals
|
||||||
Wadley
|
Wadley
|
||||||
wallstyle
|
wallstyle
|
||||||
|
|||||||
@ -2,10 +2,11 @@ These are examples that work the MDI package in LAMMPS which uses the
|
|||||||
MolSSI MDI library for coupling codes together and communicating
|
MolSSI MDI library for coupling codes together and communicating
|
||||||
between them with MDI messages.
|
between them with MDI messages.
|
||||||
|
|
||||||
In MDI lingo, one code is the driver and another code is the engine.
|
Within the MDI context, one code is the driver and another code is
|
||||||
The 2 codes can be written in any language; C++ (LAMMPS) and Python
|
the engine. The 2 codes can be written in any language; C++ (LAMMPS)
|
||||||
are illustrated here. The 2 codes can each be stand-alone codes, in
|
and Python are illustrated here. The 2 codes can each be stand-alone
|
||||||
which case they can be run on different numbers of processors. The 2
|
codes, in which case they can be run on different numbers of processors.
|
||||||
|
The 2
|
||||||
codes can communicate either via TCP (sockets) or via MPI. For the
|
codes can communicate either via TCP (sockets) or via MPI. For the
|
||||||
TCP case, the driver and engine need to be launched separately,
|
TCP case, the driver and engine need to be launched separately,
|
||||||
e.g. in 2 windows on your desktop machine. For the MPI case, a single
|
e.g. in 2 windows on your desktop machine. For the MPI case, a single
|
||||||
@ -19,87 +20,99 @@ LAMMPS supports operating in all these MDI modes. It can be an engine
|
|||||||
operating either as a stand-alone code or as a plugin. It can also be
|
operating either as a stand-alone code or as a plugin. It can also be
|
||||||
a driver and couple to an engine that is either a stand-alone code or
|
a driver and couple to an engine that is either a stand-alone code or
|
||||||
a plugin. Examples for all these use cases are in this directory.
|
a plugin. Examples for all these use cases are in this directory.
|
||||||
The example commands below illustrate how to run all the variants.
|
The Run.sh file shows how run in all the modes. Type "sh Run.sh"
|
||||||
|
to try them all out.
|
||||||
|
|
||||||
To use LAMMPS as a plugin engine, you must build it as a shared library.
|
To use LAMMPS as a plugin engine, you must build it as a shared
|
||||||
Something like this, which also builds the normal LAMMPS executable
|
library. Something like this with make, which also builds the normal
|
||||||
lmp_mpi:
|
LAMMPS executable lmp_mpi:
|
||||||
|
|
||||||
cd src
|
cd src
|
||||||
make yes-mdi
|
make yes-mdi
|
||||||
make mode=shlib mpi
|
make mode=shlib mpi
|
||||||
|
|
||||||
To use the serial_driver.py example you will need Python 3 with Numpy
|
-------------------------------------------------
|
||||||
and mpi4py available in your Python. Make sure LAMMPS and Python are
|
|
||||||
using same the same version of MPI.
|
Examples 4 and 5 use Python scripts as MDI drivers. For this you will
|
||||||
|
need Python 3 with Numpy and mpi4py installed. Make sure LAMMPS and
|
||||||
|
Python/mpi4py are using same the same version of MPI.
|
||||||
|
|
||||||
|
You will also need MDI installed in your Python. You cannot use the
|
||||||
|
LAMMPS build of the MDI library for this, b/c LAMMPS builds MDI as a
|
||||||
|
static library, not shared, which Python requires.
|
||||||
|
|
||||||
|
You can install MDI in your Python via conda:
|
||||||
|
|
||||||
|
% conda install -c conda-forge pymdi=1.4.1
|
||||||
|
|
||||||
|
or via pip:
|
||||||
|
|
||||||
|
% pip install pymdi==1.4.1
|
||||||
|
|
||||||
|
It is likely fine to leave off the version number, to get the latest
|
||||||
|
MDI version. But to be safe, 1.4.1 is the version LAMMPS is currently
|
||||||
|
using.
|
||||||
|
|
||||||
|
-------------------------------------------------
|
||||||
|
|
||||||
|
5 example use-cases are explained below.
|
||||||
|
|
||||||
|
In the first 3 examples, results running with MDI should be identical
|
||||||
|
to running without MDI (alone log files). Example #4 has no non-MDI
|
||||||
|
run. Example #5 results should match the non-MDI run of example #1.
|
||||||
|
|
||||||
|
-------------------------------------------------
|
||||||
|
|
||||||
|
* Example #1 = run ab initio MD (AIMD)
|
||||||
|
|
||||||
|
Two instances of LAMMPS operate as a driver and engine. As an engine,
|
||||||
|
LAMMPS is a surrogate for a quantum code.
|
||||||
|
|
||||||
|
You can compare the thermo output in log.aimd.alone.1 to the thermo output in
|
||||||
|
any of the log.aimd.driver* files. It should be identical.
|
||||||
|
|
||||||
|
Note that the "alone" and "driver" input scripts have options for
|
||||||
|
running in NVE vs NPT Comment in/out the appropriate line to make
|
||||||
|
change. Nothing needs to be changed in the "engine" scripts.
|
||||||
|
|
||||||
-------------------------------------------------
|
-------------------------------------------------
|
||||||
-------------------------------------------------
|
-------------------------------------------------
|
||||||
|
|
||||||
* Example #1 = run ab inito MD (AIMD)
|
* Example #2 = run LAMMPS, compute QM forces on snapshots from a long run
|
||||||
Two instances of LAMMPS operate as a driver and engine
|
|
||||||
As an engine, LAMMPS is a surrogate for a quantum code
|
|
||||||
|
|
||||||
Note that the 2 input scripts in.aimd.alone and in.aimd.driver
|
Two instances of LAMMPS operate as a driver and engine. As an engine,
|
||||||
have an option for running in NVE vs NPT mode. Comment in/out
|
LAMMPS is a surrogate for a quantum code
|
||||||
the appropriate line to change modes. Nothing needs to be
|
|
||||||
changed in the in.aimd.engine or in.aimd.engine.plugin scripts.
|
|
||||||
|
|
||||||
---
|
You can compare the thermo output in log.snapshot.alone.1 to the
|
||||||
|
thermo output in any of the log.snapshot.driver* files. It should be
|
||||||
|
identical.
|
||||||
|
|
||||||
Run the entire calculation with a single instance of LAMMPS by itself
|
You can compare the dumped forces in dump.snapshot.alone.1 to the
|
||||||
results should be identical to running this example with MDI
|
forces in any of the dump.snapshot.* files. They should be identical,
|
||||||
|
although at step 0 the forces are "zero" and may be epsilon different.
|
||||||
% lmp_mpi < in.aimd.alone
|
|
||||||
|
|
||||||
With MDI, the thermo output of the driver should match the thermo
|
|
||||||
output of the in.aimd.alone script.
|
|
||||||
|
|
||||||
---
|
|
||||||
|
|
||||||
Run with TCP: 1 proc each
|
|
||||||
|
|
||||||
% lmp_mpi -mdi "-name aimd -role DRIVER -method TCP -port 8021" -log log.aimd.driver -in in.aimd.driver
|
|
||||||
|
|
||||||
% lmp_mpi -mdi "-name LAMMPS -role ENGINE -method TCP -port 8021 -hostname localhost" -log log.aimd.engine -in in.aimd.engine
|
|
||||||
|
|
||||||
---
|
|
||||||
|
|
||||||
Run with TCP: 3 procs + 4 procs
|
|
||||||
|
|
||||||
% mpirun -np 3 lmp_mpi -mdi "-name aimd -role DRIVER -method TCP -port 8021" -log log.aimd.driver -in in.aimd.driver
|
|
||||||
|
|
||||||
% mpirun -np 4 lmp_mpi -mdi "-name LAMMPS -role ENGINE -method TCP -port 8021 -hostname localhost" -log log.aimd.engine -in in.aimd.engine
|
|
||||||
|
|
||||||
---
|
|
||||||
|
|
||||||
Run with MPI: 1 proc each
|
|
||||||
|
|
||||||
% mpirun -np 1 lmp_mpi -mdi "-name aimd -role DRIVER -method MPI" -log log.aimd.driver -in in.aimd.driver : -np 1 lmp_mpi -mdi "-name LAMMPS -role ENGINE -method MPI" -log log.aimd.engine -in in.aimd.engine
|
|
||||||
|
|
||||||
---
|
|
||||||
|
|
||||||
Run with MPI: 3 procs + 4 procs
|
|
||||||
|
|
||||||
% mpirun -np 3 lmp_mpi -mdi "-name aimd -role DRIVER -method MPI" -log log.aimd.driver -in in.aimd.driver : -np 4 lmp_mpi -mdi "-name LAMMPS -role ENGINE -method MPI" -log log.aimd.engine -in in.aimd.engine
|
|
||||||
|
|
||||||
---
|
|
||||||
|
|
||||||
Run in plugin mode: 1 proc
|
|
||||||
|
|
||||||
% lmp_mpi -mdi "-name aimd -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/src" -log log.aimd.driver.plugin -in in.aimd.driver.plugin
|
|
||||||
|
|
||||||
---
|
|
||||||
|
|
||||||
Run in plugin mode: 3 procs
|
|
||||||
|
|
||||||
% mpirun -np 3 lmp_mpi -mdi "-name aimd -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/src" -log log.aimd.driver.plugin -in in.aimd.driver.plugin
|
|
||||||
|
|
||||||
-------------------------------------------------
|
-------------------------------------------------
|
||||||
-------------------------------------------------
|
-------------------------------------------------
|
||||||
|
|
||||||
* Example #2 = Python driver runs a sequence of unrelated LAMMPS calculations
|
* Example #3 = run LAMMPS, compute QM forces on series of independent systems
|
||||||
Each calculation can be a single-point evaluation, MD run, or minimization
|
|
||||||
|
Two instances of LAMMPS operate as a driver and engine. As an engine,
|
||||||
|
LAMMPS is a surrogate for a quantum code
|
||||||
|
|
||||||
|
You can compare the thermo output in log.series.alone.1 to the thermo
|
||||||
|
output in any of the log.series.driver* files. It should be
|
||||||
|
identical.
|
||||||
|
|
||||||
|
You can compare the dumped forces in dump.series.alone.1 to the forces
|
||||||
|
in any of the dump.series.* files. They should be identical,
|
||||||
|
|
||||||
|
-------------------------------------------------
|
||||||
|
-------------------------------------------------
|
||||||
|
|
||||||
|
* Example #4 = Python driver runs a sequence of unrelated LAMMPS calculations
|
||||||
|
|
||||||
|
Each calculation can be a single-point evaluation, MD run, or
|
||||||
|
minimization
|
||||||
|
|
||||||
The sequence_driver.py code allows for optional switches in addition
|
The sequence_driver.py code allows for optional switches in addition
|
||||||
to -mdi (required) and the -plugin and -plugin_args switches which are
|
to -mdi (required) and the -plugin and -plugin_args switches which are
|
||||||
@ -128,101 +141,31 @@ copied here:
|
|||||||
# -seed 12345
|
# -seed 12345
|
||||||
# random number seed > 0, default = 12345
|
# random number seed > 0, default = 12345
|
||||||
|
|
||||||
---
|
You can compare the thermo output in any of the log.sequence.engine.*
|
||||||
|
files. It should be identical.
|
||||||
Run with TCP: 1 proc each
|
|
||||||
|
|
||||||
% python3 sequence_driver.py -mdi "-role DRIVER -name sequence -method TCP -port 8021"
|
|
||||||
|
|
||||||
% lmp_mpi -mdi "-role ENGINE -name LAMMPS -method TCP -port 8021 -hostname localhost" -log log.sequence -in in.sequence
|
|
||||||
|
|
||||||
---
|
|
||||||
|
|
||||||
Run with TCP: 2 proc + 4 procs
|
|
||||||
|
|
||||||
% mpirun -np 2 python3 sequence_driver.py -mdi "-role DRIVER -name sequence -method TCP -port 8021"
|
|
||||||
|
|
||||||
% mpirun -np 4 lmp_mpi -mdi "-role ENGINE -name LAMMPS -method TCP -port 8021 -hostname localhost" -log log.sequence -in in.sequence
|
|
||||||
|
|
||||||
---
|
|
||||||
|
|
||||||
Run with MPI: 1 proc each
|
|
||||||
|
|
||||||
% mpirun -np 1 python3 sequence_driver.py -mdi "-role DRIVER -name sequence -method MPI" : -np 1 lmp_mpi -mdi "-role ENGINE -name LAMMPS -method MPI" -log log.sequence -in in.sequence
|
|
||||||
|
|
||||||
---
|
|
||||||
|
|
||||||
Run with MPI: 2 procs + 4 procs
|
|
||||||
|
|
||||||
% mpirun -np 2 python3 sequence_driver.py -mdi "-role DRIVER -name sequence -method MPI" : -np 4 lmp_mpi -mdi "-role ENGINE -name LAMMPS -method MPI" -log log.sequence -in in.sequence
|
|
||||||
|
|
||||||
---
|
|
||||||
|
|
||||||
Run in plugin mode: 1 proc
|
|
||||||
|
|
||||||
% python3 sequence_driver.py -plugin lammps -mdi "-role DRIVER -name sequence -method LINK -plugin_path /home/sjplimp/lammps/git/src" -plugin_args "-log log.sequence -in in.sequence"
|
|
||||||
|
|
||||||
---
|
|
||||||
|
|
||||||
Run in plugin mode: 3 procs
|
|
||||||
|
|
||||||
% mpirun -np 3 python3 sequence_driver.py -plugin lammps -mdi "-role DRIVER -name sequence -method LINK -plugin_path /home/sjplimp/lammps/git/src" -plugin_args "-log log.sequence -in in.sequence"
|
|
||||||
|
|
||||||
-------------------------------------------------
|
-------------------------------------------------
|
||||||
-------------------------------------------------
|
-------------------------------------------------
|
||||||
|
|
||||||
* Example #3 = run AIMD with Python driver code and 2 LAMMPS instances as engines
|
* Example #5 = run AIMD with Python driver code and 2 LAMMPS instances as engines
|
||||||
First LAMMPS instance performs the MD timestepping
|
|
||||||
Second LAMMPS instance is surrogate QM = computes forces
|
First LAMMPS instance performs the MD timestepping. Second LAMMPS
|
||||||
|
instance is surrogate QM to compute forces.
|
||||||
|
|
||||||
The aimd_driver.py code allows for an optional switch in addition to
|
The aimd_driver.py code allows for an optional switch in addition to
|
||||||
-mdi (required) and the -plugin and -plugin_args swiches which are
|
-mdi (required) and the -plugin and -plugin_args swiches which are
|
||||||
used to link to the 2 engines as a plugin libraries. The example run
|
used to link to the 2 engines as a plugin libraries. The example run
|
||||||
commands below use the default values of the optional switch. The
|
commands below use the default values of the optional switch. The
|
||||||
switch is also explained the top of the file; the info is copied
|
switch is also explained the top of the file; the info is copied here:
|
||||||
here:
|
|
||||||
|
|
||||||
# -nsteps 5
|
# -nsteps 10
|
||||||
# number of timesteps in dynamics runs, default = 5
|
# number of timesteps in dynamics runs, default = 10
|
||||||
|
|
||||||
---
|
This calculation is the same as Example #1 with a LAMMPS driver and a
|
||||||
|
LAMMPS engine. Now there is a Python driver and two LAMMPS engines.
|
||||||
|
|
||||||
Run the entire calculation with a single instance of LAMMPS by itself
|
You can compare the thermo output in log.aimd.alone.1 output to the
|
||||||
results should be identical to running this example with MDI
|
thermo output is any of the log.sequence.engine.* files. It should be
|
||||||
|
identical for the Total Energy printed out by the Python driver script.
|
||||||
|
|
||||||
% lmp_mpi < in.aimd.alone
|
E.g. Step 10: MM energy 1.69875, QM energy -6.31535, Total energy -4.6166
|
||||||
|
|
||||||
With MDI, the driver prints the QM and Total energies. These should
|
|
||||||
match the PotEng and TotEng output of the in.aimd.alone script.
|
|
||||||
|
|
||||||
---
|
|
||||||
|
|
||||||
Run with TCP: 1 proc each
|
|
||||||
|
|
||||||
% python3 aimd_driver.py -mdi "-role DRIVER -name aimd -method TCP -port 8021"
|
|
||||||
|
|
||||||
% lmp_mpi -mdi "-role ENGINE -name MM -method TCP -port 8021 -hostname localhost" -log log.aimd.mm -in in.aimd.mm
|
|
||||||
|
|
||||||
% lmp_mpi -mdi "-role ENGINE -name QM -method TCP -port 8021 -hostname localhost" -log log.aimd.qm -in in.aimd.qm
|
|
||||||
|
|
||||||
---
|
|
||||||
|
|
||||||
Run with TCP: 2 procs + 2 procs + 3 procs
|
|
||||||
|
|
||||||
% mpirun -np 2 python3 aimd_driver.py -mdi "-role DRIVER -name aimd -method TCP -port 8021"
|
|
||||||
|
|
||||||
% mpirun -np 2 lmp_mpi -mdi "-role ENGINE -name MM -method TCP -port 8021 -hostname localhost" -log log.aimd.mm -in in.aimd.mm
|
|
||||||
|
|
||||||
% mpirun -np 3 lmp_mpi -mdi "-role ENGINE -name QM -method TCP -port 8021 -hostname localhost" -log log.aimd.qm -in in.aimd.qm
|
|
||||||
|
|
||||||
---
|
|
||||||
|
|
||||||
Run with MPI: 1 proc each
|
|
||||||
|
|
||||||
% mpirun -np 1 python3 aimd_driver.py -mdi "-role DRIVER -name aimd -method MPI" : -np 1 lmp_mpi -mdi "-role ENGINE -name MM -method MPI" -log log.aimd.mm -in in.aimd.mm : -np 1 lmp_mpi -mdi "-role ENGINE -name QM -method MPI" -log log.aimd.qm -in in.aimd.qm
|
|
||||||
|
|
||||||
---
|
|
||||||
|
|
||||||
Run with MPI: 2 procs + 2 procs + 3 procs
|
|
||||||
|
|
||||||
% mpirun -np 2 python3 aimd_driver.py -mdi "-role DRIVER -name aimd -method MPI" : -np 2 lmp_mpi -mdi "-role ENGINE -name MM -method MPI" -log log.aimd.mm -in in.aimd.mm : -np 3 lmp_mpi -mdi "-role ENGINE -name QM -method MPI" -log log.aimd.qm -in in.aimd.qm
|
|
||||||
|
|||||||
256
examples/mdi/Run.sh
Normal file
256
examples/mdi/Run.sh
Normal file
@ -0,0 +1,256 @@
|
|||||||
|
# Run all the examples
|
||||||
|
|
||||||
|
# -------------------------------------------------
|
||||||
|
# -------------------------------------------------
|
||||||
|
|
||||||
|
# Example 1 = run ab initio MD (AIMD)
|
||||||
|
|
||||||
|
# ---
|
||||||
|
|
||||||
|
# Run without MDI
|
||||||
|
|
||||||
|
lmp_mpi -log log.aimd.alone.1 < in.aimd.alone
|
||||||
|
|
||||||
|
# ---
|
||||||
|
|
||||||
|
# Run with TCP: 1 proc each
|
||||||
|
|
||||||
|
lmp_mpi -mdi "-name LMP1 -role DRIVER -method TCP -port 8021" -log log.aimd.driver.tcp.1 -in in.aimd.driver &
|
||||||
|
|
||||||
|
lmp_mpi -mdi "-name LMP2 -role ENGINE -method TCP -port 8021 -hostname localhost" -log log.aimd.engine.tcp.1 -in in.aimd.engine
|
||||||
|
|
||||||
|
# ---
|
||||||
|
|
||||||
|
# Run with TCP: 3 procs + 4 procs
|
||||||
|
|
||||||
|
mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method TCP -port 8021" -log log.aimd.driver.tcp.3 -in in.aimd.driver &
|
||||||
|
|
||||||
|
mpirun -np 4 lmp_mpi -mdi "-name LMP2 -role ENGINE -method TCP -port 8021 -hostname localhost" -log log.aimd.engine.tcp.4 -in in.aimd.engine
|
||||||
|
|
||||||
|
# ---
|
||||||
|
|
||||||
|
# Run with MPI: 1 proc each
|
||||||
|
|
||||||
|
mpirun -np 1 lmp_mpi -mdi "-name LMP1 -role DRIVER -method MPI" -log log.aimd.driver.mpi.1 -in in.aimd.driver : -np 1 lmp_mpi -mdi "-name LMP2 -role ENGINE -method MPI" -log log.aimd.engine.mpi.1 -in in.aimd.engine
|
||||||
|
|
||||||
|
# ---
|
||||||
|
|
||||||
|
# Run with MPI: 3 procs + 4 procs
|
||||||
|
|
||||||
|
mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method MPI" -log log.aimd.driver.mpi.3 -in in.aimd.driver : -np 4 lmp_mpi -mdi "-name LMP2 -role ENGINE -method MPI" -log log.aimd.engine.mpi.4 -in in.aimd.engine
|
||||||
|
|
||||||
|
# ---
|
||||||
|
|
||||||
|
# Run in plugin mode: 1 proc
|
||||||
|
|
||||||
|
lmp_mpi -mdi "-name LMP1 -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/src" -log log.aimd.driver.plugin.1 -in in.aimd.driver.plugin
|
||||||
|
mv log.aimd.engine.plugin log.aimd.engine.plugin.1
|
||||||
|
|
||||||
|
# ---
|
||||||
|
|
||||||
|
# Run in plugin mode: 3 procs
|
||||||
|
|
||||||
|
mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/src" -log log.aimd.driver.plugin.3 -in in.aimd.driver.plugin
|
||||||
|
mv log.aimd.engine.plugin log.aimd.engine.plugin.3
|
||||||
|
|
||||||
|
# -------------------------------------------------
|
||||||
|
# -------------------------------------------------
|
||||||
|
|
||||||
|
# Example 2 = run LAMMPS, compute QM forces on snapshots from a long run
|
||||||
|
|
||||||
|
# ---
|
||||||
|
|
||||||
|
# Run without MDI
|
||||||
|
|
||||||
|
lmp_mpi -log log.snapshot.alone.1 < in.snapshot.alone
|
||||||
|
mv dump.snapshot.alone dump.snapshot.alone.1
|
||||||
|
|
||||||
|
# ---
|
||||||
|
|
||||||
|
# Run with TCP: 1 proc each
|
||||||
|
|
||||||
|
lmp_mpi -mdi "-name LMP1 -role DRIVER -method TCP -port 8021" -log log.snapshot.driver.tcp.1 -in in.snapshot.driver &
|
||||||
|
|
||||||
|
lmp_mpi -mdi "-name LMP2 -role ENGINE -method TCP -port 8021 -hostname localhost" -log log.snapshot.engine.tcp.1 -in in.snapshot.engine
|
||||||
|
mv dump.snapshot.driver dump.snapshot.driver.tcp.1
|
||||||
|
|
||||||
|
# ---
|
||||||
|
|
||||||
|
# Run with TCP: 3 procs + 4 procs
|
||||||
|
|
||||||
|
mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method TCP -port 8021" -log log.snapshot.driver.tcp.3 -in in.snapshot.driver &
|
||||||
|
|
||||||
|
mpirun -np 4 lmp_mpi -mdi "-name LMP2 -role ENGINE -method TCP -port 8021 -hostname localhost" -log log.snapshot.engine.tcp.4 -in in.snapshot.engine
|
||||||
|
mv dump.snapshot.driver dump.snapshot.driver.tcp.4
|
||||||
|
|
||||||
|
# ---
|
||||||
|
|
||||||
|
# Run with MPI: 1 proc each
|
||||||
|
|
||||||
|
mpirun -np 1 lmp_mpi -mdi "-name LMP1 -role DRIVER -method MPI" -log log.snapshot.driver.mpi.1 -in in.snapshot.driver : -np 1 lmp_mpi -mdi "-name LMP2 -role ENGINE -method MPI" -log log.snapshot.engine.mpi.1 -in in.snapshot.engine
|
||||||
|
mv dump.snapshot.driver dump.snapshot.driver.mpi.1
|
||||||
|
|
||||||
|
# ---
|
||||||
|
|
||||||
|
# Run with MPI: 3 procs + 4 procs
|
||||||
|
|
||||||
|
mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method MPI" -log log.snapshot.driver.mpi.3 -in in.snapshot.driver : -np 4 lmp_mpi -mdi "-name LMP2 -role ENGINE -method MPI" -log log.snapshot.engine.mpi.3 -in in.snapshot.engine
|
||||||
|
mv dump.snapshot.driver dump.snapshot.driver.mpi.4
|
||||||
|
|
||||||
|
# ---
|
||||||
|
|
||||||
|
# Run in plugin mode: 1 proc
|
||||||
|
|
||||||
|
lmp_mpi -mdi "-name LMP1 -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/src" -log log.snapshot.driver.plugin.1 -in in.snapshot.driver.plugin
|
||||||
|
mv log.snapshot.engine.plugin log.snapshot.engine.plugin.1
|
||||||
|
mv dump.snapshot.driver.plugin dump.snapshot.driver.plugin.1
|
||||||
|
|
||||||
|
# ---
|
||||||
|
|
||||||
|
# Run in plugin mode: 3 procs
|
||||||
|
|
||||||
|
mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/src" -log log.snapshot.driver.plugin.3 -in in.snapshot.driver.plugin
|
||||||
|
mv log.snapshot.engine.plugin log.snapshot.engine.plugin.3
|
||||||
|
mv dump.snapshot.driver.plugin dump.snapshot.driver.plugin.3
|
||||||
|
|
||||||
|
# -------------------------------------------------
|
||||||
|
# -------------------------------------------------
|
||||||
|
|
||||||
|
# Example 3 = run LAMMPS, compute QM forces on series of independent systems
|
||||||
|
|
||||||
|
# ---
|
||||||
|
|
||||||
|
# Run without MDI
|
||||||
|
|
||||||
|
lmp_mpi -log log.series.alone.1 < in.series.alone
|
||||||
|
mv dump.series.alone dump.series.alone.1
|
||||||
|
|
||||||
|
# ---
|
||||||
|
|
||||||
|
# Run with TCP: 1 proc each
|
||||||
|
|
||||||
|
lmp_mpi -mdi "-name LMP1 -role DRIVER -method TCP -port 8021" -log log.series.driver.tcp.1 -in in.series.driver &
|
||||||
|
|
||||||
|
lmp_mpi -mdi "-name LMP2 -role ENGINE -method TCP -port 8021 -hostname localhost" -log log.series.engine.tcp.1 -in in.series.engine
|
||||||
|
mv dump.series.driver dump.series.driver.tcp.1
|
||||||
|
|
||||||
|
# ---
|
||||||
|
|
||||||
|
# Run with TCP: 3 procs + 4 procs
|
||||||
|
|
||||||
|
mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method TCP -port 8021" -log log.series.driver.tcp.3 -in in.series.driver &
|
||||||
|
|
||||||
|
mpirun -np 4 lmp_mpi -mdi "-name LMP2 -role ENGINE -method TCP -port 8021 -hostname localhost" -log log.series.engine.tcp.4 -in in.series.engine
|
||||||
|
mv dump.series.driver dump.series.driver.tcp.4
|
||||||
|
|
||||||
|
# ---
|
||||||
|
|
||||||
|
# Run with MPI: 1 proc each
|
||||||
|
|
||||||
|
mpirun -np 1 lmp_mpi -mdi "-name LMP1 -role DRIVER -method MPI" -log log.series.driver.mpi.1 -in in.series.driver : -np 1 lmp_mpi -mdi "-name LMP2 -role ENGINE -method MPI" -log log.series.engine.mpi.1 -in in.series.engine
|
||||||
|
mv dump.series.driver dump.series.driver.mpi.1
|
||||||
|
|
||||||
|
# ---
|
||||||
|
|
||||||
|
# Run with MPI: 3 procs + 4 procs
|
||||||
|
|
||||||
|
mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method MPI" -log log.series.driver.mpi.3 -in in.series.driver : -np 4 lmp_mpi -mdi "-name LMP2 -role ENGINE -method MPI" -log log.series.engine.mpi.4 -in in.series.engine
|
||||||
|
mv dump.series.driver dump.series.driver.mpi.4
|
||||||
|
|
||||||
|
# ---
|
||||||
|
|
||||||
|
# Run in plugin mode: 1 proc
|
||||||
|
|
||||||
|
lmp_mpi -mdi "-name LMP1 -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/src" -log log.series.driver.plugin.1 -in in.series.driver.plugin
|
||||||
|
mv log.series.engine.plugin log.series.engine.plugin.1
|
||||||
|
mv dump.series.driver.plugin dump.series.driver.plugin.1
|
||||||
|
|
||||||
|
# ---
|
||||||
|
|
||||||
|
# Run in plugin mode: 3 procs
|
||||||
|
|
||||||
|
mpirun -np 3 lmp_mpi -mdi "-name LMP1 -role DRIVER -method LINK -plugin_path /home/sjplimp/lammps/git/src" -log log.series.driver.plugin.3 -in in.series.driver.plugin
|
||||||
|
mv log.series.engine.plugin log.series.engine.plugin.3
|
||||||
|
mv dump.series.driver.plugin dump.series.driver.plugin.3
|
||||||
|
|
||||||
|
# -------------------------------------------------
|
||||||
|
# -------------------------------------------------
|
||||||
|
|
||||||
|
# Example 4 = Python driver runs a sequence of unrelated LAMMPS calculations
|
||||||
|
|
||||||
|
# ---
|
||||||
|
|
||||||
|
# Run with TCP: 1 proc each
|
||||||
|
|
||||||
|
python3 sequence_driver.py -mdi "-role DRIVER -name sequence -method TCP -port 8021" &
|
||||||
|
|
||||||
|
lmp_mpi -mdi "-role ENGINE -name LMP -method TCP -port 8021 -hostname localhost" -log log.sequence.engine.tcp.1 -in in.sequence.python
|
||||||
|
|
||||||
|
# ---
|
||||||
|
|
||||||
|
# Run with TCP: 2 proc + 4 procs
|
||||||
|
|
||||||
|
mpirun -np 2 python3 sequence_driver.py -mdi "-role DRIVER -name sequence -method TCP -port 8021" &
|
||||||
|
|
||||||
|
mpirun -np 4 lmp_mpi -mdi "-role ENGINE -name LMP -method TCP -port 8021 -hostname localhost" -log log.sequence.engine.tcp.4 -in in.sequence.python
|
||||||
|
|
||||||
|
# ---
|
||||||
|
|
||||||
|
# Run with MPI: 1 proc each
|
||||||
|
|
||||||
|
mpirun -np 1 python3 sequence_driver.py -mdi "-role DRIVER -name sequence -method MPI" : -np 1 lmp_mpi -mdi "-role ENGINE -name LAMMPS -method MPI" -log log.sequence.engine.mpi.1 -in in.sequence.python
|
||||||
|
|
||||||
|
# ---
|
||||||
|
|
||||||
|
# Run with MPI: 2 procs + 4 procs
|
||||||
|
|
||||||
|
mpirun -np 2 python3 sequence_driver.py -mdi "-role DRIVER -name sequence -method MPI" : -np 4 lmp_mpi -mdi "-role ENGINE -name LMP -method MPI" -log log.sequence.engine.mpi.4 -in in.sequence.python
|
||||||
|
|
||||||
|
# ---
|
||||||
|
|
||||||
|
# Run in plugin mode: 1 proc
|
||||||
|
|
||||||
|
python3 sequence_driver.py -plugin lammps -mdi "-role DRIVER -name sequence -method LINK -plugin_path /home/sjplimp/lammps/git/src" -plugin_args "-log log.sequence.engine.plugin.1 -in in.sequence".python
|
||||||
|
|
||||||
|
# ---
|
||||||
|
|
||||||
|
# Run in plugin mode: 3 procs
|
||||||
|
|
||||||
|
mpirun -np 3 python3 sequence_driver.py -plugin lammps -mdi "-role DRIVER -name sequence -method LINK -plugin_path /home/sjplimp/lammps/git/src" -plugin_args "-log log.sequence.engine.plugin.3 -in in.sequence".python
|
||||||
|
|
||||||
|
# -------------------------------------------------
|
||||||
|
# -------------------------------------------------
|
||||||
|
|
||||||
|
# Example 5 = run AIMD with Python driver code and 2 LAMMPS instances as engines
|
||||||
|
|
||||||
|
# ---
|
||||||
|
|
||||||
|
# Run with TCP: 1 proc each
|
||||||
|
|
||||||
|
python3 aimd_driver.py -mdi "-role DRIVER -name aimdpy -method TCP -port 8021" > log.aimdpy.driver.tcp.1 &
|
||||||
|
|
||||||
|
lmp_mpi -mdi "-role ENGINE -name MM -method TCP -port 8021 -hostname localhost" -log log.aimdpy.mm.tcp.1 -in in.aimdpy.mm &
|
||||||
|
|
||||||
|
lmp_mpi -mdi "-role ENGINE -name QM -method TCP -port 8021 -hostname localhost" -log log.aimdpy.qm.tcp.1 -in in.aimdpy.qm
|
||||||
|
|
||||||
|
# ---
|
||||||
|
|
||||||
|
# Run with TCP: 2 procs + 2 procs + 3 procs
|
||||||
|
|
||||||
|
mpirun -np 2 python3 aimd_driver.py -mdi "-role DRIVER -name aimdpy -method TCP -port 8021" > log.aimdpy.driver.tcp.2 &
|
||||||
|
|
||||||
|
mpirun -np 2 lmp_mpi -mdi "-role ENGINE -name MM -method TCP -port 8021 -hostname localhost" -log log.aimdpy.mm.tcp.2 -in in.aimdpy.mm &
|
||||||
|
|
||||||
|
mpirun -np 3 lmp_mpi -mdi "-role ENGINE -name QM -method TCP -port 8021 -hostname localhost" -log log.aimdpy.qm.tcp.3 -in in.aimdpy.qm
|
||||||
|
|
||||||
|
# ---
|
||||||
|
|
||||||
|
# Run with MPI: 1 proc each
|
||||||
|
|
||||||
|
mpirun -np 1 python3 aimd_driver.py -mdi "-role DRIVER -name aimdpy -method MPI" : -np 1 lmp_mpi -mdi "-role ENGINE -name MM -method MPI" -log log.aimdpy.mm.mpi.1 -in in.aimdpy.mm : -np 1 lmp_mpi -mdi "-role ENGINE -name QM -method MPI" -log log.aimdpy.qm.mpi.1 -in in.aimdpy.qm > log.aimdpy.driver.mpi.1
|
||||||
|
|
||||||
|
# ---
|
||||||
|
|
||||||
|
# Run with MPI: 2 procs + 2 procs + 3 procs
|
||||||
|
|
||||||
|
mpirun -np 2 python3 aimd_driver.py -mdi "-role DRIVER -name aimdpy -method MPI" : -np 2 lmp_mpi -mdi "-role ENGINE -name MM -method MPI" -log log.aimdpy.mm.mpi.2 -in in.aimdpy.mm : -np 3 lmp_mpi -mdi "-role ENGINE -name QM -method MPI" -log log.aimdpy.qm.mpi.3 -in in.aimdpy.qm > log.aimdpy.driver.mpi.2
|
||||||
@ -23,8 +23,8 @@
|
|||||||
# -plugin_args arglist
|
# -plugin_args arglist
|
||||||
# args to add when launching plugin library, only when using plugin mode
|
# args to add when launching plugin library, only when using plugin mode
|
||||||
# enclose arglist in quotes if multiple words
|
# enclose arglist in quotes if multiple words
|
||||||
# -nsteps 5
|
# -nsteps 10
|
||||||
# number of timesteps, default = 5
|
# number of timesteps, default = 10
|
||||||
|
|
||||||
import sys
|
import sys
|
||||||
import mdi
|
import mdi
|
||||||
@ -182,7 +182,7 @@ mdiarg = ""
|
|||||||
plugin = ""
|
plugin = ""
|
||||||
plugin_args = ""
|
plugin_args = ""
|
||||||
|
|
||||||
nsteps = 5
|
nsteps = 10
|
||||||
|
|
||||||
# parse command-line args
|
# parse command-line args
|
||||||
|
|
||||||
|
|||||||
1018
examples/mdi/data.series.0.7
Normal file
1018
examples/mdi/data.series.0.7
Normal file
File diff suppressed because it is too large
Load Diff
1018
examples/mdi/data.series.0.8
Normal file
1018
examples/mdi/data.series.0.8
Normal file
File diff suppressed because it is too large
Load Diff
1018
examples/mdi/data.series.0.9
Normal file
1018
examples/mdi/data.series.0.9
Normal file
File diff suppressed because it is too large
Load Diff
1018
examples/mdi/data.snapshot
Normal file
1018
examples/mdi/data.snapshot
Normal file
File diff suppressed because it is too large
Load Diff
1527
examples/mdi/dump.17Jun22.series.alone.1
Normal file
1527
examples/mdi/dump.17Jun22.series.alone.1
Normal file
File diff suppressed because it is too large
Load Diff
1527
examples/mdi/dump.17Jun22.series.driver.mpi.1
Normal file
1527
examples/mdi/dump.17Jun22.series.driver.mpi.1
Normal file
File diff suppressed because it is too large
Load Diff
1527
examples/mdi/dump.17Jun22.series.driver.mpi.4
Normal file
1527
examples/mdi/dump.17Jun22.series.driver.mpi.4
Normal file
File diff suppressed because it is too large
Load Diff
1527
examples/mdi/dump.17Jun22.series.driver.plugin.1
Normal file
1527
examples/mdi/dump.17Jun22.series.driver.plugin.1
Normal file
File diff suppressed because it is too large
Load Diff
1527
examples/mdi/dump.17Jun22.series.driver.plugin.3
Normal file
1527
examples/mdi/dump.17Jun22.series.driver.plugin.3
Normal file
File diff suppressed because it is too large
Load Diff
1527
examples/mdi/dump.17Jun22.series.driver.tcp.1
Normal file
1527
examples/mdi/dump.17Jun22.series.driver.tcp.1
Normal file
File diff suppressed because it is too large
Load Diff
1527
examples/mdi/dump.17Jun22.series.driver.tcp.4
Normal file
1527
examples/mdi/dump.17Jun22.series.driver.tcp.4
Normal file
File diff suppressed because it is too large
Load Diff
2036
examples/mdi/dump.17Jun22.snapshot.alone.1
Normal file
2036
examples/mdi/dump.17Jun22.snapshot.alone.1
Normal file
File diff suppressed because it is too large
Load Diff
2036
examples/mdi/dump.17Jun22.snapshot.driver.mpi.1
Normal file
2036
examples/mdi/dump.17Jun22.snapshot.driver.mpi.1
Normal file
File diff suppressed because it is too large
Load Diff
2036
examples/mdi/dump.17Jun22.snapshot.driver.mpi.4
Normal file
2036
examples/mdi/dump.17Jun22.snapshot.driver.mpi.4
Normal file
File diff suppressed because it is too large
Load Diff
2036
examples/mdi/dump.17Jun22.snapshot.driver.plugin.1
Normal file
2036
examples/mdi/dump.17Jun22.snapshot.driver.plugin.1
Normal file
File diff suppressed because it is too large
Load Diff
2036
examples/mdi/dump.17Jun22.snapshot.driver.plugin.3
Normal file
2036
examples/mdi/dump.17Jun22.snapshot.driver.plugin.3
Normal file
File diff suppressed because it is too large
Load Diff
2036
examples/mdi/dump.17Jun22.snapshot.driver.tcp.1
Normal file
2036
examples/mdi/dump.17Jun22.snapshot.driver.tcp.1
Normal file
File diff suppressed because it is too large
Load Diff
2036
examples/mdi/dump.17Jun22.snapshot.driver.tcp.4
Normal file
2036
examples/mdi/dump.17Jun22.snapshot.driver.tcp.4
Normal file
File diff suppressed because it is too large
Load Diff
@ -29,4 +29,4 @@ fix 1 all nve
|
|||||||
thermo_style custom step temp pe etotal press vol
|
thermo_style custom step temp pe etotal press vol
|
||||||
thermo 1
|
thermo 1
|
||||||
|
|
||||||
run 5
|
run 10
|
||||||
|
|||||||
@ -23,10 +23,9 @@ fix 1 all nve
|
|||||||
# NPT
|
# NPT
|
||||||
#fix 1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0
|
#fix 1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0
|
||||||
|
|
||||||
fix 2 all mdi/aimd
|
fix 2 all mdi/qm virial yes
|
||||||
fix_modify 2 energy yes virial yes
|
|
||||||
|
|
||||||
thermo_style custom step temp pe etotal press vol
|
thermo_style custom step temp pe etotal press vol
|
||||||
thermo 1
|
thermo 1
|
||||||
|
|
||||||
run 5
|
run 10
|
||||||
|
|||||||
@ -23,12 +23,11 @@ fix 1 all nve
|
|||||||
# NPT
|
# NPT
|
||||||
#fix 1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0
|
#fix 1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0
|
||||||
|
|
||||||
fix 2 all mdi/aimd
|
fix 2 all mdi/qm virial yes
|
||||||
fix_modify 2 energy yes virial yes
|
|
||||||
|
|
||||||
thermo_style custom step temp pe etotal press vol
|
thermo_style custom step temp pe etotal press vol
|
||||||
thermo 1
|
thermo 1
|
||||||
|
|
||||||
mdi plugin lammps mdi "-role ENGINE -name lammps -method LINK" &
|
mdi plugin lammps mdi "-role ENGINE -name LMP2 -method LINK" &
|
||||||
infile in.aimd.engine extra "-log log.aimd.engine.plugin" &
|
infile in.aimd.engine extra "-log log.aimd.engine.plugin" &
|
||||||
command "run 5"
|
command "run 10"
|
||||||
|
|||||||
@ -1,16 +1,11 @@
|
|||||||
# 3d Lennard-Jones melt - MDI engine script
|
# 3d Lennard-Jones melt - MDI engine script
|
||||||
|
|
||||||
variable x index 5
|
|
||||||
variable y index 5
|
|
||||||
variable z index 5
|
|
||||||
|
|
||||||
units lj
|
units lj
|
||||||
atom_style atomic
|
atom_style atomic
|
||||||
|
|
||||||
lattice fcc 0.8442
|
lattice fcc 1.0
|
||||||
region box block 0 $x 0 $y 0 $z
|
region box block 0 1 0 1 0 1
|
||||||
create_box 1 box
|
create_box 1 box
|
||||||
create_atoms 1 box
|
|
||||||
mass 1 1.0
|
mass 1 1.0
|
||||||
|
|
||||||
pair_style lj/cut 2.5
|
pair_style lj/cut 2.5
|
||||||
@ -19,4 +14,7 @@ pair_coeff 1 1 1.0 1.0 2.5
|
|||||||
neighbor 0.3 bin
|
neighbor 0.3 bin
|
||||||
neigh_modify delay 0 every 1 check yes
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
thermo_style custom step temp pe etotal press vol
|
||||||
|
thermo 1
|
||||||
|
|
||||||
mdi engine
|
mdi engine
|
||||||
|
|||||||
@ -19,3 +19,4 @@ fix 1 all nve
|
|||||||
thermo 10
|
thermo 10
|
||||||
|
|
||||||
mdi engine
|
mdi engine
|
||||||
|
|
||||||
37
examples/mdi/in.series.alone
Normal file
37
examples/mdi/in.series.alone
Normal file
@ -0,0 +1,37 @@
|
|||||||
|
# 3d Lennard-Jones melt - MDI driver script
|
||||||
|
|
||||||
|
variable x index 5
|
||||||
|
variable y index 5
|
||||||
|
variable z index 5
|
||||||
|
|
||||||
|
variable rho index 0.7 0.8 0.9
|
||||||
|
|
||||||
|
label LOOP
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
read_data data.series.${rho}
|
||||||
|
|
||||||
|
displace_atoms all random 0.1 0.1 0.1 48294
|
||||||
|
|
||||||
|
pair_style lj/cut 2.5
|
||||||
|
pair_coeff 1 1 1.0 1.0 2.5
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
compute 1 all pressure NULL virial
|
||||||
|
|
||||||
|
thermo_style custom step temp pe c_1 c_1[1] c_1[2] c_1[3]
|
||||||
|
|
||||||
|
run 0
|
||||||
|
|
||||||
|
write_dump all custom dump.series.alone &
|
||||||
|
id type x y z fx fy fz modify sort id append yes
|
||||||
|
|
||||||
|
clear
|
||||||
|
|
||||||
|
next rho
|
||||||
|
|
||||||
|
jump SELF LOOP
|
||||||
39
examples/mdi/in.series.driver
Normal file
39
examples/mdi/in.series.driver
Normal file
@ -0,0 +1,39 @@
|
|||||||
|
# 3d Lennard-Jones melt - MDI driver script
|
||||||
|
|
||||||
|
variable x index 5
|
||||||
|
variable y index 5
|
||||||
|
variable z index 5
|
||||||
|
|
||||||
|
variable rho index 0.7 0.8 0.9
|
||||||
|
|
||||||
|
mdi connect
|
||||||
|
|
||||||
|
label LOOP
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
read_data data.series.${rho}
|
||||||
|
|
||||||
|
displace_atoms all random 0.1 0.1 0.1 48294
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
fix 1 all mdi/qm add no virial yes connect no
|
||||||
|
variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3
|
||||||
|
|
||||||
|
thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||||
|
|
||||||
|
run 0
|
||||||
|
|
||||||
|
write_dump all custom dump.series.driver &
|
||||||
|
id type x y z f_1[1] f_1[2] f_1[3] modify sort id append yes
|
||||||
|
|
||||||
|
clear
|
||||||
|
|
||||||
|
next rho
|
||||||
|
|
||||||
|
jump SELF LOOP
|
||||||
|
|
||||||
|
mdi exit
|
||||||
38
examples/mdi/in.series.driver.plugin
Normal file
38
examples/mdi/in.series.driver.plugin
Normal file
@ -0,0 +1,38 @@
|
|||||||
|
# 3d Lennard-Jones melt - MDI driver script
|
||||||
|
|
||||||
|
variable x index 5
|
||||||
|
variable y index 5
|
||||||
|
variable z index 5
|
||||||
|
|
||||||
|
variable rho index 0.7 0.8 0.9
|
||||||
|
|
||||||
|
label LOOP
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
read_data data.series.${rho}
|
||||||
|
|
||||||
|
displace_atoms all random 0.1 0.1 0.1 48294
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
fix 1 all mdi/qm add no virial yes
|
||||||
|
variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3
|
||||||
|
|
||||||
|
thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||||
|
|
||||||
|
mdi plugin lammps mdi "-role ENGINE -name LMP2 -method LINK" &
|
||||||
|
infile in.series.engine &
|
||||||
|
extra "-log log.series.engine.plugin" &
|
||||||
|
command "run 0"
|
||||||
|
|
||||||
|
write_dump all custom dump.series.driver.plugin &
|
||||||
|
id type x y z f_1[1] f_1[2] f_1[3] modify sort id append yes
|
||||||
|
|
||||||
|
clear
|
||||||
|
|
||||||
|
next rho
|
||||||
|
|
||||||
|
jump SELF LOOP
|
||||||
17
examples/mdi/in.series.engine
Normal file
17
examples/mdi/in.series.engine
Normal file
@ -0,0 +1,17 @@
|
|||||||
|
# 3d Lennard-Jones melt - MDI engine script
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
lattice fcc 1.0
|
||||||
|
region box block 0 1 0 1 0 1
|
||||||
|
create_box 1 box
|
||||||
|
mass 1 1.0
|
||||||
|
|
||||||
|
pair_style lj/cut 2.5
|
||||||
|
pair_coeff 1 1 1.0 1.0 2.5
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
mdi engine
|
||||||
28
examples/mdi/in.snapshot.alone
Normal file
28
examples/mdi/in.snapshot.alone
Normal file
@ -0,0 +1,28 @@
|
|||||||
|
# 3d Lennard-Jones melt - MDI driver script
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
read_data data.snapshot
|
||||||
|
|
||||||
|
velocity all create 1.44 87287 loop geom
|
||||||
|
|
||||||
|
pair_style lj/cut 2.5
|
||||||
|
pair_coeff 1 1 1.0 1.0 2.5
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
fix 1 all nve
|
||||||
|
|
||||||
|
compute 1 all pressure NULL virial
|
||||||
|
|
||||||
|
thermo_style custom step temp pe c_1 c_1[1] c_1[2] c_1[3]
|
||||||
|
|
||||||
|
thermo 100
|
||||||
|
|
||||||
|
dump 1 all custom 100 dump.snapshot.alone &
|
||||||
|
id type x y z fx fy fz
|
||||||
|
dump_modify 1 sort id
|
||||||
|
|
||||||
|
run 300
|
||||||
33
examples/mdi/in.snapshot.driver
Normal file
33
examples/mdi/in.snapshot.driver
Normal file
@ -0,0 +1,33 @@
|
|||||||
|
# 3d Lennard-Jones melt - MDI driver script
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
read_data data.snapshot
|
||||||
|
|
||||||
|
velocity all create 1.44 87287 loop geom
|
||||||
|
|
||||||
|
pair_style lj/cut 2.5
|
||||||
|
pair_coeff 1 1 1.0 1.0 2.5
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
fix 1 all nve
|
||||||
|
|
||||||
|
fix 2 all mdi/qm add no every 100 virial yes
|
||||||
|
|
||||||
|
compute 1 all pressure NULL virial
|
||||||
|
variable evirial equal (f_2[1]+f_2[2]+f_2[3])/3
|
||||||
|
|
||||||
|
thermo_style custom step temp pe c_1 c_1[1] c_1[2] c_1[3]
|
||||||
|
|
||||||
|
thermo 100
|
||||||
|
|
||||||
|
dump 1 all custom 100 dump.snapshot.driver &
|
||||||
|
id type x y z f_2[1] f_2[2] f_2[3]
|
||||||
|
dump_modify 1 sort id
|
||||||
|
|
||||||
|
run 300 pre no post no every 100 &
|
||||||
|
"print 'QM eng = $(f_2/atoms)'" &
|
||||||
|
"print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'"
|
||||||
42
examples/mdi/in.snapshot.driver.plugin
Normal file
42
examples/mdi/in.snapshot.driver.plugin
Normal file
@ -0,0 +1,42 @@
|
|||||||
|
# 3d Lennard-Jones melt - MDI driver script
|
||||||
|
|
||||||
|
variable x index 5
|
||||||
|
variable y index 5
|
||||||
|
variable z index 5
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
read_data data.snapshot
|
||||||
|
|
||||||
|
velocity all create 1.44 87287 loop geom
|
||||||
|
|
||||||
|
pair_style lj/cut 2.5
|
||||||
|
pair_coeff 1 1 1.0 1.0 2.5
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
fix 1 all nve
|
||||||
|
|
||||||
|
fix 2 all mdi/qm add no every 100 virial yes
|
||||||
|
|
||||||
|
compute 1 all pressure NULL virial
|
||||||
|
variable evirial equal (f_2[1]+f_2[2]+f_2[3])/3
|
||||||
|
|
||||||
|
thermo_style custom step temp pe c_1 c_1[1] c_1[2] c_1[3]
|
||||||
|
|
||||||
|
thermo 100
|
||||||
|
|
||||||
|
dump 1 all custom 100 dump.snapshot.driver.plugin &
|
||||||
|
id type x y z f_2[1] f_2[2] f_2[3]
|
||||||
|
dump_modify 1 sort id
|
||||||
|
|
||||||
|
mdi plugin lammps mdi "-role ENGINE -name LMP2 -method LINK" &
|
||||||
|
infile in.snapshot.engine &
|
||||||
|
extra "-log log.snapshot.engine.plugin" &
|
||||||
|
command """
|
||||||
|
run 300 pre no post no every 100
|
||||||
|
"print 'QM eng = $(f_2/atoms)'"
|
||||||
|
"print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'"
|
||||||
|
"""
|
||||||
17
examples/mdi/in.snapshot.engine
Normal file
17
examples/mdi/in.snapshot.engine
Normal file
@ -0,0 +1,17 @@
|
|||||||
|
# 3d Lennard-Jones melt - MDI engine script
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
lattice fcc 1.0
|
||||||
|
region box block 0 1 0 1 0 1
|
||||||
|
create_box 1 box
|
||||||
|
mass 1 1.0
|
||||||
|
|
||||||
|
pair_style lj/cut 2.5
|
||||||
|
pair_coeff 1 1 1.0 1.0 2.5
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
mdi engine
|
||||||
@ -1,4 +1,4 @@
|
|||||||
LAMMPS (17 Feb 2022)
|
LAMMPS (2 Jun 2022)
|
||||||
# 3d Lennard-Jones melt - MDI driver script
|
# 3d Lennard-Jones melt - MDI driver script
|
||||||
|
|
||||||
variable x index 5
|
variable x index 5
|
||||||
@ -39,8 +39,8 @@ fix 1 all nve
|
|||||||
thermo_style custom step temp pe etotal press vol
|
thermo_style custom step temp pe etotal press vol
|
||||||
thermo 1
|
thermo 1
|
||||||
|
|
||||||
run 5
|
run 10
|
||||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||||
Neighbor list info ...
|
Neighbor list info ...
|
||||||
update every 1 steps, delay 0 steps, check yes
|
update every 1 steps, delay 0 steps, check yes
|
||||||
max neighbors/atom: 2000, page size: 100000
|
max neighbors/atom: 2000, page size: 100000
|
||||||
@ -54,37 +54,42 @@ Neighbor list info ...
|
|||||||
stencil: half/bin/3d
|
stencil: half/bin/3d
|
||||||
bin: standard
|
bin: standard
|
||||||
Per MPI rank memory allocation (min/avg/max) = 3.144 | 3.144 | 3.144 Mbytes
|
Per MPI rank memory allocation (min/avg/max) = 3.144 | 3.144 | 3.144 Mbytes
|
||||||
Step Temp PotEng TotEng Press Volume
|
Step Temp PotEng TotEng Press Volume
|
||||||
0 1.44 -6.7733681 -4.6176881 -5.0221006 592.27671
|
0 1.44 -6.7733681 -4.6176881 -5.0221006 592.27671
|
||||||
1 1.4377309 -6.7699814 -4.6176981 -5.0007431 592.27671
|
1 1.4377309 -6.7699814 -4.6176981 -5.0007431 592.27671
|
||||||
2 1.430825 -6.7596844 -4.6177394 -4.9363501 592.27671
|
2 1.430825 -6.7596844 -4.6177394 -4.9363501 592.27671
|
||||||
3 1.4189655 -6.7420029 -4.6178116 -4.8276957 592.27671
|
3 1.4189655 -6.7420029 -4.6178116 -4.8276957 592.27671
|
||||||
4 1.4016029 -6.7161132 -4.6179137 -4.6726332 592.27671
|
4 1.4016029 -6.7161132 -4.6179137 -4.6726332 592.27671
|
||||||
5 1.3779738 -6.6808361 -4.6180094 -4.468186 592.27671
|
5 1.3779738 -6.6808361 -4.6180094 -4.468186 592.27671
|
||||||
Loop time of 0.00427098 on 1 procs for 5 steps with 500 atoms
|
6 1.3471497 -6.6344152 -4.6177322 -4.2103477 592.27671
|
||||||
|
7 1.3081237 -6.5752633 -4.6170021 -3.8956402 592.27671
|
||||||
|
8 1.2599751 -6.502724 -4.6165412 -3.5228721 592.27671
|
||||||
|
9 1.2021373 -6.4153971 -4.6157975 -3.0910274 592.27671
|
||||||
|
10 1.1347688 -6.3153532 -4.6166043 -2.6072847 592.27671
|
||||||
|
Loop time of 0.00919691 on 1 procs for 10 steps with 500 atoms
|
||||||
|
|
||||||
Performance: 505739.085 tau/day, 1170.692 timesteps/s
|
Performance: 469723.136 tau/day, 1087.322 timesteps/s
|
||||||
73.9% CPU use with 1 MPI tasks x no OpenMP threads
|
98.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
MPI task timing breakdown:
|
MPI task timing breakdown:
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
---------------------------------------------------------------
|
---------------------------------------------------------------
|
||||||
Pair | 0.0038665 | 0.0038665 | 0.0038665 | 0.0 | 90.53
|
Pair | 0.0066536 | 0.0066536 | 0.0066536 | 0.0 | 72.35
|
||||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
Neigh | 0.0017906 | 0.0017906 | 0.0017906 | 0.0 | 19.47
|
||||||
Comm | 0.0001297 | 0.0001297 | 0.0001297 | 0.0 | 3.04
|
Comm | 0.0002554 | 0.0002554 | 0.0002554 | 0.0 | 2.78
|
||||||
Output | 0.00014902 | 0.00014902 | 0.00014902 | 0.0 | 3.49
|
Output | 0.00029976 | 0.00029976 | 0.00029976 | 0.0 | 3.26
|
||||||
Modify | 6.5249e-05 | 6.5249e-05 | 6.5249e-05 | 0.0 | 1.53
|
Modify | 9.8718e-05 | 9.8718e-05 | 9.8718e-05 | 0.0 | 1.07
|
||||||
Other | | 6.054e-05 | | | 1.42
|
Other | | 9.887e-05 | | | 1.08
|
||||||
|
|
||||||
Nlocal: 500 ave 500 max 500 min
|
Nlocal: 500 ave 500 max 500 min
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
Nghost: 1956 ave 1956 max 1956 min
|
Nghost: 1956 ave 1956 max 1956 min
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
Neighs: 19500 ave 19500 max 19500 min
|
Neighs: 19396 ave 19396 max 19396 min
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
Total # of neighbors = 19500
|
Total # of neighbors = 19396
|
||||||
Ave neighs/atom = 39
|
Ave neighs/atom = 38.792
|
||||||
Neighbor list builds = 0
|
Neighbor list builds = 1
|
||||||
Dangerous builds = 0
|
Dangerous builds = 0
|
||||||
Total wall time: 0:00:00
|
Total wall time: 0:00:00
|
||||||
83
examples/mdi/log.17Jun22.aimd.driver.mpi.1
Normal file
83
examples/mdi/log.17Jun22.aimd.driver.mpi.1
Normal file
@ -0,0 +1,83 @@
|
|||||||
|
LAMMPS (2 Jun 2022)
|
||||||
|
# 3d Lennard-Jones melt - MDI driver script
|
||||||
|
|
||||||
|
variable x index 5
|
||||||
|
variable y index 5
|
||||||
|
variable z index 5
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
lattice fcc 0.8442
|
||||||
|
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||||
|
region box block 0 $x 0 $y 0 $z
|
||||||
|
region box block 0 5 0 $y 0 $z
|
||||||
|
region box block 0 5 0 5 0 $z
|
||||||
|
region box block 0 5 0 5 0 5
|
||||||
|
create_box 1 box
|
||||||
|
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
create_atoms 1 box
|
||||||
|
Created 500 atoms
|
||||||
|
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||||
|
create_atoms CPU = 0.001 seconds
|
||||||
|
mass 1 1.0
|
||||||
|
|
||||||
|
velocity all create 1.44 87287 loop geom
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
# NVE
|
||||||
|
fix 1 all nve
|
||||||
|
# NPT
|
||||||
|
#fix 1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0
|
||||||
|
|
||||||
|
fix 2 all mdi/qm virial yes
|
||||||
|
|
||||||
|
thermo_style custom step temp pe etotal press vol
|
||||||
|
thermo 1
|
||||||
|
|
||||||
|
run 10
|
||||||
|
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||||
|
Step Temp PotEng TotEng Press Volume
|
||||||
|
0 1.44 -6.7733681 -4.6176881 -5.0221006 592.27671
|
||||||
|
1 1.4377309 -6.7699814 -4.6176981 -5.0007431 592.27671
|
||||||
|
2 1.430825 -6.7596844 -4.6177394 -4.9363501 592.27671
|
||||||
|
3 1.4189655 -6.7420029 -4.6178116 -4.8276957 592.27671
|
||||||
|
4 1.4016029 -6.7161132 -4.6179137 -4.6726332 592.27671
|
||||||
|
5 1.3779738 -6.6808361 -4.6180094 -4.468186 592.27671
|
||||||
|
6 1.3471497 -6.6344152 -4.6177322 -4.2103477 592.27671
|
||||||
|
7 1.3081237 -6.5752633 -4.6170021 -3.8956402 592.27671
|
||||||
|
8 1.2599751 -6.502724 -4.6165412 -3.5228721 592.27671
|
||||||
|
9 1.2021373 -6.4153971 -4.6157975 -3.0910274 592.27671
|
||||||
|
10 1.1347688 -6.3153532 -4.6166043 -2.6072847 592.27671
|
||||||
|
Loop time of 0.0078442 on 1 procs for 10 steps with 500 atoms
|
||||||
|
|
||||||
|
Performance: 550725.026 tau/day, 1274.826 timesteps/s
|
||||||
|
99.4% CPU use with 1 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Neigh | 1.592e-06 | 1.592e-06 | 1.592e-06 | 0.0 | 0.02
|
||||||
|
Comm | 2.6703e-05 | 2.6703e-05 | 2.6703e-05 | 0.0 | 0.34
|
||||||
|
Output | 0.00021168 | 0.00021168 | 0.00021168 | 0.0 | 2.70
|
||||||
|
Modify | 0.0075488 | 0.0075488 | 0.0075488 | 0.0 | 96.23
|
||||||
|
Other | | 5.544e-05 | | | 0.71
|
||||||
|
|
||||||
|
Nlocal: 500 ave 500 max 500 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 0 ave 0 max 0 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 0 ave 0 max 0 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 0
|
||||||
|
Ave neighs/atom = 0
|
||||||
|
Neighbor list builds = 1
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:00
|
||||||
83
examples/mdi/log.17Jun22.aimd.driver.mpi.3
Normal file
83
examples/mdi/log.17Jun22.aimd.driver.mpi.3
Normal file
@ -0,0 +1,83 @@
|
|||||||
|
LAMMPS (2 Jun 2022)
|
||||||
|
# 3d Lennard-Jones melt - MDI driver script
|
||||||
|
|
||||||
|
variable x index 5
|
||||||
|
variable y index 5
|
||||||
|
variable z index 5
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
lattice fcc 0.8442
|
||||||
|
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||||
|
region box block 0 $x 0 $y 0 $z
|
||||||
|
region box block 0 5 0 $y 0 $z
|
||||||
|
region box block 0 5 0 5 0 $z
|
||||||
|
region box block 0 5 0 5 0 5
|
||||||
|
create_box 1 box
|
||||||
|
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||||
|
1 by 1 by 3 MPI processor grid
|
||||||
|
create_atoms 1 box
|
||||||
|
Created 500 atoms
|
||||||
|
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||||
|
create_atoms CPU = 0.001 seconds
|
||||||
|
mass 1 1.0
|
||||||
|
|
||||||
|
velocity all create 1.44 87287 loop geom
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
# NVE
|
||||||
|
fix 1 all nve
|
||||||
|
# NPT
|
||||||
|
#fix 1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0
|
||||||
|
|
||||||
|
fix 2 all mdi/qm virial yes
|
||||||
|
|
||||||
|
thermo_style custom step temp pe etotal press vol
|
||||||
|
thermo 1
|
||||||
|
|
||||||
|
run 10
|
||||||
|
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||||
|
Step Temp PotEng TotEng Press Volume
|
||||||
|
0 1.44 -6.7733681 -4.6176881 -5.0221006 592.27671
|
||||||
|
1 1.4377309 -6.7699814 -4.6176981 -5.0007431 592.27671
|
||||||
|
2 1.430825 -6.7596844 -4.6177394 -4.9363501 592.27671
|
||||||
|
3 1.4189655 -6.7420029 -4.6178116 -4.8276957 592.27671
|
||||||
|
4 1.4016029 -6.7161132 -4.6179137 -4.6726332 592.27671
|
||||||
|
5 1.3779738 -6.6808361 -4.6180094 -4.468186 592.27671
|
||||||
|
6 1.3471497 -6.6344152 -4.6177322 -4.2103477 592.27671
|
||||||
|
7 1.3081237 -6.5752633 -4.6170021 -3.8956402 592.27671
|
||||||
|
8 1.2599751 -6.502724 -4.6165412 -3.5228721 592.27671
|
||||||
|
9 1.2021373 -6.4153971 -4.6157975 -3.0910274 592.27671
|
||||||
|
10 1.1347688 -6.3153532 -4.6166043 -2.6072847 592.27671
|
||||||
|
Loop time of 0.00523112 on 3 procs for 10 steps with 500 atoms
|
||||||
|
|
||||||
|
Performance: 825827.658 tau/day, 1911.638 timesteps/s
|
||||||
|
98.8% CPU use with 3 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Neigh | 5.95e-07 | 1.7073e-06 | 3.907e-06 | 0.0 | 0.03
|
||||||
|
Comm | 3.8259e-05 | 6.2707e-05 | 7.5974e-05 | 0.0 | 1.20
|
||||||
|
Output | 0.00017543 | 0.00021238 | 0.00028075 | 0.0 | 4.06
|
||||||
|
Modify | 0.004815 | 0.0048289 | 0.0048521 | 0.0 | 92.31
|
||||||
|
Other | | 0.0001254 | | | 2.40
|
||||||
|
|
||||||
|
Nlocal: 166.667 ave 176 max 150 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 2
|
||||||
|
Nghost: 0 ave 0 max 0 min
|
||||||
|
Histogram: 3 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 0 ave 0 max 0 min
|
||||||
|
Histogram: 3 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 0
|
||||||
|
Ave neighs/atom = 0
|
||||||
|
Neighbor list builds = 1
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:00
|
||||||
84
examples/mdi/log.17Jun22.aimd.driver.plugin.1
Normal file
84
examples/mdi/log.17Jun22.aimd.driver.plugin.1
Normal file
@ -0,0 +1,84 @@
|
|||||||
|
LAMMPS (2 Jun 2022)
|
||||||
|
# 3d Lennard-Jones melt - MDI driver script
|
||||||
|
|
||||||
|
variable x index 5
|
||||||
|
variable y index 5
|
||||||
|
variable z index 5
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
lattice fcc 0.8442
|
||||||
|
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||||
|
region box block 0 $x 0 $y 0 $z
|
||||||
|
region box block 0 5 0 $y 0 $z
|
||||||
|
region box block 0 5 0 5 0 $z
|
||||||
|
region box block 0 5 0 5 0 5
|
||||||
|
create_box 1 box
|
||||||
|
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
create_atoms 1 box
|
||||||
|
Created 500 atoms
|
||||||
|
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||||
|
create_atoms CPU = 0.001 seconds
|
||||||
|
mass 1 1.0
|
||||||
|
|
||||||
|
velocity all create 1.44 87287 loop geom
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
# NVE
|
||||||
|
fix 1 all nve
|
||||||
|
# NPT
|
||||||
|
#fix 1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0
|
||||||
|
|
||||||
|
fix 2 all mdi/qm virial yes
|
||||||
|
|
||||||
|
thermo_style custom step temp pe etotal press vol
|
||||||
|
thermo 1
|
||||||
|
|
||||||
|
mdi plugin lammps mdi "-role ENGINE -name LMP2 -method LINK" infile in.aimd.engine extra "-log log.aimd.engine.plugin" command "run 10"
|
||||||
|
run 10
|
||||||
|
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||||
|
Step Temp PotEng TotEng Press Volume
|
||||||
|
0 1.44 -6.7733681 -4.6176881 -5.0221006 592.27671
|
||||||
|
1 1.4377309 -6.7699814 -4.6176981 -5.0007431 592.27671
|
||||||
|
2 1.430825 -6.7596844 -4.6177394 -4.9363501 592.27671
|
||||||
|
3 1.4189655 -6.7420029 -4.6178116 -4.8276957 592.27671
|
||||||
|
4 1.4016029 -6.7161132 -4.6179137 -4.6726332 592.27671
|
||||||
|
5 1.3779738 -6.6808361 -4.6180094 -4.468186 592.27671
|
||||||
|
6 1.3471497 -6.6344152 -4.6177322 -4.2103477 592.27671
|
||||||
|
7 1.3081237 -6.5752633 -4.6170021 -3.8956402 592.27671
|
||||||
|
8 1.2599751 -6.502724 -4.6165412 -3.5228721 592.27671
|
||||||
|
9 1.2021373 -6.4153971 -4.6157975 -3.0910274 592.27671
|
||||||
|
10 1.1347688 -6.3153532 -4.6166043 -2.6072847 592.27671
|
||||||
|
Loop time of 0.00940117 on 1 procs for 10 steps with 500 atoms
|
||||||
|
|
||||||
|
Performance: 459517.175 tau/day, 1063.697 timesteps/s
|
||||||
|
96.1% CPU use with 1 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Neigh | 1.9e-06 | 1.9e-06 | 1.9e-06 | 0.0 | 0.02
|
||||||
|
Comm | 3.0131e-05 | 3.0131e-05 | 3.0131e-05 | 0.0 | 0.32
|
||||||
|
Output | 0.00030359 | 0.00030359 | 0.00030359 | 0.0 | 3.23
|
||||||
|
Modify | 0.0090041 | 0.0090041 | 0.0090041 | 0.0 | 95.78
|
||||||
|
Other | | 6.144e-05 | | | 0.65
|
||||||
|
|
||||||
|
Nlocal: 500 ave 500 max 500 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 0 ave 0 max 0 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 0 ave 0 max 0 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 0
|
||||||
|
Ave neighs/atom = 0
|
||||||
|
Neighbor list builds = 1
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:00
|
||||||
84
examples/mdi/log.17Jun22.aimd.driver.plugin.3
Normal file
84
examples/mdi/log.17Jun22.aimd.driver.plugin.3
Normal file
@ -0,0 +1,84 @@
|
|||||||
|
LAMMPS (2 Jun 2022)
|
||||||
|
# 3d Lennard-Jones melt - MDI driver script
|
||||||
|
|
||||||
|
variable x index 5
|
||||||
|
variable y index 5
|
||||||
|
variable z index 5
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
lattice fcc 0.8442
|
||||||
|
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||||
|
region box block 0 $x 0 $y 0 $z
|
||||||
|
region box block 0 5 0 $y 0 $z
|
||||||
|
region box block 0 5 0 5 0 $z
|
||||||
|
region box block 0 5 0 5 0 5
|
||||||
|
create_box 1 box
|
||||||
|
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||||
|
1 by 1 by 3 MPI processor grid
|
||||||
|
create_atoms 1 box
|
||||||
|
Created 500 atoms
|
||||||
|
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||||
|
create_atoms CPU = 0.001 seconds
|
||||||
|
mass 1 1.0
|
||||||
|
|
||||||
|
velocity all create 1.44 87287 loop geom
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
# NVE
|
||||||
|
fix 1 all nve
|
||||||
|
# NPT
|
||||||
|
#fix 1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0
|
||||||
|
|
||||||
|
fix 2 all mdi/qm virial yes
|
||||||
|
|
||||||
|
thermo_style custom step temp pe etotal press vol
|
||||||
|
thermo 1
|
||||||
|
|
||||||
|
mdi plugin lammps mdi "-role ENGINE -name LMP2 -method LINK" infile in.aimd.engine extra "-log log.aimd.engine.plugin" command "run 10"
|
||||||
|
run 10
|
||||||
|
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||||
|
Step Temp PotEng TotEng Press Volume
|
||||||
|
0 1.44 -6.7733681 -4.6176881 -5.0221006 592.27671
|
||||||
|
1 1.4377309 -6.7699814 -4.6176981 -5.0007431 592.27671
|
||||||
|
2 1.430825 -6.7596844 -4.6177394 -4.9363501 592.27671
|
||||||
|
3 1.4189655 -6.7420029 -4.6178116 -4.8276957 592.27671
|
||||||
|
4 1.4016029 -6.7161132 -4.6179137 -4.6726332 592.27671
|
||||||
|
5 1.3779738 -6.6808361 -4.6180094 -4.468186 592.27671
|
||||||
|
6 1.3471497 -6.6344152 -4.6177322 -4.2103477 592.27671
|
||||||
|
7 1.3081237 -6.5752633 -4.6170021 -3.8956402 592.27671
|
||||||
|
8 1.2599751 -6.502724 -4.6165412 -3.5228721 592.27671
|
||||||
|
9 1.2021373 -6.4153971 -4.6157975 -3.0910274 592.27671
|
||||||
|
10 1.1347688 -6.3153532 -4.6166043 -2.6072847 592.27671
|
||||||
|
Loop time of 0.00613177 on 3 procs for 10 steps with 500 atoms
|
||||||
|
|
||||||
|
Performance: 704527.327 tau/day, 1630.850 timesteps/s
|
||||||
|
99.2% CPU use with 3 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Neigh | 7.93e-07 | 1.8723e-06 | 3.996e-06 | 0.0 | 0.03
|
||||||
|
Comm | 4.4254e-05 | 7.4628e-05 | 9.321e-05 | 0.0 | 1.22
|
||||||
|
Output | 0.00019476 | 0.00024309 | 0.00032745 | 0.0 | 3.96
|
||||||
|
Modify | 0.005637 | 0.0056559 | 0.0056903 | 0.0 | 92.24
|
||||||
|
Other | | 0.0001563 | | | 2.55
|
||||||
|
|
||||||
|
Nlocal: 166.667 ave 176 max 150 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 2
|
||||||
|
Nghost: 0 ave 0 max 0 min
|
||||||
|
Histogram: 3 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 0 ave 0 max 0 min
|
||||||
|
Histogram: 3 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 0
|
||||||
|
Ave neighs/atom = 0
|
||||||
|
Neighbor list builds = 1
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:00
|
||||||
83
examples/mdi/log.17Jun22.aimd.driver.tcp.1
Normal file
83
examples/mdi/log.17Jun22.aimd.driver.tcp.1
Normal file
@ -0,0 +1,83 @@
|
|||||||
|
LAMMPS (2 Jun 2022)
|
||||||
|
# 3d Lennard-Jones melt - MDI driver script
|
||||||
|
|
||||||
|
variable x index 5
|
||||||
|
variable y index 5
|
||||||
|
variable z index 5
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
lattice fcc 0.8442
|
||||||
|
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||||
|
region box block 0 $x 0 $y 0 $z
|
||||||
|
region box block 0 5 0 $y 0 $z
|
||||||
|
region box block 0 5 0 5 0 $z
|
||||||
|
region box block 0 5 0 5 0 5
|
||||||
|
create_box 1 box
|
||||||
|
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
create_atoms 1 box
|
||||||
|
Created 500 atoms
|
||||||
|
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||||
|
create_atoms CPU = 0.001 seconds
|
||||||
|
mass 1 1.0
|
||||||
|
|
||||||
|
velocity all create 1.44 87287 loop geom
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
# NVE
|
||||||
|
fix 1 all nve
|
||||||
|
# NPT
|
||||||
|
#fix 1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0
|
||||||
|
|
||||||
|
fix 2 all mdi/qm virial yes
|
||||||
|
|
||||||
|
thermo_style custom step temp pe etotal press vol
|
||||||
|
thermo 1
|
||||||
|
|
||||||
|
run 10
|
||||||
|
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||||
|
Step Temp PotEng TotEng Press Volume
|
||||||
|
0 1.44 -6.7733681 -4.6176881 -5.0221006 592.27671
|
||||||
|
1 1.4377309 -6.7699814 -4.6176981 -5.0007431 592.27671
|
||||||
|
2 1.430825 -6.7596844 -4.6177394 -4.9363501 592.27671
|
||||||
|
3 1.4189655 -6.7420029 -4.6178116 -4.8276957 592.27671
|
||||||
|
4 1.4016029 -6.7161132 -4.6179137 -4.6726332 592.27671
|
||||||
|
5 1.3779738 -6.6808361 -4.6180094 -4.468186 592.27671
|
||||||
|
6 1.3471497 -6.6344152 -4.6177322 -4.2103477 592.27671
|
||||||
|
7 1.3081237 -6.5752633 -4.6170021 -3.8956402 592.27671
|
||||||
|
8 1.2599751 -6.502724 -4.6165412 -3.5228721 592.27671
|
||||||
|
9 1.2021373 -6.4153971 -4.6157975 -3.0910274 592.27671
|
||||||
|
10 1.1347688 -6.3153532 -4.6166043 -2.6072847 592.27671
|
||||||
|
Loop time of 2.41182 on 1 procs for 10 steps with 500 atoms
|
||||||
|
|
||||||
|
Performance: 1791.180 tau/day, 4.146 timesteps/s
|
||||||
|
0.1% CPU use with 1 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Neigh | 2.596e-06 | 2.596e-06 | 2.596e-06 | 0.0 | 0.00
|
||||||
|
Comm | 4.9627e-05 | 4.9627e-05 | 4.9627e-05 | 0.0 | 0.00
|
||||||
|
Output | 0.00063707 | 0.00063707 | 0.00063707 | 0.0 | 0.03
|
||||||
|
Modify | 2.411 | 2.411 | 2.411 | 0.0 | 99.97
|
||||||
|
Other | | 0.0001146 | | | 0.00
|
||||||
|
|
||||||
|
Nlocal: 500 ave 500 max 500 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 0 ave 0 max 0 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 0 ave 0 max 0 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 0
|
||||||
|
Ave neighs/atom = 0
|
||||||
|
Neighbor list builds = 1
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:02
|
||||||
83
examples/mdi/log.17Jun22.aimd.driver.tcp.3
Normal file
83
examples/mdi/log.17Jun22.aimd.driver.tcp.3
Normal file
@ -0,0 +1,83 @@
|
|||||||
|
LAMMPS (2 Jun 2022)
|
||||||
|
# 3d Lennard-Jones melt - MDI driver script
|
||||||
|
|
||||||
|
variable x index 5
|
||||||
|
variable y index 5
|
||||||
|
variable z index 5
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
lattice fcc 0.8442
|
||||||
|
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||||
|
region box block 0 $x 0 $y 0 $z
|
||||||
|
region box block 0 5 0 $y 0 $z
|
||||||
|
region box block 0 5 0 5 0 $z
|
||||||
|
region box block 0 5 0 5 0 5
|
||||||
|
create_box 1 box
|
||||||
|
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||||
|
1 by 1 by 3 MPI processor grid
|
||||||
|
create_atoms 1 box
|
||||||
|
Created 500 atoms
|
||||||
|
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||||
|
create_atoms CPU = 0.001 seconds
|
||||||
|
mass 1 1.0
|
||||||
|
|
||||||
|
velocity all create 1.44 87287 loop geom
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
# NVE
|
||||||
|
fix 1 all nve
|
||||||
|
# NPT
|
||||||
|
#fix 1 all npt temp 1.0 1.0 0.1 iso 1.0 1.0 1.0
|
||||||
|
|
||||||
|
fix 2 all mdi/qm virial yes
|
||||||
|
|
||||||
|
thermo_style custom step temp pe etotal press vol
|
||||||
|
thermo 1
|
||||||
|
|
||||||
|
run 10
|
||||||
|
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||||
|
Step Temp PotEng TotEng Press Volume
|
||||||
|
0 1.44 -6.7733681 -4.6176881 -5.0221006 592.27671
|
||||||
|
1 1.4377309 -6.7699814 -4.6176981 -5.0007431 592.27671
|
||||||
|
2 1.430825 -6.7596844 -4.6177394 -4.9363501 592.27671
|
||||||
|
3 1.4189655 -6.7420029 -4.6178116 -4.8276957 592.27671
|
||||||
|
4 1.4016029 -6.7161132 -4.6179137 -4.6726332 592.27671
|
||||||
|
5 1.3779738 -6.6808361 -4.6180094 -4.468186 592.27671
|
||||||
|
6 1.3471497 -6.6344152 -4.6177322 -4.2103477 592.27671
|
||||||
|
7 1.3081237 -6.5752633 -4.6170021 -3.8956402 592.27671
|
||||||
|
8 1.2599751 -6.502724 -4.6165412 -3.5228721 592.27671
|
||||||
|
9 1.2021373 -6.4153971 -4.6157975 -3.0910274 592.27671
|
||||||
|
10 1.1347688 -6.3153532 -4.6166043 -2.6072847 592.27671
|
||||||
|
Loop time of 2.39983 on 3 procs for 10 steps with 500 atoms
|
||||||
|
|
||||||
|
Performance: 1800.127 tau/day, 4.167 timesteps/s
|
||||||
|
66.7% CPU use with 3 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Neigh | 3.75e-07 | 1.3583e-06 | 2.574e-06 | 0.0 | 0.00
|
||||||
|
Comm | 5.4167e-05 | 0.00010938 | 0.00015338 | 0.0 | 0.00
|
||||||
|
Output | 0.00030885 | 0.00042099 | 0.00064497 | 0.0 | 0.02
|
||||||
|
Modify | 2.3988 | 2.3989 | 2.3989 | 0.0 | 99.96
|
||||||
|
Other | | 0.0004276 | | | 0.02
|
||||||
|
|
||||||
|
Nlocal: 166.667 ave 176 max 150 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 2
|
||||||
|
Nghost: 0 ave 0 max 0 min
|
||||||
|
Histogram: 3 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 0 ave 0 max 0 min
|
||||||
|
Histogram: 3 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 0
|
||||||
|
Ave neighs/atom = 0
|
||||||
|
Neighbor list builds = 1
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:03
|
||||||
55
examples/mdi/log.17Jun22.aimd.engine.mpi.1
Normal file
55
examples/mdi/log.17Jun22.aimd.engine.mpi.1
Normal file
@ -0,0 +1,55 @@
|
|||||||
|
LAMMPS (2 Jun 2022)
|
||||||
|
# 3d Lennard-Jones melt - MDI engine script
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
lattice fcc 1.0
|
||||||
|
Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011
|
||||||
|
region box block 0 1 0 1 0 1
|
||||||
|
create_box 1 box
|
||||||
|
Created orthogonal box = (0 0 0) to (1.5874011 1.5874011 1.5874011)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
mass 1 1.0
|
||||||
|
|
||||||
|
pair_style lj/cut 2.5
|
||||||
|
pair_coeff 1 1 1.0 1.0 2.5
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
thermo_style custom step temp pe etotal press vol
|
||||||
|
thermo 1
|
||||||
|
|
||||||
|
mdi engine
|
||||||
|
delete_atoms group all
|
||||||
|
Deleted 0 atoms, new total = 0
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||||
|
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 0 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 2.8
|
||||||
|
ghost atom cutoff = 2.8
|
||||||
|
binsize = 1.4, bins = 6 6 6
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair lj/cut, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/atomonly/newton
|
||||||
|
stencil: half/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 3.144 | 3.144 | 3.144 Mbytes
|
||||||
|
Step Temp PotEng TotEng Press Volume
|
||||||
|
0 0 -6.7733681 -6.7733681 -6.2353173 592.27671
|
||||||
|
1 0 -6.7699814 -6.7699814 -6.2120481 592.27671
|
||||||
|
2 0 -6.7596844 -6.7596844 -6.1418368 592.27671
|
||||||
|
3 0 -6.7420029 -6.7420029 -6.0231905 592.27671
|
||||||
|
4 0 -6.7161132 -6.7161132 -5.8534999 592.27671
|
||||||
|
5 0 -6.6808361 -6.6808361 -5.6291449 592.27671
|
||||||
|
6 0 -6.6344152 -6.6344152 -5.3453369 592.27671
|
||||||
|
7 0 -6.5752633 -6.5752633 -4.9977496 592.27671
|
||||||
|
8 0 -6.502724 -6.502724 -4.5844158 592.27671
|
||||||
|
9 0 -6.4153971 -6.4153971 -4.103842 592.27671
|
||||||
|
10 0 -6.3153532 -6.3153532 -3.5633405 592.27671
|
||||||
|
Total wall time: 0:00:00
|
||||||
55
examples/mdi/log.17Jun22.aimd.engine.mpi.4
Normal file
55
examples/mdi/log.17Jun22.aimd.engine.mpi.4
Normal file
@ -0,0 +1,55 @@
|
|||||||
|
LAMMPS (2 Jun 2022)
|
||||||
|
# 3d Lennard-Jones melt - MDI engine script
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
lattice fcc 1.0
|
||||||
|
Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011
|
||||||
|
region box block 0 1 0 1 0 1
|
||||||
|
create_box 1 box
|
||||||
|
Created orthogonal box = (0 0 0) to (1.5874011 1.5874011 1.5874011)
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
mass 1 1.0
|
||||||
|
|
||||||
|
pair_style lj/cut 2.5
|
||||||
|
pair_coeff 1 1 1.0 1.0 2.5
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
thermo_style custom step temp pe etotal press vol
|
||||||
|
thermo 1
|
||||||
|
|
||||||
|
mdi engine
|
||||||
|
delete_atoms group all
|
||||||
|
Deleted 0 atoms, new total = 0
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||||
|
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 0 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 2.8
|
||||||
|
ghost atom cutoff = 2.8
|
||||||
|
binsize = 1.4, bins = 6 6 6
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair lj/cut, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/atomonly/newton
|
||||||
|
stencil: half/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 3.109 | 3.109 | 3.109 Mbytes
|
||||||
|
Step Temp PotEng TotEng Press Volume
|
||||||
|
0 0 -6.7733681 -6.7733681 -6.2353173 592.27671
|
||||||
|
1 0 -6.7699814 -6.7699814 -6.2120481 592.27671
|
||||||
|
2 0 -6.7596844 -6.7596844 -6.1418368 592.27671
|
||||||
|
3 0 -6.7420029 -6.7420029 -6.0231905 592.27671
|
||||||
|
4 0 -6.7161132 -6.7161132 -5.8534999 592.27671
|
||||||
|
5 0 -6.6808361 -6.6808361 -5.6291449 592.27671
|
||||||
|
6 0 -6.6344152 -6.6344152 -5.3453369 592.27671
|
||||||
|
7 0 -6.5752633 -6.5752633 -4.9977496 592.27671
|
||||||
|
8 0 -6.502724 -6.502724 -4.5844158 592.27671
|
||||||
|
9 0 -6.4153971 -6.4153971 -4.103842 592.27671
|
||||||
|
10 0 -6.3153532 -6.3153532 -3.5633405 592.27671
|
||||||
|
Total wall time: 0:00:00
|
||||||
55
examples/mdi/log.17Jun22.aimd.engine.plugin.1
Normal file
55
examples/mdi/log.17Jun22.aimd.engine.plugin.1
Normal file
@ -0,0 +1,55 @@
|
|||||||
|
LAMMPS (2 Jun 2022)
|
||||||
|
# 3d Lennard-Jones melt - MDI engine script
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
lattice fcc 1.0
|
||||||
|
Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011
|
||||||
|
region box block 0 1 0 1 0 1
|
||||||
|
create_box 1 box
|
||||||
|
Created orthogonal box = (0 0 0) to (1.5874011 1.5874011 1.5874011)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
mass 1 1.0
|
||||||
|
|
||||||
|
pair_style lj/cut 2.5
|
||||||
|
pair_coeff 1 1 1.0 1.0 2.5
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
thermo_style custom step temp pe etotal press vol
|
||||||
|
thermo 1
|
||||||
|
|
||||||
|
mdi engine
|
||||||
|
delete_atoms group all
|
||||||
|
Deleted 0 atoms, new total = 0
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||||
|
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 0 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 2.8
|
||||||
|
ghost atom cutoff = 2.8
|
||||||
|
binsize = 1.4, bins = 6 6 6
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair lj/cut, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/atomonly/newton
|
||||||
|
stencil: half/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 3.144 | 3.144 | 3.144 Mbytes
|
||||||
|
Step Temp PotEng TotEng Press Volume
|
||||||
|
0 0 -6.7733681 -6.7733681 -6.2353173 592.27671
|
||||||
|
1 0 -6.7699814 -6.7699814 -6.2120481 592.27671
|
||||||
|
2 0 -6.7596844 -6.7596844 -6.1418368 592.27671
|
||||||
|
3 0 -6.7420029 -6.7420029 -6.0231905 592.27671
|
||||||
|
4 0 -6.7161132 -6.7161132 -5.8534999 592.27671
|
||||||
|
5 0 -6.6808361 -6.6808361 -5.6291449 592.27671
|
||||||
|
6 0 -6.6344152 -6.6344152 -5.3453369 592.27671
|
||||||
|
7 0 -6.5752633 -6.5752633 -4.9977496 592.27671
|
||||||
|
8 0 -6.502724 -6.502724 -4.5844158 592.27671
|
||||||
|
9 0 -6.4153971 -6.4153971 -4.103842 592.27671
|
||||||
|
10 0 -6.3153532 -6.3153532 -3.5633405 592.27671
|
||||||
|
Total wall time: 0:00:00
|
||||||
55
examples/mdi/log.17Jun22.aimd.engine.plugin.3
Normal file
55
examples/mdi/log.17Jun22.aimd.engine.plugin.3
Normal file
@ -0,0 +1,55 @@
|
|||||||
|
LAMMPS (2 Jun 2022)
|
||||||
|
# 3d Lennard-Jones melt - MDI engine script
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
lattice fcc 1.0
|
||||||
|
Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011
|
||||||
|
region box block 0 1 0 1 0 1
|
||||||
|
create_box 1 box
|
||||||
|
Created orthogonal box = (0 0 0) to (1.5874011 1.5874011 1.5874011)
|
||||||
|
1 by 1 by 3 MPI processor grid
|
||||||
|
mass 1 1.0
|
||||||
|
|
||||||
|
pair_style lj/cut 2.5
|
||||||
|
pair_coeff 1 1 1.0 1.0 2.5
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
thermo_style custom step temp pe etotal press vol
|
||||||
|
thermo 1
|
||||||
|
|
||||||
|
mdi engine
|
||||||
|
delete_atoms group all
|
||||||
|
Deleted 0 atoms, new total = 0
|
||||||
|
1 by 1 by 3 MPI processor grid
|
||||||
|
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||||
|
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 0 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 2.8
|
||||||
|
ghost atom cutoff = 2.8
|
||||||
|
binsize = 1.4, bins = 6 6 6
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair lj/cut, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/atomonly/newton
|
||||||
|
stencil: half/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 3.124 | 3.13 | 3.133 Mbytes
|
||||||
|
Step Temp PotEng TotEng Press Volume
|
||||||
|
0 0 -6.7733681 -6.7733681 -6.2353173 592.27671
|
||||||
|
1 0 -6.7699814 -6.7699814 -6.2120481 592.27671
|
||||||
|
2 0 -6.7596844 -6.7596844 -6.1418368 592.27671
|
||||||
|
3 0 -6.7420029 -6.7420029 -6.0231905 592.27671
|
||||||
|
4 0 -6.7161132 -6.7161132 -5.8534999 592.27671
|
||||||
|
5 0 -6.6808361 -6.6808361 -5.6291449 592.27671
|
||||||
|
6 0 -6.6344152 -6.6344152 -5.3453369 592.27671
|
||||||
|
7 0 -6.5752633 -6.5752633 -4.9977496 592.27671
|
||||||
|
8 0 -6.502724 -6.502724 -4.5844158 592.27671
|
||||||
|
9 0 -6.4153971 -6.4153971 -4.103842 592.27671
|
||||||
|
10 0 -6.3153532 -6.3153532 -3.5633405 592.27671
|
||||||
|
Total wall time: 0:00:00
|
||||||
55
examples/mdi/log.17Jun22.aimd.engine.tcp.1
Normal file
55
examples/mdi/log.17Jun22.aimd.engine.tcp.1
Normal file
@ -0,0 +1,55 @@
|
|||||||
|
LAMMPS (2 Jun 2022)
|
||||||
|
# 3d Lennard-Jones melt - MDI engine script
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
lattice fcc 1.0
|
||||||
|
Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011
|
||||||
|
region box block 0 1 0 1 0 1
|
||||||
|
create_box 1 box
|
||||||
|
Created orthogonal box = (0 0 0) to (1.5874011 1.5874011 1.5874011)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
mass 1 1.0
|
||||||
|
|
||||||
|
pair_style lj/cut 2.5
|
||||||
|
pair_coeff 1 1 1.0 1.0 2.5
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
thermo_style custom step temp pe etotal press vol
|
||||||
|
thermo 1
|
||||||
|
|
||||||
|
mdi engine
|
||||||
|
delete_atoms group all
|
||||||
|
Deleted 0 atoms, new total = 0
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||||
|
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 0 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 2.8
|
||||||
|
ghost atom cutoff = 2.8
|
||||||
|
binsize = 1.4, bins = 6 6 6
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair lj/cut, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/atomonly/newton
|
||||||
|
stencil: half/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 3.144 | 3.144 | 3.144 Mbytes
|
||||||
|
Step Temp PotEng TotEng Press Volume
|
||||||
|
0 0 -6.7733681 -6.7733681 -6.2353173 592.27671
|
||||||
|
1 0 -6.7699814 -6.7699814 -6.2120481 592.27671
|
||||||
|
2 0 -6.7596844 -6.7596844 -6.1418368 592.27671
|
||||||
|
3 0 -6.7420029 -6.7420029 -6.0231905 592.27671
|
||||||
|
4 0 -6.7161132 -6.7161132 -5.8534999 592.27671
|
||||||
|
5 0 -6.6808361 -6.6808361 -5.6291449 592.27671
|
||||||
|
6 0 -6.6344152 -6.6344152 -5.3453369 592.27671
|
||||||
|
7 0 -6.5752633 -6.5752633 -4.9977496 592.27671
|
||||||
|
8 0 -6.502724 -6.502724 -4.5844158 592.27671
|
||||||
|
9 0 -6.4153971 -6.4153971 -4.103842 592.27671
|
||||||
|
10 0 -6.3153532 -6.3153532 -3.5633405 592.27671
|
||||||
|
Total wall time: 0:00:02
|
||||||
55
examples/mdi/log.17Jun22.aimd.engine.tcp.4
Normal file
55
examples/mdi/log.17Jun22.aimd.engine.tcp.4
Normal file
@ -0,0 +1,55 @@
|
|||||||
|
LAMMPS (2 Jun 2022)
|
||||||
|
# 3d Lennard-Jones melt - MDI engine script
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
lattice fcc 1.0
|
||||||
|
Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011
|
||||||
|
region box block 0 1 0 1 0 1
|
||||||
|
create_box 1 box
|
||||||
|
Created orthogonal box = (0 0 0) to (1.5874011 1.5874011 1.5874011)
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
mass 1 1.0
|
||||||
|
|
||||||
|
pair_style lj/cut 2.5
|
||||||
|
pair_coeff 1 1 1.0 1.0 2.5
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
thermo_style custom step temp pe etotal press vol
|
||||||
|
thermo 1
|
||||||
|
|
||||||
|
mdi engine
|
||||||
|
delete_atoms group all
|
||||||
|
Deleted 0 atoms, new total = 0
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||||
|
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 0 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 2.8
|
||||||
|
ghost atom cutoff = 2.8
|
||||||
|
binsize = 1.4, bins = 6 6 6
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair lj/cut, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/atomonly/newton
|
||||||
|
stencil: half/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 3.109 | 3.109 | 3.109 Mbytes
|
||||||
|
Step Temp PotEng TotEng Press Volume
|
||||||
|
0 0 -6.7733681 -6.7733681 -6.2353173 592.27671
|
||||||
|
1 0 -6.7699814 -6.7699814 -6.2120481 592.27671
|
||||||
|
2 0 -6.7596844 -6.7596844 -6.1418368 592.27671
|
||||||
|
3 0 -6.7420029 -6.7420029 -6.0231905 592.27671
|
||||||
|
4 0 -6.7161132 -6.7161132 -5.8534999 592.27671
|
||||||
|
5 0 -6.6808361 -6.6808361 -5.6291449 592.27671
|
||||||
|
6 0 -6.6344152 -6.6344152 -5.3453369 592.27671
|
||||||
|
7 0 -6.5752633 -6.5752633 -4.9977496 592.27671
|
||||||
|
8 0 -6.502724 -6.502724 -4.5844158 592.27671
|
||||||
|
9 0 -6.4153971 -6.4153971 -4.103842 592.27671
|
||||||
|
10 0 -6.3153532 -6.3153532 -3.5633405 592.27671
|
||||||
|
Total wall time: 0:00:02
|
||||||
77
examples/mdi/log.17Jun22.aimdpy.driver.mpi.1
Normal file
77
examples/mdi/log.17Jun22.aimdpy.driver.mpi.1
Normal file
@ -0,0 +1,77 @@
|
|||||||
|
LAMMPS (2 Jun 2022)
|
||||||
|
LAMMPS (2 Jun 2022)
|
||||||
|
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||||
|
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
Created 500 atoms
|
||||||
|
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||||
|
create_atoms CPU = 0.000 seconds
|
||||||
|
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||||
|
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
Created 500 atoms
|
||||||
|
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||||
|
create_atoms CPU = 0.001 seconds
|
||||||
|
Setting up Verlet run ...
|
||||||
|
Unit style : lj
|
||||||
|
Current step : 0
|
||||||
|
Time step : 0.005
|
||||||
|
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||||
|
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||||
|
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 0 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 2.8
|
||||||
|
ghost atom cutoff = 2.8
|
||||||
|
binsize = 1.4, bins = 6 6 6
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair lj/cut, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/atomonly/newton
|
||||||
|
stencil: half/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Setting up Verlet run ...
|
||||||
|
Unit style : lj
|
||||||
|
Current step : 0
|
||||||
|
Time step : 0.005
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 3.144 | 3.144 | 3.144 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 0 -6.7733681 0 -6.7733681 -6.2353173
|
||||||
|
Step 0: MM energy 2.15568, QM energy -6.77337, Total energy -4.61769
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 1.44 0 0 2.15568 1.2132167
|
||||||
|
1 0 -6.7699814 0 -6.7699814 -6.2120481
|
||||||
|
Step 1: MM energy 2.15228, QM energy -6.76998, Total energy -4.6177
|
||||||
|
1 1.4377309 0 0 2.1522832 1.211305
|
||||||
|
2 0 -6.7596844 0 -6.7596844 -6.1418368
|
||||||
|
Step 2: MM energy 2.14195, QM energy -6.75968, Total energy -4.61774
|
||||||
|
2 1.430825 0 0 2.141945 1.2054866
|
||||||
|
3 0 -6.7420029 0 -6.7420029 -6.0231905
|
||||||
|
Step 3: MM energy 2.12419, QM energy -6.742, Total energy -4.61781
|
||||||
|
3 1.4189655 0 0 2.1241913 1.1954949
|
||||||
|
4 0 -6.7161132 0 -6.7161132 -5.8534999
|
||||||
|
Step 4: MM energy 2.0982, QM energy -6.71611, Total energy -4.61791
|
||||||
|
4 1.4016029 0 0 2.0981995 1.1808667
|
||||||
|
5 0 -6.6808361 0 -6.6808361 -5.6291449
|
||||||
|
Step 5: MM energy 2.06283, QM energy -6.68084, Total energy -4.61801
|
||||||
|
5 1.3779738 0 0 2.0628267 1.1609589
|
||||||
|
6 0 -6.6344152 0 -6.6344152 -5.3453369
|
||||||
|
Step 6: MM energy 2.01668, QM energy -6.63442, Total energy -4.61773
|
||||||
|
6 1.3471497 0 0 2.016683 1.1349892
|
||||||
|
7 0 -6.5752633 0 -6.5752633 -4.9977496
|
||||||
|
Step 7: MM energy 1.95826, QM energy -6.57526, Total energy -4.617
|
||||||
|
7 1.3081237 0 0 1.9582612 1.1021094
|
||||||
|
8 0 -6.502724 0 -6.502724 -4.5844158
|
||||||
|
Step 8: MM energy 1.88618, QM energy -6.50272, Total energy -4.61654
|
||||||
|
8 1.2599751 0 0 1.8861828 1.0615437
|
||||||
|
9 0 -6.4153971 0 -6.4153971 -4.103842
|
||||||
|
Step 9: MM energy 1.7996, QM energy -6.4154, Total energy -4.6158
|
||||||
|
9 1.2021373 0 0 1.7995995 1.0128146
|
||||||
|
10 0 -6.3153532 0 -6.3153532 -3.5633405
|
||||||
|
Step 10: MM energy 1.69875, QM energy -6.31535, Total energy -4.6166
|
||||||
|
10 1.1347688 0 0 1.6987489 0.95605588
|
||||||
|
Total wall time: 0:00:00
|
||||||
|
Total wall time: 0:00:00
|
||||||
77
examples/mdi/log.17Jun22.aimdpy.driver.mpi.2
Normal file
77
examples/mdi/log.17Jun22.aimdpy.driver.mpi.2
Normal file
@ -0,0 +1,77 @@
|
|||||||
|
LAMMPS (2 Jun 2022)
|
||||||
|
LAMMPS (2 Jun 2022)
|
||||||
|
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||||
|
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||||
|
1 by 1 by 2 MPI processor grid
|
||||||
|
Created 500 atoms
|
||||||
|
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||||
|
create_atoms CPU = 0.000 seconds
|
||||||
|
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||||
|
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||||
|
1 by 1 by 3 MPI processor grid
|
||||||
|
Created 500 atoms
|
||||||
|
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||||
|
create_atoms CPU = 0.001 seconds
|
||||||
|
Setting up Verlet run ...
|
||||||
|
Unit style : lj
|
||||||
|
Current step : 0
|
||||||
|
Time step : 0.005
|
||||||
|
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||||
|
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||||
|
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 0 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 2.8
|
||||||
|
ghost atom cutoff = 2.8
|
||||||
|
binsize = 1.4, bins = 6 6 6
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair lj/cut, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/atomonly/newton
|
||||||
|
stencil: half/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Setting up Verlet run ...
|
||||||
|
Unit style : lj
|
||||||
|
Current step : 0
|
||||||
|
Time step : 0.005
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 3.124 | 3.13 | 3.133 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 0 -6.7733681 0 -6.7733681 -6.2353173
|
||||||
|
Step 0: MM energy 2.15568, QM energy -6.77337, Total energy -4.61769
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 1.44 0 0 2.15568 1.2132167
|
||||||
|
1 0 -6.7699814 0 -6.7699814 -6.2120481
|
||||||
|
Step 1: MM energy 2.15228, QM energy -6.76998, Total energy -4.6177
|
||||||
|
1 1.4377309 0 0 2.1522832 1.211305
|
||||||
|
2 0 -6.7596844 0 -6.7596844 -6.1418368
|
||||||
|
Step 2: MM energy 2.14195, QM energy -6.75968, Total energy -4.61774
|
||||||
|
2 1.430825 0 0 2.141945 1.2054866
|
||||||
|
3 0 -6.7420029 0 -6.7420029 -6.0231905
|
||||||
|
Step 3: MM energy 2.12419, QM energy -6.742, Total energy -4.61781
|
||||||
|
3 1.4189655 0 0 2.1241913 1.1954949
|
||||||
|
4 0 -6.7161132 0 -6.7161132 -5.8534999
|
||||||
|
Step 4: MM energy 2.0982, QM energy -6.71611, Total energy -4.61791
|
||||||
|
4 1.4016029 0 0 2.0981995 1.1808667
|
||||||
|
5 0 -6.6808361 0 -6.6808361 -5.6291449
|
||||||
|
Step 5: MM energy 2.06283, QM energy -6.68084, Total energy -4.61801
|
||||||
|
5 1.3779738 0 0 2.0628267 1.1609589
|
||||||
|
6 0 -6.6344152 0 -6.6344152 -5.3453369
|
||||||
|
Step 6: MM energy 2.01668, QM energy -6.63442, Total energy -4.61773
|
||||||
|
6 1.3471497 0 0 2.016683 1.1349892
|
||||||
|
7 0 -6.5752633 0 -6.5752633 -4.9977496
|
||||||
|
Step 7: MM energy 1.95826, QM energy -6.57526, Total energy -4.617
|
||||||
|
7 1.3081237 0 0 1.9582612 1.1021094
|
||||||
|
8 0 -6.502724 0 -6.502724 -4.5844158
|
||||||
|
Step 8: MM energy 1.88618, QM energy -6.50272, Total energy -4.61654
|
||||||
|
8 1.2599751 0 0 1.8861828 1.0615437
|
||||||
|
9 0 -6.4153971 0 -6.4153971 -4.103842
|
||||||
|
Step 9: MM energy 1.7996, QM energy -6.4154, Total energy -4.6158
|
||||||
|
9 1.2021373 0 0 1.7995995 1.0128146
|
||||||
|
10 0 -6.3153532 0 -6.3153532 -3.5633405
|
||||||
|
Step 10: MM energy 1.69875, QM energy -6.31535, Total energy -4.6166
|
||||||
|
10 1.1347688 0 0 1.6987489 0.95605588
|
||||||
|
Total wall time: 0:00:00
|
||||||
|
Total wall time: 0:00:00
|
||||||
@ -4,3 +4,8 @@ Step 2: MM energy 2.14195, QM energy -6.75968, Total energy -4.61774
|
|||||||
Step 3: MM energy 2.12419, QM energy -6.742, Total energy -4.61781
|
Step 3: MM energy 2.12419, QM energy -6.742, Total energy -4.61781
|
||||||
Step 4: MM energy 2.0982, QM energy -6.71611, Total energy -4.61791
|
Step 4: MM energy 2.0982, QM energy -6.71611, Total energy -4.61791
|
||||||
Step 5: MM energy 2.06283, QM energy -6.68084, Total energy -4.61801
|
Step 5: MM energy 2.06283, QM energy -6.68084, Total energy -4.61801
|
||||||
|
Step 6: MM energy 2.01668, QM energy -6.63442, Total energy -4.61773
|
||||||
|
Step 7: MM energy 1.95826, QM energy -6.57526, Total energy -4.617
|
||||||
|
Step 8: MM energy 1.88618, QM energy -6.50272, Total energy -4.61654
|
||||||
|
Step 9: MM energy 1.7996, QM energy -6.4154, Total energy -4.6158
|
||||||
|
Step 10: MM energy 1.69875, QM energy -6.31535, Total energy -4.6166
|
||||||
@ -4,3 +4,8 @@ Step 2: MM energy 2.14195, QM energy -6.75968, Total energy -4.61774
|
|||||||
Step 3: MM energy 2.12419, QM energy -6.742, Total energy -4.61781
|
Step 3: MM energy 2.12419, QM energy -6.742, Total energy -4.61781
|
||||||
Step 4: MM energy 2.0982, QM energy -6.71611, Total energy -4.61791
|
Step 4: MM energy 2.0982, QM energy -6.71611, Total energy -4.61791
|
||||||
Step 5: MM energy 2.06283, QM energy -6.68084, Total energy -4.61801
|
Step 5: MM energy 2.06283, QM energy -6.68084, Total energy -4.61801
|
||||||
|
Step 6: MM energy 2.01668, QM energy -6.63442, Total energy -4.61773
|
||||||
|
Step 7: MM energy 1.95826, QM energy -6.57526, Total energy -4.617
|
||||||
|
Step 8: MM energy 1.88618, QM energy -6.50272, Total energy -4.61654
|
||||||
|
Step 9: MM energy 1.7996, QM energy -6.4154, Total energy -4.6158
|
||||||
|
Step 10: MM energy 1.69875, QM energy -6.31535, Total energy -4.6166
|
||||||
49
examples/mdi/log.17Jun22.aimdpy.mm.mpi.1
Normal file
49
examples/mdi/log.17Jun22.aimdpy.mm.mpi.1
Normal file
@ -0,0 +1,49 @@
|
|||||||
|
LAMMPS (2 Jun 2022)
|
||||||
|
# 3d Lennard-Jones melt - LAMMPS as MM engine for aimd_driver.py
|
||||||
|
|
||||||
|
variable x index 5
|
||||||
|
variable y index 5
|
||||||
|
variable z index 5
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
lattice fcc 0.8442
|
||||||
|
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||||
|
region box block 0 $x 0 $y 0 $z
|
||||||
|
region box block 0 5 0 $y 0 $z
|
||||||
|
region box block 0 5 0 5 0 $z
|
||||||
|
region box block 0 5 0 5 0 5
|
||||||
|
create_box 1 box
|
||||||
|
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
create_atoms 1 box
|
||||||
|
Created 500 atoms
|
||||||
|
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||||
|
create_atoms CPU = 0.001 seconds
|
||||||
|
mass 1 1.0
|
||||||
|
|
||||||
|
velocity all create 1.44 87287 loop geom
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
fix 1 all nve
|
||||||
|
|
||||||
|
mdi engine
|
||||||
|
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 1.44 0 0 2.15568 1.2132167
|
||||||
|
1 1.4377309 0 0 2.1522832 1.211305
|
||||||
|
2 1.430825 0 0 2.141945 1.2054866
|
||||||
|
3 1.4189655 0 0 2.1241913 1.1954949
|
||||||
|
4 1.4016029 0 0 2.0981995 1.1808667
|
||||||
|
5 1.3779738 0 0 2.0628267 1.1609589
|
||||||
|
6 1.3471497 0 0 2.016683 1.1349892
|
||||||
|
7 1.3081237 0 0 1.9582612 1.1021094
|
||||||
|
8 1.2599751 0 0 1.8861828 1.0615437
|
||||||
|
9 1.2021373 0 0 1.7995995 1.0128146
|
||||||
|
10 1.1347688 0 0 1.6987489 0.95605588
|
||||||
|
Total wall time: 0:00:00
|
||||||
49
examples/mdi/log.17Jun22.aimdpy.mm.mpi.2
Normal file
49
examples/mdi/log.17Jun22.aimdpy.mm.mpi.2
Normal file
@ -0,0 +1,49 @@
|
|||||||
|
LAMMPS (2 Jun 2022)
|
||||||
|
# 3d Lennard-Jones melt - LAMMPS as MM engine for aimd_driver.py
|
||||||
|
|
||||||
|
variable x index 5
|
||||||
|
variable y index 5
|
||||||
|
variable z index 5
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
lattice fcc 0.8442
|
||||||
|
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||||
|
region box block 0 $x 0 $y 0 $z
|
||||||
|
region box block 0 5 0 $y 0 $z
|
||||||
|
region box block 0 5 0 5 0 $z
|
||||||
|
region box block 0 5 0 5 0 5
|
||||||
|
create_box 1 box
|
||||||
|
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||||
|
1 by 1 by 2 MPI processor grid
|
||||||
|
create_atoms 1 box
|
||||||
|
Created 500 atoms
|
||||||
|
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||||
|
create_atoms CPU = 0.000 seconds
|
||||||
|
mass 1 1.0
|
||||||
|
|
||||||
|
velocity all create 1.44 87287 loop geom
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
fix 1 all nve
|
||||||
|
|
||||||
|
mdi engine
|
||||||
|
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 1.44 0 0 2.15568 1.2132167
|
||||||
|
1 1.4377309 0 0 2.1522832 1.211305
|
||||||
|
2 1.430825 0 0 2.141945 1.2054866
|
||||||
|
3 1.4189655 0 0 2.1241913 1.1954949
|
||||||
|
4 1.4016029 0 0 2.0981995 1.1808667
|
||||||
|
5 1.3779738 0 0 2.0628267 1.1609589
|
||||||
|
6 1.3471497 0 0 2.016683 1.1349892
|
||||||
|
7 1.3081237 0 0 1.9582612 1.1021094
|
||||||
|
8 1.2599751 0 0 1.8861828 1.0615437
|
||||||
|
9 1.2021373 0 0 1.7995995 1.0128146
|
||||||
|
10 1.1347688 0 0 1.6987489 0.95605588
|
||||||
|
Total wall time: 0:00:00
|
||||||
49
examples/mdi/log.17Jun22.aimdpy.mm.tcp.1
Normal file
49
examples/mdi/log.17Jun22.aimdpy.mm.tcp.1
Normal file
@ -0,0 +1,49 @@
|
|||||||
|
LAMMPS (2 Jun 2022)
|
||||||
|
# 3d Lennard-Jones melt - LAMMPS as MM engine for aimd_driver.py
|
||||||
|
|
||||||
|
variable x index 5
|
||||||
|
variable y index 5
|
||||||
|
variable z index 5
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
lattice fcc 0.8442
|
||||||
|
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||||
|
region box block 0 $x 0 $y 0 $z
|
||||||
|
region box block 0 5 0 $y 0 $z
|
||||||
|
region box block 0 5 0 5 0 $z
|
||||||
|
region box block 0 5 0 5 0 5
|
||||||
|
create_box 1 box
|
||||||
|
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
create_atoms 1 box
|
||||||
|
Created 500 atoms
|
||||||
|
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||||
|
create_atoms CPU = 0.001 seconds
|
||||||
|
mass 1 1.0
|
||||||
|
|
||||||
|
velocity all create 1.44 87287 loop geom
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
fix 1 all nve
|
||||||
|
|
||||||
|
mdi engine
|
||||||
|
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 1.44 0 0 2.15568 1.2132167
|
||||||
|
1 1.4377309 0 0 2.1522832 1.211305
|
||||||
|
2 1.430825 0 0 2.141945 1.2054866
|
||||||
|
3 1.4189655 0 0 2.1241913 1.1954949
|
||||||
|
4 1.4016029 0 0 2.0981995 1.1808667
|
||||||
|
5 1.3779738 0 0 2.0628267 1.1609589
|
||||||
|
6 1.3471497 0 0 2.016683 1.1349892
|
||||||
|
7 1.3081237 0 0 1.9582612 1.1021094
|
||||||
|
8 1.2599751 0 0 1.8861828 1.0615437
|
||||||
|
9 1.2021373 0 0 1.7995995 1.0128146
|
||||||
|
10 1.1347688 0 0 1.6987489 0.95605588
|
||||||
|
Total wall time: 0:00:02
|
||||||
49
examples/mdi/log.17Jun22.aimdpy.mm.tcp.2
Normal file
49
examples/mdi/log.17Jun22.aimdpy.mm.tcp.2
Normal file
@ -0,0 +1,49 @@
|
|||||||
|
LAMMPS (2 Jun 2022)
|
||||||
|
# 3d Lennard-Jones melt - LAMMPS as MM engine for aimd_driver.py
|
||||||
|
|
||||||
|
variable x index 5
|
||||||
|
variable y index 5
|
||||||
|
variable z index 5
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
lattice fcc 0.8442
|
||||||
|
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||||
|
region box block 0 $x 0 $y 0 $z
|
||||||
|
region box block 0 5 0 $y 0 $z
|
||||||
|
region box block 0 5 0 5 0 $z
|
||||||
|
region box block 0 5 0 5 0 5
|
||||||
|
create_box 1 box
|
||||||
|
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||||
|
1 by 1 by 2 MPI processor grid
|
||||||
|
create_atoms 1 box
|
||||||
|
Created 500 atoms
|
||||||
|
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||||
|
create_atoms CPU = 0.001 seconds
|
||||||
|
mass 1 1.0
|
||||||
|
|
||||||
|
velocity all create 1.44 87287 loop geom
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
fix 1 all nve
|
||||||
|
|
||||||
|
mdi engine
|
||||||
|
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 1.44 0 0 2.15568 1.2132167
|
||||||
|
1 1.4377309 0 0 2.1522832 1.211305
|
||||||
|
2 1.430825 0 0 2.141945 1.2054866
|
||||||
|
3 1.4189655 0 0 2.1241913 1.1954949
|
||||||
|
4 1.4016029 0 0 2.0981995 1.1808667
|
||||||
|
5 1.3779738 0 0 2.0628267 1.1609589
|
||||||
|
6 1.3471497 0 0 2.016683 1.1349892
|
||||||
|
7 1.3081237 0 0 1.9582612 1.1021094
|
||||||
|
8 1.2599751 0 0 1.8861828 1.0615437
|
||||||
|
9 1.2021373 0 0 1.7995995 1.0128146
|
||||||
|
10 1.1347688 0 0 1.6987489 0.95605588
|
||||||
|
Total wall time: 0:00:02
|
||||||
@ -1,4 +1,4 @@
|
|||||||
LAMMPS (17 Feb 2022)
|
LAMMPS (2 Jun 2022)
|
||||||
# 3d Lennard-Jones melt - LAMMPS as surrogate QM engine for aimd_driver.py
|
# 3d Lennard-Jones melt - LAMMPS as surrogate QM engine for aimd_driver.py
|
||||||
|
|
||||||
variable x index 5
|
variable x index 5
|
||||||
@ -20,7 +20,7 @@ Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
|||||||
create_atoms 1 box
|
create_atoms 1 box
|
||||||
Created 500 atoms
|
Created 500 atoms
|
||||||
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||||
create_atoms CPU = 0.001 seconds
|
create_atoms CPU = 0.000 seconds
|
||||||
mass 1 1.0
|
mass 1 1.0
|
||||||
|
|
||||||
pair_style lj/cut 2.5
|
pair_style lj/cut 2.5
|
||||||
@ -31,7 +31,7 @@ neigh_modify delay 0 every 1 check yes
|
|||||||
|
|
||||||
mdi engine
|
mdi engine
|
||||||
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||||
Neighbor list info ...
|
Neighbor list info ...
|
||||||
update every 1 steps, delay 0 steps, check yes
|
update every 1 steps, delay 0 steps, check yes
|
||||||
max neighbors/atom: 2000, page size: 100000
|
max neighbors/atom: 2000, page size: 100000
|
||||||
@ -45,11 +45,16 @@ Neighbor list info ...
|
|||||||
stencil: half/bin/3d
|
stencil: half/bin/3d
|
||||||
bin: standard
|
bin: standard
|
||||||
Per MPI rank memory allocation (min/avg/max) = 3.144 | 3.144 | 3.144 Mbytes
|
Per MPI rank memory allocation (min/avg/max) = 3.144 | 3.144 | 3.144 Mbytes
|
||||||
Step Temp E_pair E_mol TotEng Press
|
Step Temp E_pair E_mol TotEng Press
|
||||||
0 0 -6.7733681 0 -6.7733681 -6.2353173
|
0 0 -6.7733681 0 -6.7733681 -6.2353173
|
||||||
1 0 -6.7699814 0 -6.7699814 -6.2120481
|
1 0 -6.7699814 0 -6.7699814 -6.2120481
|
||||||
2 0 -6.7596844 0 -6.7596844 -6.1418368
|
2 0 -6.7596844 0 -6.7596844 -6.1418368
|
||||||
3 0 -6.7420029 0 -6.7420029 -6.0231905
|
3 0 -6.7420029 0 -6.7420029 -6.0231905
|
||||||
4 0 -6.7161132 0 -6.7161132 -5.8534999
|
4 0 -6.7161132 0 -6.7161132 -5.8534999
|
||||||
5 0 -6.6808361 0 -6.6808361 -5.6291449
|
5 0 -6.6808361 0 -6.6808361 -5.6291449
|
||||||
|
6 0 -6.6344152 0 -6.6344152 -5.3453369
|
||||||
|
7 0 -6.5752633 0 -6.5752633 -4.9977496
|
||||||
|
8 0 -6.502724 0 -6.502724 -4.5844158
|
||||||
|
9 0 -6.4153971 0 -6.4153971 -4.103842
|
||||||
|
10 0 -6.3153532 0 -6.3153532 -3.5633405
|
||||||
Total wall time: 0:00:00
|
Total wall time: 0:00:00
|
||||||
@ -1,4 +1,4 @@
|
|||||||
LAMMPS (17 Feb 2022)
|
LAMMPS (2 Jun 2022)
|
||||||
# 3d Lennard-Jones melt - LAMMPS as surrogate QM engine for aimd_driver.py
|
# 3d Lennard-Jones melt - LAMMPS as surrogate QM engine for aimd_driver.py
|
||||||
|
|
||||||
variable x index 5
|
variable x index 5
|
||||||
@ -31,7 +31,7 @@ neigh_modify delay 0 every 1 check yes
|
|||||||
|
|
||||||
mdi engine
|
mdi engine
|
||||||
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||||
Neighbor list info ...
|
Neighbor list info ...
|
||||||
update every 1 steps, delay 0 steps, check yes
|
update every 1 steps, delay 0 steps, check yes
|
||||||
max neighbors/atom: 2000, page size: 100000
|
max neighbors/atom: 2000, page size: 100000
|
||||||
@ -45,11 +45,16 @@ Neighbor list info ...
|
|||||||
stencil: half/bin/3d
|
stencil: half/bin/3d
|
||||||
bin: standard
|
bin: standard
|
||||||
Per MPI rank memory allocation (min/avg/max) = 3.124 | 3.13 | 3.133 Mbytes
|
Per MPI rank memory allocation (min/avg/max) = 3.124 | 3.13 | 3.133 Mbytes
|
||||||
Step Temp E_pair E_mol TotEng Press
|
Step Temp E_pair E_mol TotEng Press
|
||||||
0 0 -6.7733681 0 -6.7733681 -6.2353173
|
0 0 -6.7733681 0 -6.7733681 -6.2353173
|
||||||
1 0 -6.7699814 0 -6.7699814 -6.2120481
|
1 0 -6.7699814 0 -6.7699814 -6.2120481
|
||||||
2 0 -6.7596844 0 -6.7596844 -6.1418368
|
2 0 -6.7596844 0 -6.7596844 -6.1418368
|
||||||
3 0 -6.7420029 0 -6.7420029 -6.0231905
|
3 0 -6.7420029 0 -6.7420029 -6.0231905
|
||||||
4 0 -6.7161132 0 -6.7161132 -5.8534999
|
4 0 -6.7161132 0 -6.7161132 -5.8534999
|
||||||
5 0 -6.6808361 0 -6.6808361 -5.6291449
|
5 0 -6.6808361 0 -6.6808361 -5.6291449
|
||||||
|
6 0 -6.6344152 0 -6.6344152 -5.3453369
|
||||||
|
7 0 -6.5752633 0 -6.5752633 -4.9977496
|
||||||
|
8 0 -6.502724 0 -6.502724 -4.5844158
|
||||||
|
9 0 -6.4153971 0 -6.4153971 -4.103842
|
||||||
|
10 0 -6.3153532 0 -6.3153532 -3.5633405
|
||||||
Total wall time: 0:00:00
|
Total wall time: 0:00:00
|
||||||
@ -1,4 +1,4 @@
|
|||||||
LAMMPS (17 Feb 2022)
|
LAMMPS (2 Jun 2022)
|
||||||
# 3d Lennard-Jones melt - LAMMPS as surrogate QM engine for aimd_driver.py
|
# 3d Lennard-Jones melt - LAMMPS as surrogate QM engine for aimd_driver.py
|
||||||
|
|
||||||
variable x index 5
|
variable x index 5
|
||||||
@ -31,7 +31,7 @@ neigh_modify delay 0 every 1 check yes
|
|||||||
|
|
||||||
mdi engine
|
mdi engine
|
||||||
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||||
Neighbor list info ...
|
Neighbor list info ...
|
||||||
update every 1 steps, delay 0 steps, check yes
|
update every 1 steps, delay 0 steps, check yes
|
||||||
max neighbors/atom: 2000, page size: 100000
|
max neighbors/atom: 2000, page size: 100000
|
||||||
@ -45,11 +45,16 @@ Neighbor list info ...
|
|||||||
stencil: half/bin/3d
|
stencil: half/bin/3d
|
||||||
bin: standard
|
bin: standard
|
||||||
Per MPI rank memory allocation (min/avg/max) = 3.144 | 3.144 | 3.144 Mbytes
|
Per MPI rank memory allocation (min/avg/max) = 3.144 | 3.144 | 3.144 Mbytes
|
||||||
Step Temp E_pair E_mol TotEng Press
|
Step Temp E_pair E_mol TotEng Press
|
||||||
0 0 -6.7733681 0 -6.7733681 -6.2353173
|
0 0 -6.7733681 0 -6.7733681 -6.2353173
|
||||||
1 0 -6.7699814 0 -6.7699814 -6.2120481
|
1 0 -6.7699814 0 -6.7699814 -6.2120481
|
||||||
2 0 -6.7596844 0 -6.7596844 -6.1418368
|
2 0 -6.7596844 0 -6.7596844 -6.1418368
|
||||||
3 0 -6.7420029 0 -6.7420029 -6.0231905
|
3 0 -6.7420029 0 -6.7420029 -6.0231905
|
||||||
4 0 -6.7161132 0 -6.7161132 -5.8534999
|
4 0 -6.7161132 0 -6.7161132 -5.8534999
|
||||||
5 0 -6.6808361 0 -6.6808361 -5.6291449
|
5 0 -6.6808361 0 -6.6808361 -5.6291449
|
||||||
Total wall time: 0:00:01
|
6 0 -6.6344152 0 -6.6344152 -5.3453369
|
||||||
|
7 0 -6.5752633 0 -6.5752633 -4.9977496
|
||||||
|
8 0 -6.502724 0 -6.502724 -4.5844158
|
||||||
|
9 0 -6.4153971 0 -6.4153971 -4.103842
|
||||||
|
10 0 -6.3153532 0 -6.3153532 -3.5633405
|
||||||
|
Total wall time: 0:00:02
|
||||||
@ -1,4 +1,4 @@
|
|||||||
LAMMPS (17 Feb 2022)
|
LAMMPS (2 Jun 2022)
|
||||||
# 3d Lennard-Jones melt - LAMMPS as surrogate QM engine for aimd_driver.py
|
# 3d Lennard-Jones melt - LAMMPS as surrogate QM engine for aimd_driver.py
|
||||||
|
|
||||||
variable x index 5
|
variable x index 5
|
||||||
@ -31,7 +31,7 @@ neigh_modify delay 0 every 1 check yes
|
|||||||
|
|
||||||
mdi engine
|
mdi engine
|
||||||
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||||
Neighbor list info ...
|
Neighbor list info ...
|
||||||
update every 1 steps, delay 0 steps, check yes
|
update every 1 steps, delay 0 steps, check yes
|
||||||
max neighbors/atom: 2000, page size: 100000
|
max neighbors/atom: 2000, page size: 100000
|
||||||
@ -45,11 +45,16 @@ Neighbor list info ...
|
|||||||
stencil: half/bin/3d
|
stencil: half/bin/3d
|
||||||
bin: standard
|
bin: standard
|
||||||
Per MPI rank memory allocation (min/avg/max) = 3.124 | 3.13 | 3.133 Mbytes
|
Per MPI rank memory allocation (min/avg/max) = 3.124 | 3.13 | 3.133 Mbytes
|
||||||
Step Temp E_pair E_mol TotEng Press
|
Step Temp E_pair E_mol TotEng Press
|
||||||
0 0 -6.7733681 0 -6.7733681 -6.2353173
|
0 0 -6.7733681 0 -6.7733681 -6.2353173
|
||||||
1 0 -6.7699814 0 -6.7699814 -6.2120481
|
1 0 -6.7699814 0 -6.7699814 -6.2120481
|
||||||
2 0 -6.7596844 0 -6.7596844 -6.1418368
|
2 0 -6.7596844 0 -6.7596844 -6.1418368
|
||||||
3 0 -6.7420029 0 -6.7420029 -6.0231905
|
3 0 -6.7420029 0 -6.7420029 -6.0231905
|
||||||
4 0 -6.7161132 0 -6.7161132 -5.8534999
|
4 0 -6.7161132 0 -6.7161132 -5.8534999
|
||||||
5 0 -6.6808361 0 -6.6808361 -5.6291449
|
5 0 -6.6808361 0 -6.6808361 -5.6291449
|
||||||
Total wall time: 0:00:01
|
6 0 -6.6344152 0 -6.6344152 -5.3453369
|
||||||
|
7 0 -6.5752633 0 -6.5752633 -4.9977496
|
||||||
|
8 0 -6.502724 0 -6.502724 -4.5844158
|
||||||
|
9 0 -6.4153971 0 -6.4153971 -4.103842
|
||||||
|
10 0 -6.3153532 0 -6.3153532 -3.5633405
|
||||||
|
Total wall time: 0:00:02
|
||||||
90
examples/mdi/log.17Jun22.sequence.engine.mpi.1
Normal file
90
examples/mdi/log.17Jun22.sequence.engine.mpi.1
Normal file
@ -0,0 +1,90 @@
|
|||||||
|
LAMMPS (2 Jun 2022)
|
||||||
|
# MDI engine script to process a series of evaulate, run, minimize commands
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
lattice fcc 0.8442
|
||||||
|
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||||
|
region box block 0 1 0 1 0 1
|
||||||
|
create_box 1 box
|
||||||
|
Created orthogonal box = (0 0 0) to (1.6795962 1.6795962 1.6795962)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
mass 1 1.0
|
||||||
|
|
||||||
|
pair_style lj/cut 2.5
|
||||||
|
pair_coeff 1 1 1.0 1.0 2.5
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
fix 1 all nve
|
||||||
|
|
||||||
|
thermo 10
|
||||||
|
|
||||||
|
mdi engine
|
||||||
|
delete_atoms group all
|
||||||
|
Deleted 0 atoms, new total = 0
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 0 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 2.8
|
||||||
|
ghost atom cutoff = 2.8
|
||||||
|
binsize = 1.4, bins = 4 4 4
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair lj/cut, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/atomonly/newton
|
||||||
|
stencil: half/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 1 -3.9713146 0 -2.4947521 3.1253597
|
||||||
|
10 1.2380002 -4.3210346 0 -2.4930499 2.0015258
|
||||||
|
20 1.173596 -4.2234559 0 -2.4905682 2.3587731
|
||||||
|
30 1.2989994 -4.4124445 0 -2.4943907 1.903698
|
||||||
|
40 1.4510255 -4.6467459 0 -2.504216 1.2196259
|
||||||
|
50 1.4631454 -4.6641774 0 -2.5037518 1.2838406
|
||||||
|
60 1.2694188 -4.3794267 0 -2.5050505 2.4497113
|
||||||
|
70 1.3363814 -4.4759884 0 -2.5027378 2.2441463
|
||||||
|
80 1.402534 -4.5752515 0 -2.5043224 1.9011715
|
||||||
|
90 1.3870321 -4.5512479 0 -2.5032084 2.0040237
|
||||||
|
100 1.3635651 -4.5209384 0 -2.5075493 1.9773816
|
||||||
|
delete_atoms group all
|
||||||
|
Deleted 64 atoms, new total = 0
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 1 -4.1934138 0 -2.7168513 0.72358299
|
||||||
|
10 1.0170498 -4.2225288 0 -2.7207912 0.7556766
|
||||||
|
20 0.92567967 -4.0920979 0 -2.725274 1.2463143
|
||||||
|
30 1.0851758 -4.3346599 0 -2.73233 0.53176652
|
||||||
|
40 1.2163699 -4.5351986 0 -2.7391524 -0.077915153
|
||||||
|
50 1.2305739 -4.5558134 0 -2.7387942 -0.10711153
|
||||||
|
60 1.1172288 -4.3979372 0 -2.7482791 0.52752067
|
||||||
|
70 1.2228415 -4.5540741 0 -2.7484722 0.11937533
|
||||||
|
80 1.1776333 -4.4870195 0 -2.7481704 0.33904864
|
||||||
|
90 1.219283 -4.5483185 0 -2.747971 0.17898549
|
||||||
|
100 1.2138939 -4.5432229 0 -2.7508327 0.3076354
|
||||||
|
delete_atoms group all
|
||||||
|
Deleted 64 atoms, new total = 0
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 1 -3.8524214 0 -2.3758589 4.6814052
|
||||||
|
10 1.3356745 -4.3481612 0 -2.3759544 3.061856
|
||||||
|
20 1.1791601 -4.117932 0 -2.3768284 3.8565
|
||||||
|
30 1.3435556 -4.3613609 0 -2.3775171 3.0728735
|
||||||
|
40 1.5628445 -4.6886004 0 -2.3809628 2.0989245
|
||||||
|
50 1.4735556 -4.5569123 0 -2.3811152 2.6364099
|
||||||
|
60 1.609387 -4.7581056 0 -2.3817452 1.8988642
|
||||||
|
70 1.5014902 -4.5938759 0 -2.3768318 2.458161
|
||||||
|
80 1.3763383 -4.4089865 0 -2.3767369 3.0379808
|
||||||
|
90 1.498202 -4.5909613 0 -2.3787724 2.5543714
|
||||||
|
100 1.43934 -4.5009545 0 -2.375679 3.0923444
|
||||||
|
|
||||||
|
Total wall time: 0:00:00
|
||||||
90
examples/mdi/log.17Jun22.sequence.engine.mpi.4
Normal file
90
examples/mdi/log.17Jun22.sequence.engine.mpi.4
Normal file
@ -0,0 +1,90 @@
|
|||||||
|
LAMMPS (2 Jun 2022)
|
||||||
|
# MDI engine script to process a series of evaulate, run, minimize commands
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
lattice fcc 0.8442
|
||||||
|
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||||
|
region box block 0 1 0 1 0 1
|
||||||
|
create_box 1 box
|
||||||
|
Created orthogonal box = (0 0 0) to (1.6795962 1.6795962 1.6795962)
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
mass 1 1.0
|
||||||
|
|
||||||
|
pair_style lj/cut 2.5
|
||||||
|
pair_coeff 1 1 1.0 1.0 2.5
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
fix 1 all nve
|
||||||
|
|
||||||
|
thermo 10
|
||||||
|
|
||||||
|
mdi engine
|
||||||
|
delete_atoms group all
|
||||||
|
Deleted 0 atoms, new total = 0
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 0 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 2.8
|
||||||
|
ghost atom cutoff = 2.8
|
||||||
|
binsize = 1.4, bins = 4 4 4
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair lj/cut, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/atomonly/newton
|
||||||
|
stencil: half/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 1 -3.9713146 0 -2.4947521 3.1253597
|
||||||
|
10 1.2380002 -4.3210346 0 -2.4930499 2.0015258
|
||||||
|
20 1.173596 -4.2234559 0 -2.4905682 2.3587731
|
||||||
|
30 1.2989994 -4.4124445 0 -2.4943907 1.903698
|
||||||
|
40 1.4510255 -4.6467459 0 -2.504216 1.2196259
|
||||||
|
50 1.4631454 -4.6641774 0 -2.5037518 1.2838406
|
||||||
|
60 1.2694188 -4.3794267 0 -2.5050505 2.4497113
|
||||||
|
70 1.3363814 -4.4759884 0 -2.5027378 2.2441463
|
||||||
|
80 1.402534 -4.5752515 0 -2.5043224 1.9011715
|
||||||
|
90 1.3870321 -4.5512479 0 -2.5032084 2.0040237
|
||||||
|
100 1.3635651 -4.5209384 0 -2.5075493 1.9773816
|
||||||
|
delete_atoms group all
|
||||||
|
Deleted 64 atoms, new total = 0
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 1 -4.1934138 0 -2.7168513 0.72358299
|
||||||
|
10 1.0170498 -4.2225288 0 -2.7207912 0.7556766
|
||||||
|
20 0.92567967 -4.0920979 0 -2.725274 1.2463143
|
||||||
|
30 1.0851758 -4.3346599 0 -2.73233 0.53176652
|
||||||
|
40 1.2163699 -4.5351986 0 -2.7391524 -0.077915153
|
||||||
|
50 1.2305739 -4.5558134 0 -2.7387942 -0.10711153
|
||||||
|
60 1.1172288 -4.3979372 0 -2.7482791 0.52752067
|
||||||
|
70 1.2228415 -4.5540741 0 -2.7484722 0.11937533
|
||||||
|
80 1.1776333 -4.4870195 0 -2.7481704 0.33904864
|
||||||
|
90 1.219283 -4.5483185 0 -2.747971 0.17898549
|
||||||
|
100 1.2138939 -4.5432229 0 -2.7508327 0.3076354
|
||||||
|
delete_atoms group all
|
||||||
|
Deleted 64 atoms, new total = 0
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 1 -3.8524214 0 -2.3758589 4.6814052
|
||||||
|
10 1.3356745 -4.3481612 0 -2.3759544 3.061856
|
||||||
|
20 1.1791601 -4.117932 0 -2.3768284 3.8565
|
||||||
|
30 1.3435556 -4.3613609 0 -2.3775171 3.0728735
|
||||||
|
40 1.5628445 -4.6886004 0 -2.3809628 2.0989245
|
||||||
|
50 1.4735556 -4.5569123 0 -2.3811152 2.6364099
|
||||||
|
60 1.609387 -4.7581056 0 -2.3817452 1.8988642
|
||||||
|
70 1.5014902 -4.5938759 0 -2.3768318 2.458161
|
||||||
|
80 1.3763383 -4.4089865 0 -2.3767369 3.0379808
|
||||||
|
90 1.498202 -4.5909613 0 -2.3787724 2.5543714
|
||||||
|
100 1.43934 -4.5009545 0 -2.375679 3.0923444
|
||||||
|
|
||||||
|
Total wall time: 0:00:00
|
||||||
90
examples/mdi/log.17Jun22.sequence.engine.plugin.1
Normal file
90
examples/mdi/log.17Jun22.sequence.engine.plugin.1
Normal file
@ -0,0 +1,90 @@
|
|||||||
|
LAMMPS (2 Jun 2022)
|
||||||
|
# MDI engine script to process a series of evaulate, run, minimize commands
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
lattice fcc 0.8442
|
||||||
|
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||||
|
region box block 0 1 0 1 0 1
|
||||||
|
create_box 1 box
|
||||||
|
Created orthogonal box = (0 0 0) to (1.6795962 1.6795962 1.6795962)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
mass 1 1.0
|
||||||
|
|
||||||
|
pair_style lj/cut 2.5
|
||||||
|
pair_coeff 1 1 1.0 1.0 2.5
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
fix 1 all nve
|
||||||
|
|
||||||
|
thermo 10
|
||||||
|
|
||||||
|
mdi engine
|
||||||
|
delete_atoms group all
|
||||||
|
Deleted 0 atoms, new total = 0
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 0 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 2.8
|
||||||
|
ghost atom cutoff = 2.8
|
||||||
|
binsize = 1.4, bins = 4 4 4
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair lj/cut, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/atomonly/newton
|
||||||
|
stencil: half/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 1 -3.9713146 0 -2.4947521 3.1253597
|
||||||
|
10 1.2380002 -4.3210346 0 -2.4930499 2.0015258
|
||||||
|
20 1.173596 -4.2234559 0 -2.4905682 2.3587731
|
||||||
|
30 1.2989994 -4.4124445 0 -2.4943907 1.903698
|
||||||
|
40 1.4510255 -4.6467459 0 -2.504216 1.2196259
|
||||||
|
50 1.4631454 -4.6641774 0 -2.5037518 1.2838406
|
||||||
|
60 1.2694188 -4.3794267 0 -2.5050505 2.4497113
|
||||||
|
70 1.3363814 -4.4759884 0 -2.5027378 2.2441463
|
||||||
|
80 1.402534 -4.5752515 0 -2.5043224 1.9011715
|
||||||
|
90 1.3870321 -4.5512479 0 -2.5032084 2.0040237
|
||||||
|
100 1.3635651 -4.5209384 0 -2.5075493 1.9773816
|
||||||
|
delete_atoms group all
|
||||||
|
Deleted 64 atoms, new total = 0
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 1 -4.1934138 0 -2.7168513 0.72358299
|
||||||
|
10 1.0170498 -4.2225288 0 -2.7207912 0.7556766
|
||||||
|
20 0.92567967 -4.0920979 0 -2.725274 1.2463143
|
||||||
|
30 1.0851758 -4.3346599 0 -2.73233 0.53176652
|
||||||
|
40 1.2163699 -4.5351986 0 -2.7391524 -0.077915153
|
||||||
|
50 1.2305739 -4.5558134 0 -2.7387942 -0.10711153
|
||||||
|
60 1.1172288 -4.3979372 0 -2.7482791 0.52752067
|
||||||
|
70 1.2228415 -4.5540741 0 -2.7484722 0.11937533
|
||||||
|
80 1.1776333 -4.4870195 0 -2.7481704 0.33904864
|
||||||
|
90 1.219283 -4.5483185 0 -2.747971 0.17898549
|
||||||
|
100 1.2138939 -4.5432229 0 -2.7508327 0.3076354
|
||||||
|
delete_atoms group all
|
||||||
|
Deleted 64 atoms, new total = 0
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 1 -3.8524214 0 -2.3758589 4.6814052
|
||||||
|
10 1.3356745 -4.3481612 0 -2.3759544 3.061856
|
||||||
|
20 1.1791601 -4.117932 0 -2.3768284 3.8565
|
||||||
|
30 1.3435556 -4.3613609 0 -2.3775171 3.0728735
|
||||||
|
40 1.5628445 -4.6886004 0 -2.3809628 2.0989245
|
||||||
|
50 1.4735556 -4.5569123 0 -2.3811152 2.6364099
|
||||||
|
60 1.609387 -4.7581056 0 -2.3817452 1.8988642
|
||||||
|
70 1.5014902 -4.5938759 0 -2.3768318 2.458161
|
||||||
|
80 1.3763383 -4.4089865 0 -2.3767369 3.0379808
|
||||||
|
90 1.498202 -4.5909613 0 -2.3787724 2.5543714
|
||||||
|
100 1.43934 -4.5009545 0 -2.375679 3.0923444
|
||||||
|
|
||||||
|
Total wall time: 0:00:00
|
||||||
90
examples/mdi/log.17Jun22.sequence.engine.plugin.3
Normal file
90
examples/mdi/log.17Jun22.sequence.engine.plugin.3
Normal file
@ -0,0 +1,90 @@
|
|||||||
|
LAMMPS (2 Jun 2022)
|
||||||
|
# MDI engine script to process a series of evaulate, run, minimize commands
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
lattice fcc 0.8442
|
||||||
|
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||||
|
region box block 0 1 0 1 0 1
|
||||||
|
create_box 1 box
|
||||||
|
Created orthogonal box = (0 0 0) to (1.6795962 1.6795962 1.6795962)
|
||||||
|
1 by 1 by 3 MPI processor grid
|
||||||
|
mass 1 1.0
|
||||||
|
|
||||||
|
pair_style lj/cut 2.5
|
||||||
|
pair_coeff 1 1 1.0 1.0 2.5
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
fix 1 all nve
|
||||||
|
|
||||||
|
thermo 10
|
||||||
|
|
||||||
|
mdi engine
|
||||||
|
delete_atoms group all
|
||||||
|
Deleted 0 atoms, new total = 0
|
||||||
|
1 by 1 by 3 MPI processor grid
|
||||||
|
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 0 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 2.8
|
||||||
|
ghost atom cutoff = 2.8
|
||||||
|
binsize = 1.4, bins = 4 4 4
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair lj/cut, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/atomonly/newton
|
||||||
|
stencil: half/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 3.07 | 3.07 | 3.071 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 1 -3.9713146 0 -2.4947521 3.1253597
|
||||||
|
10 1.2380002 -4.3210346 0 -2.4930499 2.0015258
|
||||||
|
20 1.173596 -4.2234559 0 -2.4905682 2.3587731
|
||||||
|
30 1.2989994 -4.4124445 0 -2.4943907 1.903698
|
||||||
|
40 1.4510255 -4.6467459 0 -2.504216 1.2196259
|
||||||
|
50 1.4631454 -4.6641774 0 -2.5037518 1.2838406
|
||||||
|
60 1.2694188 -4.3794267 0 -2.5050505 2.4497113
|
||||||
|
70 1.3363814 -4.4759884 0 -2.5027378 2.2441463
|
||||||
|
80 1.402534 -4.5752515 0 -2.5043224 1.9011715
|
||||||
|
90 1.3870321 -4.5512479 0 -2.5032084 2.0040237
|
||||||
|
100 1.3635651 -4.5209384 0 -2.5075493 1.9773816
|
||||||
|
delete_atoms group all
|
||||||
|
Deleted 64 atoms, new total = 0
|
||||||
|
1 by 1 by 3 MPI processor grid
|
||||||
|
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 3.07 | 3.07 | 3.071 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 1 -4.1934138 0 -2.7168513 0.72358299
|
||||||
|
10 1.0170498 -4.2225288 0 -2.7207912 0.7556766
|
||||||
|
20 0.92567967 -4.0920979 0 -2.725274 1.2463143
|
||||||
|
30 1.0851758 -4.3346599 0 -2.73233 0.53176652
|
||||||
|
40 1.2163699 -4.5351986 0 -2.7391524 -0.077915153
|
||||||
|
50 1.2305739 -4.5558134 0 -2.7387942 -0.10711153
|
||||||
|
60 1.1172288 -4.3979372 0 -2.7482791 0.52752067
|
||||||
|
70 1.2228415 -4.5540741 0 -2.7484722 0.11937533
|
||||||
|
80 1.1776333 -4.4870195 0 -2.7481704 0.33904864
|
||||||
|
90 1.219283 -4.5483185 0 -2.747971 0.17898549
|
||||||
|
100 1.2138939 -4.5432229 0 -2.7508327 0.3076354
|
||||||
|
delete_atoms group all
|
||||||
|
Deleted 64 atoms, new total = 0
|
||||||
|
3 by 1 by 1 MPI processor grid
|
||||||
|
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 3.07 | 3.07 | 3.071 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 1 -3.8524214 0 -2.3758589 4.6814052
|
||||||
|
10 1.3356745 -4.3481612 0 -2.3759544 3.061856
|
||||||
|
20 1.1791601 -4.117932 0 -2.3768284 3.8565
|
||||||
|
30 1.3435556 -4.3613609 0 -2.3775171 3.0728735
|
||||||
|
40 1.5628445 -4.6886004 0 -2.3809628 2.0989245
|
||||||
|
50 1.4735556 -4.5569123 0 -2.3811152 2.6364099
|
||||||
|
60 1.609387 -4.7581056 0 -2.3817452 1.8988642
|
||||||
|
70 1.5014902 -4.5938759 0 -2.3768318 2.458161
|
||||||
|
80 1.3763383 -4.4089865 0 -2.3767369 3.0379808
|
||||||
|
90 1.498202 -4.5909613 0 -2.3787724 2.5543714
|
||||||
|
100 1.43934 -4.5009545 0 -2.375679 3.0923444
|
||||||
|
|
||||||
|
Total wall time: 0:00:00
|
||||||
90
examples/mdi/log.17Jun22.sequence.engine.tcp.1
Normal file
90
examples/mdi/log.17Jun22.sequence.engine.tcp.1
Normal file
@ -0,0 +1,90 @@
|
|||||||
|
LAMMPS (2 Jun 2022)
|
||||||
|
# MDI engine script to process a series of evaulate, run, minimize commands
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
lattice fcc 0.8442
|
||||||
|
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||||
|
region box block 0 1 0 1 0 1
|
||||||
|
create_box 1 box
|
||||||
|
Created orthogonal box = (0 0 0) to (1.6795962 1.6795962 1.6795962)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
mass 1 1.0
|
||||||
|
|
||||||
|
pair_style lj/cut 2.5
|
||||||
|
pair_coeff 1 1 1.0 1.0 2.5
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
fix 1 all nve
|
||||||
|
|
||||||
|
thermo 10
|
||||||
|
|
||||||
|
mdi engine
|
||||||
|
delete_atoms group all
|
||||||
|
Deleted 0 atoms, new total = 0
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 0 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 2.8
|
||||||
|
ghost atom cutoff = 2.8
|
||||||
|
binsize = 1.4, bins = 4 4 4
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair lj/cut, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/atomonly/newton
|
||||||
|
stencil: half/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 1 -3.9713146 0 -2.4947521 3.1253597
|
||||||
|
10 1.2380002 -4.3210346 0 -2.4930499 2.0015258
|
||||||
|
20 1.173596 -4.2234559 0 -2.4905682 2.3587731
|
||||||
|
30 1.2989994 -4.4124445 0 -2.4943907 1.903698
|
||||||
|
40 1.4510255 -4.6467459 0 -2.504216 1.2196259
|
||||||
|
50 1.4631454 -4.6641774 0 -2.5037518 1.2838406
|
||||||
|
60 1.2694188 -4.3794267 0 -2.5050505 2.4497113
|
||||||
|
70 1.3363814 -4.4759884 0 -2.5027378 2.2441463
|
||||||
|
80 1.402534 -4.5752515 0 -2.5043224 1.9011715
|
||||||
|
90 1.3870321 -4.5512479 0 -2.5032084 2.0040237
|
||||||
|
100 1.3635651 -4.5209384 0 -2.5075493 1.9773816
|
||||||
|
delete_atoms group all
|
||||||
|
Deleted 64 atoms, new total = 0
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 1 -4.1934138 0 -2.7168513 0.72358299
|
||||||
|
10 1.0170498 -4.2225288 0 -2.7207912 0.7556766
|
||||||
|
20 0.92567967 -4.0920979 0 -2.725274 1.2463143
|
||||||
|
30 1.0851758 -4.3346599 0 -2.73233 0.53176652
|
||||||
|
40 1.2163699 -4.5351986 0 -2.7391524 -0.077915153
|
||||||
|
50 1.2305739 -4.5558134 0 -2.7387942 -0.10711153
|
||||||
|
60 1.1172288 -4.3979372 0 -2.7482791 0.52752067
|
||||||
|
70 1.2228415 -4.5540741 0 -2.7484722 0.11937533
|
||||||
|
80 1.1776333 -4.4870195 0 -2.7481704 0.33904864
|
||||||
|
90 1.219283 -4.5483185 0 -2.747971 0.17898549
|
||||||
|
100 1.2138939 -4.5432229 0 -2.7508327 0.3076354
|
||||||
|
delete_atoms group all
|
||||||
|
Deleted 64 atoms, new total = 0
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 1 -3.8524214 0 -2.3758589 4.6814052
|
||||||
|
10 1.3356745 -4.3481612 0 -2.3759544 3.061856
|
||||||
|
20 1.1791601 -4.117932 0 -2.3768284 3.8565
|
||||||
|
30 1.3435556 -4.3613609 0 -2.3775171 3.0728735
|
||||||
|
40 1.5628445 -4.6886004 0 -2.3809628 2.0989245
|
||||||
|
50 1.4735556 -4.5569123 0 -2.3811152 2.6364099
|
||||||
|
60 1.609387 -4.7581056 0 -2.3817452 1.8988642
|
||||||
|
70 1.5014902 -4.5938759 0 -2.3768318 2.458161
|
||||||
|
80 1.3763383 -4.4089865 0 -2.3767369 3.0379808
|
||||||
|
90 1.498202 -4.5909613 0 -2.3787724 2.5543714
|
||||||
|
100 1.43934 -4.5009545 0 -2.375679 3.0923444
|
||||||
|
|
||||||
|
Total wall time: 0:00:00
|
||||||
90
examples/mdi/log.17Jun22.sequence.engine.tcp.4
Normal file
90
examples/mdi/log.17Jun22.sequence.engine.tcp.4
Normal file
@ -0,0 +1,90 @@
|
|||||||
|
LAMMPS (2 Jun 2022)
|
||||||
|
# MDI engine script to process a series of evaulate, run, minimize commands
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
lattice fcc 0.8442
|
||||||
|
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||||
|
region box block 0 1 0 1 0 1
|
||||||
|
create_box 1 box
|
||||||
|
Created orthogonal box = (0 0 0) to (1.6795962 1.6795962 1.6795962)
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
mass 1 1.0
|
||||||
|
|
||||||
|
pair_style lj/cut 2.5
|
||||||
|
pair_coeff 1 1 1.0 1.0 2.5
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
fix 1 all nve
|
||||||
|
|
||||||
|
thermo 10
|
||||||
|
|
||||||
|
mdi engine
|
||||||
|
delete_atoms group all
|
||||||
|
Deleted 0 atoms, new total = 0
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 0 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 2.8
|
||||||
|
ghost atom cutoff = 2.8
|
||||||
|
binsize = 1.4, bins = 4 4 4
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair lj/cut, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/atomonly/newton
|
||||||
|
stencil: half/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 1 -3.9713146 0 -2.4947521 3.1253597
|
||||||
|
10 1.2380002 -4.3210346 0 -2.4930499 2.0015258
|
||||||
|
20 1.173596 -4.2234559 0 -2.4905682 2.3587731
|
||||||
|
30 1.2989994 -4.4124445 0 -2.4943907 1.903698
|
||||||
|
40 1.4510255 -4.6467459 0 -2.504216 1.2196259
|
||||||
|
50 1.4631454 -4.6641774 0 -2.5037518 1.2838406
|
||||||
|
60 1.2694188 -4.3794267 0 -2.5050505 2.4497113
|
||||||
|
70 1.3363814 -4.4759884 0 -2.5027378 2.2441463
|
||||||
|
80 1.402534 -4.5752515 0 -2.5043224 1.9011715
|
||||||
|
90 1.3870321 -4.5512479 0 -2.5032084 2.0040237
|
||||||
|
100 1.3635651 -4.5209384 0 -2.5075493 1.9773816
|
||||||
|
delete_atoms group all
|
||||||
|
Deleted 64 atoms, new total = 0
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 1 -4.1934138 0 -2.7168513 0.72358299
|
||||||
|
10 1.0170498 -4.2225288 0 -2.7207912 0.7556766
|
||||||
|
20 0.92567967 -4.0920979 0 -2.725274 1.2463143
|
||||||
|
30 1.0851758 -4.3346599 0 -2.73233 0.53176652
|
||||||
|
40 1.2163699 -4.5351986 0 -2.7391524 -0.077915153
|
||||||
|
50 1.2305739 -4.5558134 0 -2.7387942 -0.10711153
|
||||||
|
60 1.1172288 -4.3979372 0 -2.7482791 0.52752067
|
||||||
|
70 1.2228415 -4.5540741 0 -2.7484722 0.11937533
|
||||||
|
80 1.1776333 -4.4870195 0 -2.7481704 0.33904864
|
||||||
|
90 1.219283 -4.5483185 0 -2.747971 0.17898549
|
||||||
|
100 1.2138939 -4.5432229 0 -2.7508327 0.3076354
|
||||||
|
delete_atoms group all
|
||||||
|
Deleted 64 atoms, new total = 0
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 3.077 | 3.077 | 3.077 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 1 -3.8524214 0 -2.3758589 4.6814052
|
||||||
|
10 1.3356745 -4.3481612 0 -2.3759544 3.061856
|
||||||
|
20 1.1791601 -4.117932 0 -2.3768284 3.8565
|
||||||
|
30 1.3435556 -4.3613609 0 -2.3775171 3.0728735
|
||||||
|
40 1.5628445 -4.6886004 0 -2.3809628 2.0989245
|
||||||
|
50 1.4735556 -4.5569123 0 -2.3811152 2.6364099
|
||||||
|
60 1.609387 -4.7581056 0 -2.3817452 1.8988642
|
||||||
|
70 1.5014902 -4.5938759 0 -2.3768318 2.458161
|
||||||
|
80 1.3763383 -4.4089865 0 -2.3767369 3.0379808
|
||||||
|
90 1.498202 -4.5909613 0 -2.3787724 2.5543714
|
||||||
|
100 1.43934 -4.5009545 0 -2.375679 3.0923444
|
||||||
|
|
||||||
|
Total wall time: 0:00:00
|
||||||
248
examples/mdi/log.17Jun22.series.alone.1
Normal file
248
examples/mdi/log.17Jun22.series.alone.1
Normal file
@ -0,0 +1,248 @@
|
|||||||
|
LAMMPS (2 Jun 2022)
|
||||||
|
# 3d Lennard-Jones melt - MDI driver script
|
||||||
|
|
||||||
|
variable x index 5
|
||||||
|
variable y index 5
|
||||||
|
variable z index 5
|
||||||
|
|
||||||
|
variable rho index 0.7 0.8 0.9
|
||||||
|
|
||||||
|
label LOOP
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
read_data data.series.${rho}
|
||||||
|
read_data data.series.0.7
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (0 0 0) to (8.9390354 8.9390354 8.9390354)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
500 atoms
|
||||||
|
reading velocities ...
|
||||||
|
500 velocities
|
||||||
|
read_data CPU = 0.004 seconds
|
||||||
|
|
||||||
|
displace_atoms all random 0.1 0.1 0.1 48294
|
||||||
|
Displacing atoms ...
|
||||||
|
|
||||||
|
pair_style lj/cut 2.5
|
||||||
|
pair_coeff 1 1 1.0 1.0 2.5
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
compute 1 all pressure NULL virial
|
||||||
|
|
||||||
|
thermo_style custom step temp pe c_1 c_1[1] c_1[2] c_1[3]
|
||||||
|
|
||||||
|
run 0
|
||||||
|
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||||
|
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 0 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 2.8
|
||||||
|
ghost atom cutoff = 2.8
|
||||||
|
binsize = 1.4, bins = 7 7 7
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair lj/cut, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/atomonly/newton
|
||||||
|
stencil: half/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 3.137 | 3.137 | 3.137 Mbytes
|
||||||
|
Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3]
|
||||||
|
0 0 -5.200819 -4.5647906 -4.5444385 -4.5699966 -4.5799366
|
||||||
|
Loop time of 2.729e-06 on 1 procs for 0 steps with 500 atoms
|
||||||
|
|
||||||
|
109.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Other | | 2.729e-06 | | |100.00
|
||||||
|
|
||||||
|
Nlocal: 500 ave 500 max 500 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 1956 ave 1956 max 1956 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 15687 ave 15687 max 15687 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 15687
|
||||||
|
Ave neighs/atom = 31.374
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
write_dump all custom dump.series.alone id type x y z fx fy fz modify sort id append yes
|
||||||
|
|
||||||
|
clear
|
||||||
|
|
||||||
|
next rho
|
||||||
|
|
||||||
|
jump SELF LOOP
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
read_data data.series.${rho}
|
||||||
|
read_data data.series.0.8
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (0 0 0) to (8.5498797 8.5498797 8.5498797)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
500 atoms
|
||||||
|
reading velocities ...
|
||||||
|
500 velocities
|
||||||
|
read_data CPU = 0.004 seconds
|
||||||
|
|
||||||
|
displace_atoms all random 0.1 0.1 0.1 48294
|
||||||
|
Displacing atoms ...
|
||||||
|
|
||||||
|
pair_style lj/cut 2.5
|
||||||
|
pair_coeff 1 1 1.0 1.0 2.5
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
compute 1 all pressure NULL virial
|
||||||
|
|
||||||
|
thermo_style custom step temp pe c_1 c_1[1] c_1[2] c_1[3]
|
||||||
|
|
||||||
|
run 0
|
||||||
|
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||||
|
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 0 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 2.8
|
||||||
|
ghost atom cutoff = 2.8
|
||||||
|
binsize = 1.4, bins = 7 7 7
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair lj/cut, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/atomonly/newton
|
||||||
|
stencil: half/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 3.135 | 3.135 | 3.135 Mbytes
|
||||||
|
Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3]
|
||||||
|
0 0 -6.0419499 -4.2737827 -4.2865535 -4.2176976 -4.3170971
|
||||||
|
Loop time of 1.434e-06 on 1 procs for 0 steps with 500 atoms
|
||||||
|
|
||||||
|
139.5% CPU use with 1 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Other | | 1.434e-06 | | |100.00
|
||||||
|
|
||||||
|
Nlocal: 500 ave 500 max 500 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 1956 ave 1956 max 1956 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 18734 ave 18734 max 18734 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 18734
|
||||||
|
Ave neighs/atom = 37.468
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
write_dump all custom dump.series.alone id type x y z fx fy fz modify sort id append yes
|
||||||
|
|
||||||
|
clear
|
||||||
|
|
||||||
|
next rho
|
||||||
|
|
||||||
|
jump SELF LOOP
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
read_data data.series.${rho}
|
||||||
|
read_data data.series.0.9
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (0 0 0) to (8.2207069 8.2207069 8.2207069)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
500 atoms
|
||||||
|
reading velocities ...
|
||||||
|
500 velocities
|
||||||
|
read_data CPU = 0.003 seconds
|
||||||
|
|
||||||
|
displace_atoms all random 0.1 0.1 0.1 48294
|
||||||
|
Displacing atoms ...
|
||||||
|
|
||||||
|
pair_style lj/cut 2.5
|
||||||
|
pair_coeff 1 1 1.0 1.0 2.5
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
compute 1 all pressure NULL virial
|
||||||
|
|
||||||
|
thermo_style custom step temp pe c_1 c_1[1] c_1[2] c_1[3]
|
||||||
|
|
||||||
|
run 0
|
||||||
|
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||||
|
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 0 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 2.8
|
||||||
|
ghost atom cutoff = 2.8
|
||||||
|
binsize = 1.4, bins = 6 6 6
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair lj/cut, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/atomonly/newton
|
||||||
|
stencil: half/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 3.134 | 3.134 | 3.134 Mbytes
|
||||||
|
Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3]
|
||||||
|
0 0 -6.4477578 -1.5268553 -1.5717034 -1.568693 -1.4401696
|
||||||
|
Loop time of 1.483e-06 on 1 procs for 0 steps with 500 atoms
|
||||||
|
|
||||||
|
134.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Other | | 1.483e-06 | | |100.00
|
||||||
|
|
||||||
|
Nlocal: 500 ave 500 max 500 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 1956 ave 1956 max 1956 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 20023 ave 20023 max 20023 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 20023
|
||||||
|
Ave neighs/atom = 40.046
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
write_dump all custom dump.series.alone id type x y z fx fy fz modify sort id append yes
|
||||||
|
|
||||||
|
clear
|
||||||
|
|
||||||
|
next rho
|
||||||
|
|
||||||
|
jump SELF LOOP
|
||||||
|
Total wall time: 0:00:00
|
||||||
213
examples/mdi/log.17Jun22.series.driver.mpi.1
Normal file
213
examples/mdi/log.17Jun22.series.driver.mpi.1
Normal file
@ -0,0 +1,213 @@
|
|||||||
|
LAMMPS (2 Jun 2022)
|
||||||
|
# 3d Lennard-Jones melt - MDI driver script
|
||||||
|
|
||||||
|
variable x index 5
|
||||||
|
variable y index 5
|
||||||
|
variable z index 5
|
||||||
|
|
||||||
|
variable rho index 0.7 0.8 0.9
|
||||||
|
|
||||||
|
mdi connect
|
||||||
|
|
||||||
|
label LOOP
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
read_data data.series.${rho}
|
||||||
|
read_data data.series.0.7
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (0 0 0) to (8.9390354 8.9390354 8.9390354)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
500 atoms
|
||||||
|
reading velocities ...
|
||||||
|
500 velocities
|
||||||
|
read_data CPU = 0.003 seconds
|
||||||
|
|
||||||
|
displace_atoms all random 0.1 0.1 0.1 48294
|
||||||
|
Displacing atoms ...
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
fix 1 all mdi/qm add no virial yes connect no
|
||||||
|
variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3
|
||||||
|
|
||||||
|
thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||||
|
|
||||||
|
run 0
|
||||||
|
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||||
|
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||||
|
Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||||
|
0 0 -5.200819 -4.5647906 -4.5444385 -4.5699966 -4.5799366
|
||||||
|
Loop time of 1.919e-06 on 1 procs for 0 steps with 500 atoms
|
||||||
|
|
||||||
|
0.0% CPU use with 1 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Other | | 1.919e-06 | | |100.00
|
||||||
|
|
||||||
|
Nlocal: 500 ave 500 max 500 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 0 ave 0 max 0 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 0 ave 0 max 0 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 0
|
||||||
|
Ave neighs/atom = 0
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
write_dump all custom dump.series.driver id type x y z f_1[1] f_1[2] f_1[3] modify sort id append yes
|
||||||
|
|
||||||
|
clear
|
||||||
|
|
||||||
|
next rho
|
||||||
|
|
||||||
|
jump SELF LOOP
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
read_data data.series.${rho}
|
||||||
|
read_data data.series.0.8
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (0 0 0) to (8.5498797 8.5498797 8.5498797)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
500 atoms
|
||||||
|
reading velocities ...
|
||||||
|
500 velocities
|
||||||
|
read_data CPU = 0.003 seconds
|
||||||
|
|
||||||
|
displace_atoms all random 0.1 0.1 0.1 48294
|
||||||
|
Displacing atoms ...
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
fix 1 all mdi/qm add no virial yes connect no
|
||||||
|
variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3
|
||||||
|
|
||||||
|
thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||||
|
|
||||||
|
run 0
|
||||||
|
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||||
|
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||||
|
Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||||
|
0 0 -6.0419499 -4.2737827 -4.2865535 -4.2176976 -4.3170971
|
||||||
|
Loop time of 1.141e-06 on 1 procs for 0 steps with 500 atoms
|
||||||
|
|
||||||
|
87.6% CPU use with 1 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Other | | 1.141e-06 | | |100.00
|
||||||
|
|
||||||
|
Nlocal: 500 ave 500 max 500 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 0 ave 0 max 0 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 0 ave 0 max 0 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 0
|
||||||
|
Ave neighs/atom = 0
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
write_dump all custom dump.series.driver id type x y z f_1[1] f_1[2] f_1[3] modify sort id append yes
|
||||||
|
|
||||||
|
clear
|
||||||
|
|
||||||
|
next rho
|
||||||
|
|
||||||
|
jump SELF LOOP
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
read_data data.series.${rho}
|
||||||
|
read_data data.series.0.9
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (0 0 0) to (8.2207069 8.2207069 8.2207069)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
500 atoms
|
||||||
|
reading velocities ...
|
||||||
|
500 velocities
|
||||||
|
read_data CPU = 0.002 seconds
|
||||||
|
|
||||||
|
displace_atoms all random 0.1 0.1 0.1 48294
|
||||||
|
Displacing atoms ...
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
fix 1 all mdi/qm add no virial yes connect no
|
||||||
|
variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3
|
||||||
|
|
||||||
|
thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||||
|
|
||||||
|
run 0
|
||||||
|
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||||
|
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||||
|
Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||||
|
0 0 -6.4477578 -1.5268553 -1.5717034 -1.568693 -1.4401696
|
||||||
|
Loop time of 1.019e-06 on 1 procs for 0 steps with 500 atoms
|
||||||
|
|
||||||
|
98.1% CPU use with 1 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Other | | 1.019e-06 | | |100.00
|
||||||
|
|
||||||
|
Nlocal: 500 ave 500 max 500 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 0 ave 0 max 0 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 0 ave 0 max 0 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 0
|
||||||
|
Ave neighs/atom = 0
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
write_dump all custom dump.series.driver id type x y z f_1[1] f_1[2] f_1[3] modify sort id append yes
|
||||||
|
|
||||||
|
clear
|
||||||
|
|
||||||
|
next rho
|
||||||
|
|
||||||
|
jump SELF LOOP
|
||||||
|
|
||||||
|
mdi exit
|
||||||
|
Total wall time: 0:00:00
|
||||||
213
examples/mdi/log.17Jun22.series.driver.mpi.3
Normal file
213
examples/mdi/log.17Jun22.series.driver.mpi.3
Normal file
@ -0,0 +1,213 @@
|
|||||||
|
LAMMPS (2 Jun 2022)
|
||||||
|
# 3d Lennard-Jones melt - MDI driver script
|
||||||
|
|
||||||
|
variable x index 5
|
||||||
|
variable y index 5
|
||||||
|
variable z index 5
|
||||||
|
|
||||||
|
variable rho index 0.7 0.8 0.9
|
||||||
|
|
||||||
|
mdi connect
|
||||||
|
|
||||||
|
label LOOP
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
read_data data.series.${rho}
|
||||||
|
read_data data.series.0.7
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (0 0 0) to (8.9390354 8.9390354 8.9390354)
|
||||||
|
1 by 1 by 3 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
500 atoms
|
||||||
|
reading velocities ...
|
||||||
|
500 velocities
|
||||||
|
read_data CPU = 0.004 seconds
|
||||||
|
|
||||||
|
displace_atoms all random 0.1 0.1 0.1 48294
|
||||||
|
Displacing atoms ...
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
fix 1 all mdi/qm add no virial yes connect no
|
||||||
|
variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3
|
||||||
|
|
||||||
|
thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||||
|
|
||||||
|
run 0
|
||||||
|
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||||
|
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||||
|
Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||||
|
0 0 -5.200819 -4.5647906 -4.5444385 -4.5699966 -4.5799366
|
||||||
|
Loop time of 4.00933e-06 on 3 procs for 0 steps with 500 atoms
|
||||||
|
|
||||||
|
91.5% CPU use with 3 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Other | | 4.009e-06 | | |100.00
|
||||||
|
|
||||||
|
Nlocal: 166.667 ave 177 max 150 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 1 1
|
||||||
|
Nghost: 0 ave 0 max 0 min
|
||||||
|
Histogram: 3 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 0 ave 0 max 0 min
|
||||||
|
Histogram: 3 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 0
|
||||||
|
Ave neighs/atom = 0
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
write_dump all custom dump.series.driver id type x y z f_1[1] f_1[2] f_1[3] modify sort id append yes
|
||||||
|
|
||||||
|
clear
|
||||||
|
|
||||||
|
next rho
|
||||||
|
|
||||||
|
jump SELF LOOP
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
read_data data.series.${rho}
|
||||||
|
read_data data.series.0.8
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (0 0 0) to (8.5498797 8.5498797 8.5498797)
|
||||||
|
1 by 1 by 3 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
500 atoms
|
||||||
|
reading velocities ...
|
||||||
|
500 velocities
|
||||||
|
read_data CPU = 0.003 seconds
|
||||||
|
|
||||||
|
displace_atoms all random 0.1 0.1 0.1 48294
|
||||||
|
Displacing atoms ...
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
fix 1 all mdi/qm add no virial yes connect no
|
||||||
|
variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3
|
||||||
|
|
||||||
|
thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||||
|
|
||||||
|
run 0
|
||||||
|
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||||
|
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||||
|
Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||||
|
0 0 -6.0419499 -4.2737827 -4.2865535 -4.2176976 -4.3170971
|
||||||
|
Loop time of 3.11833e-06 on 3 procs for 0 steps with 500 atoms
|
||||||
|
|
||||||
|
117.6% CPU use with 3 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Other | | 3.118e-06 | | |100.00
|
||||||
|
|
||||||
|
Nlocal: 166.667 ave 178 max 150 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 1 0 1
|
||||||
|
Nghost: 0 ave 0 max 0 min
|
||||||
|
Histogram: 3 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 0 ave 0 max 0 min
|
||||||
|
Histogram: 3 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 0
|
||||||
|
Ave neighs/atom = 0
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
write_dump all custom dump.series.driver id type x y z f_1[1] f_1[2] f_1[3] modify sort id append yes
|
||||||
|
|
||||||
|
clear
|
||||||
|
|
||||||
|
next rho
|
||||||
|
|
||||||
|
jump SELF LOOP
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
read_data data.series.${rho}
|
||||||
|
read_data data.series.0.9
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (0 0 0) to (8.2207069 8.2207069 8.2207069)
|
||||||
|
3 by 1 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
500 atoms
|
||||||
|
reading velocities ...
|
||||||
|
500 velocities
|
||||||
|
read_data CPU = 0.003 seconds
|
||||||
|
|
||||||
|
displace_atoms all random 0.1 0.1 0.1 48294
|
||||||
|
Displacing atoms ...
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
fix 1 all mdi/qm add no virial yes connect no
|
||||||
|
variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3
|
||||||
|
|
||||||
|
thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||||
|
|
||||||
|
run 0
|
||||||
|
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||||
|
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||||
|
Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||||
|
0 0 -6.4477578 -1.5268553 -1.5717034 -1.568693 -1.4401696
|
||||||
|
Loop time of 2.85467e-06 on 3 procs for 0 steps with 500 atoms
|
||||||
|
|
||||||
|
140.1% CPU use with 3 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Other | | 2.855e-06 | | |100.00
|
||||||
|
|
||||||
|
Nlocal: 166.667 ave 181 max 150 min
|
||||||
|
Histogram: 1 0 0 0 0 0 1 0 0 1
|
||||||
|
Nghost: 0 ave 0 max 0 min
|
||||||
|
Histogram: 3 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 0 ave 0 max 0 min
|
||||||
|
Histogram: 3 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 0
|
||||||
|
Ave neighs/atom = 0
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
write_dump all custom dump.series.driver id type x y z f_1[1] f_1[2] f_1[3] modify sort id append yes
|
||||||
|
|
||||||
|
clear
|
||||||
|
|
||||||
|
next rho
|
||||||
|
|
||||||
|
jump SELF LOOP
|
||||||
|
|
||||||
|
mdi exit
|
||||||
|
Total wall time: 0:00:00
|
||||||
212
examples/mdi/log.17Jun22.series.driver.plugin.1
Normal file
212
examples/mdi/log.17Jun22.series.driver.plugin.1
Normal file
@ -0,0 +1,212 @@
|
|||||||
|
LAMMPS (2 Jun 2022)
|
||||||
|
# 3d Lennard-Jones melt - MDI driver script
|
||||||
|
|
||||||
|
variable x index 5
|
||||||
|
variable y index 5
|
||||||
|
variable z index 5
|
||||||
|
|
||||||
|
variable rho index 0.7 0.8 0.9
|
||||||
|
|
||||||
|
label LOOP
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
read_data data.series.${rho}
|
||||||
|
read_data data.series.0.7
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (0 0 0) to (8.9390354 8.9390354 8.9390354)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
500 atoms
|
||||||
|
reading velocities ...
|
||||||
|
500 velocities
|
||||||
|
read_data CPU = 0.004 seconds
|
||||||
|
|
||||||
|
displace_atoms all random 0.1 0.1 0.1 48294
|
||||||
|
Displacing atoms ...
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
fix 1 all mdi/qm add no virial yes
|
||||||
|
variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3
|
||||||
|
|
||||||
|
thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||||
|
|
||||||
|
mdi plugin lammps mdi "-role ENGINE -name LMP2 -method LINK" infile in.series.engine extra "-log log.series.engine.plugin" command "run 0"
|
||||||
|
run 0
|
||||||
|
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||||
|
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||||
|
Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||||
|
0 0 -5.200819 -4.5647906 -4.5444385 -4.5699966 -4.5799366
|
||||||
|
Loop time of 2.359e-06 on 1 procs for 0 steps with 500 atoms
|
||||||
|
|
||||||
|
127.2% CPU use with 1 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Other | | 2.359e-06 | | |100.00
|
||||||
|
|
||||||
|
Nlocal: 500 ave 500 max 500 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 0 ave 0 max 0 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 0 ave 0 max 0 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 0
|
||||||
|
Ave neighs/atom = 0
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
write_dump all custom dump.series.driver.plugin id type x y z f_1[1] f_1[2] f_1[3] modify sort id append yes
|
||||||
|
|
||||||
|
clear
|
||||||
|
|
||||||
|
next rho
|
||||||
|
|
||||||
|
jump SELF LOOP
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
read_data data.series.${rho}
|
||||||
|
read_data data.series.0.8
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (0 0 0) to (8.5498797 8.5498797 8.5498797)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
500 atoms
|
||||||
|
reading velocities ...
|
||||||
|
500 velocities
|
||||||
|
read_data CPU = 0.004 seconds
|
||||||
|
|
||||||
|
displace_atoms all random 0.1 0.1 0.1 48294
|
||||||
|
Displacing atoms ...
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
fix 1 all mdi/qm add no virial yes
|
||||||
|
variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3
|
||||||
|
|
||||||
|
thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||||
|
|
||||||
|
mdi plugin lammps mdi "-role ENGINE -name LMP2 -method LINK" infile in.series.engine extra "-log log.series.engine.plugin" command "run 0"
|
||||||
|
run 0
|
||||||
|
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||||
|
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||||
|
Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||||
|
0 0 -6.0419499 -4.2737827 -4.2865535 -4.2176976 -4.3170971
|
||||||
|
Loop time of 1.468e-06 on 1 procs for 0 steps with 500 atoms
|
||||||
|
|
||||||
|
204.4% CPU use with 1 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Other | | 1.468e-06 | | |100.00
|
||||||
|
|
||||||
|
Nlocal: 500 ave 500 max 500 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 0 ave 0 max 0 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 0 ave 0 max 0 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 0
|
||||||
|
Ave neighs/atom = 0
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
write_dump all custom dump.series.driver.plugin id type x y z f_1[1] f_1[2] f_1[3] modify sort id append yes
|
||||||
|
|
||||||
|
clear
|
||||||
|
|
||||||
|
next rho
|
||||||
|
|
||||||
|
jump SELF LOOP
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
read_data data.series.${rho}
|
||||||
|
read_data data.series.0.9
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (0 0 0) to (8.2207069 8.2207069 8.2207069)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
500 atoms
|
||||||
|
reading velocities ...
|
||||||
|
500 velocities
|
||||||
|
read_data CPU = 0.003 seconds
|
||||||
|
|
||||||
|
displace_atoms all random 0.1 0.1 0.1 48294
|
||||||
|
Displacing atoms ...
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
fix 1 all mdi/qm add no virial yes
|
||||||
|
variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3
|
||||||
|
|
||||||
|
thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||||
|
|
||||||
|
mdi plugin lammps mdi "-role ENGINE -name LMP2 -method LINK" infile in.series.engine extra "-log log.series.engine.plugin" command "run 0"
|
||||||
|
run 0
|
||||||
|
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||||
|
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||||
|
Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||||
|
0 0 -6.4477578 -1.5268553 -1.5717034 -1.568693 -1.4401696
|
||||||
|
Loop time of 1.378e-06 on 1 procs for 0 steps with 500 atoms
|
||||||
|
|
||||||
|
145.1% CPU use with 1 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Other | | 1.378e-06 | | |100.00
|
||||||
|
|
||||||
|
Nlocal: 500 ave 500 max 500 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 0 ave 0 max 0 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 0 ave 0 max 0 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 0
|
||||||
|
Ave neighs/atom = 0
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
write_dump all custom dump.series.driver.plugin id type x y z f_1[1] f_1[2] f_1[3] modify sort id append yes
|
||||||
|
|
||||||
|
clear
|
||||||
|
|
||||||
|
next rho
|
||||||
|
|
||||||
|
jump SELF LOOP
|
||||||
|
Total wall time: 0:00:00
|
||||||
212
examples/mdi/log.17Jun22.series.driver.plugin.3
Normal file
212
examples/mdi/log.17Jun22.series.driver.plugin.3
Normal file
@ -0,0 +1,212 @@
|
|||||||
|
LAMMPS (2 Jun 2022)
|
||||||
|
# 3d Lennard-Jones melt - MDI driver script
|
||||||
|
|
||||||
|
variable x index 5
|
||||||
|
variable y index 5
|
||||||
|
variable z index 5
|
||||||
|
|
||||||
|
variable rho index 0.7 0.8 0.9
|
||||||
|
|
||||||
|
label LOOP
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
read_data data.series.${rho}
|
||||||
|
read_data data.series.0.7
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (0 0 0) to (8.9390354 8.9390354 8.9390354)
|
||||||
|
1 by 1 by 3 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
500 atoms
|
||||||
|
reading velocities ...
|
||||||
|
500 velocities
|
||||||
|
read_data CPU = 0.004 seconds
|
||||||
|
|
||||||
|
displace_atoms all random 0.1 0.1 0.1 48294
|
||||||
|
Displacing atoms ...
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
fix 1 all mdi/qm add no virial yes
|
||||||
|
variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3
|
||||||
|
|
||||||
|
thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||||
|
|
||||||
|
mdi plugin lammps mdi "-role ENGINE -name LMP2 -method LINK" infile in.series.engine extra "-log log.series.engine.plugin" command "run 0"
|
||||||
|
run 0
|
||||||
|
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||||
|
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||||
|
Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||||
|
0 0 -5.200819 -4.5647906 -4.5444385 -4.5699966 -4.5799366
|
||||||
|
Loop time of 3.50867e-06 on 3 procs for 0 steps with 500 atoms
|
||||||
|
|
||||||
|
114.0% CPU use with 3 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Other | | 3.509e-06 | | |100.00
|
||||||
|
|
||||||
|
Nlocal: 166.667 ave 177 max 150 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 1 1
|
||||||
|
Nghost: 0 ave 0 max 0 min
|
||||||
|
Histogram: 3 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 0 ave 0 max 0 min
|
||||||
|
Histogram: 3 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 0
|
||||||
|
Ave neighs/atom = 0
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
write_dump all custom dump.series.driver.plugin id type x y z f_1[1] f_1[2] f_1[3] modify sort id append yes
|
||||||
|
|
||||||
|
clear
|
||||||
|
|
||||||
|
next rho
|
||||||
|
|
||||||
|
jump SELF LOOP
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
read_data data.series.${rho}
|
||||||
|
read_data data.series.0.8
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (0 0 0) to (8.5498797 8.5498797 8.5498797)
|
||||||
|
1 by 1 by 3 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
500 atoms
|
||||||
|
reading velocities ...
|
||||||
|
500 velocities
|
||||||
|
read_data CPU = 0.003 seconds
|
||||||
|
|
||||||
|
displace_atoms all random 0.1 0.1 0.1 48294
|
||||||
|
Displacing atoms ...
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
fix 1 all mdi/qm add no virial yes
|
||||||
|
variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3
|
||||||
|
|
||||||
|
thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||||
|
|
||||||
|
mdi plugin lammps mdi "-role ENGINE -name LMP2 -method LINK" infile in.series.engine extra "-log log.series.engine.plugin" command "run 0"
|
||||||
|
run 0
|
||||||
|
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||||
|
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||||
|
Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||||
|
0 0 -6.0419499 -4.2737827 -4.2865535 -4.2176976 -4.3170971
|
||||||
|
Loop time of 3.225e-06 on 3 procs for 0 steps with 500 atoms
|
||||||
|
|
||||||
|
82.7% CPU use with 3 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Other | | 3.225e-06 | | |100.00
|
||||||
|
|
||||||
|
Nlocal: 166.667 ave 178 max 150 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 1 0 1
|
||||||
|
Nghost: 0 ave 0 max 0 min
|
||||||
|
Histogram: 3 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 0 ave 0 max 0 min
|
||||||
|
Histogram: 3 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 0
|
||||||
|
Ave neighs/atom = 0
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
write_dump all custom dump.series.driver.plugin id type x y z f_1[1] f_1[2] f_1[3] modify sort id append yes
|
||||||
|
|
||||||
|
clear
|
||||||
|
|
||||||
|
next rho
|
||||||
|
|
||||||
|
jump SELF LOOP
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
read_data data.series.${rho}
|
||||||
|
read_data data.series.0.9
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (0 0 0) to (8.2207069 8.2207069 8.2207069)
|
||||||
|
3 by 1 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
500 atoms
|
||||||
|
reading velocities ...
|
||||||
|
500 velocities
|
||||||
|
read_data CPU = 0.003 seconds
|
||||||
|
|
||||||
|
displace_atoms all random 0.1 0.1 0.1 48294
|
||||||
|
Displacing atoms ...
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
fix 1 all mdi/qm add no virial yes
|
||||||
|
variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3
|
||||||
|
|
||||||
|
thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||||
|
|
||||||
|
mdi plugin lammps mdi "-role ENGINE -name LMP2 -method LINK" infile in.series.engine extra "-log log.series.engine.plugin" command "run 0"
|
||||||
|
run 0
|
||||||
|
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||||
|
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||||
|
Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||||
|
0 0 -6.4477578 -1.5268553 -1.5717034 -1.568693 -1.4401696
|
||||||
|
Loop time of 2.713e-06 on 3 procs for 0 steps with 500 atoms
|
||||||
|
|
||||||
|
98.3% CPU use with 3 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Other | | 2.713e-06 | | |100.00
|
||||||
|
|
||||||
|
Nlocal: 166.667 ave 181 max 150 min
|
||||||
|
Histogram: 1 0 0 0 0 0 1 0 0 1
|
||||||
|
Nghost: 0 ave 0 max 0 min
|
||||||
|
Histogram: 3 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 0 ave 0 max 0 min
|
||||||
|
Histogram: 3 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 0
|
||||||
|
Ave neighs/atom = 0
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
write_dump all custom dump.series.driver.plugin id type x y z f_1[1] f_1[2] f_1[3] modify sort id append yes
|
||||||
|
|
||||||
|
clear
|
||||||
|
|
||||||
|
next rho
|
||||||
|
|
||||||
|
jump SELF LOOP
|
||||||
|
Total wall time: 0:00:00
|
||||||
213
examples/mdi/log.17Jun22.series.driver.tcp.1
Normal file
213
examples/mdi/log.17Jun22.series.driver.tcp.1
Normal file
@ -0,0 +1,213 @@
|
|||||||
|
LAMMPS (2 Jun 2022)
|
||||||
|
# 3d Lennard-Jones melt - MDI driver script
|
||||||
|
|
||||||
|
variable x index 5
|
||||||
|
variable y index 5
|
||||||
|
variable z index 5
|
||||||
|
|
||||||
|
variable rho index 0.7 0.8 0.9
|
||||||
|
|
||||||
|
mdi connect
|
||||||
|
|
||||||
|
label LOOP
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
read_data data.series.${rho}
|
||||||
|
read_data data.series.0.7
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (0 0 0) to (8.9390354 8.9390354 8.9390354)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
500 atoms
|
||||||
|
reading velocities ...
|
||||||
|
500 velocities
|
||||||
|
read_data CPU = 0.005 seconds
|
||||||
|
|
||||||
|
displace_atoms all random 0.1 0.1 0.1 48294
|
||||||
|
Displacing atoms ...
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
fix 1 all mdi/qm add no virial yes connect no
|
||||||
|
variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3
|
||||||
|
|
||||||
|
thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||||
|
|
||||||
|
run 0
|
||||||
|
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||||
|
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||||
|
Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||||
|
0 0 -5.200819 -4.5647906 -4.5444385 -4.5699966 -4.5799366
|
||||||
|
Loop time of 3.017e-06 on 1 procs for 0 steps with 500 atoms
|
||||||
|
|
||||||
|
99.4% CPU use with 1 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Other | | 3.017e-06 | | |100.00
|
||||||
|
|
||||||
|
Nlocal: 500 ave 500 max 500 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 0 ave 0 max 0 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 0 ave 0 max 0 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 0
|
||||||
|
Ave neighs/atom = 0
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
write_dump all custom dump.series.driver id type x y z f_1[1] f_1[2] f_1[3] modify sort id append yes
|
||||||
|
|
||||||
|
clear
|
||||||
|
|
||||||
|
next rho
|
||||||
|
|
||||||
|
jump SELF LOOP
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
read_data data.series.${rho}
|
||||||
|
read_data data.series.0.8
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (0 0 0) to (8.5498797 8.5498797 8.5498797)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
500 atoms
|
||||||
|
reading velocities ...
|
||||||
|
500 velocities
|
||||||
|
read_data CPU = 0.005 seconds
|
||||||
|
|
||||||
|
displace_atoms all random 0.1 0.1 0.1 48294
|
||||||
|
Displacing atoms ...
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
fix 1 all mdi/qm add no virial yes connect no
|
||||||
|
variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3
|
||||||
|
|
||||||
|
thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||||
|
|
||||||
|
run 0
|
||||||
|
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||||
|
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||||
|
Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||||
|
0 0 -6.0419499 -4.2737827 -4.2865535 -4.2176976 -4.3170971
|
||||||
|
Loop time of 1.977e-06 on 1 procs for 0 steps with 500 atoms
|
||||||
|
|
||||||
|
101.2% CPU use with 1 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Other | | 1.977e-06 | | |100.00
|
||||||
|
|
||||||
|
Nlocal: 500 ave 500 max 500 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 0 ave 0 max 0 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 0 ave 0 max 0 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 0
|
||||||
|
Ave neighs/atom = 0
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
write_dump all custom dump.series.driver id type x y z f_1[1] f_1[2] f_1[3] modify sort id append yes
|
||||||
|
|
||||||
|
clear
|
||||||
|
|
||||||
|
next rho
|
||||||
|
|
||||||
|
jump SELF LOOP
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
read_data data.series.${rho}
|
||||||
|
read_data data.series.0.9
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (0 0 0) to (8.2207069 8.2207069 8.2207069)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
500 atoms
|
||||||
|
reading velocities ...
|
||||||
|
500 velocities
|
||||||
|
read_data CPU = 0.004 seconds
|
||||||
|
|
||||||
|
displace_atoms all random 0.1 0.1 0.1 48294
|
||||||
|
Displacing atoms ...
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
fix 1 all mdi/qm add no virial yes connect no
|
||||||
|
variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3
|
||||||
|
|
||||||
|
thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||||
|
|
||||||
|
run 0
|
||||||
|
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||||
|
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||||
|
Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||||
|
0 0 -6.4477578 -1.5268553 -1.5717034 -1.568693 -1.4401696
|
||||||
|
Loop time of 2.042e-06 on 1 procs for 0 steps with 500 atoms
|
||||||
|
|
||||||
|
97.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Other | | 2.042e-06 | | |100.00
|
||||||
|
|
||||||
|
Nlocal: 500 ave 500 max 500 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 0 ave 0 max 0 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 0 ave 0 max 0 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 0
|
||||||
|
Ave neighs/atom = 0
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
write_dump all custom dump.series.driver id type x y z f_1[1] f_1[2] f_1[3] modify sort id append yes
|
||||||
|
|
||||||
|
clear
|
||||||
|
|
||||||
|
next rho
|
||||||
|
|
||||||
|
jump SELF LOOP
|
||||||
|
|
||||||
|
mdi exit
|
||||||
|
Total wall time: 0:00:00
|
||||||
213
examples/mdi/log.17Jun22.series.driver.tcp.3
Normal file
213
examples/mdi/log.17Jun22.series.driver.tcp.3
Normal file
@ -0,0 +1,213 @@
|
|||||||
|
LAMMPS (2 Jun 2022)
|
||||||
|
# 3d Lennard-Jones melt - MDI driver script
|
||||||
|
|
||||||
|
variable x index 5
|
||||||
|
variable y index 5
|
||||||
|
variable z index 5
|
||||||
|
|
||||||
|
variable rho index 0.7 0.8 0.9
|
||||||
|
|
||||||
|
mdi connect
|
||||||
|
|
||||||
|
label LOOP
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
read_data data.series.${rho}
|
||||||
|
read_data data.series.0.7
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (0 0 0) to (8.9390354 8.9390354 8.9390354)
|
||||||
|
1 by 1 by 3 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
500 atoms
|
||||||
|
reading velocities ...
|
||||||
|
500 velocities
|
||||||
|
read_data CPU = 0.005 seconds
|
||||||
|
|
||||||
|
displace_atoms all random 0.1 0.1 0.1 48294
|
||||||
|
Displacing atoms ...
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
fix 1 all mdi/qm add no virial yes connect no
|
||||||
|
variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3
|
||||||
|
|
||||||
|
thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||||
|
|
||||||
|
run 0
|
||||||
|
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||||
|
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||||
|
Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||||
|
0 0 -5.200819 -4.5647906 -4.5444385 -4.5699966 -4.5799366
|
||||||
|
Loop time of 9.08933e-06 on 3 procs for 0 steps with 500 atoms
|
||||||
|
|
||||||
|
95.3% CPU use with 3 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Other | | 9.089e-06 | | |100.00
|
||||||
|
|
||||||
|
Nlocal: 166.667 ave 177 max 150 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 1 1
|
||||||
|
Nghost: 0 ave 0 max 0 min
|
||||||
|
Histogram: 3 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 0 ave 0 max 0 min
|
||||||
|
Histogram: 3 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 0
|
||||||
|
Ave neighs/atom = 0
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
write_dump all custom dump.series.driver id type x y z f_1[1] f_1[2] f_1[3] modify sort id append yes
|
||||||
|
|
||||||
|
clear
|
||||||
|
|
||||||
|
next rho
|
||||||
|
|
||||||
|
jump SELF LOOP
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
read_data data.series.${rho}
|
||||||
|
read_data data.series.0.8
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (0 0 0) to (8.5498797 8.5498797 8.5498797)
|
||||||
|
1 by 1 by 3 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
500 atoms
|
||||||
|
reading velocities ...
|
||||||
|
500 velocities
|
||||||
|
read_data CPU = 0.005 seconds
|
||||||
|
|
||||||
|
displace_atoms all random 0.1 0.1 0.1 48294
|
||||||
|
Displacing atoms ...
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
fix 1 all mdi/qm add no virial yes connect no
|
||||||
|
variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3
|
||||||
|
|
||||||
|
thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||||
|
|
||||||
|
run 0
|
||||||
|
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||||
|
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||||
|
Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||||
|
0 0 -6.0419499 -4.2737827 -4.2865535 -4.2176976 -4.3170971
|
||||||
|
Loop time of 3.63567e-06 on 3 procs for 0 steps with 500 atoms
|
||||||
|
|
||||||
|
100.9% CPU use with 3 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Other | | 3.636e-06 | | |100.00
|
||||||
|
|
||||||
|
Nlocal: 166.667 ave 178 max 150 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 1 0 1
|
||||||
|
Nghost: 0 ave 0 max 0 min
|
||||||
|
Histogram: 3 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 0 ave 0 max 0 min
|
||||||
|
Histogram: 3 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 0
|
||||||
|
Ave neighs/atom = 0
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
write_dump all custom dump.series.driver id type x y z f_1[1] f_1[2] f_1[3] modify sort id append yes
|
||||||
|
|
||||||
|
clear
|
||||||
|
|
||||||
|
next rho
|
||||||
|
|
||||||
|
jump SELF LOOP
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
read_data data.series.${rho}
|
||||||
|
read_data data.series.0.9
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (0 0 0) to (8.2207069 8.2207069 8.2207069)
|
||||||
|
3 by 1 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
500 atoms
|
||||||
|
reading velocities ...
|
||||||
|
500 velocities
|
||||||
|
read_data CPU = 0.004 seconds
|
||||||
|
|
||||||
|
displace_atoms all random 0.1 0.1 0.1 48294
|
||||||
|
Displacing atoms ...
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
fix 1 all mdi/qm add no virial yes connect no
|
||||||
|
variable evirial equal (f_1[1]+f_1[2]+f_1[3])/3
|
||||||
|
|
||||||
|
thermo_style custom step temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||||
|
|
||||||
|
run 0
|
||||||
|
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||||
|
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2127)
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:210)
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 2.297 | 2.297 | 2.297 Mbytes
|
||||||
|
Step Temp f_1 v_evirial f_1[1] f_1[2] f_1[3]
|
||||||
|
0 0 -6.4477578 -1.5268553 -1.5717034 -1.568693 -1.4401696
|
||||||
|
Loop time of 3.806e-06 on 3 procs for 0 steps with 500 atoms
|
||||||
|
|
||||||
|
105.1% CPU use with 3 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Other | | 3.806e-06 | | |100.00
|
||||||
|
|
||||||
|
Nlocal: 166.667 ave 181 max 150 min
|
||||||
|
Histogram: 1 0 0 0 0 0 1 0 0 1
|
||||||
|
Nghost: 0 ave 0 max 0 min
|
||||||
|
Histogram: 3 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 0 ave 0 max 0 min
|
||||||
|
Histogram: 3 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 0
|
||||||
|
Ave neighs/atom = 0
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
write_dump all custom dump.series.driver id type x y z f_1[1] f_1[2] f_1[3] modify sort id append yes
|
||||||
|
|
||||||
|
clear
|
||||||
|
|
||||||
|
next rho
|
||||||
|
|
||||||
|
jump SELF LOOP
|
||||||
|
|
||||||
|
mdi exit
|
||||||
|
Total wall time: 0:00:00
|
||||||
58
examples/mdi/log.17Jun22.series.engine.mpi.1
Normal file
58
examples/mdi/log.17Jun22.series.engine.mpi.1
Normal file
@ -0,0 +1,58 @@
|
|||||||
|
LAMMPS (2 Jun 2022)
|
||||||
|
# 3d Lennard-Jones melt - MDI engine script
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
lattice fcc 1.0
|
||||||
|
Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011
|
||||||
|
region box block 0 1 0 1 0 1
|
||||||
|
create_box 1 box
|
||||||
|
Created orthogonal box = (0 0 0) to (1.5874011 1.5874011 1.5874011)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
mass 1 1.0
|
||||||
|
|
||||||
|
pair_style lj/cut 2.5
|
||||||
|
pair_coeff 1 1 1.0 1.0 2.5
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
mdi engine
|
||||||
|
delete_atoms group all
|
||||||
|
Deleted 0 atoms, new total = 0
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||||
|
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 0 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 2.8
|
||||||
|
ghost atom cutoff = 2.8
|
||||||
|
binsize = 1.4, bins = 7 7 7
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair lj/cut, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/atomonly/newton
|
||||||
|
stencil: half/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 3.137 | 3.137 | 3.137 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 0 -5.200819 0 -5.200819 -4.5647906
|
||||||
|
delete_atoms group all
|
||||||
|
Deleted 500 atoms, new total = 0
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||||
|
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 3.137 | 3.137 | 3.137 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 0 -6.0419499 0 -6.0419499 -4.2737827
|
||||||
|
delete_atoms group all
|
||||||
|
Deleted 500 atoms, new total = 0
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||||
|
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 3.137 | 3.137 | 3.137 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 0 -6.4477578 0 -6.4477578 -1.5268553
|
||||||
|
Total wall time: 0:00:00
|
||||||
58
examples/mdi/log.17Jun22.series.engine.mpi.4
Normal file
58
examples/mdi/log.17Jun22.series.engine.mpi.4
Normal file
@ -0,0 +1,58 @@
|
|||||||
|
LAMMPS (2 Jun 2022)
|
||||||
|
# 3d Lennard-Jones melt - MDI engine script
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
lattice fcc 1.0
|
||||||
|
Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011
|
||||||
|
region box block 0 1 0 1 0 1
|
||||||
|
create_box 1 box
|
||||||
|
Created orthogonal box = (0 0 0) to (1.5874011 1.5874011 1.5874011)
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
mass 1 1.0
|
||||||
|
|
||||||
|
pair_style lj/cut 2.5
|
||||||
|
pair_coeff 1 1 1.0 1.0 2.5
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
mdi engine
|
||||||
|
delete_atoms group all
|
||||||
|
Deleted 0 atoms, new total = 0
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||||
|
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 0 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 2.8
|
||||||
|
ghost atom cutoff = 2.8
|
||||||
|
binsize = 1.4, bins = 7 7 7
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair lj/cut, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/atomonly/newton
|
||||||
|
stencil: half/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 3.103 | 3.103 | 3.103 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 0 -5.200819 0 -5.200819 -4.5647906
|
||||||
|
delete_atoms group all
|
||||||
|
Deleted 500 atoms, new total = 0
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||||
|
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 3.103 | 3.103 | 3.103 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 0 -6.0419499 0 -6.0419499 -4.2737827
|
||||||
|
delete_atoms group all
|
||||||
|
Deleted 500 atoms, new total = 0
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||||
|
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 3.103 | 3.103 | 3.103 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 0 -6.4477578 0 -6.4477578 -1.5268553
|
||||||
|
Total wall time: 0:00:00
|
||||||
42
examples/mdi/log.17Jun22.series.engine.plugin.1
Normal file
42
examples/mdi/log.17Jun22.series.engine.plugin.1
Normal file
@ -0,0 +1,42 @@
|
|||||||
|
LAMMPS (2 Jun 2022)
|
||||||
|
# 3d Lennard-Jones melt - MDI engine script
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
lattice fcc 1.0
|
||||||
|
Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011
|
||||||
|
region box block 0 1 0 1 0 1
|
||||||
|
create_box 1 box
|
||||||
|
Created orthogonal box = (0 0 0) to (1.5874011 1.5874011 1.5874011)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
mass 1 1.0
|
||||||
|
|
||||||
|
pair_style lj/cut 2.5
|
||||||
|
pair_coeff 1 1 1.0 1.0 2.5
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
mdi engine
|
||||||
|
delete_atoms group all
|
||||||
|
Deleted 0 atoms, new total = 0
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||||
|
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 0 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 2.8
|
||||||
|
ghost atom cutoff = 2.8
|
||||||
|
binsize = 1.4, bins = 6 6 6
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair lj/cut, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/atomonly/newton
|
||||||
|
stencil: half/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 3.134 | 3.134 | 3.134 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 0 -6.4477578 0 -6.4477578 -1.5268553
|
||||||
|
Total wall time: 0:00:00
|
||||||
42
examples/mdi/log.17Jun22.series.engine.plugin.3
Normal file
42
examples/mdi/log.17Jun22.series.engine.plugin.3
Normal file
@ -0,0 +1,42 @@
|
|||||||
|
LAMMPS (2 Jun 2022)
|
||||||
|
# 3d Lennard-Jones melt - MDI engine script
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
lattice fcc 1.0
|
||||||
|
Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011
|
||||||
|
region box block 0 1 0 1 0 1
|
||||||
|
create_box 1 box
|
||||||
|
Created orthogonal box = (0 0 0) to (1.5874011 1.5874011 1.5874011)
|
||||||
|
1 by 1 by 3 MPI processor grid
|
||||||
|
mass 1 1.0
|
||||||
|
|
||||||
|
pair_style lj/cut 2.5
|
||||||
|
pair_coeff 1 1 1.0 1.0 2.5
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
mdi engine
|
||||||
|
delete_atoms group all
|
||||||
|
Deleted 0 atoms, new total = 0
|
||||||
|
3 by 1 by 1 MPI processor grid
|
||||||
|
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||||
|
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 0 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 2.8
|
||||||
|
ghost atom cutoff = 2.8
|
||||||
|
binsize = 1.4, bins = 6 6 6
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair lj/cut, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/atomonly/newton
|
||||||
|
stencil: half/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 3.104 | 3.105 | 3.107 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 0 -6.4477578 0 -6.4477578 -1.5268553
|
||||||
|
Total wall time: 0:00:00
|
||||||
58
examples/mdi/log.17Jun22.series.engine.tcp.1
Normal file
58
examples/mdi/log.17Jun22.series.engine.tcp.1
Normal file
@ -0,0 +1,58 @@
|
|||||||
|
LAMMPS (2 Jun 2022)
|
||||||
|
# 3d Lennard-Jones melt - MDI engine script
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
lattice fcc 1.0
|
||||||
|
Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011
|
||||||
|
region box block 0 1 0 1 0 1
|
||||||
|
create_box 1 box
|
||||||
|
Created orthogonal box = (0 0 0) to (1.5874011 1.5874011 1.5874011)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
mass 1 1.0
|
||||||
|
|
||||||
|
pair_style lj/cut 2.5
|
||||||
|
pair_coeff 1 1 1.0 1.0 2.5
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
mdi engine
|
||||||
|
delete_atoms group all
|
||||||
|
Deleted 0 atoms, new total = 0
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||||
|
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 0 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 2.8
|
||||||
|
ghost atom cutoff = 2.8
|
||||||
|
binsize = 1.4, bins = 7 7 7
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair lj/cut, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/atomonly/newton
|
||||||
|
stencil: half/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 3.137 | 3.137 | 3.137 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 0 -5.200819 0 -5.200819 -4.5647906
|
||||||
|
delete_atoms group all
|
||||||
|
Deleted 500 atoms, new total = 0
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||||
|
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 3.137 | 3.137 | 3.137 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 0 -6.0419499 0 -6.0419499 -4.2737827
|
||||||
|
delete_atoms group all
|
||||||
|
Deleted 500 atoms, new total = 0
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||||
|
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 3.137 | 3.137 | 3.137 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 0 -6.4477578 0 -6.4477578 -1.5268553
|
||||||
|
Total wall time: 0:00:00
|
||||||
58
examples/mdi/log.17Jun22.series.engine.tcp.4
Normal file
58
examples/mdi/log.17Jun22.series.engine.tcp.4
Normal file
@ -0,0 +1,58 @@
|
|||||||
|
LAMMPS (2 Jun 2022)
|
||||||
|
# 3d Lennard-Jones melt - MDI engine script
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
lattice fcc 1.0
|
||||||
|
Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011
|
||||||
|
region box block 0 1 0 1 0 1
|
||||||
|
create_box 1 box
|
||||||
|
Created orthogonal box = (0 0 0) to (1.5874011 1.5874011 1.5874011)
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
mass 1 1.0
|
||||||
|
|
||||||
|
pair_style lj/cut 2.5
|
||||||
|
pair_coeff 1 1 1.0 1.0 2.5
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
mdi engine
|
||||||
|
delete_atoms group all
|
||||||
|
Deleted 0 atoms, new total = 0
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||||
|
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 0 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 2.8
|
||||||
|
ghost atom cutoff = 2.8
|
||||||
|
binsize = 1.4, bins = 7 7 7
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair lj/cut, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/atomonly/newton
|
||||||
|
stencil: half/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 3.103 | 3.103 | 3.103 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 0 -5.200819 0 -5.200819 -4.5647906
|
||||||
|
delete_atoms group all
|
||||||
|
Deleted 500 atoms, new total = 0
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||||
|
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 3.103 | 3.103 | 3.103 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 0 -6.0419499 0 -6.0419499 -4.2737827
|
||||||
|
delete_atoms group all
|
||||||
|
Deleted 500 atoms, new total = 0
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||||
|
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 3.103 | 3.103 | 3.103 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 0 -6.4477578 0 -6.4477578 -1.5268553
|
||||||
|
Total wall time: 0:00:00
|
||||||
82
examples/mdi/log.17Jun22.snapshot.alone.1
Normal file
82
examples/mdi/log.17Jun22.snapshot.alone.1
Normal file
@ -0,0 +1,82 @@
|
|||||||
|
LAMMPS (2 Jun 2022)
|
||||||
|
# 3d Lennard-Jones melt - MDI driver script
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
read_data data.snapshot
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
500 atoms
|
||||||
|
reading velocities ...
|
||||||
|
500 velocities
|
||||||
|
read_data CPU = 0.005 seconds
|
||||||
|
|
||||||
|
velocity all create 1.44 87287 loop geom
|
||||||
|
|
||||||
|
pair_style lj/cut 2.5
|
||||||
|
pair_coeff 1 1 1.0 1.0 2.5
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
fix 1 all nve
|
||||||
|
|
||||||
|
compute 1 all pressure NULL virial
|
||||||
|
|
||||||
|
thermo_style custom step temp pe c_1 c_1[1] c_1[2] c_1[3]
|
||||||
|
|
||||||
|
thermo 100
|
||||||
|
|
||||||
|
dump 1 all custom 100 dump.snapshot.alone id type x y z fx fy fz
|
||||||
|
dump_modify 1 sort id
|
||||||
|
|
||||||
|
run 300
|
||||||
|
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 0 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 2.8
|
||||||
|
ghost atom cutoff = 2.8
|
||||||
|
binsize = 1.4, bins = 6 6 6
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair lj/cut, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/atomonly/newton
|
||||||
|
stencil: half/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 4.461 | 4.461 | 4.461 Mbytes
|
||||||
|
Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3]
|
||||||
|
0 1.44 -6.7733681 -6.2353173 -6.2353173 -6.2353173 -6.2353173
|
||||||
|
100 0.75627629 -5.7579933 -0.4184022 -0.48020229 -0.33571704 -0.43928726
|
||||||
|
200 0.75199164 -5.752864 -0.40524506 -0.51524578 -0.27940441 -0.42108499
|
||||||
|
300 0.75219392 -5.7527975 -0.41843911 -0.24280603 -0.42189159 -0.59061972
|
||||||
|
Loop time of 0.159268 on 1 procs for 300 steps with 500 atoms
|
||||||
|
|
||||||
|
Performance: 813725.152 tau/day, 1883.623 timesteps/s
|
||||||
|
99.5% CPU use with 1 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.10659 | 0.10659 | 0.10659 | 0.0 | 66.93
|
||||||
|
Neigh | 0.038637 | 0.038637 | 0.038637 | 0.0 | 24.26
|
||||||
|
Comm | 0.0053144 | 0.0053144 | 0.0053144 | 0.0 | 3.34
|
||||||
|
Output | 0.0048583 | 0.0048583 | 0.0048583 | 0.0 | 3.05
|
||||||
|
Modify | 0.002043 | 0.002043 | 0.002043 | 0.0 | 1.28
|
||||||
|
Other | | 0.001821 | | | 1.14
|
||||||
|
|
||||||
|
Nlocal: 500 ave 500 max 500 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 1898 ave 1898 max 1898 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 18744 ave 18744 max 18744 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 18744
|
||||||
|
Ave neighs/atom = 37.488
|
||||||
|
Neighbor list builds = 31
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:00
|
||||||
105
examples/mdi/log.17Jun22.snapshot.driver.mpi.1
Normal file
105
examples/mdi/log.17Jun22.snapshot.driver.mpi.1
Normal file
@ -0,0 +1,105 @@
|
|||||||
|
LAMMPS (2 Jun 2022)
|
||||||
|
# 3d Lennard-Jones melt - MDI driver script
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
read_data data.snapshot
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
500 atoms
|
||||||
|
reading velocities ...
|
||||||
|
500 velocities
|
||||||
|
read_data CPU = 0.003 seconds
|
||||||
|
|
||||||
|
velocity all create 1.44 87287 loop geom
|
||||||
|
|
||||||
|
pair_style lj/cut 2.5
|
||||||
|
pair_coeff 1 1 1.0 1.0 2.5
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
fix 1 all nve
|
||||||
|
|
||||||
|
fix 2 all mdi/qm add no every 100 virial yes
|
||||||
|
|
||||||
|
compute 1 all pressure NULL virial
|
||||||
|
variable evirial equal (f_2[1]+f_2[2]+f_2[3])/3
|
||||||
|
|
||||||
|
thermo_style custom step temp pe c_1 c_1[1] c_1[2] c_1[3]
|
||||||
|
|
||||||
|
thermo 100
|
||||||
|
|
||||||
|
dump 1 all custom 100 dump.snapshot.driver id type x y z f_2[1] f_2[2] f_2[3]
|
||||||
|
dump_modify 1 sort id
|
||||||
|
|
||||||
|
run 300 pre no post no every 100 "print 'QM eng = $(f_2/atoms)'" "print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'"
|
||||||
|
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 0 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 2.8
|
||||||
|
ghost atom cutoff = 2.8
|
||||||
|
binsize = 1.4, bins = 6 6 6
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair lj/cut, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/atomonly/newton
|
||||||
|
stencil: half/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 4.461 | 4.461 | 4.461 Mbytes
|
||||||
|
Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3]
|
||||||
|
0 1.44 -6.7733681 -6.2353173 -6.2353173 -6.2353173 -6.2353173
|
||||||
|
100 0.75627629 -5.7579933 -0.4184022 -0.48020229 -0.33571704 -0.43928726
|
||||||
|
Loop time of 0.052449 on 1 procs for 100 steps with 500 atoms
|
||||||
|
|
||||||
|
print 'QM eng = $(f_2/atoms)'
|
||||||
|
QM eng = -5.7579933325734575789
|
||||||
|
print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'
|
||||||
|
QM virial = -0.41840219542566597921 -0.48020228608206266818 -0.33571704057969975477 -0.43928725961523629184
|
||||||
|
Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3]
|
||||||
|
100 0.75627629 -5.7579933 -0.4184022 -0.48020229 -0.33571704 -0.43928726
|
||||||
|
200 0.75199164 -5.752864 -0.40524506 -0.51524578 -0.27940441 -0.42108499
|
||||||
|
Loop time of 0.0497171 on 1 procs for 100 steps with 500 atoms
|
||||||
|
|
||||||
|
print 'QM eng = $(f_2/atoms)'
|
||||||
|
QM eng = -5.7528640103266583949
|
||||||
|
print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'
|
||||||
|
QM virial = -0.40524505957306500292 -0.515245777483180456 -0.27940441114041408843 -0.42108499009560135251
|
||||||
|
Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3]
|
||||||
|
200 0.75199164 -5.752864 -0.40524506 -0.51524578 -0.27940441 -0.42108499
|
||||||
|
300 0.75219392 -5.7527975 -0.41843911 -0.24280603 -0.42189159 -0.59061972
|
||||||
|
Loop time of 0.0506296 on 1 procs for 100 steps with 500 atoms
|
||||||
|
|
||||||
|
Performance: 853255.432 tau/day, 1975.128 timesteps/s
|
||||||
|
100.0% CPU use with 1 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.032111 | 0.032111 | 0.032111 | 0.0 | 63.42
|
||||||
|
Neigh | 0.012403 | 0.012403 | 0.012403 | 0.0 | 24.50
|
||||||
|
Comm | 0.0016352 | 0.0016352 | 0.0016352 | 0.0 | 3.23
|
||||||
|
Output | 0.001556 | 0.001556 | 0.001556 | 0.0 | 3.07
|
||||||
|
Modify | 0.0023767 | 0.0023767 | 0.0023767 | 0.0 | 4.69
|
||||||
|
Other | | 0.0005478 | | | 1.08
|
||||||
|
|
||||||
|
Nlocal: 500 ave 500 max 500 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 1898 ave 1898 max 1898 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 18744 ave 18744 max 18744 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 18744
|
||||||
|
Ave neighs/atom = 37.488
|
||||||
|
Neighbor list builds = 31
|
||||||
|
Dangerous builds = 0
|
||||||
|
print 'QM eng = $(f_2/atoms)'
|
||||||
|
QM eng = -5.7527974697327088904
|
||||||
|
print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'
|
||||||
|
QM virial = -0.41843911315518900196 -0.24280603320322050043 -0.4218915869116203754 -0.59061971935072643536
|
||||||
|
Total wall time: 0:00:00
|
||||||
105
examples/mdi/log.17Jun22.snapshot.driver.mpi.3
Normal file
105
examples/mdi/log.17Jun22.snapshot.driver.mpi.3
Normal file
@ -0,0 +1,105 @@
|
|||||||
|
LAMMPS (2 Jun 2022)
|
||||||
|
# 3d Lennard-Jones melt - MDI driver script
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
read_data data.snapshot
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||||
|
1 by 1 by 3 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
500 atoms
|
||||||
|
reading velocities ...
|
||||||
|
500 velocities
|
||||||
|
read_data CPU = 0.004 seconds
|
||||||
|
|
||||||
|
velocity all create 1.44 87287 loop geom
|
||||||
|
|
||||||
|
pair_style lj/cut 2.5
|
||||||
|
pair_coeff 1 1 1.0 1.0 2.5
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
fix 1 all nve
|
||||||
|
|
||||||
|
fix 2 all mdi/qm add no every 100 virial yes
|
||||||
|
|
||||||
|
compute 1 all pressure NULL virial
|
||||||
|
variable evirial equal (f_2[1]+f_2[2]+f_2[3])/3
|
||||||
|
|
||||||
|
thermo_style custom step temp pe c_1 c_1[1] c_1[2] c_1[3]
|
||||||
|
|
||||||
|
thermo 100
|
||||||
|
|
||||||
|
dump 1 all custom 100 dump.snapshot.driver id type x y z f_2[1] f_2[2] f_2[3]
|
||||||
|
dump_modify 1 sort id
|
||||||
|
|
||||||
|
run 300 pre no post no every 100 "print 'QM eng = $(f_2/atoms)'" "print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'"
|
||||||
|
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 0 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 2.8
|
||||||
|
ghost atom cutoff = 2.8
|
||||||
|
binsize = 1.4, bins = 6 6 6
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair lj/cut, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/atomonly/newton
|
||||||
|
stencil: half/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 4.417 | 4.422 | 4.425 Mbytes
|
||||||
|
Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3]
|
||||||
|
0 1.44 -6.7733681 -6.2353173 -6.2353173 -6.2353173 -6.2353173
|
||||||
|
100 0.75627629 -5.7579933 -0.4184022 -0.48020229 -0.33571704 -0.43928726
|
||||||
|
Loop time of 0.0242313 on 3 procs for 100 steps with 500 atoms
|
||||||
|
|
||||||
|
print 'QM eng = $(f_2/atoms)'
|
||||||
|
QM eng = -5.7579933325734558025
|
||||||
|
print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'
|
||||||
|
QM virial = -0.41840219542566797761 -0.4802022860820577832 -0.33571704057970208623 -0.43928725961524273114
|
||||||
|
Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3]
|
||||||
|
100 0.75627629 -5.7579933 -0.4184022 -0.48020229 -0.33571704 -0.43928726
|
||||||
|
200 0.75199164 -5.752864 -0.40524506 -0.51524578 -0.27940441 -0.42108499
|
||||||
|
Loop time of 0.0269411 on 3 procs for 100 steps with 500 atoms
|
||||||
|
|
||||||
|
print 'QM eng = $(f_2/atoms)'
|
||||||
|
QM eng = -5.752864010326673494
|
||||||
|
print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'
|
||||||
|
QM virial = -0.40524505957305401171 -0.51524577748319133619 -0.27940441114042008364 -0.4210849900955495051
|
||||||
|
Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3]
|
||||||
|
200 0.75199164 -5.752864 -0.40524506 -0.51524578 -0.27940441 -0.42108499
|
||||||
|
300 0.75219392 -5.7527975 -0.41843911 -0.24280603 -0.42189159 -0.59061972
|
||||||
|
Loop time of 0.022648 on 3 procs for 100 steps with 500 atoms
|
||||||
|
|
||||||
|
Performance: 1907449.463 tau/day, 4415.392 timesteps/s
|
||||||
|
100.0% CPU use with 3 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.0091419 | 0.010422 | 0.011089 | 0.9 | 46.02
|
||||||
|
Neigh | 0.0036491 | 0.0040749 | 0.0043554 | 0.5 | 17.99
|
||||||
|
Comm | 0.004713 | 0.0056035 | 0.0073471 | 1.6 | 24.74
|
||||||
|
Output | 0.00062782 | 0.00063348 | 0.00064461 | 0.0 | 2.80
|
||||||
|
Modify | 0.0013385 | 0.0013655 | 0.0013943 | 0.1 | 6.03
|
||||||
|
Other | | 0.0005485 | | | 2.42
|
||||||
|
|
||||||
|
Nlocal: 166.667 ave 175 max 157 min
|
||||||
|
Histogram: 1 0 0 0 0 0 1 0 0 1
|
||||||
|
Nghost: 1254.33 ave 1264 max 1246 min
|
||||||
|
Histogram: 1 0 0 1 0 0 0 0 0 1
|
||||||
|
Neighs: 6248 ave 6632 max 5774 min
|
||||||
|
Histogram: 1 0 0 0 0 0 1 0 0 1
|
||||||
|
|
||||||
|
Total # of neighbors = 18744
|
||||||
|
Ave neighs/atom = 37.488
|
||||||
|
Neighbor list builds = 31
|
||||||
|
Dangerous builds = 0
|
||||||
|
print 'QM eng = $(f_2/atoms)'
|
||||||
|
QM eng = -5.752797469732716884
|
||||||
|
print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'
|
||||||
|
QM virial = -0.41843911315521897798 -0.24280603320323970729 -0.42189158691169792448 -0.590619719350719663
|
||||||
|
Total wall time: 0:00:00
|
||||||
118
examples/mdi/log.17Jun22.snapshot.driver.plugin.1
Normal file
118
examples/mdi/log.17Jun22.snapshot.driver.plugin.1
Normal file
@ -0,0 +1,118 @@
|
|||||||
|
LAMMPS (2 Jun 2022)
|
||||||
|
# 3d Lennard-Jones melt - MDI driver script
|
||||||
|
|
||||||
|
variable x index 5
|
||||||
|
variable y index 5
|
||||||
|
variable z index 5
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
read_data data.snapshot
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
500 atoms
|
||||||
|
reading velocities ...
|
||||||
|
500 velocities
|
||||||
|
read_data CPU = 0.005 seconds
|
||||||
|
|
||||||
|
velocity all create 1.44 87287 loop geom
|
||||||
|
|
||||||
|
pair_style lj/cut 2.5
|
||||||
|
pair_coeff 1 1 1.0 1.0 2.5
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
fix 1 all nve
|
||||||
|
|
||||||
|
fix 2 all mdi/qm add no every 100 virial yes
|
||||||
|
|
||||||
|
compute 1 all pressure NULL virial
|
||||||
|
variable evirial equal (f_2[1]+f_2[2]+f_2[3])/3
|
||||||
|
|
||||||
|
thermo_style custom step temp pe c_1 c_1[1] c_1[2] c_1[3]
|
||||||
|
|
||||||
|
thermo 100
|
||||||
|
|
||||||
|
dump 1 all custom 100 dump.snapshot.driver.plugin id type x y z f_2[1] f_2[2] f_2[3]
|
||||||
|
dump_modify 1 sort id
|
||||||
|
|
||||||
|
mdi plugin lammps mdi "-role ENGINE -name LMP2 -method LINK" infile in.snapshot.engine extra "-log log.snapshot.engine.plugin" command """
|
||||||
|
run 300 pre no post no every 100
|
||||||
|
"print 'QM eng = $(f_2/atoms)'"
|
||||||
|
"print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'"
|
||||||
|
"""
|
||||||
|
|
||||||
|
run 300 pre no post no every 100
|
||||||
|
"print 'QM eng = $(f_2/atoms)'"
|
||||||
|
"print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'"
|
||||||
|
|
||||||
|
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 0 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 2.8
|
||||||
|
ghost atom cutoff = 2.8
|
||||||
|
binsize = 1.4, bins = 6 6 6
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair lj/cut, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/atomonly/newton
|
||||||
|
stencil: half/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 4.461 | 4.461 | 4.461 Mbytes
|
||||||
|
Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3]
|
||||||
|
0 1.44 -6.7733681 -6.2353173 -6.2353173 -6.2353173 -6.2353173
|
||||||
|
100 0.75627629 -5.7579933 -0.4184022 -0.48020229 -0.33571704 -0.43928726
|
||||||
|
Loop time of 0.0623265 on 1 procs for 100 steps with 500 atoms
|
||||||
|
|
||||||
|
print 'QM eng = $(f_2/atoms)'
|
||||||
|
QM eng = -5.7579933325734575789
|
||||||
|
print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'
|
||||||
|
QM virial = -0.41840219542566597921 -0.48020228608206266818 -0.33571704057969975477 -0.43928725961523629184
|
||||||
|
Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3]
|
||||||
|
100 0.75627629 -5.7579933 -0.4184022 -0.48020229 -0.33571704 -0.43928726
|
||||||
|
200 0.75199164 -5.752864 -0.40524506 -0.51524578 -0.27940441 -0.42108499
|
||||||
|
Loop time of 0.0498825 on 1 procs for 100 steps with 500 atoms
|
||||||
|
|
||||||
|
print 'QM eng = $(f_2/atoms)'
|
||||||
|
QM eng = -5.7528640103266583949
|
||||||
|
print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'
|
||||||
|
QM virial = -0.40524505957306500292 -0.515245777483180456 -0.27940441114041408843 -0.42108499009560135251
|
||||||
|
Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3]
|
||||||
|
200 0.75199164 -5.752864 -0.40524506 -0.51524578 -0.27940441 -0.42108499
|
||||||
|
300 0.75219392 -5.7527975 -0.41843911 -0.24280603 -0.42189159 -0.59061972
|
||||||
|
Loop time of 0.050109 on 1 procs for 100 steps with 500 atoms
|
||||||
|
|
||||||
|
Performance: 862120.560 tau/day, 1995.649 timesteps/s
|
||||||
|
99.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.031747 | 0.031747 | 0.031747 | 0.0 | 63.36
|
||||||
|
Neigh | 0.012304 | 0.012304 | 0.012304 | 0.0 | 24.55
|
||||||
|
Comm | 0.0016113 | 0.0016113 | 0.0016113 | 0.0 | 3.22
|
||||||
|
Output | 0.0015529 | 0.0015529 | 0.0015529 | 0.0 | 3.10
|
||||||
|
Modify | 0.0023537 | 0.0023537 | 0.0023537 | 0.0 | 4.70
|
||||||
|
Other | | 0.0005398 | | | 1.08
|
||||||
|
|
||||||
|
Nlocal: 500 ave 500 max 500 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 1898 ave 1898 max 1898 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 18744 ave 18744 max 18744 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 18744
|
||||||
|
Ave neighs/atom = 37.488
|
||||||
|
Neighbor list builds = 31
|
||||||
|
Dangerous builds = 0
|
||||||
|
print 'QM eng = $(f_2/atoms)'
|
||||||
|
QM eng = -5.7527974697327088904
|
||||||
|
print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'
|
||||||
|
QM virial = -0.41843911315518900196 -0.24280603320322050043 -0.4218915869116203754 -0.59061971935072643536
|
||||||
|
Total wall time: 0:00:00
|
||||||
118
examples/mdi/log.17Jun22.snapshot.driver.plugin.3
Normal file
118
examples/mdi/log.17Jun22.snapshot.driver.plugin.3
Normal file
@ -0,0 +1,118 @@
|
|||||||
|
LAMMPS (2 Jun 2022)
|
||||||
|
# 3d Lennard-Jones melt - MDI driver script
|
||||||
|
|
||||||
|
variable x index 5
|
||||||
|
variable y index 5
|
||||||
|
variable z index 5
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
read_data data.snapshot
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||||
|
1 by 1 by 3 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
500 atoms
|
||||||
|
reading velocities ...
|
||||||
|
500 velocities
|
||||||
|
read_data CPU = 0.004 seconds
|
||||||
|
|
||||||
|
velocity all create 1.44 87287 loop geom
|
||||||
|
|
||||||
|
pair_style lj/cut 2.5
|
||||||
|
pair_coeff 1 1 1.0 1.0 2.5
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
fix 1 all nve
|
||||||
|
|
||||||
|
fix 2 all mdi/qm add no every 100 virial yes
|
||||||
|
|
||||||
|
compute 1 all pressure NULL virial
|
||||||
|
variable evirial equal (f_2[1]+f_2[2]+f_2[3])/3
|
||||||
|
|
||||||
|
thermo_style custom step temp pe c_1 c_1[1] c_1[2] c_1[3]
|
||||||
|
|
||||||
|
thermo 100
|
||||||
|
|
||||||
|
dump 1 all custom 100 dump.snapshot.driver.plugin id type x y z f_2[1] f_2[2] f_2[3]
|
||||||
|
dump_modify 1 sort id
|
||||||
|
|
||||||
|
mdi plugin lammps mdi "-role ENGINE -name LMP2 -method LINK" infile in.snapshot.engine extra "-log log.snapshot.engine.plugin" command """
|
||||||
|
run 300 pre no post no every 100
|
||||||
|
"print 'QM eng = $(f_2/atoms)'"
|
||||||
|
"print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'"
|
||||||
|
"""
|
||||||
|
|
||||||
|
run 300 pre no post no every 100
|
||||||
|
"print 'QM eng = $(f_2/atoms)'"
|
||||||
|
"print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'"
|
||||||
|
|
||||||
|
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 0 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 2.8
|
||||||
|
ghost atom cutoff = 2.8
|
||||||
|
binsize = 1.4, bins = 6 6 6
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair lj/cut, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/atomonly/newton
|
||||||
|
stencil: half/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 4.417 | 4.422 | 4.425 Mbytes
|
||||||
|
Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3]
|
||||||
|
0 1.44 -6.7733681 -6.2353173 -6.2353173 -6.2353173 -6.2353173
|
||||||
|
100 0.75627629 -5.7579933 -0.4184022 -0.48020229 -0.33571704 -0.43928726
|
||||||
|
Loop time of 0.0245664 on 3 procs for 100 steps with 500 atoms
|
||||||
|
|
||||||
|
print 'QM eng = $(f_2/atoms)'
|
||||||
|
QM eng = -5.7579933325734442562
|
||||||
|
print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'
|
||||||
|
QM virial = -0.41840219542566498001 -0.48020228608205661747 -0.33571704057970125357 -0.43928725961523629184
|
||||||
|
Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3]
|
||||||
|
100 0.75627629 -5.7579933 -0.4184022 -0.48020229 -0.33571704 -0.43928726
|
||||||
|
200 0.75199164 -5.752864 -0.40524506 -0.51524578 -0.27940441 -0.42108499
|
||||||
|
Loop time of 0.0221302 on 3 procs for 100 steps with 500 atoms
|
||||||
|
|
||||||
|
print 'QM eng = $(f_2/atoms)'
|
||||||
|
QM eng = -5.7528640103266690531
|
||||||
|
print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'
|
||||||
|
QM virial = -0.40524505957305301251 -0.51524577748319111414 -0.27940441114042025017 -0.42108499009554783976
|
||||||
|
Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3]
|
||||||
|
200 0.75199164 -5.752864 -0.40524506 -0.51524578 -0.27940441 -0.42108499
|
||||||
|
300 0.75219392 -5.7527975 -0.41843911 -0.24280603 -0.42189159 -0.59061972
|
||||||
|
Loop time of 0.0224519 on 3 procs for 100 steps with 500 atoms
|
||||||
|
|
||||||
|
Performance: 1924114.069 tau/day, 4453.968 timesteps/s
|
||||||
|
100.0% CPU use with 3 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.0096043 | 0.010493 | 0.011044 | 0.6 | 46.74
|
||||||
|
Neigh | 0.0037658 | 0.0041299 | 0.004422 | 0.4 | 18.39
|
||||||
|
Comm | 0.0048946 | 0.0055617 | 0.0068824 | 1.3 | 24.77
|
||||||
|
Output | 0.00063471 | 0.00063884 | 0.00064691 | 0.0 | 2.85
|
||||||
|
Modify | 0.0010632 | 0.0010754 | 0.0010895 | 0.0 | 4.79
|
||||||
|
Other | | 0.0005531 | | | 2.46
|
||||||
|
|
||||||
|
Nlocal: 166.667 ave 175 max 157 min
|
||||||
|
Histogram: 1 0 0 0 0 0 1 0 0 1
|
||||||
|
Nghost: 1254.33 ave 1264 max 1246 min
|
||||||
|
Histogram: 1 0 0 1 0 0 0 0 0 1
|
||||||
|
Neighs: 6248 ave 6632 max 5774 min
|
||||||
|
Histogram: 1 0 0 0 0 0 1 0 0 1
|
||||||
|
|
||||||
|
Total # of neighbors = 18744
|
||||||
|
Ave neighs/atom = 37.488
|
||||||
|
Neighbor list builds = 31
|
||||||
|
Dangerous builds = 0
|
||||||
|
print 'QM eng = $(f_2/atoms)'
|
||||||
|
QM eng = -5.7527974697327239895
|
||||||
|
print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'
|
||||||
|
QM virial = -0.41843911315521697958 -0.24280603320323956851 -0.42189158691169470483 -0.59061971935071611028
|
||||||
|
Total wall time: 0:00:00
|
||||||
105
examples/mdi/log.17Jun22.snapshot.driver.tcp.1
Normal file
105
examples/mdi/log.17Jun22.snapshot.driver.tcp.1
Normal file
@ -0,0 +1,105 @@
|
|||||||
|
LAMMPS (2 Jun 2022)
|
||||||
|
# 3d Lennard-Jones melt - MDI driver script
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
read_data data.snapshot
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
500 atoms
|
||||||
|
reading velocities ...
|
||||||
|
500 velocities
|
||||||
|
read_data CPU = 0.004 seconds
|
||||||
|
|
||||||
|
velocity all create 1.44 87287 loop geom
|
||||||
|
|
||||||
|
pair_style lj/cut 2.5
|
||||||
|
pair_coeff 1 1 1.0 1.0 2.5
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
fix 1 all nve
|
||||||
|
|
||||||
|
fix 2 all mdi/qm add no every 100 virial yes
|
||||||
|
|
||||||
|
compute 1 all pressure NULL virial
|
||||||
|
variable evirial equal (f_2[1]+f_2[2]+f_2[3])/3
|
||||||
|
|
||||||
|
thermo_style custom step temp pe c_1 c_1[1] c_1[2] c_1[3]
|
||||||
|
|
||||||
|
thermo 100
|
||||||
|
|
||||||
|
dump 1 all custom 100 dump.snapshot.driver id type x y z f_2[1] f_2[2] f_2[3]
|
||||||
|
dump_modify 1 sort id
|
||||||
|
|
||||||
|
run 300 pre no post no every 100 "print 'QM eng = $(f_2/atoms)'" "print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'"
|
||||||
|
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 0 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 2.8
|
||||||
|
ghost atom cutoff = 2.8
|
||||||
|
binsize = 1.4, bins = 6 6 6
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair lj/cut, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/atomonly/newton
|
||||||
|
stencil: half/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 4.461 | 4.461 | 4.461 Mbytes
|
||||||
|
Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3]
|
||||||
|
0 1.44 -6.7733681 -6.2353173 -6.2353173 -6.2353173 -6.2353173
|
||||||
|
100 0.75627629 -5.7579933 -0.4184022 -0.48020229 -0.33571704 -0.43928726
|
||||||
|
Loop time of 0.276735 on 1 procs for 100 steps with 500 atoms
|
||||||
|
|
||||||
|
print 'QM eng = $(f_2/atoms)'
|
||||||
|
QM eng = -5.7579933325734575789
|
||||||
|
print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'
|
||||||
|
QM virial = -0.41840219542566597921 -0.48020228608206266818 -0.33571704057969975477 -0.43928725961523629184
|
||||||
|
Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3]
|
||||||
|
100 0.75627629 -5.7579933 -0.4184022 -0.48020229 -0.33571704 -0.43928726
|
||||||
|
200 0.75199164 -5.752864 -0.40524506 -0.51524578 -0.27940441 -0.42108499
|
||||||
|
Loop time of 0.276667 on 1 procs for 100 steps with 500 atoms
|
||||||
|
|
||||||
|
print 'QM eng = $(f_2/atoms)'
|
||||||
|
QM eng = -5.7528640103266583949
|
||||||
|
print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'
|
||||||
|
QM virial = -0.40524505957306500292 -0.515245777483180456 -0.27940441114041408843 -0.42108499009560135251
|
||||||
|
Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3]
|
||||||
|
200 0.75199164 -5.752864 -0.40524506 -0.51524578 -0.27940441 -0.42108499
|
||||||
|
300 0.75219392 -5.7527975 -0.41843911 -0.24280603 -0.42189159 -0.59061972
|
||||||
|
Loop time of 0.278602 on 1 procs for 100 steps with 500 atoms
|
||||||
|
|
||||||
|
Performance: 155060.058 tau/day, 358.935 timesteps/s
|
||||||
|
26.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.049067 | 0.049067 | 0.049067 | 0.0 | 17.61
|
||||||
|
Neigh | 0.01894 | 0.01894 | 0.01894 | 0.0 | 6.80
|
||||||
|
Comm | 0.0026936 | 0.0026936 | 0.0026936 | 0.0 | 0.97
|
||||||
|
Output | 0.002919 | 0.002919 | 0.002919 | 0.0 | 1.05
|
||||||
|
Modify | 0.20406 | 0.20406 | 0.20406 | 0.0 | 73.24
|
||||||
|
Other | | 0.0009253 | | | 0.33
|
||||||
|
|
||||||
|
Nlocal: 500 ave 500 max 500 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 1898 ave 1898 max 1898 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 18744 ave 18744 max 18744 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 18744
|
||||||
|
Ave neighs/atom = 37.488
|
||||||
|
Neighbor list builds = 31
|
||||||
|
Dangerous builds = 0
|
||||||
|
print 'QM eng = $(f_2/atoms)'
|
||||||
|
QM eng = -5.7527974697327088904
|
||||||
|
print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'
|
||||||
|
QM virial = -0.41843911315518900196 -0.24280603320322050043 -0.4218915869116203754 -0.59061971935072643536
|
||||||
|
Total wall time: 0:00:01
|
||||||
105
examples/mdi/log.17Jun22.snapshot.driver.tcp.3
Normal file
105
examples/mdi/log.17Jun22.snapshot.driver.tcp.3
Normal file
@ -0,0 +1,105 @@
|
|||||||
|
LAMMPS (2 Jun 2022)
|
||||||
|
# 3d Lennard-Jones melt - MDI driver script
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
read_data data.snapshot
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981)
|
||||||
|
1 by 1 by 3 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
500 atoms
|
||||||
|
reading velocities ...
|
||||||
|
500 velocities
|
||||||
|
read_data CPU = 0.005 seconds
|
||||||
|
|
||||||
|
velocity all create 1.44 87287 loop geom
|
||||||
|
|
||||||
|
pair_style lj/cut 2.5
|
||||||
|
pair_coeff 1 1 1.0 1.0 2.5
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
fix 1 all nve
|
||||||
|
|
||||||
|
fix 2 all mdi/qm add no every 100 virial yes
|
||||||
|
|
||||||
|
compute 1 all pressure NULL virial
|
||||||
|
variable evirial equal (f_2[1]+f_2[2]+f_2[3])/3
|
||||||
|
|
||||||
|
thermo_style custom step temp pe c_1 c_1[1] c_1[2] c_1[3]
|
||||||
|
|
||||||
|
thermo 100
|
||||||
|
|
||||||
|
dump 1 all custom 100 dump.snapshot.driver id type x y z f_2[1] f_2[2] f_2[3]
|
||||||
|
dump_modify 1 sort id
|
||||||
|
|
||||||
|
run 300 pre no post no every 100 "print 'QM eng = $(f_2/atoms)'" "print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'"
|
||||||
|
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 0 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 2.8
|
||||||
|
ghost atom cutoff = 2.8
|
||||||
|
binsize = 1.4, bins = 6 6 6
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair lj/cut, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/atomonly/newton
|
||||||
|
stencil: half/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 4.417 | 4.422 | 4.425 Mbytes
|
||||||
|
Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3]
|
||||||
|
0 1.44 -6.7733681 -6.2353173 -6.2353173 -6.2353173 -6.2353173
|
||||||
|
100 0.75627629 -5.7579933 -0.4184022 -0.48020229 -0.33571704 -0.43928726
|
||||||
|
Loop time of 0.271725 on 3 procs for 100 steps with 500 atoms
|
||||||
|
|
||||||
|
print 'QM eng = $(f_2/atoms)'
|
||||||
|
QM eng = -5.7579933325734558025
|
||||||
|
print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'
|
||||||
|
QM virial = -0.41840219542566797761 -0.4802022860820577832 -0.33571704057970208623 -0.43928725961524273114
|
||||||
|
Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3]
|
||||||
|
100 0.75627629 -5.7579933 -0.4184022 -0.48020229 -0.33571704 -0.43928726
|
||||||
|
200 0.75199164 -5.752864 -0.40524506 -0.51524578 -0.27940441 -0.42108499
|
||||||
|
Loop time of 0.275711 on 3 procs for 100 steps with 500 atoms
|
||||||
|
|
||||||
|
print 'QM eng = $(f_2/atoms)'
|
||||||
|
QM eng = -5.752864010326673494
|
||||||
|
print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'
|
||||||
|
QM virial = -0.40524505957305401171 -0.51524577748319133619 -0.27940441114042008364 -0.4210849900955495051
|
||||||
|
Step Temp PotEng c_1 c_1[1] c_1[2] c_1[3]
|
||||||
|
200 0.75199164 -5.752864 -0.40524506 -0.51524578 -0.27940441 -0.42108499
|
||||||
|
300 0.75219392 -5.7527975 -0.41843911 -0.24280603 -0.42189159 -0.59061972
|
||||||
|
Loop time of 0.27674 on 3 procs for 100 steps with 500 atoms
|
||||||
|
|
||||||
|
Performance: 156103.145 tau/day, 361.350 timesteps/s
|
||||||
|
71.1% CPU use with 3 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.0086137 | 0.01236 | 0.019756 | 4.7 | 4.47
|
||||||
|
Neigh | 0.003253 | 0.0047355 | 0.0075676 | 2.9 | 1.71
|
||||||
|
Comm | 0.0065383 | 0.016521 | 0.021738 | 5.5 | 5.97
|
||||||
|
Output | 0.0011823 | 0.0011972 | 0.0012111 | 0.0 | 0.43
|
||||||
|
Modify | 0.24066 | 0.24076 | 0.24093 | 0.0 | 87.00
|
||||||
|
Other | | 0.001171 | | | 0.42
|
||||||
|
|
||||||
|
Nlocal: 166.667 ave 175 max 157 min
|
||||||
|
Histogram: 1 0 0 0 0 0 1 0 0 1
|
||||||
|
Nghost: 1254.33 ave 1264 max 1246 min
|
||||||
|
Histogram: 1 0 0 1 0 0 0 0 0 1
|
||||||
|
Neighs: 6248 ave 6632 max 5774 min
|
||||||
|
Histogram: 1 0 0 0 0 0 1 0 0 1
|
||||||
|
|
||||||
|
Total # of neighbors = 18744
|
||||||
|
Ave neighs/atom = 37.488
|
||||||
|
Neighbor list builds = 31
|
||||||
|
Dangerous builds = 0
|
||||||
|
print 'QM eng = $(f_2/atoms)'
|
||||||
|
QM eng = -5.752797469732716884
|
||||||
|
print 'QM virial = $(v_evirial) $(f_2[1]) $(f_2[2]) $(f_2[3])'
|
||||||
|
QM virial = -0.41843911315521897798 -0.24280603320323970729 -0.42189158691169792448 -0.590619719350719663
|
||||||
|
Total wall time: 0:00:01
|
||||||
45
examples/mdi/log.17Jun22.snapshot.engine.mpi.1
Normal file
45
examples/mdi/log.17Jun22.snapshot.engine.mpi.1
Normal file
@ -0,0 +1,45 @@
|
|||||||
|
LAMMPS (2 Jun 2022)
|
||||||
|
# 3d Lennard-Jones melt - MDI engine script
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
lattice fcc 1.0
|
||||||
|
Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011
|
||||||
|
region box block 0 1 0 1 0 1
|
||||||
|
create_box 1 box
|
||||||
|
Created orthogonal box = (0 0 0) to (1.5874011 1.5874011 1.5874011)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
mass 1 1.0
|
||||||
|
|
||||||
|
pair_style lj/cut 2.5
|
||||||
|
pair_coeff 1 1 1.0 1.0 2.5
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
mdi engine
|
||||||
|
delete_atoms group all
|
||||||
|
Deleted 0 atoms, new total = 0
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||||
|
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 0 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 2.8
|
||||||
|
ghost atom cutoff = 2.8
|
||||||
|
binsize = 1.4, bins = 6 6 6
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair lj/cut, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/atomonly/newton
|
||||||
|
stencil: half/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 3.144 | 3.144 | 3.144 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 0 -6.7733681 0 -6.7733681 -6.2353173
|
||||||
|
1 0 -5.7579933 0 -5.7579933 -0.4184022
|
||||||
|
2 0 -5.752864 0 -5.752864 -0.40524506
|
||||||
|
3 0 -5.7527975 0 -5.7527975 -0.41843911
|
||||||
|
Total wall time: 0:00:00
|
||||||
45
examples/mdi/log.17Jun22.snapshot.engine.mpi.3
Normal file
45
examples/mdi/log.17Jun22.snapshot.engine.mpi.3
Normal file
@ -0,0 +1,45 @@
|
|||||||
|
LAMMPS (2 Jun 2022)
|
||||||
|
# 3d Lennard-Jones melt - MDI engine script
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
lattice fcc 1.0
|
||||||
|
Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011
|
||||||
|
region box block 0 1 0 1 0 1
|
||||||
|
create_box 1 box
|
||||||
|
Created orthogonal box = (0 0 0) to (1.5874011 1.5874011 1.5874011)
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
mass 1 1.0
|
||||||
|
|
||||||
|
pair_style lj/cut 2.5
|
||||||
|
pair_coeff 1 1 1.0 1.0 2.5
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
mdi engine
|
||||||
|
delete_atoms group all
|
||||||
|
Deleted 0 atoms, new total = 0
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||||
|
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 0 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 2.8
|
||||||
|
ghost atom cutoff = 2.8
|
||||||
|
binsize = 1.4, bins = 6 6 6
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair lj/cut, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/atomonly/newton
|
||||||
|
stencil: half/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 3.109 | 3.109 | 3.109 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 0 -6.7733681 0 -6.7733681 -6.2353173
|
||||||
|
1 0 -5.7579933 0 -5.7579933 -0.4184022
|
||||||
|
2 0 -5.752864 0 -5.752864 -0.40524506
|
||||||
|
3 0 -5.7527975 0 -5.7527975 -0.41843911
|
||||||
|
Total wall time: 0:00:00
|
||||||
45
examples/mdi/log.17Jun22.snapshot.engine.plugin.1
Normal file
45
examples/mdi/log.17Jun22.snapshot.engine.plugin.1
Normal file
@ -0,0 +1,45 @@
|
|||||||
|
LAMMPS (2 Jun 2022)
|
||||||
|
# 3d Lennard-Jones melt - MDI engine script
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
lattice fcc 1.0
|
||||||
|
Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011
|
||||||
|
region box block 0 1 0 1 0 1
|
||||||
|
create_box 1 box
|
||||||
|
Created orthogonal box = (0 0 0) to (1.5874011 1.5874011 1.5874011)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
mass 1 1.0
|
||||||
|
|
||||||
|
pair_style lj/cut 2.5
|
||||||
|
pair_coeff 1 1 1.0 1.0 2.5
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
|
mdi engine
|
||||||
|
delete_atoms group all
|
||||||
|
Deleted 0 atoms, new total = 0
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
|
||||||
|
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 0 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 2.8
|
||||||
|
ghost atom cutoff = 2.8
|
||||||
|
binsize = 1.4, bins = 6 6 6
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair lj/cut, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/atomonly/newton
|
||||||
|
stencil: half/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 3.144 | 3.144 | 3.144 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 0 -6.7733681 0 -6.7733681 -6.2353173
|
||||||
|
1 0 -5.7579933 0 -5.7579933 -0.4184022
|
||||||
|
2 0 -5.752864 0 -5.752864 -0.40524506
|
||||||
|
3 0 -5.7527975 0 -5.7527975 -0.41843911
|
||||||
|
Total wall time: 0:00:00
|
||||||
Some files were not shown because too many files have changed in this diff Show More
Reference in New Issue
Block a user