Merge pull request #3628 from lammps/fix-mdi-qmmm
Add a fix mdi/qmmm command for running QMMM via MDI code coupling
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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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/v1.4.12.tar.gz" CACHE STRING "URL for MDI tarball")
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set(MDI_MD5 "7a222353ae8e03961d5365e6cd48baee" CACHE STRING "MD5 checksum for MDI tarball")
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set(MDI_URL "https://github.com/MolSSI-MDI/MDI_Library/archive/v1.4.16.tar.gz" CACHE STRING "URL for MDI tarball")
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set(MDI_MD5 "407db44e2d79447ab5c1233af1965f65" CACHE STRING "MD5 checksum for MDI tarball")
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mark_as_advanced(MDI_URL)
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mark_as_advanced(MDI_MD5)
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GetFallbackURL(MDI_URL MDI_FALLBACK)
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@ -111,6 +111,7 @@ OPT.
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* :doc:`lineforce <fix_lineforce>`
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* :doc:`manifoldforce <fix_manifoldforce>`
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* :doc:`mdi/qm <fix_mdi_qm>`
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* :doc:`mdi/qmmm <fix_mdi_qmmm>`
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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:`momentum (k) <fix_momentum>`
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@ -76,9 +76,16 @@ energy minimizations, or to evaluate the quantum energy and forces for a
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series of independent systems. The ``examples/mdi`` directory has
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example input scripts for all of these use cases.
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The package also has a :doc:`fix mdi/qmmm <fix_mdi_qmmm>` command in
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which LAMMPS operates as an MDI driver in conjunction with a quantum
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mechanics code as an MDI engine to perform QM/MM simulations. The
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LAMMPS input script partitions the system into QM and MM (molecular
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mechanics) atoms. As described below the ``examples/QUANTUM`` directory
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has examples for coupling to 3 different quantum codes in this manner.
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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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Currently, 5 example use cases are provided:
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@ -119,45 +126,26 @@ as a plugin library.
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-------------
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Currently, there are at least two quantum DFT codes which have direct MDI
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As of March 2023, these are quantum codes with MDI support provided via
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Python wrapper scripts included in the LAMMPS distribution. These can
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be used with the fix mdi/qm and fix mdi/qmmm commands to perform QM
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calculations of an entire system (e.g. AIMD) or QM/MM simulations. See
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the ``examples/QUANTUM`` sub-directories for more details:
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* LATTE - AIMD only
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* PySCF - QM/MM only
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* NWChem - AIMD or QM/MM
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There are also at least two quantum codes which have direct MDI
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support, `Quantum ESPRESSO (QE) <https://www.quantum-espresso.org/>`_
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and `INQ <https://qsg.llnl.gov/node/101.html>`_. There are also several
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QM 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 support
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which writes/read files to pass data to the quantum code itself. The
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list of QCEngine-supported and i-PI-supported quantum codes is on the
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`MDI webpage
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and `INQ <https://qsg.llnl.gov/node/101.html>`_. There are also
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several QM codes which have indirect support through QCEngine or i-PI.
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The 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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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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<https://molssi-mdi.github.io/MDI_Library/html/index.html>`_.
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Here is how to build QE as a stand-alone ``pw.x`` file which can be
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used in stand-alone mode:
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.. code-block:: bash
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git clone --branch mdi_plugin https://github.com/MolSSI-MDI/q-e.git <base_path>/q-e
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build the executable pw.x, following the `QE build guide <https://gitlab.com/QEF/q-e/-/wikis/Developers/CMake-build-system>`_
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Here is how to build QE as a shared library which can be used in plugin mode,
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which results in a ``libqemdi.so`` file in ``<base_path>/q-e/MDI/src``:
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.. code-block:: bash
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git clone --branch mdi_plugin https://github.com/MolSSI-MDI/q-e.git <base_path>/q-e
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cd <base_path>/q-e
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./configure --enable-parallel --enable-openmp --enable-shared FFLAGS="-fPIC" FCFLAGS="-fPIC" CFLAGS="-fPIC" foxflags="-fPIC" try_foxflags="-fPIC"
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make -j 4 mdi
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INQ cannot be built as a stand-alone code; it is by design a library.
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Here is how to build INQ as a shared library which can be used in
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plugin mode, which results in a ``libinqmdi.so`` file in
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``<base_path>/inq/build/examples``:
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.. code-block:: bash
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git clone --branch mdi --recurse-submodules https://gitlab.com/taylor-a-barnes/inq.git <base_path>/inq
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cd <base_path>/inq
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mkdir -p build
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cd build
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../configure --prefix=<install_path>/install
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make -j 4
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make install
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These direct- and indirect-support codes should be usable for full
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system calculations (e.g. AIMD). Whether they support QM/MM models
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depends on the individual QM code.
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@ -262,7 +262,8 @@ accelerated styles exist.
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* :doc:`lb/viscous <fix_lb_viscous>` - :doc:`fix viscous <fix_viscous>` replacement for use with a lattice-Boltzmann fluid
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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:`mdi/qm <fix_mdi_qm>` - LAMMPS operates as driver for a quantum code via the MolSSI Driver Interface (MDI)
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* :doc:`mdi/qm <fix_mdi_qm>` - LAMMPS operates as a client for a quantum code via the MolSSI Driver Interface (MDI)
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* :doc:`mdi/qmmm <fix_mdi_qmmm>` - LAMMPS operates as client for QM/MM simulation with 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:`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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@ -8,12 +8,12 @@ Syntax
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.. parsed-literal::
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fix ID group-ID mdi/qm keyword
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fix ID group-ID mdi/qm keyword value(s) keyword value(s) ...
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* ID, group-ID are documented in :doc:`fix <fix>` command
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* mdi/qm = style name of this fix command
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* zero or more keyword/value pairs may be appended
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* keyword = *virial* or *add* or *every* or *connect* or *elements*
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* keyword = *virial* or *add* or *every* or *connect* or *elements* or *mc*
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.. parsed-literal::
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@ -29,7 +29,9 @@ Syntax
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yes = perform a one-time connection to the MDI engine code
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no = do not perform the connection operation
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*elements* args = N_1 N_2 ... N_ntypes
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N_1,N_2,...N_ntypes = atomic number for each of ntypes LAMMPS atom types
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N_1,N_2,...N_ntypes = chemical symbol for each of ntypes LAMMPS atom types
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*mc* args = mcfixID
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mcfixID = ID of a Monte Carlo fix designed to work with this fix
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Examples
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""""""""
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@ -38,7 +40,7 @@ Examples
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fix 1 all mdi/qm
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fix 1 all mdi/qm virial yes
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fix 1 all mdi/qm add no every 100 elements 13 29
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fix 1 all mdi/qm add no every 100 elements C C H O
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Description
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"""""""""""
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@ -57,12 +59,27 @@ The server code must support use of the `MDI Library
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<https://molssi-mdi.github.io/MDI_Library/html/index.html>`_ as
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explained below.
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Typically, to use this fix, the input script should not define any
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other classical force field components, e.g. a pair style, bond style,
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etc.
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These are example use cases for this fix, discussed further below:
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* perform an ab initio MD (AIMD) simulation with quantum forces
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* perform an energy minimization with quantum forces
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* perform a nudged elastic band (NEB) calculation with quantum forces
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* perform a QM calculation for a series of independent systems which LAMMPS reads or generates
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* perform a QM calculation for a series of independent systems which
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LAMMPS reads or generates once
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* run a classical MD simulation and calculate QM energy/forces once
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every N steps on the current configuration
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More generally any command which calculates per-atom forces can instead
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use quantum forces by defining this fix. Examples are the Monte Carlo
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commands :doc:`fix gcmc <fix_gcmc>` and :doc:`fix atom/swap
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<fix_atom_swap>`, as well as the :doc:`compute born/matrix
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<compute_born_matrix>` command. The only requirement is that internally
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the command invokes the post_force() method of fixes such as this one,
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which will trigger the quantum calculation.
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The code coupling performed by this command is done via the `MDI
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Library <https://molssi-mdi.github.io/MDI_Library/html/index.html>`_.
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@ -72,27 +89,32 @@ for MDI. See the :doc:`Howto mdi <Howto_mdi>` page for more
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information about how LAMMPS can operate as either an MDI driver or
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engine.
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The examples/mdi directory contains input scripts using this fix in
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The ``examples/mdi`` directory contains input scripts using this fix in
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the various use cases discussed below. In each case, two instances of
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LAMMPS are used, once as an MDI driver, once as an MDI engine
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(surrogate for a QM code). The examples/mdi/README file explains how
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to launch two codes so that they communicate via the MDI library using
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either MPI or sockets. Any QM code that supports MDI could be used in
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place of LAMMPS acting as a QM surrogate. See the :doc:`Howto mdi
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<Howto_mdi>` page for a current list (March 2022) of such QM codes.
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LAMMPS are used, once as an MDI driver, once as an MDI engine (surrogate
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for a QM code). The ``examples/mdi/README`` file explains how to launch
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two codes so that they communicate via the MDI library using either MPI
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or sockets. Any QM code that supports MDI could be used in place of
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LAMMPS acting as a QM surrogate. See the :doc:`Howto mdi <Howto_mdi>`
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page for a current list (March 2022) of such QM codes. The
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``examples/QUANTUM`` directory has examples for coupling LAMMPS to 3 QM
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codes either via this fix or the :doc:`fix mdi/qmmm <fix_mdi_qmmm>`
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command.
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Note that an engine code can support MDI in either or both of two
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modes. It can be used as a stand-alone code, launched at the same
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time as LAMMPS. Or it can be used as a plugin library, which LAMMPS
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loads. See the :doc:`mdi plugin <mdi>` command for how to trigger
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LAMMPS to load a plugin library. The examples/mdi/README file
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explains how to launch the two codes in either mode.
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Note that an engine code can support MDI in either or both of two modes.
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It can be used as a stand-alone code, launched at the same time as
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LAMMPS. Or it can be used as a plugin library, which LAMMPS loads. See
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the :doc:`mdi plugin <mdi>` command for how to trigger LAMMPS to load a
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plugin library. The ``examples/mdi/README`` file and
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``examples/QUANTUM/QM-code/README`` files explain how to launch the two
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codes in either mode.
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----------
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The *virial* keyword setting of yes or no determines whether
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LAMMPS will request the QM code to also compute and return
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a 6-element symmetric virial tensor for the system.
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The *virial* keyword setting of yes or no determines whether LAMMPS
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will request the QM code to also compute and return the QM
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contribution to a stress tensor for the system which LAMMPS will
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convert to a 6-element symmetric virial tensor.
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The *add* keyword setting of *yes* or *no* determines whether the
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energy and forces and virial returned by the QM code will be added to
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@ -109,25 +131,27 @@ commands. See details below.
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The *every* keyword determines how often the QM code will be invoked
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during a dynamics run with the current LAMMPS simulation box and
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configuration of atoms. The QM code will be called once every
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*Nevery* timesteps.
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*Nevery* timesteps. By default *Nevery* = 1.
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The *connect* keyword determines whether this fix performs a one-time
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connection to the QM code. The default is *yes*. The only time a
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*no* is needed is if this command is used multiple times in an input
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script. E.g. if it used inside a loop which also uses the :doc:`clear
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<clear>` command to destroy the system (including any defined fixes).
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See the examples/mdi/in.series.driver script as an example of this,
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where LAMMPS is using the QM code to compute energy and forces for a
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series of system configurations. In this use case *connect no*
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is used along with the :doc:`mdi connect and exit <mdi>` command
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to one-time initiate/terminate the connection outside the loop.
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connection to the QM code. The default is *yes*. The only time a *no*
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is needed is if this command is used multiple times in an input script
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and the MDI coupling is between two stand-alone codes (not plugin mode).
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E.g. if it used inside a loop which also uses the :doc:`clear <clear>`
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command to destroy the system (including this fix). See the
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``examples/mdi/in.series.driver`` script as an example of this, where
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LAMMPS is using the QM code to compute energy and forces for a series of
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system configurations. In this use case *connect no* is used along with
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the :doc:`mdi connect and exit <mdi>` command to one-time
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initiate/terminate the connection outside the loop.
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The *elements* keyword allows specification of what element each
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LAMMPS atom type corresponds to. This is specified by the atomic
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number of the element, e.g. 13 for Al. An atomic number must be
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specified for each of the ntypes LAMMPS atom types. Ntypes is
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typically specified via the create_box command or in the data file
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read by the read_data command.
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LAMMPS atom type corresponds to. This is specified by the chemical
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symbol of the element, e.g. C or Al or Si. A symbol must be specified
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for each of the ntypes LAMMPS atom types. Multiple LAMMPS types can
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represent the same element. Ntypes is typically specified via the
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:doc:`create_box <create_box>` command or in the data file read by the
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:doc:`read_data <read_data>` command.
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If this keyword is specified, then this fix will send the MDI
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">ELEMENTS" command to the engine, to ensure the two codes are
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@ -136,10 +160,18 @@ not specified, then this fix will send the MDI >TYPES command to the
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engine. This is fine if both the LAMMPS driver and the MDI engine are
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initialized so that the atom type values are consistent in both codes.
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The *mc* keyword enables this fix to be used with a Monte Carlo (MC)
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fix to calculate before/after quantum energies as part of the MC
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accept/reject criterion. The :doc:`fix gcmc <fix_gcmc>` and :doc:`fix
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atom/swap <fix_atom_swap>` commands can be used in this manner.
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Specify the ID of the MC fix following the *mc* keyword. This allows
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the two fixes to coordinate when MC events are being calculated versus
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MD timesteps between the MC events.
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----------
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The following 3 example use cases are illustrated in the examples/mdi
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directory. See its README file for more details.
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The following 3 example use cases are illustrated in the
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``examples/mdi`` directory. See its README file for more details.
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(1) To run an ab initio MD (AIMD) dynamics simulation, or an energy
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minimization with QM forces, or a multi-replica NEB calculation, use
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@ -252,12 +284,6 @@ This command is part of the MDI package. It is only enabled if
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LAMMPS was built with that package. See the :doc:`Build package
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<Build_package>` page for more info.
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The QM code does not currently compute and return per-atom energy or
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per-atom virial contributions. So they will not show up as part of
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the calculations performed by the :doc:`compute pe/atom
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<compute_pe_atom>` or :doc:`compute stress/atom <compute_stress_atom>`
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commands.
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To use LAMMPS as an MDI driver in conjunction with other MDI-enabled
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codes (MD or QM codes), the :doc:`units <units>` command should be
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used to specify *real* or *metal* units. This will ensure the correct
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@ -265,12 +291,15 @@ unit conversions between LAMMPS and MDI units. The other code will
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also perform similar unit conversions into its preferred units.
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LAMMPS can also be used as an MDI driver in other unit choices it
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supports, e.g. *lj*, but then no unit conversion is performed.
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supports, e.g. *lj*, but then no unit conversion to MDI units is
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performed.
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Related commands
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""""""""""""""""
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:doc:`mdi plugin <mdi>`, :doc:`mdi engine <mdi>`
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:doc:`mdi plugin <mdi>`,
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:doc:`mdi engine <mdi>`,
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:doc:`fix mdi/qmmm <fix_mdi_qmmm>`
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Default
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"""""""
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274
doc/src/fix_mdi_qmmm.rst
Normal file
274
doc/src/fix_mdi_qmmm.rst
Normal file
@ -0,0 +1,274 @@
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.. index:: fix mdi/qmmm
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fix mdi/qmmm 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/qmmm mode keyword value(s) keyword value(s) ...
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* ID, group-ID are documented in :doc:`fix <fix>` command
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* mdi/qmmm = style name of this fix command
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* mode = *direct* or *potential*
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* zero or more keyword/value pairs may be appended
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* keyword = *virial* or *add* or *every* or *connect* or *elements*
|
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.. parsed-literal::
|
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|
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*virial* args = *yes* or *no*
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yes = request virial tensor from server code
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no = do not request virial tensor from server code
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*connect* args = *yes* or *no*
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yes = perform a one-time connection to the MDI engine code
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no = do not perform the connection operation
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*elements* args = N_1 N_2 ... N_ntypes
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N_1,N_2,...N_ntypes = chemical symbol for each of ntypes LAMMPS atom types
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Examples
|
||||
""""""""
|
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|
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.. code-block:: LAMMPS
|
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|
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fix 1 all mdi/qmmm direct
|
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fix 1 all mdi/qmmm potential virial yes
|
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fix 1 all mdi/qmmm potential virial yes elements 13 29
|
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|
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Description
|
||||
"""""""""""
|
||||
|
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.. versionadded:: TBD
|
||||
|
||||
This command enables LAMMPS to act as a client with another server code
|
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to perform a coupled QM/MM (quantum-mechanics/molecular-mechanics)
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simulation. LAMMPS will perform classical MD (molecular mechanics
|
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or MM) for the (typically larger) MM portion of the system. A quantum
|
||||
mechanics code will calculate quantum energy and forces for the QM
|
||||
portion of the system. The two codes work together to calculate the
|
||||
energy and forces due to the cross interactions between QM and MM atoms.
|
||||
The QM server code must support use of the `MDI Library
|
||||
<https://molssi-mdi.github.io/MDI_Library/html/index.html>`_ as
|
||||
explained below.
|
||||
|
||||
The partitioning of the system between QM and MM atoms is as follows.
|
||||
Atoms in the specified group are QM atoms; the remaining atoms are MM
|
||||
atoms. The input script should thus define this partitioning.
|
||||
See additional information below about other requirements for an input
|
||||
script to use this fix and perform a QM/MM simulation.
|
||||
|
||||
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), in this case 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/QUANTUM`` directory has sub-directories with example
|
||||
input scripts using this fix in tandem with different QM codes. The
|
||||
README files in the sub-directories explain how to download and build
|
||||
the various QM codes. They also explain how to launch LAMMPS and the QM
|
||||
code so that they communicate via the MDI library using either MPI or
|
||||
sockets. Any QM code that supports MDI could be used in addition to
|
||||
those discussed in the sub-directories. 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/QUANTUM`` sub-directory README files
|
||||
explains how to launch the two codes in either mode.
|
||||
|
||||
----------
|
||||
|
||||
The *mode* setting determines which QM/MM coupling algorithm is used.
|
||||
LAMMPS currently supports *direct* and *potential* algorithms, based
|
||||
on the *mode* setting. Both algorithms should give reasonably
|
||||
accurate results, but some QM codes support only one of the two modes.
|
||||
E.g. in the ``examples/QUANTUM`` directory, PySCF supports only *direct*,
|
||||
NWChem supports only *potential*, and LATTE currently supports
|
||||
neither, so it cannot be used for QM/MM simulations using this fix.
|
||||
|
||||
The *direct* option passes the coordinates and charges of each MM atom
|
||||
to the quantum code, in addition to the coordinates of each QM atom.
|
||||
The quantum code returns forces on each QM atom as well as forces on
|
||||
each MM atom. The latter is effectively the force on MM atoms due to
|
||||
the QM atoms.
|
||||
|
||||
The input script for performing a *direct* mode QM/MM simulation should
|
||||
do the following:
|
||||
|
||||
* delete all bonds (angles, dihedrals, etc) between QM atoms
|
||||
* set the charge on each QM atom to zero
|
||||
* define no bonds (angles, dihedrals, etc) which involve both QM and MM atoms
|
||||
* define a force field (pair, bonds, angles, optional kspace) for the entire system
|
||||
|
||||
The first two bullet can be performed using the :doc:`delete_bonds
|
||||
<delete_bonds>` and :doc:`set <set>` commands.
|
||||
|
||||
The third bullet is required to have a consistent model, but is not
|
||||
checked by LAMMPS.
|
||||
|
||||
The fourth bullet implies that non-bonded non-Coulombic interactions
|
||||
(e.g. van der Waals) between QM/QM and QM/MM pairs of atoms are
|
||||
computed by LAMMPS.
|
||||
|
||||
See the ``examples/QUANTUM/PySCF/in.*`` files for examples of input
|
||||
scripts for QM/MM simulations using the *direct* mode.
|
||||
|
||||
The *potential* option passes the coordinates of each QM atom and a
|
||||
Coulomb potential for each QM atom to the quantum code. The latter is
|
||||
calculated by performing a Coulombics-only calculation for the entire
|
||||
system, subtracting all QM/QM pairwise Coulombic terms, and dividing
|
||||
the Coulomb energy on each QM atom by the charge of the QM atom. The
|
||||
potential value represents the Coulombic influence of all the MM atoms
|
||||
on each QM atom.
|
||||
|
||||
The quantum code returns forces and charge on each QM atom. The new
|
||||
charges on the QM atom are used to re-calculate the MM force field,
|
||||
resulting in altered forces on the MM atoms.
|
||||
|
||||
The input script for performing a *potential* mode QM/MM simulation
|
||||
should do the following:
|
||||
|
||||
* delete all bonds (angles, dihedrals, etc) between QM atoms
|
||||
* define a hybrid pair style which includes a Coulomb-only pair sub-style
|
||||
* define no bonds (angles, dihedrals, etc) which involve both QM and MM atoms
|
||||
* define a force field (pair, bonds, angles, optional kspace) for the entire system
|
||||
|
||||
The first operation can be performed using the :doc:`delete_bonds
|
||||
<delete_bonds>` command. See the ``examples/QUANTUM/NWChem/in.*`` files
|
||||
for examples of how to do this.
|
||||
|
||||
The second operation is necessary so that this fix can calculate the
|
||||
Coulomb potential for the QM atoms.
|
||||
|
||||
The third bullet is required to have a consistent model, but is not
|
||||
checked by LAMMPS.
|
||||
|
||||
The fourth bullet implies that non-bonded non-Coulombic interactions
|
||||
(e.g. van der Waals) between QM/QM and QM/MM pairs of atoms are computed
|
||||
by LAMMPS. However, some QM codes do not want the MM code (LAMMPS) to
|
||||
compute QM/QM van der Waals interactions. NWChem is an example. In
|
||||
this case, the coefficients for those interactions need to be turned
|
||||
off, which typically requires the atom types for the QM atoms be
|
||||
different than those for the MM atoms.
|
||||
|
||||
See the ``examples/QUANTUM/NWChem/in.*`` files for examples of input
|
||||
scripts for QM/MM simulations using the *potential* mode. Those scripts
|
||||
also illustrate how to turn off QM/QM van der Waals interactions.
|
||||
|
||||
----------
|
||||
|
||||
The *virial* keyword setting of yes or no determines whether LAMMPS
|
||||
will request the QM code to also compute and return the QM
|
||||
contribution to a stress tensor for the system which LAMMPS will
|
||||
convert to a 6-element symmetric virial tensor.
|
||||
|
||||
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 this fix). As
|
||||
example would be a script which loop over a series of independent QM/MM
|
||||
simulations, e.g. each with their own data file. In this use case
|
||||
*connect no* could be 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 chemical
|
||||
symbol of the element, e.g. C or Al or Si. A symbol must be specified
|
||||
for each of the ntypes LAMMPS atom types. Multiple LAMMPS types can
|
||||
represent the same element. Ntypes is typically specified via the
|
||||
:doc:`create_box <create_box>` command or in the data file read by the
|
||||
:doc:`read_data <read_data>` command.
|
||||
|
||||
If this keyword is specified, then this fix will send the MDI
|
||||
">ELEMENTS" command to the engine, to insure the two codes are
|
||||
consistent in their definition of atomic species. If this keyword is
|
||||
not specified, then this fix will send the MDI >TYPES command to the
|
||||
engine. This is fine if both the LAMMPS driver and the MDI engine are
|
||||
initialized so that the atom type values are consistent in both codes.
|
||||
|
||||
----------
|
||||
|
||||
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>`.
|
||||
|
||||
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>`.
|
||||
|
||||
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>`. Note that
|
||||
for *direct* mode this will be quantum forces on both QM and MM atoms.
|
||||
For *potential* mode it will only be quantum forces on QM atoms; the
|
||||
forces for MM atoms will be zero.
|
||||
|
||||
No parameter of this fix can be used with the *start/stop* keywords of
|
||||
the :doc:`run <run>` command.
|
||||
|
||||
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.
|
||||
|
||||
|
||||
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
|
||||
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.
|
||||
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`mdi plugin <mdi>`,
|
||||
:doc:`mdi engine <mdi>`,
|
||||
:doc:`fix mdi/qm <fix_mdi_qm>`
|
||||
|
||||
Default
|
||||
"""""""
|
||||
|
||||
The default for the optional keywords are virial = no and connect = yes.
|
||||
@ -17,7 +17,7 @@ Syntax
|
||||
*engine* args = zero or more keyword/args pairs
|
||||
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
|
||||
N_1,N_2,...N_ntypes = chemical symbol 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)
|
||||
keyword/value pairs in any order, some are required, some are optional
|
||||
@ -35,7 +35,7 @@ Examples
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
mdi engine
|
||||
mdi engine elements 13 29
|
||||
mdi engine elements Al Cu
|
||||
mdi plugin lammps mdi "-role ENGINE -name lammps -method LINK" &
|
||||
infile in.aimd.engine extra "-log log.aimd.engine.plugin" &
|
||||
command "run 5"
|
||||
@ -173,13 +173,16 @@ commands, which are described further below.
|
||||
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.
|
||||
to. This is specified by the chemical symbol of the element,
|
||||
e.g. C or Al or Si. A symbol must be specified for each of the
|
||||
ntypes LAMMPS atom types. Each LAMMPS type must map to a unique
|
||||
element; two or more types cannot map to the same element. Ntypes
|
||||
is typically specified via the :doc:`create_box <create_box>`
|
||||
command or in the data file read by the :doc:`read_data
|
||||
<read_data>` command. Once this has been done, the MDI driver can
|
||||
send an >ELEMENTS command to the LAMMPS driver with the atomic
|
||||
number of each atom and the LAMMPS engine will be able to map it to
|
||||
a LAMMPS atom type.
|
||||
|
||||
The MD and OPTG commands perform an entire MD simulation or energy
|
||||
minimization (to convergence) with no communication from the driver
|
||||
|
||||
@ -2574,7 +2574,7 @@ nvidia
|
||||
nvk
|
||||
nvt
|
||||
Nwait
|
||||
nwchem
|
||||
NWChem
|
||||
nx
|
||||
Nx
|
||||
nxlo
|
||||
@ -2908,6 +2908,7 @@ PyLammps
|
||||
pymbar
|
||||
pymodule
|
||||
pymol
|
||||
PySCF
|
||||
pythonic
|
||||
pytorch
|
||||
pyy
|
||||
|
||||
@ -1,24 +0,0 @@
|
||||
This dir contains scripts that demonstrate how to use LAMMPS as an
|
||||
MDI engine. LAMMPS as an engine performs the MD timestepping.
|
||||
The driver is a simple Python script. Every timestep the driver
|
||||
sends one or more commands to LAMMPS.
|
||||
|
||||
--------------
|
||||
|
||||
The Script.sh file has comands to perform some very simple example
|
||||
runs.
|
||||
|
||||
--------------
|
||||
|
||||
More complex calculations using LAMMPS as an MDI engine will
|
||||
typically require the use of an MDI driver. Several MDI drivers
|
||||
support calculations with LAMMPS, and include:
|
||||
|
||||
Ab Initio Molecular Dynamics (AIMD) Driver:
|
||||
https://github.com/MolSSI-MDI/MDI_AIMD_Driver
|
||||
|
||||
Nudged Elastic Band (NEB) Driver:
|
||||
https://github.com/MolSSI-MDI/MDI_NEB_Driver
|
||||
|
||||
Metadynamics Driver:
|
||||
https://github.com/MolSSI-MDI/MDI_Metadynamics
|
||||
@ -1,16 +0,0 @@
|
||||
#!/bin/bash
|
||||
# sample launch scripts
|
||||
|
||||
|
||||
# TCP, running LAMMPS on one proc
|
||||
|
||||
python driver.py -mdi "-name driver -role DRIVER -method TCP -port 8021" &
|
||||
../../../src/lmp_mdi -mdi "-name LAMMPS -role ENGINE -method TCP -port 8021 -hostname localhost" -in lammps.in > lammps.out &
|
||||
wait
|
||||
|
||||
|
||||
# TCP, running LAMMPS on two procs
|
||||
|
||||
python driver.py -mdi "-name driver -role DRIVER -method TCP -port 8021" &
|
||||
mpiexec -n 2 ../../../src/lmp_mdi -mdi "-name LAMMPS -role ENGINE -method TCP -port 8021 -hostname localhost" -in lammps.in > lammps.out &
|
||||
wait
|
||||
@ -1,24 +0,0 @@
|
||||
import sys
|
||||
import mdi
|
||||
|
||||
use_mpi4py = False
|
||||
try:
|
||||
from mpi4py import MPI
|
||||
use_mpi4py = True
|
||||
except:
|
||||
pass
|
||||
|
||||
# Initialize the MDI Library
|
||||
mdi.MDI_Init(sys.argv[2])
|
||||
|
||||
# Connect to the engine
|
||||
comm = mdi.MDI_Accept_communicator()
|
||||
|
||||
# Determine the name of the engine
|
||||
mdi.MDI_Send_Command("<NAME", comm)
|
||||
name = mdi.MDI_Recv(mdi.MDI_NAME_LENGTH, mdi.MDI_CHAR, comm)
|
||||
|
||||
print("Engine name: " + str(name))
|
||||
|
||||
# Send the "EXIT" command to the engine
|
||||
mdi.MDI_Send_Command("EXIT", comm)
|
||||
@ -1,92 +0,0 @@
|
||||
LAMMPS data file for water
|
||||
|
||||
24 atoms
|
||||
16 bonds
|
||||
8 angles
|
||||
0 dihedrals
|
||||
0 impropers
|
||||
|
||||
2 atom types
|
||||
1 bond types
|
||||
1 angle types
|
||||
0 dihedral types
|
||||
0 improper types
|
||||
|
||||
0.0 4.9325 xlo xhi
|
||||
0.0 4.9325 ylo yhi
|
||||
0.0 4.9325 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
1 15.9994
|
||||
2 1.008
|
||||
|
||||
Pair Coeffs
|
||||
|
||||
1 0.102 3.188
|
||||
2 0.000 0.000
|
||||
|
||||
Bond Coeffs
|
||||
|
||||
1 450 0.9572
|
||||
|
||||
Angle Coeffs
|
||||
|
||||
1 55.0 104.52
|
||||
|
||||
Atoms
|
||||
|
||||
1 0 1 -0.83400 2.17919 0.196156 4.15513
|
||||
2 0 2 0.41700 2.29785 4.8353 0.126003
|
||||
3 0 2 0.41700 1.82037 1.07996 4.23498
|
||||
4 0 1 -0.83400 4.65839 0.120414 0.305758
|
||||
5 0 2 0.41700 4.67446 -0.0220991 4.29186
|
||||
6 0 2 0.41700 4.28188 0.994196 0.410515
|
||||
7 0 1 -0.83400 3.65045 2.40907 0.344349
|
||||
8 0 2 0.41700 3.52052 2.1838 4.35565
|
||||
9 0 2 0.41700 4.26579 3.14208 0.327669
|
||||
10 0 1 -0.83400 1.21327 2.62177 4.15519
|
||||
11 0 2 0.41700 1.47452 3.53837 4.0667
|
||||
12 0 2 0.41700 1.20743 2.46396 0.16677
|
||||
13 0 1 -0.83400 4.45777 4.47325 2.74192
|
||||
14 0 2 0.41700 4.53396 4.49652 1.78804
|
||||
15 0 2 0.41700 4.21354 3.56943 2.94119
|
||||
16 0 1 -0.83400 2.04119 4.41585 1.64725
|
||||
17 0 2 0.41700 2.26934 4.77582 2.50434
|
||||
18 0 2 0.41700 1.69079 3.54574 1.83793
|
||||
19 0 1 -0.83400 3.73384 1.97964 2.81949
|
||||
20 0 2 0.41700 3.41083 2.22014 1.95113
|
||||
21 0 2 0.41700 3.91914 1.04272 2.75561
|
||||
22 0 1 -0.83400 1.20859 2.09853 1.68186
|
||||
23 0 2 0.41700 1.01865 2.25693 2.60655
|
||||
24 0 2 0.41700 1.16884 1.14674 1.58832
|
||||
|
||||
Bonds
|
||||
|
||||
1 1 1 2
|
||||
2 1 1 3
|
||||
3 1 4 5
|
||||
4 1 4 6
|
||||
5 1 7 8
|
||||
6 1 7 9
|
||||
7 1 10 11
|
||||
8 1 10 12
|
||||
9 1 13 14
|
||||
10 1 13 15
|
||||
11 1 16 17
|
||||
12 1 16 18
|
||||
13 1 19 20
|
||||
14 1 19 21
|
||||
15 1 22 23
|
||||
16 1 22 24
|
||||
|
||||
Angles
|
||||
|
||||
1 1 2 1 3
|
||||
2 1 5 4 6
|
||||
3 1 8 7 9
|
||||
4 1 11 10 12
|
||||
5 1 14 13 15
|
||||
6 1 17 16 18
|
||||
7 1 20 19 21
|
||||
8 1 23 22 24
|
||||
@ -1,28 +0,0 @@
|
||||
units real
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
pair_style lj/cut/coul/long 10.0
|
||||
pair_modify mix arithmetic
|
||||
kspace_style pppm 1e-4
|
||||
special_bonds amber
|
||||
|
||||
atom_modify sort 0 0
|
||||
|
||||
read_data lammps.data
|
||||
|
||||
timestep 1.0
|
||||
|
||||
dump 1 all custom 1 dump.lammpstrj id element xu yu zu
|
||||
dump 2 all custom 1 dump.force id element fx fy fz
|
||||
dump 3 all xyz 1 dump.xyz
|
||||
dump_modify 1 element O H
|
||||
dump_modify 2 element O H
|
||||
|
||||
thermo_style multi
|
||||
thermo 1
|
||||
|
||||
fix 1 all nvt temp 300.0 300.0 70.0
|
||||
|
||||
mdi/engine
|
||||
@ -1,161 +0,0 @@
|
||||
LATTE is a semi-empirical tight-binding quantum code, developed
|
||||
primarily at Los Alamos National Labs.
|
||||
|
||||
See these links:
|
||||
|
||||
https://www.osti.gov/biblio/1526907-los-alamos-transferable-tight-binding-energetics-latte-version
|
||||
https://github.com/lanl/LATTE
|
||||
|
||||
LAMMPS has 2 ways of working with LATTE:
|
||||
|
||||
(1) Via its LATTE package and the fix latte command
|
||||
must run LAMMPS on a single processor, it calls LATTE as a library
|
||||
|
||||
(2) Via its MDI package and the code-coupling MDI library
|
||||
(a) can run LAMMPS and LATTE as stand-alone codes
|
||||
LAMMPS can be run on any number of procs
|
||||
LATTE must run on a single proc, but can use OpenMP
|
||||
(b) can run LAMMPS with LATTE as a plug-in library
|
||||
must run LAMMPS on a single processor
|
||||
|
||||
Examples for use case (1) are in the examples/latte dir. Use case (2)
|
||||
is illustrated in this dir.
|
||||
|
||||
NOTE: If you compare MDI runs in this dir to similar fix latte runs in
|
||||
examples/latte, the answers for energy and virial will be differnt.
|
||||
This is b/c the version of LATTE used by the fix latte command within
|
||||
the LATTE package is older than the version of LATTE used here.
|
||||
|
||||
------------------
|
||||
Building 3 codes needed to run these examples
|
||||
|
||||
(1) Download and build MDI
|
||||
|
||||
% git clone git@github.com:MolSSI-MDI/MDI_Library.git mdi
|
||||
% cd mdi
|
||||
% mkdir build; cd build
|
||||
% cmake .. # includes support for all langauges (incl Fortran, Python)
|
||||
% make
|
||||
|
||||
(2) Download and build LATTE with MDI support
|
||||
|
||||
% git clone git@github.com:lanl/LATTE.git latte
|
||||
% cd latte
|
||||
% git checkout skimLATTE-progress # goto branch with MDI support
|
||||
% cp makefiles/makefile.CHOICES.mdi makefile.CHOICES # so can now edit
|
||||
% edit makefile.CHOICES settings to have these settings:
|
||||
MAKELIB = OFF, SHARED = ON, MDI = ON
|
||||
MDI_PATH must point to CMake build of MDI in (1),
|
||||
e.g. /home/sjplimp/mdi/build/MDI_Library
|
||||
comment out 2 LIB lines with CUDA-CUDART_LIBRARY
|
||||
% make clean
|
||||
% make # creates liblatte.so and LATTE_DOUBLE with support for MDI
|
||||
|
||||
(3) Build LAMMPS with its MDI package
|
||||
also with the MOLECULE package for these example scripts
|
||||
|
||||
Build with traditional make
|
||||
|
||||
% cd lammps/lib/mdi
|
||||
% python Install.py -m mpi # downloads and builds MDI
|
||||
% cd ../../src
|
||||
% make yes-mdi yes-molecule
|
||||
$ make mpi # creates lmp_mpi
|
||||
|
||||
% mkdir build; cd build
|
||||
% cmake -D PKG_MDI=yes -D PKG_MOLECULE=yes ../cmake
|
||||
% make # creates lmp
|
||||
|
||||
Build with CMake
|
||||
|
||||
% cd lammps
|
||||
% mkdir build; cd build
|
||||
% cmake -D PKG_MDI=yes -D PKG_MOLECULE=yes ../cmake
|
||||
% make # creates lmp
|
||||
|
||||
(4) Copy LAMMPS and LATTE executables into this dir
|
||||
|
||||
Copy the LAMMPS executable (lmp_mpi or lmp) into this dir as lmp_mpi.
|
||||
Copy the LATTE executable LATTE_DOUBLE into this dir.
|
||||
The run commands below assume you have done this.
|
||||
|
||||
(5) Ensure LD_LIBRARY_PATH includes the dir where MDI was built in (1)
|
||||
with its libmdi.so file, e.g. mdi/build/MDI_Library. This is needed
|
||||
so when LATTE_DOUBLE runs as an executable it will able to find
|
||||
libmdi.so.
|
||||
|
||||
------------------
|
||||
Notes on LATTE usage
|
||||
|
||||
You must run this version of LATTE on a single MPI processor.
|
||||
However, you can use OpenMP with LATTE. To do this you need to build
|
||||
LATTE with OpenMP support by editing the makefile.CHOICES file to
|
||||
include -fopenmp with FFLAGS and LINKFLAGS. Also -lapack and -lblas
|
||||
need to be added to LIB, and those libraries must be available on your
|
||||
system. For best performance you should also build LATTE with its
|
||||
PROGRESS and BML libraries. Building those libs is more complex,
|
||||
see details here:
|
||||
|
||||
https://github.com/lanl/LATTE_SUPER/tree/allMachines/Laptop
|
||||
|
||||
At run time, you need to also first set an environment variable for
|
||||
the number of OpenMP threads to use, e.g.
|
||||
|
||||
% export OMP_NUM_THREADS=12
|
||||
|
||||
By default LATTE reads the latte.in file for its parameters. That
|
||||
file specifies other files LATTE will read. With MDI, the driver code
|
||||
(e.g. LAMMPS) can use the >FNAME command to specify an alternate
|
||||
filename to use instead of latte.in.
|
||||
|
||||
By default LATTE writes out a log.latte file with info about its
|
||||
calculations. An "OUTFILE= logfile" setting in latte.in can rename
|
||||
this file.
|
||||
|
||||
---------
|
||||
Run example #1: AIMD
|
||||
|
||||
* Run with MPI: 1 proc each
|
||||
|
||||
mpirun -np 1 lmp_mpi -mdi "-name LMP -role DRIVER -method MPI" \
|
||||
-in in.aimd -log log.aimd.lammps.mpi : \
|
||||
-np 1 LATTE_DOUBLE -mdi "-name LATTE -role ENGINE -method MPI"
|
||||
|
||||
* Run with MPI: 2 procs for LAMMPS, 1 for LATTE
|
||||
|
||||
mpirun -np 2 lmp_mpi -mdi "-name LMP -role DRIVER -method MPI" \
|
||||
-in in.aimd -log log.aimd.lammps.mpi : \
|
||||
-np 1 LATTE_DOUBLE -mdi "-name LATTE -role ENGINE -method MPI"
|
||||
|
||||
* Run in plugin mode: 1 proc
|
||||
|
||||
lmp_mpi -mdi \
|
||||
"-name LMP -role DRIVER -method LINK -plugin_path /home/sjplimp/latte/git" \
|
||||
-in in.aimd.plugin -log log.aimd.lammps.plugin
|
||||
|
||||
NOTE: The -plugin_path needs to point to where LATTE was built in step
|
||||
(2).
|
||||
|
||||
---------
|
||||
Run example #2: sequence of configurations
|
||||
|
||||
* Run with MPI: 1 proc each
|
||||
|
||||
mpirun -np 1 lmp_mpi -mdi "-name LMP -role DRIVER -method MPI" \
|
||||
-in in.series -log log.series.lammps.mpi : \
|
||||
-np 1 LATTE_DOUBLE -mdi "-name LATTE -role ENGINE -method MPI"
|
||||
|
||||
* Run with MPI: 2 procs for LAMMPS, 1 for LATTE
|
||||
|
||||
mpirun -np 2 lmp_mpi -mdi "-name LMP -role DRIVER -method MPI" \
|
||||
-in in.series -log log.series.lammps.mpi : \
|
||||
-np 1 LATTE_DOUBLE -mdi "-name LATTE -role ENGINE -method MPI"
|
||||
|
||||
* Run in plugin mode: 1 proc
|
||||
|
||||
lmp_mpi -mdi \
|
||||
"-name LMP -role DRIVER -method LINK -plugin_path /home/sjplimp/latte/git" \
|
||||
-in in.series.plugin -log log.series.lammps.plugin
|
||||
|
||||
NOTE: The -plugin_path needs to point to where LATTE was built in step
|
||||
(2).
|
||||
@ -1,315 +0,0 @@
|
||||
ITEM: TIMESTEP
|
||||
0
|
||||
ITEM: NUMBER OF ATOMS
|
||||
6
|
||||
ITEM: BOX BOUNDS xy xz yz pp pp pp
|
||||
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
ITEM: ATOMS id type x y z vx vy vz fx fy fz
|
||||
1 1 2.7 2.7 0 -0.601491 0.335597 -0.87242 -2.27066e-14 -1.33391e-14 2.31141e-14
|
||||
2 2 1.35 4.05 1.35 8.2897 4.55901 5.97376 2.35473 2.21578e-14 7.40069e-15
|
||||
3 2 4.05 4.05 1.35 1.7742 6.51885 0.385522 -2.35473 2.97071e-15 -2.01341e-14
|
||||
4 1 2.7 1.65327e-16 2.7 -0.325605 -1.03244 0.724324 -2.90278e-14 6.77422e-15 2.86766e-15
|
||||
5 2 1.35 1.35 4.05 2.42711 -1.49109 -2.41596 2.35473 5.79901e-15 -1.19594e-14
|
||||
6 2 4.05 1.35 4.05 1.30688 0.784281 -1.73922 -2.35473 -1.38761e-14 1.09382e-14
|
||||
ITEM: TIMESTEP
|
||||
1
|
||||
ITEM: NUMBER OF ATOMS
|
||||
6
|
||||
ITEM: BOX BOUNDS xy xz yz pp pp pp
|
||||
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
ITEM: ATOMS id type x y z vx vy vz fx fy fz
|
||||
1 1 2.69985 2.70008 -0.000218105 -0.601467 0.335616 -0.872428 0.00470101 0.00380515 -0.00141625
|
||||
2 2 1.35212 4.05114 1.35149 8.64389 4.55886 5.97363 2.34251 -0.00209926 -0.00172976
|
||||
3 2 4.0504 4.05163 1.3501 1.41949 6.51866 0.385561 -2.34936 -0.00247497 0.00051716
|
||||
4 1 2.69992 -0.00025811 2.70018 -0.325581 -1.03243 0.724334 0.00481137 0.00249244 0.00195665
|
||||
5 2 1.35065 1.34963 4.0494 2.78199 -1.49112 -2.4159 2.3517 -0.00043711 0.000874754
|
||||
6 2 4.05028 1.3502 4.04957 0.951796 0.784184 -1.73923 -2.35436 -0.00128625 -0.00020256
|
||||
ITEM: TIMESTEP
|
||||
2
|
||||
ITEM: NUMBER OF ATOMS
|
||||
6
|
||||
ITEM: BOX BOUNDS xy xz yz pp pp pp
|
||||
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
ITEM: ATOMS id type x y z vx vy vz fx fy fz
|
||||
1 1 2.6997 2.70017 -0.000436214 -0.601396 0.335673 -0.872449 0.00939888 0.00756163 -0.00288164
|
||||
2 2 1.35432 4.05228 1.35299 8.99615 4.55837 5.97323 2.32921 -0.00431846 -0.00355855
|
||||
3 2 4.05071 4.05326 1.35019 1.06567 6.5181 0.385678 -2.34304 -0.00494314 0.00103532
|
||||
4 1 2.69984 -0.000516214 2.70036 -0.325507 -1.03239 0.724364 0.00976944 0.00512657 0.00403686
|
||||
5 2 1.35139 1.34925 4.04879 3.13634 -1.49122 -2.4157 2.34776 -0.000851489 0.00177498
|
||||
6 2 4.05048 1.35039 4.04913 0.596838 0.783892 -1.73928 -2.3531 -0.00257512 -0.000406965
|
||||
ITEM: TIMESTEP
|
||||
3
|
||||
ITEM: NUMBER OF ATOMS
|
||||
6
|
||||
ITEM: BOX BOUNDS xy xz yz pp pp pp
|
||||
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
ITEM: ATOMS id type x y z vx vy vz fx fy fz
|
||||
1 1 2.69955 2.70025 -0.00065433 -0.601277 0.335769 -0.872486 0.0141006 0.0112702 -0.00439552
|
||||
2 2 1.35661 4.05342 1.35448 9.34633 4.55754 5.97255 2.31482 -0.00666433 -0.00549143
|
||||
3 2 4.05093 4.05489 1.35029 0.712875 6.51717 0.385873 -2.33577 -0.00740896 0.00154764
|
||||
4 1 2.69976 -0.000774304 2.70054 -0.325382 -1.03232 0.724417 0.0148831 0.00790884 0.00624833
|
||||
5 2 1.35222 1.34888 4.04819 3.49003 -1.49137 -2.41536 2.3429 -0.0012407 0.00270313
|
||||
6 2 4.05058 1.35059 4.0487 0.242138 0.783407 -1.73935 -2.35094 -0.00386511 -0.000612161
|
||||
ITEM: TIMESTEP
|
||||
4
|
||||
ITEM: NUMBER OF ATOMS
|
||||
6
|
||||
ITEM: BOX BOUNDS xy xz yz pp pp pp
|
||||
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
ITEM: ATOMS id type x y z vx vy vz fx fy fz
|
||||
1 1 2.6994 2.70034 -0.000872457 -0.60111 0.335902 -0.872539 0.0188131 0.0149318 -0.00595718
|
||||
2 2 1.359 4.05456 1.35597 9.69425 4.55635 5.97156 2.29933 -0.00914346 -0.00753331
|
||||
3 2 4.05107 4.05652 1.35039 0.361248 6.51586 0.386144 -2.32753 -0.00987687 0.00204727
|
||||
4 1 2.69967 -0.00103238 2.70072 -0.325204 -1.03223 0.724492 0.020161 0.0108455 0.00859866
|
||||
5 2 1.35314 1.34851 4.04758 3.84292 -1.49159 -2.41488 2.33711 -0.00160232 0.00366164
|
||||
6 2 4.0506 1.35078 4.04826 -0.112168 0.782727 -1.73946 -2.34789 -0.00515472 -0.000817084
|
||||
ITEM: TIMESTEP
|
||||
5
|
||||
ITEM: NUMBER OF ATOMS
|
||||
6
|
||||
ITEM: BOX BOUNDS xy xz yz pp pp pp
|
||||
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
ITEM: ATOMS id type x y z vx vy vz fx fy fz
|
||||
1 1 2.69925 2.70042 -0.0010906 -0.600896 0.336071 -0.872607 0.0235434 0.0185473 -0.00756588
|
||||
2 2 1.36146 4.0557 1.35747 10.0397 4.55478 5.97026 2.2827 -0.0117623 -0.00968894
|
||||
3 2 4.05111 4.05815 1.35048 0.0109366 6.51419 0.386489 -2.31832 -0.0123511 0.00252727
|
||||
4 1 2.69959 -0.00129042 2.70091 -0.324972 -1.0321 0.724592 0.0256115 0.0139425 0.0110953
|
||||
5 2 1.35414 1.34814 4.04698 4.19487 -1.49186 -2.41425 2.33039 -0.00193394 0.0046529
|
||||
6 2 4.05052 1.35098 4.04783 -0.465946 0.781852 -1.7396 -2.34393 -0.00644244 -0.00102066
|
||||
ITEM: TIMESTEP
|
||||
6
|
||||
ITEM: NUMBER OF ATOMS
|
||||
6
|
||||
ITEM: BOX BOUNDS xy xz yz pp pp pp
|
||||
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
ITEM: ATOMS id type x y z vx vy vz fx fy fz
|
||||
1 1 2.6991 2.7005 -0.00130876 -0.600633 0.336277 -0.872692 0.0282985 0.0221175 -0.00922083
|
||||
2 2 1.36401 4.05684 1.35896 10.3827 4.55279 5.96863 2.26494 -0.0145272 -0.0119629
|
||||
3 2 4.05107 4.05978 1.35058 -0.337913 6.51214 0.386904 -2.30814 -0.0148362 0.00298071
|
||||
4 1 2.69951 -0.00154843 2.70109 -0.324684 -1.03194 0.724717 0.0312427 0.0172058 0.0137455
|
||||
5 2 1.35523 1.34776 4.04638 4.54573 -1.49217 -2.41347 2.32273 -0.00223319 0.00567932
|
||||
6 2 4.05036 1.35117 4.04739 -0.819058 0.780784 -1.73977 -2.33906 -0.00772673 -0.00122181
|
||||
ITEM: TIMESTEP
|
||||
7
|
||||
ITEM: NUMBER OF ATOMS
|
||||
6
|
||||
ITEM: BOX BOUNDS xy xz yz pp pp pp
|
||||
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
ITEM: ATOMS id type x y z vx vy vz fx fy fz
|
||||
1 1 2.69895 2.70059 -0.00152695 -0.600322 0.336519 -0.872794 0.0330853 0.0256435 -0.0109212
|
||||
2 2 1.36665 4.05797 1.36045 10.7228 4.55038 5.96665 2.24601 -0.0174443 -0.0143597
|
||||
3 2 4.05094 4.0614 1.35068 -0.685154 6.50971 0.387385 -2.29698 -0.0173365 0.00340068
|
||||
4 1 2.69943 -0.00180639 2.70127 -0.324338 -1.03175 0.724871 0.0370626 0.020641 0.0165564
|
||||
5 2 1.35641 1.34739 4.04577 4.89536 -1.49253 -2.41254 2.31411 -0.0024977 0.00674323
|
||||
6 2 4.05012 1.35137 4.04696 -1.17137 0.779522 -1.73997 -2.33329 -0.00900604 -0.00141944
|
||||
ITEM: TIMESTEP
|
||||
8
|
||||
ITEM: NUMBER OF ATOMS
|
||||
6
|
||||
ITEM: BOX BOUNDS xy xz yz pp pp pp
|
||||
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
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||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
ITEM: ATOMS id type x y z vx vy vz fx fy fz
|
||||
1 1 2.6988 2.70067 -0.00174516 -0.599962 0.336797 -0.872914 0.0379108 0.0291262 -0.0126661
|
||||
2 2 1.36938 4.05911 1.36194 11.06 4.54752 5.96429 2.2259 -0.0205196 -0.0168834
|
||||
3 2 4.05073 4.06303 1.35077 -1.03064 6.50691 0.387927 -2.28482 -0.0198564 0.00378025
|
||||
4 1 2.69935 -0.0020643 2.70145 -0.323932 -1.03153 0.725054 0.0430788 0.0242538 0.0195348
|
||||
5 2 1.35768 1.34702 4.04517 5.24362 -1.49292 -2.41144 2.30452 -0.0027252 0.00784692
|
||||
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|
||||
ITEM: TIMESTEP
|
||||
9
|
||||
ITEM: NUMBER OF ATOMS
|
||||
6
|
||||
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|
||||
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
ITEM: ATOMS id type x y z vx vy vz fx fy fz
|
||||
1 1 2.69865 2.70076 -0.0019634 -0.599553 0.337109 -0.873051 0.0427817 0.0325667 -0.0144547
|
||||
2 2 1.37218 4.06025 1.36343 11.3941 4.54418 5.96155 2.20459 -0.023759 -0.019538
|
||||
3 2 4.05043 4.06466 1.35087 -1.37421 6.50372 0.388522 -2.27166 -0.0224003 0.00411244
|
||||
4 1 2.69927 -0.00232215 2.70163 -0.323464 -1.03126 0.725268 0.0492987 0.0280495 0.0226874
|
||||
5 2 1.35904 1.34664 4.04457 5.59036 -1.49335 -2.41017 2.29396 -0.00291347 0.00899259
|
||||
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|
||||
ITEM: TIMESTEP
|
||||
10
|
||||
ITEM: NUMBER OF ATOMS
|
||||
6
|
||||
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|
||||
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
ITEM: ATOMS id type x y z vx vy vz fx fy fz
|
||||
1 1 2.6985 2.70084 -0.00218168 -0.599095 0.337456 -0.873207 0.0477049 0.0359661 -0.0162858
|
||||
2 2 1.37507 4.06138 1.36492 11.7248 4.54034 5.95839 2.18206 -0.0271682 -0.0223275
|
||||
3 2 4.05004 4.06628 1.35097 -1.71572 6.50015 0.389163 -2.25748 -0.0249726 0.0043903
|
||||
4 1 2.69919 -0.00257993 2.70181 -0.322932 -1.03096 0.725515 0.0557294 0.0320331 0.0260207
|
||||
5 2 1.36048 1.34627 4.04397 5.93543 -1.4938 -2.40872 2.2824 -0.00306026 0.0101825
|
||||
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|
||||
ITEM: TIMESTEP
|
||||
11
|
||||
ITEM: NUMBER OF ATOMS
|
||||
6
|
||||
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|
||||
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
ITEM: ATOMS id type x y z vx vy vz fx fy fz
|
||||
1 1 2.69835 2.70092 -0.00240001 -0.598586 0.337838 -0.873382 0.0526872 0.0393256 -0.0181586
|
||||
2 2 1.37805 4.06252 1.36641 12.0521 4.53597 5.9548 2.15829 -0.0307526 -0.0252554
|
||||
3 2 4.04957 4.06791 1.35106 -2.05501 6.49619 0.389841 -2.24228 -0.0275775 0.00460683
|
||||
4 1 2.69911 -0.00283763 2.70199 -0.322334 -1.03061 0.725796 0.0623777 0.0362096 0.0295409
|
||||
5 2 1.362 1.3459 4.04336 6.27868 -1.49427 -2.40709 2.26985 -0.00316333 0.0114188
|
||||
6 2 4.04824 1.35215 4.04522 -2.56981 0.772563 -1.74105 -2.30093 -0.0140417 -0.00215255
|
||||
ITEM: TIMESTEP
|
||||
12
|
||||
ITEM: NUMBER OF ATOMS
|
||||
6
|
||||
ITEM: BOX BOUNDS xy xz yz pp pp pp
|
||||
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
ITEM: ATOMS id type x y z vx vy vz fx fy fz
|
||||
1 1 2.6982 2.70101 -0.00261837 -0.598027 0.338253 -0.873575 0.0577351 0.0426463 -0.0200718
|
||||
2 2 1.3811 4.06365 1.3679 12.3757 4.53105 5.95076 2.13326 -0.0345179 -0.0283253
|
||||
3 2 4.04901 4.06953 1.35116 -2.39194 6.49183 0.390547 -2.22604 -0.0302194 0.00475506
|
||||
4 1 2.69903 -0.00309524 2.70217 -0.321667 -1.03022 0.726114 0.06925 0.0405836 0.0332542
|
||||
5 2 1.36362 1.34552 4.04276 6.61997 -1.49475 -2.40527 2.25627 -0.00322051 0.0127037
|
||||
6 2 4.04756 1.35234 4.04478 -2.91602 0.770353 -1.74139 -2.29048 -0.0152721 -0.00231583
|
||||
ITEM: TIMESTEP
|
||||
13
|
||||
ITEM: NUMBER OF ATOMS
|
||||
6
|
||||
ITEM: BOX BOUNDS xy xz yz pp pp pp
|
||||
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
ITEM: ATOMS id type x y z vx vy vz fx fy fz
|
||||
1 1 2.69805 2.70109 -0.00283679 -0.597416 0.338702 -0.873788 0.0628554 0.0459295 -0.0220243
|
||||
2 2 1.38423 4.06478 1.36939 12.6954 4.52555 5.94625 2.10694 -0.0384688 -0.0315401
|
||||
3 2 4.04837 4.07115 1.35126 -2.72634 6.48707 0.39127 -2.20874 -0.0329024 0.00482793
|
||||
4 1 2.69895 -0.00335274 2.70236 -0.320929 -1.02979 0.726471 0.0763523 0.0451591 0.0371659
|
||||
5 2 1.36531 1.34515 4.04216 6.95912 -1.49523 -2.40326 2.24165 -0.00322965 0.0140393
|
||||
6 2 4.04678 1.35253 4.04434 -3.26057 0.767958 -1.74175 -2.27906 -0.0164877 -0.0024688
|
||||
ITEM: TIMESTEP
|
||||
14
|
||||
ITEM: NUMBER OF ATOMS
|
||||
6
|
||||
ITEM: BOX BOUNDS xy xz yz pp pp pp
|
||||
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
ITEM: ATOMS id type x y z vx vy vz fx fy fz
|
||||
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|
||||
2 2 1.38745 4.06591 1.37087 13.0111 4.51944 5.94124 2.07932 -0.0426096 -0.0349018
|
||||
3 2 4.04765 4.07277 1.35136 -3.05804 6.4819 0.391997 -2.19038 -0.035631 0.00481829
|
||||
4 1 2.69887 -0.00361013 2.70254 -0.320118 -1.0293 0.726868 0.0836894 0.0499393 0.0412807
|
||||
5 2 1.3671 1.34478 4.04156 7.296 -1.49572 -2.40103 2.22598 -0.00318867 0.0154277
|
||||
6 2 4.04593 1.35272 4.04391 -3.60334 0.765381 -1.74213 -2.26667 -0.0176868 -0.00261028
|
||||
ITEM: TIMESTEP
|
||||
15
|
||||
ITEM: NUMBER OF ATOMS
|
||||
6
|
||||
ITEM: BOX BOUNDS xy xz yz pp pp pp
|
||||
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
ITEM: ATOMS id type x y z vx vy vz fx fy fz
|
||||
1 1 2.69775 2.70126 -0.0032738 -0.596036 0.339698 -0.874275 0.0733392 0.0523895 -0.0260413
|
||||
2 2 1.39074 4.06704 1.37236 13.3225 4.51268 5.93571 2.05037 -0.0469451 -0.0384133
|
||||
3 2 4.04685 4.07439 1.35146 -3.3869 6.47632 0.392716 -2.17093 -0.038409 0.00471919
|
||||
4 1 2.69879 -0.00386739 2.70272 -0.319232 -1.02877 0.727309 0.0912666 0.0549279 0.0456036
|
||||
5 2 1.36896 1.3444 4.04096 7.63043 -1.49619 -2.3986 2.20924 -0.00309551 0.0168709
|
||||
6 2 4.04498 1.35291 4.04347 -3.94416 0.762625 -1.74253 -2.25329 -0.0188678 -0.0027391
|
||||
ITEM: TIMESTEP
|
||||
16
|
||||
ITEM: NUMBER OF ATOMS
|
||||
6
|
||||
ITEM: BOX BOUNDS xy xz yz pp pp pp
|
||||
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
ITEM: ATOMS id type x y z vx vy vz fx fy fz
|
||||
1 1 2.6976 2.70135 -0.00349241 -0.595266 0.340245 -0.87455 0.0787153 0.055569 -0.0281032
|
||||
2 2 1.39411 4.06817 1.37384 13.6294 4.50526 5.92964 2.02007 -0.0514799 -0.042077
|
||||
3 2 4.04596 4.07601 1.35155 -3.71274 6.47031 0.393413 -2.15039 -0.0412405 0.00452364
|
||||
4 1 2.69871 -0.00412452 2.7029 -0.318268 -1.02819 0.727794 0.0990893 0.0601283 0.0501398
|
||||
5 2 1.37091 1.34403 4.04036 7.96225 -1.49665 -2.39594 2.19142 -0.00294819 0.0183708
|
||||
6 2 4.04395 1.3531 4.04304 -4.28288 0.759692 -1.74296 -2.2389 -0.0200287 -0.00285406
|
||||
ITEM: TIMESTEP
|
||||
17
|
||||
ITEM: NUMBER OF ATOMS
|
||||
6
|
||||
ITEM: BOX BOUNDS xy xz yz pp pp pp
|
||||
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
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||||
ITEM: ATOMS id type x y z vx vy vz fx fy fz
|
||||
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|
||||
2 2 1.39755 4.0693 1.37532 13.9317 4.49714 5.92301 1.9884 -0.0562187 -0.0458954
|
||||
3 2 4.04499 4.07763 1.35165 -4.0354 6.46388 0.394073 -2.12872 -0.0441293 0.0042247
|
||||
4 1 2.69863 -0.00438149 2.70308 -0.317223 -1.02755 0.728326 0.107162 0.0655439 0.054894
|
||||
5 2 1.37294 1.34365 4.03976 8.2913 -1.49708 -2.39305 2.17248 -0.00274479 0.0199293
|
||||
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|
||||
ITEM: TIMESTEP
|
||||
18
|
||||
ITEM: NUMBER OF ATOMS
|
||||
6
|
||||
ITEM: BOX BOUNDS xy xz yz pp pp pp
|
||||
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
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||||
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|
||||
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|
||||
2 2 1.40107 4.07042 1.3768 14.229 4.48829 5.91578 1.95532 -0.0611659 -0.0498706
|
||||
3 2 4.04394 4.07924 1.35175 -4.3547 6.457 0.394679 -2.10593 -0.0470792 0.0038154
|
||||
4 1 2.69855 -0.00463829 2.70327 -0.316095 -1.02686 0.728907 0.11549 0.0711775 0.0598705
|
||||
5 2 1.37506 1.34328 4.03916 8.61741 -1.49747 -2.38993 2.15241 -0.00248344 0.0215483
|
||||
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|
||||
ITEM: TIMESTEP
|
||||
19
|
||||
ITEM: NUMBER OF ATOMS
|
||||
6
|
||||
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|
||||
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
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||||
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||||
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|
||||
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|
||||
2 2 1.40467 4.07154 1.37828 14.5213 4.47868 5.90795 1.92083 -0.0663258 -0.0540045
|
||||
3 2 4.04281 4.08086 1.35185 -4.67049 6.44967 0.395215 -2.08198 -0.050094 0.00328881
|
||||
4 1 2.69847 -0.00489492 2.70345 -0.314881 -1.02611 0.72954 0.124076 0.0770317 0.0650736
|
||||
5 2 1.37725 1.3429 4.03857 8.94041 -1.49782 -2.38655 2.13119 -0.00216234 0.0232295
|
||||
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|
||||
ITEM: TIMESTEP
|
||||
20
|
||||
ITEM: NUMBER OF ATOMS
|
||||
6
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||||
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0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
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||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
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||||
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||||
ITEM: ATOMS id type x y z vx vy vz fx fy fz
|
||||
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|
||||
2 2 1.40833 4.07266 1.37976 14.8083 4.46827 5.89948 1.88489 -0.0717024 -0.0582989
|
||||
3 2 4.0416 4.08247 1.35195 -4.98257 6.44189 0.395662 -2.05686 -0.0531772 0.00263798
|
||||
4 1 2.69839 -0.00515135 2.70363 -0.313579 -1.0253 0.730227 0.132925 0.0831089 0.0705072
|
||||
5 2 1.37953 1.34253 4.03797 9.26012 -1.49812 -2.38291 2.1088 -0.00177977 0.0249746
|
||||
6 2 4.039 1.35386 4.04129 -5.61376 0.746262 -1.74478 -2.171 -0.0244362 -0.00315046
|
||||
@ -1,315 +0,0 @@
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||||
ITEM: TIMESTEP
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||||
0
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||||
ITEM: NUMBER OF ATOMS
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||||
6
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||||
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||||
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||||
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||||
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|
||||
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|
||||
2 2 1.35 4.05 1.35 8.2897 4.55901 5.97376 2.35473 2.21578e-14 7.40069e-15
|
||||
3 2 4.05 4.05 1.35 1.7742 6.51885 0.385522 -2.35473 2.97071e-15 -2.01341e-14
|
||||
4 1 2.7 1.65327e-16 2.7 -0.325605 -1.03244 0.724324 -2.90278e-14 6.77422e-15 2.86766e-15
|
||||
5 2 1.35 1.35 4.05 2.42711 -1.49109 -2.41596 2.35473 5.79901e-15 -1.19594e-14
|
||||
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|
||||
ITEM: TIMESTEP
|
||||
1
|
||||
ITEM: NUMBER OF ATOMS
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||||
6
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||||
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||||
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||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
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||||
ITEM: ATOMS id type x y z vx vy vz fx fy fz
|
||||
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|
||||
2 2 1.35212 4.05114 1.35149 8.64389 4.55886 5.97363 2.34251 -0.00209926 -0.00172976
|
||||
3 2 4.0504 4.05163 1.3501 1.41949 6.51866 0.385561 -2.34936 -0.00247497 0.00051716
|
||||
4 1 2.69992 -0.00025811 2.70018 -0.325581 -1.03243 0.724334 0.00481137 0.00249244 0.00195665
|
||||
5 2 1.35065 1.34963 4.0494 2.78199 -1.49112 -2.4159 2.3517 -0.00043711 0.000874754
|
||||
6 2 4.05028 1.3502 4.04957 0.951796 0.784184 -1.73923 -2.35436 -0.00128625 -0.00020256
|
||||
ITEM: TIMESTEP
|
||||
2
|
||||
ITEM: NUMBER OF ATOMS
|
||||
6
|
||||
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|
||||
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|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
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||||
ITEM: ATOMS id type x y z vx vy vz fx fy fz
|
||||
1 1 2.6997 2.70017 -0.000436214 -0.601396 0.335673 -0.872449 0.00939888 0.00756163 -0.00288164
|
||||
2 2 1.35432 4.05228 1.35299 8.99615 4.55837 5.97323 2.32921 -0.00431846 -0.00355855
|
||||
3 2 4.05071 4.05326 1.35019 1.06567 6.5181 0.385678 -2.34304 -0.00494314 0.00103532
|
||||
4 1 2.69984 -0.000516214 2.70036 -0.325507 -1.03239 0.724364 0.00976944 0.00512657 0.00403686
|
||||
5 2 1.35139 1.34925 4.04879 3.13634 -1.49122 -2.4157 2.34776 -0.000851489 0.00177498
|
||||
6 2 4.05048 1.35039 4.04913 0.596838 0.783892 -1.73928 -2.3531 -0.00257512 -0.000406965
|
||||
ITEM: TIMESTEP
|
||||
3
|
||||
ITEM: NUMBER OF ATOMS
|
||||
6
|
||||
ITEM: BOX BOUNDS xy xz yz pp pp pp
|
||||
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
ITEM: ATOMS id type x y z vx vy vz fx fy fz
|
||||
1 1 2.69955 2.70025 -0.00065433 -0.601277 0.335769 -0.872486 0.0141006 0.0112702 -0.00439552
|
||||
2 2 1.35661 4.05342 1.35448 9.34633 4.55754 5.97255 2.31482 -0.00666433 -0.00549143
|
||||
3 2 4.05093 4.05489 1.35029 0.712875 6.51717 0.385873 -2.33577 -0.00740896 0.00154764
|
||||
4 1 2.69976 -0.000774304 2.70054 -0.325382 -1.03232 0.724417 0.0148831 0.00790884 0.00624833
|
||||
5 2 1.35222 1.34888 4.04819 3.49003 -1.49137 -2.41536 2.3429 -0.0012407 0.00270313
|
||||
6 2 4.05058 1.35059 4.0487 0.242138 0.783407 -1.73935 -2.35094 -0.00386511 -0.000612161
|
||||
ITEM: TIMESTEP
|
||||
4
|
||||
ITEM: NUMBER OF ATOMS
|
||||
6
|
||||
ITEM: BOX BOUNDS xy xz yz pp pp pp
|
||||
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
ITEM: ATOMS id type x y z vx vy vz fx fy fz
|
||||
1 1 2.6994 2.70034 -0.000872457 -0.60111 0.335902 -0.872539 0.0188131 0.0149318 -0.00595718
|
||||
2 2 1.359 4.05456 1.35597 9.69425 4.55635 5.97156 2.29933 -0.00914346 -0.00753331
|
||||
3 2 4.05107 4.05652 1.35039 0.361248 6.51586 0.386144 -2.32753 -0.00987687 0.00204727
|
||||
4 1 2.69967 -0.00103238 2.70072 -0.325204 -1.03223 0.724492 0.020161 0.0108455 0.00859866
|
||||
5 2 1.35314 1.34851 4.04758 3.84292 -1.49159 -2.41488 2.33711 -0.00160232 0.00366164
|
||||
6 2 4.0506 1.35078 4.04826 -0.112168 0.782727 -1.73946 -2.34789 -0.00515472 -0.000817084
|
||||
ITEM: TIMESTEP
|
||||
5
|
||||
ITEM: NUMBER OF ATOMS
|
||||
6
|
||||
ITEM: BOX BOUNDS xy xz yz pp pp pp
|
||||
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
ITEM: ATOMS id type x y z vx vy vz fx fy fz
|
||||
1 1 2.69925 2.70042 -0.0010906 -0.600896 0.336071 -0.872607 0.0235434 0.0185473 -0.00756588
|
||||
2 2 1.36146 4.0557 1.35747 10.0397 4.55478 5.97026 2.2827 -0.0117623 -0.00968894
|
||||
3 2 4.05111 4.05815 1.35048 0.0109366 6.51419 0.386489 -2.31832 -0.0123511 0.00252727
|
||||
4 1 2.69959 -0.00129042 2.70091 -0.324972 -1.0321 0.724592 0.0256115 0.0139425 0.0110953
|
||||
5 2 1.35414 1.34814 4.04698 4.19487 -1.49186 -2.41425 2.33039 -0.00193394 0.0046529
|
||||
6 2 4.05052 1.35098 4.04783 -0.465946 0.781852 -1.7396 -2.34393 -0.00644244 -0.00102066
|
||||
ITEM: TIMESTEP
|
||||
6
|
||||
ITEM: NUMBER OF ATOMS
|
||||
6
|
||||
ITEM: BOX BOUNDS xy xz yz pp pp pp
|
||||
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
ITEM: ATOMS id type x y z vx vy vz fx fy fz
|
||||
1 1 2.6991 2.7005 -0.00130876 -0.600633 0.336277 -0.872692 0.0282985 0.0221175 -0.00922083
|
||||
2 2 1.36401 4.05684 1.35896 10.3827 4.55279 5.96863 2.26494 -0.0145272 -0.0119629
|
||||
3 2 4.05107 4.05978 1.35058 -0.337913 6.51214 0.386904 -2.30814 -0.0148362 0.00298071
|
||||
4 1 2.69951 -0.00154843 2.70109 -0.324684 -1.03194 0.724717 0.0312427 0.0172058 0.0137455
|
||||
5 2 1.35523 1.34776 4.04638 4.54573 -1.49217 -2.41347 2.32273 -0.00223319 0.00567932
|
||||
6 2 4.05036 1.35117 4.04739 -0.819058 0.780784 -1.73977 -2.33906 -0.00772673 -0.00122181
|
||||
ITEM: TIMESTEP
|
||||
7
|
||||
ITEM: NUMBER OF ATOMS
|
||||
6
|
||||
ITEM: BOX BOUNDS xy xz yz pp pp pp
|
||||
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
ITEM: ATOMS id type x y z vx vy vz fx fy fz
|
||||
1 1 2.69895 2.70059 -0.00152695 -0.600322 0.336519 -0.872794 0.0330853 0.0256435 -0.0109212
|
||||
2 2 1.36665 4.05797 1.36045 10.7228 4.55038 5.96665 2.24601 -0.0174443 -0.0143597
|
||||
3 2 4.05094 4.0614 1.35068 -0.685154 6.50971 0.387385 -2.29698 -0.0173365 0.00340068
|
||||
4 1 2.69943 -0.00180639 2.70127 -0.324338 -1.03175 0.724871 0.0370626 0.020641 0.0165564
|
||||
5 2 1.35641 1.34739 4.04577 4.89536 -1.49253 -2.41254 2.31411 -0.0024977 0.00674323
|
||||
6 2 4.05012 1.35137 4.04696 -1.17137 0.779522 -1.73997 -2.33329 -0.00900604 -0.00141944
|
||||
ITEM: TIMESTEP
|
||||
8
|
||||
ITEM: NUMBER OF ATOMS
|
||||
6
|
||||
ITEM: BOX BOUNDS xy xz yz pp pp pp
|
||||
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
ITEM: ATOMS id type x y z vx vy vz fx fy fz
|
||||
1 1 2.6988 2.70067 -0.00174516 -0.599962 0.336797 -0.872914 0.0379108 0.0291262 -0.0126661
|
||||
2 2 1.36938 4.05911 1.36194 11.06 4.54752 5.96429 2.2259 -0.0205196 -0.0168834
|
||||
3 2 4.05073 4.06303 1.35077 -1.03064 6.50691 0.387927 -2.28482 -0.0198564 0.00378025
|
||||
4 1 2.69935 -0.0020643 2.70145 -0.323932 -1.03153 0.725054 0.0430788 0.0242538 0.0195348
|
||||
5 2 1.35768 1.34702 4.04517 5.24362 -1.49292 -2.41144 2.30452 -0.0027252 0.00784692
|
||||
6 2 4.04978 1.35156 4.04652 -1.52274 0.778068 -1.7402 -2.32659 -0.0102788 -0.00161245
|
||||
ITEM: TIMESTEP
|
||||
9
|
||||
ITEM: NUMBER OF ATOMS
|
||||
6
|
||||
ITEM: BOX BOUNDS xy xz yz pp pp pp
|
||||
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
ITEM: ATOMS id type x y z vx vy vz fx fy fz
|
||||
1 1 2.69865 2.70076 -0.0019634 -0.599553 0.337109 -0.873051 0.0427817 0.0325667 -0.0144547
|
||||
2 2 1.37218 4.06025 1.36343 11.3941 4.54418 5.96155 2.20459 -0.023759 -0.019538
|
||||
3 2 4.05043 4.06466 1.35087 -1.37421 6.50372 0.388522 -2.27166 -0.0224003 0.00411244
|
||||
4 1 2.69927 -0.00232215 2.70163 -0.323464 -1.03126 0.725268 0.0492987 0.0280495 0.0226874
|
||||
5 2 1.35904 1.34664 4.04457 5.59036 -1.49335 -2.41017 2.29396 -0.00291347 0.00899259
|
||||
6 2 4.04935 1.35176 4.04609 -1.87303 0.776422 -1.74045 -2.31898 -0.0115434 -0.00179972
|
||||
ITEM: TIMESTEP
|
||||
10
|
||||
ITEM: NUMBER OF ATOMS
|
||||
6
|
||||
ITEM: BOX BOUNDS xy xz yz pp pp pp
|
||||
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
ITEM: ATOMS id type x y z vx vy vz fx fy fz
|
||||
1 1 2.6985 2.70084 -0.00218168 -0.599095 0.337456 -0.873207 0.0477049 0.0359661 -0.0162858
|
||||
2 2 1.37507 4.06138 1.36492 11.7248 4.54034 5.95839 2.18206 -0.0271682 -0.0223275
|
||||
3 2 4.05004 4.06628 1.35097 -1.71572 6.50015 0.389163 -2.25748 -0.0249726 0.0043903
|
||||
4 1 2.69919 -0.00257993 2.70181 -0.322932 -1.03096 0.725515 0.0557294 0.0320331 0.0260207
|
||||
5 2 1.36048 1.34627 4.04397 5.93543 -1.4938 -2.40872 2.2824 -0.00306026 0.0101825
|
||||
6 2 4.04884 1.35195 4.04565 -2.2221 0.774587 -1.74074 -2.31042 -0.0127983 -0.00198013
|
||||
ITEM: TIMESTEP
|
||||
11
|
||||
ITEM: NUMBER OF ATOMS
|
||||
6
|
||||
ITEM: BOX BOUNDS xy xz yz pp pp pp
|
||||
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
ITEM: ATOMS id type x y z vx vy vz fx fy fz
|
||||
1 1 2.69835 2.70092 -0.00240001 -0.598586 0.337838 -0.873382 0.0526872 0.0393256 -0.0181586
|
||||
2 2 1.37805 4.06252 1.36641 12.0521 4.53597 5.9548 2.15829 -0.0307526 -0.0252554
|
||||
3 2 4.04957 4.06791 1.35106 -2.05501 6.49619 0.389841 -2.24228 -0.0275775 0.00460683
|
||||
4 1 2.69911 -0.00283763 2.70199 -0.322334 -1.03061 0.725796 0.0623777 0.0362096 0.0295409
|
||||
5 2 1.362 1.3459 4.04336 6.27868 -1.49427 -2.40709 2.26985 -0.00316333 0.0114188
|
||||
6 2 4.04824 1.35215 4.04522 -2.56981 0.772563 -1.74105 -2.30093 -0.0140417 -0.00215255
|
||||
ITEM: TIMESTEP
|
||||
12
|
||||
ITEM: NUMBER OF ATOMS
|
||||
6
|
||||
ITEM: BOX BOUNDS xy xz yz pp pp pp
|
||||
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
ITEM: ATOMS id type x y z vx vy vz fx fy fz
|
||||
1 1 2.6982 2.70101 -0.00261837 -0.598027 0.338253 -0.873575 0.0577351 0.0426463 -0.0200718
|
||||
2 2 1.3811 4.06365 1.3679 12.3757 4.53105 5.95076 2.13326 -0.0345179 -0.0283253
|
||||
3 2 4.04901 4.06953 1.35116 -2.39194 6.49183 0.390547 -2.22604 -0.0302194 0.00475506
|
||||
4 1 2.69903 -0.00309524 2.70217 -0.321667 -1.03022 0.726114 0.06925 0.0405836 0.0332542
|
||||
5 2 1.36362 1.34552 4.04276 6.61997 -1.49475 -2.40527 2.25627 -0.00322051 0.0127037
|
||||
6 2 4.04756 1.35234 4.04478 -2.91602 0.770353 -1.74139 -2.29048 -0.0152721 -0.00231583
|
||||
ITEM: TIMESTEP
|
||||
13
|
||||
ITEM: NUMBER OF ATOMS
|
||||
6
|
||||
ITEM: BOX BOUNDS xy xz yz pp pp pp
|
||||
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
ITEM: ATOMS id type x y z vx vy vz fx fy fz
|
||||
1 1 2.69805 2.70109 -0.00283679 -0.597416 0.338702 -0.873788 0.0628554 0.0459295 -0.0220243
|
||||
2 2 1.38423 4.06478 1.36939 12.6954 4.52555 5.94625 2.10694 -0.0384688 -0.0315401
|
||||
3 2 4.04837 4.07115 1.35126 -2.72634 6.48707 0.39127 -2.20874 -0.0329024 0.00482793
|
||||
4 1 2.69895 -0.00335274 2.70236 -0.320929 -1.02979 0.726471 0.0763523 0.0451591 0.0371659
|
||||
5 2 1.36531 1.34515 4.04216 6.95912 -1.49523 -2.40326 2.24165 -0.00322965 0.0140393
|
||||
6 2 4.04678 1.35253 4.04434 -3.26057 0.767958 -1.74175 -2.27906 -0.0164877 -0.0024688
|
||||
ITEM: TIMESTEP
|
||||
14
|
||||
ITEM: NUMBER OF ATOMS
|
||||
6
|
||||
ITEM: BOX BOUNDS xy xz yz pp pp pp
|
||||
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
ITEM: ATOMS id type x y z vx vy vz fx fy fz
|
||||
1 1 2.6979 2.70118 -0.00305527 -0.596753 0.339184 -0.874022 0.0680546 0.0491768 -0.0240145
|
||||
2 2 1.38745 4.06591 1.37087 13.0111 4.51944 5.94124 2.07932 -0.0426096 -0.0349018
|
||||
3 2 4.04765 4.07277 1.35136 -3.05804 6.4819 0.391997 -2.19038 -0.035631 0.00481829
|
||||
4 1 2.69887 -0.00361013 2.70254 -0.320118 -1.0293 0.726868 0.0836894 0.0499393 0.0412807
|
||||
5 2 1.3671 1.34478 4.04156 7.296 -1.49572 -2.40103 2.22598 -0.00318867 0.0154277
|
||||
6 2 4.04593 1.35272 4.04391 -3.60334 0.765381 -1.74213 -2.26667 -0.0176868 -0.00261028
|
||||
ITEM: TIMESTEP
|
||||
15
|
||||
ITEM: NUMBER OF ATOMS
|
||||
6
|
||||
ITEM: BOX BOUNDS xy xz yz pp pp pp
|
||||
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
ITEM: ATOMS id type x y z vx vy vz fx fy fz
|
||||
1 1 2.69775 2.70126 -0.0032738 -0.596036 0.339698 -0.874275 0.0733392 0.0523895 -0.0260413
|
||||
2 2 1.39074 4.06704 1.37236 13.3225 4.51268 5.93571 2.05037 -0.0469451 -0.0384133
|
||||
3 2 4.04685 4.07439 1.35146 -3.3869 6.47632 0.392716 -2.17093 -0.038409 0.00471919
|
||||
4 1 2.69879 -0.00386739 2.70272 -0.319232 -1.02877 0.727309 0.0912666 0.0549279 0.0456036
|
||||
5 2 1.36896 1.3444 4.04096 7.63043 -1.49619 -2.3986 2.20924 -0.00309551 0.0168709
|
||||
6 2 4.04498 1.35291 4.04347 -3.94416 0.762625 -1.74253 -2.25329 -0.0188678 -0.0027391
|
||||
ITEM: TIMESTEP
|
||||
16
|
||||
ITEM: NUMBER OF ATOMS
|
||||
6
|
||||
ITEM: BOX BOUNDS xy xz yz pp pp pp
|
||||
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
ITEM: ATOMS id type x y z vx vy vz fx fy fz
|
||||
1 1 2.6976 2.70135 -0.00349241 -0.595266 0.340245 -0.87455 0.0787153 0.055569 -0.0281032
|
||||
2 2 1.39411 4.06817 1.37384 13.6294 4.50526 5.92964 2.02007 -0.0514799 -0.042077
|
||||
3 2 4.04596 4.07601 1.35155 -3.71274 6.47031 0.393413 -2.15039 -0.0412405 0.00452364
|
||||
4 1 2.69871 -0.00412452 2.7029 -0.318268 -1.02819 0.727794 0.0990893 0.0601283 0.0501398
|
||||
5 2 1.37091 1.34403 4.04036 7.96225 -1.49665 -2.39594 2.19142 -0.00294819 0.0183708
|
||||
6 2 4.04395 1.3531 4.04304 -4.28288 0.759692 -1.74296 -2.2389 -0.0200287 -0.00285406
|
||||
ITEM: TIMESTEP
|
||||
17
|
||||
ITEM: NUMBER OF ATOMS
|
||||
6
|
||||
ITEM: BOX BOUNDS xy xz yz pp pp pp
|
||||
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
ITEM: ATOMS id type x y z vx vy vz fx fy fz
|
||||
1 1 2.69745 2.70143 -0.00371108 -0.594441 0.340824 -0.874845 0.0841889 0.0587168 -0.0301987
|
||||
2 2 1.39755 4.0693 1.37532 13.9317 4.49714 5.92301 1.9884 -0.0562187 -0.0458954
|
||||
3 2 4.04499 4.07763 1.35165 -4.0354 6.46388 0.394073 -2.12872 -0.0441293 0.0042247
|
||||
4 1 2.69863 -0.00438149 2.70308 -0.317223 -1.02755 0.728326 0.107162 0.0655439 0.054894
|
||||
5 2 1.37294 1.34365 4.03976 8.2913 -1.49708 -2.39305 2.17248 -0.00274479 0.0199293
|
||||
6 2 4.04284 1.35329 4.0426 -4.61936 0.756586 -1.74339 -2.2235 -0.0211679 -0.00295392
|
||||
ITEM: TIMESTEP
|
||||
18
|
||||
ITEM: NUMBER OF ATOMS
|
||||
6
|
||||
ITEM: BOX BOUNDS xy xz yz pp pp pp
|
||||
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
ITEM: ATOMS id type x y z vx vy vz fx fy fz
|
||||
1 1 2.69731 2.70152 -0.00392983 -0.593559 0.341435 -0.875162 0.0897661 0.0618346 -0.0323262
|
||||
2 2 1.40107 4.07042 1.3768 14.229 4.48829 5.91578 1.95532 -0.0611659 -0.0498706
|
||||
3 2 4.04394 4.07924 1.35175 -4.3547 6.457 0.394679 -2.10593 -0.0470792 0.0038154
|
||||
4 1 2.69855 -0.00463829 2.70327 -0.316095 -1.02686 0.728907 0.11549 0.0711775 0.0598705
|
||||
5 2 1.37506 1.34328 4.03916 8.61741 -1.49747 -2.38993 2.15241 -0.00248344 0.0215483
|
||||
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|
||||
ITEM: TIMESTEP
|
||||
19
|
||||
ITEM: NUMBER OF ATOMS
|
||||
6
|
||||
ITEM: BOX BOUNDS xy xz yz pp pp pp
|
||||
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
ITEM: ATOMS id type x y z vx vy vz fx fy fz
|
||||
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|
||||
2 2 1.40467 4.07154 1.37828 14.5213 4.47868 5.90795 1.92083 -0.0663258 -0.0540045
|
||||
3 2 4.04281 4.08086 1.35185 -4.67049 6.44967 0.395215 -2.08198 -0.050094 0.00328881
|
||||
4 1 2.69847 -0.00489492 2.70345 -0.314881 -1.02611 0.72954 0.124076 0.0770317 0.0650736
|
||||
5 2 1.37725 1.3429 4.03857 8.94041 -1.49782 -2.38655 2.13119 -0.00216234 0.0232295
|
||||
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|
||||
ITEM: TIMESTEP
|
||||
20
|
||||
ITEM: NUMBER OF ATOMS
|
||||
6
|
||||
ITEM: BOX BOUNDS xy xz yz pp pp pp
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||||
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
ITEM: ATOMS id type x y z vx vy vz fx fy fz
|
||||
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|
||||
2 2 1.40833 4.07266 1.37976 14.8083 4.46827 5.89948 1.88489 -0.0717024 -0.0582989
|
||||
3 2 4.0416 4.08247 1.35195 -4.98257 6.44189 0.395662 -2.05686 -0.0531772 0.00263798
|
||||
4 1 2.69839 -0.00515135 2.70363 -0.313579 -1.0253 0.730227 0.132925 0.0831089 0.0705072
|
||||
5 2 1.37953 1.34253 4.03797 9.26012 -1.49812 -2.38291 2.1088 -0.00177977 0.0249746
|
||||
6 2 4.039 1.35386 4.04129 -5.61376 0.746262 -1.74478 -2.171 -0.0244362 -0.00315046
|
||||
@ -1,315 +0,0 @@
|
||||
ITEM: TIMESTEP
|
||||
0
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ITEM: NUMBER OF ATOMS
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6
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||||
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|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
ITEM: ATOMS id type x y z vx vy vz fx fy fz
|
||||
1 1 2.7 2.7 0 -0.601491 0.335597 -0.87242 -2.27066e-14 -1.33391e-14 2.31141e-14
|
||||
2 2 1.35 4.05 1.35 8.2897 4.55901 5.97376 2.35473 2.21578e-14 7.40069e-15
|
||||
3 2 4.05 4.05 1.35 1.7742 6.51885 0.385522 -2.35473 2.97071e-15 -2.01341e-14
|
||||
4 1 2.7 1.65327e-16 2.7 -0.325605 -1.03244 0.724324 -2.90278e-14 6.77422e-15 2.86766e-15
|
||||
5 2 1.35 1.35 4.05 2.42711 -1.49109 -2.41596 2.35473 5.79901e-15 -1.19594e-14
|
||||
6 2 4.05 1.35 4.05 1.30688 0.784281 -1.73922 -2.35473 -1.38761e-14 1.09382e-14
|
||||
ITEM: TIMESTEP
|
||||
1
|
||||
ITEM: NUMBER OF ATOMS
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||||
6
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||||
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||||
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|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
ITEM: ATOMS id type x y z vx vy vz fx fy fz
|
||||
1 1 2.69985 2.70008 -0.000218105 -0.601467 0.335616 -0.872428 0.00470101 0.00380515 -0.00141625
|
||||
2 2 1.35212 4.05114 1.35149 8.64389 4.55886 5.97363 2.34251 -0.00209926 -0.00172976
|
||||
3 2 4.0504 4.05163 1.3501 1.41949 6.51866 0.385561 -2.34936 -0.00247497 0.00051716
|
||||
4 1 2.69992 -0.00025811 2.70018 -0.325581 -1.03243 0.724334 0.00481137 0.00249244 0.00195665
|
||||
5 2 1.35065 1.34963 4.0494 2.78199 -1.49112 -2.4159 2.3517 -0.00043711 0.000874754
|
||||
6 2 4.05028 1.3502 4.04957 0.951796 0.784184 -1.73923 -2.35436 -0.00128625 -0.00020256
|
||||
ITEM: TIMESTEP
|
||||
2
|
||||
ITEM: NUMBER OF ATOMS
|
||||
6
|
||||
ITEM: BOX BOUNDS xy xz yz pp pp pp
|
||||
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
ITEM: ATOMS id type x y z vx vy vz fx fy fz
|
||||
1 1 2.6997 2.70017 -0.000436214 -0.601396 0.335673 -0.872449 0.00939888 0.00756163 -0.00288164
|
||||
2 2 1.35432 4.05228 1.35299 8.99615 4.55837 5.97323 2.32921 -0.00431846 -0.00355855
|
||||
3 2 4.05071 4.05326 1.35019 1.06567 6.5181 0.385678 -2.34304 -0.00494314 0.00103532
|
||||
4 1 2.69984 -0.000516214 2.70036 -0.325507 -1.03239 0.724364 0.00976944 0.00512657 0.00403686
|
||||
5 2 1.35139 1.34925 4.04879 3.13634 -1.49122 -2.4157 2.34776 -0.000851489 0.00177498
|
||||
6 2 4.05048 1.35039 4.04913 0.596838 0.783892 -1.73928 -2.3531 -0.00257512 -0.000406965
|
||||
ITEM: TIMESTEP
|
||||
3
|
||||
ITEM: NUMBER OF ATOMS
|
||||
6
|
||||
ITEM: BOX BOUNDS xy xz yz pp pp pp
|
||||
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
ITEM: ATOMS id type x y z vx vy vz fx fy fz
|
||||
1 1 2.69955 2.70025 -0.00065433 -0.601277 0.335769 -0.872486 0.0141006 0.0112702 -0.00439552
|
||||
2 2 1.35661 4.05342 1.35448 9.34633 4.55754 5.97255 2.31482 -0.00666433 -0.00549143
|
||||
3 2 4.05093 4.05489 1.35029 0.712875 6.51717 0.385873 -2.33577 -0.00740896 0.00154764
|
||||
4 1 2.69976 -0.000774304 2.70054 -0.325382 -1.03232 0.724417 0.0148831 0.00790884 0.00624833
|
||||
5 2 1.35222 1.34888 4.04819 3.49003 -1.49137 -2.41536 2.3429 -0.0012407 0.00270313
|
||||
6 2 4.05058 1.35059 4.0487 0.242138 0.783407 -1.73935 -2.35094 -0.00386511 -0.000612161
|
||||
ITEM: TIMESTEP
|
||||
4
|
||||
ITEM: NUMBER OF ATOMS
|
||||
6
|
||||
ITEM: BOX BOUNDS xy xz yz pp pp pp
|
||||
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
ITEM: ATOMS id type x y z vx vy vz fx fy fz
|
||||
1 1 2.6994 2.70034 -0.000872457 -0.60111 0.335902 -0.872539 0.0188131 0.0149318 -0.00595718
|
||||
2 2 1.359 4.05456 1.35597 9.69425 4.55635 5.97156 2.29933 -0.00914346 -0.00753331
|
||||
3 2 4.05107 4.05652 1.35039 0.361248 6.51586 0.386144 -2.32753 -0.00987687 0.00204727
|
||||
4 1 2.69967 -0.00103238 2.70072 -0.325204 -1.03223 0.724492 0.020161 0.0108455 0.00859866
|
||||
5 2 1.35314 1.34851 4.04758 3.84292 -1.49159 -2.41488 2.33711 -0.00160232 0.00366164
|
||||
6 2 4.0506 1.35078 4.04826 -0.112168 0.782727 -1.73946 -2.34789 -0.00515472 -0.000817084
|
||||
ITEM: TIMESTEP
|
||||
5
|
||||
ITEM: NUMBER OF ATOMS
|
||||
6
|
||||
ITEM: BOX BOUNDS xy xz yz pp pp pp
|
||||
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
ITEM: ATOMS id type x y z vx vy vz fx fy fz
|
||||
1 1 2.69925 2.70042 -0.0010906 -0.600896 0.336071 -0.872607 0.0235434 0.0185473 -0.00756588
|
||||
2 2 1.36146 4.0557 1.35747 10.0397 4.55478 5.97026 2.2827 -0.0117623 -0.00968894
|
||||
3 2 4.05111 4.05815 1.35048 0.0109366 6.51419 0.386489 -2.31832 -0.0123511 0.00252727
|
||||
4 1 2.69959 -0.00129042 2.70091 -0.324972 -1.0321 0.724592 0.0256115 0.0139425 0.0110953
|
||||
5 2 1.35414 1.34814 4.04698 4.19487 -1.49186 -2.41425 2.33039 -0.00193394 0.0046529
|
||||
6 2 4.05052 1.35098 4.04783 -0.465946 0.781852 -1.7396 -2.34393 -0.00644244 -0.00102066
|
||||
ITEM: TIMESTEP
|
||||
6
|
||||
ITEM: NUMBER OF ATOMS
|
||||
6
|
||||
ITEM: BOX BOUNDS xy xz yz pp pp pp
|
||||
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
ITEM: ATOMS id type x y z vx vy vz fx fy fz
|
||||
1 1 2.6991 2.7005 -0.00130876 -0.600633 0.336277 -0.872692 0.0282985 0.0221175 -0.00922083
|
||||
2 2 1.36401 4.05684 1.35896 10.3827 4.55279 5.96863 2.26494 -0.0145272 -0.0119629
|
||||
3 2 4.05107 4.05978 1.35058 -0.337913 6.51214 0.386904 -2.30814 -0.0148362 0.00298071
|
||||
4 1 2.69951 -0.00154843 2.70109 -0.324684 -1.03194 0.724717 0.0312427 0.0172058 0.0137455
|
||||
5 2 1.35523 1.34776 4.04638 4.54573 -1.49217 -2.41347 2.32273 -0.00223319 0.00567932
|
||||
6 2 4.05036 1.35117 4.04739 -0.819058 0.780784 -1.73977 -2.33906 -0.00772673 -0.00122181
|
||||
ITEM: TIMESTEP
|
||||
7
|
||||
ITEM: NUMBER OF ATOMS
|
||||
6
|
||||
ITEM: BOX BOUNDS xy xz yz pp pp pp
|
||||
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
ITEM: ATOMS id type x y z vx vy vz fx fy fz
|
||||
1 1 2.69895 2.70059 -0.00152695 -0.600322 0.336519 -0.872794 0.0330853 0.0256435 -0.0109212
|
||||
2 2 1.36665 4.05797 1.36045 10.7228 4.55038 5.96665 2.24601 -0.0174443 -0.0143597
|
||||
3 2 4.05094 4.0614 1.35068 -0.685154 6.50971 0.387385 -2.29698 -0.0173365 0.00340068
|
||||
4 1 2.69943 -0.00180639 2.70127 -0.324338 -1.03175 0.724871 0.0370626 0.020641 0.0165564
|
||||
5 2 1.35641 1.34739 4.04577 4.89536 -1.49253 -2.41254 2.31411 -0.0024977 0.00674323
|
||||
6 2 4.05012 1.35137 4.04696 -1.17137 0.779522 -1.73997 -2.33329 -0.00900604 -0.00141944
|
||||
ITEM: TIMESTEP
|
||||
8
|
||||
ITEM: NUMBER OF ATOMS
|
||||
6
|
||||
ITEM: BOX BOUNDS xy xz yz pp pp pp
|
||||
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
ITEM: ATOMS id type x y z vx vy vz fx fy fz
|
||||
1 1 2.6988 2.70067 -0.00174516 -0.599962 0.336797 -0.872914 0.0379108 0.0291262 -0.0126661
|
||||
2 2 1.36938 4.05911 1.36194 11.06 4.54752 5.96429 2.2259 -0.0205196 -0.0168834
|
||||
3 2 4.05073 4.06303 1.35077 -1.03064 6.50691 0.387927 -2.28482 -0.0198564 0.00378025
|
||||
4 1 2.69935 -0.0020643 2.70145 -0.323932 -1.03153 0.725054 0.0430788 0.0242538 0.0195348
|
||||
5 2 1.35768 1.34702 4.04517 5.24362 -1.49292 -2.41144 2.30452 -0.0027252 0.00784692
|
||||
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|
||||
ITEM: TIMESTEP
|
||||
9
|
||||
ITEM: NUMBER OF ATOMS
|
||||
6
|
||||
ITEM: BOX BOUNDS xy xz yz pp pp pp
|
||||
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
ITEM: ATOMS id type x y z vx vy vz fx fy fz
|
||||
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|
||||
2 2 1.37218 4.06025 1.36343 11.3941 4.54418 5.96155 2.20459 -0.023759 -0.019538
|
||||
3 2 4.05043 4.06466 1.35087 -1.37421 6.50372 0.388522 -2.27166 -0.0224003 0.00411244
|
||||
4 1 2.69927 -0.00232215 2.70163 -0.323464 -1.03126 0.725268 0.0492987 0.0280495 0.0226874
|
||||
5 2 1.35904 1.34664 4.04457 5.59036 -1.49335 -2.41017 2.29396 -0.00291347 0.00899259
|
||||
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|
||||
ITEM: TIMESTEP
|
||||
10
|
||||
ITEM: NUMBER OF ATOMS
|
||||
6
|
||||
ITEM: BOX BOUNDS xy xz yz pp pp pp
|
||||
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
ITEM: ATOMS id type x y z vx vy vz fx fy fz
|
||||
1 1 2.6985 2.70084 -0.00218168 -0.599095 0.337456 -0.873207 0.0477049 0.0359661 -0.0162858
|
||||
2 2 1.37507 4.06138 1.36492 11.7248 4.54034 5.95839 2.18206 -0.0271682 -0.0223275
|
||||
3 2 4.05004 4.06628 1.35097 -1.71572 6.50015 0.389163 -2.25748 -0.0249726 0.0043903
|
||||
4 1 2.69919 -0.00257993 2.70181 -0.322932 -1.03096 0.725515 0.0557294 0.0320331 0.0260207
|
||||
5 2 1.36048 1.34627 4.04397 5.93543 -1.4938 -2.40872 2.2824 -0.00306026 0.0101825
|
||||
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|
||||
ITEM: TIMESTEP
|
||||
11
|
||||
ITEM: NUMBER OF ATOMS
|
||||
6
|
||||
ITEM: BOX BOUNDS xy xz yz pp pp pp
|
||||
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
ITEM: ATOMS id type x y z vx vy vz fx fy fz
|
||||
1 1 2.69835 2.70092 -0.00240001 -0.598586 0.337838 -0.873382 0.0526872 0.0393256 -0.0181586
|
||||
2 2 1.37805 4.06252 1.36641 12.0521 4.53597 5.9548 2.15829 -0.0307526 -0.0252554
|
||||
3 2 4.04957 4.06791 1.35106 -2.05501 6.49619 0.389841 -2.24228 -0.0275775 0.00460683
|
||||
4 1 2.69911 -0.00283763 2.70199 -0.322334 -1.03061 0.725796 0.0623777 0.0362096 0.0295409
|
||||
5 2 1.362 1.3459 4.04336 6.27868 -1.49427 -2.40709 2.26985 -0.00316333 0.0114188
|
||||
6 2 4.04824 1.35215 4.04522 -2.56981 0.772563 -1.74105 -2.30093 -0.0140417 -0.00215255
|
||||
ITEM: TIMESTEP
|
||||
12
|
||||
ITEM: NUMBER OF ATOMS
|
||||
6
|
||||
ITEM: BOX BOUNDS xy xz yz pp pp pp
|
||||
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
ITEM: ATOMS id type x y z vx vy vz fx fy fz
|
||||
1 1 2.6982 2.70101 -0.00261837 -0.598027 0.338253 -0.873575 0.0577351 0.0426463 -0.0200718
|
||||
2 2 1.3811 4.06365 1.3679 12.3757 4.53105 5.95076 2.13326 -0.0345179 -0.0283253
|
||||
3 2 4.04901 4.06953 1.35116 -2.39194 6.49183 0.390547 -2.22604 -0.0302194 0.00475506
|
||||
4 1 2.69903 -0.00309524 2.70217 -0.321667 -1.03022 0.726114 0.06925 0.0405836 0.0332542
|
||||
5 2 1.36362 1.34552 4.04276 6.61997 -1.49475 -2.40527 2.25627 -0.00322051 0.0127037
|
||||
6 2 4.04756 1.35234 4.04478 -2.91602 0.770353 -1.74139 -2.29048 -0.0152721 -0.00231583
|
||||
ITEM: TIMESTEP
|
||||
13
|
||||
ITEM: NUMBER OF ATOMS
|
||||
6
|
||||
ITEM: BOX BOUNDS xy xz yz pp pp pp
|
||||
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
ITEM: ATOMS id type x y z vx vy vz fx fy fz
|
||||
1 1 2.69805 2.70109 -0.00283679 -0.597416 0.338702 -0.873788 0.0628554 0.0459295 -0.0220243
|
||||
2 2 1.38423 4.06478 1.36939 12.6954 4.52555 5.94625 2.10694 -0.0384688 -0.0315401
|
||||
3 2 4.04837 4.07115 1.35126 -2.72634 6.48707 0.39127 -2.20874 -0.0329024 0.00482793
|
||||
4 1 2.69895 -0.00335274 2.70236 -0.320929 -1.02979 0.726471 0.0763523 0.0451591 0.0371659
|
||||
5 2 1.36531 1.34515 4.04216 6.95912 -1.49523 -2.40326 2.24165 -0.00322965 0.0140393
|
||||
6 2 4.04678 1.35253 4.04434 -3.26057 0.767958 -1.74175 -2.27906 -0.0164877 -0.0024688
|
||||
ITEM: TIMESTEP
|
||||
14
|
||||
ITEM: NUMBER OF ATOMS
|
||||
6
|
||||
ITEM: BOX BOUNDS xy xz yz pp pp pp
|
||||
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
ITEM: ATOMS id type x y z vx vy vz fx fy fz
|
||||
1 1 2.6979 2.70118 -0.00305527 -0.596753 0.339184 -0.874022 0.0680546 0.0491768 -0.0240145
|
||||
2 2 1.38745 4.06591 1.37087 13.0111 4.51944 5.94124 2.07932 -0.0426096 -0.0349018
|
||||
3 2 4.04765 4.07277 1.35136 -3.05804 6.4819 0.391997 -2.19038 -0.035631 0.00481829
|
||||
4 1 2.69887 -0.00361013 2.70254 -0.320118 -1.0293 0.726868 0.0836894 0.0499393 0.0412807
|
||||
5 2 1.3671 1.34478 4.04156 7.296 -1.49572 -2.40103 2.22598 -0.00318867 0.0154277
|
||||
6 2 4.04593 1.35272 4.04391 -3.60334 0.765381 -1.74213 -2.26667 -0.0176868 -0.00261028
|
||||
ITEM: TIMESTEP
|
||||
15
|
||||
ITEM: NUMBER OF ATOMS
|
||||
6
|
||||
ITEM: BOX BOUNDS xy xz yz pp pp pp
|
||||
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
ITEM: ATOMS id type x y z vx vy vz fx fy fz
|
||||
1 1 2.69775 2.70126 -0.0032738 -0.596036 0.339698 -0.874275 0.0733392 0.0523895 -0.0260413
|
||||
2 2 1.39074 4.06704 1.37236 13.3225 4.51268 5.93571 2.05037 -0.0469451 -0.0384133
|
||||
3 2 4.04685 4.07439 1.35146 -3.3869 6.47632 0.392716 -2.17093 -0.038409 0.00471919
|
||||
4 1 2.69879 -0.00386739 2.70272 -0.319232 -1.02877 0.727309 0.0912666 0.0549279 0.0456036
|
||||
5 2 1.36896 1.3444 4.04096 7.63043 -1.49619 -2.3986 2.20924 -0.00309551 0.0168709
|
||||
6 2 4.04498 1.35291 4.04347 -3.94416 0.762625 -1.74253 -2.25329 -0.0188678 -0.0027391
|
||||
ITEM: TIMESTEP
|
||||
16
|
||||
ITEM: NUMBER OF ATOMS
|
||||
6
|
||||
ITEM: BOX BOUNDS xy xz yz pp pp pp
|
||||
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
ITEM: ATOMS id type x y z vx vy vz fx fy fz
|
||||
1 1 2.6976 2.70135 -0.00349241 -0.595266 0.340245 -0.87455 0.0787153 0.055569 -0.0281032
|
||||
2 2 1.39411 4.06817 1.37384 13.6294 4.50526 5.92964 2.02007 -0.0514799 -0.042077
|
||||
3 2 4.04596 4.07601 1.35155 -3.71274 6.47031 0.393413 -2.15039 -0.0412405 0.00452364
|
||||
4 1 2.69871 -0.00412452 2.7029 -0.318268 -1.02819 0.727794 0.0990893 0.0601283 0.0501398
|
||||
5 2 1.37091 1.34403 4.04036 7.96225 -1.49665 -2.39594 2.19142 -0.00294819 0.0183708
|
||||
6 2 4.04395 1.3531 4.04304 -4.28288 0.759692 -1.74296 -2.2389 -0.0200287 -0.00285406
|
||||
ITEM: TIMESTEP
|
||||
17
|
||||
ITEM: NUMBER OF ATOMS
|
||||
6
|
||||
ITEM: BOX BOUNDS xy xz yz pp pp pp
|
||||
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
ITEM: ATOMS id type x y z vx vy vz fx fy fz
|
||||
1 1 2.69745 2.70143 -0.00371108 -0.594441 0.340824 -0.874845 0.0841889 0.0587168 -0.0301987
|
||||
2 2 1.39755 4.0693 1.37532 13.9317 4.49714 5.92301 1.9884 -0.0562187 -0.0458954
|
||||
3 2 4.04499 4.07763 1.35165 -4.0354 6.46388 0.394073 -2.12872 -0.0441293 0.0042247
|
||||
4 1 2.69863 -0.00438149 2.70308 -0.317223 -1.02755 0.728326 0.107162 0.0655439 0.054894
|
||||
5 2 1.37294 1.34365 4.03976 8.2913 -1.49708 -2.39305 2.17248 -0.00274479 0.0199293
|
||||
6 2 4.04284 1.35329 4.0426 -4.61936 0.756586 -1.74339 -2.2235 -0.0211679 -0.00295392
|
||||
ITEM: TIMESTEP
|
||||
18
|
||||
ITEM: NUMBER OF ATOMS
|
||||
6
|
||||
ITEM: BOX BOUNDS xy xz yz pp pp pp
|
||||
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
ITEM: ATOMS id type x y z vx vy vz fx fy fz
|
||||
1 1 2.69731 2.70152 -0.00392983 -0.593559 0.341435 -0.875162 0.0897661 0.0618346 -0.0323262
|
||||
2 2 1.40107 4.07042 1.3768 14.229 4.48829 5.91578 1.95532 -0.0611659 -0.0498706
|
||||
3 2 4.04394 4.07924 1.35175 -4.3547 6.457 0.394679 -2.10593 -0.0470792 0.0038154
|
||||
4 1 2.69855 -0.00463829 2.70327 -0.316095 -1.02686 0.728907 0.11549 0.0711775 0.0598705
|
||||
5 2 1.37506 1.34328 4.03916 8.61741 -1.49747 -2.38993 2.15241 -0.00248344 0.0215483
|
||||
6 2 4.04164 1.35348 4.04217 -4.95344 0.753309 -1.74385 -2.20706 -0.0222835 -0.00303744
|
||||
ITEM: TIMESTEP
|
||||
19
|
||||
ITEM: NUMBER OF ATOMS
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||||
6
|
||||
ITEM: BOX BOUNDS xy xz yz pp pp pp
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0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
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0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
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||||
ITEM: ATOMS id type x y z vx vy vz fx fy fz
|
||||
1 1 2.69716 2.7016 -0.00414866 -0.592621 0.342077 -0.8755 0.0954526 0.0649239 -0.0344841
|
||||
2 2 1.40467 4.07154 1.37828 14.5213 4.47868 5.90795 1.92083 -0.0663258 -0.0540045
|
||||
3 2 4.04281 4.08086 1.35185 -4.67049 6.44967 0.395215 -2.08198 -0.050094 0.00328881
|
||||
4 1 2.69847 -0.00489492 2.70345 -0.314881 -1.02611 0.72954 0.124076 0.0770317 0.0650736
|
||||
5 2 1.37725 1.3429 4.03857 8.94041 -1.49782 -2.38655 2.13119 -0.00216234 0.0232295
|
||||
6 2 4.04036 1.35367 4.04173 -5.28496 0.749867 -1.74431 -2.18956 -0.0233735 -0.00310338
|
||||
ITEM: TIMESTEP
|
||||
20
|
||||
ITEM: NUMBER OF ATOMS
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||||
6
|
||||
ITEM: BOX BOUNDS xy xz yz pp pp pp
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0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
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0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
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||||
ITEM: ATOMS id type x y z vx vy vz fx fy fz
|
||||
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|
||||
2 2 1.40833 4.07266 1.37976 14.8083 4.46827 5.89948 1.88489 -0.0717024 -0.0582989
|
||||
3 2 4.0416 4.08247 1.35195 -4.98257 6.44189 0.395662 -2.05686 -0.0531772 0.00263798
|
||||
4 1 2.69839 -0.00515135 2.70363 -0.313579 -1.0253 0.730227 0.132925 0.0831089 0.0705072
|
||||
5 2 1.37953 1.34253 4.03797 9.26012 -1.49812 -2.38291 2.1088 -0.00177977 0.0249746
|
||||
6 2 4.039 1.35386 4.04129 -5.61376 0.746262 -1.74478 -2.171 -0.0244362 -0.00315046
|
||||
@ -1,15 +0,0 @@
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||||
ITEM: TIMESTEP
|
||||
0
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ITEM: NUMBER OF ATOMS
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6
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0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
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||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
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||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
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|
||||
1 1 2.7 2.7 0 -2.27066e-14 -1.33391e-14 2.31141e-14
|
||||
2 2 1.35 4.05 1.35 2.35473 2.21578e-14 7.40069e-15
|
||||
3 2 4.05 4.05 1.35 -2.35473 2.97071e-15 -2.01341e-14
|
||||
4 1 2.7 1.65327e-16 2.7 -2.90278e-14 6.77422e-15 2.86766e-15
|
||||
5 2 1.35 1.35 4.05 2.35473 5.79901e-15 -1.19594e-14
|
||||
6 2 4.05 1.35 4.05 -2.35473 -1.38761e-14 1.09382e-14
|
||||
@ -1,18 +0,0 @@
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ITEM: TIMESTEP
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||||
0
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ITEM: NUMBER OF ATOMS
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||||
9
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||||
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0.0000000000000000e+00 1.6199999999999999e+01 3.3065463576978537e-16
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||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
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||||
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|
||||
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|
||||
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|
||||
3 2 4.05 4.05 1.35 -0.682428 -0.329901 -0.329901
|
||||
4 1 2.7 1.65327e-16 2.7 -8.06311e-14 -1.57101 -1.57101
|
||||
5 2 1.35 1.35 4.05 2.79365 0.684734 0.684734
|
||||
6 2 4.05 1.35 4.05 -2.79365 0.684734 0.684734
|
||||
7 1 2.7 2.7 0 -1.30843e-13 0.760572 0.760572
|
||||
8 2 1.35 4.05 1.35 0.682428 -0.329901 -0.329901
|
||||
9 2 4.05 4.05 1.35 -0.682428 -0.329901 -0.329901
|
||||
@ -1,21 +0,0 @@
|
||||
ITEM: TIMESTEP
|
||||
0
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||||
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||||
12
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||||
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||||
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
5 2 4.05 9.45 4.05 -0.999862 -1.02573 0.037629
|
||||
6 2 6.75 9.45 4.05 -1.64718 -0.119006 0.375837
|
||||
7 1 2.7 1.65327e-16 2.7 -0.211437 1.63064 -0.0728897
|
||||
8 2 1.35 1.35 4.05 0.461807 -1.3955 -1.94959
|
||||
9 2 4.05 1.35 4.05 0.708573 -1.2552 0.0543549
|
||||
10 1 5.4 0 0 0.211437 1.63064 -0.0728897
|
||||
11 2 4.05 1.35 1.35 -0.708573 -1.2552 0.0543549
|
||||
12 2 6.75 1.35 1.35 -0.461807 -1.3955 -1.94959
|
||||
@ -1,15 +0,0 @@
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||||
ITEM: TIMESTEP
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||||
0
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||||
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||||
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||||
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||||
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||||
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|
||||
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|
||||
2 2 1.35 4.05 1.35 2.35473 2.21578e-14 7.40069e-15
|
||||
3 2 4.05 4.05 1.35 -2.35473 2.97071e-15 -2.01341e-14
|
||||
4 1 2.7 1.65327e-16 2.7 -2.90278e-14 6.77422e-15 2.86766e-15
|
||||
5 2 1.35 1.35 4.05 2.35473 5.79901e-15 -1.19594e-14
|
||||
6 2 4.05 1.35 4.05 -2.35473 -1.38761e-14 1.09382e-14
|
||||
@ -1,18 +0,0 @@
|
||||
ITEM: TIMESTEP
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||||
0
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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|
||||
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|
||||
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|
||||
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|
||||
4 1 2.7 1.65327e-16 2.7 -8.06311e-14 -1.57101 -1.57101
|
||||
5 2 1.35 1.35 4.05 2.79365 0.684734 0.684734
|
||||
6 2 4.05 1.35 4.05 -2.79365 0.684734 0.684734
|
||||
7 1 2.7 2.7 0 -1.30843e-13 0.760572 0.760572
|
||||
8 2 1.35 4.05 1.35 0.682428 -0.329901 -0.329901
|
||||
9 2 4.05 4.05 1.35 -0.682428 -0.329901 -0.329901
|
||||
@ -1,21 +0,0 @@
|
||||
ITEM: TIMESTEP
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||||
0
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||||
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||||
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||||
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||||
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|
||||
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|
||||
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||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
8 2 1.35 1.35 4.05 0.461807 -1.3955 -1.94959
|
||||
9 2 4.05 1.35 4.05 0.708573 -1.2552 0.0543549
|
||||
10 1 5.4 0 0 0.211437 1.63064 -0.0728897
|
||||
11 2 4.05 1.35 1.35 -0.708573 -1.2552 0.0543549
|
||||
12 2 6.75 1.35 1.35 -0.461807 -1.3955 -1.94959
|
||||
@ -1,15 +0,0 @@
|
||||
ITEM: TIMESTEP
|
||||
0
|
||||
ITEM: NUMBER OF ATOMS
|
||||
6
|
||||
ITEM: BOX BOUNDS xy xz yz pp pp pp
|
||||
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
ITEM: ATOMS id type x y z fx fy fz
|
||||
1 1 2.7 2.7 0 -2.27066e-14 -1.33391e-14 2.31141e-14
|
||||
2 2 1.35 4.05 1.35 2.35473 2.21578e-14 7.40069e-15
|
||||
3 2 4.05 4.05 1.35 -2.35473 2.97071e-15 -2.01341e-14
|
||||
4 1 2.7 1.65327e-16 2.7 -2.90278e-14 6.77422e-15 2.86766e-15
|
||||
5 2 1.35 1.35 4.05 2.35473 5.79901e-15 -1.19594e-14
|
||||
6 2 4.05 1.35 4.05 -2.35473 -1.38761e-14 1.09382e-14
|
||||
@ -1,18 +0,0 @@
|
||||
ITEM: TIMESTEP
|
||||
0
|
||||
ITEM: NUMBER OF ATOMS
|
||||
9
|
||||
ITEM: BOX BOUNDS xy xz yz pp pp pp
|
||||
0.0000000000000000e+00 1.6199999999999999e+01 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
ITEM: ATOMS id type x y z fx fy fz
|
||||
1 1 2.7 2.7 0 -1.27436e-13 0.760572 0.760572
|
||||
2 2 1.35 4.05 1.35 0.682428 -0.329901 -0.329901
|
||||
3 2 4.05 4.05 1.35 -0.682428 -0.329901 -0.329901
|
||||
4 1 2.7 1.65327e-16 2.7 -8.06311e-14 -1.57101 -1.57101
|
||||
5 2 1.35 1.35 4.05 2.79365 0.684734 0.684734
|
||||
6 2 4.05 1.35 4.05 -2.79365 0.684734 0.684734
|
||||
7 1 2.7 2.7 0 -1.30843e-13 0.760572 0.760572
|
||||
8 2 1.35 4.05 1.35 0.682428 -0.329901 -0.329901
|
||||
9 2 4.05 4.05 1.35 -0.682428 -0.329901 -0.329901
|
||||
@ -1,21 +0,0 @@
|
||||
ITEM: TIMESTEP
|
||||
0
|
||||
ITEM: NUMBER OF ATOMS
|
||||
12
|
||||
ITEM: BOX BOUNDS xy xz yz pp pp pp
|
||||
0.0000000000000000e+00 1.0800000000000001e+01 6.6130927153957075e-16
|
||||
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
|
||||
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
|
||||
ITEM: ATOMS id type x y z fx fy fz
|
||||
1 1 2.7 8.1 0 -0.433947 2.16479 1.55466
|
||||
2 2 1.35 9.45 1.35 1.64718 -0.119006 0.375837
|
||||
3 2 4.05 9.45 1.35 0.999862 -1.02573 0.037629
|
||||
4 1 5.4 8.1 2.7 0.433947 2.16479 1.55466
|
||||
5 2 4.05 9.45 4.05 -0.999862 -1.02573 0.037629
|
||||
6 2 6.75 9.45 4.05 -1.64718 -0.119006 0.375837
|
||||
7 1 2.7 1.65327e-16 2.7 -0.211437 1.63064 -0.0728897
|
||||
8 2 1.35 1.35 4.05 0.461807 -1.3955 -1.94959
|
||||
9 2 4.05 1.35 4.05 0.708573 -1.2552 0.0543549
|
||||
10 1 5.4 0 0 0.211437 1.63064 -0.0728897
|
||||
11 2 4.05 1.35 1.35 -0.708573 -1.2552 0.0543549
|
||||
12 2 6.75 1.35 1.35 -0.461807 -1.3955 -1.94959
|
||||
@ -1,102 +0,0 @@
|
||||
LAMMPS (23 Jun 2022)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# AIMD test of two UO2 molecules with LATTE in MDI stand-alone mode
|
||||
|
||||
units metal
|
||||
atom_style full
|
||||
atom_modify sort 0 0.0
|
||||
|
||||
read_data 2uo2.lmp
|
||||
Reading data file ...
|
||||
triclinic box = (0 0 0) to (10.8 5.4 5.4) with tilt (3.3065464e-16 3.3065464e-16 3.3065464e-16)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
6 atoms
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
0 = max # of 1-2 neighbors
|
||||
0 = max # of 1-3 neighbors
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.003 seconds
|
||||
|
||||
velocity all create 300.0 87287 loop geom
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
timestep 0.00025
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
fix 2 all mdi/qm virial yes elements 92 8
|
||||
|
||||
thermo_style custom step temp pe etotal press
|
||||
thermo 1
|
||||
|
||||
dump 1 all custom 1 dump.aimd.mpi id type x y z vx vy vz fx fy fz
|
||||
|
||||
run 20
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 0
|
||||
ghost atom cutoff = 0
|
||||
binsize = 10.8, bins = 1 1 1
|
||||
0 neighbor lists, perpetual/occasional/extra = 0 0 0
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:210)
|
||||
Per MPI rank memory allocation (min/avg/max) = 6.489 | 6.489 | 6.489 Mbytes
|
||||
Step Temp PotEng TotEng Press
|
||||
0 300 -50.539035 -50.345145 -120197.6
|
||||
1 307.57345 -50.544722 -50.345937 -120123.27
|
||||
2 316.3757 -50.551342 -50.346868 -120035.12
|
||||
3 326.39203 -50.558885 -50.347938 -119933.11
|
||||
4 337.60559 -50.567341 -50.349146 -119817.17
|
||||
5 349.99734 -50.576697 -50.350493 -119687.24
|
||||
6 363.54606 -50.586939 -50.351979 -119543.23
|
||||
7 378.22834 -50.598054 -50.353605 -119385.07
|
||||
8 394.0186 -50.610024 -50.355369 -119212.67
|
||||
9 410.88903 -50.622831 -50.357273 -119025.94
|
||||
10 428.80963 -50.636457 -50.359317 -118824.77
|
||||
11 447.74819 -50.65088 -50.3615 -118609.06
|
||||
12 467.67027 -50.666079 -50.363823 -118378.7
|
||||
13 488.53922 -50.68203 -50.366287 -118133.58
|
||||
14 510.31617 -50.698708 -50.36889 -117873.58
|
||||
15 532.96002 -50.716086 -50.371633 -117598.57
|
||||
16 556.42747 -50.734137 -50.374517 -117308.44
|
||||
17 580.67298 -50.75283 -50.377541 -117003.05
|
||||
18 605.64879 -50.772136 -50.380705 -116682.27
|
||||
19 631.30497 -50.792023 -50.38401 -116345.95
|
||||
20 657.58937 -50.812455 -50.387454 -115993.97
|
||||
Loop time of 3.40001 on 1 procs for 20 steps with 6 atoms
|
||||
|
||||
Performance: 0.127 ns/day, 188.889 hours/ns, 5.882 timesteps/s
|
||||
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Bond | 1.2223e-05 | 1.2223e-05 | 1.2223e-05 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 6.0971e-05 | 6.0971e-05 | 6.0971e-05 | 0.0 | 0.00
|
||||
Output | 0.0009257 | 0.0009257 | 0.0009257 | 0.0 | 0.03
|
||||
Modify | 3.3989 | 3.3989 | 3.3989 | 0.0 | 99.97
|
||||
Other | | 6.824e-05 | | | 0.00
|
||||
|
||||
Nlocal: 6 ave 6 max 6 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 2 ave 2 max 2 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
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:03
|
||||
@ -1,102 +0,0 @@
|
||||
LAMMPS (23 Jun 2022)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# AIMD test of two UO2 molecules with LATTE in MDI stand-alone mode
|
||||
|
||||
units metal
|
||||
atom_style full
|
||||
atom_modify sort 0 0.0
|
||||
|
||||
read_data 2uo2.lmp
|
||||
Reading data file ...
|
||||
triclinic box = (0 0 0) to (10.8 5.4 5.4) with tilt (3.3065464e-16 3.3065464e-16 3.3065464e-16)
|
||||
2 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
6 atoms
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
0 = max # of 1-2 neighbors
|
||||
0 = max # of 1-3 neighbors
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.005 seconds
|
||||
|
||||
velocity all create 300.0 87287 loop geom
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
timestep 0.00025
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
fix 2 all mdi/qm virial yes elements 92 8
|
||||
|
||||
thermo_style custom step temp pe etotal press
|
||||
thermo 1
|
||||
|
||||
dump 1 all custom 1 dump.aimd.mpi id type x y z vx vy vz fx fy fz
|
||||
|
||||
run 20
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 0
|
||||
ghost atom cutoff = 0
|
||||
binsize = 10.8, bins = 1 1 1
|
||||
0 neighbor lists, perpetual/occasional/extra = 0 0 0
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:210)
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.485 | 5.987 | 6.489 Mbytes
|
||||
Step Temp PotEng TotEng Press
|
||||
0 300 -50.539035 -50.345145 -120197.6
|
||||
1 307.57345 -50.544722 -50.345937 -120123.27
|
||||
2 316.3757 -50.551342 -50.346868 -120035.12
|
||||
3 326.39203 -50.558885 -50.347938 -119933.11
|
||||
4 337.60559 -50.567341 -50.349146 -119817.17
|
||||
5 349.99734 -50.576697 -50.350493 -119687.24
|
||||
6 363.54606 -50.586939 -50.351979 -119543.23
|
||||
7 378.22834 -50.598054 -50.353605 -119385.07
|
||||
8 394.0186 -50.610024 -50.355369 -119212.67
|
||||
9 410.88903 -50.622831 -50.357273 -119025.94
|
||||
10 428.80963 -50.636457 -50.359317 -118824.77
|
||||
11 447.74819 -50.65088 -50.3615 -118609.06
|
||||
12 467.67027 -50.666079 -50.363823 -118378.7
|
||||
13 488.53922 -50.68203 -50.366287 -118133.58
|
||||
14 510.31617 -50.698708 -50.36889 -117873.58
|
||||
15 532.96002 -50.716086 -50.371633 -117598.57
|
||||
16 556.42747 -50.734137 -50.374517 -117308.44
|
||||
17 580.67298 -50.75283 -50.377541 -117003.05
|
||||
18 605.64879 -50.772136 -50.380705 -116682.27
|
||||
19 631.30497 -50.792023 -50.38401 -116345.95
|
||||
20 657.58937 -50.812455 -50.387454 -115993.97
|
||||
Loop time of 25.2055 on 2 procs for 20 steps with 6 atoms
|
||||
|
||||
Performance: 0.017 ns/day, 1400.306 hours/ns, 0.793 timesteps/s
|
||||
99.9% CPU use with 2 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Bond | 1.746e-05 | 2.5213e-05 | 3.2966e-05 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 4.3862e-05 | 5.4267e-05 | 6.4671e-05 | 0.0 | 0.00
|
||||
Output | 0.001642 | 0.0018189 | 0.0019957 | 0.4 | 0.01
|
||||
Modify | 25.203 | 25.203 | 25.203 | 0.0 | 99.99
|
||||
Other | | 0.000307 | | | 0.00
|
||||
|
||||
Nlocal: 3 ave 6 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 1 ave 2 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:26
|
||||
@ -1,103 +0,0 @@
|
||||
LAMMPS (23 Jun 2022)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# AIMD test of two UO2 molecules with LATTE in MDI plugin mode
|
||||
|
||||
units metal
|
||||
atom_style full
|
||||
atom_modify sort 0 0.0
|
||||
|
||||
read_data 2uo2.lmp
|
||||
Reading data file ...
|
||||
triclinic box = (0 0 0) to (10.8 5.4 5.4) with tilt (3.3065464e-16 3.3065464e-16 3.3065464e-16)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
6 atoms
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
0 = max # of 1-2 neighbors
|
||||
0 = max # of 1-3 neighbors
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.004 seconds
|
||||
|
||||
velocity all create 300.0 87287 loop geom
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
timestep 0.00025
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
fix 2 all mdi/qm virial yes elements 92 8
|
||||
|
||||
thermo_style custom step temp pe etotal press
|
||||
thermo 1
|
||||
|
||||
dump 1 all custom 1 dump.aimd.plugin id type x y z vx vy vz fx fy fz
|
||||
|
||||
mdi plugin latte_mdi mdi "-role ENGINE -name LATTE -method LINK" command "run 20"
|
||||
run 20
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 0
|
||||
ghost atom cutoff = 0
|
||||
binsize = 10.8, bins = 1 1 1
|
||||
0 neighbor lists, perpetual/occasional/extra = 0 0 0
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:210)
|
||||
Per MPI rank memory allocation (min/avg/max) = 6.489 | 6.489 | 6.489 Mbytes
|
||||
Step Temp PotEng TotEng Press
|
||||
0 300 -50.539035 -50.345145 -120197.6
|
||||
1 307.57345 -50.544722 -50.345937 -120123.27
|
||||
2 316.3757 -50.551342 -50.346868 -120035.12
|
||||
3 326.39203 -50.558885 -50.347938 -119933.11
|
||||
4 337.60559 -50.567341 -50.349146 -119817.17
|
||||
5 349.99734 -50.576697 -50.350493 -119687.24
|
||||
6 363.54606 -50.586939 -50.351979 -119543.23
|
||||
7 378.22834 -50.598054 -50.353605 -119385.07
|
||||
8 394.0186 -50.610024 -50.355369 -119212.67
|
||||
9 410.88903 -50.622831 -50.357273 -119025.94
|
||||
10 428.80963 -50.636457 -50.359317 -118824.77
|
||||
11 447.74819 -50.65088 -50.3615 -118609.06
|
||||
12 467.67027 -50.666079 -50.363823 -118378.7
|
||||
13 488.53922 -50.68203 -50.366287 -118133.58
|
||||
14 510.31617 -50.698708 -50.36889 -117873.58
|
||||
15 532.96002 -50.716086 -50.371633 -117598.57
|
||||
16 556.42747 -50.734137 -50.374517 -117308.44
|
||||
17 580.67298 -50.75283 -50.377541 -117003.05
|
||||
18 605.64879 -50.772136 -50.380705 -116682.27
|
||||
19 631.30497 -50.792023 -50.38401 -116345.95
|
||||
20 657.58937 -50.812455 -50.387454 -115993.97
|
||||
Loop time of 2.74435 on 1 procs for 20 steps with 6 atoms
|
||||
|
||||
Performance: 0.157 ns/day, 152.464 hours/ns, 7.288 timesteps/s
|
||||
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Bond | 1.299e-05 | 1.299e-05 | 1.299e-05 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 7.9198e-05 | 7.9198e-05 | 7.9198e-05 | 0.0 | 0.00
|
||||
Output | 0.001118 | 0.001118 | 0.001118 | 0.0 | 0.04
|
||||
Modify | 2.743 | 2.743 | 2.743 | 0.0 | 99.95
|
||||
Other | | 0.0001456 | | | 0.01
|
||||
|
||||
Nlocal: 6 ave 6 max 6 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 2 ave 2 max 2 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
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:03
|
||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
@ -1,263 +0,0 @@
|
||||
LAMMPS (23 Jun 2022)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Series of single-point calcs of 2,3,4 UO2 molecules
|
||||
# with LATTE in MDI stand-alone mode
|
||||
|
||||
variable files index 2uo2 3uo2 4uo2
|
||||
|
||||
mdi connect
|
||||
|
||||
label LOOP
|
||||
|
||||
units metal
|
||||
atom_style full
|
||||
atom_modify sort 0 0.0
|
||||
|
||||
read_data ${files}.lmp
|
||||
read_data 2uo2.lmp
|
||||
Reading data file ...
|
||||
triclinic box = (0 0 0) to (10.8 5.4 5.4) with tilt (3.3065464e-16 3.3065464e-16 3.3065464e-16)
|
||||
2 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
6 atoms
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
0 = max # of 1-2 neighbors
|
||||
0 = max # of 1-3 neighbors
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.004 seconds
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
timestep 0.001
|
||||
|
||||
fix 1 all mdi/qm virial yes elements 92 8 connect no
|
||||
|
||||
thermo_style custom step temp pe etotal press
|
||||
thermo 1
|
||||
|
||||
run 0
|
||||
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 0
|
||||
ghost atom cutoff = 0
|
||||
binsize = 10.8, bins = 1 1 1
|
||||
0 neighbor lists, perpetual/occasional/extra = 0 0 0
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:210)
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.234 | 5.236 | 5.238 Mbytes
|
||||
Step Temp PotEng TotEng Press
|
||||
0 0 -50.539035 -50.539035 -120855.2
|
||||
Loop time of 1.956e-06 on 2 procs for 0 steps with 6 atoms
|
||||
|
||||
127.8% CPU use with 2 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Bond | 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 | | 1.956e-06 | | |100.00
|
||||
|
||||
Nlocal: 3 ave 6 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 1 ave 2 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
write_dump all custom dump.series.mpi.${files} id type x y z fx fy fz modify sort id
|
||||
write_dump all custom dump.series.mpi.2uo2 id type x y z fx fy fz modify sort id
|
||||
|
||||
clear
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
|
||||
next files
|
||||
|
||||
jump SELF LOOP
|
||||
|
||||
units metal
|
||||
atom_style full
|
||||
atom_modify sort 0 0.0
|
||||
|
||||
read_data ${files}.lmp
|
||||
read_data 3uo2.lmp
|
||||
Reading data file ...
|
||||
triclinic box = (0 0 0) to (16.2 5.4 5.4) with tilt (3.3065464e-16 3.3065464e-16 3.3065464e-16)
|
||||
2 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
9 atoms
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
0 = max # of 1-2 neighbors
|
||||
0 = max # of 1-3 neighbors
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.001 seconds
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
timestep 0.001
|
||||
|
||||
fix 1 all mdi/qm virial yes elements 92 8 connect no
|
||||
|
||||
thermo_style custom step temp pe etotal press
|
||||
thermo 1
|
||||
|
||||
run 0
|
||||
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 0
|
||||
ghost atom cutoff = 0
|
||||
binsize = 16.2, bins = 1 1 1
|
||||
0 neighbor lists, perpetual/occasional/extra = 0 0 0
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:210)
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.234 | 5.236 | 5.238 Mbytes
|
||||
Step Temp PotEng TotEng Press
|
||||
0 0 -78.155679 -78.155679 -99931.431
|
||||
Loop time of 2.375e-06 on 2 procs for 0 steps with 9 atoms
|
||||
|
||||
147.4% CPU use with 2 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Bond | 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 | | 2.375e-06 | | |100.00
|
||||
|
||||
Nlocal: 4.5 ave 9 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 1.5 ave 3 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
write_dump all custom dump.series.mpi.${files} id type x y z fx fy fz modify sort id
|
||||
write_dump all custom dump.series.mpi.3uo2 id type x y z fx fy fz modify sort id
|
||||
|
||||
clear
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
|
||||
next files
|
||||
|
||||
jump SELF LOOP
|
||||
|
||||
units metal
|
||||
atom_style full
|
||||
atom_modify sort 0 0.0
|
||||
|
||||
read_data ${files}.lmp
|
||||
read_data 4uo2.lmp
|
||||
Reading data file ...
|
||||
triclinic box = (0 0 0) to (10.8 10.8 5.4) with tilt (6.6130927e-16 3.3065464e-16 3.3065464e-16)
|
||||
1 by 2 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
12 atoms
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
0 = max # of 1-2 neighbors
|
||||
0 = max # of 1-3 neighbors
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.002 seconds
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
timestep 0.001
|
||||
|
||||
fix 1 all mdi/qm virial yes elements 92 8 connect no
|
||||
|
||||
thermo_style custom step temp pe etotal press
|
||||
thermo 1
|
||||
|
||||
run 0
|
||||
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 0
|
||||
ghost atom cutoff = 0
|
||||
binsize = 10.8, bins = 1 1 1
|
||||
0 neighbor lists, perpetual/occasional/extra = 0 0 0
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:210)
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.238 | 5.238 | 5.238 Mbytes
|
||||
Step Temp PotEng TotEng Press
|
||||
0 0 -102.35713 -102.35713 -31036.168
|
||||
Loop time of 2.4445e-06 on 2 procs for 0 steps with 12 atoms
|
||||
|
||||
122.7% CPU use with 2 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Bond | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 2.444e-06 | | |100.00
|
||||
|
||||
Nlocal: 6 ave 6 max 6 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 2.5 ave 4 max 1 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
write_dump all custom dump.series.mpi.${files} id type x y z fx fy fz modify sort id
|
||||
write_dump all custom dump.series.mpi.4uo2 id type x y z fx fy fz modify sort id
|
||||
|
||||
clear
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
|
||||
next files
|
||||
|
||||
jump SELF LOOP
|
||||
|
||||
mdi exit
|
||||
Total wall time: 0:00:08
|
||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
211
examples/QUANTUM/LATTE/README
Normal file
211
examples/QUANTUM/LATTE/README
Normal file
@ -0,0 +1,211 @@
|
||||
# Test runs with coupling of LAMMPS and LATTE
|
||||
|
||||
Step 0: What LATTE currently supports
|
||||
Step 1: Build LAMMPS
|
||||
Step 2: Install or download/build MDI code coupling package
|
||||
Step 3: Download/build LATTE
|
||||
Step 4: Perform test runs in any of 3 modes
|
||||
|
||||
---------------------------------
|
||||
---------------------------------
|
||||
|
||||
Step 0: What LATTE currently supports
|
||||
|
||||
LATTE can be used with fix mdi/qm to perform QM calculations of an
|
||||
entire system, but not with fix mdi/qmmm to perform QMMM simulations.
|
||||
LATTE can calculate a QM energy and virial as well as QM forces on
|
||||
each atom.
|
||||
|
||||
LATTE does not support MPI parallelism, so run it on a single MPI
|
||||
task. But it does support multi-threading via OpenMP. By default it
|
||||
will use all the threads available on your compute node. Depending on
|
||||
the size of the problem and your hardware, it may be faster to run on
|
||||
fewer threads. Thus for a production run it is a good idea to do some
|
||||
short runs first with different thread counts to test performance.
|
||||
|
||||
For example, these commands will set the OpenMP thread count (to 4)
|
||||
before performing a run. Unsetting the environment variable will
|
||||
revert to the default (use all available threads).
|
||||
|
||||
bash:
|
||||
% export OMP_NUM_THREADS=4
|
||||
% unset OMP_NUM_THREADS
|
||||
|
||||
(t)csh:
|
||||
% setenv OMP_NUM_THREADS 4
|
||||
% unsetenv OMP_NUM_THREADS
|
||||
|
||||
All the example log files in this directory were run with OMP_NUM_THREADS = 1
|
||||
|
||||
---------------------------------
|
||||
---------------------------------
|
||||
|
||||
Step 1: Build LAMMPS
|
||||
|
||||
The MDI and molecule packags are needed. Copy the final LAMMPS
|
||||
executable into the examples/QUANTUM/LATTE directory.
|
||||
|
||||
Traditional make:
|
||||
|
||||
% cd ~/lammps/lib/mdi
|
||||
% python Install.py -m mpi
|
||||
% cd ~/lammps/src
|
||||
% make yes-mdi yes-molecule
|
||||
% make -j mpi
|
||||
% cp lmp_mpi ~/lammps/examples/QUANTUM/LATTE
|
||||
|
||||
CMake:
|
||||
|
||||
% cd ~/lammps
|
||||
% mkdir build; cd build
|
||||
% cmake -DPKG_MDI=yes -DPKG_MOLECULE=yes ../cmake
|
||||
% make -j
|
||||
% cp lmp ~/lammps/examples/QUANTUM/LATTE/lmp_mpi
|
||||
|
||||
---------------------------------
|
||||
---------------------------------
|
||||
|
||||
Step 2: Install or download/build MDI code coupling package
|
||||
|
||||
To simply use the MDI python module for the example scripts in this
|
||||
dir, you only need to install the MDI python module in your
|
||||
environment. Alternatively, you can download/build MDI itself, which
|
||||
will include its documentation and examples (as well as libraries and
|
||||
Python interface).
|
||||
|
||||
NOTE: It should be fine to leave off the version number for the python
|
||||
module installs, to just grab the latest MDI version. 1.4.16 is the
|
||||
version of MDI LAMMPS is currently using.
|
||||
|
||||
(option 1) Install MDI python module via pip:
|
||||
|
||||
% pip install 'pymdi>=1.4.14'
|
||||
|
||||
(option 2) Install MDI python module via conda:
|
||||
|
||||
% conda install -c conda-forge pymdi=1.4.16
|
||||
|
||||
(option 3) Download/build MDI code coupling package
|
||||
|
||||
(a) clone the MDI Git repo
|
||||
|
||||
% git clone https://github.com/MolSSI-MDI/MDI_Library.git mdi
|
||||
|
||||
(b) build MDI
|
||||
|
||||
% cd mdi
|
||||
% mkdir build; cd build
|
||||
% cmake ..
|
||||
% make -j
|
||||
|
||||
(c) Add a line like this to your ~/.bashrc or ~/.cshrc file so that
|
||||
Python can find MDI:
|
||||
|
||||
For bash:
|
||||
|
||||
% export PYTHONPATH="${HOME}/mdi/build/MDI_Library:${PYTHONPATH}"
|
||||
% hash -r
|
||||
|
||||
For (t)csh:
|
||||
|
||||
% setenv PYTHONPATH "${HOME}/mdi/build/MDI_Library:${PYTHONPATH}"
|
||||
% rehash
|
||||
|
||||
(d) Check import of 3 Python modules which the script that wraps
|
||||
LATTE will need:
|
||||
|
||||
% python
|
||||
>>> import numpy as np
|
||||
>>> from mpi4py import MPI
|
||||
>>> import mdi
|
||||
|
||||
---------------------------------
|
||||
---------------------------------
|
||||
|
||||
Step 3: Download/build LATTE
|
||||
|
||||
NOTE: As of March 2023, this ECP branch of the LATTE repo is the
|
||||
latest developement version of LATTE to use with LAMMPS. It will be
|
||||
become the default LATTE branch at some point in the future. This doc
|
||||
page will be updated when that happens.
|
||||
|
||||
(a) clone the ECP branch of the LATTE Git repo
|
||||
|
||||
% git clone -b ECP https://github.com/lanl/LATTE.git latte
|
||||
|
||||
(b) build LATTE as a shared library
|
||||
|
||||
% cd ~/latte
|
||||
% mkdir build; cd build
|
||||
% cmake -DBUILD_SHARED_LIBS=on ../cmake
|
||||
% make -j # should produce liblatte.so in build
|
||||
|
||||
(c) Add a line like this to your ~/.bashrc or ~/.cshrc file so that
|
||||
the liblatte.so file can be found:
|
||||
|
||||
For bash:
|
||||
|
||||
% export LD_LIBRARY_PATH="${HOME}/latte/build:${LD_LIBRARY_PATH}"
|
||||
% hash -r
|
||||
|
||||
For (t)csh:
|
||||
|
||||
% setenv LD_LIBRARY_PATH "${HOME}/latte/build:${LD_LIBRARY_PATH}"
|
||||
% rehash
|
||||
|
||||
---------------------------------
|
||||
---------------------------------
|
||||
|
||||
Step 4: Perform test runs in any of 3 modes
|
||||
|
||||
These tests are in lammps/examples/QUANTUM/LATTE
|
||||
|
||||
in.ch4 = AIMD with CH4 molecule
|
||||
in.graphene = AIMD with graphene
|
||||
in.series = series of 3 UO2 conformations
|
||||
in.sucrose = AIMD of sucrose molecule
|
||||
in.uo2 = two molecules of UO2
|
||||
in.water = eight water molecules
|
||||
|
||||
** run LAMMPS and LATTE with TCP/IP, 1 proc each
|
||||
|
||||
lmp_mpi -mdi "-name LMP -role DRIVER -method TCP -port 8021" -log log.water.tcp.1 -in in.water &
|
||||
python latte_mdi.py -mdi "-name LATTE -role ENGINE -method TCP -port 8021 -hostname localhost" latte.in.water
|
||||
|
||||
lmp_mpi -mdi "-name LMP -role DRIVER -method TCP -port 8021" -log log.uo2.tcp.1 -in in.uo2 &
|
||||
python latte_mdi.py -mdi "-name LATTE -role ENGINE -method TCP -port 8021 -hostname localhost" latte.in.uo2
|
||||
|
||||
lmp_mpi -mdi "-name LMP -role DRIVER -method TCP -port 8021" -log log.series.tcp.1 -in in.series &
|
||||
python latte_mdi.py -mdi "-name LATTE -role ENGINE -method TCP -port 8021 -hostname localhost" latte.in.uo2
|
||||
|
||||
** run LAMMPS and LATTE with MPI, 1 proc each
|
||||
|
||||
mpirun -np 1 lmp_mpi -mdi "-name LMP -role DRIVER -method MPI" -log log.water.mpi.1 -in in.water : -np 1 python latte_mdi.py -mdi "-name LATTE -role ENGINE -method MPI" latte.in.water
|
||||
|
||||
mpirun -np 1 lmp_mpi -mdi "-name LMP -role DRIVER -method MPI" -log log.water.min.mpi.1 -in in.water.min : -np 1 python latte_mdi.py -mdi "-name LATTE -role ENGINE -method MPI" latte.in.generic
|
||||
|
||||
mpirun -np 1 lmp_mpi -mdi "-name LMP -role DRIVER -method MPI" -log log.uo2.mpi.1 -in in.uo2 : -np 1 python latte_mdi.py -mdi "-name LATTE -role ENGINE -method MPI" latte.in.uo2
|
||||
|
||||
mpirun -np 1 lmp_mpi -mdi "-name LMP -role DRIVER -method MPI" -log log.ch4.mpi.1 -in in.ch4 : -np 1 python latte_mdi.py -mdi "-name LATTE -role ENGINE -method MPI" latte.in.generic
|
||||
|
||||
mpirun -np 1 lmp_mpi -mdi "-name LMP -role DRIVER -method MPI" -log log.sucrose.mpi.1 -in in.sucrose : -np 1 python latte_mdi.py -mdi "-name LATTE -role ENGINE -method MPI" latte.in.generic
|
||||
|
||||
mpirun -np 1 lmp_mpi -mdi "-name LMP -role DRIVER -method MPI" -log log.graphene.mpi.1 -in in.graphene : -np 1 python latte_mdi.py -mdi "-name LATTE -role ENGINE -method MPI" latte.in.generic
|
||||
|
||||
mpirun -np 1 lmp_mpi -mdi "-name LMP -role DRIVER -method MPI" -log log.series.mpi.1 -in in.series : -np 1 python latte_mdi.py -mdi "-name LATTE -role ENGINE -method MPI" latte.in.uo2
|
||||
|
||||
** run LATTE as plugin MDI engine, 1 proc
|
||||
|
||||
lmp_mpi -mdi "-name LMP -role DRIVER -method LINK -plugin_path ${HOME}/lammps/examples/QUANTUM/LATTE" -log log.water.plugin.1 -in in.water.plugin
|
||||
|
||||
lmp_mpi -mdi "-name LMP -role DRIVER -method LINK -plugin_path ${HOME}/lammps/examples/QUANTUM/LATTE" -log log.water.min.plugin.1 -in in.water.min.plugin
|
||||
|
||||
lmp_mpi -mdi "-name LMP -role DRIVER -method LINK -plugin_path ${HOME}/lammps/examples/QUANTUM/LATTE" -log log.uo2.plugin.1 -in in.uo2.plugin
|
||||
|
||||
lmp_mpi -mdi "-name LMP -role DRIVER -method LINK -plugin_path ${HOME}/lammps/examples/QUANTUM/LATTE" -log log.ch4.plugin.1 -in in.ch4.plugin
|
||||
|
||||
lmp_mpi -mdi "-name LMP -role DRIVER -method LINK -plugin_path ${HOME}/lammps/examples/QUANTUM/LATTE" -log log.sucrose.plugin.1 -in in.sucrose.plugin
|
||||
|
||||
lmp_mpi -mdi "-name LMP -role DRIVER -method LINK -plugin_path ${HOME}/lammps/examples/QUANTUM/LATTE" -log log.graphene.plugin.1 -in in.graphene.plugin
|
||||
|
||||
lmp_mpi -mdi "-name LMP -role DRIVER -method LINK -plugin_path ${HOME}/lammps/examples/QUANTUM/LATTE" -log log.series.plugin.1 -in in.series.plugin
|
||||
36
examples/QUANTUM/LATTE/TBparam_generic/bondints.nonortho
Normal file
36
examples/QUANTUM/LATTE/TBparam_generic/bondints.nonortho
Normal file
@ -0,0 +1,36 @@
|
||||
Noints= 34
|
||||
Element1 Element2 Kind H0 B1 B2 B3 B4 B5 R1 Rcut H0 B1 B2 B3 B4 B5 R1 Rcut
|
||||
N O sss -11.430028 -2.257346 -1.152844 0.000000 0.000000 1.200000 3.500000 4.000000 0.340064 -1.703613 -0.622348 0.036738 -0.040158 1.200000 3.500000 4.000000
|
||||
N O sps 11.597479 -1.382001 -0.765170 0.000000 0.000000 1.200000 3.500000 4.000000 -0.370946 -1.040947 -0.931097 0.252441 -0.115450 1.200000 3.500000 4.000000
|
||||
O N sps 12.143744 -0.822913 -0.676127 0.000000 0.000000 1.200000 3.500000 4.000000 -0.420014 -1.107918 -0.905594 0.188424 -0.088365 1.200000 3.500000 4.000000
|
||||
N O pps 9.465191 -1.082032 -0.769214 0.000000 0.000000 1.200000 3.500000 4.000000 -0.314073 0.499050 -2.914288 2.067657 -0.738439 1.200000 3.500000 4.000000
|
||||
N O ppp -4.676789 -2.171480 -0.288002 0.000000 0.000000 1.200000 3.500000 4.000000 0.223937 -1.991867 -0.537630 -0.081270 -0.004130 1.200000 3.500000 4.000000
|
||||
C O sss -14.369472 -2.077439 -0.875471 0.000000 0.000000 1.200000 3.500000 4.000000 0.375339 -1.547372 -0.642492 0.020614 -0.026699 1.200000 3.500000 4.000000
|
||||
C O sps 9.576296 -1.156217 -0.494803 0.000000 0.000000 1.200000 3.500000 4.000000 -0.373027 -0.776043 -1.019920 0.257539 -0.102838 1.200000 3.500000 4.000000
|
||||
O C sps 14.037374 -1.192632 -0.654572 0.000000 0.000000 1.200000 3.500000 4.000000 -0.458068 -1.035067 -0.937868 0.190562 -0.077841 1.200000 3.500000 4.000000
|
||||
C O pps 9.331152 -0.718120 -0.822100 0.000000 0.000000 1.200000 3.500000 4.000000 -0.322293 0.795473 -3.476601 2.589965 -0.897800 1.200000 3.500000 4.000000
|
||||
C O ppp -5.334367 -2.263939 -0.204910 0.000000 0.000000 1.200000 3.500000 4.000000 0.244570 -1.922717 -0.573671 -0.057280 -0.004108 1.200000 3.500000 4.000000
|
||||
C N sss -7.010061 -1.730597 -0.575559 0.000000 0.000000 1.500000 3.500000 4.000000 0.263438 -1.754525 -0.584215 -0.007801 -0.021729 1.500000 3.500000 4.000000
|
||||
C N sps 7.543283 -1.293768 -0.624363 0.000000 0.000000 1.500000 3.500000 4.000000 -0.326609 -1.197485 -0.807786 0.134891 -0.084373 1.500000 3.500000 4.000000
|
||||
N C sps 9.090970 -1.494255 -0.616711 0.000000 0.000000 1.500000 3.500000 4.000000 -0.337943 -1.335442 -0.769693 0.119373 -0.079493 1.500000 3.500000 4.000000
|
||||
C N pps 6.892240 -0.931920 -0.769164 0.000000 0.000000 1.500000 3.500000 4.000000 -0.350240 -0.467439 -1.849316 1.854403 -0.988471 1.500000 3.500000 4.000000
|
||||
C N ppp -2.903346 -2.149349 -0.253006 0.000000 0.000000 1.500000 3.500000 4.000000 0.158424 -2.114409 -0.582346 -0.051076 -0.006183 1.500000 3.500000 4.000000
|
||||
C C sss -9.404207 -1.363297 -0.507128 0.000000 0.000000 1.400000 3.500000 4.000000 0.346977 -1.519820 -0.570812 -0.013518 -0.015829 1.400000 3.500000 4.000000
|
||||
C C sps 8.662429 -1.047410 -0.661999 0.000000 0.000000 1.400000 3.500000 4.000000 -0.400467 -0.984048 -0.853949 0.157178 -0.073381 1.400000 3.500000 4.000000
|
||||
C C pps 6.811512 -0.552299 -0.776890 0.000000 0.000000 1.400000 3.500000 4.000000 -0.382417 0.102889 -2.786680 2.646356 -1.134320 1.400000 3.500000 4.000000
|
||||
C C ppp -3.550127 -1.925572 -0.132715 0.000000 0.000000 1.400000 3.500000 4.000000 0.214357 -1.948923 -0.578323 -0.034356 -0.007257 1.400000 3.500000 4.000000
|
||||
H C sss -9.072577 -1.393093 -0.430611 0.000000 0.000000 1.100000 3.500000 4.000000 0.416003 -1.459596 -0.654874 0.009140 -0.012658 1.100000 3.500000 4.000000
|
||||
H C sps 8.176008 -0.985177 -0.427403 0.000000 0.000000 1.100000 3.500000 4.000000 -0.495695 -0.901626 -1.007214 0.189808 -0.057087 1.100000 3.500000 4.000000
|
||||
H H sss -9.340000 -1.145903 -0.391777 0.000000 0.000000 0.750000 3.500000 4.000000 0.575007 -1.391261 -0.778831 0.080209 -0.017759 0.750000 3.500000 4.000000
|
||||
O O sss -12.737687 -1.851608 -0.666621 0.000000 0.000000 1.200000 3.500000 4.000000 0.296445 -1.911896 -0.663451 0.038054 -0.046608 1.200000 3.500000 4.000000
|
||||
O O sps 13.683050 -1.684554 -0.468349 0.000000 0.000000 1.200000 3.500000 4.000000 -0.362143 -1.285274 -0.939591 0.204641 -0.106438 1.200000 3.500000 4.000000
|
||||
O O pps 9.460772 -1.211748 -0.581016 0.000000 0.000000 1.200000 3.500000 4.000000 -0.312044 0.121814 -2.519352 1.681266 -0.644566 1.200000 3.500000 4.000000
|
||||
O O ppp -4.494595 -2.709223 -0.284124 0.000000 0.000000 1.200000 3.500000 4.000000 0.193010 -2.168462 -0.580629 -0.105104 0.004891 1.200000 3.500000 4.000000
|
||||
H O sss -12.230931 -1.808632 -0.421164 0.000000 0.000000 1.000000 3.500000 4.000000 0.404725 -1.702546 -0.707938 0.074904 -0.039922 1.000000 3.500000 4.000000
|
||||
H O sps 9.466088 -1.321262 -0.386336 0.000000 0.000000 1.000000 3.500000 4.000000 -0.447660 -0.952979 -1.163537 0.400616 -0.156965 1.000000 3.500000 4.000000
|
||||
N N sss -7.710330 -2.365312 -0.525527 0.000000 0.000000 1.500000 3.500000 4.000000 0.231654 -1.879002 -0.572765 -0.004579 -0.031106 1.500000 3.500000 4.000000
|
||||
N N sps 8.222314 -1.612118 -0.690081 0.000000 0.000000 1.500000 3.500000 4.000000 -0.305271 -1.385158 -0.751032 0.114531 -0.090839 1.500000 3.500000 4.000000
|
||||
N N pps 7.178570 -1.176467 -0.571049 0.000000 0.000000 1.500000 3.500000 4.000000 -0.324668 -0.547805 -1.638658 1.495168 -0.827868 1.500000 3.500000 4.000000
|
||||
N N ppp -2.829344 -2.408049 -0.387709 0.000000 0.000000 1.500000 3.500000 4.000000 0.142909 -2.162036 -0.571942 -0.071640 -0.004682 1.500000 3.500000 4.000000
|
||||
H N sss -12.095890 -1.519057 -0.277247 0.000000 0.000000 1.000000 3.500000 4.000000 0.446693 -1.500463 -0.657448 0.065741 -0.037004 1.000000 3.500000 4.000000
|
||||
H N sps 9.851338 -1.231616 -0.370836 0.000000 0.000000 1.000000 3.500000 4.000000 -0.501530 -0.785734 -1.123232 0.394878 -0.148501 1.000000 3.500000 4.000000
|
||||
7
examples/QUANTUM/LATTE/TBparam_generic/electrons.dat
Normal file
7
examples/QUANTUM/LATTE/TBparam_generic/electrons.dat
Normal file
@ -0,0 +1,7 @@
|
||||
Noelem= 5
|
||||
Element basis Numel Es Ep Ed Ef Mass HubbardU Wss Wpp Wdd Wff
|
||||
N sp 5.0 -18.58 -7.09 0.0 0.0 14.0067 15.93 0.0 -0.6950 0.0 0.0
|
||||
O sp 6.0 -23.96 -9.02 0.0 0.0 15.9994 12.15 0.0 -0.7577 0.0 0.0
|
||||
H s 1.0 -6.35 0.0 0.0 0.0 1.0079 12.85 -1.7937 0.0 0.0 0.0
|
||||
C sp 4.0 -13.75 -5.28 0.0 0.0 12.01 10.0 0.0 -0.621 0.0 0.0
|
||||
Ti sd 4.0 -5.5 0.0 -3.0 0.0 47.867 10.0 0.0 0.0 0.0 0.0
|
||||
12
examples/QUANTUM/LATTE/TBparam_generic/ppots.nonortho
Normal file
12
examples/QUANTUM/LATTE/TBparam_generic/ppots.nonortho
Normal file
@ -0,0 +1,12 @@
|
||||
Nopps= 10
|
||||
Ele1 Ele2 A0 A1 A2 A3 A4 A5 A6 C R1 Rcut
|
||||
N O 13.182426 20.050322 -46.806321 38.206953 -12.319656 0.000000 0.000000 0.000000 1.600000 1.700000
|
||||
C N 88.953762 10.294988 -27.706877 22.101434 -6.836438 0.000000 0.000000 0.000000 1.600000 1.700000
|
||||
C O 0.944093 30.116337 -59.608215 45.107654 -13.178839 0.000000 0.000000 0.000000 1.600000 1.700000
|
||||
C H 104.889589 3.971095 -23.823043 26.408093 -11.317522 0.000000 0.000000 0.000000 1.200000 1.300000
|
||||
C C 3.962931 24.467772 -51.156024 39.031644 -11.342979 0.000000 0.000000 0.000000 1.600000 1.700000
|
||||
H H 38.512100 3.887860 -37.769100 57.083500 -34.512200 0.000000 0.000000 0.000000 0.900000 1.000000
|
||||
N N 43.228899 15.004605 -36.621777 29.234888 -8.912743 0.000000 0.000000 0.000000 1.600000 1.700000
|
||||
N H 0.625470 28.081241 -63.414297 53.286361 -17.352234 0.000000 0.000000 0.000000 1.300000 1.400000
|
||||
O O 10.999870 19.303033 -45.747853 37.946431 -11.935755 0.000000 0.000000 0.000000 1.500000 1.600000
|
||||
O H 0.481176 33.175383 -81.158683 74.935408 -26.792315 0.000000 0.000000 0.000000 1.200000 1.300000
|
||||
36
examples/QUANTUM/LATTE/TBparam_water/bondints.nonortho
Normal file
36
examples/QUANTUM/LATTE/TBparam_water/bondints.nonortho
Normal file
@ -0,0 +1,36 @@
|
||||
Noints= 34
|
||||
Element1 Element2 Kind H0 B1 B2 B3 B4 B5 R1 Rcut H0 B1 B2 B3 B4 B5 R1 Rcut
|
||||
N O sss -11.430028 -2.257346 -1.152844 0.000000 0.000000 1.200000 3.500000 4.000000 0.340064 -1.703613 -0.622348 0.036738 -0.040158 1.200000 3.500000 4.000000
|
||||
N O sps 11.597479 -1.382001 -0.765170 0.000000 0.000000 1.200000 3.500000 4.000000 -0.370946 -1.040947 -0.931097 0.252441 -0.115450 1.200000 3.500000 4.000000
|
||||
O N sps 12.143744 -0.822913 -0.676127 0.000000 0.000000 1.200000 3.500000 4.000000 -0.420014 -1.107918 -0.905594 0.188424 -0.088365 1.200000 3.500000 4.000000
|
||||
N O pps 9.465191 -1.082032 -0.769214 0.000000 0.000000 1.200000 3.500000 4.000000 -0.314073 0.499050 -2.914288 2.067657 -0.738439 1.200000 3.500000 4.000000
|
||||
N O ppp -4.676789 -2.171480 -0.288002 0.000000 0.000000 1.200000 3.500000 4.000000 0.223937 -1.991867 -0.537630 -0.081270 -0.004130 1.200000 3.500000 4.000000
|
||||
C O sss -14.369472 -2.077439 -0.875471 0.000000 0.000000 1.200000 3.500000 4.000000 0.375339 -1.547372 -0.642492 0.020614 -0.026699 1.200000 3.500000 4.000000
|
||||
C O sps 9.576296 -1.156217 -0.494803 0.000000 0.000000 1.200000 3.500000 4.000000 -0.373027 -0.776043 -1.019920 0.257539 -0.102838 1.200000 3.500000 4.000000
|
||||
O C sps 14.037374 -1.192632 -0.654572 0.000000 0.000000 1.200000 3.500000 4.000000 -0.458068 -1.035067 -0.937868 0.190562 -0.077841 1.200000 3.500000 4.000000
|
||||
C O pps 9.331152 -0.718120 -0.822100 0.000000 0.000000 1.200000 3.500000 4.000000 -0.322293 0.795473 -3.476601 2.589965 -0.897800 1.200000 3.500000 4.000000
|
||||
C O ppp -5.334367 -2.263939 -0.204910 0.000000 0.000000 1.200000 3.500000 4.000000 0.244570 -1.922717 -0.573671 -0.057280 -0.004108 1.200000 3.500000 4.000000
|
||||
C N sss -7.010061 -1.730597 -0.575559 0.000000 0.000000 1.500000 3.500000 4.000000 0.263438 -1.754525 -0.584215 -0.007801 -0.021729 1.500000 3.500000 4.000000
|
||||
C N sps 7.543283 -1.293768 -0.624363 0.000000 0.000000 1.500000 3.500000 4.000000 -0.326609 -1.197485 -0.807786 0.134891 -0.084373 1.500000 3.500000 4.000000
|
||||
N C sps 9.090970 -1.494255 -0.616711 0.000000 0.000000 1.500000 3.500000 4.000000 -0.337943 -1.335442 -0.769693 0.119373 -0.079493 1.500000 3.500000 4.000000
|
||||
C N pps 6.892240 -0.931920 -0.769164 0.000000 0.000000 1.500000 3.500000 4.000000 -0.350240 -0.467439 -1.849316 1.854403 -0.988471 1.500000 3.500000 4.000000
|
||||
C N ppp -2.903346 -2.149349 -0.253006 0.000000 0.000000 1.500000 3.500000 4.000000 0.158424 -2.114409 -0.582346 -0.051076 -0.006183 1.500000 3.500000 4.000000
|
||||
C C sss -9.404207 -1.363297 -0.507128 0.000000 0.000000 1.400000 3.500000 4.000000 0.346977 -1.519820 -0.570812 -0.013518 -0.015829 1.400000 3.500000 4.000000
|
||||
C C sps 8.662429 -1.047410 -0.661999 0.000000 0.000000 1.400000 3.500000 4.000000 -0.400467 -0.984048 -0.853949 0.157178 -0.073381 1.400000 3.500000 4.000000
|
||||
C C pps 6.811512 -0.552299 -0.776890 0.000000 0.000000 1.400000 3.500000 4.000000 -0.382417 0.102889 -2.786680 2.646356 -1.134320 1.400000 3.500000 4.000000
|
||||
C C ppp -3.550127 -1.925572 -0.132715 0.000000 0.000000 1.400000 3.500000 4.000000 0.214357 -1.948923 -0.578323 -0.034356 -0.007257 1.400000 3.500000 4.000000
|
||||
H C sss -9.072577 -1.393093 -0.430611 0.000000 0.000000 1.100000 3.500000 4.000000 0.416003 -1.459596 -0.654874 0.009140 -0.012658 1.100000 3.500000 4.000000
|
||||
H C sps 8.176008 -0.985177 -0.427403 0.000000 0.000000 1.100000 3.500000 4.000000 -0.495695 -0.901626 -1.007214 0.189808 -0.057087 1.100000 3.500000 4.000000
|
||||
H H sss -9.340000 -1.145903 -0.391777 0.000000 0.000000 0.750000 3.500000 4.000000 0.575007 -1.391261 -0.778831 0.080209 -0.017759 0.750000 3.500000 4.000000
|
||||
O O sss -12.737687 -1.851608 -0.666621 0.000000 0.000000 1.200000 3.500000 4.000000 0.296445 -1.911896 -0.663451 0.038054 -0.046608 1.200000 3.500000 4.000000
|
||||
O O sps 13.683050 -1.684554 -0.468349 0.000000 0.000000 1.200000 3.500000 4.000000 -0.362143 -1.285274 -0.939591 0.204641 -0.106438 1.200000 3.500000 4.000000
|
||||
O O pps 9.460772 -1.211748 -0.581016 0.000000 0.000000 1.200000 3.500000 4.000000 -0.312044 0.121814 -2.519352 1.681266 -0.644566 1.200000 3.500000 4.000000
|
||||
O O ppp -4.494595 -2.709223 -0.284124 0.000000 0.000000 1.200000 3.500000 4.000000 0.193010 -2.168462 -0.580629 -0.105104 0.004891 1.200000 3.500000 4.000000
|
||||
H O sss -12.230931 -1.808632 -0.421164 0.000000 0.000000 1.000000 3.500000 4.000000 0.404725 -1.702546 -0.707938 0.074904 -0.039922 1.000000 3.500000 4.000000
|
||||
H O sps 9.466088 -1.321262 -0.386336 0.000000 0.000000 1.000000 3.500000 4.000000 -0.447660 -0.952979 -1.163537 0.400616 -0.156965 1.000000 3.500000 4.000000
|
||||
N N sss -7.710330 -2.365312 -0.525527 0.000000 0.000000 1.500000 3.500000 4.000000 0.231654 -1.879002 -0.572765 -0.004579 -0.031106 1.500000 3.500000 4.000000
|
||||
N N sps 8.222314 -1.612118 -0.690081 0.000000 0.000000 1.500000 3.500000 4.000000 -0.305271 -1.385158 -0.751032 0.114531 -0.090839 1.500000 3.500000 4.000000
|
||||
N N pps 7.178570 -1.176467 -0.571049 0.000000 0.000000 1.500000 3.500000 4.000000 -0.324668 -0.547805 -1.638658 1.495168 -0.827868 1.500000 3.500000 4.000000
|
||||
N N ppp -2.829344 -2.408049 -0.387709 0.000000 0.000000 1.500000 3.500000 4.000000 0.142909 -2.162036 -0.571942 -0.071640 -0.004682 1.500000 3.500000 4.000000
|
||||
H N sss -12.095890 -1.519057 -0.277247 0.000000 0.000000 1.000000 3.500000 4.000000 0.446693 -1.500463 -0.657448 0.065741 -0.037004 1.000000 3.500000 4.000000
|
||||
H N sps 9.851338 -1.231616 -0.370836 0.000000 0.000000 1.000000 3.500000 4.000000 -0.501530 -0.785734 -1.123232 0.394878 -0.148501 1.000000 3.500000 4.000000
|
||||
7
examples/QUANTUM/LATTE/TBparam_water/electrons.dat
Normal file
7
examples/QUANTUM/LATTE/TBparam_water/electrons.dat
Normal file
@ -0,0 +1,7 @@
|
||||
Noelem= 5
|
||||
Element basis Numel Es Ep Ed Ef Mass HubbardU Wss Wpp Wdd Wff
|
||||
N sp 5.0 -18.58 -7.09 0.0 0.0 14.0067 15.93 0.0 -0.6950 0.0 0.0
|
||||
O sp 6.0 -23.96 -9.02 0.0 0.0 15.9994 12.15 0.0 -0.7577 0.0 0.0
|
||||
H s 1.0 -6.35 0.0 0.0 0.0 1.0079 12.85 -1.7937 0.0 0.0 0.0
|
||||
C sp 4.0 -13.75 -5.28 0.0 0.0 12.01 10.0 0.0 -0.621 0.0 0.0
|
||||
Ti sd 4.0 -5.5 0.0 -3.0 0.0 47.867 10.0 0.0 0.0 0.0 0.0
|
||||
12
examples/QUANTUM/LATTE/TBparam_water/ppots.nonortho
Normal file
12
examples/QUANTUM/LATTE/TBparam_water/ppots.nonortho
Normal file
@ -0,0 +1,12 @@
|
||||
Nopps= 10
|
||||
Ele1 Ele2 A0 A1 A2 A3 A4 A5 A6 C R1 Rcut
|
||||
N O 13.182426 20.050322 -46.806321 38.206953 -12.319656 0.000000 0.000000 0.000000 1.600000 1.700000
|
||||
C N 88.953762 10.294988 -27.706877 22.101434 -6.836438 0.000000 0.000000 0.000000 1.600000 1.700000
|
||||
C O 0.944093 30.116337 -59.608215 45.107654 -13.178839 0.000000 0.000000 0.000000 1.600000 1.700000
|
||||
C H 104.889589 3.971095 -23.823043 26.408093 -11.317522 0.000000 0.000000 0.000000 1.200000 1.300000
|
||||
C C 3.962931 24.467772 -51.156024 39.031644 -11.342979 0.000000 0.000000 0.000000 1.600000 1.700000
|
||||
H H 38.512100 3.887860 -37.769100 57.083500 -34.512200 0.000000 0.000000 0.000000 0.900000 1.000000
|
||||
N N 43.228899 15.004605 -36.621777 29.234888 -8.912743 0.000000 0.000000 0.000000 1.600000 1.700000
|
||||
N H 0.625470 28.081241 -63.414297 53.286361 -17.352234 0.000000 0.000000 0.000000 1.300000 1.400000
|
||||
O O 10.999870 19.303033 -45.747853 37.946431 -11.935755 0.000000 0.000000 0.000000 1.500000 1.600000
|
||||
O H 0.481176 33.175383 -81.158683 74.935408 -26.792315 0.000000 0.000000 0.000000 1.200000 1.300000
|
||||
23
examples/QUANTUM/LATTE/data.ch4
Normal file
23
examples/QUANTUM/LATTE/data.ch4
Normal file
@ -0,0 +1,23 @@
|
||||
LAMMPS Description
|
||||
|
||||
5 atoms
|
||||
|
||||
2 atom types
|
||||
|
||||
0.0000000000000000 19.523000000000000 xlo xhi
|
||||
0.0000000000000000 12.757999999999999 ylo yhi
|
||||
0.0000000000000000 11.692000000000000 zlo zhi
|
||||
0.0000000000000000 0.0000000000000000 0.0000000000000000 xy xz yz
|
||||
|
||||
Masses
|
||||
|
||||
1 12.010000000000000
|
||||
2 1.0078250169754028
|
||||
|
||||
Atoms
|
||||
|
||||
1 1 1 0.0 -9.16600 2.05200 0.00000
|
||||
2 1 2 0.0 -8.09600 2.05200 0.00000
|
||||
3 1 2 0.0 -9.52300 2.75800 -0.72000
|
||||
4 1 2 0.0 -9.52300 2.32200 0.97200
|
||||
5 1 2 0.0 -9.52300 1.07500 -0.25200
|
||||
49
examples/QUANTUM/LATTE/data.graphene
Normal file
49
examples/QUANTUM/LATTE/data.graphene
Normal file
@ -0,0 +1,49 @@
|
||||
LAMMPS Description
|
||||
|
||||
32 atoms
|
||||
|
||||
1 atom types
|
||||
|
||||
0.0000000000000000 10.000000000000000 xlo xhi
|
||||
0.0000000000000000 8.0000000000000000 ylo yhi
|
||||
0.0000000000000000 20.000000000000000 zlo zhi
|
||||
4.8985871965894128E-016 1.2246467991473533E-015 1.2246467991473533E-015 xy xz yz
|
||||
|
||||
Masses
|
||||
|
||||
1 12.010000000000000
|
||||
|
||||
Atoms
|
||||
|
||||
1 1 1 0.0 4.93100 4.25000 0.00500
|
||||
2 1 1 0.0 8.62100 2.12100 0.14000
|
||||
3 1 1 0.0 3.70700 2.12600 0.14700
|
||||
4 1 1 0.0 7.38200 4.25400 0.07800
|
||||
5 1 1 0.0 2.47900 4.25400 0.08000
|
||||
6 1 1 0.0 6.15800 6.37400 -0.01000
|
||||
7 1 1 0.0 1.23700 6.38300 0.06600
|
||||
8 1 1 0.0 1.24000 2.12100 0.14600
|
||||
9 1 1 0.0 6.15500 2.12600 0.12900
|
||||
10 1 1 0.0 0.00700 4.25200 0.12200
|
||||
11 1 1 0.0 8.62100 6.38500 0.04100
|
||||
12 1 1 0.0 3.70000 6.37400 -0.01000
|
||||
13 1 1 0.0 0.00600 1.41600 0.13000
|
||||
14 1 1 0.0 4.93000 1.40800 0.14700
|
||||
15 1 1 0.0 8.61800 3.54600 0.11500
|
||||
16 1 1 0.0 3.70800 3.55300 0.08400
|
||||
17 1 1 0.0 7.39400 5.68000 0.03500
|
||||
18 1 1 0.0 2.46500 5.68000 0.03500
|
||||
19 1 1 0.0 6.16000 7.80500 0.02700
|
||||
20 1 1 0.0 1.23800 7.81100 0.06000
|
||||
21 1 1 0.0 2.47300 1.41800 0.16100
|
||||
22 1 1 0.0 7.38900 1.41700 0.14800
|
||||
23 1 1 0.0 1.24200 3.54700 0.12600
|
||||
24 1 1 0.0 6.15300 3.55300 0.07400
|
||||
25 1 1 0.0 0.00700 5.67800 0.09700
|
||||
26 1 1 0.0 4.93100 5.66800 -0.03100
|
||||
27 1 1 0.0 8.62000 7.81300 0.03900
|
||||
28 1 1 0.0 3.70100 7.80200 0.03700
|
||||
29 1 1 0.0 0.00700 -0.01000 0.08900
|
||||
30 1 1 0.0 4.93100 -0.01500 0.16100
|
||||
31 1 1 0.0 2.47300 -0.01200 0.14400
|
||||
32 1 1 0.0 7.38900 -0.01300 0.14800
|
||||
63
examples/QUANTUM/LATTE/data.sucrose
Normal file
63
examples/QUANTUM/LATTE/data.sucrose
Normal file
@ -0,0 +1,63 @@
|
||||
LAMMPS Description
|
||||
|
||||
45 atoms
|
||||
|
||||
3 atom types
|
||||
|
||||
0.0000000000000000 17.202999999999999 xlo xhi
|
||||
0.0000000000000000 18.009000000000000 ylo yhi
|
||||
0.0000000000000000 21.643000000000001 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
1 15.9994
|
||||
2 12.01
|
||||
3 1.0079
|
||||
|
||||
Atoms
|
||||
|
||||
1 1 1 0.0 8.62700 8.66700 12.48600
|
||||
2 1 1 0.0 9.11200 9.11800 10.27300
|
||||
3 1 1 0.0 8.45700 11.33100 10.49000
|
||||
4 1 1 0.0 11.72600 8.36500 10.66700
|
||||
5 1 1 0.0 8.06500 8.99400 7.93600
|
||||
6 1 2 0.0 9.62800 9.07200 11.59100
|
||||
7 1 3 0.0 9.90900 10.08300 11.89200
|
||||
8 1 2 0.0 9.07000 10.40400 9.64000
|
||||
9 1 1 0.0 6.14600 11.61000 8.00500
|
||||
10 1 1 0.0 11.07200 10.13000 8.37600
|
||||
11 1 1 0.0 6.10200 10.00900 11.62100
|
||||
12 1 2 0.0 8.14000 10.29100 8.45100
|
||||
13 1 3 0.0 8.49000 10.91200 7.62300
|
||||
14 1 1 0.0 7.41500 7.08400 14.43400
|
||||
15 1 2 0.0 10.75100 8.07000 11.65100
|
||||
16 1 3 0.0 11.24000 8.11800 12.63400
|
||||
17 1 2 0.0 7.09000 11.63400 10.17000
|
||||
18 1 3 0.0 7.06900 12.69800 9.91100
|
||||
19 1 2 0.0 7.97200 7.44200 12.14000
|
||||
20 1 3 0.0 7.54700 7.58300 11.13800
|
||||
21 1 1 0.0 11.24900 5.73000 11.78600
|
||||
22 1 2 0.0 10.26800 6.65900 11.37300
|
||||
23 1 3 0.0 10.12300 6.53400 10.29200
|
||||
24 1 2 0.0 6.78400 10.79500 8.95500
|
||||
25 1 3 0.0 6.12100 9.95500 9.19600
|
||||
26 1 2 0.0 10.47500 10.88300 9.39800
|
||||
27 1 3 0.0 10.49500 11.92100 9.06900
|
||||
28 1 3 0.0 11.09100 10.82000 10.30900
|
||||
29 1 2 0.0 8.99100 6.32000 12.11700
|
||||
30 1 3 0.0 9.23100 6.01100 13.14400
|
||||
31 1 2 0.0 6.86600 7.25300 13.14500
|
||||
32 1 3 0.0 6.17700 8.10100 13.15700
|
||||
33 1 3 0.0 6.28900 6.35300 12.94300
|
||||
34 1 2 0.0 6.24000 11.39400 11.39300
|
||||
35 1 3 0.0 6.66500 11.86500 12.28300
|
||||
36 1 3 0.0 5.23100 11.78100 11.26000
|
||||
37 1 1 0.0 8.34300 5.24100 11.48000
|
||||
38 1 3 0.0 12.00100 9.28600 10.78200
|
||||
39 1 3 0.0 12.06300 5.97500 11.33000
|
||||
40 1 3 0.0 6.99600 9.67600 11.79700
|
||||
41 1 3 0.0 7.93700 7.87600 14.60900
|
||||
42 1 3 0.0 10.95500 9.19800 8.60700
|
||||
43 1 3 0.0 5.94400 11.05900 7.24100
|
||||
44 1 3 0.0 7.94900 8.39500 8.68400
|
||||
45 1 3 0.0 8.96400 4.50300 11.48800
|
||||
41
examples/QUANTUM/LATTE/data.water
Normal file
41
examples/QUANTUM/LATTE/data.water
Normal file
@ -0,0 +1,41 @@
|
||||
LAMMPS Description
|
||||
|
||||
24 atoms
|
||||
|
||||
2 atom types
|
||||
|
||||
0.0000000000000000 6.2670000000000003 xlo xhi
|
||||
0.0000000000000000 6.2670000000000003 ylo yhi
|
||||
0.0000000000000000 6.2670000000000003 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
1 15.994915008544922
|
||||
2 1.0078250169754028
|
||||
|
||||
Atoms
|
||||
|
||||
1 1 1 0.0 3.08800 3.70000 3.12400
|
||||
2 1 2 0.0 4.05800 3.70000 3.12400
|
||||
3 1 2 0.0 2.76400 3.13200 3.84100
|
||||
4 1 1 0.0 2.47000 0.39000 1.36000
|
||||
5 1 2 0.0 1.54000 0.37000 1.73000
|
||||
6 1 2 0.0 2.48000 0.00000 0.44000
|
||||
7 1 1 0.0 1.99300 0.41700 5.25000
|
||||
8 1 2 0.0 2.39300 1.32700 5.16000
|
||||
9 1 2 0.0 0.99300 0.49700 5.31000
|
||||
10 1 1 0.0 2.05300 6.09700 3.48000
|
||||
11 1 2 0.0 2.12300 5.20700 3.02000
|
||||
12 1 2 0.0 1.11300 0.17000 3.40000
|
||||
13 1 1 0.0 4.90000 5.37700 2.14000
|
||||
14 1 2 0.0 5.51000 6.17700 2.18000
|
||||
15 1 2 0.0 3.95000 5.68700 2.21000
|
||||
16 1 1 0.0 0.92000 3.82700 0.56000
|
||||
17 1 2 0.0 0.00000 3.54700 0.27000
|
||||
18 1 2 0.0 1.23000 4.59700 0.00000
|
||||
19 1 1 0.0 0.89000 2.03700 3.41000
|
||||
20 1 2 0.0 0.72000 2.86700 2.87000
|
||||
21 1 2 0.0 1.79000 1.66700 3.19000
|
||||
22 1 1 0.0 4.45000 4.61700 5.43000
|
||||
23 1 2 0.0 4.75000 3.89700 4.81000
|
||||
24 1 2 0.0 4.06000 4.21700 6.26000
|
||||
39
examples/QUANTUM/LATTE/in.ch4
Normal file
39
examples/QUANTUM/LATTE/in.ch4
Normal file
@ -0,0 +1,39 @@
|
||||
# simple CH4 model with LATTE
|
||||
|
||||
units metal
|
||||
atom_style full
|
||||
|
||||
read_data data.ch4
|
||||
|
||||
# replicate system if requested
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
variable nrep equal v_x*v_y*v_z
|
||||
if "${nrep} > 1" then "replicate $x $y $z"
|
||||
|
||||
# initialize system
|
||||
|
||||
velocity all create 0.0 87287 loop geom
|
||||
|
||||
pair_style zero 1.0
|
||||
pair_coeff * *
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
timestep 0.00025
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
fix 2 all mdi/qm virial yes elements C H
|
||||
fix_modify 2 energy yes
|
||||
|
||||
thermo_style custom step temp pe etotal press
|
||||
|
||||
# dynamics
|
||||
|
||||
thermo 10
|
||||
run 100
|
||||
41
examples/QUANTUM/LATTE/in.ch4.plugin
Normal file
41
examples/QUANTUM/LATTE/in.ch4.plugin
Normal file
@ -0,0 +1,41 @@
|
||||
# simple CH4 model with LATTE
|
||||
|
||||
units metal
|
||||
atom_style full
|
||||
|
||||
read_data data.ch4
|
||||
|
||||
# replicate system if requested
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
variable nrep equal v_x*v_y*v_z
|
||||
if "${nrep} > 1" then "replicate $x $y $z"
|
||||
|
||||
# initialize system
|
||||
|
||||
velocity all create 0.0 87287 loop geom
|
||||
|
||||
pair_style zero 1.0
|
||||
pair_coeff * *
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
timestep 0.00025
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
fix 2 all mdi/qm virial yes elements C H
|
||||
fix_modify 2 energy yes
|
||||
|
||||
thermo_style custom step temp pe etotal press
|
||||
|
||||
# dynamics
|
||||
|
||||
thermo 10
|
||||
|
||||
mdi plugin latte_mdi mdi "-role ENGINE -name LATTE -method LINK" &
|
||||
extra latte.in.generic command "run 100"
|
||||
39
examples/QUANTUM/LATTE/in.graphene
Normal file
39
examples/QUANTUM/LATTE/in.graphene
Normal file
@ -0,0 +1,39 @@
|
||||
# graphene model with LATTE
|
||||
|
||||
units metal
|
||||
atom_style full
|
||||
|
||||
read_data data.graphene
|
||||
|
||||
# replicate system if requested
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
variable nrep equal v_x*v_y*v_z
|
||||
if "${nrep} > 1" then "replicate $x $y $z"
|
||||
|
||||
# initialize system
|
||||
|
||||
velocity all create 100.0 87287 loop geom
|
||||
|
||||
pair_style zero 1.0
|
||||
pair_coeff * *
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
timestep 0.00025
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
fix 2 all mdi/qm virial yes elements C
|
||||
fix_modify 2 energy yes
|
||||
|
||||
thermo_style custom step temp pe etotal press
|
||||
|
||||
# dynamics
|
||||
|
||||
thermo 5
|
||||
run 20
|
||||
41
examples/QUANTUM/LATTE/in.graphene.plugin
Normal file
41
examples/QUANTUM/LATTE/in.graphene.plugin
Normal file
@ -0,0 +1,41 @@
|
||||
# graphene model with LATTE
|
||||
|
||||
units metal
|
||||
atom_style full
|
||||
|
||||
read_data data.graphene
|
||||
|
||||
# replicate system if requested
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
variable nrep equal v_x*v_y*v_z
|
||||
if "${nrep} > 1" then "replicate $x $y $z"
|
||||
|
||||
# initialize system
|
||||
|
||||
velocity all create 100.0 87287 loop geom
|
||||
|
||||
pair_style zero 1.0
|
||||
pair_coeff * *
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
timestep 0.00025
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
fix 2 all mdi/qm virial yes elements C
|
||||
fix_modify 2 energy yes
|
||||
|
||||
thermo_style custom step temp pe etotal press
|
||||
|
||||
# dynamics
|
||||
|
||||
thermo 5
|
||||
|
||||
mdi plugin latte_mdi mdi "-role ENGINE -name LATTE -method LINK" &
|
||||
extra latte.in.generic command "run 20"
|
||||
@ -9,24 +9,23 @@ label LOOP
|
||||
|
||||
units metal
|
||||
atom_style full
|
||||
atom_modify sort 0 0.0
|
||||
|
||||
read_data ${files}.lmp
|
||||
read_data data.${files}
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
timestep 0.001
|
||||
|
||||
fix 1 all mdi/qm virial yes elements 92 8 connect no
|
||||
fix 1 all mdi/qm virial yes elements U O connect no
|
||||
|
||||
thermo_style custom step temp pe etotal press
|
||||
thermo 1
|
||||
|
||||
run 0
|
||||
|
||||
write_dump all custom dump.series.mpi.${files} &
|
||||
id type x y z fx fy fz modify sort id
|
||||
#write_dump all custom dump.series.mpi.${files} &
|
||||
# id type x y z fx fy fz modify sort id
|
||||
|
||||
clear
|
||||
|
||||
@ -7,23 +7,23 @@ label LOOP
|
||||
|
||||
units metal
|
||||
atom_style full
|
||||
atom_modify sort 0 0.0
|
||||
|
||||
read_data ${files}.lmp
|
||||
read_data data.${files}
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
fix 1 all mdi/qm virial yes elements 92 8
|
||||
fix 1 all mdi/qm virial yes elements U O
|
||||
fix_modify 1 energy yes
|
||||
|
||||
thermo_style custom step temp pe etotal press
|
||||
thermo 1
|
||||
|
||||
mdi plugin latte_mdi mdi "-role ENGINE -name LATTE -method LINK" &
|
||||
command "run 0"
|
||||
extra latte.in.uo2 command "run 0"
|
||||
|
||||
write_dump all custom dump.series.plugin.${files} &
|
||||
id type x y z fx fy fz modify sort id
|
||||
#write_dump all custom dump.series.plugin.${files} &
|
||||
# id type x y z fx fy fz modify sort id
|
||||
|
||||
clear
|
||||
|
||||
39
examples/QUANTUM/LATTE/in.sucrose
Normal file
39
examples/QUANTUM/LATTE/in.sucrose
Normal file
@ -0,0 +1,39 @@
|
||||
# sucrose model with LATTE
|
||||
|
||||
units metal
|
||||
atom_style full
|
||||
|
||||
read_data data.sucrose
|
||||
|
||||
# replicate system if requested
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
variable nrep equal v_x*v_y*v_z
|
||||
if "${nrep} > 1" then "replicate $x $y $z"
|
||||
|
||||
# initialize system
|
||||
|
||||
velocity all create 100.0 87287 loop geom
|
||||
|
||||
pair_style zero 1.0
|
||||
pair_coeff * *
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
timestep 0.00025
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
fix 2 all mdi/qm virial yes elements O C H
|
||||
fix_modify 2 energy yes
|
||||
|
||||
thermo_style custom step temp pe etotal press
|
||||
|
||||
# dynamics
|
||||
|
||||
thermo 10
|
||||
run 100
|
||||
41
examples/QUANTUM/LATTE/in.sucrose.plugin
Normal file
41
examples/QUANTUM/LATTE/in.sucrose.plugin
Normal file
@ -0,0 +1,41 @@
|
||||
# sucrose model with LATTE
|
||||
|
||||
units metal
|
||||
atom_style full
|
||||
|
||||
read_data data.sucrose
|
||||
|
||||
# replicate system if requested
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
variable nrep equal v_x*v_y*v_z
|
||||
if "${nrep} > 1" then "replicate $x $y $z"
|
||||
|
||||
# initialize system
|
||||
|
||||
velocity all create 100.0 87287 loop geom
|
||||
|
||||
pair_style zero 1.0
|
||||
pair_coeff * *
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
timestep 0.00025
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
fix 2 all mdi/qm virial yes elements O C H
|
||||
fix_modify 2 energy yes
|
||||
|
||||
thermo_style custom step temp pe etotal press
|
||||
|
||||
# dynamics
|
||||
|
||||
thermo 10
|
||||
|
||||
mdi plugin latte_mdi mdi "-role ENGINE -name LATTE -method LINK" &
|
||||
extra latte.in.generic command "run 100"
|
||||
@ -2,9 +2,8 @@
|
||||
|
||||
units metal
|
||||
atom_style full
|
||||
atom_modify sort 0 0.0
|
||||
|
||||
read_data 2uo2.lmp
|
||||
read_data data.2uo2
|
||||
|
||||
velocity all create 300.0 87287 loop geom
|
||||
|
||||
@ -15,12 +14,12 @@ timestep 0.00025
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
fix 2 all mdi/qm virial yes elements 92 8
|
||||
fix 2 all mdi/qm virial yes elements U O
|
||||
|
||||
thermo_style custom step temp pe etotal press
|
||||
thermo 1
|
||||
thermo 5
|
||||
|
||||
dump 1 all custom 1 dump.aimd.mpi &
|
||||
id type x y z vx vy vz fx fy fz
|
||||
#dump 1 all custom 1 dump.aimd.mpi &
|
||||
# id type x y z vx vy vz fx fy fz
|
||||
|
||||
run 20
|
||||
@ -1,10 +1,9 @@
|
||||
# AIMD test of two UO2 molecules with LATTE in MDI plugin mode
|
||||
# AIMD test of two UO2 molecules with LATTE in MDI stand-alone mode
|
||||
|
||||
units metal
|
||||
atom_style full
|
||||
atom_modify sort 0 0.0
|
||||
|
||||
read_data 2uo2.lmp
|
||||
read_data data.2uo2
|
||||
|
||||
velocity all create 300.0 87287 loop geom
|
||||
|
||||
@ -15,13 +14,13 @@ timestep 0.00025
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
fix 2 all mdi/qm virial yes elements 92 8
|
||||
fix 2 all mdi/qm virial yes elements U O
|
||||
|
||||
thermo_style custom step temp pe etotal press
|
||||
thermo 1
|
||||
thermo 5
|
||||
|
||||
dump 1 all custom 1 dump.aimd.plugin &
|
||||
id type x y z vx vy vz fx fy fz
|
||||
#dump 1 all custom 1 dump.aimd.mpi &
|
||||
# id type x y z vx vy vz fx fy fz
|
||||
|
||||
mdi plugin latte_mdi mdi "-role ENGINE -name LATTE -method LINK" &
|
||||
command "run 20"
|
||||
extra latte.in.uo2 command "run 20"
|
||||
39
examples/QUANTUM/LATTE/in.water
Normal file
39
examples/QUANTUM/LATTE/in.water
Normal file
@ -0,0 +1,39 @@
|
||||
# simple water model with LATTE
|
||||
|
||||
units metal
|
||||
atom_style full
|
||||
|
||||
read_data data.water
|
||||
|
||||
# replicate system if requested
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
variable nrep equal v_x*v_y*v_z
|
||||
if "${nrep} > 1" then "replicate $x $y $z"
|
||||
|
||||
# initialize system
|
||||
|
||||
velocity all create 0.0 87287 loop geom
|
||||
|
||||
pair_style zero 1.0
|
||||
pair_coeff * *
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
timestep 0.00025
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
fix 2 all mdi/qm virial yes elements O H
|
||||
fix_modify 2 energy yes
|
||||
|
||||
thermo_style custom step temp pe etotal press
|
||||
|
||||
# dynamics
|
||||
|
||||
thermo 10
|
||||
run 100
|
||||
39
examples/QUANTUM/LATTE/in.water.min
Normal file
39
examples/QUANTUM/LATTE/in.water.min
Normal file
@ -0,0 +1,39 @@
|
||||
# minimize water model with LATTE and FIRE
|
||||
|
||||
units metal
|
||||
atom_style full
|
||||
|
||||
read_data data.water
|
||||
|
||||
# replicate system if requested
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
variable nrep equal v_x*v_y*v_z
|
||||
if "${nrep} > 1" then "replicate $x $y $z"
|
||||
|
||||
# initialize system
|
||||
|
||||
velocity all create 0.0 87287 loop geom
|
||||
|
||||
pair_style zero 1.0
|
||||
pair_coeff * *
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
fix 2 all mdi/qm virial yes elements O H
|
||||
fix_modify 2 energy yes
|
||||
|
||||
thermo_style custom step temp pe etotal press
|
||||
|
||||
# minimization
|
||||
|
||||
thermo 10
|
||||
|
||||
min_style fire
|
||||
minimize 1.0e-4 1.0e-4 500 500
|
||||
41
examples/QUANTUM/LATTE/in.water.min.plugin
Normal file
41
examples/QUANTUM/LATTE/in.water.min.plugin
Normal file
@ -0,0 +1,41 @@
|
||||
# minimize water model with LATTE and FIRE
|
||||
|
||||
units metal
|
||||
atom_style full
|
||||
|
||||
read_data data.water
|
||||
|
||||
# replicate system if requested
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
variable nrep equal v_x*v_y*v_z
|
||||
if "${nrep} > 1" then "replicate $x $y $z"
|
||||
|
||||
# initialize system
|
||||
|
||||
velocity all create 0.0 87287 loop geom
|
||||
|
||||
pair_style zero 1.0
|
||||
pair_coeff * *
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
fix 2 all mdi/qm virial yes elements O H
|
||||
fix_modify 2 energy yes
|
||||
|
||||
thermo_style custom step temp pe etotal press
|
||||
|
||||
# minimization
|
||||
|
||||
thermo 10
|
||||
|
||||
min_style fire
|
||||
|
||||
mdi plugin latte_mdi mdi "-role ENGINE -name LATTE -method LINK" &
|
||||
extra latte.in.water command "minimize 1.0e-4 1.0e-4 500 500"
|
||||
41
examples/QUANTUM/LATTE/in.water.plugin
Normal file
41
examples/QUANTUM/LATTE/in.water.plugin
Normal file
@ -0,0 +1,41 @@
|
||||
# simple water model with LATTE
|
||||
|
||||
units metal
|
||||
atom_style full
|
||||
|
||||
read_data data.water
|
||||
|
||||
# replicate system if requested
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
variable nrep equal v_x*v_y*v_z
|
||||
if "${nrep} > 1" then "replicate $x $y $z"
|
||||
|
||||
# initialize system
|
||||
|
||||
velocity all create 0.0 87287 loop geom
|
||||
|
||||
pair_style zero 1.0
|
||||
pair_coeff * *
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
timestep 0.00025
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
fix 2 all mdi/qm virial yes elements O H
|
||||
fix_modify 2 energy yes
|
||||
|
||||
thermo_style custom step temp pe etotal press
|
||||
|
||||
# dynamics
|
||||
|
||||
thermo 10
|
||||
|
||||
mdi plugin latte_mdi mdi "-role ENGINE -name LATTE -method LINK" &
|
||||
extra latte.in.water command "run 100"
|
||||
32
examples/QUANTUM/LATTE/latte.in.generic
Normal file
32
examples/QUANTUM/LATTE/latte.in.generic
Normal file
@ -0,0 +1,32 @@
|
||||
LATTE INPUT FILE
|
||||
================
|
||||
#This input file resumes the content of MDcontroller and TBparam/control.in
|
||||
#The parser will only read it is present inside the running folder.
|
||||
#In case this file is not present Latte will read the two files as original.
|
||||
#The order of the keywords is not important in this file.
|
||||
#To get a full description of these keywords please see:
|
||||
## https://github.com/lanl/LATTE/blob/master/Manual/LATTE_manual.pdf
|
||||
|
||||
#General controls
|
||||
CONTROL{
|
||||
XCONTROL= 1
|
||||
BASISTYPE= NONORTHO
|
||||
PARAMPATH= "./TBparam_generic"
|
||||
KBT= 0.0
|
||||
ENTROPYKIND= 1
|
||||
PPOTON= 1
|
||||
SPINON= 0 SPINTOL= 1.0e-4
|
||||
ELECTRO= 1 ELECMETH= 0 ELEC_QTOL= 1.0e-8
|
||||
MAXSCF= 450
|
||||
BREAKTOL= 1.0E-6 MINSP2ITER= 22 SP2CONV= REL
|
||||
FULLQCONV= 1 QITER= 3
|
||||
QMIX= 0.25 SPINMIX= 0.25 MDMIX= 0.25
|
||||
SPARSEON= 0 THRESHOLDON= 1 NUMTHRESH= 1.0e-6 FILLINSTOP= 100 BLKSZ= 4
|
||||
MSPARSE= 1500
|
||||
SKIN= 1.0
|
||||
CHARGE= 0
|
||||
XBO= 1
|
||||
XBODISON= 1
|
||||
XBODISORDER= 5
|
||||
KON= 0
|
||||
}
|
||||
@ -2,7 +2,7 @@
|
||||
CONTROL{
|
||||
XCONTROL= 1
|
||||
BASISTYPE= NONORTHO
|
||||
PARAMPATH= './'
|
||||
PARAMPATH= "./TBparam_uo2"
|
||||
SCLTYPE= TABLE
|
||||
DEBUGON= 0
|
||||
FERMIM= 6
|
||||
@ -12,7 +12,7 @@ CONTROL{
|
||||
ENTROPYKIND= 1
|
||||
PPOTON= 2 VDWON= 0
|
||||
SPINON= 0 SPINTOL= 1.0e-4
|
||||
ELECTRO= 1 ELECMETH= 0 ELEC_ETOL= 0.001 ELEC_QTOL= 1.0e-12
|
||||
ELECTRO= 1 ELECMETH= 0 ELEC_ETOL= 0.001 ELEC_QTOL= 1.0e-5
|
||||
COULACC= 1.0e-6 COULCUT= -500.0 COULR1= 500.0
|
||||
MAXSCF= 250
|
||||
BREAKTOL= 1.0E-12 MINSP2ITER= 22 SP2CONV= REL
|
||||
32
examples/QUANTUM/LATTE/latte.in.water
Executable file
32
examples/QUANTUM/LATTE/latte.in.water
Executable file
@ -0,0 +1,32 @@
|
||||
LATTE INPUT FILE
|
||||
================
|
||||
#This input file resumes the content of MDcontroller and TBparam/control.in
|
||||
#The parser will only read it is present inside the running folder.
|
||||
#In case this file is not present Latte will read the two files as original.
|
||||
#The order of the keywords is not important in this file.
|
||||
#To get a full description of these keywords please see:
|
||||
## https://github.com/lanl/LATTE/blob/master/Manual/LATTE_manual.pdf
|
||||
|
||||
#General controls
|
||||
CONTROL{
|
||||
XCONTROL= 1
|
||||
BASISTYPE= NONORTHO
|
||||
PARAMPATH= "./TBparam_water"
|
||||
KBT= 0.0
|
||||
ENTROPYKIND= 1
|
||||
PPOTON= 1
|
||||
SPINON= 0 SPINTOL= 1.0e-4
|
||||
ELECTRO= 1 ELECMETH= 0 ELEC_QTOL= 1.0e-8
|
||||
MAXSCF= 450
|
||||
BREAKTOL= 1.0E-6 MINSP2ITER= 22 SP2CONV= REL
|
||||
FULLQCONV= 1 QITER= 3
|
||||
QMIX= 0.25 SPINMIX= 0.25 MDMIX= 0.25
|
||||
SPARSEON= 0 THRESHOLDON= 1 NUMTHRESH= 1.0e-6 FILLINSTOP= 100 BLKSZ= 4
|
||||
MSPARSE= 1500
|
||||
SKIN= 1.0
|
||||
CHARGE= 0
|
||||
XBO= 1
|
||||
XBODISON= 1
|
||||
XBODISORDER= 5
|
||||
KON= 0
|
||||
}
|
||||
758
examples/QUANTUM/LATTE/latte_mdi.py
Normal file
758
examples/QUANTUM/LATTE/latte_mdi.py
Normal file
@ -0,0 +1,758 @@
|
||||
# MDI wrapper on LATTE code
|
||||
|
||||
# native LATTE units are Angstroms and eV
|
||||
|
||||
import sys,os,time
|
||||
from ctypes import *
|
||||
|
||||
import numpy as np
|
||||
from mpi4py import MPI
|
||||
import mdi
|
||||
|
||||
# --------------------------------------------
|
||||
|
||||
ELEMENTS = [
|
||||
'H' , 'He', 'Li', 'Be', 'B' , 'C' , 'N' , 'O' , 'F' , 'Ne',
|
||||
'Na', 'Mg', 'Al', 'Si', 'P' , 'S' , 'Cl', 'Ar', 'K' , 'Ca',
|
||||
'Sc', 'Ti', 'V' , 'Cr', 'Mn', 'Fe', 'Co', 'Ni', 'Cu', 'Zn',
|
||||
'Ga', 'Ge', 'As', 'Se', 'Br', 'Kr', 'Rb', 'Sr', 'Y' , 'Zr',
|
||||
'Nb', 'Mo', 'Tc', 'Ru', 'Rh', 'Pd', 'Ag', 'Cd', 'In', 'Sn',
|
||||
'Sb', 'Te', 'I' , 'Xe', 'Cs', 'Ba', 'La', 'Ce', 'Pr', 'Nd',
|
||||
'Pm', 'Sm', 'Eu', 'Gd', 'Tb', 'Dy', 'Ho', 'Er', 'Tm', 'Yb',
|
||||
'Lu', 'Hf', 'Ta', 'W' , 'Re', 'Os', 'Ir', 'Pt', 'Au', 'Hg',
|
||||
'Tl', 'Pb', 'Bi', 'Po', 'At', 'Rn', 'Fr', 'Ra', 'Ac', 'Th',
|
||||
'Pa', 'U' , 'Np', 'Pu', 'Am', 'Cm', 'Bk', 'Cf', 'Es', 'Fm',
|
||||
'Md', 'No', 'Lr', 'Rf', 'Db', 'Sg', 'Bh', 'Hs', 'Mt', 'Ds',
|
||||
'Rg', 'Cn', 'Nh', 'Fl', 'Mc', 'Lv', 'Ts', 'Og',
|
||||
]
|
||||
|
||||
# --------------------------------------------
|
||||
# global data
|
||||
# --------------------------------------------
|
||||
|
||||
world = 0
|
||||
me = nprocs = 0
|
||||
|
||||
exitflag = False
|
||||
|
||||
AIMD = 0
|
||||
QMMM = 1
|
||||
mode = AIMD
|
||||
|
||||
# LATTE library
|
||||
|
||||
libname = "liblatte.so"
|
||||
liblatte = None
|
||||
infile = None
|
||||
|
||||
# QM inputs
|
||||
|
||||
flag_qm_natoms = flag_mm_natoms = 0
|
||||
flag_box = flag_box_displ = 0
|
||||
flag_qm_elements = flag_qm_types = 0
|
||||
flag_qm_coords = flag_qm_potential = 0
|
||||
flag_mm_elements = 0
|
||||
flag_mm_coords = flag_mm_charges = 0
|
||||
|
||||
box = np.empty(9)
|
||||
box_displ = np.empty(3)
|
||||
|
||||
qm_natoms = 0
|
||||
qm_elements = None
|
||||
qm_coords = None
|
||||
qm_potential = None
|
||||
qm_velocity = None
|
||||
qm_ntypes = 0
|
||||
qm_types = None
|
||||
qm_mass = None
|
||||
|
||||
mm_natoms = 0
|
||||
mm_coords = None
|
||||
mm_charges = None
|
||||
mm_elements = None
|
||||
|
||||
# QM outputs
|
||||
|
||||
qm_pe = 0.0
|
||||
qm_stress = np.empty(9)
|
||||
qm_forces = None
|
||||
qm_charges = None
|
||||
|
||||
mm_forces = None
|
||||
|
||||
# --------------------------------------------
|
||||
# print error message and halt
|
||||
# --------------------------------------------
|
||||
|
||||
def error(txt,mpiexists=1):
|
||||
if me == 0: print("ERROR:",txt)
|
||||
if mpiexists: world.Abort()
|
||||
sys.exit()
|
||||
|
||||
# --------------------------------------------
|
||||
# process non-MDI command-line options to LATTE
|
||||
# --------------------------------------------
|
||||
|
||||
def options(other_options):
|
||||
global infile
|
||||
|
||||
if len(other_options) != 1:
|
||||
error("No filename provided to LATTE wrapper")
|
||||
infile = other_options[0]
|
||||
|
||||
# copy infile to latte.in as required by LATTE
|
||||
|
||||
os.system("cp %s latte.in" % infile)
|
||||
|
||||
# --------------------------------------------
|
||||
# operate as an engine
|
||||
# --------------------------------------------
|
||||
|
||||
def mdi_engine(other_options):
|
||||
global world
|
||||
|
||||
# get the MPI intra-communicator for this engine
|
||||
|
||||
world = mdi.MDI_MPI_get_world_comm()
|
||||
me = world.Get_rank()
|
||||
nprocs = world.Get_size()
|
||||
|
||||
# LATTE lib can only be invoked on a single MPI task
|
||||
|
||||
if nprocs > 1:
|
||||
error("LATTE can only run on a single MPI task")
|
||||
|
||||
# process non-MDI command line args
|
||||
|
||||
options(other_options)
|
||||
|
||||
# confirm LATTE is being run as an engine
|
||||
|
||||
role = mdi.MDI_Get_Role()
|
||||
if not role == mdi.MDI_ENGINE:
|
||||
error("Must run LATTE as an MDI engine")
|
||||
|
||||
# supported MDI commands
|
||||
|
||||
mdi.MDI_Register_Node("@DEFAULT")
|
||||
mdi.MDI_Register_Command("@DEFAULT","EXIT")
|
||||
|
||||
# driver --> engine
|
||||
|
||||
mdi.MDI_Register_Command("@DEFAULT",">NATOMS")
|
||||
mdi.MDI_Register_Command("@DEFAULT",">CELL")
|
||||
mdi.MDI_Register_Command("@DEFAULT",">CELL_DISPL")
|
||||
mdi.MDI_Register_Command("@DEFAULT",">ELEMENTS")
|
||||
mdi.MDI_Register_Command("@DEFAULT",">TYPES")
|
||||
mdi.MDI_Register_Command("@DEFAULT",">COORDS")
|
||||
mdi.MDI_Register_Command("@DEFAULT",">POTENTIAL_AT_NUCLEI")
|
||||
mdi.MDI_Register_Command("@DEFAULT",">NLATTICE")
|
||||
mdi.MDI_Register_Command("@DEFAULT",">LATTICE_ELEMENTS")
|
||||
mdi.MDI_Register_Command("@DEFAULT",">CLATTICE")
|
||||
mdi.MDI_Register_Command("@DEFAULT",">LATTICE")
|
||||
|
||||
# engine --> driver
|
||||
|
||||
mdi.MDI_Register_Command("@DEFAULT","<PE")
|
||||
mdi.MDI_Register_Command("@DEFAULT","<FORCES")
|
||||
mdi.MDI_Register_Command("@DEFAULT",">LATTICE_FORCES")
|
||||
mdi.MDI_Register_Command("@DEFAULT","<STRESS")
|
||||
mdi.MDI_Register_Command("@DEFAULT","<CHARGES")
|
||||
|
||||
# load LATTE lib and set ctypes signatures for function calls
|
||||
|
||||
latte_load()
|
||||
|
||||
# one-time operation to establish a connection with the driver
|
||||
|
||||
mdicomm = mdi.MDI_Accept_Communicator()
|
||||
|
||||
# set callback to execute_command
|
||||
|
||||
mdi.MDI_Set_Execute_Command_Func(execute_command,None)
|
||||
|
||||
# infinite loop to exchange messages with driver
|
||||
# until EXIT command received
|
||||
|
||||
while not exitflag:
|
||||
command = mdi.MDI_Recv_Command(mdicomm)
|
||||
command = world.bcast(command,root=0)
|
||||
execute_command(command,mdicomm,None)
|
||||
|
||||
# --------------------------------------------
|
||||
# called in loop by mdi_engine()
|
||||
# called internally from MDI_Recv_command() until an EXIT command is received
|
||||
# command = command name
|
||||
# mdicomm = MDI communicator for all MDI commands
|
||||
# can also use world for MPI commands
|
||||
# object_ptr = ptr to data if necessary
|
||||
# --------------------------------------------
|
||||
|
||||
def execute_command(command,mdicomm,object_ptr):
|
||||
global exitflag
|
||||
|
||||
# driver says done
|
||||
|
||||
if command == "EXIT":
|
||||
exitflag = True
|
||||
|
||||
# MDI commands which setup quantum calculation
|
||||
# NOTE: not sure if it makes sense for LATTE wrapper to support >TYPES
|
||||
|
||||
elif command == ">NATOMS":
|
||||
receive_qm_natoms(mdicomm)
|
||||
|
||||
elif command == ">CELL":
|
||||
receive_box(mdicomm)
|
||||
|
||||
elif command == ">CELL_DISPL":
|
||||
receive_box_displ(mdicomm)
|
||||
|
||||
elif command == ">ELEMENTS":
|
||||
receive_qm_elements(mdicomm)
|
||||
|
||||
elif command == ">COORDS":
|
||||
receive_qm_coords(mdicomm)
|
||||
|
||||
elif command == ">POTENTIAL_AT_NUCLEI":
|
||||
receive_qm_potential(mdicomm)
|
||||
|
||||
elif command == ">NLATTICE":
|
||||
receive_mm_natoms(mdicomm)
|
||||
|
||||
elif command == ">LATTICE_ELEMENTS":
|
||||
receive_mm_elements(mdicomm)
|
||||
|
||||
elif command == ">CLATTICE":
|
||||
receive_mm_coords(mdicomm)
|
||||
|
||||
elif command == ">LATTICE":
|
||||
receive_mm_charges(mdicomm)
|
||||
|
||||
# MDI commands which retreive quantum results
|
||||
# each may also trigger the quantum calculation
|
||||
|
||||
elif command == "<PE":
|
||||
evaluate()
|
||||
ierr = mdi.MDI_Send(qm_pe,1,mdi.MDI_DOUBLE,mdicomm)
|
||||
if ierr: error("MDI: <PE data")
|
||||
|
||||
elif command == "<FORCES":
|
||||
evaluate()
|
||||
ierr = mdi.MDI_Send(qm_forces,3*qm_natoms,mdi.MDI_DOUBLE,mdicomm)
|
||||
if ierr: error("MDI: <FORCES data")
|
||||
|
||||
elif command == "<LATTICE_FORCES":
|
||||
evaluate()
|
||||
ierr = mdi.MDI_Send(mm_forces,3*mm_natoms,mdi.MDI_DOUBLE,mdicomm)
|
||||
if ierr: error("MDI: <LATTICE_FORCES data")
|
||||
|
||||
elif command == "<STRESS":
|
||||
evaluate()
|
||||
ierr = mdi.MDI_Send(qm_stress,9,mdi.MDI_DOUBLE,mdicomm)
|
||||
if ierr: error("MDI: <STRESS data")
|
||||
|
||||
elif command == "<CHARGES":
|
||||
evaluate()
|
||||
ierr = mdi.MDI_Send(qm_charges,qm_natoms,mdi.MDI_DOUBLE,mdicomm)
|
||||
if ierr: error("MDI: <CHARGES data")
|
||||
|
||||
# unrecognized command
|
||||
|
||||
else: error("Unrecognized MDI command")
|
||||
|
||||
return 0
|
||||
|
||||
# --------------------------------------------
|
||||
# receive count of QM atoms from driver
|
||||
# --------------------------------------------
|
||||
|
||||
def receive_qm_natoms(mdicomm):
|
||||
global flag_qm_natoms,qm_natoms
|
||||
flag_qm_natoms = 1
|
||||
|
||||
qm_natoms = mdi.MDI_Recv(1,mdi.MDI_INT,mdicomm)
|
||||
qm_natoms = world.bcast(qm_natoms,root=0)
|
||||
allocate("qm")
|
||||
|
||||
# --------------------------------------------
|
||||
# receive 3 simulation box edge vectors from driver
|
||||
# --------------------------------------------
|
||||
|
||||
def receive_box(mdicomm):
|
||||
global flag_box
|
||||
flag_box = 1
|
||||
|
||||
ierr = mdi.MDI_Recv(9,mdi.MDI_DOUBLE,mdicomm,buf=box)
|
||||
if ierr: error("MDI: >CELL data")
|
||||
world.Bcast(box,root=0)
|
||||
|
||||
# --------------------------------------------
|
||||
# receive simulation box displacement vector from driver
|
||||
# --------------------------------------------
|
||||
|
||||
def receive_box_displ(mdicomm):
|
||||
global flag_box_displ
|
||||
flag_box_displ = 1
|
||||
|
||||
ierr = mdi.MDI_Recv(3,mdi.MDI_DOUBLE,mdicomm,buf=box_displ)
|
||||
if ierr: error("MDI: >CELL_DISPL data")
|
||||
world.Bcast(box_displ,root=0)
|
||||
|
||||
# --------------------------------------------
|
||||
# receive QM atom coords from driver
|
||||
# --------------------------------------------
|
||||
|
||||
def receive_qm_coords(mdicomm):
|
||||
global flag_qm_coords
|
||||
flag_qm_coords = 1
|
||||
|
||||
if not qm_natoms: error("Cannot MDI >COORDS if # of QM atoms = 0")
|
||||
|
||||
ierr = mdi.MDI_Recv(3*qm_natoms,mdi.MDI_DOUBLE,mdicomm,buf=qm_coords)
|
||||
if ierr: error("MDI: >COORDS data")
|
||||
world.Bcast(qm_coords,root=0)
|
||||
|
||||
# --------------------------------------------
|
||||
# receive Coulomb potential at QM nuclei from driver
|
||||
# --------------------------------------------
|
||||
|
||||
def receive_qm_potential(mdicomm):
|
||||
global flag_qm_potential
|
||||
flag_qm_potential = 1
|
||||
|
||||
if not qm_natoms: error("Cannot MDI >POTENTIAL_AT_NUCLEI if # of QM atoms = 0")
|
||||
|
||||
ierr = mdi.MDI_Recv(qm_natoms,mdi.MDI_DOUBLE,mdicomm,buf=qm_potential)
|
||||
if ierr: error("MDI: >POTENTIAL_AT_NUCLEI data")
|
||||
world.Bcast(qm_potential,root=0)
|
||||
|
||||
# --------------------------------------------
|
||||
# receive QM atomic numbers from driver
|
||||
# --------------------------------------------
|
||||
|
||||
def receive_qm_elements(mdicomm):
|
||||
global flag_qm_elements
|
||||
flag_qm_elements = 1
|
||||
|
||||
if not qm_natoms: error("Cannot MDI >ELEMENTS if # of QM atoms = 0")
|
||||
|
||||
ierr = mdi.MDI_Recv(qm_natoms,mdi.MDI_INT,mdicomm,buf=qm_elements)
|
||||
if ierr: error("MDI: >ELEMENTS data")
|
||||
world.Bcast(qm_elements,root=0)
|
||||
|
||||
# --------------------------------------------
|
||||
# receive QM atom types from driver
|
||||
# --------------------------------------------
|
||||
|
||||
def receive_types(mdicomm):
|
||||
global flag_qm_types
|
||||
flag_qm_types = 1
|
||||
|
||||
if not qm_natoms: error("Cannot MDI >TYPES if # of QM atoms = 0")
|
||||
|
||||
ierr = mdi.MDI_Recv(qm_natoms,mdi.MDI_INT,mdicomm,buf=qm_types)
|
||||
if ierr: error("MDI: >TYPES data")
|
||||
world.Bcast(qm_types,root=0)
|
||||
|
||||
# --------------------------------------------
|
||||
# receive count of MM atoms from driver
|
||||
# --------------------------------------------
|
||||
|
||||
def receive_mm_natoms(mdicomm):
|
||||
global flag_mm_natoms,mm_natoms
|
||||
flag_mm_natoms = 1
|
||||
|
||||
mm_natoms = mdi.MDI_Recv(1,mdi.MDI_INT,mdicomm)
|
||||
mm_natoms = world.bcast(mm_natoms,root=0)
|
||||
allocate("mm")
|
||||
|
||||
# --------------------------------------------
|
||||
# receive MM atomic numbers from driver
|
||||
# --------------------------------------------
|
||||
|
||||
def receive_mm_elements(mdicomm):
|
||||
global flag_mm_elements
|
||||
flag_mm_elements = 1
|
||||
|
||||
if not mm_natoms: error("Cannot MDI >LATTICE_ELEMENTS if # of MM atoms = 0")
|
||||
|
||||
ierr = mdi.MDI_Recv(mm_natoms,mdi.MDI_INT,mdicomm,buf=mm_elements)
|
||||
if ierr: error("MDI: >LATTICE_ELEMENTS data")
|
||||
world.Bcast(mm_elements,root=0)
|
||||
|
||||
# --------------------------------------------
|
||||
# receive MM atom coords from driver
|
||||
# --------------------------------------------
|
||||
|
||||
def receive_mm_coords(mdicomm):
|
||||
global flag_mm_coords
|
||||
flag_mm_coords = 1
|
||||
|
||||
if not mm_natoms: error("Cannot MDI >CLATTICE if # of MM atoms = 0")
|
||||
|
||||
ierr = mdi.MDI_Recv(3*mm_natoms,mdi.MDI_DOUBLE,mdicomm,buf=mm_coords)
|
||||
if ierr: error("MDI: >CLATTICE data")
|
||||
world.Bcast(mm_coords,root=0)
|
||||
|
||||
# --------------------------------------------
|
||||
# receive charge on MM atoms from driver
|
||||
# --------------------------------------------
|
||||
|
||||
def receive_mm_charges(mdicomm):
|
||||
global flag_mm_charges
|
||||
flag_mm_charges = 1
|
||||
|
||||
if not mm_natoms: error("Cannot MDI >LATTICE if # of MM atoms = 0")
|
||||
|
||||
ierr = mdi.MDI_Recv(mm_natoms,mdi.MDI_DOUBLE,mdicomm,buf=mm_charges)
|
||||
if ierr: error("MDI: >LATTICE data")
|
||||
world.Bcast(mm_charges,root=0)
|
||||
|
||||
# --------------------------------------------
|
||||
# allocate persistent data for QM or MM atoms
|
||||
# called when qm_natoms or mm_natoms is reset by MDI driver
|
||||
# --------------------------------------------
|
||||
|
||||
def allocate(which):
|
||||
global qm_elements,qm_coords,qm_potential,qm_forces,qm_charges
|
||||
global qm_types,qm_mass,qm_velocity
|
||||
global mm_coords,mm_charges,mm_forces
|
||||
|
||||
if which == "qm":
|
||||
n = qm_natoms
|
||||
qm_elements = np.empty(n,dtype=np.int32)
|
||||
qm_coords = np.empty((n,3))
|
||||
qm_potential = np.empty(n)
|
||||
qm_forces = np.empty((n,3))
|
||||
qm_charges = np.empty(n)
|
||||
|
||||
qm_types = np.empty(n,dtype=np.int32)
|
||||
qm_velocity = np.empty((n,3))
|
||||
qm_velocity.fill(0.0)
|
||||
|
||||
if which == "mm":
|
||||
n = mm_natoms
|
||||
mm_elements = np.empty(n,dtype=np.int32)
|
||||
mm_coords = np.empty((n,3))
|
||||
mm_charges = np.empty(n)
|
||||
mm_forces = np.empty((n,3))
|
||||
|
||||
# --------------------------------------------
|
||||
# perform a quantum calculation via LATTE
|
||||
# NOTE: ignore change of box size each step for now, e.g. MD NPT dynamics
|
||||
# NOTE: assume periodic for now, worry about non-periodic later
|
||||
# --------------------------------------------
|
||||
|
||||
def evaluate():
|
||||
global mode
|
||||
global flag_qm_natoms,flag_mm_natoms
|
||||
global flag_box,flag_box_displ
|
||||
global flag_qm_elements,flag_qm_types,flag_qm_coords,flag_qm_potential
|
||||
global flag_mm_elements,flag_mm_coords,flag_mm_charges
|
||||
global qm_pe,qm_stress,qm_forces,qm_charges
|
||||
global mm_forces
|
||||
global dm_previous
|
||||
|
||||
# just return if the QM system was already evaluated
|
||||
# happens when multiple results are requested by driver
|
||||
|
||||
any_flag = flag_qm_natoms + flag_mm_natoms + flag_box + flag_box_displ + \
|
||||
flag_qm_elements + flag_qm_coords + flag_qm_potential + \
|
||||
flag_mm_elements + flag_mm_coords + flag_mm_charges
|
||||
if not any_flag: return
|
||||
|
||||
# if any of these MDI commands received from LAMMPS,
|
||||
# treat it as a brand new system
|
||||
|
||||
new_system = 0
|
||||
if flag_qm_natoms or flag_mm_natoms: new_system = 1
|
||||
if flag_qm_elements or flag_mm_elements: new_system = 1
|
||||
if new_system:
|
||||
if flag_mm_natoms or flag_qm_potential: mode = QMMM
|
||||
else: mode = AIMD
|
||||
|
||||
# if new system, error check that all needed MDI calls have been made
|
||||
|
||||
if new_system:
|
||||
if not flag_qm_natoms: error("QM atom count not specified")
|
||||
if not flag_qm_elements or not flag_qm_coords:
|
||||
error("QM atom properties not fully specified")
|
||||
if mode == QMMM and not flag_qm_potential:
|
||||
error("QM atom properties not fully specified")
|
||||
set_types_masses()
|
||||
|
||||
# LATTE inputs
|
||||
# box, qm_coords must be converted to Angstroms
|
||||
|
||||
bohr_to_angstrom = mdi.MDI_Conversion_factor("bohr","angstrom")
|
||||
|
||||
box_A = box * bohr_to_angstrom
|
||||
qm_coords_A = qm_coords * bohr_to_angstrom
|
||||
|
||||
# unsupported LATTE flags for now
|
||||
|
||||
#coulombflag = 0
|
||||
#neighflag = 0
|
||||
|
||||
#pbcflag = 1 # NOTE: could pass this in as latte_mdi.py command-line arg
|
||||
|
||||
#thermo_virial = 1
|
||||
#eflag_atom = 1
|
||||
#vflag_global = 1
|
||||
#vflag_atom = 0
|
||||
|
||||
#flags_latte[0] = pbcflag; # 1 for fully periodic, 0 for fully non-periodic
|
||||
#flags_latte[1] = coulombflag; # 1 for LAMMPS computes Coulombics, 0 for LATTE
|
||||
#flags_latte[2] = eflag_atom; # 1 to return per-atom energies, 0 for no
|
||||
#flags_latte[3] = vflag_global and thermo_virial; # 1 to return global/per-atom
|
||||
#flags_latte[4] = vflag_atom and thermo_virial; # virial, 0 for no
|
||||
#flags_latte[5] = neighflag; # 1 to pass neighbor list to LATTE, 0 for no
|
||||
|
||||
# setup ctypes args for liblatte.latte() function
|
||||
|
||||
flags_latte = 6*[0]
|
||||
c_flags_latte = (c_int*6)(*flags_latte)
|
||||
|
||||
c_qm_natoms = c_int(qm_natoms)
|
||||
c_qm_ntypes = c_int(qm_ntypes)
|
||||
|
||||
boxlo = [0.0,0.0,0.0]
|
||||
boxhi = [box_A[0],box_A[4],box_A[8]]
|
||||
xy = box_A[3]
|
||||
xz = box_A[6]
|
||||
yz = box_A[7]
|
||||
|
||||
c_boxlo = (c_double*3)(*boxlo)
|
||||
c_boxhi = (c_double*3)(*boxhi)
|
||||
c_xy = c_double(xy)
|
||||
c_xz = c_double(xz)
|
||||
c_yz = c_double(yz)
|
||||
|
||||
maxiter = -1
|
||||
c_maxiter = c_int(maxiter)
|
||||
|
||||
c_qm_pe = c_double(qm_pe)
|
||||
|
||||
timestep = 0.0
|
||||
c_timestep = c_double(timestep)
|
||||
|
||||
latte_stress = np.empty(6)
|
||||
c_new_system = c_int(new_system)
|
||||
|
||||
latte_error = 0
|
||||
c_latte_error = c_bool(latte_error)
|
||||
|
||||
# QMMM with QM and MM atoms
|
||||
|
||||
if mode == QMMM:
|
||||
error("QMMM not yet supported with LATTE")
|
||||
|
||||
# AIMD with only QM atoms
|
||||
|
||||
elif mode == AIMD:
|
||||
#print("Calling LATTE ...")
|
||||
time1 = time.time()
|
||||
|
||||
#print("A",c_qm_natoms.value)
|
||||
#print("B",qm_coords_A)
|
||||
#print("C",qm_types)
|
||||
#print("D",c_qm_ntypes.value)
|
||||
#print("E",qm_mass)
|
||||
#print("F",c_boxlo[0],c_boxlo[1],c_boxlo[2])
|
||||
#print("G",c_boxhi[0],c_boxhi[1],c_boxhi[2])
|
||||
#print("H",c_xy.value,c_xz.value,c_yz.value)
|
||||
#print("I",c_maxiter.value)
|
||||
#print("J",qm_velocity)
|
||||
#print("K",c_timestep.value)
|
||||
#print("L",c_new_system.value)
|
||||
|
||||
liblatte.\
|
||||
latte(c_flags_latte,byref(c_qm_natoms),qm_coords_A,
|
||||
qm_types,byref(c_qm_ntypes),qm_mass,
|
||||
c_boxlo,c_boxhi,byref(c_xy),byref(c_xz),byref(c_yz),
|
||||
qm_forces,byref(c_maxiter),byref(c_qm_pe),
|
||||
qm_velocity,byref(c_timestep),latte_stress,
|
||||
byref(c_new_system),byref(c_latte_error))
|
||||
|
||||
latte_error = c_latte_error.value
|
||||
time2 = time.time()
|
||||
#print("LATTE time:",time2-time1,latte_error)
|
||||
|
||||
# LATTE computes extensive stress values
|
||||
# MDI stress values are intensive
|
||||
# so divide latte_stress by box volume in Angstroms
|
||||
# more generally could use volume = (a x b) dot c for (a,b,c) edge vectors
|
||||
|
||||
qm_pe = c_qm_pe.value
|
||||
latte_stress /= box_A[0]*box_A[4]*box_A[8]
|
||||
|
||||
# conversion of LATTE outputs to MDI units
|
||||
# qm_pe from eV to Hartrees
|
||||
# qm_forces from eV/A to Hartrees/Bohr
|
||||
# latte_stress from eV/A^3 to Hartrees/Bohr^3
|
||||
|
||||
ev_to_hartree = mdi.MDI_Conversion_factor("electron_volt","hartree")
|
||||
angstrom_to_bohr = mdi.MDI_Conversion_factor("angstrom","bohr")
|
||||
|
||||
qm_pe *= ev_to_hartree
|
||||
qm_forces *= ev_to_hartree / angstrom_to_bohr
|
||||
latte_stress *= ev_to_hartree / \
|
||||
(angstrom_to_bohr*angstrom_to_bohr*angstrom_to_bohr)
|
||||
|
||||
qm_stress[0] = latte_stress[0]
|
||||
qm_stress[4] = latte_stress[1]
|
||||
qm_stress[8] = latte_stress[2]
|
||||
qm_stress[1] = qm_stress[3] = latte_stress[3]
|
||||
qm_stress[2] = qm_stress[6] = latte_stress[4]
|
||||
qm_stress[5] = qm_stress[7] = latte_stress[5]
|
||||
|
||||
# clear flags for all MDI commands for next QM evaluation
|
||||
|
||||
flag_qm_natoms = flag_mm_natoms = 0
|
||||
flag_box = flag_box_displ = 0
|
||||
flag_qm_elements = 0
|
||||
flag_qm_coords = flag_qm_potential = 0
|
||||
flag_mm_elements = 0
|
||||
flag_mm_coords = flag_mm_charges = 0
|
||||
|
||||
# --------------------------------------------
|
||||
# load LATTE library
|
||||
# set ctypes signatures for single function calls to LATTE lib
|
||||
# --------------------------------------------
|
||||
|
||||
def latte_load():
|
||||
global liblatte
|
||||
|
||||
liblatte = CDLL(libname,RTLD_GLOBAL)
|
||||
|
||||
nparray = np.ctypeslib.ndpointer(dtype=np.float64,ndim=2,flags="C_CONTIGUOUS")
|
||||
npvector_double = np.ctypeslib.ndpointer(dtype=np.float64,ndim=1,flags="C_CONTIGUOUS")
|
||||
npvector_int = np.ctypeslib.ndpointer(dtype=np.int32,ndim=1,flags="C_CONTIGUOUS")
|
||||
|
||||
liblatte.latte_abiversion.restype = None
|
||||
liblatte.latte_abiversion.argtypes = None
|
||||
|
||||
liblatte.latte.restype = None
|
||||
liblatte.latte.argtypes = \
|
||||
[POINTER(c_int), POINTER(c_int), nparray, npvector_int, POINTER(c_int), npvector_double,
|
||||
POINTER(c_double), POINTER(c_double), POINTER(c_double),
|
||||
POINTER(c_double), POINTER(c_double),
|
||||
nparray, POINTER(c_int), POINTER(c_double), nparray,
|
||||
POINTER(c_double), npvector_double, POINTER(c_int), POINTER(c_bool)]
|
||||
|
||||
# --------------------------------------------
|
||||
# set ntypes, qm_types, qm_mass from qm_elements and electrons.dat file
|
||||
# required inputs for LATTE latte() function
|
||||
# --------------------------------------------
|
||||
|
||||
def set_types_masses():
|
||||
global qm_ntypes,qm_types,qm_mass
|
||||
|
||||
# read latte.in file for PARAMPATH to electrons.dat file
|
||||
|
||||
lines = open(infile,'r').readlines()
|
||||
for line in lines:
|
||||
if "PARAMPATH=" not in line: continue
|
||||
words = line.split()
|
||||
parampath = words[1][1:-1]
|
||||
|
||||
if parampath[-1] == '/': efile = parampath + "electrons.dat"
|
||||
else: efile = parampath + "/electrons.dat"
|
||||
|
||||
# extract symbol/mass pairings from electrons.dat file
|
||||
# symbol2mass = dict for mass of each chemical symbol
|
||||
|
||||
lines = open(efile,'r').readlines()
|
||||
|
||||
symbol2mass = {}
|
||||
for line in lines[2:]:
|
||||
line = line.strip()
|
||||
if not line: continue
|
||||
words = line.split()
|
||||
if words[0] in symbol2mass: continue
|
||||
else: symbol2mass[words[0]] = float(words[7])
|
||||
|
||||
# symbol_list = list of unique chemical symbols
|
||||
# qm_ntypes = # of unique symbols
|
||||
|
||||
symbol_list = []
|
||||
for i in range(qm_natoms):
|
||||
symbol = ELEMENTS[qm_elements[i]-1]
|
||||
if symbol not in symbol2mass:
|
||||
error("Atom element symbol not in LATTE electrons.dat file")
|
||||
if symbol in symbol_list: continue
|
||||
symbol_list.append(symbol)
|
||||
|
||||
qm_ntypes = len(symbol_list)
|
||||
|
||||
# qm_types = chemcial type of each atom (1 to qm_types)
|
||||
# qm_mass = mass of each atom type
|
||||
|
||||
qm_mass = np.empty(qm_ntypes)
|
||||
|
||||
for i in range(qm_natoms):
|
||||
symbol = ELEMENTS[qm_elements[i]-1]
|
||||
itype = symbol_list.index(symbol)
|
||||
qm_types[i] = itype + 1
|
||||
qm_mass[itype] = symbol2mass[symbol]
|
||||
|
||||
# --------------------------------------------
|
||||
# function called by MDI driver
|
||||
# only when it invokes pyscf_mdi.py as a plugin
|
||||
# --------------------------------------------
|
||||
|
||||
def MDI_Plugin_init_latte_mdi(plugin_state):
|
||||
|
||||
# other_options = all non-MDI args
|
||||
# -mdi arg is processed and stripped internally by MDI
|
||||
|
||||
other_options = []
|
||||
|
||||
mdi.MDI_Set_plugin_state(plugin_state)
|
||||
narg = mdi.MDI_Plugin_get_argc()
|
||||
|
||||
for iarg in range(narg):
|
||||
arg = mdi.MDI_Plugin_get_arg(iarg)
|
||||
other_options.append(arg)
|
||||
|
||||
# start running as an MDI engine
|
||||
|
||||
mdi_engine(other_options)
|
||||
|
||||
# --------------------------------------------
|
||||
# main program
|
||||
# invoked when MDI driver and pyscf_mdi.py
|
||||
# are run as independent executables
|
||||
# --------------------------------------------
|
||||
|
||||
if __name__== "__main__":
|
||||
|
||||
# mdi_option = single arg in quotes that follows -mdi
|
||||
# other_options = all non-MDI args
|
||||
|
||||
mdi_option = ""
|
||||
other_options = []
|
||||
|
||||
narg = len(sys.argv)
|
||||
args = sys.argv
|
||||
|
||||
iarg = 1
|
||||
while iarg < narg:
|
||||
arg = args[iarg]
|
||||
if arg == "-mdi" or arg == "--mdi":
|
||||
if narg > iarg+1: mdi_option = sys.argv[iarg+1]
|
||||
else: error("LATTE -mdi argument not provided",0)
|
||||
iarg += 1
|
||||
else: other_options.append(arg)
|
||||
iarg += 1
|
||||
|
||||
if not mdi_option: error("LATTE -mdi option not provided",0)
|
||||
|
||||
# call MDI_Init with just -mdi option
|
||||
|
||||
mdi.MDI_Init(mdi_option)
|
||||
|
||||
# start running as an MDI engine
|
||||
|
||||
mdi_engine(other_options)
|
||||
109
examples/QUANTUM/LATTE/log.22Mar23.ch4.mpi.1
Normal file
109
examples/QUANTUM/LATTE/log.22Mar23.ch4.mpi.1
Normal file
@ -0,0 +1,109 @@
|
||||
LAMMPS (8 Feb 2023)
|
||||
# simple CH4 model with LATTE
|
||||
|
||||
units metal
|
||||
atom_style full
|
||||
|
||||
read_data data.ch4
|
||||
Reading data file ...
|
||||
triclinic box = (0 0 0) to (19.523 12.758 11.692) with tilt (0 0 0)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
5 atoms
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
0 = max # of 1-2 neighbors
|
||||
0 = max # of 1-3 neighbors
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.002 seconds
|
||||
|
||||
# replicate system if requested
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
variable nrep equal v_x*v_y*v_z
|
||||
if "${nrep} > 1" then "replicate $x $y $z"
|
||||
|
||||
# initialize system
|
||||
|
||||
velocity all create 0.0 87287 loop geom
|
||||
|
||||
pair_style zero 1.0
|
||||
pair_coeff * *
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
timestep 0.00025
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
fix 2 all mdi/qm virial yes elements C H
|
||||
fix_modify 2 energy yes
|
||||
|
||||
thermo_style custom step temp pe etotal press
|
||||
|
||||
# dynamics
|
||||
|
||||
thermo 10
|
||||
run 100
|
||||
Generated 0 of 1 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
|
||||
ghost atom cutoff = 2
|
||||
binsize = 1, bins = 20 13 12
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair zero, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton/tri
|
||||
stencil: half/bin/3d/tri
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 6.027 | 6.027 | 6.027 Mbytes
|
||||
Step Temp PotEng TotEng Press
|
||||
0 0 -23.980353 -23.980353 348.02718
|
||||
10 19.123151 -23.990297 -23.98041 18.774333
|
||||
20 0.32743246 -23.980525 -23.980355 -336.7411
|
||||
30 18.229142 -23.989832 -23.980407 -72.30124
|
||||
40 1.3944306 -23.981078 -23.980357 335.25084
|
||||
50 17.34967 -23.989376 -23.980405 109.38135
|
||||
60 2.7948439 -23.981807 -23.980362 -313.70127
|
||||
70 14.957352 -23.98813 -23.980397 -157.44458
|
||||
80 5.1636049 -23.983039 -23.980369 297.94883
|
||||
90 13.368191 -23.987306 -23.980394 192.91153
|
||||
100 7.0848846 -23.984037 -23.980374 -269.0214
|
||||
Loop time of 0.0756328 on 1 procs for 100 steps with 5 atoms
|
||||
|
||||
Performance: 28.559 ns/day, 0.840 hours/ns, 1322.179 timesteps/s, 6.611 katom-step/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 | 2.862e-06 | 2.862e-06 | 2.862e-06 | 0.0 | 0.00
|
||||
Bond | 1.987e-06 | 1.987e-06 | 1.987e-06 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 8.987e-06 | 8.987e-06 | 8.987e-06 | 0.0 | 0.01
|
||||
Output | 2.5967e-05 | 2.5967e-05 | 2.5967e-05 | 0.0 | 0.03
|
||||
Modify | 0.075581 | 0.075581 | 0.075581 | 0.0 | 99.93
|
||||
Other | | 1.178e-05 | | | 0.02
|
||||
|
||||
Nlocal: 5 ave 5 max 5 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 7 ave 7 max 7 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 10 ave 10 max 10 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 10
|
||||
Ave neighs/atom = 2
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
111
examples/QUANTUM/LATTE/log.22Mar23.ch4.plugin.1
Normal file
111
examples/QUANTUM/LATTE/log.22Mar23.ch4.plugin.1
Normal file
@ -0,0 +1,111 @@
|
||||
LAMMPS (8 Feb 2023)
|
||||
# simple CH4 model with LATTE
|
||||
|
||||
units metal
|
||||
atom_style full
|
||||
|
||||
read_data data.ch4
|
||||
Reading data file ...
|
||||
triclinic box = (0 0 0) to (19.523 12.758 11.692) with tilt (0 0 0)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
5 atoms
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
0 = max # of 1-2 neighbors
|
||||
0 = max # of 1-3 neighbors
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.004 seconds
|
||||
|
||||
# replicate system if requested
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
variable nrep equal v_x*v_y*v_z
|
||||
if "${nrep} > 1" then "replicate $x $y $z"
|
||||
|
||||
# initialize system
|
||||
|
||||
velocity all create 0.0 87287 loop geom
|
||||
|
||||
pair_style zero 1.0
|
||||
pair_coeff * *
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
timestep 0.00025
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
fix 2 all mdi/qm virial yes elements C H
|
||||
fix_modify 2 energy yes
|
||||
|
||||
thermo_style custom step temp pe etotal press
|
||||
|
||||
# dynamics
|
||||
|
||||
thermo 10
|
||||
|
||||
mdi plugin latte_mdi mdi "-role ENGINE -name LATTE -method LINK" extra latte.in.generic command "run 100"
|
||||
run 100
|
||||
Generated 0 of 1 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
|
||||
ghost atom cutoff = 2
|
||||
binsize = 1, bins = 20 13 12
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair zero, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton/tri
|
||||
stencil: half/bin/3d/tri
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 6.027 | 6.027 | 6.027 Mbytes
|
||||
Step Temp PotEng TotEng Press
|
||||
0 0 -23.980353 -23.980353 348.02718
|
||||
10 19.123151 -23.990297 -23.98041 18.774333
|
||||
20 0.32743246 -23.980525 -23.980355 -336.7411
|
||||
30 18.229142 -23.989832 -23.980407 -72.30124
|
||||
40 1.3944306 -23.981078 -23.980357 335.25084
|
||||
50 17.34967 -23.989376 -23.980405 109.38135
|
||||
60 2.7948439 -23.981807 -23.980362 -313.70127
|
||||
70 14.957352 -23.98813 -23.980397 -157.44458
|
||||
80 5.1636049 -23.983039 -23.980369 297.94883
|
||||
90 13.368191 -23.987306 -23.980394 192.91153
|
||||
100 7.0848846 -23.984037 -23.980374 -269.0214
|
||||
Loop time of 0.0679725 on 1 procs for 100 steps with 5 atoms
|
||||
|
||||
Performance: 31.778 ns/day, 0.755 hours/ns, 1471.184 timesteps/s, 7.356 katom-step/s
|
||||
90.7% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 5.878e-06 | 5.878e-06 | 5.878e-06 | 0.0 | 0.01
|
||||
Bond | 3.369e-06 | 3.369e-06 | 3.369e-06 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 1.6278e-05 | 1.6278e-05 | 1.6278e-05 | 0.0 | 0.02
|
||||
Output | 5.6299e-05 | 5.6299e-05 | 5.6299e-05 | 0.0 | 0.08
|
||||
Modify | 0.067865 | 0.067865 | 0.067865 | 0.0 | 99.84
|
||||
Other | | 2.597e-05 | | | 0.04
|
||||
|
||||
Nlocal: 5 ave 5 max 5 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 7 ave 7 max 7 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 10 ave 10 max 10 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 10
|
||||
Ave neighs/atom = 2
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
103
examples/QUANTUM/LATTE/log.22Mar23.graphene.mpi.1
Normal file
103
examples/QUANTUM/LATTE/log.22Mar23.graphene.mpi.1
Normal file
@ -0,0 +1,103 @@
|
||||
LAMMPS (8 Feb 2023)
|
||||
# graphene model with LATTE
|
||||
|
||||
units metal
|
||||
atom_style full
|
||||
|
||||
read_data data.graphene
|
||||
Reading data file ...
|
||||
triclinic box = (0 0 0) to (10 8 20) with tilt (4.8985872e-16 1.2246468e-15 1.2246468e-15)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
32 atoms
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
0 = max # of 1-2 neighbors
|
||||
0 = max # of 1-3 neighbors
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.002 seconds
|
||||
|
||||
# replicate system if requested
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
variable nrep equal v_x*v_y*v_z
|
||||
if "${nrep} > 1" then "replicate $x $y $z"
|
||||
|
||||
# initialize system
|
||||
|
||||
velocity all create 100.0 87287 loop geom
|
||||
|
||||
pair_style zero 1.0
|
||||
pair_coeff * *
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
timestep 0.00025
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
fix 2 all mdi/qm virial yes elements C
|
||||
fix_modify 2 energy yes
|
||||
|
||||
thermo_style custom step temp pe etotal press
|
||||
|
||||
# dynamics
|
||||
|
||||
thermo 5
|
||||
run 20
|
||||
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
|
||||
ghost atom cutoff = 2
|
||||
binsize = 1, bins = 11 9 20
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair zero, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton/tri
|
||||
stencil: half/bin/3d/tri
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 6.032 | 6.032 | 6.032 Mbytes
|
||||
Step Temp PotEng TotEng Press
|
||||
0 100 -247.46002 -247.05931 63327.854
|
||||
5 826.57726 -250.37499 -247.06284 62186.684
|
||||
10 2683.9104 -257.82775 -247.07314 59699.92
|
||||
15 4697.8879 -265.91019 -247.08545 57703.843
|
||||
20 5758.1468 -270.16276 -247.0895 57792.304
|
||||
Loop time of 1.62794 on 1 procs for 20 steps with 32 atoms
|
||||
|
||||
Performance: 0.265 ns/day, 90.441 hours/ns, 12.285 timesteps/s, 393.134 atom-step/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 | 2.462e-06 | 2.462e-06 | 2.462e-06 | 0.0 | 0.00
|
||||
Bond | 6.56e-07 | 6.56e-07 | 6.56e-07 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 3.2959e-05 | 3.2959e-05 | 3.2959e-05 | 0.0 | 0.00
|
||||
Output | 2.315e-05 | 2.315e-05 | 2.315e-05 | 0.0 | 0.00
|
||||
Modify | 1.6279 | 1.6279 | 1.6279 | 0.0 |100.00
|
||||
Other | | 9.915e-06 | | | 0.00
|
||||
|
||||
Nlocal: 32 ave 32 max 32 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 100 ave 100 max 100 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 48 ave 48 max 48 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 48
|
||||
Ave neighs/atom = 1.5
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:01
|
||||
105
examples/QUANTUM/LATTE/log.22Mar23.graphene.plugin.1
Normal file
105
examples/QUANTUM/LATTE/log.22Mar23.graphene.plugin.1
Normal file
@ -0,0 +1,105 @@
|
||||
LAMMPS (8 Feb 2023)
|
||||
# graphene model with LATTE
|
||||
|
||||
units metal
|
||||
atom_style full
|
||||
|
||||
read_data data.graphene
|
||||
Reading data file ...
|
||||
triclinic box = (0 0 0) to (10 8 20) with tilt (4.8985872e-16 1.2246468e-15 1.2246468e-15)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
32 atoms
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
0 = max # of 1-2 neighbors
|
||||
0 = max # of 1-3 neighbors
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.003 seconds
|
||||
|
||||
# replicate system if requested
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
variable nrep equal v_x*v_y*v_z
|
||||
if "${nrep} > 1" then "replicate $x $y $z"
|
||||
|
||||
# initialize system
|
||||
|
||||
velocity all create 100.0 87287 loop geom
|
||||
|
||||
pair_style zero 1.0
|
||||
pair_coeff * *
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
timestep 0.00025
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
fix 2 all mdi/qm virial yes elements C
|
||||
fix_modify 2 energy yes
|
||||
|
||||
thermo_style custom step temp pe etotal press
|
||||
|
||||
# dynamics
|
||||
|
||||
thermo 5
|
||||
|
||||
mdi plugin latte_mdi mdi "-role ENGINE -name LATTE -method LINK" extra latte.in.generic command "run 20"
|
||||
run 20
|
||||
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
|
||||
ghost atom cutoff = 2
|
||||
binsize = 1, bins = 11 9 20
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair zero, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton/tri
|
||||
stencil: half/bin/3d/tri
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 6.032 | 6.032 | 6.032 Mbytes
|
||||
Step Temp PotEng TotEng Press
|
||||
0 100 -247.46002 -247.05931 63327.854
|
||||
5 826.57726 -250.37499 -247.06284 62186.684
|
||||
10 2683.9104 -257.82775 -247.07314 59699.92
|
||||
15 4697.8879 -265.91019 -247.08545 57703.843
|
||||
20 5758.1468 -270.16276 -247.0895 57792.304
|
||||
Loop time of 1.655 on 1 procs for 20 steps with 32 atoms
|
||||
|
||||
Performance: 0.261 ns/day, 91.944 hours/ns, 12.085 timesteps/s, 386.708 atom-step/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 | 7.488e-06 | 7.488e-06 | 7.488e-06 | 0.0 | 0.00
|
||||
Bond | 1.768e-06 | 1.768e-06 | 1.768e-06 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 1.9365e-05 | 1.9365e-05 | 1.9365e-05 | 0.0 | 0.00
|
||||
Output | 5.8712e-05 | 5.8712e-05 | 5.8712e-05 | 0.0 | 0.00
|
||||
Modify | 1.6549 | 1.6549 | 1.6549 | 0.0 | 99.99
|
||||
Other | | 3.093e-05 | | | 0.00
|
||||
|
||||
Nlocal: 32 ave 32 max 32 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 100 ave 100 max 100 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 48 ave 48 max 48 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 48
|
||||
Ave neighs/atom = 1.5
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:01
|
||||
@ -1,6 +1,4 @@
|
||||
LAMMPS (23 Jun 2022)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
LAMMPS (8 Feb 2023)
|
||||
# Series of single-point calcs of 2,3,4 UO2 molecules
|
||||
# with LATTE in MDI stand-alone mode
|
||||
|
||||
@ -12,98 +10,14 @@ label LOOP
|
||||
|
||||
units metal
|
||||
atom_style full
|
||||
atom_modify sort 0 0.0
|
||||
|
||||
read_data ${files}.lmp
|
||||
read_data 2uo2.lmp
|
||||
read_data data.${files}
|
||||
read_data data.2uo2
|
||||
Reading data file ...
|
||||
triclinic box = (0 0 0) to (10.8 5.4 5.4) with tilt (3.3065464e-16 3.3065464e-16 3.3065464e-16)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
6 atoms
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
0 = max # of 1-2 neighbors
|
||||
0 = max # of 1-3 neighbors
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.003 seconds
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
timestep 0.001
|
||||
|
||||
fix 1 all mdi/qm virial yes elements 92 8 connect no
|
||||
|
||||
thermo_style custom step temp pe etotal press
|
||||
thermo 1
|
||||
|
||||
run 0
|
||||
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 0
|
||||
ghost atom cutoff = 0
|
||||
binsize = 10.8, bins = 1 1 1
|
||||
0 neighbor lists, perpetual/occasional/extra = 0 0 0
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:210)
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.238 | 5.238 | 5.238 Mbytes
|
||||
Step Temp PotEng TotEng Press
|
||||
0 0 -50.539035 -50.539035 -120855.2
|
||||
Loop time of 1.397e-06 on 1 procs for 0 steps with 6 atoms
|
||||
|
||||
71.6% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Bond | 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 | | 1.397e-06 | | |100.00
|
||||
|
||||
Nlocal: 6 ave 6 max 6 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 2 ave 2 max 2 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
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
write_dump all custom dump.series.mpi.${files} id type x y z fx fy fz modify sort id
|
||||
write_dump all custom dump.series.mpi.2uo2 id type x y z fx fy fz modify sort id
|
||||
|
||||
clear
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
|
||||
next files
|
||||
|
||||
jump SELF LOOP
|
||||
|
||||
units metal
|
||||
atom_style full
|
||||
atom_modify sort 0 0.0
|
||||
|
||||
read_data ${files}.lmp
|
||||
read_data 3uo2.lmp
|
||||
Reading data file ...
|
||||
triclinic box = (0 0 0) to (16.2 5.4 5.4) with tilt (3.3065464e-16 3.3065464e-16 3.3065464e-16)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
9 atoms
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
@ -119,27 +33,21 @@ Finding 1-2 1-3 1-4 neighbors ...
|
||||
|
||||
timestep 0.001
|
||||
|
||||
fix 1 all mdi/qm virial yes elements 92 8 connect no
|
||||
fix 1 all mdi/qm virial yes elements U O connect no
|
||||
|
||||
thermo_style custom step temp pe etotal press
|
||||
thermo 1
|
||||
|
||||
run 0
|
||||
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 0
|
||||
ghost atom cutoff = 0
|
||||
binsize = 16.2, bins = 1 1 1
|
||||
0 neighbor lists, perpetual/occasional/extra = 0 0 0
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:210)
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.238 | 5.238 | 5.238 Mbytes
|
||||
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:2348)
|
||||
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) = 5.239 | 5.239 | 5.239 Mbytes
|
||||
Step Temp PotEng TotEng Press
|
||||
0 0 -78.155679 -78.155679 -99931.431
|
||||
Loop time of 1.117e-06 on 1 procs for 0 steps with 9 atoms
|
||||
0 0 -50.539026 -50.539026 -120855.18
|
||||
Loop time of 4.37e-07 on 1 procs for 0 steps with 6 atoms
|
||||
|
||||
89.5% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
228.8% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
@ -150,7 +58,80 @@ 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 | | 1.117e-06 | | |100.00
|
||||
Other | | 4.37e-07 | | |100.00
|
||||
|
||||
Nlocal: 6 ave 6 max 6 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 2 ave 2 max 2 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
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
#write_dump all custom dump.series.mpi.${files} # id type x y z fx fy fz modify sort id
|
||||
|
||||
clear
|
||||
|
||||
next files
|
||||
|
||||
jump SELF LOOP
|
||||
|
||||
units metal
|
||||
atom_style full
|
||||
|
||||
read_data data.${files}
|
||||
read_data data.3uo2
|
||||
Reading data file ...
|
||||
triclinic box = (0 0 0) to (16.2 5.4 5.4) with tilt (3.3065464e-16 3.3065464e-16 3.3065464e-16)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
9 atoms
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
0 = max # of 1-2 neighbors
|
||||
0 = max # of 1-3 neighbors
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.001 seconds
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
timestep 0.001
|
||||
|
||||
fix 1 all mdi/qm virial yes elements U O connect no
|
||||
|
||||
thermo_style custom step temp pe etotal press
|
||||
thermo 1
|
||||
|
||||
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:2348)
|
||||
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) = 5.239 | 5.239 | 5.239 Mbytes
|
||||
Step Temp PotEng TotEng Press
|
||||
0 0 -78.155585 -78.155585 -99929.253
|
||||
Loop time of 4.69e-07 on 1 procs for 0 steps with 9 atoms
|
||||
|
||||
213.2% 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
|
||||
Bond | 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 | | 4.69e-07 | | |100.00
|
||||
|
||||
Nlocal: 9 ave 9 max 9 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
@ -165,12 +146,9 @@ Ave special neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
write_dump all custom dump.series.mpi.${files} id type x y z fx fy fz modify sort id
|
||||
write_dump all custom dump.series.mpi.3uo2 id type x y z fx fy fz modify sort id
|
||||
#write_dump all custom dump.series.mpi.${files} # id type x y z fx fy fz modify sort id
|
||||
|
||||
clear
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
|
||||
next files
|
||||
|
||||
@ -178,10 +156,9 @@ jump SELF LOOP
|
||||
|
||||
units metal
|
||||
atom_style full
|
||||
atom_modify sort 0 0.0
|
||||
|
||||
read_data ${files}.lmp
|
||||
read_data 4uo2.lmp
|
||||
read_data data.${files}
|
||||
read_data data.4uo2
|
||||
Reading data file ...
|
||||
triclinic box = (0 0 0) to (10.8 10.8 5.4) with tilt (6.6130927e-16 3.3065464e-16 3.3065464e-16)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
@ -202,27 +179,21 @@ Finding 1-2 1-3 1-4 neighbors ...
|
||||
|
||||
timestep 0.001
|
||||
|
||||
fix 1 all mdi/qm virial yes elements 92 8 connect no
|
||||
fix 1 all mdi/qm virial yes elements U O connect no
|
||||
|
||||
thermo_style custom step temp pe etotal press
|
||||
thermo 1
|
||||
|
||||
run 0
|
||||
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 0
|
||||
ghost atom cutoff = 0
|
||||
binsize = 10.8, bins = 1 1 1
|
||||
0 neighbor lists, perpetual/occasional/extra = 0 0 0
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:210)
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.238 | 5.238 | 5.238 Mbytes
|
||||
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:2348)
|
||||
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) = 5.239 | 5.239 | 5.239 Mbytes
|
||||
Step Temp PotEng TotEng Press
|
||||
0 0 -102.35713 -102.35713 -31036.168
|
||||
Loop time of 1.466e-06 on 1 procs for 0 steps with 12 atoms
|
||||
0 0 -102.35715 -102.35715 -31036.694
|
||||
Loop time of 4.2e-07 on 1 procs for 0 steps with 12 atoms
|
||||
|
||||
136.4% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
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
|
||||
@ -233,7 +204,7 @@ 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 | | 1.466e-06 | | |100.00
|
||||
Other | | 4.2e-07 | | |100.00
|
||||
|
||||
Nlocal: 12 ave 12 max 12 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
@ -248,16 +219,13 @@ Ave special neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
write_dump all custom dump.series.mpi.${files} id type x y z fx fy fz modify sort id
|
||||
write_dump all custom dump.series.mpi.4uo2 id type x y z fx fy fz modify sort id
|
||||
#write_dump all custom dump.series.mpi.${files} # id type x y z fx fy fz modify sort id
|
||||
|
||||
clear
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
|
||||
next files
|
||||
|
||||
jump SELF LOOP
|
||||
|
||||
mdi exit
|
||||
Total wall time: 0:00:02
|
||||
Total wall time: 0:00:00
|
||||
@ -1,6 +1,4 @@
|
||||
LAMMPS (23 Jun 2022)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
LAMMPS (8 Feb 2023)
|
||||
# Series of single-point calcs of 2,3,4 UO2 molecules
|
||||
# with LATTE in MDI plugin mode
|
||||
|
||||
@ -10,10 +8,9 @@ label LOOP
|
||||
|
||||
units metal
|
||||
atom_style full
|
||||
atom_modify sort 0 0.0
|
||||
|
||||
read_data ${files}.lmp
|
||||
read_data 2uo2.lmp
|
||||
read_data data.${files}
|
||||
read_data data.2uo2
|
||||
Reading data file ...
|
||||
triclinic box = (0 0 0) to (10.8 5.4 5.4) with tilt (3.3065464e-16 3.3065464e-16 3.3065464e-16)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
@ -27,33 +24,28 @@ Finding 1-2 1-3 1-4 neighbors ...
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.004 seconds
|
||||
read_data CPU = 0.002 seconds
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
fix 1 all mdi/qm virial yes elements 92 8
|
||||
fix 1 all mdi/qm virial yes elements U O
|
||||
fix_modify 1 energy yes
|
||||
|
||||
thermo_style custom step temp pe etotal press
|
||||
thermo 1
|
||||
|
||||
mdi plugin latte_mdi mdi "-role ENGINE -name LATTE -method LINK" command "run 0"
|
||||
mdi plugin latte_mdi mdi "-role ENGINE -name LATTE -method LINK" extra latte.in.uo2 command "run 0"
|
||||
run 0
|
||||
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 0
|
||||
ghost atom cutoff = 0
|
||||
binsize = 10.8, bins = 1 1 1
|
||||
0 neighbor lists, perpetual/occasional/extra = 0 0 0
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:210)
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.238 | 5.238 | 5.238 Mbytes
|
||||
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:2348)
|
||||
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) = 5.239 | 5.239 | 5.239 Mbytes
|
||||
Step Temp PotEng TotEng Press
|
||||
0 0 -50.539035 -50.539035 -120855.2
|
||||
Loop time of 1.396e-06 on 1 procs for 0 steps with 6 atoms
|
||||
0 0 -50.539026 -50.539026 -120855.18
|
||||
Loop time of 3.55e-07 on 1 procs for 0 steps with 6 atoms
|
||||
|
||||
143.3% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
281.7% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
@ -64,7 +56,7 @@ 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 | | 1.396e-06 | | |100.00
|
||||
Other | | 3.55e-07 | | |100.00
|
||||
|
||||
Nlocal: 6 ave 6 max 6 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
@ -79,12 +71,9 @@ Ave special neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
write_dump all custom dump.series.plugin.${files} id type x y z fx fy fz modify sort id
|
||||
write_dump all custom dump.series.plugin.2uo2 id type x y z fx fy fz modify sort id
|
||||
#write_dump all custom dump.series.plugin.${files} # id type x y z fx fy fz modify sort id
|
||||
|
||||
clear
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
|
||||
next files
|
||||
|
||||
@ -92,10 +81,9 @@ jump SELF LOOP
|
||||
|
||||
units metal
|
||||
atom_style full
|
||||
atom_modify sort 0 0.0
|
||||
|
||||
read_data ${files}.lmp
|
||||
read_data 3uo2.lmp
|
||||
read_data data.${files}
|
||||
read_data data.3uo2
|
||||
Reading data file ...
|
||||
triclinic box = (0 0 0) to (16.2 5.4 5.4) with tilt (3.3065464e-16 3.3065464e-16 3.3065464e-16)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
@ -109,33 +97,28 @@ Finding 1-2 1-3 1-4 neighbors ...
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.002 seconds
|
||||
read_data CPU = 0.001 seconds
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
fix 1 all mdi/qm virial yes elements 92 8
|
||||
fix 1 all mdi/qm virial yes elements U O
|
||||
fix_modify 1 energy yes
|
||||
|
||||
thermo_style custom step temp pe etotal press
|
||||
thermo 1
|
||||
|
||||
mdi plugin latte_mdi mdi "-role ENGINE -name LATTE -method LINK" command "run 0"
|
||||
mdi plugin latte_mdi mdi "-role ENGINE -name LATTE -method LINK" extra latte.in.uo2 command "run 0"
|
||||
run 0
|
||||
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 0
|
||||
ghost atom cutoff = 0
|
||||
binsize = 16.2, bins = 1 1 1
|
||||
0 neighbor lists, perpetual/occasional/extra = 0 0 0
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:210)
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.238 | 5.238 | 5.238 Mbytes
|
||||
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:2348)
|
||||
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) = 5.239 | 5.239 | 5.239 Mbytes
|
||||
Step Temp PotEng TotEng Press
|
||||
0 0 -78.155679 -78.155679 -99931.431
|
||||
Loop time of 1.117e-06 on 1 procs for 0 steps with 9 atoms
|
||||
0 0 -78.155585 -78.155585 -99929.253
|
||||
Loop time of 5.92e-07 on 1 procs for 0 steps with 9 atoms
|
||||
|
||||
89.5% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
168.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
@ -146,7 +129,7 @@ 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 | | 1.117e-06 | | |100.00
|
||||
Other | | 5.92e-07 | | |100.00
|
||||
|
||||
Nlocal: 9 ave 9 max 9 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
@ -161,12 +144,9 @@ Ave special neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
write_dump all custom dump.series.plugin.${files} id type x y z fx fy fz modify sort id
|
||||
write_dump all custom dump.series.plugin.3uo2 id type x y z fx fy fz modify sort id
|
||||
#write_dump all custom dump.series.plugin.${files} # id type x y z fx fy fz modify sort id
|
||||
|
||||
clear
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
|
||||
next files
|
||||
|
||||
@ -174,10 +154,9 @@ jump SELF LOOP
|
||||
|
||||
units metal
|
||||
atom_style full
|
||||
atom_modify sort 0 0.0
|
||||
|
||||
read_data ${files}.lmp
|
||||
read_data 4uo2.lmp
|
||||
read_data data.${files}
|
||||
read_data data.4uo2
|
||||
Reading data file ...
|
||||
triclinic box = (0 0 0) to (10.8 10.8 5.4) with tilt (6.6130927e-16 3.3065464e-16 3.3065464e-16)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
@ -196,28 +175,23 @@ Finding 1-2 1-3 1-4 neighbors ...
|
||||
neighbor 0.3 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
fix 1 all mdi/qm virial yes elements 92 8
|
||||
fix 1 all mdi/qm virial yes elements U O
|
||||
fix_modify 1 energy yes
|
||||
|
||||
thermo_style custom step temp pe etotal press
|
||||
thermo 1
|
||||
|
||||
mdi plugin latte_mdi mdi "-role ENGINE -name LATTE -method LINK" command "run 0"
|
||||
mdi plugin latte_mdi mdi "-role ENGINE -name LATTE -method LINK" extra latte.in.uo2 command "run 0"
|
||||
run 0
|
||||
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 0
|
||||
ghost atom cutoff = 0
|
||||
binsize = 10.8, bins = 1 1 1
|
||||
0 neighbor lists, perpetual/occasional/extra = 0 0 0
|
||||
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:210)
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.238 | 5.238 | 5.238 Mbytes
|
||||
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:2348)
|
||||
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) = 5.239 | 5.239 | 5.239 Mbytes
|
||||
Step Temp PotEng TotEng Press
|
||||
0 0 -102.35713 -102.35713 -31036.168
|
||||
Loop time of 1.048e-06 on 1 procs for 0 steps with 12 atoms
|
||||
0 0 -102.35715 -102.35715 -31036.694
|
||||
Loop time of 4.14e-07 on 1 procs for 0 steps with 12 atoms
|
||||
|
||||
190.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
483.1% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
@ -228,7 +202,7 @@ 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 | | 1.048e-06 | | |100.00
|
||||
Other | | 4.14e-07 | | |100.00
|
||||
|
||||
Nlocal: 12 ave 12 max 12 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
@ -243,14 +217,11 @@ Ave special neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
write_dump all custom dump.series.plugin.${files} id type x y z fx fy fz modify sort id
|
||||
write_dump all custom dump.series.plugin.4uo2 id type x y z fx fy fz modify sort id
|
||||
#write_dump all custom dump.series.plugin.${files} # id type x y z fx fy fz modify sort id
|
||||
|
||||
clear
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
|
||||
next files
|
||||
|
||||
jump SELF LOOP
|
||||
Total wall time: 0:00:01
|
||||
Total wall time: 0:00:00
|
||||
109
examples/QUANTUM/LATTE/log.22Mar23.sucrose.mpi.1
Normal file
109
examples/QUANTUM/LATTE/log.22Mar23.sucrose.mpi.1
Normal file
@ -0,0 +1,109 @@
|
||||
LAMMPS (8 Feb 2023)
|
||||
# sucrose model with LATTE
|
||||
|
||||
units metal
|
||||
atom_style full
|
||||
|
||||
read_data data.sucrose
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (17.203 18.009 21.643)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
45 atoms
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
0 = max # of 1-2 neighbors
|
||||
0 = max # of 1-3 neighbors
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.002 seconds
|
||||
|
||||
# replicate system if requested
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
variable nrep equal v_x*v_y*v_z
|
||||
if "${nrep} > 1" then "replicate $x $y $z"
|
||||
|
||||
# initialize system
|
||||
|
||||
velocity all create 100.0 87287 loop geom
|
||||
|
||||
pair_style zero 1.0
|
||||
pair_coeff * *
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
timestep 0.00025
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
fix 2 all mdi/qm virial yes elements O C H
|
||||
fix_modify 2 energy yes
|
||||
|
||||
thermo_style custom step temp pe etotal press
|
||||
|
||||
# dynamics
|
||||
|
||||
thermo 10
|
||||
run 100
|
||||
Generated 0 of 3 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
|
||||
ghost atom cutoff = 2
|
||||
binsize = 1, bins = 18 19 22
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair zero, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 6.059 | 6.059 | 6.059 Mbytes
|
||||
Step Temp PotEng TotEng Press
|
||||
0 100 -251.26616 -250.69742 107.21668
|
||||
10 66.857941 -251.07691 -250.69666 -492.79612
|
||||
20 59.63791 -251.03635 -250.69717 -248.43262
|
||||
30 37.423913 -250.90951 -250.69666 188.29378
|
||||
40 58.409162 -251.0293 -250.6971 -237.97667
|
||||
50 59.243304 -251.0339 -250.69695 -638.8034
|
||||
60 52.981345 -250.99824 -250.69691 -316.59797
|
||||
70 43.705344 -250.9456 -250.69703 85.920691
|
||||
80 38.818553 -250.91757 -250.69679 -13.26722
|
||||
90 53.942805 -251.00391 -250.69711 -245.17309
|
||||
100 49.969604 -250.98104 -250.69684 -243.79969
|
||||
Loop time of 8.6113 on 1 procs for 100 steps with 45 atoms
|
||||
|
||||
Performance: 0.251 ns/day, 95.681 hours/ns, 11.613 timesteps/s, 522.569 atom-step/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 | 7.518e-06 | 7.518e-06 | 7.518e-06 | 0.0 | 0.00
|
||||
Bond | 3.387e-06 | 3.387e-06 | 3.387e-06 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 9.735e-06 | 9.735e-06 | 9.735e-06 | 0.0 | 0.00
|
||||
Output | 7.2205e-05 | 7.2205e-05 | 7.2205e-05 | 0.0 | 0.00
|
||||
Modify | 8.6112 | 8.6112 | 8.6112 | 0.0 |100.00
|
||||
Other | | 3.922e-05 | | | 0.00
|
||||
|
||||
Nlocal: 45 ave 45 max 45 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: 59 ave 59 max 59 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 59
|
||||
Ave neighs/atom = 1.3111111
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:08
|
||||
111
examples/QUANTUM/LATTE/log.22Mar23.sucrose.plugin.1
Normal file
111
examples/QUANTUM/LATTE/log.22Mar23.sucrose.plugin.1
Normal file
@ -0,0 +1,111 @@
|
||||
LAMMPS (8 Feb 2023)
|
||||
# sucrose model with LATTE
|
||||
|
||||
units metal
|
||||
atom_style full
|
||||
|
||||
read_data data.sucrose
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (17.203 18.009 21.643)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
45 atoms
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
0 = max # of 1-2 neighbors
|
||||
0 = max # of 1-3 neighbors
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.003 seconds
|
||||
|
||||
# replicate system if requested
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
variable nrep equal v_x*v_y*v_z
|
||||
if "${nrep} > 1" then "replicate $x $y $z"
|
||||
|
||||
# initialize system
|
||||
|
||||
velocity all create 100.0 87287 loop geom
|
||||
|
||||
pair_style zero 1.0
|
||||
pair_coeff * *
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
timestep 0.00025
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
fix 2 all mdi/qm virial yes elements O C H
|
||||
fix_modify 2 energy yes
|
||||
|
||||
thermo_style custom step temp pe etotal press
|
||||
|
||||
# dynamics
|
||||
|
||||
thermo 10
|
||||
|
||||
mdi plugin latte_mdi mdi "-role ENGINE -name LATTE -method LINK" extra latte.in.generic command "run 100"
|
||||
run 100
|
||||
Generated 0 of 3 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
|
||||
ghost atom cutoff = 2
|
||||
binsize = 1, bins = 18 19 22
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair zero, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 6.059 | 6.059 | 6.059 Mbytes
|
||||
Step Temp PotEng TotEng Press
|
||||
0 100 -251.26616 -250.69742 107.21668
|
||||
10 66.857941 -251.07691 -250.69666 -492.79612
|
||||
20 59.63791 -251.03635 -250.69717 -248.43262
|
||||
30 37.423913 -250.90951 -250.69666 188.29378
|
||||
40 58.409162 -251.0293 -250.6971 -237.97667
|
||||
50 59.243304 -251.0339 -250.69695 -638.8034
|
||||
60 52.981345 -250.99824 -250.69691 -316.59797
|
||||
70 43.705344 -250.9456 -250.69703 85.920691
|
||||
80 38.818553 -250.91757 -250.69679 -13.26722
|
||||
90 53.942805 -251.00391 -250.69711 -245.17309
|
||||
100 49.969604 -250.98104 -250.69684 -243.79969
|
||||
Loop time of 7.36277 on 1 procs for 100 steps with 45 atoms
|
||||
|
||||
Performance: 0.293 ns/day, 81.809 hours/ns, 13.582 timesteps/s, 611.183 atom-step/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 | 2.5563e-05 | 2.5563e-05 | 2.5563e-05 | 0.0 | 0.00
|
||||
Bond | 6.88e-06 | 6.88e-06 | 6.88e-06 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 2.6855e-05 | 2.6855e-05 | 2.6855e-05 | 0.0 | 0.00
|
||||
Output | 0.00012794 | 0.00012794 | 0.00012794 | 0.0 | 0.00
|
||||
Modify | 7.3625 | 7.3625 | 7.3625 | 0.0 |100.00
|
||||
Other | | 0.0001205 | | | 0.00
|
||||
|
||||
Nlocal: 45 ave 45 max 45 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: 59 ave 59 max 59 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 59
|
||||
Ave neighs/atom = 1.3111111
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:07
|
||||
77
examples/QUANTUM/LATTE/log.22Mar23.uo2.mpi.1
Normal file
77
examples/QUANTUM/LATTE/log.22Mar23.uo2.mpi.1
Normal file
@ -0,0 +1,77 @@
|
||||
LAMMPS (8 Feb 2023)
|
||||
# AIMD test of two UO2 molecules with LATTE in MDI stand-alone mode
|
||||
|
||||
units metal
|
||||
atom_style full
|
||||
|
||||
read_data data.2uo2
|
||||
Reading data file ...
|
||||
triclinic box = (0 0 0) to (10.8 5.4 5.4) with tilt (3.3065464e-16 3.3065464e-16 3.3065464e-16)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
6 atoms
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
0 = max # of 1-2 neighbors
|
||||
0 = max # of 1-3 neighbors
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.002 seconds
|
||||
|
||||
velocity all create 300.0 87287 loop geom
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
timestep 0.00025
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
fix 2 all mdi/qm virial yes elements U O
|
||||
|
||||
thermo_style custom step temp pe etotal press
|
||||
thermo 5
|
||||
|
||||
#dump 1 all custom 1 dump.aimd.mpi # id type x y z vx vy vz fx fy fz
|
||||
|
||||
run 20
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2348)
|
||||
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) = 5.239 | 5.239 | 5.239 Mbytes
|
||||
Step Temp PotEng TotEng Press
|
||||
0 300 -50.539026 -50.345136 -120197.58
|
||||
5 349.9977 -50.576715 -50.350511 -119686.74
|
||||
10 428.81071 -50.636477 -50.359336 -118824.24
|
||||
15 532.96198 -50.716083 -50.371629 -117598.48
|
||||
20 657.59195 -50.812448 -50.387446 -115993.96
|
||||
Loop time of 0.304615 on 1 procs for 20 steps with 6 atoms
|
||||
|
||||
Performance: 1.418 ns/day, 16.923 hours/ns, 65.657 timesteps/s, 393.940 atom-step/s
|
||||
99.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Bond | 6.39e-07 | 6.39e-07 | 6.39e-07 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 2.832e-06 | 2.832e-06 | 2.832e-06 | 0.0 | 0.00
|
||||
Output | 2.8879e-05 | 2.8879e-05 | 2.8879e-05 | 0.0 | 0.01
|
||||
Modify | 0.30458 | 0.30458 | 0.30458 | 0.0 | 99.99
|
||||
Other | | 5.828e-06 | | | 0.00
|
||||
|
||||
Nlocal: 6 ave 6 max 6 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 2 ave 2 max 2 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
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
78
examples/QUANTUM/LATTE/log.22Mar23.uo2.plugin.1
Normal file
78
examples/QUANTUM/LATTE/log.22Mar23.uo2.plugin.1
Normal file
@ -0,0 +1,78 @@
|
||||
LAMMPS (8 Feb 2023)
|
||||
# AIMD test of two UO2 molecules with LATTE in MDI stand-alone mode
|
||||
|
||||
units metal
|
||||
atom_style full
|
||||
|
||||
read_data data.2uo2
|
||||
Reading data file ...
|
||||
triclinic box = (0 0 0) to (10.8 5.4 5.4) with tilt (3.3065464e-16 3.3065464e-16 3.3065464e-16)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
6 atoms
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
0 = max # of 1-2 neighbors
|
||||
0 = max # of 1-3 neighbors
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.002 seconds
|
||||
|
||||
velocity all create 300.0 87287 loop geom
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
timestep 0.00025
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
fix 2 all mdi/qm virial yes elements U O
|
||||
|
||||
thermo_style custom step temp pe etotal press
|
||||
thermo 5
|
||||
|
||||
#dump 1 all custom 1 dump.aimd.mpi # id type x y z vx vy vz fx fy fz
|
||||
|
||||
mdi plugin latte_mdi mdi "-role ENGINE -name LATTE -method LINK" extra latte.in.uo2 command "run 20"
|
||||
run 20
|
||||
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2348)
|
||||
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) = 5.239 | 5.239 | 5.239 Mbytes
|
||||
Step Temp PotEng TotEng Press
|
||||
0 300 -50.539026 -50.345136 -120197.58
|
||||
5 349.9977 -50.576715 -50.350511 -119686.74
|
||||
10 428.81071 -50.636477 -50.359336 -118824.24
|
||||
15 532.96198 -50.716083 -50.371629 -117598.48
|
||||
20 657.59195 -50.812448 -50.387446 -115993.96
|
||||
Loop time of 0.307869 on 1 procs for 20 steps with 6 atoms
|
||||
|
||||
Performance: 1.403 ns/day, 17.104 hours/ns, 64.963 timesteps/s, 389.776 atom-step/s
|
||||
100.0% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Bond | 1.987e-06 | 1.987e-06 | 1.987e-06 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 1.4031e-05 | 1.4031e-05 | 1.4031e-05 | 0.0 | 0.00
|
||||
Output | 4.9408e-05 | 4.9408e-05 | 4.9408e-05 | 0.0 | 0.02
|
||||
Modify | 0.30778 | 0.30778 | 0.30778 | 0.0 | 99.97
|
||||
Other | | 2.062e-05 | | | 0.01
|
||||
|
||||
Nlocal: 6 ave 6 max 6 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 2 ave 2 max 2 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
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
118
examples/QUANTUM/LATTE/log.22Mar23.water.min.mpi.1
Normal file
118
examples/QUANTUM/LATTE/log.22Mar23.water.min.mpi.1
Normal file
@ -0,0 +1,118 @@
|
||||
LAMMPS (8 Feb 2023)
|
||||
# minimize water model with LATTE and FIRE
|
||||
|
||||
units metal
|
||||
atom_style full
|
||||
|
||||
read_data data.water
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (6.267 6.267 6.267)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
24 atoms
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
0 = max # of 1-2 neighbors
|
||||
0 = max # of 1-3 neighbors
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.002 seconds
|
||||
|
||||
# replicate system if requested
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
variable nrep equal v_x*v_y*v_z
|
||||
if "${nrep} > 1" then "replicate $x $y $z"
|
||||
|
||||
# initialize system
|
||||
|
||||
velocity all create 0.0 87287 loop geom
|
||||
|
||||
pair_style zero 1.0
|
||||
pair_coeff * *
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
fix 2 all mdi/qm virial yes elements O H
|
||||
fix_modify 2 energy yes
|
||||
|
||||
thermo_style custom step temp pe etotal press
|
||||
|
||||
# minimization
|
||||
|
||||
thermo 10
|
||||
|
||||
min_style fire
|
||||
minimize 1.0e-4 1.0e-4 500 500
|
||||
Generated 0 of 1 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
|
||||
ghost atom cutoff = 2
|
||||
binsize = 1, bins = 7 7 7
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair zero, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Parameters for fire:
|
||||
dmax delaystep dtgrow dtshrink alpha0 alphashrink tmax tmin integrator halfstepback abcfire
|
||||
0.1 20 1.1 0.5 0.25 0.99 10 0.02 eulerimplicit yes no
|
||||
Per MPI rank memory allocation (min/avg/max) = 6.007 | 6.007 | 6.007 Mbytes
|
||||
Step Temp PotEng TotEng Press
|
||||
0 0 -104.95596 -104.95596 48235.444
|
||||
10 899.15241 -108.14682 -105.47365 73033.936
|
||||
20 1939.7634 -109.75294 -103.98606 40647.182
|
||||
30 4.8318933 -110.23114 -110.21677 5660.7758
|
||||
40 50.735818 -110.29132 -110.14048 4890.8986
|
||||
50 153.92 -110.3956 -109.938 5046.391
|
||||
60 3.0178396 -110.52031 -110.51134 1964.2113
|
||||
70 26.161764 -110.55445 -110.47667 1839.5114
|
||||
78 69.534871 -110.60152 -110.39479 2086.0227
|
||||
Loop time of 1.36163 on 1 procs for 78 steps with 24 atoms
|
||||
|
||||
100.0% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = energy tolerance
|
||||
Energy initial, next-to-last, final =
|
||||
-104.955956572959 -110.594257523305 -110.601518955931
|
||||
Force two-norm initial, final = 19.119006 0.28249145
|
||||
Force max component initial, final = 11.775801 0.096323091
|
||||
Final line search alpha, max atom move = 0 0
|
||||
Iterations, force evaluations = 78 81
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 5.729e-06 | 5.729e-06 | 5.729e-06 | 0.0 | 0.00
|
||||
Bond | 2.468e-06 | 2.468e-06 | 2.468e-06 | 0.0 | 0.00
|
||||
Neigh | 1.8056e-05 | 1.8056e-05 | 1.8056e-05 | 0.0 | 0.00
|
||||
Comm | 3.9123e-05 | 3.9123e-05 | 3.9123e-05 | 0.0 | 0.00
|
||||
Output | 3.794e-05 | 3.794e-05 | 3.794e-05 | 0.0 | 0.00
|
||||
Modify | 1.3615 | 1.3615 | 1.3615 | 0.0 | 99.99
|
||||
Other | | 6.371e-05 | | | 0.00
|
||||
|
||||
Nlocal: 24 ave 24 max 24 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 75 ave 75 max 75 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 26 ave 26 max 26 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 26
|
||||
Ave neighs/atom = 1.0833333
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 2
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:01
|
||||
120
examples/QUANTUM/LATTE/log.22Mar23.water.min.plugin.1
Normal file
120
examples/QUANTUM/LATTE/log.22Mar23.water.min.plugin.1
Normal file
@ -0,0 +1,120 @@
|
||||
LAMMPS (8 Feb 2023)
|
||||
# minimize water model with LATTE and FIRE
|
||||
|
||||
units metal
|
||||
atom_style full
|
||||
|
||||
read_data data.water
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (6.267 6.267 6.267)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
24 atoms
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
0 = max # of 1-2 neighbors
|
||||
0 = max # of 1-3 neighbors
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.004 seconds
|
||||
|
||||
# replicate system if requested
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
variable nrep equal v_x*v_y*v_z
|
||||
if "${nrep} > 1" then "replicate $x $y $z"
|
||||
|
||||
# initialize system
|
||||
|
||||
velocity all create 0.0 87287 loop geom
|
||||
|
||||
pair_style zero 1.0
|
||||
pair_coeff * *
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
fix 2 all mdi/qm virial yes elements O H
|
||||
fix_modify 2 energy yes
|
||||
|
||||
thermo_style custom step temp pe etotal press
|
||||
|
||||
# minimization
|
||||
|
||||
thermo 10
|
||||
|
||||
min_style fire
|
||||
|
||||
mdi plugin latte_mdi mdi "-role ENGINE -name LATTE -method LINK" extra latte.in.water command "minimize 1.0e-4 1.0e-4 500 500"
|
||||
minimize 1.0e-4 1.0e-4 500 500
|
||||
Generated 0 of 1 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
|
||||
ghost atom cutoff = 2
|
||||
binsize = 1, bins = 7 7 7
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair zero, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Parameters for fire:
|
||||
dmax delaystep dtgrow dtshrink alpha0 alphashrink tmax tmin integrator halfstepback abcfire
|
||||
0.1 20 1.1 0.5 0.25 0.99 10 0.02 eulerimplicit yes no
|
||||
Per MPI rank memory allocation (min/avg/max) = 6.007 | 6.007 | 6.007 Mbytes
|
||||
Step Temp PotEng TotEng Press
|
||||
0 0 -104.95596 -104.95596 48235.444
|
||||
10 899.15241 -108.14682 -105.47365 73033.936
|
||||
20 1939.7634 -109.75294 -103.98606 40647.182
|
||||
30 4.8318933 -110.23114 -110.21677 5660.7758
|
||||
40 50.735818 -110.29132 -110.14048 4890.8986
|
||||
50 153.92 -110.3956 -109.938 5046.391
|
||||
60 3.0178396 -110.52031 -110.51134 1964.2113
|
||||
70 26.161764 -110.55445 -110.47667 1839.5114
|
||||
78 69.534871 -110.60152 -110.39479 2086.0227
|
||||
Loop time of 1.26399 on 1 procs for 78 steps with 24 atoms
|
||||
|
||||
99.5% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = energy tolerance
|
||||
Energy initial, next-to-last, final =
|
||||
-104.955956572959 -110.594257523305 -110.601518955931
|
||||
Force two-norm initial, final = 19.119006 0.28249145
|
||||
Force max component initial, final = 11.775801 0.096323091
|
||||
Final line search alpha, max atom move = 0 0
|
||||
Iterations, force evaluations = 78 81
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.4828e-05 | 1.4828e-05 | 1.4828e-05 | 0.0 | 0.00
|
||||
Bond | 3.973e-06 | 3.973e-06 | 3.973e-06 | 0.0 | 0.00
|
||||
Neigh | 1.813e-05 | 1.813e-05 | 1.813e-05 | 0.0 | 0.00
|
||||
Comm | 6.9762e-05 | 6.9762e-05 | 6.9762e-05 | 0.0 | 0.01
|
||||
Output | 7.4467e-05 | 7.4467e-05 | 7.4467e-05 | 0.0 | 0.01
|
||||
Modify | 1.2636 | 1.2636 | 1.2636 | 0.0 | 99.97
|
||||
Other | | 0.0001693 | | | 0.01
|
||||
|
||||
Nlocal: 24 ave 24 max 24 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 75 ave 75 max 75 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 26 ave 26 max 26 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 26
|
||||
Ave neighs/atom = 1.0833333
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 2
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:01
|
||||
109
examples/QUANTUM/LATTE/log.22Mar23.water.mpi.1
Normal file
109
examples/QUANTUM/LATTE/log.22Mar23.water.mpi.1
Normal file
@ -0,0 +1,109 @@
|
||||
LAMMPS (8 Feb 2023)
|
||||
# simple water model with LATTE
|
||||
|
||||
units metal
|
||||
atom_style full
|
||||
|
||||
read_data data.water
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (6.267 6.267 6.267)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
24 atoms
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
0 = max # of 1-2 neighbors
|
||||
0 = max # of 1-3 neighbors
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.002 seconds
|
||||
|
||||
# replicate system if requested
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
variable nrep equal v_x*v_y*v_z
|
||||
if "${nrep} > 1" then "replicate $x $y $z"
|
||||
|
||||
# initialize system
|
||||
|
||||
velocity all create 0.0 87287 loop geom
|
||||
|
||||
pair_style zero 1.0
|
||||
pair_coeff * *
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
timestep 0.00025
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
fix 2 all mdi/qm virial yes elements O H
|
||||
fix_modify 2 energy yes
|
||||
|
||||
thermo_style custom step temp pe etotal press
|
||||
|
||||
# dynamics
|
||||
|
||||
thermo 10
|
||||
run 100
|
||||
Generated 0 of 1 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
|
||||
ghost atom cutoff = 2
|
||||
binsize = 1, bins = 7 7 7
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair zero, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 6.007 | 6.007 | 6.007 Mbytes
|
||||
Step Temp PotEng TotEng Press
|
||||
0 0 -104.95596 -104.95596 48235.444
|
||||
10 336.53106 -105.96027 -104.95977 97996.851
|
||||
20 529.06409 -106.53023 -104.95733 131519.85
|
||||
30 753.62603 -107.19952 -104.959 49296.662
|
||||
40 716.65647 -107.08803 -104.95742 28307.122
|
||||
50 824.04393 -107.40823 -104.95836 102167.59
|
||||
60 933.56146 -107.73479 -104.95933 92508.518
|
||||
70 851.18489 -107.48767 -104.95711 13993.264
|
||||
80 999.80278 -107.93147 -104.95907 36700.735
|
||||
90 998.77487 -107.9257 -104.95636 107233.54
|
||||
100 1281.4438 -108.76963 -104.95992 49702.389
|
||||
Loop time of 1.3546 on 1 procs for 100 steps with 24 atoms
|
||||
|
||||
Performance: 1.595 ns/day, 15.051 hours/ns, 73.823 timesteps/s, 1.772 katom-step/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 | 1.0596e-05 | 1.0596e-05 | 1.0596e-05 | 0.0 | 0.00
|
||||
Bond | 2.698e-06 | 2.698e-06 | 2.698e-06 | 0.0 | 0.00
|
||||
Neigh | 1.9285e-05 | 1.9285e-05 | 1.9285e-05 | 0.0 | 0.00
|
||||
Comm | 4.4683e-05 | 4.4683e-05 | 4.4683e-05 | 0.0 | 0.00
|
||||
Output | 4.9581e-05 | 4.9581e-05 | 4.9581e-05 | 0.0 | 0.00
|
||||
Modify | 1.3544 | 1.3544 | 1.3544 | 0.0 | 99.99
|
||||
Other | | 2.583e-05 | | | 0.00
|
||||
|
||||
Nlocal: 24 ave 24 max 24 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 77 ave 77 max 77 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 31 ave 31 max 31 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 31
|
||||
Ave neighs/atom = 1.2916667
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 2
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:01
|
||||
111
examples/QUANTUM/LATTE/log.22Mar23.water.plugin.1
Normal file
111
examples/QUANTUM/LATTE/log.22Mar23.water.plugin.1
Normal file
@ -0,0 +1,111 @@
|
||||
LAMMPS (8 Feb 2023)
|
||||
# simple water model with LATTE
|
||||
|
||||
units metal
|
||||
atom_style full
|
||||
|
||||
read_data data.water
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (6.267 6.267 6.267)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
24 atoms
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
0 = max # of 1-2 neighbors
|
||||
0 = max # of 1-3 neighbors
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.002 seconds
|
||||
|
||||
# replicate system if requested
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
variable nrep equal v_x*v_y*v_z
|
||||
if "${nrep} > 1" then "replicate $x $y $z"
|
||||
|
||||
# initialize system
|
||||
|
||||
velocity all create 0.0 87287 loop geom
|
||||
|
||||
pair_style zero 1.0
|
||||
pair_coeff * *
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
timestep 0.00025
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
fix 2 all mdi/qm virial yes elements O H
|
||||
fix_modify 2 energy yes
|
||||
|
||||
thermo_style custom step temp pe etotal press
|
||||
|
||||
# dynamics
|
||||
|
||||
thermo 10
|
||||
|
||||
mdi plugin latte_mdi mdi "-role ENGINE -name LATTE -method LINK" extra latte.in.water command "run 100"
|
||||
run 100
|
||||
Generated 0 of 1 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
|
||||
ghost atom cutoff = 2
|
||||
binsize = 1, bins = 7 7 7
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair zero, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 6.007 | 6.007 | 6.007 Mbytes
|
||||
Step Temp PotEng TotEng Press
|
||||
0 0 -104.95596 -104.95596 48235.444
|
||||
10 336.53106 -105.96027 -104.95977 97996.851
|
||||
20 529.06409 -106.53023 -104.95733 131519.85
|
||||
30 753.62603 -107.19952 -104.959 49296.662
|
||||
40 716.65647 -107.08803 -104.95742 28307.122
|
||||
50 824.04393 -107.40823 -104.95836 102167.59
|
||||
60 933.56146 -107.73479 -104.95933 92508.518
|
||||
70 851.18489 -107.48767 -104.95711 13993.264
|
||||
80 999.80278 -107.93147 -104.95907 36700.735
|
||||
90 998.77487 -107.9257 -104.95636 107233.54
|
||||
100 1281.4438 -108.76963 -104.95992 49702.389
|
||||
Loop time of 1.26869 on 1 procs for 100 steps with 24 atoms
|
||||
|
||||
Performance: 1.703 ns/day, 14.097 hours/ns, 78.821 timesteps/s, 1.892 katom-step/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 | 1.3605e-05 | 1.3605e-05 | 1.3605e-05 | 0.0 | 0.00
|
||||
Bond | 4.492e-06 | 4.492e-06 | 4.492e-06 | 0.0 | 0.00
|
||||
Neigh | 1.7779e-05 | 1.7779e-05 | 1.7779e-05 | 0.0 | 0.00
|
||||
Comm | 7.0791e-05 | 7.0791e-05 | 7.0791e-05 | 0.0 | 0.01
|
||||
Output | 0.00010052 | 0.00010052 | 0.00010052 | 0.0 | 0.01
|
||||
Modify | 1.2684 | 1.2684 | 1.2684 | 0.0 | 99.98
|
||||
Other | | 6.755e-05 | | | 0.01
|
||||
|
||||
Nlocal: 24 ave 24 max 24 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 77 ave 77 max 77 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 31 ave 31 max 31 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 31
|
||||
Ave neighs/atom = 1.2916667
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 2
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:01
|
||||
181
examples/QUANTUM/NWChem/README
Normal file
181
examples/QUANTUM/NWChem/README
Normal file
@ -0,0 +1,181 @@
|
||||
# Test runs with coupling of LAMMPS and NWChem PWDFT
|
||||
|
||||
Step 0: What NWChem/PWDF currently supports
|
||||
Step 1: Build LAMMPS
|
||||
Step 2: Install or download/build MDI code coupling package
|
||||
Step 3: Download/build NWChem PWDFT
|
||||
Step 4: Perform test runs in any of 3 modes
|
||||
|
||||
---------------------------------
|
||||
---------------------------------
|
||||
|
||||
Step 0: What NWChem/PWDFT currently supports
|
||||
|
||||
PWDFT can be used with fix mdi/qm to perform QM calculations of an
|
||||
entire system and with fix mdi/qmmm for QMMM simulations. For QMMM it
|
||||
can use the potential mode of fix mdi/qmmm, but not the direct mode.
|
||||
PWDFT can calculate a QM energy and QM forces on each atom, but it
|
||||
cannot compute a QM stress tensor.
|
||||
|
||||
PWDFT supports MPI parallelism, but not threading parallelism.
|
||||
|
||||
---------------------------------
|
||||
---------------------------------
|
||||
|
||||
Step 1: Build LAMMPS
|
||||
|
||||
The MDI and molecule packags are needed. Copy the final LAMMPS
|
||||
executable into the examples/QUANTUM/NWChem directory.
|
||||
|
||||
Traditional make:
|
||||
|
||||
% cd ~/lammps/lib/mdi
|
||||
% python Install.py -m mpi
|
||||
% cd ~/lammps/src
|
||||
% make yes-mdi yes-molecule
|
||||
% make -j mpi
|
||||
% cp lmp_mpi ~/lammps/examples/QUANTUM/NWChem
|
||||
|
||||
CMake:
|
||||
|
||||
% cd ~/lammps
|
||||
% mkdir build; cd build
|
||||
% cmake -DPKG_MDI=yes -DPKG_MOLECULE=yes ../cmake
|
||||
% make -j
|
||||
% cp lmp ~/lammps/examples/QUANTUM/NWChem/lmp_mpi
|
||||
|
||||
---------------------------------
|
||||
---------------------------------
|
||||
|
||||
Step 2: Install or download/build MDI code coupling package
|
||||
|
||||
To simply use the MDI python module for the example scripts in this
|
||||
dir, you only need to install the MDI python module in your
|
||||
environment. Alternatively, you can download/build MDI itself, which
|
||||
will include its documentation and examples (as well as libraries and
|
||||
Python interface).
|
||||
|
||||
NOTE: It should be fine to leave off the version number for the python
|
||||
module installs, to just grab the latest MDI version. 1.4.16 is the
|
||||
version of MDI LAMMPS is currently using.
|
||||
|
||||
(option 1) Install MDI python module via pip:
|
||||
|
||||
% pip install 'pymdi>=1.4.14'
|
||||
|
||||
(option 2) Install MDI python module via conda:
|
||||
|
||||
% conda install -c conda-forge pymdi=1.4.16
|
||||
|
||||
(option 3) Download/build MDI code coupling package
|
||||
|
||||
(a) clone the MDI Git repo
|
||||
|
||||
% git clone https://github.com/MolSSI-MDI/MDI_Library.git mdi
|
||||
|
||||
(b) build MDI
|
||||
|
||||
% cd mdi
|
||||
% mkdir build; cd build
|
||||
% cmake ..
|
||||
% make -j
|
||||
|
||||
(c) Add a line like this to your ~/.bashrc or ~/.cshrc file so that
|
||||
Python can find MDI:
|
||||
|
||||
For bash:
|
||||
|
||||
% export PYTHONPATH="${HOME}/mdi/build/MDI_Library:${PYTHONPATH}"
|
||||
% hash -r
|
||||
|
||||
For (t)csh:
|
||||
|
||||
% setenv PYTHONPATH "${HOME}/mdi/build/MDI_Library:${PYTHONPATH}"
|
||||
% rehash
|
||||
|
||||
(d) Check import of 3 Python modules which the script that wraps
|
||||
NWChem will need:
|
||||
|
||||
% python
|
||||
>>> import numpy as np
|
||||
>>> from mpi4py import MPI
|
||||
>>> import mdi
|
||||
|
||||
---------------------------------
|
||||
---------------------------------
|
||||
|
||||
Step 3: Download/build NWChem PWDFT
|
||||
|
||||
NOTE: As of March 2023, this PWDFT-only repo is part of the new
|
||||
NWChemEx (exascale) version of NWChem. It will be included in the
|
||||
NWChemEx repo when it is publicly released. This doc page will be
|
||||
updated when that happens.
|
||||
|
||||
(a) clone the PWDFT Git repo
|
||||
|
||||
% mkdir nwchem; cd nwchem
|
||||
% git clone https://github.com/ebylaska/PWDFT.git PWDFT
|
||||
|
||||
(b) build PWDFT
|
||||
|
||||
% cd ~/nwchem/PWDFT
|
||||
% cd build_library; rm -r *
|
||||
% cmake -DMAKE_LIBRARY=true -DCMAKE_POSITION_INDEPENDENT_CODE=ON ../Nwpw
|
||||
% make -j # should produce libpwdft.so in build_library
|
||||
|
||||
(c) Add a line like this to your ~/.bashrc or ~/.cshrc
|
||||
file so that the libpwdft.so file can be found:
|
||||
|
||||
For bash:
|
||||
|
||||
% export LD_LIBRARY_PATH="${HOME}/nwchem/PWDFT/build_library:${LD_LIBRARY_PATH}"
|
||||
% hash -r
|
||||
|
||||
For (t)csh:
|
||||
|
||||
% setenv LD_LIBRARY_PATH "${HOME}/nwchem/PWDFT/build_library:${LD_LIBRARY_PATH}"
|
||||
% rehash
|
||||
|
||||
---------------------------------
|
||||
---------------------------------
|
||||
|
||||
Step 4: Perform test runs in any of 3 modes
|
||||
|
||||
These tests are in lammps/examples/QUANTUM/NWChem
|
||||
|
||||
in.series = series of several W conformations
|
||||
in.water.qmmm = QMMM of two-water system, 1 QM + 1 MM
|
||||
in.zeolite.qmmm = QMMM of zeolite, MM zeolite + QM methane molecule
|
||||
|
||||
** run LAMMPS-only versions of water and zeolite problems
|
||||
|
||||
lmp_mpi -log log.water.mm.1 < in.water.mm
|
||||
|
||||
lmp_mpi -log log.zeolite.mm.1 < in.zeolite.mm
|
||||
|
||||
** run LAMMPS and PWDFT with TCP/IP, 1 or more procs each
|
||||
|
||||
lmp_mpi -mdi "-name LMP -role DRIVER -method TCP -port 8021" -log log.series.tcp.1 -in in.series &
|
||||
python nwchem_mdi.py -mdi "-name NWChem -role ENGINE -method TCP -port 8021 -hostname localhost" template.w.nw w.nw log.series.pwdft.tcp.1
|
||||
|
||||
lmp_mpi -mdi "-name LMP -role DRIVER -method TCP -port 8021" -log log.water.qmmm.tcp.1 -in in.water.qmmm &
|
||||
mpirun -np 2 python nwchem_mdi.py -mdi "-name NWChem -role ENGINE -method TCP -port 8021 -hostname localhost" template.water.nw water.nw log.water.pwdft.qmmm.tcp.2
|
||||
|
||||
lmp_mpi -mdi "-name LMP -role DRIVER -method TCP -port 8021" -log log.zeolite.qmmm.tcp.1 -in in.zeolite.qmmm &
|
||||
mpirun -np 8 python nwchem_mdi.py -mdi "-name NWChem -role ENGINE -method TCP -port 8021 -hostname localhost" template.methane.nw methane.nw log.zeolite.pwdft.qmmm.tcp.8
|
||||
|
||||
** run LAMMPS and PWDFT with MPI, 1 or more procs each
|
||||
|
||||
mpirun -np 1 lmp_mpi -mdi "-name LMP -role DRIVER -method MPI" -log log.series.mpi.1 -in in.series : -np 1 python nwchem_mdi.py -mdi "-name NWChem -role ENGINE -method MPI" template.w.nw w.nw log.series.pwdft.mpi.1
|
||||
|
||||
mpirun -np 1 lmp_mpi -mdi "-name LMP -role DRIVER -method MPI" -log log.water.qmmm.mpi.1 -in in.water.qmmm : -np 2 python nwchem_mdi.py -mdi "-name NWChem -role ENGINE -method MPI" template.water.nw water.nw log.water.pwdft.qmmm.mpi.2
|
||||
|
||||
mpirun -np 1 lmp_mpi -mdi "-name LMP -role DRIVER -method MPI" -log log.zeolite.qmmm.mpi.1 -in in.zeolite.qmmm : -np 8 python nwchem_mdi.py -mdi "-name NWChem -role ENGINE -method MPI" template.methane.nw methane.nw log.zeolite.pwdft.qmmm.mpi.8
|
||||
|
||||
** run PWDFT as plugin MDI engine, 1 or more procs
|
||||
|
||||
lmp_mpi -mdi "-name LMP -role DRIVER -method LINK -plugin_path ${HOME}/lammps/examples/QUANTUM/NWChem" -log log.series.plugin.1 -in in.series.plugin
|
||||
|
||||
mpirun -np 2 lmp_mpi -mdi "-name LMP -role DRIVER -method LINK -plugin_path ${HOME}/lammps/examples/QUANTUM/NWChem" -log log.water.qmmm.plugin.2 -in in.water.qmmm.plugin
|
||||
|
||||
mpirun -np 8 lmp_mpi -mdi "-name LMP -role DRIVER -method LINK -plugin_path ${HOME}/lammps/examples/QUANTUM/NWChem" -log log.zeolite.qmmm.plugin.8 -in in.zeolite.qmmm.plugin
|
||||
12
examples/QUANTUM/NWChem/data.w.bcc
Normal file
12
examples/QUANTUM/NWChem/data.w.bcc
Normal file
@ -0,0 +1,12 @@
|
||||
LAMMPS data file from VASP file VASP/POSCAR_bcc
|
||||
|
||||
2 atoms
|
||||
1 atom types
|
||||
0.0 3.1654062429393064 xlo xhi
|
||||
0.0 3.1654062429393064 ylo yhi
|
||||
0.0 3.1654062429393064 zlo zhi
|
||||
|
||||
Atoms
|
||||
|
||||
1 1 0 0 0
|
||||
2 1 1.5827031214696532 1.5827031214696532 1.5827031214696532
|
||||
29
examples/QUANTUM/NWChem/data.w.bcc_222
Normal file
29
examples/QUANTUM/NWChem/data.w.bcc_222
Normal file
@ -0,0 +1,29 @@
|
||||
LAMMPS data file from VASP file VASP/POSCAR_bcc_222
|
||||
|
||||
18 atoms
|
||||
1 atom types
|
||||
0.0 8.9531208783704628 xlo xhi
|
||||
0.0 3.8768150619108339 ylo yhi
|
||||
0.0 45.534159244872015 zlo zhi
|
||||
2.2382802195926157 0 0 xy xz yz
|
||||
|
||||
Atoms
|
||||
|
||||
1 1 0 0 15
|
||||
2 1 6.7148406587778462 1.2922716873036106 15.913774073227765
|
||||
3 1 4.4765604391852314 2.5845433746072226 16.827548146455531
|
||||
4 1 11.191401097963077 3.876815061910833 17.741322219683298
|
||||
5 1 6.7148406587778471 1.2922716873036111 18.655096292911061
|
||||
6 1 4.4765604391852305 2.5845433746072222 19.568870366138828
|
||||
7 1 2.2382802195926152 3.876815061910833 20.482644439366592
|
||||
8 1 6.7148406587778453 1.2922716873036111 21.396418512594359
|
||||
9 1 4.4765604391852305 2.5845433746072222 22.310192585822122
|
||||
10 1 2.2382802195926148 3.8768150619108321 23.223966659049893
|
||||
11 1 6.7148406587778453 1.2922716873036102 24.137740732277656
|
||||
12 1 4.4765604391852305 2.5845433746072195 25.051514805505423
|
||||
13 1 2.2382802195926148 3.8768150619108321 25.965288878733183
|
||||
14 1 6.7148406587778444 1.2922716873036084 26.879062951960954
|
||||
15 1 4.4765604391852314 2.5845433746072204 27.792837025188717
|
||||
16 1 2.2382802195926139 3.8768150619108304 28.706611098416481
|
||||
17 1 6.7148406587778453 1.2922716873036102 29.620385171644248
|
||||
18 1 4.4765604391852269 2.5845433746072204 30.534159244872015
|
||||
14
examples/QUANTUM/NWChem/data.w.diamond
Normal file
14
examples/QUANTUM/NWChem/data.w.diamond
Normal file
@ -0,0 +1,14 @@
|
||||
LAMMPS data file from VASP file VASP/POSCAR_diamond
|
||||
|
||||
4 atoms
|
||||
1 atom types
|
||||
0.0 2.8200563642280549 xlo xhi
|
||||
0.0 2.8200563642280549 ylo yhi
|
||||
0.0 3.9881619569478763 zlo zhi
|
||||
|
||||
Atoms
|
||||
|
||||
1 1 0 0 0
|
||||
2 1 1.4100281821140275 0 0.99704048923696909
|
||||
3 1 1.4100281821140275 1.4100281821140275 1.9940809784739382
|
||||
4 1 0 1.4100281821140275 2.991121467710907
|
||||
28
examples/QUANTUM/NWChem/data.w.fcc_001
Normal file
28
examples/QUANTUM/NWChem/data.w.fcc_001
Normal file
@ -0,0 +1,28 @@
|
||||
LAMMPS data file from VASP file VASP/POSCAR_fcc_001
|
||||
|
||||
18 atoms
|
||||
1 atom types
|
||||
0.0 4.4765604391852305 xlo xhi
|
||||
0.0 4.4765604391852305 ylo yhi
|
||||
0.0 113.81190612996821 zlo zhi
|
||||
|
||||
Atoms
|
||||
|
||||
1 1 0 0 30
|
||||
2 1 2.2382802195926152 2.2382802195926152 33.165406242939305
|
||||
3 1 0 0 36.33081248587861
|
||||
4 1 2.2382802195926152 2.2382802195926152 39.496218728817922
|
||||
5 1 0 0 42.661624971757227
|
||||
6 1 2.2382802195926152 2.2382802195926152 45.827031214696532
|
||||
7 1 0 0 48.992437457635837
|
||||
8 1 2.2382802195926152 2.2382802195926152 52.157843700575143
|
||||
9 1 0 0 55.323249943514455
|
||||
10 1 2.2382802195926152 2.2382802195926152 58.488656186453753
|
||||
11 1 0 0 61.654062429393065
|
||||
12 1 2.2382802195926152 2.2382802195926152 64.819468672332363
|
||||
13 1 0 0 67.984874915271675
|
||||
14 1 2.2382802195926152 2.2382802195926152 71.150281158210987
|
||||
15 1 0 0 74.315687401150285
|
||||
16 1 2.2382802195926152 2.2382802195926152 77.481093644089597
|
||||
17 1 0 0 80.646499887028909
|
||||
18 1 2.2382802195926152 2.2382802195926152 83.811906129968207
|
||||
19
examples/QUANTUM/NWChem/data.w.sc_001
Normal file
19
examples/QUANTUM/NWChem/data.w.sc_001
Normal file
@ -0,0 +1,19 @@
|
||||
LAMMPS data file from VASP file VASP/POSCAR_sc_001
|
||||
|
||||
9 atoms
|
||||
1 atom types
|
||||
0.0 2.5123845999742804 xlo xhi
|
||||
0.0 2.5123845999742804 ylo yhi
|
||||
0.0 50.099076799794247 zlo zhi
|
||||
|
||||
Atoms
|
||||
|
||||
1 1 0 0 15.000000000000002
|
||||
2 1 0 0 17.512384599974283
|
||||
3 1 0 0 20.024769199948562
|
||||
4 1 0 0 22.537153799922841
|
||||
5 1 0 0 25.049538399897123
|
||||
6 1 0 0 27.561922999871406
|
||||
7 1 0 0 30.074307599845682
|
||||
8 1 0 0 32.586692199819964
|
||||
9 1 0 0 35.099076799794247
|
||||
45
examples/QUANTUM/NWChem/data.water.mm
Normal file
45
examples/QUANTUM/NWChem/data.water.mm
Normal file
@ -0,0 +1,45 @@
|
||||
LAMMPS data file for water dimer in large box
|
||||
|
||||
6 atoms
|
||||
4 bonds
|
||||
2 angles
|
||||
2 atom types
|
||||
1 bond types
|
||||
1 angle types
|
||||
-6.879301 6.879301 xlo xhi
|
||||
-6.879301 6.879301 ylo yhi
|
||||
-6.879301 6.879301 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
1 15.99491
|
||||
2 1.008
|
||||
|
||||
Bond Coeffs
|
||||
|
||||
1 554.25 1.0
|
||||
|
||||
Angle Coeffs
|
||||
|
||||
1 47.744 109.4
|
||||
|
||||
Atoms
|
||||
|
||||
1 1 1 -0.8476 0.161560 -0.052912 0.033173
|
||||
2 1 2 0.4238 0.803054 0.369132 -0.511660
|
||||
3 1 2 0.4238 -0.325571 -0.669574 -0.488560
|
||||
4 2 1 -0.8476 0.021259 0.506771 2.831278
|
||||
5 2 2 0.4238 -0.721039 1.083100 2.758378
|
||||
6 2 2 0.4238 0.158220 0.181883 1.945696
|
||||
|
||||
Bonds
|
||||
|
||||
1 1 1 2
|
||||
2 1 1 3
|
||||
3 1 4 5
|
||||
4 1 4 6
|
||||
|
||||
Angles
|
||||
|
||||
1 1 2 1 3
|
||||
2 1 5 4 6
|
||||
48
examples/QUANTUM/NWChem/data.water.qmmm
Normal file
48
examples/QUANTUM/NWChem/data.water.qmmm
Normal file
@ -0,0 +1,48 @@
|
||||
LAMMPS data file for water dimer in large box - for QMMM with different types
|
||||
|
||||
6 atoms
|
||||
4 atom types
|
||||
4 bonds
|
||||
1 bond types
|
||||
2 angles
|
||||
1 angle types
|
||||
|
||||
-6.879301 6.879301 xlo xhi
|
||||
-6.879301 6.879301 ylo yhi
|
||||
-6.879301 6.879301 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
1 15.99491
|
||||
2 1.008
|
||||
3 15.99491
|
||||
4 1.008
|
||||
|
||||
Bond Coeffs
|
||||
|
||||
1 554.25 1.0
|
||||
|
||||
Angle Coeffs
|
||||
|
||||
1 47.744 109.4
|
||||
|
||||
Atoms
|
||||
|
||||
1 1 1 -0.8476 0.161560 -0.052912 0.033173
|
||||
2 1 2 0.4238 0.803054 0.369132 -0.511660
|
||||
3 1 2 0.4238 -0.325571 -0.669574 -0.488560
|
||||
4 2 3 -0.8476 0.021259 0.506771 2.831278
|
||||
5 2 4 0.4238 -0.721039 1.083100 2.758378
|
||||
6 2 4 0.4238 0.158220 0.181883 1.945696
|
||||
|
||||
Bonds
|
||||
|
||||
1 1 1 2
|
||||
2 1 1 3
|
||||
3 1 4 5
|
||||
4 1 4 6
|
||||
|
||||
Angles
|
||||
|
||||
1 1 2 1 3
|
||||
2 1 5 4 6
|
||||
114
examples/QUANTUM/NWChem/data.zeolite
Normal file
114
examples/QUANTUM/NWChem/data.zeolite
Normal file
@ -0,0 +1,114 @@
|
||||
LAMMPS data file for SiO2 zeolite with one methane moleclue
|
||||
|
||||
77 atoms
|
||||
4 atom types
|
||||
4 bonds
|
||||
1 bond types
|
||||
6 angles
|
||||
1 angle types
|
||||
-5.9266 5.9926 xlo xhi
|
||||
-5.9266 5.9926 ylo yhi
|
||||
-5.9266 5.9926 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
1 28.0855
|
||||
2 15.99491
|
||||
3 12.0
|
||||
4 1.008
|
||||
|
||||
Atoms
|
||||
|
||||
1 0 1 1.910418 0.00000 4.38651 2.18123
|
||||
2 0 1 1.910418 0.00000 -4.38651 2.18123
|
||||
3 0 1 1.910418 0.00000 4.38651 -2.18123
|
||||
4 0 1 1.910418 0.00000 -4.38651 -2.18123
|
||||
5 0 1 1.910418 2.18123 0.00000 4.38651
|
||||
6 0 1 1.910418 2.18123 0.00000 -4.38651
|
||||
7 0 1 1.910418 -2.18123 0.00000 4.38651
|
||||
8 0 1 1.910418 -2.18123 0.00000 -4.38651
|
||||
9 0 1 1.910418 4.38651 2.18123 0.00000
|
||||
10 0 1 1.910418 -4.38651 2.18123 0.00000
|
||||
11 0 1 1.910418 4.38651 -2.18123 0.00000
|
||||
12 0 1 1.910418 -4.38651 -2.18123 0.00000
|
||||
13 0 1 1.910418 4.38651 0.00000 -2.18123
|
||||
14 0 1 1.910418 -4.38651 0.00000 -2.18123
|
||||
15 0 1 1.910418 4.38651 0.00000 2.18123
|
||||
16 0 1 1.910418 -4.38651 0.00000 2.18123
|
||||
17 0 1 1.910418 0.00000 2.18123 -4.38651
|
||||
18 0 1 1.910418 0.00000 2.18123 4.38651
|
||||
19 0 1 1.910418 0.00000 -2.18123 -4.38651
|
||||
20 0 1 1.910418 0.00000 -2.18123 4.38651
|
||||
21 0 1 1.910418 2.18123 4.38651 0.00000
|
||||
22 0 1 1.910418 2.18123 -4.38651 0.00000
|
||||
23 0 1 1.910418 -2.18123 4.38651 0.00000
|
||||
24 0 1 1.910418 -2.18123 -4.38651 0.00000
|
||||
25 0 2 -0.955209 0.00000 -5.92660 2.64860
|
||||
26 0 2 -0.955209 0.00000 -5.92660 -2.64860
|
||||
27 0 2 -0.955209 2.64860 0.00000 -5.92660
|
||||
28 0 2 -0.955209 -2.64860 0.00000 -5.92660
|
||||
29 0 2 -0.955209 -5.92660 2.64860 0.00000
|
||||
30 0 2 -0.955209 -5.92660 -2.64860 0.00000
|
||||
31 0 2 -0.955209 -5.92660 0.00000 -2.64860
|
||||
32 0 2 -0.955209 -5.92660 0.00000 2.64860
|
||||
33 0 2 -0.955209 0.00000 2.64860 -5.92660
|
||||
34 0 2 -0.955209 0.00000 -2.64860 -5.92660
|
||||
35 0 2 -0.955209 2.64860 -5.92660 0.00000
|
||||
36 0 2 -0.955209 -2.64860 -5.92660 0.00000
|
||||
37 0 2 -0.955209 0.00000 3.45272 3.45272
|
||||
38 0 2 -0.955209 0.00000 -3.45272 3.45272
|
||||
39 0 2 -0.955209 0.00000 3.45272 -3.45272
|
||||
40 0 2 -0.955209 0.00000 -3.45272 -3.45272
|
||||
41 0 2 -0.955209 3.45272 0.00000 3.45272
|
||||
42 0 2 -0.955209 3.45272 0.00000 -3.45272
|
||||
43 0 2 -0.955209 -3.45272 0.00000 3.45272
|
||||
44 0 2 -0.955209 -3.45272 0.00000 -3.45272
|
||||
45 0 2 -0.955209 3.45272 3.45272 0.00000
|
||||
46 0 2 -0.955209 -3.45272 3.45272 0.00000
|
||||
47 0 2 -0.955209 3.45272 -3.45272 0.00000
|
||||
48 0 2 -0.955209 -3.45272 -3.45272 0.00000
|
||||
49 0 2 -0.955209 1.28702 1.28702 4.12598
|
||||
50 0 2 -0.955209 -1.28702 -1.28702 4.12598
|
||||
51 0 2 -0.955209 -1.28702 1.28702 -4.12598
|
||||
52 0 2 -0.955209 1.28702 -1.28702 -4.12598
|
||||
53 0 2 -0.955209 4.12598 1.28702 1.28702
|
||||
54 0 2 -0.955209 4.12598 -1.28702 -1.28702
|
||||
55 0 2 -0.955209 -4.12598 -1.28702 1.28702
|
||||
56 0 2 -0.955209 -4.12598 1.28702 -1.28702
|
||||
57 0 2 -0.955209 1.28702 4.12598 1.28702
|
||||
58 0 2 -0.955209 -1.28702 4.12598 -1.28702
|
||||
59 0 2 -0.955209 1.28702 -4.12598 -1.28702
|
||||
60 0 2 -0.955209 -1.28702 -4.12598 1.28702
|
||||
61 0 2 -0.955209 1.28702 1.28702 -4.12598
|
||||
62 0 2 -0.955209 -1.28702 -1.28702 -4.12598
|
||||
63 0 2 -0.955209 1.28702 -1.28702 4.12598
|
||||
64 0 2 -0.955209 -1.28702 1.28702 4.12598
|
||||
65 0 2 -0.955209 1.28702 4.12598 -1.28702
|
||||
66 0 2 -0.955209 -1.28702 4.12598 1.28702
|
||||
67 0 2 -0.955209 -1.28702 -4.12598 -1.28702
|
||||
68 0 2 -0.955209 1.28702 -4.12598 1.28702
|
||||
69 0 2 -0.955209 4.12598 1.28702 -1.28702
|
||||
70 0 2 -0.955209 4.12598 -1.28702 1.28702
|
||||
71 0 2 -0.955209 -4.12598 1.28702 1.28702
|
||||
72 0 2 -0.955209 -4.12598 -1.28702 -1.28702
|
||||
73 1 3 -0.66 0.00000 0.00000 0.00000
|
||||
74 1 4 0.165 0.00000 -0.89000 -0.62930
|
||||
75 1 4 0.165 0.00000 0.89000 -0.62930
|
||||
76 1 4 0.165 -0.89000 0.00000 0.62930
|
||||
77 1 4 0.165 0.89000 0.00000 0.62930
|
||||
|
||||
Bonds
|
||||
|
||||
1 1 73 74
|
||||
2 1 73 75
|
||||
3 1 73 76
|
||||
4 1 73 77
|
||||
|
||||
Angles
|
||||
|
||||
1 1 74 73 75
|
||||
2 1 74 73 76
|
||||
3 1 74 73 77
|
||||
4 1 75 73 76
|
||||
5 1 75 73 77
|
||||
6 1 76 73 77
|
||||
40
examples/QUANTUM/NWChem/in.series
Normal file
40
examples/QUANTUM/NWChem/in.series
Normal file
@ -0,0 +1,40 @@
|
||||
# multiple W conformations with NWChem
|
||||
|
||||
# configs that don't currently work well
|
||||
# w.bcc_222 w.fcc_001
|
||||
|
||||
variable datafile index w.bcc w.diamond w.sc_001
|
||||
variable p equal extract_setting(world_size)
|
||||
|
||||
mdi connect
|
||||
|
||||
label loop
|
||||
|
||||
units metal
|
||||
atom_style atomic
|
||||
atom_modify map yes
|
||||
comm_modify cutoff 2.0
|
||||
|
||||
log log.series.${datafile}.$p
|
||||
|
||||
read_data data.${datafile}
|
||||
|
||||
mass 1 183.84
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all mdi/qm elements W connect no
|
||||
fix_modify 1 energy yes
|
||||
|
||||
#dump 1 all custom 1 dump.series.${datafile}.$p id x y z fx fy fz
|
||||
|
||||
run 0
|
||||
|
||||
clear
|
||||
|
||||
next datafile
|
||||
|
||||
jump SELF loop
|
||||
|
||||
mdi exit
|
||||
38
examples/QUANTUM/NWChem/in.series.plugin
Normal file
38
examples/QUANTUM/NWChem/in.series.plugin
Normal file
@ -0,0 +1,38 @@
|
||||
# multiple W conformations with NWChem
|
||||
|
||||
# configs that don't currently work well
|
||||
# w.bcc_222 w.fcc_001
|
||||
|
||||
variable datafile index w.bcc w.diamond w.sc_001
|
||||
variable p equal extract_setting(world_size)
|
||||
|
||||
label loop
|
||||
|
||||
units metal
|
||||
atom_style atomic
|
||||
atom_modify map yes
|
||||
comm_modify cutoff 2.0
|
||||
|
||||
log log.series.plugin.${datafile}.$p
|
||||
|
||||
read_data data.${datafile}
|
||||
|
||||
mass 1 183.84
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all mdi/qm elements W
|
||||
fix_modify 1 energy yes
|
||||
|
||||
#dump 1 all custom 1 dump.series.plugin.${datafile} id x y z fx fy fz
|
||||
|
||||
mdi plugin nwchem_mdi mdi "-role ENGINE -name LATTE -method LINK" &
|
||||
extra "template.w.nw w.nw log.series.pwdft.plugin.$p" &
|
||||
command "run 0"
|
||||
|
||||
clear
|
||||
|
||||
next datafile
|
||||
|
||||
jump SELF loop
|
||||
34
examples/QUANTUM/NWChem/in.water.mm
Normal file
34
examples/QUANTUM/NWChem/in.water.mm
Normal file
@ -0,0 +1,34 @@
|
||||
# MM for water dimer
|
||||
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
|
||||
read_data data.water.mm
|
||||
|
||||
group mm molecule 1
|
||||
group qm molecule 2
|
||||
|
||||
# pair style must define stand-alone short-range Coulombics
|
||||
|
||||
pair_style lj/cut/coul/cut 6.0
|
||||
pair_coeff 1 1 0.13506 3.166
|
||||
pair_coeff 2 2 0.0 1.0
|
||||
|
||||
velocity all create 300.0 458732
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
timestep 1.0
|
||||
|
||||
thermo_style custom step cpu temp ke evdwl ecoul epair emol elong &
|
||||
pe etotal press
|
||||
|
||||
thermo 1
|
||||
|
||||
run 10
|
||||
61
examples/QUANTUM/NWChem/in.water.qmmm
Normal file
61
examples/QUANTUM/NWChem/in.water.qmmm
Normal file
@ -0,0 +1,61 @@
|
||||
# QMMM with NWChem
|
||||
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
|
||||
read_data data.water.qmmm
|
||||
|
||||
# QM atoms are 1st water
|
||||
# MM atoms are 2nd water
|
||||
|
||||
group qm molecule 1
|
||||
group mm molecule 2
|
||||
|
||||
# remove bonds/angles between QM atoms
|
||||
|
||||
delete_bonds qm multi remove special
|
||||
|
||||
# pair style must define stand-alone short-range Coulombics
|
||||
# must specify mixing explicitly b/c hybrid/overlay
|
||||
# QM O,H = types 1,2
|
||||
# MM O,H = types 3,4
|
||||
# QM O,H atoms do not LJ interact with each other
|
||||
# only MM O atoms LJ interact with other b/c MM H is zero
|
||||
# MM/QM O do LJ interact with each other, same as pair of MM O atoms
|
||||
# MM O and QM H do LJ interact with each other with non-zero H epsilon = 0.044
|
||||
# geometric mixing for epsilon, arithmetic for sigma
|
||||
# this is to provide stability for QM H atoms
|
||||
|
||||
# mixing only for MM-O/QM-O and MM-O/QM-H
|
||||
|
||||
pair_style hybrid/overlay lj/cut 6.0 coul/cut 6.0
|
||||
pair_coeff 1 1 lj/cut 0.0 3.165558
|
||||
pair_coeff 2 2 lj/cut 0.0 0.7
|
||||
pair_coeff 3 3 lj/cut 0.155394 3.165558
|
||||
pair_coeff 4 4 lj/cut 0.0 0.7
|
||||
pair_coeff 1 3 lj/cut 0.155394 3.165558
|
||||
pair_coeff 2 3 lj/cut 0.08268818537130924 1.932779
|
||||
pair_coeff * * coul/cut
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
velocity all create 300.0 87287 loop geom
|
||||
|
||||
# QMMM dynamics
|
||||
|
||||
timestep 0.1
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
fix 2 qm mdi/qmmm potential elements O H O H
|
||||
fix_modify 2 energy yes
|
||||
|
||||
thermo_style custom step cpu temp ke evdwl ecoul epair emol elong &
|
||||
f_2 pe etotal press
|
||||
|
||||
thermo 1
|
||||
run 10
|
||||
65
examples/QUANTUM/NWChem/in.water.qmmm.plugin
Normal file
65
examples/QUANTUM/NWChem/in.water.qmmm.plugin
Normal file
@ -0,0 +1,65 @@
|
||||
# QMMM with NWChem
|
||||
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
|
||||
read_data data.water.qmmm
|
||||
|
||||
# QM atoms are 1st water
|
||||
# MM atoms are 2nd water
|
||||
|
||||
group qm molecule 1
|
||||
group mm molecule 2
|
||||
|
||||
# remove bonds/angles between QM atoms
|
||||
|
||||
delete_bonds qm multi remove special
|
||||
|
||||
# pair style must define stand-alone short-range Coulombics
|
||||
# must specify mixing explicitly b/c hybrid/overlay
|
||||
# QM O,H = types 1,2
|
||||
# MM O,H = types 3,4
|
||||
# QM O,H atoms do not LJ interact with each other
|
||||
# only MM O atoms LJ interact with other b/c MM H is zero
|
||||
# MM/QM O do LJ interact with each other, same as pair of MM O atoms
|
||||
# MM O and QM H do LJ interact with each other with non-zero H epsilon = 0.044
|
||||
# geometric mixing for epsilon, arithmetic for sigma
|
||||
# this is to provide stability for QM H atoms
|
||||
|
||||
# mixing only for MM-O/QM-O and MM-O/QM-H
|
||||
|
||||
pair_style hybrid/overlay lj/cut 6.0 coul/cut 6.0
|
||||
pair_coeff 1 1 lj/cut 0.0 3.165558
|
||||
pair_coeff 2 2 lj/cut 0.0 0.7
|
||||
pair_coeff 3 3 lj/cut 0.155394 3.165558
|
||||
pair_coeff 4 4 lj/cut 0.0 0.7
|
||||
pair_coeff 1 3 lj/cut 0.155394 3.165558
|
||||
pair_coeff 2 3 lj/cut 0.08268818537130924 1.932779
|
||||
pair_coeff * * coul/cut
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
velocity all create 300.0 87287 loop geom
|
||||
|
||||
# QMMM dynamics
|
||||
|
||||
timestep 0.1
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
fix 2 qm mdi/qmmm potential elements O H O H
|
||||
fix_modify 2 energy yes
|
||||
|
||||
thermo_style custom step cpu temp ke evdwl ecoul epair emol elong &
|
||||
f_2 pe etotal press
|
||||
thermo 1
|
||||
|
||||
variable p equal extract_setting(world_size)
|
||||
|
||||
mdi plugin nwchem_mdi mdi "-role ENGINE -name NWChem -method LINK" &
|
||||
extra "template.water.nw water.nw log.water.pwdft.qmmm.plugin.$p" &
|
||||
command "run 10"
|
||||
104
examples/QUANTUM/NWChem/in.zeolite.mm
Normal file
104
examples/QUANTUM/NWChem/in.zeolite.mm
Normal file
@ -0,0 +1,104 @@
|
||||
# MM for SiO2 zeolite with one methane molecule
|
||||
|
||||
# CHIK potential
|
||||
# EPL, Carre, Horbach, Ispas, Kob, 82, 17001 (2008)
|
||||
# B = 1/rho
|
||||
|
||||
#q Si = 1.910418
|
||||
#q O = -0.955209
|
||||
#A OO = 659.595398 eV
|
||||
#B OO = 2.590066 1/Ang
|
||||
#C OO = 26.836679 eV-Ang^6
|
||||
#A SiO = 27029.419922 eV
|
||||
#B SiO = 5.158606 1/Ang
|
||||
#C SiO = 148.099091 eV-Ang^6
|
||||
#A SiSi = 3150.462646 eV
|
||||
#B SiSi = 2.851451 1/Ang
|
||||
#C SiSi = 626.7519553 eV-Ang^6
|
||||
|
||||
# LJ params for methane and O from Table 1
|
||||
# Bhatia and Nicholson, J Phys Chem C, 2012, 116, 2344-2355.
|
||||
|
||||
#q C = -0.66
|
||||
#Q H = 0.165
|
||||
#sigma C = 0.34 nm
|
||||
#sigma H = 0.265 nm
|
||||
#sigma O = 0.28 nm
|
||||
#eps/kB C = 55.082 K = 0.004745993 eV
|
||||
#eps/kB H = 7.905 K = 0.000681113 eV
|
||||
#eps/kB O = 492.7 K = 0.0424522 eV
|
||||
|
||||
# LJ params for silicon
|
||||
#e-Journal of Surf Sci and Nanotech, Inui and Iwasaki, 15, 40-49 (2017)
|
||||
|
||||
#sigma Si = 3.826 Ang
|
||||
#eps Si = 17.4 meV = 0.0174 eV
|
||||
|
||||
# C-H bond and methane angle params
|
||||
|
||||
#OPLS C-H bond k = 29.40 ev/Ang^2
|
||||
#C-H bond r0 = 1.09 Angs
|
||||
#methane angles = 109.5 degrees
|
||||
#C-H angle k/kB = 2000 K/rad^2
|
||||
|
||||
# conversions
|
||||
|
||||
#1 eV = 11606 K
|
||||
#1 eV = 23.0609 kcal/mole
|
||||
#1 kcal/mole = 503.2761 K
|
||||
#1 kcal = 4.814 kJoule
|
||||
|
||||
# -------------------------
|
||||
|
||||
units metal
|
||||
atom_style full
|
||||
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
|
||||
read_data data.zeolite
|
||||
|
||||
group mm type 1 2
|
||||
group qm type 3 4
|
||||
|
||||
# pair style must define stand-alone short-range Coulombics
|
||||
# arithmetic mixing
|
||||
|
||||
pair_style hybrid/overlay buck 6.5 lj/cut 6.5 coul/cut 6.5
|
||||
|
||||
pair_coeff 1 1 buck 3150.462646 0.35032282 626.7519553
|
||||
pair_coeff 2 2 buck 659.595398 0.38609055 26.836679
|
||||
pair_coeff 1 2 buck 27029.419922 0.19385082 148.099091
|
||||
pair_coeff 1 2 buck 27029.419922 0.19385082 148.099091
|
||||
pair_coeff 1 3 lj/cut 0.009087 3.613
|
||||
pair_coeff 1 4 lj/cut 0.00344258 3.238
|
||||
pair_coeff 2 3 lj/cut 0.01419429 3.1
|
||||
pair_coeff 2 4 lj/cut 0.00537724 2.725
|
||||
pair_coeff 3 3 lj/cut 0.004746 3.4
|
||||
pair_coeff 4 4 lj/cut 0.00068111 2.65
|
||||
pair_coeff * * coul/cut
|
||||
|
||||
bond_style harmonic
|
||||
bond_coeff 1 29.40 1.09
|
||||
|
||||
angle_style harmonic
|
||||
angle_coeff 1 0.172325 109.5
|
||||
|
||||
#velocity all create 300.0 458732
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
# dynamic or frozen zeolite
|
||||
|
||||
fix 1 all nve
|
||||
#fix 1 qm nve
|
||||
|
||||
timestep 0.0001
|
||||
|
||||
thermo_style custom step cpu temp ke evdwl ecoul epair emol elong &
|
||||
pe etotal press
|
||||
|
||||
thermo 1
|
||||
|
||||
run 3
|
||||
70
examples/QUANTUM/NWChem/in.zeolite.qmmm
Normal file
70
examples/QUANTUM/NWChem/in.zeolite.qmmm
Normal file
@ -0,0 +1,70 @@
|
||||
# QMMM for SiO2 zeolite with one methane molecule
|
||||
|
||||
units metal
|
||||
atom_style full
|
||||
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
|
||||
read_data data.zeolite
|
||||
|
||||
# MM atoms are Si,O
|
||||
# QM atoms are C,H
|
||||
|
||||
group mm type 1 2
|
||||
group qm type 3 4
|
||||
|
||||
# pair style must define stand-alone short-range Coulombics
|
||||
# must specify mixing explicitly b/c hybrid/overlay
|
||||
# MM Si,O = types 1,2
|
||||
# QM C,H = types 3,4
|
||||
# MM Si,O atoms do not LJ interact with each other (just via Buckingham)
|
||||
# QM C,H atoms do not LJ interact with each other
|
||||
# MM Si,O and QM C,H do LJ interact with each other
|
||||
|
||||
pair_style hybrid/overlay buck 6.5 lj/cut 6.5 coul/cut 6.5
|
||||
|
||||
pair_coeff 1 1 buck 3150.462646 0.35032282 626.7519553
|
||||
pair_coeff 2 2 buck 659.595398 0.38609055 26.836679
|
||||
pair_coeff 1 2 buck 27029.419922 0.19385082 148.099091
|
||||
|
||||
pair_coeff 1 3 lj/cut 0.09087 3.613
|
||||
pair_coeff 1 4 lj/cut 0.0344258 3.238
|
||||
pair_coeff 2 3 lj/cut 0.1419429 3.1
|
||||
pair_coeff 2 4 lj/cut 0.035857762359063315 1.932779
|
||||
|
||||
pair_coeff 3 3 lj/cut 0.0 3.4
|
||||
pair_coeff 4 4 lj/cut 0.0 2.65
|
||||
pair_coeff * * coul/cut
|
||||
|
||||
bond_style harmonic
|
||||
bond_coeff 1 29.40 1.09
|
||||
|
||||
angle_style harmonic
|
||||
angle_coeff 1 0.172325 109.5
|
||||
|
||||
# remove bonds/angles in QM methane molecule
|
||||
|
||||
delete_bonds qm multi remove special
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
velocity all create 300.0 458732
|
||||
|
||||
# QMMM dynamics with small timestep
|
||||
# dynamic or frozen zeolite
|
||||
|
||||
#fix 1 all nve
|
||||
fix 1 qm nve
|
||||
|
||||
fix 2 qm mdi/qmmm potential elements Si O C H
|
||||
fix_modify 2 energy yes
|
||||
|
||||
timestep 0.0001
|
||||
|
||||
thermo_style custom step cpu temp ke evdwl ecoul epair emol elong &
|
||||
f_2 pe etotal press
|
||||
thermo 1
|
||||
|
||||
run 2
|
||||
Some files were not shown because too many files have changed in this diff Show More
Reference in New Issue
Block a user