147 lines
4.5 KiB
ReStructuredText
147 lines
4.5 KiB
ReStructuredText
.. index:: pair_style pod
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.. index:: pair_style pod/kk
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pair_style pod command
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========================
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Accelerator Variants: *pod/kk*
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Syntax
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""""""
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.. code-block:: LAMMPS
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pair_style pod
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Examples
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""""""""
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.. code-block:: LAMMPS
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pair_style pod
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pair_coeff * * Ta_param.pod Ta_coefficients.pod Ta
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Description
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"""""""""""
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.. versionadded:: 22Dec2022
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Pair style *pod* defines the proper orthogonal descriptor (POD)
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potential :ref:`(Nguyen and Rohskopf) <Nguyen20222b>`,
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:ref:`(Nguyen2023) <Nguyen20232b>`, :ref:`(Nguyen2024) <Nguyen20242b>`,
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and :ref:`(Nguyen and Sema) <Nguyen20243b>`. The :doc:`fitpod
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<fitpod_command>` is used to fit the POD potential.
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Only a single pair_coeff command is used with the *pod* style which
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specifies a POD parameter file followed by a coefficient file, a
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projection matrix file, and a centroid file.
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The POD parameter file (``Ta_param.pod``) can contain blank and comment
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lines (start with #) anywhere. Each non-blank non-comment line must
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contain one keyword/value pair. See :doc:`fitpod <fitpod_command>` for
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the description of all the keywords that can be assigned in the
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parameter file.
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The coefficient file (``Ta_coefficients.pod``) contains coefficients for
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the POD potential. The top of the coefficient file can contain any
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number of blank and comment lines (start with #), but follows a strict
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format after that. The first non-blank non-comment line must contain:
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* model_coefficients: *ncoeff* *nproj* *ncentroid*
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This is followed by *ncoeff* coefficients, *nproj* projection matrix entries,
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and *ncentroid* centroid coordinates, one per line. The coefficient
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file is generated after training the POD potential using :doc:`fitpod
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<fitpod_command>`.
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As an example, if a LAMMPS indium phosphide simulation has 4 atoms
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types, with the first two being indium and the third and fourth being
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phophorous, the pair_coeff command would look like this:
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.. code-block:: LAMMPS
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pair_coeff * * pod InP_param.pod InP_coefficients.pod In In P P
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The first 2 arguments must be \* \* so as to span all LAMMPS atom types.
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The two filenames are for the parameter and coefficient files, respectively.
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The two trailing 'In' arguments map LAMMPS atom types 1 and 2 to the
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POD 'In' element. The two trailing 'P' arguments map LAMMPS atom types
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3 and 4 to the POD 'P' element.
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If a POD mapping value is specified as NULL, the mapping is not
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performed. This can be used when a *pod* potential is used as part of
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the *hybrid* pair style. The NULL values are placeholders for atom
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types that will be used with other potentials.
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Examples about training and using POD potentials are found in the
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directory lammps/examples/PACKAGES/pod and the Github repo https://github.com/cesmix-mit/pod-examples.
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----------
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Mixing, shift, table, tail correction, restart, rRESPA info
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"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
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For atom type pairs I,J and I != J, where types I and J correspond to
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two different element types, mixing is performed by LAMMPS with
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user-specifiable parameters as described above. You never need to
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specify a pair_coeff command with I != J arguments for this style.
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This pair style does not support the :doc:`pair_modify <pair_modify>`
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shift, table, and tail options.
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This pair style does not write its information to :doc:`binary restart
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files <restart>`, since it is stored in potential files. Thus, you need
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to re-specify the pair_style and pair_coeff commands in an input script
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that reads a restart file.
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This pair style can only be used via the *pair* keyword of the
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:doc:`run_style respa <run_style>` command. It does not support the
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*inner*, *middle*, *outer* keywords.
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----------
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.. include:: accel_styles.rst
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----------
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Restrictions
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""""""""""""
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This style is part of the ML-POD package. It is only enabled if LAMMPS
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was built with that package. See the :doc:`Build package
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<Build_package>` page for more info.
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Related commands
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""""""""""""""""
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:doc:`fitpod <fitpod_command>`,
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:doc:`compute pod/atom <compute_pod_atom>`,
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:doc:`compute podd/atom <compute_pod_atom>`,
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:doc:`compute pod/local <compute_pod_atom>`,
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:doc:`compute pod/global <compute_pod_atom>`
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Default
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"""""""
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none
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----------
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.. _Nguyen20222b:
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**(Nguyen and Rohskopf)** Nguyen and Rohskopf, Journal of Computational Physics, 480, 112030, (2023).
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.. _Nguyen20232b:
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**(Nguyen2023)** Nguyen, Physical Review B, 107(14), 144103, (2023).
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.. _Nguyen20242b:
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**(Nguyen2024)** Nguyen, Journal of Computational Physics, 113102, (2024).
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.. _Nguyen20243b:
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**(Nguyen and Sema)** Nguyen and Sema, https://arxiv.org/abs/2405.00306, (2024).
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