3087 lines
87 KiB
ReStructuredText
3087 lines
87 KiB
ReStructuredText
Package details
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===============
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Here is a brief description of all packages in LAMMPS. It lists authors
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(if applicable) and summarizes the package contents. It has specific
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instructions on how to install the package, including, if necessary,
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info on how to download or build any extra library it requires. It also
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gives links to documentation, example scripts, and pictures/movies (if
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available) that illustrate use of the package.
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The majority of packages can be included in a LAMMPS build with a single
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setting (``-D PKG_<NAME>=on`` for CMake) or command (``make yes-<name>``
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for make). See the :doc:`Build package <Build_package>` page for more
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info. A few packages may require additional steps; this is indicated in
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the descriptions below. The :doc:`Build extras <Build_extras>` page
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gives those details.
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.. note::
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To see the complete list of commands a package adds to LAMMPS,
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you can examine the files in its src directory, e.g. ``ls
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src/GRANULAR``. Files with names that start with fix, compute, atom,
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pair, bond, angle, etc correspond to commands with the same style name
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as contained in the file name.
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.. table_from_list::
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:columns: 6
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* :ref:`ADIOS <PKG-ADIOS>`
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* :ref:`AMOEBA <PKG-AMOEBA>`
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* :ref:`APIP <PKG-APIP>`
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* :ref:`ASPHERE <PKG-ASPHERE>`
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* :ref:`ATC <PKG-ATC>`
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* :ref:`AWPMD <PKG-AWPMD>`
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* :ref:`BOCS <PKG-BOCS>`
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* :ref:`BODY <PKG-BODY>`
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* :ref:`BPM <PKG-BPM>`
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* :ref:`BROWNIAN <PKG-BROWNIAN>`
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* :ref:`CG-DNA <PKG-CG-DNA>`
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* :ref:`CG-SPICA <PKG-CG-SPICA>`
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* :ref:`CLASS2 <PKG-CLASS2>`
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* :ref:`COLLOID <PKG-COLLOID>`
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* :ref:`COLVARS <PKG-COLVARS>`
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* :ref:`COMPRESS <PKG-COMPRESS>`
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* :ref:`CORESHELL <PKG-CORESHELL>`
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* :ref:`DIELECTRIC <PKG-DIELECTRIC>`
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* :ref:`DIFFRACTION <PKG-DIFFRACTION>`
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* :ref:`DIPOLE <PKG-DIPOLE>`
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* :ref:`DPD-BASIC <PKG-DPD-BASIC>`
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* :ref:`DPD-MESO <PKG-DPD-MESO>`
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* :ref:`DPD-REACT <PKG-DPD-REACT>`
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* :ref:`DPD-SMOOTH <PKG-DPD-SMOOTH>`
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* :ref:`DRUDE <PKG-DRUDE>`
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* :ref:`EFF <PKG-EFF>`
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* :ref:`ELECTRODE <PKG-ELECTRODE>`
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* :ref:`EXTRA-COMMAND <PKG-EXTRA-COMMAND>`
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* :ref:`EXTRA-COMPUTE <PKG-EXTRA-COMPUTE>`
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* :ref:`EXTRA-DUMP <PKG-EXTRA-DUMP>`
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* :ref:`EXTRA-FIX <PKG-EXTRA-FIX>`
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* :ref:`EXTRA-MOLECULE <PKG-EXTRA-MOLECULE>`
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* :ref:`EXTRA-PAIR <PKG-EXTRA-PAIR>`
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* :ref:`FEP <PKG-FEP>`
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* :ref:`GPU <PKG-GPU>`
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* :ref:`GRANULAR <PKG-GRANULAR>`
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* :ref:`H5MD <PKG-H5MD>`
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* :ref:`INTEL <PKG-INTEL>`
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* :ref:`INTERLAYER <PKG-INTERLAYER>`
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* :ref:`KIM <PKG-KIM>`
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* :ref:`KOKKOS <PKG-KOKKOS>`
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* :ref:`KSPACE <PKG-KSPACE>`
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* :ref:`LATBOLTZ <PKG-LATBOLTZ>`
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* :ref:`LEPTON <PKG-LEPTON>`
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* :ref:`MACHDYN <PKG-MACHDYN>`
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* :ref:`MANIFOLD <PKG-MANIFOLD>`
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* :ref:`MANYBODY <PKG-MANYBODY>`
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* :ref:`MC <PKG-MC>`
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* :ref:`MDI <PKG-MDI>`
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* :ref:`MEAM <PKG-MEAM>`
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* :ref:`MESONT <PKG-MESONT>`
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* :ref:`MGPT <PKG-MGPT>`
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* :ref:`MISC <PKG-MISC>`
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* :ref:`ML-HDNNP <PKG-ML-HDNNP>`
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* :ref:`ML-IAP <PKG-ML-IAP>`
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* :ref:`ML-PACE <PKG-ML-PACE>`
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* :ref:`ML-POD <PKG-ML-POD>`
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* :ref:`ML-QUIP <PKG-ML-QUIP>`
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* :ref:`ML-RANN <PKG-ML-RANN>`
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* :ref:`ML-SNAP <PKG-ML-SNAP>`
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* :ref:`ML-UF3 <PKG-ML-UF3>`
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* :ref:`MOFFF <PKG-MOFFF>`
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* :ref:`MOLECULE <PKG-MOLECULE>`
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* :ref:`MOLFILE <PKG-MOLFILE>`
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* :ref:`NETCDF <PKG-NETCDF>`
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* :ref:`OPENMP <PKG-OPENMP>`
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* :ref:`OPT <PKG-OPT>`
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* :ref:`ORIENT <PKG-ORIENT>`
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* :ref:`PERI <PKG-PERI>`
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* :ref:`PHONON <PKG-PHONON>`
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* :ref:`PLUGIN <PKG-PLUGIN>`
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* :ref:`PLUMED <PKG-PLUMED>`
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* :ref:`POEMS <PKG-POEMS>`
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* :ref:`PTM <PKG-PTM>`
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* :ref:`PYTHON <PKG-PYTHON>`
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* :ref:`QEQ <PKG-QEQ>`
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* :ref:`QMMM <PKG-QMMM>`
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* :ref:`QTB <PKG-QTB>`
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* :ref:`RHEO <PKG-RHEO>`
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* :ref:`REACTION <PKG-REACTION>`
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* :ref:`REAXFF <PKG-REAXFF>`
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* :ref:`REPLICA <PKG-REPLICA>`
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* :ref:`RIGID <PKG-RIGID>`
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* :ref:`SCAFACOS <PKG-SCAFACOS>`
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* :ref:`SHOCK <PKG-SHOCK>`
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* :ref:`SMTBQ <PKG-SMTBQ>`
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* :ref:`SPH <PKG-SPH>`
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* :ref:`SPIN <PKG-SPIN>`
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* :ref:`SRD <PKG-SRD>`
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* :ref:`TALLY <PKG-TALLY>`
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* :ref:`UEF <PKG-UEF>`
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* :ref:`VORONOI <PKG-VORONOI>`
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* :ref:`VTK <PKG-VTK>`
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* :ref:`YAFF <PKG-YAFF>`
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----------
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.. _PKG-ADIOS:
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ADIOS package
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------------------
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**Contents:**
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ADIOS is a high-performance I/O library. This package implements the
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:doc:`dump atom/adios <dump_adios>`, :doc:`dump custom/adios <dump_adios>` and
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:doc:`read_dump ... format adios <read_dump>`
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commands to write and read data using the ADIOS library.
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**Authors:** Norbert Podhorszki (ORNL) from the ADIOS developer team.
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.. versionadded:: 28Feb2019
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**Install:**
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This package has :ref:`specific installation instructions <adios>` on the :doc:`Build extras <Build_extras>` page.
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**Supporting info:**
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* ``src/ADIOS``: filenames -> commands
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* ``src/ADIOS/README``
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* ``examples/PACKAGES/adios``
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* https://github.com/ornladios/ADIOS2
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* :doc:`dump atom/adios <dump_adios>`
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* :doc:`dump custom/adios <dump_adios>`
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* :doc:`read_dump <read_dump>`
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----------
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.. _PKG-AMOEBA:
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AMOEBA package
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---------------
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**Contents:**
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Implementation of the AMOEBA and HIPPO polarized force fields
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originally developed by Jay Ponder's group at the U Washington at St
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Louis. The LAMMPS implementation is based on Fortran 90 code
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provided by the Ponder group in their
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`Tinker MD software <https://dasher.wustl.edu/tinker/>`_.
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**Authors:** Josh Rackers and Steve Plimpton (Sandia), Trung Nguyen (U
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Chicago)
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**Supporting info:**
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* ``src/AMOEBA``: filenames -> commands
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* :doc:`AMOEBA and HIPPO howto <Howto_amoeba>`
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* :doc:`pair_style amoeba <pair_amoeba>`
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* :doc:`pair_style hippo <pair_amoeba>`
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* :doc:`atom_style amoeba <atom_style>`
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* :doc:`angle_style amoeba <angle_amoeba>`
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* :doc:`improper_style amoeba <improper_amoeba>`
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* :doc:`fix amoeba/bitorsion <fix_amoeba_bitorsion>`
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* :doc:`fix amoeba/pitorsion <fix_amoeba_pitorsion>`
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* tools/tinker/tinker2lmp.py
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* ``examples/amoeba``
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----------
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.. _PKG-APIP:
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APIP package
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------------
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**Contents:**
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This package provides adaptive-precision interatomic potentials (APIP) as
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described in:
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D. Immel, R. Drautz and G. Sutmann, "Adaptive-precision potentials for
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large-scale atomistic simulations", J. Chem. Phys. 162, 114119 (2025)
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`link <immel2025_doi_>`_
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Adaptive-precision means, that a fast interatomic potential, such as EAM,
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is coupled to a precise interatomic potential, such as ACE.
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This package provides the required pair_styles and fixes to run an efficient,
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energy-conserving adaptive-precision simulation.
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In the context of this package, precision refers to the accuracy of an interatomic
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potential.
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.. _immel2025_doi: https://doi.org/10.1063/5.0245877
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**Authors:**
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This package was written by David Immel^1,
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Ralf Drautz^2 and Godehard Sutmann^1^2.
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^1: Forschungszentrum Juelich, Juelich, Germany
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^2: Ruhr-University Bochum, Bochum, Germany
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**Install:**
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The APIP package requires also the installation of ML-PACE, which has
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:ref:`specific installation instructions <ml-pace>` on the
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:doc:`Build extras <Build_extras>` page.
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**Supporting info:**
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* ``src/APIP``: filenames -> commands
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* :doc:`Howto APIP <Howto_apip>`
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* ``examples/PACKAGES/apip``
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* :doc:`fix atom_weight/apip <fix_atom_weight_apip>`
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* :doc:`fix lambda/apip <fix_lambda_apip>`
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* :doc:`fix lambda_thermostat/apip <fix_lambda_thermostat_apip>`
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* :doc:`pair_style eam/apip <pair_eam_apip>`
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* :doc:`pair_style lambda/zone/apip <pair_lambda_zone_apip>`
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* :doc:`pair_style lambda/input/apip <pair_lambda_input_apip>`
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* :doc:`pair_style pace/apip <pair_pace_apip>`
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----------
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.. _PKG-ASPHERE:
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ASPHERE package
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---------------
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**Contents:**
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Computes, time-integration fixes, and pair styles for aspherical
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particle models including ellipsoids, 2d lines, and 3d triangles.
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**Supporting info:**
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* ``src/ASPHERE``: filenames -> commands
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* :doc:`Howto spherical <Howto_spherical>`
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* :doc:`pair_style gayberne <pair_gayberne>`
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* :doc:`pair_style resquared <pair_resquared>`
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* :doc:`pair_style ylz <pair_ylz>`
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* `doc/PDF/pair_gayberne_extra.pdf <PDF/pair_gayberne_extra.pdf>`_
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* `doc/PDF/pair_resquared_extra.pdf <PDF/pair_resquared_extra.pdf>`_
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* ``examples/ASPHERE``
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* ``examples/ellipse``
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* https://www.lammps.org/movies.html#line
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* https://www.lammps.org/movies.html#tri
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----------
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.. _PKG-ATC:
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ATC package
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----------------
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**Contents:**
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ATC stands for atoms-to-continuum. This package implements a
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:doc:`fix atc <fix_atc>` command to either couple molecular dynamics
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with continuum finite element equations or perform on-the-fly
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conversion of atomic information to continuum fields.
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**Authors:** Reese Jones, Jeremy Templeton, Jon Zimmerman (Sandia).
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**Install:**
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This package has :ref:`specific installation instructions <atc>` on the
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:doc:`Build extras <Build_extras>` page. The ATC package requires that
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also the :ref:`MANYBODY <PKG-MANYBODY>` package is installed.
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**Supporting info:**
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* ``src/ATC``: filenames -> commands
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* ``src/ATC/README``
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* :doc:`fix atc <fix_atc>`
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* ``examples/PACKAGES/atc``
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* https://www.lammps.org/pictures.html#atc
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----------
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.. _PKG-AWPMD:
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AWPMD package
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------------------
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**Contents:**
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AWPMD stands for Antisymmetrized Wave Packet Molecular Dynamics. This
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package implements an atom, pair, and fix style which allows electrons
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to be treated as explicit particles in a classical molecular dynamics
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model.
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**Author:** Ilya Valuev (JIHT, Russia).
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**Install:**
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This package has :ref:`specific installation instructions <awpmd>` on the :doc:`Build extras <Build_extras>` page.
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**Supporting info:**
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* ``src/AWPMD``: filenames -> commands
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* ``src/AWPMD/README``
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* :doc:`pair_style awpmd/cut <pair_awpmd>`
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* ``examples/PACKAGES/awpmd``
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----------
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.. _PKG-BOCS:
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BOCS package
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-----------------
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**Contents:**
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This package provides :doc:`fix bocs <fix_bocs>`, a modified version
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of :doc:`fix npt <fix_nh>` which includes the pressure correction to
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the barostat as outlined in:
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N. J. H. Dunn and W. G. Noid, "Bottom-up coarse-grained models that
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accurately describe the structure, pressure, and compressibility of
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molecular liquids", J. Chem. Phys. 143, 243148 (2015).
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**Authors:** Nicholas J. H. Dunn and Michael R. DeLyser (The
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Pennsylvania State University)
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**Supporting info:**
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The BOCS package for LAMMPS is part of the BOCS software package:
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`https://github.com/noid-group/BOCS <https://github.com/noid-group/BOCS>`_
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See the following reference for information about the entire package:
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Dunn, NJH; Lebold, KM; DeLyser, MR; Rudzinski, JF; Noid, WG.
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"BOCS: Bottom-Up Open-Source Coarse-Graining Software."
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J. Phys. Chem. B. 122, 13, 3363-3377 (2018).
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Example inputs are in the ``examples/PACKAGES/bocs`` folder.
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----------
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.. _PKG-BODY:
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BODY package
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------------
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**Contents:**
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Body-style particles with internal structure. Computes,
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time-integration fixes, pair styles, as well as the body styles
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themselves. See the :doc:`Howto body <Howto_body>` page for an
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overview.
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**Supporting info:**
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* ``src/BODY`` filenames -> commands
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* :doc:`Howto_body <Howto_body>`
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* :doc:`atom_style body <atom_style>`
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* :doc:`fix nve/body <fix_nve_body>`
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* :doc:`pair_style body/nparticle <pair_body_nparticle>`
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* ``examples/body``
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----------
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.. _PKG-BPM:
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BPM package
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------------
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**Contents:**
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Pair styles, bond styles, fixes, and computes for bonded particle
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models for mesoscale simulations of solids and fracture. See the
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:doc:`Howto bpm <Howto_bpm>` page for an overview.
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**Authors:** Joel T. Clemmer (Sandia National Labs)
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.. versionadded:: 4May2022
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**Supporting info:**
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* ``src/BPM``: filenames -> commands
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* :doc:`Howto_bpm <Howto_bpm>`
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* :doc:`atom_style bpm/sphere <atom_style>`
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* :doc:`bond_style bpm/rotational <bond_bpm_rotational>`
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* :doc:`bond_style bpm/spring <bond_bpm_spring>`
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* :doc:`compute nbond/atom <compute_nbond_atom>`
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* :doc:`fix nve/bpm/sphere <fix_nve_bpm_sphere>`
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* :doc:`pair_style bpm/spring <pair_bpm_spring>`
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* https://www.lammps.org/movies.html#bpmpackage
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* ``examples/bpm``
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----------
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.. _PKG-BROWNIAN:
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BROWNIAN package
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---------------------
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**Contents:**
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This package provides :doc:`fix brownian, fix brownian/sphere, and
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fix brownian/asphere <fix_brownian>` as well as
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:doc:`fix propel/self <fix_propel_self>` which allow to do Brownian
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Dynamics time integration of point, spherical and aspherical particles
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and also support self-propelled particles.
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**Authors:** Sam Cameron (University of Bristol),
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Stefan Paquay (while at Brandeis University) (initial version of fix propel/self)
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.. versionadded:: 14May2021
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Example inputs are in the ``examples/PACKAGES/brownian`` folder.
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----------
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.. _PKG-CG-DNA:
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CG-DNA package
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------------------
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**Contents:**
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Several pair styles, bond styles, and integration fixes for coarse-grained
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modelling of single- and double-stranded DNA and RNA based on the oxDNA and
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oxRNA model of Doye, Louis and Ouldridge. The package includes Langevin-type
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rigid-body integrators with improved stability.
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**Author:** Oliver Henrich (University of Strathclyde, Glasgow).
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**Install:**
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The CG-DNA package requires that also the :ref:`MOLECULE <PKG-MOLECULE>`
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and :ref:`ASPHERE <PKG-ASPHERE>` packages are installed.
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**Supporting info:**
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* ``src/CG-DNA``: filenames -> commands
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* ``src/CG-DNA/README``
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* :doc:`pair_style oxdna/\* <pair_oxdna>`
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* :doc:`pair_style oxdna2/\* <pair_oxdna2>`
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* :doc:`pair_style oxrna2/\* <pair_oxrna2>`
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* :doc:`bond_style oxdna/\* <bond_oxdna>`
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* :doc:`bond_style oxdna2/\* <bond_oxdna>`
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* :doc:`bond_style oxrna2/\* <bond_oxdna>`
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* :doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`
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* ``examples/PACKAGES/cgdna``
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----------
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.. _PKG-CG-SPICA:
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CG-SPICA package
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------------------
|
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**Contents:**
|
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|
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Several pair styles and an angle style which implement the
|
|
coarse-grained SPICA (formerly called SDK) model which enables
|
|
simulation of biological or soft material systems.
|
|
|
|
**Original Author:** Axel Kohlmeyer (Temple U).
|
|
|
|
**Maintainers:** Yusuke Miyazaki and Wataru Shinoda (Okayama U).
|
|
|
|
**Supporting info:**
|
|
|
|
* ``src/CG-SPICA``: filenames -> commands
|
|
* ``src/CG-SPICA/README``
|
|
* :doc:`pair_style lj/spica/\* <pair_spica>`
|
|
* :doc:`angle_style spica <angle_spica>`
|
|
* ``examples/PACKAGES/cgspica``
|
|
* https://www.lammps.org/pictures.html#cg
|
|
* https://www.spica-ff.org/
|
|
|
|
----------
|
|
|
|
.. _PKG-CLASS2:
|
|
|
|
CLASS2 package
|
|
--------------
|
|
|
|
**Contents:**
|
|
|
|
Bond, angle, dihedral, improper, and pair styles for the COMPASS
|
|
CLASS2 molecular force field.
|
|
|
|
**Supporting info:**
|
|
|
|
* ``src/CLASS2``: filenames -> commands
|
|
* :doc:`bond_style class2 <bond_class2>`
|
|
* :doc:`angle_style class2 <angle_class2>`
|
|
* :doc:`dihedral_style class2 <dihedral_class2>`
|
|
* :doc:`improper_style class2 <improper_class2>`
|
|
* :doc:`pair_style lj/class2 <pair_class2>`
|
|
|
|
----------
|
|
|
|
.. _PKG-COLLOID:
|
|
|
|
COLLOID package
|
|
---------------
|
|
|
|
**Contents:**
|
|
|
|
Coarse-grained finite-size colloidal particles. Pair styles and fix
|
|
wall styles for colloidal interactions. Includes the Fast Lubrication
|
|
Dynamics (FLD) method for hydrodynamic interactions, which is a
|
|
simplified approximation to Stokesian dynamics.
|
|
|
|
**Authors:** This package includes Fast Lubrication Dynamics pair styles
|
|
which were created by Amit Kumar and Michael Bybee from Jonathan
|
|
Higdon's group at UIUC.
|
|
|
|
**Supporting info:**
|
|
|
|
* ``src/COLLOID``: filenames -> commands
|
|
* :doc:`fix wall/colloid <fix_wall>`
|
|
* :doc:`pair_style colloid <pair_colloid>`
|
|
* :doc:`pair_style yukawa/colloid <pair_yukawa_colloid>`
|
|
* :doc:`pair_style brownian <pair_brownian>`
|
|
* :doc:`pair_style lubricate <pair_lubricate>`
|
|
* :doc:`pair_style lubricateU <pair_lubricateU>`
|
|
* ``examples/colloid``
|
|
* ``examples/srd``
|
|
|
|
----------
|
|
|
|
.. _PKG-COLVARS:
|
|
|
|
COLVARS package
|
|
--------------------
|
|
|
|
**Contents:**
|
|
|
|
Colvars stands for collective variables, which can be used to implement
|
|
various enhanced sampling methods, including Adaptive Biasing Force,
|
|
Metadynamics, Steered MD, Umbrella Sampling and Restraints. A :doc:`fix
|
|
colvars <fix_colvars>` command is implemented which wraps a COLVARS
|
|
library, which implements these methods. simulations.
|
|
|
|
**Authors:** The COLVARS library is written and maintained by Giacomo
|
|
Fiorin (NIH, Bethesda, MD, USA) and Jerome Henin (CNRS, Paris, France),
|
|
originally for the NAMD MD code, but with portability in mind. Axel
|
|
Kohlmeyer (Temple U) provided the interface to LAMMPS.
|
|
|
|
**Install:**
|
|
|
|
This package has :ref:`specific installation instructions <colvar>` on
|
|
the :doc:`Build extras <Build_extras>` page.
|
|
|
|
**Supporting info:**
|
|
|
|
* ``src/COLVARS``: filenames -> commands
|
|
* `doc/PDF/colvars-refman-lammps.pdf <PDF/colvars-refman-lammps.pdf>`_
|
|
* ``src/COLVARS/README``
|
|
* ``lib/colvars/README``
|
|
* :doc:`fix colvars <fix_colvars>`
|
|
* :doc:`group2ndx <group2ndx>`
|
|
* :doc:`ndx2group <group2ndx>`
|
|
* ``examples/PACKAGES/colvars``
|
|
|
|
----------
|
|
|
|
.. _PKG-COMPRESS:
|
|
|
|
COMPRESS package
|
|
----------------
|
|
|
|
**Contents:**
|
|
|
|
Compressed output of dump files via the zlib compression library,
|
|
using dump styles with a "gz" in their style name.
|
|
|
|
To use this package you must have the zlib compression library
|
|
available on your system.
|
|
|
|
**Author:** Axel Kohlmeyer (Temple U).
|
|
|
|
**Install:**
|
|
|
|
This package has :ref:`specific installation instructions <compress>` on the :doc:`Build extras <Build_extras>` page.
|
|
|
|
**Supporting info:**
|
|
|
|
* ``src/COMPRESS``: filenames -> commands
|
|
* ``src/COMPRESS/README``
|
|
* ``lib/compress/README``
|
|
* :doc:`dump atom/gz <dump>`
|
|
* :doc:`dump cfg/gz <dump>`
|
|
* :doc:`dump custom/gz <dump>`
|
|
* :doc:`dump xyz/gz <dump>`
|
|
|
|
----------
|
|
|
|
.. _PKG-CORESHELL:
|
|
|
|
CORESHELL package
|
|
-----------------
|
|
|
|
**Contents:**
|
|
|
|
Compute and pair styles that implement the adiabatic core/shell model
|
|
for polarizability. The pair styles augment Born, Buckingham, and
|
|
Lennard-Jones styles with core/shell capabilities. The :doc:`compute
|
|
temp/cs <compute_temp_cs>` command calculates the temperature of a
|
|
system with core/shell particles. See the :doc:`Howto coreshell
|
|
<Howto_coreshell>` page for an overview of how to use this package.
|
|
|
|
**Author:** Hendrik Heenen (Technical U of Munich).
|
|
|
|
**Supporting info:**
|
|
|
|
* ``src/CORESHELL``: filenames -> commands
|
|
* :doc:`Howto coreshell <Howto_coreshell>`
|
|
* :doc:`Howto polarizable <Howto_polarizable>`
|
|
* :doc:`compute temp/cs <compute_temp_cs>`
|
|
* :doc:`pair_style born/coul/long/cs <pair_cs>`
|
|
* :doc:`pair_style buck/coul/long/cs <pair_cs>`
|
|
* :doc:`pair_style lj/cut/coul/long/cs <pair_lj>`
|
|
* ``examples/coreshell``
|
|
|
|
----------
|
|
|
|
.. _PKG-DIELECTRIC:
|
|
|
|
DIELECTRIC package
|
|
------------------------
|
|
|
|
**Contents:**
|
|
|
|
An atom style, multiple pair styles, several fixes, Kspace styles and a
|
|
compute for simulating systems using boundary element solvers for
|
|
computing the induced charges at the interface between two media with
|
|
different dielectric constants.
|
|
|
|
**Install:**
|
|
|
|
To use this package, also the :ref:`KSPACE <PKG-KSPACE>` and
|
|
:ref:`EXTRA-PAIR <PKG-EXTRA-PAIR>` packages need to be installed.
|
|
|
|
**Author:** Trung Nguyen and Monica Olvera de la Cruz (Northwestern U)
|
|
|
|
.. versionadded:: 2Jul2021
|
|
|
|
**Supporting info:**
|
|
|
|
* ``src/DIELECTRIC``: filenames -> commands
|
|
* :doc:`atom_style dielectric <atom_style>`
|
|
* :doc:`pair_style coul/cut/dielectric <pair_dielectric>`
|
|
* :doc:`pair_style coul/long/dielectric <pair_dielectric>`
|
|
* :doc:`pair_style lj/cut/coul/cut/dielectric <pair_dielectric>`
|
|
* :doc:`pair_style lj/cut/coul/debye/dielectric <pair_dielectric>`
|
|
* :doc:`pair_style lj/cut/coul/long/dielectric <pair_dielectric>`
|
|
* :doc:`pair_style lj/cut/coul/msm/dielectric <pair_dielectric>`
|
|
* :doc:`pair_style pppm/dielectric <kspace_style>`
|
|
* :doc:`pair_style pppm/disp/dielectric <kspace_style>`
|
|
* :doc:`pair_style msm/dielectric <kspace_style>`
|
|
* :doc:`fix_style polarize/bem/icc <fix_polarize>`
|
|
* :doc:`fix_style polarize/bem/gmres <fix_polarize>`
|
|
* :doc:`fix_style polarize/functional <fix_polarize>`
|
|
* :doc:`compute efield/atom <compute_efield_atom>`
|
|
* ``examples/PACKAGES/dielectric``
|
|
|
|
----------
|
|
|
|
.. _PKG-DIFFRACTION:
|
|
|
|
DIFFRACTION package
|
|
------------------------
|
|
|
|
**Contents:**
|
|
|
|
Two computes and a fix for calculating x-ray and electron diffraction
|
|
intensities based on kinematic diffraction theory.
|
|
|
|
**Author:** Shawn Coleman while at the U Arkansas.
|
|
|
|
**Supporting info:**
|
|
|
|
* ``src/DIFFRACTION``: filenames -> commands
|
|
* :doc:`compute saed <compute_saed>`
|
|
* :doc:`compute xrd <compute_xrd>`
|
|
* :doc:`fix saed/vtk <fix_saed_vtk>`
|
|
* ``examples/PACKAGES/diffraction``
|
|
|
|
----------
|
|
|
|
.. _PKG-DIPOLE:
|
|
|
|
DIPOLE package
|
|
--------------
|
|
|
|
**Contents:**
|
|
|
|
An atom style and several pair styles for point dipole models with
|
|
short-range or long-range interactions.
|
|
|
|
**Supporting info:**
|
|
|
|
* ``src/DIPOLE``: filenames -> commands
|
|
* :doc:`atom_style dipole <atom_style>`
|
|
* :doc:`pair_style lj/cut/dipole/cut <pair_dipole>`
|
|
* :doc:`pair_style lj/cut/dipole/long <pair_dipole>`
|
|
* :doc:`pair_style lj/long/dipole/long <pair_dipole>`
|
|
* :doc:`angle_style dipole <angle_dipole>`
|
|
* ``examples/dipole``
|
|
|
|
----------
|
|
|
|
.. _PKG-DPD-BASIC:
|
|
|
|
DPD-BASIC package
|
|
--------------------
|
|
|
|
**Contents:**
|
|
|
|
Pair styles for the basic dissipative particle dynamics (DPD) method
|
|
and DPD thermostatting.
|
|
|
|
Pair style :doc:`dpd/coul/slater/long <pair_dpd_coul_slater_long>` also
|
|
includes smeared charges for coulomb interactions and thus requires the
|
|
:ref:`KSPACE <PKG-KSPACE>` package to be installed to handle the long-range
|
|
Coulomb part of the interactions.
|
|
|
|
**Authors:** Kurt Smith (U Pittsburgh), Martin Svoboda, Martin Lisal (ICPF and UJEP), Eddy Barraud (IFPEN)
|
|
|
|
**Supporting info:**
|
|
|
|
* ``src/DPD-BASIC``: filenames -> commands
|
|
* :doc:`pair_style dpd <pair_dpd>`
|
|
* :doc:`pair_style dpd/tstat <pair_dpd>`
|
|
* :doc:`pair_style dpd/ext <pair_dpd_ext>`
|
|
* :doc:`pair_style dpd/ext/tstat <pair_dpd_ext>`
|
|
* :doc:`pair_style dpd/coul/slater/long <pair_dpd_coul_slater_long>`
|
|
* ``examples/PACKAGES/dpd-basic``
|
|
|
|
----------
|
|
|
|
.. _PKG-DPD-MESO:
|
|
|
|
DPD-MESO package
|
|
--------------------
|
|
|
|
**Contents:**
|
|
|
|
Several extensions of the dissipative particle dynamics (DPD)
|
|
method. Specifically, energy-conserving DPD (eDPD) that can model
|
|
non-isothermal processes, many-body DPD (mDPD) for simulating
|
|
vapor-liquid coexistence, and transport DPD (tDPD) for modeling
|
|
advection-diffusion-reaction systems. The equations of motion of these
|
|
DPD extensions are integrated through a modified velocity-Verlet (MVV)
|
|
algorithm.
|
|
|
|
**Author:** Zhen Li (Department of Mechanical Engineering, Clemson University)
|
|
|
|
**Supporting info:**
|
|
|
|
* ``src/DPD-MESO``: filenames -> commands
|
|
* ``src/DPD-MESO/README``
|
|
* :doc:`atom_style edpd <atom_style>`
|
|
* :doc:`pair_style edpd <pair_mesodpd>`
|
|
* :doc:`pair_style mdpd <pair_mesodpd>`
|
|
* :doc:`pair_style tdpd <pair_mesodpd>`
|
|
* :doc:`fix mvv/dpd <fix_mvv_dpd>`
|
|
* ``examples/PACKAGES/mesodpd``
|
|
* https://www.lammps.org/movies.html#mesodpd
|
|
|
|
----------
|
|
|
|
.. _PKG-DPD-REACT:
|
|
|
|
DPD-REACT package
|
|
-----------------
|
|
|
|
**Contents:**
|
|
|
|
DPD stands for dissipative particle dynamics. This package implements
|
|
coarse-grained DPD-based models for energetic, reactive molecular
|
|
crystalline materials. It includes many pair styles specific to these
|
|
systems, including for reactive DPD, where each particle has internal
|
|
state for multiple species and a coupled set of chemical reaction ODEs
|
|
are integrated each timestep. Highly accurate time integrators for
|
|
isothermal, isoenergetic, isobaric and isenthalpic conditions are
|
|
included. These enable long timesteps via the Shardlow splitting
|
|
algorithm.
|
|
|
|
**Authors:** Jim Larentzos (ARL), Tim Mattox (Engility Corp), and John
|
|
Brennan (ARL).
|
|
|
|
**Supporting info:**
|
|
|
|
* ``src/DPD-REACT``: filenames -> commands
|
|
* ``src/DPD-REACT/README``
|
|
* :doc:`compute dpd <compute_dpd>`
|
|
* :doc:`compute dpd/atom <compute_dpd_atom>`
|
|
* :doc:`fix eos/cv <fix_eos_table>`
|
|
* :doc:`fix eos/table <fix_eos_table>`
|
|
* :doc:`fix eos/table/rx <fix_eos_table_rx>`
|
|
* :doc:`fix shardlow <fix_shardlow>`
|
|
* :doc:`fix rx <fix_rx>`
|
|
* :doc:`pair_style table/rx <pair_table_rx>`
|
|
* :doc:`pair_style dpd/fdt <pair_dpd_fdt>`
|
|
* :doc:`pair_style dpd/fdt/energy <pair_dpd_fdt>`
|
|
* :doc:`pair_style exp6/rx <pair_exp6_rx>`
|
|
* :doc:`pair_style multi/lucy <pair_multi_lucy>`
|
|
* :doc:`pair_style multi/lucy/rx <pair_multi_lucy_rx>`
|
|
* ``examples/PACKAGES/dpd-react``
|
|
|
|
----------
|
|
|
|
.. _PKG-DPD-SMOOTH:
|
|
|
|
DPD-SMOOTH package
|
|
------------------
|
|
|
|
**Contents:**
|
|
|
|
A pair style for smoothed dissipative particle dynamics (SDPD), which
|
|
is an extension of smoothed particle hydrodynamics (SPH) to mesoscale
|
|
where thermal fluctuations are important (see the
|
|
:ref:`SPH package <PKG-SPH>`).
|
|
Also two fixes for moving and rigid body integration of SPH/SDPD particles
|
|
(particles of atom_style meso).
|
|
|
|
**Author:** Morteza Jalalvand (Institute for Advanced Studies in Basic
|
|
Sciences, Iran).
|
|
|
|
**Supporting info:**
|
|
|
|
* ``src/DPD-SMOOTH``: filenames -> commands
|
|
* ``src/DPD-SMOOTH/README``
|
|
* :doc:`pair_style sdpd/taitwater/isothermal <pair_sdpd_taitwater_isothermal>`
|
|
* :doc:`fix meso/move <fix_meso_move>`
|
|
* :doc:`fix rigid/meso <fix_rigid_meso>`
|
|
* ``examples/PACKAGES/dpd-smooth``
|
|
|
|
----------
|
|
|
|
.. _PKG-DRUDE:
|
|
|
|
DRUDE package
|
|
------------------
|
|
|
|
**Contents:**
|
|
|
|
Fixes, pair styles, and a compute to simulate thermalized Drude
|
|
oscillators as a model of polarization. See the :doc:`Howto drude <Howto_drude>` and :doc:`Howto drude2 <Howto_drude2>` pages
|
|
for an overview of how to use the package. There are auxiliary tools
|
|
for using this package in tools/drude.
|
|
|
|
**Authors:** Alain Dequidt (U Clermont Auvergne), Julien
|
|
Devemy (CNRS), and Agilio Padua (ENS de Lyon).
|
|
|
|
**Supporting info:**
|
|
|
|
* ``src/DRUDE``: filenames -> commands
|
|
* :doc:`Howto drude <Howto_drude>`
|
|
* :doc:`Howto drude2 <Howto_drude2>`
|
|
* :doc:`Howto polarizable <Howto_polarizable>`
|
|
* ``src/DRUDE/README``
|
|
* :doc:`fix drude <fix_drude>`
|
|
* :doc:`fix drude/transform/\* <fix_drude_transform>`
|
|
* :doc:`compute temp/drude <compute_temp_drude>`
|
|
* :doc:`pair_style thole <pair_thole>`
|
|
* :doc:`pair_style lj/cut/thole/long <pair_thole>`
|
|
* ``examples/PACKAGES/drude``
|
|
* tools/drude
|
|
|
|
----------
|
|
|
|
.. _PKG-EFF:
|
|
|
|
EFF package
|
|
----------------
|
|
|
|
**Contents:**
|
|
|
|
EFF stands for electron force field which allows a classical MD code
|
|
to model electrons as particles of variable radius. This package
|
|
contains atom, pair, fix and compute styles which implement the eFF as
|
|
described in A. Jaramillo-Botero, J. Su, Q. An, and W.A. Goddard III,
|
|
JCC, 2010. The eFF potential was first introduced by Su and Goddard,
|
|
in 2007. There are auxiliary tools for using this package in
|
|
tools/eff; see its README file.
|
|
|
|
**Author:** Andres Jaramillo-Botero (CalTech).
|
|
|
|
**Supporting info:**
|
|
|
|
* ``src/EFF``: filenames -> commands
|
|
* ``src/EFF/README``
|
|
* :doc:`atom_style electron <atom_style>`
|
|
* :doc:`fix nve/eff <fix_nve_eff>`
|
|
* :doc:`fix nvt/eff <fix_nh_eff>`
|
|
* :doc:`fix npt/eff <fix_nh_eff>`
|
|
* :doc:`fix langevin/eff <fix_langevin_eff>`
|
|
* :doc:`compute temp/eff <compute_temp_eff>`
|
|
* :doc:`pair_style eff/cut <pair_eff>`
|
|
* :doc:`pair_style eff/inline <pair_eff>`
|
|
* ``examples/PACKAGES/eff``
|
|
* tools/eff/README
|
|
* tools/eff
|
|
* https://www.lammps.org/movies.html#eff
|
|
|
|
-------------------
|
|
|
|
.. _PKG-ELECTRODE:
|
|
|
|
ELECTRODE package
|
|
-----------------
|
|
|
|
**Contents:**
|
|
|
|
The ELECTRODE package allows the user to enforce a constant potential method for
|
|
groups of atoms that interact with the remaining atoms as electrolyte.
|
|
|
|
**Authors:** The ELECTRODE package is written and maintained by Ludwig
|
|
Ahrens-Iwers (TUHH, Hamburg, Germany), Shern Tee (UQ, Brisbane, Australia) and
|
|
Robert Meissner (Helmholtz-Zentrum Hereon, Geesthacht and TUHH, Hamburg, Germany).
|
|
|
|
.. versionadded:: 4May2022
|
|
|
|
**Install:**
|
|
|
|
This package has :ref:`specific installation instructions <electrode>` on the
|
|
:doc:`Build extras <Build_extras>` page.
|
|
|
|
**Supporting info:**
|
|
|
|
* :doc:`fix electrode/conp <fix_electrode>`
|
|
* :doc:`fix electrode/conq <fix_electrode>`
|
|
* :doc:`fix electrode/thermo <fix_electrode>`
|
|
|
|
----------
|
|
|
|
.. _PKG-EXTRA-COMMAND:
|
|
|
|
EXTRA-COMMAND package
|
|
---------------------
|
|
|
|
**Contents:**
|
|
|
|
Additional command styles that are less commonly used.
|
|
|
|
**Supporting info:**
|
|
|
|
* ``src/EXTRA-COMMAND``: filenames -> commands
|
|
* :doc:`general commands <Commands_all>`
|
|
|
|
----------
|
|
|
|
.. _PKG-EXTRA-COMPUTE:
|
|
|
|
EXTRA-COMPUTE package
|
|
---------------------
|
|
|
|
**Contents:**
|
|
|
|
Additional compute styles that are less commonly used.
|
|
|
|
**Supporting info:**
|
|
|
|
* ``src/EXTRA-COMPUTE``: filenames -> commands
|
|
* :doc:`compute <compute>`
|
|
|
|
----------
|
|
|
|
.. _PKG-EXTRA-DUMP:
|
|
|
|
EXTRA-DUMP package
|
|
------------------
|
|
|
|
**Contents:**
|
|
|
|
Additional dump styles that are less commonly used.
|
|
|
|
**Supporting info:**
|
|
|
|
* ``src/EXTRA-DUMP``: filenames -> commands
|
|
* :doc:`dump <dump>`
|
|
|
|
----------
|
|
|
|
.. _PKG-EXTRA-FIX:
|
|
|
|
EXTRA-FIX package
|
|
-----------------
|
|
|
|
**Contents:**
|
|
|
|
Additional fix styles that are less commonly used.
|
|
|
|
**Supporting info:**
|
|
|
|
* ``src/EXTRA-FIX``: filenames -> commands
|
|
* :doc:`fix <fix>`
|
|
|
|
----------
|
|
|
|
.. _PKG-EXTRA-MOLECULE:
|
|
|
|
EXTRA-MOLECULE package
|
|
----------------------
|
|
|
|
**Contents:**
|
|
|
|
Additional bond, angle, dihedral, and improper styles that are less commonly used.
|
|
|
|
**Install:**
|
|
|
|
To use this package, also the :ref:`MOLECULE <PKG-MOLECULE>` package needs to be installed.
|
|
|
|
**Supporting info:**
|
|
|
|
* ``src/EXTRA-MOLECULE``: filenames -> commands
|
|
* :doc:`molecular styles <Commands_bond>`
|
|
|
|
----------
|
|
|
|
.. _PKG-EXTRA-PAIR:
|
|
|
|
EXTRA-PAIR package
|
|
------------------
|
|
|
|
**Contents:**
|
|
|
|
Additional pair styles that are less commonly used.
|
|
|
|
**Supporting info:**
|
|
|
|
* ``src/EXTRA-PAIR``: filenames -> commands
|
|
* :doc:`pair_style <pair_style>`
|
|
* ``examples/PACKAGES/dispersion``
|
|
|
|
----------
|
|
|
|
.. _PKG-FEP:
|
|
|
|
FEP package
|
|
----------------
|
|
|
|
**Contents:**
|
|
|
|
FEP stands for free energy perturbation. This package provides methods
|
|
for performing FEP simulations by using a :doc:`fix adapt/fep
|
|
<fix_adapt_fep>` command with soft-core pair potentials, which have a
|
|
"soft" in their style name. There are auxiliary tools for using this
|
|
package in ``tools/fep``; see its ``README`` file.
|
|
|
|
**Author:** Agilio Padua (ENS de Lyon)
|
|
|
|
**Supporting info:**
|
|
|
|
* ``src/FEP``: filenames -> commands
|
|
* ``src/FEP/README``
|
|
* :doc:`fix adapt/fep <fix_adapt_fep>`
|
|
* :doc:`compute fep <compute_fep>`
|
|
* :doc:`pair_style \*/soft <pair_fep_soft>`
|
|
* ``examples/PACKAGES/fep``
|
|
* tools/fep/README
|
|
* tools/fep
|
|
|
|
----------
|
|
|
|
.. _PKG-GPU:
|
|
|
|
GPU package
|
|
-----------
|
|
|
|
**Contents:**
|
|
|
|
Dozens of pair styles and a version of the PPPM long-range Coulombic
|
|
solver optimized for GPUs. All such styles have a "gpu" as a suffix
|
|
in their style name. The GPU code can be compiled with either CUDA or
|
|
OpenCL, however the OpenCL variants are no longer actively maintained
|
|
and only the CUDA versions are regularly tested. The
|
|
:doc:`Speed_gpu` page gives details of what hardware and GPU
|
|
software is required on your system, and details on how to build and
|
|
use this package. Its styles can be invoked at run time via the ``-sf
|
|
gpu`` or ``-suffix gpu`` :doc:`command-line switches <Run_options>`. See
|
|
also the :ref:`KOKKOS <PKG-KOKKOS>` package, which has GPU-enabled styles.
|
|
|
|
**Authors:** Mike Brown (Intel) while at Sandia and ORNL and Trung Nguyen
|
|
(Northwestern U) while at ORNL and later. AMD HIP support by Evgeny
|
|
Kuznetsov, Vladimir Stegailov, and Vsevolod Nikolskiy (HSE University).
|
|
|
|
**Install:**
|
|
|
|
This package has :ref:`specific installation instructions <gpu>` on the
|
|
:doc:`Build extras <Build_extras>` page.
|
|
|
|
**Supporting info:**
|
|
|
|
* ``src/GPU``: filenames -> commands
|
|
* ``src/GPU/README``
|
|
* ``lib/gpu/README``
|
|
* :doc:`Accelerator packages <Speed_packages>`
|
|
* :doc:`GPU package <Speed_gpu>`
|
|
* :doc:`Section 2.6 -sf gpu <Run_options>`
|
|
* :doc:`Section 2.6 -pk gpu <Run_options>`
|
|
* :doc:`package gpu <package>`
|
|
* :doc:`Commands <Commands_all>` pages (:doc:`pair <Commands_pair>`, :doc:`kspace <Commands_kspace>`)
|
|
for styles followed by (g)
|
|
* `Benchmarks page <https://www.lammps.org/bench.html>`_ of website
|
|
|
|
----------
|
|
|
|
.. _PKG-GRANULAR:
|
|
|
|
GRANULAR package
|
|
----------------
|
|
|
|
**Contents:**
|
|
|
|
Pair styles and fixes for finite-size granular particles, which
|
|
interact with each other and boundaries via frictional and dissipative
|
|
potentials.
|
|
|
|
**Supporting info:**
|
|
|
|
* ``src/GRANULAR``: filenames -> commands
|
|
* :doc:`Howto granular <Howto_granular>`
|
|
* :doc:`fix pour <fix_pour>`
|
|
* :doc:`fix wall/gran <fix_wall_gran>`
|
|
* :doc:`pair_style gran/hooke <pair_gran>`
|
|
* :doc:`pair_style gran/hertz/history <pair_gran>`
|
|
* ``examples/granregion``
|
|
* ``examples/pour``
|
|
* bench/in.chute
|
|
* https://www.lammps.org/pictures.html#jamming
|
|
* https://www.lammps.org/movies.html#hopper
|
|
* https://www.lammps.org/movies.html#dem
|
|
* https://www.lammps.org/movies.html#brazil
|
|
* https://www.lammps.org/movies.html#granregion
|
|
|
|
----------
|
|
|
|
.. _PKG-H5MD:
|
|
|
|
H5MD package
|
|
-----------------
|
|
|
|
**Contents:**
|
|
|
|
H5MD stands for HDF5 for MD. `HDF5 <HDF5_>`_ is a portable, binary,
|
|
self-describing file format, used by many scientific simulations.
|
|
H5MD is a format for molecular simulations, built on top of HDF5.
|
|
This package implements a :doc:`dump h5md <dump_h5md>` command to output
|
|
LAMMPS snapshots in this format.
|
|
|
|
.. _HDF5: https://www.hdfgroup.org/solutions/hdf5
|
|
|
|
To use this package you must have the HDF5 library available on your
|
|
system.
|
|
|
|
**Author:** Pierre de Buyl (KU Leuven) created both the package and the
|
|
H5MD format.
|
|
|
|
**Install:**
|
|
|
|
This package has :ref:`specific installation instructions <h5md>` on the :doc:`Build extras <Build_extras>` page.
|
|
|
|
**Supporting info:**
|
|
|
|
* ``src/H5MD``: filenames -> commands
|
|
* ``src/H5MD/README``
|
|
* ``lib/h5md/README``
|
|
* :doc:`dump h5md <dump_h5md>`
|
|
|
|
----------
|
|
|
|
.. _PKG-INTEL:
|
|
|
|
INTEL package
|
|
------------------
|
|
|
|
**Contents:**
|
|
|
|
Dozens of pair, fix, bond, angle, dihedral, improper, and kspace styles
|
|
which are optimized for Intel CPUs and KNLs (Knights Landing). All of
|
|
them have an "intel" in their style name. The :doc:`INTEL package
|
|
<Speed_intel>` page gives details of what hardware and compilers are
|
|
required on your system, and how to build and use this package. Its
|
|
styles can be invoked at run time via the ``-sf intel`` or ``-suffix intel``
|
|
:doc:`command-line switches <Run_options>`. Also see the :ref:`KOKKOS
|
|
<PKG-KOKKOS>`, :ref:`OPT <PKG-OPT>`, and :ref:`OPENMP <PKG-OPENMP>`
|
|
packages, which have styles optimized for CPUs and KNLs.
|
|
|
|
You need to have an Intel compiler, version 14 or higher to take full
|
|
advantage of this package. While compilation with GNU compilers is
|
|
supported, performance will be sub-optimal.
|
|
|
|
.. note::
|
|
|
|
the INTEL package contains styles that require using the
|
|
-restrict flag, when compiling with Intel compilers.
|
|
|
|
**Author:** Mike Brown (Intel).
|
|
|
|
**Install:**
|
|
|
|
This package has :ref:`specific installation instructions <intel>` on the :doc:`Build extras <Build_extras>` page.
|
|
|
|
**Supporting info:**
|
|
|
|
* ``src/INTEL``: filenames -> commands
|
|
* ``src/INTEL/README``
|
|
* :doc:`Accelerator packages <Speed_packages>`
|
|
* :doc:`INTEL package <Speed_intel>`
|
|
* :doc:`Section 2.6 -sf intel <Run_options>`
|
|
* :doc:`Section 2.6 -pk intel <Run_options>`
|
|
* :doc:`package intel <package>`
|
|
* Search the :doc:`commands <Commands_all>` pages (:doc:`fix <Commands_fix>`, :doc:`compute <Commands_compute>`,
|
|
:doc:`pair <Commands_pair>`, :doc:`bond, angle, dihedral, improper <Commands_bond>`, :doc:`kspace <Commands_kspace>`) for styles followed by (i)
|
|
* ``src/INTEL/TEST``
|
|
* `Benchmarks page <https://www.lammps.org/bench.html>`_ of website
|
|
|
|
----------
|
|
|
|
.. _PKG-INTERLAYER:
|
|
|
|
INTERLAYER package
|
|
------------------
|
|
|
|
**Contents:**
|
|
|
|
A collection of pair styles specifically to be used for modeling layered
|
|
materials, most commonly graphene sheets (or equivalents).
|
|
|
|
**Supporting info:**
|
|
|
|
* ``src/INTERLAYER``: filenames -> commands
|
|
* :doc:`Pair style <Commands_pair>` page
|
|
* ``examples/PACKAGES/interlayer``
|
|
|
|
----------
|
|
|
|
.. _PKG-KIM:
|
|
|
|
KIM package
|
|
-----------
|
|
|
|
**Contents:**
|
|
|
|
This package contains a command with a set of sub-commands that serve as a
|
|
wrapper on the
|
|
`Open Knowledgebase of Interatomic Models (OpenKIM) <https://openkim.org>`_
|
|
repository of interatomic models (IMs) enabling compatible ones to be used in
|
|
LAMMPS simulations.
|
|
|
|
|
|
This includes :doc:`kim init <kim_commands>`, and
|
|
:doc:`kim interactions <kim_commands>` commands to select, initialize and
|
|
instantiate the IM, a :doc:`kim query <kim_commands>` command to perform web
|
|
queries for material property predictions of OpenKIM IMs, a
|
|
:doc:`kim param <kim_commands>` command to access KIM Model Parameters from
|
|
LAMMPS, and a :doc:`kim property <kim_commands>` command to write material
|
|
properties computed in LAMMPS to standard KIM property instance format.
|
|
|
|
Support for KIM IMs that conform to the
|
|
`KIM Application Programming Interface (API) <https://openkim.org/kim-api/>`_
|
|
is provided by the :doc:`pair_style kim <pair_kim>` command.
|
|
|
|
.. note::
|
|
|
|
The command *pair_style kim* is called by *kim interactions* and is not
|
|
recommended to be directly used in input scripts.
|
|
|
|
To use this package you must have the KIM API library available on your
|
|
system. The KIM API is available for download on the
|
|
`OpenKIM website <https://openkim.org/kim-api/>`_.
|
|
When installing LAMMPS from binary, the kim-api package
|
|
is a dependency that is automatically downloaded and installed.
|
|
|
|
Information about the KIM project can be found at its website:
|
|
`https://openkim.org <https://openkim.org>`_.
|
|
The KIM project is led by Ellad Tadmor and Ryan Elliott (U Minnesota)
|
|
and is funded by the `National Science Foundation <https://www.nsf.gov/>`_.
|
|
|
|
**Authors:** Ryan Elliott (U Minnesota) is the main developer for the KIM
|
|
API and the *pair_style kim* command. Yaser Afshar (U Minnesota),
|
|
Axel Kohlmeyer (Temple U), Ellad Tadmor (U Minnesota), and
|
|
Daniel Karls (U Minnesota) contributed to the
|
|
:doc:`kim command <kim_commands>` interface in close collaboration with
|
|
Ryan Elliott.
|
|
|
|
**Install:**
|
|
|
|
This package has :ref:`specific installation instructions <kim>` on the
|
|
:doc:`Build extras <Build_extras>` page.
|
|
|
|
**Supporting info:**
|
|
|
|
* :doc:`kim command <kim_commands>`
|
|
* :doc:`pair_style kim <pair_kim>`
|
|
* ``src/KIM``: filenames -> commands
|
|
* ``src/KIM/README``
|
|
* ``lib/kim/README``
|
|
* ``examples/kim``
|
|
|
|
----------
|
|
|
|
.. _PKG-KOKKOS:
|
|
|
|
KOKKOS package
|
|
--------------
|
|
|
|
**Contents:**
|
|
|
|
Dozens of atom, pair, bond, angle, dihedral, improper, fix, compute
|
|
styles adapted to compile using the Kokkos library which can convert
|
|
them to OpenMP or CUDA code so that they run efficiently on multicore
|
|
CPUs, KNLs, or GPUs. All the styles have a "kk" as a suffix in their
|
|
style name. The :doc:`KOKKOS package <Speed_kokkos>` page gives details
|
|
of what hardware and software is required on your system, and how to
|
|
build and use this package. Its styles can be invoked at run time via
|
|
the ``-sf kk`` or ``-suffix kk`` :doc:`command-line switches <Run_options>`.
|
|
Also see the :ref:`GPU <PKG-GPU>`, :ref:`OPT <PKG-OPT>`, :ref:`INTEL
|
|
<PKG-INTEL>`, and :ref:`OPENMP <PKG-OPENMP>` packages, which have styles
|
|
optimized for CPUs, KNLs, and GPUs.
|
|
|
|
You must have a C++17 compatible compiler to use this package.
|
|
KOKKOS makes extensive use of advanced C++ features, which can
|
|
expose compiler bugs, especially when compiling for maximum
|
|
performance at high optimization levels. Please see the file
|
|
``lib/kokkos/README`` for a list of compilers and their respective
|
|
platforms, that are known to work.
|
|
|
|
**Authors:** The KOKKOS package was created primarily by Christian Trott
|
|
and Stan Moore (Sandia), with contributions from other folks as well.
|
|
It uses the open-source `Kokkos library <https://github.com/kokkos>`_
|
|
which was developed by Carter Edwards, Christian Trott, and others at
|
|
Sandia, and which is included in the LAMMPS distribution in
|
|
``lib/kokkos``.
|
|
|
|
**Install:**
|
|
|
|
This package has :ref:`specific installation instructions <kokkos>` on the :doc:`Build extras <Build_extras>` page.
|
|
|
|
**Supporting info:**
|
|
|
|
* ``src/KOKKOS``: filenames -> commands
|
|
* ``src/KOKKOS/README``
|
|
* ``lib/kokkos/README``
|
|
* :doc:`Accelerator packages <Speed_packages>`
|
|
* :doc:`KOKKOS package <Speed_kokkos>`
|
|
* :doc:`Section 2.6 -k on ... <Run_options>`
|
|
* :doc:`Section 2.6 -sf kk <Run_options>`
|
|
* :doc:`Section 2.6 -pk kokkos <Run_options>`
|
|
* :doc:`package kokkos <package>`
|
|
* Search the :doc:`commands <Commands_all>` pages (:doc:`fix <Commands_fix>`, :doc:`compute <Commands_compute>`,
|
|
:doc:`pair <Commands_pair>`, :doc:`bond, angle, dihedral, improper <Commands_bond>`,
|
|
:doc:`kspace <Commands_kspace>`) for styles followed by (k)
|
|
* `Benchmarks page <https://www.lammps.org/bench.html>`_ of website
|
|
|
|
----------
|
|
|
|
.. _PKG-KSPACE:
|
|
|
|
KSPACE package
|
|
--------------
|
|
|
|
**Contents:**
|
|
|
|
A variety of long-range Coulombic solvers, as well as pair styles which
|
|
compute the corresponding short-range pairwise Coulombic interactions.
|
|
These include Ewald, particle-particle particle-mesh (PPPM), and
|
|
multilevel summation method (MSM) solvers.
|
|
|
|
**Install:**
|
|
|
|
Building with this package requires a 1d FFT library be present on your
|
|
system for use by the PPPM solvers. This can be the KISS FFT library
|
|
provided with LAMMPS, third party libraries like FFTW, or a
|
|
vendor-supplied FFT library. See the :doc:`Build settings
|
|
<Build_settings>` page for details on how to select different FFT
|
|
options for your LAMMPS build.
|
|
|
|
**Supporting info:**
|
|
|
|
* ``src/KSPACE``: filenames -> commands
|
|
* :doc:`kspace_style <kspace_style>`
|
|
* `doc/PDF/kspace.pdf <PDF/kspace.pdf>`_
|
|
* :doc:`Howto tip3p <Howto_tip3p>`
|
|
* :doc:`Howto tip4p <Howto_tip4p>`
|
|
* :doc:`Howto spc <Howto_spc>`
|
|
* :doc:`pair_style coul <pair_coul>`
|
|
* Search the :doc:`pair style <Commands_pair>` page for styles with "long" or "msm" in name
|
|
* ``examples/peptide``
|
|
* bench/in.rhodo
|
|
|
|
----------
|
|
|
|
.. _PKG-LATBOLTZ:
|
|
|
|
LATBOLTZ package
|
|
----------------
|
|
|
|
**Contents:**
|
|
|
|
Fixes which implement a background Lattice-Boltzmann (LB) fluid, which
|
|
can be used to model MD particles influenced by hydrodynamic forces.
|
|
|
|
**Authors:** Frances Mackay and Colin Denniston (University of Western
|
|
Ontario).
|
|
|
|
**Install:**
|
|
|
|
The LATBOLTZ package requires that LAMMPS is build in :ref:`MPI parallel mode <serial>`.
|
|
|
|
**Supporting info:**
|
|
|
|
* ``src/LATBOLTZ``: filenames -> commands
|
|
* ``src/LATBOLTZ/README``
|
|
* :doc:`fix lb/fluid <fix_lb_fluid>`
|
|
* :doc:`fix lb/momentum <fix_lb_momentum>`
|
|
* :doc:`fix lb/viscous <fix_lb_viscous>`
|
|
* ``examples/PACKAGES/latboltz``
|
|
|
|
----------
|
|
|
|
.. _PKG-LEPTON:
|
|
|
|
LEPTON package
|
|
--------------
|
|
|
|
**Contents:**
|
|
|
|
Styles for pair, bond, and angle forces that evaluate the potential
|
|
function from a string using the `Lepton mathematical expression parser
|
|
<https://simtk.org/projects/lepton>`_. Lepton is a C++ library that is
|
|
bundled with `OpenMM <https://openmm.org/>`_ and can be used for
|
|
parsing, evaluating, differentiating, and analyzing mathematical
|
|
expressions. This is a more lightweight and efficient alternative for
|
|
evaluating custom potential function to an embedded Python interpreter
|
|
as used in the :ref:`PYTHON package <PKG-PYTHON>`. On the other hand,
|
|
since the potentials are evaluated form analytical expressions, they are
|
|
more precise than what can be done with :ref:`tabulated potentials
|
|
<tabulate>`.
|
|
|
|
**Authors:** Axel Kohlmeyer (Temple U). Lepton itself is developed
|
|
by Peter Eastman at Stanford University.
|
|
|
|
.. versionadded:: 8Feb2023
|
|
|
|
**Install:**
|
|
|
|
This package has :ref:`specific installation instructions <lepton>` on
|
|
the :doc:`Build extras <Build_extras>` page.
|
|
|
|
**Supporting info:**
|
|
|
|
* ``src/LEPTON``: filenames -> commands
|
|
* ``lib/lepton/README``.md
|
|
* :doc:`pair_style lepton <pair_lepton>`
|
|
* :doc:`bond_style lepton <bond_lepton>`
|
|
* :doc:`angle_style lepton <angle_lepton>`
|
|
* :doc:`dihedral_style lepton <dihedral_lepton>`
|
|
|
|
----------
|
|
|
|
.. _PKG-MACHDYN:
|
|
|
|
MACHDYN package
|
|
----------------
|
|
|
|
**Contents:**
|
|
|
|
An atom style, fixes, computes, and several pair styles which
|
|
implements smoothed Mach dynamics (SMD) for solids, which is a model
|
|
related to smoothed particle hydrodynamics (SPH) for liquids (see the
|
|
:ref:`SPH package <PKG-SPH>`).
|
|
|
|
This package solves solids mechanics problems via a state of the art
|
|
stabilized meshless method with hourglass control. It can specify
|
|
hydrostatic interactions independently from material strength models,
|
|
i.e. pressure and deviatoric stresses are separated. It provides many
|
|
material models (Johnson-Cook, plasticity with hardening,
|
|
Mie-Grueneisen, Polynomial EOS) and allows new material models to be
|
|
added. It implements rigid boundary conditions (walls) which can be
|
|
specified as surface geometries from \*.STL files.
|
|
|
|
**Author:** Georg Ganzenmuller (Fraunhofer-Institute for High-Speed
|
|
Dynamics, Ernst Mach Institute, Germany).
|
|
|
|
**Install:**
|
|
|
|
This package has :ref:`specific installation instructions <machdyn>` on the :doc:`Build extras <Build_extras>` page.
|
|
|
|
**Supporting info:**
|
|
|
|
* ``src/MACHDYN``: filenames -> commands
|
|
* ``src/MACHDYN/README``
|
|
* `doc/PDF/MACHDYN_LAMMPS_userguide.pdf <PDF/MACHDYN_LAMMPS_userguide.pdf>`_
|
|
* ``examples/PACKAGES/machdyn``
|
|
* https://www.lammps.org/movies.html#smd
|
|
|
|
----------
|
|
|
|
.. _PKG-MANIFOLD:
|
|
|
|
MANIFOLD package
|
|
---------------------
|
|
|
|
**Contents:**
|
|
|
|
Several fixes and a "manifold" class which enable simulations of
|
|
particles constrained to a manifold (a 2D surface within the 3D
|
|
simulation box). This is done by applying the RATTLE constraint
|
|
algorithm to formulate single-particle constraint functions
|
|
g(xi,yi,zi) = 0 and their derivative (i.e. the normal of the manifold)
|
|
n = grad(g).
|
|
|
|
**Author:** Stefan Paquay (until 2017: Eindhoven University of
|
|
Technology (TU/e), The Netherlands; since 2017: Brandeis University,
|
|
Waltham, MA, USA)
|
|
|
|
**Supporting info:**
|
|
|
|
* ``src/MANIFOLD``: filenames -> commands
|
|
* ``src/MANIFOLD/README``
|
|
* :doc:`Howto manifold <Howto_manifold>`
|
|
* :doc:`fix manifoldforce <fix_manifoldforce>`
|
|
* :doc:`fix nve/manifold/rattle <fix_nve_manifold_rattle>`
|
|
* :doc:`fix nvt/manifold/rattle <fix_nvt_manifold_rattle>`
|
|
* ``examples/PACKAGES/manifold``
|
|
* https://www.lammps.org/movies.html#manifold
|
|
|
|
----------
|
|
|
|
.. _PKG-MANYBODY:
|
|
|
|
MANYBODY package
|
|
----------------
|
|
|
|
**Contents:**
|
|
|
|
A variety of many-body and bond-order potentials. These include
|
|
(AI)REBO, BOP, EAM, EIM, Stillinger-Weber, and Tersoff potentials.
|
|
|
|
**Supporting info:**
|
|
|
|
* ``src/MANYBODY``: filenames -> commands
|
|
* :doc:`Pair style <Commands_pair>` page
|
|
* ``examples/comb``
|
|
* ``examples/eim``
|
|
* ``examples/nb3d``
|
|
* ``examples/shear``
|
|
* ``examples/streitz``
|
|
* ``examples/vashishta``
|
|
* bench/in.eam
|
|
|
|
----------
|
|
|
|
.. _PKG-MC:
|
|
|
|
MC package
|
|
----------
|
|
|
|
**Contents:**
|
|
|
|
Several fixes and a pair style that have Monte Carlo (MC) or MC-like
|
|
attributes. These include fixes for creating, breaking, and swapping
|
|
bonds, for performing atomic swaps, and performing grand canonical
|
|
MC (GCMC), semi-grand canonical MC (SGCMC), or similar processes in
|
|
conjunction with molecular dynamics (MD).
|
|
|
|
**Supporting info:**
|
|
|
|
* ``src/MC``: filenames -> commands
|
|
* :doc:`fix atom/swap <fix_atom_swap>`
|
|
* :doc:`fix bond/break <fix_bond_break>`
|
|
* :doc:`fix bond/create <fix_bond_create>`
|
|
* :doc:`fix bond/create/angle <fix_bond_create>`
|
|
* :doc:`fix bond/swap <fix_bond_swap>`
|
|
* :doc:`fix charge/regulation <fix_charge_regulation>`
|
|
* :doc:`fix gcmc <fix_gcmc>`
|
|
* :doc:`fix sgcmc <fix_sgcmc>`
|
|
* :doc:`fix tfmc <fix_tfmc>`
|
|
* :doc:`fix widom <fix_widom>`
|
|
* :doc:`pair_style dsmc <pair_dsmc>`
|
|
* https://www.lammps.org/movies.html#gcmc
|
|
|
|
----------
|
|
|
|
.. _PKG-MDI:
|
|
|
|
MDI package
|
|
----------------
|
|
|
|
**Contents:**
|
|
|
|
A LAMMPS command and fixes to allow client-server coupling of LAMMPS
|
|
to other atomic or molecular simulation codes or materials modeling
|
|
workflows via the `MolSSI Driver Interface
|
|
(MDI) library <https://molssi-mdi.github.io/MDI_Library/html/index.html>`_.
|
|
|
|
**Author:** Taylor Barnes - MolSSI, taylor.a.barnes at gmail.com
|
|
|
|
.. versionadded:: 14May2021
|
|
|
|
**Install:**
|
|
|
|
This package has :ref:`specific installation instructions <mdi>` on
|
|
the :doc:`Build extras <Build_extras>` page.
|
|
|
|
**Supporting info:**
|
|
|
|
* ``src/MDI/README``
|
|
* ``lib/mdi/README``
|
|
* :doc:`Howto MDI <Howto_mdi>`
|
|
* :doc:`mdi <mdi>`
|
|
* :doc:`fix mdi/qm <fix_mdi_qm>`
|
|
* ``examples/PACKAGES/mdi``
|
|
|
|
----------
|
|
|
|
.. _PKG-MEAM:
|
|
|
|
MEAM package
|
|
------------------
|
|
|
|
**Contents:**
|
|
|
|
A pair style for the modified embedded atom (MEAM) potential
|
|
translated from the Fortran version in the (obsolete) MEAM package
|
|
to plain C++. The MEAM fully replaces the MEAM package, which
|
|
has been removed from LAMMPS after the 12 December 2018 version.
|
|
|
|
**Author:** Sebastian Huetter, (Otto-von-Guericke University Magdeburg)
|
|
based on the Fortran version of Greg Wagner (Northwestern U) while at
|
|
Sandia.
|
|
|
|
**Supporting info:**
|
|
|
|
* ``src/MEAM``: filenames -> commands
|
|
* ``src/MEAM/README``
|
|
* :doc:`pair_style meam <pair_meam>`
|
|
* ``examples/meam``
|
|
|
|
----------
|
|
|
|
.. _PKG-MESONT:
|
|
|
|
MESONT package
|
|
-------------------
|
|
|
|
**Contents:**
|
|
|
|
MESONT is a LAMMPS package for simulation of nanomechanics of nanotubes
|
|
(NTs). The model is based on a coarse-grained representation of NTs as
|
|
"flexible cylinders" consisting of a variable number of
|
|
segments. Internal interactions within a NT and the van der Waals
|
|
interaction between the tubes are described by a mesoscopic force field
|
|
designed and parameterized based on the results of atomic-level
|
|
molecular dynamics simulations. The description of the force field is
|
|
provided in the papers listed in ``src/MESONT/README``.
|
|
|
|
This package used to have two independent implementations of this model:
|
|
the original implementation using a Fortran library written by the
|
|
developers of the model and a second implementation written in C++ by
|
|
Philipp Kloza (U Cambridge). Since the C++ implementation offers the
|
|
same features as the original implementation with the addition of
|
|
friction, is typically faster, and easier to compile/install, the
|
|
Fortran library based implementation has since been obsoleted and
|
|
removed from the distribution. You have to download and compile
|
|
an older version of LAMMPS if you want to use those.
|
|
|
|
**Download of potential files:**
|
|
|
|
The potential files for these pair styles are *very* large and thus are
|
|
not included in the regular downloaded packages of LAMMPS or the git
|
|
repositories. Instead, they will be automatically downloaded from a web
|
|
server when the package is installed for the first time.
|
|
|
|
**Authors of the obsoleted *mesont* styles:**
|
|
|
|
Maxim V. Shugaev (University of Virginia), Alexey N. Volkov (University
|
|
of Alabama), Leonid V. Zhigilei (University of Virginia)
|
|
|
|
.. deprecated:: 8Feb2023
|
|
|
|
**Author of the C++ styles:**
|
|
Philipp Kloza (U Cambridge)
|
|
|
|
.. versionadded:: 15Jun2020
|
|
|
|
**Supporting info:**
|
|
|
|
* ``src/MESONT``: filenames -> commands
|
|
* ``src/MESONT/README``
|
|
* :doc:`bond_style mesocnt <bond_mesocnt>`
|
|
* :doc:`angle_style mesocnt <angle_mesocnt>`
|
|
* :doc:`pair_style mesocnt <pair_mesocnt>`
|
|
* ``examples/PACKAGES/mesont``
|
|
|
|
----------
|
|
|
|
.. _PKG-MGPT:
|
|
|
|
MGPT package
|
|
-----------------
|
|
|
|
**Contents:**
|
|
|
|
A pair style which provides a fast implementation of the quantum-based
|
|
MGPT multi-ion potentials. The MGPT or model GPT method derives from
|
|
first-principles DFT-based generalized pseudopotential theory (GPT)
|
|
through a series of systematic approximations valid for mid-period
|
|
transition metals with nearly half-filled d bands. The MGPT method
|
|
was originally developed by John Moriarty at LLNL. The pair style in
|
|
this package calculates forces and energies using an optimized
|
|
matrix-MGPT algorithm due to Tomas Oppelstrup at LLNL.
|
|
|
|
**Authors:** Tomas Oppelstrup and John Moriarty (LLNL).
|
|
|
|
**Supporting info:**
|
|
|
|
* ``src/MGPT``: filenames -> commands
|
|
* ``src/MGPT/README``
|
|
* :doc:`pair_style mgpt <pair_mgpt>`
|
|
* ``examples/PACKAGES/mgpt``
|
|
|
|
----------
|
|
|
|
.. _PKG-MISC:
|
|
|
|
MISC package
|
|
------------
|
|
|
|
**Contents:**
|
|
|
|
A variety of compute, fix, pair, bond styles with specialized
|
|
capabilities that don't align with other packages. Do a directory
|
|
listing, ``ls src/MISC``, to see the list of commands.
|
|
|
|
.. note::
|
|
|
|
the MISC package contains styles that require using the
|
|
-restrict flag, when compiling with Intel compilers.
|
|
|
|
**Supporting info:**
|
|
|
|
* ``src/MISC``: filenames -> commands
|
|
* :doc:`bond_style special <bond_special>`
|
|
* :doc:`compute viscosity/cos <compute_viscosity_cos>`
|
|
* :doc:`fix accelerate/cos <fix_accelerate_cos>`
|
|
* :doc:`fix imd <fix_imd>`
|
|
* :doc:`fix ipi <fix_ipi>`
|
|
* :doc:`pair_style agni <pair_agni>`
|
|
* :doc:`pair_style list <pair_list>`
|
|
* :doc:`pair_style srp <pair_srp>`
|
|
* :doc:`pair_style tracker <pair_tracker>`
|
|
|
|
----------
|
|
|
|
.. _PKG-ML-HDNNP:
|
|
|
|
ML-HDNNP package
|
|
------------------
|
|
|
|
**Contents:**
|
|
|
|
A :doc:`pair_style hdnnp <pair_hdnnp>` command which allows to use
|
|
high-dimensional neural network potentials (HDNNPs), a form of machine learning
|
|
potentials. HDNNPs must be carefully trained prior to their application in a
|
|
molecular dynamics simulation.
|
|
|
|
.. _n2p2: https://github.com/CompPhysVienna/n2p2
|
|
|
|
To use this package you must have the `n2p2 <n2p2_>`_ library installed and
|
|
compiled on your system.
|
|
|
|
**Author:** Andreas Singraber
|
|
|
|
.. versionadded:: 27May2021
|
|
|
|
**Install:**
|
|
|
|
This package has :ref:`specific installation instructions <ml-hdnnp>` on the
|
|
:doc:`Build extras <Build_extras>` page.
|
|
|
|
**Supporting info:**
|
|
|
|
* ``src/ML-HDNNP``: filenames -> commands
|
|
* ``src/ML-HDNNP/README``
|
|
* ``lib/hdnnp/README``
|
|
* :doc:`pair_style hdnnp <pair_hdnnp>`
|
|
* ``examples/PACKAGES/hdnnp``
|
|
|
|
----------
|
|
|
|
.. _PKG-ML-IAP:
|
|
|
|
ML-IAP package
|
|
--------------
|
|
|
|
**Contents:**
|
|
|
|
A general interface for machine-learning interatomic potentials, including PyTorch.
|
|
|
|
**Install:**
|
|
|
|
To use this package, also the :ref:`ML-SNAP <PKG-ML-SNAP>` package needs
|
|
to be installed. To make the *mliappy* model available, also the
|
|
:ref:`PYTHON <PKG-PYTHON>` package needs to be installed, the version
|
|
of Python must be 3.6 or later, and the `cython <https://cython.org/>`_ software
|
|
must be installed.
|
|
|
|
**Author:** Aidan Thompson (Sandia), Nicholas Lubbers (LANL).
|
|
|
|
.. versionadded:: 30Jun2020
|
|
|
|
**Supporting info:**
|
|
|
|
* ``src/ML-IAP``: filenames -> commands
|
|
* ``src/ML-IAP/README.md``
|
|
* :doc:`pair_style mliap <pair_mliap>`
|
|
* :doc:`compute_style mliap <compute_mliap>`
|
|
* ``examples/mliap`` (see README)
|
|
|
|
When built with the *mliappy* model this package includes an extension for
|
|
coupling with Python models, including PyTorch. In this case, the Python
|
|
interpreter linked to LAMMPS will need the ``cython`` and ``numpy`` modules
|
|
installed. The provided examples build models with PyTorch, which would
|
|
therefore also needs to be installed to run those examples.
|
|
|
|
----------
|
|
|
|
.. _PKG-ML-PACE:
|
|
|
|
ML-PACE package
|
|
-------------------
|
|
|
|
**Contents:**
|
|
|
|
A pair style for the Atomic Cluster Expansion potential (ACE).
|
|
ACE is a methodology for deriving a highly accurate classical potential
|
|
fit to a large archive of quantum mechanical (DFT) data. The ML-PACE
|
|
package provides an efficient implementation for running simulations
|
|
with ACE potentials.
|
|
|
|
**Authors:**
|
|
|
|
This package was written by Yury Lysogorskiy^1,
|
|
Cas van der Oord^2, Anton Bochkarev^1,
|
|
Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1,
|
|
Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1.
|
|
|
|
^1: Ruhr-University Bochum, Bochum, Germany
|
|
|
|
^2: University of Cambridge, Cambridge, United Kingdom
|
|
|
|
^3: Sandia National Laboratories, Albuquerque, New Mexico, USA
|
|
|
|
^4: University of British Columbia, Vancouver, BC, Canada
|
|
|
|
.. versionadded:: 14May2021
|
|
|
|
**Install:**
|
|
|
|
This package has :ref:`specific installation instructions <ml-pace>` on the
|
|
:doc:`Build extras <Build_extras>` page. This package may also be compiled
|
|
as a plugin to avoid licensing conflicts when distributing binaries.
|
|
|
|
**Supporting info:**
|
|
|
|
* ``src/ML-PACE``: filenames -> commands
|
|
* :doc:`pair_style pace <pair_pace>`
|
|
* ``examples/PACKAGES/pace``
|
|
|
|
----------
|
|
|
|
.. _PKG-ML-POD:
|
|
|
|
ML-POD package
|
|
-------------------
|
|
|
|
**Contents:**
|
|
|
|
A pair style and fitpod style for Proper Orthogonal Descriptors
|
|
(POD). POD is a methodology for deriving descriptors based on the proper
|
|
orthogonal decomposition. The ML-POD package provides an efficient
|
|
implementation for running simulations with POD potentials, along with
|
|
fitting the potentials natively in LAMMPS.
|
|
|
|
**Authors:**
|
|
|
|
Ngoc Cuong Nguyen (MIT), Andrew Rohskopf (Sandia)
|
|
|
|
.. versionadded:: 22Dec2022
|
|
|
|
**Install:**
|
|
|
|
This package has :ref:`specific installation instructions <ml-pod>` on the
|
|
:doc:`Build extras <Build_extras>` page.
|
|
|
|
**Supporting info:**
|
|
|
|
* ``src/ML-POD``: filenames -> commands
|
|
* :doc:`pair_style pod <pair_pod>`
|
|
* :doc:`command_style fitpod <fitpod_command>`
|
|
* ``examples/PACKAGES/pod``
|
|
|
|
----------
|
|
|
|
.. _PKG-ML-QUIP:
|
|
|
|
ML-QUIP package
|
|
-----------------
|
|
|
|
**Contents:**
|
|
|
|
A :doc:`pair_style quip <pair_quip>` command which wraps the `QUIP
|
|
libAtoms library <quip_>`_, which includes a variety of interatomic
|
|
potentials, including Gaussian Approximation Potential (GAP) models
|
|
developed by the Cambridge University group.
|
|
|
|
.. _quip: https://github.com/libAtoms/QUIP
|
|
|
|
To use this package you must have the QUIP libAtoms library available
|
|
on your system.
|
|
|
|
**Author:** Albert Bartok (Cambridge University)
|
|
|
|
**Install:**
|
|
|
|
This package has :ref:`specific installation instructions <ml-quip>` on the
|
|
:doc:`Build extras <Build_extras>` page.
|
|
|
|
**Supporting info:**
|
|
|
|
* ``src/ML-QUIP``: filenames -> commands
|
|
* ``src/ML-QUIP/README``
|
|
* :doc:`pair_style quip <pair_quip>`
|
|
* ``examples/PACKAGES/quip``
|
|
|
|
----------
|
|
|
|
.. _PKG-ML-RANN:
|
|
|
|
ML-RANN package
|
|
-----------------
|
|
|
|
**Contents:**
|
|
|
|
A pair style for using rapid atomistic neural network (RANN) potentials.
|
|
These neural network potentials work by first generating a series of symmetry
|
|
functions from the neighbor list and then using these values as the input layer
|
|
of a neural network.
|
|
|
|
**Authors:**
|
|
|
|
This package was written by Christopher Barrett
|
|
with contributions by Doyl Dickel, Mississippi State University.
|
|
|
|
.. versionadded:: 27May2021
|
|
|
|
**Supporting info:**
|
|
|
|
* ``src/ML-RANN``: filenames -> commands
|
|
* :doc:`pair_style rann <pair_rann>`
|
|
* ``examples/PACKAGES/rann``
|
|
|
|
----------
|
|
|
|
.. _PKG-ML-SNAP:
|
|
|
|
ML-SNAP package
|
|
---------------
|
|
|
|
**Contents:**
|
|
|
|
A pair style for the spectral neighbor analysis potential (SNAP).
|
|
SNAP is methodology for deriving a highly accurate classical potential
|
|
fit to a large archive of quantum mechanical (DFT) data. Also several
|
|
computes which analyze attributes of the potential.
|
|
|
|
**Author:** Aidan Thompson (Sandia).
|
|
|
|
**Supporting info:**
|
|
|
|
* ``src/ML-SNAP``: filenames -> commands
|
|
* :doc:`pair_style snap <pair_snap>`
|
|
* :doc:`compute sna/atom <compute_sna_atom>`
|
|
* :doc:`compute sna/grid <compute_sna_atom>`
|
|
* :doc:`compute sna/grid/local <compute_sna_atom>`
|
|
* :doc:`compute snad/atom <compute_sna_atom>`
|
|
* :doc:`compute snav/atom <compute_sna_atom>`
|
|
* ``examples/snap``
|
|
|
|
----------
|
|
|
|
.. _PKG-ML-UF3:
|
|
|
|
ML-UF3 package
|
|
--------------
|
|
|
|
**Contents:**
|
|
|
|
A pair style for the ultra-fast force field potentials (UF3). UF3 is a
|
|
methodology for deriving a highly accurate classical potential which is
|
|
fast to evaluate and is fitted to a large archives of quantum mechanical
|
|
(DFT) data. The use of b-spline basis set in UF3 enables the rapid
|
|
evaluation of 2-body and 3-body interactions.
|
|
|
|
**Authors:** Ajinkya C Hire (University of Florida),
|
|
Hendrik Krass (University of Constance),
|
|
Matthias Rupp (Luxembourg Institute of Science and Technology),
|
|
Richard Hennig (University of Florida)
|
|
|
|
**Supporting info:**
|
|
|
|
* ``src/ML-UF3``: filenames -> commands
|
|
* :doc:`pair_style uf3 <pair_uf3>`
|
|
* ``examples/uf3``
|
|
* https://github.com/uf3/uf3
|
|
|
|
.. _PKG-MOFFF:
|
|
|
|
MOFFF package
|
|
------------------
|
|
|
|
**Contents:**
|
|
|
|
Pair, angle and improper styles needed to employ the MOF-FF
|
|
force field by Schmid and coworkers with LAMMPS.
|
|
MOF-FF is a first principles derived force field with the primary aim
|
|
to simulate MOFs and related porous framework materials, using spherical
|
|
Gaussian charges. It is described in S. Bureekaew et al., Phys. Stat. Sol. B
|
|
2013, 250, 1128-1141.
|
|
For the usage of MOF-FF see the example in the example directory as
|
|
well as the `MOF+ <MOFplus_>`_ website.
|
|
|
|
.. _MOFplus: https://www.mofplus.org/content/show/MOF-FF
|
|
|
|
**Author:** Hendrik Heenen (Technical U of Munich),
|
|
Rochus Schmid (Ruhr-University Bochum).
|
|
|
|
**Supporting info:**
|
|
|
|
* ``src/MOFFF``: filenames -> commands
|
|
* ``src/MOFFF/README``
|
|
* :doc:`pair_style buck6d/coul/gauss <pair_buck6d_coul_gauss>`
|
|
* :doc:`angle_style class2 <angle_class2>`
|
|
* :doc:`angle_style cosine/buck6d <angle_cosine_buck6d>`
|
|
* :doc:`improper_style inversion/harmonic <improper_inversion_harmonic>`
|
|
* ``examples/PACKAGES/mofff``
|
|
|
|
----------
|
|
|
|
.. _PKG-MOLECULE:
|
|
|
|
MOLECULE package
|
|
----------------
|
|
|
|
**Contents:**
|
|
|
|
A large number of atom, pair, bond, angle, dihedral, improper styles
|
|
that are used to model molecular systems with fixed covalent bonds.
|
|
The pair styles include the Dreiding (hydrogen-bonding) and CHARMM
|
|
force fields, and a TIP4P water model.
|
|
|
|
**Supporting info:**
|
|
|
|
* ``src/MOLECULE``: filenames -> commands
|
|
* :doc:`atom_style <atom_style>`
|
|
* :doc:`bond_style <bond_style>`
|
|
* :doc:`angle_style <angle_style>`
|
|
* :doc:`dihedral_style <dihedral_style>`
|
|
* :doc:`improper_style <improper_style>`
|
|
* :doc:`pair_style hbond/dreiding/lj <pair_hbond_dreiding>`
|
|
* :doc:`pair_style lj/charmm/coul/charmm <pair_charmm>`
|
|
* :doc:`Howto bioFF <Howto_bioFF>`
|
|
* ``examples/cmap``
|
|
* ``examples/dreiding``
|
|
* ``examples/micelle,``
|
|
* ``examples/peptide``
|
|
* bench/in.chain
|
|
* bench/in.rhodo
|
|
|
|
----------
|
|
|
|
.. _PKG-MOLFILE:
|
|
|
|
MOLFILE package
|
|
--------------------
|
|
|
|
**Contents:**
|
|
|
|
A :doc:`dump molfile <dump_molfile>` command which uses molfile plugins
|
|
that are bundled with the `VMD <vmd-home_>`_
|
|
molecular visualization and analysis program, to enable LAMMPS to dump
|
|
snapshots in formats compatible with various molecular simulation
|
|
tools.
|
|
|
|
To use this package you must have the desired VMD plugins available on
|
|
your system.
|
|
|
|
Note that this package only provides the interface code, not the
|
|
plugins themselves, which will be accessed when requesting a specific
|
|
plugin via the :doc:`dump molfile <dump_molfile>` command. Plugins can
|
|
be obtained from a VMD installation which has to match the platform
|
|
that you are using to compile LAMMPS for. By adding plugins to VMD,
|
|
support for new file formats can be added to LAMMPS (or VMD or other
|
|
programs that use them) without having to re-compile the application
|
|
itself. More information about the VMD molfile plugins can be found
|
|
at
|
|
`https://www.ks.uiuc.edu/Research/vmd/plugins/molfile <https://www.ks.uiuc.edu/Research/vmd/plugins/molfile>`_.
|
|
|
|
**Author:** Axel Kohlmeyer (Temple U).
|
|
|
|
**Install:**
|
|
|
|
This package has :ref:`specific installation instructions <molfile>` on the :doc:`Build extras <Build_extras>` page.
|
|
|
|
**Supporting info:**
|
|
|
|
* ``src/MOLFILE``: filenames -> commands
|
|
* ``src/MOLFILE/README``
|
|
* ``lib/molfile/README``
|
|
* :doc:`dump molfile <dump_molfile>`
|
|
|
|
----------
|
|
|
|
.. _PKG-NETCDF:
|
|
|
|
NETCDF package
|
|
-------------------
|
|
|
|
**Contents:**
|
|
|
|
Dump styles for writing NetCDF formatted dump files. NetCDF is a
|
|
portable, binary, self-describing file format developed on top of
|
|
HDF5. The file contents follow the AMBER NetCDF trajectory conventions
|
|
(https://ambermd.org/netcdf/nctraj.xhtml), but include extensions.
|
|
|
|
To use this package you must have the NetCDF library available on your
|
|
system.
|
|
|
|
Note that NetCDF files can be directly visualized with the following
|
|
tools:
|
|
|
|
* `Ovito <ovito_>`_ (Ovito supports the AMBER convention and the extensions mentioned above)
|
|
* `VMD <vmd-home_>`_
|
|
|
|
.. _ovito: https://www.ovito.org
|
|
|
|
.. _vmd-home: https://www.ks.uiuc.edu/Research/vmd/
|
|
|
|
**Author:** Lars Pastewka (Karlsruhe Institute of Technology).
|
|
|
|
**Install:**
|
|
|
|
This package has :ref:`specific installation instructions <netcdf>` on the :doc:`Build extras <Build_extras>` page.
|
|
|
|
**Supporting info:**
|
|
|
|
* ``src/NETCDF``: filenames -> commands
|
|
* ``src/NETCDF/README``
|
|
* ``lib/netcdf/README``
|
|
* :doc:`dump netcdf <dump_netcdf>`
|
|
|
|
----------
|
|
|
|
.. _PKG-OPENMP:
|
|
|
|
OPENMP package
|
|
----------------
|
|
|
|
**Contents:**
|
|
|
|
Hundreds of pair, fix, compute, bond, angle, dihedral, improper, and
|
|
kspace styles which are altered to enable threading on many-core CPUs
|
|
via OpenMP directives. All of them have an "omp" in their style name.
|
|
The :doc:`OPENMP package <Speed_omp>` page gives details of what hardware
|
|
and compilers are required on your system, and how to build and use
|
|
this package. Its styles can be invoked at run time via the ``-sf omp``
|
|
or ``-suffix omp`` :doc:`command-line switches <Run_options>`. Also see
|
|
the :ref:`KOKKOS <PKG-KOKKOS>`, :ref:`OPT <PKG-OPT>`, and :ref:`INTEL <PKG-INTEL>`
|
|
packages, which have styles optimized for CPUs.
|
|
|
|
**Author:** Axel Kohlmeyer (Temple U).
|
|
|
|
.. note::
|
|
|
|
To enable multi-threading support the compile flag ``-fopenmp``
|
|
and the link flag ``-fopenmp`` (for GNU compilers, you have to look up
|
|
the equivalent flags for other compilers) must be used to build LAMMPS.
|
|
When using Intel compilers, also the ``-restrict`` flag is required.
|
|
The OPENMP package can be compiled without enabling OpenMP; then
|
|
all code will be compiled as serial and the only improvement over the
|
|
regular styles are some data access optimization. These flags should
|
|
be added to the CCFLAGS and LINKFLAGS lines of your Makefile.machine.
|
|
See ``src/MAKE/OPTIONS/Makefile``.omp for an example.
|
|
|
|
Once you have an appropriate Makefile.machine, you can
|
|
install/uninstall the package and build LAMMPS in the usual manner:
|
|
|
|
**Install:**
|
|
|
|
This package has :ref:`specific installation instructions <openmp>` on
|
|
the :doc:`Build extras <Build_extras>` page.
|
|
|
|
**Supporting info:**
|
|
|
|
* ``src/OPENMP``: filenames -> commands
|
|
* ``src/OPENMP/README``
|
|
* :doc:`Accelerator packages <Speed_packages>`
|
|
* :doc:`OPENMP package <Speed_omp>`
|
|
* :doc:`Command-line option -suffix/-sf omp <Run_options>`
|
|
* :doc:`Command-line option -package/-pk omp <Run_options>`
|
|
* :doc:`package omp <package>`
|
|
* Search the :doc:`commands <Commands_all>` pages (:doc:`fix <Commands_fix>`, :doc:`compute <Commands_compute>`,
|
|
:doc:`pair <Commands_pair>`, :doc:`bond, angle, dihedral, improper <Commands_bond>`,
|
|
:doc:`kspace <Commands_kspace>`) for styles followed by (o)
|
|
* `Benchmarks page <https://www.lammps.org/bench.html>`_ of website
|
|
|
|
----------
|
|
|
|
.. _PKG-OPT:
|
|
|
|
OPT package
|
|
-----------
|
|
|
|
**Contents:**
|
|
|
|
A handful of pair styles which are optimized for improved CPU
|
|
performance on single or multiple cores. These include EAM, LJ,
|
|
CHARMM, and Morse potentials. The styles have an "opt" suffix in
|
|
their style name. The :doc:`OPT package <Speed_opt>` page gives
|
|
details of how to build and use this package. Its styles can be
|
|
invoked at run time via the ``-sf opt`` or ``-suffix opt`` :doc:`command-line switches <Run_options>`. See also the :ref:`KOKKOS <PKG-KOKKOS>`,
|
|
:ref:`INTEL <PKG-INTEL>`, and :ref:`OPENMP <PKG-OPENMP>` packages, which
|
|
have styles optimized for CPU performance.
|
|
|
|
**Authors:** James Fischer (High Performance Technologies), David Richie,
|
|
and Vincent Natoli (Stone Ridge Technology).
|
|
|
|
**Install:**
|
|
|
|
This package has :ref:`specific installation instructions <opt>` on the :doc:`Build extras <Build_extras>` page.
|
|
|
|
**Supporting info:**
|
|
|
|
* ``src/OPT``: filenames -> commands
|
|
* :doc:`Accelerator packages <Speed_packages>`
|
|
* :doc:`OPT package <Speed_opt>`
|
|
* :doc:`Section 2.6 -sf opt <Run_options>`
|
|
* Search the :doc:`pair style <Commands_pair>` page for styles followed by (t)
|
|
* `Benchmarks page <https://www.lammps.org/bench.html>`_ of website
|
|
|
|
.. _PKG-ORIENT:
|
|
|
|
ORIENT package
|
|
--------------
|
|
|
|
**Contents:**
|
|
|
|
A few fixes that apply orientation dependent forces for studying
|
|
grain boundary migration.
|
|
|
|
**Supporting info:**
|
|
|
|
* ``src/ORIENT``: filenames -> commands
|
|
* :doc:`fix orient/bcc <fix_orient>`
|
|
* :doc:`fix orient/fcc <fix_orient>`
|
|
* :doc:`fix orient/eco <fix_orient_eco>`
|
|
|
|
----------
|
|
|
|
.. _PKG-PERI:
|
|
|
|
PERI package
|
|
------------
|
|
|
|
**Contents:**
|
|
|
|
An atom style, several pair styles which implement different
|
|
Peridynamics materials models, and several computes which calculate
|
|
diagnostics. Peridynamics is a particle-based meshless continuum
|
|
model.
|
|
|
|
**Authors:** The original package was created by Mike Parks (Sandia).
|
|
Additional Peridynamics models were added by Rezwanur Rahman and John
|
|
Foster (UTSA).
|
|
|
|
**Supporting info:**
|
|
|
|
* ``src/PERI``: filenames -> commands
|
|
* :doc:`Peridynamics Howto <Howto_peri>`
|
|
* `doc/PDF/PDLammps_overview.pdf <PDF/PDLammps_overview.pdf>`_
|
|
* `doc/PDF/PDLammps_EPS.pdf <PDF/PDLammps_EPS.pdf>`_
|
|
* `doc/PDF/PDLammps_VES.pdf <PDF/PDLammps_VES.pdf>`_
|
|
* :doc:`atom_style peri <atom_style>`
|
|
* :doc:`pair_style peri/\* <pair_peri>`
|
|
* :doc:`compute damage/atom <compute_damage_atom>`
|
|
* :doc:`compute plasticity/atom <compute_plasticity_atom>`
|
|
* ``examples/peri``
|
|
* https://www.lammps.org/movies.html#peri
|
|
|
|
----------
|
|
|
|
.. _PKG-PHONON:
|
|
|
|
PHONON package
|
|
-------------------
|
|
|
|
**Contents:**
|
|
|
|
A :doc:`fix phonon <fix_phonon>` command that calculates dynamical
|
|
matrices, which can then be used to compute phonon dispersion
|
|
relations, directly from molecular dynamics simulations.
|
|
And a :doc:`dynamical_matrix <dynamical_matrix>` as well as a
|
|
:doc:`third_order <third_order>` command to compute the dynamical matrix
|
|
and third order tensor from finite differences.
|
|
|
|
**Install:**
|
|
|
|
The fix phonon command also requires that the :ref:`KSPACE <PKG-KSPACE>`
|
|
package is installed.
|
|
|
|
|
|
**Authors:** Ling-Ti Kong (Shanghai Jiao Tong University) for "fix phonon"
|
|
and Charlie Sievers (UC Davis) for "dynamical_matrix" and "third_order"
|
|
|
|
**Supporting info:**
|
|
|
|
* ``src/PHONON``: filenames -> commands
|
|
* ``src/PHONON/README``
|
|
* :doc:`fix phonon <fix_phonon>`
|
|
* :doc:`dynamical_matrix <dynamical_matrix>`
|
|
* :doc:`third_order <third_order>`
|
|
* ``examples/PACKAGES/phonon``
|
|
|
|
----------
|
|
|
|
.. _PKG-PLUGIN:
|
|
|
|
PLUGIN package
|
|
--------------
|
|
|
|
**Contents:**
|
|
|
|
A :doc:`plugin <plugin>` command that can load and unload several
|
|
kind of styles in LAMMPS from shared object files at runtime without
|
|
having to recompile and relink LAMMPS.
|
|
|
|
When the environment variable ``LAMMPS_PLUGIN_PATH`` is set, then LAMMPS
|
|
will search the directory (or directories) listed in this path for files
|
|
with names that end in ``plugin.so`` (e.g. ``helloplugin.so``) and will
|
|
try to load the contained plugins automatically at start-up.
|
|
|
|
**Authors:** Axel Kohlmeyer (Temple U)
|
|
|
|
.. versionadded:: 8Apr2021
|
|
|
|
**Supporting info:**
|
|
|
|
* ``src/PLUGIN``: filenames -> commands
|
|
* :doc:`plugin command <plugin>`
|
|
* :doc:`Information on writing plugins <Developer_plugins>`
|
|
* ``examples/plugin``
|
|
|
|
----------
|
|
|
|
.. _PKG-PLUMED:
|
|
|
|
PLUMED package
|
|
-------------------
|
|
|
|
**Contents:**
|
|
|
|
The fix plumed command allows you to use the PLUMED free energy plugin
|
|
for molecular dynamics to analyze and bias your LAMMPS trajectory on
|
|
the fly. The PLUMED library is called from within the LAMMPS input
|
|
script by using the :doc:`fix plumed <fix_plumed>` command.
|
|
|
|
**Authors:** The `PLUMED library <https://www.plumed.org>`_ is written
|
|
and maintained by Massimilliano Bonomi, Giovanni Bussi, Carlo Camiloni,
|
|
and Gareth Tribello.
|
|
|
|
**Install:**
|
|
|
|
This package has :ref:`specific installation instructions <plumed>` on the
|
|
:doc:`Build extras <Build_extras>` page. This package may also be compiled
|
|
as a plugin to avoid licensing conflicts when distributing binaries.
|
|
|
|
**Supporting info:**
|
|
|
|
* ``src/PLUMED/README``
|
|
* ``lib/plumed/README``
|
|
* :doc:`fix plumed <fix_plumed>`
|
|
* ``examples/PACKAGES/plumed``
|
|
|
|
----------
|
|
|
|
.. _PKG-POEMS:
|
|
|
|
POEMS package
|
|
-------------
|
|
|
|
**Contents:**
|
|
|
|
A fix that wraps the Parallelizable Open source Efficient Multibody
|
|
Software (POEMS) library, which is able to simulate the dynamics of
|
|
articulated body systems. These are systems with multiple rigid
|
|
bodies (collections of particles) whose motion is coupled by
|
|
connections at hinge points.
|
|
|
|
**Author:** Rudra Mukherjee (JPL) while at RPI.
|
|
|
|
**Install:**
|
|
|
|
This package has :ref:`specific installation instructions <poems>` on the :doc:`Build extras <Build_extras>` page.
|
|
|
|
**Supporting info:**
|
|
|
|
* ``src/POEMS``: filenames -> commands
|
|
* ``src/POEMS/README``
|
|
* ``lib/poems/README``
|
|
* :doc:`fix poems <fix_poems>`
|
|
* ``examples/rigid``
|
|
|
|
----------
|
|
|
|
.. _PKG-PTM:
|
|
|
|
PTM package
|
|
----------------
|
|
|
|
**Contents:**
|
|
|
|
A :doc:`compute ptm/atom <compute_ptm_atom>` command that calculates
|
|
local structure characterization using the Polyhedral Template
|
|
Matching methodology.
|
|
|
|
**Author:** Peter Mahler Larsen (MIT).
|
|
|
|
**Supporting info:**
|
|
|
|
* ``src/PTM``: filenames not starting with ptm\_ -> commands
|
|
* ``src/PTM``: filenames starting with ptm\_ -> supporting code
|
|
* ``src/PTM/LICENSE``
|
|
* :doc:`compute ptm/atom <compute_ptm_atom>`
|
|
|
|
----------
|
|
|
|
.. _PKG-PYTHON:
|
|
|
|
PYTHON package
|
|
--------------
|
|
|
|
**Contents:**
|
|
|
|
A :doc:`python <python>` command which allow you to execute Python code
|
|
from a LAMMPS input script. The code can be in a separate file or
|
|
embedded in the input script itself. See the :doc:`Python call
|
|
<Python_call>` page for an overview of using Python from LAMMPS in this
|
|
manner and all the :doc:`Python <Python_head>` manual pages for other
|
|
ways to use LAMMPS and Python together.
|
|
|
|
.. note::
|
|
|
|
Building with the PYTHON package assumes you have a Python development
|
|
environment (headers and libraries) available on your system, which needs
|
|
to be Python version 3.6 or later.
|
|
|
|
**Install:**
|
|
|
|
This package has :ref:`specific installation instructions <python>` on the :doc:`Build extras <Build_extras>` page.
|
|
|
|
**Supporting info:**
|
|
|
|
* ``src/PYTHON``: filenames -> commands
|
|
* :doc:`Python call <Python_head>`
|
|
* ``lib/python/README``
|
|
* ``examples/python``
|
|
|
|
----------
|
|
|
|
.. _PKG-QEQ:
|
|
|
|
QEQ package
|
|
-----------
|
|
|
|
**Contents:**
|
|
|
|
Several fixes for performing charge equilibration (QEq) via different
|
|
algorithms. These can be used with pair styles that perform QEq as
|
|
part of their formulation.
|
|
|
|
**Supporting info:**
|
|
|
|
* ``src/QEQ``: filenames -> commands
|
|
* :doc:`fix qeq/\* <fix_qeq>`
|
|
* ``examples/qeq``
|
|
* ``examples/streitz``
|
|
|
|
----------
|
|
|
|
.. _PKG-QMMM:
|
|
|
|
QMMM package
|
|
-----------------
|
|
|
|
**Contents:**
|
|
|
|
A :doc:`fix qmmm <fix_qmmm>` command which allows LAMMPS to be used as
|
|
the MM code in a QM/MM simulation. This is currently only available
|
|
in combination with the `Quantum ESPRESSO <espresso_>`_ package.
|
|
|
|
.. _espresso: https://www.quantum-espresso.org
|
|
|
|
To use this package you must have Quantum ESPRESSO (QE) available on
|
|
your system and include its coupling library in the compilation and
|
|
then compile LAMMPS as a library. For QM/MM calculations you then
|
|
build a custom binary with MPI support, that sets up 3 partitions with
|
|
MPI sub-communicators (for inter- and intra-partition communication)
|
|
and then calls the corresponding library interfaces on each partition
|
|
(2x LAMMPS and 1x QE).
|
|
|
|
The current implementation supports an ONIOM style mechanical coupling
|
|
and a multi-pole based electrostatic coupling to the Quantum ESPRESSO
|
|
plane wave DFT package. The QM/MM interface has been written in a
|
|
manner that coupling to other QM codes should be possible without
|
|
changes to LAMMPS itself.
|
|
|
|
**Authors:** Axel Kohlmeyer (Temple U). Mariella Ippolito and Carlo Cavazzoni (CINECA, Italy)
|
|
|
|
**Install:**
|
|
|
|
This package has :ref:`specific installation instructions <qmmm>`
|
|
on the :doc:`Build extras <Build_extras>` page.
|
|
|
|
**Supporting info:**
|
|
|
|
* ``src/QMMM``: filenames -> commands
|
|
* ``src/QMMM/README``
|
|
* ``lib/qmmm/README``
|
|
* :doc:`fix phonon <fix_phonon>`
|
|
* ``lib/qmmm/example-ec/README``
|
|
* ``lib/qmmm/example-mc/README``
|
|
|
|
----------
|
|
|
|
.. _PKG-QTB:
|
|
|
|
QTB package
|
|
----------------
|
|
|
|
**Contents:**
|
|
|
|
Two fixes which provide a self-consistent quantum treatment of
|
|
vibrational modes in a classical molecular dynamics simulation. By
|
|
coupling the MD simulation to a colored thermostat, it introduces zero
|
|
point energy into the system, altering the energy power spectrum and
|
|
the heat capacity to account for their quantum nature. This is useful
|
|
when modeling systems at temperatures lower than their classical
|
|
limits or when temperatures ramp across the classical limits in a
|
|
simulation.
|
|
|
|
**Author:** Yuan Shen (Stanford U).
|
|
|
|
**Supporting info:**
|
|
|
|
* ``src/QTB``: filenames -> commands
|
|
* ``src/QTB/README``
|
|
* :doc:`fix qtb <fix_qtb>`
|
|
* :doc:`fix qbmsst <fix_qbmsst>`
|
|
* ``examples/PACKAGES/qtb``
|
|
|
|
----------
|
|
|
|
.. _PKG-REACTION:
|
|
|
|
REACTION package
|
|
---------------------
|
|
|
|
**Contents:**
|
|
|
|
This package implements the REACTER protocol, which allows for complex
|
|
bond topology changes (reactions) during a running MD simulation when
|
|
using classical force fields. Topology changes are defined in pre- and
|
|
post-reaction molecule templates and can include creation and deletion
|
|
of bonds, angles, dihedrals, impropers, atom types, bond types, angle
|
|
types, dihedral types, improper types, and/or atomic charges. Other
|
|
options currently available include reaction constraints (e.g., angle
|
|
and Arrhenius constraints), deletion of reaction byproducts or other
|
|
small molecules, creation of new atoms or molecules bonded to existing
|
|
atoms, and using LAMMPS variables for input parameters.
|
|
|
|
**Author:** Jacob R. Gissinger (NASA Langley Research Center).
|
|
|
|
**Supporting info:**
|
|
|
|
* ``src/REACTION``: filenames -> commands
|
|
* ``src/REACTION/README``
|
|
* :doc:`fix bond/react <fix_bond_react>`
|
|
* ``examples/PACKAGES/reaction``
|
|
* `2017 LAMMPS Workshop <https://www.lammps.org/workshops/Aug17/pdf/gissinger.pdf>`_
|
|
* `2019 LAMMPS Workshop <https://www.lammps.org/workshops/Aug19/talk_gissinger.pdf>`_
|
|
* `2021 LAMMPS Workshop <https://www.lammps.org/workshops/Aug21/talk/jacob-gissinger/>`_
|
|
* `REACTER website (reacter.org) <https://www.reacter.org/>`_
|
|
|
|
----------
|
|
|
|
.. _PKG-REAXFF:
|
|
|
|
REAXFF package
|
|
------------------
|
|
|
|
**Contents:**
|
|
|
|
A pair style which implements the ReaxFF potential in C/C++. ReaxFF
|
|
is a universal reactive force field. See the ``src/REAXFF/README`` file
|
|
for more info on differences between the two packages. Also two fixes
|
|
for monitoring molecules as bonds are created and destroyed.
|
|
|
|
**Author:** Hasan Metin Aktulga (MSU) while at Purdue University.
|
|
|
|
**Supporting info:**
|
|
|
|
* ``src/REAXFF``: filenames -> commands
|
|
* ``src/REAXFF/README``
|
|
* :doc:`pair_style reaxff <pair_reaxff>`
|
|
* :doc:`fix reaxff/bonds <fix_reaxff_bonds>`
|
|
* :doc:`fix reaxff/species <fix_reaxff_species>`
|
|
* ``examples/reaxff``
|
|
|
|
----------
|
|
|
|
.. _PKG-REPLICA:
|
|
|
|
REPLICA package
|
|
---------------
|
|
|
|
**Contents:**
|
|
|
|
A collection of multi-replica methods which can be used when running
|
|
multiple LAMMPS simulations (replicas). See the :doc:`Howto replica <Howto_replica>` page for an overview of how to run
|
|
multi-replica simulations in LAMMPS. Methods in the package include
|
|
nudged elastic band (NEB), parallel replica dynamics (PRD),
|
|
temperature accelerated dynamics (TAD), parallel tempering, and a
|
|
verlet/split algorithm for performing long-range Coulombics on one set
|
|
of processors, and the remainder of the force field calculation on
|
|
another set.
|
|
|
|
**Supporting info:**
|
|
|
|
* ``src/REPLICA``: filenames -> commands
|
|
* :doc:`Howto replica <Howto_replica>`
|
|
* :doc:`neb <neb>`
|
|
* :doc:`prd <prd>`
|
|
* :doc:`tad <tad>`
|
|
* :doc:`temper <temper>`,
|
|
* :doc:`temper/npt <temper_npt>`,
|
|
* :doc:`temper/grem <temper_grem>`,
|
|
* :doc:`run_style verlet/split <run_style>`
|
|
* ``examples/neb``
|
|
* ``examples/prd``
|
|
* ``examples/tad``
|
|
* ``examples/PACKAGES/grem``
|
|
|
|
----------
|
|
|
|
.. _PKG-RHEO:
|
|
|
|
RHEO package
|
|
------------
|
|
|
|
**Contents:**
|
|
|
|
Pair styles, bond styles, fixes, and computes for reproducing
|
|
hydrodynamics and elastic objects. See the :doc:`Howto rheo
|
|
<Howto_rheo>` page for an overview.
|
|
|
|
**Install:**
|
|
|
|
This package has :ref:`specific installation instructions <rheo>` on the :doc:`Build extras <Build_extras>` page.
|
|
|
|
**Authors:** Joel T. Clemmer (Sandia National Labs),
|
|
Thomas C. O'Connor (Carnegie Mellon University)
|
|
|
|
.. versionadded:: 29Aug2024
|
|
|
|
**Supporting info:**
|
|
|
|
* ``src/RHEO`` filenames -> commands
|
|
* :doc:`Howto_rheo <Howto_rheo>`
|
|
* :doc:`atom_style rheo <atom_style>`
|
|
* :doc:`atom_style rheo/thermal <atom_style>`
|
|
* :doc:`bond_style rheo/shell <bond_rheo_shell>`
|
|
* :doc:`compute rheo/property/atom <compute_rheo_property_atom>`
|
|
* :doc:`fix rheo <fix_rheo>`
|
|
* :doc:`fix rheo/oxidation <fix_rheo_oxidation>`
|
|
* :doc:`fix rheo/pressure <fix_rheo_pressure>`
|
|
* :doc:`fix rheo/thermal <fix_rheo_thermal>`
|
|
* :doc:`fix rheo/viscosity <fix_rheo_viscosity>`
|
|
* :doc:`pair_style rheo <pair_rheo>`
|
|
* :doc:`pair_style rheo/solid <pair_rheo_solid>`
|
|
* https://www.lammps.org/movies.html#rheopackage
|
|
* ``examples/rheo``
|
|
|
|
----------
|
|
|
|
.. _PKG-RIGID:
|
|
|
|
RIGID package
|
|
-------------
|
|
|
|
**Contents:**
|
|
|
|
Fixes which enforce rigid constraints on collections of atoms or
|
|
particles. This includes SHAKE and RATTLE, as well as various
|
|
rigid-body integrators for a few large bodies or many small bodies.
|
|
Also several computes which calculate properties of rigid bodies.
|
|
|
|
**Supporting info:**
|
|
|
|
* ``src/RIGID``: filenames -> commands
|
|
* :doc:`compute erotate/rigid <compute_erotate_rigid>`
|
|
* :doc:`fix shake <fix_shake>`
|
|
* :doc:`fix rattle <fix_shake>`
|
|
* :doc:`fix rigid/\* <fix_rigid>`
|
|
* ``examples/ASPHERE``
|
|
* ``examples/rigid``
|
|
* bench/in.rhodo
|
|
* https://www.lammps.org/movies.html#box
|
|
* https://www.lammps.org/movies.html#star
|
|
|
|
----------
|
|
|
|
.. _PKG-SCAFACOS:
|
|
|
|
SCAFACOS package
|
|
---------------------
|
|
|
|
**Contents:**
|
|
|
|
A KSpace style which wraps the `ScaFaCoS Coulomb solver library <http://www.scafacos.de>`_ to compute long-range Coulombic
|
|
interactions.
|
|
|
|
To use this package you must have the ScaFaCoS library available on
|
|
your system.
|
|
|
|
**Author:** Rene Halver (JSC) wrote the scafacos LAMMPS command.
|
|
|
|
ScaFaCoS itself was developed by a consortium of German research
|
|
facilities with a BMBF (German Ministry of Science and Education)
|
|
funded project in 2009-2012. Participants of the consortium were the
|
|
Universities of Bonn, Chemnitz, Stuttgart, and Wuppertal as well as
|
|
the Forschungszentrum Juelich.
|
|
|
|
**Install:**
|
|
|
|
This package has :ref:`specific installation instructions <scafacos>` on the :doc:`Build extras <Build_extras>` page.
|
|
The SCAFACOS package requires that LAMMPS is build in :ref:`MPI parallel mode <serial>`.
|
|
|
|
**Supporting info:**
|
|
|
|
* ``src/SCAFACOS``: filenames -> commands
|
|
* ``src/SCAFACOS/README``
|
|
* :doc:`kspace_style scafacos <kspace_style>`
|
|
* :doc:`kspace_modify <kspace_modify>`
|
|
* ``examples/PACKAGES/scafacos``
|
|
|
|
----------
|
|
|
|
.. _PKG-SHOCK:
|
|
|
|
SHOCK package
|
|
-------------
|
|
|
|
**Contents:**
|
|
|
|
Fixes for running impact simulations where a shock-wave passes through
|
|
a material.
|
|
|
|
**Supporting info:**
|
|
|
|
* ``src/SHOCK``: filenames -> commands
|
|
* :doc:`fix append/atoms <fix_append_atoms>`
|
|
* :doc:`fix msst <fix_msst>`
|
|
* :doc:`fix nphug <fix_nphug>`
|
|
* :doc:`fix wall/piston <fix_wall_piston>`
|
|
* ``examples/hugoniostat``
|
|
* ``examples/msst``
|
|
|
|
----------
|
|
|
|
.. _PKG-SMTBQ:
|
|
|
|
SMTBQ package
|
|
------------------
|
|
|
|
**Contents:**
|
|
|
|
Pair styles which implement Second Moment Tight Binding models.
|
|
One with QEq charge equilibration (SMTBQ) for the description of
|
|
ionocovalent bonds in oxides, and two more as plain SMATB models.
|
|
|
|
**Authors:** SMTBQ: Nicolas Salles, Emile Maras, Olivier Politano, and Robert
|
|
Tetot (LAAS-CNRS, France);
|
|
SMATB: Daniele Rapetti (Politecnico di Torino)
|
|
|
|
**Supporting info:**
|
|
|
|
* ``src/SMTBQ``: filenames -> commands
|
|
* ``src/SMTBQ/README``
|
|
* :doc:`pair_style smtbq <pair_smtbq>`
|
|
* :doc:`pair_style smatb <pair_smatb>`, :doc:`pair_style smatb/single <pair_smatb>`
|
|
* ``examples/PACKAGES/smtbq``
|
|
|
|
----------
|
|
|
|
.. _PKG-SPH:
|
|
|
|
SPH package
|
|
----------------
|
|
|
|
**Contents:**
|
|
|
|
An atom style, fixes, computes, and several pair styles which
|
|
implements smoothed particle hydrodynamics (SPH) for liquids. See the
|
|
related :ref:`MACHDYN package <PKG-MACHDYN>` package for smooth Mach dynamics
|
|
(SMD) for solids.
|
|
|
|
This package contains ideal gas, Lennard-Jones equation of states, Tait,
|
|
and full support for complete (i.e. internal-energy dependent) equations
|
|
of state. It allows for plain or Monaghans XSPH integration of the
|
|
equations of motion. It has options for density continuity or density
|
|
summation to propagate the density field. It has :doc:`set <set>`
|
|
command options to set the internal energy and density of particles from
|
|
the input script and allows the same quantities to be output with
|
|
thermodynamic output or to dump files via the :doc:`compute
|
|
property/atom <compute_property_atom>` command.
|
|
|
|
**Author:** Georg Ganzenmuller (Fraunhofer-Institute for High-Speed
|
|
Dynamics, Ernst Mach Institute, Germany).
|
|
|
|
**Supporting info:**
|
|
|
|
* ``src/SPH``: filenames -> commands
|
|
* ``src/SPH/README``
|
|
* `doc/PDF/SPH_LAMMPS_userguide.pdf <PDF/SPH_LAMMPS_userguide.pdf>`_
|
|
* ``examples/PACKAGES/sph``
|
|
* https://www.lammps.org/movies.html#sph
|
|
|
|
.. note::
|
|
|
|
Please note that the SPH PDF guide file has not been updated for
|
|
many years and thus does not reflect the current *syntax* of the
|
|
SPH package commands. For that please refer to the LAMMPS manual.
|
|
|
|
.. note::
|
|
|
|
Please also note, that the :ref:`RHEO package <PKG-RHEO>` offers
|
|
similar functionality in a more modern and flexible implementation.
|
|
|
|
----------
|
|
|
|
.. _PKG-SPIN:
|
|
|
|
SPIN package
|
|
------------
|
|
|
|
**Contents:**
|
|
|
|
Model atomic magnetic spins classically, coupled to atoms moving in
|
|
the usual manner via MD. Various pair, fix, and compute styles.
|
|
|
|
**Author:** Julien Tranchida (Sandia).
|
|
|
|
**Supporting info:**
|
|
|
|
* ``src/SPIN``: filenames -> commands
|
|
* :doc:`Howto spins <Howto_spins>`
|
|
* :doc:`pair_style spin/dipole/cut <pair_spin_dipole>`
|
|
* :doc:`pair_style spin/dipole/long <pair_spin_dipole>`
|
|
* :doc:`pair_style spin/dmi <pair_spin_dmi>`
|
|
* :doc:`pair_style spin/exchange <pair_spin_exchange>`
|
|
* :doc:`pair_style spin/exchange/biquadratic <pair_spin_exchange>`
|
|
* :doc:`pair_style spin/magelec <pair_spin_magelec>`
|
|
* :doc:`pair_style spin/neel <pair_spin_neel>`
|
|
* :doc:`fix nve/spin <fix_nve_spin>`
|
|
* :doc:`fix langevin/spin <fix_langevin_spin>`
|
|
* :doc:`fix precession/spin <fix_precession_spin>`
|
|
* :doc:`compute spin <compute_spin>`
|
|
* :doc:`neb/spin <neb_spin>`
|
|
* ``examples/SPIN``
|
|
|
|
----------
|
|
|
|
.. _PKG-SRD:
|
|
|
|
SRD package
|
|
-----------
|
|
|
|
**Contents:**
|
|
|
|
A pair of fixes which implement the Stochastic Rotation Dynamics (SRD)
|
|
method for coarse-graining of a solvent, typically around large
|
|
colloidal particles.
|
|
|
|
**Supporting info:**
|
|
|
|
* ``src/SRD``: filenames -> commands
|
|
* :doc:`fix srd <fix_srd>`
|
|
* :doc:`fix wall/srd <fix_wall_srd>`
|
|
* ``examples/srd``
|
|
* ``examples/ASPHERE``
|
|
* https://www.lammps.org/movies.html#tri
|
|
* https://www.lammps.org/movies.html#line
|
|
* https://www.lammps.org/movies.html#poly
|
|
|
|
----------
|
|
|
|
.. _PKG-TALLY:
|
|
|
|
TALLY package
|
|
------------------
|
|
|
|
**Contents:**
|
|
|
|
Several compute styles that can be called when pairwise interactions
|
|
are calculated to tally information (forces, heat flux, energy,
|
|
stress, etc) about individual interactions.
|
|
|
|
**Author:** Axel Kohlmeyer (Temple U).
|
|
|
|
**Supporting info:**
|
|
|
|
* ``src/TALLY``: filenames -> commands
|
|
* ``src/TALLY/README``
|
|
* :doc:`compute \*/tally <compute_tally>`
|
|
* ``examples/PACKAGES/tally``
|
|
|
|
----------
|
|
|
|
.. _PKG-UEF:
|
|
|
|
UEF package
|
|
----------------
|
|
|
|
**Contents:**
|
|
|
|
A fix style for the integration of the equations of motion under
|
|
extensional flow with proper boundary conditions, as well as several
|
|
supporting compute styles and an output option.
|
|
|
|
**Author:** David Nicholson (MIT).
|
|
|
|
**Supporting info:**
|
|
|
|
* ``src/UEF``: filenames -> commands
|
|
* ``src/UEF/README``
|
|
* :doc:`fix nvt/uef <fix_nh_uef>`
|
|
* :doc:`fix npt/uef <fix_nh_uef>`
|
|
* :doc:`compute pressure/uef <compute_pressure_uef>`
|
|
* :doc:`compute temp/uef <compute_temp_uef>`
|
|
* :doc:`dump cfg/uef <dump_cfg_uef>`
|
|
* ``examples/uef``
|
|
|
|
----------
|
|
|
|
.. _PKG-VORONOI:
|
|
|
|
VORONOI package
|
|
---------------
|
|
|
|
**Contents:**
|
|
|
|
A compute command which calculates the Voronoi tesselation of a
|
|
collection of atoms by wrapping the `Voro++ library
|
|
<https://math.lbl.gov/voro++/>`_. This can be used to calculate the
|
|
local volume or each atoms or its near neighbors.
|
|
|
|
To use this package you must have the Voro++ library available on your
|
|
system.
|
|
|
|
**Author:** Daniel Schwen (INL) while at LANL. The open-source Voro++
|
|
library was written by Chris Rycroft (Harvard U) while at UC Berkeley
|
|
and LBNL.
|
|
|
|
**Install:**
|
|
|
|
This package has :ref:`specific installation instructions <voronoi>` on the :doc:`Build extras <Build_extras>` page.
|
|
|
|
**Supporting info:**
|
|
|
|
* ``src/VORONOI``: filenames -> commands
|
|
* ``src/VORONOI/README``
|
|
* ``lib/voronoi/README``
|
|
* :doc:`compute voronoi/atom <compute_voronoi_atom>`
|
|
* ``examples/voronoi``
|
|
|
|
----------
|
|
|
|
.. _PKG-VTK:
|
|
|
|
VTK package
|
|
----------------
|
|
|
|
**Contents:**
|
|
|
|
A :doc:`dump vtk <dump_vtk>` command which outputs snapshot info in the
|
|
`VTK format <vtk_>`_, enabling visualization by `Paraview <paraview_>`_ or
|
|
other visualization packages.
|
|
|
|
.. _vtk: https://www.vtk.org
|
|
|
|
.. _paraview: https://www.paraview.org
|
|
|
|
To use this package you must have VTK library available on your
|
|
system.
|
|
|
|
**Authors:** Richard Berger (JKU) and Daniel Queteschiner (DCS Computing).
|
|
|
|
**Install:**
|
|
|
|
This package has :ref:`specific installation instructions <vtk>` on the :doc:`Build extras <Build_extras>` page.
|
|
|
|
**Supporting info:**
|
|
|
|
* ``src/VTK``: filenames -> commands
|
|
* ``src/VTK/README``
|
|
* ``lib/vtk/README``
|
|
* :doc:`dump vtk <dump_vtk>`
|
|
|
|
----------
|
|
|
|
.. _PKG-YAFF:
|
|
|
|
YAFF package
|
|
-----------------
|
|
|
|
**Contents:**
|
|
|
|
Some potentials that are also implemented in the Yet Another Force Field (`YAFF <yaff_>`_) code.
|
|
The expressions and their use are discussed in the following papers
|
|
|
|
* Vanduyfhuys et al., J. Comput. Chem., 36 (13), 1015-1027 (2015) `link <vanduyfhuys2015_>`_
|
|
* Vanduyfhuys et al., J. Comput. Chem., 39 (16), 999-1011 (2018) `link <vanduyfhuys2018_>`_
|
|
|
|
which discuss the `QuickFF <quickff_>`_ methodology.
|
|
|
|
.. _vanduyfhuys2015: https://doi.org/10.1002/jcc.23877
|
|
.. _vanduyfhuys2018: https://doi.org/10.1002/jcc.25173
|
|
.. _quickff: https://molmod.github.io/QuickFF
|
|
.. _yaff: https://github.com/molmod/yaff
|
|
|
|
**Author:** Steven Vandenbrande.
|
|
|
|
.. versionadded:: 1Feb2019
|
|
|
|
**Supporting info:**
|
|
|
|
* ``src/YAFF/README``
|
|
* :doc:`angle_style cross <angle_cross>`
|
|
* :doc:`angle_style mm3 <angle_mm3>`
|
|
* :doc:`bond_style mm3 <bond_mm3>`
|
|
* :doc:`improper_style distharm <improper_distharm>`
|
|
* :doc:`improper_style sqdistharm <improper_sqdistharm>`
|
|
* :doc:`pair_style mm3/switch3/coulgauss/long <pair_lj_switch3_coulgauss_long>`
|
|
* :doc:`pair_style lj/switch3/coulgauss/long <pair_lj_switch3_coulgauss_long>`
|
|
* ``examples/PACKAGES/yaff``
|