129 lines
26 KiB
ReStructuredText
129 lines
26 KiB
ReStructuredText
User packages
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=============
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This is a list of user packages in LAMMPS. The link for each package
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name gives more details.
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User packages have been contributed by users, and begin with the
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"user" prefix. If a contribution is a single command (single file),
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it is typically in the USER-MISC package. User packages don't
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necessarily meet the requirements of the :doc:`standard packages <Packages_standard>`. This means the developers will try
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to keep things working and usually can answer technical questions
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about compiling the package. If you have problems using a specific
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feature provided in a user package, you may need to contact the
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contributor directly to get help. Information on how to submit
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additions you make to LAMMPS as single files or as a standard or user
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package is explained on the :doc:`Modify contribute <Modify_contribute>`
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doc page.
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The "Example" column is a sub-directory in the examples directory of
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the distribution which has an input script that uses the package.
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E.g. "peptide" refers to the examples/peptide directory; USER/atc
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refers to the examples/USER/atc directory. The "Library" column
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indicates whether an extra library is needed to build and use the
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package:
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* no = no library
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* sys = system library: you likely have it on your machine
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* int = internal library: provided with LAMMPS, but you may need to build it
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* ext = external library: you will need to download and install it on your machine
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+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
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| Package | Description | Doc page | Example | Library |
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+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
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| :ref:`USER-ADIOS <PKG-USER-ADIOS>` | dump output via ADIOS | :doc:`dump adios <dump_adios>` | USER/adios | ext |
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+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
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| :ref:`USER-ATC <PKG-USER-ATC>` | Atom-to-Continuum coupling | :doc:`fix atc <fix_atc>` | USER/atc | int |
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+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
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| :ref:`USER-AWPMD <PKG-USER-AWPMD>` | wave packet MD | :doc:`pair_style awpmd/cut <pair_awpmd>` | USER/awpmd | int |
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+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
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| :ref:`USER-BOCS <PKG-USER-BOCS>` | BOCS bottom up coarse graining | :doc:`fix bocs <fix_bocs>` | USER/bocs | no |
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+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
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| :ref:`USER-BROWNIAN <PKG-USER-BROWNIAN>` | Brownian dynamics and self-propelled particles | :doc:`fix brownian <fix_brownian>`, :doc:`fix propel/self <fix_propel_self>` | USER/brownian | no |
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+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
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| :ref:`USER-CGDNA <PKG-USER-CGDNA>` | coarse-grained DNA force fields | src/USER-CGDNA/README | USER/cgdna | no |
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+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
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| :ref:`USER-CGSDK <PKG-USER-CGSDK>` | SDK coarse-graining model | :doc:`pair_style lj/sdk <pair_sdk>` | USER/cgsdk | no |
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+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
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| :ref:`USER-COLVARS <PKG-USER-COLVARS>` | collective variables library | :doc:`fix colvars <fix_colvars>` | USER/colvars | int |
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+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
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| :ref:`USER-DIFFRACTION <PKG-USER-DIFFRACTION>` | virtual x-ray and electron diffraction | :doc:`compute xrd <compute_xrd>` | USER/diffraction | no |
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+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
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| :ref:`USER-DPD <PKG-USER-DPD>` | reactive dissipative particle dynamics | src/USER-DPD/README | USER/dpd | no |
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+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
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| :ref:`USER-DRUDE <PKG-USER-DRUDE>` | Drude oscillators | :doc:`Howto drude <Howto_drude>` | USER/drude | no |
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+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
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| :ref:`USER-EFF <PKG-USER-EFF>` | electron force field | :doc:`pair_style eff/cut <pair_eff>` | USER/eff | no |
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+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
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| :ref:`USER-FEP <PKG-USER-FEP>` | free energy perturbation | :doc:`compute fep <compute_fep>` | USER/fep | no |
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+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
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| :ref:`USER-H5MD <PKG-USER-H5MD>` | dump output via HDF5 | :doc:`dump h5md <dump_h5md>` | n/a | ext |
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+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
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| :ref:`USER-HDNNP <PKG-USER-HDNNP>` | High-dimensional neural network potentials | :doc:`pair_style hdnnp <pair_hdnnp>` | USER/hdnnp | ext |
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+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
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| :ref:`USER-INTEL <PKG-USER-INTEL>` | optimized Intel CPU and KNL styles | :doc:`Speed intel <Speed_intel>` | `Benchmarks <https://www.lammps.org/bench.html>`_ | no |
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+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
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| :ref:`USER-LB <PKG-USER-LB>` | Lattice Boltzmann fluid | :doc:`fix lb/fluid <fix_lb_fluid>` | USER/lb | no |
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+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
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| :ref:`USER-MANIFOLD <PKG-USER-MANIFOLD>` | motion on 2d surfaces | :doc:`fix manifoldforce <fix_manifoldforce>` | USER/manifold | no |
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+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
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| :ref:`USER-MDI <PKG-USER-MDI>` | client-server coupling | :doc:`MDI Howto <Howto_mdi>` | USER/mdi | ext |
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+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
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| :ref:`USER-MEAMC <PKG-USER-MEAMC>` | modified EAM potential (C++) | :doc:`pair_style meam/c <pair_meamc>` | meamc | no |
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+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
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| :ref:`USER-MESODPD <PKG-USER-MESODPD>` | mesoscale DPD models | :doc:`pair_style edpd <pair_mesodpd>` | USER/mesodpd | no |
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+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
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| :ref:`USER-MESONT <PKG-USER-MESONT>` | mesoscopic tubular potential model for nanotubes | pair style :doc:`mesont/tpm <pair_mesont_tpm>`, :doc:`mesocnt <pair_mesocnt>` | USER/mesont | int |
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+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
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| :ref:`USER-MGPT <PKG-USER-MGPT>` | fast MGPT multi-ion potentials | :doc:`pair_style mgpt <pair_mgpt>` | USER/mgpt | no |
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+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
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| :ref:`USER-MISC <PKG-USER-MISC>` | single-file contributions | USER-MISC/README | USER/misc | no |
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+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
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| :ref:`USER-MOFFF <PKG-USER-MOFFF>` | styles for `MOF-FF <MOFplus_>`_ force field | :doc:`pair_style buck6d/coul/gauss <pair_buck6d_coul_gauss>` | USER/mofff | no |
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+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
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| :ref:`USER-MOLFILE <PKG-USER-MOLFILE>` | `VMD <https://www.ks.uiuc.edu/Research/vmd/>`_ molfile plug-ins | :doc:`dump molfile <dump_molfile>` | n/a | ext |
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+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
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| :ref:`USER-NETCDF <PKG-USER-NETCDF>` | dump output via NetCDF | :doc:`dump netcdf <dump_netcdf>` | n/a | ext |
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+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
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| :ref:`USER-OMP <PKG-USER-OMP>` | OpenMP-enabled styles | :doc:`Speed omp <Speed_omp>` | `Benchmarks <https://www.lammps.org/bench.html>`_ | no |
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+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
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| :ref:`USER-PACE <PKG-USER-PACE>` | Fast implementation of Atomic Cluster Expansion (ACE) potential | :doc:`pair pace <pair_pace>` | USER/pace | ext |
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+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
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| :ref:`USER-PHONON <PKG-USER-PHONON>` | phonon dynamical matrix | :doc:`fix phonon <fix_phonon>` | USER/phonon | no |
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+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
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| :ref:`USER-PLUMED <PKG-USER-PLUMED>` | :ref:`PLUMED <PLUMED>` free energy library | :doc:`fix plumed <fix_plumed>` | USER/plumed | ext |
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+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
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| :ref:`USER-PTM <PKG-USER-PTM>` | Polyhedral Template Matching | :doc:`compute ptm/atom <compute_ptm_atom>` | n/a | no |
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+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
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| :ref:`USER-QMMM <PKG-USER-QMMM>` | QM/MM coupling | :doc:`fix qmmm <fix_qmmm>` | USER/qmmm | ext |
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+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
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| :ref:`USER-QTB <PKG-USER-QTB>` | quantum nuclear effects | :doc:`fix qtb <fix_qtb>` :doc:`fix qbmsst <fix_qbmsst>` | qtb | no |
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+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
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| :ref:`USER-QUIP <PKG-USER-QUIP>` | QUIP/libatoms interface | :doc:`pair_style quip <pair_quip>` | USER/quip | ext |
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+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
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| :ref:`USER-REACTION <PKG-USER-REACTION>` | chemical reactions in classical MD | :doc:`fix bond/react <fix_bond_react>` | USER/reaction | no |
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+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
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| :ref:`USER-REAXC <PKG-USER-REAXC>` | ReaxFF potential (C/C++) | :doc:`pair_style reaxc <pair_reaxc>` | reax | no |
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+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
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| :ref:`USER-SCAFACOS <PKG-USER-SCAFACOS>` | wrapper on ScaFaCoS solver | :doc:`kspace_style scafacos <kspace_style>` | USER/scafacos | ext |
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+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
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| :ref:`USER-SDPD <PKG-USER-SDPD>` | smoothed dissipative particle dynamics | :doc:`pair_style sdpd/taitwater/isothermal <pair_sdpd_taitwater_isothermal>` | USER/sdpd | no |
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+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
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| :ref:`USER-SMD <PKG-USER-SMD>` | smoothed Mach dynamics | `SMD User Guide <PDF/SMD_LAMMPS_userguide.pdf>`_ | USER/smd | ext |
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+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
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| :ref:`USER-SMTBQ <PKG-USER-SMTBQ>` | second moment tight binding QEq potential | :doc:`pair_style smtbq <pair_smtbq>` | USER/smtbq | no |
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+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
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| :ref:`USER-SPH <PKG-USER-SPH>` | smoothed particle hydrodynamics | `SPH User Guide <PDF/SPH_LAMMPS_userguide.pdf>`_ | USER/sph | no |
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+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
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| :ref:`USER-TALLY <PKG-USER-TALLY>` | pairwise tally computes | :doc:`compute XXX/tally <compute_tally>` | USER/tally | no |
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+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
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| :ref:`USER-UEF <PKG-USER-UEF>` | extensional flow | :doc:`fix nvt/uef <fix_nh_uef>` | USER/uef | no |
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+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
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| :ref:`USER-VTK <PKG-USER-VTK>` | dump output via VTK | :doc:`compute vtk <dump_vtk>` | n/a | ext |
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+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
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| :ref:`USER-YAFF <PKG-USER-YAFF>` | additional styles implemented in YAFF | :doc:`angle_style cross <angle_cross>` | USER/yaff | no |
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+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
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.. _MOFplus: https://www.mofplus.org/content/show/MOF-FF
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.. _PLUMED: https://www.plumed.org
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