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Packages
========
This section gives a quick overview of the add-on packages that extend
LAMMPS functionality.
| 4.1 :ref:`Standard packages <pkg_1>`
| 4.2 :ref:`User packages <pkg_2>`
|
LAMMPS includes many optional packages, which are groups of files that
enable a specific set of features. For example, force fields for
molecular systems or granular systems are in packages. You can see
the list of all packages by typing "make package" from within the src
directory of the LAMMPS distribution.
See :ref:`Section_start 3 <start_3>` of the manual for
details on how to include/exclude specific packages as part of the
LAMMPS build process, and for more details about the differences
between standard packages and user packages.
Unless otherwise noted below, every package is independent of all the
others. I.e. any package can be included or excluded in a LAMMPS
build, independent of all other packages. However, note that some
packages include commands derived from commands in other packages. If
the other package is not installed, the derived command from the new
package will also not be installed when you include the new one.
E.g. the pair lj/cut/coul/long/omp command from the USER-OMP package
will not be installed as part of the USER-OMP package if the KSPACE
package is not also installed, since it contains the pair
lj/cut/coul/long command. If you later install the KSPACE pacakge and
the USER-OMP package is already installed, both the pair
lj/cut/coul/long and lj/cut/coul/long/omp commands will be installed.
The two tables below list currently available packages in LAMMPS, with
a one-line descriptions of each. The sections below give a few more
details, including instructions for building LAMMPS with the package,
either via the make command or the Make.py tool described in :ref:`Section 2.4 <start_4>`.
.. _pkg_1:
Standard packages
-----------------------------
The current list of standard packages is as follows.
+-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
| Package | Description | Author(s) | Doc page | Example | Library |
+-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
| ASPHERE | aspherical particles | - | :ref:`Section_howto 6.14 <howto_14>` | ellipse | - |
+-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
| BODY | body-style particles | - | :doc:`body <body>` | body | - |
+-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
| CLASS2 | class 2 force fields | - | :doc:`pair_style lj/class2 <pair_class2>` | - | - |
+-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
| COLLOID | colloidal particles | - | :doc:`atom_style colloid <atom_style>` | colloid | - |
+-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
| COMPRESS | I/O compression | Axel Kohlmeyer (Temple U) | :doc:`dump */gz <dump>` | - | - |
+-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
| CORESHELL | adiabatic core/shell model | Hendrik Heenen (Technical U of Munich) | :ref:`Section_howto 6.25 <howto_25>` | coreshell | - |
+-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
| DIPOLE | point dipole particles | - | :doc:`pair_style dipole/cut <pair_dipole>` | dipole | - |
+-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
| FLD | Fast Lubrication Dynamics | Kumar & Bybee & Higdon (1) | :doc:`pair_style lubricateU <pair_lubricateU>` | - | - |
+-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
| GPU | GPU-enabled styles | Mike Brown (ORNL) | :doc:`Section accelerate <accelerate_gpu>` | gpu | lib/gpu |
+-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
| GRANULAR | granular systems | - | :ref:`Section_howto 6.6 <howto_6>` | pour | - |
+-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
| KIM | openKIM potentials | Smirichinski & Elliot & Tadmor (3) | :doc:`pair_style kim <pair_kim>` | kim | KIM |
+-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
| KOKKOS | Kokkos-enabled styles | Trott & Edwards (4) | :doc:`Section_accelerate <accelerate_kokkos>` | kokkos | lib/kokkos |
+-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
| KSPACE | long-range Coulombic solvers | - | :doc:`kspace_style <kspace_style>` | peptide | - |
+-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
| MANYBODY | many-body potentials | - | :doc:`pair_style tersoff <pair_tersoff>` | shear | - |
+-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
| MEAM | modified EAM potential | Greg Wagner (Sandia) | :doc:`pair_style meam <pair_meam>` | meam | lib/meam |
+-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
| MC | Monte Carlo options | - | :doc:`fix gcmc <fix_gcmc>` | - | - |
+-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
| MOLECULE | molecular system force fields | - | :ref:`Section_howto 6.3 <howto_3>` | peptide | - |
+-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
| OPT | optimized pair styles | Fischer & Richie & Natoli (2) | :doc:`Section accelerate <accelerate_opt>` | - | - |
+-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
| PERI | Peridynamics models | Mike Parks (Sandia) | :doc:`pair_style peri <pair_peri>` | peri | - |
+-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
| POEMS | coupled rigid body motion | Rudra Mukherjee (JPL) | :doc:`fix poems <fix_poems>` | rigid | lib/poems |
+-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
| PYTHON | embed Python code in an input script | - | :doc:`python <python>` | python | lib/python |
+-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
| REAX | ReaxFF potential | Aidan Thompson (Sandia) | :doc:`pair_style reax <pair_reax>` | reax | lib/reax |
+-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
| REPLICA | multi-replica methods | - | :ref:`Section_howto 6.5 <howto_5>` | tad | - |
+-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
| RIGID | rigid bodies | - | :doc:`fix rigid <fix_rigid>` | rigid | - |
+-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
| SHOCK | shock loading methods | - | :doc:`fix msst <fix_msst>` | - | - |
+-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
| SNAP | quantum-fit potential | Aidan Thompson (Sandia) | :doc:`pair snap <pair_snap>` | snap | - |
+-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
| SRD | stochastic rotation dynamics | - | :doc:`fix srd <fix_srd>` | srd | - |
+-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
| VORONOI | Voronoi tesselations | Daniel Schwen (LANL) | :doc:`compute voronoi/atom <compute_voronoi_atom>` | - | Voro++ |
+-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
| XTC | dumps in XTC format | - | :doc:`dump <dump>` | - | - |
+-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
| | | | | | |
+-----------+--------------------------------------+----------------------------------------+----------------------------------------------------+-----------+------------+
The "Authors" column lists a name(s) if a specific person is
responible for creating and maintaining the package.
More details on
multiple authors are give below.
(1) The FLD package was created by Amit Kumar and Michael Bybee from
Jonathan Higdon's group at UIUC.
(2) The OPT package was created by James Fischer (High Performance
Technologies), David Richie, and Vincent Natoli (Stone Ridge
Technolgy).
(3) The KIM package was created by Valeriu Smirichinski, Ryan Elliott,
and Ellad Tadmor (U Minn).
(4) The KOKKOS package was created primarily by Christian Trott
(Sandia). It uses the Kokkos library which was developed by Carter
Edwards, Christian, and collaborators at Sandia.
The "Doc page" column links to either a portion of the
:doc:`Section_howto <Section_howto>` of the manual, or an input script
command implemented as part of the package.
The "Example" column is a sub-directory in the examples directory of
the distribution which has an input script that uses the package.
E.g. "peptide" refers to the examples/peptide directory.
The "Library" column lists an external library which must be built
first and which LAMMPS links to when it is built. If it is listed as
lib/package, then the code for the library is under the lib directory
of the LAMMPS distribution. See the lib/package/README file for info
on how to build the library. If it is not listed as lib/package, then
it is a third-party library not included in the LAMMPS distribution.
See the src/package/README or src/package/Makefile.lammps file for
info on where to download the library. :ref:`Section start <start_3_3>` of the manual also gives details
on how to build LAMMPS with both kinds of auxiliary libraries.
Except where explained below, all of these packages can be installed,
and LAMMPS re-built, by issuing these commands from the src dir.
.. parsed-literal::
make yes-package
make machine
or
Make.py -p package -a machine
To un-install the package and re-build LAMMPS without it:
.. parsed-literal::
make no-package
make machine
or
Make.py -p ^package -a machine
"Package" is the name of the package in lower-case letters,
e.g. asphere or rigid, and "machine" is the build target, e.g. mpi or
serial.
Build instructions for COMPRESS package
-----------------------------
Build instructions for GPU package
------------------------
Build instructions for KIM package
------------------------
Build instructions for KOKKOS package
---------------------------
Build instructions for KSPACE package
---------------------------
Build instructions for MEAM package
-------------------------
Build instructions for POEMS package
--------------------------
Build instructions for PYTHON package
---------------------------
Build instructions for REAX package
-------------------------
Build instructions for VORONOI package
----------------------------
Build instructions for XTC package
------------------------
----------
.. _pkg_2:
User packages
-------------------------
The current list of user-contributed packages is as follows:
+------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
| Package | Description | Author(s) | Doc page | Example | Pic/movie | Library |
+------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
| USER-ATC | atom-to-continuum coupling | Jones & Templeton & Zimmerman (1) | :doc:`fix atc <fix_atc>` | USER/atc | `atc <atc_>`_ | lib/atc |
+------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
| USER-AWPMD | wave-packet MD | Ilya Valuev (JIHT) | :doc:`pair_style awpmd/cut <pair_awpmd>` | USER/awpmd | - | lib/awpmd |
+------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
| USER-CG-CMM | coarse-graining model | Axel Kohlmeyer (Temple U) | :doc:`pair_style lj/sdk <pair_sdk>` | USER/cg-cmm | `cg <cg_>`_ | - |
+------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
| USER-COLVARS | collective variables | Fiorin & Henin & Kohlmeyer (2) | :doc:`fix colvars <fix_colvars>` | USER/colvars | `colvars <colvars>`_ | lib/colvars |
+------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
| USER-CUDA | NVIDIA GPU styles | Christian Trott (U Tech Ilmenau) | :doc:`Section accelerate <accelerate_cuda>` | USER/cuda | - | lib/cuda |
+------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
| USER-DIFFRACTION | virutal x-ray and electron diffraction | Shawn Coleman (ARL) | :doc:`compute xrd <compute_xrd>` | USER/diffraction | - | - |
+------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
| USER-DRUDE | Drude oscillators | Dequidt & Devemy & Padua (3) | :doc:`tutorial <tutorial_drude>` | USER/drude | - | - |
+------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
| USER-EFF | electron force field | Andres Jaramillo-Botero (Caltech) | :doc:`pair_style eff/cut <pair_eff>` | USER/eff | `eff <eff_>`_ | - |
+------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
| USER-FEP | free energy perturbation | Agilio Padua (U Blaise Pascal Clermont-Ferrand) | :doc:`compute fep <compute_fep>` | USER/fep | - | - |
+------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
| USER-H5MD | dump output via HDF5 | Pierre de Buyl (KU Leuven) | :doc:`dump h5md <dump_h5md>` | - | - | lib/h5md |
+------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
| USER-INTEL | Vectorized CPU and Intel(R) coprocessor styles | W. Michael Brown (Intel) | :doc:`Section accelerate <accelerate_intel>` | examples/intel | - | - |
+------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
| USER-LB | Lattice Boltzmann fluid | Colin Denniston (U Western Ontario) | :doc:`fix lb/fluid <fix_lb_fluid>` | USER/lb | - | - |
+------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
| USER-MGPT | fast MGPT multi-ion potentials | Tomas Oppelstrup & John Moriarty (LLNL) | :doc:`pair_style mgpt <pair_mgpt>` | USER/mgpt | - | - |
+------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
| USER-MISC | single-file contributions | USER-MISC/README | USER-MISC/README | - | - | - |
+------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
| USER-MOLFILE | `VMD <VMD_>`_ molfile plug-ins | Axel Kohlmeyer (Temple U) | :doc:`dump molfile <dump_molfile>` | - | - | VMD-MOLFILE |
+------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
| USER-OMP | OpenMP threaded styles | Axel Kohlmeyer (Temple U) | :doc:`Section accelerate <accelerate_omp>` | - | - | - |
+------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
| USER-PHONON | phonon dynamical matrix | Ling-Ti Kong (Shanghai Jiao Tong U) | :doc:`fix phonon <fix_phonon>` | USER/phonon | - | - |
+------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
| USER-QMMM | QM/MM coupling | Axel Kohlmeyer (Temple U) | :doc:`fix qmmm <fix_qmmm>` | USER/qmmm | - | lib/qmmm |
+------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
| USER-QTB | quantum nuclear effects | Yuan Shen (Stanford) | :doc:`fix qtb <fix_qtb>` :doc:`fix_qbmsst <fix_qbmsst>` | qtb | - | - |
+------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
| USER-QUIP | QUIP/libatoms interface | Albert Bartok-Partay (U Cambridge) | :doc:`pair_style quip <pair_quip>` | USER/quip | - | lib/quip |
+------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
| USER-REAXC | C version of ReaxFF | Metin Aktulga (LBNL) | :doc:`pair_style reaxc <pair_reax_c>` | reax | - | - |
+------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
| USER-SMD | smoothed Mach dynamics | Georg Ganzenmuller (EMI) | `userguide.pdf <PDF/SMD_LAMMPS_userguide.pdf>`_ | USER/smd | - | - |
+------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
| USER-SMTBQ | Second Moment Tight Binding - QEq potential | Salles & Maras & Politano & Tetot (4) | :doc:`pair_style smtbq <pair_smtbq>` | USER/smtbq | - | - |
+------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
| USER-SPH | smoothed particle hydrodynamics | Georg Ganzenmuller (EMI) | `userguide.pdf <PDF/SPH_LAMMPS_userguide.pdf>`_ | USER/sph | `sph <sph_>`_ | - |
+------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
| USER-TALLY | Pairwise tallied computes | Axel Kohlmeyer (Temple U) | :doc:`compute <...>/tally <compute_tally>` | USER/tally | - | - |
+------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
| | | | | | | |
+------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
.. _atc: http://lammps.sandia.gov/pictures.html#atc
.. _cg: http://lammps.sandia.gov/pictures.html#cg
.. _eff: http://lammps.sandia.gov/movies.html#eff
.. _sph: http://lammps.sandia.gov/movies.html#sph
.. _VMD: http://www.ks.uiuc.edu/Research/vmd
The "Authors" column lists a name(s) if a specific person is
responible for creating and maintaining the package.
(1) The ATC package was created by Reese Jones, Jeremy Templeton, and
Jon Zimmerman (Sandia).
(2) The COLVARS package was created by Axel Kohlmeyer (Temple U) using
the colvars module library written by Giacomo Fiorin (Temple U) and
Jerome Henin (LISM, Marseille, France).
(3) The DRUDE package was created by Alain Dequidt (U Blaise Pascal
Clermont-Ferrand) and co-authors Julien Devemy (CNRS) and Agilio Padua
(U Blaise Pascal).
(4) The SMTBQ package was created by Nicolas Salles, Emile Maras,
Olivier Politano, and Robert Tetot (LAAS-CNRS, France).
If the Library is not listed as lib/package, then it is a third-party
library not included in the LAMMPS distribution. See the
src/package/Makefile.lammps file for info on where to download the
library from.
The "Doc page" column links to either a portion of the
:doc:`Section_howto <Section_howto>` of the manual, or an input script
command implemented as part of the package, or to additional
documentation provided within the package.
The "Example" column is a sub-directory in the examples directory of
the distribution which has an input script that uses the package.
E.g. "peptide" refers to the examples/peptide directory. USER/cuda
refers to the examples/USER/cuda directory.
The "Library" column lists an external library which must be built
first and which LAMMPS links to when it is built. If it is listed as
lib/package, then the code for the library is under the lib directory
of the LAMMPS distribution. See the lib/package/README file for info
on how to build the library. If it is not listed as lib/package, then
it is a third-party library not included in the LAMMPS distribution.
See the src/package/Makefile.lammps file for info on where to download
the library. :ref:`Section start <start_3_3>` of the
manual also gives details on how to build LAMMPS with both kinds of
auxiliary libraries.
Except where explained below, all of these packages can be installed,
and LAMMPS re-built, by issuing these commands from the src dir.
.. parsed-literal::
make yes-user-package
make machine
or
Make.py -p package -a machine
To un-install the package and re-build LAMMPS without it:
.. parsed-literal::
make no-user-package
make machine
or
Make.py -p ^package -a machine
"Package" is the name of the package (in this case without the user
prefix) in lower-case letters, e.g. drude or phonon, and "machine" is
the build target, e.g. mpi or serial.
USER-ATC package
----------------
This package implements a "fix atc" command which can be used in a
LAMMPS input script. This fix can be employed to either do concurrent
coupling of MD with FE-based physics surrogates or on-the-fly
post-processing of atomic information to continuum fields.
See the doc page for the fix atc command to get started. At the
bottom of the doc page are many links to additional documentation
contained in the doc/USER/atc directory.
There are example scripts for using this package in examples/USER/atc.
This package uses an external library in lib/atc which must be
compiled before making LAMMPS. See the lib/atc/README file and the
LAMMPS manual for information on building LAMMPS with external
libraries.
The primary people who created this package are Reese Jones (rjones at
sandia.gov), Jeremy Templeton (jatempl at sandia.gov) and Jon
Zimmerman (jzimmer at sandia.gov) at Sandia. Contact them directly if
you have questions.
----------
USER-AWPMD package
------------------
This package contains a LAMMPS implementation of the Antisymmetrized
Wave Packet Molecular Dynamics (AWPMD) method.
See the doc page for the pair_style awpmd/cut command to get started.
There are example scripts for using this package in examples/USER/awpmd.
This package uses an external library in lib/awpmd which must be
compiled before making LAMMPS. See the lib/awpmd/README file and the
LAMMPS manual for information on building LAMMPS with external
libraries.
The person who created this package is Ilya Valuev at the JIHT in
Russia (valuev at physik.hu-berlin.de). Contact him directly if you
have questions.
----------
USER-CG-CMM package
-------------------
This package implements 3 commands which can be used in a LAMMPS input
script:
* pair_style lj/sdk
* pair_style lj/sdk/coul/long
* angle_style sdk
These styles allow coarse grained MD simulations with the
parametrization of Shinoda, DeVane, Klein, Mol Sim, 33, 27 (2007)
(SDK), with extensions to simulate ionic liquids, electrolytes, lipids
and charged amino acids.
See the doc pages for these commands for details.
There are example scripts for using this package in
examples/USER/cg-cmm.
This is the second generation implementation reducing the the clutter
of the previous version. For many systems with electrostatics, it will
be faster to use pair_style hybrid/overlay with lj/sdk and coul/long
instead of the combined lj/sdk/coul/long style. since the number of
charged atom types is usually small. For any other coulomb
interactions this is now required. To exploit this property, the use
of the kspace_style pppm/cg is recommended over regular pppm. For all
new styles, input file backward compatibility is provided. The old
implementation is still available through appending the /old
suffix. These will be discontinued and removed after the new
implementation has been fully validated.
The current version of this package should be considered beta
quality. The CG potentials work correctly for "normal" situations, but
have not been testing with all kinds of potential parameters and
simulation systems.
The person who created this package is Axel Kohlmeyer at Temple U
(akohlmey at gmail.com). Contact him directly if you have questions.
----------
USER-COLVARS package
--------------------
This package implements the "fix colvars" command which can be
used in a LAMMPS input script.
This fix allows to use "collective variables" to implement
Adaptive Biasing Force, Metadynamics, Steered MD, Umbrella
Sampling and Restraints. This code consists of two parts:
* A portable collective variable module library written and maintained
* by Giacomo Fiorin (ICMS, Temple University, Philadelphia, PA, USA) and
* Jerome Henin (LISM, CNRS, Marseille, France). This code is located in
* the directory lib/colvars and needs to be compiled first. The colvars
* fix and an interface layer, exchanges information between LAMMPS and
* the collective variable module.
See the doc page of :doc:`fix colvars <fix_colvars>` for more details.
There are example scripts for using this package in
examples/USER/colvars
This is a very new interface that does not yet support all
features in the module and will see future optimizations
and improvements. The colvars module library is also available
in NAMD has been thoroughly used and tested there. Bugs and
problems are likely due to the interface layers code.
Thus the current version of this package should be considered
beta quality.
The person who created this package is Axel Kohlmeyer at Temple U
(akohlmey at gmail.com). Contact him directly if you have questions.
----------
USER-CUDA package
-----------------
This package provides acceleration of various LAMMPS pair styles, fix
styles, compute styles, and long-range Coulombics via PPPM for NVIDIA
GPUs.
See this section of the manual to get started:
:ref:`Section_accelerate <acc_7>`
There are example scripts for using this package in
examples/USER/cuda.
This package uses an external library in lib/cuda which must be
compiled before making LAMMPS. See the lib/cuda/README file and the
LAMMPS manual for information on building LAMMPS with external
libraries.
The person who created this package is Christian Trott at the
University of Technology Ilmenau, Germany (christian.trott at
tu-ilmenau.de). Contact him directly if you have questions.
----------
USER-DIFFRACTION package
------------------------
This package contains the commands neeed to calculate x-ray and
electron diffraction intensities based on kinematic diffraction
theory.
See these doc pages and their related commands to get started:
* :doc:`compute xrd <compute_xrd>`
* :doc:`compute saed <compute_saed>`
* :doc:`fix saed/vtk <fix_saed_vtk>`
The person who created this package is Shawn P. Coleman
(shawn.p.coleman8.ctr at mail.mil) while at the University of
Arkansas. Contact him directly if you have questions.
----------
USER-DRUDE package
------------------
This package implements methods for simulating polarizable systems
in LAMMPS using thermalized Drude oscillators.
See these doc pages and their related commands to get started:
* :doc:`Drude tutorial <tutorial_drude>`
* :doc:`fix drude <fix_drude>`
* :doc:`compute temp/drude <compute_temp_drude>`
* :doc:`fix langevin/drude <fix_langevin_drude>`
* :doc:`fix drude/transform/... <fix_drude_transform>`
* :doc:`pair thole <pair_thole>`
There are auxiliary tools for using this package in tools/drude.
The person who created this package is Alain Dequidt at Universite
Blaise Pascal Clermont-Ferrand (alain.dequidt at univ-bpclermont.fr)
Contact him directly if you have questions. Co-authors: Julien Devemy,
Agilio Padua.
----------
USER-EFF package
----------------
This package contains a LAMMPS implementation of the electron Force
Field (eFF) currently under development at Caltech, 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.
eFF can be viewed as an approximation to QM wave packet dynamics and
Fermionic molecular dynamics, combining the ability of electronic
structure methods to describe atomic structure, bonding, and chemistry
in materials, and of plasma methods to describe nonequilibrium
dynamics of large systems with a large number of highly excited
electrons. We classify it as a mixed QM-classical approach rather than
a conventional force field method, which introduces QM-based terms (a
spin-dependent repulsion term to account for the Pauli exclusion
principle and the electron wavefunction kinetic energy associated with
the Heisenberg principle) that reduce, along with classical
electrostatic terms between nuclei and electrons, to the sum of a set
of effective pairwise potentials. This makes eFF uniquely suited to
simulate materials over a wide range of temperatures and pressures
where electronically excited and ionized states of matter can occur
and coexist.
The necessary customizations to the LAMMPS core are in place to
enable the correct handling of explicit electron properties during
minimization and dynamics.
See the doc page for the pair_style eff/cut command to get started.
There are example scripts for using this package in
examples/USER/eff.
There are auxiliary tools for using this package in tools/eff.
The person who created this package is Andres Jaramillo-Botero at
CalTech (ajaramil at wag.caltech.edu). Contact him directly if you
have questions.
----------
USER-FEP package
----------------
This package provides methods for performing free energy perturbation
simulations with soft-core pair potentials in LAMMPS.
See these doc pages and their related commands to get started:
* :doc:`fix adapt/fep <fix_adapt_fep>`
* :doc:`compute fep <compute_fep>`
* :doc:`soft pair styles <pair_lj_soft>`
The person who created this package is Agilio Padua at Universite
Blaise Pascal Clermont-Ferrand (agilio.padua at univ-bpclermont.fr)
Contact him directly if you have questions.
----------
USER-H5MD package
-----------------
This package contains a :doc:`dump h5md <dump_h5md>` command for
performing a dump of atom properties in HDF5 format. `HDF5 files <HDF5_>`_ are binary, portable and self-describing and can be
examined and used by a variety of auxiliary tools. The output HDF5
files are structured in a format called H5MD, which was designed to
store molecular data, and can be used and produced by various MD and
MD-related codes. The :doc:`dump h5md <doc/dump_h5md>` command gives a
citation to a paper describing the format.
.. _HDF5: http://www.hdfgroup.org/HDF5/
The person who created this package and the underlying H5MD format is
Pierre de Buyl at KU Leuven (see http://pdebuyl.be). Contact him
directly if you have questions.
----------
USER-INTEL package
------------------
This package provides options for performing neighbor list and
non-bonded force calculations in single, mixed, or double precision
and also a capability for accelerating calculations with an
Intel(R) Xeon Phi(TM) coprocessor.
See this section of the manual to get started:
:ref:`Section_accelerate <acc_9>`
The person who created this package is W. Michael Brown at Intel
(michael.w.brown at intel.com). Contact him directly if you have questions.
----------
USER-LB package
---------------
This package contains a LAMMPS implementation of a background
Lattice-Boltzmann fluid, which can be used to model MD particles
influenced by hydrodynamic forces.
See this doc page and its related commands to get started:
:doc:`fix lb/fluid <fix_lb_fluid>`
The people who created this package are Frances Mackay (fmackay at
uwo.ca) and Colin (cdennist at uwo.ca) Denniston, University of
Western Ontario. Contact them directly if you have questions.
----------
USER-MGPT package
-----------------
This package contains a fast implementation for LAMMPS of
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 Lawrence
Livermore National Lab (LLNL).
In the general matrix representation of MGPT, which can also be
applied to f-band actinide metals, the multi-ion potentials are
evaluated on the fly during a simulation through d- or f-state matrix
multiplication, and the forces that move the ions are determined
analytically. The *mgpt* pair style in this package calculates forces
and energies using an optimized matrix-MGPT algorithm due to Tomas
Oppelstrup at LLNL.
See this doc page to get started:
:doc:`pair_style mgpt <pair_mgpt>`
The persons who created the USER-MGPT package are Tomas Oppelstrup
(oppelstrup2@llnl.gov) and John Moriarty (moriarty2@llnl.gov)
Contact them directly if you have any questions.
----------
USER-MISC package
-----------------
The files in this package are a potpourri of (mostly) unrelated
features contributed to LAMMPS by users. Each feature is a single
pair of files (*.cpp and *.h).
More information about each feature can be found by reading its doc
page in the LAMMPS doc directory. The doc page which lists all LAMMPS
input script commands is as follows:
:ref:`Section_commands <cmd_5>`
User-contributed features are listed at the bottom of the fix,
compute, pair, etc sections.
The list of features and author of each is given in the
src/USER-MISC/README file.
You should contact the author directly if you have specific questions
about the feature or its coding.
----------
USER-MOLFILE package
--------------------
This package contains a dump molfile command which uses molfile
plugins that are bundled with the
`VMD <http://www.ks.uiuc.edu/Research/vmd>`_ molecular visualization and
analysis program, to enable LAMMPS to dump its information in formats
compatible with various molecular simulation tools.
The package only provides the interface code, not the plugins. These
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 recompile the
application itself.
See this doc page to get started:
:ref:`dump molfile <acc_5>`
The person who created this package is Axel Kohlmeyer at Temple U
(akohlmey at gmail.com). Contact him directly if you have questions.
----------
USER-OMP package
----------------
This package provides OpenMP multi-threading support and
other optimizations of various LAMMPS pair styles, dihedral
styles, and fix styles.
See this section of the manual to get started:
:ref:`Section_accelerate <acc_5>`
The person who created this package is Axel Kohlmeyer at Temple U
(akohlmey at gmail.com). Contact him directly if you have questions.
----------
USER-PHONON package
-------------------
This package contains a fix phonon command that calculates dynamical
matrices, which can then be used to compute phonon dispersion
relations, directly from molecular dynamics simulations.
See this doc page to get started:
:doc:`fix phonon <fix_phonon>`
The person who created this package is Ling-Ti Kong (konglt at
sjtu.edu.cn) at Shanghai Jiao Tong University. Contact him directly
if you have questions.
----------
USER-QMMM package
-----------------
This package provides a fix qmmm command which allows LAMMPS to be
used in a QM/MM simulation, currently only in combination with pw.x
code from the `Quantum ESPRESSO <espresso_>`_ package.
.. _espresso: http://www.quantum-espresso.org
The current implementation only supports an ONIOM style mechanical
coupling to the Quantum ESPRESSO plane wave DFT package.
Electrostatic coupling is in preparation and the interface has been
written in a manner that coupling to other QM codes should be possible
without changes to LAMMPS itself.
See this doc page to get started:
:doc:`fix qmmm <fix_qmmm>`
as well as the lib/qmmm/README file.
The person who created this package is Axel Kohlmeyer at Temple U
(akohlmey at gmail.com). Contact him directly if you have questions.
----------
USER-QTB package
----------------
This package provides a self-consistent quantum treatment of the
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, alter the energy power spectrum and the
heat capacity towards their quantum nature. This package could be of
interest if one wants to model systems at temperatures lower than
their classical limits or when temperatures ramp up across the
classical limits in the simulation.
See these two doc pages to get started:
:doc:`fix qtb <fix_qtb>` provides quantum nulcear correction through a
colored thermostat and can be used with other time integration schemes
like :doc:`fix nve <fix_nve>` or :doc:`fix nph <fix_nh>`.
:doc:`fix qbmsst <fix_qbmsst>` enables quantum nuclear correction of a
multi-scale shock technique simulation by coupling the quantum thermal
bath with the shocked system.
The person who created this package is Yuan Shen (sy0302 at
stanford.edu) at Stanford University. Contact him directly if you
have questions.
----------
USER-REAXC package
------------------
This package contains a implementation for LAMMPS of the ReaxFF force
field. ReaxFF uses distance-dependent bond-order functions to
represent the contributions of chemical bonding to the potential
energy. It was originally developed by Adri van Duin and the Goddard
group at CalTech.
The USER-REAXC version of ReaxFF (pair_style reax/c), implemented in
C, should give identical or very similar results to pair_style reax,
which is a ReaxFF implementation on top of a Fortran library, a
version of which library was originally authored by Adri van Duin.
The reax/c version should be somewhat faster and more scalable,
particularly with respect to the charge equilibration calculation. It
should also be easier to build and use since there are no complicating
issues with Fortran memory allocation or linking to a Fortran library.
For technical details about this implemention of ReaxFF, see
this paper:
Parallel and Scalable Reactive Molecular Dynamics: Numerical Methods
and Algorithmic Techniques, H. M. Aktulga, J. C. Fogarty,
S. A. Pandit, A. Y. Grama, Parallel Computing, in press (2011).
See the doc page for the pair_style reax/c command for details
of how to use it in LAMMPS.
The person who created this package is Hasan Metin Aktulga (hmaktulga
at lbl.gov), while at Purdue University. Contact him directly, or
Aidan Thompson at Sandia (athomps at sandia.gov), if you have
questions.
----------
USER-SMD package
----------------
This package implements smoothed Mach dynamics (SMD) in
LAMMPS. Currently, the package has the following features:
* Does liquids via traditional Smooth Particle Hydrodynamics (SPH)
* Also solves solids mechanics problems via a state of the art
stabilized meshless method with hourglass control.
* Can specify hydrostatic interactions independently from material
strength models, i.e. pressure and deviatoric stresses are separated.
* Many material models available (Johnson-Cook, plasticity with
hardening, Mie-Grueneisen, Polynomial EOS). Easy to add new
material models.
* Rigid boundary conditions (walls) can be loaded as surface geometries
from *.STL files.
See the file doc/PDF/SMD_LAMMPS_userguide.pdf to get started.
There are example scripts for using this package in examples/USER/smd.
The person who created this package is Georg Ganzenmuller at the
Fraunhofer-Institute for High-Speed Dynamics, Ernst Mach Institute in
Germany (georg.ganzenmueller at emi.fhg.de). Contact him directly if
you have questions.
----------
USER-SMTBQ package
------------------
This package implements the Second Moment Tight Binding - QEq (SMTB-Q)
potential for the description of ionocovalent bonds in oxides.
There are example scripts for using this package in
examples/USER/smtbq.
See this doc page to get started:
:doc:`pair_style smtbq <pair_smtbq>`
The persons who created the USER-SMTBQ package are Nicolas Salles,
Emile Maras, Olivier Politano, Robert Tetot, who can be contacted at
these email addreses: lammps@u-bourgogne.fr, nsalles@laas.fr. Contact
them directly if you have any questions.
----------
USER-SPH package
----------------
This package implements smoothed particle hydrodynamics (SPH) in
LAMMPS. Currently, the package has the following features:
* Tait, ideal gas, Lennard-Jones equation of states, full support for
complete (i.e. internal-energy dependent) equations of state
* Plain or Monaghans XSPH integration of the equations of motion
* Density continuity or density summation to propagate the density field
* Commands to set internal energy and density of particles from the
input script
* Output commands to access internal energy and density for dumping and
thermo output
See the file doc/PDF/SPH_LAMMPS_userguide.pdf to get started.
There are example scripts for using this package in examples/USER/sph.
The person who created this package is Georg Ganzenmuller at the
Fraunhofer-Institute for High-Speed Dynamics, Ernst Mach Institute in
Germany (georg.ganzenmueller at emi.fhg.de). Contact him directly if
you have questions.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Section_commands.html#comm
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