Homec4science
Diffusion lammps (lammm-master) Browse

lammps/doc/Section_packages.html
65bcbb90734blammm-master

Last Change
Raw File

Section_packages.html
View Options

<HTML>
<CENTER><A HREF = "Section_commands.html">Previous Section</A> - <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> -
<A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A> - <A HREF = "Section_accelerate.html">Next
Section</A>
</CENTER>
<HR>
<H3>4. Packages
</H3>
<P>This section gives a quick overview of the add-on packages that extend
LAMMPS functionality.
</P>
4.1 <A HREF = "#pkg_1">Standard packages</A><BR>
4.2 <A HREF = "#pkg_2">User packages</A> <BR>
<P>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.
</P>
<P>See <A HREF = "Section_start.html#start_3">this section</A> 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 in LAMMPS.
</P>
<P>Below, the packages currently availabe in LAMMPS are listed. For
standard packages, just a one-line description is given. For user
packages, more details are provided.
</P>
<HR>
<HR>
<H4><A NAME = "pkg_1"></A>4.1 Standard packages
</H4>
<P>The current list of standard packages is as follows:
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD >Package</TD><TD > Description</TD><TD > Author(s)</TD><TD > Doc page</TD><TD > Example</TD><TD > Library</TD></TR>
<TR ALIGN="center"><TD >ASPHERE</TD><TD > aspherical particles</TD><TD > -</TD><TD > <A HREF = "Section_howto.html#howto_14">howto</A></TD><TD > ellipse</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >CLASS2</TD><TD > class 2 force fields</TD><TD > -</TD><TD > <A HREF = "pair_class2.html">pair_style lj/class2</A></TD><TD > -</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >COLLOID</TD><TD > colloidal particles</TD><TD > -</TD><TD > <A HREF = "atom_style.html">atom_style colloid</A></TD><TD > colloid</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >DIPOLE</TD><TD > point dipole particles</TD><TD > -</TD><TD > <A HREF = "pair_dipole.html">pair_style dipole/cut</A></TD><TD > dipole</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >FLD</TD><TD > Fast Lubrication Dynamics</TD><TD > Kumar & Bybee & Higdon (1)</TD><TD > <A HREF = "pair_lubricateU.html">pair_style lubricateU</A></TD><TD > -</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >GPU</TD><TD > GPU-enabled potentials</TD><TD > Mike Brown (ORNL)</TD><TD > <A HREF = "Section_accelerate.html#acc_3">accelerate</A></TD><TD > gpu</TD><TD > lib/gpu</TD></TR>
<TR ALIGN="center"><TD >GRANULAR</TD><TD > granular systems</TD><TD > -</TD><TD > <A HREF = "Section_howto.html#howto_6">howto</A></TD><TD > pour</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >KSPACE</TD><TD > long-range Coulombic solvers</TD><TD > -</TD><TD > <A HREF = "kspace_style.html">kspace_style</A></TD><TD > peptide</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >MANYBODY</TD><TD > many-body potentials</TD><TD > -</TD><TD > <A HREF = "pair_tersoff.html">pair_style tersoff</A></TD><TD > shear</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >MEAM</TD><TD > modified EAM potential</TD><TD > Greg Wagner (Sandia)</TD><TD > <A HREF = "pair_meam.html">pair_style meam</A></TD><TD > meam</TD><TD > lib/meam</TD></TR>
<TR ALIGN="center"><TD >MC</TD><TD > Monte Carlo options</TD><TD > -</TD><TD > <A HREF = "fix_gcmc.html">fix gcmc</A></TD><TD > -</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >MOLECULE</TD><TD > molecular system force fields</TD><TD > -</TD><TD > <A HREF = "Section_howto.html#howto_3">howto</A></TD><TD > peptide</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >OPT</TD><TD > optimized pair potentials</TD><TD > Fischer & Richie & Natoli (2)</TD><TD > <A HREF = "Section_accelerate.html#acc_1">howto</A></TD><TD > -</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >PERI</TD><TD > Peridynamics models</TD><TD > Mike Parks (Sandia)</TD><TD > <A HREF = "pair_peri.html">pair_style peri</A></TD><TD > peri</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >POEMS</TD><TD > coupled rigid body motion</TD><TD > Rudra Mukherjee (JPL)</TD><TD > <A HREF = "fix_poems.html">fix poems</A></TD><TD > rigid</TD><TD > lib/poems</TD></TR>
<TR ALIGN="center"><TD >REAX</TD><TD > ReaxFF potential</TD><TD > Aidan Thompson (Sandia)</TD><TD > <A HREF = "pair_reax.html">pair_style reax</A></TD><TD > reax</TD><TD > lib/reax</TD></TR>
<TR ALIGN="center"><TD >REPLICA</TD><TD > multi-replica methods</TD><TD > -</TD><TD > <A HREF = "Section_howto.html#howto_5">howto</A></TD><TD > tad</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >SHOCK</TD><TD > shock loading methods</TD><TD > -</TD><TD > <A HREF = "fix_msst.html">fix msst</A></TD><TD > -</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >SRD</TD><TD > stochastic rotation dynamics</TD><TD > -</TD><TD > <A HREF = "fix_srd.html">fix srd</A></TD><TD > srd</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >XTC</TD><TD > dumps in XTC format</TD><TD > -</TD><TD > <A HREF = "dump.html">dump</A></TD><TD > -</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >
</TD></TR></TABLE></DIV>
<P>The "Authors" column lists a name(s) if a specific person is
responible for creating and maintaining the package.
</P>
<P>(1) The FLD package was created by Amit Kumar and Michael Bybee from
Jonathan Higdon's group at UIUC.
</P>
<P>(2) The OPT package was created by James Fischer (High Performance
Technologies), David Richie, and Vincent Natoli (Stone Ridge
Technolgy).
</P>
<P>The "Doc page" column links to either a portion of the
<A HREF = "Section_howto.html">Section_howto</A> of the manual, or an input script
command implemented as part of the package.
</P>
<P>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.
</P>
<P>The "Library" column lists an external library which must be built first and which LAMMPS links to when it is built. These are in the lib directory of the distribution. <A HREF = "Section_start.html#start_3_3">This section</A> of the manual gives details on the 2-step build process with external libraries.
</P>
<HR>
<HR>
<H4><A NAME = "pkg_2"></A>4.2 User packages
</H4>
<P>The current list of user-contributed packages is as follows:
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD >Package</TD><TD > Description</TD><TD > Author(s)</TD><TD > Doc page</TD><TD > Example</TD><TD > Pic/movie</TD><TD > Library</TD></TR>
<TR ALIGN="center"><TD >USER-MISC</TD><TD > single-file contributions</TD><TD > USER-MISC/README</TD><TD > -</TD><TD > -</TD><TD > -</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >USER-ATC</TD><TD > atom-to-continuum coupling</TD><TD > Jones & Templeton & Zimmerman (2)</TD><TD > <A HREF = "fix_atc.html">fix atc</A></TD><TD > USER/atc</TD><TD > <A HREF = "http://lammps.sandia.gov/pictures.html#atc">atc</A></TD><TD > lib/atc</TD></TR>
<TR ALIGN="center"><TD >USER-AWPMD</TD><TD > wave-packet MD</TD><TD > Ilya Valuev (JIHT)</TD><TD > <A HREF = "pair_awpmd.html">pair_style awpmd/cut</A></TD><TD > USER/awpmd</TD><TD > -</TD><TD > lib/awpmd</TD></TR>
<TR ALIGN="center"><TD >USER-CG-CMM</TD><TD > coarse-graining model</TD><TD > Axel Kohlmeyer (Temple U)</TD><TD > <A HREF = "pair_sdk.html">pair_style lj/sdk</A></TD><TD > USER/cg-cmm</TD><TD > <A HREF = "http://lammps.sandia.gov/pictures.html#cg">cg</A></TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >USER-CUDA</TD><TD > NVIDIA GPU styles</TD><TD > Christian Trott (U Tech Ilmenau)</TD><TD > <A HREF = "Section_accelerate.html#acc_4">accelerate</A></TD><TD > USER/cuda</TD><TD > -</TD><TD > lib/cuda</TD></TR>
<TR ALIGN="center"><TD >USER-EFF</TD><TD > electron force field</TD><TD > Andres Jaramillo-Botero (Caltech)</TD><TD > <A HREF = "pair_eff.html">pair_style eff/cut</A></TD><TD > USER/eff</TD><TD > <A HREF = "http://lammps.sandia.gov/movies.html#eff">eff</A></TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >USER-EWALDN</TD><TD > Ewald for 1/R^n</TD><TD > Pieter in' t Veld (BASF)</TD><TD > <A HREF = "kspace_style.html">kspace_style</A></TD><TD > -</TD><TD > -</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >USER-OMP</TD><TD > OpenMP threaded styles</TD><TD > Axel Kohlmeyer (Temple U)</TD><TD > <A HREF = "Section_accelerate.html#acc_2">accelerate</A></TD><TD > -</TD><TD > -</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >USER-REAXC</TD><TD > C version of ReaxFF</TD><TD > Metin Aktulga (LBNL)</TD><TD > <A HREF = "pair_reax_c.html">pair_style reaxc</A></TD><TD > reax</TD><TD > -</TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >USER-SPH</TD><TD > smoothed particle hydrodynamics</TD><TD > Georg Ganzenmuller (EMI)</TD><TD > <A HREF = "USER/sph/SPH_LAMMPS_userguide.pdf">SPH_LAMMPS_userguide.pdf</A></TD><TD > USER/sph</TD><TD > <A HREF = "http://lammps.sandia.gov/movies.html#sph">sph</A></TD><TD > -</TD></TR>
<TR ALIGN="center"><TD >
</TD></TR></TABLE></DIV>
<P>The "Authors" column lists a name(s) if a specific person is
responible for creating and maintaining the package.
</P>
<P>(2) The ATC package was created by Reese Jones, Jeremy Templeton, and Jon Zimmerman (Sandia).
</P>
<P>The "Doc page" column links to either a portion of the
<A HREF = "Section_howto.html">Section_howto</A> of the manual, or an input script
command implemented as part of the package, or to additional
documentation provided witht he package.
</P>
<P>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.
</P>
<P>The "Library" column lists an external library which must be built
first and which LAMMPS links to when it is built. These are in the
lib directory of the distribution. <A HREF = "Section_start.html#start_3_3">This
section</A> of the manual gives details on
the 2-step build process with external libraries.
</P>
<P>More details on each package, from the USER-blah/README file
is given below.
</P>
<HR>
<H4>USER-MISC package
</H4>
<P>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).
</P>
<P>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:
</P>
<P><A HREF = "Section_commands.html#cmd_5">Section_commands</A>
</P>
<P>User-contributed features are listed at the bottom of the fix,
compute, pair, etc sections.
</P>
<P>The list of features and author of each is given in the
src/USER-MISC/README file.
</P>
<P>You should contact the author directly if you have specific questions
about the feature or its coding.
</P>
<HR>
<H4>USER-ATC package
</H4>
<P>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.
</P>
<P>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.
</P>
<P>There are example scripts for using this package in examples/USER/atc.
</P>
<P>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.
</P>
<P>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.
</P>
<HR>
<H4>USER-AWPMD package
</H4>
<P>This package contains a LAMMPS implementation of the Antisymmetrized
Wave Packet Molecular Dynamics (AWPMD) method.
</P>
<P>See the doc page for the pair_style awpmd/cut command to get started.
</P>
<P>There are example scripts for using this package in examples/USER/awpmd.
</P>
<P>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.
</P>
<P>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.
</P>
<HR>
<H4>USER-CG-CMM package
</H4>
<P>This package implements 3 commands which can be used in a LAMMPS input
script:
</P>
<UL><LI>pair_style lj/sdk
<LI>pair_style lj/sdk/coul/long
<LI>angle_style sdk
</UL>
<P>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.
</P>
<P>See the doc pages for these commands for details.
</P>
<P>There are example scripts for using this package in
examples/USER/cg-cmm.
</P>
<P>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.
</P>
<P>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.
</P>
<P>The person who created this package is Axel Kohlmeyer at Temple U
(akohlmey at gmail.com). Contact him directly if you have questions.
</P>
<HR>
<H4>USER-CUDA package
</H4>
<P>This package provides acceleration of various LAMMPS pair styles, fix
styles, compute styles, and long-range Coulombics via PPPM for NVIDIA
GPUs.
</P>
<P>See this section of the manual to get started:
</P>
<P><A HREF = "Section_accelerate.html#acc_4">Section_accelerate</A>
</P>
<P>There are example scripts for using this package in
examples/USER/cuda.
</P>
<P>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.
</P>
<P>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.
</P>
<HR>
<H4>USER-EFF package
</H4>
<P>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.
</P>
<P>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.
</P>
<P>The necessary customizations to the LAMMPS core are in place to
enable the correct handling of explicit electron properties during
minimization and dynamics.
</P>
<P>See the doc page for the pair_style eff/cut command to get started.
</P>
<P>There are example scripts for using this package in
examples/USER/eff.
</P>
<P>There are auxiliary tools for using this package in tools/eff.
</P>
<P>The person who created this package is Andres Jaramillo-Botero at
CalTech (ajaramil at wag.caltech.edu). Contact him directly if you
have questions.
</P>
<HR>
<H4>USER-EWALDN package
</H4>
<P>This package implements 3 commands which can be used in a LAMMPS input
script: pair_style lj/coul, pair_style buck/coul, and kspace_style
ewald/n.
</P>
<P>The "kspace_style ewald/n" command is similar to standard Ewald for
charges, but also enables the Lennard-Jones interaction, or any 1/r^N
interaction to be of infinite extent, instead of being cutoff. LAMMPS
pair potentials for long-range Coulombic interactions, such as
lj/cut/coul/long can be used with ewald/n. The two new pair_style
commands provide the modifications for the short-range LJ and
Buckingham interactions that can also be used with ewald/n.
</P>
<P>Another advantage of kspace_style ewald/n is that it can be used with
non-orthogonal (triclinic symmetry) simulation boxes, either for just
long-range Coulombic interactions, or for both Coulombic and 1/r^N LJ
or Buckingham, which is not currently possible for other kspace styles
such as PPPM and ewald.
</P>
<P>See the doc pages for these commands for details.
</P>
<P>The person who created these files is Pieter in' t Veld while at
Sandia. He is now at BASF (pieter.intveld at basf.com). Contact him
directly if you have questions.
</P>
<HR>
<H4>USER-OMP package
</H4>
<P>This package provides OpenMP multi-threading support and
other optimizations of various LAMMPS pair styles, dihedral
styles, and fix styles.
</P>
<P>See this section of the manual to get started:
</P>
<P><A HREF = "Section_accelerate.html#acc_2">Section_accelerate</A>
</P>
<P>The person who created this package is Axel Kohlmeyer at Temple U
(akohlmey at gmail.com). Contact him directly if you have questions.
</P>
<HR>
<H4>USER-REAXC package
</H4>
<P>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.
</P>
<P>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.
</P>
<P>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.
</P>
<P>For technical details about this implemention of ReaxFF, see
this paper:
</P>
<P>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).
</P>
<P>See the doc page for the pair_style reax/c command for details
of how to use it in LAMMPS.
</P>
<P>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.
</P>
<HR>
<H4>USER-SPH package
</H4>
<P>This package implements smoothed particle hydrodynamics (SPH) in
LAMMPS. Currently, the package has the following features:
</P>
<P>* 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
</P>
<P>See the file doc/USER/sph/SPH_LAMMPS_userguide.pdf to get started.
</P>
<P>There are example scripts for using this package in examples/USER/sph.
</P>
<P>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.
</P>
</HTML>
c4science · Help