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423 lines
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<HTML>
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<CENTER><A HREF = "Section_commands.html">Previous Section</A> - <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> -
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<A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A> - <A HREF = "Section_accelerate.html">Next
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Section</A>
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</CENTER>
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<HR>
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<H3>4. Packages
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</H3>
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<P>This section gives a quick overview of the add-on packages that extend
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LAMMPS functionality.
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</P>
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4.1 <A HREF = "#pkg_1">Standard packages</A><BR>
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4.2 <A HREF = "#pkg_2">User packages</A> <BR>
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<P>LAMMPS includes many optional packages, which are groups of files that
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enable a specific set of features. For example, force fields for
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molecular systems or granular systems are in packages. You can see
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the list of all packages by typing "make package" from within the src
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directory of the LAMMPS distribution.
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</P>
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<P>See <A HREF = "Section_start.html#start_3">Section_start 3</A> of the manual for
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details on how to include/exclude specific packages as part of the
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LAMMPS build process, and for more details about the differences
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between standard packages and user packages in LAMMPS.
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</P>
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<P>Below, the packages currently availabe in LAMMPS are listed. For
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standard packages, just a one-line description is given. For user
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packages, more details are provided.
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</P>
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<HR>
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<HR>
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<H4><A NAME = "pkg_1"></A>4.1 Standard packages
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</H4>
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<P>The current list of standard packages is as follows:
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</P>
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<DIV ALIGN=center><TABLE BORDER=1 >
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<TR ALIGN="center"><TD >Package</TD><TD > Description</TD><TD > Author(s)</TD><TD > Doc page</TD><TD > Example</TD><TD > Library</TD></TR>
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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<TR ALIGN="center"><TD >
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</TD></TR></TABLE></DIV>
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<P>The "Authors" column lists a name(s) if a specific person is
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responible for creating and maintaining the package.
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</P>
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<P>(1) The FLD package was created by Amit Kumar and Michael Bybee from
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Jonathan Higdon's group at UIUC.
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</P>
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<P>(2) The OPT package was created by James Fischer (High Performance
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Technologies), David Richie, and Vincent Natoli (Stone Ridge
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Technolgy).
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</P>
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<P>The "Doc page" column links to either a portion of the
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<A HREF = "Section_howto.html">Section_howto</A> of the manual, or an input script
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command implemented as part of the package.
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</P>
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<P>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.
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</P>
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<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.
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</P>
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<HR>
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<HR>
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<H4><A NAME = "pkg_2"></A>4.2 User packages
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</H4>
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<P>The current list of user-contributed packages is as follows:
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</P>
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<DIV ALIGN=center><TABLE BORDER=1 >
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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<TR ALIGN="center"><TD >
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</TD></TR></TABLE></DIV>
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<P>The "Authors" column lists a name(s) if a specific person is
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responible for creating and maintaining the package.
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</P>
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<P>(2) The ATC package was created by Reese Jones, Jeremy Templeton, and Jon Zimmerman (Sandia).
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</P>
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<P>The "Doc page" column links to either a portion of the
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<A HREF = "Section_howto.html">Section_howto</A> of the manual, or an input script
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command implemented as part of the package, or to additional
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documentation provided witht he package.
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</P>
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<P>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/cuda
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refers to the examples/USER/cuda directory.
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</P>
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<P>The "Library" column lists an external library which must be built
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first and which LAMMPS links to when it is built. These are in the
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lib directory of the distribution. <A HREF = "Section_start.html#start_3_3">This
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section</A> of the manual gives details on
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the 2-step build process with external libraries.
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</P>
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<P>More details on each package, from the USER-blah/README file
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is given below.
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</P>
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<HR>
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<H4>USER-MISC package
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</H4>
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<P>The files in this package are a potpourri of (mostly) unrelated
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features contributed to LAMMPS by users. Each feature is a single
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pair of files (*.cpp and *.h).
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</P>
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<P>More information about each feature can be found by reading its doc
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page in the LAMMPS doc directory. The doc page which lists all LAMMPS
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input script commands is as follows:
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</P>
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<P><A HREF = "Section_commands.html#cmd_5">Section_commands</A>
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</P>
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<P>User-contributed features are listed at the bottom of the fix,
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compute, pair, etc sections.
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</P>
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<P>The list of features and author of each is given in the
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src/USER-MISC/README file.
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</P>
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<P>You should contact the author directly if you have specific questions
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about the feature or its coding.
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</P>
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<HR>
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<H4>USER-ATC package
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</H4>
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<P>This package implements a "fix atc" command which can be used in a
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LAMMPS input script. This fix can be employed to either do concurrent
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coupling of MD with FE-based physics surrogates or on-the-fly
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post-processing of atomic information to continuum fields.
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</P>
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<P>See the doc page for the fix atc command to get started. At the
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bottom of the doc page are many links to additional documentation
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contained in the doc/USER/atc directory.
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</P>
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<P>There are example scripts for using this package in examples/USER/atc.
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</P>
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<P>This package uses an external library in lib/atc which must be
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compiled before making LAMMPS. See the lib/atc/README file and the
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LAMMPS manual for information on building LAMMPS with external
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libraries.
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</P>
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<P>The primary people who created this package are Reese Jones (rjones at
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sandia.gov), Jeremy Templeton (jatempl at sandia.gov) and Jon
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Zimmerman (jzimmer at sandia.gov) at Sandia. Contact them directly if
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you have questions.
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</P>
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<HR>
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<H4>USER-AWPMD package
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</H4>
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<P>This package contains a LAMMPS implementation of the Antisymmetrized
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Wave Packet Molecular Dynamics (AWPMD) method.
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</P>
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<P>See the doc page for the pair_style awpmd/cut command to get started.
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</P>
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<P>There are example scripts for using this package in examples/USER/awpmd.
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</P>
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<P>This package uses an external library in lib/awpmd which must be
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compiled before making LAMMPS. See the lib/awpmd/README file and the
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LAMMPS manual for information on building LAMMPS with external
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libraries.
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</P>
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<P>The person who created this package is Ilya Valuev at the JIHT in
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Russia (valuev at physik.hu-berlin.de). Contact him directly if you
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have questions.
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</P>
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<HR>
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<H4>USER-CG-CMM package
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</H4>
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<P>This package implements 3 commands which can be used in a LAMMPS input
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script:
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</P>
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<UL><LI>pair_style lj/sdk
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<LI>pair_style lj/sdk/coul/long
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<LI>angle_style sdk
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</UL>
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<P>These styles allow coarse grained MD simulations with the
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parametrization of Shinoda, DeVane, Klein, Mol Sim, 33, 27 (2007)
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(SDK), with extensions to simulate ionic liquids, electrolytes, lipids
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and charged amino acids.
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</P>
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<P>See the doc pages for these commands for details.
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</P>
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<P>There are example scripts for using this package in
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examples/USER/cg-cmm.
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</P>
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<P>This is the second generation implementation reducing the the clutter
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of the previous version. For many systems with electrostatics, it will
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be faster to use pair_style hybrid/overlay with lj/sdk and coul/long
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instead of the combined lj/sdk/coul/long style. since the number of
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charged atom types is usually small. For any other coulomb
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interactions this is now required. To exploit this property, the use
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of the kspace_style pppm/cg is recommended over regular pppm. For all
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new styles, input file backward compatibility is provided. The old
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implementation is still available through appending the /old
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suffix. These will be discontinued and removed after the new
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implementation has been fully validated.
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</P>
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<P>The current version of this package should be considered beta
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quality. The CG potentials work correctly for "normal" situations, but
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have not been testing with all kinds of potential parameters and
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simulation systems.
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</P>
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<P>The person who created this package is Axel Kohlmeyer at Temple U
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(akohlmey at gmail.com). Contact him directly if you have questions.
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</P>
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<HR>
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<H4>USER-CUDA package
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</H4>
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<P>This package provides acceleration of various LAMMPS pair styles, fix
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styles, compute styles, and long-range Coulombics via PPPM for NVIDIA
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GPUs.
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</P>
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<P>See this section of the manual to get started:
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</P>
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<P><A HREF = "Section_accelerate.html#acc_4">Section_accelerate</A>
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</P>
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<P>There are example scripts for using this package in
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examples/USER/cuda.
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</P>
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<P>This package uses an external library in lib/cuda which must be
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compiled before making LAMMPS. See the lib/cuda/README file and the
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LAMMPS manual for information on building LAMMPS with external
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libraries.
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</P>
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<P>The person who created this package is Christian Trott at the
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University of Technology Ilmenau, Germany (christian.trott at
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tu-ilmenau.de). Contact him directly if you have questions.
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</P>
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<HR>
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<H4>USER-EFF package
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</H4>
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<P>This package contains a LAMMPS implementation of the electron Force
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Field (eFF) currently under development at Caltech, as described in
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A. Jaramillo-Botero, J. Su, Q. An, and W.A. Goddard III, JCC,
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2010. The eFF potential was first introduced by Su and Goddard, in
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2007.
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</P>
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<P>eFF can be viewed as an approximation to QM wave packet dynamics and
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Fermionic molecular dynamics, combining the ability of electronic
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structure methods to describe atomic structure, bonding, and chemistry
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in materials, and of plasma methods to describe nonequilibrium
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dynamics of large systems with a large number of highly excited
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electrons. We classify it as a mixed QM-classical approach rather than
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a conventional force field method, which introduces QM-based terms (a
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spin-dependent repulsion term to account for the Pauli exclusion
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principle and the electron wavefunction kinetic energy associated with
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the Heisenberg principle) that reduce, along with classical
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electrostatic terms between nuclei and electrons, to the sum of a set
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of effective pairwise potentials. This makes eFF uniquely suited to
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simulate materials over a wide range of temperatures and pressures
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where electronically excited and ionized states of matter can occur
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and coexist.
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</P>
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<P>The necessary customizations to the LAMMPS core are in place to
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enable the correct handling of explicit electron properties during
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minimization and dynamics.
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</P>
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<P>See the doc page for the pair_style eff/cut command to get started.
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</P>
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<P>There are example scripts for using this package in
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examples/USER/eff.
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</P>
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<P>There are auxiliary tools for using this package in tools/eff.
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</P>
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<P>The person who created this package is Andres Jaramillo-Botero at
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CalTech (ajaramil at wag.caltech.edu). Contact him directly if you
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have questions.
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</P>
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<HR>
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<H4>USER-EWALDN package
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</H4>
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<P>This package implements 3 commands which can be used in a LAMMPS input
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script: pair_style lj/coul, pair_style buck/coul, and kspace_style
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ewald/n.
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</P>
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<P>The "kspace_style ewald/n" command is similar to standard Ewald for
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charges, but also enables the Lennard-Jones interaction, or any 1/r^N
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interaction to be of infinite extent, instead of being cutoff. LAMMPS
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pair potentials for long-range Coulombic interactions, such as
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lj/cut/coul/long can be used with ewald/n. The two new pair_style
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|
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>
|