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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">Section_howto 6.14</A></TD><TD > ellipse</TD><TD > -</TD></TR>
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<TR ALIGN="center"><TD >BODY</TD><TD > body-style particles</TD><TD > -</TD><TD > <A HREF = "body.html">body</A></TD><TD > body</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 >CORESHELL</TD><TD > adiabatic core/shell model</TD><TD > Hendrik Heenen (Technical U of Munich)</TD><TD > <A HREF = "Section_howto.html#howto_25">Section_howto 6.25</A></TD><TD > coreshell</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 styles</TD><TD > Mike Brown (ORNL)</TD><TD > <A HREF = "accelerate_gpu.html">Section 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">Section_howto 6.6</A></TD><TD > pour</TD><TD > -</TD></TR>
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<TR ALIGN="center"><TD >KIM</TD><TD > openKIM potentials</TD><TD > Smirichinski & Elliot & Tadmor (3)</TD><TD > <A HREF = "pair_kim.html">pair_style kim</A></TD><TD > kim</TD><TD > KIM</TD></TR>
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<TR ALIGN="center"><TD >KOKKOS</TD><TD > Kokkos-enabled styles</TD><TD > Trott & Edwards (4)</TD><TD > <A HREF = "accelerate_kokkos.html">Section_accelerate</A></TD><TD > kokkos</TD><TD > lib/kokkos</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">Section_howto 6.3</A></TD><TD > peptide</TD><TD > -</TD></TR>
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<TR ALIGN="center"><TD >OPT</TD><TD > optimized pair styles</TD><TD > Fischer & Richie & Natoli (2)</TD><TD > <A HREF = "accelerate_opt.html">Section accelerate</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 >PYTHON</TD><TD > embed Python code in an input script</TD><TD > -</TD><TD > <A HREF = "python.html">python</A></TD><TD > python</TD><TD > lib/python</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">Section_howto 6.5</A></TD><TD > tad</TD><TD > -</TD></TR>
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<TR ALIGN="center"><TD >RIGID</TD><TD > rigid bodies</TD><TD > -</TD><TD > <A HREF = "fix_rigid.html">fix rigid</A></TD><TD > rigid</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 >SNAP</TD><TD > quantum-fit potential</TD><TD > Aidan Thompson (Sandia)</TD><TD > <A HREF = "pair_snap.html">pair snap</A></TD><TD > snap</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 >VORONOI</TD><TD > Voronoi tesselations</TD><TD > Daniel Schwen (LANL)</TD><TD > <A HREF = "compute_voronoi_atom.html">compute voronoi/atom</A></TD><TD > -</TD><TD > Voro++</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>(3) The KIM package was created by Valeriu Smirichinski, Ryan Elliott,
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and Ellad Tadmor (U Minn).
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</P>
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<P>(4) The KOKKOS package was created primarily by Christian Trott
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(Sandia). It uses the Kokkos library which was developed by Carter
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Edwards, Christian, and collaborators at 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.
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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
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first and which LAMMPS links to when it is built. If it is listed as
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lib/package, then the code for the library is under the lib directory
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of the LAMMPS distribution. See the lib/package/README file for info
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on how to build the library. If it is not listed as lib/package, then
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it is a third-party library not included in the LAMMPS distribution.
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See the src/package/README or src/package/Makefile.lammps file for
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info on where to download the library. <A HREF = "Section_start.html#start_3_3">Section
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start</A> of the manual also gives details
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on how to build LAMMPS with both kinds of auxiliary 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-ATC</TD><TD > atom-to-continuum coupling</TD><TD > Jones & Templeton & Zimmerman (1)</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-COLVARS</TD><TD > collective variables</TD><TD > Fiorin & Henin & Kohlmeyer (2)</TD><TD > <A HREF = "fix_colvars.html">fix colvars</A></TD><TD > USER/colvars</TD><TD > <A HREF = "colvars">colvars</A></TD><TD > lib/colvars</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 = "accelerate_cuda.html">Section accelerate</A></TD><TD > USER/cuda</TD><TD > -</TD><TD > lib/cuda</TD></TR>
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<TR ALIGN="center"><TD >USER-DIFFRACTION</TD><TD > virutal x-ray and electron diffraction</TD><TD > Shawn Coleman (ARL)</TD><TD ><A HREF = "compute_xrd.html">compute xrd</A></TD><TD > USER/diffraction</TD><TD > -</TD><TD > -</TD></TR>
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<TR ALIGN="center"><TD >USER-DRUDE</TD><TD > Drude oscillators</TD><TD > Dequidt & Devemy & Padua (3)</TD><TD > <A HREF = "tutorial_drude.html">tutorial</A></TD><TD > USER/drude</TD><TD > -</TD><TD > -</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-FEP</TD><TD > free energy perturbation</TD><TD > Agilio Padua (U Blaise Pascal Clermont-Ferrand)</TD><TD > <A HREF = "compute_fep.html">compute fep</A></TD><TD > USER/fep</TD><TD > -</TD><TD > -</TD></TR>
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<TR ALIGN="center"><TD >USER-INTEL</TD><TD > Vectorized CPU and Intel(R) coprocessor styles</TD><TD > W. Michael Brown (Intel)</TD><TD > <A HREF = "accelerate_intel.html">Section accelerate</A></TD><TD > examples/intel</TD><TD > -</TD><TD > -</TD></TR>
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<TR ALIGN="center"><TD >USER-LB</TD><TD > Lattice Boltzmann fluid</TD><TD > Colin Denniston (U Western Ontario)</TD><TD > <A HREF = "fix_lb_fluid.html">fix lb/fluid</A></TD><TD > USER/lb</TD><TD > -</TD><TD > -</TD></TR>
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<TR ALIGN="center"><TD >USER-MISC</TD><TD > single-file contributions</TD><TD > USER-MISC/README</TD><TD > USER-MISC/README</TD><TD > -</TD><TD > -</TD><TD > -</TD></TR>
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<TR ALIGN="center"><TD >USER-MOLFILE</TD><TD > <A HREF = "http://www.ks.uiuc.edu/Research/vmd">VMD</A> molfile plug-ins</TD><TD > Axel Kohlmeyer (Temple U)</TD><TD > <A HREF = "dump_molfile.html">dump molfile</A></TD><TD > -</TD><TD > -</TD><TD > VMD-MOLFILE</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 = "accelerate_omp.html">Section accelerate</A></TD><TD > -</TD><TD > -</TD><TD > -</TD></TR>
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<TR ALIGN="center"><TD >USER-PHONON</TD><TD > phonon dynamical matrix</TD><TD > Ling-Ti Kong (Shanghai Jiao Tong U)</TD><TD > <A HREF = "fix_phonon.html">fix phonon</A></TD><TD > USER/phonon</TD><TD > -</TD><TD > -</TD></TR>
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<TR ALIGN="center"><TD >USER-QMMM</TD><TD > QM/MM coupling</TD><TD > Axel Kohlmeyer (Temple U)</TD><TD > <A HREF = "fix_qmmm.html">fix qmmm</A></TD><TD > USER/qmmm</TD><TD > -</TD><TD > lib/qmmm</TD></TR>
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<TR ALIGN="center"><TD >USER-QTB</TD><TD > quantum nuclear effects</TD><TD > Yuan Shen (Stanford)</TD><TD > <A HREF = "fix_qtb.html">fix qtb</A> <A HREF = "fix_qbmsst.html">fix_qbmsst</A></TD><TD > qtb</TD><TD > -</TD><TD > -</TD></TR>
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<TR ALIGN="center"><TD >USER-QUIP</TD><TD > QM/MM coupling</TD><TD > Albert Bartok-Partay (U Cambridge)</TD><TD > <A HREF = "fix_quip.html">fix quip</A></TD><TD > USER/quip</TD><TD > -</TD><TD > lib/quip</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">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>If the Library is not listed as lib/package, then it is a third-party
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library not included in the LAMMPS distribution. See the
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src/package/Makefile.lammps file for info on where to download the
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library from.
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</P>
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<P>(2) The ATC package was created by Reese Jones, Jeremy Templeton, and
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Jon Zimmerman (Sandia).
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</P>
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<P>(2) The COLVARS package was created by Axel Kohlmeyer (Temple U) using
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the colvars module library written by Giacomo Fiorin (Temple U) and
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Jerome Henin (LISM, Marseille, France).
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</P>
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<P>(3) The DRUDE package was created by Alain Dequidt (U Blaise Pascal
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Clermont-Ferrand) and co-authors Julien Devemy (CNRS) and Agilio Padua
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(U Blaise Pascal).
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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. If it is listed as
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lib/package, then the code for the library is under the lib directory
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of the LAMMPS distribution. See the lib/package/README file for info
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on how to build the library. If it is not listed as lib/package, then
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it is a third-party library not included in the LAMMPS distribution.
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See the src/package/Makefile.lammps file for info on where to download
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the library. <A HREF = "Section_start.html#start_3_3">Section start</A> of the
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manual also gives details on how to build LAMMPS with both kinds of
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auxiliary libraries.
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</P>
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<P>More details on each package, from the USER-*/README file is given
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below.
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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
|
|
</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-COLVARS package
|
|
</H4>
|
|
<P>This package implements the "fix colvars" command which can be
|
|
used in a LAMMPS input script.
|
|
</P>
|
|
<P>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:
|
|
</P>
|
|
<UL><LI>A portable collective variable module library written and maintained
|
|
<LI>by Giacomo Fiorin (ICMS, Temple University, Philadelphia, PA, USA) and
|
|
<LI>Jerome Henin (LISM, CNRS, Marseille, France). This code is located in
|
|
<LI>the directory lib/colvars and needs to be compiled first. The colvars
|
|
<LI>fix and an interface layer, exchanges information between LAMMPS and
|
|
<LI>the collective variable module.
|
|
</UL>
|
|
<P>See the doc page of <A HREF = "fix_colvars.html">fix colvars</A> for more details.
|
|
</P>
|
|
<P>There are example scripts for using this package in
|
|
examples/USER/colvars
|
|
</P>
|
|
<P>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.
|
|
</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_7">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-DIFFRACTION package
|
|
</H4>
|
|
<P>This package contains the commands neeed to calculate x-ray and
|
|
electron diffraction intensities based on kinematic diffraction
|
|
theory.
|
|
</P>
|
|
<P>See these doc pages and their related commands to get started:
|
|
</P>
|
|
<UL><LI><A HREF = "compute_xrd.html">compute xrd</A>
|
|
<LI><A HREF = "compute_saed.html">compute saed</A>
|
|
<LI><A HREF = "fix_saed_vtk.html">fix saed/vtk</A>
|
|
</UL>
|
|
<P>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.
|
|
</P>
|
|
<HR>
|
|
|
|
<H4>USER-DRUDE package
|
|
</H4>
|
|
<P>This package implements methods for simulating polarizable systems
|
|
in LAMMPS using thermalized Drude oscillators.
|
|
</P>
|
|
<P>See these doc pages and their related commands to get started:
|
|
</P>
|
|
<UL><LI><A HREF = "tutorial_drude.html">Drude tutorial</A>
|
|
<LI><A HREF = "fix_drude.html">fix drude</A>
|
|
<LI><A HREF = "compute_temp_drude.html">compute temp/drude</A>
|
|
<LI><A HREF = "fix_langevin_drude.html">fix langevin/drude</A>
|
|
<LI><A HREF = "fix_drude_transform.html">fix drude/transform/...</A>
|
|
<LI><A HREF = "pair_thole.html">pair thole</A>
|
|
</UL>
|
|
<P>There are auxiliary tools for using this package in tools/drude.
|
|
</P>
|
|
<P>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.
|
|
</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-FEP package
|
|
</H4>
|
|
<P>This package provides methods for performing free energy perturbation
|
|
simulations with soft-core pair potentials in LAMMPS.
|
|
</P>
|
|
<P>See these doc pages and their related commands to get started:
|
|
</P>
|
|
<UL><LI><A HREF = "fix_adapt_fep.html">fix adapt/fep</A>
|
|
<LI><A HREF = "compute_fep.html">compute fep</A>
|
|
<LI><A HREF = "pair_lj_soft.html">soft pair styles</A>
|
|
</UL>
|
|
<P>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.
|
|
</P>
|
|
<HR>
|
|
|
|
<H4>USER-INTEL package
|
|
</H4>
|
|
<P>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.
|
|
</P>
|
|
<P>See this section of the manual to get started:
|
|
</P>
|
|
<P><A HREF = "Section_accelerate.html#acc_9">Section_accelerate</A>
|
|
</P>
|
|
<P>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.
|
|
</P>
|
|
<HR>
|
|
|
|
<H4>USER-LB package
|
|
</H4>
|
|
<P>This package contains a LAMMPS implementation of a background
|
|
Lattice-Boltzmann fluid, which can be used to model MD particles
|
|
influenced by hydrodynamic forces.
|
|
</P>
|
|
<P>See this doc page and its related commands to get started:
|
|
</P>
|
|
<P><A HREF = "fix_lb_fluid.html">fix lb/fluid</A>
|
|
</P>
|
|
<P>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.
|
|
</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-MOLFILE package
|
|
</H4>
|
|
<P>This package contains a dump molfile command which uses molfile
|
|
plugins that are bundled with the
|
|
<A HREF = "http://www.ks.uiuc.edu/Research/vmd">VMD</A> molecular visualization and
|
|
analysis program, to enable LAMMPS to dump its information in formats
|
|
compatible with various molecular simulation tools.
|
|
</P>
|
|
<P>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.
|
|
</P>
|
|
<P>See this doc page to get started:
|
|
</P>
|
|
<P><A HREF = "dump_molfile.html#acc_5">dump molfile</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-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_5">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-PHONON package
|
|
</H4>
|
|
<P>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.
|
|
</P>
|
|
<P>See this doc page to get started:
|
|
</P>
|
|
<P><A HREF = "fix_phonon.html">fix phonon</A>
|
|
</P>
|
|
<P>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.
|
|
</P>
|
|
<HR>
|
|
|
|
<H4>USER-QMMM package
|
|
</H4>
|
|
<P>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 <A HREF = "http://www.quantum-espresso.org">Quantum ESPRESSO</A> package.
|
|
</P>
|
|
|
|
|
|
<P>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.
|
|
</P>
|
|
<P>See this doc page to get started:
|
|
</P>
|
|
<P><A HREF = "fix_qmmm.html">fix qmmm</A>
|
|
</P>
|
|
<P>as well as the lib/qmmm/README file.
|
|
</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-QTB package
|
|
</H4>
|
|
<P>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.
|
|
</P>
|
|
<P>See these two doc pages to get started:
|
|
</P>
|
|
<P><A HREF = "fix_qtb.html">fix qtb</A> provides quantum nulcear correction through a
|
|
colored thermostat and can be used with other time integration schemes
|
|
like <A HREF = "fix_nve.html">fix nve</A> or <A HREF = "fix_nh.html">fix nph</A>.
|
|
</P>
|
|
<P><A HREF = "fix_qbmsst.html">fix qbmsst</A> enables quantum nuclear correction of a
|
|
multi-scale shock technique simulation by coupling the quantum thermal
|
|
bath with the shocked system.
|
|
</P>
|
|
<P>The person who created this package is Yuan Shen (sy0302 at
|
|
stanford.edu) at Stanford University. 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>
|