<li>force-field compatibility with common CHARMM, AMBER, DREIDING, OPLS, GROMACS, COMPASS options</li>
<li>access to <aclass="reference external"href="http://openkim.org">KIM archive</a> of potentials via <aclass="reference internal"href="pair_kim.html"><spanclass="doc">pair kim</span></a></li>
<li>hybrid potentials: multiple pair, bond, angle, dihedral, improper potentials can be used in one simulation</li>
<li>overlaid potentials: superposition of multiple pair potentials</li>
<li>energy minimization via conjugate gradient or steepest descent relaxation</li>
<li>rRESPA hierarchical timestepping</li>
<li>rerun command for post-processing of dump files</li>
</ul>
</div>
<divclass="section"id="diagnostics">
<h3>1.2.7. Diagnostics</h3>
<ulclass="simple">
<li>see the various flavors of the <aclass="reference internal"href="fix.html"><spanclass="doc">fix</span></a> and <aclass="reference internal"href="compute.html"><spanclass="doc">compute</span></a> commands</li>
<li>Various pre- and post-processing serial tools are packaged
with LAMMPS; see these <aclass="reference internal"href="Section_tools.html"><spanclass="doc">doc pages</span></a>.</li>
<li>Our group has also written and released a separate toolkit called
<aclass="reference external"href="http://www.sandia.gov/~sjplimp/pizza.html">Pizza.py</a> which provides tools for doing setup, analysis,
plotting, and visualization for LAMMPS simulations. Pizza.py is
written in <aclass="reference external"href="http://www.python.org">Python</a> and is available for download from <aclass="reference external"href="http://www.sandia.gov/~sjplimp/pizza.html">the Pizza.py WWW site</a>.</li>
</ul>
</div>
<divclass="section"id="specialized-features">
<h3>1.2.11. Specialized features</h3>
<p>These are LAMMPS capabilities which you may not think of as typical
molecular dynamics options:</p>
<ulclass="simple">
<li><aclass="reference internal"href="balance.html"><spanclass="doc">static</span></a> and <aclass="reference internal"href="fix_balance.html"><spanclass="doc">dynamic load-balancing</span></a></li>
<li><aclass="reference internal"href="fix_ipi.html"><spanclass="doc">path-integral molecular dynamics (PIMD)</span></a> and <aclass="reference internal"href="fix_pimd.html"><spanclass="doc">this as well</span></a></li>
<li>Monte Carlo via <aclass="reference internal"href="fix_gcmc.html"><spanclass="doc">GCMC</span></a> and <aclass="reference internal"href="fix_tfmc.html"><spanclass="doc">tfMC</span></a> and <spanclass="xref doc">atom swapping</span></li>
<li><aclass="reference internal"href="pair_dsmc.html"><spanclass="doc">Direct Simulation Monte Carlo</span></a> for low-density fluids</li>
<li>perform sophisticated analyses of your MD simulation</li>
<li>visualize your MD simulation</li>
<li>plot your output data</li>
</ul>
<p>A few tools for pre- and post-processing tasks are provided as part of
the LAMMPS package; they are described in <aclass="reference internal"href="Section_tools.html"><spanclass="doc">this section</span></a>. However, many people use other codes or
write their own tools for these tasks.</p>
<p>As noted above, our group has also written and released a separate
toolkit called <aclass="reference external"href="http://www.sandia.gov/~sjplimp/pizza.html">Pizza.py</a> which addresses some of the listed
bullets. It provides tools for doing setup, analysis, plotting, and
visualization for LAMMPS simulations. Pizza.py is written in
<aclass="reference external"href="http://www.python.org">Python</a> and is available for download from <aclass="reference external"href="http://www.sandia.gov/~sjplimp/pizza.html">the Pizza.py WWW site</a>.</p>
<p>LAMMPS requires as input a list of initial atom coordinates and types,
molecular topology information, and force-field coefficients assigned
to all atoms and bonds. LAMMPS will not build molecular systems and
assign force-field parameters for you.</p>
<p>For atomic systems LAMMPS provides a <aclass="reference internal"href="create_atoms.html"><spanclass="doc">create_atoms</span></a>
command which places atoms on solid-state lattices (fcc, bcc,
user-defined, etc). Assigning small numbers of force field
coefficients can be done via the <aclass="reference internal"href="pair_coeff.html"><spanclass="doc">pair coeff</span></a>, <aclass="reference internal"href="bond_coeff.html"><spanclass="doc">bond coeff</span></a>, <aclass="reference internal"href="angle_coeff.html"><spanclass="doc">angle coeff</span></a>, etc commands.
For molecular systems or more complicated simulation geometries, users
typically use another code as a builder and convert its output to
LAMMPS input format, or write their own code to generate atom
coordinate and molecular topology for LAMMPS to read in.</p>
<p>For complicated molecular systems (e.g. a protein), a multitude of
topology information and hundreds of force-field coefficients must
typically be specified. We suggest you use a program like
<aclass="reference external"href="http://www.scripps.edu/brooks">CHARMM</a> or <aclass="reference external"href="http://amber.scripps.edu">AMBER</a> or other molecular builders to setup
such problems and dump its information to a file. You can then
reformat the file as LAMMPS input. Some of the tools in <aclass="reference internal"href="Section_tools.html"><spanclass="doc">this section</span></a> can assist in this process.</p>
<p>Similarly, LAMMPS creates output files in a simple format. Most users
post-process these files with their own analysis tools or re-format
them for input into other programs, including visualization packages.
If you are convinced you need to compute something on-the-fly as
LAMMPS runs, see <aclass="reference internal"href="Section_modify.html"><spanclass="doc">Section_modify</span></a> for a discussion
of how you can use the <aclass="reference internal"href="dump.html"><spanclass="doc">dump</span></a> and <aclass="reference internal"href="compute.html"><spanclass="doc">compute</span></a> and
<aclass="reference internal"href="fix.html"><spanclass="doc">fix</span></a> commands to print out data of your choosing. Keep in
mind that complicated computations can slow down the molecular
dynamics timestepping, particularly if the computations are not
parallel, so it is often better to leave such analysis to
post-processing codes.</p>
<p>A very simple (yet fast) visualizer is provided with the LAMMPS
package - see the <aclass="reference internal"href="Section_tools.html#xmovie"><spanclass="std std-ref">xmovie</span></a> tool in <aclass="reference internal"href="Section_tools.html"><spanclass="doc">this section</span></a>. It creates xyz projection views of
atomic coordinates and animates them. We find it very useful for
debugging purposes. For high-quality visualization we recommend the
<p>CHARMM, AMBER, NAMD, NWCHEM, and Tinker are designed primarily for
modeling biological molecules. CHARMM and AMBER use
atom-decomposition (replicated-data) strategies for parallelism; NAMD
and NWCHEM use spatial-decomposition approaches, similar to LAMMPS.
Tinker is a serial code. DL_POLY includes potentials for a variety of
biological and non-biological materials; both a replicated-data and
spatial-decomposition version exist.</p>
<hrclass="docutils"/>
</div>
<divclass="section"id="open-source-distribution">
<spanid="intro-4"></span><h2>1.4. Open source distribution</h2>
<p>LAMMPS comes with no warranty of any kind. As each source file states
in its header, it is a copyrighted code that is distributed free-of-
charge, under the terms of the <aclass="reference external"href="http://www.gnu.org/copyleft/gpl.html">GNU Public License</a> (GPL). This
is often referred to as open-source distribution - see
<aclass="reference external"href="http://www.gnu.org">www.gnu.org</a> or <aclass="reference external"href="http://www.opensource.org">www.opensource.org</a> for more
details. The legal text of the GPL is in the LICENSE file that is
included in the LAMMPS distribution.</p>
<p>Here is a summary of what the GPL means for LAMMPS users:</p>
<p>(1) Anyone is free to use, modify, or extend LAMMPS in any way they
choose, including for commercial purposes.</p>
<p>(2) If you distribute a modified version of LAMMPS, it must remain
open-source, meaning you distribute it under the terms of the GPL.
You should clearly annotate such a code as a derivative version of
LAMMPS.</p>
<p>(3) If you release any code that includes LAMMPS source code, then it
must also be open-sourced, meaning you distribute it under the terms
of the GPL.</p>
<p>(4) If you give LAMMPS files to someone else, the GPL LICENSE file and
source file headers (including the copyright and GPL notices) should
remain part of the code.</p>
<p>In the spirit of an open-source code, these are various ways you can
contribute to making LAMMPS better. You can send email to the
<aclass="reference external"href="http://lammps.sandia.gov/authors.html">developers</a> on any of these
items.</p>
<ulclass="simple">
<li>Point prospective users to the <aclass="reference external"href="http://lammps.sandia.gov">LAMMPS WWW Site</a>. Mention it in
talks or link to it from your WWW site.</li>
<li>If you find an error or omission in this manual or on the <aclass="reference external"href="http://lammps.sandia.gov">LAMMPS WWW Site</a>, or have a suggestion for something to clarify or include,
<li>If you find a bug, <aclass="reference internal"href="Section_errors.html#err-2"><spanclass="std std-ref">Section_errors 2</span></a>
describes how to report it.</li>
<li>If you publish a paper using LAMMPS results, send the citation (and
any cool pictures or movies if you like) to add to the Publications,
Pictures, and Movies pages of the <aclass="reference external"href="http://lammps.sandia.gov">LAMMPS WWW Site</a>, with links
and attributions back to you.</li>
<li>Create a new Makefile.machine that can be added to the src/MAKE
directory.</li>
<li>The tools sub-directory of the LAMMPS distribution has various
stand-alone codes for pre- and post-processing of LAMMPS data. More
details are given in <aclass="reference internal"href="Section_tools.html"><spanclass="doc">Section_tools</span></a>. If you write
a new tool that users will find useful, it can be added to the LAMMPS
distribution.</li>
<li>LAMMPS is designed to be easy to extend with new code for features
like potentials, boundary conditions, diagnostic computations, etc.
<aclass="reference internal"href="Section_modify.html"><spanclass="doc">This section</span></a> gives details. If you add a
feature of general interest, it can be added to the LAMMPS
distribution.</li>
<li>The Benchmark page of the <aclass="reference external"href="http://lammps.sandia.gov">LAMMPS WWW Site</a> lists LAMMPS
performance on various platforms. The files needed to run the
benchmarks are part of the LAMMPS distribution. If your machine is
sufficiently different from those listed, your timing data can be
added to the page.</li>
<li>You can send feedback for the User Comments page of the <aclass="reference external"href="http://lammps.sandia.gov">LAMMPS WWW Site</a>. It might be added to the page. No promises.</li>
<li>Cash. Small denominations, unmarked bills preferred. Paper sack OK.
Leave on desk. VISA also accepted. Chocolate chip cookies
<spanid="intro-5"></span><h2>1.5. Acknowledgments and citations</h2>
<p>LAMMPS development has been funded by the <aclass="reference external"href="http://www.doe.gov">US Department of Energy</a> (DOE), through its CRADA, LDRD, ASCI, and Genomes-to-Life
programs and its <aclass="reference external"href="http://www.sc.doe.gov/ascr/home.html">OASCR</a> and <aclass="reference external"href="http://www.er.doe.gov/production/ober/ober_top.html">OBER</a> offices.</p>
<p>Specifically, work on the latest version was funded in part by the US
Department of Energy’s Genomics:GTL program
(<aclass="reference external"href="http://www.doegenomestolife.org">www.doegenomestolife.org</a>) under the <aclass="reference external"href="http://www.genomes2life.org">project</a>, “Carbon
Sequestration in Synechococcus Sp.: From Molecular Machines to
Hierarchical Modeling”.</p>
<p>The following paper describe the basic parallel algorithms used in
LAMMPS. If you use LAMMPS results in your published work, please cite
this paper and include a pointer to the <aclass="reference external"href="http://lammps.sandia.gov">LAMMPS WWW Site</a>
<p>Other papers describing specific algorithms used in LAMMPS are listed
under the <aclass="reference external"href="http://lammps.sandia.gov/cite.html">Citing LAMMPS link</a> of
the LAMMPS WWW page.</p>
<p>The <aclass="reference external"href="http://lammps.sandia.gov/papers.html">Publications link</a> on the
LAMMPS WWW page lists papers that have cited LAMMPS. If your paper is
not listed there for some reason, feel free to send us the info. If
the simulations in your paper produced cool pictures or animations,
we’ll be pleased to add them to the
<aclass="reference external"href="http://lammps.sandia.gov/pictures.html">Pictures</a> or
<aclass="reference external"href="http://lammps.sandia.gov/movies.html">Movies</a> pages of the LAMMPS WWW
site.</p>
<p>The core group of LAMMPS developers is at Sandia National Labs:</p>
<ulclass="simple">
<li>Steve Plimpton, sjplimp at sandia.gov</li>
<li>Aidan Thompson, athomps at sandia.gov</li>
<li>Paul Crozier, pscrozi at sandia.gov</li>
</ul>
<p>The following folks are responsible for significant contributions to
the code, or other aspects of the LAMMPS development effort. Many of
the packages they have written are somewhat unique to LAMMPS and the
code would not be as general-purpose as it is without their expertise
and efforts.</p>
<ulclass="simple">
<li>Axel Kohlmeyer (Temple U), akohlmey at gmail.com, SVN and Git repositories, indefatigable mail list responder, USER-CG-CMM and USER-OMP packages</li>
<li>Roy Pollock (LLNL), Ewald and PPPM solvers</li>
<li>Mike Brown (ORNL), brownw at ornl.gov, GPU package</li>
<li>Greg Wagner (Sandia), gjwagne at sandia.gov, MEAM package for MEAM potential</li>
<li>Mike Parks (Sandia), mlparks at sandia.gov, PERI package for Peridynamics</li>
<li>Rudra Mukherjee (JPL), Rudranarayan.M.Mukherjee at jpl.nasa.gov, POEMS package for articulated rigid body motion</li>
<li>Reese Jones (Sandia) and collaborators, rjones at sandia.gov, USER-ATC package for atom/continuum coupling</li>
<li>Ilya Valuev (JIHT), valuev at physik.hu-berlin.de, USER-AWPMD package for wave-packet MD</li>
<li>Christian Trott (U Tech Ilmenau), christian.trott at tu-ilmenau.de, USER-CUDA package</li>
<li>Andres Jaramillo-Botero (Caltech), ajaramil at wag.caltech.edu, USER-EFF package for electron force field</li>
<li>Christoph Kloss (JKU), Christoph.Kloss at jku.at, USER-LIGGGHTS package for granular models and granular/fluid coupling</li>
<li>Metin Aktulga (LBL), hmaktulga at lbl.gov, USER-REAXC package for C version of ReaxFF</li>
<li>Georg Gunzenmuller (EMI), georg.ganzenmueller at emi.fhg.de, USER-SPH package</li>
</ul>
<p>As discussed in <aclass="reference internal"href="Section_history.html"><spanclass="doc">Section_history</span></a>, LAMMPS
originated as a cooperative project between DOE labs and industrial
partners. Folks involved in the design and testing of the original
version of LAMMPS were the following:</p>
<ulclass="simple">
<li>John Carpenter (Mayo Clinic, formerly at Cray Research)</li>
<li>Terry Stouch (Lexicon Pharmaceuticals, formerly at Bristol Myers Squibb)</li>
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