<p>The LAMMPS distribution includes an examples sub-directory with many
sample problems. Many are 2d models that run quickly are are
straightforward to visualize, requiring at most a couple of minutes to
run on a desktop machine. Each problem has an input script (in.*) and
produces a log file (log.*) when it runs. Some use a data file
(data.*) of initial coordinates as additional input. A few sample log
file run on different machines and different numbers of processors are
included in the directories to compare your answers to. E.g. a log
file like log.date.crack.foo.P means the “crack” example was run on P
processors of machine “foo” on that date (i.e. with that version of
LAMMPS).</p>
<p>Many of the input files have commented-out lines for creating dump
files and image files.</p>
<p>If you uncomment the <aclass="reference internal"href="dump.html"><spanclass="doc">dump</span></a> command in the input script, a
text dump file will be produced, which can be animated by various
<aclass="reference external"href="http://lammps.sandia.gov/viz.html">visualization programs</a>. It can
also be animated using the xmovie tool described in the <aclass="reference internal"href="Section_tools.html"><spanclass="doc">Additional Tools</span></a> section of the LAMMPS documentation.</p>
<p>If you uncomment the <aclass="reference internal"href="dump.html"><spanclass="doc">dump image</span></a> command in the input
script, and assuming you have built LAMMPS with a JPG library, JPG
snapshot images will be produced when the simulation runs. They can
be quickly post-processed into a movie using commands described on the
<p>Animations of many of the examples can be viewed on the Movies section
of the <aclass="reference external"href="http://lammps.sandia.gov">LAMMPS web site</a>.</p>
<p>There are two kinds of sub-directories in the examples dir. Lowercase
dirs contain one or a few simple, quick-to-run problems. Uppercase
dirs contain up to several complex scripts that illustrate a
particular kind of simulation method or model. Some of these run for
longer times, e.g. to measure a particular quantity.</p>
<p>Lists of both kinds of directories are given below.</p>
<hrclass="docutils"/>
<divclass="section"id="lowercase-directories">
<h2>7.1. Lowercase directories</h2>
<tableborder="1"class="docutils">
<colgroup>
<colwidth="16%"/>
<colwidth="84%"/>
</colgroup>
<tbodyvalign="top">
<trclass="row-odd"><td>accelerate</td>
<td>run with various acceleration options (OpenMP, GPU, Phi)</td>
</tr>
<trclass="row-even"><td>balance</td>
<td>dynamic load balancing, 2d system</td>
</tr>
<trclass="row-odd"><td>body</td>
<td>body particles, 2d system</td>
</tr>
<trclass="row-even"><td>colloid</td>
<td>big colloid particles in a small particle solvent, 2d system</td>
</tr>
<trclass="row-odd"><td>comb</td>
<td>models using the COMB potential</td>
</tr>
<trclass="row-even"><td>coreshell</td>
<td>core/shell model using CORESHELL package</td>
</tr>
<trclass="row-odd"><td>crack</td>
<td>crack propagation in a 2d solid</td>
</tr>
<trclass="row-even"><td>deposit</td>
<td>deposit atoms and molecules on a surface</td>
</tr>
<trclass="row-odd"><td>dipole</td>
<td>point dipolar particles, 2d system</td>
</tr>
<trclass="row-even"><td>dreiding</td>
<td>methanol via Dreiding FF</td>
</tr>
<trclass="row-odd"><td>eim</td>
<td>NaCl using the EIM potential</td>
</tr>
<trclass="row-even"><td>ellipse</td>
<td>ellipsoidal particles in spherical solvent, 2d system</td>
</tr>
<trclass="row-odd"><td>flow</td>
<td>Couette and Poiseuille flow in a 2d channel</td>
</tr>
<trclass="row-even"><td>friction</td>
<td>frictional contact of spherical asperities between 2d surfaces</td>
</tr>
<trclass="row-odd"><td>hugoniostat</td>
<td>Hugoniostat shock dynamics</td>
</tr>
<trclass="row-even"><td>indent</td>
<td>spherical indenter into a 2d solid</td>
</tr>
<trclass="row-odd"><td>kim</td>
<td>use of potentials in Knowledge Base for Interatomic Models (KIM)</td>
</tr>
<trclass="row-even"><td>meam</td>
<td>MEAM test for SiC and shear (same as shear examples)</td>
</tr>
<trclass="row-odd"><td>melt</td>
<td>rapid melt of 3d LJ system</td>
</tr>
<trclass="row-even"><td>micelle</td>
<td>self-assembly of small lipid-like molecules into 2d bilayers</td>
</tr>
<trclass="row-odd"><td>min</td>
<td>energy minimization of 2d LJ melt</td>
</tr>
<trclass="row-even"><td>msst</td>
<td>MSST shock dynamics</td>
</tr>
<trclass="row-odd"><td>nb3b</td>
<td>use of nonbonded 3-body harmonic pair style</td>
</tr>
<trclass="row-even"><td>neb</td>
<td>nudged elastic band (NEB) calculation for barrier finding</td>
</tr>
<trclass="row-odd"><td>nemd</td>
<td>non-equilibrium MD of 2d sheared system</td>
</tr>
<trclass="row-even"><td>obstacle</td>
<td>flow around two voids in a 2d channel</td>
</tr>
<trclass="row-odd"><td>peptide</td>
<td>dynamics of a small solvated peptide chain (5-mer)</td>
</tr>
<trclass="row-even"><td>peri</td>
<td>Peridynamic model of cylinder impacted by indenter</td>
</tr>
<trclass="row-odd"><td>pour</td>
<td>pouring of granular particles into a 3d box, then chute flow</td>
</tr>
<trclass="row-even"><td>prd</td>
<td>parallel replica dynamics of vacancy diffusion in bulk Si</td>
</tr>
<trclass="row-odd"><td>python</td>
<td>using embedded Python in a LAMMPS input script</td>
</tr>
<trclass="row-even"><td>qeq</td>
<td>use of the QEQ package for charge equilibration</td>
</tr>
<trclass="row-odd"><td>reax</td>
<td>RDX and TATB models using the ReaxFF</td>
</tr>
<trclass="row-even"><td>rigid</td>
<td>rigid bodies modeled as independent or coupled</td>
</tr>
<trclass="row-odd"><td>shear</td>
<td>sideways shear applied to 2d solid, with and without a void</td>
</tr>
<trclass="row-even"><td>snap</td>
<td>NVE dynamics for BCC tantalum crystal using SNAP potential</td>
</tr>
<trclass="row-odd"><td>srd</td>
<td>stochastic rotation dynamics (SRD) particles as solvent</td>
</tr>
<trclass="row-even"><td>streitz</td>
<td>use of Streitz/Mintmire potential with charge equilibration</td>
</tr>
<trclass="row-odd"><td>tad</td>
<td>temperature-accelerated dynamics of vacancy diffusion in bulk Si</td>
</tr>
<trclass="row-even"><td>vashishta</td>
<td>use of the Vashishta potential</td>
</tr>
</tbody>
</table>
<p>Here is how you can run and visualize one of the sample problems:</p>
<preclass="literal-block">
cd indent
cp ../../src/lmp_linux . # copy LAMMPS executable to this dir
lmp_linux -in in.indent # run the problem
</pre>
<p>Running the simulation produces the files <em>dump.indent</em> and
<em>log.lammps</em>. You can visualize the dump file of snapshots with a
variety of 3rd-party tools highlighted on the
<aclass="reference external"href="http://lammps.sandia.gov/viz.html">Visualization</a> page of the LAMMPS
web site.</p>
<p>If you uncomment the <aclass="reference internal"href="dump_image.html"><spanclass="doc">dump image</span></a> line(s) in the input
script a series of JPG images will be produced by the run (assuming
you built LAMMPS with JPG support; see <aclass="reference internal"href="Section_start.html"><spanclass="doc">Section start 2.2</span></a> for details). These can be viewed
individually or turned into a movie or animated by tools like
ImageMagick or QuickTime or various Windows-based tools. See the
<aclass="reference internal"href="dump_image.html"><spanclass="doc">dump image</span></a> doc page for more details. E.g. this
Imagemagick command would create a GIF file suitable for viewing in a
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