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<p class="caption"><span class="caption-text">User Documentation</span></p>
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<ul class="current">
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<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
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<li class="toctree-l1 current"><a class="current reference internal" href="#">7. Example problems</a><ul>
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<li class="toctree-l2"><a class="reference internal" href="#lowercase-directories">7.1. Lowercase directories</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#uppercase-directories">7.2. Uppercase directories</a></li>
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</ul>
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</li>
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<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
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<p class="caption"><span class="caption-text">Index</span></p>
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<li class="toctree-l1"><a class="reference internal" href="computes.html">Computes</a></li>
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<li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
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<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
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<li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
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<li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
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<li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>
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<li>7. Example problems</li>
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<div class="section" id="example-problems">
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<h1>7. Example problems</h1>
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<p>The LAMMPS distribution includes an examples sub-directory with many
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sample problems. Many are 2d models that run quickly are are
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straightforward to visualize, requiring at most a couple of minutes to
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run on a desktop machine. Each problem has an input script (in.*) and
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produces a log file (log.*) when it runs. Some use a data file
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(data.*) of initial coordinates as additional input. A few sample log
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file run on different machines and different numbers of processors are
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included in the directories to compare your answers to. E.g. a log
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file like log.date.crack.foo.P means the “crack” example was run on P
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processors of machine “foo” on that date (i.e. with that version of
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LAMMPS).</p>
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<p>Many of the input files have commented-out lines for creating dump
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files and image files.</p>
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<p>If you uncomment the <a class="reference internal" href="dump.html"><span class="doc">dump</span></a> command in the input script, a
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text dump file will be produced, which can be animated by various
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<a class="reference external" href="http://lammps.sandia.gov/viz.html">visualization programs</a>. It can
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also be animated using the xmovie tool described in the <a class="reference internal" href="Section_tools.html"><span class="doc">Additional Tools</span></a> section of the LAMMPS documentation.</p>
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<p>If you uncomment the <a class="reference internal" href="dump.html"><span class="doc">dump image</span></a> command in the input
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script, and assuming you have built LAMMPS with a JPG library, JPG
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snapshot images will be produced when the simulation runs. They can
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be quickly post-processed into a movie using commands described on the
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<a class="reference internal" href="dump_image.html"><span class="doc">dump image</span></a> doc page.</p>
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<p>Animations of many of the examples can be viewed on the Movies section
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of the <a class="reference external" href="http://lammps.sandia.gov">LAMMPS web site</a>.</p>
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<p>There are two kinds of sub-directories in the examples dir. Lowercase
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dirs contain one or a few simple, quick-to-run problems. Uppercase
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dirs contain up to several complex scripts that illustrate a
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particular kind of simulation method or model. Some of these run for
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longer times, e.g. to measure a particular quantity.</p>
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<p>Lists of both kinds of directories are given below.</p>
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<hr class="docutils" />
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<div class="section" id="lowercase-directories">
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<h2>7.1. Lowercase directories</h2>
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<table border="1" class="docutils">
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<colgroup>
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<col width="16%" />
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<col width="84%" />
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</colgroup>
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<tbody valign="top">
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<tr class="row-odd"><td>accelerate</td>
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<td>run with various acceleration options (OpenMP, GPU, Phi)</td>
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</tr>
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<tr class="row-even"><td>balance</td>
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<td>dynamic load balancing, 2d system</td>
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</tr>
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<tr class="row-odd"><td>body</td>
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<td>body particles, 2d system</td>
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</tr>
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<tr class="row-even"><td>colloid</td>
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<td>big colloid particles in a small particle solvent, 2d system</td>
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</tr>
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<tr class="row-odd"><td>comb</td>
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<td>models using the COMB potential</td>
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</tr>
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<tr class="row-even"><td>coreshell</td>
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<td>core/shell model using CORESHELL package</td>
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</tr>
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<tr class="row-odd"><td>crack</td>
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<td>crack propagation in a 2d solid</td>
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</tr>
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<tr class="row-even"><td>deposit</td>
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<td>deposit atoms and molecules on a surface</td>
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</tr>
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<tr class="row-odd"><td>dipole</td>
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<td>point dipolar particles, 2d system</td>
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</tr>
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<tr class="row-even"><td>dreiding</td>
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<td>methanol via Dreiding FF</td>
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</tr>
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<tr class="row-odd"><td>eim</td>
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<td>NaCl using the EIM potential</td>
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</tr>
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<tr class="row-even"><td>ellipse</td>
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<td>ellipsoidal particles in spherical solvent, 2d system</td>
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</tr>
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<tr class="row-odd"><td>flow</td>
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<td>Couette and Poiseuille flow in a 2d channel</td>
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</tr>
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<tr class="row-even"><td>friction</td>
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<td>frictional contact of spherical asperities between 2d surfaces</td>
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</tr>
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<tr class="row-odd"><td>hugoniostat</td>
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<td>Hugoniostat shock dynamics</td>
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</tr>
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<tr class="row-even"><td>indent</td>
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<td>spherical indenter into a 2d solid</td>
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</tr>
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<tr class="row-odd"><td>kim</td>
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<td>use of potentials in Knowledge Base for Interatomic Models (KIM)</td>
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</tr>
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<tr class="row-even"><td>meam</td>
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<td>MEAM test for SiC and shear (same as shear examples)</td>
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</tr>
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<tr class="row-odd"><td>melt</td>
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<td>rapid melt of 3d LJ system</td>
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</tr>
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<tr class="row-even"><td>micelle</td>
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<td>self-assembly of small lipid-like molecules into 2d bilayers</td>
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</tr>
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<tr class="row-odd"><td>min</td>
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<td>energy minimization of 2d LJ melt</td>
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</tr>
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<tr class="row-even"><td>msst</td>
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<td>MSST shock dynamics</td>
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</tr>
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<tr class="row-odd"><td>nb3b</td>
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<td>use of nonbonded 3-body harmonic pair style</td>
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</tr>
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<tr class="row-even"><td>neb</td>
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<td>nudged elastic band (NEB) calculation for barrier finding</td>
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</tr>
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<tr class="row-odd"><td>nemd</td>
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<td>non-equilibrium MD of 2d sheared system</td>
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</tr>
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<tr class="row-even"><td>obstacle</td>
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<td>flow around two voids in a 2d channel</td>
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</tr>
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<tr class="row-odd"><td>peptide</td>
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<td>dynamics of a small solvated peptide chain (5-mer)</td>
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</tr>
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<tr class="row-even"><td>peri</td>
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<td>Peridynamic model of cylinder impacted by indenter</td>
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</tr>
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<tr class="row-odd"><td>pour</td>
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<td>pouring of granular particles into a 3d box, then chute flow</td>
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</tr>
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<tr class="row-even"><td>prd</td>
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<td>parallel replica dynamics of vacancy diffusion in bulk Si</td>
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</tr>
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<tr class="row-odd"><td>python</td>
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<td>using embedded Python in a LAMMPS input script</td>
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</tr>
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<tr class="row-even"><td>qeq</td>
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<td>use of the QEQ package for charge equilibration</td>
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</tr>
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<tr class="row-odd"><td>reax</td>
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<td>RDX and TATB models using the ReaxFF</td>
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</tr>
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<tr class="row-even"><td>rigid</td>
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<td>rigid bodies modeled as independent or coupled</td>
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</tr>
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<tr class="row-odd"><td>shear</td>
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<td>sideways shear applied to 2d solid, with and without a void</td>
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</tr>
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<tr class="row-even"><td>snap</td>
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<td>NVE dynamics for BCC tantalum crystal using SNAP potential</td>
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</tr>
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<tr class="row-odd"><td>srd</td>
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<td>stochastic rotation dynamics (SRD) particles as solvent</td>
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</tr>
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<tr class="row-even"><td>streitz</td>
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<td>use of Streitz/Mintmire potential with charge equilibration</td>
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</tr>
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<tr class="row-odd"><td>tad</td>
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<td>temperature-accelerated dynamics of vacancy diffusion in bulk Si</td>
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</tr>
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<tr class="row-even"><td>vashishta</td>
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<td>use of the Vashishta potential</td>
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</tr>
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</tbody>
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</table>
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<p>Here is how you can run and visualize one of the sample problems:</p>
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<pre class="literal-block">
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cd indent
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cp ../../src/lmp_linux . # copy LAMMPS executable to this dir
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lmp_linux -in in.indent # run the problem
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</pre>
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<p>Running the simulation produces the files <em>dump.indent</em> and
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<em>log.lammps</em>. You can visualize the dump file of snapshots with a
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variety of 3rd-party tools highlighted on the
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<a class="reference external" href="http://lammps.sandia.gov/viz.html">Visualization</a> page of the LAMMPS
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web site.</p>
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<p>If you uncomment the <a class="reference internal" href="dump_image.html"><span class="doc">dump image</span></a> line(s) in the input
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script a series of JPG images will be produced by the run (assuming
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you built LAMMPS with JPG support; see <a class="reference internal" href="Section_start.html"><span class="doc">Section start 2.2</span></a> for details). These can be viewed
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individually or turned into a movie or animated by tools like
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ImageMagick or QuickTime or various Windows-based tools. See the
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<a class="reference internal" href="dump_image.html"><span class="doc">dump image</span></a> doc page for more details. E.g. this
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Imagemagick command would create a GIF file suitable for viewing in a
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browser.</p>
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<pre class="literal-block">
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% convert -loop 1 *.jpg foo.gif
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</pre>
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</div>
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<hr class="docutils" />
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<div class="section" id="uppercase-directories">
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<h2>7.2. Uppercase directories</h2>
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<table border="1" class="docutils">
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<colgroup>
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<col width="11%" />
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<col width="89%" />
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</colgroup>
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<tbody valign="top">
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<tr class="row-odd"><td>ASPHERE</td>
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<td>various aspherical particle models, using ellipsoids, rigid bodies, line/triangle particles, etc</td>
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</tr>
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<tr class="row-even"><td>COUPLE</td>
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<td>examples of how to use LAMMPS as a library</td>
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</tr>
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<tr class="row-odd"><td>DIFFUSE</td>
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<td>compute diffusion coefficients via several methods</td>
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</tr>
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<tr class="row-even"><td>ELASTIC</td>
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<td>compute elastic constants at zero temperature</td>
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</tr>
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<tr class="row-odd"><td>ELASTIC_T</td>
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<td>compute elastic constants at finite temperature</td>
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</tr>
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<tr class="row-even"><td>KAPPA</td>
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<td>compute thermal conductivity via several methods</td>
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</tr>
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<tr class="row-odd"><td>MC</td>
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<td>using LAMMPS in a Monte Carlo mode to relax the energy of a system</td>
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</tr>
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<tr class="row-even"><td>USER</td>
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<td>examples for USER packages and USER-contributed commands</td>
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</tr>
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<tr class="row-odd"><td>VISCOSITY</td>
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<td>compute viscosity via several methods</td>
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</tr>
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</tbody>
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</table>
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<p>Nearly all of these directories have README files which give more
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details on how to understand and use their contents.</p>
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<p>The USER directory has a large number of sub-directories which
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correspond by name to a USER package. They contain scripts that
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illustrate how to use the command(s) provided in that package. Many
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of the sub-directories have their own README files which give further
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instructions. See the <a class="reference internal" href="Section_packages.html"><span class="doc">Section packages</span></a> doc
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page for more info on specific USER packages.</p>
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</div>
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<footer>
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<a href="Section_perf.html" class="btn btn-neutral float-right" title="8. Performance & scalability" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
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<p>
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© Copyright 2013 Sandia Corporation.
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</p>
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