438 lines
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HTML
438 lines
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HTML
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<div class="lammps_version">Version: <b>19 Nov 2024</b></div>
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<li class="toctree-l1"><a class="reference internal" href="Speed.html">7. Accelerate performance</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Howto.html">8. Howto discussions</a></li>
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<li class="toctree-l1 current"><a class="current reference internal" href="#">9. Example scripts</a><ul>
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<li class="toctree-l2"><a class="reference internal" href="#lowercase-directories">9.1. Lowercase directories</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#uppercase-directories">9.2. Uppercase directories</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Tools.html">10. Auxiliary tools</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Library.html">1. LAMMPS Library Interfaces</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Modify.html">3. Modifying & extending LAMMPS</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="breadcrumb-item active"><span class="section-number">9. </span>Example scripts</li>
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<p><span class="math notranslate nohighlight">\(\renewcommand{\AA}{\text{Å}}\)</span></p>
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<section id="example-scripts">
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<h1><span class="section-number">9. </span>Example scripts<a class="headerlink" href="#example-scripts" title="Link to this heading"></a></h1>
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<p>The LAMMPS distribution includes an examples subdirectory with many
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sample problems. Many are 2d models that run quickly and 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="https://www.lammps.org/viz.html">visualization programs</a>.</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="https://www.lammps.org/movies.html">LAMMPS website</a>.</p>
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<p>There are two kinds of subdirectories in the examples folder. Lower
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case named directories contain one or a few simple, quick-to-run
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problems. Upper case named directories contain up to several complex
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scripts that illustrate a particular kind of simulation method or
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model. Some of these run for longer times, e.g. to measure a
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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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<section id="lowercase-directories">
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<h2><span class="section-number">9.1. </span>Lowercase directories<a class="headerlink" href="#lowercase-directories" title="Link to this heading"></a></h2>
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<table class="docutils align-default">
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<tbody>
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<tr class="row-odd"><td><p>accelerate</p></td>
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<td><p>run with various acceleration options (OpenMP, GPU, Phi)</p></td>
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</tr>
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<tr class="row-even"><td><p>airebo</p></td>
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<td><p>polyethylene with AIREBO potential</p></td>
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</tr>
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<tr class="row-odd"><td><p>atm</p></td>
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<td><p>Axilrod-Teller-Muto potential example</p></td>
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</tr>
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<tr class="row-even"><td><p>balance</p></td>
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<td><p>dynamic load balancing, 2d system</p></td>
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</tr>
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<tr class="row-odd"><td><p>body</p></td>
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<td><p>body particles, 2d system</p></td>
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</tr>
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<tr class="row-even"><td><p>bpm</p></td>
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<td><p>BPM simulations of pouring elastic grains and plate impact</p></td>
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</tr>
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<tr class="row-odd"><td><p>cmap</p></td>
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<td><p>CMAP 5-body contributions to CHARMM force field</p></td>
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</tr>
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<tr class="row-even"><td><p>colloid</p></td>
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<td><p>big colloid particles in a small particle solvent, 2d system</p></td>
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</tr>
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<tr class="row-odd"><td><p>comb</p></td>
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<td><p>models using the COMB potential</p></td>
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</tr>
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<tr class="row-even"><td><p>controller</p></td>
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<td><p>use of fix controller as a thermostat</p></td>
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</tr>
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<tr class="row-odd"><td><p>coreshell</p></td>
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<td><p>core/shell model using CORESHELL package</p></td>
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</tr>
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<tr class="row-even"><td><p>crack</p></td>
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<td><p>crack propagation in a 2d solid</p></td>
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</tr>
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<tr class="row-odd"><td><p>deposit</p></td>
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<td><p>deposit atoms and molecules on a surface</p></td>
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</tr>
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<tr class="row-even"><td><p>dipole</p></td>
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<td><p>point dipolar particles, 2d system</p></td>
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</tr>
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<tr class="row-odd"><td><p>dreiding</p></td>
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<td><p>methanol via Dreiding FF</p></td>
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</tr>
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<tr class="row-even"><td><p>eim</p></td>
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<td><p>NaCl using the EIM potential</p></td>
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</tr>
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<tr class="row-odd"><td><p>ellipse</p></td>
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<td><p>ellipsoidal particles in spherical solvent, 2d system</p></td>
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</tr>
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<tr class="row-even"><td><p>flow</p></td>
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<td><p>Couette and Poiseuille flow in a 2d channel</p></td>
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</tr>
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<tr class="row-odd"><td><p>friction</p></td>
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<td><p>frictional contact of spherical asperities between 2d surfaces</p></td>
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</tr>
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<tr class="row-even"><td><p>mc</p></td>
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<td><p>Monte Carlo features via fix gcmc, widom and other commands</p></td>
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</tr>
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<tr class="row-odd"><td><p>granregion</p></td>
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<td><p>use of fix wall/region/gran as boundary on granular particles</p></td>
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</tr>
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<tr class="row-even"><td><p>hugoniostat</p></td>
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<td><p>Hugoniostat shock dynamics</p></td>
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</tr>
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<tr class="row-odd"><td><p>hyper</p></td>
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<td><p>global and local hyperdynamics of diffusion on Pt surface</p></td>
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</tr>
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<tr class="row-even"><td><p>indent</p></td>
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<td><p>spherical indenter into a 2d solid</p></td>
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</tr>
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<tr class="row-odd"><td><p>kim</p></td>
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<td><p>use of potentials from the <a class="reference external" href="https://openkim.org">OpenKIM Repository</a></p></td>
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</tr>
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<tr class="row-even"><td><p>mdi</p></td>
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<td><p>use of the MDI package and MolSSI MDI code coupling library</p></td>
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</tr>
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<tr class="row-odd"><td><p>meam</p></td>
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<td><p>MEAM test for SiC and shear (same as shear examples)</p></td>
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</tr>
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<tr class="row-even"><td><p>melt</p></td>
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<td><p>rapid melt of 3d LJ system</p></td>
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</tr>
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<tr class="row-odd"><td><p>micelle</p></td>
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<td><p>self-assembly of small lipid-like molecules into 2d bilayers</p></td>
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</tr>
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<tr class="row-even"><td><p>min</p></td>
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<td><p>energy minimization of 2d LJ melt</p></td>
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</tr>
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<tr class="row-odd"><td><p>msst</p></td>
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<td><p>MSST shock dynamics</p></td>
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</tr>
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<tr class="row-even"><td><p>multi</p></td>
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<td><p>multi neighboring for systems with large interaction disparities</p></td>
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</tr>
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<tr class="row-odd"><td><p>nb3b</p></td>
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<td><p>use of non-bonded 3-body harmonic pair style</p></td>
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</tr>
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<tr class="row-even"><td><p>neb</p></td>
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<td><p>nudged elastic band (NEB) calculation for barrier finding</p></td>
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</tr>
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<tr class="row-odd"><td><p>nemd</p></td>
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<td><p>non-equilibrium MD of 2d sheared system</p></td>
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</tr>
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<tr class="row-even"><td><p>obstacle</p></td>
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<td><p>flow around two voids in a 2d channel</p></td>
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</tr>
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<tr class="row-odd"><td><p>peptide</p></td>
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<td><p>dynamics of a small solvated peptide chain (5-mer)</p></td>
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</tr>
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<tr class="row-even"><td><p>peri</p></td>
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<td><p>Peridynamic model of cylinder impacted by indenter</p></td>
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</tr>
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<tr class="row-odd"><td><p>pour</p></td>
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<td><p>pouring of granular particles into a 3d box, then chute flow</p></td>
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</tr>
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<tr class="row-even"><td><p>prd</p></td>
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<td><p>parallel replica dynamics of vacancy diffusion in bulk Si</p></td>
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</tr>
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<tr class="row-odd"><td><p>python</p></td>
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<td><p>using embedded Python in a LAMMPS input script</p></td>
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</tr>
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<tr class="row-even"><td><p>qeq</p></td>
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<td><p>use of the QEQ package for charge equilibration</p></td>
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</tr>
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<tr class="row-odd"><td><p>rdf-adf</p></td>
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<td><p>computing radial and angle distribution functions for water</p></td>
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</tr>
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<tr class="row-even"><td><p>reax</p></td>
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<td><p>RDX and TATB models using the ReaxFF</p></td>
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</tr>
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<tr class="row-odd"><td><p>rerun</p></td>
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<td><p>use of rerun and read_dump commands</p></td>
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</tr>
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<tr class="row-even"><td><p>rheo</p></td>
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<td><p>RHEO simulations of fluid flows and phase transitions</p></td>
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</tr>
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<tr class="row-odd"><td><p>rigid</p></td>
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<td><p>rigid bodies modeled as independent or coupled</p></td>
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</tr>
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<tr class="row-even"><td><p>shear</p></td>
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<td><p>sideways shear applied to 2d solid, with and without a void</p></td>
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</tr>
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<tr class="row-odd"><td><p>snap</p></td>
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<td><p>NVE dynamics for BCC tantalum crystal using SNAP potential</p></td>
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</tr>
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<tr class="row-even"><td><p>srd</p></td>
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<td><p>stochastic rotation dynamics (SRD) particles as solvent</p></td>
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</tr>
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<tr class="row-odd"><td><p>streitz</p></td>
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<td><p>use of Streitz/Mintmire potential with charge equilibration</p></td>
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</tr>
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<tr class="row-even"><td><p>tad</p></td>
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<td><p>temperature-accelerated dynamics of vacancy diffusion in bulk Si</p></td>
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</tr>
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<tr class="row-odd"><td><p>threebody</p></td>
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<td><p>regression test input for a variety of manybody potentials</p></td>
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</tr>
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<tr class="row-even"><td><p>tracker</p></td>
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<td><p>track interactions in LJ melt</p></td>
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</tr>
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<tr class="row-odd"><td><p>vashishta</p></td>
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<td><p>use of the Vashishta potential</p></td>
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</tr>
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<tr class="row-even"><td><p>voronoi</p></td>
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<td><p>Voronoi tesselation via compute voronoi/atom command</p></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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<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="nb">cd</span><span class="w"> </span>indent
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cp<span class="w"> </span>../../src/lmp_linux<span class="w"> </span>.<span class="w"> </span><span class="c1"># copy LAMMPS executable to this dir</span>
|
|
lmp_linux<span class="w"> </span>-in<span class="w"> </span><span class="k">in</span>.indent<span class="w"> </span><span class="c1"># run the problem</span>
|
|
</pre></div>
|
|
</div>
|
|
<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 third-party tools highlighted on the
|
|
<a class="reference external" href="https://www.lammps.org/viz.html">Visualization</a> page of the LAMMPS
|
|
website.</p>
|
|
<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
|
|
script a series of JPG images will be produced by the run (assuming
|
|
you built LAMMPS with JPG support; see the
|
|
<a class="reference internal" href="Build_settings.html"><span class="doc">Build_settings</span></a> page 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
|
|
<a class="reference internal" href="dump_image.html"><span class="doc">dump image</span></a> page for more details. E.g. this
|
|
Imagemagick command would create a GIF file suitable for viewing in a
|
|
browser.</p>
|
|
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>%<span class="w"> </span>convert<span class="w"> </span>-loop<span class="w"> </span><span class="m">1</span><span class="w"> </span>*.jpg<span class="w"> </span>foo.gif
|
|
</pre></div>
|
|
</div>
|
|
</section>
|
|
<hr class="docutils" />
|
|
<section id="uppercase-directories">
|
|
<h2><span class="section-number">9.2. </span>Uppercase directories<a class="headerlink" href="#uppercase-directories" title="Link to this heading"></a></h2>
|
|
<table class="docutils align-default">
|
|
<tbody>
|
|
<tr class="row-odd"><td><p>ASPHERE</p></td>
|
|
<td><p>various aspherical particle models, using ellipsoids, rigid bodies, line/triangle particles, etc</p></td>
|
|
</tr>
|
|
<tr class="row-even"><td><p>COUPLE</p></td>
|
|
<td><p>examples of how to use LAMMPS as a library</p></td>
|
|
</tr>
|
|
<tr class="row-odd"><td><p>DIFFUSE</p></td>
|
|
<td><p>compute diffusion coefficients via several methods</p></td>
|
|
</tr>
|
|
<tr class="row-even"><td><p>ELASTIC</p></td>
|
|
<td><p>compute elastic constants at zero temperature</p></td>
|
|
</tr>
|
|
<tr class="row-odd"><td><p>ELASTIC_T</p></td>
|
|
<td><p>compute elastic constants at finite temperature</p></td>
|
|
</tr>
|
|
<tr class="row-even"><td><p>HEAT</p></td>
|
|
<td><p>compute thermal conductivity for LJ and water via fix ehex</p></td>
|
|
</tr>
|
|
<tr class="row-odd"><td><p>KAPPA</p></td>
|
|
<td><p>compute thermal conductivity via several methods</p></td>
|
|
</tr>
|
|
<tr class="row-even"><td><p>MC-LOOP</p></td>
|
|
<td><p>using LAMMPS in a Monte Carlo mode to relax the energy of a system in a input script loop</p></td>
|
|
</tr>
|
|
<tr class="row-odd"><td><p>PACKAGES</p></td>
|
|
<td><p>examples for specific packages and contributed commands</p></td>
|
|
</tr>
|
|
<tr class="row-even"><td><p>SPIN</p></td>
|
|
<td><p>examples for features of the SPIN package</p></td>
|
|
</tr>
|
|
<tr class="row-odd"><td><p>UNITS</p></td>
|
|
<td><p>examples that run the same simulation in lj, real, metal units</p></td>
|
|
</tr>
|
|
<tr class="row-even"><td><p>VISCOSITY</p></td>
|
|
<td><p>compute viscosity via several methods</p></td>
|
|
</tr>
|
|
</tbody>
|
|
</table>
|
|
<p>Nearly all of these directories have README files which give more
|
|
details on how to understand and use their contents.</p>
|
|
<p>The PACKAGES directory has a large number of subdirectories which
|
|
correspond by name to specific packages. They contain scripts that
|
|
illustrate how to use the command(s) provided in those packages. Many
|
|
of the subdirectories have their own README files which give further
|
|
instructions. See the <a class="reference internal" href="Packages_details.html"><span class="doc">Packages_details</span></a> doc
|
|
page for more info on specific packages.</p>
|
|
</section>
|
|
</section>
|
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