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<li class="toctree-l2"><a class="reference internal" href="Python_formats.html">2.7. Output Readers</a></li>
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<li class="toctree-l2 current"><a class="current reference internal" href="#">2.8. Example Python scripts</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Python_error.html">2.9. Handling LAMMPS errors</a></li>
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<li class="breadcrumb-item active"><span class="section-number">2.8. </span>Example Python 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-python-scripts">
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<h1><span class="section-number">2.8. </span>Example Python scripts<a class="headerlink" href="#example-python-scripts" title="Link to this heading"></a></h1>
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<p>The <code class="docutils literal notranslate"><span class="pre">python/examples</span></code> directory has Python scripts which show how Python
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can run LAMMPS, grab data, change it, and put it back into LAMMPS.</p>
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<p>These are the Python scripts included as demos in the <code class="docutils literal notranslate"><span class="pre">python/examples</span></code>
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directory of the LAMMPS distribution, to illustrate the kinds of
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things that are possible when Python wraps LAMMPS. If you create your
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own scripts, send them to us and we can include them in the LAMMPS
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distribution.</p>
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<table class="docutils align-default">
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<tbody>
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<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">trivial.py</span></code></p></td>
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<td><p>read/run a LAMMPS input script through Python</p></td>
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</tr>
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<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">demo.py</span></code></p></td>
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<td><p>invoke various LAMMPS library interface routines</p></td>
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</tr>
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<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">simple.py</span></code></p></td>
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<td><p>run in parallel, similar to <code class="docutils literal notranslate"><span class="pre">examples/COUPLE/simple/simple.cpp</span></code></p></td>
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</tr>
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<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">split.py</span></code></p></td>
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<td><p>same as <code class="docutils literal notranslate"><span class="pre">simple.py</span></code> but running in parallel on a subset of procs</p></td>
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</tr>
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<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">gui.py</span></code></p></td>
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<td><p>GUI go/stop/temperature-slider to control LAMMPS</p></td>
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</tr>
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<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">plot.py</span></code></p></td>
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<td><p>real-time temperature plot with GnuPlot via Pizza.py</p></td>
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</tr>
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<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">viz_TOOL.py</span></code></p></td>
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<td><p>real-time viz via some viz package</p></td>
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</tr>
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<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">vizplotgui_TOOL.py</span></code></p></td>
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<td><p>combination of <code class="docutils literal notranslate"><span class="pre">viz_TOOL.py</span></code> and <code class="docutils literal notranslate"><span class="pre">plot.py</span></code> and <code class="docutils literal notranslate"><span class="pre">gui.py</span></code></p></td>
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</tr>
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</tbody>
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</table>
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<p>For the <code class="docutils literal notranslate"><span class="pre">viz_TOOL.py</span></code> and <code class="docutils literal notranslate"><span class="pre">vizplotgui_TOOL.py</span></code> commands, replace <code class="docutils literal notranslate"><span class="pre">TOOL</span></code>
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with <code class="docutils literal notranslate"><span class="pre">gl</span></code> or <code class="docutils literal notranslate"><span class="pre">atomeye</span></code> or <code class="docutils literal notranslate"><span class="pre">pymol</span></code> or <code class="docutils literal notranslate"><span class="pre">vmd</span></code>, depending on what
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visualization package you have installed.</p>
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<p>Note that for GL, you need to be able to run the Pizza.py GL tool,
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which is included in the pizza subdirectory. See the Pizza.py doc pages for more info:</p>
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<ul class="simple">
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<li><p><a class="reference external" href="https://lammps.github.io/pizza">https://lammps.github.io/pizza</a></p></li>
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</ul>
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<p>Note that for AtomEye, you need version 3, and there is a line in the
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scripts that specifies the path and name of the executable. See the
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AtomEye web pages for more details:</p>
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<ul class="simple">
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<li><p><a class="reference external" href="http://li.mit.edu/Archive/Graphics/A/">http://li.mit.edu/Archive/Graphics/A/</a></p></li>
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<li><p><a class="reference external" href="http://li.mit.edu/Archive/Graphics/A3/A3.html">http://li.mit.edu/Archive/Graphics/A3/A3.html</a></p></li>
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</ul>
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<p>The latter link is to AtomEye 3 which has the scripting capability
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needed by these Python scripts.</p>
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<p>Note that for PyMol, you need to have built and installed the
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open-source version of PyMol in your Python, so that you can import it
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from a Python script. See the PyMol web pages for more details:</p>
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<blockquote>
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<div><ul class="simple">
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<li><p><a class="reference external" href="https://www.pymol.org">https://www.pymol.org</a></p></li>
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<li><p><a class="reference external" href="https://github.com/schrodinger/pymol-open-source">https://github.com/schrodinger/pymol-open-source</a></p></li>
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</ul>
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</div></blockquote>
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<p>The latter link is to the open-source version.</p>
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<p>Note that for VMD, you need a fairly current version (1.8.7 works for
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me) and there are some lines in the <code class="docutils literal notranslate"><span class="pre">pizza/vmd.py</span></code> script for 4 PIZZA
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variables that have to match the VMD installation on your system.</p>
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<hr class="docutils" />
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<p>See the <code class="docutils literal notranslate"><span class="pre">python/README</span></code> file for instructions on how to run them and the
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source code for individual scripts for comments about what they do.</p>
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<p>Here are screenshots of the <code class="docutils literal notranslate"><span class="pre">vizplotgui_tool.py</span></code> script in action for
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different visualization package options:</p>
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<p><a class="reference internal" href="_images/screenshot_gl.jpg"><img alt="pyex1" src="_images/screenshot_gl.jpg" style="width: 24%;" /></a> <a class="reference internal" href="_images/screenshot_atomeye.jpg"><img alt="pyex2" src="_images/screenshot_atomeye.jpg" style="width: 24%;" /></a> <a class="reference internal" href="_images/screenshot_pymol.jpg"><img alt="pyex3" src="_images/screenshot_pymol.jpg" style="width: 24%;" /></a> <a class="reference internal" href="_images/screenshot_vmd.jpg"><img alt="pyex4" src="_images/screenshot_vmd.jpg" style="width: 24%;" /></a></p>
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Click to see larger versions of the images.</section>
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