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<p><span class="math notranslate nohighlight">\(\renewcommand{\AA}{\text{Å}}\)</span></p>
<section id="lammps-non-features">
<h1><span class="section-number">1.4. </span>LAMMPS non-features<a class="headerlink" href="#lammps-non-features" title="Link to this heading"></a></h1>
<p>LAMMPS is designed to be a fast, parallel engine for molecular
dynamics (MD) simulations. It provides only a modest amount of
functionality for setting up simulations and analyzing their output.</p>
<p>Originally, LAMMPS was not conceived and designed for:</p>
<ul class="simple">
<li><p>being run through a GUI</p></li>
<li><p>building molecular systems, or building molecular topologies</p></li>
<li><p>assign force-field coefficients automagically</p></li>
<li><p>perform sophisticated analysis of your MD simulation</p></li>
<li><p>visualize your MD simulation interactively</p></li>
<li><p>plot your output data</p></li>
</ul>
<p>Over the years many of these limitations have been reduced or
removed. In part through features added to LAMMPS and in part
through external tools that either closely interface with LAMMPS
or extend LAMMPS.</p>
<p>Here are suggestions on how to perform these tasks:</p>
<ul>
<li><p><strong>GUI:</strong> LAMMPS can be built as a library and a Python module that
wraps the library interface is provided. Thus, GUI interfaces can be
written in Python or C/C++ that run LAMMPS and visualize or plot its
output. Examples of this are provided in the python directory and
described on the <a class="reference internal" href="Python_head.html"><span class="doc">Python</span></a> doc page.</p>
<p>Since version 2 August 2023 <a class="reference internal" href="Tools.html#lammps-gui"><span class="std std-ref">a LAMMPS-GUI tool</span></a> is
included in LAMMPS. Also, there are several external wrappers or GUI
front ends that are mentioned on the <a class="reference external" href="https://www.lammps.org/prepost.html">Pre-/post-processing tools page</a> of the LAMMPS homepage.</p>
</li>
<li><p><strong>Builder:</strong> Several pre-processing tools are packaged with LAMMPS.
Some of them convert input files in formats produced by other MD codes
such as CHARMM, AMBER, or Insight into LAMMPS input formats. Some of
them are simple programs that will build simple molecular systems,
such as linear bead-spring polymer chains. The moltemplate program is
a true molecular builder that will generate complex molecular models.
See the <a class="reference internal" href="Tools.html"><span class="doc">Tools</span></a> page for details on tools packaged with
LAMMPS. The <a class="reference external" href="https://www.lammps.org/prepost.html">Pre-/post-processing tools page</a> of the LAMMPS homepage
describes a variety of third party tools for this task. Furthermore,
some internal LAMMPS commands allow reconstructing, or selectively adding
topology information, as well as provide the option to insert molecule
templates instead of atoms for building bulk molecular systems.</p></li>
<li><p><strong>Force-field assignment:</strong> The conversion tools described in the previous
bullet for CHARMM, AMBER, and Insight will also assign force field
coefficients in the LAMMPS format, assuming you provide CHARMM, AMBER,
or BIOVIA (formerly Accelrys) force field files. The tools
<a class="reference external" href="https://parmed.github.io/ParmEd/html/index.html">ParmEd</a> and
<a class="reference external" href="https://github.com/shirtsgroup/InterMol">InterMol</a> are particularly
powerful and flexible in converting force field and topology data
between various MD simulation programs.</p></li>
<li><p><strong>Simulation analysis:</strong> If you want to perform analysis on-the-fly as
your simulation runs, see the <a class="reference internal" href="compute.html"><span class="doc">compute</span></a> and <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> doc pages, which list commands that can be used in a LAMMPS
input script. Also see the <a class="reference internal" href="Modify.html"><span class="doc">Modify</span></a> page for info on
how to add your own analysis code or algorithms to LAMMPS. For
post-processing, LAMMPS output such as <a class="reference internal" href="dump.html"><span class="doc">dump file snapshots</span></a> can be converted into formats used by other MD or
post-processing codes. To some degree, that conversion can be done
directly inside LAMMPS by interfacing to the VMD molfile plugins. The
<a class="reference internal" href="rerun.html"><span class="doc">rerun</span></a> command also allows post-processing of existing
trajectories, and through being able to read a variety of file
formats, this can also be used for analyzing trajectories from other
MD codes. Some post-processing tools packaged with LAMMPS will do
these conversions. Scripts provided in the tools/python directory can
extract and massage data in dump files to make it easier to import
into other programs. See the <a class="reference internal" href="Tools.html"><span class="doc">Tools</span></a> page for details on
these various options.</p>
<p>The <a class="reference external" href="https://www.lammps.org/prepost.html">Pre-/post-processing page</a>
on the LAMMPS homepage lists some external packages for analysis of MD
simulation data, including data produced by LAMMPS.</p>
</li>
<li><p><strong>Visualization:</strong> LAMMPS can produce NETPBM, JPG, or PNG format
snapshot images on-the-fly via its <a class="reference internal" href="dump_image.html"><span class="doc">dump image</span></a>
command and pass them to an external program, <a class="reference external" href="https://ffmpeg.org/">FFmpeg</a>, to generate movies from them. The
<a class="reference internal" href="Tools.html#lammps-gui"><span class="std std-ref">LAMMPS-GUI tool</span></a> has an <em>Snapshot Image Viewer</em>
which uses <a class="reference internal" href="dump_image.html"><span class="doc">dump image</span></a> and allows to modify the
visualization settings interactively. It also has a <em>Slide Show</em>
feature where images created by <a class="reference internal" href="dump_image.html"><span class="doc">dump image</span></a> are
collected during a simulation and can be animated interactively or
exported to a movie with FFmpeg.</p>
<p>For high-quality, interactive visualization, there are many excellent
and free tools available. See the <a class="reference external" href="https://www.lammps.org/viz.html">Visualization Tools</a> page of the LAMMPS website for
visualization packages that can process LAMMPS output data.</p>
</li>
<li><p><strong>Plotting:</strong> See the next bullet about Pizza.py as well as the
<a class="reference internal" href="Python_head.html"><span class="doc">Python</span></a> page for examples of plotting LAMMPS
output. Scripts provided with the <em>python</em> tool in the <code class="docutils literal notranslate"><span class="pre">tools</span></code>
directory will extract and process data in log and dump files to make
it easier to analyze and plot. See the <a class="reference internal" href="Tools.html"><span class="doc">Tools</span></a> doc page
for more discussion of the various tools.</p>
<p>The <a class="reference internal" href="Tools.html#lammps-gui"><span class="std std-ref">LAMMPS-GUI tool</span></a> has an <em>Chart Viewer</em> where
<a class="reference internal" href="thermo_style.html"><span class="doc">thermodynamic data</span></a> computed by LAMMPS is
collected during the simulation and plotted immediately.</p>
</li>
<li><p><strong>Pizza.py:</strong> Our group has also written a separate toolkit called
<a class="reference external" href="https://lammps.github.io/pizza">Pizza.py</a> which can do certain kinds of
setup, analysis, plotting, and visualization (via OpenGL) for LAMMPS
simulations. It thus provides some functionality for several of the
above bullets. Pizza.py is written in <a class="reference external" href="https://www.python.org">Python</a>
and is available for download from <a class="reference external" href="https://sjplimp.github.io/download.html">this page</a>.</p></li>
</ul>
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