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<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Introduction &mdash; LAMMPS 15 May 2015 version documentation</title>
<title>1. Introduction &mdash; LAMMPS 15 May 2015 version documentation</title>
@ -32,7 +32,9 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/>
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/>
<link rel="next" title="2. Getting Started" href="Section_start.html"/>
<link rel="prev" title="LAMMPS Documentation" href="Manual.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -71,31 +73,42 @@
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">Introduction</a><ul>
<li><a class="reference internal" href="#what-is-lammps">What is LAMMPS</a></li>
<li><a class="reference internal" href="#lammps-features">LAMMPS features</a><ul>
<li><a class="reference internal" href="#general-features">General features</a></li>
<li><a class="reference internal" href="#particle-and-model-types">Particle and model types</a></li>
<li><a class="reference internal" href="#force-fields">Force fields</a></li>
<li><a class="reference internal" href="#atom-creation">Atom creation</a></li>
<li><a class="reference internal" href="#ensembles-constraints-and-boundary-conditions">Ensembles, constraints, and boundary conditions</a></li>
<li><a class="reference internal" href="#integrators">Integrators</a></li>
<li><a class="reference internal" href="#diagnostics">Diagnostics</a></li>
<li><a class="reference internal" href="#output">Output</a></li>
<li><a class="reference internal" href="#multi-replica-models">Multi-replica models</a></li>
<li><a class="reference internal" href="#pre-and-post-processing">Pre- and post-processing</a></li>
<li><a class="reference internal" href="#specialized-features">Specialized features</a></li>
<ul class="current">
<li class="toctree-l1 current"><a class="current reference internal" href="">1. Introduction</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#what-is-lammps">1.1. What is LAMMPS</a></li>
<li class="toctree-l2"><a class="reference internal" href="#lammps-features">1.2. LAMMPS features</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#general-features">1.2.1. General features</a></li>
<li class="toctree-l3"><a class="reference internal" href="#particle-and-model-types">1.2.2. Particle and model types</a></li>
<li class="toctree-l3"><a class="reference internal" href="#force-fields">1.2.3. Force fields</a></li>
<li class="toctree-l3"><a class="reference internal" href="#atom-creation">1.2.4. Atom creation</a></li>
<li class="toctree-l3"><a class="reference internal" href="#ensembles-constraints-and-boundary-conditions">1.2.5. Ensembles, constraints, and boundary conditions</a></li>
<li class="toctree-l3"><a class="reference internal" href="#integrators">1.2.6. Integrators</a></li>
<li class="toctree-l3"><a class="reference internal" href="#diagnostics">1.2.7. Diagnostics</a></li>
<li class="toctree-l3"><a class="reference internal" href="#output">1.2.8. Output</a></li>
<li class="toctree-l3"><a class="reference internal" href="#multi-replica-models">1.2.9. Multi-replica models</a></li>
<li class="toctree-l3"><a class="reference internal" href="#pre-and-post-processing">1.2.10. Pre- and post-processing</a></li>
<li class="toctree-l3"><a class="reference internal" href="#specialized-features">1.2.11. Specialized features</a></li>
</ul>
</li>
<li><a class="reference internal" href="#lammps-non-features">LAMMPS non-features</a></li>
<li><a class="reference internal" href="#open-source-distribution">Open source distribution</a></li>
<li><a class="reference internal" href="#acknowledgments-and-citations">Acknowledgments and citations</a></li>
<li class="toctree-l2"><a class="reference internal" href="#lammps-non-features">1.3. LAMMPS non-features</a></li>
<li class="toctree-l2"><a class="reference internal" href="#open-source-distribution">1.4. Open source distribution</a></li>
<li class="toctree-l2"><a class="reference internal" href="#acknowledgments-and-citations">1.5. Acknowledgments and citations</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</div>
</div>
@ -118,7 +131,7 @@
<ul class="wy-breadcrumbs">
<li><a href="Manual.html">Docs</a> &raquo;</li>
<li>Introduction</li>
<li>1. Introduction</li>
<li class="wy-breadcrumbs-aside">
@ -133,7 +146,7 @@
<div itemprop="articleBody">
<div class="section" id="introduction">
<h1>Introduction<a class="headerlink" href="#introduction" title="Permalink to this headline"></a></h1>
<h1>1. Introduction<a class="headerlink" href="#introduction" title="Permalink to this headline"></a></h1>
<p>This section provides an overview of what LAMMPS can and can&#8217;t do,
describes what it means for LAMMPS to be an open-source code, and
acknowledges the funding and people who have contributed to LAMMPS
@ -147,7 +160,7 @@ over the years.</p>
<div class="line"><br /></div>
</div>
<div class="section" id="what-is-lammps">
<span id="intro-1"></span><h2>What is LAMMPS<a class="headerlink" href="#what-is-lammps" title="Permalink to this headline"></a></h2>
<span id="intro-1"></span><h2>1.1. What is LAMMPS<a class="headerlink" href="#what-is-lammps" title="Permalink to this headline"></a></h2>
<p>LAMMPS is a classical molecular dynamics code that models an ensemble
of particles in a liquid, solid, or gaseous state. It can model
atomic, polymeric, biological, metallic, granular, and coarse-grained
@ -198,14 +211,14 @@ LAMMPS are listed in <a class="reference internal" href="#intro-5"><span>this se
<hr class="docutils" />
</div>
<div class="section" id="lammps-features">
<span id="intro-2"></span><h2>LAMMPS features<a class="headerlink" href="#lammps-features" title="Permalink to this headline"></a></h2>
<span id="intro-2"></span><h2>1.2. LAMMPS features<a class="headerlink" href="#lammps-features" title="Permalink to this headline"></a></h2>
<p>This section highlights LAMMPS features, with pointers to specific
commands which give more details. If LAMMPS doesn&#8217;t have your
favorite interatomic potential, boundary condition, or atom type, see
<a class="reference internal" href="Section_modify.html"><em>Section_modify</em></a>, which describes how you can add
it to LAMMPS.</p>
<div class="section" id="general-features">
<h3>General features<a class="headerlink" href="#general-features" title="Permalink to this headline"></a></h3>
<h3>1.2.1. General features<a class="headerlink" href="#general-features" title="Permalink to this headline"></a></h3>
<ul class="simple">
<li>runs on a single processor or in parallel</li>
<li>distributed-memory message-passing parallelism (MPI)</li>
@ -224,7 +237,7 @@ it to LAMMPS.</p>
</ul>
</div>
<div class="section" id="particle-and-model-types">
<h3>Particle and model types<a class="headerlink" href="#particle-and-model-types" title="Permalink to this headline"></a></h3>
<h3>1.2.2. Particle and model types<a class="headerlink" href="#particle-and-model-types" title="Permalink to this headline"></a></h3>
<p>(<a class="reference internal" href="atom_style.html"><em>atom style</em></a> command)</p>
<ul class="simple">
<li>atoms</li>
@ -242,7 +255,7 @@ it to LAMMPS.</p>
</ul>
</div>
<div class="section" id="force-fields">
<h3>Force fields<a class="headerlink" href="#force-fields" title="Permalink to this headline"></a></h3>
<h3>1.2.3. Force fields<a class="headerlink" href="#force-fields" title="Permalink to this headline"></a></h3>
<p>(<a class="reference internal" href="pair_style.html"><em>pair style</em></a>, <a class="reference internal" href="bond_style.html"><em>bond style</em></a>,
<a class="reference internal" href="angle_style.html"><em>angle style</em></a>, <a class="reference internal" href="dihedral_style.html"><em>dihedral style</em></a>,
<a class="reference internal" href="improper_style.html"><em>improper style</em></a>, <a class="reference internal" href="kspace_style.html"><em>kspace style</em></a>
@ -271,7 +284,7 @@ commands)</p>
</ul>
</div>
<div class="section" id="atom-creation">
<h3>Atom creation<a class="headerlink" href="#atom-creation" title="Permalink to this headline"></a></h3>
<h3>1.2.4. Atom creation<a class="headerlink" href="#atom-creation" title="Permalink to this headline"></a></h3>
<p>(<a class="reference internal" href="read_data.html"><em>read_data</em></a>, <a class="reference internal" href="lattice.html"><em>lattice</em></a>,
<a class="reference internal" href="create_atoms.html"><em>create_atoms</em></a>, <a class="reference internal" href="delete_atoms.html"><em>delete_atoms</em></a>,
<a class="reference internal" href="displace_atoms.html"><em>displace_atoms</em></a>, <a class="reference internal" href="replicate.html"><em>replicate</em></a> commands)</p>
@ -284,7 +297,7 @@ commands)</p>
</ul>
</div>
<div class="section" id="ensembles-constraints-and-boundary-conditions">
<h3>Ensembles, constraints, and boundary conditions<a class="headerlink" href="#ensembles-constraints-and-boundary-conditions" title="Permalink to this headline"></a></h3>
<h3>1.2.5. Ensembles, constraints, and boundary conditions<a class="headerlink" href="#ensembles-constraints-and-boundary-conditions" title="Permalink to this headline"></a></h3>
<p>(<a class="reference internal" href="fix.html"><em>fix</em></a> command)</p>
<ul class="simple">
<li>2d or 3d systems</li>
@ -304,7 +317,7 @@ commands)</p>
</ul>
</div>
<div class="section" id="integrators">
<h3>Integrators<a class="headerlink" href="#integrators" title="Permalink to this headline"></a></h3>
<h3>1.2.6. Integrators<a class="headerlink" href="#integrators" title="Permalink to this headline"></a></h3>
<p>(<a class="reference internal" href="run.html"><em>run</em></a>, <a class="reference internal" href="run_style.html"><em>run_style</em></a>, <a class="reference internal" href="minimize.html"><em>minimize</em></a> commands)</p>
<ul class="simple">
<li>velocity-Verlet integrator</li>
@ -316,13 +329,13 @@ commands)</p>
</ul>
</div>
<div class="section" id="diagnostics">
<h3>Diagnostics<a class="headerlink" href="#diagnostics" title="Permalink to this headline"></a></h3>
<h3>1.2.7. Diagnostics<a class="headerlink" href="#diagnostics" title="Permalink to this headline"></a></h3>
<ul class="simple">
<li>see the various flavors of the <a class="reference internal" href="fix.html"><em>fix</em></a> and <a class="reference internal" href="compute.html"><em>compute</em></a> commands</li>
</ul>
</div>
<div class="section" id="output">
<h3>Output<a class="headerlink" href="#output" title="Permalink to this headline"></a></h3>
<h3>1.2.8. Output<a class="headerlink" href="#output" title="Permalink to this headline"></a></h3>
<p>(<a class="reference internal" href="dump.html"><em>dump</em></a>, <a class="reference internal" href="restart.html"><em>restart</em></a> commands)</p>
<ul class="simple">
<li>log file of thermodynamic info</li>
@ -337,14 +350,14 @@ commands)</p>
</ul>
</div>
<div class="section" id="multi-replica-models">
<h3>Multi-replica models<a class="headerlink" href="#multi-replica-models" title="Permalink to this headline"></a></h3>
<h3>1.2.9. Multi-replica models<a class="headerlink" href="#multi-replica-models" title="Permalink to this headline"></a></h3>
<p><a class="reference internal" href="neb.html"><em>nudged elastic band</em></a>
<a class="reference internal" href="prd.html"><em>parallel replica dynamics</em></a>
<a class="reference internal" href="tad.html"><em>temperature accelerated dynamics</em></a>
<a class="reference internal" href="temper.html"><em>parallel tempering</em></a></p>
</div>
<div class="section" id="pre-and-post-processing">
<h3>Pre- and post-processing<a class="headerlink" href="#pre-and-post-processing" title="Permalink to this headline"></a></h3>
<h3>1.2.10. Pre- and post-processing<a class="headerlink" href="#pre-and-post-processing" title="Permalink to this headline"></a></h3>
<ul class="simple">
<li>Various pre- and post-processing serial tools are packaged
with LAMMPS; see these <a class="reference internal" href="Section_tools.html"><em>doc pages</em></a>.</li>
@ -355,7 +368,7 @@ written in <a class="reference external" href="http://www.python.org">Python</a>
</ul>
</div>
<div class="section" id="specialized-features">
<h3>Specialized features<a class="headerlink" href="#specialized-features" title="Permalink to this headline"></a></h3>
<h3>1.2.11. Specialized features<a class="headerlink" href="#specialized-features" title="Permalink to this headline"></a></h3>
<p>These are LAMMPS capabilities which you may not think of as typical
molecular dynamics options:</p>
<ul class="simple">
@ -379,7 +392,7 @@ molecular dynamics options:</p>
</div>
</div>
<div class="section" id="lammps-non-features">
<span id="intro-3"></span><h2>LAMMPS non-features<a class="headerlink" href="#lammps-non-features" title="Permalink to this headline"></a></h2>
<span id="intro-3"></span><h2>1.3. LAMMPS non-features<a class="headerlink" href="#lammps-non-features" title="Permalink to this headline"></a></h2>
<p>LAMMPS is designed to efficiently compute Newton&#8217;s equations of motion
for a system of interacting particles. Many of the tools needed to
pre- and post-process the data for such simulations are not included
@ -472,7 +485,7 @@ spatial-decomposition version exist.</p>
<hr class="docutils" />
</div>
<div class="section" id="open-source-distribution">
<span id="intro-4"></span><h2>Open source distribution<a class="headerlink" href="#open-source-distribution" title="Permalink to this headline"></a></h2>
<span id="intro-4"></span><h2>1.4. Open source distribution<a class="headerlink" href="#open-source-distribution" title="Permalink to this headline"></a></h2>
<p>LAMMPS comes with no warranty of any kind. As each source file states
in its header, it is a copyrighted code that is distributed free-of-
charge, under the terms of the <a class="reference external" href="http://www.gnu.org/copyleft/gpl.html">GNU Public License</a> (GPL). This
@ -534,7 +547,7 @@ encouraged.</li>
<hr class="docutils" />
</div>
<div class="section" id="acknowledgments-and-citations">
<span id="intro-5"></span><h2>Acknowledgments and citations<a class="headerlink" href="#acknowledgments-and-citations" title="Permalink to this headline"></a></h2>
<span id="intro-5"></span><h2>1.5. Acknowledgments and citations<a class="headerlink" href="#acknowledgments-and-citations" title="Permalink to this headline"></a></h2>
<p>LAMMPS development has been funded by the <a class="reference external" href="http://www.doe.gov">US Department of Energy</a> (DOE), through its CRADA, LDRD, ASCI, and Genomes-to-Life
programs and its <a class="reference external" href="http://www.sc.doe.gov/ascr/home.html">OASCR</a> and <a class="reference external" href="http://www.er.doe.gov/production/ober/ober_top.html">OBER</a> offices.</p>
<p>Specifically, work on the latest version was funded in part by the US
@ -603,6 +616,15 @@ version of LAMMPS were the following:</p>
</div>
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