Page MenuHomec4science
Files F103389767

pair_list.html
No OneTemporary
Actions

File Metadata

Created
Sat, Mar 1, 17:34

pair_list.html
View Options

<!DOCTYPE html>
<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]-->
<!--[if gt IE 8]><!--> <html class="no-js" lang="en" > <!--<![endif]-->
<head>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>pair_style list command &mdash; LAMMPS documentation</title>
<link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
<link rel="stylesheet" href="_static/sphinxcontrib-images/LightBox2/lightbox2/css/lightbox.css" type="text/css" />
<link rel="top" title="LAMMPS documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
</head>
<body class="wy-body-for-nav" role="document">
<div class="wy-grid-for-nav">
<nav data-toggle="wy-nav-shift" class="wy-nav-side">
<div class="wy-side-nav-search">
<a href="Manual.html" class="icon icon-home"> LAMMPS
</a>
<div role="search">
<form id="rtd-search-form" class="wy-form" action="search.html" method="get">
<input type="text" name="q" placeholder="Search docs" />
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
</div>
</div>
<div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation">
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></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>
&nbsp;
</nav>
<section data-toggle="wy-nav-shift" class="wy-nav-content-wrap">
<nav class="wy-nav-top" role="navigation" aria-label="top navigation">
<i data-toggle="wy-nav-top" class="fa fa-bars"></i>
<a href="Manual.html">LAMMPS</a>
</nav>
<div class="wy-nav-content">
<div class="rst-content">
<div role="navigation" aria-label="breadcrumbs navigation">
<ul class="wy-breadcrumbs">
<li><a href="Manual.html">Docs</a> &raquo;</li>
<li>pair_style list command</li>
<li class="wy-breadcrumbs-aside">
<a href="http://lammps.sandia.gov">Website</a>
<a href="Section_commands.html#comm">Commands</a>
</li>
</ul>
<hr/>
</div>
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div itemprop="articleBody">
<div class="section" id="pair-style-list-command">
<span id="index-0"></span><h1>pair_style list command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="nb">list</span> <span class="n">listfile</span> <span class="n">cutoff</span> <span class="n">keyword</span>
</pre></div>
</div>
<ul class="simple">
<li>listfile = name of file with list of pairwise interactions</li>
<li>cutoff = global cutoff (distance units)</li>
<li>keyword = optional flag <em>nocheck</em> or <em>check</em> (default is <em>check</em>)</li>
</ul>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="nb">list</span> <span class="n">restraints</span><span class="o">.</span><span class="n">txt</span> <span class="mf">200.0</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">hybrid</span><span class="o">/</span><span class="n">overlay</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span> <span class="mf">1.1225</span> <span class="nb">list</span> <span class="n">pair_list</span><span class="o">.</span><span class="n">txt</span> <span class="mf">300.0</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span> <span class="mf">1.0</span> <span class="mf">1.0</span>
<span class="n">pair_coeff</span> <span class="mi">3</span><span class="o">*</span> <span class="mi">3</span><span class="o">*</span> <span class="nb">list</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
<p>Style <em>list</em> computes interactions between explicitly listed pairs of
atoms with the option to select functional form and parameters for
each individual pair. Because the parameters are set in the list
file, the pair_coeff command has no parameters (but still needs to be
provided). The <em>check</em> and <em>nocheck</em> keywords enable/disable a test
that checks whether all listed bonds were present and computed.</p>
<p>This pair style can be thought of as a hybrid between bonded,
non-bonded, and restraint interactions. It will typically be used as
an additional interaction within the <em>hybrid/overlay</em> pair style. It
currently supports three interaction styles: a 12-6 Lennard-Jones, a
Morse and a harmonic potential.</p>
<p>The format of the list file is as follows:</p>
<ul class="simple">
<li>one line per pair of atoms</li>
<li>empty lines will be ignored</li>
<li>comment text starts with a &#8216;#&#8217; character</li>
<li>line syntax: <em>ID1 ID2 style coeffs cutoff</em></li>
</ul>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">ID1</span> <span class="o">=</span> <span class="n">atom</span> <span class="n">ID</span> <span class="n">of</span> <span class="n">first</span> <span class="n">atom</span>
<span class="n">ID2</span> <span class="o">=</span> <span class="n">atom</span> <span class="n">ID</span> <span class="n">of</span> <span class="n">second</span> <span class="n">atom</span>
<span class="n">style</span> <span class="o">=</span> <span class="n">style</span> <span class="n">of</span> <span class="n">interaction</span>
<span class="n">coeffs</span> <span class="o">=</span> <span class="nb">list</span> <span class="n">of</span> <span class="n">coeffs</span>
<span class="n">cutoff</span> <span class="o">=</span> <span class="n">cutoff</span> <span class="k">for</span> <span class="n">interaction</span> <span class="p">(</span><span class="n">optional</span><span class="p">)</span>
</pre></div>
</div>
<p>The cutoff parameter is optional. If not specified, the global cutoff
is used.</p>
<p>Here is an example file:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># this is a comment</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="mi">15</span> <span class="mi">259</span> <span class="n">lj126</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">50.0</span>
<span class="mi">15</span> <span class="mi">603</span> <span class="n">morse</span> <span class="mf">10.0</span> <span class="mf">1.2</span> <span class="mf">2.0</span> <span class="mf">10.0</span> <span class="c1"># and another comment</span>
<span class="mi">18</span> <span class="mi">470</span> <span class="n">harmonic</span> <span class="mf">50.0</span> <span class="mf">1.2</span> <span class="mf">5.0</span>
</pre></div>
</div>
<p>The style <em>lj126</em> computes pairwise interactions with the formula</p>
<img alt="_images/pair_lj.jpg" class="align-center" src="_images/pair_lj.jpg" />
<p>and the coefficients:</p>
<ul class="simple">
<li>epsilon (energy units)</li>
<li>sigma (distance units)</li>
</ul>
<p>The style <em>morse</em> computes pairwise interactions with the formula</p>
<img alt="_images/pair_morse.jpg" class="align-center" src="_images/pair_morse.jpg" />
<p>and the coefficients:</p>
<ul class="simple">
<li>D0 (energy units)</li>
<li>alpha (1/distance units)</li>
<li>r0 (distance units)</li>
</ul>
<p>The style <em>harmonic</em> computes pairwise interactions with the formula</p>
<img alt="_images/bond_harmonic.jpg" class="align-center" src="_images/bond_harmonic.jpg" />
<p>and the coefficients:</p>
<ul class="simple">
<li>K (energy units)</li>
<li>r0 (distance units)</li>
</ul>
<p>Note that the usual 1/2 factor is included in K.</p>
<hr class="docutils" />
<p><strong>Mixing, shift, table, tail correction, restart, rRESPA info</strong>:</p>
<p>This pair style does not support mixing since all parameters are
explicit for each pair.</p>
<p>The <a class="reference internal" href="pair_modify.html"><span class="doc">pair_modify</span></a> shift option is supported by this
pair style.</p>
<p>The <a class="reference internal" href="pair_modify.html"><span class="doc">pair_modify</span></a> table and tail options are not
relevant for this pair style.</p>
<p>This pair style does not write its information to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>, so pair_style and pair_coeff commands need
to be specified in an input script that reads a restart file.</p>
<p>This pair style can only be used via the <em>pair</em> keyword of the
<a class="reference internal" href="run_style.html"><span class="doc">run_style respa</span></a> command. It does not support the
<em>inner</em>, <em>middle</em>, <em>outer</em> keywords.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>This pair style does not use a neighbor list and instead identifies
atoms by their IDs. This has two consequences: 1) The cutoff has to be
chosen sufficiently large, so that the second atom of a pair has to be
a ghost atom on the same node on which the first atom is local;
otherwise the interaction will be skipped. You can use the <em>check</em>
option to detect, if interactions are missing. 2) Unlike other pair
styles in LAMMPS, an atom I will not interact with multiple images of
atom J (assuming the images are within the cutoff distance), but only
with the nearest image.</p>
<p>This style is part of the USER-MISC package. It is only enabled if
LAMMPS is build with that package. See the <span class="xref std std-ref">Making of LAMMPS</span> section for more info.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a>,
<a class="reference internal" href="pair_hybrid.html"><span class="doc">pair_style hybrid/overlay</span></a>,
<a class="reference internal" href="pair_lj.html"><span class="doc">pair_style lj/cut</span></a>,
<a class="reference internal" href="pair_morse.html"><span class="doc">pair_style morse</span></a>,
<a class="reference internal" href="bond_harmonic.html"><span class="doc">bond_style harmonic</span></a></p>
<p><strong>Default:</strong> none</p>
</div>
</div>
</div>
</div>
<footer>
<hr/>
<div role="contentinfo">
<p>
&copy; Copyright 2013 Sandia Corporation.
</p>
</div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
</footer>
</div>
</div>
</section>
</div>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true
};
</script>
<script type="text/javascript" src="_static/jquery.js"></script>
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
<script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
<script type="text/javascript" src="_static/sphinxcontrib-images/LightBox2/lightbox2/js/jquery-1.11.0.min.js"></script>
<script type="text/javascript" src="_static/sphinxcontrib-images/LightBox2/lightbox2/js/lightbox.min.js"></script>
<script type="text/javascript" src="_static/sphinxcontrib-images/LightBox2/lightbox2-customize/jquery-noconflict.js"></script>
<script type="text/javascript" src="_static/js/theme.js"></script>
<script type="text/javascript">
jQuery(function () {
SphinxRtdTheme.StickyNav.enable();
});
</script>
</body>
</html>

Event Timeline

c4science · Help