forked from lijiext/lammps
315 lines
12 KiB
HTML
315 lines
12 KiB
HTML
|
|
|
|
<!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 — LAMMPS 15 May 2015 version 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 15 May 2015 version 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 & 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 & 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>
|
|
|
|
</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> »</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<a class="headerlink" href="#pair-style-list-command" title="Permalink to this headline">¶</a></h1>
|
|
<div class="section" id="syntax">
|
|
<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline">¶</a></h2>
|
|
<div class="highlight-python"><div class="highlight"><pre>pair_style list listfile cutoff keyword
|
|
</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<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h2>
|
|
<div class="highlight-python"><div class="highlight"><pre>pair_style list restraints.txt 200.0
|
|
pair_coeff * *
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>pair_style hybrid/overlay lj/cut 1.1225 list pair_list.txt 300.0
|
|
pair_coeff * * lj/cut 1.0 1.0
|
|
pair_coeff 3* 3* list
|
|
</pre></div>
|
|
</div>
|
|
</div>
|
|
<div class="section" id="description">
|
|
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></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 ‘#’ character</li>
|
|
<li>line syntax: <em>ID1 ID2 style coeffs cutoff</em></li>
|
|
</ul>
|
|
<div class="highlight-python"><div class="highlight"><pre>ID1 = atom ID of first atom
|
|
ID2 = atom ID of second atom
|
|
style = style of interaction
|
|
coeffs = list of coeffs
|
|
cutoff = cutoff for interaction (optional)
|
|
</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-python"><div class="highlight"><pre><span class="c"># this is a comment</span>
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>15 259 lj126 1.0 1.0 50.0
|
|
15 603 morse 10.0 1.2 2.0 10.0 # and another comment
|
|
18 470 harmonic 50.0 1.2 5.0
|
|
</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"><em>pair_modify</em></a> shift option is supported by this
|
|
pair style.</p>
|
|
<p>The <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></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"><em>binary restart files</em></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"><em>run_style respa</em></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<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></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<a class="headerlink" href="#related-commands" title="Permalink to this headline">¶</a></h2>
|
|
<p><a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a>,
|
|
<a class="reference internal" href="pair_hybrid.html"><em>pair_style hybrid/overlay</em></a>,
|
|
<a class="reference internal" href="pair_lj.html"><em>pair_style lj/cut</em></a>,
|
|
<a class="reference internal" href="pair_morse.html"><em>pair_style morse</em></a>,
|
|
<a class="reference internal" href="bond_harmonic.html"><em>bond_style harmonic</em></a></p>
|
|
<p><strong>Default:</strong> none</p>
|
|
</div>
|
|
</div>
|
|
|
|
|
|
</div>
|
|
</div>
|
|
<footer>
|
|
|
|
|
|
<hr/>
|
|
|
|
<div role="contentinfo">
|
|
<p>
|
|
© Copyright .
|
|
</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:'15 May 2015 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> |