forked from lijiext/lammps
289 lines
12 KiB
HTML
289 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 kim command — 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 & 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 kim 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-kim-command">
|
||
|
|
<span id="index-0"></span><h1>pair_style kim 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="n">kim</span> <span class="n">virialmode</span> <span class="n">model</span> <span class="n">printflag</span>
|
||
|
|
</pre></div>
|
||
|
|
</div>
|
||
|
|
<ul class="simple">
|
||
|
|
<li>virialmode = KIMvirial or LAMMPSvirial</li>
|
||
|
|
<li>model = name of KIM model (potential)</li>
|
||
|
|
<li>printflag = 1/0 do or do not print KIM descriptor file, optional</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="n">kim</span> <span class="n">KIMvirial</span> <span class="n">model_Ar_P_Morse</span>
|
||
|
|
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">Ar</span> <span class="n">Ar</span>
|
||
|
|
</pre></div>
|
||
|
|
</div>
|
||
|
|
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">kim</span> <span class="n">KIMvirial</span> <span class="n">model_Ar_P_Morse</span> <span class="mi">1</span>
|
||
|
|
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">Ar</span> <span class="n">Ar</span>
|
||
|
|
</pre></div>
|
||
|
|
</div>
|
||
|
|
</div>
|
||
|
|
<div class="section" id="description">
|
||
|
|
<h2>Description</h2>
|
||
|
|
<p>This pair style is a wrapper on the <a class="reference external" href="https://openkim.org">Knowledge Base for Interatomic Models (KIM)</a> repository of interatomic potentials,
|
||
|
|
so that they can be used by LAMMPS scripts.</p>
|
||
|
|
<p>In KIM lingo, a potential is a “model” and a model contains both the
|
||
|
|
analytic formulas that define the potential as well as the parameters
|
||
|
|
needed to run it for one or more materials, including coefficients and
|
||
|
|
cutoffs.</p>
|
||
|
|
<p>The argument <em>virialmode</em> determines how the global virial is
|
||
|
|
calculated. If <em>KIMvirial</em> is specified, the KIM model performs the
|
||
|
|
global virial calculation (if it knows how). If <em>LAMMPSvirial</em> is
|
||
|
|
specified, LAMMPS computes the global virial using its fdotr mechanism.</p>
|
||
|
|
<p>The argument <em>model</em> is the name of the KIM model for a specific
|
||
|
|
potential as KIM defines it. In principle, LAMMPS can invoke any KIM
|
||
|
|
model. You should get an error or warning message from either LAMMPS
|
||
|
|
or KIM if there is an incompatibility.</p>
|
||
|
|
<p>The argument <em>printflag</em> is optional. If it is set to a non-zero
|
||
|
|
value then a KIM dsecriptor file is printed when KIM is invoked. This
|
||
|
|
can be useful for debugging. The default is to not print this file.</p>
|
||
|
|
<p>Only a single pair_coeff command is used with the <em>kim</em> style which
|
||
|
|
specifies the mapping of LAMMPS atom types to KIM elements. This is
|
||
|
|
done by specifying N additional arguments after the * * in the
|
||
|
|
pair_coeff command, where N is the number of LAMMPS atom types:</p>
|
||
|
|
<ul class="simple">
|
||
|
|
<li>N element names = mapping of KIM elements to atom types</li>
|
||
|
|
</ul>
|
||
|
|
<p>As an example, imagine the KIM model supports Si and C atoms. If your
|
||
|
|
LAMMPS simulation has 4 atom types and you want the 1st 3 to be Si,
|
||
|
|
and the 4th to be C, you would use the following pair_coeff command:</p>
|
||
|
|
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">Si</span> <span class="n">Si</span> <span class="n">Si</span> <span class="n">C</span>
|
||
|
|
</pre></div>
|
||
|
|
</div>
|
||
|
|
<p>The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
|
||
|
|
The first three Si arguments map LAMMPS atom types 1,2,3 to Si as
|
||
|
|
defined within KIM. The final C argument maps LAMMPS atom type 4 to C
|
||
|
|
as defined within KIM. If a mapping value is specified as NULL, the
|
||
|
|
mapping is not performed. This can only be used when a <em>kim</em>
|
||
|
|
potential is used as part of the <em>hybrid</em> pair style. The NULL values
|
||
|
|
are placeholders for atom types that will be used with other
|
||
|
|
potentials.</p>
|
||
|
|
<hr class="docutils" />
|
||
|
|
<p>In addition to the usual LAMMPS error messages, the KIM library itself
|
||
|
|
may generate errors, which should be printed to the screen. In this
|
||
|
|
case it is also useful to check the kim.log file for additional error
|
||
|
|
information. This file kim.log should be generated in the same
|
||
|
|
directory where LAMMPS is running.</p>
|
||
|
|
<p>To download, build, and install the KIM library on your system, see
|
||
|
|
the lib/kim/README file. Once you have done this and built LAMMPS
|
||
|
|
with the KIM package installed you can run the example input scripts
|
||
|
|
in examples/kim.</p>
|
||
|
|
<hr class="docutils" />
|
||
|
|
<p><strong>Mixing, shift, table, tail correction, restart, rRESPA info</strong>:</p>
|
||
|
|
<p>This pair style does not support the <a class="reference internal" href="pair_modify.html"><span class="doc">pair_modify</span></a>
|
||
|
|
mix, shift, table, and tail options.</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>, since KIM stores the potential parameters.
|
||
|
|
Thus, you need to re-specify the pair_style and pair_coeff commands 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 is part of the KIM package. It is only enabled if
|
||
|
|
LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
|
||
|
|
<p>This current version of pair_style kim is compatible with the
|
||
|
|
kim-api package version 1.6.0 and higher.</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></p>
|
||
|
|
<p><strong>Default:</strong> none</p>
|
||
|
|
</div>
|
||
|
|
</div>
|
||
|
|
|
||
|
|
|
||
|
|
</div>
|
||
|
|
</div>
|
||
|
|
<footer>
|
||
|
|
|
||
|
|
|
||
|
|
<hr/>
|
||
|
|
|
||
|
|
<div role="contentinfo">
|
||
|
|
<p>
|
||
|
|
© 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>
|