Homec4science
Diffusion lammps (efficient_neuronet) Browse

lammps/doc/html/fix_qeq_reax.html
ebf04bdf161befficient_neuronet

Last Change
Raw File

fix_qeq_reax.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>fix qeq/reax 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>fix qeq/reax 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="fix-qeq-reax-command">
<span id="index-0"></span><h1>fix qeq/reax command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">qeq</span><span class="o">/</span><span class="n">reax</span> <span class="n">Nevery</span> <span class="n">cutlo</span> <span class="n">cuthi</span> <span class="n">tolerance</span> <span class="n">params</span>
</pre></div>
</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command</li>
<li>qeq/reax = style name of this fix command</li>
<li>Nevery = perform QEq every this many steps</li>
<li>cutlo,cuthi = lo and hi cutoff for Taper radius</li>
<li>tolerance = precision to which charges will be equilibrated</li>
<li>params = reax/c or a filename</li>
</ul>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">qeq</span><span class="o">/</span><span class="n">reax</span> <span class="mi">1</span> <span class="mf">0.0</span> <span class="mf">10.0</span> <span class="mf">1.0e-6</span> <span class="n">reax</span><span class="o">/</span><span class="n">c</span>
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">qeq</span><span class="o">/</span><span class="n">reax</span> <span class="mi">1</span> <span class="mf">0.0</span> <span class="mf">10.0</span> <span class="mf">1.0e-6</span> <span class="n">param</span><span class="o">.</span><span class="n">qeq</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
<p>Perform the charge equilibration (QEq) method as described in <a class="reference internal" href="#rappe"><span class="std std-ref">(Rappe and Goddard)</span></a> and formulated in <a class="reference internal" href="neb.html#nakano"><span class="std std-ref">(Nakano)</span></a>. It is
typically used in conjunction with the ReaxFF force field model as
implemented in the <a class="reference internal" href="pair_reax_c.html"><span class="doc">pair_style reax/c</span></a> command, but
it can be used with any potential in LAMMPS, so long as it defines and
uses charges on each atom. The <a class="reference internal" href="fix_qeq_comb.html"><span class="doc">fix qeq/comb</span></a>
command should be used to perform charge equliibration with the <a class="reference internal" href="pair_comb.html"><span class="doc">COMB potential</span></a>. For more technical details about the
charge equilibration performed by fix qeq/reax, see the
<a class="reference internal" href="pair_reax_c.html#aktulga"><span class="std std-ref">(Aktulga)</span></a> paper.</p>
<p>The QEq method minimizes the electrostatic energy of the system by
adjusting the partial charge on individual atoms based on interactions
with their neighbors. It reqires some parameters for each atom type.
If the <em>params</em> setting above is the word &#8220;reax/c&#8221;, then these are
extracted from the <a class="reference internal" href="pair_reax_c.html"><span class="doc">pair_style reax/c</span></a> command and
the ReaxFF force field file it reads in. If a file name is specified
for <em>params</em>, then the parameters are taken from the specified file
and the file must contain one line for each atom type. The latter
form must be used when performing QeQ with a non-ReaxFF potential.
Each line should be formatted as follows:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">itype</span> <span class="n">chi</span> <span class="n">eta</span> <span class="n">gamma</span>
</pre></div>
</div>
<p>where <em>itype</em> is the atom type from 1 to Ntypes, <em>chi</em> denotes the
electronegativity in eV, <em>eta</em> denotes the self-Coulomb
potential in eV, and <em>gamma</em> denotes the valence orbital
exponent. Note that these 3 quantities are also in the ReaxFF
potential file, except that eta is defined here as twice the eta value
in the ReaxFF file. Note that unlike the rest of LAMMPS, the units
of this fix are hard-coded to be A, eV, and electronic charge.</p>
</div>
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. No global scalar or vector or per-atom
quantities are stored by this fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>. No parameter of this fix can
be used with the <em>start/stop</em> keywords of the <a class="reference internal" href="run.html"><span class="doc">run</span></a> command.</p>
<p>This fix is invoked during <a class="reference internal" href="minimize.html"><span class="doc">energy minimization</span></a>.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>This fix is part of the USER-REAXC 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 fix does not correctly handle interactions
involving multiple periodic images of the same atom. Hence, it should not
be used for periodic cell dimensions less than 10 angstroms.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><a class="reference internal" href="pair_reax_c.html"><span class="doc">pair_style reax/c</span></a></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="rappe"><strong>(Rappe)</strong> Rappe and Goddard III, Journal of Physical Chemistry, 95,
3358-3363 (1991).</p>
<p id="nakano"><strong>(Nakano)</strong> Nakano, Computer Physics Communications, 104, 59-69 (1997).</p>
<p id="aktulga">(Aktulga) Aktulga, Fogarty, Pandit, Grama, Parallel Computing, 38,
245-259 (2012).</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>
c4science · Help