forked from lijiext/lammps
271 lines
11 KiB
HTML
271 lines
11 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>fix qeq/reax 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>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<a class="headerlink" href="#fix-qeq-reax-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>fix ID group-ID qeq/reax Nevery cutlo cuthi tolerance params
|
|
</pre></div>
|
|
</div>
|
|
<ul class="simple">
|
|
<li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><em>fix</em></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<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h2>
|
|
<div class="highlight-python"><div class="highlight"><pre>fix 1 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
|
|
fix 1 all qeq/reax 1 0.0 10.0 1.0e-6 param.qeq
|
|
</pre></div>
|
|
</div>
|
|
</div>
|
|
<div class="section" id="description">
|
|
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
|
|
<p>Perform the charge equilibration (QEq) method as described in <a class="reference internal" href="#rappe"><span>(Rappe and Goddard)</span></a> and formulated in <a class="reference internal" href="neb.html#nakano"><span>(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"><em>pair_style reax/c</em></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"><em>fix qeq/comb</em></a>
|
|
command should be used to perform charge equliibration with the <a class="reference internal" href="pair_comb.html"><em>COMB potential</em></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>(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 “reax/c”, then these are
|
|
extracted from the <a class="reference internal" href="pair_reax_c.html"><em>pair_style reax/c</em></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-python"><div class="highlight"><pre>itype chi eta gamma
|
|
</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<a class="headerlink" href="#restart-fix-modify-output-run-start-stop-minimize-info" title="Permalink to this headline">¶</a></h2>
|
|
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><em>binary restart files</em></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>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"><em>run</em></a> command.</p>
|
|
<p>This fix is invoked during <a class="reference internal" href="minimize.html"><em>energy minimization</em></a>.</p>
|
|
</div>
|
|
<div class="section" id="restrictions">
|
|
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></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>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<a class="headerlink" href="#related-commands" title="Permalink to this headline">¶</a></h2>
|
|
<p><a class="reference internal" href="pair_reax_c.html"><em>pair_style reax/c</em></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>
|
|
© 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> |