Homec4science
Diffusion lammps (lammm-master-deprecated) Browse

lammps/doc/html/pair_exp6_rx.html
57fb84393a7alammm-master-deprecated

Last Change
Raw File

pair_exp6_rx.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 exp6/rx 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">
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">pair_style exp6/rx command</a><ul>
<li><a class="reference internal" href="#syntax">Syntax</a></li>
<li><a class="reference internal" href="#examples">Examples</a></li>
<li><a class="reference internal" href="#description">Description</a></li>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
</ul>
</li>
</ul>
</div>
</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 exp6/rx 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-exp6-rx-command">
<span id="index-0"></span><h1>pair_style exp6/rx 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">exp6</span><span class="o">/</span><span class="n">rx</span> <span class="n">cutoff</span>
</pre></div>
</div>
<ul class="simple">
<li>cutoff = global cutoff for DPD interactions (distance units)</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">exp6</span><span class="o">/</span><span class="n">rx</span> <span class="mf">10.0</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">exp6</span><span class="o">.</span><span class="n">params</span> <span class="n">h2o</span> <span class="n">h2o</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">10.0</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">exp6</span><span class="o">.</span><span class="n">params</span> <span class="n">h2o</span> <span class="mi">1</span><span class="n">fluid</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">10.0</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">exp6</span><span class="o">.</span><span class="n">params</span> <span class="mi">1</span><span class="n">fluid</span> <span class="mi">1</span><span class="n">fluid</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">10.0</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
<p>Style <em>exp6/rx</em> is used in reaction DPD simulations, where the
coarse-grained (CG) particles are composed of <em>m</em> species whose
reaction rate kinetics are determined from a set of <em>n</em> reaction rate
equations through the <a class="reference internal" href="fix_rx.html"><span class="doc">fix rx</span></a> command. The species of
one CG particle can interact with a species in a neighboring CG
particle through a site-site interaction potential model. The
<em>exp6/rx</em> style computes an exponential-6 potential given by</p>
<img alt="_images/pair_exp6_rx.jpg" class="align-center" src="_images/pair_exp6_rx.jpg" />
<p>where the <em>epsilon</em> parameter determines the depth of the potential
minimum located at <em>Rm</em>, and <em>alpha</em> determines the softness of the repulsion.</p>
<p>The coefficients must be defined for each species in a given particle
type via the <a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a> command as in the examples
above, where the first argument is the filename that includes the
exponential-6 parameters for each species. The file includes the
species tag followed by the <em>alpha</em>, <em>epsilon</em> and <em>Rm</em>
parameters. The format of the file is described below.</p>
<p>The second and third arguments specify the site-site interaction
potential between two species contained within two different
particles. The species tags must either correspond to the species
defined in the reaction kinetics files specified with the <a class="reference internal" href="fix_rx.html"><span class="doc">fix rx</span></a> command or they must correspond to the tag &#8220;1fluid&#8221;,
signifying interaction with a product species mixture determined
through a one-fluid approximation. The interaction potential is
weighted by the geometric average of the concentrations of the two
species. The coarse-grained potential is stored before and after the
reaction kinetics solver is applied, where the difference is defined
to be the internal chemical energy (uChem).</p>
<p>The fourth and fifth arguments specify the <em>Rm</em> and <em>epsilon</em> scaling exponents.</p>
<p>The final argument specifies the interaction cutoff.</p>
<hr class="docutils" />
<p>The format of a tabulated file is as follows (without the
parenthesized comments):</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># exponential-6 parameters for various species (one or more comment or blank lines)</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">h2o</span> <span class="n">exp6</span> <span class="mf">11.00</span> <span class="mf">0.02</span> <span class="mf">3.50</span> <span class="p">(</span><span class="n">species</span><span class="p">,</span> <span class="n">exp6</span><span class="p">,</span> <span class="n">alpha</span><span class="p">,</span> <span class="n">Rm</span><span class="p">,</span> <span class="n">epsilon</span><span class="p">)</span>
<span class="n">no2</span> <span class="n">exp6</span> <span class="mf">13.60</span> <span class="mf">0.01</span> <span class="mf">3.70</span>
<span class="o">...</span>
<span class="n">co2</span> <span class="n">exp6</span> <span class="mf">13.00</span> <span class="mf">0.03</span> <span class="mf">3.20</span>
</pre></div>
</div>
<p>A section begins with a non-blank line whose 1st character is not a
&#8220;#&#8221;; blank lines or lines starting with &#8220;#&#8221; can be used as comments
between sections.</p>
<p>Following a blank line, the next N lines list the species and their
corresponding parameters. The first argument is the species tag, the
second argument is the exp6 tag, the 3rd argument is the <em>alpha</em>
parameter (energy units), the 4th argument is the <em>epsilon</em> parameter
(energy-distance^6 units), and the 5th argument is the <em>Rm</em> parameter
(distance units). If a species tag of &#8220;1fluid&#8221; is listed as a pair
coefficient, a one-fluid approximation is specified where a
concentration-dependent combination of the parameters is computed
through the following equations:</p>
<img alt="_images/pair_exp6_rx_oneFluid.jpg" class="align-center" src="_images/pair_exp6_rx_oneFluid.jpg" />
<p>where</p>
<img alt="_images/pair_exp6_rx_oneFluid2.jpg" class="align-center" src="_images/pair_exp6_rx_oneFluid2.jpg" />
<p>and xa and xb are the mole fractions of a and b, respectively, which
comprise the gas mixture.</p>
<hr class="docutils" />
<p><strong>Mixing, shift, table, tail correction, restart, rRESPA info</strong>:</p>
<p>This pair style does not support mixing. Thus, coefficients for all
I,J pairs must be specified explicitly.</p>
<p>This style does not support the <a class="reference internal" href="pair_modify.html"><span class="doc">pair_modify</span></a> shift option
for the energy of the exp() and 1/r^6 portion of the pair interaction.</p>
<p>This style does not support the pair_modify tail option for adding long-range
tail corrections to energy and pressure for the A,C terms in the
pair interaction.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>This command is part of the USER-DPD package. It is only enabled if
LAMMPS was built with that package. See the <span class="xref std std-ref">Making 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></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>
c4science · Help