Homec4science
Diffusion lammps (efficient_neuronet) Browse

lammps/doc/html/pair_dpd_fdt.html
076464e41187efficient_neuronet

Last Change
Raw File

pair_dpd_fdt.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 dpd/fdt 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>pair_style dpd/fdt 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-dpd-fdt-command">
<span id="index-0"></span><h1>pair_style dpd/fdt command</h1>
</div>
<div class="section" id="pair-style-dpd-fdt-energy-command">
<h1>pair_style dpd/fdt/energy 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">style</span> <span class="n">args</span>
</pre></div>
</div>
<ul class="simple">
<li>style = <em>dpd/fdt</em> or <em>dpd/fdt/energy</em></li>
<li>args = list of arguments for a particular style</li>
</ul>
<pre class="literal-block">
<em>dpd/fdt</em> args = T cutoff seed
T = temperature (temperature units)
cutoff = global cutoff for DPD interactions (distance units)
seed = random # seed (positive integer)
<em>dpd/fdt/energy</em> args = cutoff seed
cutoff = global cutoff for DPD interactions (distance units)
seed = random # seed (positive integer)
</pre>
</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">dpd</span><span class="o">/</span><span class="n">fdt</span> <span class="mf">300.0</span> <span class="mf">2.5</span> <span class="mi">34387</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">3.0</span> <span class="mf">1.0</span> <span class="mf">2.5</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">dpd</span><span class="o">/</span><span class="n">fdt</span><span class="o">/</span><span class="n">energy</span> <span class="mf">2.5</span> <span class="mi">34387</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">3.0</span> <span class="mf">1.0</span> <span class="mf">0.1</span> <span class="mf">2.5</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
<p>Styles <em>dpd/fdt</em> and <em>dpd/fdt/energy</em> set the fluctuation-dissipation
theorem parameters and compute the conservative force for dissipative
particle dynamics (DPD). The conservative force on atom I due to atom
J is given by</p>
<img alt="_images/pair_dpd_conservative.jpg" class="align-center" src="_images/pair_dpd_conservative.jpg" />
<p>where the weighting factor, omega_ij, varies between 0 and 1, and is
chosen to have the following functional form:</p>
<img alt="_images/pair_dpd_omega.jpg" class="align-center" src="_images/pair_dpd_omega.jpg" />
<p>where Rij is a unit vector in the direction Ri - Rj, and Rc is the
cutoff. Note that alternative definitions of the weighting function
exist, but would have to be implemented as a separate pair style
command.</p>
<p>These pair style differ from the other dpd styles in that the
dissipative and random forces are not computed within the pair style.
This style can be combined with the <a class="reference internal" href="fix_shardlow.html"><span class="doc">fix shardlow</span></a>
to perform the stochastic integration of the dissipative and random
forces through the Shardlow splitting algorithm approach.</p>
<p>The pairwise energy associated with styles <em>dpd/fdt</em> and
<em>dpd/fdt/energy</em> is only due to the conservative force term Fc, and is
shifted to be zero at the cutoff distance Rc. The pairwise virial is
calculated using only the conservative term.</p>
<p>For style <em>dpd/fdt</em>, the fluctuation-dissipation theorem defines gamma
to be set equal to sigma*sigma/(2 T), where T is the set point
temperature specified as a pair style parameter in the above examples.
This style can be combined with <a class="reference internal" href="fix_shardlow.html"><span class="doc">fix shardlow</span></a> to
perform DPD simulations under isothermal and isobaric conditions (see
<a class="reference internal" href="#lisal"><span class="std std-ref">(Lisal)</span></a>). The following coefficients must be defined for
each pair of atoms types via the <a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a> command
as in the examples above, or in the data file or restart files read by
the <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> or <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a>
commands:</p>
<ul class="simple">
<li>A (force units)</li>
<li>sigma (force*time^(1/2) units)</li>
<li>cutoff (distance units)</li>
</ul>
<p>The last coefficient is optional. If not specified, the global DPD
cutoff is used.</p>
<p>For style <em>dpd/fdt/energy</em>, the fluctuation-dissipation theorem
defines gamma to be set equal to sigma*sigma/(2 dpdTheta), where
dpdTheta is the average internal temperature for the pair.
Furthermore, the fluctuation-dissipation defines alpha*alpha to be set
equal to 2*kB*kappa, where kappa is the mesoparticle thermal
conductivity parameter. This style can be combined with <a class="reference internal" href="fix_shardlow.html"><span class="doc">fix shardlow</span></a> to perform DPD simulations under
isoenergetic and isoenthalpic conditions (see <a class="reference internal" href="#lisal"><span class="std std-ref">(Lisal)</span></a>). The
following coefficients must be defined for each pair of atoms types
via the <a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a> command as in the examples above,
or in the data file or restart files read by the
<a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> or <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a>
commands:</p>
<ul class="simple">
<li>A (force units)</li>
<li>sigma (force*time^(1/2) units)</li>
<li>kappa (1/time units)</li>
<li>cutoff (distance units)</li>
</ul>
<p>The last coefficient is optional. If not specified, the global DPD
cutoff is used.</p>
<p>For style <em>dpd/fdt/energy</em>, the particle internal temperature is
related to the particle internal energy through a mesoparticle
equation of state. Thus, an an additional <a class="reference internal" href="fix.html"><span class="doc">fix eos</span></a> must be
specified.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>These commands are part of the USER-DPD package. They are 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>Pair styles <em>dpd/fdt</em> and <em>dpd/fdt/energy</em> require use of the
<span class="xref doc">communicate vel yes</span> option so that velocites are
stored by ghost atoms.</p>
<p>Pair style <em>dpd/fdt/energy</em> requires <a class="reference internal" href="atom_style.html"><span class="doc">atom_style dpd</span></a>
to be used in order to properly account for the particle internal
energies and temperatures.</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>, <a class="reference internal" href="fix_shardlow.html"><span class="doc">fix shardlow</span></a></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="lisal"><strong>(Lisal)</strong> M. Lisal, J.K. Brennan, J. Bonet Avalos, &#8220;Dissipative
particle dynamics as isothermal, isobaric, isoenergetic, and
isoenthalpic conditions using Shardlow-like splitting algorithms.&#8221;,
J. Chem. Phys., 135, 204105 (2011).</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