Homec4science
Diffusion lammps (lammm-master-deprecated) Browse

lammps/doc/pair_mdf.html
1aeecfb0cfcflammm-master-deprecated

Last Change
Raw File

pair_mdf.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 lj/mdf command &mdash; LAMMPS 15 Dec 2015 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 Dec 2015 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 lj/mdf 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-lj-mdf-command">
<span id="index-0"></span><h1>pair_style lj/mdf command<a class="headerlink" href="#pair-style-lj-mdf-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-buck-mdf-command">
<h1>pair_style buck/mdf command<a class="headerlink" href="#pair-style-buck-mdf-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-lennard-mdf-command">
<h1>pair_style lennard/mdf command<a class="headerlink" href="#pair-style-lennard-mdf-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>pair_style style args
</pre></div>
</div>
<ul class="simple">
<li>style = <em>lj/mdf</em> or <em>buck/mdf</em> or <em>lennard/mdf</em></li>
<li>args = list of arguments for a particular style</li>
</ul>
<pre class="literal-block">
<em>lj/mdf</em> args = cutoff1 cutoff2
cutoff1 = inner cutoff for the start of the tapering function
cutoff1 = out cutoff for the end of the tapering function
<em>buck/mdf</em> args = cutoff1 cutoff2
cutoff1 = inner cutoff for the start of the tapering function
cutoff1 = out cutoff for the end of the tapering function
<em>lennard/mdf</em> args = cutoff1 cutoff2
cutoff1 = inner cutoff for the start of the tapering function
cutoff1 = out cutoff for the end of the tapering function
</pre>
</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>pair_style lj/mdf 2.5 3.0
pair_coeff * * 1 1
pair_coeff 1 1 1 1.1 2.8 3.0 3.2
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>pair_style buck 2.5 3.0
pair_coeff * * 100.0 1.5 200.0
pair_coeff * * 100.0 1.5 200.0 3.0 3.5
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>pair_style lennard/mdf 2.5 3.0
pair_coeff * * 1 1
pair_coeff 1 1 1 1.1 2.8 3.0 3.2
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>The <em>lj/mdf</em>, <em>buck/mdf</em> and <em>lennard/mdf</em> compute the standard 12-6
Lennard-Jones and Buckingham potential with the addition of a taper
function that ramps the energy and force smoothly to zero between an
inner and outer cutoff.</p>
<img alt="Eqs/pair_mdf-1.jpg" class="align-center" src="Eqs/pair_mdf-1.jpg" />
<p>The tapering, <em>f(r)</em>, is done by using the Mei, Davenport, Fernando
function <a class="reference internal" href="#mei"><span>(Mei)</span></a>.</p>
<img alt="Eqs/pair_mdf-2.jpg" class="align-center" src="Eqs/pair_mdf-2.jpg" />
<p>where</p>
<img alt="Eqs/pair_mdf-3.jpg" class="align-center" src="Eqs/pair_mdf-3.jpg" />
<p>Here <em>r_m</em> is the inner cutoff radius and <em>r_cut</em> is the outer cutoff
radius.</p>
<hr class="docutils" />
<p>For the <em>lj/mdf</em> pair_style, the potential energy, <em>E(r)</em>, is the
standard 12-6 Lennard-Jones written in the epsilon/sigma form:</p>
<img alt="Eqs/pair_mdf-4.jpg" class="align-center" src="Eqs/pair_mdf-4.jpg" />
<p>The following coefficients must be defined for each pair of atoms
types via the pair_coeff 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"><em>read_data</em></a> or
<a class="reference internal" href="read_restart.html"><em>read_restart commands</em></a>, or by mixing as described
below:</p>
<ul class="simple">
<li>epsilon (energy units)</li>
<li>sigma (distance units)</li>
<li>r_m (distance units)</li>
<li>r_*cut* (distance units)</li>
</ul>
<hr class="docutils" />
<p>For the <em>buck/mdf</em> pair_style, the potential energy, <em>E(r)</em>, is the
standard 12-6 Lennard-Jones written in the epsilon/sigma form:</p>
<img alt="Eqs/pair_mdf-5.jpg" class="align-center" src="Eqs/pair_mdf-5.jpg" />
<ul class="simple">
<li>A (energy units)</li>
<li>rho (distance units)</li>
<li>C (energy-distance^6 units)</li>
<li>r_m (distance units)</li>
<li>r_*cut*$ (distance units)</li>
</ul>
<hr class="docutils" />
<p>For the <em>lennard/mdf</em> pair_style, the potential energy, <em>E(r)</em>, is the
standard 12-6 Lennard-Jones written in the $A/B$ form:</p>
<img alt="Eqs/pair_mdf-6.jpg" class="align-center" src="Eqs/pair_mdf-6.jpg" />
<p>The following coefficients must be defined for each pair of atoms
types via the pair_coeff command as in the examples above, or in the
data file or restart files read by the read_data or read_restart
commands, or by mixing as described below:</p>
<ul class="simple">
<li>A (energy-distance^12 units)</li>
<li>B (energy-distance^6 units)</li>
<li>r_m (distance units)</li>
<li>r_*cut* (distance units)</li>
</ul>
<hr class="docutils" />
<p><strong>Mixing, shift, table, tail correction, restart, rRESPA info</strong>:</p>
<p>For atom type pairs I,J and I != J, the epsilon and sigma coefficients
and cutoff distance for all of the lj/cut pair styles can be mixed.
The default mix value is <em>geometric</em>. See the &#8220;pair_modify&#8221; command
for details.</p>
<p>All of the <em>lj/cut</em> pair styles support the
<a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> shift option for the energy of the
Lennard-Jones portion of the pair interaction.</p>
<p>The <em>lj/cut/coul/long</em> and <em>lj/cut/tip4p/long</em> pair styles support the
<a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> table option since they can tabulate
the short-range portion of the long-range Coulombic interaction.</p>
<p>All of the <em>lj/cut</em> pair styles support the
<a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> tail option for adding a long-range
tail correction to the energy and pressure for the Lennard-Jones
portion of the pair interaction.</p>
<p>All of the <em>lj/cut</em> pair styles write their information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>, so pair_style and pair_coeff commands do
not need to be specified in an input script that reads a restart file.</p>
<p>The <em>lj/cut</em> and <em>lj/cut/coul/long</em> pair styles support the use of the
<em>inner</em>, <em>middle</em>, and <em>outer</em> keywords of the <a class="reference internal" href="run_style.html"><em>run_style respa</em></a> command, meaning the pairwise forces can be
partitioned by distance at different levels of the rRESPA hierarchy.
The other styles only support the <em>pair</em> keyword of run_style respa.
See the <a class="reference internal" href="run_style.html"><em>run_style</em></a> command for details.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>These pair styles can only be used if LAMMPS was built with the
USER-MISC package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a>
section for more info on packages.</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_coeff.html"><em>pair_coeff</em></a></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="mei"><strong>(Mei)</strong> Mei, Davenport, Fernando, Phys Rev B, 43 4653 (1991)</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:'15 Dec 2015',
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