Page MenuHomec4science
Files F90788496

pair_thole.html
No OneTemporary
Actions

File Metadata

Created
Mon, Nov 4, 18:49

pair_thole.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 thole 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 thole 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-thole-command">
<span id="index-0"></span><h1>pair_style thole command<a class="headerlink" href="#pair-style-thole-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 thole damp cutoff
</pre></div>
</div>
<ul class="simple">
<li>thole = style name</li>
<li>damp = global damping parameter</li>
<li>cutoff = global cutoff</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>pair_style hybrid/overlay ... thole 2.6 12.0
pair_coeff 1 1 thole 1.0
pair_coeff 1 2 thole 1.0 2.6 10.0
pair_coeff * 2 thole 1.0 2.6
</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>thole</em> pair style is meant to be used with force fields that
include explicit polarization through Drude dipoles. This link
describes how to use the <a class="reference internal" href="tutorial_drude.html"><em>thermalized Drude oscillator model</em></a> in LAMMPS and polarizable models in LAMMPS
are discussed in <a class="reference internal" href="Section_howto.html#howto-25"><span>this Section</span></a>.</p>
<p>The <em>thole</em> pair style should be used as a sub-style within in the
<a class="reference internal" href="pair_hybrid.html"><em>pair_hybrid/overlay</em></a> command, in conjunction with a
main pair style including Coulomb interactions, i.e. any pair style
containing <em>coul/cut</em> or <em>coul/long</em> in its style name.</p>
<p>The <em>thole</em> pair style computes the Coulomb interaction damped at
short distances by a function</p>
<div class="math">
\[\begin{equation} T_{ij}(r_{ij}) = 1 - \left( 1 +
\frac{s_{ij} r_{ij} }{2} \right)
\exp \left( - s_{ij} r_{ij} \right) \end{equation}\]</div>
<p>This function results from an adaptation to point charges
<a class="reference internal" href="tutorial_drude.html#noskov"><span>(Noskov)</span></a> of the dipole screening scheme originally proposed
by <a class="reference internal" href="tutorial_drude.html#thole"><span>Thole</span></a>. The scaling coefficient <span class="math">\(s_{ij}\)</span> is determined
by the polarizability of the atoms, <span class="math">\(\alpha_i\)</span>, and by a Thole
damping parameter <span class="math">\(a\)</span>. This Thole damping parameter usually takes
a value of 2.6, but in certain force fields the value can depend upon
the atom types. The mixing rule for Thole damping parameters is the
arithmetic average, and for polarizabilities the geometric average
between the atom-specific values.</p>
<div class="math">
\[\begin{equation} s_{ij} = \frac{ a_{ij} }{
(\alpha_{ij})^{1/3} } = \frac{ (a_i + a_j)/2 }{
[(\alpha_i\alpha_j)^{1/2}]^{1/3} } \end{equation}\]</div>
<p>The damping function is only applied to the interactions between the
point charges representing the induced dipoles on polarizable sites,
that is, charges on Drude particles, <span class="math">\(q_{D,i}\)</span>, and opposite
charges, <span class="math">\(-q_{D,i}\)</span>, located on the respective core particles
(to which each Drude particle is bonded). Therefore, Thole screening
is not applied to the full charge of the core particle <span class="math">\(q_i\)</span>, but
only to the <span class="math">\(-q_{D,i}\)</span> part of it.</p>
<p>The interactions between core charges are subject to the weighting
factors set by the <a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a> command. The
interactions between Drude particles and core charges or
non-polarizable atoms are also subject to these weighting factors. The
Drude particles inherit the 1-2, 1-3 and 1-4 neighbor relations from
their respective cores.</p>
<p>The following coefficients must be defined for each pair of atoms
types via the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command as in the example
above.</p>
<ul class="simple">
<li>alpha (distance units^3)</li>
<li>damp</li>
<li>cutoff (distance units)</li>
</ul>
<p>The last two coefficients are optional. If not specified the global
Thole damping parameter or global cutoff specified in the pair_style
command are used. In order to specify a cutoff (third argument) a damp
parameter (second argument) must also be specified.</p>
<p><strong>Mixing</strong>:</p>
<p>The <em>thole</em> pair style does not support mixing. Thus, coefficients
for all I,J pairs must be specified explicitly.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>These pair styles are part of the USER-DRUDE 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>Making LAMMPS</span></a> section for more info.</p>
<p>This pair_style should currently not be used with the <a class="reference internal" href="dihedral_charmm.html"><em>charmm dihedral style</em></a> if the latter has non-zero 1-4 weighting
factors. This is because the <em>thole</em> pair style does not know which
pairs are 1-4 partners of which dihedrals.</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="fix_drude.html"><em>fix drude</em></a>, <a class="reference internal" href="fix_langevin_drude.html"><em>fix langevin/drude</em></a>, <a class="reference internal" href="fix_drude_transform.html"><em>fix drude/transform</em></a>, <a class="reference internal" href="compute_temp_drude.html"><em>compute temp/drude</em></a></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="noskov"><strong>(Noskov)</strong> Noskov, Lamoureux and Roux, J Phys Chem B, 109, 6705 (2005).</p>
<p id="thole"><strong>(Thole)</strong> Chem Phys, 59, 341 (1981).</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>

Event Timeline

c4science · Help