Homec4science
Diffusion lammps (lammm-master) Browse

lammps/doc/html/angle_dipole.html
db1e17197fcflammm-master

Last Change
Raw File

angle_dipole.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>angle_style dipole 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>angle_style dipole 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="angle-style-dipole-command">
<span id="index-0"></span><h1>angle_style dipole command</h1>
</div>
<div class="section" id="angle-style-dipole-omp-command">
<h1>angle_style dipole/omp command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
angle_style dipole
</pre>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
angle_style dipole
angle_coeff 6 2.1 180.0
</pre>
</div>
<div class="section" id="description">
<h2>Description</h2>
<p>The <em>dipole</em> angle style is used to control the orientation of a dipolar
atom within a molecule <a class="reference internal" href="#orsi"><span class="std std-ref">(Orsi)</span></a>. Specifically, the <em>dipole</em> angle
style restrains the orientation of a point dipole mu_j (embedded in atom
&#8216;j&#8217;) with respect to a reference (bond) vector r_ij = r_i - r_j, where &#8216;i&#8217;
is another atom of the same molecule (typically, &#8216;i&#8217; and &#8216;j&#8217; are also
covalently bonded).</p>
<p>It is convenient to define an angle gamma between the &#8216;free&#8217; vector mu_j
and the reference (bond) vector r_ij:</p>
<img alt="_images/angle_dipole_gamma.jpg" class="align-center" src="_images/angle_dipole_gamma.jpg" />
<p>The <em>dipole</em> angle style uses the potential:</p>
<img alt="_images/angle_dipole_potential.jpg" class="align-center" src="_images/angle_dipole_potential.jpg" />
<p>where K is a rigidity constant and gamma0 is an equilibrium (reference)
angle.</p>
<p>The torque on the dipole can be obtained by differentiating the
potential using the &#8216;chain rule&#8217; as in appendix C.3 of
<a class="reference internal" href="pair_gayberne.html#allen"><span class="std std-ref">(Allen)</span></a>:</p>
<img alt="_images/angle_dipole_torque.jpg" class="align-center" src="_images/angle_dipole_torque.jpg" />
<p>Example: if gamma0 is set to 0 degrees, the torque generated by
the potential will tend to align the dipole along the reference
direction defined by the (bond) vector r_ij (in other words, mu_j is
restrained to point towards atom &#8216;i&#8217;).</p>
<p>The dipolar torque T_j must be counterbalanced in order to conserve
the local angular momentum. This is achieved via an additional force
couple generating a torque equivalent to the opposite of T_j:</p>
<img alt="_images/angle_dipole_couple.jpg" class="align-center" src="_images/angle_dipole_couple.jpg" />
<p>where F_i and F_j are applied on atoms i and j, respectively.</p>
<p>The following coefficients must be defined for each angle type via the
<a class="reference internal" href="angle_coeff.html"><span class="doc">angle_coeff</span></a> command as in the example 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>K (energy)</li>
<li>gamma0 (degrees)</li>
</ul>
<hr class="docutils" />
<p>Styles with a <em>gpu</em>, <em>intel</em>, <em>kk</em>, <em>omp</em>, or <em>opt</em> suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed in <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a>
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.</p>
<p>These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. 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>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <a class="reference internal" href="Section_start.html#start-6"><span class="std std-ref">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>This angle style can only be used if LAMMPS was built with the
USER-MISC package. See the <a class="reference internal" href="Section_start.html#start-2-3"><span class="std std-ref">Making LAMMPS</span></a>
section for more info on packages.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">In the &#8220;Angles&#8221; section of the data file, the atom ID &#8216;j&#8217;
corresponding to the dipole to restrain must come before the atom ID
of the reference atom &#8216;i&#8217;. A third atom ID &#8216;k&#8217; must also be provided,
although &#8216;k&#8217; is just a &#8216;dummy&#8217; atom which can be any atom; it may be
useful to choose a convention (e.g., &#8216;k&#8217;=&#8217;i&#8217;) and adhere to it. For
example, if ID=1 for the dipolar atom to restrain, and ID=2 for the
reference atom, the corresponding line in the &#8220;Angles&#8221; section of the
data file would read: X X 1 2 2</p>
</div>
<p>The &#8220;newton&#8221; command for intramolecular interactions must be &#8220;on&#8221;
(which is the default).</p>
<p>This angle style should not be used with SHAKE.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><a class="reference internal" href="angle_coeff.html"><span class="doc">angle_coeff</span></a>, <a class="reference internal" href="angle_hybrid.html"><span class="doc">angle_hybrid</span></a></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="orsi"><strong>(Orsi)</strong> Orsi &amp; Essex, The ELBA force field for coarse-grain modeling of
lipid membranes, PloS ONE 6(12): e28637, 2011.</p>
<p id="allen"><strong>(Allen)</strong> Allen &amp; Tildesley, Computer Simulation of Liquids,
Clarendon Press, Oxford, 1987.</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