Homec4science
Diffusion lammps (lammm-master-deprecated) Browse

lammps/doc/html/angle_cosine_periodic.html
7d77aea42d30lammm-master-deprecated

Last Change
Raw File

angle_cosine_periodic.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 cosine/periodic 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"/>
<link rel="up" title="Angle Styles" href="angles.html"/>
<link rel="next" title="angle_style cosine/shift command" href="angle_cosine_shift.html"/>
<link rel="prev" title="angle_style cosine/delta command" href="angle_cosine_delta.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">
<p class="caption"><span class="caption-text">User Documentation</span></p>
<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>
<p class="caption"><span class="caption-text">Index</span></p>
<ul class="current">
<li class="toctree-l1"><a class="reference internal" href="tutorials.html">Tutorials</a></li>
<li class="toctree-l1"><a class="reference internal" href="commands.html">Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="fixes.html">Fixes</a></li>
<li class="toctree-l1"><a class="reference internal" href="computes.html">Computes</a></li>
<li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
<li class="toctree-l1 current"><a class="reference internal" href="angles.html">Angle Styles</a><ul class="current">
<li class="toctree-l2"><a class="reference internal" href="angle_charmm.html">angle_style charmm command</a></li>
<li class="toctree-l2"><a class="reference internal" href="angle_charmm.html#angle-style-charmm-intel-command">angle_style charmm/intel command</a></li>
<li class="toctree-l2"><a class="reference internal" href="angle_charmm.html#angle-style-charmm-kk-command">angle_style charmm/kk command</a></li>
<li class="toctree-l2"><a class="reference internal" href="angle_charmm.html#angle-style-charmm-omp-command">angle_style charmm/omp command</a></li>
<li class="toctree-l2"><a class="reference internal" href="angle_class2.html">angle_style class2 command</a></li>
<li class="toctree-l2"><a class="reference internal" href="angle_class2.html#angle-style-class2-omp-command">angle_style class2/omp command</a></li>
<li class="toctree-l2"><a class="reference internal" href="angle_cosine.html">angle_style cosine command</a></li>
<li class="toctree-l2"><a class="reference internal" href="angle_cosine.html#angle-style-cosine-omp-command">angle_style cosine/omp command</a></li>
<li class="toctree-l2"><a class="reference internal" href="angle_cosine_delta.html">angle_style cosine/delta command</a></li>
<li class="toctree-l2"><a class="reference internal" href="angle_cosine_delta.html#angle-style-cosine-delta-omp-command">angle_style cosine/delta/omp command</a></li>
<li class="toctree-l2 current"><a class="current reference internal" href="#">angle_style cosine/periodic command</a></li>
<li class="toctree-l2"><a class="reference internal" href="#angle-style-cosine-periodic-omp-command">angle_style cosine/periodic/omp command</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#syntax">Syntax</a></li>
<li class="toctree-l3"><a class="reference internal" href="#examples">Examples</a></li>
<li class="toctree-l3"><a class="reference internal" href="#description">Description</a></li>
<li class="toctree-l3"><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li class="toctree-l3"><a class="reference internal" href="#related-commands">Related commands</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="angle_cosine_shift.html">angle_style cosine/shift command</a></li>
<li class="toctree-l2"><a class="reference internal" href="angle_cosine_shift.html#angle-style-cosine-shift-omp-command">angle_style cosine/shift/omp command</a></li>
<li class="toctree-l2"><a class="reference internal" href="angle_cosine_shift_exp.html">angle_style cosine/shift/exp command</a></li>
<li class="toctree-l2"><a class="reference internal" href="angle_cosine_shift_exp.html#angle-style-cosine-shift-exp-omp-command">angle_style cosine/shift/exp/omp command</a></li>
<li class="toctree-l2"><a class="reference internal" href="angle_cosine_squared.html">angle_style cosine/squared command</a></li>
<li class="toctree-l2"><a class="reference internal" href="angle_cosine_squared.html#angle-style-cosine-squared-omp-command">angle_style cosine/squared/omp command</a></li>
<li class="toctree-l2"><a class="reference internal" href="angle_dipole.html">angle_style dipole command</a></li>
<li class="toctree-l2"><a class="reference internal" href="angle_dipole.html#angle-style-dipole-omp-command">angle_style dipole/omp command</a></li>
<li class="toctree-l2"><a class="reference internal" href="angle_fourier.html">angle_style fourier command</a></li>
<li class="toctree-l2"><a class="reference internal" href="angle_fourier.html#angle-style-fourier-omp-command">angle_style fourier/omp command</a></li>
<li class="toctree-l2"><a class="reference internal" href="angle_fourier_simple.html">angle_style fourier/simple command</a></li>
<li class="toctree-l2"><a class="reference internal" href="angle_fourier_simple.html#angle-style-fourier-simple-omp-command">angle_style fourier/simple/omp command</a></li>
<li class="toctree-l2"><a class="reference internal" href="angle_harmonic.html">angle_style harmonic command</a></li>
<li class="toctree-l2"><a class="reference internal" href="angle_harmonic.html#angle-style-harmonic-intel-command">angle_style harmonic/intel command</a></li>
<li class="toctree-l2"><a class="reference internal" href="angle_harmonic.html#angle-style-harmonic-kk-command">angle_style harmonic/kk command</a></li>
<li class="toctree-l2"><a class="reference internal" href="angle_harmonic.html#angle-style-harmonic-omp-command">angle_style harmonic/omp command</a></li>
<li class="toctree-l2"><a class="reference internal" href="angle_hybrid.html">angle_style hybrid command</a></li>
<li class="toctree-l2"><a class="reference internal" href="angle_none.html">angle_style none command</a></li>
<li class="toctree-l2"><a class="reference internal" href="angle_quartic.html">angle_style quartic command</a></li>
<li class="toctree-l2"><a class="reference internal" href="angle_quartic.html#angle-style-quartic-omp-command">angle_style quartic/omp command</a></li>
<li class="toctree-l2"><a class="reference internal" href="angle_sdk.html">angle_style sdk command</a></li>
<li class="toctree-l2"><a class="reference internal" href="angle_table.html">angle_style table command</a></li>
<li class="toctree-l2"><a class="reference internal" href="angle_table.html#angle-style-table-omp-command">angle_style table/omp command</a></li>
<li class="toctree-l2"><a class="reference internal" href="angle_zero.html">angle_style zero command</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
<li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</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><a href="angles.html">Angle Styles</a> &raquo;</li>
<li>angle_style cosine/periodic 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 class="rst-footer-buttons" style="margin-bottom: 1em" role="navigation" aria-label="footer navigation">
<a href="angle_cosine_shift.html" class="btn btn-neutral float-right" title="angle_style cosine/shift command" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
<a href="angle_cosine_delta.html" class="btn btn-neutral" title="angle_style cosine/delta command" accesskey="p"><span class="fa fa-arrow-circle-left"></span> Previous</a>
</div>
</div>
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div itemprop="articleBody">
<div class="section" id="angle-style-cosine-periodic-command">
<span id="index-0"></span><h1>angle_style cosine/periodic command</h1>
</div>
<div class="section" id="angle-style-cosine-periodic-omp-command">
<h1>angle_style cosine/periodic/omp command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
angle_style cosine/periodic
</pre>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
angle_style cosine/periodic
angle_coeff * 75.0 1 6
</pre>
</div>
<div class="section" id="description">
<h2>Description</h2>
<p>The <em>cosine/periodic</em> angle style uses the following potential, which
is commonly used in the <a class="reference internal" href="Section_howto.html#howto-4"><span class="std std-ref">DREIDING</span></a> force
field, particularly for organometallic systems where <em>n</em> = 4 might be
used for an octahedral complex and <em>n</em> = 3 might be used for a
trigonal center:</p>
<img alt="_images/angle_cosine_periodic.jpg" class="align-center" src="_images/angle_cosine_periodic.jpg" />
<p>where C, B and n are coefficients defined for each angle type.</p>
<p>See <a class="reference internal" href="#cosine-mayo"><span class="std std-ref">(Mayo)</span></a> for a description of the DREIDING force field</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>C (energy)</li>
<li>B = 1 or -1</li>
<li>n = 1, 2, 3, 4, 5 or 6 for periodicity</li>
</ul>
<p>Note that the prefactor C is specified and not the overall force
constant K = C / n^2. When B = 1, it leads to a minimum for the
linear geometry. When B = -1, it leads to a maximum for the linear
geometry.</p>
<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 5</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-7"><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 5</span></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>This angle style can only be used if LAMMPS was built with the
MOLECULE package (which it is by default). 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 on packages.</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></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="cosine-mayo"><strong>(Mayo)</strong> Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
(1990).</p>
</div>
</div>
</div>
</div>
<footer>
<div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
<a href="angle_cosine_shift.html" class="btn btn-neutral float-right" title="angle_style cosine/shift command" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
<a href="angle_cosine_delta.html" class="btn btn-neutral" title="angle_style cosine/delta command" accesskey="p"><span class="fa fa-arrow-circle-left"></span> Previous</a>
</div>
<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