Homec4science
Diffusion lammps (lammm-master) Browse

lammps/doc/html/dihedral_class2.html
b611b8e05617lammm-master

Last Change
Raw File

dihedral_class2.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>dihedral_style class2 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>dihedral_style class2 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="dihedral-style-class2-command">
<span id="index-0"></span><h1>dihedral_style class2 command</h1>
</div>
<div class="section" id="dihedral-style-class2-omp-command">
<h1>dihedral_style class2/omp command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">class2</span>
</pre></div>
</div>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">class2</span>
<span class="n">dihedral_coeff</span> <span class="mi">1</span> <span class="mi">100</span> <span class="mi">75</span> <span class="mi">100</span> <span class="mi">70</span> <span class="mi">80</span> <span class="mi">60</span>
<span class="n">dihedral_coeff</span> <span class="o">*</span> <span class="n">mbt</span> <span class="mf">3.5945</span> <span class="mf">0.1704</span> <span class="o">-</span><span class="mf">0.5490</span> <span class="mf">1.5228</span>
<span class="n">dihedral_coeff</span> <span class="o">*</span> <span class="n">ebt</span> <span class="mf">0.3417</span> <span class="mf">0.3264</span> <span class="o">-</span><span class="mf">0.9036</span> <span class="mf">0.1368</span> <span class="mf">0.0</span> <span class="o">-</span><span class="mf">0.8080</span> <span class="mf">1.0119</span> <span class="mf">1.1010</span>
<span class="n">dihedral_coeff</span> <span class="mi">2</span> <span class="n">at</span> <span class="mf">0.0</span> <span class="o">-</span><span class="mf">0.1850</span> <span class="o">-</span><span class="mf">0.7963</span> <span class="o">-</span><span class="mf">2.0220</span> <span class="mf">0.0</span> <span class="o">-</span><span class="mf">0.3991</span> <span class="mf">110.2453</span> <span class="mf">105.1270</span>
<span class="n">dihedral_coeff</span> <span class="o">*</span> <span class="n">aat</span> <span class="o">-</span><span class="mf">13.5271</span> <span class="mf">110.2453</span> <span class="mf">105.1270</span>
<span class="n">dihedral_coeff</span> <span class="o">*</span> <span class="n">bb13</span> <span class="mf">0.0</span> <span class="mf">1.0119</span> <span class="mf">1.1010</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
<p>The <em>class2</em> dihedral style uses the potential</p>
<img alt="_images/dihedral_class2.jpg" class="align-center" src="_images/dihedral_class2.jpg" />
<p>where Ed is the dihedral term, Embt is a middle-bond-torsion term,
Eebt is an end-bond-torsion term, Eat is an angle-torsion term, Eaat
is an angle-angle-torsion term, and Ebb13 is a bond-bond-13 term.</p>
<p>Theta1 and theta2 are equilibrium angles and r1 r2 r3 are equilibrium
bond lengths.</p>
<p>See <a class="reference internal" href="pair_modify.html#sun"><span class="std std-ref">(Sun)</span></a> for a description of the COMPASS class2 force field.</p>
<p>Coefficients for the Ed, Embt, Eebt, Eat, Eaat, and Ebb13 formulas
must be defined for each dihedral type via the
<a class="reference internal" href="dihedral_coeff.html"><span class="doc">dihedral_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>
<p>These are the 6 coefficients for the Ed formula:</p>
<ul class="simple">
<li>K1 (energy)</li>
<li>phi1 (degrees)</li>
<li>K2 (energy)</li>
<li>phi2 (degrees)</li>
<li>K3 (energy)</li>
<li>phi3 (degrees)</li>
</ul>
<p>For the Embt formula, each line in a
<a class="reference internal" href="dihedral_coeff.html"><span class="doc">dihedral_coeff</span></a> command in the input script lists
5 coefficients, the first of which is &#8220;mbt&#8221; to indicate they are
MiddleBondTorsion coefficients. In a data file, these coefficients
should be listed under a &#8220;MiddleBondTorsion Coeffs&#8221; heading and you
must leave out the &#8220;mbt&#8221;, i.e. only list 4 coefficients after the
dihedral type.</p>
<ul class="simple">
<li>mbt</li>
<li>A1 (energy/distance)</li>
<li>A2 (energy/distance)</li>
<li>A3 (energy/distance)</li>
<li>r2 (distance)</li>
</ul>
<p>For the Eebt formula, each line in a
<a class="reference internal" href="dihedral_coeff.html"><span class="doc">dihedral_coeff</span></a> command in the input script lists
9 coefficients, the first of which is &#8220;ebt&#8221; to indicate they are
EndBondTorsion coefficients. In a data file, these coefficients
should be listed under a &#8220;EndBondTorsion Coeffs&#8221; heading and you must
leave out the &#8220;ebt&#8221;, i.e. only list 8 coefficients after the dihedral
type.</p>
<ul class="simple">
<li>ebt</li>
<li>B1 (energy/distance)</li>
<li>B2 (energy/distance)</li>
<li>B3 (energy/distance)</li>
<li>C1 (energy/distance)</li>
<li>C2 (energy/distance)</li>
<li>C3 (energy/distance)</li>
<li>r1 (distance)</li>
<li>r3 (distance)</li>
</ul>
<p>For the Eat formula, each line in a
<a class="reference internal" href="dihedral_coeff.html"><span class="doc">dihedral_coeff</span></a> command in the input script lists
9 coefficients, the first of which is &#8220;at&#8221; to indicate they are
AngleTorsion coefficients. In a data file, these coefficients should
be listed under a &#8220;AngleTorsion Coeffs&#8221; heading and you must leave out
the &#8220;at&#8221;, i.e. only list 8 coefficients after the dihedral type.</p>
<ul class="simple">
<li>at</li>
<li>D1 (energy/radian)</li>
<li>D2 (energy/radian)</li>
<li>D3 (energy/radian)</li>
<li>E1 (energy/radian)</li>
<li>E2 (energy/radian)</li>
<li>E3 (energy/radian)</li>
<li>theta1 (degrees)</li>
<li>theta2 (degrees)</li>
</ul>
<p>Theta1 and theta2 are specified in degrees, but LAMMPS converts them
to radians internally; hence the units of D and E are in
energy/radian.</p>
<p>For the Eaat formula, each line in a
<a class="reference internal" href="dihedral_coeff.html"><span class="doc">dihedral_coeff</span></a> command in the input script lists
4 coefficients, the first of which is &#8220;aat&#8221; to indicate they are
AngleAngleTorsion coefficients. In a data file, these coefficients
should be listed under a &#8220;AngleAngleTorsion Coeffs&#8221; heading and you
must leave out the &#8220;aat&#8221;, i.e. only list 3 coefficients after the
dihedral type.</p>
<ul class="simple">
<li>aat</li>
<li>M (energy/radian^2)</li>
<li>theta1 (degrees)</li>
<li>theta2 (degrees)</li>
</ul>
<p>Theta1 and theta2 are specified in degrees, but LAMMPS converts them
to radians internally; hence the units of M are in energy/radian^2.</p>
<p>For the Ebb13 formula, each line in a
<a class="reference internal" href="dihedral_coeff.html"><span class="doc">dihedral_coeff</span></a> command in the input script lists
4 coefficients, the first of which is &#8220;bb13&#8221; to indicate they are
BondBond13 coefficients. In a data file, these coefficients should be
listed under a &#8220;BondBond13 Coeffs&#8221; heading and you must leave out the
&#8220;bb13&#8221;, i.e. only list 3 coefficients after the dihedral type.</p>
<ul class="simple">
<li>bb13</li>
<li>N (energy/distance^2)</li>
<li>r1 (distance)</li>
<li>r3 (distance)</li>
</ul>
<hr class="docutils" />
<p>Styles with a <em>cuda</em>, <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 USER-CUDA, 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_accelerate</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 dihedral style can only be used if LAMMPS was built with the
CLASS2 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 on packages.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><a class="reference internal" href="dihedral_coeff.html"><span class="doc">dihedral_coeff</span></a></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="sun"><strong>(Sun)</strong> Sun, J Phys Chem B 102, 7338-7364 (1998).</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