Homec4science
Diffusion lammps (lammps-icms) Browse

lammps/doc/html/dihedral_coeff.html
db1e17197fcflammps-icms

Last Change
Raw File

dihedral_coeff.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_coeff 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_coeff 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-coeff-command">
<span id="index-0"></span><h1>dihedral_coeff command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
dihedral_coeff N args
</pre>
<ul class="simple">
<li>N = dihedral type (see asterisk form below)</li>
<li>args = coefficients for one or more dihedral types</li>
</ul>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
dihedral_coeff 1 80.0 1 3
dihedral_coeff * 80.0 1 3 0.5
dihedral_coeff 2* 80.0 1 3 0.5
</pre>
</div>
<div class="section" id="description">
<h2>Description</h2>
<hr class="docutils" />
<p>Specify the dihedral force field coefficients for one or more dihedral types.
The number and meaning of the coefficients depends on the dihedral style.
Dihedral coefficients can also be set in the data file read by the
<a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> command or in a restart file.</p>
<p>N can be specified in one of two ways. An explicit numeric value can
be used, as in the 1st example above. Or a wild-card asterisk can be
used to set the coefficients for multiple dihedral types. This takes the
form &#8220;*&#8221; or &#8220;*n&#8221; or &#8220;n*&#8221; or &#8220;m*n&#8221;. If N = the number of dihedral types,
then an asterisk with no numeric values means all types from 1 to N. A
leading asterisk means all types from 1 to n (inclusive). A trailing
asterisk means all types from n to N (inclusive). A middle asterisk
means all types from m to n (inclusive).</p>
<p>Note that using a dihedral_coeff command can override a previous setting
for the same dihedral type. For example, these commands set the coeffs
for all dihedral types, then overwrite the coeffs for just dihedral type 2:</p>
<pre class="literal-block">
dihedral_coeff * 80.0 1 3
dihedral_coeff 2 200.0 1 3
</pre>
<p>A line in a data file that specifies dihedral coefficients uses the exact
same format as the arguments of the dihedral_coeff command in an input
script, except that wild-card asterisks should not be used since
coefficients for all N types must be listed in the file. For example,
under the &#8220;Dihedral Coeffs&#8221; section of a data file, the line that
corresponds to the 1st example above would be listed as</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="mi">1</span> <span class="mf">80.0</span> <span class="mi">1</span> <span class="mi">3</span>
</pre></div>
</div>
<p>The <a class="reference internal" href="dihedral_class2.html"><span class="doc">dihedral_style class2</span></a> is an exception to
this rule, in that an additional argument is used in the input script
to allow specification of the cross-term coefficients. See its doc
page for details.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">When comparing the formulas and coefficients for various LAMMPS
dihedral styles with dihedral equations defined by other force fields,
note that some force field implementations divide/multiply the energy
prefactor <em>K</em> by the multiple number of torsions that contain the J-K
bond in an I-J-K-L torsion. LAMMPS does not do this, i.e. the listed
dihedral equation applies to each individual dihedral. Thus you need
to define <em>K</em> appropriately to account for this difference if
necessary.</p>
</div>
<hr class="docutils" />
<p>Here is an alphabetic list of dihedral styles defined in LAMMPS. Click on
the style to display the formula it computes and coefficients
specified by the associated <a class="reference internal" href="#"><span class="doc">dihedral_coeff</span></a> command.</p>
<p>Note that there are also additional dihedral styles submitted by users
which are included in the LAMMPS distribution. The list of these with
links to the individual styles are given in the dihedral section of
<a class="reference internal" href="Section_commands.html#cmd-5"><span class="std std-ref">this page</span></a>.</p>
<ul class="simple">
<li><a class="reference internal" href="dihedral_none.html"><span class="doc">dihedral_style none</span></a> - turn off dihedral interactions</li>
<li><a class="reference internal" href="dihedral_hybrid.html"><span class="doc">dihedral_style hybrid</span></a> - define multiple styles of dihedral interactions</li>
<li><a class="reference internal" href="dihedral_charmm.html"><span class="doc">dihedral_style charmm</span></a> - CHARMM dihedral</li>
<li><a class="reference internal" href="dihedral_class2.html"><span class="doc">dihedral_style class2</span></a> - COMPASS (class 2) dihedral</li>
<li><a class="reference internal" href="dihedral_harmonic.html"><span class="doc">dihedral_style harmonic</span></a> - harmonic dihedral</li>
<li><a class="reference internal" href="dihedral_helix.html"><span class="doc">dihedral_style helix</span></a> - helix dihedral</li>
<li><a class="reference internal" href="dihedral_multi_harmonic.html"><span class="doc">dihedral_style multi/harmonic</span></a> - multi-harmonic dihedral</li>
<li><a class="reference internal" href="dihedral_opls.html"><span class="doc">dihedral_style opls</span></a> - OPLS dihedral</li>
</ul>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>This command must come after the simulation box is defined by a
<a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a>, <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a>, or
<a class="reference internal" href="create_box.html"><span class="doc">create_box</span></a> command.</p>
<p>A dihedral style must be defined before any dihedral coefficients are
set, either in the input script or in a data file.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><a class="reference internal" href="dihedral_style.html"><span class="doc">dihedral_style</span></a></p>
<p><strong>Default:</strong> none</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