Homec4science
Diffusion lammps (lammm-master-deprecated) Browse

lammps/doc/html/bond_style.html
3b4412d782eflammm-master-deprecated

Last Change
Raw File

bond_style.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>bond_style 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>bond_style 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="bond-style-command">
<span id="index-0"></span><h1>bond_style command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">style</span> <span class="n">args</span>
</pre></div>
</div>
<ul class="simple">
<li>style = <em>none</em> or <em>hybrid</em> or <em>class2</em> or <em>fene</em> or <em>fene/expand</em> or <em>harmonic</em> or <em>morse</em> or <em>nonlinear</em> or <em>quartic</em></li>
</ul>
<pre class="literal-block">
args = none for any style except <em>hybrid</em>
<em>hybrid</em> args = list of one or more styles
</pre>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">harmonic</span>
<span class="n">bond_style</span> <span class="n">fene</span>
<span class="n">bond_style</span> <span class="n">hybrid</span> <span class="n">harmonic</span> <span class="n">fene</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
<p>Set the formula(s) LAMMPS uses to compute bond interactions between
pairs of atoms. In LAMMPS, a bond differs from a pairwise
interaction, which are set via the <a class="reference internal" href="pair_style.html"><span class="doc">pair_style</span></a>
command. Bonds are defined between specified pairs of atoms and
remain in force for the duration of the simulation (unless the bond
breaks which is possible in some bond potentials). The list of bonded
atoms is read in by a <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> command from a data or restart file.
By contrast, pair potentials are typically defined between all pairs
of atoms within a cutoff distance and the set of active interactions
changes over time.</p>
<p>Hybrid models where bonds are computed using different bond potentials
can be setup using the <em>hybrid</em> bond style.</p>
<p>The coefficients associated with a bond style can be specified in a
data or restart file or via the <a class="reference internal" href="bond_coeff.html"><span class="doc">bond_coeff</span></a> command.</p>
<p>All bond potentials store their coefficient data in binary restart
files which means bond_style and <a class="reference internal" href="bond_coeff.html"><span class="doc">bond_coeff</span></a> commands
do not need to be re-specified in an input script that restarts a
simulation. See the <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a> command for
details on how to do this. The one exception is that bond_style
<em>hybrid</em> only stores the list of sub-styles in the restart file; bond
coefficients need to be re-specified.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">When both a bond and pair style is defined, the
<a class="reference internal" href="special_bonds.html"><span class="doc">special_bonds</span></a> command often needs to be used to
turn off (or weight) the pairwise interaction that would otherwise
exist between 2 bonded atoms.</p>
</div>
<p>In the formulas listed for each bond style, <em>r</em> is the distance
between the 2 atoms in the bond.</p>
<hr class="docutils" />
<p>Here is an alphabetic list of bond 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="bond_coeff.html"><span class="doc">bond_coeff</span></a> command.</p>
<p>Note that there are also additional bond 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 bond 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="bond_none.html"><span class="doc">bond_style none</span></a> - turn off bonded interactions</li>
<li><a class="reference internal" href="bond_zero.html"><span class="doc">bond_style zero</span></a> - topology but no interactions</li>
<li><a class="reference internal" href="bond_hybrid.html"><span class="doc">bond_style hybrid</span></a> - define multiple styles of bond interactions</li>
<li><a class="reference internal" href="bond_class2.html"><span class="doc">bond_style class2</span></a> - COMPASS (class 2) bond</li>
<li><a class="reference internal" href="bond_fene.html"><span class="doc">bond_style fene</span></a> - FENE (finite-extensible non-linear elastic) bond</li>
<li><a class="reference internal" href="bond_fene_expand.html"><span class="doc">bond_style fene/expand</span></a> - FENE bonds with variable size particles</li>
<li><a class="reference internal" href="bond_harmonic.html"><span class="doc">bond_style harmonic</span></a> - harmonic bond</li>
<li><a class="reference internal" href="bond_morse.html"><span class="doc">bond_style morse</span></a> - Morse bond</li>
<li><a class="reference internal" href="bond_nonlinear.html"><span class="doc">bond_style nonlinear</span></a> - nonlinear bond</li>
<li><a class="reference internal" href="bond_quartic.html"><span class="doc">bond_style quartic</span></a> - breakable quartic bond</li>
<li><a class="reference internal" href="bond_table.html"><span class="doc">bond_style table</span></a> - tabulated by bond length</li>
</ul>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>Bond styles can only be set for atom styles that allow bonds to be
defined.</p>
<p>Most bond styles are part of the MOLECULE 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 class="std std-ref">Making LAMMPS</span></a> section for more info on packages.
The doc pages for individual bond potentials tell if it is part of a
package.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><a class="reference internal" href="bond_coeff.html"><span class="doc">bond_coeff</span></a>, <a class="reference internal" href="delete_bonds.html"><span class="doc">delete_bonds</span></a></p>
</div>
<div class="section" id="default">
<h2>Default</h2>
<p>bond_style 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