forked from lijiext/lammps
268 lines
12 KiB
HTML
268 lines
12 KiB
HTML
|
|
|
|
<!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>compute bond/local command — 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 & 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 & 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>
|
|
|
|
</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> »</li>
|
|
|
|
<li>compute bond/local 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="compute-bond-local-command">
|
|
<span id="index-0"></span><h1>compute bond/local command</h1>
|
|
<div class="section" id="syntax">
|
|
<h2>Syntax</h2>
|
|
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">bond</span><span class="o">/</span><span class="n">local</span> <span class="n">input1</span> <span class="n">input2</span> <span class="o">...</span>
|
|
</pre></div>
|
|
</div>
|
|
<ul class="simple">
|
|
<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><span class="doc">compute</span></a> command</li>
|
|
<li>bond/local = style name of this compute command</li>
|
|
<li>one or more keywords may be appended</li>
|
|
<li>keyword = <em>dist</em> or <em>eng</em></li>
|
|
</ul>
|
|
<pre class="literal-block">
|
|
<em>dist</em> = bond distance
|
|
<em>eng</em> = bond energy
|
|
<em>force</em> = bond force
|
|
</pre>
|
|
</div>
|
|
<div class="section" id="examples">
|
|
<h2>Examples</h2>
|
|
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">bond</span><span class="o">/</span><span class="n">local</span> <span class="n">eng</span>
|
|
<span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">bond</span><span class="o">/</span><span class="n">local</span> <span class="n">dist</span> <span class="n">eng</span> <span class="n">force</span>
|
|
</pre></div>
|
|
</div>
|
|
</div>
|
|
<div class="section" id="description">
|
|
<h2>Description</h2>
|
|
<p>Define a computation that calculates properties of individual bond
|
|
interactions. The number of datums generated, aggregated across all
|
|
processors, equals the number of bonds in the system, modified
|
|
by the group parameter as explained below.</p>
|
|
<p>The local data stored by this command is generated by looping over all
|
|
the atoms owned on a processor and their bonds. A bond will only be
|
|
included if both atoms in the bond are in the specified compute group.
|
|
Any bonds that have been broken (see the <a class="reference internal" href="bond_style.html"><span class="doc">bond_style</span></a>
|
|
command) by setting their bond type to 0 are not included. Bonds that
|
|
have been turned off (see the <a class="reference internal" href="fix_shake.html"><span class="doc">fix shake</span></a> or
|
|
<a class="reference internal" href="delete_bonds.html"><span class="doc">delete_bonds</span></a> commands) by setting their bond type
|
|
negative are written into the file, but their energy will be 0.0.</p>
|
|
<p>Note that as atoms migrate from processor to processor, there will be
|
|
no consistent ordering of the entries within the local vector or array
|
|
from one timestep to the next. The only consistency that is
|
|
guaranteed is that the ordering on a particular timestep will be the
|
|
same for local vectors or arrays generated by other compute commands.
|
|
For example, bond output from the <a class="reference internal" href="compute_property_local.html"><span class="doc">compute property/local</span></a> command can be combined
|
|
with data from this command and output by the <a class="reference internal" href="dump.html"><span class="doc">dump local</span></a>
|
|
command in a consistent way.</p>
|
|
<p>Here is an example of how to do this:</p>
|
|
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="nb">property</span><span class="o">/</span><span class="n">local</span> <span class="n">batom1</span> <span class="n">batom2</span> <span class="n">btype</span>
|
|
<span class="n">compute</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">bond</span><span class="o">/</span><span class="n">local</span> <span class="n">dist</span> <span class="n">eng</span>
|
|
<span class="n">dump</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">local</span> <span class="mi">1000</span> <span class="n">tmp</span><span class="o">.</span><span class="n">dump</span> <span class="n">index</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="n">c_2</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_2</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span>
|
|
</pre></div>
|
|
</div>
|
|
<p><strong>Output info:</strong></p>
|
|
<p>This compute calculates a local vector or local array depending on the
|
|
number of keywords. The length of the vector or number of rows in the
|
|
array is the number of bonds. If a single keyword is specified, a
|
|
local vector is produced. If two or more keywords are specified, a
|
|
local array is produced where the number of columns = the number of
|
|
keywords. The vector or array can be accessed by any command that
|
|
uses local values from a compute as input. See <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">this section</span></a> for an overview of LAMMPS output
|
|
options.</p>
|
|
<p>The output for <em>dist</em> will be in distance <a class="reference internal" href="units.html"><span class="doc">units</span></a>. The
|
|
output for <em>eng</em> will be in energy <a class="reference internal" href="units.html"><span class="doc">units</span></a>. The output for
|
|
<em>force</em> will be in force <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
|
|
</div>
|
|
<div class="section" id="restrictions">
|
|
<h2>Restrictions</h2>
|
|
<blockquote>
|
|
<div>none</div></blockquote>
|
|
</div>
|
|
<div class="section" id="related-commands">
|
|
<h2>Related commands</h2>
|
|
<p><a class="reference internal" href="dump.html"><span class="doc">dump local</span></a>, <a class="reference internal" href="compute_property_local.html"><span class="doc">compute property/local</span></a></p>
|
|
<p><strong>Default:</strong> none</p>
|
|
</div>
|
|
</div>
|
|
|
|
|
|
</div>
|
|
</div>
|
|
<footer>
|
|
|
|
|
|
<hr/>
|
|
|
|
<div role="contentinfo">
|
|
<p>
|
|
© 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> |