Homec4science
Diffusion lammps (lammm-master-deprecated) Browse

lammps/doc/html/compute_body_local.html
29d04c1fbbf7lammm-master-deprecated

Last Change
Raw File

compute_body_local.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>compute body/local 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>compute body/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-body-local-command">
<span id="index-0"></span><h1>compute body/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">body</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>body/local = style name of this compute command</li>
<li>one or more keywords may be appended</li>
<li>keyword = <em>id</em> or <em>type</em> or <em>integer</em></li>
</ul>
<pre class="literal-block">
<em>id</em> = atom ID of the body particle
<em>type</em> = atom type of the body particle
<em>integer</em> = 1,2,3,etc = index of fields defined by body style
</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">body</span><span class="o">/</span><span class="n">local</span> <span class="nb">type</span> <span class="mi">1</span> <span class="mi">2</span> <span class="mi">3</span>
<span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">body</span><span class="o">/</span><span class="n">local</span> <span class="mi">3</span> <span class="mi">6</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
<p>Define a computation that calculates properties of individual body
sub-particles. The number of datums generated, aggregated across all
processors, equals the number of body sub-particles plus the number of
non-body particles in the system, modified by the group parameter as
explained below. See <a class="reference internal" href="Section_howto.html#howto-14"><span class="std std-ref">Section_howto 14</span></a>
of the manual and the <a class="reference internal" href="body.html"><span class="doc">body</span></a> doc page for more details on
using body particles.</p>
<p>The local data stored by this command is generated by looping over all
the atoms. An atom will only be included if it is in the group. If
the atom is a body particle, then its N sub-particles will be looped
over, and it will contribute N datums to the count of datums. If it
is not a body particle, it will contribute 1 datum.</p>
<p>For both body particles and non-body particles, the <em>id</em> keyword
will store the ID of the particle.</p>
<p>For both body particles and non-body particles, the <em>type</em> keyword
will store the type of the particle.</p>
<p>The <em>integer</em> keywords mean different things for body and non-body
particles. If the atom is not a body particle, only its <em>x</em>, <em>y</em>, <em>z</em>
coordinates can be referenced, using the <em>integer</em> keywords 1,2,3.
Note that this means that if you want to access more fields than this
for body particles, then you cannot include non-body particles in the
group.</p>
<p>For a body particle, the <em>integer</em> keywords refer to fields calculated
by the body style for each sub-particle. The body style, as specified
by the <a class="reference internal" href="atom_style.html"><span class="doc">atom_style body</span></a>, determines how many fields
exist and what they are. See the <a class="reference internal" href="body.html"><span class="doc">body</span></a> doc page for
details of the different styles.</p>
<p>Here is an example of how to output body information using the <a class="reference internal" href="dump.html"><span class="doc">dump local</span></a> command with this compute. If fields 1,2,3 for the
body sub-particles are x,y,z coordinates, then the dump file will be
formatted similar to the output of a <a class="reference internal" href="dump.html"><span class="doc">dump atom or custom</span></a>
command.</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="n">body</span><span class="o">/</span><span class="n">local</span> <span class="nb">type</span> <span class="mi">1</span> <span class="mi">2</span> <span class="mi">3</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_1</span><span class="p">[</span><span class="mi">4</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 datums as described above. 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 <a class="reference internal" href="units.html"><span class="doc">units</span></a> for output values depend on the body style.</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></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