Homec4science
Diffusion lammps (lammm-master) Browse

lammps/doc/compute_com_chunk.html
c6213f36d34clammm-master

Last Change
Raw File

compute_com_chunk.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 com/chunk command &mdash; LAMMPS 15 May 2015 version 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 15 May 2015 version 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 com/chunk command</li>
<li class="wy-breadcrumbs-aside">
<a href="http://lammps.sandia.gov">Homepage</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-com-chunk-command">
<span id="index-0"></span><h1>compute com/chunk command<a class="headerlink" href="#compute-com-chunk-command" title="Permalink to this headline">¶</a></h1>
<div class="section" id="syntax">
<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline">¶</a></h2>
<div class="highlight-python"><div class="highlight"><pre>compute ID group-ID com/chunk chunkID
</pre></div>
</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><em>compute</em></a> command</li>
<li>com/chunk = style name of this compute command</li>
<li>chunkID = ID of <a class="reference internal" href="compute_chunk_atom.html"><em>compute chunk/atom</em></a> command</li>
</ul>
</div>
<div class="section" id="examples">
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h2>
<div class="highlight-python"><div class="highlight"><pre>compute 1 fluid com/chunk molchunk
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
<p>Define a computation that calculates the center-of-mass for multiple
chunks of atoms.</p>
<p>In LAMMPS, chunks are collections of atoms defined by a <a class="reference internal" href="compute_chunk_atom.html"><em>compute chunk/atom</em></a> command, which assigns each atom
to a single chunk (or no chunk). The ID for this command is specified
as chunkID. For example, a single chunk could be the atoms in a
molecule or atoms in a spatial bin. See the <a class="reference internal" href="compute_chunk_atom.html"><em>compute chunk/atom</em></a> doc page and &#8220;<a class="reference internal" href="Section_howto.html#howto-23"><span>Section_howto 23</span></a> for details of how chunks can be
defined and examples of how they can be used to measure properties of
a system.</p>
<p>This compute calculates the x,y,z coordinates of the center-of-mass
for each chunk, which includes all effects due to atoms passing thru
periodic boundaries.</p>
<p>Note that only atoms in the specified group contribute to the
calculation. The <a class="reference internal" href="compute_chunk_atom.html"><em>compute chunk/atom</em></a> command
defines its own group; atoms will have a chunk ID = 0 if they are not
in that group, signifying they are not assigned to a chunk, and will
thus also not contribute to this calculation. You can specify the
&#8220;all&#8221; group for this command if you simply want to include atoms with
non-zero chunk IDs.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">The coordinates of an atom contribute to the chunk&#8217;s
center-of-mass in &#8220;unwrapped&#8221; form, by using the image flags
associated with each atom. See the <a class="reference internal" href="dump.html"><em>dump custom</em></a> command
for a discussion of &#8220;unwrapped&#8221; coordinates. See the Atoms section of
the <a class="reference internal" href="read_data.html"><em>read_data</em></a> command for a discussion of image flags
and how they are set for each atom. You can reset the image flags
(e.g. to 0) before invoking this compute by using the <a class="reference internal" href="set.html"><em>set image</em></a> command.</p>
</div>
<p>The simplest way to output the results of the compute com/chunk
calculation to a file is to use the <a class="reference internal" href="fix_ave_time.html"><em>fix ave/time</em></a>
command, for example:</p>
<div class="highlight-python"><div class="highlight"><pre>compute cc1 all chunk/atom molecule
compute myChunk all com/chunk cc1
fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector
</pre></div>
</div>
<p><strong>Output info:</strong></p>
<p>This compute calculates a global array where the number of rows = the
number of chunks <em>Nchunk</em> as calculated by the specified <a class="reference internal" href="compute_chunk_atom.html"><em>compute chunk/atom</em></a> command. The number of columns =
3 for the x,y,z center-of-mass coordinates of each chunk. These
values can be accessed by any command that uses global array values
from a compute as input. See <a class="reference internal" href="Section_howto.html#howto-15"><span>Section_howto 15</span></a> for an overview of LAMMPS output
options.</p>
<p>The array values are &#8220;intensive&#8221;. The array values will be in
distance <a class="reference internal" href="units.html"><em>units</em></a>.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
<blockquote>
<div>none</div></blockquote>
</div>
<div class="section" id="related-commands">
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline">¶</a></h2>
<p><a class="reference internal" href="compute_com.html"><em>compute com</em></a></p>
<p><strong>Default:</strong> none</p>
</div>
</div>
</div>
</div>
<footer>
<hr/>
<div role="contentinfo">
<p>
&copy; Copyright .
</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:'15 May 2015 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="_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