Homec4science
Diffusion lammps (lammm-devel) Browse

lammps/doc/html/group2ndx.html
58be921a0932lammm-devel

Last Change
Raw File

group2ndx.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>group2ndx 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>group2ndx 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="group2ndx-command">
<span id="index-0"></span><h1>group2ndx command</h1>
</div>
<div class="section" id="ndx2group-command">
<h1>ndx2group command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">group2ndx</span> <span class="n">file</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="o">...</span>
<span class="n">ndx2group</span> <span class="n">file</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="o">...</span>
</pre></div>
</div>
<ul class="simple">
<li>file = name of index file to write out or read in</li>
<li>zero or more group IDs may be appended</li>
</ul>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">group2ndx</span> <span class="n">allindex</span><span class="o">.</span><span class="n">ndx</span>
<span class="n">group2ndx</span> <span class="n">someindex</span><span class="o">.</span><span class="n">ndx</span> <span class="n">upper</span> <span class="n">lower</span> <span class="n">mobile</span>
<span class="n">ndx2group</span> <span class="n">someindex</span><span class="o">.</span><span class="n">ndx</span>
<span class="n">ndx2group</span> <span class="n">someindex</span><span class="o">.</span><span class="n">ndx</span> <span class="n">mobile</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
<p>Write or read a Gromacs style index file in text format that associates
atom IDs with the corresponding group definitions. This index file can be
used with in combination with Gromacs analysis tools or to import group
definitions into the <a class="reference internal" href="fix_colvars.html"><span class="doc">fix colvars</span></a> input file. It can
also be used to save and restore group definitions for static groups.</p>
<p>The <em>group2ndx</em> command will write group definitions to an index file.
Without specifying any group IDs, all groups will be written to the index
file. When specifying group IDs, only those groups will be written to the
index file. In order to follow the Gromacs conventions, the group <em>all</em>
will be renamed to <em>System</em> in the index file.</p>
<p>The <em>ndx2group</em> command will create of update group definitions from those
stored in an index file. Without specifying any group IDs, all groups except
<em>System</em> will be read from the index file and the corresponding groups
recreated. If a group of the same name already exists, it will be completely
reset. When specifying group IDs, those groups, if present, will be read
from the index file and restored.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>This command requires that atoms have atom IDs, since this is the
information that is written to the index file.</p>
<p>These commands are part of the USER-COLVARS 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.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><a class="reference internal" href="group.html"><span class="doc">group</span></a>, <a class="reference internal" href="dump.html"><span class="doc">dump</span></a>, <a class="reference internal" href="fix_colvars.html"><span class="doc">fix colvars</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