forked from lijiext/lammps
259 lines
9.2 KiB
HTML
259 lines
9.2 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 vacf command — 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 & 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 vacf 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-vacf-command">
|
|
<span id="index-0"></span><h1>compute vacf command<a class="headerlink" href="#compute-vacf-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 vacf
|
|
</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>vacf = style name of this compute 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 all vacf
|
|
compute 1 upper vacf
|
|
</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 velocity auto-correlation
|
|
function (VACF), averaged over a group of atoms. Each atom’s
|
|
contribution to the VACF is its current velocity vector dotted into
|
|
its initial velocity vector at the time the compute was specified.</p>
|
|
<p>A vector of four quantites is calculated by this compute. The first 3
|
|
elements of the vector are vx * vx0 (and similarly for the y and z
|
|
components), summed and averaged over atoms in the group. Vx is the
|
|
current x-component of velocity for the atom, vx0 is the initial
|
|
x-component of velocity for the atom. The 4th element of the vector
|
|
is the total VACF, i.e. (vx*vx0 + vy*vy0 + vz*vz0), summed and
|
|
averaged over atoms in the group.</p>
|
|
<p>The integral of the VACF versus time is proportional to the diffusion
|
|
coefficient of the diffusing atoms. This can be computed in the
|
|
following manner, using the <a class="reference internal" href="variable.html"><em>variable trap()</em></a> function:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>compute 2 all vacf
|
|
fix 5 all vector 1 c_2[4]
|
|
variable diff equal dt*trap(f_5)
|
|
thermo_style custom step v_diff
|
|
</pre></div>
|
|
</div>
|
|
<div class="admonition warning">
|
|
<p class="first admonition-title">Warning</p>
|
|
<p class="last">If you want the quantities calculated by this compute
|
|
to be continuous when running from a <a class="reference internal" href="read_restart.html"><em>restart file</em></a>,
|
|
then you should use the same ID for this compute, as in the original
|
|
run. This is so that the fix this compute creates to store per-atom
|
|
quantities will also have the same ID, and thus be initialized
|
|
correctly with time=0 atom velocities from the restart file.</p>
|
|
</div>
|
|
<p><strong>Output info:</strong></p>
|
|
<p>This compute calculates a global vector of length 4, which can be
|
|
accessed by indices 1-4 by any command that uses global vector values
|
|
from a compute as input. See <a class="reference internal" href="Section_howto.html#howto-15"><span>this section</span></a> for an overview of LAMMPS output
|
|
options.</p>
|
|
<p>The vector values are “intensive”. The vector values will be in
|
|
velocity^2 <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_msd.html"><em>compute msd</em></a></p>
|
|
<p><strong>Default:</strong> none</p>
|
|
</div>
|
|
</div>
|
|
|
|
|
|
</div>
|
|
</div>
|
|
<footer>
|
|
|
|
|
|
<hr/>
|
|
|
|
<div role="contentinfo">
|
|
<p>
|
|
© 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="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> |