forked from lijiext/lammps
297 lines
12 KiB
HTML
297 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 centro/atom 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 centro/atom 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-centro-atom-command">
|
|
<span id="index-0"></span><h1>compute centro/atom 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">centro</span><span class="o">/</span><span class="n">atom</span> <span class="n">lattice</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>centro/atom = style name of this compute command</li>
|
|
<li>lattice = <em>fcc</em> or <em>bcc</em> or N = # of neighbors per atom to include</li>
|
|
</ul>
|
|
</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">centro</span><span class="o">/</span><span class="n">atom</span> <span class="n">fcc</span>
|
|
</pre></div>
|
|
</div>
|
|
<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">centro</span><span class="o">/</span><span class="n">atom</span> <span class="mi">8</span>
|
|
</pre></div>
|
|
</div>
|
|
</div>
|
|
<div class="section" id="description">
|
|
<h2>Description</h2>
|
|
<p>Define a computation that calculates the centro-symmetry parameter for
|
|
each atom in the group. In solid-state systems the centro-symmetry
|
|
parameter is a useful measure of the local lattice disorder around an
|
|
atom and can be used to characterize whether the atom is part of a
|
|
perfect lattice, a local defect (e.g. a dislocation or stacking
|
|
fault), or at a surface.</p>
|
|
<p>The value of the centro-symmetry parameter will be 0.0 for atoms not
|
|
in the specified compute group.</p>
|
|
<p>This parameter is computed using the following formula from
|
|
<a class="reference internal" href="#kelchner"><span class="std std-ref">(Kelchner)</span></a></p>
|
|
<img alt="_images/centro_symmetry.jpg" class="align-center" src="_images/centro_symmetry.jpg" />
|
|
<p>where the <em>N</em> nearest neighbors or each atom are identified and Ri and
|
|
Ri+N/2 are vectors from the central atom to a particular pair of
|
|
nearest neighbors. There are N*(N-1)/2 possible neighbor pairs that
|
|
can contribute to this formula. The quantity in the sum is computed
|
|
for each, and the N/2 smallest are used. This will typically be for
|
|
pairs of atoms in symmetrically opposite positions with respect to the
|
|
central atom; hence the i+N/2 notation.</p>
|
|
<p><em>N</em> is an input parameter, which should be set to correspond to the
|
|
number of nearest neighbors in the underlying lattice of atoms. If
|
|
the keyword <em>fcc</em> or <em>bcc</em> is used, <em>N</em> is set to 12 and 8
|
|
respectively. More generally, <em>N</em> can be set to a positive, even
|
|
integer.</p>
|
|
<p>For an atom on a lattice site, surrounded by atoms on a perfect
|
|
lattice, the centro-symmetry parameter will be 0. It will be near 0
|
|
for small thermal perturbations of a perfect lattice. If a point
|
|
defect exists, the symmetry is broken, and the parameter will be a
|
|
larger positive value. An atom at a surface will have a large
|
|
positive parameter. If the atom does not have <em>N</em> neighbors (within
|
|
the potential cutoff), then its centro-symmetry parameter is set to
|
|
0.0.</p>
|
|
<p>Only atoms within the cutoff of the pairwise neighbor list are
|
|
considered as possible neighbors. Atoms not in the compute group are
|
|
included in the <em>N</em> neighbors used in this calculation.</p>
|
|
<p>The neighbor list needed to compute this quantity is constructed each
|
|
time the calculation is performed (e.g. each time a snapshot of atoms
|
|
is dumped). Thus it can be inefficient to compute/dump this quantity
|
|
too frequently or to have multiple compute/dump commands, each with a
|
|
<em>centro/atom</em> style.</p>
|
|
<p><strong>Output info:</strong></p>
|
|
<p>This compute calculates a per-atom vector, which can be accessed by
|
|
any command that uses per-atom values from a compute as input. See
|
|
<a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">Section_howto 15</span></a> for an overview of
|
|
LAMMPS output options.</p>
|
|
<p>The per-atom vector values are unitless values >= 0.0. Their
|
|
magnitude depends on the lattice style due to the number of
|
|
contibuting neighbor pairs in the summation in the formula above. And
|
|
it depends on the local defects surrounding the central atom, as
|
|
described above.</p>
|
|
<p>Here are typical centro-symmetry values, from a a nanoindentation
|
|
simulation into gold (FCC). These were provided by Jon Zimmerman
|
|
(Sandia):</p>
|
|
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Bulk</span> <span class="n">lattice</span> <span class="o">=</span> <span class="mi">0</span>
|
|
<span class="n">Dislocation</span> <span class="n">core</span> <span class="o">~</span> <span class="mf">1.0</span> <span class="p">(</span><span class="mf">0.5</span> <span class="n">to</span> <span class="mf">1.25</span><span class="p">)</span>
|
|
<span class="n">Stacking</span> <span class="n">faults</span> <span class="o">~</span> <span class="mf">5.0</span> <span class="p">(</span><span class="mf">4.0</span> <span class="n">to</span> <span class="mf">6.0</span><span class="p">)</span>
|
|
<span class="n">Free</span> <span class="n">surface</span> <span class="o">~</span> <span class="mf">23.0</span>
|
|
</pre></div>
|
|
</div>
|
|
<p>These values are <em>not</em> normalized by the square of the lattice
|
|
parameter. If they were, normalized values would be:</p>
|
|
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Bulk</span> <span class="n">lattice</span> <span class="o">=</span> <span class="mi">0</span>
|
|
<span class="n">Dislocation</span> <span class="n">core</span> <span class="o">~</span> <span class="mf">0.06</span> <span class="p">(</span><span class="mf">0.03</span> <span class="n">to</span> <span class="mf">0.075</span><span class="p">)</span>
|
|
<span class="n">Stacking</span> <span class="n">faults</span> <span class="o">~</span> <span class="mf">0.3</span> <span class="p">(</span><span class="mf">0.24</span> <span class="n">to</span> <span class="mf">0.36</span><span class="p">)</span>
|
|
<span class="n">Free</span> <span class="n">surface</span> <span class="o">~</span> <span class="mf">1.38</span>
|
|
</pre></div>
|
|
</div>
|
|
<p>For BCC materials, the values for dislocation cores and free surfaces
|
|
would be somewhat different, due to their being only 8 neighbors instead
|
|
of 12.</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="compute_cna_atom.html"><span class="doc">compute cna/atom</span></a></p>
|
|
<p><strong>Default:</strong> none</p>
|
|
<hr class="docutils" />
|
|
<p id="kelchner"><strong>(Kelchner)</strong> Kelchner, Plimpton, Hamilton, Phys Rev B, 58, 11085 (1998).</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> |