Homec4science
Diffusion lammps (master) Browse

lammps/doc/html/fix_store_state.html
57fb84393a7amaster

Last Change
Raw File

fix_store_state.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>fix store/state 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">
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">fix store/state command</a><ul>
<li><a class="reference internal" href="#syntax">Syntax</a></li>
<li><a class="reference internal" href="#examples">Examples</a></li>
<li><a class="reference internal" href="#description">Description</a></li>
<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
<li><a class="reference internal" href="#default">Default</a></li>
</ul>
</li>
</ul>
</div>
</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>fix store/state 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="fix-store-state-command">
<span id="index-0"></span><h1>fix store/state command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">store</span><span class="o">/</span><span class="n">state</span> <span class="n">N</span> <span class="n">input1</span> <span class="n">input2</span> <span class="o">...</span> <span class="n">keyword</span> <span class="n">value</span> <span class="o">...</span>
</pre></div>
</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command</li>
<li>store/state = style name of this fix command</li>
<li>N = store atom attributes every N steps, N = 0 for initial store only</li>
<li>input = one or more atom attributes</li>
</ul>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">possible</span> <span class="n">attributes</span> <span class="o">=</span> <span class="nb">id</span><span class="p">,</span> <span class="n">mol</span><span class="p">,</span> <span class="nb">type</span><span class="p">,</span> <span class="n">mass</span><span class="p">,</span>
<span class="n">x</span><span class="p">,</span> <span class="n">y</span><span class="p">,</span> <span class="n">z</span><span class="p">,</span> <span class="n">xs</span><span class="p">,</span> <span class="n">ys</span><span class="p">,</span> <span class="n">zs</span><span class="p">,</span> <span class="n">xu</span><span class="p">,</span> <span class="n">yu</span><span class="p">,</span> <span class="n">zu</span><span class="p">,</span> <span class="n">xsu</span><span class="p">,</span> <span class="n">ysu</span><span class="p">,</span> <span class="n">zsu</span><span class="p">,</span> <span class="n">ix</span><span class="p">,</span> <span class="n">iy</span><span class="p">,</span> <span class="n">iz</span><span class="p">,</span>
<span class="n">vx</span><span class="p">,</span> <span class="n">vy</span><span class="p">,</span> <span class="n">vz</span><span class="p">,</span> <span class="n">fx</span><span class="p">,</span> <span class="n">fy</span><span class="p">,</span> <span class="n">fz</span><span class="p">,</span>
<span class="n">q</span><span class="p">,</span> <span class="n">mux</span><span class="p">,</span> <span class="n">muy</span><span class="p">,</span> <span class="n">muz</span><span class="p">,</span> <span class="n">mu</span><span class="p">,</span>
<span class="n">radius</span><span class="p">,</span> <span class="n">diameter</span><span class="p">,</span> <span class="n">omegax</span><span class="p">,</span> <span class="n">omegay</span><span class="p">,</span> <span class="n">omegaz</span><span class="p">,</span>
<span class="n">angmomx</span><span class="p">,</span> <span class="n">angmomy</span><span class="p">,</span> <span class="n">angmomz</span><span class="p">,</span> <span class="n">tqx</span><span class="p">,</span> <span class="n">tqy</span><span class="p">,</span> <span class="n">tqz</span><span class="p">,</span>
<span class="n">c_ID</span><span class="p">,</span> <span class="n">c_ID</span><span class="p">[</span><span class="n">N</span><span class="p">],</span> <span class="n">f_ID</span><span class="p">,</span> <span class="n">f_ID</span><span class="p">[</span><span class="n">N</span><span class="p">],</span> <span class="n">v_name</span><span class="p">,</span>
<span class="n">d_name</span><span class="p">,</span> <span class="n">i_name</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="nb">id</span> <span class="o">=</span> <span class="n">atom</span> <span class="n">ID</span>
<span class="n">mol</span> <span class="o">=</span> <span class="n">molecule</span> <span class="n">ID</span>
<span class="nb">type</span> <span class="o">=</span> <span class="n">atom</span> <span class="nb">type</span>
<span class="n">mass</span> <span class="o">=</span> <span class="n">atom</span> <span class="n">mass</span>
<span class="n">x</span><span class="p">,</span><span class="n">y</span><span class="p">,</span><span class="n">z</span> <span class="o">=</span> <span class="n">unscaled</span> <span class="n">atom</span> <span class="n">coordinates</span>
<span class="n">xs</span><span class="p">,</span><span class="n">ys</span><span class="p">,</span><span class="n">zs</span> <span class="o">=</span> <span class="n">scaled</span> <span class="n">atom</span> <span class="n">coordinates</span>
<span class="n">xu</span><span class="p">,</span><span class="n">yu</span><span class="p">,</span><span class="n">zu</span> <span class="o">=</span> <span class="n">unwrapped</span> <span class="n">atom</span> <span class="n">coordinates</span>
<span class="n">xsu</span><span class="p">,</span><span class="n">ysu</span><span class="p">,</span><span class="n">zsu</span> <span class="o">=</span> <span class="n">scaled</span> <span class="n">unwrapped</span> <span class="n">atom</span> <span class="n">coordinates</span>
<span class="n">ix</span><span class="p">,</span><span class="n">iy</span><span class="p">,</span><span class="n">iz</span> <span class="o">=</span> <span class="n">box</span> <span class="n">image</span> <span class="n">that</span> <span class="n">the</span> <span class="n">atom</span> <span class="ow">is</span> <span class="ow">in</span>
<span class="n">vx</span><span class="p">,</span><span class="n">vy</span><span class="p">,</span><span class="n">vz</span> <span class="o">=</span> <span class="n">atom</span> <span class="n">velocities</span>
<span class="n">fx</span><span class="p">,</span><span class="n">fy</span><span class="p">,</span><span class="n">fz</span> <span class="o">=</span> <span class="n">forces</span> <span class="n">on</span> <span class="n">atoms</span>
<span class="n">q</span> <span class="o">=</span> <span class="n">atom</span> <span class="n">charge</span>
<span class="n">mux</span><span class="p">,</span><span class="n">muy</span><span class="p">,</span><span class="n">muz</span> <span class="o">=</span> <span class="n">orientation</span> <span class="n">of</span> <span class="n">dipolar</span> <span class="n">atom</span>
<span class="n">mu</span> <span class="o">=</span> <span class="n">magnitued</span> <span class="n">of</span> <span class="n">dipole</span> <span class="n">moment</span> <span class="n">of</span> <span class="n">atom</span>
<span class="n">radius</span><span class="p">,</span><span class="n">diameter</span> <span class="o">=</span> <span class="n">radius</span><span class="o">.</span><span class="n">diameter</span> <span class="n">of</span> <span class="n">spherical</span> <span class="n">particle</span>
<span class="n">omegax</span><span class="p">,</span><span class="n">omegay</span><span class="p">,</span><span class="n">omegaz</span> <span class="o">=</span> <span class="n">angular</span> <span class="n">velocity</span> <span class="n">of</span> <span class="n">spherical</span> <span class="n">particle</span>
<span class="n">angmomx</span><span class="p">,</span><span class="n">angmomy</span><span class="p">,</span><span class="n">angmomz</span> <span class="o">=</span> <span class="n">angular</span> <span class="n">momentum</span> <span class="n">of</span> <span class="n">aspherical</span> <span class="n">particle</span>
<span class="n">tqx</span><span class="p">,</span><span class="n">tqy</span><span class="p">,</span><span class="n">tqz</span> <span class="o">=</span> <span class="n">torque</span> <span class="n">on</span> <span class="n">finite</span><span class="o">-</span><span class="n">size</span> <span class="n">particles</span>
<span class="n">c_ID</span> <span class="o">=</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">compute</span> <span class="k">with</span> <span class="n">ID</span>
<span class="n">c_ID</span><span class="p">[</span><span class="n">I</span><span class="p">]</span> <span class="o">=</span> <span class="n">Ith</span> <span class="n">column</span> <span class="n">of</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="n">array</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">compute</span> <span class="k">with</span> <span class="n">ID</span>
<span class="n">f_ID</span> <span class="o">=</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">fix</span> <span class="k">with</span> <span class="n">ID</span>
<span class="n">f_ID</span><span class="p">[</span><span class="n">I</span><span class="p">]</span> <span class="o">=</span> <span class="n">Ith</span> <span class="n">column</span> <span class="n">of</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="n">array</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">fix</span> <span class="k">with</span> <span class="n">ID</span>
<span class="n">v_name</span> <span class="o">=</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">an</span> <span class="n">atom</span><span class="o">-</span><span class="n">style</span> <span class="n">variable</span> <span class="k">with</span> <span class="n">name</span>
<span class="n">d_name</span> <span class="o">=</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="n">floating</span> <span class="n">point</span> <span class="n">vector</span> <span class="n">name</span><span class="p">,</span> <span class="n">managed</span> <span class="n">by</span> <span class="n">fix</span> <span class="nb">property</span><span class="o">/</span><span class="n">atom</span>
<span class="n">i_name</span> <span class="o">=</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="n">integer</span> <span class="n">vector</span> <span class="n">name</span><span class="p">,</span> <span class="n">managed</span> <span class="n">by</span> <span class="n">fix</span> <span class="nb">property</span><span class="o">/</span><span class="n">atom</span>
</pre></div>
</div>
<ul class="simple">
<li>zero or more keyword/value pairs may be appended</li>
<li>keyword = <em>com</em></li>
</ul>
<pre class="literal-block">
<em>com</em> value = <em>yes</em> or <em>no</em>
</pre>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">store</span><span class="o">/</span><span class="n">state</span> <span class="mi">0</span> <span class="n">x</span> <span class="n">y</span> <span class="n">z</span>
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">store</span><span class="o">/</span><span class="n">state</span> <span class="mi">0</span> <span class="n">xu</span> <span class="n">yu</span> <span class="n">zu</span> <span class="n">com</span> <span class="n">yes</span>
<span class="n">fix</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">store</span><span class="o">/</span><span class="n">state</span> <span class="mi">1000</span> <span class="n">vx</span> <span class="n">vy</span> <span class="n">vz</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
<p>Define a fix that stores attributes for each atom in the group at the
time the fix is defined. If <em>N</em> is 0, then the values are never
updated, so this is a way of archiving an atom attribute at a given
time for future use in a calculation or output. See the discussion of
<a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a> that take fixes as
inputs.</p>
<p>If <em>N</em> is not zero, then the attributes will be updated every <em>N</em>
steps.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">Actually, only atom attributes specified by keywords like <em>xu</em>
or <em>vy</em> or <em>radius</em> are initially stored immediately at the point in
your input script when the fix is defined. Attributes specified by a
compute, fix, or variable are not initially stored until the first run
following the fix definition begins. This is because calculating
those attributes may require quantities that are not defined in
between runs.</p>
</div>
<p>The list of possible attributes is the same as that used by the <a class="reference internal" href="dump.html"><span class="doc">dump custom</span></a> command, which describes their meaning.</p>
<p>If the <em>com</em> keyword is set to <em>yes</em> then the <em>xu</em>, <em>yu</em>, and <em>zu</em>
inputs store the position of each atom relative to the center-of-mass
of the group of atoms, instead of storing the absolute position.</p>
<p>The requested values are stored in a per-atom vector or array as
discussed below. Zeroes are stored for atoms not in the specified
group.</p>
</div>
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>This fix writes the per-atom values it stores to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>, so that the values can be restored when a
simulation is restarted. See the <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a>
command for info on how to re-specify a fix in an input script that
reads a restart file, so that the operation of the fix continues in an
uninterrupted fashion.</p>
<p>None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options are relevant to this
fix.</p>
<p>If a single input is specified, this fix produces a per-atom vector.
If multiple inputs are specified, a per-atom array is produced where
the number of columns for each atom is the number of inputs. These
can be accessed by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>. The per-atom values be
accessed on any timestep.</p>
<p>No parameter of this fix can be used with the <em>start/stop</em> keywords of
the <a class="reference internal" href="run.html"><span class="doc">run</span></a> command. This fix is not invoked during <a class="reference internal" href="minimize.html"><span class="doc">energy minimization</span></a>.</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 custom</span></a>, <a class="reference internal" href="compute_property_atom.html"><span class="doc">compute property/atom</span></a>,
<a class="reference internal" href="fix_property_atom.html"><span class="doc">fix property/atom</span></a>, <a class="reference internal" href="variable.html"><span class="doc">variable</span></a></p>
</div>
<div class="section" id="default">
<h2>Default</h2>
<p>The option default is com = no.</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