Homec4science
Diffusion lammps (lammm-master-deprecated) Browse

lammps/doc/fix_append_atoms.html
5affb6c013bdlammm-master-deprecated

Last Change
Raw File

fix_append_atoms.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 append/atoms command &mdash; LAMMPS 9 Dec 2015 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 9 Dec 2015 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>fix append/atoms 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-append-atoms-command">
<span id="index-0"></span><h1>fix append/atoms command<a class="headerlink" href="#fix-append-atoms-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>fix ID group-ID append/atoms face ... keyword value ...
</pre></div>
</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><em>fix</em></a> command</li>
<li>append/atoms = style name of this fix command</li>
<li>face = <em>zhi</em></li>
<li>zero or more keyword/value pairs may be appended</li>
<li>keyword = <em>basis</em> or <em>size</em> or <em>freq</em> or <em>temp</em> or <em>random</em> or <em>units</em></li>
</ul>
<pre class="literal-block">
<em>basis</em> values = M itype
M = which basis atom
itype = atom type (1-N) to assign to this basis atom
<em>size</em> args = Lz
Lz = z size of lattice region appended in a single event(distance units)
<em>freq</em> args = freq
freq = the number of timesteps between append events
<em>temp</em> args = target damp seed extent
target = target temperature for the region between zhi-extent and zhi (temperature units)
damp = damping parameter (time units)
seed = random number seed for langevin kicks
extent = extent of thermostated region (distance units)
<em>random</em> args = xmax ymax zmax seed
<em>xmax</em>, <em>ymax</em>, <em>zmax</em> = maximum displacement in particular direction (distance units)
<em>seed</em> = random number seed for random displacement
<em>units</em> value = <em>lattice</em> or <em>box</em>
<em>lattice</em> = the wall position is defined in lattice units
<em>box</em> = the wall position is defined in simulation box units
</pre>
</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>fix 1 all append/atoms zhi size 5.0 freq 295 units lattice
fix 4 all append/atoms zhi size 15.0 freq 5 units box
fix A all append/atoms zhi size 1.0 freq 1000 units lattice
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
<p>This fix creates atoms on a lattice, appended on the zhi edge of the
system box. This can be useful when a shock or wave is propagating
from zlo. This allows the system to grow with time to accommodate an
expanding wave. A simulation box must already exist, which is
typically created via the <a class="reference internal" href="create_box.html"><em>create_box</em></a> command.
Before using this command, a lattice must also be defined using the
<a class="reference internal" href="lattice.html"><em>lattice</em></a> command.</p>
<p>This fix will automatically freeze atoms on the zhi edge of the
system, so that overlaps are avoided when new atoms are appended.</p>
<p>The <em>basis</em> keyword specifies an atom type that will be assigned to
specific basis atoms as they are created. See the
<a class="reference internal" href="lattice.html"><em>lattice</em></a> command for specifics on how basis atoms are
defined for the unit cell of the lattice. By default, all created
atoms are assigned type = 1 unless this keyword specifies differently.</p>
<p>The <em>size</em> keyword defines the size in z of the chunk of material to
be added.</p>
<p>The <em>random</em> keyword will give the atoms random displacements around
their lattice points to simulate some initial temperature.</p>
<p>The <em>temp</em> keyword will cause a region to be thermostated with a
Langevin thermostat on the zhi boundary. The size of the region is
measured from zhi and is set with the <em>extent</em> argument.</p>
<p>The <em>units</em> keyword determines the meaning of the distance units used
to define a wall position, but only when a numeric constant is used.
A <em>box</em> value selects standard distance units as defined by the
<a class="reference internal" href="units.html"><em>units</em></a> command, e.g. Angstroms for units = real or metal.
A <em>lattice</em> value means the distance units are in lattice spacings.
The <a class="reference internal" href="lattice.html"><em>lattice</em></a> command must have been previously used to
define the lattice spacings.</p>
</div>
<hr class="docutils" />
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
<h2>Restart, fix_modify, output, run start/stop, minimize info<a class="headerlink" href="#restart-fix-modify-output-run-start-stop-minimize-info" title="Permalink to this headline">¶</a></h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>. None of the <a class="reference internal" href="fix_modify.html"><em>fix_modify</em></a> options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span>output commands</span></a>. No parameter of this fix can
be used with the <em>start/stop</em> keywords of the <a class="reference internal" href="run.html"><em>run</em></a> command.
This fix is not invoked during <a class="reference internal" href="minimize.html"><em>energy minimization</em></a>.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
<p>This fix style is part of the SHOCK package. It is only enabled if
LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
<p>The boundary on which atoms are added with append/atoms must be
shrink/minimum. The opposite boundary may be any boundary type other
than periodic.</p>
</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="fix_wall_piston.html"><em>fix wall/piston</em></a> command</p>
</div>
<div class="section" id="default">
<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline">¶</a></h2>
<p>The keyword defaults are size = 0.0, freq = 0, units = lattice. All
added atoms are of type 1 unless the basis keyword is used.</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:'9 Dec 2015',
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