forked from lijiext/lammps
324 lines
14 KiB
HTML
324 lines
14 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 temp/asphere 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 temp/asphere 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-temp-asphere-command">
|
|
<span id="index-0"></span><h1>compute temp/asphere 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">temp</span><span class="o">/</span><span class="n">asphere</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="compute.html"><span class="doc">compute</span></a> command</li>
|
|
<li>temp/asphere = style name of this compute command</li>
|
|
<li>zero or more keyword/value pairs may be appended</li>
|
|
<li>keyword = <em>bias</em> or <em>dof</em></li>
|
|
</ul>
|
|
<pre class="literal-block">
|
|
<em>bias</em> value = bias-ID
|
|
bias-ID = ID of a temperature compute that removes a velocity bias
|
|
<em>dof</em> value = <em>all</em> or <em>rotate</em>
|
|
all = compute temperature of translational and rotational degrees of freedom
|
|
rotate = compute temperature of just rotational degrees of freedom
|
|
</pre>
|
|
</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">temp</span><span class="o">/</span><span class="n">asphere</span>
|
|
<span class="n">compute</span> <span class="n">myTemp</span> <span class="n">mobile</span> <span class="n">temp</span><span class="o">/</span><span class="n">asphere</span> <span class="n">bias</span> <span class="n">tempCOM</span>
|
|
<span class="n">compute</span> <span class="n">myTemp</span> <span class="n">mobile</span> <span class="n">temp</span><span class="o">/</span><span class="n">asphere</span> <span class="n">dof</span> <span class="n">rotate</span>
|
|
</pre></div>
|
|
</div>
|
|
</div>
|
|
<div class="section" id="description">
|
|
<h2>Description</h2>
|
|
<p>Define a computation that calculates the temperature of a group of
|
|
aspherical particles, including a contribution from both their
|
|
translational and rotational kinetic energy. This differs from the
|
|
usual <a class="reference internal" href="compute_temp.html"><span class="doc">compute temp</span></a> command, which assumes point
|
|
particles with only translational kinetic energy.</p>
|
|
<p>Only finite-size particles (aspherical or spherical) can be included
|
|
in the group. For 3d finite-size particles, each has 6 degrees of
|
|
freedom (3 translational, 3 rotational). For 2d finite-size
|
|
particles, each has 3 degrees of freedom (2 translational, 1
|
|
rotational).</p>
|
|
<div class="admonition note">
|
|
<p class="first admonition-title">Note</p>
|
|
<p class="last">This choice for degrees of freedom (dof) assumes that all
|
|
finite-size aspherical or spherical particles in your model will
|
|
freely rotate, sampling all their rotational dof. It is possible to
|
|
use a combination of interaction potentials and fixes that induce no
|
|
torque or otherwise constrain some of all of your particles so that
|
|
this is not the case. Then there are less dof and you should use the
|
|
<a class="reference internal" href="compute_modify.html"><span class="doc">compute_modify extra</span></a> command to adjust the dof
|
|
accordingly.</p>
|
|
</div>
|
|
<p>For example, an aspherical particle with all three of its shape
|
|
parameters the same is a sphere. If it does not rotate, then it
|
|
should have 3 dof instead of 6 in 3d (or 2 instead of 3 in 2d). A
|
|
uniaxial aspherical particle has two of its three shape parameters the
|
|
same. If it does not rotate around the axis perpendicular to its
|
|
circular cross section, then it should have 5 dof instead of 6 in 3d.
|
|
The latter is the case for uniaxial ellipsoids in a <a class="reference internal" href="pair_gayberne.html"><span class="doc">GayBerne model</span></a> since there is no induced torque around the
|
|
optical axis. It will also be the case for biaxial ellipsoids when
|
|
exactly two of the semiaxes have the same length and the corresponding
|
|
relative well depths are equal.</p>
|
|
<p>The translational kinetic energy is computed the same as is described
|
|
by the <a class="reference internal" href="compute_temp.html"><span class="doc">compute temp</span></a> command. The rotational
|
|
kinetic energy is computed as 1/2 I w^2, where I is the inertia tensor
|
|
for the aspherical particle and w is its angular velocity, which is
|
|
computed from its angular momentum.</p>
|
|
<div class="admonition note">
|
|
<p class="first admonition-title">Note</p>
|
|
<p class="last">For <a class="reference internal" href="dimension.html"><span class="doc">2d models</span></a>, particles are treated as
|
|
ellipsoids, not ellipses, meaning their moments of inertia will be the
|
|
same as in 3d.</p>
|
|
</div>
|
|
<p>A kinetic energy tensor, stored as a 6-element vector, is also
|
|
calculated by this compute. The formula for the components of the
|
|
tensor is the same as the above formula, except that v^2 and w^2 are
|
|
replaced by vx*vy and wx*wy for the xy component, and the appropriate
|
|
elements of the inertia tensor are used. The 6 components of the
|
|
vector are ordered xx, yy, zz, xy, xz, yz.</p>
|
|
<p>The number of atoms contributing to the temperature is assumed to be
|
|
constant for the duration of the run; use the <em>dynamic</em> option of the
|
|
<a class="reference internal" href="compute_modify.html"><span class="doc">compute_modify</span></a> command if this is not the case.</p>
|
|
<p>This compute subtracts out translational degrees-of-freedom due to
|
|
fixes that constrain molecular motion, such as <a class="reference internal" href="fix_shake.html"><span class="doc">fix shake</span></a> and <a class="reference internal" href="fix_rigid.html"><span class="doc">fix rigid</span></a>. This means the
|
|
temperature of groups of atoms that include these constraints will be
|
|
computed correctly. If needed, the subtracted degrees-of-freedom can
|
|
be altered using the <em>extra</em> option of the
|
|
<a class="reference internal" href="compute_modify.html"><span class="doc">compute_modify</span></a> command.</p>
|
|
<p>See <a class="reference internal" href="Section_howto.html#howto-16"><span class="std std-ref">this howto section</span></a> of the manual for
|
|
a discussion of different ways to compute temperature and perform
|
|
thermostatting.</p>
|
|
<hr class="docutils" />
|
|
<p>The keyword/value option pairs are used in the following ways.</p>
|
|
<p>For the <em>bias</em> keyword, <em>bias-ID</em> refers to the ID of a temperature
|
|
compute that removes a “bias” velocity from each atom. This allows
|
|
compute temp/sphere to compute its thermal temperature after the
|
|
translational kinetic energy components have been altered in a
|
|
prescribed way, e.g. to remove a flow velocity profile. Thermostats
|
|
that use this compute will work with this bias term. See the doc
|
|
pages for individual computes that calculate a temperature and the doc
|
|
pages for fixes that perform thermostatting for more details.</p>
|
|
<p>For the <em>dof</em> keyword, a setting of <em>all</em> calculates a temperature
|
|
that includes both translational and rotational degrees of freedom. A
|
|
setting of <em>rotate</em> calculates a temperature that includes only
|
|
rotational degrees of freedom.</p>
|
|
<hr class="docutils" />
|
|
<p><strong>Output info:</strong></p>
|
|
<p>This compute calculates a global scalar (the temperature) and a global
|
|
vector of length 6 (KE tensor), which can be accessed by indices 1-6.
|
|
These values can be used by any command that uses global scalar or
|
|
vector values from a compute as input. See <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">this section</span></a> for an overview of LAMMPS output
|
|
options.</p>
|
|
<p>The scalar value calculated by this compute is “intensive”. The
|
|
vector values are “extensive”.</p>
|
|
<p>The scalar value will be in temperature <a class="reference internal" href="units.html"><span class="doc">units</span></a>. The
|
|
vector values will be in energy <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
|
|
</div>
|
|
<div class="section" id="restrictions">
|
|
<h2>Restrictions</h2>
|
|
<p>This compute is part of the ASPHERE 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 class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
|
|
<p>This compute requires that atoms store angular momementum and a
|
|
quaternion as defined by the <a class="reference internal" href="atom_style.html"><span class="doc">atom_style ellipsoid</span></a>
|
|
command.</p>
|
|
<p>All particles in the group must be finite-size. They cannot be point
|
|
particles, but they can be aspherical or spherical as defined by their
|
|
shape attribute.</p>
|
|
</div>
|
|
<div class="section" id="related-commands">
|
|
<h2>Related commands</h2>
|
|
<p><a class="reference internal" href="compute_temp.html"><span class="doc">compute temp</span></a></p>
|
|
<p><strong>Default:</strong> none</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> |