forked from lijiext/lammps
317 lines
16 KiB
HTML
317 lines
16 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>fix nvt/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>fix nvt/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="fix-nvt-asphere-command">
|
|
<span id="index-0"></span><h1>fix nvt/asphere command</h1>
|
|
</div>
|
|
<div class="section" id="fix-nvt-asphere-omp-command">
|
|
<h1>fix nvt/asphere/omp 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">nvt</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="fix.html"><span class="doc">fix</span></a> command</li>
|
|
<li>nvt/asphere = style name of this fix command</li>
|
|
<li>additional thermostat related keyword/value pairs from the <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a> command can be appended</li>
|
|
</ul>
|
|
</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">nvt</span><span class="o">/</span><span class="n">asphere</span> <span class="n">temp</span> <span class="mf">300.0</span> <span class="mf">300.0</span> <span class="mf">100.0</span>
|
|
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">nvt</span><span class="o">/</span><span class="n">asphere</span> <span class="n">temp</span> <span class="mf">300.0</span> <span class="mf">300.0</span> <span class="mf">100.0</span> <span class="n">drag</span> <span class="mf">0.2</span>
|
|
</pre></div>
|
|
</div>
|
|
</div>
|
|
<div class="section" id="description">
|
|
<h2>Description</h2>
|
|
<p>Perform constant NVT integration to update position, velocity,
|
|
orientation, and angular velocity each timestep for aspherical or
|
|
ellipsoidal particles in the group using a Nose/Hoover temperature
|
|
thermostat. V is volume; T is temperature. This creates a system
|
|
trajectory consistent with the canonical ensemble.</p>
|
|
<p>This fix differs from the <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a> command, which
|
|
assumes point particles and only updates their position and velocity.</p>
|
|
<p>The thermostat is applied to both the translational and rotational
|
|
degrees of freedom for the aspherical particles, assuming a compute is
|
|
used which calculates a temperature that includes the rotational
|
|
degrees of freedom (see below). The translational degrees of freedom
|
|
can also have a bias velocity removed from them before thermostatting
|
|
takes place; see the description below.</p>
|
|
<p>Additional parameters affecting the thermostat are specified by
|
|
keywords and values documented with the <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a>
|
|
command. See, for example, discussion of the <em>temp</em> and <em>drag</em>
|
|
keywords.</p>
|
|
<p>This fix computes a temperature each timestep. To do this, the fix
|
|
creates its own compute of style “temp/asphere”, as if this command
|
|
had been issued:</p>
|
|
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_temp</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>
|
|
</pre></div>
|
|
</div>
|
|
<p>See the <a class="reference internal" href="compute_temp_asphere.html"><span class="doc">compute temp/asphere</span></a> command for
|
|
details. Note that the ID of the new compute is the fix-ID +
|
|
underscore + “temp”, and the group for the new compute is the same as
|
|
the fix group.</p>
|
|
<p>Note that this is NOT the compute used by thermodynamic output (see
|
|
the <a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style</span></a> command) with ID = <em>thermo_temp</em>.
|
|
This means you can change the attributes of this fix’s temperature
|
|
(e.g. its degrees-of-freedom) via the
|
|
<a class="reference internal" href="compute_modify.html"><span class="doc">compute_modify</span></a> command or print this temperature
|
|
during thermodynamic output via the <a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style custom</span></a> command using the appropriate compute-ID.
|
|
It also means that changing attributes of <em>thermo_temp</em> will have no
|
|
effect on this fix.</p>
|
|
<p>Like other fixes that perform thermostatting, this fix can be used
|
|
with <a class="reference internal" href="compute.html"><span class="doc">compute commands</span></a> that calculate a temperature
|
|
after removing a “bias” from the atom velocities. E.g. removing the
|
|
center-of-mass velocity from a group of atoms or only calculating
|
|
temperature on the x-component of velocity or only calculating
|
|
temperature for atoms in a geometric region. This is not done by
|
|
default, but only if the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> command is used
|
|
to assign a temperature compute to this fix that includes such a bias
|
|
term. See the doc pages for individual <a class="reference internal" href="compute.html"><span class="doc">compute commands</span></a> to determine which ones include a bias. In
|
|
this case, the thermostat works in the following manner: the current
|
|
temperature is calculated taking the bias into account, bias is
|
|
removed from each atom, thermostatting is performed on the remaining
|
|
thermal degrees of freedom, and the bias is added back in.</p>
|
|
<hr class="docutils" />
|
|
<p>Styles with a <em>gpu</em>, <em>intel</em>, <em>kk</em>, <em>omp</em>, or <em>opt</em> suffix are
|
|
functionally the same as the corresponding style without the suffix.
|
|
They have been optimized to run faster, depending on your available
|
|
hardware, as discussed in <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a>
|
|
of the manual. The accelerated styles take the same arguments and
|
|
should produce the same results, except for round-off and precision
|
|
issues.</p>
|
|
<p>These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
|
USER-OMP and OPT packages, respectively. They are only enabled if
|
|
LAMMPS was built with those packages. 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>You can specify the accelerated styles explicitly in your input script
|
|
by including their suffix, or you can use the <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
|
|
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
|
|
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
|
|
more instructions on how to use the accelerated styles effectively.</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 state of the Nose/Hoover thermostat to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. 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>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>temp</em> option is supported by this
|
|
fix. You can use it to assign a <a class="reference internal" href="compute.html"><span class="doc">compute</span></a> you have
|
|
defined to this fix which will be used in its thermostatting
|
|
procedure.</p>
|
|
<p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>energy</em> option is supported by this
|
|
fix to add the energy change induced by Nose/Hoover thermostatting to
|
|
the system’s potential energy as part of <a class="reference internal" href="thermo_style.html"><span class="doc">thermodynamic output</span></a>.</p>
|
|
<p>This fix computes the same global scalar and global vector of
|
|
quantities as does the <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a> command.</p>
|
|
<p>This fix can ramp its target temperature over multiple runs, using the
|
|
<em>start</em> and <em>stop</em> keywords of the <a class="reference internal" href="run.html"><span class="doc">run</span></a> command. See the
|
|
<a class="reference internal" href="run.html"><span class="doc">run</span></a> command for details of how to do this.</p>
|
|
<p>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>
|
|
<p>This fix 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 fix requires that atoms store torque and 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="fix_nh.html"><span class="doc">fix nvt</span></a>, <a class="reference internal" href="fix_nve_asphere.html"><span class="doc">fix nve_asphere</span></a>, <a class="reference internal" href="fix_npt_asphere.html"><span class="doc">fix npt_asphere</span></a>, <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</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> |