Homec4science
Diffusion lammps (lammm-devel) Browse

lammps/doc/fix_langevin_eff.html
c6213f36d34clammm-devel

Last Change
Raw File

fix_langevin_eff.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 langevin/eff command &mdash; LAMMPS 15 May 2015 version 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 15 May 2015 version 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 langevin/eff command</li>
<li class="wy-breadcrumbs-aside">
<a href="http://lammps.sandia.gov">Homepage</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-langevin-eff-command">
<span id="index-0"></span><h1>fix langevin/eff command<a class="headerlink" href="#fix-langevin-eff-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 langevin/eff Tstart Tstop damp seed keyword values ...
</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>langevin/eff = style name of this fix command</li>
<li>Tstart,Tstop = desired temperature at start/end of run (temperature units)</li>
<li>damp = damping parameter (time units)</li>
<li>seed = random number seed to use for white noise (positive integer)</li>
<li>zero or more keyword/value pairs may be appended</li>
</ul>
<pre class="literal-block">
keyword = <em>scale</em> or <em>tally</em> or <em>zero</em>
<em>scale</em> values = type ratio
type = atom type (1-N)
ratio = factor by which to scale the damping coefficient
<em>tally</em> values = <em>no</em> or <em>yes</em>
<em>no</em> = do not tally the energy added/subtracted to atoms
<em>yes</em> = do tally the energy added/subtracted to atoms
</pre>
<pre class="literal-block">
<em>zero</em> value = <em>no</em> or <em>yes</em>
<em>no</em> = do not set total random force to zero
<em>yes</em> = set total random force to zero
</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 3 boundary langevin/eff 1.0 1.0 10.0 699483
fix 1 all langevin/eff 1.0 1.1 10.0 48279 scale 3 1.5
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Apply a Langevin thermostat as described in <a class="reference internal" href="#schneider"><span>(Schneider)</span></a>
to a group of nuclei and electrons in the <a class="reference internal" href="pair_eff.html"><em>electron force field</em></a> model. Used with <a class="reference internal" href="fix_nve_eff.html"><em>fix nve/eff</em></a>,
this command performs Brownian dynamics (BD), since the total force on
each atom will have the form:</p>
<div class="highlight-python"><div class="highlight"><pre>F = Fc + Ff + Fr
Ff = - (m / damp) v
Fr is proportional to sqrt(Kb T m / (dt damp))
</pre></div>
</div>
<p>Fc is the conservative force computed via the usual inter-particle
interactions (<a class="reference internal" href="pair_style.html"><em>pair_style</em></a>).</p>
<p>The Ff and Fr terms are added by this fix on a per-particle basis.</p>
<p>The operation of this fix is exactly like that described by the <a class="reference internal" href="fix_langevin.html"><em>fix langevin</em></a> command, except that the thermostatting
is also applied to the radial electron velocity for electron
particles.</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<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>. Because the state of the random number generator
is not saved in restart files, this means you cannot do &#8220;exact&#8221;
restarts with this fix, where the simulation continues on the same as
if no restart had taken place. However, in a statistical sense, a
restarted simulation should produce the same behavior.</p>
<p>The <a class="reference internal" href="fix_modify.html"><em>fix_modify</em></a> <em>temp</em> option is supported by this
fix. You can use it to assign a temperature <a class="reference internal" href="compute.html"><em>compute</em></a>
you have defined to this fix which will be used in its thermostatting
procedure, as described above. For consistency, the group used by
this fix and by the compute should be the same.</p>
<p>The <a class="reference internal" href="fix_modify.html"><em>fix_modify</em></a> <em>energy</em> option is supported by this
fix to add the energy change induced by Langevin thermostatting to the
system&#8217;s potential energy as part of <a class="reference internal" href="thermo_style.html"><em>thermodynamic output</em></a>. Note that use of this option requires
setting the <em>tally</em> keyword to <em>yes</em>.</p>
<p>This fix computes a global scalar which can be accessed by various
<a class="reference internal" href="Section_howto.html#howto-15"><span>output commands</span></a>. The scalar is the
cummulative energy change due to this fix. The scalar value
calculated by this fix is &#8220;extensive&#8221;. Note that calculation of this
quantity requires setting the <em>tally</em> keyword to <em>yes</em>.</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"><em>run</em></a> command. See the
<a class="reference internal" href="run.html"><em>run</em></a> command for details of how to do this.</p>
<p>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>
<blockquote>
<div>none</div></blockquote>
<p>This fix is part of the USER-EFF 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>
</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_langevin.html"><em>fix langevin</em></a></p>
</div>
<div class="section" id="default">
<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline"></a></h2>
<p>The option defaults are scale = 1.0 for all types and tally = no.</p>
<hr class="docutils" />
<p id="dunweg"><strong>(Dunweg)</strong> Dunweg and Paul, Int J of Modern Physics C, 2, 817-27 (1991).</p>
<p id="schneider"><strong>(Schneider)</strong> Schneider and Stoll, Phys Rev B, 17, 1302 (1978).</p>
</div>
</div>
</div>
</div>
<footer>
<hr/>
<div role="contentinfo">
<p>
&copy; Copyright .
</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:'15 May 2015 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="_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