Homec4science
Diffusion lammps (lammm-master-deprecated) Browse

lammps/doc/fix_qtb.html
490401bd6a57lammm-master-deprecated

Last Change
Raw File

fix_qtb.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 qtb command &mdash; LAMMPS 17 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 17 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 qtb 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-qtb-command">
<span id="index-0"></span><h1>fix qtb command<a class="headerlink" href="#fix-qtb-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 qtb 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>qtb = style name of this fix</li>
<li>zero or more keyword/value pairs may be appended</li>
<li>keyword = <em>temp</em> or <em>damp</em> or <em>seed</em> or <em>f_max</em> or <em>N_f</em></li>
</ul>
<pre class="literal-block">
<em>temp</em> value = target quantum temperature (temperature units)
<em>damp</em> value = damping parameter (time units) inverse of friction &lt;i&gt;&amp;gamma&lt;/i&gt;;
<em>seed</em> value = random number seed (positive integer)
<em>f_max</em> value = upper cutoff frequency of the vibration spectrum (1/time units)
<em>N_f</em> value = number of frequency bins (positive integer)
</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 nve
fix 1 all qtb temp 110 damp 200 seed 35082 f_max 0.3 N_f 100 (liquid methane modeled with the REAX force field, real units)
fix 2 all nph iso 1.01325 1.01325 1
fix 2 all qtb temp 300 damp 1 seed 47508 f_max 120.0 N_f 100 (quartz modeled with the BKS force field, metal units)
</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 command performs the quantum thermal bath scheme proposed by
<a class="reference internal" href="#dammak"><span>(Dammak)</span></a> to include self-consistent quantum nuclear effects,
when used in conjunction with the <a class="reference internal" href="fix_nve.html"><em>fix nve</em></a> or <a class="reference internal" href="fix_nh.html"><em>fix nph</em></a> commands.</p>
<p>Classical molecular dynamics simulation does not include any quantum
nuclear effect. Quantum treatment of the vibrational modes will
introduce zero point energy into the system, alter the energy power
spectrum and bias the heat capacity from the classical limit. Missing
all the quantum nuclear effects, classical MD cannot model systems at
temperatures lower than their classical limits. This effect is
especially important for materials with a large population of hydrogen
atoms and thus higher classical limits.</p>
<p>The equation of motion implemented by this command follows a Langevin
form:</p>
<center><font size="4"><i> m<sub>i</sub>a<sub>i</sub> = f<sub>i</sub>
+ R<sub>i</sub> -
m<sub>i</sub>&gamma;v<sub>i</sub>. </i></font></center><p>Here &lt;i&gt;m&lt;sub&gt;i&lt;/sub&gt;&lt;/i&gt;, &lt;i&gt;a&lt;sub&gt;i&lt;/sub&gt;&lt;/i&gt;, &lt;i&gt;f&lt;sub&gt;i&lt;/sub&gt;
&lt;/i&gt;, &lt;i&gt;R&lt;sub&gt;i&lt;/sub&gt;&lt;/i&gt;, &lt;i&gt;&amp;gamma;&lt;/i&gt; and &lt;i&gt;v&lt;sub&gt;i&lt;/sub&gt; &lt;/i&gt;
represent mass, acceleration, force exerted by all other atoms, random
force, frictional coefficient (the inverse of damping parameter damp),
and velocity. The random force &lt;i&gt;R&lt;sub&gt;i&lt;/sub&gt;&lt;/i&gt; is &#8220;colored&#8221; so
that any vibrational mode with frequency &lt;i&gt;&amp;omega;&lt;/i&gt; will have a
temperature-sensitive energy &lt;i&gt;&amp;theta;&lt;/i&gt;(&lt;i&gt;&amp;omega;,T&lt;/i&gt;) which
resembles the energy expectation for a quantum harmonic oscillator
with the same natural frequency:</p>
<center><font size="4"> <i>&theta;</i>(<i>&omega;,T</i>) =
&#8463;&omega;/2 +
&#8463;&omega;[</i>exp(<i>&#8463;&omega;/k</i><sub>B</sub><i>T</i>)<i>-1</i>]<i><sup>-1</sup></i>
</font></center><p>To efficiently generate the random forces, we employ the method
of <a class="reference internal" href="#barrat"><span>(Barrat)</span></a>, that circumvents the need to generate all
random forces for all times before the simulation. The memory
requirement of this approach is less demanding and independent
of the simulation duration. Since the total random force &lt;i&gt;R&lt;/i&gt;&lt;sub&gt;tot&lt;/sub&gt;
does not necessarily vanish for a finite number of atoms,
&lt;i&gt;R&lt;sub&gt;i&lt;/sub&gt;&lt;/i&gt; is replaced by &lt;i&gt;R&lt;sub&gt;i&lt;/sub&gt;&lt;/i&gt; - &lt;i&gt;R&lt;/i&gt;&lt;sub&gt;tot&lt;/sub&gt;/&lt;i&gt;N&lt;/i&gt;&lt;sub&gt;tot&lt;/sub&gt;
to avoid collective motion of the system.</p>
<p>The <em>temp</em> parameter sets the target quantum temperature. LAMMPS will
still have an output temperature in its thermo style. That is the
instantaneous classical temperature &lt;i&gt;T&lt;/i&gt;&lt;sup&gt;cl&lt;/sup&gt; derived from
the atom velocities at thermal equilibrium. A non-zero
&lt;i&gt;T&lt;/i&gt;&lt;sup&gt;cl&lt;/sup&gt; will be present even when the quantum
temperature approaches zero. This is associated with zero-point energy
at low temperatures.</p>
<center><font size="4"> <i>T</i><sup>cl</sup> = &sum;
<i>m<sub>i</sub>v<sub>i</sub><sup>2</sup>/3Nk</i><sub>B</sub>
</font></center><p>The <em>damp</em> parameter is specified in time units, and it equals the
inverse of the frictional coefficient &lt;i&gt;&amp;gamma;&lt;/i&gt;. &lt;i&gt;&amp;gamma;&lt;/i&gt;
should be as small as possible but slightly larger than the timescale
of anharmonic coupling in the system which is about 10 ps to 100
ps. When &lt;i&gt;&amp;gamma;&lt;/i&gt; is too large, it gives an energy spectrum that
differs from the desired Bose-Einstein spectrum. When &lt;i&gt;&amp;gamma;&lt;/i&gt;
is too small, the quantum thermal bath coupling to the system will be
less significant than anharmonic effects, reducing to a classical
limit. We find that setting &lt;i&gt;&amp;gamma;&lt;/i&gt; between 5 THz and 1 THz
could be appropriate depending on the system.</p>
<p>The random number <em>seed</em> is a positive integer used to initiate a
Marsaglia random number generator. Each processor uses the input seed
to generate its own unique seed and its own stream of random
numbers. Thus the dynamics of the system will not be identical on two
runs on different numbers of processors.</p>
<p>The <em>f_max</em> parameter truncate the noise frequency domain so that
vibrational modes with frequencies higher than <em>f_max</em> will not be
modulated. If we denote &amp;Delta;&lt;i&gt;t&lt;/i&gt; as the time interval for the
MD integration, <em>f_max</em> is always reset by the code to make
&lt;i&gt;&amp;alpha;&lt;/i&gt; = (int)(2*f_max*&amp;Delta;&lt;i&gt;t&lt;/i&gt;)&lt;sup&gt;&lt;i&gt;-1&lt;/i&gt;&lt;/sup&gt; a
positive integer and print out relative information. An appropriate
value for the cutoff frequency <em>f_max</em> would be around 2~3
&lt;i&gt;f&lt;/i&gt;&lt;sub&gt;D&lt;/sub&gt;, where &lt;i&gt;f&lt;/i&gt;&lt;sub&gt;D&lt;/sub&gt; is the Debye
frequency.</p>
<p>The <em>N_f</em> parameter is the frequency grid size, the number of points
from 0 to <em>f_max</em> in the frequency domain that will be
sampled. &lt;i&gt;3&amp;times;2&lt;/i&gt; <em>N_f</em> per-atom random numbers are required
in the random force generation and there could be as many atoms as in
the whole simulation that can migrate into every individual
processor. A larger <em>N_f</em> provides a more accurate sampling of the
spectrum while consumes more memory. With fixed <em>f_max</em> and
&lt;i&gt;&amp;gamma;&lt;/i&gt;, <em>N_f</em> should be big enough to converge the classical
temperature &lt;i&gt;T&lt;/i&gt;&lt;sup&gt;cl&lt;/sup&gt; as a function of target quantum bath
temperature. Memory usage per processor could be from 10 to 100
Mbytes.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">Unlike the <a class="reference internal" href="fix_nh.html"><em>fix nvt</em></a> command which performs
Nose/Hoover thermostatting AND time integration, this fix does NOT
perform time integration. It only modifies forces to a colored
thermostat. Thus you must use a separate time integration fix, like
<a class="reference internal" href="fix_nve.html"><em>fix nve</em></a> or <a class="reference internal" href="fix_nh.html"><em>fix nph</em></a> to actually update the
velocities and positions of atoms (as shown in the
examples). Likewise, this fix should not normally be used with other
fixes or commands that also specify system temperatures , e.g. <a class="reference internal" href="fix_nh.html"><em>fix nvt</em></a> and <a class="reference internal" href="fix_temp_rescale.html"><em>fix temp/rescale</em></a>.</p>
</div>
<hr class="docutils" />
<p><strong>Restart, fix_modify, output, run start/stop, minimizie info:</strong></p>
<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. However, in a statistical sense, a restarted
simulation should produce similar behaviors of the system.</p>
<p>This fix is not invoked during <a class="reference internal" href="minimize.html"><em>energy minimization</em></a>.</p>
</div>
<hr class="docutils" />
<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 USER-QTB 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>
<hr class="docutils" />
<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_nve.html"><em>fix nve</em></a>, <a class="reference internal" href="fix_nh.html"><em>fix nph</em></a>, <a class="reference internal" href="fix_langevin.html"><em>fix langevin</em></a>, <a class="reference internal" href="fix_qbmsst.html"><em>fix qbmsst</em></a></p>
</div>
<hr class="docutils" />
<div class="section" id="default">
<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline">¶</a></h2>
<p>The keyword defaults are temp = 300, damp = 1, seed = 880302,
f_max=200.0 and N_f = 100.</p>
<hr class="docutils" />
<p id="dammak"><strong>(Dammak)</strong> Dammak, Chalopin, Laroche, Hayoun, and Greffet, Phys Rev
Lett, 103, 190601 (2009).</p>
<p id="barrat"><strong>(Barrat)</strong> Barrat and Rodney, J. Stat. Phys, 144, 679 (2011).</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:'17 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