Homec4science
Diffusion lammps (lammm-devel) Browse

lammps/doc/fix_ti_spring.html
77f5eba53086lammm-devel

Last Change
Raw File

fix_ti_spring.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 ti/spring 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 ti/spring 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-ti-spring-command">
<span id="index-0"></span><h1>fix ti/spring command<a class="headerlink" href="#fix-ti-spring-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 ti/spring K t_switch t_equil 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>ti/spring = style name of this fix command</li>
<li>K = spring constant (force/distance units)</li>
<li>t_switch/t_equil = number of steps of the switching/equilibration procedure</li>
<li>zero or more keyword/value pairs may be appended to args</li>
<li>keyword = <em>function</em></li>
</ul>
<pre class="literal-block">
<em>function</em> value = function-ID
function-ID = ID of the switching function (1 or 2)
</pre>
<p><strong>Example:</strong></p>
<div class="highlight-python"><div class="highlight"><pre>fix ref all ti/spring 50.0 2000 1000 function 2
</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 allows you to compute the free energy of solids by performing
a thermodynamic integration between the solid of interest and an
Einstein crystal <a class="reference internal" href="#frenkel"><span>(Frenkel)</span></a>. The thermodynamic integration
is performed using the nonequilibrium method of Adiabatic Switching
<a class="reference internal" href="#watanabe"><span>(Watanabe,</span></a> <a class="reference internal" href="#dekoning96"><span>de Koning96)</span></a>.</p>
<p>A spring force is applied independently to each atom in the group to
tether it to its initial position. The initial position for each atom
is its location at the time the fix command was issued. More details
about the springs are available in <a class="reference internal" href="fix_spring_self.html"><em>fix spring/self</em></a>. The forces on the atoms are
dynamically scaled during the simulation, the rescaling is done in the
following manner:</p>
<img alt="_images/fix_ti_spring_force.jpg" class="align-center" src="_images/fix_ti_spring_force.jpg" />
<p>where F_harm is the force due to the springs, F_solid is the total
force on the atoms due to the interatomic potential and lambda is the
coupling parameter of the thermodynamic integration.</p>
<p>The fix acts as follows: during the first <em>t_equil</em> steps after the
fix is defined the value of lambda is zero, this is the period to
equilibrate the system in the lambda = 0 state. After this the value
of lambda changes continuously from 0 to 1 according to the function
defined using the keyword <em>function</em> (described below), this is done
in <em>t_switch</em> steps. Then comes the second equilibration period of
<em>t_equil</em> to equilibrate the system in the lambda = 1 state. After
that the switching back to the lambda = 0 state is made using
<em>t_switch</em> timesteps and following the same switching function. After
this period the value of lambda is kept equal to zero and the fix has
no action in the dynamics of the system anymore.</p>
<p>The description of thermodynamic integration in both directions is
done in <a class="reference internal" href="#dekoning97"><span>de Koning97</span></a>, the main reason is to try to
eliminate the dissipated heat due to the nonequilibrium process.</p>
<p>The <em>function</em> keyword allows the use of two different switching
rates, the option <em>1</em> results in a constant rescaling where the lambda
parameter changes at a constant rate during the switching time
according to the switching function</p>
<img alt="_images/fix_ti_spring_function_1.jpg" class="align-center" src="_images/fix_ti_spring_function_1.jpg" />
<p>where tau is the scaled time variable t/t_switch. The option number
<em>2</em> performs the switching at a rate defined by the following
switching function</p>
<img alt="_images/fix_ti_spring_function_2.jpg" class="align-center" src="_images/fix_ti_spring_function_2.jpg" />
<p>This function has zero slope as lambda approaches its extreme values
(0 and 1), according to (<a class="reference internal" href="#dekoning96"><span>de Koning96)</span></a> this results in
smaller fluctuations on the integral to be computed on the
thermodynamic integration.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">It is importante to keep the center of mass fixed
during the thermodynamic integration, a non-zero total velocity will
result in divergencies during the integration due to the fact that the
atoms are &#8216;attatched&#8217; to its equilibrium positions by the Einstein
crystal. Check the option <em>zero</em> of <a class="reference external" href="fix_langevin_html">fix langevin</a>
and <a class="reference internal" href="velocity.html"><em>velocity</em></a>. The use of the Nose-Hoover thermostat
(<code class="xref doc docutils literal"><span class="pre">fix</span> <span class="pre">nvt</span></code>) is NOT recommended due to its well documented
issues with the canonical sampling of harmonic degrees of freedom
(notice that the <em>chain</em> option will NOT solve this problem). The
Langevin thermostat (<a class="reference external" href="fix_langevin.html&quot;">fix langevin</a>) works fine.</p>
</div>
</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>This fix writes the original coordinates of tethered atoms to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>, so that the spring effect will be the
same in a restarted simulation. See the <a class="reference internal" href="read_restart.html"><em>read restart</em></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"><em>fix modify</em></a> <em>energy</em> option is supported by this
fix to add the energy stored in the per-atom springs to the system&#8217;s
potential energy as part of <a class="reference internal" href="thermo_style.html"><em>thermodynamic output</em></a>.</p>
<p>This fix computes a global scalar and a global vector quantities which
can be accessed by various <a class="reference internal" href="Section_howto.html#howto-15"><span>output commands</span></a>. The scalar is an energy which
is the sum of the spring energy for each atom, where the per-atom
energy is 0.5 * K * r^2. The vector has 2 positions, the first one is
the coupling parameter lambda and the second one is the time
derivative of lambda. The scalar and vector values calculated by this
fix are &#8220;extensive&#8221;.</p>
<p>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.</p>
<p>The forces due to this fix are imposed during an energy minimization,
invoked by the <a class="reference internal" href="minimize.html"><em>minimize</em></a> command.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">If you want the per-atom spring energy to be included
in the total potential energy of the system (the quantity being
minimized), you MUST enable the <a class="reference internal" href="fix_modify.html"><em>fix modify</em></a> <em>energy</em>
option for this fix.</p>
</div>
<p>An example script using this command is provided in the
examples/USER/misc/ti directory.</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_spring.html"><em>fix spring</em></a>, <a class="reference internal" href="fix_ti_rs.html"><em>fix ti/rs</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 command is part of the USER-MISC package. It is only enabled if
LAMMPS was built with those packages. 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="default">
<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline"></a></h2>
<p>The keyword default is function = 1.</p>
<hr class="docutils" />
<p id="frenkel"><strong>(Frenkel)</strong> Daan Frenkel and Anthony J. C. Ladd, J. Chem. Phys. 81, 3188
(1984).</p>
<p id="watanabe"><strong>(Watanabe)</strong> M. Watanabe and W. P. Reinhardt, Phys Rev Lett, 65, 3301 (1990).</p>
<p id="dekoning96"><strong>(de Koning 96)</strong> M. de Koning and A. Antonelli, Phys Rev E, 53, 465 (1996).</p>
<p id="dekoning97"><strong>(de Koning 97)</strong> M. de Koning and A. Antonelli, Phys Rev B, 55, 735 (1997).</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