git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13798 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
@ -1,298 +1,156 @@
|
||||
<HTML>
|
||||
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
|
||||
</CENTER>
|
||||
|
||||
|
||||
<!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/rs command — 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 & 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 ti/rs 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-ti-rs-command">
|
||||
<span id="index-0"></span><h1>fix ti/rs command<a class="headerlink" href="#fix-ti-rs-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/rs lambda_initial lambda_final 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/rs = style name of this fix command</li>
|
||||
<li>lambda_initial/lambda_final = initial/final values of the coupling parameter</li>
|
||||
<li>t_switch/t_equil = number of steps of the switching/equilibration procedure</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, 2 or 3)
|
||||
</pre>
|
||||
<p><strong>Example:</strong></p>
|
||||
<div class="highlight-python"><div class="highlight"><pre>fix ref all ti/rs 50.0 2000 1000
|
||||
fix vf vacancy ti/rs 10.0 70000 50000 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 temperature dependence
|
||||
|
||||
|
||||
<HR>
|
||||
|
||||
<H3>fix ti/rs command
|
||||
</H3>
|
||||
<P><B>Syntax:</B>
|
||||
</P>
|
||||
<PRE>fix ID group-ID ti/rs lambda_initial lambda_final t_switch t_equil keyword value ...
|
||||
</PRE>
|
||||
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
|
||||
|
||||
<LI>ti/rs = style name of this fix command
|
||||
|
||||
<LI>lambda_initial/lambda_final = initial/final values of the coupling parameter
|
||||
|
||||
<LI>t_switch/t_equil = number of steps of the switching/equilibration procedure
|
||||
|
||||
<LI>keyword = <I>function</I>
|
||||
|
||||
<PRE> <I>function</I> value = function-ID
|
||||
function-ID = ID of the switching function (1, 2 or 3)
|
||||
</PRE>
|
||||
|
||||
</UL>
|
||||
<P><B>Example:</B>
|
||||
</P>
|
||||
<PRE>fix ref all ti/rs 50.0 2000 1000
|
||||
fix vf vacancy ti/rs 10.0 70000 50000 function 2
|
||||
</PRE>
|
||||
<P><B>Description:</B>
|
||||
</P>
|
||||
<P>This fix allows you to compute the free energy temperature dependence
|
||||
by performing a thermodynamic integration procedure known as
|
||||
Reversible Scaling <a class="reference internal" href="#dekoning99"><span>(de Koning99,</span></a> <span class="xref std std-ref">de Koning00a)</span>. The thermodynamic integration is performed
|
||||
Reversible Scaling <A HREF = "#deKoning99">(de Koning99,</A> <A HREF = "#deKoning00a"">de
|
||||
Koning00a)</A>. The thermodynamic integration is performed
|
||||
using the nonequilibrium method of Adiabatic Switching
|
||||
<a class="reference internal" href="fix_ti_spring.html#watanabe"><span>(Watanabe,</span></a> <a class="reference internal" href="fix_ti_spring.html#dekoning96"><span>de Koning96)</span></a>.</p>
|
||||
<p>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_rs_force.jpg" class="align-center" src="_images/fix_ti_rs_force.jpg" />
|
||||
<p>where F_int is the total force on the atoms due to the interatomic
|
||||
<A HREF = "#Watanabe">(Watanabe,</A> <A HREF = "#deKoning96">de Koning96)</A>.
|
||||
</P>
|
||||
<P>The forces on the atoms are dynamically scaled during the simulation,
|
||||
the rescaling is done in the following manner:
|
||||
</P>
|
||||
<CENTER><IMG SRC = "Eqs/fix_ti_rs_force.jpg">
|
||||
</CENTER>
|
||||
<P>where F_int 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 <em>lambda_initial</em> , this is the
|
||||
period to equilibrate the system in the lambda = <em>lambda_initial</em>
|
||||
integration.
|
||||
</P>
|
||||
<P>The fix acts as follows: during the first <I>t_equil</I> steps after the
|
||||
fix is defined the value of lambda is <I>lambda_initial</I> , this is the
|
||||
period to equilibrate the system in the lambda = <I>lambda_initial</I>
|
||||
state. After this the value of lambda changes continuously from
|
||||
<em>lambda_initial</em> to <em>lambda_final</em> 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 = <em>lambda_final</em>
|
||||
state. After that the switching back to the lambda = <em>lambda_initial</em>
|
||||
state is done using <em>t_switch</em> timesteps and following the same
|
||||
<I>lambda_initial</I> to <I>lambda_final</I> according to the function defined
|
||||
using the keyword <I>function</I> (described below), this is done in
|
||||
<I>t_switch</I> steps. Then comes the second equilibration period of
|
||||
<I>t_equil</I> to equilibrate the system in the lambda = <I>lambda_final</I>
|
||||
state. After that the switching back to the lambda = <I>lambda_initial</I>
|
||||
state is done using <I>t_switch</I> timesteps and following the same
|
||||
switching function. After this period the value of lambda is kept
|
||||
equal to <em>lambda_initial</em> indefinitely or until a <a class="reference internal" href="unfix.html"><em>unfix</em></a>
|
||||
erase the fix.</p>
|
||||
<p>The description of thermodynamic integration in both directions is
|
||||
done in <a class="reference internal" href="#dekoning00b"><span>de Koning00b</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 three different switching
|
||||
rates. The option <em>1</em> results in a constant rescaling where the lambda
|
||||
equal to <I>lambda_initial</I> indefinitely or until a <A HREF = "unfix.html">unfix</A>
|
||||
erase the fix.
|
||||
</P>
|
||||
<P>The description of thermodynamic integration in both directions is
|
||||
done in <A HREF = "#deKoning00b">de Koning00b</A>, the main reason is to try to
|
||||
eliminate the dissipated heat due to the nonequilibrium process.
|
||||
</P>
|
||||
<P>The <I>function</I> keyword allows the use of three different switching
|
||||
rates. The option <I>1</I> 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_rs_function_1.jpg" class="align-center" src="_images/fix_ti_rs_function_1.jpg" />
|
||||
<p>where tau is the scaled time variable t/t_switch. This switching
|
||||
according to the switching function
|
||||
</P>
|
||||
<CENTER><IMG SRC = "Eqs/fix_ti_rs_function_1.jpg">
|
||||
</CENTER>
|
||||
<P>where tau is the scaled time variable t/t_switch. This switching
|
||||
function has the characteristic that the temperature scaling is faster
|
||||
at temperatures closer to the final temperature of the procedure. The
|
||||
option number <em>2</em> performs the switching at a rate defined by the
|
||||
following switching function</p>
|
||||
<img alt="_images/fix_ti_rs_function_2.jpg" class="align-center" src="_images/fix_ti_rs_function_2.jpg" />
|
||||
<p>This switching function has the characteristic that the temperature
|
||||
option number <I>2</I> performs the switching at a rate defined by the
|
||||
following switching function
|
||||
</P>
|
||||
<CENTER><IMG SRC = "Eqs/fix_ti_rs_function_2.jpg">
|
||||
</CENTER>
|
||||
<P>This switching function has the characteristic that the temperature
|
||||
scaling occurs at a constant rate during all the procedure. The option
|
||||
number <em>3</em> performs the switching at a rate defined by the following
|
||||
switching function</p>
|
||||
<img alt="_images/fix_ti_rs_function_3.jpg" class="align-center" src="_images/fix_ti_rs_function_3.jpg" />
|
||||
<p>This switching function has the characteristic that the temperature
|
||||
number <I>3</I> performs the switching at a rate defined by the following
|
||||
switching function
|
||||
</P>
|
||||
<CENTER><IMG SRC = "Eqs/fix_ti_rs_function_3.jpg">
|
||||
</CENTER>
|
||||
<P>This switching function has the characteristic that the temperature
|
||||
scaling is faster at temperatures closer to the initial temperature of
|
||||
the procedure.</p>
|
||||
<p>An example script using this command is provided in the
|
||||
examples/USER/misc/ti directory.</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>.</p>
|
||||
<p>This fix computes a global vector quantitie which can be accessed by
|
||||
various <a class="reference internal" href="Section_howto.html#howto-15"><span>output commands</span></a>. The vector has
|
||||
the procedure.
|
||||
</P>
|
||||
<P>An example script using this command is provided in the
|
||||
examples/USER/misc/ti directory.
|
||||
</P>
|
||||
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
|
||||
</P>
|
||||
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
|
||||
files</A>.
|
||||
</P>
|
||||
<P>This fix computes a global vector quantitie which can be accessed by
|
||||
various <A HREF = "Section_howto.html#howto_15">output commands</A>. 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 “extensive”.</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>
|
||||
<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_ti_spring.html"><em>fix ti/spring</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="dekoning99"><strong>(de Koning 99)</strong> M. de Koning, A. Antonelli and S. Yip, Phys Rev Lett, 83, 3973 (1999).</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="dekoning00a"><strong>(de Koning 00a)</strong> M. de Koning, A. Antonelli and S. Yip, J Chem Phys, 115, 11025 (2000).</p>
|
||||
<p id="dekoning00b"><strong>(de Koning 00b)</strong> M. de Koning et al., Computing in Science & Engineering, 2, 88 (2000).</p>
|
||||
</div>
|
||||
</div>
|
||||
values calculated by this fix are "extensive".
|
||||
</P>
|
||||
<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
|
||||
the <A HREF = "run.html">run</A> command.
|
||||
</P>
|
||||
<P>The forces due to this fix are imposed during an energy minimization,
|
||||
invoked by the <A HREF = "minimize.html">minimize</A> command.
|
||||
</P>
|
||||
<P><B>Related commands:</B>
|
||||
</P>
|
||||
<P><A HREF = "fix_ti_spring.html">fix ti/spring</A>
|
||||
</P>
|
||||
<P><B>Restrictions:</B>
|
||||
</P>
|
||||
<P>This command is part of the USER-MISC package. It is only enabled if
|
||||
LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
|
||||
LAMMPS</A> section for more info.
|
||||
</P>
|
||||
<P><B>Default:</B>
|
||||
</P>
|
||||
<P>The keyword default is function = 1.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<A NAME = "deKoning99"></A>
|
||||
|
||||
</div>
|
||||
</div>
|
||||
<footer>
|
||||
|
||||
<P><B>(de Koning 99)</B> M. de Koning, A. Antonelli and S. Yip, Phys Rev Lett, 83, 3973 (1999).
|
||||
</P>
|
||||
<A NAME = "Watanabe"></A>
|
||||
|
||||
<hr/>
|
||||
<P><B>(Watanabe)</B> M. Watanabe and W. P. Reinhardt, Phys Rev Lett, 65, 3301 (1990).
|
||||
</P>
|
||||
<A NAME = "deKoning96"></A>
|
||||
|
||||
<div role="contentinfo">
|
||||
<p>
|
||||
© 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>.
|
||||
<P><B>(de Koning 96)</B> M. de Koning and A. Antonelli, Phys Rev E, 53, 465 (1996).
|
||||
</P>
|
||||
<A NAME = "deKoning00a"></A>
|
||||
|
||||
</footer>
|
||||
<P><B>(de Koning 00a)</B> M. de Koning, A. Antonelli and S. Yip, J Chem Phys, 115, 11025 (2000).
|
||||
</P>
|
||||
<A NAME = "deKoning00b"></A>
|
||||
|
||||
</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="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>
|
||||
<P><B>(de Koning 00b)</B> M. de Koning et al., Computing in Science & Engineering, 2, 88 (2000).
|
||||
</P>
|
||||
</HTML>
|
||||
|
||||
Reference in New Issue
Block a user