forked from lijiext/lammps
352 lines
17 KiB
HTML
352 lines
17 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 ehex 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 ehex 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-ehex-command">
|
|
<span id="index-0"></span><h1>fix ehex 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">ehex</span> <span class="n">nevery</span> <span class="n">F</span> <span class="n">keyword</span> <span class="n">value</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>ehex = style name of this fix command</li>
|
|
<li>nevery = add/subtract heat every this many timesteps</li>
|
|
<li>F = energy flux into the reservoir (energy/time units)</li>
|
|
<li>zero or more keyword/value pairs may be appended to args</li>
|
|
<li>keyword = <em>region</em> or <em>constrain</em> or <em>com</em> or <em>hex</em></li>
|
|
</ul>
|
|
<pre class="literal-block">
|
|
<em>region</em> value = region-ID
|
|
region-ID = ID of region (reservoir) atoms must be in for added thermostatting force
|
|
<em>constrain</em> value = none
|
|
apply the constraint algorithm (SHAKE or RATTLE) again at the end of the timestep
|
|
<em>com</em> value = none
|
|
rescale all sites of a constrained cluster of atom if its COM is in the reservoir
|
|
<em>hex</em> value = none
|
|
omit the coordinate correction to recover the HEX algorithm
|
|
</pre>
|
|
</div>
|
|
<div class="section" id="examples">
|
|
<h2>Examples</h2>
|
|
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># Lennard-Jones, from examples/in.ehex.lj</span>
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">fnve</span> <span class="nb">all</span> <span class="n">nve</span>
|
|
<span class="c1"># specify regions rhot and rcold</span>
|
|
<span class="o">...</span>
|
|
<span class="n">fix</span> <span class="n">fhot</span> <span class="nb">all</span> <span class="n">ehex</span> <span class="mi">1</span> <span class="mf">0.15</span> <span class="n">region</span> <span class="n">rhot</span>
|
|
<span class="n">fix</span> <span class="n">fcold</span> <span class="nb">all</span> <span class="n">ehex</span> <span class="mi">1</span> <span class="o">-</span><span class="mf">0.15</span> <span class="n">region</span> <span class="n">rcold</span>
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># SPC/E water, from examples/in.ehex.spce</span>
|
|
<span class="n">fix</span> <span class="n">fnve</span> <span class="nb">all</span> <span class="n">nve</span>
|
|
<span class="c1"># specify regions rhot and rcold</span>
|
|
<span class="o">...</span>
|
|
<span class="n">fix</span> <span class="n">fhot</span> <span class="nb">all</span> <span class="n">ehex</span> <span class="mi">1</span> <span class="mf">0.075</span> <span class="n">region</span> <span class="n">rhot</span> <span class="n">constrain</span> <span class="n">com</span>
|
|
<span class="n">fix</span> <span class="n">fcold</span> <span class="nb">all</span> <span class="n">ehex</span> <span class="mi">1</span> <span class="o">-</span><span class="mf">0.075</span> <span class="n">region</span> <span class="n">rcold</span> <span class="n">constrain</span> <span class="n">com</span>
|
|
<span class="n">fix</span> <span class="n">frattle</span> <span class="nb">all</span> <span class="n">rattle</span> <span class="mi">1</span><span class="n">e</span><span class="o">-</span><span class="mi">10</span> <span class="mi">400</span> <span class="mi">0</span> <span class="n">b</span> <span class="mi">1</span> <span class="n">a</span> <span class="mi">1</span>
|
|
</pre></div>
|
|
</div>
|
|
</div>
|
|
<div class="section" id="description">
|
|
<h2>Description</h2>
|
|
<p>This fix implements the asymmetric version of the enhanced heat
|
|
exchange algorithm <a class="reference internal" href="#wirnsberger"><span class="std std-ref">(Wirnsberger)</span></a>. The eHEX algorithm is
|
|
an extension of the heat exchange algorithm <a class="reference internal" href="#ikeshoji"><span class="std std-ref">(Ikeshoji)</span></a> and
|
|
adds an additional coordinate integration to account for higher-order
|
|
truncation terms in the operator splitting. The original HEX
|
|
algorithm (implemented as <a class="reference internal" href="fix_heat.html"><span class="doc">fix heat</span></a>) is known to
|
|
exhibit a slight energy drift limiting the accessible simulation times
|
|
to a few nanoseconds. This issue is greatly improved by the new
|
|
algorithm decreasing the energy drift by at least a factor of a
|
|
hundred (LJ and SPC/E water) with little computational overhead.</p>
|
|
<p>In both algorithms (non-translational) kinetic energy is constantly
|
|
swapped between regions (reservoirs) to impose a heat flux onto the
|
|
system. The equations of motion are therefore modified if a particle
|
|
<span class="math">\(i\)</span> is located inside a reservoir <span class="math">\(\Gamma_k\)</span> where <span class="math">\(k>0\)</span>. We
|
|
use <span class="math">\(\Gamma_0\)</span> to label those parts of the simulation box which
|
|
are not thermostatted.) The input parameter <em>region-ID</em> of this fix
|
|
corresponds to <span class="math">\(k\)</span>. The energy swap is modelled by introducing an
|
|
additional thermostatting force to the equations of motion, such that
|
|
the time evolution of coordinates and momenta of particle <span class="math">\(i\)</span>
|
|
becomes <a class="reference internal" href="#wirnsberger"><span class="std std-ref">(Wirnsberger)</span></a></p>
|
|
<img alt="_images/fix_ehex_eom.jpg" class="align-center" src="_images/fix_ehex_eom.jpg" />
|
|
<p>The thermostatting force is given by</p>
|
|
<img alt="_images/fix_ehex_f.jpg" class="align-center" src="_images/fix_ehex_f.jpg" />
|
|
<p>where <span class="math">\(m_i\)</span> is the mass and <span class="math">\(k(\mathbf r_i)\)</span> maps the particle
|
|
position to the respective reservoir. The quantity
|
|
<span class="math">\(F_{\Gamma_{k(\mathbf r_i)}}\)</span> corresponds to the input parameter
|
|
<em>F</em>, which is the energy flux into the reservoir. Furthermore,
|
|
<span class="math">\(K_{\Gamma_{k(\mathbf r_i)}}\)</span> and <span class="math">\(v_{\Gamma_{k(\mathbf r_i)}}\)</span>
|
|
denote the non-translational kinetic energy and the centre of mass
|
|
velocity of that reservoir. The thermostatting force does not affect
|
|
the centre of mass velocities of the individual reservoirs and the
|
|
entire simulation box. A derivation of the equations and details on
|
|
the numerical implementation with velocity Verlet in LAMMPS can be
|
|
found in reference “(Wirnsberger)”#_Wirnsberger.</p>
|
|
<div class="admonition note">
|
|
<p class="first admonition-title">Note</p>
|
|
<p class="last">This fix only integrates the thermostatting force and must be
|
|
combined with another integrator, such as <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a>, to
|
|
solve the full equations of motion.</p>
|
|
</div>
|
|
<p>This fix is different from a thermostat such as <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a>
|
|
or <a class="reference internal" href="fix_temp_rescale.html"><span class="doc">fix temp/rescale</span></a> in that energy is
|
|
added/subtracted continually. Thus if there isn’t another mechanism
|
|
in place to counterbalance this effect, the entire system will heat or
|
|
cool continuously.</p>
|
|
<div class="admonition note">
|
|
<p class="first admonition-title">Note</p>
|
|
<p class="last">If heat is subtracted from the system too aggressively so that
|
|
the group’s kinetic energy would go to zero, then LAMMPS will halt
|
|
with an error message. Increasing the value of <em>nevery</em> means that
|
|
heat is added/subtracted less frequently but in larger portions. The
|
|
resulting temperature profile will therefore be the same.</p>
|
|
</div>
|
|
<p>This fix will default to <a class="reference internal" href="fix_heat.html"><span class="doc">fix_heat</span></a> (HEX algorithm) if
|
|
the keyword <em>hex</em> is specified.</p>
|
|
<hr class="docutils" />
|
|
<p><strong>Compatibility with SHAKE and RATTLE (rigid molecules)</strong>:</p>
|
|
<p>This fix is compatible with <a class="reference internal" href="fix_shake.html"><span class="doc">fix shake</span></a> and <span class="xref doc">fix rattle</span>. If either of these constraining algorithms is
|
|
specified in the input script and the keyword <em>constrain</em> is set, the
|
|
bond distances will be corrected a second time at the end of the
|
|
integration step. It is recommended to specify the keyword <em>com</em> in
|
|
addition to the keyword <em>constrain</em>. With this option all sites of a
|
|
constrained cluster are rescaled, if its centre of mass is located
|
|
inside the region. Rescaling all sites of a cluster by the same factor
|
|
does not introduce any velocity components along fixed bonds. No
|
|
rescaling takes place if the centre of mass lies outside the region.</p>
|
|
<div class="admonition note">
|
|
<p class="first admonition-title">Note</p>
|
|
<p class="last">You can only use the keyword <em>com</em> along with <em>constrain</em>.</p>
|
|
</div>
|
|
<p>To achieve the highest accuracy it is recommended to use <span class="xref doc">fix rattle</span> with the keywords <em>constrain</em> and <em>com</em> as
|
|
shown in the second example. Only if RATTLE is employed, the velocity
|
|
constraints will be satisfied.</p>
|
|
<div class="admonition note">
|
|
<p class="first admonition-title">Note</p>
|
|
<p class="last">Even if RATTLE is used and the keywords <em>com</em> and <em>constrain</em>
|
|
are both set, the coordinate constraints will not necessarily be
|
|
satisfied up to the target precision. The velocity constraints are
|
|
satisfied as long as all sites of a cluster are rescaled (keyword
|
|
<em>com</em>) and the cluster does not span adjacent reservoirs. The current
|
|
implementation of the eHEX algorithm introduces a small error in the
|
|
bond distances, which goes to zero with order three in the
|
|
timestep. For example, in a simulation of SPC/E water with a timestep
|
|
of 2 fs the maximum relative error in the bond distances was found to
|
|
be on the order of <span class="math">\(10^{-7}\)</span> for relatively large
|
|
temperature gradients. A higher precision can be achieved by
|
|
decreasing the timestep.</p>
|
|
</div>
|
|
</div>
|
|
<hr class="docutils" />
|
|
<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>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
|
|
are relevant to this fix.</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"><span class="doc">run</span></a> command. 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 RIGID 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>
|
|
</div>
|
|
<div class="section" id="related-commands">
|
|
<h2>Related commands</h2>
|
|
<p><a class="reference internal" href="fix_heat.html"><span class="doc">fix heat</span></a>, <a class="reference internal" href="fix_thermal_conductivity.html"><span class="doc">fix thermal/conductivity</span></a>, <a class="reference internal" href="compute_temp.html"><span class="doc">compute temp</span></a>, <a class="reference internal" href="compute_temp_region.html"><span class="doc">compute temp/region</span></a></p>
|
|
<p><strong>Default:</strong> none</p>
|
|
<hr class="docutils" />
|
|
<p id="ikeshoji"><strong>(Ikeshoji)</strong> Ikeshoji and Hafskjold, Molecular Physics, 81, 251-261 (1994).</p>
|
|
<p id="wirnsberger"><strong>(Wirnsberger)</strong> Wirnsberger, Frenkel, and Dellago, J Chem Phys, 143,
|
|
124104 (2015).</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> |