Homec4science
Diffusion lammps (lammps-icms) Browse

lammps/doc/fix_nh_eff.html
d205583a4f59lammps-icms

Last Change
Raw File

fix_nh_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 nvt/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">
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">fix nvt/eff command</a></li>
<li><a class="reference internal" href="#fix-npt-eff-command">fix npt/eff command</a></li>
<li><a class="reference internal" href="#fix-nph-eff-command">fix nph/eff command</a><ul>
<li><a class="reference internal" href="#syntax">Syntax</a></li>
<li><a class="reference internal" href="#examples">Examples</a></li>
<li><a class="reference internal" href="#description">Description</a></li>
<li><a class="reference internal" href="#restart-fix-modify-output-run-start-stop-minimize-info">Restart, fix_modify, output, run start/stop, minimize info</a></li>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
<li><a class="reference internal" href="#default">Default</a></li>
</ul>
</li>
</ul>
</div>
</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 nvt/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-nvt-eff-command">
<span id="index-0"></span><h1>fix nvt/eff command<a class="headerlink" href="#fix-nvt-eff-command" title="Permalink to this headline">¶</a></h1>
</div>
<div class="section" id="fix-npt-eff-command">
<h1>fix npt/eff command<a class="headerlink" href="#fix-npt-eff-command" title="Permalink to this headline">¶</a></h1>
</div>
<div class="section" id="fix-nph-eff-command">
<h1>fix nph/eff command<a class="headerlink" href="#fix-nph-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 style_name 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>style_name = <em>nvt/eff</em> or <em>npt/eff</em> or <em>nph/eff</em></li>
</ul>
<pre class="literal-block">
one or more keyword value pairs may be appended
keyword = <em>temp</em> or <em>iso</em> or <em>aniso</em> or <em>tri</em> or <em>x</em> or <em>y</em> or <em>z</em> or <em>xy</em> or <em>yz</em> or <em>xz</em> or <em>couple</em> or <em>tchain</em> or <em>pchain</em> or <em>mtk</em> or <em>tloop</em> or <em>ploop</em> or <em>nreset</em> or <em>drag</em> or <em>dilate</em>
<em>temp</em> values = Tstart Tstop Tdamp
Tstart,Tstop = external temperature at start/end of run
Tdamp = temperature damping parameter (time units)
<em>iso</em> or <em>aniso</em> or <em>tri</em> values = Pstart Pstop Pdamp
Pstart,Pstop = scalar external pressure at start/end of run (pressure units)
Pdamp = pressure damping parameter (time units)
<em>x</em> or <em>y</em> or <em>z</em> or <em>xy</em> or <em>yz</em> or <em>xz</em> values = Pstart Pstop Pdamp
Pstart,Pstop = external stress tensor component at start/end of run (pressure units)
Pdamp = stress damping parameter (time units)
<em>couple</em> = <em>none</em> or <em>xyz</em> or <em>xy</em> or <em>yz</em> or <em>xz</em>
<em>tchain</em> value = length of thermostat chain (1 = single thermostat)
<em>pchain</em> values = length of thermostat chain on barostat (0 = no thermostat)
<em>mtk</em> value = <em>yes</em> or <em>no</em> = add in MTK adjustment term or not
<em>tloop</em> value = number of sub-cycles to perform on thermostat
<em>ploop</em> value = number of sub-cycles to perform on barostat thermostat
<em>nreset</em> value = reset reference cell every this many timesteps
<em>drag</em> value = drag factor added to barostat/thermostat (0.0 = no drag)
<em>dilate</em> value = <em>all</em> or <em>partial</em>
</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 nvt/eff temp 300.0 300.0 0.1
fix 1 part npt/eff temp 300.0 300.0 0.1 iso 0.0 0.0 1.0
fix 2 part npt/eff temp 300.0 300.0 0.1 tri 5.0 5.0 1.0
fix 2 ice nph/eff x 1.0 1.0 0.5 y 2.0 2.0 0.5 z 3.0 3.0 0.5 yz 0.1 0.1 0.5 xz 0.2 0.2 0.5 xy 0.3 0.3 0.5 nreset 1000
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
<p>These commands perform time integration on Nose-Hoover style
non-Hamiltonian equations of motion for nuclei and electrons in the
group for the <a class="reference internal" href="pair_eff.html"><em>electron force field</em></a> model. The fixes
are designed to generate positions and velocities sampled from the
canonical (nvt), isothermal-isobaric (npt), and isenthalpic (nph)
ensembles. This is achieved by adding some dynamic variables which
are coupled to the particle velocities (thermostatting) and simulation
domain dimensions (barostatting). In addition to basic thermostatting
and barostatting, these fixes can also create a chain of thermostats
coupled to the particle thermostat, and another chain of thermostats
coupled to the barostat variables. The barostat can be coupled to the
overall box volume, or to individual dimensions, including the <em>xy</em>,
<em>xz</em> and <em>yz</em> tilt dimensions. The external pressure of the barostat
can be specified as either a scalar pressure (isobaric ensemble) or as
components of a symmetric stress tensor (constant stress ensemble).
When used correctly, the time-averaged temperature and stress tensor
of the particles will match the target values specified by
Tstart/Tstop and Pstart/Pstop.</p>
<p>The operation of these fixes is exactly like that described by the
<a class="reference internal" href="fix_nh.html"><em>fix nvt, npt, and nph</em></a> commands, except that the radius
and radial velocity of electrons are also updated. Likewise the
temperature and pressure calculated by the fix, using the computes it
creates (as discussed in the <a class="reference internal" href="fix_nh.html"><em>fix nvt, npt, and nph</em></a>
doc page), are performed with computes that include the eFF contribution
to the temperature or kinetic energy from the electron radial velocity.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">there are two different pressures that can be reported
for eFF when defining the pair_style (see <code class="xref doc docutils literal"><span class="pre">pair</span> <span class="pre">eff/cut</span></code> to understand these settings), one
(default) that considers electrons do not contribute radial virial
components (i.e. electrons treated as incompressible &#8216;rigid&#8217; spheres)
and one that does. The radial electronic contributions to the virials
are only tallied if the flexible pressure option is set, and this will
affect both global and per-atom quantities. In principle, the true
pressure of a system is somewhere in between the rigid and the
flexible eFF pressures, but, for most cases, the difference between
these two pressures will not be significant over long-term averaged
runs (i.e. even though the energy partitioning changes, the total
energy remains similar).</p>
</div>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">currently, there is no available option for the user
to set or create temperature distributions that include the radial
electronic degrees of freedom with the <a class="reference internal" href="velocity.html"><em>velocity</em></a>
command, so the the user must allow for these degrees of freedom to
equilibrate (i.e. equi-partitioning of energy) through time
integration.</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>See the doc page for the <a class="reference internal" href="fix_nh.html"><em>fix nvt, npt, and nph</em></a> commands
for details.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
<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>
<p>Other restriction discussed on the doc page for the <a class="reference internal" href="fix_nh.html"><em>fix nvt, npt, and nph</em></a> commands also apply.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">The temperature for systems (regions or groups) with
only electrons and no nuclei is 0.0 (i.e. not defined) in the current
temperature calculations, a practical example would be a uniform
electron gas or a very hot plasma, where electrons remain delocalized
from the nuclei. This is because, even though electron virials are
included in the temperature calculation, these are averaged over the
nuclear degrees of freedom only. In such cases a corrective term must
be added to the pressure to get the correct kinetic contribution.</p>
</div>
</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_nh.html"><em>fix nvt</em></a>, <a class="reference internal" href="fix_nh.html"><em>fix nph</em></a>, <a class="reference internal" href="fix_nh.html"><em>fix npt</em></a>,
<a class="reference internal" href="fix_modify.html"><em>fix_modify</em></a>, <a class="reference internal" href="run_style.html"><em>run_style</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 keyword defaults are tchain = 3, pchain = 3, mtk = yes, tloop =
ploop = 1, nreset = 0, drag = 0.0, dilate = all, and couple = none.</p>
<hr class="docutils" />
<p id="martyna"><strong>(Martyna)</strong> Martyna, Tobias and Klein, J Chem Phys, 101, 4177 (1994).</p>
<p id="parrinello"><strong>(Parrinello)</strong> Parrinello and Rahman, J Appl Phys, 52, 7182 (1981).</p>
<p id="tuckerman"><strong>(Tuckerman)</strong> Tuckerman, Alejandre, Lopez-Rendon, Jochim, and
Martyna, J Phys A: Math Gen, 39, 5629 (2006).</p>
<p id="shinoda"><strong>(Shinoda)</strong> Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004).</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