forked from lijiext/lammps
345 lines
17 KiB
HTML
345 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 temp/berendsen 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 temp/berendsen 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-temp-berendsen-command">
|
|
<span id="index-0"></span><h1>fix temp/berendsen command<a class="headerlink" href="#fix-temp-berendsen-command" title="Permalink to this headline">¶</a></h1>
|
|
</div>
|
|
<div class="section" id="fix-temp-berendsen-cuda-command">
|
|
<h1>fix temp/berendsen/cuda command<a class="headerlink" href="#fix-temp-berendsen-cuda-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 temp/berendsen Tstart Tstop Tdamp
|
|
</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>temp/berendsen = style name of this fix command</li>
|
|
<li>Tstart,Tstop = desired temperature at start/end of run</li>
|
|
</ul>
|
|
<div class="highlight-python"><div class="highlight"><pre>Tstart can be a variable (see below)
|
|
</pre></div>
|
|
</div>
|
|
<ul class="simple">
|
|
<li>Tdamp = temperature damping parameter (time units)</li>
|
|
</ul>
|
|
</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 temp/berendsen 300.0 300.0 100.0
|
|
</pre></div>
|
|
</div>
|
|
</div>
|
|
<div class="section" id="description">
|
|
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
|
|
<p>Reset the temperature of a group of atoms by using a Berendsen
|
|
thermostat <a class="reference internal" href="#berendsen"><span>(Berendsen)</span></a>, which rescales their velocities
|
|
every timestep.</p>
|
|
<p>The thermostat is applied to only the translational degrees of freedom
|
|
for the particles, which is an important consideration for finite-size
|
|
particles which have rotational degrees of freedom are being
|
|
thermostatted with this fix. The translational degrees of freedom can
|
|
also have a bias velocity removed from them before thermostatting
|
|
takes place; see the description below.</p>
|
|
<p>The desired temperature at each timestep is a ramped value during the
|
|
run from <em>Tstart</em> to <em>Tstop</em>. The <em>Tdamp</em> parameter is specified in
|
|
time units and determines how rapidly the temperature is relaxed. For
|
|
example, a value of 100.0 means to relax the temperature in a timespan
|
|
of (roughly) 100 time units (tau or fmsec or psec - see the
|
|
<a class="reference internal" href="units.html"><em>units</em></a> command).</p>
|
|
<p><em>Tstart</em> can be specified as an equal-style <a class="reference internal" href="variable.html"><em>variable</em></a>.
|
|
In this case, the <em>Tstop</em> setting is ignored. If the value is a
|
|
variable, it should be specified as v_name, where name is the variable
|
|
name. In this case, the variable will be evaluated each timestep, and
|
|
its value used to determine the target temperature.</p>
|
|
<p>Equal-style variables can specify formulas with various mathematical
|
|
functions, and include <a class="reference internal" href="thermo_style.html"><em>thermo_style</em></a> command
|
|
keywords for the simulation box parameters and timestep and elapsed
|
|
time. Thus it is easy to specify a time-dependent temperature.</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 velocities to effect
|
|
thermostatting. Thus you must use a separate time integration fix,
|
|
like <a class="reference internal" href="fix_nve.html"><em>fix nve</em></a> to actually update the positions of atoms
|
|
using the modified velocities. Likewise, this fix should not normally
|
|
be used on atoms that also have their temperature controlled by
|
|
another fix - e.g. by <a class="reference internal" href="fix_nh.html"><em>fix nvt</em></a> or <a class="reference internal" href="fix_langevin.html"><em>fix langevin</em></a> commands.</p>
|
|
</div>
|
|
<p>See <a class="reference internal" href="Section_howto.html#howto-16"><span>this howto section</span></a> of the manual for
|
|
a discussion of different ways to compute temperature and perform
|
|
thermostatting.</p>
|
|
<p>This fix computes a temperature each timestep. To do this, the fix
|
|
creates its own compute of style “temp”, as if this command had been
|
|
issued:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>compute fix-ID_temp group-ID temp
|
|
</pre></div>
|
|
</div>
|
|
<p>See the <a class="reference internal" href="compute_temp.html"><em>compute temp</em></a> command for details. Note
|
|
that the ID of the new compute is the fix-ID + underscore + “temp”,
|
|
and the group for the new compute is the same as the fix group.</p>
|
|
<p>Note that this is NOT the compute used by thermodynamic output (see
|
|
the <a class="reference internal" href="thermo_style.html"><em>thermo_style</em></a> command) with ID = <em>thermo_temp</em>.
|
|
This means you can change the attributes of this fix’s temperature
|
|
(e.g. its degrees-of-freedom) via the
|
|
<a class="reference internal" href="compute_modify.html"><em>compute_modify</em></a> command or print this temperature
|
|
during thermodynamic output via the <a class="reference internal" href="thermo_style.html"><em>thermo_style custom</em></a> command using the appropriate compute-ID.
|
|
It also means that changing attributes of <em>thermo_temp</em> will have no
|
|
effect on this fix.</p>
|
|
<p>Like other fixes that perform thermostatting, this fix can be used
|
|
with <a class="reference internal" href="compute.html"><em>compute commands</em></a> that calculate a temperature
|
|
after removing a “bias” from the atom velocities. E.g. removing the
|
|
center-of-mass velocity from a group of atoms or only calculating
|
|
temperature on the x-component of velocity or only calculating
|
|
temperature for atoms in a geometric region. This is not done by
|
|
default, but only if the <a class="reference internal" href="fix_modify.html"><em>fix_modify</em></a> command is used
|
|
to assign a temperature compute to this fix that includes such a bias
|
|
term. See the doc pages for individual <a class="reference internal" href="compute.html"><em>compute commands</em></a> to determine which ones include a bias. In
|
|
this case, the thermostat works in the following manner: the current
|
|
temperature is calculated taking the bias into account, bias is
|
|
removed from each atom, thermostatting is performed on the remaining
|
|
thermal degrees of freedom, and the bias is added back in.</p>
|
|
<hr class="docutils" />
|
|
<p>Styles with a <em>cuda</em> suffix are functionally the same as the
|
|
corresponding style without the suffix. They have been optimized to
|
|
run faster, depending on your available hardware, as discussed in
|
|
<a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a> of the manual. The
|
|
accelerated styles take the same arguments and should produce the same
|
|
results, except for round-off and precision issues.</p>
|
|
<p>These accelerated styles are part of the USER-CUDA package. They are
|
|
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>You can specify the accelerated styles explicitly in your input script
|
|
by including their suffix, or you can use the <a class="reference internal" href="Section_start.html#start-7"><span>-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
|
|
use the <a class="reference internal" href="suffix.html"><em>suffix</em></a> command in your input script.</p>
|
|
<p>See <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a> of the manual for
|
|
more instructions on how to use the accelerated styles effectively.</p>
|
|
</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<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>The <a class="reference internal" href="fix_modify.html"><em>fix_modify</em></a> <em>temp</em> option is supported by this
|
|
fix. You can use it to assign a temperature <a class="reference internal" href="compute.html"><em>compute</em></a>
|
|
you have defined to this fix which will be used in its thermostatting
|
|
procedure, as described above. For consistency, the group used by
|
|
this fix and by the compute should be the same.</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 change implied by a velocity rescaling to the
|
|
system’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 which can be accessed by various
|
|
<a class="reference internal" href="Section_howto.html#howto-15"><span>output commands</span></a>. The scalar is the
|
|
cummulative energy change due to this fix. The scalar value
|
|
calculated by this fix is “extensive”.</p>
|
|
<p>This fix can ramp its target temperature over multiple runs, using the
|
|
<em>start</em> and <em>stop</em> keywords of the <a class="reference internal" href="run.html"><em>run</em></a> command. See the
|
|
<a class="reference internal" href="run.html"><em>run</em></a> command for details of how to do this.</p>
|
|
<p>This fix is not invoked during <a class="reference internal" href="minimize.html"><em>energy minimization</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 fix can be used with dynamic groups as defined by the
|
|
<a class="reference internal" href="group.html"><em>group</em></a> command. Likewise it can be used with groups to
|
|
which atoms are added or deleted over time, e.g. a deposition
|
|
simulation. However, the conservation properties of the thermostat
|
|
and barostat are defined for systems with a static set of atoms. You
|
|
may observe odd behavior if the atoms in a group vary dramatically
|
|
over time or the atom count becomes very small.</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_nve.html"><em>fix nve</em></a>, <a class="reference internal" href="fix_nh.html"><em>fix nvt</em></a>, <a class="reference internal" href="fix_temp_rescale.html"><em>fix temp/rescale</em></a>, <a class="reference internal" href="fix_langevin.html"><em>fix langevin</em></a>,
|
|
<a class="reference internal" href="fix_modify.html"><em>fix_modify</em></a>, <a class="reference internal" href="compute_temp.html"><em>compute temp</em></a>,
|
|
<a class="reference internal" href="fix_press_berendsen.html"><em>fix press/berendsen</em></a></p>
|
|
<p><strong>Default:</strong> none</p>
|
|
<hr class="docutils" />
|
|
<p id="berendsen"><strong>(Berendsen)</strong> Berendsen, Postma, van Gunsteren, DiNola, Haak, J Chem
|
|
Phys, 81, 3684 (1984).</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> |