forked from lijiext/lammps
310 lines
14 KiB
HTML
310 lines
14 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>compute temp/deform 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>compute temp/deform 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="compute-temp-deform-command">
|
|
<span id="index-0"></span><h1>compute temp/deform command</h1>
|
|
<div class="section" id="syntax">
|
|
<h2>Syntax</h2>
|
|
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">temp</span><span class="o">/</span><span class="n">deform</span>
|
|
</pre></div>
|
|
</div>
|
|
<ul class="simple">
|
|
<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><span class="doc">compute</span></a> command</li>
|
|
<li>temp/deform = style name of this compute command</li>
|
|
</ul>
|
|
</div>
|
|
<div class="section" id="examples">
|
|
<h2>Examples</h2>
|
|
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">myTemp</span> <span class="nb">all</span> <span class="n">temp</span><span class="o">/</span><span class="n">deform</span>
|
|
</pre></div>
|
|
</div>
|
|
</div>
|
|
<div class="section" id="description">
|
|
<h2>Description</h2>
|
|
<p>Define a computation that calculates the temperature of a group of
|
|
atoms, after subtracting out a streaming velocity induced by the
|
|
simulation box changing size and/or shape, for example in a
|
|
non-equilibrium MD (NEMD) simulation. The size/shape change is
|
|
induced by use of the <a class="reference internal" href="fix_deform.html"><span class="doc">fix deform</span></a> command. A compute
|
|
of this style is created by the <a class="reference internal" href="fix_nvt_sllod.html"><span class="doc">fix nvt/sllod</span></a>
|
|
command to compute the thermal temperature of atoms for thermostatting
|
|
purposes. A compute of this style can also be used by any command
|
|
that computes a temperature, e.g. <a class="reference internal" href="thermo_modify.html"><span class="doc">thermo_modify</span></a>,
|
|
<a class="reference internal" href="fix_temp_rescale.html"><span class="doc">fix temp/rescale</span></a>, <a class="reference internal" href="fix_nh.html"><span class="doc">fix npt</span></a>, etc.</p>
|
|
<p>The deformation fix changes the box size and/or shape over time, so
|
|
each atom in the simulation box can be thought of as having a
|
|
“streaming” velocity. For example, if the box is being sheared in x,
|
|
relative to y, then atoms at the bottom of the box (low y) have a
|
|
small x velocity, while atoms at the top of the box (hi y) have a
|
|
large x velocity. This position-dependent streaming velocity is
|
|
subtracted from each atom’s actual velocity to yield a thermal
|
|
velocity which is used to compute the temperature.</p>
|
|
<div class="admonition note">
|
|
<p class="first admonition-title">Note</p>
|
|
<p class="last"><a class="reference internal" href="fix_deform.html"><span class="doc">Fix deform</span></a> has an option for remapping either
|
|
atom coordinates or velocities to the changing simulation box. When
|
|
using this compute in conjunction with a deforming box, fix deform
|
|
should NOT remap atom positions, but rather should let atoms respond
|
|
to the changing box by adjusting their own velocities (or let <a class="reference internal" href="fix_deform.html"><span class="doc">fix deform</span></a> remap the atom velocities, see it’s remap
|
|
option). If fix deform does remap atom positions, then they appear to
|
|
move with the box but their velocity is not changed, and thus they do
|
|
NOT have the streaming velocity assumed by this compute. LAMMPS will
|
|
warn you if fix deform is defined and its remap setting is not
|
|
consistent with this compute.</p>
|
|
</div>
|
|
<p>After the streaming velocity has been subtracted from each atom, the
|
|
temperature is calculated by the formula KE = dim/2 N k T, where KE =
|
|
total kinetic energy of the group of atoms (sum of 1/2 m v^2), dim = 2
|
|
or 3 = dimensionality of the simulation, N = number of atoms in the
|
|
group, k = Boltzmann constant, and T = temperature. Note that v in
|
|
the kinetic energy formula is the atom’s thermal velocity.</p>
|
|
<p>A kinetic energy tensor, stored as a 6-element vector, is also
|
|
calculated by this compute for use in the computation of a pressure
|
|
tensor. The formula for the components of the tensor is the same as
|
|
the above formula, except that v^2 is replaced by vx*vy for the xy
|
|
component, etc. The 6 components of the vector are ordered xx, yy,
|
|
zz, xy, xz, yz.</p>
|
|
<p>The number of atoms contributing to the temperature is assumed to be
|
|
constant for the duration of the run; use the <em>dynamic</em> option of the
|
|
<a class="reference internal" href="compute_modify.html"><span class="doc">compute_modify</span></a> command if this is not the case.</p>
|
|
<p>The removal of the box deformation velocity component by this fix is
|
|
essentially computing the temperature after a “bias” has been removed
|
|
from the velocity of the atoms. If this compute is used with a fix
|
|
command that performs thermostatting then this bias will be subtracted
|
|
from each atom, thermostatting of the remaining thermal velocity will
|
|
be performed, and the bias will be added back in. Thermostatting
|
|
fixes that work in this way include <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a>, <a class="reference internal" href="fix_temp_rescale.html"><span class="doc">fix temp/rescale</span></a>, <a class="reference internal" href="fix_temp_berendsen.html"><span class="doc">fix temp/berendsen</span></a>, and <a class="reference internal" href="fix_langevin.html"><span class="doc">fix langevin</span></a>.</p>
|
|
<div class="admonition note">
|
|
<p class="first admonition-title">Note</p>
|
|
<p class="last">The temperature calculated by this compute is only accurate if
|
|
the atoms are indeed moving with a stream velocity profile that
|
|
matches the box deformation. If not, then the compute will subtract
|
|
off an incorrect stream velocity, yielding a bogus thermal
|
|
temperature. You should NOT assume that your atoms are streaming at
|
|
the same rate the box is deforming. Rather, you should monitor their
|
|
velocity profile, e.g. via the <a class="reference internal" href="fix_ave_spatial.html"><span class="doc">fix ave/spatial</span></a>
|
|
command. And you can compare the results of this compute to <a class="reference internal" href="compute_temp_profile.html"><span class="doc">compute temp/profile</span></a>, which actually calculates the
|
|
stream profile before subtracting it. If the two computes do not give
|
|
roughly the same temperature, then your atoms are not streaming
|
|
consistent with the box deformation. See the <a class="reference internal" href="fix_deform.html"><span class="doc">fix deform</span></a> command for more details on ways to get atoms
|
|
to stream consistently with the box deformation.</p>
|
|
</div>
|
|
<p>This compute subtracts out degrees-of-freedom due to fixes that
|
|
constrain molecular motion, such as <a class="reference internal" href="fix_shake.html"><span class="doc">fix shake</span></a> and
|
|
<a class="reference internal" href="fix_rigid.html"><span class="doc">fix rigid</span></a>. This means the temperature of groups of
|
|
atoms that include these constraints will be computed correctly. If
|
|
needed, the subtracted degrees-of-freedom can be altered using the
|
|
<em>extra</em> option of the <a class="reference internal" href="compute_modify.html"><span class="doc">compute_modify</span></a> command.</p>
|
|
<p>See <a class="reference internal" href="Section_howto.html#howto-16"><span class="std std-ref">this howto section</span></a> of the manual for
|
|
a discussion of different ways to compute temperature and perform
|
|
thermostatting.</p>
|
|
<p><strong>Output info:</strong></p>
|
|
<p>This compute calculates a global scalar (the temperature) and a global
|
|
vector of length 6 (KE tensor), which can be accessed by indices 1-6.
|
|
These values can be used by any command that uses global scalar or
|
|
vector values from a compute as input. See <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">this section</span></a> for an overview of LAMMPS output
|
|
options.</p>
|
|
<p>The scalar value calculated by this compute is “intensive”. The
|
|
vector values are “extensive”.</p>
|
|
<p>The scalar value will be in temperature <a class="reference internal" href="units.html"><span class="doc">units</span></a>. The
|
|
vector values will be in energy <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
|
|
</div>
|
|
<div class="section" id="restrictions">
|
|
<h2>Restrictions</h2>
|
|
<blockquote>
|
|
<div>none</div></blockquote>
|
|
</div>
|
|
<div class="section" id="related-commands">
|
|
<h2>Related commands</h2>
|
|
<p><a class="reference internal" href="compute_temp_ramp.html"><span class="doc">compute temp/ramp</span></a>, <a class="reference internal" href="compute_temp_profile.html"><span class="doc">compute temp/profile</span></a>, <a class="reference internal" href="fix_deform.html"><span class="doc">fix deform</span></a>,
|
|
<a class="reference internal" href="fix_nvt_sllod.html"><span class="doc">fix nvt/sllod</span></a></p>
|
|
<p><strong>Default:</strong> none</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> |