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>compute temp/profile 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/profile 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-profile-command">
|
|
<span id="index-0"></span><h1>compute temp/profile 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">profile</span> <span class="n">xflag</span> <span class="n">yflag</span> <span class="n">zflag</span> <span class="n">binstyle</span> <span class="n">args</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/profile = style name of this compute command</li>
|
|
<li>xflag,yflag,zflag = 0/1 for whether to exclude/include this dimension</li>
|
|
<li>binstyle = <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>xyz</em></li>
|
|
</ul>
|
|
<pre class="literal-block">
|
|
<em>x</em> arg = Nx
|
|
<em>y</em> arg = Ny
|
|
<em>z</em> arg = Nz
|
|
<em>xy</em> args = Nx Ny
|
|
<em>yz</em> args = Ny Nz
|
|
<em>xz</em> args = Nx Nz
|
|
<em>xyz</em> args = Nx Ny Nz
|
|
Nx,Ny,Nz = number of velocity bins in x,y,z dimensions
|
|
</pre>
|
|
<ul class="simple">
|
|
<li>zero or more keyword/value pairs may be appended</li>
|
|
<li>keyword = <em>out</em></li>
|
|
</ul>
|
|
<pre class="literal-block">
|
|
<em>out</em> value = <em>tensor</em> or <em>bin</em>
|
|
</pre>
|
|
</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="n">flow</span> <span class="n">temp</span><span class="o">/</span><span class="n">profile</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mi">1</span> <span class="n">x</span> <span class="mi">10</span>
|
|
<span class="n">compute</span> <span class="n">myTemp</span> <span class="n">flow</span> <span class="n">temp</span><span class="o">/</span><span class="n">profile</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mi">1</span> <span class="n">x</span> <span class="mi">10</span> <span class="n">out</span> <span class="nb">bin</span>
|
|
<span class="n">compute</span> <span class="n">myTemp</span> <span class="n">flow</span> <span class="n">temp</span><span class="o">/</span><span class="n">profile</span> <span class="mi">0</span> <span class="mi">1</span> <span class="mi">1</span> <span class="n">xyz</span> <span class="mi">20</span> <span class="mi">20</span> <span class="mi">20</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 spatially-averaged center-of-mass
|
|
velocity field, before computing the kinetic energy. This can be
|
|
useful for thermostatting a collection of atoms undergoing a complex
|
|
flow, e.g. via a profile-unbiased thermostat (PUT) as described in
|
|
<a class="reference internal" href="fix_nvt_sllod.html#evans"><span class="std std-ref">(Evans)</span></a>. A compute of this style can 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 <em>xflag</em>, <em>yflag</em>, <em>zflag</em> settings determine which components of
|
|
average velocity are subtracted out.</p>
|
|
<p>The <em>binstyle</em> setting and its <em>Nx</em>, <em>Ny</em>, <em>Nz</em> arguments determine
|
|
how bins are setup to perform spatial averaging. “Bins” can be 1d
|
|
slabs, 2d pencils, or 3d bricks depending on which <em>binstyle</em> is used.
|
|
The simulation box is partitioned conceptually into <em>Nx</em> by <em>Ny</em> by
|
|
<em>Nz</em> bins. Depending on the <em>binstyle</em>, you may only specify one or
|
|
two of these values; the others are effectively set to 1 (no binning
|
|
in that dimension). For non-orthogonal (triclinic) simulation boxes,
|
|
the bins are “tilted” slabs or pencils or bricks that are parallel to
|
|
the tilted faces of the box. See the <a class="reference internal" href="region.html"><span class="doc">region prism</span></a>
|
|
command for a discussion of the geometry of tilted boxes in LAMMPS.</p>
|
|
<p>When a temperature is computed, the center-of-mass velocity for the
|
|
set of atoms that are both in the compute group and in the same
|
|
spatial bin is calculated. This bias velocity is then subtracted from
|
|
the velocities of individual atoms in the bin to yield a thermal
|
|
velocity for each atom. Note that if there is only one atom in the
|
|
bin, its thermal velocity will thus be 0.0.</p>
|
|
<p>After the spatially-averaged velocity field has been subtracted from
|
|
each atom, the temperature is calculated by the formula KE = (dim/2 N
|
|
- dim*Nx*Ny*Nz) 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. The dim*Nx*Ny*Nz term are degrees of freedom
|
|
subtracted to adjust for the removal of the center-of-mass velocity in
|
|
each of Nx*Ny*Nz bins, as discussed in the <a class="reference internal" href="fix_nvt_sllod.html#evans"><span class="std std-ref">(Evans)</span></a> paper.</p>
|
|
<p>If the <em>out</em> keyword is used with a <em>tensor</em> value, which is the
|
|
default, 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>If the <em>out</em> keyword is used with a <em>bin</em> value, the count of atoms
|
|
and computed temperature for each bin are stored for output, as an
|
|
array of values, as described below. The temperature of each bin is
|
|
calculated as described above, where the bias velocity is subtracted
|
|
and only the remaining thermal velocity of atoms in the bin
|
|
contributes to the temperature. See the note below for how the
|
|
temperature is normalized by the degrees-of-freedom of atoms in the
|
|
bin.</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 spatially-averaged velocity field 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>
|
|
<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>
|
|
<div class="admonition note">
|
|
<p class="first admonition-title">Note</p>
|
|
<p class="last">When using the <em>out</em> keyword with a value of <em>bin</em>, the
|
|
calculated temperature for each bin does not include the
|
|
degrees-of-freedom adjustment described in the preceeding paragraph,
|
|
for fixes that constrain molecular motion. It does include the
|
|
adjustment due to the <em>extra</em> option, which is applied to each bin.</p>
|
|
</div>
|
|
<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. Using this compute in conjunction with a
|
|
thermostatting fix, as explained there, will effectively implement a
|
|
profile-unbiased thermostat (PUT), as described in <a class="reference internal" href="fix_nvt_sllod.html#evans"><span class="std std-ref">(Evans)</span></a>.</p>
|
|
<p><strong>Output info:</strong></p>
|
|
<p>This compute calculates a global scalar (the temperature). Depending
|
|
on the setting of the <em>out</em> keyword, it also calculates a global
|
|
vector or array. For <em>out</em> = <em>tensor</em>, it calculates a vector of
|
|
length 6 (KE tensor), which can be accessed by indices 1-6. For <em>out</em>
|
|
= <em>bin</em> it calculates a global array which has 2 columns and N rows,
|
|
where N is the number of bins. The first column contains the number
|
|
of atoms in that bin. The second contains the temperature of that
|
|
bin, calculated as described above. The ordering of rows in the array
|
|
is as follows. Bins in x vary fastest, then y, then z. Thus for a
|
|
10x10x10 3d array of bins, there will be 1000 rows. The bin with
|
|
indices ix,iy,iz = 2,3,4 would map to row M = (iz-1)*10*10 + (iy-1)*10
|
|
+ ix = 322, where the rows are numbered from 1 to 1000 and the bin
|
|
indices are numbered from 1 to 10 in each dimension.</p>
|
|
<p>These values can be used by any command that uses global scalar or
|
|
vector or array 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”. The array values are “intensive”.</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>. The first column
|
|
of array values are counts; the values in the second column will be in
|
|
temperature <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
|
|
</div>
|
|
<div class="section" id="restrictions">
|
|
<h2>Restrictions</h2>
|
|
<p>You should not use too large a velocity-binning grid, especially in
|
|
3d. In the current implementation, the binned velocity averages are
|
|
summed across all processors, so this will be inefficient if the grid
|
|
is too large, and the operation is performed every timestep, as it
|
|
will be for most thermostats.</p>
|
|
</div>
|
|
<div class="section" id="related-commands">
|
|
<h2>Related commands</h2>
|
|
<p><a class="reference internal" href="compute_temp.html"><span class="doc">compute temp</span></a>, <a class="reference internal" href="compute_temp_ramp.html"><span class="doc">compute temp/ramp</span></a>, <a class="reference internal" href="compute_temp_deform.html"><span class="doc">compute temp/deform</span></a>, <a class="reference internal" href="compute_pressure.html"><span class="doc">compute pressure</span></a></p>
|
|
</div>
|
|
<div class="section" id="default">
|
|
<h2>Default</h2>
|
|
<p>The option default is out = tensor.</p>
|
|
<hr class="docutils" />
|
|
<p id="evans"><strong>(Evans)</strong> Evans and Morriss, Phys Rev Lett, 56, 2172-2175 (1986).</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> |