ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14349 f3b2605a-c512-4ea7-a41b-209d697bcdaa

Browse Source
This commit is contained in:
sjplimp
2015-12-10 17:23:56 +00:00
parent 8550cacf18
commit 28bf73fbf7
688 changed files with 6410 additions and 6513 deletions
Download Patch File Download Diff File Expand all files Collapse all files

45
doc/compute_temp_deform.html
View File

@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>compute temp/deform command &mdash; LAMMPS 15 May 2015 version documentation</title>
<title>compute temp/deform command &mdash; LAMMPS 10 Dec 2015 version documentation</title>
@ -32,7 +32,7 @@
<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/>
<link rel="top" title="LAMMPS 10 Dec 2015 version documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
@ -162,19 +162,18 @@ 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&#8217;s actual velocity to yield a thermal
velocity which is used to compute the temperature.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last"><a class="reference internal" href="fix_deform.html"><em>Fix deform</em></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"><em>fix deform</em></a> remap the atom
velocities, see it&#8217;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 class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last"><a class="reference internal" href="fix_deform.html"><em>Fix deform</em></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"><em>fix deform</em></a> remap the atom velocities, see it&#8217;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 =
@ -198,12 +197,12 @@ 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"><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_temp_berendsen.html"><em>fix temp/berendsen</em></a>, and <a class="reference internal" href="fix_langevin.html"><em>fix langevin</em></a>.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</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
<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"><em>fix ave/spatial</em></a>
@ -256,7 +255,7 @@ vector values will be in energy <a class="reference internal" href="units.html">
<div role="contentinfo">
<p>
&copy; Copyright .
&copy; 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>.
@ -277,7 +276,7 @@ vector values will be in energy <a class="reference internal" href="units.html">
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'15 May 2015 version',
VERSION:'10 Dec 2015 version',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true