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

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2015-12-10 17:23:56 +00:00
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doc/compute_hexorder_atom.html
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>compute hexorder/atom command &mdash; LAMMPS 15 May 2015 version documentation</title>
<title>compute hexorder/atom 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>
@ -191,18 +191,18 @@ specified compute group, as well as for atoms that have less than
time the calculation is performed (i.e. each time a snapshot of atoms
is dumped). Thus it can be inefficient to compute/dump this quantity
too frequently.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">If you have a bonded system, then the settings of
<a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a> command can remove pairwise
interactions between atoms in the same bond, angle, or dihedral. This
is the default setting for the <a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a>
command, and means those pairwise interactions do not appear in the
neighbor list. Because this fix uses the neighbor list, it also means
those pairs will not be included in the order parameter. This difficulty
can be circumvented by writing a dump file, and using the
<a class="reference internal" href="rerun.html"><em>rerun</em></a> command to compute the order parameter for snapshots
in the dump file. The rerun script can use a
those pairs will not be included in the order parameter. This
difficulty can be circumvented by writing a dump file, and using the
<a class="reference internal" href="rerun.html"><em>rerun</em></a> command to compute the order parameter for
snapshots in the dump file. The rerun script can use a
<a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a> command that includes all pairs in
the neighbor list.</p>
</div>
@ -241,7 +241,7 @@ options.</p>
<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>.
@ -262,7 +262,7 @@ options.</p>
<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