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2015-12-10 17:23:56 +00:00
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doc/create_atoms.html
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@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>create_atoms command &mdash; LAMMPS 15 May 2015 version documentation</title>
<title>create_atoms 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>
@ -233,14 +233,13 @@ inside the simulation box and is also consistent with the region
volume. See the <a class="reference internal" href="region.html"><em>region</em></a> command for details. Note that
a region can be specified so that its &#8220;volume&#8221; is either inside or
outside a geometric boundary.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">Particles generated by the <em>random</em> style will
typically be highly overlapped which will cause many interatomic
potentials to compute large energies and forces. Thus you should
either perform an <a class="reference internal" href="minimize.html"><em>energy minimization</em></a> or run dynamics
with <a class="reference internal" href="fix_nve_limit.html"><em>fix nve/limit</em></a> to equilibrate such a system,
before running normal dynamics.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">Particles generated by the <em>random</em> style will typically be
highly overlapped which will cause many interatomic potentials to
compute large energies and forces. Thus you should either perform an
<a class="reference internal" href="minimize.html"><em>energy minimization</em></a> or run dynamics with <a class="reference internal" href="fix_nve_limit.html"><em>fix nve/limit</em></a> to equilibrate such a system, before
running normal dynamics.</p>
</div>
<p>Note that this command adds particles to those that already exist.
This means it can be used to add particles to a system previously read
@ -281,15 +280,15 @@ created in parallel.</p>
<p>Also note that because of the random rotations, it may be important to
use a lattice with a large enough spacing that adjacent molecules will
not overlap, regardless of their relative orientations.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">If the <a class="reference internal" href="create_box.html"><em>create_box</em></a> command is used to
create the simulation box, followed by the create_atoms command with
its <em>mol</em> option for adding molecules, then you typically need to use
the optional keywords allowed by the <a class="reference internal" href="create_box.html"><em>create_box</em></a>
command for extra bonds (angles,etc) or extra special neighbors. This
is because by default, the <a class="reference internal" href="create_box.html"><em>create_box</em></a> command sets
up a non-molecular system which doesn&#8217;t allow molecules to be added.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">If the <a class="reference internal" href="create_box.html"><em>create_box</em></a> command is used to create
the simulation box, followed by the create_atoms command with its
<em>mol</em> option for adding molecules, then you typically need to use the
optional keywords allowed by the <a class="reference internal" href="create_box.html"><em>create_box</em></a> command
for extra bonds (angles,etc) or extra special neighbors. This is
because by default, the <a class="reference internal" href="create_box.html"><em>create_box</em></a> command sets up a
non-molecular system which doesn&#8217;t allow molecules to be added.</p>
</div>
<hr class="docutils" />
<p>This is the meaning of the other allowed keywords.</p>
@ -440,7 +439,7 @@ random, and <em>units</em> = lattice.</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>.
@ -461,7 +460,7 @@ random, and <em>units</em> = lattice.</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