jianmu
/
lammps
forked from lijiext/lammps
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity
lammps/doc/delete_bonds.html

333 lines
14 KiB
HTML
Raw Blame History

<!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>delete_bonds command &mdash; 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 &amp; 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 &amp; 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>
&nbsp;
</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> &raquo;</li>
<li>delete_bonds 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="delete-bonds-command">
<span id="index-0"></span><h1>delete_bonds command<a class="headerlink" href="#delete-bonds-command" title="Permalink to this headline"></a></h1>
<div class="section" id="syntax">
<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>delete_bonds group-ID style arg keyword ...
</pre></div>
</div>
<ul>
<li><p class="first">group-ID = group ID</p>
</li>
<li><dl class="first docutils">
<dt>style = <em>multi</em> or <em>atom</em> or <em>bond</em> or <em>angle</em> or <em>dihedral</em> or</dt>
<dd><p class="first last"><em>improper</em> or <em>stats</em></p>
</dd>
</dl>
</li>
</ul>
<pre class="literal-block">
<em>multi</em> arg = none
<em>atom</em> arg = an atom type or range of types (see below)
<em>bond</em> arg = a bond type or range of types (see below)
<em>angle</em> arg = an angle type or range of types (see below)
<em>dihedral</em> arg = a dihedral type or range of types (see below)
<em>improper</em> arg = an improper type or range of types (see below)
<em>stats</em> arg = none
</pre>
<ul class="simple">
<li>zero or more keywords may be appended</li>
<li>keyword = <em>any</em> or <em>undo</em> or <em>remove</em> or <em>special</em></li>
</ul>
</div>
<div class="section" id="examples">
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>delete_bonds frozen multi remove
delete_bonds all atom 4 special
delete_bonds all bond 0*3 special
delete_bonds all stats
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Turn off (or on) molecular topology interactions, i.e. bonds, angles,
dihedrals, impropers. This command is useful for deleting
interactions that have been previously turned off by bond-breaking
potentials. It is also useful for turning off topology interactions
between frozen or rigid atoms. Pairwise interactions can be turned
off via the <a class="reference internal" href="neigh_modify.html"><em>neigh_modify exclude</em></a> command. The
<a class="reference internal" href="fix_shake.html"><em>fix shake</em></a> command also effectively turns off certain
bond and angle interactions.</p>
<p>For all styles, by default, an interaction is only turned off (or on)
if all the atoms involved are in the specified group. See the <em>any</em>
keyword to change the behavior.</p>
<p>Several of the styles (<em>atom</em>, <em>bond</em>, <em>angle</em>, <em>dihedral</em>,
<em>improper</em>) take a <em>type</em> as an argument. The specified <em>type</em> should
be an integer from 0 to N, where N is the number of relevant types
(atom types, bond types, etc). A value of 0 is only relevant for
style <em>bond</em>; see details below. In all cases, a wildcard asterisk
can be used in place of or in conjunction with the <em>type</em> argument to
specify a range of types. This takes the form &#8220;*&#8221; or &#8220;<em>n&#8221; or &#8220;n</em>&#8221; or
&#8220;m*n&#8221;. If N = the number of types, then an asterisk with no numeric
values means all types from 0 to N. A leading asterisk means all
types from 0 to n (inclusive). A trailing asterisk means all types
from n to N (inclusive). A middle asterisk means all types from m to
n (inclusive). Note that it is fine to include a type of 0 for
non-bond styles; it will simply be ignored.</p>
<p>For style <em>multi</em> all bond, angle, dihedral, and improper interactions
of any type, involving atoms in the group, are turned off.</p>
<p>Style <em>atom</em> is the same as style <em>multi</em> except that in addition, one
or more of the atoms involved in the bond, angle, dihedral, or
improper interaction must also be of the specified atom type.</p>
<p>For style <em>bond</em>, only bonds are candidates for turn-off, and the bond
must also be of the specified type. Styles <em>angle</em>, <em>dihedral</em>, and
<em>improper</em> are treated similarly.</p>
<p>For style <em>bond</em>, you can set the type to 0 to delete bonds that have
been previously broken by a bond-breaking potential (which sets the
bond type to 0 when a bond is broken); e.g. see the <a class="reference internal" href="bond_style.html"><em>bond_style quartic</em></a> command.</p>
<p>For style <em>stats</em> no interactions are turned off (or on); the status
of all interactions in the specified group is simply reported. This
is useful for diagnostic purposes if bonds have been turned off by a
bond-breaking potential during a previous run.</p>
<p>The default behavior of the delete_bonds command is to turn off
interactions by toggling their type to a negative value, but not to
permanently remove the interaction. E.g. a bond_type of 2 is set to
-2. The neighbor list creation routines will not include such an
interaction in their interaction lists. The default is also to not
alter the list of 1-2, 1-3, 1-4 neighbors computed by the
<a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a> command and used to weight pairwise
force and energy calculations. This means that pairwise computations
will proceed as if the bond (or angle, etc) were still turned on.</p>
<p>Several keywords can be appended to the argument list to alter the
default behaviors.</p>
<p>The <em>any</em> keyword changes the requirement that all atoms in the bond
(angle, etc) must be in the specified group in order to turn-off the
interaction. Instead, if any of the atoms in the interaction are in
the specified group, it will be turned off (or on if the <em>undo</em>
keyword is used).</p>
<p>The <em>undo</em> keyword inverts the delete_bonds command so that the
specified bonds, angles, etc are turned on if they are currently
turned off. This means a negative value is toggled to positive. For
example, for style <em>angle</em>, if <em>type</em> is specified as 2, then all
angles with current type = -2, are reset to type = 2. Note that the
<a class="reference internal" href="fix_shake.html"><em>fix shake</em></a> command also sets bond and angle types
negative, so this option should not be used on those interactions.</p>
<p>The <em>remove</em> keyword is invoked at the end of the delete_bonds
operation. It causes turned-off bonds (angles, etc) to be removed
from each atom&#8217;s data structure and then adjusts the global bond
(angle, etc) counts accordingly. Removal is a permanent change;
removed bonds cannot be turned back on via the <em>undo</em> keyword.
Removal does not alter the pairwise 1-2, 1-3, 1-4 weighting list.</p>
<p>The <em>special</em> keyword is invoked at the end of the delete_bonds
operation, after (optional) removal. It re-computes the pairwise 1-2,
1-3, 1-4 weighting list. The weighting list computation treats
turned-off bonds the same as turned-on. Thus, turned-off bonds must
be removed if you wish to change the weighting list.</p>
<p>Note that the choice of <em>remove</em> and <em>special</em> options affects how
1-2, 1-3, 1-4 pairwise interactions will be computed across bonds that
have been modified by the delete_bonds command.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>This command requires inter-processor communication to acquire ghost
atoms, to coordinate the deleting of bonds, angles, etc between atoms
shared by multiple processors. This means that your system must be
ready to perform a simulation before using this command (force fields
setup, atom masses set, etc). Just as would be needed to run
dynamics, the force field you define should define a cutoff
(e.g. through a <a class="reference internal" href="pair_style.html"><em>pair_style</em></a> command) which is long
enough for a processor to acquire the ghost atoms its needs to compute
bond, angle, etc interactions.</p>
<p>If deleted bonds (angles, etc) are removed but the 1-2, 1-3, 1-4
weighting list is not recomputed, this can cause a later <a class="reference internal" href="fix_shake.html"><em>fix shake</em></a> command to fail due to an atom&#8217;s bonds being
inconsistent with the weighting list. This should only happen if the
group used in the fix command includes both atoms in the bond, in
which case you probably should be recomputing the weighting list.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline"></a></h2>
<p><a class="reference internal" href="neigh_modify.html"><em>neigh_modify</em></a> exclude,
<a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a>, <a class="reference internal" href="fix_shake.html"><em>fix shake</em></a></p>
<p><strong>Default:</strong> none</p>
</div>
</div>
</div>
</div>
<footer>
<hr/>
<div role="contentinfo">
<p>
&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>.
</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>
Reference in New Issue View Git Blame Copy Permalink