485 lines
28 KiB
HTML
485 lines
28 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>delete_bonds 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"/>
|
|
<link rel="up" title="Commands" href="commands.html"/>
|
|
<link rel="next" title="dielectric command" href="dielectric.html"/>
|
|
<link rel="prev" title="delete_atoms command" href="delete_atoms.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">
|
|
|
|
|
|
|
|
<p class="caption"><span class="caption-text">User Documentation</span></p>
|
|
<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>
|
|
<p class="caption"><span class="caption-text">Index</span></p>
|
|
<ul class="current">
|
|
<li class="toctree-l1"><a class="reference internal" href="tutorials.html">Tutorials</a></li>
|
|
<li class="toctree-l1 current"><a class="reference internal" href="commands.html">Commands</a><ul class="current">
|
|
<li class="toctree-l2"><a class="reference internal" href="angle_coeff.html">angle_coeff command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="angle_style.html">angle_style command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="atom_modify.html">atom_modify command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="atom_style.html">atom_style command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="balance.html">balance command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="bond_coeff.html">bond_coeff command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="bond_style.html">bond_style command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="bond_write.html">bond_write command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="boundary.html">boundary command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="box.html">box command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="change_box.html">change_box command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="clear.html">clear command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="comm_modify.html">comm_modify command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="comm_style.html">comm_style command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute.html">compute command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="compute_modify.html">compute_modify command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="create_atoms.html">create_atoms command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="create_bonds.html">create_bonds command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="create_box.html">create_box command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="delete_atoms.html">delete_atoms command</a></li>
|
|
<li class="toctree-l2 current"><a class="current reference internal" href="#">delete_bonds command</a><ul>
|
|
<li class="toctree-l3"><a class="reference internal" href="#syntax">Syntax</a></li>
|
|
<li class="toctree-l3"><a class="reference internal" href="#examples">Examples</a></li>
|
|
<li class="toctree-l3"><a class="reference internal" href="#description">Description</a></li>
|
|
<li class="toctree-l3"><a class="reference internal" href="#restrictions">Restrictions</a></li>
|
|
<li class="toctree-l3"><a class="reference internal" href="#related-commands">Related commands</a></li>
|
|
</ul>
|
|
</li>
|
|
<li class="toctree-l2"><a class="reference internal" href="dielectric.html">dielectric command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="dihedral_coeff.html">dihedral_coeff command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="dihedral_style.html">dihedral_style command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="dimension.html">dimension command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="displace_atoms.html">displace_atoms command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="dump.html">dump command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="dump.html#dump-custom-vtk-command"><code class="docutils literal"><span class="pre">dump</span> <span class="pre">custom/vtk</span></code> command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="dump.html#dump-h5md-command"><code class="docutils literal"><span class="pre">dump</span> <span class="pre">h5md</span></code> command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="dump.html#dump-image-command"><code class="docutils literal"><span class="pre">dump</span> <span class="pre">image</span></code> command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="dump.html#dump-movie-command"><code class="docutils literal"><span class="pre">dump</span> <span class="pre">movie</span></code> command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="dump.html#dump-molfile-command"><code class="docutils literal"><span class="pre">dump</span> <span class="pre">molfile</span></code> command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="dump_custom_vtk.html">dump custom/vtk command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="dump_h5md.html">dump h5md command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="dump_image.html">dump image command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="dump_image.html#dump-movie-command">dump movie command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="dump_modify.html">dump_modify command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="dump_molfile.html">dump molfile command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="echo.html">echo command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="fix.html">fix command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="fix_modify.html">fix_modify command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="group.html">group command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="group2ndx.html">group2ndx command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="group2ndx.html#ndx2group-command">ndx2group command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="if.html">if command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="improper_coeff.html">improper_coeff command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="improper_style.html">improper_style command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="include.html">include command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="info.html">info command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="jump.html">jump command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="kspace_modify.html">kspace_modify command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="kspace_style.html">kspace_style command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="label.html">label command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="lattice.html">lattice command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="log.html">log command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="mass.html">mass command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="min_modify.html">min_modify command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="min_style.html">min_style command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="minimize.html">minimize command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="molecule.html">molecule command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="neb.html">neb command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="neigh_modify.html">neigh_modify command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="neighbor.html">neighbor command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="newton.html">newton command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="next.html">next command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="package.html">package command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="pair_coeff.html">pair_coeff command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="pair_modify.html">pair_modify command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="pair_style.html">pair_style command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="pair_write.html">pair_write command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="partition.html">partition command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="prd.html">prd command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="print.html">print command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="processors.html">processors command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="python.html">python command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="quit.html">quit command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="read_data.html">read_data command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="read_dump.html">read_dump command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="read_restart.html">read_restart command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="region.html">region command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="replicate.html">replicate command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="rerun.html">rerun command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="reset_timestep.html">reset_timestep command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="restart.html">restart command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="run.html">run command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="run_style.html">run_style command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="set.html">set command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="shell.html">shell command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="special_bonds.html">special_bonds command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="suffix.html">suffix command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="tad.html">tad command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="temper.html">temper command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="thermo.html">thermo command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="thermo_modify.html">thermo_modify command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="thermo_style.html">thermo_style command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="timer.html">timer command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="timestep.html">timestep command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="uncompute.html">uncompute command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="undump.html">undump command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="unfix.html">unfix command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="units.html">units command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="variable.html">variable command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="velocity.html">velocity command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="write_coeff.html">write_coeff command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="write_data.html">write_data command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="write_dump.html">write_dump command</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="write_restart.html">write_restart command</a></li>
|
|
</ul>
|
|
</li>
|
|
<li class="toctree-l1"><a class="reference internal" href="fixes.html">Fixes</a></li>
|
|
<li class="toctree-l1"><a class="reference internal" href="computes.html">Computes</a></li>
|
|
<li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
|
|
<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
|
|
<li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
|
|
<li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
|
|
<li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</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><a href="commands.html">Commands</a> »</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 class="rst-footer-buttons" style="margin-bottom: 1em" role="navigation" aria-label="footer navigation">
|
|
|
|
<a href="dielectric.html" class="btn btn-neutral float-right" title="dielectric command" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
|
|
|
|
|
|
<a href="delete_atoms.html" class="btn btn-neutral" title="delete_atoms command" accesskey="p"><span class="fa fa-arrow-circle-left"></span> Previous</a>
|
|
|
|
</div>
|
|
|
|
</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</h1>
|
|
<div class="section" id="syntax">
|
|
<h2>Syntax</h2>
|
|
<pre class="literal-block">
|
|
delete_bonds group-ID style arg keyword ...
|
|
</pre>
|
|
<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>
|
|
<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>
|
|
</li>
|
|
<li><p class="first">zero or more keywords may be appended</p>
|
|
</li>
|
|
<li><p class="first">keyword = <em>any</em> or <em>undo</em> or <em>remove</em> or <em>special</em></p>
|
|
</li>
|
|
</ul>
|
|
</div>
|
|
<div class="section" id="examples">
|
|
<h2>Examples</h2>
|
|
<pre class="literal-block">
|
|
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 class="section" id="description">
|
|
<h2>Description</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"><span class="doc">neigh_modify exclude</span></a> command. The
|
|
<a class="reference internal" href="fix_shake.html"><span class="doc">fix shake</span></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 “*” or “*n” or “n*” or
|
|
“m*n”. 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"><span class="doc">bond_style quartic</span></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"><span class="doc">special_bonds</span></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"><span class="doc">fix shake</span></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’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</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"><span class="doc">pair_style</span></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"><span class="doc">fix shake</span></a> command to fail due to an atom’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</h2>
|
|
<p><a class="reference internal" href="neigh_modify.html"><span class="doc">neigh_modify</span></a> exclude,
|
|
<a class="reference internal" href="special_bonds.html"><span class="doc">special_bonds</span></a>, <a class="reference internal" href="fix_shake.html"><span class="doc">fix shake</span></a></p>
|
|
<p><strong>Default:</strong> none</p>
|
|
</div>
|
|
</div>
|
|
|
|
|
|
</div>
|
|
</div>
|
|
<footer>
|
|
|
|
<div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
|
|
|
|
<a href="dielectric.html" class="btn btn-neutral float-right" title="dielectric command" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
|
|
|
|
|
|
<a href="delete_atoms.html" class="btn btn-neutral" title="delete_atoms command" accesskey="p"><span class="fa fa-arrow-circle-left"></span> Previous</a>
|
|
|
|
</div>
|
|
|
|
|
|
<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> |