fix_bond_swap.html
No OneTemporary
Actions

Subscribers

None

File Metadata

Created: Sun, Dec 29, 09:46

fix_bond_swap.html
View Options



	<!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>fix bond/swap 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"/>


	<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 & 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>



	</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>fix bond/swap 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="fix-bond-swap-command">
	<span id="index-0"></span><h1>fix bond/swap command</h1>
	<div class="section" id="syntax">
	<h2>Syntax</h2>
	<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">bond</span><span class="o">/</span><span class="n">swap</span> <span class="n">Nevery</span> <span class="n">fraction</span> <span class="n">cutoff</span> <span class="n">seed</span>
	</pre></div>
	</div>
	<ul class="simple">
	<li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command</li>
	<li>bond/swap = style name of this fix command</li>
	<li>Nevery = attempt bond swapping every this many steps</li>
	<li>fraction = fraction of group atoms to consider for swapping</li>
	<li>cutoff = distance at which swapping will be considered (distance units)</li>
	<li>seed = random # seed (positive integer)</li>
	</ul>
	</div>
	<div class="section" id="examples">
	<h2>Examples</h2>
	<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">bond</span><span class="o">/</span><span class="n">swap</span> <span class="mi">50</span> <span class="mf">0.5</span> <span class="mf">1.3</span> <span class="mi">598934</span>
	</pre></div>
	</div>
	</div>
	<div class="section" id="description">
	<h2>Description</h2>
	<p>In a simulation of polymer chains, this command attempts to swap bonds
	between two different chains, effectively grafting the end of one
	chain onto another chain and vice versa. This is done via Monte Carlo
	rules using the Boltzmann acceptance criterion. The purpose is to
	equilibrate the polymer chain conformations more rapidly than dynamics
	alone would do it, by enabling instantaneous large conformational
	changes in a dense polymer melt. The polymer chains should thus more
	rapidly converge to the proper end-to-end distances and radii of
	gyration. It is designed for use with systems of
	<a class="reference internal" href="bond_fene.html"><span class="doc">FENE</span></a> or <a class="reference internal" href="bond_harmonic.html"><span class="doc">harmonic</span></a> bead-spring
	polymer chains where each polymer is a linear chain of monomers, but
	LAMMPS does not enforce this requirement, i.e. any
	<a class="reference internal" href="bond_style.html"><span class="doc">bond_style</span></a> can be used.</p>
	<p>A schematic of the kinds of bond swaps that can occur is shown here:</p>
	<img alt="_images/bondswap.jpg" class="align-center" src="_images/bondswap.jpg" />
	<p>On the left, the red and blue chains have two monomers A1 and B1 close
	to each other, which are currently bonded to monomers A2 and B2
	respectively within their own chains. The bond swap operation will
	attempt to delete the A1-A2 and B1-B2 bonds and replace them with
	A1-B2 and B1-A2 bonds. If the swap is energetically favorable, the
	two chains on the right are the result and each polymer chain has
	undergone a dramatic conformational change. This reference,
	<a class="reference internal" href="#sides"><span class="std std-ref">(Sides)</span></a> provides more details on how the algorithm works and
	its application:</p>
	<p>The bond swapping operation is invoked every <em>Nevery</em> timesteps. If
	any bond is swapped, a re-build of the neighbor lists is triggered,
	since a swap alters the list of which neighbors are considered for
	pairwise interaction. At each invocation, each processor considers a
	random specified <em>fraction</em> of its atoms as potential swapping
	monomers for this timestep. Choosing a small <em>fraction</em> value can
	reduce the likelihood of a reverse swap occurring soon after an
	initial swap.</p>
	<p>For each monomer A1, its neighbors are examined to find a possible B1
	monomer. Both A1 and B1 must be in the fix group, their separation
	must be less than the specified <em>cutoff</em>, and the molecule IDs of A1
	and B1 must be the same (see below). If a suitable partner is found,
	the energy change due to swapping the 2 bonds is computed. This
	includes changes in pairwise, bond, and angle energies due to the
	altered connectivity of the 2 chains. Dihedral and improper
	interactions are not allowed to be defined when this fix is used.</p>
	<p>If the energy decreases due to the swap operation, the bond swap is
	accepted. If the energy increases it is accepted with probability
	exp(-delta/kT) where delta is the increase in energy, k is the
	Boltzmann constant, and T is the current temperature of the system.
	Whether the swap is accepted or rejected, no other swaps are attempted
	by this processor on this timestep.</p>
	<p>The criterion for matching molecule IDs is how bond swaps performed by
	this fix conserve chain length. To use this features you must setup
	the molecule IDs for your polymer chains in a certain way, typically
	in the data file, read by the <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> comand.
	Consider a system of 6-mer chains. You have 2 choices. If the
	molecule IDs for monomers on each chain are set to 1,2,3,4,5,6 then
	swaps will conserve chain length. For a particular momoner there will
	be only one other monomer on another chain which is a potential swap
	partner. If the molecule IDs for monomers on each chain are set to
	1,2,3,3,2,1 then swaps will conserve chain length but swaps will be
	able to occur at either end of a chain. Thus for a particular monomer
	there will be 2 possible swap partners on another chain. In this
	scenario, swaps can also occur within a single chain, i.e. the two
	ends of a chain swap with each other.</p>
	<div class="admonition note">
	<p class="first admonition-title">Note</p>
	<p class="last">If your simulation uses molecule IDs in the usual way, where all
	monomers on a single chain are assigned the same ID (different for
	each chain), then swaps will only occur within the same chain. If you
	assign the same molecule ID to all monomers in all chains then
	inter-chain swaps will occur, but they will not conserve chain length.
	Neither of these scenarios is probably what you want for this fix.</p>
	</div>
	<div class="admonition note">
	<p class="first admonition-title">Note</p>
	<p class="last">When a bond swap occurs the image flags of monomers in the new
	polymer chains can become inconsistent. See the <a class="reference internal" href="dump.html"><span class="doc">dump</span></a>
	command for a discussion of image flags. This is not an issue for
	running dynamics, but can affect calculation of some diagnostic
	quantities or the printing of unwrapped coordinates to a dump file.</p>
	</div>
	<hr class="docutils" />
	<p>This fix computes a temperature each time it is invoked for use by the
	Boltzmann criterion. To do this, the fix creates its own compute of
	style <em>temp</em>, as if this command had been issued:</p>
	<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_temp</span> <span class="nb">all</span> <span class="n">temp</span>
	</pre></div>
	</div>
	<p>See the <a class="reference internal" href="compute_temp.html"><span class="doc">compute temp</span></a> command for details. Note
	that the ID of the new compute is the fix-ID with underscore + “temp”
	appended and the group for the new compute is “all”, so that the
	temperature of the entire system is used.</p>
	<p>Note that this is NOT the compute used by thermodynamic output (see
	the <a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style</span></a> command) with ID = <em>thermo_temp</em>.
	This means you can change the attributes of this fix’s temperature
	(e.g. its degrees-of-freedom) via the
	<a class="reference internal" href="compute_modify.html"><span class="doc">compute_modify</span></a> command or print this temperature
	during thermodyanmic output via the <a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style custom</span></a> command using the appropriate compute-ID.
	It also means that changing attributes of <em>thermo_temp</em> will have no
	effect on this fix.</p>
	<hr class="docutils" />
	<p><strong>Restart, fix_modify, thermo output, run start/stop, minimize info:</strong></p>
	<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. Because the state of the random number generator
	is not saved in restart files, this means you cannot do “exact”
	restarts with this fix, where the simulation continues on the same as
	if no restart had taken place. However, in a statistical sense, a
	restarted simulation should produce the same behavior. Also note that
	each processor generates possible swaps independently of other
	processors. Thus if you repeat the same simulation on a different number
	of processors, the specific swaps performed will be different.</p>
	<p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>temp</em> option is supported by this
	fix. You can use it to assign a <a class="reference internal" href="compute.html"><span class="doc">compute</span></a> you have
	defined to this fix which will be used to compute the temperature for
	the Boltzmann criterion.</p>
	<p>This fix computes two statistical quantities as a global 2-vector of
	output, which can be accessed by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>. The first component of the
	vector is the cummulative number of swaps performed by all processors.
	The second component of the vector is the cummulative number of swaps
	attempted (whether accepted or rejected). Note that a swap “attempt”
	only occurs when swap partners meeting the criteria described above
	are found on a particular timestep. The vector values calculated by
	this fix are “intensive”.</p>
	<p>No parameter of this fix can be used with the <em>start/stop</em> keywords of
	the <a class="reference internal" href="run.html"><span class="doc">run</span></a> command. This fix is not invoked during <a class="reference internal" href="minimize.html"><span class="doc">energy minimization</span></a>.</p>
	</div>
	<div class="section" id="restrictions">
	<h2>Restrictions</h2>
	<p>This fix is part of the MC package. It is only enabled if LAMMPS was
	built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
	<p>The setings of the “special_bond” command must be 0,1,1 in order to
	use this fix, which is typical of bead-spring chains with FENE or
	harmonic bonds. This means that pairwise interactions between bonded
	atoms are turned off, but are turned on between atoms two or three
	hops away along the chain backbone.</p>
	<p>Currently, energy changes in dihedral and improper interactions due to
	a bond swap are not considered. Thus a simulation that uses this fix
	cannot use a dihedral or improper potential.</p>
	</div>
	<div class="section" id="related-commands">
	<h2>Related commands</h2>
	<p><a class="reference internal" href="fix_atom_swap.html"><span class="doc">fix atom/swap</span></a></p>
	<p><strong>Default:</strong> none</p>
	<hr class="docutils" />
	<p id="sides"><strong>(Sides)</strong> Sides, Grest, Stevens, Plimpton, J Polymer Science B, 42,
	199-208 (2004).</p>
	</div>
	</div>


	</div>
	</div>
	<footer>


	<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>

fix_bond_swap.htmlNo OneTemporaryActions

File Metadata

fix_bond_swap.htmlView Options

Event Timeline

fix_bond_swap.html
No OneTemporary
Actions

fix_bond_swap.html
View Options