Page MenuHomec4science
Files F90807296

pair_srp.html
No OneTemporary
Actions

File Metadata

Created
Mon, Nov 4, 22:47

pair_srp.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>pair_style srp command &mdash; LAMMPS 15 May 2015 version 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 15 May 2015 version 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>pair_style srp command</li>
<li class="wy-breadcrumbs-aside">
<a href="http://lammps.sandia.gov">Homepage</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="pair-style-srp-command">
<span id="index-0"></span><h1>pair_style srp command<a class="headerlink" href="#pair-style-srp-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>
<p>pair_style srp cutoff bond_type dist keyword value ...</p>
<ul class="simple">
<li>cutoff = global cutoff for SRP interactions (distance units)</li>
<li>bond_type = bond type to apply SRP interactions</li>
<li>distance = <em>min</em> or <em>mid</em></li>
<li>zero or more keyword/value pairs may be appended</li>
<li>keyword = <em>exclude</em></li>
</ul>
<pre class="literal-block">
<em>exclude</em> value = <em>yes</em> or <em>no</em>
</pre>
</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>pair_style hybrid dpd 1.0 1.0 12345 srp 0.8 1 mid exclude yes
pair_coeff 1 1 dpd 60.0 4.5 1.0
pair_coeff 1 2 none
pair_coeff 2 2 srp 100.0 0.8
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>pair_style hybrid dpd 1.0 1.0 12345 srp 0.8 * min exclude yes
pair_coeff 1 1 dpd 60.0 50 1.0
pair_coeff 1 2 none
pair_coeff 2 2 srp 40.0
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>pair_style hybrid srp 0.8 2 mid
pair_coeff 1 1 none
pair_coeff 1 2 none
pair_coeff 2 2 srp 100.0 0.8
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
<p>Style <em>srp</em> computes a soft segmental repulsive potential (SRP) that
acts between pairs of bonds. This potential is useful for preventing
bonds from passing through one another when a soft non-bonded
potential acts between beads in, for example, DPD polymer chains. An
example input script that uses this command is provided in
examples/USER/srp.</p>
<p>Bonds of type <em>btype</em> interact with one another through a
bond-pairwise potential, such that the force on bond <em>i</em> due to bond
<em>j</em> is as follows</p>
<img alt="_images/pair_srp1.jpg" class="align-center" src="_images/pair_srp1.jpg" />
<p>where <em>r</em> and <em>rij</em> are the distance and unit vector between the two
bonds. The bondtype can also be specified as an asterisk (*) and then
this interaction applied to all bonds.
The <em>mid</em> option computes <em>r</em> and <em>rij</em> from the midpoint
distance between bonds. The <em>min</em> option computes <em>r</em> and <em>rij</em> from
the minimum distance between bonds. The force acting on a bond is
mapped onto the two bond atoms according to the lever rule,</p>
<img alt="_images/pair_srp2.jpg" class="align-center" src="_images/pair_srp2.jpg" />
<p>where <em>L</em> is the normalized distance from the atom to the point of
closest approach of bond <em>i</em> and <em>j</em>. The <em>mid</em> option takes <em>L</em> as
0.5 for each interaction as described in <a class="reference internal" href="#sirk"><span>(Sirk)</span></a>.</p>
<p>The following coefficients must be defined via the
<a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command as in the examples above, or in
the data file or restart file read by the <a class="reference internal" href="read_data.html"><em>read_data</em></a>
or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a> commands:</p>
<ul class="simple">
<li><em>C</em> (force units)</li>
<li><em>rc</em> (distance units)</li>
</ul>
<p>The last coefficient is optional. If not specified, the global cutoff
is used.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">Pair style srp considers each bond of type <em>btype</em> as
a fictitious particle of type <em>bptype</em>, where <em>bptype</em> is the largest
atom type in the system. These &#8220;bond particles&#8221; are inserted at the
beginning of the run, and serve as placeholders that define the
position of the bonds. This allows neighbor lists to be constructed
and pairwise interactions to be computed in almost the same way as is
done for point particles. Because bonds interact only with other
bonds, <a class="reference internal" href="pair_hybrid.html"><em>pair_style hybrid</em></a> should be used to turn off
interactions between atom type <em>bptype</em> and all other types of atoms.
An error will be flagged if <a class="reference internal" href="pair_hybrid.html"><em>pair_style hybrid</em></a> is
not used. Further, only bond particles should be given an atom type
of <em>bptype</em>; a check is done at the beginning of the run to ensure
there are no regular atoms of <em>bptype</em>.</p>
</div>
<p>The optional <em>exclude</em> keyword determines if forces are computed
between first neighbor (directly connected) bonds. For a setting of
<em>no</em>, first neighbor forces are computed; for <em>yes</em> they are not computed. A setting of <em>no</em>
cannot be used with the <em>min</em> option for distance calculation because the the minimum distance between
directly connected bonds is zero.</p>
<p>Pair style <em>srp</em> turns off normalization of thermodynamic properties
by particle number, as if the command <a class="reference internal" href="thermo_modify.html"><em>thermo_modify norm no</em></a> had been issued.</p>
<p>The pairwise energy associated with style <em>srp</em> is shifted to be zero
at the cutoff distance <em>rc</em>.</p>
<hr class="docutils" />
<p><strong>Mixing, shift, table, tail correction, restart, rRESPA info</strong>:</p>
<p>This pair styles does not support mixing.</p>
<p>This pair style does not support the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a>
shift option for the energy of the pair interaction. Note that as
discussed above, the energy term is already shifted to be 0.0 at the
cutoff distance <em>rc</em>.</p>
<p>The <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> table option is not relevant for
this pair style.</p>
<p>This pair style does not support the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a>
tail option for adding long-range tail corrections to energy and
pressure.</p>
<p>This pair style writes global and per-atom information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>. Pair srp should be used with <a class="reference internal" href="pair_hybrid.html"><em>pair_style hybrid</em></a>, thus the pair_coeff commands need to be
specified in the input script when reading a restart file.</p>
<p>This pair style can only be used via the <em>pair</em> keyword of the
<a class="reference internal" href="run_style.html"><em>run_style respa</em></a> command. It does not support the
<em>inner</em>, <em>middle</em>, <em>outer</em> keywords.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
<p>This pair style is part of the USER-MISC package. It is only enabled
if LAMMPS was built with that package. See the Making LAMMPS section
for more info.</p>
<p>This pair style must be used with <a class="reference internal" href="pair_hybrid.html"><em>pair_style hybrid</em></a>.</p>
<p>This pair style requires the <a class="reference internal" href="newton.html"><em>newton</em></a> command to be <em>on</em>
for non-bonded interactions.</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="pair_hybrid.html"><em>pair_style hybrid</em></a>, <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a>,
<a class="reference internal" href="pair_dpd.html"><em>pair dpd</em></a></p>
</div>
<div class="section" id="default">
<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline">¶</a></h2>
<p>The default keyword value is exclude = yes.</p>
<hr class="docutils" />
<p id="sirk"><strong>(Sirk)</strong> Sirk TW, Sliozberg YR, Brennan JK, Lisal M, Andzelm JW, J
Chem Phys, 136 (13) 134903, 2012.</p>
</div>
</div>
</div>
</div>
<footer>
<hr/>
<div role="contentinfo">
<p>
&copy; Copyright .
</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:'15 May 2015 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="_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>

Event Timeline

c4science · Help