Homec4science
Diffusion lammps (efficient_neuronet) Browse

lammps/doc/pair_line_lj.html
2f8eae4d354eefficient_neuronet

Last Change
Raw File

pair_line_lj.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 line/lj 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>pair_style line/lj 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="pair-style-line-lj-command">
<span id="index-0"></span><h1>pair_style line/lj command<a class="headerlink" href="#pair-style-line-lj-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>pair_style line/lj cutoff
</pre></div>
</div>
<p>cutoff = global cutoff for interactions (distance units)</p>
</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 line/lj 3.0
pair_coeff * * 1.0 1.0 1.0 0.8 1.12
pair_coeff 1 2 1.0 2.0 1.0 1.5 1.12 5.0
pair_coeff 1 2 1.0 0.0 1.0 1.0 2.5
</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>line/lj</em> treats particles which are line segments as a set of
small spherical particles that tile the line segment length as
explained below. Interactions between two line segments, each with N1
and N2 spherical particles, are calculated as the pairwise sum of
N1*N2 Lennard-Jones interactions. Interactions between a line segment
with N spherical particles and a point particle are treated as the
pairwise sum of N Lennard-Jones interactions. See the <a class="reference internal" href="pair_lj.html"><em>pair_style lj/cut</em></a> doc page for the definition of Lennard-Jones
interactions.</p>
<p>The set of non-overlapping spherical sub-particles that represent a
line segment are generated in the following manner. Their size is a
function of the line segment length and the specified sub-particle
size for that particle type. If a line segment has a length L and is
of type I, then the number of spheres N that represent the segment is
calculated as N = L/sizeI, rounded up to an integer value. Thus if L
is not evenly divisibly by sizeI, N is incremented to include one
extra sphere. The centers of the spheres are spaced equally along the
line segment. Imagine N+1 equally-space points, which include the 2
end points of the segment. The sphere centers are halfway between
each pair of points.</p>
<p>The LJ interaction between 2 spheres on different line segments (or a
sphere on a line segment and a point particles) is computed with
sub-particle epsilon, sigma, and cutoff values that are set by the
pair_coeff command, as described below. If the distance bewteen the 2
spheres is greater than the sub-particle cutoff, there is no
interaction. This means that some pairs of sub-particles on 2 line
segments may interact, but others may not.</p>
<p>For purposes of creating the neighbor list for pairs of interacting
line segments or lines/point particles, a regular particle-particle
cutoff is used, as defined by the <em>cutoff</em> setting above in the
pair_style command or overridden with an optional argument in the
pair_coeff command for a type pair as discussed below. The distance
between the centers of 2 line segments, or the center of a line
segment and a point particle, must be less than this distance (plus
the neighbor skin; see the <a class="reference external" href="neighbor">neighbor</a> command), for the pair
of particles to be included in the neighbor list.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">This means that a too-short value for the <em>cutoff</em> setting can
exclude a pair of particles from the neighbor list even if pairs of
their sub-particle spheres would interact, based on the sub-particle
cutoff specified in the pair_coeff command. E.g. sub-particles at the
ends of the line segments that are close to each other. Which may not
be what you want, since it means the ends of 2 line segments could
pass through each other. It is up to you to specify a <em>cutoff</em>
setting that is consistent with the length of the line segments you
are using and the sub-particle cutoff settings.</p>
</div>
<p>For style <em>line/lj</em>, the following coefficients must be defined for
each pair of atom types 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 files 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>sizeI (distance units)</li>
<li>sizeJ (distance units)</li>
<li>epsilon (energy units)</li>
<li>sigma (distance units)</li>
<li>subcutoff (distance units)</li>
<li>cutoff (distance units)</li>
</ul>
<p>The <em>sizeI</em> and <em>sizeJ</em> coefficients are the sub-particle sizes for
line particles of type I and type J. They are used to define the N
sub-particles per segment as described above. These coefficients are
actually stored on a per-type basis. Thus if there are multiple
pair_coeff commmands that involve type I, as either the first or
second atom type, you should use consistent values for sizeI or sizeJ
in all of them. If you do not do this, the last value specified for
sizeI will apply to all segments of type I. If typeI or typeJ refers
to point particles, the corresponding sizeI or sizeJ is ignored; it
can be set to 0.0.</p>
<p>The <em>epsilon</em>, <em>sigma</em>, and <em>subcutoff</em> coefficients are used to
compute an LJ interactions between a pair of sub-particles on 2 line
segments (of type I and J), or between a sub particle/point particle
pair. As discussed above, the <em>subcutoff</em> and <em>cutoff</em> params are
different. The latter is only used for building the neighbor list
when the distance between centers of two line segments or one segment
and a point particle is calculated.</p>
<p>The <em>cutoff</em> coefficient is optional. If not specified, the global
cutoff is used.</p>
<hr class="docutils" />
<p><strong>Mixing, shift, table, tail correction, restart, rRESPA info</strong>:</p>
<p>For atom type pairs I,J and I != J, coeffiecients must be specified.
No default mixing rules are used.</p>
<p>This pair style does not support the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a>
shift, table, and tail options.</p>
<p>This pair style does not write its information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>.</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 style is part of the ASPHERE package. It is only enabled if
LAMMPS was built with that package. See the <span class="xref std std-ref">Making LAMMPS</span> section for more info.</p>
<p>Defining particles to be line segments so they participate in
line/line or line/particle interactions requires the use the
<a class="reference internal" href="atom_style.html"><em>atom_style line</em></a> command.</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_coeff.html"><em>pair_coeff</em></a>, <a class="reference internal" href="pair_tri_lj.html"><em>pair_style tri/lj</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>
c4science · Help