Homec4science
Diffusion lammps (lammps-icms) Browse

lammps/doc/html/pair_multi_lucy_rx.html
db1e17197fcflammps-icms

Last Change
Raw File

pair_multi_lucy_rx.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 multi/lucy/rx 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 multi/lucy/rx 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-multi-lucy-rx-command">
<span id="index-0"></span><h1>pair_style multi/lucy/rx command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
pair_style multi/lucy/rx style N keyword ...
</pre>
<ul class="simple">
<li>style = <em>lookup</em> or <em>linear</em> = method of interpolation</li>
<li>N = use N values in <em>lookup</em>, <em>linear</em> tables</li>
</ul>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
pair_style multi/lucy/rx linear 1000
pair_coeff * * multibody.table ENTRY1 h2o h2o 7.0
pair_coeff * * multibody.table ENTRY1 h2o 1fluid 7.0
</pre>
</div>
<div class="section" id="description">
<h2>Description</h2>
<p>Style <em>multi/lucy/rx</em> is used in reaction DPD simulations, where the
coarse-grained (CG) particles are composed of <em>m</em> species whose
reaction rate kinetics are determined from a set of <em>n</em> reaction rate
equations through the <a class="reference internal" href="fix_rx.html"><span class="doc">fix rx</span></a> command. The species of
one CG particle can interact with a species in a neighboring CG
particle through a site-site interaction potential model. Style
<em>multi/lucy/rx</em> computes the site-site density-dependent force
following from the many-body form described in <a class="reference internal" href="#moore"><span class="std std-ref">(Moore)</span></a> and
<a class="reference internal" href="#warren"><span class="std std-ref">(Warren)</span></a> as</p>
<img alt="_images/pair_multi_lucy.jpg" class="align-center" src="_images/pair_multi_lucy.jpg" />
<p>which consists of a density-dependent function, A(rho), and a
radial-dependent weight function, omegaDD(rij). The radial-dependent
weight function, omegaDD(rij), is taken as the Lucy function:</p>
<img alt="_images/pair_multi_lucy2.jpg" class="align-center" src="_images/pair_multi_lucy2.jpg" />
<p>The density-dependent energy for a given particle is given by:</p>
<img alt="_images/pair_multi_lucy_energy.jpg" class="align-center" src="_images/pair_multi_lucy_energy.jpg" />
<p>See the supporting information of <a class="reference internal" href="#brennan"><span class="std std-ref">(Brennan)</span></a> or the
publication by <a class="reference internal" href="#moore"><span class="std std-ref">(Moore)</span></a> for more details on the functional
form.</p>
<p>An interpolation table is used to evaluate the density-dependent
energy (Integral(A(rho)drho) and force (A(rho)). Note that the
pre-factor to the energy is computed after the interpolation, thus the
Integral(A(rho)drho will have units of energy / length^4.</p>
<p>The interpolation table is created as a pre-computation by fitting
cubic splines to the file values and interpolating the
density-dependent energy and force at each of <em>N</em> densities. During a
simulation, the tables are used to interpolate the density-dependent
energy and force as needed for each pair of particles separated by a
distance <em>R</em>. The interpolation is done in one of 2 styles: <em>lookup</em>
and <em>linear</em>.</p>
<p>For the <em>lookup</em> style, the density is used to find the nearest table
entry, which is the density-dependent energy and force.</p>
<p>For the <em>linear</em> style, the density is used to find the 2 surrounding
table values from which the density-dependent energy and force are
computed by linear interpolation.</p>
<p>The following coefficients must be defined for each pair of atoms
types via the <a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a> command as in the examples
above.</p>
<ul class="simple">
<li>filename</li>
<li>keyword</li>
<li>species1</li>
<li>species2</li>
<li>cutoff (distance units)</li>
</ul>
<p>The filename specifies a file containing the tabulated
density-dependent energy and force. The keyword specifies a section
of the file. The cutoff is an optional coefficient. If not
specified, the outer cutoff in the table itself (see below) will be
used to build an interpolation table that extend to the largest
tabulated distance. If specified, only file values up to the cutoff
are used to create the interpolation table. The format of this file
is described below.</p>
<p>The species tags define the site-site interaction potential between
two species contained within two different particles. The species
tags must either correspond to the species defined in the reaction
kinetics files specified with the <a class="reference internal" href="fix_rx.html"><span class="doc">fix rx</span></a> command or they
must correspond to the tag &#8220;1fluid&#8221;, signifying interaction with a
product species mixture determined through a one-fluid approximation.
The interaction potential is weighted by the geometric average of the
concentrations of the two species. The coarse-grained potential is
stored before and after the reaction kinetics solver is applied, where
the difference is defined to be the internal chemical energy (uChem).</p>
<hr class="docutils" />
<p>The format of a tabulated file is a series of one or more sections,
defined as follows (without the parenthesized comments):</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># Density-dependent function (one or more comment or blank lines)</span>
</pre></div>
</div>
<pre class="literal-block">
DD-FUNCTION (keyword is first text on line)
N 500 R 1.0 10.0 (N, R, RSQ parameters)
(blank)
1 1.0 25.5 102.34 (index, density, energy/r^4, force)
2 1.02 23.4 98.5
...
500 10.0 0.001 0.003
</pre>
<p>A section begins with a non-blank line whose 1st character is not a
&#8220;#&#8221;; blank lines or lines starting with &#8220;#&#8221; can be used as comments
between sections. The first line begins with a keyword which
identifies the section. The line can contain additional text, but the
initial text must match the argument specified in the pair_coeff
command. The next line lists (in any order) one or more parameters
for the table. Each parameter is a keyword followed by one or more
numeric values.</p>
<p>The parameter &#8220;N&#8221; is required and its value is the number of table
entries that follow. Note that this may be different than the <em>N</em>
specified in the <a class="reference internal" href="#"><span class="doc">pair_style multi/lucy/rx</span></a>
command. Let Ntable = <em>N</em> in the pair_style command, and Nfile = &#8220;N&#8221;
in the tabulated file. What LAMMPS does is a preliminary
interpolation by creating splines using the Nfile tabulated values as
nodal points. It uses these to interpolate the density-dependent
energy and force at Ntable different points. The resulting tables of
length Ntable are then used as described above, when computing the
density-dependent energy and force. This means that if you want the
interpolation tables of length Ntable to match exactly what is in the
tabulated file (with effectively no preliminary interpolation), you
should set Ntable = Nfile, and use the &#8220;RSQ&#8221; parameter. This is
because the internal table abscissa is always RSQ (separation distance
squared), for efficient lookup.</p>
<p>All other parameters are optional. If &#8220;R&#8221; or &#8220;RSQ&#8221; does not appear,
then the distances in each line of the table are used as-is to perform
spline interpolation. In this case, the table values can be spaced in
<em>density</em> uniformly or however you wish to position table values in
regions of large gradients.</p>
<p>If used, the parameters &#8220;R&#8221; or &#8220;RSQ&#8221; are followed by 2 values <em>rlo</em>
and <em>rhi</em>. If specified, the density associated with each
density-dependent energy and force value is computed from these 2
values (at high accuracy), rather than using the (low-accuracy) value
listed in each line of the table. The density values in the table
file are ignored in this case. For &#8220;R&#8221;, distances uniformly spaced
between <em>rlo</em> and <em>rhi</em> are computed; for &#8220;RSQ&#8221;, squared distances
uniformly spaced between <em>rlo*rlo</em> and <em>rhi*rhi</em> are computed.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">If you use &#8220;R&#8221; or &#8220;RSQ&#8221;, the tabulated distance values in the
file are effectively ignored, and replaced by new values as described
in the previous paragraph. If the density value in the table is not
very close to the new value (i.e. round-off difference), then you will
be assigning density-dependent energy and force values to a different
density, which is probably not what you want. LAMMPS will warn if
this is occurring.</p>
</div>
<p>Following a blank line, the next N lines list the tabulated values.
On each line, the 1st value is the index from 1 to N, the 2nd value is
r (in density units), the 3rd value is the density-dependent function
value (in energy units / length^4), and the 4th is the force (in force
units). The density values must increase from one line to the next.</p>
<p>Note that one file can contain many sections, each with a tabulated
potential. LAMMPS reads the file section by section until it finds
one that matches the specified keyword.</p>
<hr class="docutils" />
<p><strong>Mixing, shift, table, tail correction, restart, rRESPA info</strong>:</p>
<p>This pair style does not support mixing. Thus, coefficients for all
I,J pairs must be specified explicitly.</p>
<p>The <a class="reference internal" href="pair_modify.html"><span class="doc">pair_modify</span></a> shift, table, and tail options are
not relevant for this pair style.</p>
<p>This pair style writes the settings for the &#8220;pair_style multi/lucy/rx&#8221; command
to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>, so a pair_style command does
not need to specified in an input script that reads a restart file.
However, the coefficient information is not stored in the restart
file, since it is tabulated in the potential files. Thus, pair_coeff
commands do need to be specified in the restart input script.</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"><span class="doc">run_style respa</span></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</h2>
<p>This command is part of the USER-DPD 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>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="warren"><strong>(Warren)</strong> Warren, Phys Rev E, 68, 066702 (2003).</p>
<p id="brennan"><strong>(Brennan)</strong> Brennan, J Chem Phys Lett, 5, 2144-2149 (2014).</p>
<p id="moore"><strong>(Moore)</strong> Moore, J Chem Phys, 144, 104501 (2016).</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