Homec4science
Diffusion lammps (lammm-master-deprecated) Browse

lammps/doc/html/pair_colloid.html
f876973bcccblammm-master-deprecated

Last Change
Raw File

pair_colloid.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 colloid 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 colloid 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-colloid-command">
<span id="index-0"></span><h1>pair_style colloid command</h1>
</div>
<div class="section" id="pair-style-colloid-gpu-command">
<h1>pair_style colloid/gpu command</h1>
</div>
<div class="section" id="pair-style-colloid-omp-command">
<h1>pair_style colloid/omp command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">colloid</span> <span class="n">cutoff</span>
</pre></div>
</div>
<ul class="simple">
<li>cutoff = global cutoff for colloidal interactions (distance units)</li>
</ul>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">colloid</span> <span class="mf">10.0</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mi">25</span> <span class="mf">1.0</span> <span class="mf">10.0</span> <span class="mf">10.0</span>
<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mi">144</span> <span class="mf">1.0</span> <span class="mf">0.0</span> <span class="mf">0.0</span> <span class="mf">3.0</span>
<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">2</span> <span class="mf">75.398</span> <span class="mf">1.0</span> <span class="mf">0.0</span> <span class="mf">10.0</span> <span class="mf">9.0</span>
<span class="n">pair_coeff</span> <span class="mi">2</span> <span class="mi">2</span> <span class="mf">39.478</span> <span class="mf">1.0</span> <span class="mf">10.0</span> <span class="mf">10.0</span> <span class="mf">25.0</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
<p>Style <em>colloid</em> computes pairwise interactions between large colloidal
particles and small solvent particles using 3 formulas. A colloidal
particle has a size &gt; sigma; a solvent particle is the usual
Lennard-Jones particle of size sigma.</p>
<p>The colloid-colloid interaction energy is given by</p>
<img alt="_images/pair_colloid_cc.jpg" class="align-center" src="_images/pair_colloid_cc.jpg" />
<p>where A_cc is the Hamaker constant, a1 and a2 are the radii of the two
colloidal particles, and Rc is the cutoff. This equation results from
describing each colloidal particle as an integrated collection of
Lennard-Jones particles of size sigma and is derived in
<a class="reference internal" href="pair_resquared.html#everaers"><span class="std std-ref">(Everaers)</span></a>.</p>
<p>The colloid-solvent interaction energy is given by</p>
<img alt="_images/pair_colloid_cs.jpg" class="align-center" src="_images/pair_colloid_cs.jpg" />
<p>where A_cs is the Hamaker constant, a is the radius of the colloidal
particle, and Rc is the cutoff. This formula is derived from the
colloid-colloid interaction, letting one of the particle sizes go to
zero.</p>
<p>The solvent-solvent interaction energy is given by the usual
Lennard-Jones formula</p>
<img alt="_images/pair_colloid_ss.jpg" class="align-center" src="_images/pair_colloid_ss.jpg" />
<p>with A_ss set appropriately, which results from letting both particle
sizes go to zero.</p>
<p>When used in combination with <a class="reference internal" href="#"><span class="doc">pair_style yukawa/colloid</span></a>, the two terms become the so-called
DLVO potential, which combines electrostatic repulsion and van der
Waals attraction.</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, or in the data file or restart files read by the
<a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> or <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a>
commands, or by mixing as described below:</p>
<ul class="simple">
<li>A (energy units)</li>
<li>sigma (distance units)</li>
<li>d1 (distance units)</li>
<li>d2 (distance units)</li>
<li>cutoff (distance units)</li>
</ul>
<p>A is the Hamaker energy prefactor and should typically be set as
follows:</p>
<ul class="simple">
<li>A_cc = colloid/colloid = 4 pi^2 = 39.5</li>
<li>A_cs = colloid/solvent = sqrt(A_cc*A_ss)</li>
<li>A_ss = solvent/solvent = 144 (assuming epsilon = 1, so that 144/36 = 4)</li>
</ul>
<p>Sigma is the size of the solvent particle or the constituent particles
integrated over in the colloidal particle and should typically be set
as follows:</p>
<ul class="simple">
<li>Sigma_cc = colloid/colloid = 1.0</li>
<li>Sigma_cs = colloid/solvent = arithmetic mixing between colloid sigma and solvent sigma</li>
<li>Sigma_ss = solvent/solvent = 1.0 or whatever size the solvent particle is</li>
</ul>
<p>Thus typically Sigma_cs = 1.0, unless the solvent particle&#8217;s size !=
1.0.</p>
<p>D1 and d2 are particle diameters, so that d1 = 2*a1 and d2 = 2*a2 in
the formulas above. Both d1 and d2 must be values &gt;= 0. If d1 &gt; 0
and d2 &gt; 0, then the pair interacts via the colloid-colloid formula
above. If d1 = 0 and d2 = 0, then the pair interacts via the
solvent-solvent formula. I.e. a d value of 0 is a Lennard-Jones
particle of size sigma. If either d1 = 0 or d2 = 0 and the other is
larger, then the pair interacts via the colloid-solvent formula.</p>
<p>Note that the diameter of a particular particle type may appear in
multiple pair_coeff commands, as it interacts with other particle
types. You should insure the particle diameter is specified
consistently each time it appears.</p>
<p>The last coefficient is optional. If not specified, the global cutoff
specified in the pair_style command is used. However, you typically
want different cutoffs for interactions between different particle
sizes. E.g. if colloidal particles of diameter 10 are used with
solvent particles of diameter 1, then a solvent-solvent cutoff of 2.5
would correspond to a colloid-colloid cutoff of 25. A good
rule-of-thumb is to use a colloid-solvent cutoff that is half the big
diameter + 4 times the small diameter. I.e. 9 = 5 + 4 for the
colloid-solvent cutoff in this case.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">When using pair_style colloid for a mixture with 2 (or more)
widely different particles sizes (e.g. sigma=10 colloids in a
background sigma=1 LJ fluid), you will likely want to use these
commands for efficiency: <a class="reference internal" href="neighbor.html"><span class="doc">neighbor multi</span></a> and
<a class="reference internal" href="comm_modify.html"><span class="doc">comm_modify multi</span></a>.</p>
</div>
<hr class="docutils" />
<p>Styles with a <em>gpu</em>, <em>intel</em>, <em>kk</em>, <em>omp</em>, or <em>opt</em> suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed in <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a>
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.</p>
<p>These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. 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>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
more instructions on how to use the accelerated styles effectively.</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, the A, sigma, d1, and d2
coefficients and cutoff distance for this pair style can be mixed. A
is an energy value mixed like a LJ epsilon. D1 and d2 are distance
values and are mixed like sigma. The default mix value is
<em>geometric</em>. See the &#8220;pair_modify&#8221; command for details.</p>
<p>This pair style supports the <a class="reference internal" href="pair_modify.html"><span class="doc">pair_modify</span></a> shift
option for the energy of the pair interaction.</p>
<p>The <a class="reference internal" href="pair_modify.html"><span class="doc">pair_modify</span></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"><span class="doc">pair_modify</span></a>
tail option for adding long-range tail corrections to energy and
pressure.</p>
<p>This pair style writes its information to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads 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"><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 style is part of the COLLOID 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>Normally, this pair style should be used with finite-size particles
which have a diameter, e.g. see the <a class="reference internal" href="atom_style.html"><span class="doc">atom_style sphere</span></a> command. However, this is not a requirement,
since the only definition of particle size is via the pair_coeff
parameters for each type. In other words, the physical radius of the
particle is ignored. Thus you should insure that the d1,d2 parameters
you specify are consistent with the physical size of the particles of
that type.</p>
<p>Per-particle polydispersity is not yet supported by this pair style;
only per-type polydispersity is enabled via the pair_coeff parameters.</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="everaers"><strong>(Everaers)</strong> Everaers, Ejtehadi, Phys Rev E, 67, 041710 (2003).</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