Homec4science
Diffusion lammps (efficient_neuronet) Browse

lammps/doc/pair_gayberne.html
311649293d08efficient_neuronet

Last Change
Raw File

pair_gayberne.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 gayberne 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 gayberne 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-gayberne-command">
<span id="index-0"></span><h1>pair_style gayberne command<a class="headerlink" href="#pair-style-gayberne-command" title="Permalink to this headline">¶</a></h1>
</div>
<div class="section" id="pair-style-gayberne-gpu-command">
<h1>pair_style gayberne/gpu command<a class="headerlink" href="#pair-style-gayberne-gpu-command" title="Permalink to this headline">¶</a></h1>
</div>
<div class="section" id="pair-style-gayberne-intel-command">
<h1>pair_style gayberne/intel command<a class="headerlink" href="#pair-style-gayberne-intel-command" title="Permalink to this headline">¶</a></h1>
</div>
<div class="section" id="pair-style-gayberne-omp-command">
<h1>pair_style gayberne/omp command<a class="headerlink" href="#pair-style-gayberne-omp-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 gayberne gamma upsilon mu cutoff
</pre></div>
</div>
<ul class="simple">
<li>gamma = shift for potential minimum (typically 1)</li>
<li>upsilon = exponent for eta orientation-dependent energy function</li>
<li>mu = exponent for chi orientation-dependent energy function</li>
<li>cutoff = global cutoff for interactions (distance units)</li>
</ul>
</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 gayberne 1.0 1.0 1.0 10.0
pair_coeff * * 1.0 1.7 1.7 3.4 3.4 1.0 1.0 1.0
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
<p>The <em>gayberne</em> styles compute a Gay-Berne anisotropic LJ interaction
<a class="reference internal" href="#berardi"><span>(Berardi)</span></a> between pairs of ellipsoidal particles or an
ellipsoidal and spherical particle via the formulas</p>
<img alt="_images/pair_gayberne.jpg" class="align-center" src="_images/pair_gayberne.jpg" />
<p>where A1 and A2 are the transformation matrices from the simulation
box frame to the body frame and r12 is the center to center vector
between the particles. Ur controls the shifted distance dependent
interaction based on the distance of closest approach of the two
particles (h12) and the user-specified shift parameter gamma. When
both particles are spherical, the formula reduces to the usual
Lennard-Jones interaction (see details below for when Gay-Berne treats
a particle as &#8220;spherical&#8221;).</p>
<p>For large uniform molecules it has been shown that the energy
parameters are approximately representable in terms of local contact
curvatures <a class="reference internal" href="pair_resquared.html#everaers"><span>(Everaers)</span></a>:</p>
<img alt="_images/pair_gayberne2.jpg" class="align-center" src="_images/pair_gayberne2.jpg" />
<p>The variable names utilized as potential parameters are for the most
part taken from <a class="reference internal" href="pair_resquared.html#everaers"><span>(Everaers)</span></a> in order to be consistent with
the <a class="reference internal" href="pair_resquared.html"><em>RE-squared pair potential</em></a>. Details on the
upsilon and mu parameters are given
<a class="reference external" href="PDF/pair_resquared_extra.pdf">here</a>.</p>
<p>More details of the Gay-Berne formulation are given in the references
listed below and in <a class="reference external" href="PDF/pair_gayberne_extra.pdf">this supplementary document</a>.</p>
<p>Use of this pair style requires the NVE, NVT, or NPT fixes with the
<em>asphere</em> extension (e.g. <a class="reference internal" href="fix_nve_asphere.html"><em>fix nve/asphere</em></a>) in
order to integrate particle rotation. Additionally, <a class="reference internal" href="atom_style.html"><em>atom_style ellipsoid</em></a> should be used since it defines the
rotational state and the size and shape of each ellipsoidal particle.</p>
<p>The following coefficients must be defined for each pair of atoms
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, or by mixing as described below:</p>
<ul class="simple">
<li>epsilon = well depth (energy units)</li>
<li>sigma = minimum effective particle radii (distance units)</li>
<li>epsilon_i_a = relative well depth of type I for side-to-side interactions</li>
<li>epsilon_i_b = relative well depth of type I for face-to-face interactions</li>
<li>epsilon_i_c = relative well depth of type I for end-to-end interactions</li>
<li>epsilon_j_a = relative well depth of type J for side-to-side interactions</li>
<li>epsilon_j_b = relative well depth of type J for face-to-face interactions</li>
<li>epsilon_j_c = relative well depth of type J for end-to-end interactions</li>
<li>cutoff (distance units)</li>
</ul>
<p>The last coefficient is optional. If not specified, the global
cutoff specified in the pair_style command is used.</p>
<p>It is typical with the Gay-Berne potential to define <em>sigma</em> as the
minimum of the 3 shape diameters of the particles involved in an I,I
interaction, though this is not required. Note that this is a
different meaning for <em>sigma</em> than the <a class="reference internal" href="pair_resquared.html"><em>pair_style resquared</em></a> potential uses.</p>
<p>The epsilon_i and epsilon_j coefficients are actually defined for atom
types, not for pairs of atom types. Thus, in a series of pair_coeff
commands, they only need to be specified once for each atom type.</p>
<p>Specifically, if any of epsilon_i_a, epsilon_i_b, epsilon_i_c are
non-zero, the three values are assigned to atom type I. If all the
epsilon_i values are zero, they are ignored. If any of epsilon_j_a,
epsilon_j_b, epsilon_j_c are non-zero, the three values are assigned
to atom type J. If all three epsilon_j values are zero, they are
ignored. Thus the typical way to define the epsilon_i and epsilon_j
coefficients is to list their values in &#8220;pair_coeff I J&#8221; commands when
I = J, but set them to 0.0 when I != J. If you do list them when I !=
J, you should insure they are consistent with their values in other
pair_coeff commands, since only the last setting will be in effect.</p>
<p>Note that if this potential is being used as a sub-style of
<a class="reference internal" href="pair_hybrid.html"><em>pair_style hybrid</em></a>, and there is no &#8220;pair_coeff I I&#8221;
setting made for Gay-Berne for a particular type I (because I-I
interactions are computed by another hybrid pair potential), then you
still need to insure the epsilon a,b,c coefficients are assigned to
that type. e.g. in a &#8220;pair_coeff I J&#8221; command.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">If the epsilon a = b = c for an atom type, and if the
shape of the particle itself is spherical, meaning its 3 shape
parameters are all the same, then the particle is treated as an LJ
sphere by the Gay-Berne potential. This is significant because if two
LJ spheres interact, then the simple Lennard-Jones formula is used to
compute their interaction energy/force using the specified epsilon and
sigma as the standard LJ parameters. This is much cheaper to compute
than the full Gay-Berne formula. To treat the particle as a LJ sphere
with sigma = D, you should normally set epsilon a = b = c = 1.0, set
the pair_coeff sigma = D, and also set the 3 shape parameters for the
particle to D. The one exception is that if the 3 shape parameters
are set to 0.0, which is a valid way in LAMMPS to specify a point
particle, then the Gay-Berne potential will treat that as shape
parameters of 1.0 (i.e. a LJ particle with sigma = 1), since it
requires finite-size particles. In this case you should still set the
pair_coeff sigma to 1.0 as well.</p>
</div>
<hr class="docutils" />
<p>Styles with a <em>cuda</em>, <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"><em>Section_accelerate</em></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 USER-CUDA, 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>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>-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><em>suffix</em></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></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 epsilon and sigma coefficients
and cutoff distance for this pair style can be mixed. The default mix
value is <em>geometric</em>. See the &#8220;pair_modify&#8221; command for details.</p>
<p>This pair styles supports the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> shift
option for the energy of the Lennard-Jones portion of the pair
interaction, but only for sphere-sphere interactions. There is no
shifting performed for ellipsoidal interactions due to the anisotropic
dependence of the interaction.</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 its information to <a class="reference internal" href="restart.html"><em>binary restart files</em></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"><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>The <em>gayberne</em> style is part of the ASPHERE 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>Making LAMMPS</span></a> section for more info.</p>
<p>These pair style require that atoms store torque and a quaternion to
represent their orientation, as defined by the
<a class="reference internal" href="atom_style.html"><em>atom_style</em></a>. It also require they store a per-type
<code class="xref doc docutils literal"><span class="pre">shape</span></code>. The particles cannot store a per-particle
diameter.</p>
<p>This pair style requires that atoms be ellipsoids as defined by the
<a class="reference internal" href="atom_style.html"><em>atom_style ellipsoid</em></a> command.</p>
<p>Particles acted on by the potential can be finite-size aspherical or
spherical particles, or point particles. Spherical particles have all
3 of their shape parameters equal to each other. Point particles have
all 3 of their shape parameters equal to 0.0.</p>
<p>The Gay-Berne potential does not become isotropic as r increases
<a class="reference internal" href="pair_resquared.html#everaers"><span>(Everaers)</span></a>. The distance-of-closest-approach
approximation used by LAMMPS becomes less accurate when high-aspect
ratio ellipsoids are used.</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="fix_nve_asphere.html"><em>fix nve/asphere</em></a>,
<a class="reference internal" href="compute_temp_asphere.html"><em>compute temp/asphere</em></a>, <a class="reference internal" href="pair_resquared.html"><em>pair_style resquared</em></a></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="everaers"><strong>(Everaers)</strong> Everaers and Ejtehadi, Phys Rev E, 67, 041710 (2003).</p>
<p id="berardi"><strong>(Berardi)</strong> Berardi, Fava, Zannoni, Chem Phys Lett, 297, 8-14 (1998).
Berardi, Muccioli, Zannoni, J Chem Phys, 128, 024905 (2008).</p>
<p id="perram"><strong>(Perram)</strong> Perram and Rasmussen, Phys Rev E, 54, 6565-6572 (1996).</p>
<p id="allen"><strong>(Allen)</strong> Allen and Germano, Mol Phys 104, 3225-3235 (2006).</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="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