Homec4science
Diffusion lammps (efficient_neuronet) Browse

lammps/doc/html/pair_airebo.html
7baaf2dfe210efficient_neuronet

Last Change
Raw File

pair_airebo.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 airebo 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 airebo 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-airebo-command">
<span id="index-0"></span><h1>pair_style airebo command</h1>
</div>
<div class="section" id="pair-style-airebo-omp-command">
<h1>pair_style airebo/omp command</h1>
</div>
<div class="section" id="pair-style-airebo-morse-command">
<h1>pair_style airebo/morse command</h1>
</div>
<div class="section" id="pair-style-airebo-morse-omp-command">
<h1>pair_style airebo/morse/omp command</h1>
</div>
<div class="section" id="pair-style-rebo-command">
<h1>pair_style rebo command</h1>
</div>
<div class="section" id="pair-style-rebo-omp-command">
<h1>pair_style rebo/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">style</span> <span class="n">cutoff</span> <span class="n">LJ_flag</span> <span class="n">TORSION_flag</span>
</pre></div>
</div>
<ul class="simple">
<li>style = <em>airebo</em> or <em>airebo/morse</em> or <em>rebo</em></li>
<li>cutoff = LJ or Morse cutoff (sigma scale factor) (AIREBO and AIREBO-M only)</li>
<li>LJ_flag = 0/1 to turn off/on the LJ or Morse term (AIREBO and AIREBO-M only, optional)</li>
<li>TORSION_flag = 0/1 to turn off/on the torsion term (AIREBO and AIREBO-M only, optional)</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">airebo</span> <span class="mf">3.0</span>
<span class="n">pair_style</span> <span class="n">airebo</span> <span class="mf">2.5</span> <span class="mi">1</span> <span class="mi">0</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="o">../</span><span class="n">potentials</span><span class="o">/</span><span class="n">CH</span><span class="o">.</span><span class="n">airebo</span> <span class="n">H</span> <span class="n">C</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">airebo</span><span class="o">/</span><span class="n">morse</span> <span class="mf">3.0</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="o">../</span><span class="n">potentials</span><span class="o">/</span><span class="n">CH</span><span class="o">.</span><span class="n">airebo</span><span class="o">-</span><span class="n">m</span> <span class="n">H</span> <span class="n">C</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">rebo</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="o">../</span><span class="n">potentials</span><span class="o">/</span><span class="n">CH</span><span class="o">.</span><span class="n">airebo</span> <span class="n">H</span> <span class="n">C</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
<p>The <em>airebo</em> pair style computes the Adaptive Intermolecular Reactive
Empirical Bond Order (AIREBO) Potential of <a class="reference internal" href="#stuart"><span class="std std-ref">(Stuart)</span></a> for a
system of carbon and/or hydrogen atoms. Note that this is the initial
formulation of AIREBO from 2000, not the later formulation.</p>
<p>The <em>airebo/morse</em> pair style computes the AIREBO-M potential, which
is equivalent to AIREBO, but replaces the LJ term with a Morse potential.
The Morse potentials are parameterized by high-quality quantum chemistry
(MP2) calculations and do not diverge as quickly as particle density
increases. This allows AIREBO-M to retain accuracy to much higher pressures
than AIREBO (up to 40 GPa for Polyethylene). Details for this potential
and its parameterization are given in <a class="reference internal" href="#oconnor"><span class="std std-ref">(O&#8217;Conner)</span></a>.</p>
<p>The <em>rebo</em> pair style computes the Reactive Empirical Bond Order (REBO)
Potential of <a class="reference internal" href="#brenner"><span class="std std-ref">(Brenner)</span></a>. Note that this is the so-called
2nd generation REBO from 2002, not the original REBO from 1990.
As discussed below, 2nd generation REBO is closely related to the
intial AIREBO; it is just a subset of the potential energy terms.</p>
<p>The AIREBO potential consists of three terms:</p>
<img alt="_images/pair_airebo.jpg" class="align-center" src="_images/pair_airebo.jpg" />
<p>By default, all three terms are included. For the <em>airebo</em> style, if
the two optional flag arguments to the pair_style command are
included, the LJ and torsional terms can be turned off. Note that
both or neither of the flags must be included. If both of the LJ an
torsional terms are turned off, it becomes the 2nd-generation REBO
potential, with a small caveat on the spline fitting procedure
mentioned below. This can be specified directly as pair_style <em>rebo</em>
with no additional arguments.</p>
<p>The detailed formulas for this potential are given in
<a class="reference internal" href="#stuart"><span class="std std-ref">(Stuart)</span></a>; here we provide only a brief description.</p>
<p>The E_REBO term has the same functional form as the hydrocarbon REBO
potential developed in <a class="reference internal" href="#brenner"><span class="std std-ref">(Brenner)</span></a>. The coefficients for
E_REBO in AIREBO are essentially the same as Brenner&#8217;s potential, but
a few fitted spline values are slightly different. For most cases the
E_REBO term in AIREBO will produce the same energies, forces and
statistical averages as the original REBO potential from which it was
derived. The E_REBO term in the AIREBO potential gives the model its
reactive capabilities and only describes short-ranged C-C, C-H and H-H
interactions (r &lt; 2 Angstroms). These interactions have strong
coordination-dependence through a bond order parameter, which adjusts
the attraction between the I,J atoms based on the position of other
nearby atoms and thus has 3- and 4-body dependence.</p>
<p>The E_LJ term adds longer-ranged interactions (2 &lt; r &lt; cutoff) using a
form similar to the standard <a class="reference internal" href="pair_lj.html"><span class="doc">Lennard Jones potential</span></a>.
The E_LJ term in AIREBO contains a series of switching functions so
that the short-ranged LJ repulsion (1/r^12) does not interfere with
the energetics captured by the E_REBO term. The extent of the E_LJ
interactions is determined by the <em>cutoff</em> argument to the pair_style
command which is a scale factor. For each type pair (C-C, C-H, H-H)
the cutoff is obtained by multiplying the scale factor by the sigma
value defined in the potential file for that type pair. In the
standard AIREBO potential, sigma_CC = 3.4 Angstroms, so with a scale
factor of 3.0 (the argument in pair_style), the resulting E_LJ cutoff
would be 10.2 Angstroms.</p>
<p>The E_TORSION term is an explicit 4-body potential that describes
various dihedral angle preferences in hydrocarbon configurations.</p>
<hr class="docutils" />
<p>Only a single pair_coeff command is used with the <em>airebo</em>, <em>airebo</em>
or <em>rebo</em> style which specifies an AIREBO or AIREBO-M potential file
with parameters for C and H. Note that the <em>rebo</em> style in LAMMPS
uses the same AIREBO-formatted potential file. These are mapped to
LAMMPS atom types by specifying N additional arguments after the
filename in the pair_coeff command, where N is the number of LAMMPS
atom types:</p>
<ul class="simple">
<li>filename</li>
<li>N element names = mapping of AIREBO elements to atom types</li>
</ul>
<p>See the <a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a> doc page for alternate ways
to specify the path for the potential file.</p>
<p>As an example, if your LAMMPS simulation has 4 atom types and you want
the 1st 3 to be C, and the 4th to be H, you would use the following
pair_coeff command:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">CH</span><span class="o">.</span><span class="n">airebo</span> <span class="n">C</span> <span class="n">C</span> <span class="n">C</span> <span class="n">H</span>
</pre></div>
</div>
<p>The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
The first three C arguments map LAMMPS atom types 1,2,3 to the C
element in the AIREBO file. The final H argument maps LAMMPS atom
type 4 to the H element in the SW file. If a mapping value is
specified as NULL, the mapping is not performed. This can be used
when a <em>airebo</em> potential is used as part of the <em>hybrid</em> pair style.
The NULL values are placeholders for atom types that will be used with
other potentials.</p>
<p>The parameters/coefficients for the AIREBO potentials are listed in
the CH.airebo file to agree with the original <a class="reference internal" href="#stuart"><span class="std std-ref">(Stuart)</span></a>
paper. Thus the parameters are specific to this potential and the way
it was fit, so modifying the file should be done cautiously.</p>
<p>Similarly the parameters/coefficients for the AIREBO-M potentials are
listed in the CH.airebo-m file to agree with the <a class="reference internal" href="#oconnor"><span class="std std-ref">(O&#8217;Connor)</span></a>
paper. Thus the parameters are specific to this potential and the way
it was fit, so modifying the file should be done cautiously. The
AIREBO-M Morse potentials were parameterized using a cutoff of
3.0 (sigma). Modifying this cutoff may impact simulation accuracy.</p>
<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"><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 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 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>These pair styles do not support the <a class="reference internal" href="pair_modify.html"><span class="doc">pair_modify</span></a>
mix, shift, table, and tail options.</p>
<p>These pair styles do not write their information to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>, since it is stored in potential files. Thus, you
need to re-specify the pair_style and pair_coeff commands in an input
script that reads a restart file.</p>
<p>These pair styles 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. They do not support the
<em>inner</em>, <em>middle</em>, <em>outer</em> keywords.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>These pair styles are part of the MANYBODY package. They are only
enabled if LAMMPS was built with that package (which it is by
default). 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>These pair potentials require the <a class="reference internal" href="newton.html"><span class="doc">newton</span></a> setting to be
&#8220;on&#8221; for pair interactions.</p>
<p>The CH.airebo and CH.airebo-m potential files provided with LAMMPS
(see the potentials directory) are parameterized for metal <a class="reference internal" href="units.html"><span class="doc">units</span></a>.
You can use the AIREBO, AIREBO-M or REBO potential with any LAMMPS units,
but you would need to create your own AIREBO or AIREBO-M potential file
with coefficients listed in the appropriate units, if your simulation
doesn&#8217;t use &#8220;metal&#8221; units.</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="stuart"><strong>(Stuart)</strong> Stuart, Tutein, Harrison, J Chem Phys, 112, 6472-6486
(2000).</p>
<p id="brenner"><strong>(Brenner)</strong> Brenner, Shenderova, Harrison, Stuart, Ni, Sinnott, J
Physics: Condensed Matter, 14, 783-802 (2002).</p>
<p id="oconnor"><strong>(O&#8217;Connor)</strong> O&#8217;Connor et al., J. Chem. Phys. 142, 024903 (2015).</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