Homec4science
Diffusion lammps (efficient_neuronet) Browse

lammps/doc/pair_adp.html
c16f3a8c2300efficient_neuronet

Last Change
Raw File

pair_adp.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 adp 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 adp command</li>
<li class="wy-breadcrumbs-aside">
<a href="http://lammps.sandia.gov">Homepage</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-adp-command">
<span id="index-0"></span><h1>pair_style adp command<a class="headerlink" href="#pair-style-adp-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="pair-style-adp-omp-command">
<h1>pair_style adp/omp command<a class="headerlink" href="#pair-style-adp-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 adp
</pre></div>
</div>
</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 adp
pair_coeff * * Ta.adp Ta
pair_coeff * * ../potentials/AlCu.adp Al Al Cu
</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>adp</em> computes pairwise interactions for metals and metal alloys
using the angular dependent potential (ADP) of <a class="reference internal" href="#mishin"><span>(Mishin)</span></a>,
which is a generalization of the <a class="reference internal" href="pair_eam.html"><em>embedded atom method (EAM) potential</em></a>. The LAMMPS implementation is discussed in
<a class="reference internal" href="#singh"><span>(Singh)</span></a>. The total energy Ei of an atom I is given by</p>
<img alt="_images/pair_adp.jpg" class="align-center" src="_images/pair_adp.jpg" />
<p>where F is the embedding energy which is a function of the atomic
electron density rho, phi is a pair potential interaction, alpha and
beta are the element types of atoms I and J, and s and t = 1,2,3 and
refer to the cartesian coordinates. The mu and lambda terms represent
the dipole and quadruple distortions of the local atomic environment
which extend the original EAM framework by introducing angular forces.</p>
<p>Note that unlike for other potentials, cutoffs for ADP potentials are
not set in the pair_style or pair_coeff command; they are specified in
the ADP potential files themselves. Likewise, the ADP potential files
list atomic masses; thus you do not need to use the <a class="reference internal" href="mass.html"><em>mass</em></a>
command to specify them.</p>
<p>The NIST WWW site distributes and documents ADP potentials:</p>
<div class="highlight-python"><div class="highlight"><pre>http://www.ctcms.nist.gov/potentials
</pre></div>
</div>
<p>Note that these must be converted into the extended DYNAMO <em>setfl</em>
format discussed below.</p>
<p>The NIST site is maintained by Chandler Becker (cbecker at nist.gov)
who is good resource for info on interatomic potentials and file
formats.</p>
<hr class="docutils" />
<p>Only a single pair_coeff command is used with the <em>adp</em> style which
specifies an extended DYNAMO <em>setfl</em> file, which contains information
for M elements. 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 extended <em>setfl</em> elements to atom types</li>
</ul>
<p>See the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> doc page for alternate ways to
specify the path for the potential file.</p>
<p>As an example, the potentials/AlCu.adp file, included in the
potentials directory of the LAMMPS distrbution, is an extended <em>setfl</em>
file which has tabulated ADP values for w elements and their alloy
interactions: Cu and Al. If your LAMMPS simulation has 4 atoms types
and you want the 1st 3 to be Al, and the 4th to be Cu, you would use
the following pair_coeff command:</p>
<div class="highlight-python"><div class="highlight"><pre>pair_coeff * * AlCu.adp Al Al Al Cu
</pre></div>
</div>
<p>The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
The first three Al arguments map LAMMPS atom types 1,2,3 to the Al
element in the extended <em>setfl</em> file. The final Cu argument maps
LAMMPS atom type 4 to the Al element in the extended <em>setfl</em> file.
Note that there is no requirement that your simulation use all the
elements specified by the extended <em>setfl</em> file.</p>
<p>If a mapping value is specified as NULL, the mapping is not performed.
This can be used when an <em>adp</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><em>Adp</em> files in the <em>potentials</em> directory of the LAMMPS distribution
have an &#8221;.adp&#8221; suffix. A DYNAMO <em>setfl</em> file extended for ADP is
formatted as follows. Basically it is the standard <em>setfl</em> format
with additional tabulated functions u and w added to the file after
the tabulated pair potentials. See the <a class="reference internal" href="pair_eam.html"><em>pair_eam</em></a>
command for further details on the <em>setfl</em> format.</p>
<ul class="simple">
<li>lines 1,2,3 = comments (ignored)</li>
<li>line 4: Nelements Element1 Element2 ... ElementN</li>
<li>line 5: Nrho, drho, Nr, dr, cutoff</li>
</ul>
<p>Following the 5 header lines are Nelements sections, one for each
element, each with the following format:</p>
<ul class="simple">
<li>line 1 = atomic number, mass, lattice constant, lattice type (e.g. FCC)</li>
<li>embedding function F(rho) (Nrho values)</li>
<li>density function rho(r) (Nr values)</li>
</ul>
<p>Following the Nelements sections, Nr values for each pair potential
phi(r) array are listed for all i,j element pairs in the same format
as other arrays. Since these interactions are symmetric (i,j = j,i)
only phi arrays with i &gt;= j are listed, in the following order: i,j =
(1,1), (2,1), (2,2), (3,1), (3,2), (3,3), (4,1), ..., (Nelements,
Nelements). The tabulated values for each phi function are listed as
r*phi (in units of eV-Angstroms), since they are for atom pairs, the
same as for <a class="reference internal" href="pair_eam.html"><em>other EAM files</em></a>.</p>
<p>After the phi(r) arrays, each of the u(r) arrays are listed in the
same order with the same assumptions of symmetry. Directly following
the u(r), the w(r) arrays are listed. Note that phi(r) is the only
array tabulated with a scaling by r.</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"><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, where types I and J correspond to
two different element types, no special mixing rules are needed, since
the ADP potential files specify alloy interactions explicitly.</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>, since it is stored in tabulated 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>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 pair style is part of the MANYBODY package. It is only enabled
if LAMMPS was built with that package (which it is by default).</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_eam.html"><em>pair_eam</em></a></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="mishin"><strong>(Mishin)</strong> Mishin, Mehl, and Papaconstantopoulos, Acta Mater, 53, 4029
(2005).</p>
<p id="singh"><strong>(Singh)</strong> Singh and Warner, Acta Mater, 58, 5797-5805 (2010),</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="_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