Homec4science
Diffusion lammps (efficient_neuronet) Browse

lammps/doc/html/pair_coeff.html
6571ee32dc09efficient_neuronet

Last Change
Raw File

pair_coeff.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_coeff 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_coeff 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-coeff-command">
<span id="index-0"></span><h1>pair_coeff command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_coeff</span> <span class="n">I</span> <span class="n">J</span> <span class="n">args</span>
</pre></div>
</div>
<ul class="simple">
<li>I,J = atom types (see asterisk form below)</li>
<li>args = coefficients for one or more pairs of atom types</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_coeff</span> <span class="mi">1</span> <span class="mi">2</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">2.5</span>
<span class="n">pair_coeff</span> <span class="mi">2</span> <span class="o">*</span> <span class="mf">1.0</span> <span class="mf">1.0</span>
<span class="n">pair_coeff</span> <span class="mi">3</span><span class="o">*</span> <span class="mi">1</span><span class="o">*</span><span class="mi">2</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">2.5</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">1.0</span> <span class="mf">1.0</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">nialhjea</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mi">2</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="mi">3</span> <span class="n">morse</span><span class="o">.</span><span class="n">table</span> <span class="n">ENTRY1</span>
<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">2</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">2.5</span> <span class="p">(</span><span class="k">for</span> <span class="n">pair_style</span> <span class="n">hybrid</span><span class="p">)</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
<p>Specify the pairwise force field coefficients for one or more pairs of
atom types. The number and meaning of the coefficients depends on the
pair style. Pair coefficients can also be set in the data file read
by the <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> command or in a restart file.</p>
<p>I and J can be specified in one of two ways. Explicit numeric values
can be used for each, as in the 1st example above. I &lt;= J is
required. LAMMPS sets the coefficients for the symmetric J,I
interaction to the same values.</p>
<p>A wildcard asterisk can be used in place of or in conjunction with the
I,J arguments to set the coefficients for multiple pairs of atom
types. This takes the form &#8220;*&#8221; or &#8220;<em>n&#8221; or &#8220;n</em>&#8221; or &#8220;m*n&#8221;. If N = the
number of atom types, then an asterisk with no numeric values means all
types from 1 to N. A leading asterisk means all types from 1 to n
(inclusive). A trailing asterisk means all types from n to N
(inclusive). A middle asterisk means all types from m to n
(inclusive). Note that only type pairs with I &lt;= J are considered; if
asterisks imply type pairs where J &lt; I, they are ignored.</p>
<p>Note that a pair_coeff command can override a previous setting for the
same I,J pair. For example, these commands set the coeffs for all I,J
pairs, then overwrite the coeffs for just the I,J = 2,3 pair:</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="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">2.5</span>
<span class="n">pair_coeff</span> <span class="mi">2</span> <span class="mi">3</span> <span class="mf">2.0</span> <span class="mf">1.0</span> <span class="mf">1.12</span>
</pre></div>
</div>
<p>A line in a data file that specifies pair coefficients uses the exact
same format as the arguments of the pair_coeff command in an input
script, with the exception of the I,J type arguments. In each line of
the &#8220;Pair Coeffs&#8221; section of a data file, only a single type I is
specified, which sets the coefficients for type I interacting with
type I. This is because the section has exactly N lines, where N =
the number of atom types. For this reason, the wild-card asterisk
should also not be used as part of the I argument. Thus in a data
file, the line corresponding to the 1st example above would be listed
as</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="mi">2</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">2.5</span>
</pre></div>
</div>
<p>For many potentials, if coefficients for type pairs with I != J are
not set explicitly by a pair_coeff command, the values are inferred
from the I,I and J,J settings by mixing rules; see the
<a class="reference internal" href="pair_modify.html"><span class="doc">pair_modify</span></a> command for a discussion. Details on
this option as it pertains to individual potentials are described on
the doc page for the potential.</p>
<p>Many pair styles, typically for many-body potentials, use tabulated
potential files as input, when specifying the pair_coeff command.
Potential files provided with LAMMPS are in the potentials directory
of the distribution. For some potentials, such as EAM, other archives
of suitable files can be found on the Web. They can be used with
LAMMPS so long as they are in the format LAMMPS expects, as discussed
on the individual doc pages.</p>
<p>When a pair_coeff command using a potential file is specified, LAMMPS
looks for the potential file in 2 places. First it looks in the
location specified. E.g. if the file is specified as &#8220;niu3.eam&#8221;, it
is looked for in the current working directory. If it is specified as
&#8221;../potentials/niu3.eam&#8221;, then it is looked for in the potentials
directory, assuming it is a sister directory of the current working
directory. If the file is not found, it is then looked for in the
directory specified by the LAMMPS_POTENTIALS environment variable.
Thus if this is set to the potentials directory in the LAMMPS distro,
then you can use those files from anywhere on your system, without
copying them into your working directory. Environment variables are
set in different ways for different shells. Here are example settings
for</p>
<p>csh, tcsh:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="o">%</span> <span class="n">setenv</span> <span class="n">LAMMPS_POTENTIALS</span> <span class="o">/</span><span class="n">path</span><span class="o">/</span><span class="n">to</span><span class="o">/</span><span class="n">lammps</span><span class="o">/</span><span class="n">potentials</span>
</pre></div>
</div>
<p>bash:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="o">%</span> <span class="n">export</span> <span class="n">LAMMPS_POTENTIALS</span><span class="o">=/</span><span class="n">path</span><span class="o">/</span><span class="n">to</span><span class="o">/</span><span class="n">lammps</span><span class="o">/</span><span class="n">potentials</span>
</pre></div>
</div>
<p>Windows:</p>
<pre class="literal-block">
% set LAMMPS_POTENTIALS=&quot;C:\Path to LAMMPS\Potentials&quot;
</pre>
<hr class="docutils" />
<p>The alphabetic list of pair styles defined in LAMMPS is given on the
<a class="reference internal" href="pair_style.html"><span class="doc">pair_style</span></a> doc page. They are also given in more
compact form in the pair section of <a class="reference internal" href="Section_commands.html#cmd-5"><span class="std std-ref">this page</span></a>.</p>
<p>Click on the style to display the formula it computes, arguments
specified in the pair_style command, and coefficients specified by the
associated <a class="reference internal" href="#"><span class="doc">pair_coeff</span></a> command.</p>
<p>Note that there are also additional pair styles (not listed on the
<a class="reference internal" href="pair_style.html"><span class="doc">pair_style</span></a> doc page) submitted by users which are
included in the LAMMPS distribution. The list of these with links to
the individual styles are given in the pair section of <a class="reference internal" href="Section_commands.html#cmd-5"><span class="std std-ref">this page</span></a>.</p>
<p>There are also additional accelerated pair styles (not listed on the
<a class="reference internal" href="pair_style.html"><span class="doc">pair_style</span></a> doc page) included in the LAMMPS
distribution for faster performance on CPUs and GPUs. The list of
these with links to the individual styles are given in the pair
section of <a class="reference internal" href="Section_commands.html#cmd-5"><span class="std std-ref">this page</span></a>.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>This command must come after the simulation box is defined by a
<a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a>, <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a>, or
<a class="reference internal" href="create_box.html"><span class="doc">create_box</span></a> command.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><a class="reference internal" href="pair_style.html"><span class="doc">pair_style</span></a>, <a class="reference internal" href="pair_modify.html"><span class="doc">pair_modify</span></a>,
<a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a>, <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a>,
<a class="reference internal" href="pair_write.html"><span class="doc">pair_write</span></a></p>
<p><strong>Default:</strong> none</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