forked from lijiext/lammps
337 lines
15 KiB
HTML
337 lines
15 KiB
HTML
|
|
|
|
<!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 lj/gromacs command — 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 & 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 & 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>
|
|
|
|
</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> »</li>
|
|
|
|
<li>pair_style lj/gromacs 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-lj-gromacs-command">
|
|
<span id="index-0"></span><h1>pair_style lj/gromacs command<a class="headerlink" href="#pair-style-lj-gromacs-command" title="Permalink to this headline">¶</a></h1>
|
|
</div>
|
|
<div class="section" id="pair-style-lj-gromacs-cuda-command">
|
|
<h1>pair_style lj/gromacs/cuda command<a class="headerlink" href="#pair-style-lj-gromacs-cuda-command" title="Permalink to this headline">¶</a></h1>
|
|
</div>
|
|
<div class="section" id="pair-style-lj-gromacs-gpu-command">
|
|
<h1>pair_style lj/gromacs/gpu command<a class="headerlink" href="#pair-style-lj-gromacs-gpu-command" title="Permalink to this headline">¶</a></h1>
|
|
</div>
|
|
<div class="section" id="pair-style-lj-gromacs-omp-command">
|
|
<h1>pair_style lj/gromacs/omp command<a class="headerlink" href="#pair-style-lj-gromacs-omp-command" title="Permalink to this headline">¶</a></h1>
|
|
</div>
|
|
<div class="section" id="pair-style-lj-gromacs-coul-gromacs-command">
|
|
<h1>pair_style lj/gromacs/coul/gromacs command<a class="headerlink" href="#pair-style-lj-gromacs-coul-gromacs-command" title="Permalink to this headline">¶</a></h1>
|
|
</div>
|
|
<div class="section" id="pair-style-lj-gromacs-coul-gromacs-cuda-command">
|
|
<h1>pair_style lj/gromacs/coul/gromacs/cuda command<a class="headerlink" href="#pair-style-lj-gromacs-coul-gromacs-cuda-command" title="Permalink to this headline">¶</a></h1>
|
|
</div>
|
|
<div class="section" id="pair-style-lj-gromacs-coul-gromacs-omp-command">
|
|
<h1>pair_style lj/gromacs/coul/gromacs/omp command<a class="headerlink" href="#pair-style-lj-gromacs-coul-gromacs-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 style args
|
|
</pre></div>
|
|
</div>
|
|
<ul class="simple">
|
|
<li>style = <em>lj/gromacs</em> or <em>lj/gromacs/coul/gromacs</em></li>
|
|
<li>args = list of arguments for a particular style</li>
|
|
</ul>
|
|
<pre class="literal-block">
|
|
<em>lj/gromacs</em> args = inner outer
|
|
inner, outer = global switching cutoffs for Lennard Jones
|
|
<em>lj/gromacs/coul/gromacs</em> args = inner outer (inner2) (outer2)
|
|
inner, outer = global switching cutoffs for Lennard Jones (and Coulombic if only 2 args)
|
|
inner2, outer2 = global switching cutoffs for Coulombic (optional)
|
|
</pre>
|
|
</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 lj/gromacs 9.0 12.0
|
|
pair_coeff * * 100.0 2.0
|
|
pair_coeff 2 2 100.0 2.0 8.0 10.0
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>pair_style lj/gromacs/coul/gromacs 9.0 12.0
|
|
pair_style lj/gromacs/coul/gromacs 8.0 10.0 7.0 9.0
|
|
pair_coeff * * 100.0 2.0
|
|
</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>lj/gromacs</em> styles compute shifted LJ and Coulombic interactions
|
|
with an additional switching function S(r) that ramps the energy and force
|
|
smoothly to zero between an inner and outer cutoff. It is a commonly
|
|
used potential in the <a class="reference external" href="http://www.gromacs.org">GROMACS</a> MD code and for
|
|
the coarse-grained models of <a class="reference internal" href="#marrink"><span>(Marrink)</span></a>.</p>
|
|
<img alt="_images/pair_gromacs.jpg" class="align-center" src="_images/pair_gromacs.jpg" />
|
|
<p>r1 is the inner cutoff; rc is the outer cutoff. The coefficients A, B,
|
|
and C are computed by LAMMPS to perform the shifting and smoothing.
|
|
The function
|
|
S(r) is actually applied once to each term of the LJ formula and once
|
|
to the Coulombic formula, so there are 2 or 3 sets of A,B,C coefficients
|
|
depending on which pair_style is used. The boundary conditions
|
|
applied to the smoothing function are as follows: S’(r1) = S’‘(r1) = 0,
|
|
S(rc) = -E(rc), S’(rc) = -E’(rc), and S’‘(rc) = -E’‘(rc),
|
|
where E(r) is the corresponding term
|
|
in the LJ or Coulombic potential energy function.
|
|
Single and double primes denote first and second
|
|
derivatives with respect to r, respectively.</p>
|
|
<p>The inner and outer cutoff for the LJ and Coulombic terms can be the
|
|
same or different depending on whether 2 or 4 arguments are used in
|
|
the pair_style command. The inner LJ cutoff must be > 0, but the
|
|
inner Coulombic cutoff can be >= 0.</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 (energy units)</li>
|
|
<li>sigma (distance units)</li>
|
|
<li>inner (distance units)</li>
|
|
<li>outer (distance units)</li>
|
|
</ul>
|
|
<p>Note that sigma is defined in the LJ formula as the zero-crossing
|
|
distance for the potential, not as the energy minimum at 2^(1/6)
|
|
sigma.</p>
|
|
<p>The last 2 coefficients are optional inner and outer cutoffs for style
|
|
<em>lj/gromacs</em>. If not specified, the global <em>inner</em> and <em>outer</em> values
|
|
are used.</p>
|
|
<p>The last 2 coefficients cannot be used with style
|
|
<em>lj/gromacs/coul/gromacs</em> because this force field does not allow
|
|
varying cutoffs for individual atom pairs; all pairs use the global
|
|
cutoff(s) specified in the pair_style command.</p>
|
|
<hr class="docutils" />
|
|
<p>Styles <em>intel</em>, <em>kk</em>, with a <em>cuda</em>, <em>gpu</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 all of the lj/cut pair styles can be mixed.
|
|
The default mix value is <em>geometric</em>. See the “pair_modify” command
|
|
for details.</p>
|
|
<p>None of the GROMACS pair styles support the
|
|
<a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> shift option, since the Lennard-Jones
|
|
portion of the pair interaction is already smoothed to 0.0 at the
|
|
cutoff.</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>None of the GROMACS pair styles 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, since there are no corrections for
|
|
a potential that goes to 0.0 at the cutoff.</p>
|
|
<p>All of the GROMACS pair styles write their 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>All of the GROMACS pair styles 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. They do 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>
|
|
<blockquote>
|
|
<div>none</div></blockquote>
|
|
</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></p>
|
|
<p><strong>Default:</strong> none</p>
|
|
<hr class="docutils" />
|
|
<p id="marrink"><strong>(Marrink)</strong> Marrink, de Vries, Mark, J Phys Chem B, 108, 750-760 (2004).</p>
|
|
</div>
|
|
</div>
|
|
|
|
|
|
</div>
|
|
</div>
|
|
<footer>
|
|
|
|
|
|
<hr/>
|
|
|
|
<div role="contentinfo">
|
|
<p>
|
|
© 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> |