Homec4science
Diffusion lammps (master) Browse

lammps/doc/html/bond_table.html
8db7ef436481master

Last Change
Raw File

bond_table.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>bond_style table 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"/>
<link rel="up" title="Bond Styles" href="bonds.html"/>
<link rel="next" title="bond_style zero command" href="bond_zero.html"/>
<link rel="prev" title="bond_style quartic command" href="bond_quartic.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">
<p class="caption"><span class="caption-text">User Documentation</span></p>
<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>
<p class="caption"><span class="caption-text">Index</span></p>
<ul class="current">
<li class="toctree-l1"><a class="reference internal" href="tutorials.html">Tutorials</a></li>
<li class="toctree-l1"><a class="reference internal" href="commands.html">Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="fixes.html">Fixes</a></li>
<li class="toctree-l1"><a class="reference internal" href="computes.html">Computes</a></li>
<li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
<li class="toctree-l1 current"><a class="reference internal" href="bonds.html">Bond Styles</a><ul class="current">
<li class="toctree-l2"><a class="reference internal" href="bond_class2.html">bond_style class2 command</a></li>
<li class="toctree-l2"><a class="reference internal" href="bond_class2.html#bond-style-class2-omp-command">bond_style class2/omp command</a></li>
<li class="toctree-l2"><a class="reference internal" href="bond_fene.html">bond_style fene command</a></li>
<li class="toctree-l2"><a class="reference internal" href="bond_fene.html#bond-style-fene-intel-command">bond_style fene/intel command</a></li>
<li class="toctree-l2"><a class="reference internal" href="bond_fene.html#bond-style-fene-kk-command">bond_style fene/kk command</a></li>
<li class="toctree-l2"><a class="reference internal" href="bond_fene.html#bond-style-fene-omp-command">bond_style fene/omp command</a></li>
<li class="toctree-l2"><a class="reference internal" href="bond_fene_expand.html">bond_style fene/expand command</a></li>
<li class="toctree-l2"><a class="reference internal" href="bond_fene_expand.html#bond-style-fene-expand-omp-command">bond_style fene/expand/omp command</a></li>
<li class="toctree-l2"><a class="reference internal" href="bond_harmonic.html">bond_style harmonic command</a></li>
<li class="toctree-l2"><a class="reference internal" href="bond_harmonic.html#bond-style-harmonic-intel-command">bond_style harmonic/intel command</a></li>
<li class="toctree-l2"><a class="reference internal" href="bond_harmonic.html#bond-style-harmonic-kk-command">bond_style harmonic/kk command</a></li>
<li class="toctree-l2"><a class="reference internal" href="bond_harmonic.html#bond-style-harmonic-omp-command">bond_style harmonic/omp command</a></li>
<li class="toctree-l2"><a class="reference internal" href="bond_harmonic_shift.html">bond_style harmonic/shift command</a></li>
<li class="toctree-l2"><a class="reference internal" href="bond_harmonic_shift.html#bond-style-harmonic-shift-omp-command">bond_style harmonic/shift/omp command</a></li>
<li class="toctree-l2"><a class="reference internal" href="bond_harmonic_shift_cut.html">bond_style harmonic/shift/cut command</a></li>
<li class="toctree-l2"><a class="reference internal" href="bond_harmonic_shift_cut.html#bond-style-harmonic-shift-cut-omp-command">bond_style harmonic/shift/cut/omp command</a></li>
<li class="toctree-l2"><a class="reference internal" href="bond_hybrid.html">bond_style hybrid command</a></li>
<li class="toctree-l2"><a class="reference internal" href="bond_morse.html">bond_style morse command</a></li>
<li class="toctree-l2"><a class="reference internal" href="bond_morse.html#bond-style-morse-omp-command">bond_style morse/omp command</a></li>
<li class="toctree-l2"><a class="reference internal" href="bond_none.html">bond_style none command</a></li>
<li class="toctree-l2"><a class="reference internal" href="bond_nonlinear.html">bond_style nonlinear command</a></li>
<li class="toctree-l2"><a class="reference internal" href="bond_nonlinear.html#bond-style-nonlinear-omp-command">bond_style nonlinear/omp command</a></li>
<li class="toctree-l2"><a class="reference internal" href="bond_quartic.html">bond_style quartic command</a></li>
<li class="toctree-l2"><a class="reference internal" href="bond_quartic.html#bond-style-quartic-omp-command">bond_style quartic/omp command</a></li>
<li class="toctree-l2 current"><a class="current reference internal" href="#">bond_style table command</a></li>
<li class="toctree-l2"><a class="reference internal" href="#bond-style-table-omp-command">bond_style table/omp command</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#syntax">Syntax</a></li>
<li class="toctree-l3"><a class="reference internal" href="#examples">Examples</a></li>
<li class="toctree-l3"><a class="reference internal" href="#description">Description</a></li>
<li class="toctree-l3"><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li class="toctree-l3"><a class="reference internal" href="#related-commands">Related commands</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="bond_zero.html">bond_style zero command</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
<li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
<li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</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><a href="bonds.html">Bond Styles</a> &raquo;</li>
<li>bond_style table 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 class="rst-footer-buttons" style="margin-bottom: 1em" role="navigation" aria-label="footer navigation">
<a href="bond_zero.html" class="btn btn-neutral float-right" title="bond_style zero command" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
<a href="bond_quartic.html" class="btn btn-neutral" title="bond_style quartic command" accesskey="p"><span class="fa fa-arrow-circle-left"></span> Previous</a>
</div>
</div>
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div itemprop="articleBody">
<div class="section" id="bond-style-table-command">
<span id="index-0"></span><h1>bond_style table command</h1>
</div>
<div class="section" id="bond-style-table-omp-command">
<h1>bond_style table/omp command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
bond_style table style N
</pre>
<ul class="simple">
<li>style = <em>linear</em> or <em>spline</em> = method of interpolation</li>
<li>N = use N values in table</li>
</ul>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
bond_style table linear 1000
bond_coeff 1 file.table ENTRY1
</pre>
</div>
<div class="section" id="description">
<h2>Description</h2>
<p>Style <em>table</em> creates interpolation tables of length <em>N</em> from bond
potential and force values listed in a file(s) as a function of bond
length. The files are read by the <a class="reference internal" href="bond_coeff.html"><span class="doc">bond_coeff</span></a>
command.</p>
<p>The interpolation tables are created by fitting cubic splines to the
file values and interpolating energy and force values at each of <em>N</em>
distances. During a simulation, these tables are used to interpolate
energy and force values as needed. The interpolation is done in one
of 2 styles: <em>linear</em> or <em>spline</em>.</p>
<p>For the <em>linear</em> style, the bond length is used to find 2 surrounding
table values from which an energy or force is computed by linear
interpolation.</p>
<p>For the <em>spline</em> style, a cubic spline coefficients are computed and
stored at each of the <em>N</em> values in the table. The bond length is
used to find the appropriate set of coefficients which are used to
evaluate a cubic polynomial which computes the energy or force.</p>
<p>The following coefficients must be defined for each bond type via the
<a class="reference internal" href="bond_coeff.html"><span class="doc">bond_coeff</span></a> command as in the example above.</p>
<ul class="simple">
<li>filename</li>
<li>keyword</li>
</ul>
<p>The filename specifies a file containing tabulated energy and force
values. The keyword specifies a section of the file. The format of
this file is described below.</p>
<hr class="docutils" />
<p>The format of a tabulated file is as follows (without the
parenthesized comments):</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># Bond potential for harmonic (one or more comment or blank lines)</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">HAM</span> <span class="p">(</span><span class="n">keyword</span> <span class="ow">is</span> <span class="n">the</span> <span class="n">first</span> <span class="n">text</span> <span class="n">on</span> <span class="n">line</span><span class="p">)</span>
<span class="n">N</span> <span class="mi">101</span> <span class="n">FP</span> <span class="mi">0</span> <span class="mi">0</span> <span class="n">EQ</span> <span class="mf">0.5</span> <span class="p">(</span><span class="n">N</span><span class="p">,</span> <span class="n">FP</span><span class="p">,</span> <span class="n">EQ</span> <span class="n">parameters</span><span class="p">)</span>
<span class="p">(</span><span class="n">blank</span> <span class="n">line</span><span class="p">)</span>
<span class="mi">1</span> <span class="mf">0.00</span> <span class="mf">338.0000</span> <span class="mf">1352.0000</span> <span class="p">(</span><span class="n">index</span><span class="p">,</span> <span class="n">bond</span><span class="o">-</span><span class="n">length</span><span class="p">,</span> <span class="n">energy</span><span class="p">,</span> <span class="n">force</span><span class="p">)</span>
<span class="mi">2</span> <span class="mf">0.01</span> <span class="mf">324.6152</span> <span class="mf">1324.9600</span>
<span class="o">...</span>
<span class="mi">101</span> <span class="mf">1.00</span> <span class="mf">338.0000</span> <span class="o">-</span><span class="mf">1352.0000</span>
</pre></div>
</div>
<p>A section begins with a non-blank line whose 1st character is not a
&#8220;#&#8221;; blank lines or lines starting with &#8220;#&#8221; can be used as comments
between sections. The first line begins with a keyword which
identifies the section. The line can contain additional text, but the
initial text must match the argument specified in the
<a class="reference internal" href="bond_coeff.html"><span class="doc">bond_coeff</span></a> command. The next line lists (in any
order) one or more parameters for the table. Each parameter is a
keyword followed by one or more numeric values.</p>
<p>The parameter &#8220;N&#8221; is required and its value is the number of table
entries that follow. Note that this may be different than the <em>N</em>
specified in the <a class="reference internal" href="bond_style.html"><span class="doc">bond_style table</span></a> command. Let
Ntable = <em>N</em> in the bond_style command, and Nfile = &#8220;N&#8221; in the
tabulated file. What LAMMPS does is a preliminary interpolation by
creating splines using the Nfile tabulated values as nodal points. It
uses these to interpolate as needed to generate energy and force
values at Ntable different points. The resulting tables of length
Ntable are then used as described above, when computing energy and
force for individual bond lengths. This means that if you want the
interpolation tables of length Ntable to match exactly what is in the
tabulated file (with effectively no preliminary interpolation), you
should set Ntable = Nfile.</p>
<p>The &#8220;FP&#8221; parameter is optional. If used, it is followed by two values
fplo and fphi, which are the derivatives of the force at the innermost
and outermost bond lengths. These values are needed by the spline
construction routines. If not specified by the &#8220;FP&#8221; parameter, they
are estimated (less accurately) by the first two and last two force
values in the table.</p>
<p>The &#8220;EQ&#8221; parameter is also optional. If used, it is followed by a the
equilibrium bond length, which is used, for example, by the <a class="reference internal" href="fix_shake.html"><span class="doc">fix shake</span></a> command. If not used, the equilibrium bond
length is to the distance in the table with the lowest potential energy.</p>
<p>Following a blank line, the next N lines list the tabulated values.
On each line, the 1st value is the index from 1 to N, the 2nd value is
the bond length r (in distance units), the 3rd value is the energy (in
energy units), and the 4th is the force (in force units). The bond
lengths must range from a LO value to a HI value, and increase from
one line to the next. If the actual bond length is ever smaller than
the LO value or larger than the HI value, then the bond energy and
force is evaluated as if the bond were the LO or HI length.</p>
<p>Note that one file can contain many sections, each with a tabulated
potential. LAMMPS reads the file section by section until it finds
one that matches the specified keyword.</p>
<hr class="docutils" />
<p>Styles with a <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 5</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 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 5</span></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>This bond style can only be used if LAMMPS was built with the
MOLECULE 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 on packages.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><a class="reference internal" href="bond_coeff.html"><span class="doc">bond_coeff</span></a>, <a class="reference internal" href="delete_bonds.html"><span class="doc">delete_bonds</span></a></p>
<p><strong>Default:</strong> none</p>
</div>
</div>
</div>
</div>
<footer>
<div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
<a href="bond_zero.html" class="btn btn-neutral float-right" title="bond_style zero command" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
<a href="bond_quartic.html" class="btn btn-neutral" title="bond_style quartic command" accesskey="p"><span class="fa fa-arrow-circle-left"></span> Previous</a>
</div>
<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