Homec4science
Diffusion lammps (lammm-devel) Browse

lammps/doc/angle_table.html
607c4aa2a3e1lammm-devel

Last Change
Raw File

angle_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>angle_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"/>
<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>angle_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>
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div itemprop="articleBody">
<div class="section" id="angle-style-table-command">
<span id="index-0"></span><h1>angle_style table command<a class="headerlink" href="#angle-style-table-command" title="Permalink to this headline"></a></h1>
</div>
<div class="section" id="angle-style-table-omp-command">
<h1>angle_style table/omp command<a class="headerlink" href="#angle-style-table-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>angle_style table style N
</pre></div>
</div>
<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<a class="headerlink" href="#examples" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>angle_style table linear 1000
angle_coeff 3 file.table ENTRY1
</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>table</em> creates interpolation tables of length <em>N</em> from angle
potential and derivative values listed in a file(s) as a function of
angle The files are read by the <a class="reference internal" href="angle_coeff.html"><em>angle_coeff</em></a>
command.</p>
<p>The interpolation tables are created by fitting cubic splines to the
file values and interpolating energy and derivative values at each of
<em>N</em> angles. During a simulation, these tables are used to interpolate
energy and force values on individual atoms 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 angle is used to find 2 surrounding table
values from which an energy or its derivative 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 angle is used to
find the appropriate set of coefficients which are used to evaluate a
cubic polynomial which computes the energy or derivative.</p>
<p>The following coefficients must be defined for each angle type via the
<a class="reference internal" href="angle_coeff.html"><em>angle_coeff</em></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
derivative 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-python"><div class="highlight"><pre><span class="c"># Angle potential for harmonic (one or more comment or blank lines)</span>
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>HAM (keyword is the first text on line)
N 181 FP 0 0 EQ 90.0 (N, FP, EQ parameters)
(blank line)
N 181 FP 0 0 (N, FP parameters)
1 0.0 200.5 2.5 (index, angle, energy, derivative)
2 1.0 198.0 2.5
...
181 180.0 0.0 0.0
</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="angle_coeff.html"><em>angle_coeff</em></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="angle_style.html"><em>angle_style table</em></a> command. Let
Ntable = <em>N</em> in the angle_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 derivative
values at Ntable different points. The resulting tables of length
Ntable are then used as described above, when computing energy and
force for individual angles and their atoms. 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 2nd derivatives at the innermost and
outermost angle settings. 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
derivative values in the table.</p>
<p>The &#8220;EQ&#8221; parameter is also optional. If used, it is followed by a the
equilibrium angle value, which is used, for example, by the <a class="reference internal" href="fix_shake.html"><em>fix shake</em></a> command. If not used, the equilibrium angle is
set to 180.0.</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 angle value (in degrees), the 3rd value is the energy (in energy
units), and the 4th is -dE/d(theta) (also in energy units). The 3rd
term is the energy of the 3-atom configuration for the specified
angle. The last term is the derivative of the energy with respect to
the angle (in degrees, not radians). Thus the units of the last term
are still energy, not force. The angle values must increase from one
line to the next. The angle values must also begin with 0.0 and end
with 180.0, i.e. span the full range of possible angles.</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>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>
</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 angle 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>Making LAMMPS</span></a> section for more info on packages.</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="angle_coeff.html"><em>angle_coeff</em></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