forked from lijiext/lammps
355 lines
18 KiB
HTML
355 lines
18 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>fix saed/vtk 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>fix saed/vtk 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="fix-saed-vtk-command">
|
|
<span id="index-0"></span><h1>fix saed/vtk command</h1>
|
|
<div class="section" id="syntax">
|
|
<h2>Syntax</h2>
|
|
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">saed</span><span class="o">/</span><span class="n">vtk</span> <span class="n">Nevery</span> <span class="n">Nrepeat</span> <span class="n">Nfreak</span> <span class="n">c_ID</span> <span class="n">attribute</span> <span class="n">args</span> <span class="o">...</span> <span class="n">keyword</span> <span class="n">args</span> <span class="o">...</span>
|
|
</pre></div>
|
|
</div>
|
|
<ul class="simple">
|
|
<li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command</li>
|
|
<li>saed/vtk = style name of this fix command</li>
|
|
<li>Nevery = use input values every this many timesteps</li>
|
|
<li>Nrepeat = # of times to use input values for calculating averages</li>
|
|
<li>Nfreq = calculate averages every this many timesteps</li>
|
|
<li>c_ID = saed compute ID</li>
|
|
</ul>
|
|
<pre class="literal-block">
|
|
keyword = <em>file</em> or <em>ave</em> or <em>start</em> or <em>file</em> or <em>overwrite</em>:l
|
|
<em>ave</em> args = <em>one</em> or <em>running</em> or <em>window M</em>
|
|
one = output a new average value every Nfreq steps
|
|
running = output cumulative average of all previous Nfreq steps
|
|
window M = output average of M most recent Nfreq steps
|
|
<em>start</em> args = Nstart
|
|
Nstart = start averaging on this timestep
|
|
<em>file</em> arg = filename
|
|
filename = name of file to output time averages to
|
|
<em>overwrite</em> arg = none = overwrite output file with only latest output
|
|
</pre>
|
|
</div>
|
|
<div class="section" id="examples">
|
|
<h2>Examples</h2>
|
|
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">saed</span> <span class="mf">0.0251</span> <span class="n">Al</span> <span class="n">O</span> <span class="n">Kmax</span> <span class="mf">1.70</span> <span class="n">Zone</span> <span class="mi">0</span> <span class="mi">0</span> <span class="mi">1</span> <span class="n">dR_Ewald</span> <span class="mf">0.01</span> <span class="n">c</span> <span class="mf">0.5</span> <span class="mf">0.5</span> <span class="mf">0.5</span>
|
|
<span class="n">compute</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">saed</span> <span class="mf">0.0251</span> <span class="n">Ni</span> <span class="n">Kmax</span> <span class="mf">1.70</span> <span class="n">Zone</span> <span class="mi">0</span> <span class="mi">0</span> <span class="mi">0</span> <span class="n">c</span> <span class="mf">0.05</span> <span class="mf">0.05</span> <span class="mf">0.05</span> <span class="n">manual</span> <span class="n">echo</span>
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">saed</span><span class="o">/</span><span class="n">vtk</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mi">1</span> <span class="n">c_1</span> <span class="n">file</span> <span class="n">Al2O3_001</span><span class="o">.</span><span class="n">saed</span>
|
|
<span class="n">fix</span> <span class="n">saed</span><span class="o">/</span><span class="n">vtk</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mi">1</span> <span class="n">c_2</span> <span class="n">file</span> <span class="n">Ni_000</span><span class="o">.</span><span class="n">saed</span>
|
|
</pre></div>
|
|
</div>
|
|
</div>
|
|
<div class="section" id="description">
|
|
<h2>Description</h2>
|
|
<p>Time average computed intensities from <a class="reference internal" href="compute_saed.html"><span class="doc">compute saed</span></a> and
|
|
write output to a file in the 3rd generation vtk image data format for
|
|
visualization directly in parallelized visualization software packages
|
|
like ParaView and VisIt. Note that if no time averaging is done, this
|
|
command can be used as a convenient way to simply output diffraction
|
|
intensities at a single snapshot.</p>
|
|
<p>To produce output in the image data vtk format ghost data is added
|
|
outside the <em>Kmax</em> range assigned in the compute saed. The ghost data is
|
|
assigned a value of -1 and can be removed setting a minimum isovolume
|
|
of 0 within the vizualiziton software. SAED images can be created by
|
|
visualizing a spherical slice of the data that is centered at
|
|
R_Ewald*[h k l]/norm([h k l]), where R_Ewald=1/lambda.</p>
|
|
<p>The group specified within this command is ignored. However, note that
|
|
specified values may represent calculations performed by saed computes
|
|
which store their own “group” definitions.</p>
|
|
<p>Fix saed/vtk is designed to work only with <a class="reference internal" href="compute_saed.html"><span class="doc">compute saed</span></a>
|
|
values, e.g.</p>
|
|
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">3</span> <span class="n">top</span> <span class="n">saed</span> <span class="mf">0.0251</span> <span class="n">Al</span> <span class="n">O</span>
|
|
<span class="n">fix</span> <span class="n">saed</span><span class="o">/</span><span class="n">vtk</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mi">1</span> <span class="n">c_3</span> <span class="n">file</span> <span class="n">Al2O3_001</span><span class="o">.</span><span class="n">saed</span>
|
|
</pre></div>
|
|
</div>
|
|
<hr class="docutils" />
|
|
<p>The <em>Nevery</em>, <em>Nrepeat</em>, and <em>Nfreq</em> arguments specify on what
|
|
timesteps the input values will be used in order to contribute to the
|
|
average. The final averaged quantities are generated on timesteps
|
|
that are a multiple of <em>Nfreq</em>. The average is over <em>Nrepeat</em>
|
|
quantities, computed in the preceding portion of the simulation every
|
|
<em>Nevery</em> timesteps. <em>Nfreq</em> must be a multiple of <em>Nevery</em> and
|
|
<em>Nevery</em> must be non-zero even if <em>Nrepeat</em> is 1.
|
|
Also, the timesteps
|
|
contributing to the average value cannot overlap,
|
|
i.e. Nrepeat*Nevery can not exceed Nfreq.</p>
|
|
<p>For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on
|
|
timesteps 90,92,94,96,98,100 will be used to compute the final average
|
|
on timestep 100. Similarly for timesteps 190,192,194,196,198,200 on
|
|
timestep 200, etc. If Nrepeat=1 and Nfreq = 100, then no time
|
|
averaging is done; values are simply generated on timesteps
|
|
100,200,etc.</p>
|
|
<hr class="docutils" />
|
|
<p>The output for fix ave/time/saed is a file writen with the 3rd generation
|
|
vtk image data formatting. The filename assigned by the <em>file</em> keyword is
|
|
appended with _N.vtk where N is an index (0,1,2...) to account for multiple
|
|
diffraction intensity outputs.</p>
|
|
<p>By default the header contains the following information (with example data):</p>
|
|
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># vtk DataFile Version 3.0 c_SAED</span>
|
|
<span class="n">Image</span> <span class="n">data</span> <span class="nb">set</span>
|
|
<span class="n">ASCII</span>
|
|
<span class="n">DATASET</span> <span class="n">STRUCTURED_POINTS</span>
|
|
<span class="n">DIMENSIONS</span> <span class="mi">337</span> <span class="mi">219</span> <span class="mi">209</span>
|
|
<span class="n">ASPECT_RATIO</span> <span class="mf">0.00507953</span> <span class="mf">0.00785161</span> <span class="mf">0.00821458</span>
|
|
<span class="n">ORIGIN</span> <span class="o">-</span><span class="mf">0.853361</span> <span class="o">-</span><span class="mf">0.855826</span> <span class="o">-</span><span class="mf">0.854316</span>
|
|
<span class="n">POINT_DATA</span> <span class="mi">15424827</span>
|
|
<span class="n">SCALARS</span> <span class="n">intensity</span> <span class="nb">float</span>
|
|
<span class="n">LOOKUP_TABLE</span> <span class="n">default</span>
|
|
<span class="o">...</span><span class="n">data</span>
|
|
</pre></div>
|
|
</div>
|
|
<p>In this example, kspace is sampled across a 337 x 219 x 209 point mesh
|
|
where the mesh spacing is approximately 0.005, 0.007, and 0.008
|
|
inv(length) units in the k1, k2, and k3 directions, respectively.
|
|
The data is shifted by -0.85, -0.85, -0.85 inv(length) units so that
|
|
the origin will lie at 0, 0, 0. Here, 15,424,827 kspace points are
|
|
sampled in total.</p>
|
|
<hr class="docutils" />
|
|
<p>Additional optional keywords also affect the operation of this fix.</p>
|
|
<p>The <em>ave</em> keyword determines how the values produced every <em>Nfreq</em>
|
|
steps are averaged with values produced on previous steps that were
|
|
multiples of <em>Nfreq</em>, before they are accessed by another output
|
|
command or written to a file.</p>
|
|
<p>If the <em>ave</em> setting is <em>one</em>, then the values produced on timesteps
|
|
that are multiples of <em>Nfreq</em> are independent of each other; they are
|
|
output as-is without further averaging.</p>
|
|
<p>If the <em>ave</em> setting is <em>running</em>, then the values produced on
|
|
timesteps that are multiples of <em>Nfreq</em> are summed and averaged in a
|
|
cumulative sense before being output. Each output value is thus the
|
|
average of the value produced on that timestep with all preceding
|
|
values. This running average begins when the fix is defined; it can
|
|
only be restarted by deleting the fix via the <a class="reference internal" href="unfix.html"><span class="doc">unfix</span></a>
|
|
command, or by re-defining the fix by re-specifying it.</p>
|
|
<p>If the <em>ave</em> setting is <em>window</em>, then the values produced on
|
|
timesteps that are multiples of <em>Nfreq</em> are summed and averaged within
|
|
a moving “window” of time, so that the last M values are used to
|
|
produce the output. E.g. if M = 3 and Nfreq = 1000, then the output
|
|
on step 10000 will be the average of the individual values on steps
|
|
8000,9000,10000. Outputs on early steps will average over less than M
|
|
values if they are not available.</p>
|
|
<p>The <em>start</em> keyword specifies what timestep averaging will begin on.
|
|
The default is step 0. Often input values can be 0.0 at time 0, so
|
|
setting <em>start</em> to a larger value can avoid including a 0.0 in a
|
|
running or windowed average.</p>
|
|
<p>The <em>file</em> keyword allows a filename to be specified. Every <em>Nfreq</em>
|
|
steps, the vector of saed intensity data is written to a new file using
|
|
the 3rd generation vtk format. The base of each file is assigned by
|
|
the <em>file</em> keyword and this string is appended with _N.vtk where N is
|
|
an index (0,1,2...) to account for situations with multiple diffraction
|
|
intensity outputs.</p>
|
|
<p>The <em>overwrite</em> keyword will continuously overwrite the output file
|
|
with the latest output, so that it only contains one timestep worth of
|
|
output. This option can only be used with the <em>ave running</em> setting.</p>
|
|
</div>
|
|
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
|
|
<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
|
|
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
|
|
are relevant to this fix.</p>
|
|
<p>No parameter of this fix can be used with the <em>start/stop</em> keywords of
|
|
the <a class="reference internal" href="run.html"><span class="doc">run</span></a> command. This fix is not invoked during <a class="reference internal" href="minimize.html"><span class="doc">energy minimization</span></a>.</p>
|
|
</div>
|
|
<div class="section" id="restrictions">
|
|
<h2>Restrictions</h2>
|
|
<p>The attributes for fix_saed_vtk must match the values assigned in the
|
|
associated <a class="reference internal" href="compute_saed.html"><span class="doc">compute_saed</span></a> command.</p>
|
|
</div>
|
|
<div class="section" id="related-commands">
|
|
<h2>Related commands</h2>
|
|
<p><a class="reference internal" href="compute_saed.html"><span class="doc">compute_saed</span></a></p>
|
|
</div>
|
|
<div class="section" id="default">
|
|
<h2>Default</h2>
|
|
<p>The option defaults are ave = one, start = 0, no file output.</p>
|
|
<hr class="docutils" />
|
|
<p id="coleman"><strong>(Coleman)</strong> Coleman, Spearot, Capolungo, MSMSE, 21, 055020
|
|
(2013).</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> |