Homec4science
Diffusion lammps (lammps-icms) Browse

lammps/doc/html/write_dump.html
57fb84393a7alammps-icms

Last Change
Raw File

write_dump.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>write_dump 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">
<!-- Local TOC -->
<div class="local-toc"><ul>
<li><a class="reference internal" href="#">write_dump command</a><ul>
<li><a class="reference internal" href="#syntax">Syntax</a></li>
<li><a class="reference internal" href="#examples">Examples</a></li>
<li><a class="reference internal" href="#description">Description</a></li>
<li><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li><a class="reference internal" href="#related-commands">Related commands</a></li>
<li><a class="reference internal" href="#default">Default</a></li>
</ul>
</li>
</ul>
</div>
</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>write_dump 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="write-dump-command">
<span id="index-0"></span><h1>write_dump command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">write_dump</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">style</span> <span class="n">file</span> <span class="n">dump</span><span class="o">-</span><span class="n">args</span> <span class="n">modify</span> <span class="n">dump_modify</span><span class="o">-</span><span class="n">args</span>
</pre></div>
</div>
<ul class="simple">
<li>group-ID = ID of the group of atoms to be dumped</li>
<li>style = any of the supported <a class="reference internal" href="dump.html"><span class="doc">dump styles</span></a></li>
<li>file = name of file to write dump info to</li>
<li>dump-args = any additional args needed for a particular <a class="reference internal" href="dump.html"><span class="doc">dump style</span></a></li>
<li>modify = all args after this keyword are passed to <a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify</span></a> (optional)</li>
<li>dump-modify-args = args for <a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify</span></a> (optional)</li>
</ul>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">write_dump</span> <span class="nb">all</span> <span class="n">atom</span> <span class="n">dump</span><span class="o">.</span><span class="n">atom</span>
<span class="n">write_dump</span> <span class="n">subgroup</span> <span class="n">atom</span> <span class="n">dump</span><span class="o">.</span><span class="n">run</span><span class="o">.</span><span class="n">bin</span>
<span class="n">write_dump</span> <span class="nb">all</span> <span class="n">custom</span> <span class="n">dump</span><span class="o">.</span><span class="n">myforce</span><span class="o">.*</span> <span class="nb">id</span> <span class="nb">type</span> <span class="n">x</span> <span class="n">y</span> <span class="n">vx</span> <span class="n">fx</span>
<span class="n">write_dump</span> <span class="n">flow</span> <span class="n">custom</span> <span class="n">dump</span><span class="o">.%.</span><span class="n">myforce</span> <span class="nb">id</span> <span class="nb">type</span> <span class="n">c_myF</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="n">v_ke</span> <span class="n">modify</span> <span class="n">sort</span> <span class="nb">id</span>
<span class="n">write_dump</span> <span class="nb">all</span> <span class="n">xyz</span> <span class="n">system</span><span class="o">.</span><span class="n">xyz</span> <span class="n">modify</span> <span class="n">sort</span> <span class="nb">id</span> <span class="n">elements</span> <span class="n">O</span> <span class="n">H</span>
<span class="n">write_dump</span> <span class="nb">all</span> <span class="n">image</span> <span class="n">snap</span><span class="o">*.</span><span class="n">jpg</span> <span class="nb">type</span> <span class="nb">type</span> <span class="n">size</span> <span class="mi">960</span> <span class="mi">960</span> <span class="n">modify</span> <span class="n">backcolor</span> <span class="n">white</span>
<span class="n">write_dump</span> <span class="nb">all</span> <span class="n">image</span> <span class="n">snap</span><span class="o">*.</span><span class="n">jpg</span> <span class="n">element</span> <span class="n">element</span> <span class="o">&amp;</span>
<span class="n">bond</span> <span class="n">atom</span> <span class="mf">0.3</span> <span class="n">shiny</span> <span class="mf">0.1</span> <span class="n">ssao</span> <span class="n">yes</span> <span class="mi">6345</span> <span class="mf">0.2</span> <span class="n">size</span> <span class="mi">1600</span> <span class="mi">1600</span> <span class="o">&amp;</span>
<span class="n">modify</span> <span class="n">backcolor</span> <span class="n">white</span> <span class="n">element</span> <span class="n">C</span> <span class="n">C</span> <span class="n">O</span> <span class="n">H</span> <span class="n">N</span> <span class="n">C</span> <span class="n">C</span> <span class="n">C</span> <span class="n">O</span> <span class="n">H</span> <span class="n">H</span> <span class="n">S</span> <span class="n">O</span> <span class="n">H</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
<p>Dump a single snapshot of atom quantities to one or more files for the
current state of the system. This is a one-time immediate operation,
in contrast to the <a class="reference internal" href="dump.html"><span class="doc">dump</span></a> command which will will set up a
dump style to write out snapshots periodically during a running
simulation.</p>
<p>The syntax for this command is mostly identical to that of the
<a class="reference internal" href="dump.html"><span class="doc">dump</span></a> and <a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify</span></a> commands as if
they were concatenated together, with the following exceptions: There
is no need for a dump ID or dump frequency and the keyword <em>modify</em> is
added. The latter is so that the full range of
<a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify</span></a> options can be specified for the single
snapshot, just as they can be for multiple snapshots. The <em>modify</em>
keyword separates the arguments that would normally be passed to the
<em>dump</em> command from those that would be given the <em>dump_modify</em>. Both
support optional arguments and thus LAMMPS needs to be able to cleanly
separate the two sets of args.</p>
<p>Note that if the specified filename uses wildcard characters &#8220;*&#8221; or
&#8220;%&#8221;, as supported by the <a class="reference internal" href="dump.html"><span class="doc">dump</span></a> commmand, they will operate
in the same fashion to create the new filename(s). Normally, <a class="reference internal" href="dump_image.html"><span class="doc">dump image</span></a> files require a filename with a &#8220;*&#8221; character
for the timestep. That is not the case for the write_dump command; no
wildcard &#8220;*&#8221; character is necessary.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>All restrictions for the <a class="reference internal" href="dump.html"><span class="doc">dump</span></a> and
<a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify</span></a> commands apply to this command as well,
with the exception of the <a class="reference internal" href="dump_image.html"><span class="doc">dump image</span></a> filename not
requiring a wildcard &#8220;*&#8221; character, as noted above.</p>
<p>Since dumps are normally written during a <a class="reference internal" href="run.html"><span class="doc">run</span></a> or <a class="reference internal" href="minimize.html"><span class="doc">energy minimization</span></a>, the simulation has to be ready to run
before this command can be used. Similarly, if the dump requires
information from a compute, fix, or variable, the information needs to
have been calculated for the current timestep (e.g. by a prior run),
else LAMMPS will generate an error message.</p>
<p>For example, it is not possible to dump per-atom energy with this
command before a run has been performed, since no energies and forces
have yet been calculated. See the <a class="reference internal" href="variable.html"><span class="doc">variable</span></a> doc page
sectinn on Variable Accuracy for more information on this topic.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><a class="reference internal" href="dump.html"><span class="doc">dump</span></a>, <a class="reference internal" href="dump_image.html"><span class="doc">dump image</span></a>,
<a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify</span></a></p>
</div>
<div class="section" id="default">
<h2>Default</h2>
<p>The defaults are listed on the doc pages for the <a class="reference internal" href="dump.html"><span class="doc">dump</span></a> and
<a class="reference internal" href="dump_image.html"><span class="doc">dump image</span></a> and <a class="reference internal" href="dump_modify.html"><span class="doc">dump_modify</span></a>
commands.</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