Homec4science
Diffusion lammps (lammm-master-deprecated) Browse

lammps/doc/html/write_restart.html
ebf04bdf161blammm-master-deprecated

Last Change
Raw File

write_restart.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_restart 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>write_restart 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-restart-command">
<span id="index-0"></span><h1>write_restart command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">write_restart</span> <span class="n">file</span> <span class="n">keyword</span> <span class="n">value</span> <span class="o">...</span>
</pre></div>
</div>
<ul class="simple">
<li>file = name of file to write restart information to</li>
<li>zero or more keyword/value pairs may be appended</li>
<li>keyword = <em>fileper</em> or <em>nfile</em></li>
</ul>
<pre class="literal-block">
<em>fileper</em> arg = Np
Np = write one file for every this many processors
<em>nfile</em> arg = Nf
Nf = write this many files, one from each of Nf processors
</pre>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">write_restart</span> <span class="n">restart</span><span class="o">.</span><span class="n">equil</span>
<span class="n">write_restart</span> <span class="n">restart</span><span class="o">.</span><span class="n">equil</span><span class="o">.</span><span class="n">mpiio</span>
<span class="n">write_restart</span> <span class="n">poly</span><span class="o">.%.*</span> <span class="n">nfile</span> <span class="mi">10</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
<p>Write a binary restart file of the current state of the simulation.</p>
<p>During a long simulation, the <a class="reference internal" href="restart.html"><span class="doc">restart</span></a> command is
typically used to output restart files periodically. The
write_restart command is useful after a minimization or whenever you
wish to write out a single current restart file.</p>
<p>Similar to <a class="reference internal" href="dump.html"><span class="doc">dump</span></a> files, the restart filename can contain
two wild-card characters. If a &#8220;*&#8221; appears in the filename, it is
replaced with the current timestep value. If a &#8220;%&#8221; character appears
in the filename, then one file is written by each processor and the
&#8220;%&#8221; character is replaced with the processor ID from 0 to P-1. An
additional file with the &#8220;%&#8221; replaced by &#8220;base&#8221; is also written, which
contains global information. For example, the files written for
filename restart.% would be restart.base, restart.0, restart.1, ...
restart.P-1. This creates smaller files and can be a fast mode of
output and subsequent input on parallel machines that support parallel
I/O. The optional <em>fileper</em> and <em>nfile</em> keywords discussed below can
alter the number of files written.</p>
<p>The restart file can also be written in parallel as one large binary
file via the MPI-IO library, which is part of the MPI standard for
versions 2.0 and above. Using MPI-IO requires two steps. First,
build LAMMPS with its MPIIO package installed, e.g.</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">make</span> <span class="n">yes</span><span class="o">-</span><span class="n">mpiio</span> <span class="c1"># installs the MPIIO package</span>
<span class="n">make</span> <span class="n">g</span><span class="o">++</span> <span class="c1"># build LAMMPS for your platform</span>
</pre></div>
</div>
<p>Second, use a restart filename which contains &#8221;.mpiio&#8221;. Note that it
does not have to end in &#8221;.mpiio&#8221;, just contain those characters.
Unlike MPI-IO dump files, a particular restart file must be both
written and read using MPI-IO.</p>
<p>Restart files can be read by a <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a>
command to restart a simulation from a particular state. Because the
file is binary (to enable exact restarts), it may not be readable on
another machine. In this case, you can use the <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">-r command-line switch</span></a> to convert a restart file to a data
file.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">Although the purpose of restart files is to enable restarting a
simulation from where it left off, not all information about a
simulation is stored in the file. For example, the list of fixes that
were specified during the initial run is not stored, which means the
new input script must specify any fixes you want to use. Even when
restart information is stored in the file, as it is for some fixes,
commands may need to be re-specified in the new input script, in order
to re-use that information. Details are usually given in the
documentation of the respective command. Also, see the
<a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a> command for general information about
what is stored in a restart file.</p>
</div>
<hr class="docutils" />
<p>The optional <em>nfile</em> or <em>fileper</em> keywords can be used in conjunction
with the &#8220;%&#8221; wildcard character in the specified restart file name.
As explained above, the &#8220;%&#8221; character causes the restart file to be
written in pieces, one piece for each of P processors. By default P =
the number of processors the simulation is running on. The <em>nfile</em> or
<em>fileper</em> keyword can be used to set P to a smaller value, which can
be more efficient when running on a large number of processors.</p>
<p>The <em>nfile</em> keyword sets P to the specified Nf value. For example, if
Nf = 4, and the simulation is running on 100 processors, 4 files will
be written, by processors 0,25,50,75. Each will collect information
from itself and the next 24 processors and write it to a restart file.</p>
<p>For the <em>fileper</em> keyword, the specified value of Np means write one
file for every Np processors. For example, if Np = 4, every 4th
processor (0,4,8,12,etc) will collect information from itself and the
next 3 processors and write it to a restart file.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>This command requires inter-processor communication to migrate atoms
before the restart file is written. This means that your system must
be ready to perform a simulation before using this command (force
fields setup, atom masses initialized, etc).</p>
<p>To write and read restart files in parallel with MPI-IO, the MPIIO
package must be installed.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><a class="reference internal" href="restart.html"><span class="doc">restart</span></a>, <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a>,
<a class="reference internal" href="write_data.html"><span class="doc">write_data</span></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