Homec4science
Diffusion lammps (lammps-icms) Browse

lammps/doc/fix_tune_kspace.html
e2ec56c17156lammps-icms

Last Change
Raw File

fix_tune_kspace.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>fix tune/kspace command &mdash; LAMMPS 17 Dec 2015 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 17 Dec 2015 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>fix tune/kspace 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-tune-kspace-command">
<span id="index-0"></span><h1>fix tune/kspace command<a class="headerlink" href="#fix-tune-kspace-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>fix ID group-ID tune/kspace N
</pre></div>
</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><em>fix</em></a> command</li>
<li>tune/kspace = style name of this fix command</li>
<li>N = invoke this fix every N steps</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>fix 2 all tune/kspace 100
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
<p>This fix tests each kspace style (Ewald, PPPM, and MSM), and
automatically selects the fastest style to use for the remainder
of the run. If the fastest style is Ewald or PPPM, the fix also
adjusts the coulomb cutoff towards optimal speed. Future versions
of this fix will automatically select other kspace parameters
to use for maximum simulation speed. The kspace parameters may
include the style, cutoff, grid points in each direction, order,
Ewald parameter, MSM parallelization cut-point, MPI tasks to use, etc.</p>
<p>The rationale for this fix is to provide the user with
as-fast-as-possible simulations that include long-range electrostatics
(kspace) while meeting the user-prescribed accuracy requirement. A
simple heuristic could never capture the optimal combination of
parameters for every possible run-time scenario. But by performing
short tests of various kspace parameter sets, this fix allows
parameters to be tailored specifically to the user&#8217;s machine, MPI
ranks, use of threading or accelerators, the simulated system, and the
simulation details. In addition, it is possible that parameters could
be evolved with the simulation on-the-fly, which is useful for systems
that are dynamically evolving (e.g. changes in box size/shape or
number of particles).</p>
<p>When this fix is invoked, LAMMPS will perform short timed tests of
various parameter sets to determine the optimal parameters. Tests are
performed on-the-fly, with a new test initialized every N steps. N should
be chosen large enough so that adequate CPU time lapses between tests,
thereby providing statistically significant timings. But N should not be
chosen to be so large that an unfortunate parameter set test takes an
inordinate amount of wall time to complete. An N of 100 for most problems
seems reasonable. Once an optimal parameter set is found, that set is
used for the remainder of the run.</p>
<p>This fix uses heristics to guide it&#8217;s selection of parameter sets to test,
but the actual timed results will be used to decide which set to use in the
simulation.</p>
<p>It is not necessary to discard trajectories produced using sub-optimal
parameter sets, or a mix of various parameter sets, since the user-prescribed
accuracy will have been maintained throughout. However, some users may prefer
to use this fix only to discover the optimal parameter set for a given setup
that can then be used on subsequent production runs.</p>
<p>This fix starts with kspace parameters that are set by the user with the
<a class="reference internal" href="kspace_style.html"><em>kspace_style</em></a> and <a class="reference internal" href="kspace_modify.html"><em>kspace_modify</em></a>
commands. The prescribed accuracy will be maintained by this fix throughout
the simulation.</p>
<p>None of the <a class="reference internal" href="fix_modify.html"><em>fix_modify</em></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"><em>run</em></a> command. This fix is not invoked during <a class="reference internal" href="minimize.html"><em>energy minimization</em></a>.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
<p>This fix is part of the KSPACE package. It is only enabled if LAMMPS was
built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
<p>Do not set &#8220;neigh_modify once yes&#8221; or else this fix will never be
called. Reneighboring is required.</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="kspace_style.html"><em>kspace_style</em></a>, <a class="reference internal" href="boundary.html"><em>boundary</em></a>
<a class="reference internal" href="kspace_modify.html"><em>kspace_modify</em></a>, <a class="reference internal" href="pair_lj.html"><em>pair_style lj/cut/coul/long</em></a>, <a class="reference internal" href="pair_charmm.html"><em>pair_style lj/charmm/coul/long</em></a>, <a class="reference internal" href="pair_lj_long.html"><em>pair_style lj/long</em></a>, <a class="reference internal" href="pair_lj_long.html"><em>pair_style lj/long/coul/long</em></a>,
<a class="reference internal" href="pair_buck.html"><em>pair_style buck/coul/long</em></a></p>
</div>
<div class="section" id="default">
<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline">¶</a></h2>
<hr class="docutils" />
</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:'17 Dec 2015',
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