Homec4science
Diffusion lammps (lammm-devel) Browse

lammps/doc/html/fix_wall_reflect.html
548fa007a63alammm-devel

Last Change
Raw File

fix_wall_reflect.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 wall/reflect 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>fix wall/reflect 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-wall-reflect-command">
<span id="index-0"></span><h1>fix wall/reflect command</h1>
</div>
<div class="section" id="fix-wall-reflect-kk-command">
<h1>fix wall/reflect/kk 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">wall</span><span class="o">/</span><span class="n">reflect</span> <span class="n">face</span> <span class="n">arg</span> <span class="o">...</span> <span class="n">keyword</span> <span class="n">value</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>wall/reflect = style name of this fix command</li>
<li>one or more face/arg pairs may be appended</li>
<li>face = <em>xlo</em> or <em>xhi</em> or <em>ylo</em> or <em>yhi</em> or <em>zlo</em> or <em>zhi</em></li>
</ul>
<pre class="literal-block">
<em>xlo</em>,<em>ylo</em>,<em>zlo</em> arg = EDGE or constant or variable
EDGE = current lo edge of simulation box
constant = number like 0.0 or -30.0 (distance units)
variable = <a class="reference internal" href="variable.html"><span class="doc">equal-style variable</span></a> like v_x or v_wiggle
<em>xhi</em>,<em>yhi</em>,<em>zhi</em> arg = EDGE or constant or variable
EDGE = current hi edge of simulation box
constant = number like 50.0 or 100.3 (distance units)
variable = <a class="reference internal" href="variable.html"><span class="doc">equal-style variable</span></a> like v_x or v_wiggle
</pre>
<ul class="simple">
<li>zero or more keyword/value pairs may be appended</li>
<li>keyword = <em>units</em></li>
</ul>
<pre class="literal-block">
<em>units</em> value = <em>lattice</em> or <em>box</em>
<em>lattice</em> = the wall position is defined in lattice units
<em>box</em> = the wall position is defined in simulation box units
</pre>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">xwalls</span> <span class="nb">all</span> <span class="n">wall</span><span class="o">/</span><span class="n">reflect</span> <span class="n">xlo</span> <span class="n">EDGE</span> <span class="n">xhi</span> <span class="n">EDGE</span>
<span class="n">fix</span> <span class="n">walls</span> <span class="nb">all</span> <span class="n">wall</span><span class="o">/</span><span class="n">reflect</span> <span class="n">xlo</span> <span class="mf">0.0</span> <span class="n">ylo</span> <span class="mf">10.0</span> <span class="n">units</span> <span class="n">box</span>
<span class="n">fix</span> <span class="n">top</span> <span class="nb">all</span> <span class="n">wall</span><span class="o">/</span><span class="n">reflect</span> <span class="n">zhi</span> <span class="n">v_pressdown</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
<p>Bound the simulation with one or more walls which reflect particles
in the specified group when they attempt to move thru them.</p>
<p>Reflection means that if an atom moves outside the wall on a timestep
by a distance delta (e.g. due to <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a>), then it is
put back inside the face by the same delta, and the sign of the
corresponding component of its velocity is flipped.</p>
<p>When used in conjunction with <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> and <a class="reference internal" href="run_style.html"><span class="doc">run_style verlet</span></a>, the resultant time-integration algorithm is
equivalent to the primitive splitting algorithm (PSA) described by
<a class="reference internal" href="#bond"><span class="std std-ref">Bond</span></a>. Because each reflection event divides
the corresponding timestep asymmetrically, energy conservation is only
satisfied to O(dt), rather than to O(dt^2) as it would be for
velocity-Verlet integration without reflective walls.</p>
<p>Up to 6 walls or faces can be specified in a single command: <em>xlo</em>,
<em>xhi</em>, <em>ylo</em>, <em>yhi</em>, <em>zlo</em>, <em>zhi</em>. A <em>lo</em> face reflects particles
that move to a coordinate less than the wall position, back in the
<em>hi</em> direction. A <em>hi</em> face reflects particles that move to a
coordinate higher than the wall position, back in the <em>lo</em> direction.</p>
<p>The position of each wall can be specified in one of 3 ways: as the
EDGE of the simulation box, as a constant value, or as a variable. If
EDGE is used, then the corresponding boundary of the current
simulation box is used. If a numeric constant is specified then the
wall is placed at that position in the appropriate dimension (x, y, or
z). In both the EDGE and constant cases, the wall will never move.
If the wall position is a variable, it should be specified as v_name,
where name is an <a class="reference internal" href="variable.html"><span class="doc">equal-style variable</span></a> name. In this
case the variable is evaluated each timestep and the result becomes
the current position of the reflecting wall. Equal-style variables
can specify formulas with various mathematical functions, and include
<a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style</span></a> command keywords for the simulation
box parameters and timestep and elapsed time. Thus it is easy to
specify a time-dependent wall position.</p>
<p>The <em>units</em> keyword determines the meaning of the distance units used
to define a wall position, but only when a numeric constant or
variable is used. It is not relevant when EDGE is used to specify a
face position. In the variable case, the variable is assumed to
produce a value compatible with the <em>units</em> setting you specify.</p>
<p>A <em>box</em> value selects standard distance units as defined by the
<a class="reference internal" href="units.html"><span class="doc">units</span></a> command, e.g. Angstroms for units = real or metal.
A <em>lattice</em> value means the distance units are in lattice spacings.
The <a class="reference internal" href="lattice.html"><span class="doc">lattice</span></a> command must have been previously used to
define the lattice spacings.</p>
<hr class="docutils" />
<p>Here are examples of variable definitions that move the wall position
in a time-dependent fashion using equal-style
<a class="reference internal" href="variable.html"><span class="doc">variables</span></a>.</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">ramp</span> <span class="n">equal</span> <span class="n">ramp</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="mi">10</span><span class="p">)</span>
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">wall</span><span class="o">/</span><span class="n">reflect</span> <span class="n">xlo</span> <span class="n">v_ramp</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">linear</span> <span class="n">equal</span> <span class="n">vdisplace</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="mi">20</span><span class="p">)</span>
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">wall</span><span class="o">/</span><span class="n">reflect</span> <span class="n">xlo</span> <span class="n">v_linear</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">wiggle</span> <span class="n">equal</span> <span class="n">swiggle</span><span class="p">(</span><span class="mf">0.0</span><span class="p">,</span><span class="mf">5.0</span><span class="p">,</span><span class="mf">3.0</span><span class="p">)</span>
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">wall</span><span class="o">/</span><span class="n">reflect</span> <span class="n">xlo</span> <span class="n">v_wiggle</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">wiggle</span> <span class="n">equal</span> <span class="n">cwiggle</span><span class="p">(</span><span class="mf">0.0</span><span class="p">,</span><span class="mf">5.0</span><span class="p">,</span><span class="mf">3.0</span><span class="p">)</span>
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">wall</span><span class="o">/</span><span class="n">reflect</span> <span class="n">xlo</span> <span class="n">v_wiggle</span>
</pre></div>
</div>
<p>The ramp(lo,hi) function adjusts the wall position linearly from lo to
hi over the course of a run. The vdisplace(c0,velocity) function does
something similar using the equation position = c0 + velocity*delta,
where delta is the elapsed time.</p>
<p>The swiggle(c0,A,period) function causes the wall position to
oscillate sinusoidally according to this equation, where omega = 2 PI
/ period:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">position</span> <span class="o">=</span> <span class="n">c0</span> <span class="o">+</span> <span class="n">A</span> <span class="n">sin</span><span class="p">(</span><span class="n">omega</span><span class="o">*</span><span class="n">delta</span><span class="p">)</span>
</pre></div>
</div>
<p>The cwiggle(c0,A,period) function causes the wall position to
oscillate sinusoidally according to this equation, which will have an
initial wall velocity of 0.0, and thus may impose a gentler
perturbation on the particles:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">position</span> <span class="o">=</span> <span class="n">c0</span> <span class="o">+</span> <span class="n">A</span> <span class="p">(</span><span class="mi">1</span> <span class="o">-</span> <span class="n">cos</span><span class="p">(</span><span class="n">omega</span><span class="o">*</span><span class="n">delta</span><span class="p">))</span>
</pre></div>
</div>
<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"><span class="doc">Section_accelerate</span></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 class="std std-ref">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 class="std std-ref">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
</div>
<hr class="docutils" />
<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. No global or per-atom quantities are stored
by this fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>. 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>Any dimension (xyz) that has a reflecting wall must be non-periodic.</p>
<p>A reflecting wall should not be used with rigid bodies such as those
defined by a &#8220;fix rigid&#8221; command. This is because the wall/reflect
displaces atoms directly rather than exerts a force on them. For
rigid bodies, use a soft wall instead, such as <a class="reference internal" href="fix_wall.html"><span class="doc">fix wall/lj93</span></a>. LAMMPS will flag the use of a rigid
fix with fix wall/reflect with a warning, but will not generate an
error.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><a class="reference internal" href="fix_wall.html"><span class="doc">fix wall/lj93</span></a>, <a class="reference internal" href="fix_oneway.html"><span class="doc">fix oneway</span></a></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="bond"><strong>(Bond)</strong> Bond and Leimkuhler, SIAM J Sci Comput, 30, p 134 (2007).</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