Homec4science
Diffusion lammps (efficient_neuronet) Browse

lammps/doc/fix_imd.html
c6213f36d34cefficient_neuronet

Last Change
Raw File

fix_imd.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 imd command &mdash; LAMMPS 15 May 2015 version 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 15 May 2015 version 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 imd command</li>
<li class="wy-breadcrumbs-aside">
<a href="http://lammps.sandia.gov">Homepage</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-imd-command">
<span id="index-0"></span><h1>fix imd command<a class="headerlink" href="#fix-imd-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 imd trate port keyword values ...
</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>imd = style name of this fix command</li>
<li>port = port number on which the fix listens for an IMD client</li>
<li>keyword = <em>unwrap</em> or <em>fscale</em> or <em>trate</em></li>
</ul>
<pre class="literal-block">
<em>unwrap</em> arg = <em>on</em> or <em>off</em>
off = coordinates are wrapped back into the principal unit cell (default)
on = &quot;unwrapped&quot; coordinates using the image flags used
<em>fscale</em> arg = factor
factor = floating point number to scale IMD forces (default: 1.0)
<em>trate</em> arg = transmission rate of coordinate data sets (default: 1)
<em>nowait</em> arg = <em>on</em> or <em>off</em>
off = LAMMPS waits to be connected to an IMD client before continuing (default)
on = LAMMPS listens for an IMD client, but continues with the run
</pre>
</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 vmd all imd 5678
fix comm all imd 8888 trate 5 unwrap on fscale 10.0
</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 implements the &#8220;Interactive MD&#8221; (IMD) protocol which allows
realtime visualization and manipulation of MD simulations through the
IMD protocol, as initially implemented in VMD and NAMD. Specifically
it allows LAMMPS to connect an IMD client, for example the <a class="reference external" href="http://www.ks.uiuc.edu/Research/vmd">VMD visualization program</a>, so that it can monitor the progress of the
simulation and interactively apply forces to selected atoms.</p>
<p>If LAMMPS is compiled with the preprocessor flag -DLAMMPS_ASYNC_IMD
then fix imd will use POSIX threads to spawn a IMD communication
thread on MPI rank 0 in order to offload data reading and writing
from the main execution thread and potentially lower the inferred
latencies for slow communication links. This feature has only been
tested under linux.</p>
<p>There are example scripts for using this package with LAMMPS in
examples/USER/imd. Additional examples and a driver for use with the
Novint Falcon game controller as haptic device can be found at:
<a class="reference external" href="http://sites.google.com/site/akohlmey/software/vrpn-icms">http://sites.google.com/site/akohlmey/software/vrpn-icms</a>.</p>
<p>The source code for this fix includes code developed by the
Theoretical and Computational Biophysics Group in the Beckman
Institute for Advanced Science and Technology at the University of
Illinois at Urbana-Champaign. We thank them for providing a software
interface that allows codes like LAMMPS to hook to <a class="reference external" href="http://www.ks.uiuc.edu/Research/vmd">VMD</a>.</p>
<p>Upon initialization of the fix, it will open a communication port on
the node with MPI task 0 and wait for an incoming connection. As soon
as an IMD client is connected, the simulation will continue and the
fix will send the current coordinates of the fix&#8217;s group to the IMD
client at every trate MD step. When using r-RESPA, trate applies to
the steps of the outmost RESPA level. During a run with an active IMD
connection also the IMD client can request to apply forces to selected
atoms of the fix group.</p>
<p>The port number selected must be an available network port number. On
many machines, port numbers &lt; 1024 are reserved for accounts with
system manager privilege and specific applications. If multiple imd
fixes would be active at the same time, each needs to use a different
port number.</p>
<p>The <em>nowait</em> keyword controls the behavior of the fix when no IMD
client is connected. With the default setting of <em>off</em>, LAMMPS will
wait until a connection is made before continuing with the
execution. Setting <em>nowait</em> to <em>on</em> will have the LAMMPS code be ready
to connect to a client, but continue with the simulation. This can for
example be used to monitor the progress of an ongoing calculation
without the need to be permanently connected or having to download a
trajectory file.</p>
<p>The <em>trate</em> keyword allows to select how often the coordinate data is
sent to the IMD client. It can also be changed on request of the IMD
client through an IMD protocol message. The <em>unwrap</em> keyword allows
to send &#8220;unwrapped&#8221; coordinates to the IMD client that undo the
wrapping back of coordinates into the principle unit cell, as done by
default in LAMMPS. The <em>fscale</em> keyword allows to apply a scaling
factor to forces transmitted by the IMD client. The IMD protocols
stipulates that forces are transferred in kcal/mol/angstrom under the
assumption that coordinates are given in angstrom. For LAMMPS runs
with different units or as a measure to tweak the forces generated by
the manipulation of the IMD client, this option allows to make
adjustments.</p>
<p>To connect VMD to a listening LAMMPS simulation on the same machine
with fix imd enabled, one needs to start VMD and load a coordinate or
topology file that matches the fix group. When the VMD command
prompts appears, one types the command line:</p>
<div class="highlight-python"><div class="highlight"><pre>imd connect localhost 5678
</pre></div>
</div>
<p>This assumes that <em>fix imd</em> was started with 5678 as a port
number for the IMD protocol.</p>
<p>The steps to do interactive manipulation of a running simulation in
VMD are the following:</p>
<p>In the Mouse menu of the VMD Main window, select &#8220;Mouse -&gt; Force -&gt;
Atom&#8221;. You may alternately select &#8220;Residue&#8221;, or &#8220;Fragment&#8221; to apply
forces to whole residues or fragments. Your mouse can now be used to
apply forces to your simulation. Click on an atom, residue, or
fragment and drag to apply a force. Click quickly without moving the
mouse to turn the force off. You can also use a variety of 3D position
trackers to apply forces to your simulation. Game controllers or haptic
devices with force-feedback such as the Novint Falcon or Sensable
PHANTOM allow you to feel the resistance due to inertia or interactions
with neighbors that the atoms experience you are trying to move, as if
they were real objects. See the <a class="reference external" href="http://www.ks.uiuc.edu/Research/vmd/imd/">VMD IMD Homepage</a> and the
<a class="reference external" href="http://sites.google.com/site/akohlmey/software/vrpn-icms">VRPN-ICMS Homepage</a> for more details.</p>
<p>If IMD control messages are received, a line of text describing the
message and its effect will be printed to the LAMMPS output screen, if
screen output is active.</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<a class="headerlink" href="#restart-fix-modify-output-run-start-stop-minimize-info" title="Permalink to this headline">¶</a></h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>. None of the <a class="reference internal" href="fix_modify.html"><em>fix_modify</em></a> options
are relevant to this fix. No global scalar or vector or per-atom
quantities are stored by this fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span>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"><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 USER-MISC 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>When used in combination with VMD, a topology or coordinate file has
to be loaded, which matches (in number and ordering of atoms) the
group the fix is applied to. The fix internally sorts atom IDs by
ascending integer value; in VMD (and thus the IMD protocol) those will
be assigned 0-based consecutive index numbers.</p>
<p>When using multiple active IMD connections at the same time, each
needs to use a different port number.</p>
<p><strong>Related commands:</strong> none</p>
<p><strong>Default:</strong> none</p>
</div>
</div>
</div>
</div>
<footer>
<hr/>
<div role="contentinfo">
<p>
&copy; Copyright .
</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:'15 May 2015 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="_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