Homec4science
Diffusion lammps (lammps-icms) Browse

lammps/doc/html/fix_pimd.html
db1e17197fcflammps-icms

Last Change
Raw File

fix_pimd.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 pimd 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 pimd 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-pimd-command">
<span id="index-0"></span><h1>fix pimd 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">pimd</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>pimd = style name of this fix command</li>
<li>zero or more keyword/value pairs may be appended</li>
<li>keyword = <em>method</em> or <em>fmass</em> or <em>sp</em> or <em>temp</em> or <em>nhc</em></li>
</ul>
<pre class="literal-block">
<em>method</em> value = <em>pimd</em> or <em>nmpimd</em> or <em>cmd</em>
<em>fmass</em> value = scaling factor on mass
<em>sp</em> value = scaling factor on Planck constant
<em>temp</em> value = temperature (temperarate units)
<em>nhc</em> value = Nc = number of chains in Nose-Hoover thermostat
</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="mi">1</span> <span class="nb">all</span> <span class="n">pimd</span> <span class="n">method</span> <span class="n">nmpimd</span> <span class="n">fmass</span> <span class="mf">1.0</span> <span class="n">sp</span> <span class="mf">2.0</span> <span class="n">temp</span> <span class="mf">300.0</span> <span class="n">nhc</span> <span class="mi">4</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
<p>This command performs quantum molecular dynamics simulations based on
the Feynman path integral to include effects of tunneling and
zero-point motion. In this formalism, the isomorphism of a quantum
partition function for the original system to a classical partition
function for a ring-polymer system is exploited, to efficiently sample
configurations from the canonical ensemble <a class="reference internal" href="#feynman"><span class="std std-ref">(Feynman)</span></a>.
The classical partition function and its components are given
by the following equations:</p>
<img alt="_images/fix_pimd.jpg" class="align-center" src="_images/fix_pimd.jpg" />
<p>The interested user is referred to any of the numerous references on
this methodology, but briefly, each quantum particle in a path
integral simulation is represented by a ring-polymer of P quasi-beads,
labeled from 1 to P. During the simulation, each quasi-bead interacts
with beads on the other ring-polymers with the same imaginary time
index (the second term in the effective potential above). The
quasi-beads also interact with the two neighboring quasi-beads through
the spring potential in imaginary-time space (first term in effective
potential). To sample the canonical ensemble, a Nose-Hoover massive
chain thermostat is applied <a class="reference internal" href="#pimd-tuckerman"><span class="std std-ref">(Tuckerman)</span></a>. With the
massive chain algorithm, a chain of NH thermostats is coupled to each
degree of freedom for each quasi-bead. The keyword <em>temp</em> sets the
target temperature for the system and the keyword <em>nhc</em> sets the
number <em>Nc</em> of thermostats in each chain. For example, for a
simulation of N particles with P beads in each ring-polymer, the total
number of NH thermostats would be 3 x N x P x Nc.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">This fix implements a complete velocity-verlet integrator
combined with NH massive chain thermostat, so no other time
integration fix should be used.</p>
</div>
<p>The <em>method</em> keyword determines what style of PIMD is performed. A
value of <em>pimd</em> is standard PIMD. A value of <em>nmpimd</em> is for
normal-mode PIMD. A value of <em>cmd</em> is for centroid molecular dynamics
(CMD). The difference between the styles is as follows.</p>
<p>In standard PIMD, the value used for a bead&#8217;s fictitious mass is
arbitrary. A common choice is to use Mi = m/P, which results in the
mass of the entire ring-polymer being equal to the real quantum
particle. But it can be difficult to efficiently integrate the
equations of motion for the stiff harmonic interactions in the ring
polymers.</p>
<p>A useful way to resolve this issue is to integrate the equations of
motion in a normal mode representation, using Normal Mode
Path-Integral Molecular Dynamics (NMPIMD) <a class="reference internal" href="#cao1"><span class="std std-ref">(Cao1)</span></a>. In NMPIMD,
the NH chains are attached to each normal mode of the ring-polymer and
the fictitious mass of each mode is chosen as Mk = the eigenvalue of
the Kth normal mode for k &gt; 0. The k = 0 mode, referred to as the
zero-frequency mode or centroid, corresponds to overall translation of
the ring-polymer and is assigned the mass of the real particle.</p>
<p>Motion of the centroid can be effectively uncoupled from the other
normal modes by scaling the fictitious masses to achieve a partial
adiabatic separation. This is called a Centroid Molecular Dynamics
(CMD) approximation <a class="reference internal" href="#cao2"><span class="std std-ref">(Cao2)</span></a>. The time-evolution (and resulting
dynamics) of the quantum particles can be used to obtain centroid time
correlation functions, which can be further used to obtain the true
quantum correlation function for the original system. The CMD method
also uses normal modes to evolve the system, except only the k &gt; 0
modes are thermostatted, not the centroid degrees of freedom.</p>
<p>The keyword <em>fmass</em> sets a further scaling factor for the fictitious
masses of beads, which can be used for the Partial Adiabatic CMD
<a class="reference internal" href="#hone"><span class="std std-ref">(Hone)</span></a>, or to be set as P, which results in the fictitious
masses to be equal to the real particle masses.</p>
<p>The keyword <em>sp</em> is a scaling factor on Planck&#8217;s constant, which can
be useful for debugging or other purposes. The default value of 1.0
is appropriate for most situations.</p>
<p>The PIMD algorithm in LAMMPS is implemented as a hyper-parallel scheme
as described in <a class="reference internal" href="#calhoun"><span class="std std-ref">(Calhoun)</span></a>. In LAMMPS this is done by using
<a class="reference internal" href="Section_howto.html#howto-5"><span class="std std-ref">multi-replica feature</span></a> in LAMMPS, where
each quasi-particle system is stored and simulated on a separate
partition of processors. The following diagram illustrates this
approach. The original system with 2 ring polymers is shown in red.
Since each ring has 4 quasi-beads (imaginary time slices), there are 4
replicas of the system, each running on one of the 4 partitions of
processors. Each replica (shown in green) owns one quasi-bead in each
ring.</p>
<img alt="_images/pimd.jpg" class="align-center" src="_images/pimd.jpg" />
<p>To run a PIMD simulation with M quasi-beads in each ring polymer using
N MPI tasks for each partition&#8217;s domain-decomposition, you would use P
= MxN processors (cores) and run the simulation as follows:</p>
<pre class="literal-block">
mpirun -np P lmp_mpi -partition MxN -in script
</pre>
<p>Note that in the LAMMPS input script for a multi-partition simulation,
it is often very useful to define a <a class="reference internal" href="variable.html"><span class="doc">uloop-style variable</span></a> such as</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">ibead</span> <span class="n">uloop</span> <span class="n">M</span> <span class="n">pad</span>
</pre></div>
</div>
<p>where M is the number of quasi-beads (partitions) used in the
calculation. The uloop variable can then be used to manage I/O
related tasks for each of the partitions, e.g.</p>
<pre class="literal-block">
dump dcd all dcd 10 system_${ibead}.dcd
restart 1000 system_${ibead}.restart1 system_${ibead}.restart2
read_restart system_${ibead}.restart2
</pre>
</div>
<div class="section" id="restrictions">
<h2>Restrictions</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 class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
<p>A PIMD simulation can be initialized with a single data file read via
the <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> command. However, this means all
quasi-beads in a ring polymer will have identical positions and
velocities, resulting in identical trajectories for all quasi-beads.
To avoid this, users can simply initialize velocities with different
random number seeds assigned to each partition, as defined by the
uloop variable, e.g.</p>
<div class="highlight-default"><div class="highlight"><pre><span></span>velocity all create 300.0 1234${ibead} rot yes dist gaussian
</pre></div>
</div>
</div>
<div class="section" id="default">
<h2>Default</h2>
<p>The keyword defaults are method = pimd, fmass = 1.0, sp = 1.0, temp = 300.0,
and nhc = 2.</p>
<hr class="docutils" />
<p id="feynman"><strong>(Feynman)</strong> R. Feynman and A. Hibbs, Chapter 7, Quantum Mechanics and
Path Integrals, McGraw-Hill, New York (1965).</p>
<p id="pimd-tuckerman"><strong>(Tuckerman)</strong> M. Tuckerman and B. Berne, J Chem Phys, 99, 2796 (1993).</p>
<p id="cao1"><strong>(Cao1)</strong> J. Cao and B. Berne, J Chem Phys, 99, 2902 (1993).</p>
<p id="cao2"><strong>(Cao2)</strong> J. Cao and G. Voth, J Chem Phys, 100, 5093 (1994).</p>
<p id="hone"><strong>(Hone)</strong> T. Hone, P. Rossky, G. Voth, J Chem Phys, 124,
154103 (2006).</p>
<p id="calhoun"><strong>(Calhoun)</strong> A. Calhoun, M. Pavese, G. Voth, Chem Phys Letters, 262,
415 (1996).</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