Homec4science
Diffusion lammps (lammm-master) Browse

lammps/doc/html/temper.html
7baaf2dfe210lammm-master

Last Change
Raw File

temper.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>temper 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>temper 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="temper-command">
<span id="index-0"></span><h1>temper command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">temper</span> <span class="n">N</span> <span class="n">M</span> <span class="n">temp</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID</span> <span class="n">seed1</span> <span class="n">seed2</span> <span class="n">index</span>
</pre></div>
</div>
<ul class="simple">
<li>N = total # of timesteps to run</li>
<li>M = attempt a tempering swap every this many steps</li>
<li>temp = initial temperature for this ensemble</li>
<li>fix-ID = ID of the fix that will control temperature during the run</li>
<li>seed1 = random # seed used to decide on adjacent temperature to partner with</li>
<li>seed2 = random # seed for Boltzmann factor in Metropolis swap</li>
<li>index = which temperature (0 to N-1) I am simulating (optional)</li>
</ul>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span>temper 100000 100 $t tempfix 0 58728
temper 40000 100 $t tempfix 0 32285 $w
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
<p>Run a parallel tempering or replica exchange simulation using multiple
replicas (ensembles) of a system. Two or more replicas must be used.</p>
<p>Each replica runs on a partition of one or more processors. Processor
partitions are defined at run-time using the -partition command-line
switch; see <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">Section_start 6</span></a> of the
manual. Note that if you have MPI installed, you can run a
multi-replica simulation with more replicas (partitions) than you have
physical processors, e.g you can run a 10-replica simulation on one or
two processors. You will simply not get the performance speed-up you
would see with one or more physical processors per replica. See <a class="reference internal" href="Section_howto.html#howto-5"><span class="std std-ref">this section</span></a> of the manual for further
discussion.</p>
<p>Each replica&#8217;s temperature is controlled at a different value by a fix
with <em>fix-ID</em> that controls temperature. Most thermostat fix styles
(with and without included time integration) are supported. The command
will print an error message and abort, if the chosen fix is unsupported.
The desired temperature is specified by <em>temp</em>, which is typically a
variable previously set in the input script, so that each partition is
assigned a different temperature. See the <a class="reference internal" href="variable.html"><span class="doc">variable</span></a>
command for more details. For example:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span>variable t world 300.0 310.0 320.0 330.0
fix myfix all nvt temp $t $t 100.0
temper 100000 100 $t myfix 3847 58382
</pre></div>
</div>
<p>would define 4 temperatures, and assign one of them to the thermostat
used by each replica, and to the temper command.</p>
<p>As the tempering simulation runs for <em>N</em> timesteps, a temperature swap
between adjacent ensembles will be attempted every <em>M</em> timesteps. If
<em>seed1</em> is 0, then the swap attempts will alternate between odd and
even pairings. If <em>seed1</em> is non-zero then it is used as a seed in a
random number generator to randomly choose an odd or even pairing each
time. Each attempted swap of temperatures is either accepted or
rejected based on a Boltzmann-weighted Metropolis criterion which uses
<em>seed2</em> in the random number generator.</p>
<p>As a tempering run proceeds, multiple log files and screen output
files are created, one per replica. By default these files are named
log.lammps.M and screen.M where M is the replica number from 0 to N-1,
with N = # of replicas. See the <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">section on command-line switches</span></a> for info on how to change these
names.</p>
<p>The main screen and log file (log.lammps) will list information about
which temperature is assigned to each replica at each thermodynamic
output timestep. E.g. for a simulation with 16 replicas:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Running</span> <span class="n">on</span> <span class="mi">16</span> <span class="n">partitions</span> <span class="n">of</span> <span class="n">processors</span>
<span class="n">Step</span> <span class="n">T0</span> <span class="n">T1</span> <span class="n">T2</span> <span class="n">T3</span> <span class="n">T4</span> <span class="n">T5</span> <span class="n">T6</span> <span class="n">T7</span> <span class="n">T8</span> <span class="n">T9</span> <span class="n">T10</span> <span class="n">T11</span> <span class="n">T12</span> <span class="n">T13</span> <span class="n">T14</span> <span class="n">T15</span>
<span class="mi">0</span> <span class="mi">0</span> <span class="mi">1</span> <span class="mi">2</span> <span class="mi">3</span> <span class="mi">4</span> <span class="mi">5</span> <span class="mi">6</span> <span class="mi">7</span> <span class="mi">8</span> <span class="mi">9</span> <span class="mi">10</span> <span class="mi">11</span> <span class="mi">12</span> <span class="mi">13</span> <span class="mi">14</span> <span class="mi">15</span>
<span class="mi">500</span> <span class="mi">1</span> <span class="mi">0</span> <span class="mi">3</span> <span class="mi">2</span> <span class="mi">5</span> <span class="mi">4</span> <span class="mi">6</span> <span class="mi">7</span> <span class="mi">8</span> <span class="mi">9</span> <span class="mi">10</span> <span class="mi">11</span> <span class="mi">12</span> <span class="mi">13</span> <span class="mi">14</span> <span class="mi">15</span>
<span class="mi">1000</span> <span class="mi">2</span> <span class="mi">0</span> <span class="mi">4</span> <span class="mi">1</span> <span class="mi">5</span> <span class="mi">3</span> <span class="mi">6</span> <span class="mi">7</span> <span class="mi">8</span> <span class="mi">9</span> <span class="mi">10</span> <span class="mi">11</span> <span class="mi">12</span> <span class="mi">14</span> <span class="mi">13</span> <span class="mi">15</span>
<span class="mi">1500</span> <span class="mi">2</span> <span class="mi">1</span> <span class="mi">4</span> <span class="mi">0</span> <span class="mi">5</span> <span class="mi">3</span> <span class="mi">6</span> <span class="mi">7</span> <span class="mi">9</span> <span class="mi">8</span> <span class="mi">10</span> <span class="mi">11</span> <span class="mi">12</span> <span class="mi">14</span> <span class="mi">13</span> <span class="mi">15</span>
<span class="mi">2000</span> <span class="mi">2</span> <span class="mi">1</span> <span class="mi">3</span> <span class="mi">0</span> <span class="mi">6</span> <span class="mi">4</span> <span class="mi">5</span> <span class="mi">7</span> <span class="mi">10</span> <span class="mi">8</span> <span class="mi">9</span> <span class="mi">11</span> <span class="mi">12</span> <span class="mi">14</span> <span class="mi">13</span> <span class="mi">15</span>
<span class="mi">2500</span> <span class="mi">2</span> <span class="mi">1</span> <span class="mi">3</span> <span class="mi">0</span> <span class="mi">6</span> <span class="mi">4</span> <span class="mi">5</span> <span class="mi">7</span> <span class="mi">11</span> <span class="mi">8</span> <span class="mi">9</span> <span class="mi">10</span> <span class="mi">12</span> <span class="mi">14</span> <span class="mi">13</span> <span class="mi">15</span>
<span class="o">...</span>
</pre></div>
</div>
<p>The column headings T0 to TN-1 mean which temperature is currently
assigned to the replica 0 to N-1. Thus the columns represent replicas
and the value in each column is its temperature (also numbered 0 to
N-1). For example, a 0 in the 4th column (column T3, step 2500) means
that the 4th replica is assigned temperature 0, i.e. the lowest
temperature. You can verify this time sequence of temperature
assignments for the Nth replica by comparing the Nth column of screen
output to the thermodynamic data in the corresponding log.lammps.N or
screen.N files as time proceeds.</p>
<p>You can have each replica create its own dump file in the following
manner:</p>
<pre class="literal-block">
variable rep world 0 1 2 3 4 5 6 7
dump 1 all atom 1000 dump.temper.$<em>rep</em>
</pre>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">Each replica&#8217;s dump file will contain a continuous trajectory
for its atoms where the temperature varies over time as swaps take
place involving that replica. If you want a series of dump files,
each with snapshots (from all replicas) that are all at a single
temperature, then you will need to post-process the dump files using
the information from the log.lammps file. E.g. you could produce one
dump file with snapshots at 300K (from all replicas), another with
snapshots at 310K, etc. Note that these new dump files will not
contain &#8220;continuous trajectories&#8221; for individual atoms, because two
successive snapshots (in time) may be from different replicas.</p>
</div>
<p>The last argument <em>index</em> in the temper command is optional and is
used when restarting a tempering run from a set of restart files (one
for each replica) which had previously swapped to new temperatures.
The <em>index</em> value (from 0 to N-1, where N is the # of replicas)
identifies which temperature the replica was simulating on the
timestep the restart files were written. Obviously, this argument
must be a variable so that each partition has the correct value. Set
the variable to the <em>N</em> values listed in the log file for the previous
run for the replica temperatures at that timestep. For example if the
log file listed the following for a simulation with 5 replicas:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="mi">500000</span> <span class="mi">2</span> <span class="mi">4</span> <span class="mi">0</span> <span class="mi">1</span> <span class="mi">3</span>
</pre></div>
</div>
<p>then a setting of</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">w</span> <span class="n">world</span> <span class="mi">2</span> <span class="mi">4</span> <span class="mi">0</span> <span class="mi">1</span> <span class="mi">3</span>
</pre></div>
</div>
<p>would be used to restart the run with a tempering command like the
example above with $w as the last argument.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>This command can only be used if LAMMPS was built with the REPLICA
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 on packages.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><a class="reference internal" href="variable.html"><span class="doc">variable</span></a>, <a class="reference internal" href="prd.html"><span class="doc">prd</span></a>, <a class="reference internal" href="neb.html"><span class="doc">neb</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