forked from lijiext/lammps
330 lines
14 KiB
HTML
330 lines
14 KiB
HTML
|
|
|
|
<!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 — 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 & 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 & 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>
|
|
|
|
</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> »</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<a class="headerlink" href="#temper-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>temper N M temp fix-ID seed1 seed2 index
|
|
</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<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h2>
|
|
<div class="highlight-python"><div class="highlight"><pre>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<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></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>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>this section</span></a> of the manual for further
|
|
discussion.</p>
|
|
<p>Each replica’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"><em>variable</em></a>
|
|
command for more details. For example:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>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>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-python"><div class="highlight"><pre>Running on 16 partitions of processors
|
|
Step T0 T1 T2 T3 T4 T5 T6 T7 T8 T9 T10 T11 T12 T13 T14 T15
|
|
0 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
|
|
500 1 0 3 2 5 4 6 7 8 9 10 11 12 13 14 15
|
|
1000 2 0 4 1 5 3 6 7 8 9 10 11 12 14 13 15
|
|
1500 2 1 4 0 5 3 6 7 9 8 10 11 12 14 13 15
|
|
2000 2 1 3 0 6 4 5 7 10 8 9 11 12 14 13 15
|
|
2500 2 1 3 0 6 4 5 7 11 8 9 10 12 14 13 15
|
|
...
|
|
</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>
|
|
<div class="highlight-python"><div class="highlight"><pre>variable rep world 0 1 2 3 4 5 6 7
|
|
dump 1 all atom 1000 dump.temper.$*rep*
|
|
</pre></div>
|
|
</div>
|
|
<div class="admonition note">
|
|
<p class="first admonition-title">Note</p>
|
|
<p class="last">Each replica’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 “continuous trajectories” 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-python"><div class="highlight"><pre>500000 2 4 0 1 3
|
|
</pre></div>
|
|
</div>
|
|
<p>then a setting of</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>variable w world 2 4 0 1 3
|
|
</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<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></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>Making LAMMPS</span></a> section
|
|
for more info on packages.</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="variable.html"><em>variable</em></a>, <a class="reference internal" href="prd.html"><em>prd</em></a>, <a class="reference internal" href="neb.html"><em>neb</em></a></p>
|
|
<p><strong>Default:</strong> none</p>
|
|
</div>
|
|
</div>
|
|
|
|
|
|
</div>
|
|
</div>
|
|
<footer>
|
|
|
|
|
|
<hr/>
|
|
|
|
<div role="contentinfo">
|
|
<p>
|
|
© 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> |