forked from lijiext/lammps
309 lines
14 KiB
HTML
309 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>fix nph/body 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>fix nph/body 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-nph-body-command">
|
||
|
|
<span id="index-0"></span><h1>fix nph/body command<a class="headerlink" href="#fix-nph-body-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 nph/body args keyword value ...
|
||
|
|
</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>nph/body = style name of this fix command</li>
|
||
|
|
<li>additional barostat related keyword/value pairs from the <a class="reference internal" href="fix_nh.html"><em>fix nph</em></a> command can be appended</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>fix 1 all nph/body iso 0.0 0.0 1000.0
|
||
|
|
fix 2 all nph/body x 5.0 5.0 1000.0
|
||
|
|
fix 2 all nph/body x 5.0 5.0 1000.0 drag 0.2
|
||
|
|
fix 2 water nph/body aniso 0.0 0.0 1000.0 dilate partial
|
||
|
|
</pre></div>
|
||
|
|
</div>
|
||
|
|
</div>
|
||
|
|
<div class="section" id="description">
|
||
|
|
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
|
||
|
|
<p>Perform constant NPH integration to update position, velocity,
|
||
|
|
orientation, and angular velocity each timestep for body
|
||
|
|
particles in the group using a Nose/Hoover pressure
|
||
|
|
barostat. P is pressure; H is enthalpy. This creates a system
|
||
|
|
trajectory consistent with the isenthalpic ensemble.</p>
|
||
|
|
<p>This fix differs from the <a class="reference internal" href="fix_nh.html"><em>fix nph</em></a> command, which assumes
|
||
|
|
point particles and only updates their position and velocity.</p>
|
||
|
|
<p>Additional parameters affecting the barostat are specified by keywords
|
||
|
|
and values documented with the <a class="reference internal" href="fix_nh.html"><em>fix nph</em></a> command. See,
|
||
|
|
for example, discussion of the <em>aniso</em>, and <em>dilate</em> keywords.</p>
|
||
|
|
<p>The particles in the fix group are the only ones whose velocities and
|
||
|
|
positions are updated by the velocity/position update portion of the
|
||
|
|
NPH integration.</p>
|
||
|
|
<p>Regardless of what particles are in the fix group, a global pressure is
|
||
|
|
computed for all particles. Similarly, when the size of the simulation
|
||
|
|
box is changed, all particles are re-scaled to new positions, unless the
|
||
|
|
keyword <em>dilate</em> is specified with a value of <em>partial</em>, in which case
|
||
|
|
only the particles in the fix group are re-scaled. The latter can be
|
||
|
|
useful for leaving the coordinates of particles in a solid substrate
|
||
|
|
unchanged and controlling the pressure of a surrounding fluid.</p>
|
||
|
|
<hr class="docutils" />
|
||
|
|
<p>This fix computes a temperature and pressure each timestep. To do
|
||
|
|
this, the fix creates its own computes of style “temp/body” and
|
||
|
|
“pressure”, as if these commands had been issued:</p>
|
||
|
|
<div class="highlight-python"><div class="highlight"><pre>compute fix-ID_temp all temp/body
|
||
|
|
compute fix-ID_press all pressure fix-ID_temp
|
||
|
|
</pre></div>
|
||
|
|
</div>
|
||
|
|
<p>See the <a class="reference internal" href="compute_temp_body.html"><em>compute temp/body</em></a> and <a class="reference internal" href="compute_pressure.html"><em>compute pressure</em></a> commands for details. Note that the
|
||
|
|
IDs of the new computes are the fix-ID + underscore + “temp” or fix_ID
|
||
|
|
+ underscore + “press”, and the group for the new computes is “all”
|
||
|
|
since pressure is computed for the entire system.</p>
|
||
|
|
<p>Note that these are NOT the computes used by thermodynamic output (see
|
||
|
|
the <a class="reference internal" href="thermo_style.html"><em>thermo_style</em></a> command) with ID = <em>thermo_temp</em>
|
||
|
|
and <em>thermo_press</em>. This means you can change the attributes of this
|
||
|
|
fix’s temperature or pressure via the
|
||
|
|
<a class="reference internal" href="compute_modify.html"><em>compute_modify</em></a> command or print this temperature
|
||
|
|
or pressure during thermodynamic output via the <a class="reference internal" href="thermo_style.html"><em>thermo_style custom</em></a> command using the appropriate compute-ID.
|
||
|
|
It also means that changing attributes of <em>thermo_temp</em> or
|
||
|
|
<em>thermo_press</em> will have no effect on this fix.</p>
|
||
|
|
<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"><em>Section_accelerate</em></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>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>-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
|
||
|
|
use the <a class="reference internal" href="suffix.html"><em>suffix</em></a> command in your input script.</p>
|
||
|
|
<p>See <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a> of the manual for
|
||
|
|
more instructions on how to use the accelerated styles effectively.</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>This fix writes the state of the Nose/Hoover barostat to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>. See the <a class="reference internal" href="read_restart.html"><em>read_restart</em></a>
|
||
|
|
command for info on how to re-specify a fix in an input script that
|
||
|
|
reads a restart file, so that the operation of the fix continues in an
|
||
|
|
uninterrupted fashion.</p>
|
||
|
|
<p>The <a class="reference internal" href="fix_modify.html"><em>fix_modify</em></a> <em>temp</em> and <em>press</em> options are
|
||
|
|
supported by this fix. You can use them to assign a
|
||
|
|
<a class="reference internal" href="compute.html"><em>compute</em></a> you have defined to this fix which will be used
|
||
|
|
in its thermostatting or barostatting procedure. If you do this, note
|
||
|
|
that the kinetic energy derived from the compute temperature should be
|
||
|
|
consistent with the virial term computed using all atoms for the
|
||
|
|
pressure. LAMMPS will warn you if you choose to compute temperature
|
||
|
|
on a subset of atoms.</p>
|
||
|
|
<p>The <a class="reference internal" href="fix_modify.html"><em>fix_modify</em></a> <em>energy</em> option is supported by this
|
||
|
|
fix to add the energy change induced by Nose/Hoover barostatting to
|
||
|
|
the system’s potential energy as part of <a class="reference internal" href="thermo_style.html"><em>thermodynamic output</em></a>.</p>
|
||
|
|
<p>This fix computes the same global scalar and global vector of
|
||
|
|
quantities as does the <a class="reference internal" href="fix_nh.html"><em>fix nph</em></a> command.</p>
|
||
|
|
<p>This fix can ramp its target pressure over multiple runs, using the
|
||
|
|
<em>start</em> and <em>stop</em> keywords of the <a class="reference internal" href="run.html"><em>run</em></a> command. See the
|
||
|
|
<a class="reference internal" href="run.html"><em>run</em></a> command for details of how to do this.</p>
|
||
|
|
<p>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 BODY 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>This fix requires that atoms store torque and angular momementum and a
|
||
|
|
quaternion as defined by the <a class="reference internal" href="atom_style.html"><em>atom_style body</em></a>
|
||
|
|
command.</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="fix_nh.html"><em>fix nph</em></a>, <a class="reference internal" href="fix_nve_body.html"><em>fix nve_body</em></a>, <a class="reference internal" href="fix_nvt_body.html"><em>fix nvt_body</em></a>, <a class="reference internal" href="fix_npt_body.html"><em>fix npt_body</em></a>, <a class="reference internal" href="fix_modify.html"><em>fix_modify</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>
|