Homec4science
Diffusion lammps (efficient_neuronet) Browse

lammps/doc/fix_npt_sphere.html
8b6f939ef9aeefficient_neuronet

Last Change
Raw File

fix_npt_sphere.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 npt/sphere 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 npt/sphere 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-npt-sphere-command">
<span id="index-0"></span><h1>fix npt/sphere command<a class="headerlink" href="#fix-npt-sphere-command" title="Permalink to this headline">¶</a></h1>
</div>
<div class="section" id="fix-npt-sphere-omp-command">
<h1>fix npt/sphere/omp command<a class="headerlink" href="#fix-npt-sphere-omp-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 npt/sphere 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>npt/sphere = style name of this fix command</li>
<li>additional thermostat and barostat related keyword/value pairs from the <a class="reference internal" href="fix_nh.html"><em>fix npt</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 npt/sphere temp 300.0 300.0 100.0 iso 0.0 0.0 1000.0
fix 2 all npt/sphere temp 300.0 300.0 100.0 x 5.0 5.0 1000.0
fix 2 all npt/sphere temp 300.0 300.0 100.0 x 5.0 5.0 1000.0 drag 0.2
fix 2 water npt/sphere temp 300.0 300.0 100.0 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 NPT integration to update position, velocity, and
angular velocity each timestep for finite-sizex spherical particles in
the group using a Nose/Hoover temperature thermostat and Nose/Hoover
pressure barostat. P is pressure; T is temperature. This creates a
system trajectory consistent with the isothermal-isobaric ensemble.</p>
<p>This fix differs from the <a class="reference internal" href="fix_nh.html"><em>fix npt</em></a> command, which
assumes point particles and only updates their position and velocity.</p>
<p>The thermostat is applied to both the translational and rotational
degrees of freedom for the spherical particles, assuming a compute is
used which calculates a temperature that includes the rotational
degrees of freedom (see below). The translational degrees of freedom
can also have a bias velocity removed from them before thermostatting
takes place; see the description below.</p>
<p>Additional parameters affecting the thermostat and barostat are
specified by keywords and values documented with the <a class="reference internal" href="fix_nh.html"><em>fix npt</em></a> command. See, for example, discussion of the <em>temp</em>,
<em>iso</em>, <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
NPT 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 &#8220;temp/sphere&#8221; and
&#8220;pressure&#8221;, as if these commands had been issued:</p>
<div class="highlight-python"><div class="highlight"><pre>compute fix-ID_temp all temp/sphere
compute fix-ID_press all pressure fix-ID_temp
</pre></div>
</div>
<p>See the <a class="reference internal" href="compute_temp_sphere.html"><em>compute temp/sphere</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 + &#8220;temp&#8221; or fix_ID
+ underscore + &#8220;press&#8221;, and the group for the new computes is &#8220;all&#8221;
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&#8217;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>
<p>Like other fixes that perform thermostatting, this fix can be used
with <a class="reference internal" href="compute.html"><em>compute commands</em></a> that calculate a temperature
after removing a &#8220;bias&#8221; from the atom velocities. E.g. removing the
center-of-mass velocity from a group of atoms or only calculating
temperature on the x-component of velocity or only calculating
temperature for atoms in a geometric region. This is not done by
default, but only if the <a class="reference internal" href="fix_modify.html"><em>fix_modify</em></a> command is used
to assign a temperature compute to this fix that includes such a bias
term. See the doc pages for individual <a class="reference internal" href="compute.html"><em>compute commands</em></a> to determine which ones include a bias. In
this case, the thermostat works in the following manner: the current
temperature is calculated taking the bias into account, bias is
removed from each atom, thermostatting is performed on the remaining
thermal degrees of freedom, and the bias is added back in.</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 thermostat and 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 thermostatting and
barostatting to the system&#8217;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 npt</em></a> command.</p>
<p>This fix can ramp its target temperature and 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 requires that atoms store torque and angular velocity (omega)
and a radius as defined by the <a class="reference internal" href="atom_style.html"><em>atom_style sphere</em></a>
command.</p>
<p>All particles in the group must be finite-size spheres. They cannot
be point particles.</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 npt</em></a>, <a class="reference internal" href="fix_nve_sphere.html"><em>fix nve_sphere</em></a>, <a class="reference internal" href="fix_nvt_sphere.html"><em>fix nvt_sphere</em></a>, <a class="reference internal" href="fix_npt_asphere.html"><em>fix npt_asphere</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>
&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