Homec4science
Diffusion lammps (lammm-master) Browse

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

Last Change
Raw File

create_box.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>create_box 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>create_box 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="create-box-command">
<span id="index-0"></span><h1>create_box command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">create_box</span> <span class="n">N</span> <span class="n">region</span><span class="o">-</span><span class="n">ID</span> <span class="n">keyword</span> <span class="n">value</span> <span class="o">...</span>
</pre></div>
</div>
<ul class="simple">
<li>N = # of atom types to use in this simulation</li>
<li>region-ID = ID of region to use as simulation domain</li>
<li>zero or more keyword/value pairs may be appended</li>
<li>keyword = <em>bond/types</em> or <em>angle/types</em> or <em>dihedral/types</em> or <em>improper/types</em> or <em>extra/bond/per/atom</em> or <em>extra/angle/per/atom</em> or <em>extra/dihedral/per/atom</em> or <em>extra/improper/per/atom</em></li>
</ul>
<pre class="literal-block">
<em>bond/types</em> value = # of bond types
<em>angle/types</em> value = # of angle types
<em>dihedral/types</em> value = # of dihedral types
<em>improper/types</em> value = # of improper types
<em>extra/bond/per/atom</em> value = # of bonds per atom
<em>extra/angle/per/atom</em> value = # of angles per atom
<em>extra/dihedral/per/atom</em> value = # of dihedrals per atom
<em>extra/improper/per/atom</em> value = # of impropers per atom
<em>extra/special/per/atom</em> value = # of special neighbors per atom
</pre>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">create_box</span> <span class="mi">2</span> <span class="n">mybox</span>
<span class="n">create_box</span> <span class="mi">2</span> <span class="n">mybox</span> <span class="n">bond</span><span class="o">/</span><span class="n">types</span> <span class="mi">2</span> <span class="n">extra</span><span class="o">/</span><span class="n">bond</span><span class="o">/</span><span class="n">per</span><span class="o">/</span><span class="n">atom</span> <span class="mi">1</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
<p>This command creates a simulation box based on the specified region.
Thus a <a class="reference internal" href="region.html"><span class="doc">region</span></a> command must first be used to define a
geometric domain. It also partitions the simulation box into a
regular 3d grid of rectangular bricks, one per processor, based on the
number of processors being used and the settings of the
<a class="reference internal" href="processors.html"><span class="doc">processors</span></a> command. The partitioning can later be
changed by the <a class="reference internal" href="balance.html"><span class="doc">balance</span></a> or <a class="reference internal" href="fix_balance.html"><span class="doc">fix balance</span></a> commands.</p>
<p>The argument N is the number of atom types that will be used in the
simulation.</p>
<p>If the region is not of style <em>prism</em>, then LAMMPS encloses the region
(block, sphere, etc) with an axis-aligned orthogonal bounding box
which becomes the simulation domain.</p>
<p>If the region is of style <em>prism</em>, LAMMPS creates a non-orthogonal
simulation domain shaped as a parallelepiped with triclinic symmetry.
As defined by the <a class="reference internal" href="region.html"><span class="doc">region prism</span></a> command, the
parallelepiped has its &#8220;origin&#8221; at (xlo,ylo,zlo) and is defined by 3
edge vectors starting from the origin given by A = (xhi-xlo,0,0); B =
(xy,yhi-ylo,0); C = (xz,yz,zhi-zlo). <em>Xy,xz,yz</em> can be 0.0 or
positive or negative values and are called &#8220;tilt factors&#8221; because they
are the amount of displacement applied to faces of an originally
orthogonal box to transform it into the parallelipiped.</p>
<p>By default, a <em>prism</em> region used with the create_box command must
have tilt factors (xy,xz,yz) that do not skew the box more than half
the distance of the parallel box length. For example, if xlo = 2 and
xhi = 12, then the x box length is 10 and the xy tilt factor must be
between -5 and 5. Similarly, both xz and yz must be between
-(xhi-xlo)/2 and +(yhi-ylo)/2. Note that this is not a limitation,
since if the maximum tilt factor is 5 (as in this example), then
configurations with tilt = ..., -15, -5, 5, 15, 25, ... are all
geometrically equivalent. If you wish to define a box with tilt
factors that exceed these limits, you can use the <a class="reference internal" href="box.html"><span class="doc">box tilt</span></a>
command, with a setting of <em>large</em>; a setting of <em>small</em> is the
default.</p>
<p>See <a class="reference internal" href="Section_howto.html#howto-12"><span class="std std-ref">Section_howto 12</span></a> of the doc pages
for a geometric description of triclinic boxes, as defined by LAMMPS,
and how to transform these parameters to and from other commonly used
triclinic representations.</p>
<p>When a prism region is used, the simulation domain should normally be
periodic in the dimension that the tilt is applied to, which is given
by the second dimension of the tilt factor (e.g. y for xy tilt). This
is so that pairs of atoms interacting across that boundary will have
one of them shifted by the tilt factor. Periodicity is set by the
<a class="reference internal" href="boundary.html"><span class="doc">boundary</span></a> command. For example, if the xy tilt factor
is non-zero, then the y dimension should be periodic. Similarly, the
z dimension should be periodic if xz or yz is non-zero. LAMMPS does
not require this periodicity, but you may lose atoms if this is not
the case.</p>
<p>Also note that if your simulation will tilt the box, e.g. via the <a class="reference internal" href="fix_deform.html"><span class="doc">fix deform</span></a> command, the simulation box must be setup to
be triclinic, even if the tilt factors are initially 0.0. You can
also change an orthogonal box to a triclinic box or vice versa by
using the <a class="reference internal" href="change_box.html"><span class="doc">change box</span></a> command with its <em>ortho</em> and
<em>triclinic</em> options.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">If the system is non-periodic (in a dimension), then you should
not make the lo/hi box dimensions (as defined in your
<a class="reference internal" href="region.html"><span class="doc">region</span></a> command) radically smaller/larger than the extent
of the atoms you eventually plan to create, e.g. via the
<a class="reference internal" href="create_atoms.html"><span class="doc">create_atoms</span></a> command. For example, if your atoms
extend from 0 to 50, you should not specify the box bounds as -10000
and 10000. This is because as described above, LAMMPS uses the
specified box size to layout the 3d grid of processors. A huge
(mostly empty) box will be sub-optimal for performance when using
&#8220;fixed&#8221; boundary conditions (see the <a class="reference internal" href="boundary.html"><span class="doc">boundary</span></a>
command). When using &#8220;shrink-wrap&#8221; boundary conditions (see the
<a class="reference internal" href="boundary.html"><span class="doc">boundary</span></a> command), a huge (mostly empty) box may cause
a parallel simulation to lose atoms the first time that LAMMPS
shrink-wraps the box around the atoms.</p>
</div>
<hr class="docutils" />
<p>The optional keywords can be used to create a system that allows for
bond (angle, dihedral, improper) interactions, or for molecules with
special 1-2,1-3,1-4 neighbors to be added later. These optional
keywords serve the same purpose as the analogous keywords that can be
used in a data file which are recognized by the
<a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> command when it sets up a system.</p>
<p>Note that if these keywords are not used, then the create_box command
creates an atomic (non-molecular) simulation that does not allow bonds
between pairs of atoms to be defined, or a <a class="reference internal" href="bond_style.html"><span class="doc">bond potential</span></a> to be specified, or for molecules with
special neighbors to be added to the system by commands such as
<a class="reference internal" href="create_atoms.html"><span class="doc">create_atoms mol</span></a>, <a class="reference internal" href="fix_deposit.html"><span class="doc">fix deposit</span></a>
or <a class="reference internal" href="fix_pour.html"><span class="doc">fix pour</span></a>.</p>
<p>As an example, see the examples/deposit/in.deposit.molecule script,
which deposits molecules onto a substrate. Initially there are no
molecules in the system, but they are added later by the <a class="reference internal" href="fix_deposit.html"><span class="doc">fix deposit</span></a> command. The create_box command in the
script uses the bond/types and extra/bond/per/atom keywords to allow
this. If the added molecule contained more than 1 special bond
(allowed by default), an extra/special/per/atom keyword would also
need to be specified.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>An <a class="reference internal" href="atom_style.html"><span class="doc">atom_style</span></a> and <a class="reference internal" href="region.html"><span class="doc">region</span></a> must have
been previously defined to use this command.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a>, <a class="reference internal" href="create_atoms.html"><span class="doc">create_atoms</span></a>,
<a class="reference internal" href="region.html"><span class="doc">region</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