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<title>GAMGI Tutorials: Occupancy rules</title>
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<h1>Occupancy rules</h1>
<div id="notebook">
<ul>
<li><span>Page 1</span></li>
<li><a href="occupancy_page2.html">Page 2</a></li>
</ul>
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<div class="contents">
The <a href="../interfaces/cell/link_occupancy.html">occupancy rules</a>
implemented in GAMGI, determining which nodes in crystallographic cells
should be occupied, is a powerful tool to build non crystalline structures,
for example to generate starting configurations to simulate liquid mixtures.
<p/>
This tutorial shows how to use occupancy rules to create usefull
structures in a spherical cell volume and in a conventional cell
volume. We create first a spherical volume and second a conventional
volume, for a cubic cell, plus Si, C template atoms, and link them
together using several different occupancy rules, to exemplify the method.
<p/>
Structures as those created in this tutorial can be seen in the
figure at <a href="http://www.gamgi.org/images/screenshot08_4b.png">
http://www.gamgi.org/images/screenshot08_4b.png</a>.
<h3>Spherical volume</h3>
<ol>
<li>
Press <b>Cell->Create</b> and set <b>System</b> to <b>c</b>, <b>Lattice</b>
to <b>P</b> and the lattice parameter <b>a</b> to <b>1</b>.
In the <b>Type</b> page, choose <b>Sphere</b>, with radius
<b>Length</b> equal to <b>5</b>. Press <b>Ok</b> to create the cell.</li>
<li>To improve visibility, press <b>Layer->Modify</b>, change
<b>Projection</b> to <b>Orthographic</b> and press <b>Ok</b>.</li>
<li>Press <b>Atom->Create</b>, write <b>Si</b> in the <b>Element</b>
entry and press the mouse over the screen (outside the cell), to create
a Si template atom. Repeat the task to create a <b>C</b> template atom.</li>
<li>Press <b>Cell->Link</b>, then press over the cell, then press
over the Si atom, and select the method <b>Crystal</b>.
Go to the <b>Occupancy</b> page, set the <b>Rules</b> to
(<b>*2</b>, <b>*2</b>, <b>*2</b>) and press <b>Ok</b>.
A cube with 3x3x3 nodes in the center of the sphere
is now occupied with Si atoms.</li>
<li>Repeat the <b>Cell->Link</b> task, this time linking the cell
with the C atom, using as pattern rule (<b>___*****</b>, <b>___*****</b>,
<b>___*****</b>), and press <b>Ok</b>. All nodes around the 3x3x3 central
nodes are now occupied with C atoms.</li>
</ol>
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