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<title>GAMGI Tutorials: Multilayer nanostructure</title>
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<h1>Multilayer nanostructure</h1>
<div id="notebook">
<ul>
<li><span>Page 1</span></li>
</ul>
</div>
<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 an unlimited range
of non crystalline structures, to simulate liquid mixtures, for example.
Coupled with changes in the cell origin node, they can be used to build
arbitrary multi-layer 3D nanostructures.
<p/>
This tutorial shows how to create a G letter, with a contour three-atom thick,
over a substrate formed also by three atomic layers of a different element.
<p/>
First we create a cell with the proper dimensions, a Si atom to describe
the substrate and a Cu atom to describe the adatoms, then link sucessively
the substrate atom and the adatom with the cell to create the proper structure.
<p/>
The final structure, with an orthographic layer and a directional light,
can be seen in the figure at
<a href="http://www.gamgi.org/images/screenshot12_4b.png">
http://www.gamgi.org/images/screenshot12_4b.png</a>.
<h3>Nanostructure</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, set the number of cells along
a, b, c directions to <b>38</b>, <b>26</b> and <b>5</b>, respectively.
This provides the grid of nodes that is needed to link the atoms.
In the <b>View</b> page, set <b>Borders</b> to <b>Edges</b>
and disable <b>Nodes</b>, to reduce visual cluttering to a minimum.
Press <b>Ok</b> to create the cell.</li>
<li>
Press <b>Atom->Create</b> and set <b>Style</b> to <b>Solid</b>,
<b>Size</b> to <b>1.0</b> and <b>Variancy</b> to <b>1.0</b>,
to guarantee that the atom spheres are built with the atom radius.
Write <b>Si</b> in the <b>Element</b> entry, set <b>Radius</b>
to <b>0.5</b> and press the mouse over the screen (outside the
cell), to create a Si template atom. Repeat the task to create
a Cu template atom with the same radius.</li>
<li>Select <b>Light->Create</b> and press <b>Ok</b>, to give a
tridimensional aspect to the atoms. If computer rendering becomes
too slow, select <b>Atom->Config</b>, change <b>Slices</b> to <b>4</b>
and in the end change back to <b>16</b>.</li>
<li>Press <b>Cell->Modify</b> and then press over the cell,
to get its data.
Go to the <b>Origin</b> page, set the <b>Node</b> coordinates
to <b>0</b>, <b>0</b>, <b>1</b> and press <b>Ok</b>, to change
the cell origin.
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 rules over the <b>a</b>,
<b>b</b>, <b>c</b> directions to <b>*</b>, <b>*</b>, <b>*1</b>,
respectively, and press <b>Ok</b>. The Si three-layer substrate
is in place.</li>
<li>Repeat the <b>Cell->Modify</b> task, to change the cell
origin to the coordinates <b>7</b>, <b>19</b>, <b>4</b>, and
press <b>Ok</b>.
Repeat the <b>Cell->Link</b> task, to link the cell with
the Cu atom, using as pattern rule <b>*1</b>, <b>*13</b>,
<b>*1</b>, and press <b>Ok</b>. The left segment of the G letter
is in place.</li>
<li>Repeat the <b>Cell->Modify</b> task, to change the cell
origin to the coordinates <b>19</b>, <b>11</b>, <b>4</b>, and
press <b>Ok</b>.
Repeat the <b>Cell->Link</b> task, to link the cell with
the Cu atom, using as pattern rule <b>*1</b>, <b>*5</b>,
<b>*1</b>, and press <b>Ok</b>. The bottom right segment of the
G letter is in place.</li>
<li>Repeat the <b>Cell->Modify</b> task, to change the cell
origin to the coordinates <b>19</b>, <b>27</b>, <b>4</b>, and
press <b>Ok</b>.
Repeat the <b>Cell->Link</b> task, to link the cell with
the Cu atom, using as pattern rule <b>*1</b>, <b>*5</b>,
<b>*1</b>, and press <b>Ok</b>. The top right segment of the
G letter is in place.</li>
<li>Repeat the <b>Cell->Modify</b> task, to change the cell
origin to the coordinates <b>13</b>, <b>7</b>, <b>4</b>, and
press <b>Ok</b>.
Repeat the <b>Cell->Link</b> task, to link the cell with
the Cu atom, using as pattern rule <b>*4</b>, <b>*1</b>,
<b>*1</b>, and press <b>Ok</b>. The bottom segment of the
G letter is in place.</li>
<li>Repeat the <b>Cell->Modify</b> task, to change the cell
origin to the coordinates <b>13</b>, <b>31</b>, <b>4</b>, and
press <b>Ok</b>.
Repeat the <b>Cell->Link</b> task, to link the cell with
the Cu atom, using as pattern rule <b>*4</b>, <b>*1</b>,
<b>*1</b>, and press <b>Ok</b>. The top segment of the
G letter is in place.</li>
<li>Repeat the <b>Cell->Modify</b> task, to change the cell
origin to the coordinates <b>16</b>, <b>15</b>, <b>4</b>, and
press <b>Ok</b>.
Repeat the <b>Cell->Link</b> task, to link the cell with the Cu atom,
using as pattern rule <b>*1</b>, <b>*1</b>, <b>*1</b>, and press
<b>Ok</b>. The inner segment of the G letter is in place. The whole
structure, containing 3159 Si atoms and 630 Cu atoms, is terminated.
</li>
</ol>
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