The
occupancy rules
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.
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.
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.
The final structure, with an orthographic layer and a directional light,
can be seen in the figure at
http://www.gamgi.org/images/screenshot12_4b.png.
Nanostructure
-
Press Cell->Create and set System to c, Lattice
to P and the lattice parameter a to 1.
In the Type page, set the number of cells along
a, b, c directions to 38, 26 and 5, respectively.
This provides the grid of nodes that is needed to link the atoms.
In the View page, set Borders to Edges
and disable Nodes, to reduce visual cluttering to a minimum.
Press Ok to create the cell.
-
Press Atom->Create and set Style to Solid,
Size to 1.0 and Variancy to 1.0,
to guarantee that the atom spheres are built with the atom radius.
Write Si in the Element entry, set Radius
to 0.5 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.
- Select Light->Create and press Ok, to give a
tridimensional aspect to the atoms. If computer rendering becomes
too slow, select Atom->Config, change Slices to 4
and in the end change back to 16.
- Press Cell->Modify and then press over the cell,
to get its data.
Go to the Origin page, set the Node coordinates
to 0, 0, 1 and press Ok, to change
the cell origin.
Press Cell->Link, then press over the cell, then press
over the Si atom, and select the method Crystal.
Go to the Occupancy page, set the rules over the a,
b, c directions to *, *, *1,
respectively, and press Ok. The Si three-layer substrate
is in place.
- Repeat the Cell->Modify task, to change the cell
origin to the coordinates 7, 19, 4, and
press Ok.
Repeat the Cell->Link task, to link the cell with
the Cu atom, using as pattern rule *1, *13,
*1, and press Ok. The left segment of the G letter
is in place.
- Repeat the Cell->Modify task, to change the cell
origin to the coordinates 19, 11, 4, and
press Ok.
Repeat the Cell->Link task, to link the cell with
the Cu atom, using as pattern rule *1, *5,
*1, and press Ok. The bottom right segment of the
G letter is in place.
- Repeat the Cell->Modify task, to change the cell
origin to the coordinates 19, 27, 4, and
press Ok.
Repeat the Cell->Link task, to link the cell with
the Cu atom, using as pattern rule *1, *5,
*1, and press Ok. The top right segment of the
G letter is in place.
- Repeat the Cell->Modify task, to change the cell
origin to the coordinates 13, 7, 4, and
press Ok.
Repeat the Cell->Link task, to link the cell with
the Cu atom, using as pattern rule *4, *1,
*1, and press Ok. The bottom segment of the
G letter is in place.
- Repeat the Cell->Modify task, to change the cell
origin to the coordinates 13, 31, 4, and
press Ok.
Repeat the Cell->Link task, to link the cell with
the Cu atom, using as pattern rule *4, *1,
*1, and press Ok. The top segment of the
G letter is in place.
- Repeat the Cell->Modify task, to change the cell
origin to the coordinates 16, 15, 4, and
press Ok.
Repeat the Cell->Link task, to link the cell with the Cu atom,
using as pattern rule *1, *1, *1, and press
Ok. The inner segment of the G letter is in place. The whole
structure, containing 3159 Si atoms and 630 Cu atoms, is terminated.
