The
occupancy rules
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.
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.
Structures as those created in this tutorial can be seen in the
figure at
http://www.gamgi.org/images/screenshot08_4b.png.
Spherical volume
-
Press Cell->Create and set System to c, Lattice
to P and the lattice parameter a to 1.
In the Type page, choose Sphere, with radius
Length equal to 5. Press Ok to create the cell.
- To improve visibility, press Layer->Modify, change
Projection to Orthographic and press Ok.
- Press Atom->Create, write Si in the Element
entry and press the mouse over the screen (outside the cell), to create
a Si template atom. Repeat the task to create a C template atom.
- 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 to
(*2, *2, *2) and press Ok.
A cube with 3x3x3 nodes in the center of the sphere
is now occupied with Si atoms.
- Repeat the Cell->Link task, this time linking the cell
with the C atom, using as pattern rule (___*****, ___*****,
___*****), and press Ok. All nodes around the 3x3x3 central
nodes are now occupied with C atoms.
