Step 1 - Set up Atomic Species

Somewhat obviously, we need two atomic species for this simulation - an oxygen, and a silicon. First, however, we’ll create some suitable atom types by hand.

Forcefield tab, Atom Types section

Click the [+] Add button located at the top-right

Select silicon in the periodic table dialog

Change the Charge of the new atom type to 2, the SR Form to LJ, and in the SR Parameters box enter 0.175, 1.03 (corresponding to the Lennard-Jones epsilon and sigma respectively)

Click the [+] Add button again, and choose oxygen from the periodic table

Change the Charge of the oxygen atom type to -1, the SR Form to LJ, and the SR Parameters to 0.165, 3.5

Atom types created in this way are named after the symbol of the relevant element.

Now let’s generate our atomic species, assign the relevant atom types, and create a basic site for each. First, the silicon:

Species ⇨ Create… ⇨ Atomic…

Select silicon from the periodic table

Si species tab, Contents & Forcefield section

In the list of Atoms change the AtomType for the atom to Si

Si species tab, Sites section

Select the silicon atom in the viewer, and click Create in the toolbar to create a site

And now, the oxygen:

Species ⇨ Create… ⇨ Atomic…

Select oxygen from the periodic table

O species tab, Contents & Forcefield section

In the list of Atoms change the AtomType for the atom to O

O species tab, Analysis Sites section

Select the oxygen atom in the viewer, and click Create in the toolbar to create a site

---

Back to Overview Next Step