Step 3 - Set up a Configuration
To create our silica configuration we’ll use the “relative random mix” generator as a basis.
Configuration ⇨ Create ⇨ Relative random mix
Choose both the silicon and the oxygen species and continue
Double-click the new configuration tab and rename it to
Bulk
Let’s set-up the parameters in the generator first of all. The relative random mix uses the population of the first species (referred to as A) as the reference, and sets the population of all other species relative to the first, based on user defined ratios. So, here we will use the silicon species as A and set its population explicitly, and set the relative population of species B (the oxygen) to be twice that of A, thus giving us SiO2.
Select the Parameters node in the generator
Change the value of the populationA variable to
1500
Set ratioB to
2
If, for some reason, your atomic species are defined the other way round with oxygen appearing first, you’ll need to set populationA to
3000and ratioB to0.5.
The density of bulk, amorphous silica is 0.0664 atoms Å-3. We use units of atoms Å-3 here as this allows us to add both atomic components using the same density value. If we had chosen units of g cm-3 we would have to know the individual densities of silicon and oxygen in amorphous silica.
Change the value of the rho variable to
0.0664.
Finally, the box. We will still use relative lengths and tell Dissolve to scale the box according to our species population and density (the default behaviour), but we will create a monoclinic box rather than a cubic one:
Choose the Box node
Set the angle γ to 120 degrees
We’re all set up, so click to recreate the box using our new parameters. If you zoom the viewer out (mouse wheel) then you should then see a monoclinic box of silica!