Step 6 - Analyse the Structure

We’ll introduce another analysis module, CalculateAngle, to finish off this tutorial. CalculateAngle is similar to CalculateDAngle, but is more flexible, assumes less about the connectivity between the sites, and gives more comprehensive output. We’ll use it to calculate the Si–O–Si angle, and the correlations of that angle with the individual Si–O bonds.

Create an empty layer, and add a copy of the CalculateAngle module to it.

Layer ⇨ Create… ⇨ Empty

Show the module palette for the layer by clicking the Show Palette button at the top left of the tab

Drag a CalculateAngle module from the Analysis group in the Module Palette on the left

Now let’s set it up.

Select the CalculateAngle module to display its options

Open the Calculation settings group

Change the RangeAB Min and Max values to 1.2 and 2.1 respectively, and corresponding to the range of the Si–O bonds

Change the RangeBC Min and Max values to 1.2 and 2.1 as well

Change the AngleRange BinWidth to 5.0

Open the Sites settings group

Change SiteB to be the one located on the oxygen, and change SiteA and SiteC to be the one located on the silicon

Tick the ExcludeSameSiteAC option, as otherwise we’ll get a spike at zero in the resulting angle data

Let’s open up the CalculateAngle module in a separate tab so that we can see the graphs for the calculated properties, and start Dissolve running once more.

Analysis layer tab

Double-click the CalculateAngle module to open it in a new tab

Ctrl-R

The three graphs on the first page of CalculateAngles tabs shows the two radial distribution functions A–B and B–C, and the A–B–C angle. The RDFs should mirror those calculated by the NeutronSQ module (peak at around 1.6 Å) while the normalised angle graph tells us that all the Si–O–Si angles are predominantly greater than 120°.

The second and third tabs display us the distance-angle correlation graphs, which are both identical in the present case.

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