Python interface and reconstructing various RDF species combinations

OVITO
1

I’m using the very helpfully fast ovito RDF calculations via the python interface for the first time, but I’m interested in something beyond just total and all the A-B pair partials. There are two things I want, and one is straightforward, but the other I’m just not sure how to do efficiently. I was hoping someone here could suggest documentation to look at or a specific approach I could try.

  1. I want the A-* RDF, i.e. properly weighted sum of \sum_i w_i \mathrm{rdf}(A, B_i). I suppose the weights would just be the number fraction of B_i, x(B_i), right? If so, how can I get those? Is there a pipeline modifier that would return that info?

  2. I sometimes want both total and various A-B partials. I can presumably attach two
    CoordinationAnalysisModifiers, one with partial=True, one without. Could I instead reconstruct the total from a weighted sum of the partials? If so, what are the weights? Is it, as I suspect, x(A)^2 for A-A and 2 x(A) x(B) for A != B (presumably once I figure out the correct formula I can evaluate it with whatever strategy works for question 1)?

2

Please have a look at section “Element-wise RDFs” in the online documentation of the Coordination analysis modifier for the explanation how to compute the total RDF from the partial ones. Coordination analysis — OVITO User Manual 3.9.4 documentation

3

Thanks, that does confirm what I expected for the weights, and it’s good to know that the GUI docs explain some of the details that the python docs skip.

Is there a modifier I can use in the python interface to compute the concentrations that are mentioned in that section?

4

Since you are using Python, you can directly calculate the concentrations from the particle types property array, e.g. like this

numpy.unique(data.particles.particle_types, return_counts = True)[1]/data.particles.count
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