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Regarding the Honeycutt-Anderson indices

May i know how to generate the Honeycutt-Anderson indices using Ovito


there is no out of the box modifier for that in OVITO, but you can develop a short python script that can be used with OVITO's python scripting interface ovitos. If you like you can have a look at the introductory pages in the in the scripting manual first.

You can start from the following code example given in the manual, that explains how to generate bonds using the CreateBonds modifier and then characterize those bonds by using the CommonNeighborAnalysis modifier. So most of the work is already done:

Let me know if you have further questions,