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atom selection

I want to visualize my simulation——oxygen absorption on the polyhedron of platinum.I only need the platinum and the obsorbed oxygen atoms,how can I make the other oxygen atoms disappear?Thanks!

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What would be a good criterion, in your eyes, for discriminating absorbed oxygens from the non-absorbed ones? Perhaps the number of platinum atoms within some short range of an oxygen atom can be used to decide whether that oxygen is absorbed or not.

That is something you can compute using OVITO's Compute property modifier. This modifier provides a special mode, which allows you to take into account neighboring atoms in the computation within a specified cutoff radius. This tool lets you to selectively count neighbor atoms of a certain species within the cutoff range around the central atom.

Once you have the computed the number of platinum neighbor atoms around each atom, you can use the Expression selection modifier to select those oxygen atoms which have no or only very few platinum atoms in their vicinity. Finally, use the Delete Selected modifier to hide these selected atoms.

If this approach doesn't give you satisfactory results, I can propose another technique, maybe more precise, which is based on the Construct Surface Mesh modifier of OVITO (for generating a geometric representation of the polyhedron formed by the platinum atoms) and a user-defined Python modifier function for testing which oxygen atoms are located within that polyhedral region. This approach requires OVITO Pro though.


Thank you very much,I will have a try!