Cluster visualizations in OVITO

[jo_nas]

Hello OVITO Team,

I hope you are doing well.

I would like to reproduce the types of visualizations shown in the attached figures using OVITO .

Specifically, I am interested in extractin g:

1. The coordination polyhedra around selected atoms (similar to Figures (c)–(f )).

2. The central atom, first-shell atoms, and second-shell atoms with different col ors.

3. The different cluster connection types (1-atom, 2-atom, 3-atom, and 4-atom connections), as illustrated in the second fi gure.

4. A visualization similar to these published figures, where only the relevant atoms and their coordination polyhedra are disp layed.

However, I do not know how to generate the visualizations shown in the attached f igures.

Could you please advise:

• Is it possible to create these figures directly i n OVITO?

• Which modifiers should be used?

• Is a Python script required, or can this be done through the graphical interface?

• If possible, could you provide an example workflow or script?

Thank you very much for your time and assistance.

Best regards,

[utt]

Please check the following threads where a similar question has been discussed before:

The cluster structures?

Hi OVITO Team, I hope you are well. Please, could you provide me with a Python script to reproduce the structures and distances shown in the attached image (1-atom to 4-atom icosahedral connections)? I tried with Voronoi analysis, expression selection, invert, and delete tools, but I couldn’t get this result. I’m looking for a script that can detect icosahedral clusters (like <0,0,12,0>), find their connections, and show the distances between them. Thank you very much for your help! Best r…

Connection of atomic clusters

Dear Dr. @utt Thank you, Daniel, for your explanation. I will try this approach and see how it works. I really appreciate your time and the detailed guidance you provided in advance. Thanks again for explaining it so clearly. Best regards, abdo