Connection of atomic clusters

[Ab_do]

Dear OVITO Team @utt @kalcher @stukowski ,

Thank you once again for your kind and valuable support.

I have a follow-up question related to atomic clustering. Could you please take a look at the image I’ve included below? I would like to understand how to reproduce this type of visualization and analysis using OVITO or its Python scripting interface.

As I am still a beginner with OVITO, I would greatly appreciate any clear explanation, step-by-step guidance, or example scripts that could help me achieve a similar result. If possible, visual illustrations or screenshots for each step would be especially helpful.

Thank you very much for your time and continued support.
abdo

[utt]

I don’t think there’s a fully automated way to generate images like this.

However, here’s how I would approach it:

1. Start with a larger chunk of crystal.
   
   
2. Use the Create Bonds modifier or Voronoi analysis to generate the bonds you’re interested in.
   
   
3. Select your central particle(s) using either manual selection or expression selection.
4. Add the visible “shell” of atoms to the selection by using Expand Selection modifier in bonds mode.
5. Invert the selection.
6. Delete the selected particles to isolate your region of interest.
   
   

You may need to manually delete any unwanted dangling atoms (Manual Selection + Delete Selected) or create additional bonds to complete the schematic.

To add annotations, you can use text label overlays. For automatically annotating distances between central atoms, use the Measure Distances and Angles viewport layer.

[Ab_do]

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