spatial correlation matrix

OVITO
1

Dear OVITO Team,

I hope this message finds you well.

Could you please advise me on how to compute or extract the spatial correlation matrix
Cij, as shown in the picture below, using a Python script in OVITO Pro? I would greatly appreciate any guidance or examples you can provide.

Thank you very much in advance for your support!

Best regards,

spatial correlation
spatial correlation1011×454 247 KB

2

@stukowski

3

This is not a standard function of the software and it is not clear from the diagram what type of correlation is being considered here and how the calculation looks like.

Could you please provide further details on the analysis approach? Then perhaps I can say more about how this procedure can be implemented using OVITO’s Python API.

4

Dear Dr. @stukowski,

Thank you very much for your reply and for your time.
I’m still new to this kind of analysis
I would like to calculate the spatial correlation index matrix Cij, between different types of atomic clusters (such as icosahedral, FCC-like, HCP-like, etc.) identified in Fe and Fe97.2​Ni2.8, amorphous alloys, based on LAMMPS simulation data.
If there is a way to implement such a calculation using OVITO’s Python API — possibly by combining cluster identification modifiers

I would greatly appreciate your guidance.

5

@stukowski
I have another question related to this topic. Could you please take a look at the image below? I would like to understand how to reproduce this kind of result using OVITO or its Python scripting interface.

As a beginner, I would really appreciate any explanation or steps you can suggest to help me achieve this.

Thank you very much for your time and support.
crystal
with this script:

6

You can use modifiers such as Common Neighbor Analysis, Polyhedral Template Matching, or other system-specific modifiers to identify “crystal-like” structures. Afterwards, you can use OVITO’s “Export File” function to export the count of atoms belonging to each identified crystal structure as a “Table of Values”.
Normalization and plotting can then be performed using your plotting tool of choice.

1 Like
7

Dear @utt ,

Thank you for giving your time to explain and for your excellent work on OVITO.

I followed these steps:

  1. Add Modifier
  2. Common Neighbor Analysis (CNA)

However, it does not display the “crystal-like” structures as shown in the reference image. I also tried Add Modifier → Spatial Correlation, but it shows nothing.

Is there a Python script example available to compute or visualize the Spatial Correlation Index (Cij) correctly?

Thank you again for your help and support.

Zcst
Zcst1270×615 173 KB

8

From the context, it is unclear what you mean by the Spatial Correlation Index (Cij). Perhaps this is explained in more detail in the paper from which you obtained the figure.

Please understand that we cannot find out for you how high-level research results in the literature were produced or obtained by others. It makes more sense to ask the authors of this study directly and have the calculation method explained to you by them. We can only provide you with information on the integrated low-level functions available in OVITO and explain how to access their their output data.

1 Like
9

Dear Dr. @utt

Thank you, 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