I am a new user hoping to perform an advanced analysis on an Fe80Ni20 amorphous alloy simulation. My goal is to create a spatial correlation matrix for different cluster types (ICO-like, crystal-like, etc.), and I would be very grateful for your assistance.
While I understand the first step is to classify atoms using the Polyhedral Template Matching (PTM) modifier, I am unsure how to proceed with the subsequent calculations.
Would it be possible for you to provide a step-by-step guide on how to compute the spatial correlation index from this classified data? Specifically, I am looking for the Python scripting steps required to generate the final matrix. A structured guide would be immensely helpful for a beginner.
Any help you could offer would be greatly appreciated.
You want to calculate the “spatial correlation index”. These are probably the numbers in this matrix. But it is not clear to me how this index is defined and what kind of correlation it describes. Can you describe this in more detail? Then we can think about how this statistical quantity could be calculated with OVITO.
The PTM function can be used to uniquely classify each atom in the material as either “crystal-like”, “ICO”, “ICO-like” or “OTHER”. But I am wondering what statistical correlation should be considered. Between which pairs of atoms in the system? There seems to be a missing piece.
Thank you very much for your help and for taking the time to look into this.
Yes, you’re right — and I’ve added more details in the explanation below, along with a figure (see image attached) to clarify what I mean.
I’m hoping this can be computed using OVITO, either through built-in modifiers or by scripting with Python. I’d really appreciate your thoughts on whether this kind of analysis is possible within OVITO’s framework.
Yes, this quantity could be calculated. OVITO offers all the basic functions required for this (classification of atoms, creation of clusters, search for neighboring atoms). However, Python programming likely is required to implement the calculation of the Cij indices described. The algorithm is not trivial.
Please understand that we cannot offer this complex development work as a free service, but we can advise you on the use of individual OVITO functions if necessary and respond to specific questions.
My recommendation would be to contact the authors of the paper first. Perhaps they have an easy way to share their finished calculation tool with you. Then you don’t have to redo the work.
