Author Topic: Polyhedral Template Matching Reclassification  (Read 537 times)


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Polyhedral Template Matching Reclassification
« on: February 08, 2019, 05:17:43 PM »

 I am fairly new to identifying crystal structures. Currently I am using polyhedral template matching to identify structures in binary alloys. Could anyone please describe why when a certain crystal structure, say HCP, is deselected (not allowing Ovito to classify as such) the atoms that were originally classified as HCP could be reclassified as something different than the category "other" ? Is this due to the change in the histogram for RMSD and corresponding chosen RMSD cutoff?


Constanze Kalcher

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Re: Polyhedral Template Matching Reclassification
« Reply #1 on: February 08, 2019, 05:38:20 PM »
Hi Ryan,

for each input particle, the PTM tries to determine a mapping of the local neighborhood to each active candidate structure. If such a mapping exists, a RMSD value is calculated, which is a measure of the spatial deviation from the ideal structure template (the quality of the match). The structural type with the lowest RMSD value is finally assigned to the particle.
You as a user can set a global RMSD cutoff, which limits the assignment of structural types to a range of RMSD values. Particles whose RMSD exceeds the threshold are assigned the "Other" structure type.
So I think what happens in your case is that if you deactivate the HCP structure type, the calculated RMSD values for a another structure type are still below the global cutoff, then they will be marked as such.

Does that answer your question?